bluuebunny/crossref_metadata_2025 huggingface dataset:
In situ observation of vacancy dynamics during resistance changes of oxide devices
Authors: Choi Sang-Jun , Park Gyeong-Su , Kim Ki-Hong , Yang Woo-Young , Bae Hyung-Jin , Lee Kyung-Jin , Lee Hyung-ik , Park Seong Yong , Heo Sung , Shin Hyun-Joon , Lee Sangbin , Cho Soohaeng
Published: September 2011

We report that the charged oxygen vacancies are the key element to induce a resistive switching in copper oxide resistive devices and an external bias drifts the charged vacancies at the metal/oxide Schottky interface causing the switching phenomenon by in situ transmission electron microscopy. Notable results are that the switching polarity is determined by the charge of the vacancies and that the voltage inducing non-volatile switching behavior originates from the Schottky barrier at the interface, which clarifies the origin of resistive switching and provides a design strategy for oxide resistive devices.
Correlations between microstructure and Q-factor of tunable thin film bulk acoustic wave resonators
Authors: Vorobiev A. , Gevorgian S. , Löffler M. , Olsson E.
Published: September 2011

Correlations between microstructure and Q-factor of tunable solidly mounted Ba0.25Sr0.75TiO3 (BSTO) thin film bulk acoustic wave resonators are studied using analysis of test structures prepared at different growth temperatures of the BSTO films varying in the range 450-650 °C. The observed changes in the Q-factor with growth temperature are correlated with related changes in microstructure, including the grain size, texture misalignment, interfacial amorphous layer, surface roughness, and deterioration of the Bragg reflector layers. The correlations are established through analysis of corresponding extrinsic acoustic loss mechanisms, including Rayleigh scattering at localized defects, acoustic attenuation by amorphous layer, generation of the shear waves leaking into the substrate, waves scattering by surface roughness, and resonance broadening by local thickness variations. It is shown that the waves scattering by surface roughness at the BSTO film interfaces is the main loss mechanism limiting the Q-factor of the BSTO thin film bulk acoustic wave resonators.
The effects of strong temperature anisotropy on the kinetic structure of collisionless slow shocks and reconnection exhausts. II. Theory
Authors: Liu Yi-Hsin , Drake J. F. , Swisdak M.
Published: September 2011

Simulations of collisionless oblique propagating slow shocks have revealed the existence of a transition associated with a critical temperature anisotropy ɛ = 1 − μ0(P|| − P⊥)/B2 = 0.25 (Y.-H. Liu, J. F. Drake, and M. Swisdak, Phys. Plasmas 18, 062110 (2011)). An explanation for this phenomenon is proposed here based on anisotropic fluid theory, in particular, the anisotropic derivative nonlinear-Schrödinger-Burgers equation, with an intuitive model of the energy closure for the downstream counter-streaming ions. The anisotropy value of 0.25 is significant because it is closely related to the degeneracy point of the slow and intermediate modes and corresponds to the lower bound of the coplanar to non-coplanar transition that occurs inside a compound slow shock (SS)/rotational discontinuity (RD) wave. This work implies that it is a pair of compound SS/RD waves that bound the outflows in magnetic reconnection, instead of a pair of switch-off slow shocks as in Petschek’s model. This fact might explain the rareness of in-situ observations of Petschek-reconnection-associated switch-off slow shocks.
Molecular doping effect in bottom-gate, bottom-contact pentacene thin-film transistors
Authors: Wakatsuki Yusuke , Noda Kei , Wada Yasuo , Toyabe Toru , Matsushige Kazumi
Published: September 2011

A bottom-gate, bottom-contact (BGBC) organic thin-film transistor (OTFT) with carrier-doped regions over source-drain electrodes was investigated. Device simulation with our originally developed device simulator demonstrates that heavily doped layers (p+ layers) on top of the source-drain contact region can compensate the deficiency of charge carriers at the source-channel interface during transistor operation, leading to the increase of the drain current and the apparent field-effect mobility. The phenomena expected with the device simulation were experimentally confirmed in typical BGBC pentacene thin-film transistors. The 5-nm-thick p+ layers, located 10 nm (or 20 nm) over the source-drain electrodes, were prepared by coevaporation of pentacene and 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane as an acceptor dopant. Since the molecular doping in this study can increase the drain current without positive shift of threshold voltage, p+ layers were formed precisely on top of the source-drain regions. This study shows that common inferior characteristics of bottom-contact OTFT devices mainly derive from the supply shortage of charge carriers to the channel region. The importance of reliable molecular doping techniques or heavily doped semiconductor materials for improving OTFT device performance is clearly suggested.
The spin-polarized extended Brueckner orbitals
Authors: Luzanov A. V. , Prezhdo O. V.
Published: September 2011

Conventional natural and Brueckner orbitals (BOs) are rather frequently used for improving active orbital spaces in various configuration interaction (CI) approaches. However, the natural and Brueckner single-determinant models per se fail to give an adequate picture of highly correlated and quasidegenerate states such as open-shell singlet and dissociative states. We suggest the use of the spin-polarized extended BOs formally defining them in the same manner as in Löwdin's spin-extended Hartree-Fock method. Such BO orbitals turn out to be quite flexible and particularly useful for analyzing highly correlated electronic states. It is shown that the extended BOs always exist, unlike the usual unrestricted BOs. We discuss difficulties related to violation of size-consistency for spin projected determinant models. The working algorithm is proposed for computing BOs within the full CI and related complete active space methodology. The extended BOs are analyzed in terms of the special density-like matrices associated with spin-up and spin-down BO orbitals. From these density matrices, the corresponding spin-polarization diagrams are produced for effectively unpaired (essentially correlated) electrons. We illustrate the approach by calculations on cyclic hydrogen clusters (H4, H6, and H8), certain carbene diradicals and monoradicals, and low-lying excited states. The computations show that the BO spin-projected determinant provides a strong overlap with the multi-configurational state even for quasidegenerate states and bond breaking processes.
Applying x-ray microscopy and finite element modeling to identify the mechanism of stress-assisted void growth in through-silicon vias
Authors: Kong L. W. , Lloyd J. R. , Yeap K. B , Zschech E. , Rudack A. , Liehr M. , Diebold A.
Published: September 2011

Fabricating through-silicon vias (TSVs) is challenging, especially for conformally filled TSVs, often hampered by the seam line and void inside the TSVs. Stress-assisted void growth in TSVs has been studied by finite element stress modeling and x-ray computed tomography (XCT). Because x-ray imaging does not require TSVs to be physically cross-sectioned, the same TSV can be imaged before and after annealing. Using 8 keV laboratory-based XCT, voids formed during copper electroplating are observed in as-deposited samples and void growth is observed at the void location after annealing. We hypothesize that the mechanism generating voids is hydrostatic stress-assisted void growth. Stresses in a copper-filled TSV with a pre-existing void were simulated by finite element methods. The peaks of the hydrostatic stress and its gradient are shown to be around the edge of the void. Comparing simulated results and experimental data shows that void growth in TSVs is stress-assisted: vacancies diffuse and coalesce at the void as a result of the hydrostatic stress gradient.
Voltage dependence of a stochastic model of activation of an alpha helical S4 sensor in a K channel membrane
Authors: Vaccaro S. R.
Published: September 2011

The voltage dependence of the ionic and gating currents of a K channel is dependent on the activation barriers of a voltage sensor with a potential function which may be derived from the principal electrostatic forces on an S4 segment in an inhomogeneous dielectric medium. By variation of the parameters of a voltage-sensing domain model, consistent with x-ray structures and biophysical data, the lowest frequency of the survival probability of each stationary state derived from a solution of the Smoluchowski equation provides a good fit to the voltage dependence of the slowest time constant of the ionic current in a depolarized membrane, and the gating current exhibits a rising phase that precedes an exponential relaxation. For each depolarizing potential, the calculated time dependence of the survival probabilities of the closed states of an alpha helical S4 sensor are in accord with an empirical model of the ionic and gating currents recorded during the activation process.
Thermocapillary actuation of binary drops on solid surfaces
Authors: Zhao Yuejun , Liu Fangjie , Chen Chuan-Hua
Published: September 2011

On hydrophobic solid surfaces, aqueous drops are typically not conducive to thermocapillary actuation. This letter reports thermal mobilization of water drops by encapsulating them with a long-chain alcohol. On a parylene-coated silicon substrate, a water-heptanol binary drop can assume a unique shape: the dome-shaped water drop is capped by a layer of heptanol, and the heptanol cap protrudes through a “foot” to a precursor film. For intermediate drop diameters, the speed of the binary drop is linearly proportional to its diameter and the imposed temperature gradient, with an offset accounting for the hysteresis force.
Light-induced resistance effect of Pd doped carbon film/SiO2/Si
Authors: Ma Ming , Xue Qingzhong , Li Jianpeng , Zhen Yuhua , Wang Sheng
Published: September 2011

The Pd doped amorphous carbon (a-C:Pd) films were deposited on n-Si substrates with a native SiO2 layer using direct current magnetron sputtering. The light-induced spatial sensitivity of the resistance of the a-C:Pd/SiO2/Si structure was investigated. It is found that the a-C:Pd/SiO2/Si shows a huge resistance change (∼15 000%) when the different positions of the sample surface were illuminated by a laser. The light-induced spatial sensitivity of the resistance of the a-C:Pd/SiO2/Si is attributed to the eminent photosensitivity of the a-C:Pd/SiO2/Si structure which is caused by the Pd doping and the different carrier density distribution in the illuminated and unilluminated regions.
Realization of size controllable graphene micro/nanogap with a micro/nanowire mask method for organic field-effect transistors
Authors: Liao Zhiyu , Wan Qing , Liu Huixuan , Tang Qingxin
Published: September 2011

A size controllable graphene micro/nanogap fabrication method using micro/nanowire as mask is presented. The gap dimension can be adjusted by the diameter of the mask wire. As a typical application, copper phthalocyanine (CuPc) film organic field-effect transistors (OFETs) were fabricated with the graphene micro/nanogap bottom electrodes. The ultrathin thickness of the graphene, combined with its good compatibility with organic semiconductors, and high electrical conductivity produced high-performance CuPc film device with mobility at 0.053 cm2/Vs and on/off ratio at 105, showing promising potential in low-cost and light-weight electronics.
Platypus (Ornithorhynchus anatinus) body size, condition and population structure in Tasmanian river catchments: variability and potential mucormycosis impacts
Authors: Gust Nick , Griffiths Josh
Published: September 2011

Context Despite widespread interest in platypus (Ornithorhynchus anatinus) conservation, it is unclear how their fundamental morphometric and demographic characteristics differ over a range of scales. This hampers impact assessments and understanding of platypus ecology. Although the ulcerative fungal disease mucormycosis has infected platypuses in Tasmania for three decades, its population level impacts and conservation significance remain unknown. Aims This study examined morphometric and demographic patterns in Tasmanian platypuses to provide a basis for investigating impacts of mucormycosis or other anthropogenic disturbances. It also sought to identify important spatial scales of natural variability and the magnitude of seasonal variation in platypus body size, condition and population structure. The hypothesis of higher mucormycosis prevalence and mortality in adult males was also investigated. Methods Extensive live-trapping surveys were conducted from January 2008 to July 2009 in 75 streams and 18 river catchments across Tasmania including King Island. The sex, age, body size, tail volume index, health and moult condition of 195 individuals were assessed, and population age and sex structures characterised. Sampling focussed on assessing variability within and between river catchments and compared populations in river catchments with contrasting disease status. Key results Differences in platypus morphometrics within and between catchments and seasonal moulting patterns were detected. Adult males had higher fat stores than adult females, especially during winter. This study also provided the first evidence of population level consequences of disease in platypuses. The demographic group most commonly affected by mucormycosis was confirmed to be adult males. Differences in male age structure among catchments of varying disease status were consistent with the hypothesis of higher adult male mortality rates and turnover in currently affected catchments. Conclusions More than 25 years after mucormycosis was first detected in Tasmanian platypuses, the disease continues to play a low-level, ongoing role in affected populations. Implications The present study provides the first systematic multi-scale spatial investigation of platypus mucormycosis, which contributes to unravelling the epidemiology of the disease and detecting its impacts. By identifying the magnitude and important scales of morphometric and demographic differences in Tasmanian platypuses the study also assists researchers choose comparable demographic groups and spatial scales for meaningful comparisons in future impact studies.
Carcinogenic bacterial pathogen
Helicobacter pylori
triggers DNA double-strand breaks and a DNA damage response in its host cells
Authors: Toller Isabella M. , Neelsen Kai J. , Steger Martin , Hartung Mara L. , Hottiger Michael O. , Stucki Manuel , Kalali Behnam , Gerhard Markus , Sartori Alessandro A. , Lopes Massimo , Müller Anne
Published: September 2011

The bacterial pathogen
Helicobacter pylori
chronically infects the human gastric mucosa and is the leading risk factor for the development of gastric cancer. The molecular mechanisms of
H. pylori
-associated gastric carcinogenesis remain ill defined. In this study, we examined the possibility that
H. pylori
directly compromises the genomic integrity of its host cells. We provide evidence that the infection introduces DNA double-strand breaks (DSBs) in primary and transformed murine and human epithelial and mesenchymal cells. The induction of DSBs depends on the direct contact of live bacteria with mammalian cells. The infection-associated DNA damage is evident upon separation of nuclear DNA by pulse field gel electrophoresis and by high-magnification microscopy of metaphase chromosomes. Bacterial adhesion (e.g., via blood group antigen-binding adhesin) is required to induce DSBs; in contrast, the
H. pylori
virulence factors vacuolating cytotoxin A, γ-glutamyl transpeptidase, and the cytotoxin-associated gene (Cag) pathogenicity island are dispensable for DSB induction. The DNA discontinuities trigger a damage-signaling and repair response involving the sequential ataxia telangiectasia mutated (ATM)-dependent recruitment of repair factors—p53-binding protein (53BP1) and mediator of DNA damage checkpoint protein 1 (MDC1)—and histone H2A variant X (H2AX) phosphorylation. Although most breaks are repaired efficiently upon termination of the infection, we observe that prolonged active infection leads to saturation of cellular repair capabilities. In summary, we conclude that DNA damage followed by potentially imprecise repair is consistent with the carcinogenic properties of
H. pylori
and with its mutagenic properties in vitro and in vivo and may contribute to the genetic instability and frequent chromosomal aberrations that are a hallmark of gastric cancer.
SOCS1 is essential for regulatory T cell functions by preventing loss of Foxp3 expression as well as IFN-γ and IL-17A production
Authors: Takahashi Reiko , Nishimoto Shuhei , Muto Go , Sekiya Takashi , Tamiya Taiga , Kimura Akihiro , Morita Rimpei , Asakawa Mayako , Chinen Takatoshi , Yoshimura Akihiko
Published: September 2011

Regulatory T cells (Treg cells) maintain immune homeostasis by limiting inflammatory responses. SOCS1 (suppressor of cytokine signaling 1), a negative regulator of cytokine signaling, is necessary for the suppressor functions of Treg cells in vivo, yet detailed mechanisms remain to be clarified. We found that Socs1−/− Treg cells produced high levels of IFN-γ and rapidly lost Foxp3 when transferred into Rag2−/− mice or cultured in vitro, even though the CNS2 (conserved noncoding DNA sequence 2) in the Foxp3 enhancer region was fully demethylated. Socs1−/− Treg cells showed hyperactivation of STAT1 and STAT3. Because Foxp3 expression was stable and STAT1 activation was at normal levels in Ifnγ−/−Socs1−/− Treg cells, the restriction of IFN-γ–STAT1 signaling by SOCS1 is suggested to be necessary for stable Foxp3 expression. However, Ifnγ−/−Socs1−/− Treg cells had hyperactivated STAT3 and higher IL-17A (IL-17) production compared with Ifnγ−/−Socs1+/+ Treg cells and could not suppress colitis induced by naive T cells in Rag2−/− mice. In vitro experiments suggested that cytokines produced by Socs1−/− Treg cells and Ifnγ−/−Socs1−/− Treg cells modulated antigen-presenting cells for preferential Th1 and Th17 induction, respectively. We propose that SOCS1 plays important roles in Treg cell integrity and function by maintaining Foxp3 expression and by suppressing IFN-γ and IL-17 production driven by STAT1 and STAT3, respectively.
Structural basis for the role of the Sir3 AAA+ domain in silencing: interaction with Sir4 and unmethylated histone H3K79
Authors: Ehrentraut Stefan , Hassler Markus , Oppikofer Mariano , Kueng Stephanie , Weber Jan M. , Mueller Jonathan W. , Gasser Susan M. , Ladurner Andreas G. , Ehrenhofer-Murray Ann E.
Published: September 2011

The silent information regulator 2/3/4 (Sir2/3/4) complex is required for gene silencing at the silent mating-type loci and at telomeres in Saccharomyces cerevisiae. Sir3 is closely related to the origin recognition complex 1 subunit and consists of an N-terminal bromo-adjacent homology (BAH) domain and a C-terminal AAA+ ATPase-like domain. Here, through a combination of structure biology and exhaustive mutagenesis, we identified unusual, silencing-specific features of the AAA+ domain of Sir3. Structural analysis of the putative nucleotide-binding pocket in this domain reveals a shallow groove that would preclude nucleotide binding. Mutation of this site has little effect on Sir3 function in vivo. In contrast, several surface regions are shown to be necessary for the Sir3 silencing function. Interestingly, the Sir3 AAA+ domain is shown here to bind chromatin in vitro in a manner sensitive to histone H3K79 methylation. Moreover, an exposed loop on the surface of this Sir3 domain is found to interact with Sir4. In summary, the unique folding of this conserved Sir3 AAA+ domain generates novel surface regions that mediate Sir3–Sir4 and Sir3–nucleosome interactions, both being required for the proper assembly of heterochromatin in living cells.
Transcriptional regulation of xenobiotic detoxification in Drosophila
Authors: Misra Jyoti R. , Horner Michael A. , Lam Geanette , Thummel Carl S.
Published: September 2011

Living organisms, from bacteria to humans, display a coordinated transcriptional response to xenobiotic exposure, inducing enzymes and transporters that facilitate detoxification. Several transcription factors have been identified in vertebrates that contribute to this regulatory response. In contrast, little is known about this pathway in insects. Here we show that the Drosophila Nrf2 (NF-E2-related factor 2) ortholog CncC (cap ‘n’ collar isoform-C) is a central regulator of xenobiotic detoxification responses. A binding site for CncC and its heterodimer partner Maf (muscle aponeurosis fibromatosis) is sufficient and necessary for robust transcriptional responses to three xenobiotic compounds: phenobarbital (PB), chlorpromazine, and caffeine. Genetic manipulations that alter the levels of CncC or its negative regulator, Keap1 (Kelch-like ECH-associated protein 1), lead to predictable changes in xenobiotic-inducible gene expression. Transcriptional profiling studies reveal that more than half of the genes regulated by PB are also controlled by CncC. Consistent with these effects on detoxification gene expression, activation of the CncC/Keap1 pathway in Drosophila is sufficient to confer resistance to the lethal effects of the pesticide malathion. These studies establish a molecular mechanism for the regulation of xenobiotic detoxification in Drosophila and have implications for controlling insect populations and the spread of insect-borne human diseases.
On the inappropriate use of Kimura‐2‐parameter (K2P) divergences in the DNA‐barcoding literature
Authors: Srivathsan Amrita , Meier Rudolf
Published: September 2011

Here we present evidence, based on 10 datasets comprising 5283 sequences for 200 genera, that the use of the Kimura‐2‐parameter (K2P) model in DNA‐barcoding studies is poorly justified. We demonstrate that K2P is neither expected nor confirmed to be an appropriate model for closely related COI sequences. In addition, we show that the use of uncorrected distances yields higher or similar identification success rates for neighbour‐joining trees and distance‐based identification techniques. K2P also does not widen the barcoding gap for closely related sequences. We conclude that the spread of K2P through the barcoding literature is difficult to explain, and urge the use of evidence‐based approaches to DNA barcoding.

© The Willi Hennig Society 2011.
Top spoilage losses in maize silage sealed with plastic films with different permeabilities to oxygen
Authors: Bernardes T. F. , Nussio L. G. , do Amaral R. C.
Published: September 2011

The quality of plastic films used for horizontal silos is important to limit losses in the upper silage layer. The aim of this work was to study the effectiveness of different plastic films in reducing the top losses in maize silage. The following treatments were evaluated: (i) coextruded polyethylene/polyamide oxygen barrier film (OB), (ii) polyethylene film (PE), (iii) polyvinyl chloride film (PVC), and (iv) coextruded PE/polyvinyl alcohol film (PVOH). These treatments differed according to oxygen permeability with values of 75, 722, 982 and 289 cm3 m−2 per 24 hour respectively. OB and PVOH films had better temperature and fermentation profiles than the more permeable films. The OB film was effective in reducing the dry‐matter (DM) losses during storage (82 g kg−1), and the PVOH film had an intermediate value of DM loss (101 g kg−1). PE and PVC films had higher losses (138 and 145 g kg−1 respectively). Oxygen permeability of the films promoted a positive correlation with DM losses (P < 0·05; r2 = 0·945). The results indicate that O2 permeability through the plastic film is a crucial factor for maintaining silage quality in the upper layer of the silo when it is perfectly sealed.
The transcriptional organization of the Bacillus subtilis 168 chromosome region between the spoVAF and serA genetic loci
Authors: Azevedo Vasco , Sorokin Alexei , Ehrlich S. Dusko , Serror Pascale
Published: September 2011

The genetic organization of the spoVAF–serA area of the Bacillus subtilis chromosome and its putative transcription map have been derived from analysis of the nucleotide sequence. In order to confirm this transcription map as regards size of transcripts and to determine growth conditions for their appearance, we undertook Northern hybridization analysis of total RNA from vegetatively growing and sporulating cells. Twenty‐three distinct transcripts were thus identified, 14 of which were predicted from sequence analysis and nine of which were not predicted. Eight of the latter are homologous to open reading frames identified by sequence analysis but were not expected, since no obvious promoter or terminator was found in the sequence. The last unexpected transcript does not correspond to an ORF and might identify a novel gene. Three predicted transcripts were not detected. The transcripts were classified in four groups as (i) constitutive, (ii) regulated by nutritional depletion, (iii) specific for sporulation, and (iv) possibly regulated temporally. These studies demonstrate that systematic Northern analysis of a bacterial chromosome region is a useful complement to sequence analysis.
Sulfite oxidase controls sulfur metabolism under SO2 exposure in Arabidopsis thaliana
Authors: RANDEWIG DÖRTE , HAMISCH DOMENICA , HERSCHBACH CORNELIA , EIBLMEIER MONIKA , GEHL CHRISTIAN , JURGELEIT JENS , SKERRA JESSICA , MENDEL RALF R. , RENNENBERG HEINZ , HÄNSCH ROBERT
Published: September 2011

In the present study, the significance of sulfite oxidase (SO) for sulfite detoxification and sulfur assimilation was investigated. In response to sulfur dioxide (SO2) exposure, a remarkable expansion of sulfate and a significant increase of GSH pool were observed in wild‐type and SO‐overexpressing Arabidopsis. These metabolic changes were connected with a negative feedback inhibition of adenosine 5′‐phosphosulfate reductase (APR), but no alterations in gas exchange parameters or visible symptoms of injury. However, Arabidopsis SO‐KO mutants were consistently negatively affected upon 600 nL L−1 SO2 exposure for 60 h and showed phenotypical symptoms of injury with small necrotic spots on the leaves. The mean was reduced by about 60% over the fumigation period, accompanied by a reduction of net CO2 assimilation and SO2 uptake of about 50 and 35%. Moreover, sulfur metabolism was completely distorted. Whereas sulfate pool was kept constant, thiol‐levels strongly increased. This demonstrates that SO should be the only protagonist for back‐oxidizing and detoxification of sulfite. Based on these results, it is suggested that co‐regulation of SO and APR controls sulfate assimilation pathway and stabilizes sulfite distribution into organic sulfur compounds. In conclusion, a sulfate–sulfite cycle driven by APR and SO can be postulated for fine‐tuning of sulfur distribution that is additionally used for sulfite detoxification, when plants are exposed to atmospheric SO2.
Hydraulic architecture of two species differing in wood density: opposing strategies in co‐occurring tropical pioneer trees
Authors: MCCULLOH KATHERINE A. , JOHNSON DANIEL M. , MEINZER FREDERICK C. , VOELKER STEVEN L. , LACHENBRUCH BARBARA , DOMEC JEAN‐CHRISTOPHE
Published: September 2011

Co‐occurring species often have different strategies for tolerating daily cycles of water stress. One underlying parameter that can link together the suite of traits that enables a given strategy is wood density. Here we compare hydraulic traits of two pioneer species from a tropical forest in Panama that differ in wood density: Miconia argentea and Anacardium excelsum. As hypothesized, the higher wood density of Miconia was associated with smaller diameter vessels and fibres, more water stress‐resistant leaves and stems, and roughly half the capacitance of the lower wood density Anacardium. However, the scaling of hydraulic parameters such as the increases in leaf area and measures of hydraulic conductivity with stem diameter was remarkably similar between the two species. The collection of traits exhibited by Miconia allowed it to tolerate more water stress than Anacardium, which relied more heavily on its capacitance to buffer daily water potential fluctuations. This work demonstrates the importance of examining a range of hydraulic traits throughout the plant and highlights the spectrum of possible strategies for coping with daily and seasonal water stress cycles.
The TFL1 homologue KSN is a regulator of continuous flowering in rose and strawberry
Authors: Iwata Hikaru , Gaston Amèlia , Remay Arnaud , Thouroude Tatiana , Jeauffre Julien , Kawamura Koji , Oyant Laurence Hibrand‐Saint , Araki Takashi , Denoyes Béatrice , Foucher Fabrice
Published: September 2011

Flowering is a key event in plant life, and is finely tuned by environmental and endogenous signals to adapt to different environments. In horticulture, continuous flowering (CF) is a popular trait introduced in a wide range of cultivated varieties. It played an essential role in the tremendous success of modern roses and woodland strawberries in gardens. CF genotypes flower during all favourable seasons, whereas once‐flowering (OF) genotypes only flower in spring. Here we show that in rose and strawberry continuous flowering is controlled by orthologous genes of the TERMINAL FLOWER 1 (TFL1) family. In rose, six independent pairs of CF/OF mutants differ in the presence of a retrotransposon in the second intron of the TFL1 homologue. Because of an insertion of the retrotransposon, transcription of the gene is blocked in CF roses and the absence of the floral repressor provokes continuous blooming. In OF‐climbing mutants, the retrotransposon has recombined to give an allele bearing only the long terminal repeat element, thus restoring a functional allele. In OF roses, seasonal regulation of the TFL1 homologue may explain the seasonal flowering, with low expression in spring to allow the first bloom. In woodland strawberry, Fragaria vesca, a 2‐bp deletion in the coding region of the TFL1 homologue introduces a frame shift and is responsible for CF behaviour. A diversity analysis has revealed that this deletion is always associated with the CF phenotype. Our results demonstrate a new role of TFL1 in perennial plants in maintaining vegetative growth and modifying flowering seasonality.
Systematic screening of FBN1 gene unclassified missense variants for splice abnormalities
Authors: Robinson DO , Lin F , Lyon M , Raponi M , Cross E , White HE , Cox H , Clayton‐Smith J , Baralle D
Published: September 2011

Robinson DO, Lin F, Lyon M, Raponi M, Cross E, White HE, Cox H, Clayton‐Smith J, Baralle D. Systematic screening of FBN1 gene unclassified missense variants for splice abnormalities.

Defects at the level of pre‐mRNA splicing are a common source of genetic mutation but such mutations are not always easy to identify from DNA sequence data alone. Clinical practice has only recently begun to incorporate analysis for this type of abnormality. Some base changes at the DNA level currently viewed as unclassified variants or missense mutations may influence RNA splicing. To address this problem for fibrillin 1 (FBN1) gene missense mutations we have carried out RNA analysis and in silico analysis with splice site prediction programs on 40 cases with 36 different mutations. Direct analysis of RNA from blood was performed by cDNA preparation, PCR amplification of specific FBN1 fragments, gel electrophoresis and sequencing of the PCR products. Of the 36 missense base changes, direct RNA analysis identified 2 which caused an abnormality of splicing. In silico analysis using five splice site prediction programs did not always accurately predict the splicing seen by direct RNA analysis. In conclusion, some apparent missense mutations have an effect on splicing which can be identified by direct RNA analysis, however, in silico analysis of splice sites is not always accurate, should be carried out with more than one prediction program and results should be used with caution.
Atopic eczema: How to tackle the most common atopic symptom
Authors: Wahn Ulrich , Staab Doris , Nilsson Lennart
Published: September 2011

The disease management of atopic eczema includes topical and systemic treatments as well as the control of allergic and non‐allergic trigger factors. The basis for topical treatment is the regular use of emollients. In addition, anti‐inflammatory treatment with – preferably mild – topical steroids is the treatment of choice. At least‐one third of the children with atopic eczema during the first years suffer from clinically relevant food allergy requiring elimination diets for at least one or two years. The most common cause of superinfection is Staphylococcus aureus. Recent data suggests that it may induce purulent superinfection as well as enhance the inflammatory process by superantigen mediated T‐cell activation. Also, a number of alternative treatment strategies have been investigated during the last decade: the use of γ‐linoleic acid has been shown to be of limited benefit, while studies on interferon‐γ and on high‐dose intravenous γ‐globulin are still anecdotal. The long‐term effectiveness of disease management in atopic eczema depends largely on the understanding of the disease process as well as on the compliance of the parents. Thus, coping with the problem will be easier if the patient or the parents have been educated in understanding the pathogenesis, the role of trigger factors, the possibilities of prevention and the different treatment strategies.
Report of the Fourth International Workshop on molecular blood group genotyping
Authors: Daniels G. , van der Schoot C. E. , Olsson M. L.
Published: September 2011

The fourth International Society of Blood Transfusion (ISBT) workshop on molecular blood group genotyping was held in 2010, with a feedback meeting at the ISBT Congress in Berlin, Germany. Fifty laboratories participated, 17 more than in 2008. Six samples were distributed. Samples 1–3 were DNA samples for all red cell blood group tests available to the participants. Of the 46 laboratories that tested these samples, 37 obtained completely correct results, although the extent of testing varied considerably. Sample 4, also a DNA sample, was an Rh problem in which RHDΨ and RHCE*ceCF were present, but the participants were only informed that the donor’s red cells typed as positive with some monoclonal anti‐D. Of the 42 laboratories that participated in this exercise, seven performed the sequencing necessary to obtain the correct result. Samples 5 and 6 were plasma samples from RhD‐negative pregnant women, for foetal RhD testing. These were sent to 25 laboratories, and two incorrect results were reported. Overall, the level of accuracy was about equal to that of the previous workshop. The main conclusion for the last two workshops can be reiterated: with greater care and attention to detail, very high standards could be set for molecular blood group genotyping.
Immunohistochemical Aspects of Anti‐microbial Properties in Goat Submandibular Glands
Authors: Habata I. , Yasui T. , Fujimori O. , Tsukise A.
Published: September 2011

With 7 figures and 1 table

Salivary glands are known as the principal source of anti‐microbial substances, which are considered to be essential components of saliva. The distribution of anti‐microbial substances in the submandibular glands of Japanese miniature (Shiba) goat was studied using immunohistochemical methods as performed by physical development procedures. In the goat, anti‐microbial substances such as lysozyme, IgA, lactoferrin and β‐defensin were demonstrated to be immunolocalized in the submandibular glands, especially in the serous demilunes and duct cells. The results obtained are discussed with regard to the specific functions of the saliva. The presence and secretion of anti‐microbial substances suggest that they participate in the maintenance of oral health among the elements of saliva.
Magnetic Resonance Imaging of Normal Nasal Cavity and Paranasal Sinuses in Cats
Authors: Conchou F. , Sautet J. , Raharison F. , Mogicato G.
Published: September 2011

With 6 figures

A detailed description of the nasal cavity and paranasal sinuses in clinically normal cats using magnetic resonance imaging (MRI) is presented. The heads of seven normal cats were imaged using a 1.5‐T MR unit and two sequences spin echo (SE) T1‐weighted and fast spin echo (FSE) T2‐weighted. Eighteen relevant MR scans were taken in the transverse (12 scans) and dorsal (six scans) planes. Anatomical structures were identified and labelled using anatomical texts, sectioned specimen heads and previous studies. MR scans revealed the soft‐tissue structure of the head. Identified relevant anatomical structures seen on MRI will assist clinicians to better understand MR images and evaluate pathological conditions that affect the nasal region.
Estimation of heritability of benzoxazinoid production in rye (Secale cereale) using gas chromatographic analysis
Authors: Brooks Ashley M. , Danehower David A. , Murphy J. Paul , Reberg‐Horton S. Chris , Burton James D.
Published: September 2011

With 4 tables

The 2,4‐dihydroxy‐1,4‐benzoxazin‐3‐one (DIBOA) content of Secale cereale is strongly associated with allelopathy. This has led to interest in developing allelopathic cultivars with increased DIBOA to improve weed control in this important cover crop. Objectives of this study were to determine heritability estimates for DIBOA in rye and determine the utility of gas chromatography (GC) as a screening tool in a rye allelopathy breeding programme. A synthetic population of half‐sib families varying in production of DIBOA was analysed. DIBOA concentrations ranged from 0.52 to 1.15 mg/g dwt tissue (mean = 0.70 mg/g dwt). Analysis of variance indicated significant variability for DIBOA content in rye harvested at the flag leaf stage. Year × location × genotype and block (year × location) interactions were also significant. Several genotypes were consistently ‘high’ or ‘low’ DIBOA producers across all locations and years. Narrow sense heritability estimates were 0.18 ± 0.04 SE on a per plot basis and 0.57 ± 0.07 SE on an entry mean basis. GC analysis was determined to be a good system for moderate throughput screening of lines.
Human epicardial fat: what is new and what is missing?
Authors: Sacks Harold S , Fain John N
Published: September 2011

1. Putative physiological functions of human epicardial adipose tissue (EAT) include: (i) lipid storage for the energy needs of the myocardium; (ii) thermoregulation, whereby brown fat components of EAT generate heat by non‐shivering thermogenesis in response to core cooling; (iii) neuroprotection of the cardiac autonomic ganglia and nerves; and (iv) regulation of vasomotion and luminal size of the coronary arteries. Under pathophysiological circumstances, EAT may play an adverse paracrine role in cardiac arrhythmias and in lipotoxic cardiomyopathy, but of major current interest is its hypothetical role as an immunological organ contributing to inflammation around coronary artery disease (CAD).

2. The amount of EAT measured either by echocardiographic thickness over the free wall of the right ventricle or as volume by computed tomography expands in patients with obesity both without and with CAD. The mechanisms other than obesity governing the increase in EAT volume in CAD are unknown, but EAT around CAD is infiltrated by chronic inflammatory cells and overexpresses genes for adipokines that have pro‐ or anti‐inflammatory actions and regulate oxidative stress plus angiogenesis.

3. Many cross‐sectional studies have shown positive associations between increased EAT mass and stable CAD burden. One prospective population‐based epidemiological study suggested that EAT volume at baseline is a predictor of acute myocardial infarction, but was without significant incremental predictive value after adjustment for established cardiovascular risk factors. However, strategies are needed to obtain robust epidemiological, interventional and experimental evidence to prove or disprove the hypothesis that EAT is a cardiovascular risk factor locally contributing to CAD.
Serum cortisol and dehydroepiandrosterone‐sulfate levels in schizophrenic patients and their first‐degree relatives
Authors: Yıldırım Osman , Dogan Orhan , Semiz Murat , Kilicli Fatih
Published: September 2011

Aims:  Alterations in cortisol and dehydroepiandrosterone sulfate (DHEA‐S) levels are thought to play a role in the pathophysiology of neuropsychiatric disorders, including schizophrenia. The aim of this study was to investigate the role of serum cortisol and DHEA‐S in the pathophysiology of schizophrenia.

Methods:  Sixty schizophrenic patients, 70 healthy first‐degree relatives, and 60 healthy volunteers were included. Sociodemographic characteristics, data regarding disease duration and severity, as well as ongoing and previous drug use were recorded. Serum cortisol and DHEA‐S levels were measured.

Results:  Serum cortisol and DHEA‐S levels were significantly higher in the schizophrenia group compared with the first‐degree relatives and controls (P < 0.05). Serum cortisol levels in the first‐degree relatives were significantly higher than in the healthy controls (P < 0.05). There was no significant difference between the first‐degree relatives and healthycontrols in terms of DHEA‐S levels and between the three groups in terms of serum cortisol/DHEA‐S ratios.

Conclusions:  Elevated serum cortisol levels in schizophrenic patients might be associated with the role of cortisol in the pathophysiology of schizophrenia. Also, the elevation of serum cortisol levels in first‐degree relatives compared to controls suggests that similar pathophysiological processes might have a role in individuals without any disease symptoms, but with a genetic predisposition for schizophrenia. Elevated serum DHEA‐S levels might be the result of a compensatory response to elevated cortisol levels. Serum cortisol and DHEA‐S levels may be used as a biological marker for the diagnosis of schizophrenia; however, further studies with larger sample sizes are warranted to support this finding.
Bacterial sulfur cycling shapes microbial communities in surface sediments of an ultramafic hydrothermal vent field
Authors: Schauer Regina , Røy Hans , Augustin Nico , Gennerich Hans‐Hermann , Peters Marc , Wenzhoefer Frank , Amann Rudolf , Meyerdierks Anke
Published: September 2011

The ultramafic‐hosted Logatchev hydrothermal field (LHF) is characterized by vent fluids, which are enriched in dissolved hydrogen and methane compared with fluids from basalt‐hosted systems. Thick sediment layers in LHF are partly covered by characteristic white mats. In this study, these sediments were investigated in order to determine biogeochemical processes and key organisms relevant for primary production. Temperature profiling at two mat‐covered sites showed a conductive heating of the sediments. Elemental sulfur was detected in the overlying mat and metal‐sulfides in the upper sediment layer. Microprofiles revealed an intensive hydrogen sulfide flux from deeper sediment layers. Fluorescence in situ hybridization showed that filamentous and vibrioid, Arcobacter‐related Epsilonproteobacteria dominated the overlying mats. This is in contrast to sulfidic sediments in basalt‐hosted fields where mats of similar appearance are composed of large sulfur‐oxidizing Gammaproteobacteria. Epsilonproteobacteria (7–21%) and Deltaproteobacteria (20–21%) were highly abundant in the surface sediment layer. The physiology of the closest cultivated relatives, revealed by comparative 16S rRNA sequence analysis, was characterized by the capability to metabolize sulfur components. High sulfate reduction rates as well as sulfide depleted in 34S further confirmed the importance of the biogeochemical sulfur cycle. In contrast, methane was found to be of minor relevance for microbial life in mat‐covered surface sediments. Our data indicate that in conductively heated surface sediments microbial sulfur cycling is the driving force for bacterial biomass production although ultramafic‐hosted systems are characterized by fluids with high levels of dissolved methane and hydrogen.
Genomic content of uncultured Bacteroidetes from contrasting oceanic provinces in the North Atlantic Ocean
Authors: Gómez‐Pereira Paola R. , Schüler Margarete , Fuchs Bernhard M. , Bennke Christin , Teeling Hanno , Waldmann Jost , Richter Michael , Barbe Valérie , Bataille Elodie , Glöckner Frank Oliver , Amann Rudolf
Published: September 2011

Bacteroidetes are widespread in marine systems where they play a crucial role in organic matter degradation. Whole genome analysis of several strains has revealed a broad glycolytic and proteolytic potential. In this study, we used a targeted metagenomic approach to investigate the degradation capabilities of distinct Bacteroidetes clades from two contrasting regions of the North Atlantic Ocean, the Polar Biome (BPLR) and the North Atlantic Subtropical (NAST). We present here the analysis of 76 Bacteroidetes fosmids, of which 28 encode the 16S rRNA gene as phylogenetic marker, and their comparison to complete Bacteroidetes genomes. Almost all of the 16S rRNA harbouring fosmids belonged to clades that we previously identified in BPLR and NAST. The majority of sequenced fosmids could be assigned to Bacteroidetes affiliated with the class Flavobacteria. We also present novel genomic information on the classes Cytophagia and Sphingobacteria, suggesting a capability of the latter for attachment to algal surfaces. In our fosmid set we identified a larger potential for polysaccharide degradation and cell surface attachment in the phytoplankton‐rich BPLR. Particularly, two flavobacterial fosmids, one affiliated with the genus Polaribacter, showed a whole armoury of enzymes that likely function in degradation of sulfated polysaccharides known to be major constituents of phytoplankton cell walls. Genes involved in protein and peptidoglycan degradation, although present in both fosmid sets, seemed to have a slight preponderance in NAST. This study provides support for the hypothesis of a distinct specialization among marine Bacteroidetes for the degradation of certain types of polymers.
Rhodoferax‐related pufM gene cluster dominates the aerobic anoxygenic phototrophic communities in German freshwater lakes
Authors: Salka Ivette , Čuperová Zuzana , Mašín Michal , Koblížek Michal , Grossart Hans‐Peter
Published: September 2011

The presence of aerobic anoxygenic phototrophs (AAPs) has been repeatedly reported from various marine environments, but their distribution in freshwater lakes was neglected until recently. We investigated the phylogenetic composition of AAP communities in 10 lakes in Northeastern Germany with different trophic status including oligotrophic Lake Stechlin and humic matter rich Lake Grosse Fuchskuhle. The AAP community was composed by members of Alpha‐ and Betaproteobacteria, but their contribution varied largely among the studied lakes. Our results show that AAP community composition in the studied lakes was affected mostly by pH and humic matter content. While alkaline lakes were mostly composed of Betaproteobacteria, the acidic and humic matter rich south‐west (SW) basin of Lake Grosse Fuchskule was dominated (87%) by Alphaproteobacteria. The most frequent group within Betaproteobacteria was a cluster of pufM genes which was phylogenetically related to Rhodoferax representing 38.5% of all retrieved sequences. Alphaproteobacteria‐related sequences had a broader phylogenetic diversity including six different taxa dominated by Sphingomonas‐ and Rhodobacter‐like bacteria in lakes with alkaline to neutral pH. In the acidic and humic matter‐rich SW basin of Lake Grosse Fuchskuhle, however, Methylobacterium‐related sequences dominated the AAP community. We suggest that the variable AAP community structure might reflect the potential of these bacteria to cope with the contrasting conditions in freshwater environments.