bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contribution of the myosin VI tail domain to processive stepping and intramolecular tension sensing
Authors: Dunn Alexander R. , Chuan Peiying , Bryant Zev , Spudich James A. 
Published: April 2010

Myosin VI is proposed to act as both a molecular transporter and as an anchor in vivo. A portion of the molecule
C
-terminal to the canonical lever arm, termed the medial tail (MT), has been proposed to act as either a lever arm extension or as a dimerization motif. We describe constructs in which the MT is interrupted by a glycine-rich molecular swivel. Disruption of the MT results in decreased processive run lengths measured using single-molecule fluorescence microscopy and a decreased step size under applied load as measured in an optical trap. We used single-molecule gold nanoparticle tracking and optical trapping to examine the mechanism of coordination between the heads of dimeric myosin VI. We detect two rate-limiting kinetic processes at low (< 200 micromolar) ATP concentrations. Our data can be explained by a model in which intramolecular tension greatly increases the affinity of the lead head for ADP, likely by slowing ADP release from the lead head. This mechanism likely increases both the motor’s processivity and its ability to act as an anchor under physiological conditions.
Quality assessment of protein model-structures using evolutionary conservation
Authors: Kalman Matan , Ben-Tal Nir 
Published: April 2010

Abstract
Motivation: Programs that evaluate the quality of a protein structural model are important both for validating the structure determination procedure and for guiding the model-building process. Such programs are based on properties of native structures that are generally not expected for faulty models. One such property, which is rarely used for automatic structure quality assessment, is the tendency for conserved residues to be located at the structural core and for variable residues to be located at the surface.
Results: We present ConQuass, a novel quality assessment program based on the consistency between the model structure and the protein's conservation pattern. We show that it can identify problematic structural models, and that the scores it assigns to the server models in CASP8 correlate with the similarity of the models to the native structure. We also show that when the conservation information is reliable, the method's performance is comparable and complementary to that of the other single-structure quality assessment methods that participated in CASP8 and that do not use additional structural information from homologs.
Availability: A perl implementation of the method, as well as the various perl and R scripts used for the analysis are available at http://bental.tau.ac.il/ConQuass/.
Contact: nirb@tauex.tau.ac.il
Supplementary information: Supplementary data are available at Bioinformatics online.
Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation
Authors: Liebermeister Wolfram , Uhlendorf Jannis , Klipp Edda 
Published: April 2010

Abstract
Motivation: Standard rate laws are a key requisite for systematically turning metabolic networks into kinetic models. They should provide simple, general and biochemically plausible formulae for reaction velocities and reaction elasticities. At the same time, they need to respect thermodynamic relations between the kinetic constants and the metabolic fluxes and concentrations.
Results: We present a family of reversible rate laws for reactions with arbitrary stoichiometries and various types of regulation, including mass–action, Michaelis–Menten and uni–uni reversible Hill kinetics as special cases. With a thermodynamically safe parameterization of these rate laws, parameter sets obtained by model fitting, sampling or optimization are guaranteed to lead to consistent chemical equilibrium states. A reformulation using saturation values yields simple formulae for rates and elasticities, which can be easily adjusted to the given stationary flux distributions. Furthermore, this formulation highlights the role of chemical potential differences as thermodynamic driving forces. We compare the modular rate laws to the thermodynamic–kinetic modelling formalism and discuss a simplified rate law in which the reaction rate directly depends on the reaction affinity. For automatic handling of modular rate laws, we propose a standard syntax and semantic annotations for the Systems Biology Markup Language.
Availability: An online tool for inserting the rate laws into SBML models is freely available at www.semanticsbml.org
Contact: wolfram.liebermeister@biologie.hu-berlin.de
Supplementary Information: Supplementary data are available at Bioinformatics online.
Transgenerational marking of cephalopods with an enriched barium isotope: a promising tool for empirically estimating post-hatching movement and population connectivity
Authors: Pecl Gretta T. , Doubleday Zoë A. , Danyushevsky Leonid , Gilbert Sarah , Moltschaniwskyj Natalie A. 
Published: April 2010

Abstract
Pecl, G. T., Doubleday, Z. A., Danyushevsky, L., Gilbert, S., and Moltschaniwskyj, N. A. 2010. Transgenerational marking of cephalopods with an enriched barium isotope: a promising tool for empirically estimating post-hatching movement and population connectivity. – ICES Journal of Marine Science, 67: 1372–1380. Quantifying the movement of very small and young individuals, determining sources of recruitment, and identifying the contribution of populations from different regions and periods to fished stocks is a major ecological challenge. Transgenerational isotope labelling (TRAIL), a technique which enables offspring to be marked on a mass scale, is applied for the first time to cephalopods, facilitating field studies quantifying population connectivity. Four species were used: Sepioteuthis australis, Euprymna tasmanica, Octopus pallidus, and Octopus maorum. Gravid females were injected with the enriched stable isotope 137Ba in different body tissues at several different doses. Isotopic ratios 138Ba:137Ba were then quantified using laser ablation inductively coupled plasma-mass spectrometry on the hard structures (statoliths and stylets) of offspring produced by the injected females. Day-old hatchlings from both squid species had statoliths with isotopic ratios significantly different from natural ratios and control animals, but variability in the ratios in hatchlings produced by different females was independent of dose or injection location. No differences were observed in the statoliths and stylets removed from hatchlings and juveniles, respectively, from the two octopus species, although isotopic shifts were evident in the hard structures of the adults injected. The use of TRAIL is a technique that offers considerable potential to advance the understanding of post-hatching dispersal and population connectivity in cephalopod populations.
Nutrition as a facilitator of host‐race formation: the shift of a stem‐boring beetle to a gall host
Authors: BLAIR CATHERINE P. , SCHLANGER RITA V. , DIAMOND SARAH E. , ABRAHAMSON WARREN G. 
Published: April 2010

1. The importance of host‐race formation to herbivorous insect diversity depends on the likelihood that successful populations can be established on a new plant host. A previously unexplored ecological aid to success on a novel host is better nutritional quality. The role of nutrition was examined in the shift of the stem‐boring beetle Mordellistena convicta to fly‐induced galls on goldenrod and the establishment there of a genetically distinct gall host race.2. First, larvae of the host race inhabiting stems of Solidago gigantea were transplanted into stems and galls of greenhouse‐grown S. gigantea plants. At the end of larval development, the mean mass of larvae transplanted to galls was significantly greater than the mass of larvae transplanted to stems, indicating a likely nutritional benefit during the shift. This advantage was slightly but significantly diminished when the gall‐inducing fly feeding at the centre of the gall died early in the season. Additionally, there was a suggestion of a trade‐off in the increased mortality of smaller beetle larvae transplanted into galls.3. In a companion experiment, S. gigantea gall‐race beetle larvae were likewise transplanted to S. gigantea stems and galls. Besides the expected greater mass in galls, the larvae also exhibited adaptations to the gall nutritional environment: larger inherent size, altered tunnelling behaviour, and no diminution of mass pursuant to gall‐inducer mortality.4. In a third line of inquiry, chemical analyses of field‐collected S. gigantea plants revealed higher levels of mineral elements important to insect nutrition in galls as compared with stems.
Dormancy, germination and seed bank storage: a study in support of ex situ conservation of macrophytes of southwest Australian temporary pools
Authors: TUCKETT R. E. , MERRITT D. J. , HAY F. R. , HOPPER S. D. , DIXON K. W. 
Published: April 2010

Summary1. Vernal pools and rock pools (gnammas) in the Southwest Australian Floristic Region are forms of temporary wetlands that are under threat. Some of their aquatic macrophytes are rare and/or endemic, and there is a need to develop off‐site seed banks to assure their conservation. Here, we report results of the first comprehensive study of the seed germination, dormancy and seed storage behaviour of nine indigenous macrophyte species.2. Seeds of Glossostigma drummondii, Myriophyllum balladoniense, M. lapidicola, M. petreaum and Triglochin linearis were non‐dormant, whereas those of Damasonium minus, Glossostigma sp. (currently undescribed), G. trichodes and Myriophyllum crispatum were dormant. Non‐dormant seeds germinated over a range of temperatures (5–20 °C) but temperatures at which highest germination occurred were species specific. All species demonstrated a germination preference for the light. Warm stratification substantially increased germination of dormant Glossostigma trichodes seeds and all dormancy‐breaking treatments partially overcame dormancy in Glossostigma spp.3. Seeds possessed orthodox storage behaviour (tolerating drying to 5% moisture content and storage at −18 °C) and are thus amenable to seed banking as a means of ex situ conservation.4. It appears that seeds of most species are able to germinate upon inundation as long as they are situated at the soil surface. Thus, species are opportunistic and respond to the first rains of the season providing prompt ecological cuing in an environment vulnerable to rapid drying events. Maintaining the integrity of the soil crust may be an important first step for on‐site conservation if seeds are in the superficial layers.
SEM evaluation of root canal debridement with Sonicare CanalBrush irrigation
Authors: Salman M. I. , Baumann M. A. , Hellmich M. , Roggendorf M. J. , Termaat S. 
Published: April 2010

Salman MI, Baumann MA, Hellmich M, Roggendorf MJ, Termaat S. SEM evaluation of root canal debridement with Sonicare CanalBrush irrigation. International Endodontic Journal, 43, 363–369, 2010.AbstractAim  To determine the efficacy of Sonicare CanalBrush irrigation for root canal cleaning.Methodology  Fifty human molar root canals were shaped with sequential NiTi rotary instruments up to size F3 (size 30, 0.09 taper; ProTaper system) and then enlarged apically with a Profile size 40, 0.04 taper. Five different irrigation protocols were tested (n = 10 canals per group) with 2 mL of distilled water (control, group I) or 2.5% NaOCl (control group II and test groups III, IV and V) between instrument size changes. Group III–IV received a final rinse with 17% EDTA for one min. This was extended by 30 s in group IV, whereas group V received this additional 30 s of 17% EDTA sonically dispersed with a Sonicare CanalBrush. For cleanliness evaluations, roots were split longitudinally, examined with scanning electron microscopy and scored according to Hülsmann et al. (1997) for debris and smear layer on the surface of the root canal wall. Walls were assessed at the coronal, middle and apical thirds. Data were analysed with the Kruskal–Wallis and Mann–Whitney tests.Results  Irrigation with 17% EDTA significantly reduced debris and smear layer scores (P < 0.05) compared to controls. The coronal and middle thirds had lower debris and smear layer scores than the apical third (P < 0.05). In all thirds, sonic agitation of the irrigant with a CanalBrush (group V) resulted in significantly cleaner canal walls compared to all other groups (P < 0.05).Conclusions  Irrigation by agitation with the Sonicare CanalBrush improved root canal debridement in the coronal, middle and particularly the apical thirds of the root canal.
Short‐ and long‐term sealing ability of Gutta‐flow and AH‐Plus using an ex vivo fluid transport model
Authors: Vasiliadis L. , Kodonas K. , Economides N. , Gogos C. , Stavrianos C. 
Published: April 2010

Vasiliadis L, Kodonas K, Economides N, Gogos C, Stavrianos C. Short‐ and long‐term sealing ability of Gutta‐flow and AH‐Plus using an ex vivo fluid transport model. International Endodontic Journal, 43, 377–381, 2010.AbstractAim  To use the fluid transport model to evaluate the ex vivo short‐ and long‐term microleakage along root canals filled with Gutta‐flow or AH‐Plus using the cold lateral compaction technique.Methodology  A total of 38 single‐rooted human teeth were used for the assessment of microleakage. The crowns of the teeth were sectioned below their cemento–enamel junctions to adjust the length of the roots to approximately 15 mm. The root canals were instrumented using the step‐back technique and filled using cold lateral condensation. The sealer employed was either Gutta‐flow (Group A) or AH‐Plus (Group B). Microleakage along the root canals was evaluated using a fluid transport model after periods of 1 week and 3 months.Results  The microleakage values (μL h−1) for group A were 0.36 ± 0.33 at 1 week and 0.41 ± 0.36 at 3 months. Group B showed mean microleakage values 0.2 ± 0.31 at 1 week and 0.28 ± 0.38 at 3 months. Statistical analysis indicated no significant differences (P > 0.05) between the two groups after either 1 week or 3 months.Conclusions  There was no significant difference between AH‐plus and Gutta‐flow in terms of sealing ability.
Irrigant flow in the root canal: experimental validation of an unsteady Computational Fluid Dynamics model using high‐speed imaging
Authors: Boutsioukis C. , Verhaagen B. , Versluis M. , Kastrinakis E. , Van Der Sluis L. W. M. 
Published: April 2010

Boutsioukis C, Verhaagen B, Versluis M, Kastrinakis E, van der Sluis LWM. Irrigant flow in the root canal: experimental validation of an unsteady Computational Fluid Dynamics model using high‐speed imaging. International Endodontic Journal43, 393–403, 2010.AbstractAim  To compare the results of a Computational Fluid Dynamics (CFD) simulation of the irrigant flow within a prepared root canal, during final irrigation with a syringe and a needle, with experimental high‐speed visualizations and theoretical calculations of an identical geometry and to evaluate the effect of off‐centre positioning of the needle inside the root canal.Methodology  A CFD model was created to simulate irrigant flow from a side‐vented needle inside a prepared root canal. Calculations were carried out for four different positions of the needle inside a prepared root canal. An identical root canal model was made from poly‐dimethyl‐siloxane (PDMS). High‐speed imaging of the flow seeded with particles and Particle Image Velocimetry (PIV) were combined to obtain the velocity field inside the root canal experimentally. Computational, theoretical and experimental results were compared to assess the validity of the computational model.Results  Comparison between CFD computations and experiments revealed good agreement in the velocity magnitude and vortex location and size. Small lateral displacements of the needle inside the canal had a limited effect on the flow field.Conclusions  High‐speed imaging experiments together with PIV of the flow inside a simulated root canal showed a good agreement with the CFD model, even though the flow was unsteady. Therefore, the CFD model is able to predict reliably the flow in similar domains.
Cytotoxicity of chlorhexidine on human osteoblastic cells is related to intracellular glutathione levels
Authors: Lee T.‐H. , Hu C.‐C. , Lee S.‐S. , Chou M.‐Y. , Chang Y.‐C. 
Published: April 2010

Lee T‐H, Hu C‐C, Lee S‐S, Chou M‐Y, Chang Y‐C. Cytotoxicity of chlorhexidine on human osteoblastic cells is related to intracellular glutathione levels. International Endodontic Journal, 43, 430–435, 2010.AbstractAim  To evaluate the mechanisms of cytotoxicity of chlorhexidine (CHX) in human osteoblastic cells in vitro.Methodology  Cytotoxicity, cell proliferation and collagen synthesis assays were performed to elucidate the toxic effects of CHX on the human osteoblastic cell line U2OS. To determine whether glutathione (GSH) levels were important in the cytotoxicity of CHX, cells were pre‐treated with 2‐oxothiazolidine‐4‐carboxylic acid (OTZ) to boost GSH levels or buthionine sulfoximine (BSO) to deplete GSH.Results  CHX demonstrated a cytotoxic effect to U2OS cells in a dose‐dependent manner (P < 0.05). The 50% inhibition concentration of CHX was approximately 0.005%. CHX also inhibited cell proliferation and collagen synthesis (P < 0.05). The addition of OTZ acted as a protective effect on the CHX‐induced cytotoxicity (P < 0.05). In contrast, the addition of BSO enhanced the CHX‐induced cytotoxicity (P < 0.05).Conclusions  The levels of CHX tested inhibited cell growth, proliferation and collagen synthesis on U2OS cells. CHX has significant potential for periapical toxicity. GSH depletion might be one of the mechanisms underlying CHX cytotoxicity.
Cardiospecific expression of AAV vectors
Authors: Kupatt C. 
Published: April 2010

Adenoviral vectors have been set for cardiomyocyte gene therapy with considerable transfection rates. However, due to adenoviral immunogenicity, adenoviral transfected cells are frequently subject to specific cellular immune reactions leading to loss of cells and transgene expression. Non‐pathogenic adeno associated vectors lacking immunogenicity have been utilized alternately. Tropism of the most common AAV serotype 2, favoring liver of muscle transfection, has been altered by use of serotypes 1, 6 and 9.We used a model of chronic (4 weeks) regional myocardial transfection of the pig to investigate transfection efficacy of AAV vectors, which were applied to the target region by retroinfusion. Cardiac restriction was ensured by utilization of an MLC‐2v promoter‐CMV‐enhancer construct, fused to a luciferase reporter gene, the activity of which was analyzed.Compared to the wildtype (WT) AAV 2 vector, which barely exceeded background luciferase activity, a vector lacking the heparin binding site of the envelope (AAV2 ΔHep) improved expression only slightly. Substantial increase to 40 000 RLU/mg tissue) was achieved by the addition of VEGF‐A, which enhances vascular permeability. A further 15‐fold increase of luciferase activity was achieved by applying an equal amount of AAV6 virus particles to a pig heart, with a further 5–10 fold increase achieved by utilization of AAV serotype 9.Functionally relevant gene transfer was ensured by applying AAV9 hVEGF/PDGF (0.2/0.4 × 1013 virus particles, respectively). 4 weeks after retroinfusion into pig hearts suffering from chronic total LAD‐occlusion (induced by a reduction stent), we found a significant increase of blood flow and regional myocardial function.We conclude that AAV9 is a more efficient AAV vector when compared to WT‐ or ΔHep‐AAV2 or AAV6. Functionally relevant gene expression, as performed by VEGF‐A/PDGF transfection, opens the door for utilization of this vector system for xenotransplant organ priming.
Negative costimulation to prevent human anti‐pig T cell responses
Authors: Schwinzer R. , Plege A. 
Published: April 2010

Genetic modification of pigs [e.g. transgenic expression of human complement regulatory molecules or inactivation of α(1,3)‐galactosyltransferase] enabled the development of promising strategies to overcome hyperacute rejection after pig‐to‐primate xenotransplantation. However, cellular rejection still remains a hurdle for successful xenograft survival. Our group focuses on the inhibition of human anti‐pig T cell responses by targeting ‘‘negative’’ costimulatory pathways. We tested the hypothesis that over‐expression of the human negative costimulatory ligands PD‐L1 and PD‐L2 on pig cells will result in reduced human anti‐pig T cell responses. To this end, pig cell lines stably over‐expressing human PD‐Ligands (L23‐PD‐L1/L2 cells) and appropriate controls (L23‐GFP cells) were generated and used for in vitro stimulation of purified human CD4+ T cells. Furthermore, the effect of PD‐L expression on cellular cytotoxicity was tested by 51Cr‐release assays using L23‐PD‐L1/L2 and L23‐GFP cells as targets and IL‐2‐activated human CD8+ T cells and NK cells as effector. CD4+ T cells responded with significantly reduced proliferation to L23‐PD‐L1 or L23‐PD‐L2 cells and produced less IL‐2, IFNγ, TNFα, IL‐4, and IL‐5 than cells stimulated with mock‐transfected B cells. The concentration of IL‐10, however, was increased in CD4+ T cells responding to stimulation with PD‐L1 or PD‐L2 transfectants. Furthermore, in cultures of CD4+ T cells stimulated for 3 weeks with PD‐L1 or PD‐L2 transfectants a CD4+CD25highFoxp3+ subset showed up that effectively suppressed the activation of conventional CD4+ T cells. CD8+ T cells and NK cells acquired cytolytic potential and up‐regulated the PD‐1 receptor during cultivation with IL‐2. Both cell types lysed L23‐GFP cells very effectively but were less potent on L23‐PD‐L1 targets (reduced cytotoxicity of about 50%). When cytotoxic effector cells were used that do not express PD‐1 (293‐95L cells), L23‐GFP and L23‐PD‐L1 cells were lysed with similar intensity suggesting that PD‐1/PD‐L1 interactions are required for PD‐L1 mediated protection. Flow cytometric studies revealed that a proportion of activated CD8+PD‐1+ T cells underwent apoptosis when exposed to PD‐L1 expressing L23 cells. Together these observations support the assumption that PD‐1/PD‐Ligand pathways are interesting targets to prevent human anti‐pig cellular immune responses after xenotransplantation [1]. PD‐L over‐expression might not only empede the initiation of a human anti‐pig T cell response by suppressing CD4+ T cells but may also protect pig cells from destruction by human cytotoxic effectors. Supported by the Deutsche Forschungsgemeinschaft (Transregio Forscher‐gruppe ‘‘Xenotransplantation’’, FOR 535).Reference1. Plege A, Borns K, Baars W, Schwinzer R. Suppression of human T‐cell activation and expansion of regulatory T cells by pig cells overexpressing PD‐ligands. Transplantation 2009; 87: 975–982.