bluuebunny/crossref_metadata_2025 huggingface dataset:
Bacterial community structure corresponds to performance during cathodic nitrate reduction
Authors: Wrighton Kelly C , Virdis Bernardino , Clauwaert Peter , Read Suzanne T , Daly Rebecca A , Boon Nico , Piceno Yvette , Andersen Gary L , Coates John D , Rabaey Korneel
Published: June 2010

Microbial fuel cells (MFCs) have applications other than electricity production, including the capacity to power desirable reactions in the cathode chamber. However, current knowledge of the microbial ecology and physiology of biocathodes is minimal, and as a result more research dedicated to understanding the microbial communities active in cathode biofilms is required. Here we characterize the microbiology of denitrifying bacterial communities stimulated by reducing equivalents generated from the anodic oxidation of acetate. We analyzed biofilms isolated from two types of cathodic denitrification systems: (1) a loop format where the effluent from the carbon oxidation step in the anode is subjected to a nitrifying reactor which is fed to the cathode chamber and (2) an alternative non-loop format where anodic and cathodic feed streams are separated. The results of our study indicate the superior performance of the loop reactor in terms of enhanced current production and nitrate removal rates. We hypothesized that phylogenetic or structural features of the microbial communities could explain the increased performance of the loop reactor. We used PhyloChip with 16S rRNA (cDNA) and fluorescent in situ hybridization to characterize the active bacterial communities. Our study results reveal a greater richness, as well as an increased phylogenetic diversity, active in denitrifying biofilms than was previously identified in cathodic systems. Specifically, we identified Proteobacteria, Firmicutes and Chloroflexi members that were dominant in denitrifying cathodes. In addition, our study results indicate that it is the structural component, in terms of bacterial richness and evenness, rather than the phylogenetic affiliation of dominant bacteria, that best corresponds to cathode performance.
Postprandial remodeling of the gut microbiota in Burmese pythons
Authors: Costello Elizabeth K , Gordon Jeffrey I , Secor Stephen M , Knight Rob
Published: June 2010

The vertebrate gut microbiota evolved in an environment typified by periodic fluctuations in nutrient availability, yet little is known about its responses to host feeding and fasting. As many model species (for example, mice) are adapted to lifestyles of frequent small meals, we turned to the Burmese python, a sit-and-wait foraging snake that consumes large prey at long intervals (>1 month), to examine the effects of a dynamic nutrient milieu on the gut microbiota. We used multiplexed 16S rRNA gene pyrosequencing to characterize bacterial communities harvested from the intestines of fasted and digesting snakes, and from their rodent meal. In this unprecedented survey of a reptilian host, we found that Bacteroidetes and Firmicutes numerically dominated the python gut. In the large intestine, fasting was associated with increased abundances of the genera Bacteroides, Rikenella, Synergistes and Akkermansia, and with reduced overall diversity. A marked postprandial shift in bacterial community configuration occurred. Between 12 h and 3 days after feeding, Firmicutes, including the taxa Clostridium, Lactobacillus and Peptostreptococcaceae, gradually outnumbered the fasting-dominant Bacteroidetes, and overall ‘species’-level diversity increased significantly. Most lineages seemed to be indigenous to the python rather than ingested with the meal, but a dietary source of Lactobacillus could not be ruled out. Thus, the observed large-scale alterations of the gut microbiota that accompany the Burmese python's own dramatic physiological and morphological changes during feeding and fasting emphasize the need to consider both microbial and host cellular responses to nutrient flux. The Burmese python may provide a unique model for dissecting these interrelationships.
Amino acid residues in the β3 strand and subsequent loop of the conserved ETS domain that mediate basic leucine zipper (bZIP) recruitment and potentially distinguish functional attributes of Ets proteins
Authors: Shimokawa Toshibumi , Nunomura Satoshi , Enomoto Yukinori , Ra Chisei
Published: June 2010

Ets family members share a conserved DNA-binding ETS domain, and serve a variety of roles in development, differentiation and oncogenesis. Besides DNA binding, the ETS domain also participates in protein–protein interactions with other structurally unrelated transcription factors. Although this mechanism appears to confer tissue- or development stage-specific functions on individual Ets proteins, the biological significance of many of these interactions remains to be evaluated, because their molecular basis has been elusive. We previously demonstrated a direct interaction between the ETS domain of the widely expressed GABPα (GA-binding protein α) and the granulocyte inducer C/EBPα (CCAAT/enhancer-binding protein α), and suggested its involvement in co-operative transcriptional activation of myeloid-specific genes, such as human FCAR encoding FcαR [Fc receptor for IgA (CD89)]. By deletion analysis, we identified helix α3 and the β3/β4 region as the C/EBPα-interacting region. Domain-swapping of individual sub-domains with those of other Ets proteins allowed us to highlight β-strand 3 and the subsequent loop, which when exchanged by those of Elf-1 (E74-like factor 1) reduced the ability to recruit C/EBPα. Further analysis identified a four-amino acid swap mutation of this region (I387L/C388A/K393Q/F395L) that reduces both physical interaction and co-operative transcriptional activation with C/EBPα without affecting its transactivation capacity by itself. Moreover, re-ChIP (re-chromatin immunoprecipitation) analysis demonstrated that GABPα recruits C/EBPα to the FCAR promoter, depending on these residues. The identified amino acid residues could confer the specificity of the action on the Ets proteins in diverse biological processes through mediating the recruitment of its partner factor.
The human megakaryocytic cell line UT‐7/TPO expresses functional platelet agonist signals mediated through GPVI and thromboxane receptor
Authors: Kawaguchi Tatsuya , Hashimoto Ryuji , Yokota Hiroshi
Published: June 2010

We have demonstrated that a unique megakaryocytic cell line UT‐7/TPO could respond to one of the primary platelet signals through GP (glycoprotein) VI and a secondary signal of the AA (arachidonic acid) cascade. Unlike other megakaryocytic cell lines, UT‐7/TPO was found to express GPVI and its associate signal molecule of FcRγ (Fc receptor γ chain). When UT‐7/TPO was stimulated with the GPVI agonist convulxin, the [Ca2+]i (intracellular Ca2+) was elevated in a convulxin concentration‐dependent manner, and [Ca2+]i elevation was blocked by pretreatment with the Src family kinase inhibitor PP2 and the phospholipase inhibitor U73122. These results strongly indicate that endogenously expressed GPVI signal molecules are functional in UT‐7/TPO. Concerning the AA cascade, the expression of COX (cyclooxygenase)‐1 and TX (thromboxane) synthase was observed, and this cell line was able to produce TX by exogenous AA, followed by [Ca2+]i elevation mediated through the TX receptor. It is worth noting that convulxin stimulation did not cause TX generation, even through the GPVI pathway and the AA cascade are functional in this cell line. As there are many reports that convulxin‐stimulated platelets failed to produce TX, it is suggested that UT‐7/TPO has the same property as the platelets in regards to convulxin stimulation. Thus, UT‐7/TPO is useful for the observation of both the GPVI pathway and AA cascade without requiring either the induction of differentiation or GPVI transfection. Furthermore, this cell line provides a new tool for research on platelet activation signals.
Promotion of human adipose‐derived stem cell proliferation mediated by exogenous nucleosides
Authors: Rodríguez‐Serrano Fernando , Álvarez Pablo , Caba Octavio , Picón Manuel , Marchal Juan A. , Perán Macarena , Prados José , Melguizo Consolación , Rama Ana R. , Boulaiz Houria , Aránega Antonia
Published: June 2010

Adult stem cells are becoming the best option for regenerative medicine because they have low tumourigenic potential and permit autologous transplantation, even withoutin vitroculture. Our objectives were to evaluate the effects of exogenous nucleosides on the proliferation of hASCs (human adipose‐derived stem cells), with or without co‐treatment with 5‐aza (5‐azacytidine), and to analyse the expression of lamin A/C during cardiomyocyte differentiation of these cells. We isolated hASCs from human lipoaspirates that were positive for mesenchymal stem cell markers. We found that 5‐aza induces a dose‐dependent inhibition of hASC proliferation [IC50 (inhibitory concentration 50): 5.37 μM], whereas exogenous nucleosides significantly promote the proliferation of hASCs and partially revert the antiproliferative effect of the drug. Multipotentiality of isolated hASCs was confirmed by adipogenic, osteogenic and cardiomyogenic induction. 5‐Aza‐induced cells expressed cardiac troponins I and T and myosin light chain 2, myocardial markers that were directly correlated with lamin A/C expression. Our results support the importance of the nucleoside supplementation of media to improve conditions for the expansion and maintenance of hASCs in culture. In addition, the quantification of lamin A/C expression appears to be a good marker for the characterization of cardiomyocyte differentiation of stem cells that has rarely been used.
Association of putative functional variants in the PLAU gene and the PLAUR gene with myocardial infarction
Authors: Xu Jing , Li Wenlong , Bao Xunna , Ding Hu , Chen Jingzhou , Zhang Weili , Sun Kai , Wang Jizheng , Wang Xiaojian , Wang Hu , Yu Hui , Song Weihua , Ma Weiwei , Zhang Lin , Wang Changxin , Wang Daowen , Hui Rutai
Published: June 2010

uPA (urokinase-plasminogen activator) and its receptor (uPAR) have been implicated in a broad spectrum of pathophysiological processes, including fibrinolysis, proteolysis, inflammation, atherogenesis and plaque destabilization, all of which are involved in the pathogenesis of MI (myocardial infarction). We hypothesized that putative functional genetic variation in the two genes encoding uPA and uPAR (PLAU and PLAUR respectively) might influence the susceptibility to MI. We genotyped rs4065 [3′-UTR (untranslated region) *141C>T) and rs2227564 (Pro141Leu) in the PLAU gene as well as rs344781 (−516T>C) in the PLAUR gene in 633 MI patients and 1237 gender- and age-matched control subjects. Our results showed that the T allele of rs4065 was significantly associated with an increased risk of MI, with an adjusted OR (odds ratio) of 1.38 [95% CI (confidence interval), 1.07–1.78; P=0.012) under the dominant model, 1.4 (95% CI, 1.12–1.75; P=0.003) under the additive model and 2.5 (95% CI, 1.15–5.41; P=0.02) under the recessive model. The findings were then replicated in another independent case-control study including 545 MI patients and 597 control subjects. In conclusion, our results suggest that rs4065 might be a previously unknown genetic risk factor for MI in the Chinese Han population.
High Temperature Properties and Decomposition of Inorganic Salts Part 3, Nitrates and Nitrites
Authors: Stern Kurt H.
Published: June 2010

The literature dealing with the high-temperature behavior of inorganic nitrates and nitrites has been critically reviewed. Values of (GTo−H298o)/T of the reactants and products of the decomposition reactions were calculated and have been tabulated from 298 K up to as high a temperature as possible. Equilibrium constants and partial pressures were tabulated. Auxiliary data on phase transitions and densities have also been included. Qualitative information about the thermal decomposition of the salts is reviewed.
Microwave Spectra of Molecules of Astrophysical Interest: 1. Formaldehyde, Formamide, and Thioformaldehyde
Authors: Johnson Donald R , Lovas Frank J. , Kirchhoff William H.
Published: June 2010

The available data on the microwave spectra of formaldehyde, formamide, and thioformaldehyde are critically reviewed for information applicable to radio astronomy. Molecular data such as rotational constants, centrifugal distortion parameters, dipole moments, hyperfine coupling constants, and structural parameters are tabulated. Observed rotational transitions are presented for the astronomically interesting isotopic forms of these molecules when available. Detailed centrifugal distortion calculations have been carried out for the most abundant isotopic forms of these molecules, namely, H212C16O, H213C16O, 14NH212CH16O, and H212C32S. Transitions have been predicted and tabulated for the frequency ranges 1 MHz to 300 GHz for H212C16O,100 MHz to 300 GHz for H213C16O,500 MHz to 180 GHz for 14NH212CH16O,100 MHz to 300 GHz for H212C32S. All predicted transitions include 95 percent confidence limits; measured transition error limits have been reproduced from the original literature. References are given for all data included.
Osmotic Coefficients and Mean Activity Coefficients of Uni-univalent Electrolytes in Water at 25°C
Authors: Hamer Walter J. , Wu Yung-Chi
Published: June 2010

This paper gives values for the osmotic coefficients and mean activity coefficients of uni-univalent electrolytes in aqueous solutions at 25 °C. The values are expressed on the molality or weight basis. The data available in the literature have been corrected to the presently accepted scales of atomic weights (1969) and temperature (IPST 1968) and, where necessary, to the absolute electrical units of 1969 and the fundamental constants of 1963. The selected values of osmotic coefficients and mean activity coefficients for individual electrolytes have been made internally consistent thermodynamically. In some cases estimated values are given; in other cases, references only are given when the data are sparse or unsuited to critical evaluation. Values of the osmotic coefficients and mean activity coefficients of 79 compounds are given together with the standard deviation, variance, and normalized standard deviation of their fit to equations which express these quantities as functions of electrolyte concentration. Finally, literature references are given to data on 51 additional uni-univalent electrolytes.
The Viscosity and Thermal Conductivity Coefficients of Gaseous and Liquid Fluorine
Authors: Hanley H. J. M. , Prydz R.
Published: June 2010

Tables of values for the viscosity and thermal conductivity of fluorine are presented in the range 70–300 K for pressures up to 200 atmospheres. Experimental results were reviewed but were judged to be unreliable. Accordingly, dilute gas values were determined from kinetic theory using the m-6–8 potential, and dense gas and liquid values were obtained from the modified Enskog theory. The critical point anomaly in the thermal conductivity coefficient is also discussed.
Colour Constancy: Influence of Viewing Behaviour on Grey Settings
Authors: Golz Jürgen
Published: June 2010

In numerous studies on colour constancy or colour induction subjects have to adjust a test field so that it looks achromatic. Their viewing behaviour during these settings is often not controlled or reported. Here I show that the results of grey settings depend on whether subjects visually explore the stimulus by looking around or fixate their gaze exclusively on the test field. Two different viewing instructions are compared with regard to the degree of constancy as measured by the shift of grey settings in coloured surrounds. In variegated surrounds (but not in uniform surrounds) there is a robust effect of viewing condition for all subjects and all surround chromaticities tested, in that exploration increases colour constancy compared to fixating the test field. Values of a colour constancy index are increased by as much as 20% (where 100% colour constancy means that the subject chooses as grey the mean chromaticity of the surround) with an average across all subjects and surrounds of 12.6%. Thus, if this factor is not experimentally controlled, it could inflate variance, reduce comparability between different studies, and even lead to unwarranted conclusions if viewing behaviour unpredictably differs between experimental conditions.
Higher Prevalence of Synaesthesia in Art Students
Authors: Rothen Nicolas , Meier Beat
Published: June 2010

Synaesthesia may facilitate the expression of creativity. Therefore synaesthetes may be more common in the world of creative art. To test this possibility, we used behavioural and phenomenological measures to assess the existence of grapheme–colour synaesthesia in a sample of art students ( N = 99) and a control sample ( N = 96). We found a prevalence of about 7% in the former and about 2% in the latter. Our findings suggest that synaesthesia may indeed be more common in art students.
Structures of a platelet-derived growth factor/propeptide complex and a platelet-derived growth factor/receptor complex
Authors: Hye-Ryong Shim Ann , Liu Heli , Focia Pamela J. , Chen Xiaoyan , Lin P. Charles , He Xiaolin
Published: June 2010

Platelet-derived growth factors (PDGFs) and their receptors (PDGFRs) are prototypic growth factors and receptor tyrosine kinases which have critical functions in development. We show that PDGFs share a conserved region in their prodomain sequences which can remain noncovalently associated with the mature cystine-knot growth factor domain after processing. The structure of the PDGF-A/propeptide complex reveals this conserved, hydrophobic association mode. We also present the structure of the complex between PDGF-B and the first three Ig domains of PDGFRβ, showing that two PDGF-B protomers clamp PDGFRβ at their dimerization seam. The PDGF-B:PDGFRβ interface is predominantly hydrophobic, and PDGFRs and the PDGF propeptides occupy overlapping positions on mature PDGFs, rationalizing the need of propeptides by PDGFs to cover functionally important hydrophobic surfaces during secretion. A large-scale structural organization and rearrangement is observed for PDGF-B upon receptor binding, in which the PDGF-B L1 loop, disordered in the structure of the free form, adopts a highly specific conformation to form hydrophobic interactions with the third Ig domain of PDGFRβ. Calorimetric data also shows that the membrane-proximal homotypic PDGFRα interaction, albeit required for activation, contributes negatively to ligand binding. The structural and biochemical data together offer insights into PDGF-PDGFR signaling, as well as strategies for PDGF-antagonism.
Open Elite? Social Mobility, Marriage, and Family in Florence, 1282–1494*
Authors: Padgett John F.
Published: June 2010

This article statistically analyzes quantitative data from numerous sources in order to assess changes in marriage patterns, family structure, and rates of social mobility during the period from 1282 to 1494. During this period, three systems of social stratification coexisted — wealth, political office, and age of family — but these contending status systems were not consistent in their rankings of families. Each status system was conservative in the sense that elite families at the top of that hierarchy married each other in order to stabilize their position. But because of inconsistency in rankings, contradiction within the elite opened up the Florentine marriage system to widespread upward social mobility by new men. In their own families, successful new men aggressively imitated their economically and politically declining status superiors. Sharp class divisions thereby blurred into continuous and negotiable status gradients. These open-elite patterns of social mobility, present throughout the early Florentine Renaissance, were most extreme during the Albizzi regime, immediately following the Ciompi Revolt.
Family Matters: William of Orange and the Habsburgs after the Abdication of Charles V (1555–67)*
Authors: Geevers Liesbeth
Published: June 2010

The Habsburgs and the Nassaus, who collaborated during the reign of Charles V, clashed sharply during the reign of Philip II: William of Nassau, Prince of Orange, became the leader of the Dutch Revolt. Instead of focusing on religious and political matters in the Netherlands, this article examines the underlying development of both men's dynastic identity to explain this new hostility. I argue that Habsburg family affairs — the division of the dynasty into two branches — led to an increasingly Spanish dynastic identity on Philip's part, while William could not, or would not, break free from his German-focused family identity, leading to a crucial loss of common ground between the two men.
Folding-competent and Folding-defective Forms of Ricin A Chain Have Different Fates after Retrotranslocation from the Endoplasmic Reticulum
Authors: Li Shuyu , Spooner Robert A. , Allen Stuart C. H. , Guise Christopher P. , Ladds Graham , Schnöder Tina , Schmitt Manfred J. , Lord J. Michael , Roberts Lynne M.
Published: June 2010

We report that a toxic polypeptide retaining the potential to refold upon dislocation from the endoplasmic reticulum (ER) to the cytosol (ricin A chain; RTA) and a misfolded version that cannot (termed RTAΔ), follow ER-associated degradation (ERAD) pathways in Saccharomyces cerevisiae that substantially diverge in the cytosol. Both polypeptides are dislocated in a step mediated by the transmembrane Hrd1p ubiquitin ligase complex and subsequently degraded. Canonical polyubiquitylation is not a prerequisite for this interaction because a catalytically inactive Hrd1p E3 ubiquitin ligase retains the ability to retrotranslocate RTA, and variants lacking one or both endogenous lysyl residues also require the Hrd1p complex. In the case of native RTA, we established that dislocation also depends on other components of the classical ERAD-L pathway as well as an ongoing ER–Golgi transport. However, the dislocation pathways deviate strikingly upon entry into the cytosol. Here, the CDC48 complex is required only for RTAΔ, although the involvement of individual ATPases (Rpt proteins) in the 19S regulatory particle (RP) of the proteasome, and the 20S catalytic chamber itself, is very different for the two RTA variants. We conclude that cytosolic ERAD components, particularly the proteasome RP, can discriminate between structural features of the same substrate.
Homolonto: generating homology relationships by pairwise alignment of ontologies and application to vertebrate anatomy
Authors: Parmentier Gilles , Bastian Frederic B. , Robinson-Rechavi Marc
Published: June 2010

Motivation: The anatomy of model species is described in ontologies, which are used to standardize the annotations of experimental data, such as gene expression patterns. To compare such data between species, we need to establish relations between ontologies describing different species.

Results: We present a new algorithm, and its implementation in the software Homolonto, to create new relationships between anatomical ontologies, based on the homology concept. Homolonto uses a supervised ontology alignment approach. Several alignments can be merged, forming homology groups. We also present an algorithm to generate relationships between these homology groups. This has been used to build a multi-species ontology, for the database of gene expression evolution Bgee.

Availability: download section of the Bgee website http://bgee.unil.ch/

Contact:  marc.robinson-rechavi@unil.ch

Supplementary information:  Supplementary data are available at Bioinformatics online.
A computational genomics pipeline for prokaryotic sequencing projects
Authors: Kislyuk Andrey O. , Katz Lee S. , Agrawal Sonia , Hagen Matthew S. , Conley Andrew B. , Jayaraman Pushkala , Nelakuditi Viswateja , Humphrey Jay C. , Sammons Scott A. , Govil Dhwani , Mair Raydel D. , Tatti Kathleen M. , Tondella Maria L. , Harcourt Brian H. , Mayer Leonard W. , Jordan I. King
Published: June 2010

Motivation: New sequencing technologies have accelerated research on prokaryotic genomes and have made genome sequencing operations outside major genome sequencing centers routine. However, no off-the-shelf solution exists for the combined assembly, gene prediction, genome annotation and data presentation necessary to interpret sequencing data. The resulting requirement to invest significant resources into custom informatics support for genome sequencing projects remains a major impediment to the accessibility of high-throughput sequence data.

Results: We present a self-contained, automated high-throughput open source genome sequencing and computational genomics pipeline suitable for prokaryotic sequencing projects. The pipeline has been used at the Georgia Institute of Technology and the Centers for Disease Control and Prevention for the analysis of Neisseria meningitidis and Bordetella bronchiseptica genomes. The pipeline is capable of enhanced or manually assisted reference-based assembly using multiple assemblers and modes; gene predictor combining; and functional annotation of genes and gene products. Because every component of the pipeline is executed on a local machine with no need to access resources over the Internet, the pipeline is suitable for projects of a sensitive nature. Annotation of virulence-related features makes the pipeline particularly useful for projects working with pathogenic prokaryotes.

Availability and implementation: The pipeline is licensed under the open-source GNU General Public License and available at the Georgia Tech Neisseria Base (http://nbase.biology.gatech.edu/). The pipeline is implemented with a combination of Perl, Bourne Shell and MySQL and is compatible with Linux and other Unix systems.

Contact:  king.jordan@biology.gatech.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
A more precise characterization of chaperonin substrates
Authors: Raineri Emanuele , Ribeca Paolo , Serrano Luis , Maier Tobias
Published: June 2010

Motivation: Molecular chaperones prevent the aggregation of their substrate proteins and thereby ensure that they reach their functional native state. The bacterial GroEL/ES chaperonin system is understood in great detail on a structural, mechanistic and functional level; its interactors in Escherichia coli have been identified and characterized. However, a long-standing question in the field is: What makes a protein a chaperone substrate?

Results: Here we identify, using a bioinformatics-based approach a simple set of quantities, which characterize the GroEL-substrate proteome. We define three novel parameters differentiating GroEL interactors from other cellular proteins: lower rate of evolution, hydrophobicity and aggregation propensity. Combining them with other known features to a simple Bayesian predictor allows us to identify known homologous and heterologous GroEL substrateproteins. We discuss our findings in relation to established mechanisms of protein folding and evolutionary buffering by chaperones.

Contact:  tobias.maier@crg.es

Supplementary information:  Supplementary data is available at Bioinformatics online.
Mutagenesis of 18 Type III Effectors Reveals Virulence Function of XopZPXO99 in Xanthomonas oryzae pv. oryzae
Authors: Song Congfeng , Yang Bing
Published: June 2010

Xanthomonas oryzae pv. oryzae depends on a type III secretion system (T3SS) to translocate effectors into host cells for its ability to cause bacterial blight of rice. All type III (T3) effectors with known function in X. oryzae pv. oryzae belong to a family of transcription activator-like (TAL) effectors. However, other, non–TAL-related effector genes are present in the genome, although their role in virulence and their mode of action have yet to be elucidated. Here, we report the generation of mutants for 18 non-TAL T3 effector genes and the identification of one that contributes to the virulence of strain PXO99A. XopZPXO99 encodes a predicted 1,414-amino-acid protein of unknown function. PXO99A contains two identical copies of the gene due to a duplication of 212 kb in the genome. Strains with knockout mutations of one copy of XopZPXO99 did not exhibit any visible virulence defect. However, strains with mutations in both copies of XopZPXO99 displayed reduced virulence in terms of lesion length and bacterial multiplication compared with PXO99A. The introduction of one genomic copy of XopZPXO99 restores the mutant to full virulence. Transient expression of XopZPXO99 in Nicotiana benthamiana leaves suppresses host basal defense, which is otherwise induced by a T3SS mutant of PXO99A, suggesting a role for XopZPXO99 in interfering with host innate immunity during X. oryzae pv. oryzae infection. XopZPXO99-related genes are found in all Xanthomonas spp. whose genomic sequences have been determined, suggesting a conserved role for this type of effector gene in pathogenesis of Xanthomonas spp. Our results indicate that XopZPXO99 encodes a novel T3 effector and contributes virulence to X. oryzae pv. oryzae strains for bacterial blight of rice.
Effector-Triggered and Pathogen-Associated Molecular Pattern–Triggered Immunity Differentially Contribute to Basal Resistance to Pseudomonas syringae
Authors: Zhang Jie , Lu Haibin , Li Xinyan , Li Yan , Cui Haitao , Wen Chi-Kuang , Tang Xiaoyan , Su Zhen , Zhou Jian-Min
Published: June 2010

Pathogens induce pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI) in plants. PAMPs are microbial molecules recognized by host plants as nonself signals, whereas pathogen effectors are evolved to aid in parasitism but are sometimes recognized by specific intracellular resistance proteins. In the absence of detectable ETI determining classical incompatible interactions, basal resistance exists during compatible and nonhost interactions. What triggers the basal resistance has remained elusive. Here, we provide evidence that ETI contributes to basal resistance during both compatible and nonhost Arabidopsis–Pseudomonas syringae interactions. Mutations in RAR1 and NDR1, two genes required for ETI, compromise basal resistance in both compatible and nonhost interactions. Complete nonhost resistance to P. syringae pv. tabaci required a functional type III secretion system. PTI appears to play a greater role in nonhost resistance than basal resistance during compatible interactions, because abrogation of PTI compromises basal resistance during nonhost but not compatible interactions. Strikingly, simultaneous abrogation of ETI and flagellin-induced PTI rendered plants completely susceptible to the nonadapted bacterium P. syringae pv. tabaci, indicating that ETI and PTI act synergistically during nonhost resistance. Thus, both nonhost resistance and basal resistance to virulent bacteria can be unified under PTI and ETI.
Development of an Advisory System for Grapevine Powdery Mildew in Eastern North America: A Reassessment of Epidemic Progress
Authors: Moyer Michelle M. , Gadoury David M. , Magarey Peter A. , Wilcox Wayne F. , Seem Robert C.
Published: June 2010

Historical data indicated that year-to-year variation in severity of powdery mildew fruit infection in New York was not directly related to annual variations in temperature or relative humidity through their known effects upon conidial germination, colony expansion, or latent period. Although severity of fruit infection varied from 0.02 to 61% among years, these environmental factors generally remained in the optimal range for the pathogen, with only slight year-to-year variations during the brief period that fruit were susceptible to infection. Vineyard experiments in New York and Australia indicated that colony growth was slower and sparser than would be expected from previous lab studies. Additional experiments indicated that transient exposure to temperatures near 4°C for a few hours had a debilitating effect on mildew colonies and produced growth similar to that observed on ontogenically-resistant tissues: slow and sparse with epidermal necrosis. Additional studies on seasonal release of ascospores from overwintering cleistothecia indicated that a large proportion of inoculum was often released prior to local grapevine budbreak at multiple sites in the eastern USA. These findings may represent key elements in forecasting potential severity of fruit infection in cool climates such as New York.

Accepted for publication 28 January 2010. Published 26 May 2010.
Validation of a Preclinical Spinal Safety Model
Authors: Westin B. David , Walker Suellen M. , Deumens Ronald , Grafe Marjorie , Yaksh Tony L.
Published: June 2010

Background

Preclinical studies demonstrate increased neuroapoptosis after general anesthesia in early life. Neuraxial techniques may minimize potential risks, but there has been no systematic evaluation of spinal analgesic safety in developmental models. We aimed to validate a preclinical model for evaluating dose-dependent efficacy, spinal cord toxicity, and long-term function after intrathecal morphine in the neonatal rat.

Methods

Lumbar intrathecal injections were performed in anesthetized rats aged postnatal day (P) 3, 10, and 21. The relationship between injectate volume and segmental spread was assessed postmortem and by in vivo imaging. To determine the antinociceptive dose, mechanical withdrawal thresholds were measured at baseline and 30 min after intrathecal morphine. To evaluate toxicity, doses up to the maximum tolerated were administered, and spinal cord histopathology, apoptosis, and glial response were evaluated 1 and 7 days after P3 or P21 injection. Sensory thresholds and gait analysis were evaluated at P35.

Results

Intrathecal injection can be reliably performed at all postnatal ages and injectate volume influences segmental spread. Intrathecal morphine produced spinally mediated analgesia at all ages with lower dose requirements in younger pups. High-dose intrathecal morphine did not produce signs of spinal cord toxicity or alter long-term function.

Conclusions

The therapeutic ratio for intrathecal morphine (toxic dose/antinociceptive dose) was at least 300 at P3 and at least 20 at P21 (latter doses limited by side effects). These data provide relative efficacy and safety for comparison with other analgesic preparations and contribute supporting evidence for the validity of this preclinical neonatal safety model.
Thoracic Epidural Anesthesia Attenuates Endotoxin-induced Impairment of Gastrointestinal Organ Perfusion
Authors: Schäper Jörn , Ahmed Raees , Perschel Frank Holger , Schäfer Michael , Habazettl Helmut , Welte Martin
Published: June 2010

Background

Systemic inflammation can be associated with a redistribution of organ blood flow and a decrease in gastrointestinal perfusion. Regional sympathetic blockade by means of thoracic epidural anesthesia (TEA) has been shown to improve intestinal microcirculation during systemic inflammation. This study tests the hypothesis that during systemic inflammation, TEA attenuates the impairment of gastrointestinal organ perfusion without compromising blood flow to vital organs.

Methods

Eighteen rats were anesthetized, hemodynamically monitored, and mechanically ventilated with room air. By using fluorescent microspheres, organ perfusion was quantified at baseline, 30 min after the start of epidural infusion of either 2% lidocaine (TEA) or normal saline (control), and after 60 and 120 min of intravenous Escherichia coli lipopolysaccharide infusion in TEA and control animals.

Results

Blood pressure initially was lower in TEA animals, but it was comparable to controls during endotoxemia. Gastrointestinal organ perfusion significantly decreased after 120 min of endotoxemia in the controls but not in the TEA animals (-23 +/- 27% vs. -6 +/- 26%, mean +/- SD, P < 0.05). Perfusion of the vital organs such as the heart, brain, liver, and kidneys was comparable between controls and TEA after 120 min of endotoxemia.

Conclusions

TEA attenuates the impairment of gastrointestinal organ perfusion during endotoxemia. Hence, the protective effects of TEA on intestinal microcirculation during endotoxemia may be due to a higher total organ blood flow compared with endotoxemic control animals. Furthermore, in the course of endotoxemia, TEA provides hemodynamic stability and does not compromise blood flow to vital organs.
Skin Conductance Fluctuations Correlate Poorly with Postoperative Self-report Pain Measures in School-aged Children
Authors: Choo Eugene K. , Magruder William , Montgomery Carolyne J. , Lim Joanne , Brant Rollin , Ansermino J. Mark
Published: June 2010

Background

The number of fluctuations of skin conductance per second (NFSC) has been shown to correlate with induced pain and self-report pain scales. This study aimed to evaluate the validity and feasibility of NFSC as an objective measurement of nociception intensity in school-aged children after surgery.

Methods

After approval by the research ethics board and obtaining consent, 100 subjects participated in this prospective observational study. Preoperatively, NFSC was measured for 60 s at rest and during response to a self-report pain scale (numeric rating scale [NRS], Faces Pain Scale-Revised) and anxiety scoring (NRS). Postoperative measurements were repeated every 10 min for 30 min or until NRS pain score was <or= 4 for two consecutive scores. Spearman rank correlation coefficients were calculated to investigate the relationship between NFSC and NRS pain, Faces Pain Scale-Revised, and NRS anxiety. The clinical utility of using NFSC in determining NRS pain threshold was investigated using receiver operator characteristics analysis. For clinical relevance, a cutoff NFSC was chosen that optimizes both specificity and sensitivity. Although selecting a low cutoff value increases the sensitivity of the NFSC in diagnosing pain, it does so at the expense of specificity.

Results

Data from 90 subjects (64.4% male) aged 7-17 yr (median age 13 yr) were analyzed (217 postoperative datasets). NFSC correlated weakly with NRS pain scores (P = 0.21; P < 0.002). NFSC did not correlate with NRS anxiety scores (P = 0.15, P < 0.03). NRS pain scores correlated strongly with Faces Pain Scale-Revised (P = 0.89, P < 0.0001) and weakly with NRS anxiety scores (P = 0.34, P < 0.0001). A threshold of 0.23 NFSC predicted severe pain (NRS >or= 7) with 56.3% sensitivity (95% CI = 37.7-73.6%) and 78.4% specificity (95% CI = 71.7-84.1%). The area under receiver operator characteristic curve for NFSC was 69.1%.

Conclusions

NFSC measurement is feasible in a perioperative setting but was not specific for postoperative pain intensity and was unable to identify analgesia requirements when compared with self-report measures.
Eavesdropping in crabs: an agency for lady detection
Authors: Milner Richard N. C. , Jennions Michael D. , Backwell Patricia R. Y.
Published: June 2010

Although conspicuous courtship displays are an effective way of attracting the attention of receptive females, they could provide valuable information to rival males on the location of these females. In fiddler crabs, males that see a receptive female wave their single, greatly enlarged claw in a highly conspicuous courtship display. We test whether other males use this courtship display to alert them to the presence of receptive females that they cannot directly see. We show that male fiddler crabs (
Uca mjoebergi
) eavesdrop on the courtship displays of nearby males to detect mate-searching females. This allows males to begin waving before a female becomes visible. Furthermore, males appear to adjust their waving according to the information available: eavesdropping males wave 12 times faster than non-courting males but only 1.7 times slower than males in full visual contact with the female.
Size mapping of electric field-assisted production of polycaprolactone particles
Authors: Enayati M. , Ahmad Z. , Stride E. , Edirisinghe M.
Published: June 2010

In this investigation, biodegradable polycaprolactone polymeric particles (300–4500 nm in diameter) were prepared by jetting a solution in an electric field. An extensive study has been carried out to determine how the size and size distribution of the particles generated can be controlled by systematically varying the polymer concentration in solution (and thereby its viscosity and electrical conductivity), and also the selected flow rate (2–50 µl min
−1
) and applied voltage (0–15 kV) during particle generation. Change in these parameters affects the mode of jetting, and within the stable cone-jet mode window, an increase in the applied voltage (approx. 15 kV) resulted in a reduction in particle size and this was more pronounced at high flow rates (such as; 30, 40 and 50 µl min
−1
) in the same region. The carrier particles were more polydisperse at the peripheral regions of the stable cone-jet mode, as defined in the applied voltage-flow rate parametric map. The effect of loading a drug on the particle size, size distribution and encapsulation efficiency was also studied. Release from drug-loaded particles was investigated using UV spectrophotometry over 45 days. This work demonstrates a powerful method of generating drug-loaded polymeric particles, with the ability to control size and polydispersivity, which has great potential in several categories of biotechnology requiring carrier particles, such as drug delivery and gene therapy.
Nanostructure and molecular mechanics of spider dragline silk protein assemblies
Authors: Keten Sinan , Buehler Markus J.
Published: June 2010

Spider silk is a self-assembling biopolymer that outperforms most known materials in terms of its mechanical performance, despite its underlying weak chemical bonding based on H-bonds. While experimental studies have shown that the molecular structure of silk proteins has a direct influence on the stiffness, toughness and failure strength of silk, no molecular-level analysis of the nanostructure and associated mechanical properties of silk assemblies have been reported. Here, we report atomic-level structures of MaSp1 and MaSp2 proteins from the
Nephila clavipes
spider dragline silk sequence, obtained using replica exchange molecular dynamics, and subject these structures to mechanical loading for a detailed nanomechanical analysis. The structural analysis reveals that poly-alanine regions in silk predominantly form distinct and orderly beta-sheet crystal domains, while disorderly regions are formed by glycine-rich repeats that consist of 3
1
-helix type structures and beta-turns. Our structural predictions are validated against experimental data based on dihedral angle pair calculations presented in Ramachandran plots, alpha-carbon atomic distances, as well as secondary structure content. Mechanical shearing simulations on selected structures illustrate that the nanoscale behaviour of silk protein assemblies is controlled by the distinctly different secondary structure content and hydrogen bonding in the crystalline and semi-amorphous regions. Both structural and mechanical characterization results show excellent agreement with available experimental evidence. Our findings set the stage for extensive atomistic investigations of silk, which may contribute towards an improved understanding of the source of the strength and toughness of this biological superfibre.
Predicting the onset of high-frequency self-excited oscillations in elastic-walled tubes
Authors: Whittaker Robert J. , Heil Matthias , Jensen Oliver E. , Waters Sarah L.
Published: June 2010

We present a theoretical description of flow-induced self-excited oscillations in the Starling resistor—a pre-stretched thin-walled elastic tube that is mounted on two rigid tubes and enclosed in a pressure chamber. Assuming that the flow through the elastic tube is driven by imposing the flow rate at the downstream end, we study the development of small-amplitude long-wavelength high-frequency oscillations, combining the results of two previous studies in which we analysed the fluid and solid mechanics of the problem in isolation. We derive a one-dimensional eigenvalue problem for the frequencies and mode shapes of the oscillations, and determine the slow growth or decay of the normal modes by considering the system’s energy budget. We compare the theoretical predictions for the mode shapes, frequencies and growth rates with the results of direct numerical simulations, based on the solution of the three-dimensional Navier–Stokes equations, coupled to the equations of shell theory, and find good agreement between the results. Our results provide the first asymptotic predictions for the onset of self-excited oscillations in three-dimensional collapsible tube flows.
Neutral shells and their applications in the design of electromagnetic shields
Authors: Liu L. P.
Published: June 2010

We present a simple design of electromagnetic shields for both field expelling and field confinement. Motivated by the concept of neutral inclusions in the theory of composites, we introduce two concepts of neutral shells, and use neutral shells to construct our designs of electromagnetic shields. We also discuss the relationships between electromagnetic shields and cloaking structures and argue that the designed shields are capable of ‘cloaking’ for plane waves in the long-wavelength limit.
Ruminant diets and the Miocene extinction of European great apes
Authors: Merceron Gildas , Kaiser Thomas M. , Kostopoulos Dimitris S. , Schulz Ellen
Published: June 2010

The successful evolutionary radiations of European hominoids and pliopithecoids came to an end during the Late Miocene. Using ruminant diets as environmental proxies, it becomes possible to detect variations in vegetation over time with the potential to explain fluctuations in primate diversity along a NW–SE European transect. Analysis shows that ruminants had diverse diets when primate diversity reached its peak, with more grazers in eastern Europe and more browsers farther west. After the drop in primate diversity, grazers accounted for a greater part of western and central European communities. Eastwards, the converse trend was evident with more browsing ruminants. These opposite trends indicate habitat loss and an increase in environmental uniformity that may have severely favoured the decline of primate diversity.
Harnessing disorder: onychophorans use highly unstructured proteins, not silks, for prey capture
Authors: Haritos Victoria S. , Niranjane Ajay , Weisman Sarah , Trueman Holly E. , Sriskantha Alagacone , Sutherland Tara D.
Published: June 2010

Onychophora are ancient, carnivorous soft-bodied invertebrates which capture their prey in slime that originates from dedicated glands located on either side of the head. While the biochemical composition of the slime is known, its unusual nature and the mechanism of ensnaring thread formation have remained elusive. We have examined gene expression in the slime gland from an Australian onychophoran,
Euperipatoides rowelli
, and matched expressed sequence tags to separated proteins from the slime. The analysis revealed three categories of protein present: unique high-molecular-weight proline-rich proteins, and smaller concentrations of lectins and small peptides, the latter two likely to act as protease inhibitors and antimicrobial agents. The predominant proline-rich proteins (200 kDa+) are composed of tandem repeated motifs and distinguished by an unusually high proline and charged residue content. Unlike the highly structured proteins such as silks used for prey capture by spiders and insects, these proteins lack ordered secondary structure over their entire length. We propose that on expulsion of slime from the gland onto prey, evaporative water loss triggers a glass transition change in the protein solution, resulting in adhesive and enmeshing thread formation, assisted by cross-linking of complementary charged and hydrophobic regions of the protein.
Euperipatoides rowelli
has developed an entirely new method of capturing prey by harnessing disordered proteins rather than structured, silk-like proteins.