bluuebunny/crossref_metadata_2025 huggingface dataset:
Capillary pressure and liquid wicking in three-dimensional nonwoven materials
Authors: Mao N. , Russell S. J.
Published: August 2008

The capillary pressure and liquid wicking in fibrous nonwoven materials depend on the structural arrangement of fibers in three dimensions, which is influenced by the method and conditions used to manufacture the material. By adapting the hydraulic radius mechanism and drag force theory, a model is established for predicting the directional capillary pressure in three-dimensional nonwoven materials. As a case study, equations to predict the velocity of liquid wicking in a one-dimensional wicking strip test for nonwovens having a three-dimensional fiber orientation distribution are given based on the newly established capillary pressure model. These models and equations are based on measurable structural parameters including the fiber orientation distribution, fiber diameter, and fabric porosity.
Path integral calculation of free energies: Quantum effects on the melting temperature of neon
Authors: Ramírez R. , Herrero C. P. , Antonelli A. , Hernández E. R.
Published: August 2008

The path integral formulation has been combined with several methods to determine free energies of quantum many-body systems, such as adiabatic switching and reversible scaling. These techniques are alternatives to the standard thermodynamic integration method. A quantum Einstein crystal is used as a model to demonstrate the accuracy and reliability of these free energy methods in quantum simulations. Our main interest focuses on the calculation of the melting temperature of Ne at ambient pressure, taking into account quantum effects in the atomic dynamics. The free energy of the solid was calculated by considering a quantum Einstein crystal as reference state, while for the liquid, the reference state was defined by the classical limit of the fluid. Our findings indicate that, while quantum effects in the melting temperature of this system are small, they still amount to about 6% of the melting temperature, and are therefore not negligible. The particle density as well as the melting enthalpy and entropy of the solid and liquid phases at coexistence is compared to results obtained in the classical limit and also to available experimental data.
Effect of thickness on structural, electrical, and electrochemical properties of platinum/titanium bilayer counterelectrode
Authors: Zhou Conghua , Hu Hao , Yang Ying , Chen Bolei , Zhang Jing , Wu Sujuan , Xu Sheng , Xiong Xiaodong , Han Hongwei , Zhao Xingzhong
Published: August 2008

To strengthen the adhesion of platinum layer to counterelectrodes of dye sensitized solar cells, titanium thin film has been utilized as adhesion layer between platinum and substrate [Wei et al., Appl. Phys. Lett. 90, 153122 (2007)]. In our study, platinum/titanium bilayer counterelectrodes were fabricated by magnetron sputtering. The structural, electrical, and electrochemical properties of the bilayer counterelectrode were studied by varying the thickness of both platinum and titanium layers. The influence of both electrochemical active surface and crystallite size on charge transfer resistance of the bilayer counterelectrode was explored. From these evaluations, it was found that the as-prepared titanium layer was almost amorphous, and intermetallic phase was formed between platinum and titanium layers. As expected, sheet resistance of the electrode decreased with the increase in deposition time of both platinum and titanium layers. Metal titanium was found to be inert in the catalyzing reduction in tri-iodide. With the increment of deposition time of platinum layers, charge transfer resistance of the electrode decreased quickly first, and then reached a plateau after which it changed slightly. This outcome differs from that reported before. Careful examination showed that such a behavior was related closely to the electrochemical active surface area of electrode and platinum crystallite size. For a given electrolyte, charge transfer resistance decreased with the increase in electrochemical active surface and increased with the increment of the latter. Thus, a competition was observed between the two factors, which supports the suggestion of former researchers.
Assignment of Raman-active vibrational modes of MgTiO3
Authors: Wang Chun-Hai , Jing Xi-Ping , Feng Wei , Lu Jing
Published: August 2008

MgTiO 3 ceramic sample was synthesized and its Raman spectra were recorded. The Raman-active vibrational modes of MgTiO3 were calculated using first-principle calculations (density functional theory). Based on experimental data and calculation results, the Raman peaks were assigned as 225 cm−1 (Ag), 306 cm−1 (Ag), 398 cm−1 (Ag), 500 cm−1 (Ag), 715 cm−1 (Ag) and 281 cm−1 (Eg), 328 cm−1 (Eg), 353 cm−1 (Eg), 486 cm−1 (Eg), 641 cm−1 (Eg). The assignment was supported by the polarized Raman spectrum. Meanwhile, the symmetry coordinates of MgTiO3 primitive cell were analyzed and employed to expand the Raman-active modes.
Time delays and energy transport velocities in three dimensional ideal cloaking devices
Authors: Chen Huanyang , Chan C. T.
Published: August 2008

We obtain the energy transport velocity distribution for a three dimensional ideal cloak explicitly. Near the operation frequency, the energy transport velocity has a rather peculiar distribution. The transport velocity along the direction pointing at the center of the cloak is found to be a constant, while the transport velocity approaches zero at the inner boundary of the cloak. A ray pointing right into the center of the cloak will experience abrupt changes in velocities when it impinges on the inner surface of the cloak. This peculiar distribution causes long time delays for beams passing through the ideal cloak within a geometric optics description.
Microwave dielectric resonator biosensor for aqueous glucose solution
Authors: Kim Jongchul , Babajanyan Arsen , Hovsepyan Artur , Lee Kiejin , Friedman Barry
Published: August 2008

We report a near-field microwave biosensor based on a dielectric resonator to detect glucose concentration. A microwave biosensor with a high Q dielectric resonator allows observation of the small variation of the glucose concentration by measuring the shift of the resonance frequency and the microwave reflection coefficient S11. We observed the concentration of glucose with a detectable resolution up to 5mg∕ml at an operating frequency of about f=1.68GHz. The change in the glucose concentration is directly related to the change in the reflection coefficient due to the electromagnetic interaction between the dielectric resonator and the glucose solution.
Collisionless instability of thin current sheets in the presence of sheared parallel flows
Authors: Roytershteyn V. , Daughton W.
Published: August 2008

The first results of an ongoing investigation of the influence of sheared parallel flows on the onset of collisionless magnetic reconnection in thin current sheets are reported. In particular, an exact kinetic equilibrium that incorporates flow with a symmetric profile into the well-known Harris model is proposed and its linear stability is described. The complete linearized Vlasov–Maxwell system is solved using a numerical approach that introduces no approximations regarding the shape of the particle orbits or relative magnitude of the different components of the electromagnetic potentials. Thus accurate results are obtained in a difficult, but practically important limit where the characteristic length scales for the variation of the equilibrium magnetic field and flow are comparable to the ion kinetic length scales. In particular, the dispersion relation for an instability that produces magnetic reconnection is traced as a function of the flow speed V0 at the center of the sheet, starting with the collisionless tearing mode at V0=0. The effects of the sheared flow are shown to qualitatively depend on the thickness of the current sheet. In relatively thick sheets the characteristic features of the dispersion relation depend mostly on the value of the flow shear. In this regime there exist regions of the parameter space where the flow is destabilizing. However, the growth rate of the instability never significantly exceeds that of the collisionless tearing mode and the mode is always stabilized at high enough values of V0. When the sheet is thinner than the ion gyroradius in the asymptotic magnetic field, the flow shear introduces strong non-Maxwellian features into the equilibrium distribution function. In this regime, the flow is purely stabilizing for the equilibrium considered. The instability produces magnetic reconnection in all the parameter regimes considered. Finally, the results of the linear analysis are verified using large-scale particle-in-cell simulations.
Holographic imaging using the phase coherent photorefractive effect in ZnSe quantum wells
Authors: Kabir A. , Ajward A. M. , Wagner H. P.
Published: August 2008

We demonstrate wide-field real-time, and depth-resolved holographic imaging of various reflecting objects using the all-optical phase coherent photorefractive effect in ZnSe quantum wells. In contrast to current photorefractive quantum well devices, these devices use the coherence of excitons as a basis for holography. This has the advantage that the entire depth-resolved information of the object can be obtained from the brightness profile of the holographic image with a resolution of a few micrometers. In addition, the high diffraction efficiency and short refresh time of the phase coherent photorefractive effect allow high-speed video acquisition of moving objects.
Nanocrystalline glass-coated FeNiMoB microwires
Authors: Komova E. , Varga M. , Varga R. , Vojtanik P. , Bednarcik J. , Kovac J. , Provencio M. , Vazquez M.
Published: August 2008

The evolution of the structure of glass-coated Fe40Ni38Mo4B16 amorphous microwire with thermal treatments and its interplay with magnetism has been studied. As shown by x-ray diffraction, a primary crystallization process resulted into formation of γ-(Fe,Ni) nanocrystallites embedded in a residual amorphous matrix. The evolution of the saturation magnetization and the switching field after different thermal treatment was studied. Amorphous glass-coated microwires based on FeNi exhibit magnetic bistability even in the nanocrystalline state. This is explained by the high magnetoelastic anisotropy, which is also responsible for magnetic hardening after annealing at the temperatures above 670 K.
Ion-beam induced fcc-bcc transition in ultrathin Fe films for ferromagnetic patterning
Authors: Rupp W. , Biedermann A. , Kamenik B. , Ritter R. , Klein Ch. , Platzgummer E. , Schmid M. , Varga P.
Published: August 2008

Ar + ion irradiation is used to induce a structural change from fcc to bcc in a 1.5nm thick Fe film epitaxially grown on a Cu(100) crystal. Scanning tunneling microscopy and low-energy electron diffraction show the nucleation of bcc nanocrystals, which grow with increasing ion dose. As a consequence of the structural change, the irradiated iron film becomes strongly ferromagnetic at room temperature. We present a model for the process of the transformation and demonstrate writing a magnetic pattern at the 100nm scale by ion-beam projection lithography.
Using metal-insulator-semiconductor structures to investigate dielectrics charging in capacitive microelectromechanical switches
Authors: San Hai-sheng , Chen Xu-yuan , Xu Peng , Li Gang , Zhan Lin-xian
Published: August 2008

Capacitance-voltage characteristics measured on metal-insulator-semiconductor structures are used to investigate dielectrics charging in the capacitive microelectromechanical switches. An analytical model based on this method has been established. Effects of electrical stress on charge accumulation in silicon-rich nitride were experimentally investigated. The charging parameters of the silicon-rich nitride were extracted by the exponential curve fitting method. The experimental results show that three main physical processes dominate the charging behavior of the silicon-rich nitride. It is expected that the accumulated charges can be eliminated by using an offset square-wave voltage to actuate the switches.
Systemic Darwinism
Authors: Winther Rasmus Grønfeldt
Published: August 2008

Darwin's 19th century evolutionary theory of descent with modification through natural selection opened up a multidimensional and integrative conceptual space for biology. We explore three dimensions of this space: explanatory pattern, levels of selection, and degree of difference among units of the same type. Each dimension is defined by a respective pair of poles: law and narrative explanation, organismic and hierarchical selection, and variational and essentialist thinking. As a consequence of conceptual debates in the 20th century biological sciences, the poles of each pair came to be seen as mutually exclusive opposites. A significant amount of 21st century research focuses on systems (e.g., genomic, cellular, organismic, and ecological/global). Systemic Darwinism is emerging in this context. It follows a “compositional paradigm” according to which complex systems and their hierarchical networks of parts are the focus of biological investigation. Through the investigation of systems, Systemic Darwinism promises to reintegrate each dimension of Darwin's original logical space. Moreover, this ideally and potentially unified theory of biological ontology coordinates and integrates a plurality of mathematical biological theories (e.g., self-organization/structure, cladistics/history, and evolutionary genetics/function). Integrative Systemic Darwinism requires communal articulation from a plurality of perspectives. Although it is more general than these, it draws on previous advances in Systems Theory, Systems Biology, and Hierarchy Theory. Systemic Darwinism would greatly further bioengineering research and would provide a significantly deeper and more critical understanding of biological reality.
The protonmotive force is required for maintaining ATP homeostasis and viability of hypoxic, nonreplicating
Mycobacterium tuberculosis
Authors: Rao Srinivasa P. S. , Alonso Sylvie , Rand Lucinda , Dick Thomas , Pethe Kevin
Published: August 2008

The persistence of
Mycobacterium tuberculosis
despite prolonged chemotherapy represents a major obstacle for the control of tuberculosis. The mechanisms used by Mtb to persist in a quiescent state are largely unknown. Chemical genetic and genetic approaches were used here to study the physiology of hypoxic nonreplicating mycobacteria. We found that the intracellular concentration of ATP is five to six times lower in hypoxic nonreplicating Mtb cells compared with aerobic replicating bacteria, making them exquisitely sensitive to any further depletion. We show that
de novo
ATP synthesis is essential for the viability of hypoxic nonreplicating mycobacteria, requiring the cytoplasmic membrane to be fully energized. In addition, the anaerobic electron transport chain was demonstrated to be necessary for the generation of the protonmotive force. Surprisingly, the alternate ndh-2, but not -1, was shown to be the electron donor to the electron transport chain and to be essential to replenish the [NAD
+
] pool in hypoxic nonreplicating Mtb. Finally, we describe here the high bactericidal activity of the F
0
F
1
ATP synthase inhibitor R207910 on hypoxic nonreplicating bacteria, supporting the potential of this drug candidate for shortening the time of tuberculosis therapy.
The
Bacillus subtilis
iron-sparing response is mediated by a Fur-regulated small RNA and three small, basic proteins
Authors: Gaballa Ahmed , Antelmann Haike , Aguilar Claudio , Khakh Sukhjit K. , Song Kyung-Bok , Smaldone Gregory T. , Helmann John D.
Published: August 2008

Regulation of bacterial iron homeostasis is often controlled by the iron-sensing ferric uptake repressor (Fur). The
Bacillus subtilis
Fur protein acts as an iron-dependent repressor for siderophore biosynthesis and iron transport proteins. Here, we demonstrate that Fur also coordinates an iron-sparing response that acts to repress the expression of iron-rich proteins when iron is limiting. When Fur is inactive, numerous iron-containing proteins are down-regulated, including succinate dehydrogenase, aconitase, cytochromes, and biosynthetic enzymes for heme, cysteine, and branched chain amino acids. As a result, a
fur
mutant grows slowly in a variety of nutrient conditions. Depending on the growth medium, rapid growth can be restored by mutations in one or more of the molecular effectors of the iron-sparing response. These effectors include the products of three Fur-regulated operons that encode a small RNA (FsrA) and three small, basic proteins (FbpA, FbpB, and FbpC). Extensive complementarity between FsrA and the leader region of the succinate dehydrogenase operon is consistent with an RNA-mediated translational repression mechanism for this target. Thus, iron deprivation in
B. subtilis
activates pathways to remodel the proteome to preserve iron for the most critical cellular functions.
Domestication and early agriculture in the Mediterranean Basin: Origins, diffusion, and impact
Authors: Zeder Melinda A.
Published: August 2008

The past decade has witnessed a quantum leap in our understanding of the origins, diffusion, and impact of early agriculture in the Mediterranean Basin. In large measure these advances are attributable to new methods for documenting domestication in plants and animals. The initial steps toward plant and animal domestication in the Eastern Mediterranean can now be pushed back to the 12th millennium cal B.P. Evidence for herd management and crop cultivation appears at least 1,000 years earlier than the morphological changes traditionally used to document domestication. Different species seem to have been domesticated in different parts of the Fertile Crescent, with genetic analyses detecting multiple domestic lineages for each species. Recent evidence suggests that the expansion of domesticates and agricultural economies across the Mediterranean was accomplished by several waves of seafaring colonists who established coastal farming enclaves around the Mediterranean Basin. This process also involved the adoption of domesticates and domestic technologies by indigenous populations and the local domestication of some endemic species. Human environmental impacts are seen in the complete replacement of endemic island faunas by imported mainland fauna and in today's anthropogenic, but threatened, Mediterranean landscapes where sustainable agricultural practices have helped maintain high biodiversity since the Neolithic.
Paleoindian demography and the extraterrestrial impact hypothesis
Authors: Buchanan Briggs , Collard Mark , Edinborough Kevan
Published: August 2008

Recently it has been suggested that one or more large extraterrestrial (ET) objects struck northern North America 12,900 ± 100 calendar years before present (calBP) [Firestone RB,
et al.
(2007)
Proc Natl Acad Sci USA
104: 16016–16021]. This impact is claimed to have triggered the Younger Dryas major cooling event and resulted in the extinction of the North American megafauna. The impact is also claimed to have caused major cultural changes and population decline among the Paleoindians. Here, we report a study in which ≈1,500 radiocarbon dates from archaeological sites in Canada and the United States were used to test the hypothesis that the ET resulted in population decline among the Paleoindians. Following recent studies [e.g., Gamble C, Davies W, Pettitt P, Hazelwood L, Richards M (2005)
Camb Archaeol J
15:193–223), the summed probability distribution of the calibrated dates was used to identify probable changes in human population size between 15,000 and 9,000 calBP. Subsequently, potential biases were evaluated by modeling and spatial analysis of the dated occupations. The results of the analyses were not consistent with the predictions of extraterrestrial impact hypothesis. No evidence of a population decline among the Paleoindians at 12,900 ± 100 calBP was found. Thus, minimally, the study suggests the extraterrestrial impact hypothesis should be amended.
The leaf ionome as a multivariable system to detect a plant's physiological status
Authors: Baxter Ivan R. , Vitek Olga , Lahner Brett , Muthukumar Balasubramaniam , Borghi Monica , Morrissey Joe , Guerinot Mary Lou , Salt David E.
Published: August 2008

The contention that quantitative profiles of biomolecules contain information about the physiological state of the organism has motivated a variety of high-throughput molecular profiling experiments. However, unbiased discovery and validation of biomolecular signatures from these experiments remains a challenge. Here we show that the
Arabidopsis thaliana
(
Arabidopsis
) leaf ionome, or elemental composition, contains such signatures, and we establish statistical models that connect these multivariable signatures to defined physiological responses, such as iron (Fe) and phosphorus (P) homeostasis. Iron is essential for plant growth and development, but potentially toxic at elevated levels. Because of this, shoot Fe concentrations are tightly regulated and show little variation over a range of Fe concentrations in the environment, making them a poor probe of a plant's Fe status. By evaluating the shoot ionome in plants grown under different Fe nutritional conditions, we have established a multivariable ionomic signature for the Fe response status of
Arabidopsis
. This signature has been validated against known Fe-response proteins and allows the high-throughput detection of the Fe status of plants with a false negative/positive rate of 18%/16%. A “metascreen” of previously collected ionomic data from 880
Arabidopsis
mutants and natural accessions for this Fe response signature successfully identified the known Fe mutants
frd1
and
frd3
. A similar approach has also been taken to identify and use a shoot ionomic signature associated with P homeostasis. This study establishes that multivariable ionomic signatures of physiological states associated with mineral nutrient homeostasis do exist in
Arabidopsis
and are in principle robust enough to detect specific physiological responses to environmental or genetic perturbations.
Bayesian motion estimation accounts for a surprising bias in 3D vision
Authors: Welchman Andrew E. , Lam Judith M. , Bülthoff Heinrich H.
Published: August 2008

Determining the approach of a moving object is a vital survival skill that depends on the brain combining information about lateral translation and motion-in-depth. Given the importance of sensing motion for obstacle avoidance, it is surprising that humans make errors, reporting an object will miss them when it is on a collision course with their head. Here we provide evidence that biases observed when participants estimate movement in depth result from the brain's use of a “prior” favoring slow velocity. We formulate a Bayesian model for computing 3D motion using independently estimated parameters for the shape of the visual system's slow velocity prior. We demonstrate the success of this model in accounting for human behavior in separate experiments that assess both sensitivity and bias in 3D motion estimation. Our results show that a surprising perceptual error in 3D motion perception reflects the importance of prior probabilities when estimating environmental properties.
Activation of DegP chaperone-protease via formation of large cage-like oligomers upon binding to substrate proteins
Authors: Jiang Jiansen , Zhang Xuefeng , Chen Yong , Wu Yi , Zhou Z. Hong , Chang Zengyi , Sui Sen-Fang
Published: August 2008

Cells use molecular chaperones and proteases to implement the essential quality control mechanism of proteins. The DegP (HtrA) protein, essential for the survival of
Escherichia coli
cells at elevated temperatures with homologues found in almost all organisms uniquely has both functions. Here we report a mechanism for DegP to activate both functions via formation of large cage-like 12- and 24-mers after binding to substrate proteins. Cryo-electron microscopic and biochemical studies revealed that both oligomers are consistently assembled by blocks of DegP trimers, via pairwise PDZ1–PDZ2 interactions between neighboring trimers. Such interactions simultaneously eliminate the inhibitory effects of the PDZ2 domain. Additionally, both DegP oligomers were also observed in extracts of
E. coli
cells, strongly implicating their physiological importance.
Adhesion molecules (VCAM‐1 and ICAM‐1) and C‐reactive protein in women with history of preeclampsia
Authors: PORTELINHA ANA , BELO LUÍS , TEJERA EDUARDO , REBELO IRENE
Published: August 2008

Several studies suggest that women with previous preeclampsia (PE) are at increased risk of cardiovascular disease (CVD). We examined circulating concentrations of adhesion molecules and C‐reactive protein (CRP), markers for endothelial and inflammatory reactions, in addition to blood pressure and anthropometric measurements in 58 women with a history of PE and 49 control women with no pathology associated to pregnancy. Soluble adhesion molecules were measured by standard commercial ELISA methods and plasma CRP levels by automated enzymatic assays. Systolic and diastolic blood pressures and waist‐to‐hip ratios were significantly higher in women with history of PE than in control group. There were no significant differences in circulating levels of sICAM‐1, sVCAM‐1 and CRP in the study population. Women with a history of PE do not have a persistent inflammatory state that could induce overexpression of these molecules, which was supported by normal levels of CRP. The study supports the existence of common risk factors for PE and CVD, namely obesity and hypertension.
Computational prediction of human proteins that can be secreted into the bloodstream
Authors: Cui Juan , Liu Qi , Puett David , Xu Ying
Published: August 2008

We present a novel computational method for predicting which proteins from highly and abnormally expressed genes in diseased human tissues, such as cancers, can be secreted into the bloodstream, suggesting possible marker proteins for follow-up serum proteomic studies. A main challenging issue in tackling this problem is that our understanding about the downstream localization after proteins are secreted outside the cells is very limited and not sufficient to provide useful hints about secretion to the bloodstream. To bypass this difficulty, we have taken a data mining approach by first collecting, through extensive literature searches, human proteins that are known to be secreted into the bloodstream due to various pathological conditions as detected by previous proteomic studies, and then asking the question: ‘what do these secreted proteins have in common in terms of their physical and chemical properties, amino acid sequence and structural features that can be used to predict them?’ We have identified a list of features, such as signal peptides, transmembrane domains, glycosylation sites, disordered regions, secondary structural content, hydrophobicity and polarity measures that show relevance to protein secretion. Using these features, we have trained a support vector machine-based classifier to predict protein secretion to the bloodstream. On a large test set containing 98 secretory proteins and 6601 non-secretory proteins of human, our classifier achieved ∼90% prediction sensitivity and ∼98% prediction specificity. Several additional datasets are used to further assess the performance of our classifier. On a set of 122 proteins that were found to be of abnormally high abundance in human blood due to various cancers, our program predicted 62 as blood-secreted proteins. By applying our program to abnormally highly expressed genes in gastric cancer and lung cancer tissues detected through microarray gene expression studies, we predicted 13 and 31 as blood secreted, respectively, suggesting that they could serve as potential biomarkers for these two cancers, respectively. Our study demonstrated that our method can provide highly useful information to link genomic and proteomic studies for disease biomarker discovery. Our software can be accessed at http://csbl1.bmb.uga.edu/cgi-bin/Secretion/secretion.cgi.

Contact:  xyn@bmb.uga.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Detection of stoichiometric inconsistencies in biomolecular models
Authors: Gevorgyan Albert , Poolman Mark G. , Fell David A.
Published: August 2008

Motivation: Metabolic modelling provides a mathematically rigorous basis for system-level analysis of biochemical networks. However, the growing sizes of metabolic models can lead to serious problems in their construction and validation. In this work, we describe a relatively poorly investigated type of modelling error, called stoichiometric inconsistencies. These errors are caused by incorrect definitions of reaction stoichiometries and result in conflicts between two fundamental physical constraints to be satisfied by any valid metabolic model: positivity of molecular masses of all metabolites and mass conservation in all interconversions.

Results: We introduce formal definitions of stoichiometric inconsistencies, inconsistent net stoichiometries, elementary leakage modes and other important fundamental properties of incorrectly defined biomolecular networks. Algorithms are described for the verification of stoichiometric consistency of a model, detection of unconserved metabolites and inconsistent minimal net stoichiometries. The usefulness of these algorithms for effective resolving of inconsistencies and for detection of input errors is demonstrated on a published genome-scale metabolic model of Saccharomyces cerevisiae and one of Streptococcus agalactiae constructed using the KEGG database.

Availability:  http://mudshark.brookes.ac.uk/index.php/Albert_Gevorgyan

Contact:  dfell@brookes.ac.uk
SeqMap: mapping massive amount of oligonucleotides to the genome
Authors: Jiang Hui , Wong Wing Hung
Published: August 2008

Summary: SeqMap is a tool for mapping large amount of short sequences to the genome. It is designed for finding all the places in a reference genome where each sequence may come from. This task is essential to the analysis of data from ultra high-throughput sequencing machines. With a carefully designed index-filtering algorithm and an efficient implementation, SeqMap can map tens of millions of short sequences to a genome of several billions of nucleotides. Multiple substitutions and insertions/deletions of the nucleotide bases in the sequences can be tolerated and therefore detected. SeqMap supports FASTA input format and various output formats, and provides command line options for tuning almost every aspect of the mapping process. A typical mapping can be done in a few hours on a desktop PC. Parallel use of SeqMap on a cluster is also very straightforward.

Contact:  whwong@stanford.edu
The Rx Gene Confers Resistance to a Range of Potexviruses in Transgenic Nicotiana Plants
Authors: Baurès Isabelle , Candresse Thierry , Leveau Aymeric , Bendahmane Abdelhafid , Sturbois Bénédicte
Published: August 2008

Rx-mediated resistance was analyzed in Rx-expressing transgenic Nicotiana plants. The infection outcome of nine Potato virus X isolates mutated at amino acid positions 121 and 127 of the coat protein (CP) confirmed the key role of these amino acids but provided a more complex picture than previously reported. In particular, in Rx-expressing Nicotiana spp., eliciting activity modulated by amino acid 121 was conditioned by the nature of amino acid 127. These results suggest that the specificity of recognition might be modulated by host factors that are somehow subtly modified between Rx-expressing potato and Rx-expressing transgenic Nicotiana plants. Moreover, the CP of three Potexviruses, Narcissus mosaic virus (NMV), White clover mosaic virus (WClMV), and Cymbidium mosaic virus (CymMV), are all recognized by the Rx-based machinery and able to trigger an Rx-dependant hypersensitive response. A smaller elicitor of 90 amino acids was identified in the CP of NMV and WClMV, which contains the previously identified key positions 121 and 127. This elicitor is only weakly conserved (approximately 40% identity) among the CP of the various recognized viruses, suggesting that the Rx molecular machinery targets a conserved structural element of the Potexvirus CP rather than a conserved amino acid motif.
Amino Acid Sequence of Bacterial Microbe-Associated Molecular Pattern flg22 Is Required for Virulence
Authors: Naito Kana , Taguchi Fumiko , Suzuki Tomoko , Inagaki Yoshishige , Toyoda Kazuhiro , Shiraishi Tomonori , Ichinose Yuki
Published: August 2008

Flagellin proteins derived from Pseudomonas syringae pv. tabaci 6605 and flg22Pa (QRLSTGSRINSAKDDAAGLQIA), one of the microbe-associated molecular patterns (MAMP) in bacterial flagellin, induce cell death and growth inhibition in Arabidopsis thaliana. To examine the importance of aspartic acid (D) at position 43 from the N-terminus of a flagellin in its elicitor activity, D43 was replaced with valine (V) and alanine (A) in P. syringae pv. tabaci flagellin and flg22Pta. The abilities of flagellins from P. syringae pv. tabaci D43V and D43A to induce cell death and growth inhibition were reduced, whereas the abilities of flg22PtaD43V and flg22PtaD43A were abolished. These results indicate that D43 is important for elicitor activity in P. syringae pv. tabaci. When tobacco plants were inoculated with each bacterium by the spray method, both P. syringae pv. tabaci D43V and D43A mutants had remarkably reduced ability to cause disease symptoms. Both mutants had reduced or no swimming and swarming motilities and adhesion ability. In P. syringae pv. tabaci D43V, little flagellin protein was detected and few flagella were observed by electron microscopy. These results indicate that mutant flagella are unstable and that flagellar motility is impaired. Thus, the amino acid residue required for MAMP activity is important for the intrinsic flagellar function.
Expression of a Class 1 Hemoglobin Gene and Production of Nitric Oxide in Response to Symbiotic and Pathogenic Bacteria in Lotus japonicus
Authors: Nagata Maki , Murakami Ei-ichi , Shimoda Yoshikazu , Shimoda-Sasakura Fuyuko , Kucho Ken-ichi , Suzuki Akihiro , Abe Mikiko , Higashi Shiro , Uchiumi Toshiki
Published: August 2008

Symbiotic nitrogen fixation by the collaboration between leguminous plants and rhizobia is an important system in the global nitrogen cycle, and some molecular aspects during the early stage of host-symbiont recognition have been revealed. To understand the responses of a host plant against various bacteria, we examined expression of hemoglobin (Hb) genes and production of nitric oxide (NO) in Lotus japonicus after inoculation with rhizobia or plant pathogens. When the symbiotic rhizobium Mesorhizobium loti was inoculated, expression of LjHb1 and NO production were induced transiently in the roots at 4 h after inoculation. In contrast, inoculation with the nonsymbiotic rhizobia Sinorhizobium meliloti and Bradyrhizobium japonicum induced neither expression of LjHb1 nor NO production. When L. japonicus was inoculated with plant pathogens (Ralstonia solanacearum or Pseudomonas syringae), continuous NO production was observed in roots but induction of LjHb1 did not occur. These results suggest that modulation of NO levels and expression of class 1 Hb are involved in the establishment of the symbiosis.
The Vitamin Riboflavin and Its Derivative Lumichrome Activate the LasR Bacterial Quorum-Sensing Receptor
Authors: Rajamani Sathish , Bauer Wolfgang D. , Robinson Jayne B. , Farrow John M. , Pesci Everett C. , Teplitski Max , Gao Mengsheng , Sayre Richard T. , Phillips Donald A.
Published: August 2008

Many bacteria use quorum sensing (QS) as an intercellular signaling mechanism to regulate gene expression in local populations. Plant and algal hosts, in turn, secrete compounds that mimic bacterial QS signals, allowing these hosts to manipulate QS-regulated gene expression in bacteria. Lumichrome, a derivative of the vitamin riboflavin, was purified and chemically identified from culture filtrates of the alga Chlamydomonas as a QS signal-mimic compound capable of stimulating the Pseudomonas aeruginosa LasR QS receptor. LasR normally recognizes the N-acyl homoserine lactone (AHL) signal, N-3-oxo-dodecanoyl homoserine lactone. Authentic lumichrome and riboflavin stimulated the LasR receptor in bioassays and lumichrome activated LasR in gel shift experiments. Amino acid substitutions in LasR residues required for AHL binding altered responses to both AHLs and lumichrome or riboflavin. These results and docking studies indicate that the AHL binding pocket of LasR recognizes both AHLs and the structurally dissimilar lumichrome or riboflavin. Bacteria, plants, and algae commonly secrete riboflavin or lumichrome, raising the possibility that these compounds could serve as either QS signals or as interkingdom signal mimics capable of manipulating QS in bacteria with a LasR-like receptor.
Large-Scale Gene Discovery in the Septoria Tritici Blotch Fungus Mycosphaerella graminicola with a Focus on In Planta Expression
Authors: Kema Gert H. J. , van der Lee Theo A. J. , Mendes Odette , Verstappen Els C. P. , Lankhorst René Klein , Sandbrink Hans , van der Burgt Ate , Zwiers Lute-Harm , Csukai Michael , Waalwijk Cees
Published: August 2008

The foliar disease septoria tritici blotch, caused by the fungus Mycosphaerella graminicola, is currently the most important wheat disease in Europe. Gene expression was examined under highly different conditions, using 10 expressed sequence tag libraries generated from M. graminicola isolate IPO323 using seven in vitro and three in planta growth conditions. To identify fungal clones in the interaction libraries, we developed a selection method based on hybridization with the entire genomic DNA of M. graminicola, to selectively enrich these libraries for fungal genes. Assembly of the 27,007 expressed sequence tags resulted in 9,190 unigenes, representing 5.2 Mb of the estimated 39-Mb genome size of M. graminicola. All libraries contributed significantly to the number of unigenes, especially the in planta libraries representing different stages of pathogenesis, which covered 15% of the library-specific unigenes. Even under presymptomatic conditions (5 days postinoculation), when fungal biomass is less than 5%, this method enabled us to efficiently capture fungal genes expressed during pathogenesis. Many of these genes were uniquely expressed in planta, indicating that in planta gene expression significantly differed from in vitro expression. Examples of gene discovery included a number of cell wall–degrading enzymes, a broad set of genes involved in signal transduction (n = 11) and a range of ATP-binding cassette (n = 20) and major facilitator superfamily transporter genes (n = 12) potentially involved in protection against antifungal compounds or the secretion of pathogenicity factors. In addition, evidence is provided for a mycovirus in M. graminicola that is highly expressed under various stress conditions, in particular, under nitrogen starvation. Our analyses provide a unique window on in vitro and in planta gene expression of M. graminicola.
Sex-linked markers and microsatellite locus duplication in the cichlid species
Oreochromis tanganicae
Authors: Cnaani Avner , Kocher Thomas D
Published: August 2008

Cichlid species of the genus
Oreochromis
vary in their genetic sex-determination systems. In this study, we used microsatellite DNA markers to characterize the sex-determination system in
Oreochromis tanganicae
. Markers on linkage group 3 were associated with phenotypic sex, with an inheritance pattern typical of a female heterogametic species (WZ–ZZ). Further, locus duplication was observed for two separate microsatellite markers on the sex chromosome. These results further advance our understanding of the rapidly evolving sex-determination systems among these closely related tilapia species.
Avian migrants adjust migration in response to environmental conditions
en route
Authors: Tøttrup Anders P , Thorup Kasper , Rainio Kalle , Yosef Reuven , Lehikoinen Esa , Rahbek Carsten
Published: August 2008

The onset of migration in birds is assumed to be primarily under endogenous control in long-distance migrants. Recently, climate changes appear to have been driving a rapid change in breeding area arrival. However, little is known about the climatic factors affecting migratory birds during the migration cycle, or whether recently reported phenological changes are caused by plastic behavioural responses or evolutionary change. Here, we investigate how environmental conditions in the wintering areas as well as
en route
towards breeding areas affect timing of migration. Using data from 1984 to 2004 covering the entire migration period every year from observatories located in the Middle East and northern Europe, we show that passage of the Sahara Desert is delayed and correlated with improved conditions in the wintering areas. By contrast, migrants travel more rapidly through Europe, and adjust their breeding area arrival time in response to improved environmental conditions
en route
. Previous studies have reported opposing results from a different migration route through the Mediterranean region (Italy). We argue that the simplest explanation for different phenological patterns at different latitudes and between migratory routes appears to be phenotypic responses to spatial variability in conditions
en route
.
Immune activation suppresses plasma testosterone level: a meta-analysis
Authors: Boonekamp Jelle J , Ros Albert H.F , Verhulst Simon
Published: August 2008

Females often select mates on the basis of sexual signals, which can be reliable indicators of male quality when the costliness of these signals prevents cheating. The immunocompetence handicap hypothesis (ICHH) provides a mechanistic explanation of these costs, by proposing a trade-off between immune function and sexual displays. This trade-off arises because testosterone enhances sexual signals, but suppresses immune function. Many studies have investigated the ICHH by administrating testosterone, and a recent meta-analysis found little evidence that testosterone suppressed immune function. However, another component of the ICHH, which has received less empirical interest, suggests that there may also be an interaction in the other direction, with immune activation suppressing testosterone levels. We present a meta-analysis to test for this effect. Overall, there was a strong suppressive effect of experimental immune activation on testosterone levels (r=−0.52), regardless of whether live pathogens or non-pathogenic antigens were used to challenge the immune system. The latter is important because it shows that immune activationper sesuppresses testosterone levels. Thus, a trade-off between immunocompetence and sexual displays may primarily be generated by the effect of immune activation on testosterone, rather than the opposite effect that has received most attention.
Frictionless multiple impacts in multibody systems. II. Numerical algorithm and simulation results
Authors: Liu Caishan , Zhao Zhen , Brogliato Bernard
Published: August 2008

Part I of this paper develops a framework that is an extension of the Darboux–Keller shock dynamics towards frictionless multiple impacts between bodies composed of rate-independent materials. A numerical algorithm is proposed in this paper, in which the impulsive differential equation is discretized with respect to the primary impulse corresponding to the contact with the highest potential energy, and the integration step size is estimated at the momentum level. This algorithm respects the energetic constraints and avoids the stiff ordinary differential equation problem arising by directly using the compliant model. The well-known example of Newton's cradle, as well as Bernoulli's system, is used to illustrate the developments.
Evidence of an inflammatory-like response in non-normally pigmented tissues of two scleractinian corals
Authors: Palmer Caroline V , Mydlarz Laura D , Willis Bette L
Published: August 2008

Increasing evidence of links between climate change, anthropogenic stress and coral disease underscores the importance of understanding the mechanisms by which reef-building corals resist infection and recover from injury. Cellular inflammation and melanin-producing signalling pathway are two mechanisms employed by invertebrates to remove foreign organisms such as pathogens, but they have not been recorded previously in scleractinian corals. This study demonstrates the presence of the phenoloxidase (PO) activating melanin pathway in two species of coral,
Acropora millepora
and a massive species of
Porites
, which both develop local pigmentation in response to interactions with a variety of organisms.
l
-DOPA (3-(3,4-dihydroxyphenyl)-
l
-alanine) substrate-based enzyme activation assays demonstrated PO activity in healthy tissues of both species and upregulation in pigmented tissues of
A. millepora
. Histological staining conclusively identified the presence of melanin in
Porites
tissues. These results demonstrate that the PO pathway is active in both coral species. Moreover, the upregulation of PO activity in areas of non-normal pigmentation in
A. millepora
and increased melanin production in pigmented
Porites
tissues suggest the presence of a generalized defence response to localized stress. Interspecific differences in the usage of pathways involved in innate immunity may underlie the comparative success of massive
Porites
sp. as long-lived stress tolerators.
Can't tell the caterpillars from the trees: countershading enhances survival in a woodland
Authors: Rowland Hannah M , Cuthill Innes C , Harvey Ian F , Speed Michael P , Ruxton Graeme D
Published: August 2008

Perception of the body's outline and three-dimensional shape arises from visual cues such as shading, contour, perspective and texture. When a uniformly coloured prey animal is illuminated from above by sunlight, a shadow may be cast on the body, generating a brightness contrast between the dorsal and ventral surfaces. For animals such as caterpillars, which live among flat leaves, a difference in reflectance over the body surface may degrade the degree of background matching and provide cues to shape from shading. This may make otherwise cryptic prey more conspicuous to visually hunting predators. Cryptically coloured prey are expected to match their substrate in colour, pattern and texture (though disruptive patterning is an exception), but they may also abolish self-shadowing and therefore either reduce shape cues or maintain their degree of background matching through countershading: a gradation of pigment on the body of an animal so that the surface closest to illumination is darker. In this study, we report the results from a series of field experiments where artificial prey resembling lepidopteran larvae were presented on the upper surfaces of beech tree branches so that they could be viewed by free-living birds. We demonstrate that countershading is superior to uniform coloration in terms of reducing attack by free-living predators. This result persisted even when we fixed prey to the underside of branches, simulating the resting position of many tree-living caterpillars. Our experiments provide the first demonstration, in an ecologically valid visual context, that shadowing on bodies (such as lepidopteran larvae) provides cues that visually hunting predators use to detect potential prey species, and that countershading counterbalances shadowing to enhance cryptic protection.