bluuebunny/crossref_metadata_2025 huggingface dataset:
Anticyclonic and cyclonic eddies of subtropical origin in the subantarctic zone south of Africa
Authors: Arhan Michel , Speich Sabrina , Messager Christophe , Dencausse Guillaume , Fine Rana , Boye Marie
Published: August 2011

Two eddies, one anticyclonic and the other cyclonic, intersected in the Subantarctic Zone south of South Africa during a hydrographic transect, are described using a large set of measurements including full depth hydrography, Acoustic Doppler Current Profiler velocities, biogeochemical tracers, air‐sea fluxes and altimetric sea surface height. Both eddies have a subtropical origin. The anticyclone is an Agulhas ring with convected core water of ∼12°C, and swirl velocities of 1 m s−1. It was 9.5 months old when sampled and had crossed the Agulhas Ridge. Though sampled in summer, it was releasing ∼200 W m−2 (sensible plus latent heat flux) to the atmosphere. It was observed adjacent to the Subantarctic Front, illustrating the usual encounters of such structures with this front. The cyclone, marked by pronounced low oxygen and CFC anomalies revealing an origin at the continental slope, was 4.5 months old. It had swirl speeds of 0.3 m s−1, and was coupled with the anticyclone when observed. From their kinematics and water mass properties both structures were found to transport subtropical water down to ∼900 m, the water trapped below this depth being either from the northern Subantarctic Zone, or local water. The two structures illustrate the capacity of eddies in the region to transfer subtropical and alongslope water properties into the Subantarctic Zone.
The ethics of collaborative authorship
Authors: Teixeira da Silva Jaime A
Published: August 2011

The changing nature of scientific research towards international, interdisciplinary research teams requires a redefinition of ‘authorship’ in scientific publishing.
Treatment of doxorubicin-resistant MCF7/Dx cells with nitric oxide causes histone glutathionylation and reversal of drug resistance
Authors: de Luca Anastasia , Moroni Noemi , Serafino Annalucia , Primavera Alessandra , Pastore Anna , Pedersen Jens Z. , Petruzzelli Raffaele , Farrace Maria Grazia , Pierimarchi Pasquale , Moroni Gabriella , Federici Giorgio , Sinibaldi Vallebona Paola , Lo Bello Mario
Published: August 2011

Acquired drug resistance was found to be suppressed in the doxorubicin-resistant breast cancer cell line MCF7/Dx after pre-treatment with GSNO (nitrosoglutathione). The effect was accompanied by enhanced protein glutathionylation and accumulation of doxorubicin in the nucleus. Among the glutathionylated proteins, we identified three members of the histone family; this is, to our knowledge, the first time that histone glutathionylation has been reported. Formation of the potential NO donor dinitrosyl–diglutathionyl–iron complex, bound to GSTP1-1 (glutathione transferase P1-1), was observed in both MCF7/Dx cells and drug-sensitive MCF7 cells to a similar extent. In contrast, histone glutathionylation was found to be markedly increased in the resistant MCF7/Dx cells, which also showed a 14-fold higher amount of GSTP1-1 and increased glutathione concentration compared with MCF7 cells. These results suggest that the increased cytotoxic effect of combined doxorubicin and GSNO treatment involves the glutathionylation of histones through a mechanism that requires high glutathione levels and increased expression of GSTP1-1. Owing to the critical role of histones in the regulation of gene expression, the implication of this finding may go beyond the phenomenon of doxorubicin resistance.
Nucleated polymerization with secondary pathways. I. Time evolution of the principal moments
Authors: Cohen Samuel I. A. , Vendruscolo Michele , Welland Mark E. , Dobson Christopher M. , Terentjev Eugene M. , Knowles Tuomas P. J.
Published: August 2011

Self-assembly processes resulting in linear structures are often observed in molecular biology, and include the formation of functional filaments such as actin and tubulin, as well as generally dysfunctional ones such as amyloid aggregates. Although the basic kinetic equations describing these phenomena are well-established, it has proved to be challenging, due to their non-linear nature, to derive solutions to these equations except for special cases. The availability of general analytical solutions provides a route for determining the rates of molecular level processes from the analysis of macroscopic experimental measurements of the growth kinetics, in addition to the phenomenological parameters, such as lag times and maximal growth rates that are already obtainable from standard fitting procedures. We describe here an analytical approach based on fixed-point analysis, which provides self-consistent solutions for the growth of filamentous structures that can, in addition to elongation, undergo internal fracturing and monomer-dependent nucleation as mechanisms for generating new free ends acting as growth sites. Our results generalise the analytical expression for sigmoidal growth kinetics from the Oosawa theory for nucleated polymerisation to the case of fragmenting filaments. We determine the corresponding growth laws in closed form and derive from first principles a number of relationships which have been empirically established for the kinetics of the self-assembly of amyloid fibrils.
Finite-size scaling relations for a four-dimensional Ising model on Creutz cellular automatons
Authors: Merdan Z. , Güzelsoy E.
Published: August 2011

The four-dimensional Ising model is simulated on Creutz cellular automatons using finite lattices with linear dimensions 4 ≤ L ≤ 8. The temperature variations and finite-size scaling plots of the specific heat and the Binder parameter verify the theoretically predicted expression near the infinite lattice critical temperature for 7, 14, and 21 independent simulations. Approximate values for the critical temperature of the infinite lattice of Tc(∞) = 6.6965(35), 6.6961(30), 6.6960(12), 6.6800(3), 6.6801(2), 6.6802(1) and 6.6925(22) (without the logarithmic factor), 6.6921(22) (without the logarithmic factor), 6.6909(2) (without the logarithmic factor), 6.6822(13) (with the logarithmic factor), 6.6819(11) (with the logarithmic factor), and 6.6808(8) (with the logarithmic factor) are obtained from the intersection points of the specific heat curves, the Binder parameter curves, and straight line fits of specific heat maxima for 7, 14, and 21 independent simulations, respectively. As the number of independent simulations increases, the results, 6.6802(1) and 6.6808(8), are in very good agreement with the results of a series expansion of Tc(∞), 6.6817(15) and 6.6802(2), the dynamic Monte Carlo value Tc(∞) = 6.6803(1), the cluster Monte Carlo value Tc(∞) = 6.680(1), and the Monte Carlo value using the Metropolis-Wolff cluster algorithm Tc(∞) = 6.6802632 ± 5 · 10−5. The average values calculated for the critical exponent of the specific heat are α =− 0.0402(15), − 0.0393(12), − 0.0391(11) with 7, 14, and 21 independent simulations, respectively. As the number of independent simulations increases, the result, α =− 0.0391(11), agrees with the series expansions result, α =− 0.12 ± 0.03 and the Monte Carlo result using the Metropolis-Wolff cluster algorithm, α ≥ 0 ± 0.04. However, α =− 0.0391(11) is inconsistent with the renormalization group prediction of α = 0.
Energy design for protein-protein interactions
Authors: Ravikant D. V. S. , Elber Ron
Published: August 2011

Proteins bind to other proteins efficiently and specifically to carry on many cell functions such as signaling, activation, transport, enzymatic reactions, and more. To determine the geometry and strength of binding of a protein pair, an energy function is required. An algorithm to design an optimal energy function, based on empirical data of protein complexes, is proposed and applied. Emphasis is made on negative design in which incorrect geometries are presented to the algorithm that learns to avoid them. For the docking problem the search for plausible geometries can be performed exhaustively. The possible geometries of the complex are generated on a grid with the help of a fast Fourier transform algorithm. A novel formulation of negative design makes it possible to investigate iteratively hundreds of millions of negative examples while monotonically improving the quality of the potential. Experimental structures for 640 protein complexes are used to generate positive and negative examples for learning parameters. The algorithm designed in this work finds the correct binding structure as the lowest energy minimum in 318 cases of the 640 examples. Further benchmarks on independent sets confirm the significant capacity of the scoring function to recognize correct modes of interactions.
Quantum transport of electrons through axially symmetric junctions of zigzag and armchair nanotubes
Authors: Klymenko Yu. O.
Published: August 2011

An analytic approach is developed in the nearest neighbor approximation for describing electron transport through axially symmetric junctions of zigzag and armchair nanotubes. This method yields an analytic expression for the electron transmission probability and can be used to establish selection rules for electron scattering. Oscillations in the gap width in the electron transmission spectrum are predicted as a function of the nanotube diameter and the minimum gap size is determined. The thresholds for the appearance of steps in the electron transmission coefficient are also found and it is shown that, except in its initial section, the origin of the steps is associated with the electronic characteristics of armchair nanotubes, alone.
Local and quasilocal energy levels of electrons on nanotube surfaces and in rings in magnetic fields
Authors: Ermolaev A. M. , Kofanov S. V. , Rashba G. I.
Published: August 2011

The Lifshitz local perturbation technique is used to examine impurity states of electrons on nanotube surfaces and in rings in magnetic fields. It is shown that an impurity in the form of a thin ring on a tube can form local and quasilocal electron states. The positions and widths of the impurity levels are found. These quantities on tubes and rings are calculated numerically for the parameters of semiconductor structures.
Theoretical study of the structural elements of a single-wall gold nanotube with chirality (5,3) in a Hubbard model
Authors: Filippova E. R. , Mironov G. I.
Published: August 2011

The method of static fluctuations is used in a Hubbard model for theoretical study of nanoclusters of single-wall gold nanotubes with chirality (5,3) consisting of N = 15, 20, 23, and 40 gold atoms. The Fourier transforms of anticommutator Green functions and correlation functions of the nanosystems are calculated and energy spectra are constructed.
1,2-Dibromoethane on Cu(100): Bonding structure and transformation to C2H4
Authors: Lin Jong-Liang , Lin Yi-Shiue , Shih Jain-Jung , Kuo Kuan-Huang , Lin Shu-Kuan , Wu Tz-Shiuan , Shiu Ming-Yi
Published: August 2011

Temperature-programmed reaction/desorption, mass spectrometry, reflection-absorption infrared spectroscopy, x-ray photoelectron spectroscopy, and density functional theory calculations have been employed to explore the reaction and bonding structure of 1,2-C2H4Br2 on Cu(100). Both the trans and gauche conformers are found to dissociate by breaking the C-Br bonds on clean Cu(100) at 115 K, forming C2H4 and Br atoms. Theoretical investigations for the possible paths of 1,2-C2H4Br2 → C2H4 + 2Br on Cu(100) suggest that the barriers of the trans and gauche molecules are in the ranges of 0–4.2 and 0–6.5 kcal/mol, respectively. The C-Br scission temperature of C2H4Br2 is much lower than that (∼170 K) of C2H5Br on Cu(100). Adsorbed Br atoms can decrease the dissociation rate of the 1,2-C2H4Br2 molecules impinging the surface. The 1,2-C2H4Br2 molecules adsorbed in the first monolayer are structurally distorted. Both the trans and gauche molecules exist in the second monolayer, but with no preferential adsorption orientation. However, the trans molecule is the predominant species in the third or higher layer formed at 115 K. The layer structure is not thermally stable. Upon heating the surface to 150 K, the orientation of the trans 1,2-C2H4Br2 molecules in the layer changes, leading to the rotation of the BrCCBr skeletal plane toward the surface normal on average and the considerable growth of the CH2 scissoring peak. On oxygen-precovered Cu(100), decomposition of 1,2-C2H4Br2 to form C2H4 is hampered and no oxygenated hydrocarbons are formed. The presence of the oxygen atoms also increases the adsorption energy of the second-layer molecules.
Quantum phenomena in the radial thermal expansion of bundles of single-walled carbon nanotubes doped with 3He. A giant isotope effect
Authors: Dolbin A. V. , Esel’son V. B. , Gavrilko V. G. , Manzhelii V. G. , Vinnikov N. A. , Popov S. N. , Sundqvist B.
Published: August 2011

The coefficient of radial thermal expansion αr of bundles of single-walled carbon nanotubes saturated with 3He up to a molar concentration of 9.4% has been studied over temperatures of 2.1–9.5 K by high-sensitivity capacitance dilatometry. In the interval 2.1–7 K a negative αr was observed, with a magnitude exceeding the largest negative values for pure and 4He-saturated nanotubes by three and two orders of magnitude, respectively. The contributions of the two He isotope impurities to the negative thermal expansion of the nanotube bundles are most likely related to spatial redistribution of 4He and 3He atoms by tunneling at the surface of and inside nanotube bundles. The isotope effect turned out to be huge, probably owing to a higher tunneling probability for 3He atoms.
Dynamics of He atoms adsorbed on a carbon nanotube
Authors: Strzhemechny Mikhail A. , Legchenkova Irina V.
Published: August 2011

The spectrum of a helium atom adsorbed on an armchair single-walled carbon nanotube is calculated. It is shown that a helium adatom tunnels over the surface of the nanotube within a band of width 10 K (for 4He) to 14 K (for 3He). The undersaturated system of helium adatoms on nanotubes can be used for studying quantum transport. The dynamics of this system can also be an important contributor to the large negative expansion coefficients of nanotube bundles with adsorbed helium.
Bi-relaxation behaviors in epitaxial multiferroic double-perovskite BiFe0.5Mn0.5O3/CaRuO3 heterostructures
Authors: Miao J. , Zhang X. , Zhan Q. , Jiang Y. , Chew K.-H.
Published: August 2011

Multiferroic double-perovskite BiFe0.5Mn0.5O3 thin film heterostructures were epitaxially grown on CaRuO3-buffered (001) SrTiO3 by pulse laser deposition. Typical Vogel-Fulcher relaxorlike dielectric and magnetic susceptibilities were observed, implying the film exhibits the properties of an electric relaxor and a magnetic relaxor. Polarization and size of polar nanoregions (PNRs) were determined by fitting the dielectric constant to a multi-polarization mechanism model. It was found that PNRs of 7-11 nm decrease from 0.67 μC/cm2 to 0.11 μC/cm2, as the temperature increases from 380 K to 460 K. A weak ferromagnetism was observed via magnetic hysteresis loops up to 300 K.
Self-assembly of metallic double-dot single-electron device
Authors: Guttman A. , Mahalu D. , Sperling J. , Cohen-Hoshen E. , Bar-Joseph I.
Published: August 2011

We present an approach that allows forming a nanometric double dot single electron device. It uses chemical synthesis of metallic nanoparticles to form dimeric structures, e-beam lithography to define electrodes and gates, and electrostatic trapping to place the dimers in between the electrodes. We demonstrate a control of its charge configuration and conductance properties over a wide range of external voltages. This approach can be straightforwardly generalized to other material systems and may allow realizing quantum information devices.
High purity chemical etching and thermal passivation process for Ge(001) as nanostructure template
Authors: Blumenstein Christian , Meyer Sebastian , Ruff Andreas , Schmid Benjamin , Schäfer Jörg , Claessen Ralph
Published: August 2011

An advanced two-step cleaning process of the Ge(001) surface for nanoscience requirements is presented. First, wet-chemical etching with a variant of the Piranha solution (H2SO4, H2O2, H2O) is used to remove contaminants as well as the native oxide layer. Second, passivation of the surface is achieved by a rapid thermal oxidation step, leading to a homogeneous protective oxide layer. The thickness of the oxide layer is tuned to be thick enough to protect the surface, yet thin enough to be completely removed by thermal treatment in ultra-high vacuum. The application of this recipe results in an outstandingly clean and atomically flat surface, with carbon contamination at the detection limit of x-ray photoelectron spectroscopy. Scanning tunneling microscopy and electron diffraction reveal a long range ordered surface with typical terrace diameters of ∼100 nm, suitable for the growth of atomic-scale nanostructures.
Photosensitivity at 1550 nm and Bragg grating inscription in As2Se3 chalcogenide microwires
Authors: Ahmad Raja , Rochette Martin
Published: August 2011

We present the experimental observation of photosensitivity in As2Se3 glass at a wavelength of 1550 nm. We utilize this photosensitivity to induce the Bragg gratings using a laser source at a wavelength of 1550 nm. We also quantify the photosensitivity thresholds related to exposition intensity and exposition time. Further, we demonstrate that As2Se3 microwire Bragg gratings are widely tunable in wavelength as the microwire can withstand an applied longitudinal strain of 2.7 × 104 μɛ.
Ultra-low voltage air-stable polyelectrolyte gated n-type organic thin film transistors
Authors: Malti Abdellah , Gabrielsson Erik O. , Berggren Magnus , Crispin Xavier
Published: August 2011

Complementary circuits, processing digital signals, are a cornerstone of modern electronics. Such circuits require both p- and n-type transistors. Polyelectrolytes are used as gate insulators in organic thin film transistors (OTFTs) to establish an electric double layer capacitor upon gate bias that allows low operational voltages (<1 V). However, stable and low-voltage operating n-channel organic transistors have proven difficult to construct. Here, we report ultra-low voltage n-channel organic polymer-based transistors that are stable in ambient atmosphere. Our n-type OTFTs exhibit on/off ratios around 103 for an applied drain potential as low as 0.1 V. Since small ions are known to promote electrochemical reactions within the semiconductor’s channel bulk and typically slow down the transistor, we use a solid polycationic gate insulator that suppresses penetration of anions into the n-channel semiconductor. As a result, our n-channel OTFTs switch on in under 5 ms and off in less than 1 ms.
Molecular relationships of the bear cuscus, Ailurops ursinus (Marsupialia: Phalangeridae)
Authors: Kirsch JAW , Wolman MA
Published: August 2011

DNA-hybridisation experiments, involving seven species of Phalangeridae and two outgroup taxa
in a complete 9 x 9 matrix, unequivocally placed the bear cuscus, Ailurops ursinus, nearest to the
Phalangerini (Phalanger and Spilocuscus), with Trichosurini (Trichosurus) sister to both; and
confirmed earlier molecular studies indicating that the ground cuscus, Strigocuscus gymnotis, is
not a trichosurin but is closest to Phalanger. Our results thus conflict with the most thorough
cladistic-anatomical study of phalangerids, which placed the bear cuscus outside all other
Phalangeridae as the sole living member of Subfamily Ailuropinae; instead, we suggest that
Ailurops should be considered representative of a tribe of Phalangerinae, Ailuropini, while
Trichosurus (and presumably Wyulda, which was not examined here, as well as fossil
Strigocuscus) would be removed from Phalangerinae and be considered a second subfamily of
Phalangeridae, Trichosurinae, limited to Australia. Our estimate of the time of divergence of
Ailurops and other phalangerines is about 16 myrbp; of Trichosurinae and Phalangerinae, about 21
myrbp. Thus, a single Early Miocene vicariant event between Australia and Papua New Guinea,
which isolated phalangerines in the latter region, followed by dispersal of the included ailuropins
to (or vicariant separation on) Sulawesi, would be sufficient to account for family-level
cladogenesis in Phalangeridae.
Autumnal body mass reduction in Antechinus swainsonii (Dasyuridae) in the Snowy Mountains.
Authors: Green K
Published: August 2011

Autumnal body mass reduction in a seasonally snow-covered environment is reported for
Antechinus swainsonii (Marsupialia: Dasyuridae), thus extending the phylogenetic spectrum in
which this phenomenon is known. Above 1600 m altitude the average mass of individual A.
swainsonii falls from 48.6 g to 42.6 g (a 12.3% loss) from April to May. The difference in mass
results from a reduction in lean mass rather than a metabolisation of fat reserves. In A.
swainsonii, the need to increase body mass in late summer only to lose it in autumn prior to a
winter beneath the snow seems superfluous. However, the higher mass may be necessary to
survive the harsher microclimate in autumn before conditions ameliorate beneath the snow
cover. Survival from April to May is higher in heavier animals (that do lose mass in autumn)
than lighter animals (with mass in April equal to that of animals after loss of body mass). These
lighter animals disappear from the population in autumn. With snow cover in place, A.
swainsonii is able to increase mass in winter.
Life Underground: The Biology Of Subterranean Rodents
Authors: Lacey EA , Patton JL , Cameron GN
Published: August 2011

SUBTERRANEAN rodents are intriguing subjects
for research. On the one hand they display extreme
variability in social organisation and life history, and
exhibit a range of unique adaptations in morphology
and physiology that allow exploitation of different
habitats. On the other hand, field studies of
subterranean rodents are exceptionally challenging as
the animals are seldom observed. Subterranean
rodents are also widely distributed, occurring on all
continents except Australia and Antarctica. Life
underground: The biology of subterranean rodents
provides an excellent summary of what we know
(and what we do not know) about this cryptic group
of mammals, and also succeeds in conveying the joys
and frustrations of studying them.
Regenerative phenotype in mice with a point mutation in transforming growth factor β type I receptor (
TGFBR1
)
Authors: Liu Jun , Johnson Kristen , Li Jie , Piamonte Victoria , Steffy Brian M. , Hsieh Mindy H. , Ng Nicholas , Zhang Jay , Walker John R. , Ding Sheng , Muneoka Ken , Wu Xu , Glynne Richard , Schultz Peter G.
Published: August 2011

Regeneration of peripheral differentiated tissue in mammals is rare, and regulators of this process are largely unknown. We carried out a forward genetic screen in mice using
N
-ethyl-
N
-nitrosourea mutagenesis to identify genetic mutations that affect regenerative healing in vivo. More than 400 pedigrees were screened for closure of a through-and-through punch wound in the mouse ear. This led to the identification of a single pedigree with a heritable, fast, and regenerative wound-healing phenotype. Within 5 wk after ear-punch, a threefold decrease in the diameter of the wound was observed in the mutant mice compared with the wild-type mice. At 22 wk, new cartilage, hair follicles, and sebaceous glands were observed in the newly generated tissue. This trait was mapped to a point mutation in a receptor for TGF-β,
TGFBR1
. Mouse embryonic fibroblasts from the affected mice had increased expression of a subset of TGF-β target genes, suggesting that the mutation caused partial activation of the receptor. Further, bone marrow stromal cells from the mutant mice more readily differentiated to chondrogenic precursors, providing a plausible explanation for the enhanced development of cartilage islands in the regenerated ears. This mutant mouse strain provides a unique model to further explore regeneration in mammals and, in particular, the role of TGFBR1 in chondrogenesis and regenerative wound healing.
The effects of features of examination questions on the performance of students with dyslexia
Authors: Crisp Victoria , Johnson Martin , Novaković Nadežda
Published: August 2011

This research investigated whether features of examination questions influence students with dyslexia differently to others, potentially affecting whether they have a fair opportunity to show their knowledge, understanding and skills. A number of science examination questions were chosen. For some questions two slightly different versions were created. A total of 54 students considered by their teachers to have dyslexia and a matched control group of 51 students took the test under exam conditions. A dyslexia screening assessment was administered where possible and some students were interviewed. Facility values and Rasch analysis were used to compare performance between the versions of the same question and between those with and without dyslexia. Chi‐square statistics found no statistically significant differences in performance between groups or between question versions. However, some tentative implications for good practice can be inferred (e.g. avoiding ambiguous pronouns, using bullet points).
The effects of process parameters on yield and properties of iron nanoparticles from ferrocene in a low-pressure plasma
Authors: Panchal V , Lahoti G , Bhandarkar U , Neergat M
Published: August 2011

The effects of process parameters on iron nanoparticle formation and properties while using ferrocene as a precursor in a low-pressure capacitively coupled plasma are investigated. The L18 array of the Taguchi method, followed by the L4 array, is used with the notional objective of increasing the yield of nanoparticles. A study of the size, shape and composition of the particles (using transmission electron microscopy, high-resolution transmission electron microscopy, Raman spectroscopy, x-ray diffraction, CHON and inductively coupled plasma-atomic emission spectroscopy analysis) gives an insight into the role played by various process parameters. Pressure is the most critical parameter in increasing nanoparticle yield, whereas hydrogen flow plays a key role in determining the nanoparticle size and composition. Atomic hydrogen helps in removing amorphous carbon and reducing the nanoparticle size. RF power plays an important role in the dissociation of ferrocene thus also affecting the composition. Nanoparticles obtained using optimized conditions are a mixture of Fe3O4 and Fe2O3 with cluster size 25–40 nm in diameter that are further made up of 2–4 nm crystallites. Magnetic property measurements indicate that the nanoparticles are super-paramagnetic in nature.
Frequency dependent magnetization of superconductor strip
Authors: Thakur Kailash Prasad , Raj Ashish , Brandt Ernst Helmut , Sastry Pamidi V P S S
Published: August 2011

The full text of the corrigendum is available in the pdf provided.
ChimeraScan: a tool for identifying chimeric transcription in sequencing data
Authors: Iyer Matthew K. , Chinnaiyan Arul M. , Maher Christopher A.
Published: August 2011

Summary: Next generation sequencing (NGS) technologies have enabled de novo gene fusion discovery that could reveal candidates with therapeutic significance in cancer. Here we present an open-source software package, ChimeraScan, for the discovery of chimeric transcription between two independent transcripts in high-throughput transcriptome sequencing data.

Availability:  http://chimerascan.googlecode.com

Contact:  cmaher@dom.wustl.edu

Supplementary Information:  Supplementary data are available at Bioinformatics online.
A phylogenetic mixture model for the identification of functionally divergent protein residues
Authors: Gaston Daniel , Susko Edward , Roger Andrew J.
Published: August 2011

Motivation: To understand the evolution of molecular function within protein families, it is important to identify those amino acid residues responsible for functional divergence; i.e. those sites in a protein family that affect cofactor, protein or substrate binding preferences; affinity; catalysis; flexibility; or folding. Type I functional divergence (FD) results from changes in conservation (evolutionary rate) at a site between protein subfamilies, whereas type II FD occurs when there has been a shift in preferences for different amino acid chemical properties. A variety of methods have been developed for identifying both site types in protein subfamilies, both from phylogenetic and information-theoretic angles. However, evaluation of the performance of these methods has typically relied upon a handful of reasonably well-characterized biological datasets or analyses of a single biological example. While experimental validation of many truly functionally divergent sites (true positives) can be relatively straightforward, determining that particular sites do not contribute to functional divergence (i.e. false positives and true negatives) is much more difficult, resulting in noisy ‘gold standard’ examples.

Results:We describe a novel, phylogeny-based functional divergence classifier, FunDi. Unlike previous approaches, FunDi uses a unified mixture model-based approach to detect type I and type II FD. To assess FunDi's overall classification performance relative to other methods, we introduce two methods for simulating functionally divergent datasets. We find that the FunDi method performs better than several other predictors over a wide variety of simulation conditions.

Availability:http://rogerlab.biochem.dal.ca/Software

Contact:  andrew.roger@dal.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
Conserved and differential gene interactions in dynamical biological systems
Authors: Ouyang Zhengyu , Song Mingzhou , Güth Robert , Ha Thomas J. , Larouche Matt , Goldowitz Dan
Published: August 2011

Motivation: While biological systems operated from a common genome can be conserved in various ways, they can also manifest highly diverse dynamics and functions. This is because the same set of genes can interact differentially across specific molecular contexts. For example, differential gene interactions give rise to various stages of morphogenesis during cerebellar development. However, after over a decade of efforts toward reverse engineering biological networks from high-throughput omic data, gene networks of most organisms remain sketchy. This hindrance has motivated us to develop comparative modeling to highlight conserved and differential gene interactions across experimental conditions, without reconstructing complete gene networks first.

Results: We established a comparative dynamical system modeling (CDSM) approach to identify conserved and differential interactions across molecular contexts. In CDSM, interactions are represented by ordinary differential equations and compared across conditions through statistical heterogeneity and homogeneity tests. CDSM demonstrated a consistent superiority over differential correlation and reconstruct-then-compare in simulation studies. We exploited CDSM to elucidate gene interactions important for cellular processes poorly understood during mouse cerebellar development. We generated hypotheses on 66 differential genetic interactions involved in expansion of the external granule layer. These interactions are implicated in cell cycle, differentiation, apoptosis and morphogenesis. Additional 1639 differential interactions among gene clusters were also identified when we compared gene interactions during the presence of Rhombic lip versus the presence of distinct internal granule layer. Moreover, compared with differential correlation and reconstruct-then-compare, CDSM makes fewer assumptions on data and thus is applicable to a wider range of biological assays.

Availability: Source code in C++ and R is available for non-commercial organizations upon request from the corresponding author. The cerebellum gene expression dataset used in this article is available upon request from the Goldowitz lab (dang@cmmt.ubc.ca, http://grits.dglab.org/).

Contact:  joemsong@cs.nmsu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Absynte: a web tool to analyze the evolution of orthologous archaeal and bacterial gene clusters
Authors: Despalins Arnaud , Marsit Souhir , Oberto Jacques
Published: August 2011

Summary: Absynte (Archaeal and Bacterial Synteny Explorer) is a web-based service designed to display local syntenies in completely sequenced prokaryotic chromosomes. The genomic contexts are determined with a multiple center star clustering topology on the basis of a user-provided protein sequence and all (or a set of) chromosomes from the publicly available archaeal and bacterial genomes. The results consist in a dynamic web page where a consistent color-coding permits a rapid visual evaluation of the relative positioning of genes with similar sequences within the synteny. Each gene composing the synteny can be further queried interactively using either local or remote databases. Absynte results can be exported in .CSV or high-resolution, .PDF formats for printing, archival, further editing or publication purposes. Performance, real-time computation, user-friendliness and daily database updates constitute the principal advantages of Absynte over similar web services.

Availability:  http://archaea.u-psud.fr/absynte

Contact:  jacques.oberto@igmors.u-psud.fr
Protein Quality and Physical Characteristics of Kisra (Fermented Sorghum Pancake‐like Flatbread) Made from Tannin and Non‐Tannin Sorghum Cultivars
Authors: AwadElkareem Amir Mahgoub , Taylor John R. N.
Published: August 2011

Kisra is a naturally lactic acid bacteria‐ and yeast‐fermented sorghum thin pancake‐like flatbread produced in Sudan. Kisra has considerable potential as the basis for development of a gluten‐free sandwich wrap. To help direct cultivar selection for commercial production of these products, two white, tan plant non‐tannin Type I, one white Type II tannin, and one red Type III tannin sorghum cultivars were evaluated with respect to kisra protein quality and physical characteristics. Kisra from the non‐tannin sorghums were flexible and had an open‐textured structure with many regular gas cells, whereas those from the tannin sorghums were more brittle, denser in structure, and contained far fewer and smaller gas cells. Kisra from the tannin sorghums had the lowest reactive lysine content, in vitro protein digestibility, and Protein Digestibility Corrected Amino Score (PDCAAS), with values being lowest for the Type III sorghum. PDCAAS of kisra from the Type III sorghum was only 0.12, less than half of that from the Type I sorghums. As the tannins in tannin sorghums adversely affect kisra protein quality and physical characteristics, white tan plant, non‐tannin sorghum cultivars are most suitable for kisra production and for development of wrap‐type sorghum‐based baked goods.
Enzymatic Process for Corn Dry‐Grind High‐Solids Fermentation
Authors: Kaur Prabhjot , Rausch Kent D. , Tumbleson M. E. , Singh Vijay
Published: August 2011

A modified dry‐grind process that combined the use of conventional amylases (glucoamylase [GA]), phytase, and granular starch hydrolyzing enzymes (GSHE) to achieve low liquefaction viscosities and low glucose concentrations during simultaneous saccharification and fermentation (SSF) with a high slurry solids content (>33% w/w) was developed. Doses of GSHE and GA were optimized for the modified process. At 35% solids content, the modified process had 80% lower slurry viscosity, 24% lower peak glucose concentration, 7.5% higher final ethanol concentration, and 51% higher fermentation rate compared with the conventional dry‐grind process. At 40% solids content, the modified process had lower viscosities, lower peak and residual glucose concentrations, and higher ethanol concentrations than the conventional process; however, the results were in contrast to those for 35% solids content. At 40% solids content, SSF did not run to completion for conventional or modified processes, and more than 2.5% w/v of residual glucose was left in the fermentation broth. Final ethanol concentration achieved with the modified process at 40% solids content was 19.5% v/v, similar to the ethanol concentration achieved with the modified process at 35% solids content. At 35% slurry solids content, a GSHE level of 1.25 μL/g db of corn and a GA level of 0.25 μL/g db of corn were selected as optimum enzyme doses for the modified process.
Pantoea rodasii sp. nov., Pantoea rwandensis sp. nov. and Pantoea wallisii sp. nov., isolated from Eucalyptus
Authors: Brady Carrie L. , Cleenwerck Ilse , van der Westhuizen Lorinda , Venter Stephanus N. , Coutinho Teresa A. , De Vos Paul
Published: August 2011

Several Gram-negative-staining, facultatively anaerobic bacterial isolates were obtained from Eucalyptus seedlings showing symptoms of bacterial blight and dieback in Colombia, Rwanda and South Africa. Partial 16S rRNA gene sequencing, together with partial gyrB sequencing, placed the isolates in the genus

Pantoea

and indicated that they constituted three novel species. Multilocus sequence analysis (MLSA) based on partial sequences of gyrB, rpoB, infB and atpD revealed

Pantoea dispersa

,

Pantoea eucrina

and

Pantoea cypripedii

as their closest phylogenetic relatives. DNA–DNA hybridization studies confirmed the classification of the new isolates as three novel species and phenotypic tests allowed them to be differentiated from their closest phylogenetic neighbours. The names Pantoea rodasii sp. nov. [type strain LMG 26273T = BD 943T (deposited with the Plant Pathogenic and Plant Protecting Bacteria Collection, South Africa) = BCC 581T (deposited with the Bacterial Culture Collection, Forestry and Agricultural Institute, South Africa)], Pantoea rwandensis sp. nov. (type strain LMG 26275T = BD 944T = BCC 571T) and Pantoea wallisii sp. nov. (type strain LMG 26277T = BD 946T = BCC 682T) are proposed.
Class Cariacotrichea, a novel ciliate taxon from the anoxic Cariaco Basin, Venezuela
Authors: Orsi William , Edgcomb Virginia , Faria Jose , Foissner Wilhelm , Fowle William H. , Hohmann Tine , Suarez Paula , Taylor Craig , Taylor Gordon T. , Vd'ačný Peter , Epstein Slava S.
Published: August 2011

The majority of environmental micro-organisms identified with the rRNA approach have never been visualized. Thus, their reliable classification and taxonomic assignment is often difficult or even impossible. In our preliminary 18S rRNA gene sequencing work from the world’s largest anoxic marine environment, the Cariaco Basin (Caribbean Sea, Venezuela), we detected a ciliate clade, designated previously as CAR_H [Stoeck, S., Taylor, G. T. & Epstein, S. S. (2003). Appl Environ Microbiol
63, 5656–5663]. Here, we combine the traditional rRNA detection method of fluorescent in situ hybridization (FISH) with scanning electron microscopy (SEM) and confirm the phylogenetic separation of the CAR_H sequences from all other ciliate classes by showing an outstanding morphological feature of this group: a unique, archway-shaped kinety surrounding the oral apparatus and extending to the posterior body end in CAR_H cells. Based on this specific feature and the molecular phylogenies, we propose a novel ciliate class, Cariacotrichea nov. cl.
Methanolinea mesophila sp. nov., a hydrogenotrophic methanogen isolated from rice field soil, and proposal of the archaeal family Methanoregulaceae fam. nov. within the order

Methanomicrobiales
Authors: Sakai Sanae , Ehara Masayuki , Tseng I-Cheng , Yamaguchi Takashi , Bräuer Suzanna L. , Cadillo-Quiroz Hinsby , Zinder Stephen H. , Imachi Hiroyuki
Published: August 2011

A novel mesophilic, hydrogenotrophic methanogen, designated strain TNRT, was isolated from an anaerobic, propionate-degradation enrichment culture that was originally established from a rice field soil sample from Taiwan. Cells were non-motile rods, 2.0–6.5 µm long by 0.3 µm wide. Filamentous (up to about 100 µm) and coccoid (about 1 µm in diameter) cells were also observed in cultures in the late exponential phase of growth. Strain TNRT grew at 20–40 °C (optimally at 37 °C), at pH 6.5–7.4 (optimally at pH 7.0) and in the presence of 0–25 g NaCl l−1 (optimally at 0 g NaCl l−1). The strain utilized H2/CO2 and formate for growth and produced methane. The G+C content of the genomic DNA was 56.4 mol%. Based on sequences of both the 16S rRNA gene and the methanogen-specific marker gene mcrA, strain TNRT was related most closely to

Methanolinea tarda

NOBI-1T; levels of sequence similarities were 94.8 and 86.4 %, respectively. The 16S rRNA gene sequence similarity indicates that strain TNRT and

M. tarda

NOBI-1T represent different species within the same genus. This is supported by shared phenotypic properties, including substrate usage and cell morphology, and differences in growth temperature. Based on these genetic and phenotypic properties, strain TNRT is considered to represent a novel species of the genus

Methanolinea

, for which the name Methanolinea mesophila sp. nov. is proposed; the type strain is TNRT ( = NBRC 105659T = DSM 23604T). In addition, we also suggest family status for the E1/E2 group within the order

Methanomicrobiales

, for which the name Methanoregulaceae fam. nov. is proposed; the type genus of family is Methanoregula.
Lmo0036, an ornithine and putrescine carbamoyltransferase in Listeria monocytogenes, participates in arginine deiminase and agmatine deiminase pathways and mediates acid tolerance
Authors: Chen Jianshun , Cheng Changyong , Xia Ye , Zhao Hanxin , Fang Chun , Shan Ying , Wu Beibei , Fang Weihuan
Published: August 2011

Listeria monocytogenesis a foodborne pathogen causing listeriosis. Acid is one of the stresses that foodborne pathogens encounter most frequently. The ability to survive and proliferate in acidic environments is a prerequisite for infection. However, there is limited knowledge about the molecular basis of adaptation ofL. monocytogenesto acid. Arginine deiminase (ADI) and agmatine deiminase (AgDI) systems are implicated in bacterial tolerance to acidic environments. Homologues of ADI and AgDI systems have been found inL. monocytogeneslineages I and II strains. Sequence analysis indicated thatlmo0036encodes a putative carbamoyltransferase containing conserved motifs and residues important for substrate binding. Lmo0036 acted as an ornithine carbamoyltransferase and putrescine carbamoyltransferase, representing the first example, to our knowledge, that catalyses reversible ornithine and putrescine carbamoyltransfer reactions. Catabolic ornithine and putrescine carbamoyltransfer reactions constitute the second step of ADI and AgDI pathways. However, the equilibrium ofin vitrocarbamoyltransfer reactions was overwhelmingly towards the anabolic direction, suggesting that catabolic carbamoyltransferase was probably the limiting step of the pathways.lmo0036was induced at the transcriptional level whenL. monocytogeneswas subjected to low-pH stress. Its expression product inEscherichia coliexhibited higher catabolic carbamoyltransfer activities under acidic conditions. Consistently, absence of this enzyme impaired the growth ofListeriaunder mild acidic conditions (pH 4.8) and reduced its survival in synthetic human gastric fluid (pH 2.5), and corresponded to a loss in ammonia production, indicating that Lmo0036 was responsible for acid tolerance at both sublethal and lethal pH levels. Furthermore, Lmo0036 played a possible role inListeriavirulence.
A novel C-terminal mutation resulting in constitutive activation of the Listeria monocytogenes central virulence regulatory factor PrfA
Authors: Xayarath Bobbi , Smart Jennifer I. , Mueller Kimberly J. , Freitag Nancy E.
Published: August 2011

The environmental bacteriumListeria monocytogenessurvives and replicates in a variety of diverse ecological niches that range from the soil to the cytosol of infected mammalian cells. The ability ofL. monocytogenesto replicate within an infected host requires the expression of a number of secreted bacterial gene products whose expression is regulated by the transcriptional activator PrfA. PrfA becomes activated following bacterial entry into host cells; however, the mechanism by which this activation occurs remains unknown. Here we describe a novel C-terminal mutation that results in the high-level constitutive activation of PrfA and yet, in contrast with other describedprfA*activation mutations, only modestly increases PrfA DNA binding affinity.L. monocytogenesstrains containing theprfAP219S mutation exhibited high levels of PrfA-dependent virulence gene expression, were hyperinvasive in tissue culture models of infection, were fully motile and were hypervirulent in mice. In contrast with PrfA G145S and other mutationally activated PrfA proteins, the PrfA P219S protein readily formed homodimers and did not exhibit a dramatic increase in its DNA-binding affinity for target promoters. Interestingly, theprfAP219S mutation is located adjacent to theprfAK220 residue that has been previously reported to contribute to PrfA DNA binding activity.prfAP219S therefore appears to constitutively activate PrfA via a novel mechanism which minimally affects PrfA DNA bindingin vitro.
Mucoid morphotype variation of Burkholderia multivorans during chronic cystic fibrosis lung infection is correlated with changes in metabolism, motility, biofilm formation and virulence
Authors: Silva Inês N. , Ferreira Ana S. , Becker Jörg D. , Zlosnik James E. A. , Speert David P. , He Ji , Mil-Homens Dalila , Moreira Leonilde M.
Published: August 2011

Burkholderia cepaciacomplex (Bcc) bacteria are opportunistic pathogens infecting hosts such as cystic fibrosis (CF) patients. Long-termBcc infection of CF patients’ airways has been associated with emergence of phenotypic variation. Here we studied twoBurkholderia multivoransclonal isolates displaying different morphotypes from a chronically infected CF patient to evaluate trait development during lung infection. Expression profiling of mucoid D2095 and non-mucoid D2214 isolates revealed decreased expression of genes encoding products related to virulence-associated traits and metabolism in D2214. Furthermore, D2214 showed no exopolysaccharide production, lower motility and chemotaxis, and more biofilm formation, particularly under microaerophilic conditions, than the clonal mucoid isolate D2095. WhenGalleria mellonellawas used as acute infection model, D2214 at a cell number of approximately 7×106c.f.u. caused a higher survival rate than D2095, although 6 days post-infection most of the larvae were dead. Infection with the same number of cells by mucoid D2095 caused larval death by day 4. The decreased expression of genes involved in carbon and nitrogen metabolism may reflect lower metabolic needs of D2214 caused by lack of exopolysaccharide, but also by the attenuation of pathways not required for survival. As a result, D2214 showed higher survival than D2095 in minimal medium for 28 days under aerobic conditions. Overall, adaptation duringBcc chronic lung infections gave rise to genotypic and phenotypic variation among isolates, contributing to their fitness while maintaining their capacity for survival in this opportunistic human niche.
The value of work‐based projects in management education
Authors: Rogers Beth
Published: August 2011

Purpose

National policy appears to be supportive of part‐time management education, but many researchers have observed difficult challenges in this type of skills development. This paper seeks to discuss how academic assessments that are also work‐based projects could benefit all stakeholders in management education.

Design/methodology/approach

This premise is based on prior literature sources together with an example from the author's own teaching practice – a part‐time Master's programme focused on sales managers.

Findings

It is possible for company sponsors and their employees to achieve considerable benefits from management education when assignments are used to address their change projects.

Originality/value

This paper demonstrates how, even in the most outcome‐oriented of management functions, part‐time education can provide mutual value for all stakeholders.