bluuebunny/crossref_metadata_2025 huggingface dataset:
A Catechin‐rich Beverage Improves Obesity and Blood Glucose Control in Patients With Type 2 Diabetes
Authors: Nagao Tomonori , Meguro Shinichi , Hase Tadashi , Otsuka Kazuhiro , Komikado Masanori , Tokimitsu Ichiro , Yamamoto Takashi , Yamamoto Kunio
Published: November 2008

We investigated the effects of continuous ingestion of a catechin‐rich beverage in patients with type 2 diabetes who were not receiving insulin (Ins) therapy in a double‐blind controlled study. The participants ingested green tea containing either 582.8 mg of catechins (catechin group; n = 23) or 96.3 mg of catechins (control group; n = 20) per day for 12 weeks. At week 12, the decrease in waist circumference was significantly greater in the catechin group than in the control group. Adiponectin, which is negatively correlated with visceral adiposity, increased significantly only in the catechin group. Although the increase in Ins at week 12 was significantly greater in the catechin group than in the control group, no apparent difference was noted between the two groups in glucose and hemoglobin A1c. In patients treated with insulinotropic agents, the increase in Ins at week 12 was significantly greater in the catechin group than in the control group. This significant increase in Ins levels was observed only in the catechin group. In the catechin group receiving other treatments, Ins levels remained unchanged. In addition, in patients treated with insulinotropic agents, the decrease in hemoglobin A1c at week 12 was significantly greater in the catechin group than in the control group. These results suggest that a catechin‐rich beverage might have several therapeutic uses: in the prevention of obesity; in the recovery of Ins‐secretory ability; and, as a way to maintain low hemoglobin A1c levels in type 2 diabetic patients who do not yet require Ins therapy.
Real-time analysis of amyloid fibril formation of α-synuclein using a fibrillation-state-specific fluorescent probe of JC-1
Authors: Lee Jung-Ho , Lee In-Hwan , Choe Young-Jun , Kang Sungsoo , Kim Hui Young , Gai Wei-Ping , Hahn Ji-Sook , Paik Seung R.
Published: November 2008

α-Synuclein is a pathological component of PD (Parkinson's disease) by participating in Lewy body formation. JC-1 (5,5′,6,6′-tetrachloro-1,1,3,3′-tetraethylbenzimidazolyl carbocyanine iodide) has been shown to interact with α-synuclein at the acidic C-terminal region with a Kd of 2.6 μM. JC-1 can discriminated between the fibrillation states of α-synuclein (monomeric, oligomeric intermediate and fibrillar forms) by emitting the enhanced binding fluorescence of different colours at 590, 560 and 538 nm respectively with the common excitation at 490 nm. The fibrillation-state-specific interaction of JC-1 allowed us to perform real-time analyses of the α-synuclein fibrillation in the presence of iron as a fibrillation inducer, rifampicin as a fibrillation inhibitor, baicalein as a defibrillation agent and dequalinium as a protofibril inducer. In addition, various α-synuclein fibrils with different morphologies prepared with specific ligands such as metal ions, glutathione, eosin and lipids were monitored with their characteristic JC-1-binding fluorescence spectra. FRET (fluorescence resonance energy transfer) between thioflavin-T and JC-1 was also employed to specifically identify the amyloid fibrils of α-synuclein. Taken together, we have introduced JC-1 as a powerful and versatile probe to explore the molecular mechanism of the fibrillation process of α-synuclein in vitro. It could be also useful in high-throughput drug screening. The specific α-synuclein interaction of JC-1 would therefore contribute to our complete understanding of the molecular aetiology of PD and eventual development of diagnostic/therapeutic strategies for various α-synucleinopathies.
Identification of nucleation sites and formation mechanism of inverted pyramids in 4H-SiC epilayers
Authors: Shrivastava A. , Muzykov P. , Sudarshan T. S.
Published: November 2008

Growth of high quality epilayers on low off-cut (≤4°) 4H-SiC substrates is essential for the fabrication of high performance power devices. Morphological defects such as “inverted pyramids” are device killers and hence knowing their origin and developing methods to eliminate them are essential. The nucleation sites and formation mechanism of the inverted pyramid defects, investigated using atomic force microscopy and KOH etching, are reported in this study. Partial dislocations, bounding the stacking faults, mostly aligned along the ⟨11–20⟩ directions, were found at the base of the inverted pyramid defects. It is shown that in addition to the basal plane dislocations, localized defects, attributed to clusters of impurities, serve as nucleation centers for stacking faults, and eventually the formation of inverted pyramid defects. A geometrical model is formulated to explain the formation mechanism of inverted pyramid defects.
Local distribution of the elements in the β phase of niobium-titanium superconducting alloy
Authors: Ksenofontov V. A. , Lazareva M. B. , Mazilova T. I. , Mikhaĭlovskiĭ I. M. , Storozhilov G. E. , Chernyĭ O. V.
Published: November 2008

A high-resolution atomic probe is used to analyze the chemical composition of an optimally thermo-mechanically worked niobium-titanium nanostructured superconducting alloy. Variations of the elemental composition in the matrix are found at the mesoscale level, and it is shown that they are much larger than technological nonuniformities of the chemical composition of the alloy. Nanoscale nonuniformities are found in the structure of the β phase. It is established that the order parameter of the titanium atoms is 1 and there is no clustering of the atoms and no short-range chemical order.
Effect of the electric polarization on the modulation wave vector of the antiferromagnetic structure of TbMnO3
Authors: Chupis I. E. , Ushakova I. V.
Published: November 2008

The effect of electric polarization on the temperature and field dependences of the modulation vector k of the antiferromagnetic structure in terbium manganite is analyzed. It is shown that in contrast to anharmonicity the electric polarization increases k, which could be why a nonmonotonic temperature dependence of the modulation vector is observed in TbMnO3.
Transport properties of cobaltites containing holmium
Authors: Chiang Yu. N. , Khirnyĭ V. F. , Shevchenko O. G. , Kozlovskiĭ A. A. , Semenov A. V. , Puzikov V. M. , Deĭneka T. G.
Published: November 2008

The temperature and magnetic field dependences of the electric resistance of ceramic samples Ho0.55Sr0.45CoO3−δ and Ho0.45Sr0.55CoO3−δ at temperatures ranging from room to liquid-nitrogen temperature and magnetic fields to 7kOe, applied perpendicular to the direction of current transport, are studied. Electric conduction in these samples is of the semiconductor type, and the magnetoresistance in a narrow temperature interval and comparable fields changed sign, ranging from −50 to +120%. A nonlinear dependence of the resistance of the samples on the magnitude of the transport current for weak currents and high sensitivity of the resistance to a weak magnetic field are observed. Analysis of the data shows a magnetic contribution (the presence of low-spin (S=1) states t2g5eg1 or high-spin (S=2) states t2g4eg2 of the Co3+ ions) to the mechanism of interelectronic correlations under conditions of percolation conductivity of the systems investigated. The corresponding activation energies are estimated.
Low-temperature electrical discharge through solid xenon
Authors: Gordon E. B. , Matyushenko V. I. , Sizov V. D. , Smirnov B. M.
Published: November 2008

A uniform self-sustained electrical discharge through solid xenon is realized and studied. The multiplication of electrons proceeds in the noble gas above the xenon crystal interface, whereas a positive feedback is realized on account of multiple exciton formation by excess electrons drifting through the crystal: molecular excitons emit VUV photons which knock out secondary electrons from photosensitive cathode. The discharge is stimulated by a short electrical spark along the sample axes. The electrical properties of the discharge and the electroluminescence spectra of solid xenon in the UV and visible are studied. Electrical discharge in solid xenon proves to be an effective source of UV radiation and a convenient tool for studying processes involving excitons and electrons in solid xenon at high pressures.
Structure of the high-temperature phase of tetrafluoromethane CF4
Authors: Klimenko N. A. , Gal’tsov N. N. , Prokhvatilov A. I.
Published: November 2008

X-Ray studies of the structure of the high-temperature β phase and the α-β orientational phase transition of carbon tetrafluoride have been performed. It has been found that β-CF4 possesses a monoclinic cell with the parameters a=13.732Å, b=12.815Å, c=13.429Å, and β=93.6°, which is similar to the unit cell of the high-temperature phase of silane SiH4. In both substances, the high-temperature phase contains molecules which are oriented in 32 different ways in the monoclinic lattice. It is pointed out that the structures determined for β-CF4 and β-SiH4 are related to the structures of the low-temperature phases of heavy methane tetrahalides α-CCl4 and α-CBr4. It is suggested that the orientational structures of β-CF4 and the low-temperature phases of heavy methane tetrahalides are very similar to one another. It is determined that the phase transition in CF4 is first-order phase transition, just as in silane, and is accompanied by a large volume jump reaching ΔV∕V=4.5%.
Particle size effect on diffusion in tubes with dead ends: Nonmonotonic size dependence of effective diffusion constant
Authors: Dagdug Leonardo , Berezhkovskii Alexander M. , Makhnovskii Yurii A. , Zitserman Vladimir Yu.
Published: November 2008

Diffusion of a spherical particle of radius r in a tube with identical periodic dead ends is analyzed. It is shown that the effective diffusion constant follows the Stokes–Einstein relation, Deff(r)∝1∕r, only when r is larger or much smaller than the radius of the dead end entrance. In between, Deff(r) not only deviates from the 1∕r behavior but may also even become a nonmonotonic function, which increases with the particle radius for a certain range of r.
Dynamic electronic response of a quantum dot driven by time-dependent voltage
Authors: Zheng Xiao , Jin Jinshuang , Yan YiJing
Published: November 2008

We present a comprehensive theoretical investigation on the dynamic electronic response of a noninteracting quantum dot system to various forms of time-dependent voltage applied to the single contact lead. Numerical simulations are carried out by implementing a recently developed hierarchical equations of motion formalism [J. S. Jin et al., J. Chem. Phys. 128, 234703 (2008)], which is formally exact for a fermionic system interacting with grand canonical fermionic reservoirs, in the presence of arbitrary time-dependent applied chemical potentials. The dynamical characteristics of the transient transport current evaluated in both linear and nonlinear-response regimes are analyzed, and the equivalent classic circuit corresponding to the coupled dot-lead system is also discussed.
Shock structure analysis in chemically reacting gas mixtures by a relaxation-time kinetic model
Authors: Groppi M. , Aoki K. , Spiga G. , Tritsch V.
Published: November 2008

The shock structure in a gas mixture undergoing a bimolecular chemical reaction is studied by means of a reactive kinetic relaxation model. The relevant nonlinear integrodifferential equations are numerically solved in one space dimension with upstream and downstream asymptotic equilibrium conditions satisfying the reactive Rankine–Hugoniot relations and entropy condition. Numerical results are presented, emphasizing the role of Mach number, upstream concentration fractions, and change in the chemical composition across the shock.
Carbides in stainless steels: Results from ab initio investigations
Authors: Henriksson K. O. E. , Sandberg N. , Wallenius J.
Published: November 2008

The useful properties of steels are due to a complicated microstructure containing iron and chromium carbides. Only some basic physical properties of these carbides are known with high precision, although the carbides may have a vital impact on the performance and longevity of the steel. To improve on this situation, we have performed extensive density-functional theory calculations of several carbides. The quantitative results are in perfect agreement with the relative empirical stability of the carbides. Also, in contradiction with experimental data, we find that Cr23C6 responsible for the hardness of stainless steels is not the most stable chromium-dominated carbide.
Photoresponses in polycrystalline silicon phototransistors incorporating germanium quantum dots in the gate dielectrics
Authors: Tseng S. S. , Chen I. H. , Li P. W.
Published: November 2008

Polycrystalline silicon (poly-Si) thin-film transistors (TFTs) incorporating germanium (Ge) quantum dots (QDs) in the gate oxide were fabricated as efficient blue to near ultraviolet phototransistors for light detection and amplification. Under 405–450 nm light illumination, Ge QDs poly-Si TFTs exhibit not only strong photoresponses in the drive current but also much improved subthreshold characteristics than that measured in darkness. This originates from the fact that only photoexcited holes within Ge QDs are injected into the active channel via vertical electric field and contribute excess mobile carriers for photocurrent but without the associated photogenerated electron induced junction barrier lowering.
The quantitative genetics of sex differences in parenting
Authors: Walling Craig A. , Stamper Clare E. , Smiseth Per T. , Moore Allen J.
Published: November 2008

Sex differences in parenting are common in species where both males and females provide care. Although there is a considerable body of game and optimality theory for why the sexes should differ in parental care, genetics can also play a role, and no study has examined how genetic influences might influence differences in parenting. We investigated the extent that genetic variation influenced differences in parenting, whether the evolution of differences could be constrained by shared genetic influences, and how sex-specific patterns of genetic variation underlying parental care might dictate which behaviors are free to evolve in the burying beetle
Nicrophorus vespilloides
. Females provided more direct care than males but did not differ in levels of indirect care or the number of offspring they were willing to rear. We found low to moderate levels of heritability and evolvability for all 3 parenting traits in both sexes. Intralocus sexual conflict was indicated by moderately strong intersex genetic correlations, but these were not so strong as to represent an absolute constraint to the evolution of sexual dimorphism in care behavior. Instead, the pattern of genetic correlations between parental behaviors showed sex-specific tradeoffs. Thus, differences in the genetic correlations between parental traits within a sex create sex-specific lines of least evolutionary resistance, which in turn produce the specific patterns of sex differences in parental care. Our results therefore suggest a mechanism for the evolution of behavioral specialization during biparental care if uniparental and biparental care behaviors share the same genetic influences.
Cross-talk between histone H3 tails produces cooperative nucleosome acetylation
Authors: Li Shanshan , Shogren-Knaak Michael A.
Published: November 2008

Acetylation of histone proteins by the yeast Spt-Ada-Gcn5-acetyltansferase (SAGA) complex has served as a paradigm for understanding how posttranslational modifications of chromatin regulate eukaryotic gene expression. Nonetheless, it has been unclear to what extent the structural complexity of the chromatin substrate modulates SAGA activity. By using chromatin model systems, we have found that SAGA-mediated histone acetylation is highly cooperative (cooperativity constant of 1.97 ± 0.15), employing the binding of multiple noncontiguous nucleosomes to facilitate maximal acetylation activity. Studies with various chromatin substrates, including those containing novel asymmetric histone octamers, indicate that this cooperativity occurs only when both H3 histone tails within a nucleosome are properly oriented and unacetylated. We propose that modulation of maximal SAGA activity through this dual-tail recognition could facilitate coregulation of spatially proximal genes by promoting cooperative nucleosome acetylation between genes.
Computing the stability diagram of the Trp-cage miniprotein
Authors: Paschek Dietmar , Hempel Sascha , García Angel E.
Published: November 2008

We report molecular dynamics simulations of the equilibrium folding/unfolding thermodynamics of an all-atom model of the Trp-cage miniprotein in explicit solvent. Simulations are used to sample the folding/unfolding free energy difference and its derivatives along 2 isochores. We model the Δ

G
u
(P,T)

landscape using the simulation data and propose a stablility diagram model for Trp-cage. We find the proposed diagram to exhibit features similar to globular proteins with increasing hydrostatic pressure destabilizing the native fold. The observed energy differences Δ

E
u

are roughly linearly temperature-dependent and approach Δ

E
u

= 0 with decreasing temperature, suggesting that the system approached the region of cold denaturation. In the low-temperature denatured state, the native helical secondary structure elements are largely preserved, whereas the protein conformation changes to an “open-clamp” configuration. A tighter packing of water around nonpolar sites, accompanied by an increasing solvent-accessible surface area of the unfolded ensemble, seems to stabilize the unfolded state at elevated pressures.
The goat domestication process inferred from large-scale mitochondrial DNA analysis of wild and domestic individuals
Authors: Naderi Saeid , Rezaei Hamid-Reza , Pompanon François , Blum Michael G. B. , Negrini Riccardo , Naghash Hamid-Reza , Balkız Özge , Mashkour Marjan , Gaggiotti Oscar E. , Ajmone-Marsan Paolo , Kence Aykut , Vigne Jean-Denis , Taberlet Pierre
Published: November 2008

The emergence of farming during the Neolithic transition, including the domestication of livestock, was a critical point in the evolution of human kind. The goat (
Capra hircus
) was one of the first domesticated ungulates. In this study, we compared the genetic diversity of domestic goats to that of the modern representatives of their wild ancestor, the bezoar, by analyzing 473 samples collected over the whole distribution range of the latter species. This partly confirms and significantly clarifies the goat domestication scenario already proposed by archaeological evidence. All of the mitochondrial DNA haplogroups found in current domestic goats have also been found in the bezoar. The geographic distribution of these haplogroups in the wild ancestor allowed the localization of the main domestication centers. We found no haplotype that could have been domesticated in the eastern half of the Iranian Plateau, nor further to the east. A signature of population expansion in bezoars of the C haplogroup suggests an early domestication center on the Central Iranian Plateau (Yazd and Kerman Provinces) and in the Southern Zagros (Fars Province), possibly corresponding to the management of wild flocks. However, the contribution of this center to the current domestic goat population is rather low (1.4%). We also found a second domestication center covering a large area in Eastern Anatolia, and possibly in Northern and Central Zagros. This last domestication center is the likely origin of almost all domestic goats today. This finding is consistent with archaeological data identifying Eastern Anatolia as an important domestication center.
High tolerance for ionizable residues in the hydrophobic interior of proteins
Authors: Isom Daniel G. , Cannon Brian R. , Castañeda Carlos A. , Robinson Aaron , García-Moreno E. Bertrand
Published: November 2008

Internal ionizable groups are quite rare in water-soluble globular proteins. Presumably, this reflects the incompatibility between charges and the hydrophobic environment in the protein interior. Here we show that proteins can have an inherently high tolerance for internal ionizable groups. The 25 internal positions in staphylococcal nuclease were substituted one at a time with Lys, Glu, or Asp without abolishing enzymatic activity and without detectable changes in the conformation of the protein. Similar results with substitutions of 6 randomly chosen internal positions in ribonuclease H with Lys and Glu suggest that the ability of proteins to tolerate internal ionizable groups might be a property common to many proteins. Eighty-six of the 87 substitutions made were destabilizing, but in all but one case the proteins remained in the native state at neutral pH. By comparing the stability of each variant protein at two different pH values it was established that the p
K
a
values of most of the internal ionizable groups are shifted; many of the internal ionizable groups are probably neutral at physiological pH values. These studies demonstrate that special structural adaptations are not needed for ionizable groups to exist stably in the hydrophobic interior of proteins. The studies suggest that enzymes and other proteins that use internal ionizable groups for functional purposes could have evolved through the random accumulation of mutations that introduced ionizable groups at internal positions, followed by evolutionary adaptation and optimization to modulate stability, dynamics, and other factors necessary for function.
Altered functional properties of a
TRPM2
variant in Guamanian ALS and PD
Authors: Hermosura Meredith C. , Cui Aaron M. , Go Ramon Christopher V. , Davenport Bennett , Shetler Cory M. , Heizer Justin W. , Schmitz Carsten , Mocz Gabor , Garruto Ralph M. , Perraud Anne-Laure
Published: November 2008

Two related neurodegenerative disorders, Western Pacific amyotrophic lateral sclerosis (ALS) and parkinsonism–dementia (PD), originally occurred at a high incidence on Guam, in the Kii peninsula of Japan, and in southern West New Guinea more than 50 years ago. These three foci shared a unique mineral environment characterized by the presence of severely low levels of Ca
2+
and Mg
2+
, coupled with high levels of bioavailable transition metals in the soil and drinking water. Epidemiological studies suggest that genetic factors also contribute to the etiology of these disorders. Here, we report that a variant of the transient receptor potential melastatin 2 (
TRPM2
) gene may confer susceptibility to these diseases.
TRPM2
encodes a calcium-permeable cation channel highly expressed in the brain that has been implicated in mediating cell death induced by oxidants. We found a heterozygous variant of
TRPM2
in a subset of Guamanian ALS (ALS-G) and PD (PD-G) cases. This variant,
TRPM2

P1018L

, produces a missense change in the channel protein whereby proline 1018 (Pro
1018
) is replaced by leucine (Leu
1018
). Functional studies revealed that, unlike WT TRPM2, P1018L channels inactivate. Our results suggest that the ability of TRPM2 to maintain sustained ion influx is a physiologically important function and that its disruption may, under certain conditions, contribute to disease states.
A single-cell view on the ecophysiology of anaerobic phototrophic bacteria
Authors: Musat Niculina , Halm Hannah , Winterholler Bärbel , Hoppe Peter , Peduzzi Sandro , Hillion Francois , Horreard Francois , Amann Rudolf , Jørgensen Bo B. , Kuypers Marcel M. M.
Published: November 2008

Quantitative information on the ecophysiology of individual microorganisms is generally limited because it is difficult to assign specific metabolic activities to identified single cells. Here, we develop and apply a method, Halogen In Situ Hybridization-Secondary Ion Mass Spectroscopy (HISH-SIMS), and show that it allows simultaneous phylogenetic identification and quantitation of metabolic activities of single microbial cells in the environment. Using HISH-SIMS, individual cells of the anaerobic, phototropic bacteria
Chromatium okenii
,
Lamprocystis purpurea
, and
Chlorobium clathratiforme
inhabiting the oligotrophic, meromictic Lake Cadagno were analyzed with respect to H
13
CO
3
−
and
15
NH
4
+
assimilation. Metabolic rates were found to vary greatly between individual cells of the same species, showing that microbial populations in the environment are heterogeneous, being comprised of physiologically distinct individuals. Furthermore,
C. okenii
, the least abundant species representing ≈0.3% of the total cell number, contributed more than 40% of the total uptake of ammonium and 70% of the total uptake of carbon in the system, thereby emphasizing that numerically inconspicuous microbes can play a significant role in the nitrogen and carbon cycles in the environment. By introducing this quantification method for the ecophysiological roles of individual cells, our study opens a variety of possibilities of research in environmental microbiology, especially by increasing the ability to examine the ecophysiological roles of individual cells, including those of less abundant and less active microbes, and by the capacity to track not only nitrogen and carbon but also phosphorus, sulfur, and other biological element flows within microbial communities.
SubtelomericACS-containing Proto-silencers Act as Antisilencers in Replication Factors Mutants inSaccharomyces cerevisiae
Authors: Rehman Muhammad Attiq , Wang Dongliang , Fourel Genevieve , Gilson Eric , Yankulov Krassimir
Published: November 2008

Subtelomeric genes are either fully active or completely repressed and can switch their state about once per 20 generations. This meta-stable telomeric position effect is mediated by strong repression signals emitted by the telomere and relayed/enhanced by weaker repressor elements called proto-silencers. In addition, subtelomeric regions contain sequences with chromatin partitioning and antisilencing activities referred to as subtelomeric antisilencing regions. Using extensive mutational analysis of subtelomeric elements, we show that ARS consensus sequence (ACS)-containing proto-silencers convert to antisilencers in several replication factor mutants. We point out the significance of the B1 auxiliary sequence next to ACS in mediating these effects. In contrast, an origin-derived ACS does not convert to antisilencer in mutants and its B1 element has little bearing on silencing. These results are specific for the analyzed ACS and in addition to the effects of each mutation (relative to wild type) on global silencing. Another line of experiments shows that Mcm5p possesses antisilencing activity and is recruited to telomeres in an ACS-dependent manner. Mcm5p persists at this location at the late stages of S phase. We propose that telomeric ACS are not static proto-silencers but conduct finely tuned silencing and antisilencing activities mediated by ACS-bound factors.
A Dual Role for Actin and Microtubule Cytoskeleton in the Transport of Golgi Units from the Nurse Cells to the Oocyte Across Ring Canals
Authors: Nicolas Emmanuelle , Chenouard Nicolas , Olivo-Marin Jean-Christophe , Guichet Antoine
Published: November 2008

Axis specification during Drosophila embryonic development requires transfer of maternal components during oogenesis from nurse cells (NCs) into the oocyte through cytoplasmic bridges. We found that the asymmetrical distribution of Golgi, between nurse cells and the oocyte, is sustained by an active transport process. We have characterized actin basket structures that asymmetrically cap the NC side of Ring canals (RCs) connecting the oocyte. Our results suggest that these actin baskets structurally support transport mechanisms of RC transit. In addition, our tracking analysis indicates that Golgi are actively transported to the oocyte rather than diffusing. We observed that RC transit is microtubule-based and mediated at least by dynein. Finally, we show that actin networks may be involved in RC crossing through a myosin II step process, as well as in dispatching Golgi units inside the oocyte subcompartments.
Role of an Ancestral D-Bifunctional Protein Containing Two Sterol-Carrier Protein-2 Domains in Lipid Uptake and Trafficking inToxoplasma
Authors: Lige Bao , Jayabalasingham Bamini , Zhang Hui , Pypaert Marc , Coppens Isabelle
Published: November 2008

The inability to synthesize cholesterol is universal among protozoa. The intracellular pathogen Toxoplasma depends on host lipoprotein-derived cholesterol to replicate in mammalian cells. Mechanisms of cholesterol trafficking in this parasite must be important for delivery to proper organelles. We characterized a unique d-bifunctional protein variant expressed by Toxoplasma consisting of one N-terminal d-3-hydroxyacyl-CoA dehydrogenase domain fused to two tandem sterol carrier protein-2 (SCP-2) domains. This multidomain protein undergoes multiple cleavage steps to release free SCP-2. The most C-terminal SCP-2 carries a PTS1 that directs the protein to vesicles before processing. Abrogation of this signal results in SCP-2 accumulation in the cytoplasm. Cholesterol specifically binds to parasite SCP-2 but with 10-fold lower affinity than phosphatidylcholine. In mammalian cells and Toxoplasma, the two parasite SCP-2 domains promote the circulation of various lipids between organelles and to the surface. Compared with wild-type parasites, TgHAD-2SCP-2–transfected parasites replicate faster and show enhanced uptake of cholesterol and oleate, which are incorporated into neutral lipids that accumulate at the basal end of Toxoplasma. This work provides the first evidence that the lipid transfer capability of an ancestral eukaryotic SCP-2 domain can influence the lipid metabolism of an intracellular pathogen to promote its multiplication in mammalian cells.
Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature
Authors: Wu Jiansheng , Liu Hongde , Duan Xueye , Ding Yan , Wu Hongtao , Bai Yunfei , Sun Xiao
Published: November 2008

Motivation: In this work, we aim to develop a computational approach for predicting DNA-binding sites in proteins from amino acid sequences. To avoid overfitting with this method, all available DNA-binding proteins from the Protein Data Bank (PDB) are used to construct the models. The random forest (RF) algorithm is used because it is fast and has robust performance for different parameter values. A novel hybrid feature is presented which incorporates evolutionary information of the amino acid sequence, secondary structure (SS) information and orthogonal binary vector (OBV) information which reflects the characteristics of 20 kinds of amino acids for two physical–chemical properties (dipoles and volumes of the side chains). The numbers of binding and non-binding residues in proteins are highly unbalanced, so a novel scheme is proposed to deal with the problem of imbalanced datasets by downsizing the majority class.

Results: The results show that the RF model achieves 91.41% overall accuracy with Matthew's correlation coefficient of 0.70 and an area under the receiver operating characteristic curve (AUC) of 0.913. To our knowledge, the RF method using the hybrid feature is currently the computationally optimal approach for predicting DNA-binding sites in proteins from amino acid sequences without using three-dimensional (3D) structural information. We have demonstrated that the prediction results are useful for understanding protein–DNA interactions.

Availability: DBindR web server implementation is freely available at http://www.cbi.seu.edu.cn/DBindR/DBindR.htm.

Contact:  xsun@seu.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
The SNPMaP package for R: a framework for genome-wide association using DNA pooling on microarrays
Authors: Davis Oliver S. P. , Plomin Robert , Schalkwyk Leonard C.
Published: November 2008

Summary: Large-scale genome-wide association (GWA) studies using thousands of high-density SNP microarrays are becoming an essential tool in the search for loci related to heritable variation in many phenotypes. However, the cost of GWA remains beyond the reach of many researchers. Fortunately, the majority of statistical power can still be obtained by estimating allele frequencies from DNA pools, reducing the cost to that of tens, rather than thousands of arrays. We present a set of software tools for processing SNPMaP (SNP microarrays and pooling) data from CEL files to Relative Allele Scores in the rich R statistical computing environment.

Availability: The SNPMaP package is available from http://cran.r-project.org/ under the GNU General Public License version 3 or later.

Contact:  snpmap@iop.kcl.ac.uk

Supplementary information: Additional resources and test datasets are available at http://sgdp.iop.kcl.ac.uk/snpmap/
MINOMICS: visualizing prokaryote transcriptomics and proteomics data in a genomic context
Authors: Brouwer Rutger W. W. , van Hijum Sacha A. F. T. , Kuipers Oscar P.
Published: November 2008

Summary: We have developed MINOMICS, a tool that allows facile and in-depth visualization of prokaryotic transcriptomic and proteomic data in conjunction with genomics data. MINOMICS generates interactive linear genome maps in which multiple experimental datasets are displayed together with operon, regulatory motif, transcriptional promoter and transcriptional terminator information.

Availability: MINOMICS is freely accessible at http://www.minomics.nl

Contact:  sacha.vanhijum@nizo.nl; o.p.kuipers@rug.nl

Supplementary information:  http://bioinformatics.biol.rug.nl/supplementary/minomics/
Stability of Vitamin E in Wheat Flour and Whole Wheat Flour During Storage
Authors: Nielsen Merete M⊘ller , Hansen Åse
Published: November 2008

The stability of vitamin E during 297 days of storage of wheat flour and whole wheat flour ground on a stone mill or a roller mill, respectively, were studied. One day after milling, the total content of vitamin E, expressed in vitamin E equivalents (α‐TE), was 18.7 α‐TE and 10.8 α‐TE for stone‐milled and roller‐milled wheat flour, respectively. The difference in total vitamin E content was primarily due to the absence of the germ and bran fractions in the roller‐milled flour. The total loss of vitamin E during storage was 24% for stone‐milled wheat flour but 50% for roller‐milled wheat flour. These results indicate that vitamin E, which is present in high amounts in wheat germ, functions as an antioxidant in the stone‐milled wheat flour. Hexanal formation showed that lipid oxidation in roller‐milled flour occurred just after milling, whereas the formation of hexanal in the germ fraction displayed a lack period of 22 days, confirming that vitamin E functions as an effective antioxidant in the wheat germ. Results showed no significant difference in total loss of vitamin E for stone‐milled and roller‐milled whole wheat flour. Total loss after 297 days of storage for both milling methods was ≈32%.
Effects of Selected Barley Cultivars and Their Pearling Fractions on Inhibition of Human LDL Oxidation In Vitro Using a Modified Conjugated Dienes Method
Authors: Abdel‐Aal E.‐S. M. , Gamel T. H.
Published: November 2008

Oxidation of LDL cholesterol is an important factor in the development of atherosclerosis and heart disease. In this study, selected Canadian and Egyptian barley cultivars and their pearling fractions were evaluated for antioxidant capacity to inhibit human LDL oxidation in vitro. Measurement of conjugated dienes (CD) at 234 nm was optimized to determine the degree of LDL oxidation. Dilution of oxidized LDL with iso‐propanol gave a distinct diene conjugation peak. Significant differences in total phenols content (TPC) were found between the cultivars tested, with the hulless barley having greater TPC and inhibition capacity compared with hulled barleys. The outer layers fraction contained the highest TPC, lowest CD formation, and longest lag time, whereas the inner, or endosperm fraction, had the lowest inhibition effects. The middle pearling and hull fractions possessed intermediate inhibition effects. The inhibitory effect of barley extracts was dependent on phenols concentration following a linear or quadratic pattern. The results suggest that barley whole meals, outer layers, middle pearling, or hull fraction would be a potential LDL antioxidant.
Rheological Properties of Wheat Flour Dough and Their Relationship with Bread Volume. II. Dynamic Oscillation Measurements
Authors: Van Bockstaele Filip , De Leyn Ingrid , Eeckhout Mia , Dewettinck Koen
Published: November 2008

The rheological properties of 17 pure European wheat cultivars were analyzed and evaluated in relation to the bread volume. Rheological testing included two empirical rheological methods, farinograph and alveograph, in addition to more fundamental rheological methods, specifically the creep‐recovery and dynamic oscillation measurements. The four rheological methods revealed large differences in dough rheological properties among the 17 wheat cultivars. Phase angle δ and the moduli were strongly correlated. The dynamic oscillation parameters also correlated significantly with protein content, Zeleny sedimentation value, damaged starch content, and farinograph water absorption. A nonlinear relationship (power) between the maximum creep or recovery strain and the dynamic moduli was found for both shear stresses (100 and 250 Pa). Phase angle δ showed a positive relationship with the maximum creep or recovery strain. The dynamic oscillation parameters could be related to the bread volume. Phase angle δ could explain ≈70% of the variance in bread volume among the wheat cultivars. The dynamic moduli showed an inverse relationship with the bread volume. A nonlinear relationship with the bread volume could be established for G′ (r2 = 0.75), G″ (r2 = 0.72), and |G*| (r2 = 0.74).
Phylogenetic Analysis of Bean yellow mosaic virus Isolates from Four Continents: Relationship Between the Seven Groups Found and Their Hosts and Origins
Authors: Wylie S. J. , Coutts B. A. , Jones M. G. K. , Jones R. A. C.
Published: November 2008

Genetic diversity of Bean yellow mosaic virus (BYMV) was studied by comparing sequences from the coat protein (CP) and genome-linked viral protein (VPg) genes of isolates from four continents. CP sequences compared were those of 17 new isolates and 47 others already on the database, while the VPg sequences used were from four new isolates and 10 from the database. Phylogenetic analysis of the CP sequences revealed seven distinct groups, six polytypic and one monotypic. The largest and most genetically diverse polytypic group, which had intragroup diversity of 0.061 nucleotide substitutions per site, contained isolates from natural infections in eight host species. These original isolation hosts included both wild (four) and domesticated (four) species and were from monocotyledonous and dicotyledonous plant families, indicating a generalized natural host range strategy. Only one of the other five polytypic groups spanned both monocotyledons and dicotyledons, and all contained isolates from fewer species (one to four), all of which were domesticated and had lower intragroup diversity (0.019 to 0.045 nucleotide substitutions per site), indicating host specialization. Phylogenetic analysis of the fewer VPg sequences revealed three polytypic and two monotypic groupings. These groups also correlated with original natural isolation hosts, but the branch topologies were sometimes incongruous with those formed by CPs. Also, intragroup diversity was generally higher for VPgs than for CPs. A plausible explanation for the groups found when the 64 different CP sequences were compared is that the generalized group represents the original ancestral type from which the specialist host groups evolved in response to domestication of plants after the advent of agriculture. Data on the geographical origins of the isolates within each group did not reveal whether the specialized groups might have coevolved with their principal natural hosts where these were first domesticated, but this seems plausible.
AFLP Analysis of Intraspecific Variation BetweenMonilinia laxaIsolates from Different Hosts
Authors: Gril Tjasa , Celar Franci , Munda Alenka , Javornik Branka , Jakse Jernej
Published: November 2008

We analyzed with an amplified fragment length polymorphism (AFLP) marker system the genetic diversity and relationships among 67 Monilinia laxa isolates obtained from different host plants. From a total of 1,089 amplified bands scored using 20 primer combinations with two selective nucleotides, 354 were polymorphic and further used in genetic diversity analysis. Genetic relationships among isolates were assessed with different phenetic approaches, including unweighted pair group method with arithmetic mean clustering and principal coordinate analysis; the population's differentiation estimate was analyzed by molecular variance; and model-based clustering was employed to infer population structure. All four analyses clearly showed significant differences between isolates from apple trees and isolates from other host plants. No further grouping according to any other host plant was observed. The results indicate host specialization of apple isolates and support the taxonomic grouping of apple isolates.
Pepino mosaic virus on Tomato Seed: Virus Location and Mechanical Transmission
Authors: Ling Kai-Shu
Published: November 2008

In just a few years, Pepino mosaic virus (PepMV) has become a major threat to greenhouse tomato production around the world. Although tomato seed is suspected to spread the disease, its importance as an initial virus inoculum for PepMV has not been established. To determine the potential for seed transmission, a tomato seed lot highly contaminated with PepMV was used for large-scale seedling grow-out tests. None of 10,000 grow-out seedlings was infected as determined by symptom expression, enzyme-linked immunosorbent assay (ELISA), or infectivity assay on Nicotiana benthamiana. Even though PepMV was not seed transmitted on tomato, the virus was effectively transmitted to tomato and N. benthamiana seedlings through mechanical transmission with seed extract. To examine the exact location where PepMV particles accumulated on the tomato seed, seed coats and embryos were carefully isolated and tested separately by ELISA, real-time RT-PCR, and bioassay on N. benthamiana. PepMV was detected in the seed coat fraction in both immature and mature tomato seeds, but not in the embryo. However, in N. benthamiana, the virus was neither seedborne nor seed-transmitted. Because PepMV is seedborne in tomato, efficient mechanical transmission of PepMV from the virus-contaminated tomato seed to seedlings could initiate a disease epidemic in a new tomato growing area. Thus, it is important to plant certified tomato seed that has been tested free of PepMV.
Outbreak of Bacterial Blossom Blight Caused by Pseudomonas viridiflava on Actinidia chinensis Kiwifruit Plants in Italy
Authors: Balestra G. M. , Mazzaglia A. , Rossetti A.
Published: November 2008

During the springs from 2006 to 2008, a new disease was observed on 4- to 5-year-old Actinidia chinensis (cv. Jin Tao) trees in different commercial kiwifruit-production areas in northern Italy (Lombardy). Initially, disease occurrence was sporadic but later became widespread. Symptoms on flowers appeared as a dark brown rot of anthers, filaments, sepals, and whole buds. Blossoms abscised prematurely from buds. Symptoms appeared as confluent brown spots often present on rolled margins. Bacteria were isolated from symptomatic tissue on nutrient agar medium supplemented with 5% sucrose. The isolated bacteria were aerobic; produced a diffusible fluorescent pigment on King's B medium; levan, oxidase, and arginine dihydrydrolase negative, and catalase positive; rotted potato tuber tissue; caused a hypersensitive response on tobacco; and failed to reduce nitrate or utilize sucrose and were ice nuclease-positive at –5°C, suggesting the organism was P. viridiflava (1,3). Inoculation of 2-year-old A. chinensis cv. Jin Tao plants were carried out in the greenhouse under controlled environmental conditions (15 to 27°C, night/day; relative humidity up to 70%) by spraying five plants in bloom with a suspension (1 × 108 CFU/ml) of isolated bacteria with a hand-held sprayer that produced large spray droplets. Symptoms, similar to those in nature, were observed on flowers and buds 3 to 5 days after inoculation and on leaves after 7 to 10 days. Using the same tests described above with the original strains, the strains that were isolated from symptomatic tissue were identified as Pseudomonas viridiflava. Seven bacterial strains (PV508–PV1108) were identified by sequencing 1,481 bp of their 16S rDNA region (2) and using BlastN (4) for the most similar sequences in the INSD (GenBank, EMBL, and DDBJ). Our sequences shared 99.53% (1,474 of 1,481 bp) to 99.9% (1480 of 1,481 bp) identity with the analogous sequences of P. viridiflava available in the database. To our knowledge, this is the first report of an outbreak of blossom blight caused by P. viridiflava on A. chinensis cv. Jin Tao kiwifruit plants in Italy. Previously, it was reported on A. deliciosa cv. Hayward (3). Because of the risk of bacterial contamination among the different cultivars of kiwifruit, further investigation and development of control measures are in progress.

References: (1) R. A. Lelliott and D. E. Stead. Methods for the Diagnosis of Bacterial Diseases of Plants. Blackwell Scientific, Oxford, UK, 1987. (2) E. R. B. Moore et al. Syst. Appl. Microbiol. 19:478, 1996. (3) L. Varvaro et al. Inf. Fitopatol. 6:49, 1990. (4) Z. Zhang et al. J. Comput. Biol. 7(1-2):203, 2000.