bluuebunny/crossref_metadata_2025 huggingface dataset:
High‐level production in Pichia pastoris of an anti‐p185HER‐2 single‐chain antibody fragment using an alternative secretion expression vector
Authors: Gurkan Cemal , Symeonides Stefan N. , Ellar David J.
Published: December 2008

The methylotrophic yeast Pichia pastoris has become a highly popular expression host for the recombinant production of a wide variety of proteins. Initial success with this system was greatly facilitated by the development of versatile expression vectors that were almost exclusively based on the strong, tightly regulated promoter of the P. pastoris major alcohol oxidase gene (AOX1). For example, pIB4 is an Escherichia coli–P. pastoris shuttle vector that also uses the AOX1 promoter to allow intracellular expression of endogenous and foreign genes in the latter organism. Since the eukaryotic advantages of P. pastoris would be best harnessed through the secretory targeting of the recombinant proteins, we modified the pIB4 vector by adding the Saccharomyces cerevisiae α‐factor secretion signal immediately upstream of its multiple cloning site. Here we describe the construction of this modified vector, pIB4α, and its successful use for the high‐level expression and secretion of a functional single‐chain antibody fragment (scFv), C6.5, which targets p185HER‐2, a cell‐surface glycoprotein overexpressed in about 30% of human breast and ovarian cancers. The PCR strategy used for the subcloning of the C6.5 construct into pIB4α also introduced a short DNA sequence coding for a C‐terminal hexahistidine tag, which allowed subsequent purification of the secreted scFv, by immobilized‐metal‐affinity chromatography, to a yield of 70 mg·l−1 of shake‐flask culture. In conclusion, our results suggest that the secretion expression vector pIB4α not only complements the original pIB4 vector for intracellular expression in P. pastoris, but might also constitute an attractive alternative to the commercially available secretion expression vectors.
Adhesion and proliferation of human vascular cells on UV‐light‐modified polymers
Authors: Heitz Johannes , Gumpenberger Thomas , Kahr Heike , Romanin Christoph
Published: December 2008

We studied the adhesion and proliferation of human umbilical‐vein endothelial cells (HUVEC) and human aortic smooth‐muscle cells (HASMC) on modified polymer samples. The polymers under investigation were either PTFE (polytetrafluoroethylene) or PET [poly(ethylene terephthalate)], which are among the most frequently employed biomaterials in reconstructive medicine. The polymer surfaces were modified by exposure to the UV light of an excited‐xenon‐dimer (Xe2*) excimer lamp (Heraeus‐Noblelight, Hanau, Germany) at a wavelength of 172 nm in an NH3 atmosphere. On modified PTFE, this resulted in a significant increase in the number of adhering HUVEC or HASMC 1 day after seeding and in the formation of a confluent cell layer after 3–4 days. On PET, HUVEC adhesion and proliferation rates were already high on untreated samples and could not be significantly increased by the UV‐light treatment, but the cells were distributed more homogenously on the treated samples. Cell proliferation was in all cases comparable with, or even better than, that obtained on standard polystyrene (PS) Petri dishes used in cell cultivation. As on PS Petri dishes, the proliferation of HASMC on modified PTFE was faster than that of HUVEC under similar culture conditions.
Engineering conduits to resemble natural vascular tissue
Authors: Buján Julia , García‐Honduvilla Natalio , Bellón Juan Manuel
Published: December 2008

Research on the use of biomaterials as vascular substitutes has been dominated in the past by studies focusing on the properties of the materials used. These need to be resistant to protein absorption and should allow cell colonization and integration of the biomaterial within recipient tissue. Despite promising perspectives related both to the appearance of new synthetic materials with biomedical applications and to developments in arterial replacement techniques, there are still many unresolved problems. These include the appearance of occlusive phenomena when using medium‐ or small‐calibre arterial substitutes, and the lack of growth and adaptability of the biomaterial to changes in the host. Notwithstanding, the tissue‐engineering techniques developed in recent decades have vastly improved prosthetic behaviour at the blood/biomaterial interface. There is also no doubt that developments in engineered arterial grafts made of natural biomaterials colonized with cells harvested from the recipient patient are drawing us closer and closer to achieving the living graft.
The production of hypericins and hyperforin byin vitrocultures of St. John's wort (Hypericum perforatum)
Authors: Kirakosyan Ara , Sirvent Tara Michelle , Gibson Donna Marie , Kaufman Peter B.
Published: December 2008

St. John's wort (Hypericum perforatumL.) is a herbaceous perennial distributed throughout the World that has been widely used in traditional medicine.H. perforatumproduces several types of biologically active compound, including the hypericins – a family of light‐activated anthraquinones, localized within specialized glands found predominantly on flowers and leaves – and the hyperforins – a family of prenylated acylphloroglucinols localized in the reproductive structures of the plant. Hypericins are known to be toxic to mammals and display antiviral and anticancer activity, but the role of these compounds within the plant is unknown. Hyperforins display potent antimicrobial activity and are thought to be the primary bioactive ingredient for anti‐depressive effects of the herb. The introduction ofH. perforatumfrom Europe into the U.S.A. occurred in the 17th Century. Since the plant is considered a noxious weed, few efforts have been carried out to analyse populations in the context of secondary‐metabolite concentrations. But in terms of secondary‐metabolite studies,H. perforatumis an ideal model system to study the biosyntheses of aromatic polyketides and regulation of those pathways by environmental and genetic influences. This is due, in part, to the ease of conducting these studies in plant tissue culture. This review describes the progress of secondary‐metabolite studies currently underway usingH. perforatum. Specifically, this Review focuses on the production and regulation of the hypericins and the hyperforin in wild populations, field cultivation, greenhouse studies and plant tissue culture. Additionally, factors optimizing compound production – particularly inin vitrocultures – are presented and reviewed.
Cross-Modal Interactions of Auditory and Somatic Inputs in the Brainstem and Midbrain and Their Imbalance in Tinnitus and Deafness
Authors: Dehmel S. , Cui Y. L. , Shore S. E.
Published: December 2008

Purpose

This review outlines the anatomical and functional bases of somatosensory influences on auditory processing in the normal brainstem and midbrain. It then explores how interactions between the auditory and somatosensory system are modified through deafness, and their impact on tinnitus is discussed.

Method

Literature review, tract tracing, immunohistochemistry, and in vivo electrophysiological recordings were used.

Results

Somatosensory input originates in the dorsal root ganglia and trigeminal ganglia, and is transmitted directly and indirectly through 2nd-order nuclei to the ventral cochlear nucleus, dorsal cochlear nucleus (DCN), and inferior colliculus. The glutamatergic somatosensory afferents can be segregated from auditory nerve inputs by the type of vesicular glutamate transporters present in their terminals. Electrical stimulation of the somatosensory input results in a complex combination of excitation and inhibition, and alters the rate and timing of responses to acoustic stimulation. Deafness increases the spontaneous rates of those neurons that receive excitatory somatosensory input and results in a greater sensitivity of DCN neurons to trigeminal stimulation.

Conclusions

Auditory-somatosensory bimodal integration is already present in 1st-order auditory nuclei. The balance of excitation and inhibition elicited by somatosensory input is altered following deafness. The increase in somatosensory influence on auditory neurons when their auditory input is diminished could be due to cross-modal reinnervation or increased synaptic strength, and may contribute to mechanisms underlying somatic tinnitus.
Laser-induced magnesium production from magnesium oxide using reducing agents
Authors: Mohamed M. S. , Yabe T. , Baasandash C. , Sato Y. , Mori Y. , Shi-Hua Liao , Sato H. , Uchida S.
Published: December 2008

Experiments for laser induced production of magnesium (Mg) from magnesium oxide (MgO) using reducing agents (R) were conducted. In these experiments, continuous wave CO2 focused laser is focused on a mixture of magnesium oxide and reducing agent. High power density of focused laser leads to high temperature and the reduction reaction resulting in Mg production. The resultant vapor is collected on a copper plate and analyzed in terms of magnesium deposition efficiency. Deposition efficiencies with various reducing agents such as Zr, C, and Si have been measured to be 60, 9.2, and 12.1 mg/kJ respectively. An excess addition of reducing agent over their corresponding reaction stoichiometric amounts is found to be optimum condition for the most of performed laser induced reactions. In addition, utilizing solar-pumped laser in Mg production with reducing agent will reduce CO2 emission and produce magnesium with high-energy efficiency and large throughput.
A unified theoretical framework for fluctuating-charge models in atom-space and in bond-space
Authors: Chen Jiahao , Hundertmark Dirk , Martínez Todd J.
Published: December 2008

Our previously introduced QTPIE (charge transfer with polarization current equilibration) model [J. Chen and T. J. Martínez, Chem. Phys. Lett. 438, 315 (2007)] is a fluctuating-charge model with correct asymptotic behavior. Unlike most other fluctuating-charge models, QTPIE is formulated in terms of charge-transfer variables and pairwise electronegativities, not atomic charge variables and electronegativities. The pairwise character of the electronegativities in QTPIE allows us to avoid spurious charge transfer when bonds are broken. However, the increased number of variables leads to considerable computational expense and a rank-deficient set of working equations, which is numerically inconvenient. Here, we show that QTPIE can be exactly reformulated in terms of atomic charge variables, leading to a considerable reduction in computational complexity. The transformation between atomic and bond variables is generally applicable to arbitrary fluctuating charge models and uncovers an underlying topological framework that can be used to understand the relation between fluctuating-charge models and the classical theory of electrical circuits.
Estimating errors in free energy calculations from thermodynamic integration using fitted data
Authors: de Miguel Enrique
Published: December 2008

A procedure to estimate the statistical uncertainties associated with free energies computed from thermodynamic integration using fitted data is described. The method involves generating synthetic data sets from the actual simulation data and performing an analysis of the resulting distribution of free energy values. These values follow a Gaussian distribution, and the corresponding standard deviation is associated with the error in the computed value of the free energy. The impact of these uncertainties on the coexistence pressure is examined for first-order transitions. The approach is demonstrated with an examination of finite-size effects at the freezing transition of hard spheres.
Strong stretching theory for diblock copolymers in thin films
Authors: Heckmann Marianne , Drossel Barbara
Published: December 2008

We investigate the microphases of diblock copolymers confined to thin films in the strong segregation limit. We evaluate the free energies of the possible phases and present phase diagrams for block copolymers with a cylindrical bulk phase in dependence of the film thickness and the walls’ preference for one of the monomers. We find four stable types of phases, which were also found in studies based on self-consistent field theory and dynamic density functional theory. We argue that perforated lamellas are not a stable phase.
Oblique ion collection in the drift approximation: How magnetized Mach probes really work
Authors: Hutchinson I. H.
Published: December 2008

The anisotropic fluid equations governing a frictionless obliquely flowing plasma around an essentially arbitrarily shaped three-dimensional ion-absorbing object in a strong magnetic field are solved analytically in the quasineutral drift approximation, neglecting parallel temperature gradients. The effects of transverse displacements traversing the magnetic presheath are also quantified. It is shown that the parallel collection flux density dependence upon the external Mach number is n∞csexp[−1−(M∥∞−M⊥cotθ)], where θ is the angle (in the plane of field and drift velocity) of the object-surface to the magnetic-field and M∥∞ is the external parallel flow. The perpendicular drift, M⊥, appearing here consists of the external E∧B drift plus a weighted sum of the ion and electron diamagnetic drifts that depends upon the total angle of the surface to the magnetic field. It is that somewhat counterintuitive combination that an oblique (transverse) Mach probe experiment measures.
High-frequency properties of a graphene nanoribbon field-effect transistor
Authors: Ryzhii M. , Satou A. , Ryzhii V. , Otsuji T.
Published: December 2008

We propose an analytical device model for a graphene nanoribbon field-effect transistor (GNR-FET) under the dc and ac operating conditions. The GNR-FET under consideration is based on a heterostructure, which consists of an array of nanoribbons clad between the highly conducting substrate (the back gate) and the top gate controlling the dc and ac source-drain currents. Using the model developed, we derive explicit analytical formulas for the GNR-FET transconductance as a function of the signal frequency, collision frequency of electrons, and the top gate length. The transition from the ballistic to strongly collisional electron transport is considered.
Ab initio modeling of spin and charge ordering and lattice dynamics in CaFeO3 crystals
Authors: Alexandrov V. E. , Kotomin E. A. , Maier J. , Evarestov R. A.
Published: December 2008

Results of first-principles simulations on both orthorhombic and monoclinic phases of CaFeO3 crystal are presented. The obtained atomic structures are consistent with x-ray diffraction data. The transition from a metallic orthorhombic to a narrow-gap semiconducting monoclinic phase is ascribed to the larger distortion of the Fe–O–Fe bond angle in the latter case. Calculations of Raman and optic active phonon modes at the Γ point of the Brillouin zone are performed and discussed. The isotopic substitution technique is applied to analyze the vibration modes obtained. The found charge/spin disproportionation is analyzed and compared with available experimental estimates.
Secondary electron emission from freely supported nanowires
Authors: Suzuki Makoto , Kumagai Kazuhiro , Sekiguchi Takashi , Cassell Alan M. , Saito Tsutomu , Yang Cary Y.
Published: December 2008

We present secondary electron (SE) emission results from freely supported carbon/silicon nitride (Si3N4) hybrid nanowires using scanning electron microscopy. We found that, contrary to bulk materials, the SE emission from insulating or electrically isolated metallic nanowires is strongly suppressed by the penetrating beam. A mechanism of the SE suppression by the positive specimen charging is proposed, which is based on a total emission yield calculation using the Monte Carlo technique. This finding provides an important basis for studying low-energy electron emission from nanostructures under a penetrating electron beam.
Influence of magnetic anisotropy and its distribution on the hysteresis loops upon patterning thin films
Authors: Boukari S. , Venuat J. , Carvalho A. , Arabski J. , Beaurepaire E.
Published: December 2008

We compare the hysteresis loops of ferromagnetic films and dots down to 0.2 μm. Samples are made of Co–Pt multilayers with different Co thicknesses so as to vary the perpendicular magnetic anisotropy. We determined the first- and second-order anisotropies of the films, as well as the first-order anisotropy distribution, and show that from these quantities the switching field distribution of dots can be predicted. We also explain through a simple criterion—the relation between the anisotropy distribution and the minimum nucleation field—why in some cases the hysteresis loops recorded along the easy axis on the films undergo a dramatic change after patterning.
Magnetism in

n

anopatterned graphite film
Authors: Chen Li , Yu Decai , Liu Feng
Published: December 2008

Using first-principles calculations, we show that nanopatterned graphite films (NPGFs) can exhibit magnetism in analogy to graphene-based nanostructures (GBNs). In particular, graphite films with patterned nanoscale triangular holes and channels with zigzag edges all have ferromagnetic ground states. The magnetic moments are localized at the edges with a behavior similar to that of GBNs. Our findings suggest that the NPGFs form a unique class of magnetic materials.
A kinetic theory for particulate systems with bimodal and anisotropic velocity fluctuations
Authors: Ozarkar Shailesh S. , Sangani Ashok S. , Kushch Volodymyr I. , Koch Donald L.
Published: December 2008

Observations of bubbles rising near a wall under conditions of large Reynolds and small Weber numbers have indicated that the velocity component of the bubbles parallel to the wall is significantly reduced upon collision with a wall. To understand the effect of such bubble-wall collisions on the flow of bubbly liquids bounded by walls, a model is developed and examined in detail by numerical simulations and theory. The model is a system of bubbles in which the velocity of the bubbles parallel to the wall is significantly reduced upon collision with the channel wall while the bubbles in the bulk are acted upon by gravity and linear drag forces. The inertial forces are accounted for by modeling the bubbles as rigid particles with mass equal to the virtual mass of the bubbles. The standard kinetic theory for granular materials modified to account for the viscous and gravity forces and supplemented with boundary conditions derived assuming an isotropic Maxwellian velocity distribution is inadequate for describing the behavior of the bubble-phase continuum near the walls since the velocity distribution of the bubbles near the walls is significantly bimodal and anisotropic. A kinetic theory that accounts for such a velocity distribution is described. The bimodal nature is captured by treating the system as consisting of two species with the bubbles (modeled as particles) whose most recent collision was with a channel wall treated as one species and those whose last collision was with another bubble as the other species. The theory is shown to be in very good agreement with the results of numerical simulations and provides closure relations that may be used in the analysis of bidisperse particulate systems as well as bounded bubbly flows.
Wettability inversion induced by weak electron irradiation
Authors: Aronov Daniel , Molotskii Michel
Published: December 2008

We investigate a wettability modification of ultrathin dielectric films induced by an electron irradiation. The effect of wettability inversion, transition from hydrophobic to hydrophilic state, is predicted for low irradiation doses. It is supposed that the inversion is caused by a change in the basic mechanism of the influence of an electron irradiation on the interface free energy. For high irradiation doses, the effect of the decrease in wettability under electron irradiation is caused by the interactions of an excess charge in the film with its image charges. At low doses, the mechanism is referred to the interaction of surface charges, which function as hydrophilic adsorption centers, with water molecules. The predicted effect of the wettability inversion has been experimentally verified with electron irradiation of silicon dioxide ultrathin films. A dramatic reduction in water drop surface tension on the liquid/vapor interface has been observed. Such reduction is explained by drop charging as a result of carriers tunneling from semiconductor through ultrathin oxide layer.
Midinfrared quantum cascade detector with a spectrally broad response
Authors: Hofstetter Daniel , Giorgetta Fabrizio R. , Baumann Esther , Yang Quankui , Manz Christian , Köhler Klaus
Published: December 2008

A midinfrared quantum cascade detector with a spectrally broad (ΔE∕E=27.3%) response is designed, fabricated, and tested. This detector consists of 26 differently designed active region stages in order to cover a wavelength region from 4.7to7.4μm. The device could be operated above room temperature and showed peak responsivities of 13mA∕W at 10K and 1.25mA∕W at room temperature. A background limited detectivity of 1.55×1010 Jones was seen up to a temperature TBLIP of 110K.
Room temperature surface piezoelectricity in SrTiO3 ceramics via piezoresponse force microscopy
Authors: Kholkin Andrei , Bdikin Igor , Ostapchuk Tetyana , Petzelt Jan
Published: December 2008

Sr Ti O 3 ceramics are investigated by piezoresponse force microscopy. Piezoelectric contrast is observed on polished surfaces in both vertical and lateral regimes and depends on the grain orientation varying in both sign (polarization direction) and amplitude. The observed contrast is attested to the surface piezoelectricity due to the flexoelectric effect (strain gradient-induced polarization) caused by the surface relaxation. The estimated flexoelectric coefficient is approximately one order of magnitude smaller as compared to that recently measured in SrTiO3 single crystals. The observed enhancement of piezoresponse signal at the grain boundaries is explained by the dipole moments associated with inhomogeneous distribution of oxygen vacancies.
Effects of interfacial oxygen-deficient layer on resistance switching in Cr-doped SrTiO3 thin films
Authors: Phan Bach Thang , Lee Jaichan
Published: December 2008

We investigated resistance switching in Cr-doped SrTiO3 thin films with an oxygen-deficient layer at the interface. Impedance spectroscopy showed the Maxwell–Wagner relaxation due to the high-resistance oxygen-deficient layer in addition to a bulk layer of lower resistance. The high oxygen-deficient layer significantly limits the carrier injection, thus resulting in the disappearance of resistance switching. The resistance switching was recovered by reducing the oxygen vacancy concentration at the top interface by cooling or postannealing at high oxygen ambient pressures.
Key scattering mechanisms for holes in strained SiGe/Ge/SiGe square quantum wells
Authors: Quang Doan Nhat , Tung Nguyen Huyen , Hien Do Thi , Hai Tran Thi
Published: December 2008

We present a theory of the low-temperature transport of holes confined in the Ge strained channel of single-side modulation-doped SiGe/Ge/SiGe square quantum wells (QWs). Besides the well-known scattering mechanisms such as remote impurities and surface roughness, the theory includes misfit deformation potential. We prove that due to the effect from doping-induced band bending, the surface roughness and misfit deformation potential scatterings are considerably strengthened. Accordingly, these are found to be the key scattering mechanisms in the SiGe/Ge/SiGe system, which are still a subject under debate. Our theory can explain all recent experimental data about the transport properties of interest, namely, the carrier-density dependences of the hole mobility and the ratio of the transport to quantum lifetimes. Further, the calculated hole mobility in Ge strained QWs exhibits a special channel-width dependence with a sharp peak, which was observed but has not been explained so far.
Surface strain and its impact on the electrical resistivity of GaN channel in AlGaN/GaN high electron mobility transistor
Authors: Mahadik Nadeemullah A. , Qadri Syed B. , Rao Mulpuri V.
Published: December 2008

Localized strain in AlGaN/GaN high electron mobility transistor (HEMT) device structures was studied by high resolution x-ray diffraction and rocking curve measurements, and the results were compared with the corresponding channel sheet resistance measurements. The map of in-plane tensile strain on the HEMT wafer showed a near one-to-one correspondence with the electrical resistivity. The in-plane strain variation in the range of (2.295–3.539)×10−4 resulted in a corresponding sheet resistance variation between 345 and 411 Ω/◻.
Transparent resistive random access memory and its characteristics for nonvolatile resistive switching
Authors: Seo Jung Won , Park Jae-Woo , Lim Keong Su , Yang Ji-Hwan , Kang Sang Jung
Published: December 2008

This report covers the fabrication of a fully transparent resistive random access memory (TRRAM) device based on an ITO (indium tin oxide)/ZnO/ITO capacitor structure and its resistive switching characteristics. The fabricated TRRAM has a transmittance of 81% (including the substrate) in the visible region and an excellent switching behavior under 3V. The retention measurement suggests that the memory property of the TRRAM device could be maintained for more than 10years. We believe that the TRRAM device presented in this work could be a milestone of future see-through electronic devices.
Phylogeny in cryptic weevils: molecules, morphology and new genera of western Palaearctic Cryptorhynchinae (Coleoptera:Curculionidae)
Authors: Astrin Jonas J. , Stüben Peter E.
Published: December 2008

A phylogeny is presented for the western Palaearctic representatives of the weevil subfamily Cryptorhynchinae using a combination of phenotypic and genotypic characters. This phylogeny is the first for the extremely species-rich Cryptorhynchinae to use molecular data (mitochondrial CO1 and 16S as well as nuclear ribosomal 28S). The results of this study show the need for molecular tools within this morphologically cryptic group of weevils and provide a scaffold based on which genus assignment can be tested. The present study mostly corroborates the current subdivision into genera (but many of the subgeneric groups are questioned). Three new genera are described: Montanacalles gen. nov. (type species: Kyklioacalles nevadaensis Stüben, 2001), Coloracalles gen. nov. (type species: Acalles humerosus Fairmaire, 1862) and Elliptacalles gen. nov. (type species: Acalles longus Desbrochers, 1892). Relevant external characters and the male genitalia of all discussed taxa are illustrated. Three species are transferred to different genera: Kyklioacalles aubei (Boheman, 1837) (formerly: Acalles), Ruteria major (Solari A. & F., 1907) and Ruteria minosi (Bahr & Bayer, 2005) (both formerly Echinodera).
A phylogeny of the family Fanniidae Schnabl (Insecta:Diptera:Calyptratae) based on adult morphological characters, with special reference to the Austral species of the genus Fannia
Authors: Domínguez M. C. , Roig-Juñent S. A.
Published: December 2008

The present study proposed a phylogenetic hypothesis of the family Fanniidae based on a cladistic analysis using characters from adult external morphology and female and male terminalia. The main purpose of this study was to clarify the phylogenetic position of newly described or poorly known species, mostly from southern South America, the Neotropics, Africa, Australia and New Zealand. In total, 151 characters from adult male and female external morphology and terminalia were scored for 78 species of Fanniidae. Ten continuous characters were included and analysed as such. Three genera of Fanniidae and all the species-groups and subgroups proposed for the genus Fannia, except for the admirabilis-group and the setifer-subgroup were included as terminal taxa. An heuristic parsimony analysis under implied weights was performed. The analysis recovered the monophyly of the Fanniidae and the genus Fannia, as well as the monophyly of several species-groups within Fannia. Male and female external morphological characters were, in general, highly homoplasious, whereas characters from male terminalia showed low level of homoplasy and provided resolution at suprageneric nodes and species-groups.
Evidence for polyphyly in Hemigenia and Microcorys (Lamiaceae: Westringieae)
Authors: Guerin G. R.
Published: December 2008

The phylogeny of tribe Westringieae (Lamiaceae: subfamily Prostantheroideae) was examined on the basis of combined morphological and molecular chloroplast trnT–trnF data. The analyses confirm that the tribe is monophyletic, with Prostanthera Labill. sister to the remaining genera. Both Hemigenia R.Br. and Microcorys R.Br. are shown to be polyphyletic, hence changes to generic delimitations are inevitable. Of note, the typical section of Hemigenia is polyphyletic with a large group of Western Australia species placed in a separate clade. A new section of Hemigenia is required to accommodate species currently placed in the typical section which do not belong with the type species, H. purpurea R.Br.
Characterizing heterogeneous cellular responses to perturbations
Authors: Slack Michael D. , Martinez Elisabeth D. , Wu Lani F. , Altschuler Steven J.
Published: December 2008

Cellular populations have been widely observed to respond heterogeneously to perturbation. However, interpreting the observed heterogeneity is an extremely challenging problem because of the complexity of possible cellular phenotypes, the large dimension of potential perturbations, and the lack of methods for separating meaningful biological information from noise. Here, we develop an image-based approach to characterize cellular phenotypes based on patterns of signaling marker colocalization. Heterogeneous cellular populations are characterized as mixtures of phenotypically distinct subpopulations, and responses to perturbations are summarized succinctly as probabilistic redistributions of these mixtures. We apply our method to characterize the heterogeneous responses of cancer cells to a panel of drugs. We find that cells treated with drugs of (dis-)similar mechanism exhibit (dis-)similar patterns of heterogeneity. Despite the observed phenotypic diversity of cells observed within our data, low-complexity models of heterogeneity were sufficient to distinguish most classes of drug mechanism. Our approach offers a computational framework for assessing the complexity of cellular heterogeneity, investigating the degree to which perturbations induce redistributions of a limited, but nontrivial, repertoire of underlying states and revealing functional significance contained within distinct patterns of heterogeneous responses.
Genome-scale reconstruction of the Lrp regulatory network in
Escherichia coli
Authors: Cho Byung-Kwan , Barrett Christian L. , Knight Eric M. , Park Young Seoub , Palsson Bernhard Ø.
Published: December 2008

Broad-acting transcription factors (TFs) in bacteria form regulons. Here, we present a 4-step method to fully reconstruct the leucine-responsive protein (Lrp) regulon in
Escherichia coli
K-12 MG 1655 that regulates nitrogen metabolism. Step 1 is composed of obtaining high-resolution ChIP-chip data for Lrp, the RNA polymerase and expression profiles under multiple environmental conditions. We identified 138 unique and reproducible Lrp-binding regions and classified their binding state under different conditions. In the second step, the analysis of these data revealed 6 distinct regulatory modes for individual ORFs. In the third step, we used the functional assignment of the regulated ORFs to reconstruct 4 types of regulatory network motifs around the metabolites that are affected by the corresponding gene products. In the fourth step, we determined how leucine, as a signaling molecule, shifts the regulatory motifs for particular metabolites. The physiological structure that emerges shows the regulatory motifs for different amino acid fall into the traditional classification of amino acid families, thus elucidating the structure and physiological functions of the Lrp-regulon. The same procedure can be applied to other broad-acting TFs, opening the way to full bottom-up reconstruction of the transcriptional regulatory network in bacterial cells.
Symptomatic partial rotator cuff tears: Diagnostic performance of ultrasound and magnetic resonance imaging with surgical correlation
Authors: Vlychou M. , Dailiana Z. , Fotiadou A. , Papanagiotou M. , Fezoulidis I.V. , Malizos K.
Published: December 2008

Background: The painful shoulder is a relatively common clinical entity that may be attributed to a variety of pathologies, including partial rotator cuff tears. Conservative treatment or surgical intervention may be offered, depending on the extent of the partial tear and the degree of patient discomfort.

Purpose: To apply ultrasound (US) imaging in order to evaluate the prevalence of partial rotator cuff tears in patients with painful shoulders.

Material and Methods: Fifty-six patients (17 men, 39 women; mean age 53.7 years) were included in the study, with symptomatic impingement syndrome of the shoulder after having failed to respond to conservative treatment. All patients underwent US and magnetic resonance imaging (MRI) scans prior to surgical intervention.

Results: Arthroscopy or mini-open surgery revealed 53 cases with partial tears of the rotator cuff and three with extensive tendinopathy. Both imaging modalities detected successfully 44 cases of partial tears of the supraspinatus tendon. US imaging yielded a sensitivity of 95.6%, a specificity of 70%, an accuracy of 91%, and a positive predictive accuracy of 93.6%. The corresponding values for MRI were 97.7%, 63.6%, 91%, and 91.7%, respectively.

Conclusion: US imaging can be considered almost equally effective in detecting partial tears of the rotator cuff compared to MRI, particularly located in the area of the supraspinatus tendon. MRI may be reserved for doubtful or complex cases, in which delineation of adjacent structures is mandatory prior to surgical intervention.
The TP53INP2 Protein Is Required for Autophagy in Mammalian Cells
Authors: Nowak Jonathan , Archange Cendrine , Tardivel-Lacombe Joël , Pontarotti Pierre , Pébusque Marie-Josèphe , Vaccaro Maria Inés , Velasco Guillermo , Dagorn Jean-Charles , Iovanna Juan Lucio
Published: December 2008

Using a bioinformatic approach, we identified a TP53INP1-related gene encoding a protein with 30% identity with tumor protein 53-induced nuclear protein 1 (TP53INP1), which was named TP53INP2. TP53INP1 and TP53INP2 sequences were found in several species ranging from Homo sapiens to Drosophila melanogaster, but orthologues were found neither in earlier eukaryotes nor in prokaryotes. To gain insight into the function of the TP53INP2 protein, we carried out a yeast two-hybrid screening that showed that TP53INP2 binds to the LC3-related proteins GABARAP and GABARAP-like2, and then we demonstrated by coimmunoprecipitation that TP53INP2 interacts with these proteins, as well as with LC3 and with the autophagosome transmembrane protein VMP1. TP53INP2 translocates from the nucleus to the autophagosome structures after activation of autophagy by rapamycin or starvation. Also, we showed that TP53INP2 expression is necessary for autophagosome development because its small interfering RNA-mediated knockdown strongly decreases sensitivity of mammalian cells to autophagy. Finally, we found that interactions between TP53INP2 and LC3 or the LC3-related proteins GABARAP and GABARAP-like2 require autophagy and are modulated by wortmannin as judged by bioluminescence resonance energy transfer assays. We suggest that TP53INP2 is a scaffold protein that recruits LC3 and/or LC3-related proteins to the autophagosome membrane by interacting with the transmembrane protein VMP1. It is concluded that TP53INP2 is a novel gene involved in the autophagy of mammalian cells.
Specific Activation of Mitogen-activated Protein Kinase by Transforming Growth Factor-β Receptors in Lipid Rafts Is Required for Epithelial Cell Plasticity
Authors: Zuo Wei , Chen Ye-Guang
Published: December 2008

Transforming growth factor (TGF)-β regulates a spectrum of cellular events, including cell proliferation, differentiation, and migration. In addition to the canonical Smad pathway, TGF-β can also activate mitogen-activated protein kinase (MAPK), phosphatidylinositol 3-kinase (PI3K)/Akt, and small GTPases in a cell-specific manner. Here, we report that cholesterol depletion interfered with TGF-β–induced epithelial-mesenchymal transition (EMT) and cell migration. This interference is due to impaired activation of MAPK mediated by cholesterol-rich lipid rafts. Cholesterol-depleting agents specifically inhibited TGF-β–induced activation of extracellular signal-regulated kinase (ERK) and p38, but not Smad2/3 or Akt. Activation of ERK or p38 is required for both TGF-β–induced EMT and cell migration, whereas PI3K/Akt is necessary only for TGF-β–promoted cell migration but not for EMT. Although receptor heterocomplexes could be formed in both lipid raft and nonraft membrane compartments in response to TGF-β, receptor localization in lipid rafts, but not in clathrin-coated pits, is important for TGF-β–induced MAPK activation. Requirement of lipid rafts for MAPK activation was further confirmed by specific targeting of the intracellular domain of TGF-β type I receptor to different membrane locations. Together, our findings establish a novel link between cholesterol and EMT and cell migration, that is, cholesterol-rich lipid rafts are required for TGF-β–mediated MAPK activation, an event necessary for TGF-β–directed epithelial plasticity.
Estimation of errors introduced by confocal imaging into the data on segmentation gene expression in Drosophila
Authors: Myasnikova Ekaterina , Surkova Svetlana , Panok Lena , Samsonova Maria , Reinitz John
Published: December 2008

Motivation: Currently the confocal scanning microscopy of fluorescently tagged molecules is extensively employed to acquire quantitative data on gene expression at cellular resolution. Following this approach, we generated a large dataset on the expression of segmentation genes in the Drosophila blastoderm, that is widely used in systems biology studies. As data accuracy is of critical importance for the success of studies in this field, we took a shot to evaluate possible errors introduced in the data by acquisition and processing methods. This article deals with errors introduced by confocal microscope.

Results: In confocal imaging, the inevitable photon noise is commonly reduced by the averaging of multiple frames. The averaging may introduce errors into the data, if single frames are clipped by microscope hardware. A method based on censoring technique is used to estimate and correct this type of errors. Additional source of errors is the quantification of blurred images. To estimate and correct these errors, the Richardson–Lucy deconvolution method was modified to provide the higher accuracy of data read off from blurred images of the Drosophila blastoderm. We have found that the sizes of errors introduced by confocal imaging make up ∼5–7% of the mean intensity values and do not disguise the dynamic behavior and characteristic features of gene expression patterns. We also defined a range of microscope parameters for the acquisition of sufficiently accurate data.

Availability:  http://urchin.spbcas.ru/downloads/step/step.htm

Contact:  myasnikova@spbcas.ru

Supplementary information:  Supplementary data are available at Bioinformatics online.
Thiophanate-Methyl and Propiconazole Sensitivity in Sclerotinia homoeocarpa Populations from Golf Courses in Wisconsin and Massachusetts
Authors: Koch Paul L. , Grau Craig R. , Jo Young-Ki , Jung Geunhwa
Published: December 2008

Management of dollar spot, caused by the fungus Sclerotinia homoeocarpa, is dependent upon repeated fungicide applications in intensively managed turfgrass such as golf course putting greens and fairways. Repeated fungicide applications could potentially select for fungicide-resistant isolates and result in a reduction of disease control. The objectives of this study were to determine the degree of S. homoeocarpa in vitro sensitivity to the fungicides thiophanate-methyl and propiconazole using isolates collected from golf course putting greens, fairways, and roughs; and to determine the relationships of golf course age and fungicide history to the frequency of fungicide-insensitive isolates within the population. More than 1,400 S. homoeocarpa isolates were collected from putting greens, fairways, and roughs at six Wisconsin golf courses and one Massachusetts golf course and subjected to in vitro fungicide sensitivity assays with single discriminatory concentrations of thiophanate-methyl and propiconazole. Five of seven pathogen populations from rough areas were not significantly different from one another in propiconazole sensitivity. These populations were collectively the most sensitive to both fungicides and therefore, served as baseline populations for comparison with fungicide-exposed populations from putting greens and fairways. Greater propiconazole insensitivity was observed in populations collected from fairways and putting greens that received more frequent applications of the fungicide than those isolated from the roughs. In nearly all the golf courses, the frequency of thiophanate-methyl insensitivity was higher among isolates of S. homoeocarpa collected from fairways than from roughs regardless of the age of the golf course or history of benzimidazole use. Thus, while the development of resistance to propiconazole can be predicted in part by the relative frequency of demethylation inhibitor fungicide applications, the occurrence of populations resistant to thiophanate-methyl appears to be unrelated to recent use of the benzimidazole class of fungicides.
First Report of Pepper veinal mottle virus in Tomato and Pepper in Taiwan
Authors: Cheng Y. H. , Wang R. Y. , Chen C. C. , Chang C. A. , Jan F.-J.
Published: December 2008

In May of 2006, samples from tomato plants (Solanum lycopersicum cv. Known-you 301) exhibiting necrotic symptoms on stems, petioles, and leaves were collected from Chiayi County, Taiwan. Double-antibody sandwich-ELISAs were performed using Cucumber mosaic virus, Tomato mosaic virus, Potato virus Y, Watermelon silver mottle virus, and Chilli veinal mottle virus (ChiVMV) polyclonal antibodies. Three of eight samples reacted with antibodies against ChiVMV but not with the others. Using the potyvirus degenerate primers (Hrp 5/Pot 1) (2), an expected 1.5-kb DNA fragment including the 3′-end of the NIb gene, the complete coat protein (CP) gene, and the 3′-nontranslatable region of the virus was amplified from total RNA isolated from these three samples by reverse transcription (RT)-PCR. A homology search in GenBank indicated that the new tomato-infecting virus in Taiwan belongs to Pepper veinal mottle virus (PVMV) since they shared >90% amino acid identity in the CP gene. A virus culture (Tom1) isolated from one of the diseased tomatoes was then established in Chenopodium quinoa and Nicotiana benthamiana and the CP gene was amplified and sequenced (GenBank Accession No. EU719647). Comparisons of the 807-nt CP gene with those of five PVMV isolates available in GenBank showed 81.5 to 93.1% nucleotide and 90.0 to 97.8% amino acid identity. Tom1 induced irregular necrotic lesions on stems, petioles, and leaves of tomato while inducing only mild mottle symptoms on pepper. Serological cross reaction between ChiVMV and PVMV has been observed previously (1,3) and also found in this study. To differentiate these two potyviruses by RT-PCR, primer pair CPVMVup/dw (5′-TATTC(T/C)TCAGTGTGG(A/T/C)T(T/C)CCACCAT and 5′-(T/C)C(A/T)C(A/T)(A/T/G)(A/T)AA(A/G)CCATAA(A/C)(A/C)ATA(A/G)T(T/C)T) was designed on the basis of the comparison of the CP gene and the 3′-nontranslatable region of the PVMV and ChiVMV. DNA fragments of 171 and 259 bp are expected to be amplified from ChiVMV and PVMV, respectively, by RT-PCR with primers CPVMVup/dw. In a field survey done in 2006, samples from diseased peppers (Capsicum annuum) that reacted with the polyclonal antibodies against ChiVMV were further identified by RT-PCR with primers CPVMVup/dw, indicating that both ChiVMV and PVMV infected pepper crops (Capsicum spp.) in Taiwan. A pepper isolate (Pep1) of PVMV was obtained from Nantou County through three times of single lesion passages on C. quinoa and then propagated on N. benthamiana. The CP gene of Pep1 was amplified and sequenced (GenBank Accession No. EU719646) and found to share 99.1% nucleotide and 100% amino acid identity with that of Tom1. Pep1 caused mild mottle symptoms on leaves of both tomato and pepper. To our knowledge, this is the first report of the presence of PVMV in Taiwan as well as in East Asia.

References: (1) B. Moury et al. Phytopathology 95:227, 2005. (2) S. S. Pappu et al. Plant Dis. 82:1121, 1998. (3) W. S. Tsai et al. Plant Pathol. 58:408, 2008.
Genetic Diversity Among Viruses Associated with Sugarcane Mosaic Disease in Tucumán, Argentina
Authors: Perera M. F. , Filippone M. P. , Ramallo C. J. , Cuenya M. I. , García M. L. , Ploper L. D. , Castagnaro A. P.
Published: December 2008

Sugarcane leaves with mosaic symptoms were collected in 2006–07 in Tucumán (Argentina) and analyzed by reverse-transcriptase polymerase chain reaction (RT-PCR) restriction fragment length polymorphism (RFLP) and sequencing of a fragment of the Sugarcane mosaic virus (SCMV) and Sorghum mosaic virus (SrMV) coat protein (CP) genes. SCMV was detected in 96.6% of samples, with 41% showing the RFLP profile consistent with strain E. The remaining samples produced eight different profiles that did not match other known strains. SCMV distribution seemed to be more related to sugarcane genotype than to geographical origin, and sequence analyses of CP genes showed a greater genetic diversity compared with other studies. SrMV was detected in 63.2% of samples and most of these were also infected by SCMV, indicating that, unlike other countries and other Argentinean provinces, where high levels of co-infection are infrequent, co-existence is common in Tucumán. RFLP analysis showed the presence of SrMV strains M (68%) and I (14%), while co-infection between M and H strains was present in 18% of samples. Other SCMV subgroup members and the Sugarcane streak mosaic virus (SCSMV) were not detected. Our results also showed that sequencing is currently the only reliable method to assess SCMV and SrMV genetic diversity, because RT-PCR-RFLP may not be sufficiently discriminating.
In Vitro-Transcribed Chrysanthemum stunt viroid RNA Is Infectious to Chrysanthemum and Other Plants
Authors: Matsushita Yosuke , Penmetcha Kumar K. R.
Published: December 2008

Chrysanthemum stunt viroid (CSVd), a noncoding RNA, is known to cause chrysanthemum stunt disease, which affects the yield of flowers. To gain insights into CSVd replication, infection, and the reasons for the spreading of CSVd disease in chrysanthemum plants, we prepared linear CSVd RNA and analyzed its ability to cause disease in chrysanthemum plants. We found that linear CSVd replicated as efficiently as CSVd RNA isolated from the infected chrysanthemum plants. Additionally, the linear CSVd RNA was evaluated for its ability to infect other plants as well, which revealed that CSVd has a wide host range for its replication. Importantly, the CSVd isolated from these hosts is infectious to chrysanthemum plants, and thus potentially contributes to the spreading of the disease to chrysanthemum plants.