bluuebunny/crossref_metadata_2025 huggingface dataset:
WOLOSZYNSKIA HALOPHILA (BIECHELER) COMB. NOV.: A BLOOM‐FORMING COLD‐WATER DINOFLAGELLATE CO‐OCCURRING WITH SCRIPPSIELLA HANGOEI (DINOPHYCEAE) IN THE BALTIC SEA1
Authors: Kremp Anke , Elbrächter Malte , Schweikert Michael , Wolny Jennifer L. , Gottschling Marc
Published: June 2005

Molecular analyses and subsequent morphological reinvestigation of clonal isolates germinated from cysts previously assigned to Scrippsiella hangoei (Schiller) Larsen revealed considerable differences to vegetative cell isolates of this cold‐water dinoflagellate from the northern Baltic Sea. The presence of hexagonal platelets on the cell surface and a characteristic acrobase on the episome agree with the description of Gymnodinium halophilum Biecheler. However, the arrangement of amphiesmal vesicles in more than nine latitudinal series indicates allocation of this dinoflagellate to Woloszynskia Thompson. We therefore reassign G. halophilum to Woloszynskia halophila. This species exhibits ultrastructural characteristics similar to Polarella glacialis Montresor et al. and symbiontic Gymnodinium Stein, such as stalked pyrenoids and a central eyespot consisting of multiple layers of crystal‐filled vacuoles. A close relationship between these dinoflagellates is also supported by 28s rRNA sequence data. The preference for high salinities identifies W. halophila as a marine species. The spiny resting cysts of W. halophila are identical to the cysts formed during the massive encystment events previously attributed to S. hangoei in the Baltic Sea. This suggests that W. halophila is a significant contributor to the dinoflagellate spring blooms in the Baltic Sea. Scrippsiella hangoei clones, in turn, produce noncalcareous and smooth‐walled cysts when crossed with a complementary mating type.
MYCOSPORINE‐LIKE AMINO ACIDS AND PHYLOGENIES IN GREEN ALGAE: PRASIOLA AND ITS RELATIVES FROM THE TREBOUXIOPHYCEAE (CHLOROPHYTA)1
Authors: Karsten Ulf , Friedl Thomas , Schumann Rhena , Hoyer Kirsten , Lembcke Sebastian
Published: June 2005

A UV‐absorbing mycosporine‐like amino acid (324 nm‐MAA), so far only known from the green macroalgal genus Prasiola (Trebouxiophyceae), was also identified in other morphologically diverse green algae closely related to Prasiola spp. in 18S rDNA phylogenies. Using HPLC, a second UV‐absorbing compound was found only in Myrmecia incisa Reisigal among all studied strains. This substance showed an absorption maximum at 322 nm and hence was designated as putative 322 nm‐MAA. Preliminary UV‐exposure experiments indicated that all species containing one or the other MAA showed a strong accumulation of the respective compound, thus supporting their function as putative UV sunscreen. Both UV‐absorbing substances were only identified in the studied members of the Trebouxiophyceae but were absent in members of the Ulvophyceae and Chlorophyceae. When mapped on an 18S rDNA phylogeny, the distribution of 324 nm‐MAA was found to be scattered within the Trebouxiophyceae but was consistent with a distribution that follows phylogenetic patterns rather than ecological adaptations. The 324 nm‐MAA was also detected in two phylogenetically related species from freshwater as well as from subaerial habitats, Watanabea reniformis Hanagata et al. and isolate UR7/5, which were phylogenetically independent of Prasiola and its closer allies. MAAs were absent in another Trebouxiophyceae clade comprising lichen photobionts (Coccomyxa pringsheimii Jaag) as well as freshwater picoplanktonic algae (Choricystis minor (Skuja) Fott). The data presented suggest a chemotaxonomic value of the 324 nm‐MAA in green algal taxonomy. To address the paraphyly of the genus Myrmecia Printz as presently circumscribed, we propose the new combination Lobosphaera incisa.
ELEMENTAL AND BIOCHEMICAL COMPOSITION OF RHINOMONAS RETICULATA (CRYPTOPHYTA) IN RELATION TO LIGHT AND NITRATE‐TO‐PHOSPHATE SUPPLY RATIOS1
Authors: Leonardos Nikos , Geider Richard J.
Published: June 2005

The biochemical basis for variations in the critical nitrogen‐to‐phosphorus (N:P) ratio, which defines the transition between N‐ and P‐limitation of growth rate, is currently not well understood. To assess this issue, we cultured the cryptophyte Rhinomonas reticulata NOVARINO in chemostats with inflow nitrate‐to‐phosphate ratios ranging from 5 to 60 mol N·(mol P)−1 at two light intensities. The nitrate‐to‐phosphate ratio marking the transition between N‐ and P‐limitation was independent of light intensity and was between 30 and 45 mol N/mol P. In N‐limited cells, the particulate N:P ratio was stable at around 23 mol N/mol P over a range of inflow nitrate‐to‐phosphate from 5 to 30, whereas in P‐limited cells this ratio was around 90 mol N/mol P at inflow nitrate‐to‐phosphate ratios of 45 and 60. Cell phosphorus decreased with increasing nitrate‐to‐phosphate ratio up to the critical nitrate‐to‐phosphate ratio for each light intensity, above which they remained stable. The C:P of R. reticulata cells increased with increasing inflow nitrate‐to‐phosphate from around the Redfield value (106 mol C/mol P) to around 700. There was a significant effect of light on C:P in the N‐ limited cells, with higher C:P under high light conditions that was not observed in the P‐limited chemostats. Cellular RNA was not influenced by light but was greatly influenced by the type of nutrient limitation. In contrast, chl a, C, N, and protein were not influenced by the nitrate‐to‐phosphate in the inflow medium. Total protein per RNA was independent of light intensity but exhibited a maximum at inflow nitrate‐to‐phosphate of 30. Our results suggest a strong “two‐level” homeostatic mechanism of cellular N and P content in R. reticulata with two distinct states that are determined by the type of nutrient limitation and not by light.
MORPHOLOGICAL REVERSION OF SPIRULINA (ARTHROSPIRA) PLATENSIS (CYANOPHYTA): FROM LINEAR TO HELICAL1
Authors: Wang Zhi Ping , Zhao Ying
Published: June 2005

The cyanobacterium Spirulina Turpin is characterized by its regularly coiled trichomes. Under some conditions, its helical filaments can convert to abnormal morphologies, such as irregularly curved and even linear shapes, that had been considered as a permanent degeneration that could not be reversed. However, here we found that the linear filaments of Spirulina platensis Geitler could spontaneously revert to the helical form with the same morphology as the original filaments. Further studies showed that the ultrastructural, physiological, and biochemical characteristics of linear filaments were different from those of the original filaments, whereas they were the same for the reverted and the original filaments. The SDS‐PAGE analysis revealed at least four proteins or subunits related to Spirulina morphogenesis: The 21.9‐kDa and the 20.3‐kDa proteins were highly expressed in the helical filaments, whereas the 52.0‐kDa and the 31.8‐kDa proteins were highly expressed in the linear filaments. The random amplified polymorphic DNA analysis with 96 random primers showed that the genetic background of the reverted filaments was the same as that of the original filaments but distinct from that of the linear filaments. The results indicated that linear filaments of Spirulina could revert to the original morphology under certain conditions, and their other distinctive traits were regained.
MOLECULAR SYSTEMATICS OF THE GRACILARIACEAE (GRACILARIALES, RHODOPHYTA) WITH EMPHASIS ON SOUTHERN AFRICA1
Authors: Iyer Revel , Tronchin Enrico M. , Bolton John J. , Coyne Vernon E.
Published: June 2005

Southern Africa has economically exploited populations of terete gracilarioids on the cool temperate west coast and numerous species of endemic and Indo‐Pacific tropical Gracilariaceae on the south and east coasts. Gross morphological characters have been the main means of identification, and incorrect applications have led to a number of misidentifications. In this study, small subunit rDNA and RUBISCO spacer sequences were used to determine phylogenetic relationships. Whereas rDNA sequences successfully differentiate major groups within the family as well as species belonging to the Gracilariopsis and the Curdiea/Melanthalia clade, RUBISCO spacer sequencing was required to distinguish between species of Gracilaria. The southern African gracilarioid complex (stringy, terete, elongate members of the Gracilariaceae) was resolved into three species: Gracilaria gracilis, Gracilariopsis longissima, and Gracilariopsis funicularis. South African Gracilaria protea was shown to be conspecific with tropical Indian Ocean G. corticata. Apart from G. gracilis and G. corticata, South African Gracilaria species were differentiated into a temperate‐tropical terete grouping and a temperate‐tropical flattened grouping.
SYSTEMATICS OF THE CALCIFIED GENERA OF THE GALAXAURACEAE (NEMALIALES, RHODOPHYTA) WITH AN EMPHASIS ON TAIWAN SPECIES1
Authors: Wang Wei‐Lung , Liu Shao‐Lun , Lin Showe‐Mei
Published: June 2005

The current separation of the calcified genera Actinotrichia Decaisne, Galaxaura Lamouroux, and Tricleocarpa Huisman et Borowitzka in the Galaxauraceae is largely based on type of life history (whether the gametophytes and tetrasporophytes are isomorphic or heteromorphic with respect to gross morphology or cortical‐cell features) and on features of postfertilization development (such as the composition of the pericarp). We reexamined the phylogenetic relationships of these genera based on comparative rbcL sequence analysis, types of life cycle, and cystocarp development. Four distinct assemblages have been identified: an Actinotrichia clade, a Tricleocarpa clade, a Galaxaura clade (containing the type species), and a Dichotomaria clade made of a number of formerly Galaxaura species (D. obtusata [Ellis et Solander] Lamarck, D. marginata [Ellis et Solander] Lamarck, and D. diesingiana [Zanardini] Huisman, Harper and Saunders). Key differences between Dichotomaria and Galaxaura include the habit of the gametophytic and tetrasporophytic generations (isomorphic in Dichotomaria and dimorphic in Galaxaura) as well as the presence or absence of a persistent pericarp in the cystocarp (present in Dichotomaria and absent in Galaxaura). Molecular data do not support monophyly for the putatively pantropical species Galaxaura rugosa, Dichotomaria obtusata, and D. marginata, all of which we conclude are in need of taxonomic revision.
DO PLASTID‐RELATED CHARACTERS SUPPORT THE CHROMALVEOLATE HYPOTHESIS?1
Authors: Bodył Andrzej
Published: June 2005

According to the idea of secondary endosymbiosis, plastids with three and four envelope membranes have evolved from either red or green algal endosymbionts engulfed by phagotrophic protozoans. Although this hypothesis is nowadays commonly accepted, the number of secondary endosymbioses still remains controversial. One of the models, known as the ”chromalveolate” hypothesis, postulates that the 4 membrane‐bound plastids of Chromista and the 3 or 4 membrane‐bound plastids of Alveolata result from a single secondary endosymbiosis involving a rhodophyte as the endosymbiont. Although this model has found many followers, a variety of data clearly contradict it. The ideas that became the direct inspiration for formulation of the “chromalveolate” hypothesis are also now questionable. In this comment, I discuss all these problems in the light of the most recent phylogenetic, cytological, and genomic data.
Slider Air Bearing Design Enhancements for High Speed Flexible Disk Recording
Authors: White James
Published: June 2005

The current effort was motivated largely by the fact that computing and communication platforms are becoming more portable and mobile with increased demands for both speed and disk storage. This work makes use of an asymmetric opposed slider arrangement to provide both static and dynamic improvements to the recording head air bearing interface for high speed flexible disk applications. The combination of a longitudinally slotted rail opposed by an uninterrupted rail that functions as a noncontact hydrodynamic pressure pad causes the disk to deflect at the submicron level over critical areas of the slider interface. This allows the required static minimum flying height to be focused over the recording transducer while higher clearances are positioned elsewhere, resulting in minimized exposure to contact between slider and disk. The high stiffness and low flying height of the air film at the recording element together with the low stiffness and high flying height of the opposing air film provides a noncontact air bearing interface that is especially immune to mechanical shock. A computer code called FLEXTRAN was developed that provides both static and dynamic numerical solutions of the air bearing interface composed of two opposed gimbal mounted sliders loaded against a high speed flexible disk. Simulations of the asymmetric opposed slider configuration are presented and compared with those of other slider air bearing designs.
Numerical Study of Slider Bearings With Limited Corrugation
Authors: Huynh B. Phuoc
Published: June 2005

Influence of corrugation of limited extent on the performance of fixed-incline slider bearings of infinite width is investigated numerically. Effects of the corrugated section’s parameters like its location, length, and corrugation amplitude, on pressure distribution in the bearing’s fluid film, its load supporting capacity W and flow rate, are considered. When this section is near the entrance to the bearing gap, pressure and W are reduced in comparison with the smooth wall case. As this section is located further downstream, peak pressure and W increase, whereas flow rate decreases. These effects are reinforced by longer corrugated section and larger corrugation amplitude. The results thus point to a simple way to substantially enhance a bearing’s load-supporting capacity.
A Finite Element Study of the Residual Stress and Deformation in Hemispherical Contacts
Authors: Jackson Robert , Chusoipin Itti , Green Itzhak
Published: June 2005

This work presents a finite element model (FEM) of the residual stresses and strains that are formed after an elastoplastic hemispherical contact is unloaded. The material is modeled as elastic perfectly plastic and follows the von Mises yield criterion. The FEM produces contours for the normalized axial and radial displacements as functions of the removed interference depth and location on the surface of the hemisphere. Contour plots of the von Mises stress and other stress components are also presented to show the formation of the residual stress distribution with increasing plastic deformation. This work shows that high residual von Mises stresses appear in the material pileup near the edge of the contact area after complete unloading. Values are defined for the minimum normalized interference, that when removed, results in plastic residual stresses. This work also defines an interference at which the maximum residual stress transitions from a location below the contact region and along the axis of symmetry to one near to the surface at the edge of the contact radius (within the pileup).
A Molecular Dynamics Analysis of Surface Interference and Tip Shape and Size Effects on Atomic-Scale Friction
Authors: Yang J. , Komvopoulos K.
Published: June 2005

Molecular dynamics simulations of a rigid diamond tip sliding on a face-centered-cubic copperlike substrate were performed in order to examine the dependence of the friction coefficient on the tip–substrate interference and the shape and size of the tip. For a square-base prismatic tip, the friction force is mainly due to interactions of atoms at the front face of the tip and substrate atoms ahead of the tip, while the normal force is due to interactions of atoms at the tip base and substrate atoms under the tip. However, for a pyramidal tip, both normal and friction forces are mainly due to interactions between atoms at the front face of the tip and substrate atoms in the vicinity of the sliding tip. Consequently, the friction coefficient is either sensitive (square-base prismatic tip) or insensitive (pyramidal tip) to the tip–substrate interference distance. In addition, tip size and orientation effects on the friction coefficient were observed with square- and triangle-base prismatic tips, respectively. Lower friction coefficients were obtained with a larger base area and edge-front sliding with a triangle-base prismatic tip. The results provide insight into atomic-scale friction anisotropies due to the effects of the tip size and shape and the tip–substrate interference.
An Elastoplastic Microasperity Contact Model for Metallic Materials
Authors: Lin and Li Po , Lin Jen Fin
Published: June 2005

In the present study, the formulas for the asperity contact loads (Fec and Fpc) corresponding to the critical interferences at the inception of elastoplastic and fully plastic deformations are employed to establish their relation with the ratio of these two critical interferences (δec and δpc). The critical interference ratio δpc/δec can thus be expressed as a function of the critical contact load ratio, Fpc/Fec, whose value was obtained from the experimental results of metallic materials. The interference δpc corresponding to the inception of fully plastic deformation can thus be determined. The dimensionless analyses of asperity contact area, average contact pressure, and contact load in the elastic and fully plastic regime reveals that these parameters in the elastoplastic regime can be expressed in power form and to be as a function of dimensionless interference δ/δec. The coefficients and exponents of the power form expressions can be determined by the boundary conditions set at the two ends of this regime. Four models are proposed in this study to compare the contact behaviors in the elastoplastic regime. The applications in contact of rough surfaces are also presented and discussed.
Finite Element Simulation of Dynamic Instabilities in Frictional Sliding Contact
Authors: Baillet L. , Linck V. , D’Errico S. , Laulagnet B. , Berthier Y.
Published: June 2005

This paper describes tools for numerical modeling which enable the understanding of the appearance of vibrations of a structure generated by the frictional contact between two bodies (the excitation source being friction). The dynamic finite element code PLASTD is used to reproduce transitory phenomena generated at the contact interface. This code includes contact and friction algorithms based upon a formulation which uses Lagrange multipliers. A numerical study of the dynamic response of a 2D mechanical model composed of a deformable body in relative translation and unilateral contact with Coulomb friction with a rigid surface is presented. The steady sliding solution is generically unstable and leads to a dynamic response which leads to the generation of instabilities characterized by the appearance of steady-state pulses. It is important to notice that those instabilities appear even with a constant friction coefficient of Coulomb. These simulations provided the local contact conditions (kinematics, tribological state, contact stresses, etc). The kinematics shows the existence of local impacts and sliding at high frequencies. Furthermore, local contact normal stress is found to be much higher than that expected for a smooth surface. Finally, a 3D simulation of brakes is carried out, focusing on the vibrations of the disk and the brake pad which produce noise and are due to the interface instabilities.
Relationship Between Temperature Distribution in EHL Film and Dimple Formation
Authors: Yagi Kazuyuki , Kyogoku Keiji , Nakahara Tsunamitsu
Published: June 2005

This paper describes an experimental study on dimple formation under elastohydrodynamic lubrication (EHL) conditions. The oil film thickness between a ball surface and a glass disk was measured using optical interferometry, and the temperatures of both the surfaces and of the oil film averaged across it were measured using an infrared emission technique. It was found that the temperature profile across the oil film varies abruptly along the sliding direction, and the Couette flow decreases due to the viscosity wedge action as the oil flow is close to the dimple zone. The maximum temperature rise in the dimple zone sometimes reached over 400 K, thus, the phase transition of the oil from liquid to glass may not occur.
Contact Fatigue Analysis of an Elastic-Plastic Layered Medium With a Surface Crack in Sliding Contact With a Fractal Surface
Authors: Gong Z.-Q. , Komvopoulos K.
Published: June 2005

Contact fatigue of a layered medium consisting of an elastic surface layer and three elastic-plastic underlying layers in sliding contact with a rigid and rough surface was analyzed with the finite element method. To include multiscale roughness effects and self-affine surface features, the topography of the rough surface was characterized by scale-invariant fractal geometry. A contact algorithm was used to identify the critical segment of the rough surface to be used in the contact fatigue simulations. The tensile and shear stress intensity factors and the direction and dominant mode of crack growth were determined from the crack-tip stresses. The effect of surface cracking on the evolution of plasticity in the second layer and the significance of topography (fractal) parameters on crack growth are interpreted in terms of the contact pressure, stress intensity factors, and maximum equivalent plastic strain. It is shown that a transition from tensile to shear dominant mode of fatigue crack growth occurs as the crack tip approaches the interface, resulting in further crack growth almost parallel to the layer interface. The obtained results illustrate the important role of surface roughness in contact fatigue of layered media.
Finite Element Analysis of a Contact With Friction Between an Elastic Body and a Thin Soft Layer
Authors: Linck Vannina , Bayada Guy , Baillet Laurent , Sassi Taoufik , Sabil Jalila
Published: June 2005

When studying a mechanical system involving contact between two bodies such as a disc and brake pad system, finite element simulations are often used to predict the phenomena involved. However, due to model size and calculation time problems, when modeling this type of mechanical system on a scale of about 100 mm, it is difficult to model as well a layer (for example a third body layer) on a scale of approximately 10 μm. In quasi-static problems it is possible to simulate the contact between an elastic body and a thin elastic layer bonded to a rigid surface, by considering the contact between this elastic body and a rigid surface with a specific contact law. This paper shows that it is possible to implement this specific contact law in a dynamic finite element code to simulate thin layers undergoing quasi-static and dynamic problems without physical contact instabilities. This specific contact law saves a large amount of calculation time. Once the specific contact law has been validated, the influence of the layer thickness is studied.
Effect of Laser Surface Modifications Tribological Performance of 1080 Carbon Steel
Authors: Aldajah S. H. , Ajayi O. O. , Fenske G. R. , Xu Z.
Published: June 2005

High-power laser surface treatments in the form of glazing, shock peening, cladding, and alloying can significantly affect material surface properties. In this paper, effects of laser glazing, laser shock peening, and their combination on the tribological behavior of 1080 carbon steel were investigated. Laser glazing is a process in which a high-power laser beam melts the top layer of the surface, followed by rapid cooling and resolidification. This results in a new surface layer microstructure and properties. Laser shock peening, on the other hand, is a mechanical process in which a laser generates pressure pulses on the surface of the metal, similar to shot peening. Five conditions were evaluated: untreated (baseline), laser shock peened only (PO), laser glazed only, laser glazed then shock peened last, and laser shock peened then glazed last (PFGL). In pin-on-disc testing, all laser-treated surfaces reduced dry friction when sliding against alumina, with the PFGL surface having maximum friction reduction of 43%, especially in the early stage of testing. Under lubricated conditions, all laser-treated surfaces except the PO sample lowered friction against alumina. Similarly, all glazed samples showed reduced wear by a factor of 2–3, whereas the peening alone did not change wear significantly. These tribological results are associated with changes in the near-surface microstructure and properties.
Numerical Simulation for Three Dimensional Elastic-Plastic Contact with Hardening Behavior
Authors: Wang Fan , Keer Leon M.
Published: June 2005

An elastic-plastic contact (EPC) solution and code is developed using a modified semi-analytical method. The indentation tests with different hardening behavior are simulated by using the developed EPC code. The distributions of contact pressure, residual stress and plastic strain are obtained and compared with the results of the finite element method models without hardening. Some techniques, such as fast Fourier transform and fast convergence method, are used to increase the computation speed.
Viscoplastic Lubrication Analysis in a Metal-Rolling Inlet Zone Using Parametric Quadratic Programming
Authors: Wu C. W. , Ma G. J. , Sun H. S.
Published: June 2005

A mathematical programming solution based on finite element method is used to analyze wall slip of viscoplastic lubrication in a metal-rolling inlet zone. Slip velocity can be directly obtained by parametric quadratic programming without an iterative process between the oil film pressure and the slip velocity. It is found that wall slip causes the oil film thickness to decrease dramatically. The initial limiting shear strength and proportional constant of the viscoplastic lubricant have a larger effect on the oil film pressure than the rolling speed. The nonsensitivity of oil film thickness to the rolling speed is a great particular advantage to metal-rolling processing.
A new species of Harposporium parasitic on nematodes
Authors: Li Xuan , Luo Hong , Zhang Keqin
Published: June 2005

A new species, Harposporium thaumasium X. Li et K.Q. Zhang, was isolated from forest soil in Yunnan, China. This species produces small, curved conidia, singly or in groups, from globose or ellipsoid phialides. Unlike other known Harposporium, this species produced novel arthroconidia that did not disarticulate at septa but germinated to produce typical phialides and infective conidia. Solitary or catenulate chlamydospores were also produced within infected nematodes and in pure culture. Narrowly elliptical to D-shaped accessory conidia were produced, only on potato dextrose agar and dextrose yeast agar, from mono- or poly-phialidic conidiogenous cells resembling Hirsutella; thus, on these nutrient media, four different spore types were formed. Infection tests showed that curved conidia of the species were capable of killing bacteria-feeding nematodes (Panagrellus redivivus) when ingested, and the infection was initiated by lodging of the conidia in the gut region. Accessory conidia were not observed to be infective or adhesive.Key words: endoparasitic fungi, Harposporium thaumasium sp.nov., ingested conidia, nematode.
Phylogeny of tribe Brassiceae (Brassicaceae) based on chloroplast restriction site polymorphisms and nuclear ribosomal internal transcribed spacer and chloroplasttrnL intron sequences
Authors: Warwick Suzanne I , Sauder Connie A
Published: June 2005

Using sequence data from the ITS region (internal transcribed spacers ITS-1 and ITS-2 of nuclear DNA and the 5.8 rRNA gene), chloroplast DNA (cpDNA) sequence data from the trnL intron, and cpDNA restriction site polymorphism data, we examined the evolutionary relationships of the tribe Brassiceae (Brassicaceae). A group of approximately 50 genera, it is distinguished by the presence of conduplicate cotyledons and (or) heteroarthrocarpic fruit. cpDNA restriction site data and ITS, trnL, and combined ITS/trnL sequence data were obtained for 22, 104, 94, and 87 taxa in the tribe, respectively. Results from maximum parsimony analyses of the cpDNA and ITS and ITS/trnL sequence data showed a monophyletic origin for the tribe, with the inclusion of controversial members Calepina, Conringia, and Orychophragmus. ITS- and ITS/trnL-based clades corresponded to taxonomic subtribes: Vellinae, Zillinae, and Savignyinae; but as with previous cpDNA studies, there was little support for subtribes Brassicinae, Raphaninae, and Moricandiinae. Although there was no support for the Rapa/Oleracea or Nigra cpDNA lineages, many cpDNA subclades within each of them were evident in the ITS- and ITS/trnL-based phylogeny. The trnL sequence data provided little or no resolution of tribal or subtribal limits. The ITS data indicated polyphyletic origins for Brassica, Diplotaxis, and Erucastrum.Key words: Brassiceae, Calepina, Conringia, Orychophragmus, ITS, trnL, cpDNA restriction site polymorphisms.
Ultrastructure of the early stages of Colletotrichum acutatum infection of strawberry tissues
Authors: Arroyo Francisco T , Moreno Javier , García-Herdugo Gregorio , Santos Berta De los , Barrau Carmen , Porras María , Blanco César , Romero Fernando
Published: June 2005

The early stages of the infection of attached leaves and petioles of strawberry (Fragaria ×ananassa Duch. 'Camarosa') by Colletotrichum acutatum Simmonds were studied using scanning and transmission electron microscopy. Pre-penetration events of these tissues were similar, but the production of secondary conidia (microcyclic conidiation) was detected only on leaves. At the ultrastructural level, different stages of maturation of appressoria were observed and described. In young appressoria, the cell wall was composed of two layers and the plasma membrane displayed a wavy appearance. In the following stage, the appressorium developed a third electron-transparent layer between the cell wall and the plasma membrane. This new electron-transparent material was especially visible in the region of the appressorium near the cuticle. The plasma membrane of this appressorium showed a smooth appearance. Afterwards, a penetration peg emerged through the pore penetrating the cuticle and reached the epidermal wall where it enlarged to form an intramural infection vesicle. Both structures of infection, the penetration peg and the intramural infection vesicle, produced during the early phases of infection of strawbery tissues by C. acutatum, have not been previously reported and confirm that its invasion strategy is that of a subcuticular intramural pathogen. Once the infection was well established, abundant subcuticular and intramural hyphae were produced on petioles, causing severe degradation of the host cell walls. Occasionally, the cuticle appeared disrupted in those regions where the host walls were very degraded and dilated. Differences between colonization of petioles and leaves were observed.Key words: Colletotrichum acutatum, Fragaria ×ananassa, infection vesicle, invasion strategy, penetration peg.
Dothidea sambuci and Diaporthe spiculosa
Authors: Shoemaker R A , Hambleton S
Published: June 2005

Recently, it has been proposed that the type for Dothidea be formally conserved as Sphaeria sambuci Pers. (Dothidea sambuci (Pers.) Fr.:Fr.) and additionally that an epitype specimen be established for that species. A description, illustrations, and DNA sequence data are given based on the epitype. In a search for original or type specimens, a specimen labeled Dothidea sambuci was examined from Fries's Herbarium. It is a mixed collection of a few immature stromata morphologically similar to those of Dothidea sambuci and mature perithecia of Diaporthe spiculosa (Pers.:Fr.) Nitschke, which is described and illustrated with brief remarks on its nomenclature.Key words: Sambucus, Aureobasidium, Hormonema, Dothideomycetes, phylogeny.
Spontaneous revegetation of mined peatlands in eastern Canada
Authors: Poulin Monique , Rochefort Line , Quinty François , Lavoie Claude
Published: June 2005

Many North American peatlands previously mined for horticultural peat have been abandoned recently, allowing natural recolonization to occur. The two dominant methods for peat extraction, hand block-cutting and vacuum-mining, have created distinctly different abandoned surfaces, leading to different recolonization patterns. Both types of exploitation can be found throughout eastern Canada where we conducted a vast survey of 26 abandoned mined peatlands in the provinces of Québec and New Brunswick. The aim of this study is to describe the revegetation patterns and to assess the impact of local and regional variables as well as the time since abandonment on Sphagnum re-colonization. We inventoried the vegetation structure in all trenches (2571) and baulks (2595) of abandoned block-cut areas as well as in all vacuum fields (395) of the mechanically mined areas. We also conducted detailed species relevés in 242 of these peat fields. In comparison to vacuum-mined peatlands, block-cut peatlands regenerated remarkably well. Approximately 80% of all baulks and trenches in block-cut peatlands had 50% or higher cover of ericaceous shrubs compared with only 16% found on vacuum fields. Herb cover in the three types of abandoned fields was similar to that in natural peatlands. However, Sphagnum percent cover was below 2% in baulks and vacuum fields and was 30% on average in the trenches, which is clearly below cover estimates in natural peatlands. Sphagnum cover and richness were both higher in trenches with thin residual peat deposit, and Sphagnum richness increased with latitude. Our surveys revealed that abandoned mined peatlands have a high diversity of peatland vascular plants species and a low diversity of non-peatland species.Key words: cutover peatlands, regeneration, milled peatlands, block-cut peatlands, vacuum-mined peatlands, colonization patterns.
Pleomorphic conidiogenesis among strains of Knufia cryptophialidica
Authors: Tsuneda A , Currah R S
Published: June 2005

Pleomorphic conidiogenesis was examined in four strains of Knufia cryptophialidica Hutchison & Untereiner in culture. The ex-type strain (DAOM 216555) was the most plastic, exhibiting various patterns of conidiogenesis, and was the only strain that produced phialides, that is, the most important diagnostic structure of the genus, although many of these phialides were aberrant and produced abnormally swollen conidia that appeared to lack cytoplasm. Subsequently, hyphae emerged from the aberrant phialides and some of these hyphae later disarticulated to form thallic-arthric conidia. The ex-type strain ceased to produce normal phialides after several serial transfers onto malt extract agar. Endoconidiogenesis in K. cryptophialidica, reported here for the first time, involved subdivision of conidiogenous cells by septation and schizolysis through the septa, and their release was by rupture and subsequent degeneration of the conidiogenous cell wall. Both thallic-arthric and endogenous conidia occurred in all strains and may serve as more reliable diagnostic characters of K. cryptophialidica than phialidic conidia.Key words: black meristematic fungus, endoconidia, phialides.
Life cycles and biomass allocation in seed- and ramet-derived plants of Cryptotaenia canadensis (Apiaceae), a monocarpic species of eastern North America
Authors: Hawkins Tracy S , Baskin Jerry M , Baskin Carol C
Published: June 2005

Life cycles, survivorship, and biomass allocation for seed- and ramet-derived plants of Cryptotaenia canadensis (L.) DC. were studied to determine if variation existed between plant derivations, and how these attributes contribute to persistence of the species within a temperate forest habitat. Seed-derived plants behaved as biennials, reproducing both sexually and asexually in the second growing season. Ramet-derived plants reproduced sexually and asexually annually. Annual survivorship was greater for seed-derived juveniles; however, fewer seed-derived plants flowered than did ramet-derived plants. Biomass allocation for plants harvested at four growth stages over two complete life cycles was significantly different between plant derivations during vegetative growth stages. During reproductive growth stages, biomass allocation did not differ between ramet- and seed-derived plants harvested in the same year. Regressions showed a strong correlation between sexual reproductive mass and vegetative mass for both plant derivations, with no significant difference between slopes or intercepts. Ramet mass was less dependent on plant size, and differences between slopes and intercepts were not significant. Regressions of sexual versus asexual reproductive mass varied with year and cohort. Equivalent reproductive output in conjunction with temporal differences in life cycle phenologies between plant derivations optimize this species' ability to persist in its natural habitat.Key words: allometry, Apiaceae, biomass allocation, Cryptotaenia canadensis, monocarpic.
Population genetics ofGaultheria shallonin British Columbia and the implications for management using biocontrol
Authors: Wilkin J E , Shamoun S F , Ritland C , Ritland K , El-Kassaby Y A
Published: June 2005

Gaultheria shallon Pursh. (salal), an ericaceous shrub native to the Pacific Northwest, often out-competes regenerating conifer species in managed forests. A naturally occurring fungus, Valdensinia heterodoxa Peyronel, is being considered as a potential biocontrol agent for salal. Knowledge of the genetic diversity and population structure of salal will help assess the effectiveness and the potential risks of using a biocontrol agent in natural populations. Salal samples were collected from five populations, four on Vancouver Island and one on coastal mainland British Columbia. DNA fingerprints were obtained based on 230 amplified fragment length polymorphisms (AFLPs), of which 99.1% were variable. While salal has been reported to be a polyploid, it is likely that over time it is moving toward a diploid state. Based on a comparison of allele frequencies with known diploids, the AFLP loci used in this study appear to follow a diploid pattern; however, the levels of variation reported in this study may be an underestimation depending on the ploidy of salal. An intensively sampled population on Vancouver Island (Shawnigan Lake) showed isolation by distance and low kinship correlations, indicative of more sexual reproduction than expected for a predominantly clonal population. Our findings suggest that salal may be clonal at a very local scale (less than 5 m), and that with high levels of diversity within populations and little differentiation among populations, developing an effective biocontrol for salal may be challenging.Key words: population structure, genetic diversity, AFLP, biocontrol, Gaultheria shallon.
CELLULAR DNA REPLICASES: Components and Dynamics at the Replication Fork
Authors: Johnson Aaron , O'Donnell Mike
Published: June 2005

▪ Abstract  Chromosomal DNA replicases are multicomponent machines that have evolved clever strategies to perform their function. Although the structure of DNA is elegant in its simplicity, the job of duplicating it is far from simple. At the heart of the replicase machinery is a heteropentameric AAA+ clamp-loading machine that couples ATP hydrolysis to load circular clamp proteins onto DNA. The clamps encircle DNA and hold polymerases to the template for processive action. Clamp-loader and sliding clamp structures have been solved in both prokaryotic and eukaryotic systems. The heteropentameric clamp loaders are circular oligomers, reflecting the circular shape of their respective clamp substrates. Clamps and clamp loaders also function in other DNA metabolic processes, including repair, checkpoint mechanisms, and cell cycle progression. Twin polymerases and clamps coordinate their actions with a clamp loader and yet other proteins to form a replisome machine that advances the replication fork.
MONITORING ENERGY BALANCE: Metabolites of Fatty Acid Synthesis as Hypothalamic Sensors
Authors: Dowell Paul , Hu Zhiyuan , Lane M. Daniel
Published: June 2005

▪ Abstract  Because energy balance is important for survival, a system is required to monitor energy status and to make appropriate adjustments in energy intake and energy expenditure. In higher animals, a centrally located system has evolved to accomplish this task. When caloric intake exceeds expenditure, the surplus is channeled into energy storage pathways, primarily the synthesis of fatty acids, which are converted into fat and stored in adipose tissue. Thus, metabolic flux through the pathway of fatty acid synthesis, located in the lipogenic tissues, reflects the “energy status” of the animal. The enzymatic machinery of this pathway is also expressed in the brain, notably the hypothalamus. In the hypothalamus, intermediates in this pathway appear to serve as energy sensors that signal higher brain centers to produce appropriate responses, e.g., altered food intake and energy expenditure.
STRUCTURAL STUDIES BY ELECTRON TOMOGRAPHY: From Cells to Molecules
Authors: Lučić Vladan , Förster Friedrich , Baumeister Wolfgang
Published: June 2005

▪ Abstract  Electron tomography (ET) is uniquely suited to obtain three-dimensional reconstructions of pleomorphic structures, such as cells, organelles or supramolecular assemblies. Although the principles of ET have been known for decades, its use has gathered momentum only in recent years, thanks to technological advances and its combination with improved specimen preparation techniques. The rapid freezing/freeze-substitution preparation is applicable to whole cells and tissues, and it is the method of choice for ET investigations of cellular ultrastructure. The frozen-hydrated preparation provides the best possible structural preservation and allows the imaging of molecules, complexes, and supramolecular assemblies in their native state and their natural environment. Devoid of staining and chemical fixation artifacts, cryo-ET provides a faithful representation of both the surface and internal structure of molecules. In combination with advanced computational methods, such as molecular identification based on pattern recognition techniques, cryo-ET is currently the most promising approach to comprehensively map macromolecular architecture inside cellular tomograms.
THE MAMMALIAN UNFOLDED PROTEIN RESPONSE
Authors: Schröder Martin , Kaufman Randal J.
Published: June 2005

▪ Abstract  In the endoplasmic reticulum (ER), secretory and transmembrane proteins fold into their native conformation and undergo posttranslational modifications important for their activity and structure. When protein folding in the ER is inhibited, signal transduction pathways, which increase the biosynthetic capacity and decrease the biosynthetic burden of the ER to maintain the homeostasis of this organelle, are activated. These pathways are called the unfolded protein response (UPR). In this review, we briefly summarize principles of protein folding and molecular chaperone function important for a mechanistic understanding of UPR-signaling events. We then discuss mechanisms of signal transduction employed by the UPR in mammals and our current understanding of the remodeling of cellular processes by the UPR. Finally, we summarize data that demonstrate that UPR signaling feeds into decision making in other processes previously thought to be unrelated to ER function, e.g., eukaryotic starvation responses and differentiation programs.
FROM PROTEIN SYNTHESIS TO GENETIC INSERTION
Authors: Zamecnik Paul
Published: June 2005

▪ Abstract  In 1946, 14C-cyanide made its appearance as an offshoot of the Atomic Energy Program. Our colleague Robert Loftfield built it into 14C-alanine by the Strecker synthesis, and a lusty program directed toward uncovering the unknown mechanism of protein synthesis grew out of this beginning. The necessity for an undiscovered series of steps and enzymes was soon evident. A cell free system was developed, and a succession of components necessary for this new pathway tumbled out. ATP dependence, amino acid activation, the ribosome as the site of polypeptide formation, discovery of tRNA as the translation molecule linking the gene and protein sequence, and GTP as the essential energy ingredient in peptide chain extension all appeared from our laboratory within the next decade. A little later the AP4N family, whose functions remain imperfectly defined, of intracellular molecules was discovered. Isolation of specific species of RNA became a high priority, and we sequenced a small segment of the 3′ end of the Rous sarcoma virus, just inside the poly(A) tail, at the same time the Gilbert group at Harvard was sequencing the 5′ end. The sequence identity and polarity of the two ends suggested a circular intermediate in replication and predicted correctly that a synthetic antisense oligonucleotide targeted against this sequence might be a specific inhibitor of replication. More recently, we have evolved a technique that appears to achieve a trinucleotide insertion into tissue culture cells bearing a specific Δ508 mRNA triplet deletion, resulting in phenotypic reversion in the tissue culture.
PROTEIN FAMILIES AND THEIR EVOLUTION—A STRUCTURAL PERSPECTIVE
Authors: Orengo Christine A. , Thornton Janet M.
Published: June 2005

▪ Abstract  We can now assign about two thirds of the sequences from completed genomes to as few as 1400 domain families for which structures are known and thus more ancient evolutionary relationships established. About 200 of these domain families are common to all kingdoms of life and account for nearly 50% of domain structure annotations in the genomes. Some of these domain families have been very extensively duplicated within a genome and combined with different domain partners giving rise to different multidomain proteins. The ways in which these domain combinations evolve tend to be specific to the organism so that less than 15% of the protein families found within a genome appear to be common to all kingdoms of life. Recent analyses of completed genomes, exploiting the structural data, have revealed the extent to which duplication of these domains and modifications of their functions can expand the functional repertoire of the organism, contributing to increasing complexity.
ZONA PELLUCIDA DOMAIN PROTEINS
Authors: Jovine Luca , Darie Costel C. , Litscher Eveline S. , Wassarman Paul M.
Published: June 2005

▪ Abstract  Many eukaryotic proteins share a sequence designated as the zona pellucida (ZP) domain. This structural element, present in extracellular proteins from a wide variety of organisms, from nematodes to mammals, consists of ∼260 amino acids with eight conserved cysteine (Cys) residues and is located close to the C terminus of the polypeptide. ZP domain proteins are often glycosylated, modular structures consisting of multiple types of domains. Predictions can be made about some of the structural features of the ZP domain and ZP domain proteins. The functions of ZP domain proteins vary tremendously, from serving as structural components of egg coats, appendicularian mucous houses, and nematode dauer larvae, to serving as mechanotransducers in flies and receptors in mammals and nonmammals. Generally, ZP domain proteins are present in filaments and/or matrices, which is consistent with the role of the domain in protein polymerization. A general mechanism for assembly of ZP domain proteins has been presented. It is likely that the ZP domain plays a common role despite its presence in proteins of widely diverse functions.