bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantitation of changes in protein phosphorylation: A simple method based on stable isotope labeling and mass spectrometry
Authors: Bonenfant Débora , Schmelzle Tobias , Jacinto Estela , Crespo José L. , Mini Thierry , Hall Michael N. , Jenoe Paul
Published: February 2003

Reversible protein phosphorylation plays an important role in many cellular processes. However, a simple and reliable method to measure changes in the extent of phosphorylation is lacking. Here, we present a method to quantitate the changes in phosphorylation occurring in a protein in response to a stimulus. The method consists of three steps: (
i
) enzymatic digestion in H
2
16
O or isotopically enriched H
2
18
O to label individual pools of differentially phosphorylated proteins; (
ii
) affinity selection of phosphopeptides from the combined digests by immobilized metal-affinity chromatography; and (
iii
) dephosphorylation with alkaline phosphatase to allow for quantitation of changes of phosphorylation by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. We applied this strategy to the analysis of the yeast nitrogen permease reactivator protein kinase involved in the target of rapamycin signaling pathway. Alteration in the extent of phosphorylation at Ser-353 and Ser-357 could be easily assessed and quantitated both in wild-type yeast cells treated with rapamycin and in cells lacking the SIT4 phosphatase responsible for dephosphorylating nitrogen permease reactivator protein. The method described here is simple and allows quantitation of relative changes in the level of phosphorylation in signaling proteins, thus yielding information critical for understanding the regulation of complex protein phosphorylation cascades.
Expanding expression of the 5-lipoxygenase pathway within the arterial wall during human atherogenesis
Authors: Spanbroek Rainer , Gräbner Rolf , Lötzer Katharina , Hildner Markus , Urbach Anja , Rühling Katharina , Moos Michael P. W. , Kaiser Brigitte , Cohnert Tina U. , Wahlers Thorsten , Zieske Arthur , Plenz Gabriele , Robenek Horst , Salbach Peter , Kühn Hartmut , Rådmark Olof , Samuelsson Bengt , Habenicht Andreas J. R.
Published: February 2003

Oxidation products of low-density lipoproteins have been suggested to promote inflammation during atherogenesis, and reticulocyte-type 15-lipoxygenase has been implicated to mediate this oxidation. In addition, the 5-lipoxygenase cascade leads to formation of leukotrienes, which exhibit strong proinflammatory activities in cardiovascular tissues. Here, we studied both lipoxygenase pathways in human atherosclerosis. The 5-lipoxygenase pathway was abundantly expressed in arterial walls of patients afflicted with various lesion stages of atherosclerosis of the aorta and of coronary and carotid arteries. 5-lipoxygenase localized to macrophages, dendritic cells, foam cells, mast cells, and neutrophilic granulocytes, and the number of 5-lipoxygenase expressing cells markedly increased in advanced lesions. By contrast, reticulocyte-type 15-lipoxygenase was expressed at levels that were several orders of magnitude lower than 5-lipoxygenase in both normal and diseased arteries, and its expression could not be related to lesion pathology. Our data support a model of atherogenesis in which 5-lipoxygenase cascade-dependent inflammatory circuits consisting of several leukocyte lineages and arterial wall cells evolve within the blood vessel wall during critical stages of lesion development. They raise the possibility that antileukotriene drugs may be an effective treatment regimen in late-stage disease.
Coarse-grained stochastic processes for microscopic lattice systems
Authors: Katsoulakis Markos A. , Majda Andrew J. , Vlachos Dionisios G.
Published: February 2003

Diverse scientific disciplines ranging from materials science to catalysis to biomolecular dynamics to climate modeling involve nonlinear interactions across a large range of physically significant length scales. Here a class of coarse-grained stochastic processes and corresponding Monte Carlo simulation methods, describing computationally feasible mesoscopic length scales, are derived directly from microscopic lattice systems. It is demonstrated below that the coarse-grained stochastic models can capture large-scale structures while retaining significant microscopic information. The requirement of detailed balance is used as a systematic design principle to guarantee correct noise fluctuations for the coarse-grained model. The coarse-grained stochastic algorithms provide large computational savings without increasing programming complexity or computer time per executive event compared to microscopic Monte Carlo simulations.
Oncogenic targeting of an activated tyrosine kinase to the Golgi apparatus in a glioblastoma
Authors: Charest Alan , Kheifets Vicky , Park Julie , Lane Keara , McMahon Kevin , Nutt Cathy L. , Housman David
Published: February 2003

Activating oncogenic mutations of receptor tyrosine kinases (RTKs) have been reported in several types of cancers. In many cases, genomic rearrangements lead to the fusion of unrelated genes to the DNA coding for the kinase domain of RTKs. All RTK-derived fusion proteins reported so far display oligomerization sequences within the 5′ fusion partners that are responsible for oncogenic activation. Here, we report a mechanism by which an altered RTK gains oncogenic potential in a glioblastoma cell line. A microdeletion on 6q21 results in the fusion ofFIG, a gene coding for a Golgi apparatus-associated protein, to the kinase domain of the protooncogene c-ROS. The fused protein product FIG-ROS is a potent oncogene, and its transforming potential resides in its ability to interact with and become localized to the Golgi apparatus. Thus we have found a RTK fusion protein whose subcellular location leads to constitutive kinase activation and results in oncogenic transformation.
Observation of liquid–liquid phase separation for eye lens γS-crystallin
Authors: Annunziata Onofrio , Ogun Olutayo , Benedek George B.
Published: February 2003

γS-crystallin (γS) is an important human and bovine eye lens protein involved in maintaining the transparency of the eye. By adding small amounts of polyethylene glycol (PEG) to the binary aqueous bovine γS solutions, we have observed liquid–liquid phase separation (LLPS) at −8°C and revealed that, in the binary γS–water system, this phase transition would occur at −28°C. We have measured both the effect of PEG concentration on the LLPS temperature and protein/PEG partitioning between the two liquid coexisting phases. We use our measurements of protein/PEG partitioning to determine the nature and the magnitude of the γS-PEG interactions and to quantitatively assess the effectiveness of PEG as a crystallizing agent for γS. We use our measurements of LLPS temperature as a function of protein and PEG concentration to successfully determine the location of the critical point for the binary γS-water system. This phase transition cannot be observed in the absence of PEG because it is inaccessible due to the freezing of the system. Our findings indicate that the effective interactions between γS molecules in the binary γS–water system are attractive. We compare the magnitude of the attraction found for γS with the results obtained for the other γ-crystallins for which the critical temperature is located above the freezing point of the system. This work suggests that PEG can be used to reveal the existence of LLPS for a much wider range of binary protein–water systems than known previously.
Dentate gyrus volume is reduced before onset of plaque formation in PDAPP mice: A magnetic resonance microscopy and stereologic analysis
Authors: Redwine Jeffrey M. , Kosofsky Barry , Jacobs Russell E. , Games Dora , Reilly John F. , Morrison John H. , Young Warren G. , Bloom Floyd E.
Published: February 2003

High-resolution magnetic resonance microscopy (MRM) was used to determine regional brain volumetric changes in a mouse model of Alzheimer's disease. These transgenic (Tg) mice overexpress human mutant amyloid precursor protein (APP) V717F under control of platelet-derived growth factor promoter (PDAPP mice), and cortical and hippocampal β-amyloid (Aβ) deposits accumulate in heterozygotes after 8–10 mos. We used MRM to obtain 3D volumetric data on mouse brains imaged in their skulls to define genotype- and age-related changes. Hippocampal, cerebellar, and brain volumes and corpus callosum length were quantified in 40-, 100-, 365-, and 630-day-old mice. Measurements taken at age 100 days, before Aβ deposition, revealed a 12.3% reduction of hippocampus volume in Tg mice compared with WT controls. This reduction persisted without progression to age 21 mos. A significant 18% increase in hippocampal volume occurred between 40 and 630 days in WT mice, and no corresponding significant increase occurred in Tg mice. Cavalieri volume estimates of hippocampal subfields from 100-day-old Tg mice further localized a 28% volume deficit in the dentate gyrus. In addition, corpus callosum length was reduced by ≈25% in Tg mice at all ages analyzed. In summary, reduced hippocampal volume and corpus callosum length can be detected by MRM before Aβ deposition. We conclude that overexpression of APP and amyloid may initiate pathologic changes before the appearance of plaques, suggesting novel targets for the treatment of Alzheimer's disease and further reinforcing the need for early diagnosis and treatment.
Crowding-dependent production of colony-stimulating factors by cultured syngeneic or allogeneic hematopoietic cells
Authors: Metcalf Donald , Di Rago Ladina , Mifsud Sandra
Published: February 2003

Mitogenic stimulationin vitroof mouse T lymphocytes induces the production of the hematopoietic cytokines granulocyte–macrophage colony-stimulating factor and IL-3. The present experiments showed that simple crowding of murine spleen or lymph node cells was a sufficient inducing stimulus. Crowding did not have this consequence for thymus or marrow cells or spleen cells fromnu/nuorRag-1−/− mice lacking T lymphocytes. Crowding for as short a period as 24 h was sufficient to allow subsequent cytokine production in sparse cultures. Purified T lymphocytes also exhibited low levels of crowding induction of cytokine production and cytokine production was enhanced by IL-2 and IFN-γ. However, IFN-γ−/− spleen cells exhibited similar crowding-induced colony-stimulating factor production to that of control spleen cells. Excess cell crowding inhibited cytokine production. This inhibition was not caused by receptor internalization of cytokines but may contribute to the failure to observe IL-3 production in lymphoid organsin vivo. Coculture of allogeneic spleen or peritoneal cells was a strong inducing signal for colony-stimulating factor production but this parameter was unable to detect autoreactivity of T lymphocytes in mice that lack suppressor of cytokine signaling 1 and exhibit T lymphocyte activation.
RETRACTED: β-Arrestin-mediated PDE4 cAMP phosphodiesterase recruitment regulates β-adrenoceptor switching from G
s
to G
i
Authors: Baillie George S. , Sood Arvind , McPhee Ian , Gall Irene , Perry Stephen J. , Lefkowitz Robert J. , Houslay Miles D.
Published: February 2003

Phosphorylation of the β
2
adrenoreceptor (β
2
AR) by cAMP-activated protein kinase A (PKA) switches its predominant coupling from stimulatory guanine nucleotide regulatory protein (G
s
) to inhibitory guanine nucleotide regulatory protein (G
i
). β-Arrestins recruit the cAMP-degrading PDE4 phosphodiesterases to the β
2
AR, thus controlling PKA activity at the membrane. Here we investigate a role for PDE4 recruitment in regulating G protein switching by the β
2
AR. In human embryonic kidney 293 cells overexpressing a recombinant β
2
AR, stimulation with isoprenaline recruits β-arrestins 1 and 2 as well as both PDE4D3 and PDE4D5 to the receptor and stimulates receptor phosphorylation by PKA. The PKA phosphorylation status of the β
2
AR is enhanced markedly when cells are treated with the selective PDE4-inhibitor rolipram or when they are transfected with a catalytically inactive PDE4D mutant (PDE4D5-D556A) that competitively inhibits isoprenaline-stimulated recruitment of native PDE4 to the β
2
AR. Rolipram and PDE4D5-D556A also enhance β
2
AR-mediated activation of extracellular signal-regulated kinases ERK1/2. This is consistent with a switch in coupling of the receptor from G
s
to G
i
, because the ERK1/2 activation is sensitive to both inhibitors of PKA (H89) and G
i
(pertussis toxin). In cardiac myocytes, the β
2
AR also switches from G
s
to G
i
coupling. Treating primary cardiac myocytes with isoprenaline induces recruitment of PDE4D3 and PDE4D5 to membranes and activates ERK1/2. Rolipram robustly enhances this activation in a manner sensitive to both pertussis toxin and H89. Adenovirus-mediated expression of PDE4D5-D556A also potentiates ERK1/2 activation. Thus, receptor-stimulated β-arrestin-mediated recruitment of PDE4 plays a central role in the regulation of G protein switching by the β
2
AR in a physiological system, the cardiac myocyte.
A biomimetic motility assay provides insight into the mechanism of actin-based motility
Authors: Wiesner Sebastian , Helfer Emmanuele , Didry Dominique , Ducouret Guylaine , Lafuma Françoise , Carlier Marie-France , Pantaloni Dominique
Published: February 2003

Abiomimetic motility assay is used to analyze the mechanism of force production by site-directed polymerization of actin. Polystyrene microspheres, functionalized in a controlled fashion by the N-WASP protein, the ubiquitous activator of Arp2/3 complex, undergo actin-based propulsion in a medium that consists of five pure proteins. We have analyzed the dependence of velocity on N-WASP surface density, on the concentration of capping protein, and on external force. Movement was not slowed down by increasing the diameter of the beads (0.2 to 3 μm) nor by increasing the viscosity of the medium by 105-fold. This important result shows that forces due to actin polymerization are balanced by internal forces due to transient attachment of filament ends at the surface. These forces are greater than the viscous drag. Using Alexa®488-labeled Arp2/3, we show that Arp2/3 is incorporated in the actin tail like G-actin by barbed end branching of filaments at the bead surface, not by side branching, and that filaments are more densely branched upon increasing gelsolin concentration. These data support models in which the rates of filament branching and capping control velocity, and autocatalytic branching of filament ends, rather than filament nucleation, occurs at the particle surface.
Rac and Cdc42 play distinct roles in regulating PI(3,4,5)P3 and polarity during neutrophil chemotaxis
Authors: Srinivasan Supriya , Wang Fei , Glavas Suzana , Ott Alexander , Hofmann Fred , Aktories Klaus , Kalman Daniel , Bourne Henry R.
Published: February 2003

Neutrophils exposed to chemoattractants polarize and accumulate polymerized actin at the leading edge. In neutrophil-like HL-60 cells, this asymmetry depends on a positive feedback loop in which accumulation of a membrane lipid, phosphatidylinositol (PI) 3,4,5-trisphosphate (PI[3,4,5]P3), leads to activation of Rac and/or Cdc42, and vice versa. We now report that Rac and Cdc42 play distinct roles in regulating this asymmetry. In the absence of chemoattractant, expression of constitutively active Rac stimulates accumulation at the plasma membrane of actin polymers and of GFP-tagged fluorescent probes for PI(3,4,5)P3 (the PH domain of Akt) and activated Rac (the p21-binding domain of p21-activated kinase). Dominant negative Rac inhibits chemoattractant-stimulated accumulation of actin polymers and membrane translocation of both fluorescent probes and attainment of morphologic polarity. Expression of constitutively active Cdc42 or of two different protein inhibitors of Cdc42 fails to mimic effects of the Rac mutants on actin or PI(3,4,5)P3. Instead, Cdc42 inhibitors prevent cells from maintaining a persistent leading edge and frequently induce formation of multiple, short lived leading edges containing actin polymers, PI(3,4,5)P3, and activated Rac. We conclude that Rac plays a dominant role in the PI(3,4,5)P3-dependent positive feedback loop required for forming a leading edge, whereas location and stability of the leading edge are regulated by Cdc42.
The intramitochondrial dynamin-related GTPase, Mgm1p, is a component of a protein complex that mediates mitochondrial fusion
Authors: Wong Edith D. , Wagner Jennifer A. , Scott Sidney V. , Okreglak Voytek , Holewinske Timothy J. , Cassidy-Stone Ann , Nunnari Jodi
Published: February 2003

Abalance between fission and fusion events determines the morphology of mitochondria. In yeast, mitochondrial fission is regulated by the outer membrane–associated dynamin-related GTPase, Dnm1p. Mitochondrial fusion requires two integral outer membrane components, Fzo1p and Ugo1p. Interestingly, mutations in a second mitochondrial-associated dynamin-related GTPase, Mgm1p, produce similar phenotypes to fzo1 and ugo cells. Specifically, mutations in MGM1 cause mitochondrial fragmentation and a loss of mitochondrial DNA that are suppressed by abolishing DNM1-dependent fission. In contrast to fzo1ts mutants, blocking DNM1-dependent fission restores mitochondrial fusion in mgm1ts cells during mating. Here we show that blocking DNM1-dependent fission in Δmgm1 cells fails to restore mitochondrial fusion during mating. To examine the role of Mgm1p in mitochondrial fusion, we looked for molecular interactions with known fusion components. Immunoprecipitation experiments revealed that Mgm1p is associated with both Ugo1p and Fzo1p in mitochondria, and that Ugo1p and Fzo1p also are associated with each other. In addition, genetic analysis of specific mgm1 alleles indicates that Mgm1p's GTPase and GTPase effector domains are required for its ability to promote mitochondrial fusion and that Mgm1p self-interacts, suggesting that it functions in fusion as a self-assembling GTPase. Mgm1p's localization within mitochondria has been controversial. Using protease protection and immuno-EM, we have shown previously that Mgm1p localizes to the intermembrane space, associated with the inner membrane. To further test our conclusions, we have used a novel method using the tobacco etch virus protease and confirm that Mgm1p is present in the intermembrane space compartment in vivo. Taken together, these data suggest a model where Mgm1p functions in fusion to remodel the inner membrane and to connect the inner membrane to the outer membrane via its interactions with Ugo1p and Fzo1p, thereby helping to coordinate the behavior of the four mitochondrial membranes during fusion.
The role of the lissencephaly protein Pac1 during nuclear migration in budding yeast
Authors: Lee Wei-Lih , Oberle Jessica R. , Cooper John A.
Published: February 2003

During mitosis in Saccharomyces cerevisiae, the mitotic spindle moves into the mother–bud neck via dynein-dependent sliding of cytoplasmic microtubules along the cortex of the bud. Here we show that Pac1, the yeast homologue of the human lissencephaly protein LIS1, plays a key role in this process. First, genetic interactions placed Pac1 in the dynein/dynactin pathway. Second, cells lacking Pac1 failed to display microtubule sliding in the bud, resulting in defective mitotic spindle movement and nuclear segregation. Third, Pac1 localized to the plus ends (distal tips) of cytoplasmic microtubules in the bud. This localization did not depend on the dynein heavy chain Dyn1. Moreover, the Pac1 fluorescence intensity at the microtubule end was enhanced in cells lacking dynactin or the cortical attachment molecule Num1. Fourth, dynein heavy chain Dyn1 also localized to the tips of cytoplasmic microtubules in wild-type cells. Dynein localization required Pac1 and, like Pac1, was enhanced in cells lacking the dynactin component Arp1 or the cortical attachment molecule Num1. Our results suggest that Pac1 targets dynein to microtubule tips, which is necessary for sliding of microtubules along the bud cortex. Dynein must remain inactive until microtubule ends interact with the bud cortex, at which time dynein and Pac1 appear to be offloaded from the microtubule to the cortex.
The ZO-1–associated Y-box factor ZONAB regulates epithelial cell proliferation and cell density
Authors: Balda Maria S. , Garrett Michelle D. , Matter Karl
Published: February 2003

Epithelial tight junctions regulate paracellular permeability, restrict apical/basolateral intramembrane diffusion of lipids, and have been proposed to participate in the control of epithelial cell proliferation and differentiation. Previously, we have identified ZO-1–associated nucleic acid binding proteins (ZONAB), a Y-box transcription factor whose nuclear localization and transcriptional activity is regulated by the tight junction–associated candidate tumor suppressor ZO-1. Now, we found that reduction of ZONAB expression using an antisense approach or by RNA interference strongly reduced proliferation of MDCK cells. Transfection of wild-type or ZONAB-binding fragments of ZO-1 reduced proliferation as well as nuclear ZONAB pools, indicating that promotion of proliferation by ZONAB requires its nuclear accumulation. Overexpression of ZONAB resulted in increased cell density in mature monolayers, and depletion of ZONAB or overexpression of ZO-1 reduced cell density. ZONAB was found to associate with cell division kinase (CDK) 4, and reduction of nuclear ZONAB levels resulted in reduced nuclear CDK4. Thus, our data indicate that tight junctions can regulate epithelial cell proliferation and cell density via a ZONAB/ZO-1–based pathway. Although this regulatory process may also involve regulation of transcription by ZONAB, our data suggest that one mechanism by which ZONAB and ZO-1 influence proliferation is by regulating the nuclear accumulation of CDK4.
Mechanism of filopodia initiation by reorganization of a dendritic network
Authors: Svitkina Tatyana M. , Bulanova Elena A. , Chaga Oleg Y. , Vignjevic Danijela M. , Kojima Shin-ichiro , Vasiliev Jury M. , Borisy Gary G.
Published: February 2003

Afilopodium protrudes by elongation of bundled actin filaments in its core. However, the mechanism of filopodia initiation remains unknown. Using live-cell imaging with GFP-tagged proteins and correlative electron microscopy, we performed a kinetic-structural analysis of filopodial initiation in B16F1 melanoma cells. Filopodial bundles arose not by a specific nucleation event, but by reorganization of the lamellipodial dendritic network analogous to fusion of established filopodia but occurring at the level of individual filaments. Subsets of independently nucleated lamellipodial filaments elongated and gradually associated with each other at their barbed ends, leading to formation of cone-shaped structures that we term Λ-precursors. An early marker of initiation was the gradual coalescence of GFP-vasodilator-stimulated phosphoprotein (GFP-VASP) fluorescence at the leading edge into discrete foci. The GFP-VASP foci were associated with Λ-precursors, whereas Arp2/3 was not. Subsequent recruitment of fascin to the clustered barbed ends of Λ-precursors initiated filament bundling and completed formation of the nascent filopodium. We propose a convergent elongation model of filopodia initiation, stipulating that filaments within the lamellipodial dendritic network acquire privileged status by binding a set of molecules (including VASP) to their barbed ends, which protect them from capping and mediate association of barbed ends with each other.
Rae1 is an essential mitotic checkpoint regulator that cooperates with Bub3 to prevent chromosome missegregation
Authors: Babu J. Ramesh , Jeganathan Karthik B. , Baker Darren J. , Wu Xiaosheng , Kang-Decker Ningling , van Deursen Jan M.
Published: February 2003

The WD-repeat proteins Rae1 and Bub3 show extensive sequence homology, indicative of functional similarity. However, previous studies have suggested that Rae1 is involved in the mRNA export pathway and Bub3 in the mitotic checkpoint. To determine the in vivo roles of Rae1 and Bub3 in mammals, we generated knockout mice that have these genes deleted individually or in combination. Here we show that haplo-insufficiency of either Rae1 or Bub3 results in a similar phenotype involving mitotic checkpoint defects and chromosome missegregation. We also show that overexpression of Rae1 can correct for Rae1 haplo-insufficiency and, surprisingly, Bub3 haplo-insufficiency. Rae1-null and Bub3-null mice are embryonic lethal, although cells from these mice did not have a detectable defect in nuclear export of mRNA. Unlike null mice, compound haplo-insufficient Rae1/Bub3 mice are viable. However, cells from these mice exhibit much greater rates of premature sister chromatid separation and chromosome missegregation than single haplo-insufficient cells. Finally, we show that mice with mitotic checkpoint defects are more susceptible to dimethylbenzanthrene-induced tumorigenesis than wild-type mice. Thus, our data demonstrate a novel function for Rae1 and characterize Rae1 and Bub3 as related proteins with essential, overlapping, and cooperating roles in the mitotic checkpoint.
EPLIN regulates actin dynamics by cross-linking and stabilizing filaments
Authors: Maul Raymond S. , Song Yuhong , Amann Kurt J. , Gerbin Sachi C. , Pollard Thomas D. , Chang David D.
Published: February 2003

Epithelial protein lost in neoplasm (EPLIN) is a cytoskeleton-associated protein encoded by a gene that is down-regulated in transformed cells. EPLIN increases the number and size of actin stress fibers and inhibits membrane ruffling induced by Rac. EPLIN has at least two actin binding sites. Purified recombinant EPLIN inhibits actin filament depolymerization and cross-links filaments in bundles. EPLIN does not affect the kinetics of spontaneous actin polymerization or elongation at the barbed end, but inhibits branching nucleation of actin filaments by Arp2/3 complex. Side binding activity may stabilize filaments and account for the inhibition of nucleation mediated by Arp2/3 complex. We propose that EPLIN promotes the formation of stable actin filament structures such as stress fibers at the expense of more dynamic actin filament structures such as membrane ruffles. Reduced expression of EPLIN may contribute to the motility of invasive tumor cells.
Anthrax toxin rafts into cells
Authors: Kurzchalia Teymuras
Published: February 2003

Anthrax toxin binds to a plasma membrane receptor and after endocytosis exerts its deadly effects on the cell. Until now, however, the mechanism of initial toxin uptake was unknown. In this issue, Abrami et al. (2003) demonstrate that toxin oligomerization clusters the anthrax receptor into lipid rafts and this complex is internalized via the clathrin-dependent pathway.
Dynactin polices two-way organelle traffic
Authors: Dell Karen R.
Published: February 2003

How is the bidirectional motion of organelles controlled? In this issue, Deacon et al. (2003) reveal the unexpected finding that dynactin (previously known to control dynein-based motility) binds to kinesin II and regulates anterograde movement of Xenopus melanosomes. This result suggests that dynactin may be a key player in coordinating vesicle traffic in this system.
Nucleotide polymorphisms in three genes support host and geographic speciation in tree pathogens belonging toGremmeniellaspp.
Authors: Dusabenyagasani M , Laflamme G , Hamelin R C
Published: February 2003

We detected nucleotide polymorphisms within the genus Gremmeniella in DNA sequences of β-tubulin, glyceraldehyde phosphate dehydrogenase, and mitochondrial small subunit rRNA (mtSSU rRNA) genes. A group-I intron was present in strains originating from fir (Abies spp.) in the mtSSU rRNA locus. This intron in the mtSSU rRNA locus of strains isolated from Abies sachalinensis (Fridr. Schmidt) M.T. Mast in Asia was also found in strains isolated from Abies balsamea (L.) Mill. in North America. Phylogenetic analyses yielded trees that grouped strains by host of origin with strong branch support. Asian strains of Gremmeniella abietina (Lagerberg) Morelet var. abietina isolated from fir (A. sachalinensis) were more closely related to G. abietina var. balsamea from North America, which is found on spruce (Picea spp.) and balsam fir, and European and North American races of G. abietina var. abietina from pines (Pinus spp.) were distantly related. Likewise, North American isolates of Gremmeniella laricina (Ettinger) O. Petrini, L.E. Petrini, G. Laflamme, & G.B. Ouellette, a pathogen of larch, was more closely related to G. laricina from Europe than to G. abietina var. abietina from North America. These data suggest that host specialization might have been the leading evolutionary force shaping Gremmeniella spp., with geographic separation acting as a secondary factor.Key words: Gremmeniella, geographic separation, host specialization, mitochondrial rRNA, nuclear genes.
Morphogenesis of stem gall tissues induced by larvae of two cecidomyiid species (Diptera: Cecidomyiidae) onSuaeda monoica(Chenopodiaceae)
Authors: Dorchin Netta , Freidberg Amnon , Aloni Roni
Published: February 2003

Izeniola obesula Dorchin and Stefaniola defoliata Dorchin (Diptera: Cecidomyiidae: Lasiopterini) are monophagous gall midges each inducing a unique kind of gall on stems of the salt marsh plant Suaeda monoica Gmelin (Chenopodiaceae). The morphogenesis of these two types of galls was studied in relation to the life history of the midges as observed both in the field and the laboratory. Izeniola obesula larvae penetrate the pith parenchyma through the growing shoot apex, causing intensive cell proliferation and inducing differentiation of novel vascular tissues and a sclerenchyma sheath around their chambers. Vascular differentiation in this gall originates from the larval chamber, a phenomenon attributed to local stimulation by the larva. It is suggested that the sclerenchyma layer in these galls is also induced by insect activity. Stefaniola defoliata larvae penetrate the stem laterally and reside inside the primary phloem, causing proliferation of phloem parenchyma, and are later encapsulated by secondary xylem tissue. Both galls are associated with a symbiotic fungus that grows along the inner walls of the larval chambers. The possible hormonal mechanisms controlling morphogenesis of the galls are discussed.Key words: gall morphogenesis, phytohormones, sclerenchyma, vascular differentiation.
Site factors determining epiphytic lichen distribution in a dieback-affected spruce-fir forest on Whiteface Mountain, New York: stemflow chemistry
Authors: Schmull Michaela , Hauck Markus , Vann David R , Johnson Arthur H , Runge Michael
Published: February 2003

Epiphytic lichen diversity in a dieback-affected forest of red spruce (Picea rubens Sarg.) and balsam fir (Abies balsamea (L.) Mill.) on Whiteface Mountain, New York, U.S.A., was higher on dead compared with living trees and on fir compared with spruce. Diversity differed more between living and dead spruce than between living and dead fir. Cover of all lichen species that occurred on more than 50% of the sample trees, except for two species, decreased with increasing mean concentration of NO3in stemflow. Concentrations of NO3were higher on living spruce compared with dead spruce and with living and dead fir. The negative correlations between lichen cover and NO3concentration may reflect either a decrease of lichen abundance caused by toxic effects of higher NO3concentrations or a removal of NO3from stemflow by epiphytic lichens. Experimental exposure of Hypogymnia physodes to NaNO3reduced chlorophyll concentrations. This result, together with estimations of lichen and needle biomass, indicates that a dependence of lichen cover on NO3concentrations in stemflow may be the cause for the negative correlations. The sulphur concentration in stemflow did not affect lichen abundance on Whiteface Mountain. The manganese concentration in stemflow may have an effect on single species.Key words: forest dieback, manganese, nitrate assimilation, nitrate toxicity, precipitation chemistry, sulphur.
Flower mites and nectar production in six hummingbird-pollinated plants with contrasting flower longevities
Authors: Lara Carlos , Ornelas Juan Francisco
Published: February 2003

Hummingbird flower mites and hummingbirds may compete intensely for the nectar secreted by their host plants. Here, we present the results from field experiments in which flower mites were excluded from flowers of six hummingbird-pollinated plants with contrasting flower longevities. Nectar measurements were taken on flowers from which mites were excluded and those without mite exclusion over their lifespans. The exclusion of mites had a significant positive effect on the amount of nectar available in plants with long-lived flowers. In contrast, nectar availability in short-lived flowers was not significantly reduced after mite exclusion. The significance of the mite-exclusion treatment was independent of floral morph and flower age. Results also suggest that the magnitude of the mite-exclusion treatment depends on the volume of nectar produced by the flower throughout its lifetime. The treatment effect was detected when nectar consumption, presumably by flower mites, exceeded 13% of the nectar produced by the flowers; nectar availability was not significantly reduced when nectar volume was < 7 µL per flower. It appears that flower mites consume proportionately more nectar in long-lived flowers than in short-lived flowers. Parasitic hummingbird flower mites seem to be preferentially taking advantage of plant-pollinator interactions in which flowers last several days and produce large volumes of nectar. The consequences of this finding concerning planthummingbirdmite interactions await further investigation. As a working hypothesis, we propose that nectar production has increased over evolutionary time not only by the selective pressures imposed by the pollinators, but also to compensate for the reduction they suffer after exploitation by nectar robbers and thieves such as flower mites.Key words: Ascidae, flower longevity, hummingbird pollination, multiple-species interactions, mutualism exploitation, nectar theft.
Slug tests in a confined aquifer: experimental results in a large soil tank and numerical modeling
Authors: Chapuis Robert P , Chenaf Djaouida
Published: February 2003

Variable-head (slug) tests in a confined aquifer can be interpreted using different methods that either consider or neglect the influence of the instantaneous deformation of an elastic solid matrix. This paper defines a unified interpretation for slug tests: it is based on the velocity graph describing the conservation equation underlying all methods. If the storativity S has no influence, the velocity graph is a straight line. If S has an influence, the theory considering this influence predicts the graph should be a curve. Numerous slug tests were performed in a large tank containing a confined aquifer. Other tests were used to determine independently the transmissivity T and S values of the confined aquifer which are compared with those obtained from slug tests. The velocity graphs of the slug tests provided straight lines instead of the smooth curves as predicted by the theory. A numerical analysis of these tests in the sand tank was performed using a finite element method. The analysis gave straight lines instead of curves for any S value and therefore confirmed the experimental observation (in velocity graphs) that slug test results do not depend of S and thus cannot be used to determine the S value.Key words: slug test, hydraulic conductivity, storativity, numerical modeling.
Evaluation of preconsolidation pressure and the overconsolidation ratio from piezocone tests of clay deposits in Quebec
Authors: Demers Denis , Leroueil Serge
Published: February 2003

The preconsolidation pressure and overconsolidation ratio profiles are the most important factors related to the mechanical behaviour of clay deposits. They are interpreted on the basis of a limited number of laboratory tests, but the near-continuous information provided by the piezocone can allow local data to be extrapolated to an entire site. Numerous methods have been proposed for relating piezocone data to preconsolidation pressure and the overconsolidation ratio, but their validity is still uncertain. In this paper, nine methods are compared on the basis of data collected on 31 sensitive clay sites in Quebec whose preconsolidation pressure profiles are well known. Each method is briefly presented and the most promising are identified. The simplest method, which directly relates preconsolidation pressure to net tip resistance, also appears to be the most effective.Key words: clay, preconsolidation pressure, overconsolidation ratio, piezocone, correlations.
Specific surface: determination and relevance
Authors: Santamarina J C , Klein K A , Wang Y H , Prencke E
Published: February 2003

Specific surface captures the combined effects of particle size and slenderness in a measurement that is independent and complementary to grain-size distribution. There are various methods to measure specific surface, including gas adsorption in dry conditions and selective molecular absorption in aqueous suspensions. The measurement procedure can have an important effect on measured values, yet such sensitivity is informative in itself. The amount of surface in a soil mass determines the balance between surface-related forces and gravimetricskeletal forces acting on a soil particle, affects fabric formation, supports rich energy coupling mechanisms, governs conduction, and controls sorption and retardation during chemical diffusion.Key words: specific surface, surface area, methylene blue, gas adsorption, fabric, Atterberg limits, grain-size distribution.
Influence of generalized initial state and principal stress rotation on the undrained response of sands
Authors: Sivathayalan S , Vaid Y P
Published: February 2003

The dependence of the undrained behaviour of sand on the initial stress state and the orientation of principal stresses with respect to the bedding planes is assessed under generalized loading paths using hollow cylinder torsional shear tests. The undrained tests were carried out using displacement-controlled loading to confidently capture the post-peak strain-softening response. Undrained behaviour of sands under identical initial states is shown to be dependent on the direction of principal stresses, during and prior to undrained shear, in relation to the direction of bedding planes. The minimum undrained strength of the strain-softening sand is found to be highly influenced by the initial stress state (confining stress, direction of principal stresses, and static shear), even though the friction angle mobilized at the instant of minimum strength is unique. A mere rotation of principal stresses at constant deviator stress alone can lead to a strain-softening response that may culminate in limited or unlimited flow deformation. The susceptibility of sand to liquefaction due to stress rotation increases as the direction of the major principal stress approaches the orientation of the bedding plane. The potential for flow deformation is strongly dependent on the direction of the major principal stress in relation to the bedding planes, and the steady state strength is not uniquely related to the void ratio alone.Key words: liquefaction, hollow cylinder torsion test, principal stress direction, static shear, steady state strength, minimum undrained strength.
Contrasting failure behaviour of two large landslides in clay and silt
Authors: Fletcher Lara , Hungr Oldrich , Evans S G
Published: February 2003

Two large landslides in overconsolidated glaciolacustrine clay and silt, located in river valleys in British Columbia, were found to be quite similar in their main aspects. However, their failure behaviour was very different. One continues to exhibit intermittent, mainly ductile deformations with limited mobility which are typical of compound landslides in stiff clay. The other suddenly developed into an extremely rapid flow slide of 6.4 Mm3, damming a large river in the course of a few minutes and projecting a wave onto the opposite bank. The flow slide followed a period of strong infiltration. A comparison of the two cases explains the difference in their failure behaviour. Three possible mechanisms for brittle flow slide formation are proposed, the first based on the undrained brittleness of soil at the rupture surface, the second on the high internal strength of the sliding body, and the third on macroscopic brittleness developed by pre-failure ductile deformation and softening. Both latter mechanisms are facilitated by the presence of nonplastic units in the sliding mass.Key words: overconsolidated clay, silt, landslide, flow slide, brittleness, glaciolacustrine deposits.
Prediction of impending failure of embankments on soft ground
Authors: Hunter Gavan , Fell Robin
Published: February 2003

The deformation behaviour and excess pore pressure response of 13 well-monitored embankments on soft ground that were constructed to failure have been analyzed. The analysis shows that by monitoring lateral displacement at the toe of the embankment and vertical displacement at the toe and about 5 m beyond the toe, the onset of impending failure of embankments on soft ground can be detected while the slope is at about 7090% of the failure height. This equates to an actual factor of safety of around 1.25. Monitoring of borehole inclinometers at the toe of the embankment, cracking of the embankment, and the pore pressure response and deformation during pauses in construction can provide useful additional data for detection of an impending failure.Key words: embankment on soft ground, deformation, pore pressure, failure, factor of safety.
Field and monitoring data of debris-flow events in the Swiss Alps
Authors: Hürlimann M , Rickenmann D , Graf C
Published: February 2003

Debris flow is a common process in the Swiss Alps and in other mountainous parts of the world. The understanding of debris-flow behaviour is essential to assess the hazards they present. An important approach towards improving the knowledge of debris-flow processes is the gathering of real-time data by debris-flow observation stations. Observation stations were established in three Swiss debris flow prone watersheds and equipped with video cameras, ultrasonic devices, a radar device, geophones, and rain gauges. In 2000, four significant debris flows were observed. The data provided useful information on the mechanics of debris flows and on the efficiency of the measuring devices. The observed debris flows are characterized by volumes between 5 000 and 35 000 m3, front velocities ranging from 2 to 5 m/s, and peak discharges between 20 and 125 m3/s. The analysis of the monitoring data revealed that ultrasonic and radar devices are very helpful tools, whereas the quality of the geophone signal strongly depends on the substrate on which the instrument is installed (i.e., bedrock versus unconsolidated material). Video images are useful to verify the data obtained by the other devices. A dynamic analysis of one debris flow was carried out and the simulated results are in fair agreement with the observed data.Key words: debris flow, Swiss Alps, monitoring, dynamic analysis.
An overview of soil heterogeneity: quantification and implications on geotechnical field problems
Authors: Elkateb Tamer , Chalaturnyk Rick , Robertson Peter K
Published: February 2003

Engineering judgment and reliance on factors of safety have been the conventional tools for dealing with soil heterogeneity in geotechnical practice. This paper presents a review of recent advances in treating soil variability. It presents the implications of geostatistical techniques and up-scaling methods used for quantifying the heterogeneous permeability of soil as addressed in the petroleum industry. Moreover, the interest of geotechnical practice to incorporate the statistical properties of soil in a probabilistic design framework is also discussed. This ranges from conventional Monte Carlo simulation based design and stochastic finite element analysis to the recent techniques that take into account the effect of spatial correlation of soil properties. Example applications of these techniques to different types of field problems, such as foundation settlement, seepage flow, and liquefaction assessment, are discussed with emphasis on the limitations of the current practice and trends for future research. In addition, different decision making algorithms are addressed with examples of their applications to geotechnical field problems.Key words: heterogeneity, spatial variability, geostatistics, stochastic analysis, decision making.
The shaft capacity of pipe piles in sand
Authors: Gavin Kenneth G , Lehane Barry M
Published: February 2003

This paper describes results from an experimental programme that investigated factors affecting the shaft capacity of open-ended (pipe) piles in sand. A number of jacked pile installations in a test chamber filled with loose sand were performed using both open- and closed-ended, 114 mm diameter piles. The test series was designed to investigate the effects of in situ stress level, pile end condition, and degree of plugging on the development of pile shaft resistance. The results indicate that the maximum local shaft resistance that can develop at a given location on a pipe pile may be expressed as a function of the incremental filling ratio of the soil plug during installation, the cone penetration test (CPT) qc value, and the relative position of the pile toe. The experimental results allowed a simple expression to be developed for the plug resistance during pile installation, and this is used in conjunction with a popular design method for closed-ended piles to provide a means of estimating the shaft capacity of open-ended piles. The new approach is shown to provide good estimates of overall shaft capacity and skin friction distribution.Key words: shaft capacity, pipe piles, sand.
A method for correlating large penetration test (LPT) to standard penetration test (SPT) blow counts
Authors: Daniel Chris R , Howie John A , Sy Alex
Published: February 2003

The standard penetration test (SPT) split-spoon sampler is too small for investigations in gravelly soils. For this reason, several researchers have developed scaled-up versions of the SPT, commonly referred to as "large penetration tests" (LPT), and attempted to correlate the measured blow counts to SPT blow counts. Several LPTs have been in use worldwide; each with different drill rods, sampler dimensions, and hammer energies; hence existing published LPTSPT correlations differ for each system. This paper summarizes the LPT data in the literature and presents a fundamental method for predicting LPTSPT correlations. The proposed method is based on wave equation analyses of SPT and LPT and considers variations in test equipment, penetration resistance, and energy. It is shown that the method provides a unified approach for assimilating the various published LPTSPT correlations. Additional SPT and LPT data were collected at a sand research site to check the proposed method and to expand the LPT database. The observed and predicted correlation factors are shown to be in good agreement. The proposed correlation method will be useful as a logical framework for the comparison of LPT data collected throughout the world. Additional research will be required to extend this procedure to gravel sites.Key words: large penetration test, LPT, fundamental correlation method, wave equation analysis, grain size effects.