bluuebunny/crossref_metadata_2025 huggingface dataset:
SATB1-Binding Sequences and
Alu
-Like Motifs Define a Unique Chromatin Context in the Vicinity of Human Immunodeficiency Virus Type 1 Integration Sites
Authors: Kumar Pavan P. , Mehta Sameet , Purbey Prabhat Kumar , Notani Dimple , Jayani Ranveer S. , Purohit Hemant J. , Raje Dhananjay V. , Ravi Dyavar S. , Bhonde Ramesh R. , Mitra Debashis , Galande Sanjeev
Published: March 2007

Retroviral integration has recently been shown to be nonrandom, favoring transcriptionally active regions of chromatin. However, the mechanism for integration site selection by retroviruses is not clear. We show here the occurrence of
Alu
-like motifs in the sequences flanking the reported viral integration sites that are significantly different from those obtained from the randomly picked sequences from the human genome, suggesting that unique primary sequence features exist in the genomic regions targeted by human immunodeficiency virus type 1 (HIV-1). Additionally, these sequences were preferentially bound by SATB1, the T lineage-restricted chromatin organizer, in vitro and in vivo.
Alu
repeats make up nearly 10% of the human genome and have been implicated in the regulation of transcription. To specifically isolate sequences flanking the viral integration sites and also harboring both
Alu
-like repeats and SATB1-binding sites, we combined chromatin immunoprecipitation with sequential PCRs. The cloned sequences flanking HIV-1 integration sites were specifically immunoprecipitated and amplified from the pool of anti-SATB1-immunoprecipitated genomic DNA fragments isolated from HIV-1 NL4.3-infected Jurkat T-cell chromatin. Moreover, many of these sequences were preferentially partitioned in the DNA associated tightly with the nuclear matrix and not in the chromatin loops. Strikingly, many of these regions were disfavored for integration when SATB1 was silenced, providing unequivocal evidence for its role in HIV-1 integration site selection. We propose that definitive sequence features such as the
Alu
-like motifs and SATB1-binding sites provide a unique chromatin context in vivo which is preferentially targeted by the HIV-1 integration machinery.
Full-Length, Glycosylated NSP4 Is Localized to Plasma Membrane Caveolae by a Novel Raft Isolation Technique
Authors: Storey Stephen M. , Gibbons Thomas F. , Williams Cecelia V. , Parr Rebecca D. , Schroeder Friedhelm , Ball Judith M.
Published: March 2007

Rotavirus NSP4, initially characterized as an endoplasmic reticulum intracellular receptor, is a multifunctional viral enterotoxin that induces diarrhea in murine pups. There have been recent reports of the secretion of a cleaved NSP4 fragment (residues 112 to 175) and of the association of NSP4 with LC3-positive autophagosomes, raft membranes, and microtubules. To determine if NSP4 traffics to a specific subset of rafts at the plasma membrane, we isolated caveolae from plasma membrane-enriched material that yielded caveola membranes free of endoplasmic reticulum and nonraft plasma membrane markers. Analyses of the newly isolated caveolae from rotavirus-infected MDCK cells revealed full-length, high-mannose glycosylated NSP4. The lack of Golgi network-specific processing of the caveolar NSP4 glycans supports studies showing that NSP4 bypasses the Golgi apparatus. Confocal imaging showed the colocalization of NSP4 with caveolin-1 early and late in infection, elucidating the temporal and spatial NSP4-caveolin-1 association during infection. These data were extended with fluorescent resonance energy transfer analyses that confirmed the NSP4 and caveolin-1 interaction in that the specific fluorescently tagged antibodies were within 10 nm of each other during infection. Cells transfected with NSP4 showed patterns of staining and colocalization with caveolin-1 similar to those of infected cells. This study presents an endoplasmic reticulum contaminant-free caveola isolation protocol; describes the presence of full-length, endoglycosidase H-sensitive NSP4 in plasma membrane caveolae; provides confirmation of the NSP4-caveolin interaction in the presence and absence of other viral proteins; and provides a final plasma membrane destination for Golgi network-bypassing NSP4 transport.
Sustained Induction of NF-κB Is Required for Efficient Expression of Latent Human Immunodeficiency Virus Type 1
Authors: Williams Samuel A. , Kwon Hakju , Chen Lin-Feng , Greene Warner C.
Published: March 2007

Cells harboring infectious, but transcriptionally latent, human immunodeficiency virus type 1 (HIV-1) proviruses currently pose an insurmountable barrier to viral eradication in infected patients. To better understand the molecular basis for HIV-1 latency, we used the J-Lat model of postintegration HIV-1 latency to assess the kinetic relationship between the induction of NF-κB and the activation of latent HIV-1 gene expression. Chromatin immunoprecipitation analyses revealed an oscillating pattern of RelA recruitment to the HIV-1 long terminal repeat (LTR) during continuous tumor necrosis factor alpha (TNF-α) stimulation. RNA polymerase II (Pol II) recruitment to the HIV-1 LTR closely mirrored RelA binding. Transient stimulation of cells with TNF-α for 15 min induced only a single round of RelA and RNA Pol II binding and failed to induce robust expression of latent HIV-1. Efficient formation of elongated HIV-1 transcripts required sustained induction by NF-κB, which promoted de novo synthesis of Tat. Cyclin-dependent kinase 9 (CDK9) and serine-2-phosphorylated RNA Pol II were rapidly recruited to the HIV-1 LTR after NF-κB induction; however, these elongating polymerase complexes were progressively dephosphorylated in the absence of Tat. Okadaic acid promoted sustained serine-2 phosphorylation of the C-terminal domain of RNA Pol II and stimulated efficient transcriptional elongation and HIV-1 expression in the absence of Tat. These findings underscore important differences between NF-κB and Tat stimulation of RNA Pol II elongation. While NF-κB binding to the HIV-1 LTR induces serial waves of efficient RNA Pol II initiation, elongation is impaired by the action of an okadaic acid-sensitive phosphatase that dephosphorylates the C-terminal domain of RNA Pol II. Conversely, the action of this phosphatase is overcome in the presence of Tat, promoting very efficient RNA Pol II elongation.
Cell-to-Cell Spread of Borna Disease Virus Proceeds in the Absence of the Virus Primary Receptor and Furin-Mediated Processing of the Virus Surface Glycoprotein
Authors: Clemente Roberto , de la Torre Juan C.
Published: March 2007

Borna disease virus (BDV) is an enveloped virus with a nonsegmented negative-strand RNA genome whose organization is characteristic ofMononegavirales. BDV cell entry follows a receptor-mediated endocytosis pathway, which is initiated by the recognition of an as-yet-unidentified receptor at the cell surface by the virus glycoprotein G. BDV G is synthesized as a precursor (GPC) that is cleaved by the cellular protease furin to produce the mature glycoproteins GP1 and GP2, which have been implicated in receptor recognition and pH-dependent fusion events, respectively. BDV is highly neurotropic and its spread in cultured cells proceeds in the absence of detectable extracellular virus or syncytium formation. BDV spread has been proposed to be strictly dependent on the expression and correct processing of BDV G. Here we present evidence that cell-to-cell spread of BDV required neither the expression of cellular receptors involved in virus primary infection, nor the furin-mediated processing of BDV G. We also show that in furin-deficient cells, the release of BDV particles induced by the treatment of BDV-infected cells with hypertonic buffer was not significantly affected, while virion infectivity was dramatically impaired, correlating with the decreased incorporation of BDV G species into viral particles. These findings support the view that the propagation of BDV within the central nervous systems of infected hosts involves both a primary infection that follows a receptor-mediated endocytosis pathway and a subsequent cell-to-cell spread that is independent of the expression of the primary receptor and does not require the processing of BDV G into GP1 and GP2.
Genetic Structure and Population Variability of Tomato Yellow Leaf Curl China Virus
Authors: Ge Linmei , Zhang Jiangtao , Zhou Xueping , Li Hongye
Published: March 2007

Geminiviruses have circular single-stranded DNA genomes and are important pathogens in tropical and subtropical regions, but their population diversity and variability are poorly understood. Here, we have investigated variations accumulating in Tomato yellow leaf curl China virus (TYLCCNV), a geminivirus in the genus
Begomovirus
of the family
Geminiviridae
. The population variation was analyzed in a naturally infected tomato (
Solanum lycopersicom
) plant and in
Nicotiana benthamiana
and tomato plants experimentally infected with a swarm of TYLCCNV DNA clones to provide an identical sequence for initiation of infection. Our results demonstrate that the population of TYLCCNV in a naturally infected tomato plant was genetically heterogeneous and that rapid mutation occurred in the populations amplified from
N. benthamiana
and tomato plants that had been infected with cloned DNA. This feature of the population of TYLCCNV in these plants consisted of the consensus sequence and a pool of mutants that are not identical but are closely related to the consensus sequence, and it coincides with the quasispecies concept described for many RNA viruses. The mutation frequency was circa 10
−4
in
N. benthamiana
and tomato at 60 days postinoculation, a value comparable to that reported for plant RNA viruses. The quasispecies-like nature of the TYLCCNV populations suggested that TYLCCNV is capable of rapid evolution and adaptation in response to changing agricultural practices.
Generation and Characterization of a Recombinant Vesicular Stomatitis Virus Expressing the Glycoprotein of Borna Disease Virus
Authors: Perez Mar , Clemente Roberto , Robison Clinton S. , Jeetendra E. , Jayakar Himangi R. , Whitt Michael A. , de la Torre Juan C.
Published: March 2007

Borna disease virus (BDV) is an enveloped virus with a nonsegmented negative-strand RNA genome whose organization is characteristic of mononegavirales. However, based on its unique genetics and biological features, BDV is considered to be the prototypic member of a new virus family,Bornaviridae, within the orderMononegavirales. BDV cell entry occurs via receptor-mediated endocytosis, a process initiated by the recognition of an as yet unidentified receptor at the cell surface by the BDV surface glycoprotein (G). The paucity of cell-free virus associated with BDV infection has hindered studies aimed at the elucidation of cellular receptors and detailed mechanisms involved in BDV cell entry. To overcome this problem, we generated and characterized a replication-competent recombinant vesicular stomatitis virus expressing BDV G (rVSVΔG*/BDVG). Cells infected with rVSVΔG*/BDVG produced high titers (107PFU/ml) of cell-free virus progeny, but this virus exhibited a highly attenuated phenotype both in cell culture and in vivo. Attenuation of rVSVΔG*/BDVG was associated with a delayed kinetics of viral RNA replication and altered genome/N mRNA ratios compared to results for rVSVΔG*/VSVG. Likewise, incorporation of BDV G into virions appeared to be restricted despite its high levels of expression and efficient processing in rVSVΔG*/BDVG-infected cells. Notably, rVSVΔG*/BDVG recreated the cell tropism and entry pathway of bona fide BDV. Our results indicate that rVSVΔG*/BDVG represents a unique tool for the investigation of BDV G-mediated cell entry, as well as the roles of BDV G in host immune responses and pathogenesis associated with BDV infection.
Large Hepatitis Delta Antigen Is a Novel Clathrin Adaptor-Like Protein
Authors: Huang Cheng , Chang Shin C. , Yu I-Chen , Tsay Yeou-Guang , Chang Ming-Fu
Published: March 2007

Clathrin-mediated endocytosis is a common pathway for viral entry, but little is known about the direct association of viral protein with clathrin in the cytoplasm. In this study, a putative clathrin box known to be conserved in clathrin adaptors was identified at the C terminus of the large hepatitis delta antigen (HDAg-L). Similar to clathrin adaptors, HDAg-L directly interacted with the N terminus of the clathrin heavy chain through the clathrin box. HDAg-L is a nucleocytoplasmic shuttle protein important for the assembly of hepatitis delta virus (HDV). Here, we demonstrated that brefeldin A and wortmannin, inhibitors of clathrin-mediated exocytosis and endosomal trafficking, respectively, specifically blocked HDV assembly but had no effect on the assembly of the small surface antigen of hepatitis B virus. In addition, cytoplasm-localized HDAg-L inhibited the clathrin-mediated endocytosis of transferrin and the degradation of epidermal growth factor receptor. These results indicate that HDAg-L is a new clathrin adaptor-like protein, and it may be involved in the maturation and pathogenesis of HDV coinfection or superinfection with hepatitis B virus through interaction with clathrin.
Brachiopod diversification during the Early–Mid Ordovician: an example from the Dawan Formation, Yichang area, central China
Authors: Zhan Renbin , Jin Jisuo , Chen Pengfei
Published: March 2007

Systematic and statistical study of brachiopods from the Dawan Formation of the Yichang area, western Hubei Province, central China, indicates that, at generic and specific levels, the α diversity of Early to Mid Ordovician brachiopods in the study area reached the first acme at the beginning of the Corymbograptus deflexus Biozone, marked by the diverse Sinorthis typica Community. This diversity maximum of brachiopods occurred approximately one biozone later than that of the Upper Yangtze Platform. In taxonomic constituents, the main contributors to the diversity maximum were orthoids, which experienced a major increase in the number of genera in the upper Didymograptellus eobifidus Biozone and the lower C. deflexus Biozone. In brachiopod communities or associations, orthoids and pentameroids were the dominant elements. Analyses of Early–Mid Ordovician brachiopods from the Upper Yangtze Platform indicate that a high level of brachiopod community organization, with temporal and spatial stability, was achieved by the Sinorthis Community, which persisted from the D. eobifidus to the Azygograptus suecicus biozones (early Arenig). In the D. eobifidus Biozone, the Sinorthis Community thrived across a wide ecological range (BA3 to upper BA4) in the siliciclastic facies of the central part of the Upper Yangtze Platform and, by the latest D. eobifidus interval, invaded more carbonate-rich substrates in more offshore settings in the northeastern part of the platform (the present Yichang area).
Giant dinosaur eggs from the Tiantai basin, Zhejiang Province, China
Authors: Jin Xingsheng , Azuma Yoichi , Jackson Frankie D , Varricchio David J
Published: March 2007

Giant dinosaur eggs occur within the mid-Cretaceous Liangtoutang Formation of the Tiantai basin in Zhejiang Province of southeastern China. The 43 cm × 14.5 cm eggs represent the first discovery of Macroelongatoolithus xixiaensis specimens from the region. The eggshell exhibits variation in surface ornamentation and eggshell thickness, with smoother and thicker eggshell characteristic of the poles. The Tiantai eggs differ from the stratigraphically younger type specimen of Macroelongatoolithus xixiaensis from Henan Province in their mammillary to continuous layer ratio. Three new features potentially useful for phylogenetic analysis and previously unreported in Macroelongatoolithus and other eggs in the oofamily Elongatoolithidae include prismatic columns, tabular structure within the prisms, and "splaying" of the crystals in the upper mammillae that extend into the overlying continuous layer. Microstructural features of the two nearly complete eggs suggest that the specimens are referable to a potentially large theropod dinosaur. Paleogeographic distribution of these large theropod eggs includes the Late Cretaceous Zoumagang Formation of Henan Province and the mid-Cretaceous Liangtoutang Formation of Zhejiang Province in central and southeastern China and possibly the Lower Cretaceous Cedar Mountain Formation and mid-Cretaceous Dakota Formation of Utah, USA.
Paleoenvironmental and basin analysis of the late Neoproterozoic (Ediacaran) upper Conception and St. John's groups, west Conception Bay, Newfoundland
Authors: Ichaso Aitor A , Dalrymple Robert W , Narbonne Guy M
Published: March 2007

The Conception and St. John's groups consist of deep-marine, fine-grained siliciclastic–volcaniclastic rocks with abundant impressions of Ediacaran body fossils. Based on previous tectonic reconstructions, these strata are interpreted to have accumulated during the transition from a fore arc (phase 1, ca. 630–560 Ma) to a strike-slip pull-apart basin (phase 2, ca. 560–540 Ma). The Drook and Mistaken Point formations accumulated during phase 1 and are characterized by tabular, thick- to medium-bedded turbidites (east-southeast paleoflow directions), contourites (southwest paleoflow directions), and volcanic ash beds. The high proportion of each bed consisting of TE(Bouma turbidite division) mudstone, and the lack of correlation between bed thickness and basal grain size, suggest ponding of the turbidity currents. The differences in paleoflow directions and texture between Conception Bay and equivalent units at Mistaken Point imply that the two areas may have been geographically isolated from each other; phase 1 deposition in the study area is inferred to have taken place in the basin-plain portion of a transversely supplied, partially confined sub-basin. This "west Conception sub-basin" is bounded to the east by outcrops of the older Harbour Main Group that we speculate may have been a topographic high separating the sub-basin from the main fore-arc basin located to the present-day east. The Trepassey and Fermeuse formations represent phase 2 and are characterized by tabular thin-bedded turbidites, slump deposits, and volumetrically minor amounts of volcanic ash that accumulated on a southwesterly prograding slope. The regional consistency of lithologies and paleoflow directions throughout the Avalon Peninsula suggest that basin differentiation was minimal at this time.
Late Ordovician - Early Silurian cryptospore occurrences on Anticosti Island (Île d'Anticosti), Quebec, Canada
Authors: Richardson Jeffery G , Ausich William I
Published: March 2007

Residues from Hirnantian (Upper Ordovician) and Aeronian (Lower Silurian) strata of Anticosti Island, Quebec, Canada, have yielded the oldest occurrence of terrestrial-based palynomorphs (cryptospores) from eastern North America. A low-abundance, low-diversity cryptospore assemblage containing specimens of Pseudodyadospora, Velatitetras, and alete monads has been recovered from the Velleda Member of the Ellis Bay Formation (Upper Ordovician, Hirnantian). The Gun River Formation (Lower Silurian, Aeronian) contains a low-abundance, low-diversity assemblage composed of specimens of Velatitetras, Laevolcancis, and alete monads. The occurrence of these assemblages provides evidence for early land plants in this part of North America during the Late Ordovician and Early Silurian, and documents the existence of a terrestrial-based flora during and after the Saharan (Late Ordovician) glaciation.
Unsupervised Bayesian reconstruction of individual life histories from otolith signatures: case study of Sr:Ca transects of European eel (Anguilla anguilla) otoliths
Authors: Fablet Ronan , Daverat Françoise , Pontual Hélène De
Published: March 2007

The reconstruction of individual life histories from chemical otolith measures is stated as an unsupervised signal-processing issue embedded in a Bayesian framework. This computational methodology was applied to a set of 192 European eel (Anguilla anguilla) otoliths. It provided a robust and unsupervised analysis of the individual chronologies of habitat use (either river, estuary, or coastal) from Sr:Ca measures acquired along an otolith growth axis. Links between Sr:Ca values and habitat, age, and season and the likelihood of the transitions from one habitat type to another were modelled. Major movement characteristics such as age at transition between habitats and time spent in each habitat were estimated. As a straightforward output, an unsupervised classification of habitat use patterns showed great variability. Using a hidden Markov model, 37 patterns of habitat use were found, with 20 different patterns accounting for 90% of the sample. In accordance with literature, residence behaviour was observed (28% of the eels). However, about 72% changed habitat once or several times, mainly before age 4. The potential application of this method to any other measures taken along an otolith growth axis to reconstruct individual chronologies gives a new insight in life history tactics analysis.
Guidelines for developing and updating Bayesian belief networks applied to ecological modeling and conservation
Authors: Marcot Bruce G , Steventon J Douglas , Sutherland Glenn D , McCann Robert K
Published: March 2007

Bayesian belief networks (BBNs) are useful tools for modeling ecological predictions and aiding resource-management decision-making. We provide practical guidelines for developing, testing, and revising BBNs. Primary steps in this process include creating influence diagrams of the hypothesized "causal web" of key factors affecting a species or ecological outcome of interest; developing a first, alpha-level BBN model from the influence diagram; revising the model after expert review; testing and calibrating the model with case files to create a beta-level model; and updating the model structure and conditional probabilities with new validation data, creating the final-application gamma-level model. We illustrate and discuss these steps with an empirically based BBN model of factors influencing probability of capture of northern flying squirrels (Glaucomys sabrinus (Shaw)). Testing and updating BBNs, especially with peer review and calibration, are essential to ensure their credibility and reduce bias. Our guidelines provide modelers with insights that allow them to avoid potentially spurious or unreliable models.
Comparison of early height growth between white spruce seedlings and rooted cuttings
Authors: Beaulieu J , Bernier-Cardou M
Published: March 2007

Early height growth of eastern white spruce (Picea glauca (Moench) Voss) rooted cuttings was compared with that of seedlings using annual measurements collected over 5 years in a farm field test replicated on three sites. The experiment included 148 full-sib families obtained from controlled crossings of superior trees selected for a white spruce breeding population in Quebec. Fifteen additional seedlots were used as controls. The average growth rate of seedlings (37.3 cm·year–1) was slightly larger than that of rooted cuttings (36.2 cm·year–1). The yearly growth rate increased over the test period, and it did so at a somewhat higher rate for the seedlings. The relative size of the estimated variance components and the moderate rank correlations of full-sib family height growth features between the two propagule types suggest that tree breeders should favour seedlings over rooted cuttings to rank families for selection purposes, but vegetative propagation would prove useful for bulking up scarce valuable genotypes.
Effects of nitrogen supply and wood species on Tsuga canadensis and Betula alleghaniensis seedling growth on decaying wood
Authors: Marx Laura M , Walters Michael B
Published: March 2007

Eastern hemlock (Tsuga canadensis (L.) Carrière) and yellow birch (Betula alleghaniensis Britt.) in primary Michigan forests depend on decaying wood for seedling-establishment sites, but seedling densities vary across wood species (hemlock, yellow birch, and sugar maple (Acer saccharum Marsh.)). We collected seedlings and wood from a natural field experiment and conducted a companion greenhouse experiment to determine whether seedling mass and nitrogen (N) content varied with wood species and whether they were related to wood inorganic N supply. Yellow birch seedlings were largest on hemlock wood in the field (P = 0.003) and greenhouse (but P > 0.05), while hemlock seedling mass did not vary across wood species. N concentration and N mineralization rate varied by species (N concentration: hemlock < yellow birch < maple; N mineralization rate: hemlock > yellow birch ≈ maple), but neither seedling mass nor N content was significantly correlated with wood inorganic N supply. In the greenhouse, yellow birch seedlings responded to fertilization with N when growing on hemlock and maple but not yellow birch wood and appear to be limited by phosphorus when growing on yellow birch wood. We conclude that yellow birch seedling growth varies with wood species, and is limited by both N and phosphorus, while hemlock seedlings are unresponsive to variation in wood species during the first two growing seasons.
Snag dynamics in partially harvested and unmanaged northern hardwood forests
Authors: Vanderwel Mark C , Caspersen John P , Woods Murray E
Published: March 2007

We used data from hardwood-dominated permanent sample plots in Ontario to estimate the probability of a tree falling during the 5 year period in which it dies ("tree fall"), and likewise the 5 year probability of snag fall. Tree fall probabilities ranged from 5% to 31% across species, with smaller dead trees more likely to be downed than larger ones. Expected half-lives (median time from death to fall) for 25 cm diameter snags varied from 5 to 13 years among species. Fall rates were higher for 10 cm diameter snags but relatively constant for 20–60 cm diameter snags. Recent harvesting substantially increased the probabilities of both tree fall and snag fall, with the former effect most pronounced for small individuals. We used these estimated fall rates to simulate snag dynamics in uneven-aged sugar maple (Acer saccharum Marsh.) stands. Mean snag densities were 32 and 50 snags/ha in selection-management and old-growth scenarios, respectively. Fifty-four percent of this difference was attributable to the lower density of live trees in the selection-management scenario, while 31% was attributable to losses of snags during harvesting. Silvicultural practices that strategically increase tree mortality rates, together with snag retention, as far as safety permits, during harvesting, could represent an effective approach to snag management under the selection system.
Tree mortality patterns following prescribed fires in a mixed conifer forest
Authors: Kobziar Leda , Moghaddas Jason , Stephens Scott L
Published: March 2007

During the late fall of 2002 we administered three burns in mixed conifer forest sites in the north-central Sierra Nevada. Eight months later we measured fire-induced injury and mortality in 1300 trees. Using logistic regression, an array of crown scorch, stem damage, fuels, and fire-behavior variables were examined for their influence on tree mortality. In Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco), white fir (Abies concolor (Gord. & Glend.) Lindl.), and incense cedar (Calocedrus decurrens (Torr.) Florin), smaller trees with greater total crown damage had higher mortality rates. Smaller stem diameters and denser canopies predicted mortality best in ponderosa pine (Pinus ponderosa Dougl. ex P. Laws. & C. Laws). Duff consumption and bark char severity increased model discrimination for white fir and incense cedar and California black oak (Quercus kelloggii Newberry), respectively. In tanoak (Lithocarpus densiflorus (Hook. & Arn.) Rehd.), greater total crown damage in shorter trees resulted in higher mortality rates. Along with tree diameter and consumption of large (>7.6 cm diameter at breast height, DBH) rotten downed woody debris, fire intensity was a significant predictor of overall tree mortality for all species. Mortality patterns for white fir in relation to crown damage were similar among sites, while those for incense cedar were not, which suggests that species in replicated sites responded differently to similar burns. Our results demonstrate actual fire-behavior data incorporated into mortality models, and can be used to design prescribed burns for targeted reduction of tree density in mixed conifer forests.
Pathogenicity of Leptographium longiclavatum associated with Dendroctonus ponderosae to Pinus contorta
Authors: Lee Sangwon , Kim Jae-Jin , Breuil Colette
Published: March 2007

We assessed the pathogenicity of Leptographium longiclavatum sp. nov., a recently reported fungal associate of the mountain pine beetle, Dendroctonus ponderosae (Hopkins, 1902). In September 2003, 30 lodgepole pines (Pinus contorta Dougl. ex Loud. var latifolia Engelm. ex S. Wats) between 98 and 130 years old were inoculated with L. longiclavatum, the known pathogen Ophiostoma clavigerum, or an agar control. Inoculation densities consisted of 200 and 800 points/m2 in a 60 cm wide band at breast height. The inoculated trees were examined in July 2004, 9 months after inoculation. Five of six trees inoculated with L. longiclavatum at high density (800 points/m2) developed yellow crowns, while the foliage of all trees inoculated at low density (200 points/m2) remained green. Both O. clavigerum and L. longiclavatum generated significantly longer necrotic lesions in the phloem and more occlusions in the sapwood than in the agar controls. In addition, the sapwood colonized by both fungi had a reduced moisture content compared with controls. These results suggest that L. longiclavatum is pathogenic and may contribute to the mortality of mountain pine beetle infested pines.
Disturbance history affects dead wood abundance in Newfoundland boreal forests
Authors: Moroni Martin T
Published: March 2007

Dead wood (dead standing tree (snag), woody debris (WD), buried wood, and stump) abundance was estimated in Newfoundland balsam fir (Abies balsamea (L.) Mill.) and black spruce (Picea mariana (Mill.) BSP) forests regrown following natural and anthropogenic disturbances. Although harvesting left few snags standing, natural disturbances generated many snags. Most were still standing 2 years after natural disturbance, but almost all had fallen after 33–34 years. Snag abundance then increased in stands aged 86–109 years. Natural disturbances generated little WD 0–2 years following disturbance. Harvesting, however, immediately generated large amounts of WD. Thirty-two to forty-one years following disturbance, most harvesting slash had decomposed, but naturally disturbed sites had large amounts of WD from collapsed snags. Harvested sites contained less WD 32–72 years following disturbance than naturally disturbed sites. Amounts of WD in black spruce regrown following harvesting and fire converged 63–72 years following disturbance, despite significant initial differences in WD quantities, diameter distribution, and decay classes. Abundance of WD increased from sites regrown 32–72 years following disturbance to older sites. Precommercial thinning had a minor impact on dead wood stocks. Stumps contained minor biomass. Buried wood and WD biomass were equivalent at some sites.
A population-viability-based risk assessment of Marbled Murrelet nesting habitat policy in British Columbia
Authors: Steventon J Douglas , Sutherland Glenn D , Arcese Peter
Published: March 2007

The Marbled Murrelet (Brachyramphus marmoratus Gmelin) is a small threatened seabird of the Pacific coast of North America. Through simulation modelling we varied the long-term minimum amounts and quality (nesting density) of old-forest nesting habitat to examine effects on murrelet population viability, our measure of population resilience. Applying diffusion approximations we estimated population longevity and persistence probability under uncertainties of at-sea demography and onshore edge effects affecting nesting success, time scale, spatial scale, and subpopulation structure. We cast our analysis in a Bayesian belief and decision network framework. We also applied the framework to spatially explicit land-use and murrelet inventory data for the northern mainland region of the British Columbia coast. We found a diminishing expected value of persistence probability (EVP), for a single independent population, below a nesting capacity of ≈5000 nesting pairs (≈15 000 birds), accelerating below 2000 pairs. A strategy of multiple semi-independent subpopulations provided a higher joint EVP across a wide range of total nesting capacity. There was little improvement in EVP, for any number of subpopulations, above 10 000 – 12 000 pairs (≈36 000 birds, 45%–60% of coastwide population estimate in 2001). Depending on estimates of nesting density, 12 000 pairs would require between 0.6 and 1.2 million ha of potential old-forest nesting habitat.
DIVIDE AND CONQUER? THE ROLE OF GOVERNANCE FOR THE ADAPTABILITY OF INDUSTRIAL DISTRICTS
Authors: PRESS KERSTIN
Published: March 2007

This paper develops a simulation model of the behavior of industrial districts in the face of changes in their environment. By applying Kauffman's N/K-C model to the question of optimum governance in industrial districts facing an external shock, the paper sheds light on the optimum co-ordination mechanism among agents in interdependent industrial networks. Simulation results indicate that collective governance structures with agents adjusting for the sake of the district as a whole perform best in adaptation, whereas individualistic governance modes deliver the worst results. Alliance and leader firm governance forms position themselves in-between these two extremes. However, both modes of governance can be preferable to the collective one if the observation and punishment mechanisms in the district's local culture are not strong enough to impose solidarity among its agents. In this case, a prisoner's dilemma emerges and the collective governance form is replaced by the inferior individualistic one. Through these results, the model highlights the link between governance and district adaptability. It provides an explanation for the trend in Italian districts towards more hierarchical governance structures. Moreover, the identification of the role played by governance structure for district adaptability in changing environments could serve as guidance for future research.
WAVELET TRANSFORMS GENERATED BY SPLINES
Authors: AVERBUCH AMIR Z. , ZHELUDEV VALERY A.
Published: March 2007

In this paper, we design a new family of biorthogonal wavelet transforms that are based on polynomial and discrete splines. The wavelet transforms are constructed via lifting steps, where the prediction and update filters are derived from various types of interpolatory and quasi-interpolatory splines. The transforms use finite and infinite impulse response (IIR) filters and are implemented in a fast lifting mode. We analyze properties of the generated scaling functions and wavelets. In the case when the prediction filter is derived from a polynomial interpolatory spline of even order, the synthesis scaling function and wavelet are splines of the same order. We formulate conditions for the IIR filter to generate an exponentially decaying scaling function.
SparkMaster: automated calcium spark analysis with ImageJ
Authors: Picht Eckard , Zima Aleksey V. , Blatter Lothar A. , Bers Donald M.
Published: March 2007

Ca sparks are elementary Ca-release events from intracellular Ca stores that are observed in virtually all types of muscle. Typically, Ca sparks are measured in the line-scan mode with confocal laser-scanning microscopes, yielding two-dimensional images (distance vs. time). The manual analysis of these images is time consuming and prone to errors as well as investigator bias. Therefore, we developed SparkMaster, an automated analysis program that allows rapid and reliable spark analysis. The underlying analysis algorithm is adapted from the threshold-based standard method of spark analysis developed by Cheng et al. ( Biophys J 76: 606–617, 1999) and is implemented here in the freely available image-processing software ImageJ. SparkMaster offers a graphical user interface through which all analysis parameters and output options are selected. The analysis includes general image parameters (number of detected sparks, spark frequency) and individual spark parameters (amplitude, full width at half-maximum amplitude, full duration at half-maximum amplitude, full width, full duration, time to peak, maximum steepness of spark upstroke, time constant of spark decay). We validated the algorithm using images with synthetic sparks embedded into backgrounds with different signal-to-noise ratios to determine an analysis criteria at which a high sensitivity is combined with a low frequency of false-positive detections. Finally, we applied SparkMaster to analyze experimental data of sparks measured in intact and permeabilized ventricular cardiomyocytes, permeabilized mammalian skeletal muscle, and intact smooth muscle cells. We found that SparkMaster provides a reliable, easy to use, and fast way of analyzing Ca sparks in a wide variety of experimental conditions.
Multiparametric Auditory Receptive Field Organization Across Five Cortical Fields in the Albino Rat
Authors: Polley Daniel B. , Read Heather L. , Storace Douglas A. , Merzenich Michael M.
Published: March 2007

The auditory cortex of the rat is becoming an increasingly popular model system for studies of experience-dependent receptive field plasticity. However, the relative position of various fields within the auditory core and the receptive field organization within each field have yet to be fully described in the normative case. In this study, the macro- and micro-organizational features of the auditory cortex were studied in pentobarbital-anesthetized adult rats with a combination of physiological and anatomical methods. Dense microelectrode mapping procedures were used to identify the relative position of five tonotopically organized fields within the auditory core: primary auditory cortex (AI), the posterior auditory field (PAF), the anterior auditory field (AAF), the ventral auditory field (VAF), and the suprarhinal auditory field (SRAF). AI and AAF both featured short-latency, sharply tuned responses with predominantly monotonic intensity-response functions. SRAF and PAF were both characterized by longer-latency, broadly tuned responses. VAF directly abutted the ventral boundary of AI but was almost exclusively composed of low-threshold nonmonotonic intensity-tuned responses. Dual injection of retrograde tracers into AI and VAF was used to demonstrate that the sources of thalamic input from the medial geniculate body to each area were essentially nonoverlapping. An analysis of receptive field parameters beyond characteristic frequency revealed independent spatially ordered representations for features related to spectral tuning, intensity tuning, and onset response properties in AI, AAF, VAF, and SRAF. These data demonstrate that despite its greatly reduced physical scale, the rat auditory cortex features a surprising degree of organizational complexity and detail.
Treatment Outcomes of Autologous Chondrocyte Implantation for Full-Thickness Articular Cartilage Defects of the Trochlea
Authors: Mandelbaum Bert , Browne Jon E. , Fu Freddie , Micheli Lyle J. , Moseley J. Bruce , Erggelet Christoph , Anderson Allen F.
Published: March 2007

Background

The treatment of trochlear cartilage lesions is challenging given the likely presence of other patellofemoral joint pathologies, the topography of the area, and the limited available treatment options. Only 1 other study has examined the effectiveness of autologous chondrocyte implantation for lesions of the patellofemoral joint.

Hypothesis

Patients treated with autologous chondrocyte implantation for moderate to large isolated lesions located on the trochlea will report improvement in the modified overall condition scale score of the Cincinnati Knee Rating System at a minimum 2-year follow-up.

Study Design

Case series; Level of evidence, 4.

Methods

Using modified scales of the Cincinnati Knee Rating System, 40 Cartilage Repair Registry patients rated their overall condition and symptoms at baseline and at a mean follow-up of 59 ± 18 months. Factors likely to affect outcomes also were analyzed.

Results

At baseline, patients were between ages 16 to 48 years, had a mean total defect size of 4.5 cm2, and reported an overall condition score of 3.1 points (poor). Many failed a prior marrow-stimulation procedure (48%). Other procedures performed before baseline included tibiofemoral osteotomy in 23% and lateral release or Fulkerson for patella maltracking in 13%. Forty-three percent were receiving workers’ compensation at baseline. Patients reported statistically significant improvement in their mean overall condition (3.1 points preoperatively to 6.4 points postoperatively), pain (2.6 to 6.2 points), and swelling (3.9 to 6.3 points) scores. Eleven patients experienced 17 subsequent procedures, and no patients had a failed implantation.

Conclusion

Autologous chondrocyte implantation appears to improve function and reduce symptoms in young to middle-aged patients with symptomatic, full-thickness articular cartilage lesions of the trochlea.
Studies of associations between disability in multiple sclerosis, skin type, gender and ultraviolet radiation
Authors: Woolmore J.A. , Stone M. , Pye E.M. , Partridge J.M. , Boggild M. , Young C. , Jones P.W. , Fryer A.A. , Hawkins C.P. , Strange R.C.
Published: March 2007

Recent studies suggest ultraviolet radiation (UVR)/vitamin D is protective against the development of multiple sclerosis (MS). We determined if outcome in MS is associated with the surrogate for host pigmentation, skin type, and parameters of UVR exposure. We used a validated questionnaire to determine skin type and UVR exposure during childhood (0-16 years), and early adult life (17-40 years), in 448 Caucasians with MS. Outcome was assessed using the Kurtzke Expanded Disability Status Score (EDSS) and Multiple Sclerosis Severity Scale (MSSS). We studied the association of skin type and exposure with dichotomized values of EDSS (< and ≥6) and MSSS (continuous variable) using logistic and linear regression analyses, respectively. Sex, onset age and MS duration were significantly associated with outcome in all patients. In 169 females with established disease (≥10 years), sun sensitive skin types 1 and 2 were associated with reduced risk of EDSS ≥6 (odds ratio =0.50; 95% CI = 0.26-0.97), and higher MSSS values (coefficient = -0.86; 95% CI = -1.67 to -0.05). Parameters of UVR exposure were not significantly associated with outcome. These preliminary data show an association between skin type and disability in female MS patients. They are compatible with independent studies suggesting that exposure mediates MS pathogenesis via vitamin D. Further studies are required to properly assess these potentially important findings. Multiple Sclerosis 2007; 13: 369-375. http://msj.sagepub.com
Group Treatment for Race-related Stresses among Minority Vietnam Veterans
Authors: Loo Chalsa M. , Ueda Salvador S. , Morton Robert K.
Published: March 2007

Treatment for symptoms arising from exposure to adverse race-related events is critical to culturally competent healthcare delivery to ethnic minorities, particularly in light of recent findings demonstrating significant relationships between adverse race-related events and post-traumatic stress disorder (PTSD) and general psychiatric distress. This article offers a developmental model consisting of stages by which psychological symptoms develop in response to race-related stressors in the military. This article also describes a model of group treatment for ethnic minority veterans related to psychological symptoms arising from exposure to race-related stressors. Both models were used in a race-related support group for Pacific Islander Vietnam veterans diagnosed with PTSD. A combined approach of group intervention, psychosocial education, identity reframing, cognitive differentiation, and cognitive restructuring, which included `depersonalizing discrimination' and rejection of faulty beliefs, appear to offer an effective approach to treating psychological sequelae arising from adverse race-related events. This article offers an intervention model that is linked to a developmental model of race-related stressors for Asian American Pacific Islander minority personnel in the military.
Making memories matter
Authors: Carlson Matt
Published: March 2007

The death of an eminent journalist prompts a flurry of memorializing discourse in the news media situating the deceased in a framework that makes sense of his or her accomplishments in the present both to working journalists and to news audiences. This article tracks the discourse in newspapers, magazines, and television following the deaths of television news anchor David Brinkley and newspaper columnist Mary McGrory. In these texts, journalists interpret the lives and work of McGrory and Brinkley in a manner that bolsters the cultural authority of journalists by acting on the collective memory of journalism's societal role. In this way, particularistic discussion of deceased journalists occasions a general discussion of the contemporary state of journalism.
Communicating separation?
Authors: Arnold Anne-Katrin , Schneider Beate
Published: March 2007

Western European countries currently face much immigration from Eastern Europe and Asia. In Germany, Turkish migrants are the largest ethnic minority. Cohabitation is not yet a success story: some observers even fear the development of two separate cultures. Accordingly, public debate about the role of mass and ethnic media has risen. But what role do mass media and ethnic media play in the integration process? What is the role of'ethnic journalists'?

In this article we discuss theoretical approaches to integration, cultural identity, and media consumption. We analyze the link between all three and present results pointing to the strong impact an ethnic online community has on the building of a hybrid cultural identity between majority and minority culture. We also discuss our findings on ethnic journalists' acculturation, self-conception, and audience evaluation.
The AP2 transcription factors DORNRÖSCHEN and DORNRÖSCHEN-LIKE redundantly controlArabidopsisembryo patterning via interaction with PHAVOLUTA
Authors: Chandler John W. , Cole Melanie , Flier Annegret , Grewe Britta , Werr Wolfgang
Published: March 2007

DORNRÖSCHEN (DRN) (also known as ENHANCER OF SHOOT REGENERATION1; ESR1) and DRN-LIKE (DRNL;also known as ESR2) are two linked paralogues encoding AP2 domain-containing proteins. drn mutants show embryo cell patterning defects and, similarly to drnl mutants, disrupt cotyledon development at incomplete penetrance. drn drnl double mutants with weak or strong drnl alleles show more highly penetrant and extreme phenotypes,including a pin-like embryo without cotyledons, confirming a high degree of functional redundancy for the two genes in embryo patterning. Altered expression of PIN1::PIN1-GFP and DR5::GFP in drn mutant embryos places DRN upstream of auxin transport and response. A yeast two-hybrid screen with DRN followed by co-immunoprecipitation and bimolecular fluorescence complementation revealed PHAVOLUTA (PHV) to be a protein interaction partner in planta. drn phv double mutants show an increased penetrance of embryo cell division defects. DRNL can also interact with PHV and both DRN and DRNL can heterodimerise with additional members of the class III HD-ZIP family, PHABULOSA, REVOLUTA, CORONA and ATHB8. Interactions involve the PAS-like C-terminal regions of these proteins and the DRN/DRNL AP2 domain.