bluuebunny/crossref_metadata_2025 huggingface dataset:
Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin
Authors: Ruscio Jory Z. , Kumar Deept , Shukla Maulik , Prisant Michael G. , Murali T. M. , Onufriev Alexey V.
Published: July 2008

Myoglobin is a globular protein involved in oxygen storage and transport. No consensus yet exists on the atomic level mechanism by which oxygen and other small nonpolar ligands move between the myoglobin's buried heme, which is the ligand binding site, and surrounding solvent. This study uses room temperature molecular dynamics simulations to provide a complete atomic level picture of ligand migration in myoglobin. Multiple trajectories—providing a cumulative total of 7 μs of simulation—are analyzed. Our simulation results are consistent with and tie together previous experimental findings. Specifically, we characterize: (
i
) Explicit full trajectories in which the CO ligand shuttles between the internal binding site and the solvent and (
ii
) pattern and structural origins of transient voids available for ligand migration. The computations are performed both in sperm whale myoglobin wild-type and in sperm whale V68F myoglobin mutant, which is experimentally known to slow ligand-binding kinetics. On the basis of these independent, but mutually consistent ligand migration and transient void computations, we find that there are two discrete dynamical pathways for ligand migration in myoglobin. Trajectory hops between these pathways are limited to two bottleneck regions. Ligand enters and exits the protein matrix in common identifiable portals on the protein surface. The pathways are located in the “softer” regions of the protein matrix and go between its helices and in its loop regions. Localized structural fluctuations are the primary physical origin of the simulated CO migration pathways inside the protein.
An
in vivo
gene deletion system for determining temporal requirement of bacterial virulence factors
Authors: Liu Yancheng , Gao Ping , Banga Simran , Luo Zhao-Qing
Published: July 2008

Analysis of phenotypes associated with specific mutants has been instrumental in determining the roles of a bacterial gene in a biological process. However, this technique does not allow one to address whether a specific gene or gene set is necessary to maintain such a process once it has been established. In the study of microbial pathogenesis, it is important but difficult to determine the temporal requirement of essential pathogenic determinants in the entire infection cycle. Here we report a Cre/
lox
P-based genetic system that allowed inducible deletion of specific bacterial genes after the pathogen had been phagocytosed by host cells. Using this system, we have examined the temporal requirement of the Dot/Icm type IV protein transporter of
Legionella pneumophila
during infection. We found that deletion of single essential
dot
/
icm
genes did not prevent the internalized bacteria from completing one cycle of intracellular replication. Further analyses indicate that the observed phenotypes were due to the high stability of the examined Dot/Icm protein. However, postinfection deletion within 8 h of the gene coding for the Dot/Icm substrate,
SdhA
, abolishes intracellular bacterial growth. This result indicates that the Dot/Icm transporter is important for intracellular bacterial growth after the initial biogenesis of the vacuole. Our study has provided a technical concept for analyzing the temporal requirement of specific bacterial proteins or protein complexes in infection or development.
Mass spectrometry reveals modularity and a complete subunit interaction map of the eukaryotic translation factor eIF3
Authors: Zhou Min , Sandercock Alan M. , Fraser Christopher S. , Ridlova Gabriela , Stephens Elaine , Schenauer Matthew R. , Yokoi-Fong Theresa , Barsky Daniel , Leary Julie A. , Hershey John W. , Doudna Jennifer A. , Robinson Carol V.
Published: July 2008

The eukaryotic initiation factor 3 (eIF3) plays an important role in translation initiation, acting as a docking site for several eIFs that assemble on the 40S ribosomal subunit. Here, we use mass spectrometry to probe the subunit interactions within the human eIF3 complex. Our results show that the 13-subunit complex can be maintained intact in the gas phase, enabling us to establish unambiguously its stoichiometry and its overall subunit architecture via tandem mass spectrometry and solution disruption experiments. Dissociation takes place as a function of ionic strength to form three stable modules eIF3(c:d:e:l:k), eIF3(f:h:m), and eIF3(a:b:i:g). These modules are linked by interactions between subunits eIF3b:c and eIF3c:h. We confirmed our interaction map with the homologous yeast eIF3 complex that contains the five core subunits found in the human eIF3 and supplemented our data with results from immunoprecipitation. These results, together with the 27 subcomplexes identified with increasing ionic strength, enable us to define a comprehensive interaction map for this 800-kDa species. Our interaction map allows comparison of free eIF3 with that bound to the hepatitis C virus internal ribosome entry site (HCV-IRES) RNA. We also compare our eIF3 interaction map with related complexes, containing evolutionarily conserved protein domains, and reveal the location of subunits containing RNA recognition motifs proximal to the decoding center of the 40S subunit of the ribosome.
MEF2C, a transcription factor that facilitates learning and memory by negative regulation of synapse numbers and function
Authors: Barbosa Ana C. , Kim Mi-Sung , Ertunc Mert , Adachi Megumi , Nelson Erika D. , McAnally John , Richardson James A. , Kavalali Ege T. , Monteggia Lisa M. , Bassel-Duby Rhonda , Olson Eric N.
Published: July 2008

Learning and memory depend on the activity-dependent structural plasticity of synapses and changes in neuronal gene expression. We show that deletion of the MEF2C transcription factor in the CNS of mice impairs hippocampal-dependent learning and memory. Unexpectedly, these behavioral changes were accompanied by a marked increase in the number of excitatory synapses and potentiation of basal and evoked synaptic transmission. Conversely, neuronal expression of a superactivating form of MEF2C results in a reduction of excitatory postsynaptic sites without affecting learning and memory performance. We conclude that MEF2C limits excessive synapse formation during activity-dependent refinement of synaptic connectivity and thus facilitates hippocampal-dependent learning and memory.
Complementary functions of ATM and H2AX in development and suppression of genomic instability
Authors: Zha Shan , Sekiguchi JoAnn , Brush James W. , Bassing Craig H. , Alt Frederick W.
Published: July 2008

Upon DNA damage, histone H2AX is phosphorylated by ataxia-telangiectasia mutated (ATM) and other phosphoinositide 3-kinase-related protein kinases. To elucidate further the potential overlapping and unique functions of ATM and H2AX, we asked whether they have synergistic functions in the development and maintenance of genomic stability by inactivating both genes in mouse germ line. Combined ATM/H2AX deficiency caused embryonic lethality and dramatic cellular genomic instability. Mechanistically, severe genomic instability in the double-deficient cells is associated with a requirement for H2AX to repair oxidative DNA damage resulting from ATM deficiency. We discuss these findings in the context of synergies between ATM and other repair factors.
Nitric Oxide Bioavailability in the Microcirculation: Insights from Mathematical Models
Authors: TSOUKIAS NIKOLAOS M.
Published: July 2008

Over the last 30 years nitric oxide (NO) has emerged as a key signaling molecule involved in a number of physiological functions, including in the regulation of microcirculatory tone. Despite significant scientific contributions, fundamental questions about NO's role in the microcirculation remain unanswered. Mathematical modeling can assist in investigations of microcirculatory NO physiology and address experimental limitations in quantifying vascular NO concentrations. The number of mathematical models investigating the fate of NO in the vasculature has increased over the last few years, and new models are continuously emerging, incorporating an increasing level of complexity and detail. Models investigate mechanisms that affect NO availability in health and disease. They examine the significance of NO release from nonendothelial sources, the effect of transient release, and the complex interaction of NO with other substances, such as heme‐containing proteins and reactive oxygen species. Models are utilized to test and generate hypotheses for the mechanisms that regulate NO‐dependent signaling in the microcirculation.
Chemokine Signaling to Lymphocyte Integrins Under Shear Flow
Authors: ALON RONEN , FEIGELSON SARA W.
Published: July 2008

The arrest of lymphocytes at target vascular sites depends on the rapid activation of their integrins by specialized endothelial chemokines. For over a decade, the mechanisms by which these chemokines trigger initial integrin‐mediated adhesiveness and subsequent adhesion strengthening and crawling over endothelial surfaces have been dissected in vitro using flow chamber setups. These studies revealed that lymph node chemokines and subsets of inflammatory chemokines, collectively termed “arrest chemokines,” can trigger the fastest measurable inside‐out integrin activation events. Recent studies indicate that shear forces applied on lymphocytes are instrumental in these rapid activation processes. Different GTPases have been implicated in these activation processes. As these enzymes contribute to successive integrin activation and redistribution processes in both early and prolonged contacts there is a growing need to dissect in vitro and validate in vivo specific signaling routes involved in early and late integrin activation events controlling lymphocyte arrest and their subsequent crawling to sites of diapedesis. In this article, we present an overview of both early and recent shear‐flow studies of integrin activation in lymphocytes and discuss future perspectives of integrin activation research in vitro and in vivo.
The Cochlear Pericytes
Authors: SHI XIAORUI , HAN WEIJIU , YAMAMOTO HIROSHI , TANG WENXUE , LIN XI , XIU RUIJUAN , TRUNE DENNIS R. , NUTTALL ALFRED L.
Published: July 2008

Objectives: Cochlear pericytes are not well characterized. The aim of this study was to further advance the characterization of cochlear pericyte location and distribution, with particular focus on pericyte‐related proteins on the capillaries of the cochlear lateral wall that are functionally integral to structure, contraction, and gap junction transport. Materials and Methods: Cochlear pericytes were identified by the immunofluorescence labeling of pericyte marker proteins, including alpha–smooth muscle actin (α‐SMA), desmin, Thy‐1, tropomyosin, and NG2, and by morphological identification, using fluorescence, electron, and differential interference contrast microscopy. Results: Pericytes were predominately found in the capillary network of the cochlear lateral wall, with considerable morphological heterogeneity across different types of microvessels. For example, pericytes on the vessels of the spiral ligament (V/SL) strongly expressed a gap junction protein, connexin 40, and were positive for α‐SMA, tropomyosin, and desmin. In contrast, pericytes on the vessels of the stria vascularis (V/SV) were positive for desmin, and were negative for α‐SMA and tropomyosin. Conclusions: The capillary networks of the cochlear lateral wall comprise a rich population of pericytes. These pericytes are morphologically heterogeneous, with protein expression potentially indicative of function.
Systems Biology of Vascular Endothelial Growth Factors
Authors: GABHANN FEILIM MAC , POPEL ALEKSANDER S.
Published: July 2008

Several cytokine families have roles in the development, maintenance, and remodeling of the microcirculation. Of these, the vascular endothelial growth factor (VEGF) family is one of the best studied and one of the most complex. Five VEGF ligand genes and five cell‐surface receptor genes are known in the human, and each of these may be transcribed as multiple splice isoforms to generate an extensive family of proteins, many of which are subject to further proteolytic processing. Using the VEGF family as an example, we describe the current knowledge of growth‐factor expression, processing, and transport in vivo. Experimental studies and computational simulations are being used to measure and predict the activity of these molecules, and we describe avenues of research that seek to fill the remaining gaps in our understanding of VEGF family behavior.
BioMAJ: a flexible framework for databanks synchronization and processing
Authors: Filangi Olivier , Beausse Yoann , Assi Anthony , Legrand Ludovic , Larré Jean-Marc , Martin Véronique , Collin Olivier , Caron Christophe , Leroy Hugues , Allouche David
Published: July 2008

Large- and medium-scale computational molecular biology projects require accurate bioinformatics software and numerous heterogeneous biological databanks, which are distributed around the world. BioMAJ provides a flexible, robust, fully automated environment for managing such massive amounts of data. The JAVA application enables automation of the data update cycle process and supervision of the locally mirrored data repository. We have developed workflows that handle some of the most commonly used bioinformatics databases. A set of scripts is also available for post-synchronization data treatment consisting of indexation or format conversion (for NCBI blast, SRS, EMBOSS, GCG, etc.). BioMAJ can be easily extended by personal homemade processing scripts. Source history can be kept via html reports containing statements of locally managed databanks.

Availability:  http://biomaj.genouest.org. BioMAJ is free open software. It is freely available under the CECILL version 2 license.

Contact:  biomaj@genouest.org
Back to the future: using landscape ecology to understand changing patterns of land use in Canada, and its effects on the sustainability of coastal ecosystems
Authors: Mercer Clarke Colleen S. L. , Roff John C. , Bard Shannon M.
Published: July 2008

Mercer Clarke, C. S. L., Roff, J. C., and Bard, S. M. 2008. Back to the future: using landscape ecology to understand changing patterns of land use in Canada, and its effects on the sustainability of coastal ecosystems. – ICES Journal of Marine Science, 65: 1534–1539. In Canada, concerns are mounting that the coastal environments may be more affected by human activities than is evidenced by current monitoring and assessment of environmental quality. Holistically orientated approaches to coastal management have concluded that indicators of coastal sustainability must include a wider array of factors that go beyond marine ecosystem health to include the health and well-being of coastal terrestrial environments and human communities. Research is needed to bridge the disciplinary and jurisdictional barriers that hamper better understanding of the relationships between terrestrial and marine ecosystems, and to help recognize the role of humans as both a contributing and an affected species in the coastal ecotone. Our examination of past and current knowledge of conditions along the Atlantic shore of Nova Scotia led us to challenge the predominant view that all is well along Canadian coasts. Using an interdisciplinary approach derived from landscape ecology, we examined international, national, and local efforts to assess management indicators against factors that gauge their relevance to marine- and land-development planning and management. We propose a new context for indicators, one that challenges scientists to provide decision-makers with information that can be used to drive social change, avoiding or mitigating human activities and sustaining coastal ecosystems.
Pollution fingerprints in eels as models for the chemical status of rivers
Authors: Belpaire C. , Goemans G. , Geeraerts C. , Quataert P. , Parmentier K.
Published: July 2008

Belpaire, C., Goemans, G., Geeraerts, C., Quataert, P., and Parmentier, K. 2008. Pollution fingerprints in eels as models for the chemical status of rivers. – ICES Journal of Marine Science, 65: 1483–1491. The 2006 EU Water Framework Directive (WFD) proposed the monitoring of a selection of priority substances in the aquatic phase, including lipophilic substances. However, there are strong arguments for measuring lipophilic substances in biota. Yellow eel is a good candidate because it is widespread, sedentary, and accumulates many lipophilic substances in its muscle tissue. Several authors have described the indicative value of measured concentrations, yet few studies have investigated to what extent the spectrum of contaminants present characterizes the local environmental pollution pressure. To evaluate the value of the pollution profile of an eel as a fingerprint of the chemical status of the local environment, two datasets were selected from the Flemish Eel Pollutant Network database. The pollution profiles in individual eels along a river (even at distances <5 km) proved to be significantly different. Analysis of pooled contaminant data from multiple sites and sampling years within rivers allows characterization of river-specific chemical pressures. These results highlight the usefulness of eels as bio-indicators for monitoring pollution with lipophilic chemicals, such as polychlorinated biphenyls and organochlorine pesticides, in rivers. As such, eels may be used effectively within the monitoring programme for a selection of priority substances referred to in the WFD.
First Report of Powdery Mildew of Chickpea (Cicer arietinum) Caused by Leveillula taurica in Washington State
Authors: Attanayake K. P. R. N. , Glawe D. A. , McPhee K. E. , Dugan F. M. , Chen W.
Published: July 2008

In Oct. 2007, powdery mildew was found in chickpea fields in an experimental farm near Pullman, Whitman County, Washington. Although disease signs were observed on all chickpea cultivars in the fields, high incidence was seen only on cvs. Dwelley and Spanish White. To our knowledge this is the first record of powdery mildew caused by Leveillula taurica on chickpea in WA. The pathogen has also been reported from chickpea in California and elsewhere, e.g., Ethiopia, India, Iran, Morocco, Pakistan, Sudan, Turkey, and the former USSR.

Accepted for publication 4 May 2008. Published 2 July 2008.
Amphibian malformations and inbreeding
Authors: Williams Rod N , Bos David H , Gopurenko David , DeWoody J.Andrew
Published: July 2008

Inbreeding may lead to morphological malformations in a wide variety of taxa. We used genetic markers to evaluate whether malformed urodeles were more inbred and/or had less genetic diversity than normal salamanders. We captured 687 adult and 1259 larval tiger salamanders (
Ambystoma tigrinum tigrinum
), assessed each individual for gross malformations, and surveyed genetic variation among malformed and normal individuals using both cytoplasmic and nuclear markers. The most common malformations in both adults and larvae were brachydactyly, ectrodactyly and polyphalangy. The overall frequency of adults with malformations was 0.078 compared to 0.081 in larval samples. Genetic diversity was high in both normal and malformed salamanders, and there were no significant difference in measures of inbreeding (
f
and
F
), allele frequencies, mean individual heterozygosity or mean internal relatedness. Environmental contaminants or other extrinsic factors may lead to genome alternations that ultimately cause malformations, but our data indicate that inbreeding is not a causal mechanism.
The modelling of avian visual perception predicts behavioural rejection responses to foreign egg colours
Authors: Cassey Phillip , Honza Marcel , Grim Tomas , Hauber Mark E
Published: July 2008

How do birds tell the colours of their own and foreign eggs apart? We demonstrate that perceptual modelling of avian visual discrimination can predict behavioural rejection responses to foreign eggs in the nest of wild birds. We use a photoreceptor noise-limited colour opponent model of visual perception to evaluate its accuracy as a predictor of behavioural rates of experimental egg discrimination in the song thrush
Turdus philomelos
. The visual modelling of experimental and natural eggshell colours suggests that photon capture from the ultraviolet and short wavelength-sensitive cones elicits egg rejection decisions in song thrushes, while inter-clutch variation of egg coloration provides sufficient contrasts for detecting conspecific parasitism in this species. Biologically realistic sensory models provide an important tool for relating variability of behavioural responses to perceived phenotypic variation.
Female bushcrickets fuel their metabolism with male nuptial gifts
Authors: Voigt Christian C , Kretzschmar Antje S , Speakman John R , Lehmann Gerlind U.C
Published: July 2008

In many arthropods, such as bushcrickets, males donate protein-rich nuptial gifts—so-called spermatophores—to females, which females ingest while the sperm enter the female's reproductive tract. Previously, it was shown that females route spermatophore nutrients over the course of hours and days to egg production or body synthesis. We investigated whether female bushcrickets fuel their metabolism with spermatophores immediately after consumption. We fed two male groups diets that were either enriched or depleted in
13
C, and then tracked the isotopic changes in exhaled breath in female bushcrickets after spermatophore consumption. Within 3 hours, the stable carbon isotope ratio (
δ
13
C) of female breath converged on the ratio of the male donor of the nuptial gift. This supports the idea that females quickly routed nutrients to metabolism, receiving immediate benefits from spermatophore feeding.
Multiscale investigation of the functional properties of the human femur
Authors: Cristofolini Luca , Taddei Fulvia , Baleani Massimiliano , Baruffaldi Fabio , Stea Susanna , Viceconti Marco
Published: July 2008

The mechanical strength of human bones has often been investigated in the past. Bone failure is related to musculoskeletal loading, tissue properties, bone metabolism, etc. This is intrinsically a multiscale problem. However, organ-level performance in most cases is investigated as a separate problem, incorporating only part (if any) of the information available at a higher scale (body level) or at a lower one (tissue level, cell level). A multiscale approach is proposed, where models available at different levels are integrated. A middle-out strategy is taken: the main model to be investigated is at the organ level. The organ-level model incorporates as an input the outputs from the body-level (musculoskeletal loads), tissue-level (constitutive equations) and cell-level models (bone remodelling). In this paper, this approach is exemplified by a clinically relevant application: fractures of the proximal femur. We report how a finite-element model of the femur (organ level) becomes part of a multiscale model. A significant effort is related to model validation: a number of experiments were designed to quantify the model's sensitivity and accuracy. When possible, the clinical accuracy and the clinical impact of a model should be assessed. Whereas a large amount of information is available at all scales, only organ-level models are really mature in this perspective. More work is needed in the future to integrate all levels fully, while following a sound scientific method to assess the relevance and validity of such an integrated model.
DNA methylation and heterochromatinization in the male-specific region of the primitive Y chromosome of papaya
Authors: Zhang Wenli , Wang Xiue , Yu Qingyi , Ming Ray , Jiang Jiming
Published: July 2008

Sex chromosomes evolved from autosomes. Recombination suppression in the sex-determining region and accumulation of deleterious mutations lead to degeneration of the Y chromosomes in many species with heteromorphic X/Y chromosomes. However, how the recombination suppressed domain expands from the sex-determining locus to the entire Y chromosome remains elusive. The Y chromosome of papaya (Carica papaya) diverged from the X chromosome approximately 2–3 million years ago and represents one of the most recently emerged Y chromosomes. Here, we report that the male-specific region of the Y chromosome (MSY) spans ∼13% of the papaya Y chromosome. Interestingly, the centromere of the Y chromosome is embedded in the MSY. The centromeric domain within the MSY has accumulated significantly more DNA than the corresponding X chromosomal domain, which leads to abnormal chromosome pairing. We observed four knob-like heterochromatin structures specific to the MSY. Fluorescence in situ hybridization and immunofluorescence assay revealed that the DNA sequences associated with the heterochromatic knobs are highly divergent and heavily methylated compared with the sequences in the corresponding X chromosomal domains. These results suggest that DNA methylation and heterochromatinization play an important role in the early stage of sex chromosome evolution.
Identification ofPlasmodium falciparumRhopH3 protein peptides that specifically bind to erythrocytes and inhibit merozoite invasion
Authors: Pinzón Carlos Giovanni , Curtidor Hernando , Reyes Claudia , Méndez David , Patarroyo Manuel Elkin
Published: July 2008

The identification of sequences involved in binding to erythrocytes is an important step for understanding the molecular basis of merozoite–erythrocyte interactions that take place during invasion of thePlasmodium falciparummalaria parasite into host cells. Several molecules located in the apical organelles (micronemes, rhoptry, dense granules) of the invasive‐stage parasite are essential for erythrocyte recognition, invasion, and establishment of the nascent parasitophorous vacuole. Particularly, it has been demonstrated that rhoptry proteins play an important role in binding to erythrocyte surface receptors, among which is thePfRhopH3 protein, which triggers important immune responses in patients from endemic regions. It has also been reported that anti‐RhopH3 antibodies inhibit in vitro invasion of erythrocytes, further supporting its direct involvement in erythrocyte invasion processes. In this study,PfRhopH3 consecutive peptides were synthesized and tested in erythrocyte binding assays for identifying those regions mediating binding to erythrocytes. FourteenPfRhopH3 peptides presenting high specific binding activity were found, whose bindings were saturable and presented nanomolar dissociation constants. These high‐activity binding peptides (HABPs) were characterized by having α‐helical structural elements, as determined by circular dichroism, and having receptors of a possible sialic acid‐dependent and/or glycoprotein‐dependent nature, as evidenced in enzyme‐treated erythrocyte binding assays and further corroborated by cross‐linking assay results. Furthermore, these HABPs inhibited merozoite in vitro invasion of normal erythrocytes at 200 μM by up to 60% and 90%, suggesting that some RhopH3 protein regions are involved in theP. falciparumerythrocyte invasion.
Structural basis for the activation of FGFR by NCAM
Authors: Kochoyan Arthur , Poulsen Flemming M. , Berezin Vladimir , Bock Elisabeth , Kiselyov Vladislav V.
Published: July 2008

The fibroblast growth factor receptor (FGFR) can be activated through direct interaction with the neural cell adhesion molecule (NCAM). The extracellular part of the FGFR consists of three immunoglobulin‐like (Ig) modules, and that of the NCAM consists of five Ig and two fibronectin type III (F3) modules. NCAM–FGFR interactions are mediated by the third FGFR Ig module and the second NCAM F3 module. Using surface plasmon resonance and nuclear magnetic resonance analyses, the present study demonstrates that the second Ig module of FGFR also is involved in binding to the NCAM. The second Ig module residues involved in binding were identified and shown to be localized on the “opposite sides” of the module, indicating that when NCAMs are clustered (e.g., due to homophilic binding), high‐affinity FGFR binding sites may be formed by the neighboring NCAMs.
Efficient production of membrane‐integrated and detergent‐soluble G protein‐coupled receptors inEscherichia coli
Authors: Link A. James , Skretas Georgios , Strauch Eva‐Maria , Chari Nandini S. , Georgiou George
Published: July 2008

G protein‐coupled receptors (GPCRs) are notoriously difficult to express, particularly in microbial systems. Using GPCR fusions with the green fluorescent protein (GFP), we conducted studies to identify bacterial host effector genes that result in a general and significant enhancement in the amount of membrane‐integrated human GPCRs that can be produced inEscherichia coli. We show that coexpression of the membrane‐bound AAA+ protease FtsH greatly enhances the expression yield of four different class I GPCRs, irrespective of the presence of GFP. Using this new expression system, we produced 0.5 and 2 mg/L of detergent‐solubilized and purified full‐length central cannabinoid receptor (CB1) and bradykinin receptor 2 (BR2) in shake flask cultures, respectively, two proteins that had previously eluded expression in microbial systems.
Forest history of the last 12 000 years based on plant macrofossil analysis of sediment from Marion Lake, southwestern British Columbia
Authors: Wainman Newton , Mathewes Rolf W.
Published: July 2008

The forest history around Marion Lake in southwestern British Columbia is reconstructed using plant macrofossil analysis. A comparison with a previous reconstruction based on pollen and spore analysis reveals a good correspondence between pollen and macrofossil zones. Significant improvements in the reconstruction of forest history are possible by combining the study of pollen and macrofossils. Thuja plicata macrofossils do not appear at Marion Lake until 6000 BP, contradicting previous suggestions of red cedar presence as early as 10 000 BP. Although not common at present, Taxus brevifolia may have been an important component of the forest prior to the arrival of Thuja. Fluvial input of macrofossils is important at Marion Lake. Charcoal also appears to enter the lake primarily during periods of high runoff and erosion in the watershed, suggesting the need for caution in the interpretation of charcoal data from stream-fed lakes. Increases in total influx coincide with evidence for increased precipitation after 7000 BP. Marked reductions in macrofossil influx coincide with periods of peat deposition upstream from the present lake. Relative percentages of conifer needles are unaffected by changes in influx.
Stromatographium and Acrostroma gen.nov.: two tropical hyphomycete genera with distinctive synnema anatomies
Authors: Seifert Keith A.
Published: July 2008

The type species of two monotypic anamorph genera of Hyphomycetes are described and illustrated, and their conidiomatal anatomies are contrasted. Stromatographium stromaticum, the anamorph of Fluviostroma wrightii (Ascomycetes, Sphaeriales), has conidiomata referred to as amphistromatic synnemata, with pseudoparenchymatous stromata at both ends of the stipe. Stromatostilbella is considered a synonym of Stromatographium v. Höhnel. Acrostroma annellosynnema gen. et sp. nov. (teleomorph unknown) produces conidiomata termed acrostromatic synnemata, because they have an apical pseudoparenchymatous stroma from which conidiophores arise.
The role of Sphagnum fimbriatum in secondary succession in a road salt impacted bog
Authors: Wilcox Douglas A. , Andrus Richard E.
Published: July 2008

Secondary succession of Sphagnum mosses was studied for 7 years along a belt transect in a bog that had been impacted by sodium chloride highway deicing salts. Laboratory studies on Sphagnum fimbriatum Wils., the dominant recolonizing species, were conducted to determine its salt tolerance level and ability to reproduce from spores and fragments across a salt gradient. Vegetative reproduction was also compared with that of four other recolonizing species. Sphagnum fimbriatum represented a high percentage of all recolonizing Sphagnum and generally began growing on low hummocks in quadrats where the salt content of the interstitial peat pore waters had dropped to about 300 mg/L as chloride. This salt concentration was also found to be the basic tolerance limit for mature plants and reproducing spores and fragments. The success of Sphagnum fimbriatum as a pioneer species seems to be associated with its prolific production and probable dispersal of spores, its superior vegetative reproduction, its tolerance of mineralized waters, and its ability to grow on hummocks out of direct contact with mineralized waters.
Processes of understory seedling recruitment 1 year after prescribed fire in an Arizona ponderosa pine community
Authors: Vose James M. , White Alan S.
Published: July 2008

We monitored seed rain, buried seed germination, and vegetative reproduction to determine the processes of understory species seedling recruitment after prescribed fire in an Arizona ponderosa pine (Pinus ponderosa) stand. Stands were burned with both backing and strip head fires. These fires were restricted to surface fuels, with fuel consumption ranging from 25 to 95% and total heat yield ranging from 1 600 to 42 082 kJ/m2. We identified seed rain from surviving plants the year after burning, as well as residual seeds surviving the burn, as being the major contributors of propagules for recruitment of herbaceous seedlings. Several seedlings were present in both the early-spring and late-fall inventory. We hypothesize that the early recruitment was mainly due to germination of seeds immediately after burning or early the next spring and that seed rain from surviving plants provided propagules for seedlings detected in the late-fall inventory. The pattern of seed rain reflected the phenologies of cool-season and warm-season plants. Buried seed populations were not found to be an important source of new seedlings. Ceanothus fendleri was the only species to sprout prolifically after burning.
An investigation of chromosome numbers in the genus Brachiaria (Poaceae: Paniceae) in relation to morphology and taxonomy
Authors: Basappa G. P. , Muniyamma M. , Chinnappa C. C.
Published: July 2008

Determinations of chromosome number and morphological studies of 260 populations, belonging to 32 taxa, of the genus Brachiaria from the Indian subcontinent reveal that all sexually reproducing taxa have no chromosome races. Six agamic taxa, viz., B. brizantha var. brizantha (n = 27), B. brizantha var. ciliata (n = 18), B. decumbens (n = 18), B. hybrida (n = 27), B. mutica (n = 18), and B. setigera var. albistyla (n = 14), have consistently shown uniformity in chromosome numbers, based on x = 7, 8, and 9. Brachiaria setigera var. setigera, a genetically unstable apomict, is the only taxon that tends to have a heteroploid series (n = 16, 17, 18, 21, and 32). The population of B. setigera var. setigera with n = 17 is based on a secondary base number of x = 17. There are 6 diploids, 20 tetraploids, 5 hexaploids, and 3 octoploids in the genus. Aneuploidy and triploidy are characteristically absent in the genus, although their plausible existence in the B. setigera complex cannot be ruled out. In several species certain previously reported chromosome numbers that deviate from the present study are found to be the result of erroneous identifications or the result of taxonomically complex situations such as those found in B. brizantha, the B. distachya complex, and the B. ramosa complex.
Mesocyparis borealis gen. et sp. nov.: fossil Cupressaceae from the early Tertiary of Saskatchewan, Canada
Authors: McIver E. E. , Basinger J. F.
Published: July 2008

Fossil cedar foliage of the Cupressinocladus interruptus type, with associated seeds and cones, is locally abundant in Paleocene deposits of the Ravenscrag Formation, southwestern Saskatchewan, Canada. Vegetative remains of this type occur frequently in early Tertiary plant assemblages throughout the northern hemisphere, indicating that this now extinct cedar was once widespread. For the first time this cedar can be described on the basis of both vegetative and reproductive morphology. Foliage is frond-like with a characteristic opposite branching pattern. Seed cones are globose and woody and bear four equal and decussate scales with prominent umbos. Seeds bear large, equal, semicircular wings. The fossil cedar appears most closely related to extant Cupressaceae such as Thuja, Chamaecyparis, and Heyderia. Foliage closely resembles that of Thuja, while cones are most similar to those of Chamaecyparis. The fossil differs sufficiently in foliage and seed cone structure to preclude assignment to an extant genus and is here assigned to Mesocyparis borealis gen. et sp. nov. Similarities among such extant genera as Thuja, Chamaecyparis, Heyderia, and Thujopsis and the fossil Mesocyparis borealis suggest that all may belong to a single natural group. Furthermore, this group may be more closely related to the southern hemispheric genera Libocedrus, Papuacedrus, and Austrocedrus than present classification schemes imply. Our examination of the Cupressaceae indicates that a revision of present systems of classification is required to accommodate evidence from both extant and extinct cedars.
Why is Rhinanthus minor (Scrophulariaceae) such a good invader?
Authors: Hulst Robert Van , Shipley Bill , Thériault Andrée
Published: July 2008

Rhinanthus minor L. is an annual grassland hemiparasite often found where other annuals are rare or absent. In addition to its invasive abilities, R. minor has other characteristics seldom found in annuals: virtual lack of a seed bank; few seeds per plant; seeds too big to be readily dispersed under natural conditions; and a Deevey type I or II survivorship curve. A combination of correlative and experimental studies was performed to investigate the variables influencing fecundity and survivorship in R. minor. Fecundity is positively correlated with surrounding vegetation biomass and negatively with R. minor density. Survivorship is negatively correlated with surrounding vegetation biomass and with R. minor density. Presumably, R. minor is an effective invader in relatively unproductive grassland because its finite rate of increase is a nonlinear function of the biomass of the surrounding vegetation, being maximized when the surrounding vegetation is dense enough to allow effective root parasitism (increasing R. minor fecundity) but not so dense that young R. minor plants are outcompeted for light (decreasing R. minor survivorship).
A double-stranded RNA mycovirus from the maize rust Puccinia sorghi
Authors: Pryor A. , Boelen M. G.
Published: July 2008

Evidence is presented for the occurrence of a double-stranded RNA (dsRNA) mycovirus in germinated uredospores of the maize rust fungus Puccinia sorghi Schw. Isometric particles of about 40 nm diameter copurified with six or seven dsRNAs ranging in size from about 6500 to approximately 500 base pairs. Several polypeptide subunits with a molecular mass of around 89 000 copurified with the mycovirus. Similar particles or dsRNA were not observed in the related maize rust Puccinia polysora.
An undescribed species of Microascus from the Cave of Ramioul
Authors: Malloch David , Hubart J. M.
Published: July 2008

An isolate of a fungus from decaying meat in the Cave of Ramioul, Belgium, is presented as the undescribed species Microascus caviariformis sp.nov. It grows fastest and reproduces most abundantly on media low in soluble sugars and appears to be strongly adapted to growth on proteinaceous substrata at temperatures below 25 °C. Production of a prolific and typical Scopulariopsis anamorph and relatively rapid growth on standard media are typical of most Microascus species, while its very narrow ascospores and slowly developing ascomatal ostiola are more characteristic of the genus Pithoascus. The apparent presence of a germ pore in the ascospores suggests the former genus to be more appropriate.
Morphometric analysis of western North American Antennaria (Asteraceae: Inuleae). I. Sexual species of sections Alpinae, Dioicae, and Plantaginifoliae
Authors: Bayer Randall J.
Published: July 2008

Eight sexual species of Antennaria Gaertner from sections Alpinae, Dioicae, and Plantaginifoliae have been recognized based on morphometric analyses such as principal components and cluster analyses. These taxa include A. aromatica Evert (Alpinae), A. corymbosa Nelson (Dioicae), A. marginata Greene (Dioicae), A. media Greene (Alpinae), A. microphylla Rydb. (Dioicae), A. racemosa Hook. (Plantaginifoliae), A. rosulata Rydb. (Dioicae), and A. umbrinella Rydb. (Dioicae). Taxa having both diploid and polyploid cytotypes are A. aromatica, A. marginata, A. media, A. microphylla, and A. umbrinella, whereas A. corymbosa, A. racemosa, and A. rosulata are strictly sexually reproducing diploids.
Four parameters of the wound response of loblolly and shortleaf pines to inoculation with the blue-staining fungus associated with the southern pine beetle
Authors: Cook Stephen P. , Hain Fred P.
Published: July 2008

The wound response of loblolly, Pinus taeda L., and shortleaf, P. echinata Mill., pine was examined for 14 days following wounding and inoculation of the trees with Ceratocystis minor (Hedgecock) Hunt, a fungal associate of the southern pine beetle, Dendroctonus frontalis Zimmermann. Lesion length increased at a constant rate during June, while during July there was an initially rapid lesion formation followed by a leveling off for both tree species. Lesion enlargement occurred faster from days 2 through 7 in July for both species, and at the end of the 14-day study periods, the loblolly pines had a longer average lesion length than did the shortleaf pines during both months. During June, there was an initial increase in resin flow rate followed by a decrease in resin flow rate for several days and then an increased resin flow rate to levels similar to or above the rate measured prior to wounding. During July, the initial increase in resin flow rate following inoculation was not observed. Average soluble-sugar content decreased and monoterpene concentration increased in the lesion inner bark tissue. Inner bark monoterpene composition also changed, with the percentage of α-pinene increasing or remaining unchanged in loblolly pine and decreasing in the shortleaf pine. The observed differences in tree response to fungal invasion may be important in determining if an individual can repel or impede invasion by D. frontalis at different times during the summer.
Fossil chrysophycean cyst flora in a small meromictic lake in southern Ontario, and its paleoecological interpretation
Authors: Rybak Mariusz , Rybak Izabela , Dickman Mike
Published: July 2008

Fossil chrysophycean cysts were identified and counted from the laminated sediment core from Crawford Lake. Thirty-two morphotypes have been described, most of them for the first time. The detailed description of the cysts is presented, including scanning electron photomicrographs. The abundance of certain morphotypes appears to be related to lake paleoproductivity. On this basis, fossil cyst flora have been divided into three characteristic groups: eutrophic–, mesotrophic–, and oligotrophic–meromictic forms. Our data demonstrate that chrysophycean cyst distribution can reflect lake conditions and, therefore, are potentially useful in paleoecological studies.
Ontogénie des périthèces d'Endocarpon pusillum (Pyrénolichen, Verrucariacées)
Authors: Wagner Jean
Published: July 2008

The comparative ontogeny of perithecia of numerous Verrucariaceae indicates that species studied to date show a peculiar, verrucariacean, stage. It is distinguished, at the time of perithecial cavity aperture opening, by short periphysoids and a domelike sporophytic apparatus. The development and structure of the perithecia of Endocarpon pusillum Hedw. are of the ascolocular type. This species is related to the genus Verrucaria, but differs from the genus Dermatocarpon, especially Dermatocarpon miniatum (L.) Mann.
Morphological variation within and among six populations of Trillium erectum in southern Ontario
Authors: Ringius Gordon S. , Chmielewski Jerry G.
Published: July 2008

Phenotypic variation within populations and among populations was examined in six populations of Trillium erectum from southern Ontario. The general symmetry of the flower was confirmed, although there was a tendency for the lower petals and sepals to be longer than the upper ones. Within populations, variation related to the overall expansion of the aerial shoot after emergence from the soil accounted for most of the variation. However, the expansion of the shoot was not uniform and independent growth components were found for the floral and vegetative variables. Only about one-third of the variation in floral variables was dependent on plant size. Also, within the flower, anthers, and filaments varied independently. Among-population differentiation was high and appeared to be determined by complex relationships among variables that are unique to each population. Several variables showed a correlation with underlying bedrock: populations located on Paleozoic limestone consist of plants that are smaller than those in populations located on Precambrian rocks. Whether the correlation between plant size and parental bedrock is causal is unknown.
Cytogeography of the Solidago spathulata–glutinosa complex (Compositae: Astereae)
Authors: Ringius Gordon S. , Semple John C.
Published: July 2008

One hundred and eight new chromosome counts are reported for the Solidago spathulata–glutinosa complex: 49 diploids (2n = 18) and 59 tetraploids (2n = 36). Only diploids are known in S. spathulata, which occurs along the Pacific coast from southern California to northern Oregon. Diploids, tetraploids, and one hexaploid are known in S. glutinosa, which occurs across North America. Solidago glutinosa ssp. glutinosa is composed of diploids only and is widespread in the Rocky Mountains from Mexico to Alaska and across the Canadian prairies. It also occurs disjunctly on the northern shores of Lake Superior and Lake Huron and farther east on the Gaspé Peninsula in Quebec. Solidago glutinosa ssp. glutinosa var. chlorolepis was found to be diploid (first report). Tetraploids of S. glutinosa ssp. randii were found in scattered locations in northeastern North America and around most of the upper Great Lakes, where they occur sympatrically with diploid populations of ssp. glutinosa. A single hexaploid population of ssp. randii was reported previously from West Virginia; no hexaploids were encountered in this study.
Cryptic seed abortion and the estimation of ovule fertilization
Authors: Nakamura Robert R. , Stanton Maureen L.
Published: July 2008

In a natural population of Raphanus sativus L. 41% of all fertilized ovules aborted before seed maturation. However, in mature fruits over 75% of the abortion was undetected. The cryptic abortion of developing seeds was likely due to the early time of abortion and the corky nature of the pericarp. The results are important for the accurate measurement of ovule fertilization and seed abortion in ecological studies of plant reproduction.
Predicting deposition of debris flows in mountain channels
Authors: Benda Lee E. , Cundy Terrance W.
Published: July 2008

An empirical model for predicting deposition of coarse-textured debris flows in confined mountain channels is developed based on field measurements of 14 debris flows in the Pacific Northwest, U.S.A. The model uses two criteria for deposition: channel slope (less than 3.5°) and tributary junction angle (greater than 70°). The model is tested by predicting travel distances of 15 debris flows in the Oregon Coast Range and six debris flows in the Washington Cascades, U.S.A. The model is further tested on 44 debris flows in two lithological types in the Oregon Coast Range using aerial photos and topographic maps; on these flows only the approximate travel distance is known. The model can be used by resource professionals to identify the potential for impacts from debris flows. Key words: debris flow, deposition, travel, erosion.