bluuebunny/crossref_metadata_2025 huggingface dataset:
The response of plant diversity to ecosystem retrogression: evidence from contrasting long‐term chronosequences
Authors: A. Wardle David , D. Bardgett Richard , R. Walker Lawrence , A. Peltzer Duane , Lagerström Anna
Published: September 2007

Following catastrophic disturbances, succession and vegetation development occur, but in the prolonged absence of these disturbances a decline (retrogressive) phase follows in which nutrient availability and tree biomass declines considerably. We measured plant diversity across six long‐term chronosequences that each included retrogressive stages in Australia, New Zealand, Alaska, Hawaii and Sweden. In contrast to theories predicting negative or hump‐shaped responses of tree diversity to biomass or soil fertility, tree species richness often peaked coincidentally with tree basal area (a surrogate of tree biomass), and declined during retrogression. Similar patterns were found regardless of whether or not species richness estimates were rarefraction‐adjusted to correct for variation in stem densities across plots. The Shannon‐Weiner diversity index sometimes showed the same pattern, but in two chronosequences was least when tree basal area peaked; this was driven by the domination of total basal area by single tree species in both cases. The decline in tree diversity during retrogression was often associated with reduced relative amounts of total phosphorus in soil. In contrast, total vascular plant species richness often increased during retrogression. These results demonstrate that forests with high tree diversity and biomass do not persist indefinitely in the long‐term absence of catastrophic disturbance, and that similar patterns occur across the boreal, temperate and subtropical zones.
Modeling species distributions by breaking the assumption of self‐similarity
Authors: Hui Cang , A. McGeoch Melodie
Published: September 2007

Species distributions are commonly measured as the number of sites, or geographic grid cells occupied. These data may then be used to model species distributions and to examine patterns in both intraspecific and interspecific distributions. Harte et al. (1999) used a model based on a bisection rule and assuming self‐similarity in species distributions to do so. However, this approach has also been criticized for several reasons. Here we show that the self‐similarity in species distributions breaks down according to a power relationship with spatial scales, and we therefore adopt a power‐scaling assumption for modeling species occupancy distributions. The outcomes of models based on these two assumptions (self‐similar and power‐scaling) have not previously been compared. Based on Harte's bisection method and an occupancy probability transition model under these two assumptions (self‐similar and power‐scaling), we compared the scaling pattern of occupancy (also known as the area‐of‐occupancy) and the spatial distribution of species. The two assumptions of species distribution lead to a relatively similar interspecific occupancy frequency distribution pattern, although the spatial distribution of individual species and the scaling pattern of occupancy differ significantly. The bimodality in occupancy frequency distributions that is common in species communities, is confirmed to a result for certain mathematical and statistical properties of the probability distribution of occupancy. The results thus demonstrate that the use of the bisection method in combination with a power‐scaling assumption is more appropriate for modeling species distributions than the use of a self‐similarity assumption, particularly at fine scales.
Any way the wind blows ‐ frequent wind dispersal drives species sorting in ephemeral aquatic communities
Authors: Vanschoenwinkel Bram , Gielen Saïdja , Seaman Maitland , Brendonck Luc
Published: September 2007

Despite an upsurge of interest in spatial interactions between communities and in the impact of dispersal on ecological and evolutionary processes, dispersal patterns and dynamics in natural metacommunities remain poorly understood. Although passive aerial dispersal of freshwater invertebrates is generally accepted, the frequency and relative importance of wind as a vector is still subject of considerable debate. We assessed the importance of wind dispersal in an invertebrate metacommunity in a cluster of 36 temporary rock pools on an isolated mountaintop in South Africa. Wind dispersal was quantified every four days using nine windsocks (about 1.5 m above rock base), placed in the field during one month. Distance to the nearest pool varied from 2 up to 16 m. Wind direction and speed were monitored for the entire period. About 850 propagules (mostly resting eggs) of 17 taxa were captured. The presence of water in the pools (level of exposure of the dormant propagule bank) and the dominant wind direction were the key factors affecting the yield. Wind speed was much less important.

Our results suggest that wind dispersal of propagules from temporary aquatic systems is more frequent than previously thought. This may stabilise the metacommunity by mediating gene flow among populations and facilitating rapid (re)colonisation of patches. On the other hand, wind erosion of the dormant propagule bank may lead to egg bank depletion and local extinction.

The measured frequent wind dispersal most likely fuels strong species sorting processes ultimately shaping the structure of the local communities as observed in an earlier study. To elucidate the link between local dispersal rates and their contribution to long range dispersal is a major challenge for future research on aerial dispersal of aquatic invertebrates.
Effect of Strain Rate on the Dynamic Hardness in Metals
Authors: Almasri Amin H. , Voyiadjis George Z.
Published: September 2007

Traditionally, the hardness of materials is determined from indentation tests at low loading rates (static). However, considerably less work has been conducted in studying the dynamic hardness of materials using relatively high loading rates. In the present work, two models are used to predict strain rate dependency in hardness. The first model is a power law expression that is based on the dependence of the yield stress on the strain rate. This model is relatively simple in implementation, and it is quite easy to determine its parameters from simple uniaxial experiments. The second model is a micromechanical based model using Taylor’s hardening law. It utilizes the behavior of dislocation densities at high strain rates in metals in order to relate dynamic hardness to strain rates. The latter model also accounts for any changes in temperature that could exist. A finite element is also run and compared with the two models proposed in this work. Results from both models are compared with available experimental results for oxygen-free high-conductivity copper and 1018 cold rolled steel, and both models show reasonably good agreement with the experimental results.
Chloride Content Effect on the Corrosion Fatigue Properties of Superduplex Stainless Steels
Authors: Gironès A. , Anglada M. , Mateo A.
Published: September 2007

The corrosion fatigue performance of a superduplex stainless steel in two different chloride-bearing solutions (30g∕l and 60g∕lNaCl) is explored in the present paper. Fatigue life results and surface damage analysis show a strong influence of the applied strain amplitude, as well as of the chloride content, on the cyclic response. Moreover, there is an interaction between both factors because corrosion fatigue mechanisms at low and high strain amplitudes are not comparable, since ferrite is only fully plastically active at high strains. Whereas a detrimental effect of the 30g∕lNaCl solution on the fatigue strength is observed, longer fatigue lives were attained in 60g∕lNaCl solution, even longer than in air. Surface damage inspection and residual solutions analysis support a critical anodic dissolution rate, which would act as a polishing effect, as the main reason for this unexpected result.
Effect of Nozzle-Traveling Velocity on Oil Cavitation Jet Peening of Aluminum Alloy, AA 6063-T6
Authors: Grinspan A. Sahaya , Gnanamoorthy R.
Published: September 2007

A new surface modification process was developed to introduce compressive residual stresses at the surface of components. In this process, instead of oil droplets a high-velocity cavitation jet (cloud of oil bubbles) impinges on the surface of the component to be peened. The impact pressure generated during implosion of cavitation bubbles causes severe plastic deformation at the surface. Consequently, beneficial compressive stresses are developed at the surface. In order to find the potential of this process, aluminum alloy AA6063-T6 specimens were peened at a constant cavitation number with various nozzle-traveling velocities. Residual stress induced by oil jet cavitation peening was measured using X-ray diffraction. Oil cavitation jet peening results in a smooth and hard surface. The developed compressive residual stresses at the peened surface are about 52%, 42%, and 35% of yield strength in samples for peened at nozzle traveling velocities of 0.05mm∕s, 0.10mm∕s, and 0.15mm∕s, respectively.
Simple Experiments to Help Students Understand Magnetic Phenomena
Authors: Browne Kerry , Jackson David P.
Published: September 2007

The principles of magnetism are a common topic in most introductory physics courses, yet curricular materials exploring the behavior of permanent magnets and magnetic materials are surprisingly rare in the literature. We reviewed the literature to see how magnetism is typically covered in introductory textbooks and curricula. We found that while most texts contain a relatively complete description of magnetism and its relation to current-carrying wires, few devote much space to the development of a model that explains the magnetic phenomena students are most familiar with, e.g., the interaction between permanent magnets and ferromagnetic materials.1 We also found that while there are a wide variety of published articles exploring the various principles of magnetic induction, only a few of these explore the basic interactions between common magnets, ferromagnetic materials, and current-carrying wires.2,3 The activities described in this paper were designed to provide a structured series of simple experiments to help students develop a model of magnetism capable of explaining these phenomena.
Response to Comments on "A Semi-Empirical Approach to Projecting Future Sea-Level Rise"
Authors: Rahmstorf Stefan
Published: September 2007

Additional analysis performed in response to Holgate
et al
. and Schmith
et al
. shows that the semi-empirical method for projecting future sea-level rise passes the test of predicting one half of the data set based on the other half. It further shows that the conclusions are robust with respect to choices of data binning, smoothing, and detrending.
Genomic Minimalism in the Early Diverging Intestinal Parasite
Giardia lamblia
Authors: Morrison Hilary G. , McArthur Andrew G. , Gillin Frances D. , Aley Stephen B. , Adam Rodney D. , Olsen Gary J. , Best Aaron A. , Cande W. Zacheus , Chen Feng , Cipriano Michael J. , Davids Barbara J. , Dawson Scott C. , Elmendorf Heidi G. , Hehl Adrian B. , Holder Michael E. , Huse Susan M. , Kim Ulandt U. , Lasek-Nesselquist Erica , Manning Gerard , Nigam Anuranjini , Nixon Julie E. J. , Palm Daniel , Passamaneck Nora E. , Prabhu Anjali , Reich Claudia I. , Reiner David S. , Samuelson John , Svard Staffan G. , Sogin Mitchell L.
Published: September 2007

The genome of the eukaryotic protist Giardia lamblia, an important human intestinal parasite, is compact in structure and content, contains few introns or mitochondrial relics, and has simplified machinery for DNA replication, transcription, RNA processing, and most metabolic pathways. Protein kinases comprise the single largest protein class and reflect Giardia's requirement for a complex signal transduction network for coordinating differentiation. Lateral gene transfer from bacterial and archaeal donors has shaped Giardia's genome, and previously unknown gene families, for example, cysteine-rich structural proteins, have been discovered. Unexpectedly, the genome shows little evidence of heterozygosity, supporting recent speculations that this organism is sexual. This genome sequence will not only be valuable for investigating the evolution of eukaryotes, but will also be applied to the search for new therapeutics for this parasite.
Correlated Evolution and Dietary Change in Fossil Stickleback
Authors: Purnell Mark A. , Bell Michael A. , Baines David C. , Hart Paul J. B. , Travis Matthew P.
Published: September 2007

The importance of trophic ecology in adaptation and evolution is well known, yet direct evidence that feeding controls microevolution over extended evolutionary time scales, available only from the fossil record, is conspicuously lacking. Through quantitative analysis of tooth microwear, we show that rapid evolutionary change in Miocene stickleback was associated with shifts in feeding, providing direct evidence from the fossil record for changes in trophic niche and resource exploitation driving directional, microevolutionary change over thousands of years. These results demonstrate the potential for tooth microwear analysis to provide powerful insights into trophic ecology during aquatic adaptive radiations.
Phase II, Randomized, Multicenter, Double-Blind, Placebo-Controlled Trial of a Polyclonal Anti-
Staphylococcus aureus
Capsular Polysaccharide Immune Globulin in Treatment of
Staphylococcus aureus
Bacteremia
Authors: Rupp Mark E. , Holley H. Preston , Lutz Jon , Dicpinigaitis Peter V. , Woods Christopher W. , Levine Donald P. , Veney Naomi , Fowler Vance G.
Published: September 2007

New treatment modalities are needed for the treatment of infections due to multidrug-resistant
Staphylococcus aureus. S. aureus
capsular polysaccharide immune globulin (Altastaph) is a polyclonal immune globulin preparation that is being developed as adjunctive therapy for persons with
S. aureus
infections complicated by bacteremia. In a phase II, multicenter, randomized, double-blind, placebo-controlled trial, 40 subjects with documented
S. aureus
bacteremia received standard therapy plus either Altastaph at 200 mg/kg of body weight in each of two infusions 24 h apart or placebo. During the 42-day observation period, antibody pharmacokinetics and safety were the primary characteristics studied. Information regarding the resolution of bacteremia and fever was also analyzed. Anti-type-5 and anti-type-8 capsular antibody levels peaked after the second infusion at 550 μg/ml and 419 μg/ml, respectively, and remained above 100 μg/ml at day 28. A total of 316 adverse events were noted in 39 of 40 subjects. Infusion-related adverse events in Altastaph recipients were infrequent and similar to those among recipients of commercial intravenously administered immunoglobulin G products. Five of 21 (23%) subjects in the Altastaph group died, whereas 2 of 18 (11%) subjects in the placebo group died (
P
= 0.42). Compared to the control patients, the Altastaph recipients had a shorter median time to the resolution of fever (2 days and 7 days, respectively;
P
= 0.09) and a shorter length of hospital stay (9 days and 14 days, respectively;
P
= 0.03). However, these findings are exploratory, and there were few differences in the other variables measured. High levels of opsonizing antibodies were maintained for the initial 4 weeks. Although the study was not powered to show efficacy, these preliminary findings and safety profile suggest that Altastaph may be an effective adjunct to antibiotics and warrants further investigation (ClinicalTrials.gov number NCT00063089).
Impact of Nucleoside Reverse Transcriptase Inhibitors on Mitochondria in Human Immunodeficiency Virus Type 1-Infected Children Receiving Highly Active Antiretroviral Therapy
Authors: Saitoh Akihiko , Fenton Terence , Alvero Carmelita , Fletcher Courtney V. , Spector Stephen A.
Published: September 2007

Mitochondrial toxicity induced by nucleoside reverse transcriptase inhibitors (NRTIs) has been reported to be responsible for various adverse effects. The relative impact of NRTIs on the mitochondria of human immunodeficiency virus (HIV) type 1 (HIV-1)-infected children receiving highly active antiretroviral therapy (HAART) is unknown. Mitochondrial DNA (mtDNA) levels were quantified longitudinally from peripheral blood mononuclear cells (PBMCs) in 31 HIV-1-infected children from Pediatric AIDS Clinical Trial Group Study 382 who were receiving HAART, including nelfinavir, efavirenz, and different NRTIs, and who had had undetectable plasma HIV-1 RNA levels for >2 years. The median mtDNA levels in PBMCs increased from 137 copies/cell at the baseline to 179 copies/cell at week 48 (P= 0.01) and 198 copies/cell at week 104 (P< 0.001). Before the initiation of HAART, children who received regimens containing didanosine had mtDNA levels persistently lower than those in children not receiving didanosine (106 versus 140 copies/cell;P= 0.008). During HAART, the median increase in the mtDNA level from the baseline to week 104 was the lowest in children who received regimens containing didanosine (+26 copies/cell) compared to those in children who received other regimens (+79 copies/cell) (P= 0.02). A multivariate analysis also demonstrated that didanosine, as part of HAART, was the only NRTI associated with the change in mtDNA levels (P= 0.007). Children receiving didanosine-containing antiretroviral regimens have the lowest mtDNA levels in PBMCs and may be at greater risk for long-term adverse effects due to mitochondrial toxicity. This may be of particular importance in resource-limited countries where didanosine is widely used for the treatment of HIV-infected children.
DNA Polymorphisms in the
pepA
and PPE18 Genes among Clinical Strains of
Mycobacterium tuberculosis
: Implications for Vaccine Efficacy
Authors: Hebert Andrea M. , Talarico Sarah , Yang Dong , Durmaz Riza , Marrs Carl F. , Zhang Lixin , Foxman Betsy , Yang Zhenhua
Published: September 2007

Tuberculosis continues to be a leading cause of death worldwide. Development of an effective vaccine against
Mycobacterium tuberculosis
is necessary to reduce the global burden of this disease. Mtb72F, consisting of the protein products of the
pepA
and PPE18 genes, is the first subunit tuberculosis vaccine to undergo phase I clinical trials. To obtain insight into the ability of Mtb72F to induce an immune response capable of recognizing different strains of
M. tuberculosis
, we investigated the genomic diversity of the
pepA
and PPE18 genes among 225 clinical strains of
M. tuberculosis
from two different geographical locations, Arkansas and Turkey, representing a broad range of genotypes of
M. tuberculosis
. A combination of single nucleotide polymorphisms (SNPs) and insertion/deletions resulting in amino acid changes in the PPE18 protein occurred in 47 (20.9%) of the 225 study strains, whereas SNPs resulted in amino acid changes in the PepA protein in 14 (6.2%) of the 225 study strains. Of the 122 Arkansas study strains and the 103 Turkey study strains, 32 (26.2%) and 15 (14.6%), respectively, had at least one genetic change leading to an alteration of the amino acid sequence of the PPE18 protein, and many of the changes occurred in regions previously reported to be potential T-cell epitopes. Thus, immunity induced by Mtb72F may not recognize a proportion of
M. tuberculosis
clinical strains.
Evidence for a Common Role for the Serine-Type
Plasmodium falciparum
Serine Repeat Antigen Proteases: Implications for Vaccine and Drug Design
Authors: McCoubrie Joanne E. , Miller Susanne K. , Sargeant Tobias , Good Robert T. , Hodder Anthony N. , Speed Terence P. , de Koning-Ward Tania F. , Crabb Brendan S.
Published: September 2007

Serine repeat antigens (SERAs) are a family of secreted “cysteine-like” proteases of
Plasmodium
parasites. Several SERAs possess an atypical active-site serine residue in place of the canonical cysteine. The human malaria parasite
Plasmodium falciparum
possesses six “serine-type” (
SERA1
to
SERA5
and
SERA9
) and three “cysteine-type” (
SERA6
to
SERA8
) SERAs. Here, we investigate the importance of the serine-type SERAs to blood-stage parasite development and examine the extent of functional redundancy among this group. We attempted to knock out the four
P. falciparum
serine-type
SERA
genes that have not been disrupted previously.
SERA1
,
SERA4
, and
SERA9
knockout lines were generated, while only
SERA5
, the most strongly expressed member of the SERA family, remained refractory to genetic deletion. Interestingly, we discovered that while
SERA4
-null parasites completed the blood-stage cycle normally, they exhibited a twofold increase in the level of
SERA5
mRNA. The inability to disrupt
SERA5
and the apparent compensatory increase in
SERA5
expression in response to the deletion of
SERA4
provides evidence for an important blood-stage function for the serine-type SERAs and supports the notion of functional redundancy among this group. Such redundancy is consistent with our phylogenetic analysis, which reveals a monophyletic grouping of the serine-type SERAs across the genus
Plasmodium
and a predominance of postspeciation expansion. While SERA5 is to some extent further validated as a target for vaccine and drug development, our data suggest that the expression level of other serine-type SERAs is the only barrier to escape from anti-SERA5-specific interventions.
Gamma Interferon Confers Resistance to Infection withStaphylococcus aureusin Human Vascular Endothelial Cells by Cooperative Proinflammatory and Enhanced Intrinsic Antibacterial Activities
Authors: Beekhuizen Henry , van de Gevel Joke S.
Published: September 2007

Vascular endothelium is an exposed target in systemic endovascularStaphylococcus aureusinfections. We reported earlier that the proinflammatory and procoagulant activities of primary human umbilical vein endothelial cells (ECs) after binding and ingestion ofS. aureusorganisms provide the cells effective means for leukocyte-mediated bacterial elimination. Expanding on this, we now show that these ECs exhibit a modest intrinsic capacity for eliminating intracellularS. aureusthat was influenced by cytokines relevant toS. aureusinfections. Using various EC infection assays, we showed that gamma interferon (IFN-γ), applied to cultures of ECs prior to or after infection withS. aureus, markedly reduced the level of infection, illustrated by lower percentages ofS. aureus-infected ECs and less intracellular bacteria per infected cell. IFN-γ-activated ECs had unaltered abilities to bindS. aureusand processed ingested bacteria by a seemingly conventional phagocytic pathway. IFN-γ treatment rescued EC monolayers from severe injury by virulent clinicalS. aureusstrains or excessive bacterial numbers. Mechanistically, IFN-γ controlsS. aureusinfection via IFN-γ receptor, most likely through stimulation of intrinsic endothelial antibacterial mechanisms but independent of processes that deprive bacteria of intracellularl-tryptophan or iron. The antibacterial activity of IFN-γ-stimulated ECs coincided with sustained or slightly elevated endothelial proinflammatory responses that supported monocyte recruitment. In conclusion, we identify IFN-γ as a potent regulatory Th1 cytokine possessing exclusive abilities to augment intrinsic antistaphylocccal effector mechanisms in human ECs without ablating theS. aureus-induced proinflammatory EC responses and, as such, coordinating a protective efficacy of ECs against blood-borneS. aureusinfection.
Dysregulated Immune Profiles for Skin and Dendritic Cells Are Associated with Increased Host Susceptibility toHaemophilus ducreyiInfection in Human Volunteers
Authors: Humphreys Tricia L. , Li Lang , Li Xiaoman , Janowicz Diane M. , Fortney Kate R. , Zhao Qianqian , Li Wei , McClintick Jeanette , Katz Barry P. , Wilkes David S. , Edenberg Howard J. , Spinola Stanley M.
Published: September 2007

In experimentally infected human volunteers, the cutaneous immune response toHaemophilus ducreyiis orchestrated by serum, polymorphonuclear leukocytes, macrophages, T cells, and myeloid dendritic cells (DC). This response either leads to spontaneous resolution of infection or progresses to pustule formation, which is associated with the failure of phagocytes to ingest the organism and the presence of Th1 and regulatory T cells. In volunteers who are challenged twice, some subjects form at least one pustule twice (PP group), while others have all inoculated sites resolve twice (RR group). Here, we infected PP and RR subjects withH. ducreyiand used microarrays to profile gene expression in infected and wounded skin. The PP and RR groups shared a core response toH. ducreyi. Additional transcripts that signified effective immune function were differentially expressed in RR infected sites, while those that signified a hyperinflammatory, dysregulated response were differentially expressed in PP infected sites. To examine whether DC drove these responses, we profiled gene expression inH. ducreyi-infected and uninfected monocyte-derived DC. Both groups had a common response that was typical of a type 1 DC (DC1) response. RR DC exclusively expressed many additional transcripts indicative of DC1. PP DC exclusively expressed differentially regulated transcripts characteristic of DC1 and regulatory DC. The data suggest that DC from the PP and RR groups respond differentially toH. ducreyi.PP DC may promote a dysregulated T-cell response that contributes to phagocytic failure, while RR DC may promote a Th1 response that facilitates bacterial clearance.
Sialyl-Lewis x-Independent Infection of Human Myeloid Cells by
Anaplasma phagocytophilum
Strains HZ and HGE1
Authors: Sarkar Madhubanti , Reneer Dexter V. , Carlyon Jason A.
Published: September 2007

Anaplasma phagocytophilum
, the causative agent of human granulocytic anaplasmosis, is an obligate intracellular bacterium that infects neutrophils and neutrophil precursors. Bacterial recognition of P-selectin glycoprotein ligand-1 (PSGL-1) and the α2,3-sialylated- and α1,3-fucosylated-moiety sialyl-Lewis x (sLe
x
), which modifies the PSGL-1 N terminus, is important for adhesion to and invasion of myeloid cells. We have previously demonstrated that
A. phagocytophilum
organisms of the NCH-1 strain that utilize an sLe
x
-modified PSGL-1-independent means of entry can be enriched for by cultivation in undersialylated HL-60 cells that are unable to construct sLe
x
. Because it was unknown whether other
A. phagocytophilum
isolates share this ability, we extended our studies to the geographically diverse strains HZ and HGE1. HL-60 A2 is a clonal cell line that is defective for sialylation and α1,3-fucosyltransferase. HL-60 A2 cell surfaces, therefore, not only lack sLe
x
but also are virtually devoid of any other sialic acid- and/or α1,3-fucose-modified glycan. By cultivating HZ and HGE1 in HL-60 A2 cells, we enriched for bacterial subpopulations (termed HZA2 and HGE1A2) that bind and/or infect myeloid cells in the absence of sialic acid and α1,3-fucose and in the presence of antibody that blocks the N terminus of PSGL-1. Thus, multiple
A. phagocytophilum
isolates share the ability to use sLe
x
-modified PSGL-1-dependent and -independent routes of entry into myeloid cells. HZA2 and HGE1A2 represent enriched bacterial populations that will aid dissection of the complexities of the interactions between
A. phagocytophilum
and host myeloid cells.
Australian and Thai Isolates of
Burkholderia pseudomallei
Are Distinct by Multilocus Sequence Typing: Revision of a Case of Mistaken Identity
Authors: J. Currie Bart , Thomas Annette D. , Godoy Daniel , Dance David A. , Cheng Allen C. , Ward Linda , Mayo Mark , Pitt Tyrone L. , Spratt Brian G.
Published: September 2007

A recent study using multilocus sequence typing (MLST) of
Burkholderia pseudomallei
isolates found a sequence type (ST60) to be common to both Thailand and Australia, contradicting earlier studies showing complete distinction between isolates from these regions. The ST60 isolates reportedly from Australia had been obtained for MLST from United Kingdom and U.S. collections. We have located and characterized the original Australian isolates; they were collected in 1983, and they are neither ST60 nor
B. pseudomallei
isolates. The
B. pseudomallei
MLST database has been corrected, and there is no ST common to isolates verified as obtained from Australia or from Thailand.
Evaluation of Cytomegalovirus (CMV) DNA Quantification in Dried Blood Spots: Retrospective Study of CMV Congenital Infection
Authors: Vauloup-Fellous Christelle , Ducroux Aurélie , Couloigner Vincent , Marlin Sandrine , Picone Olivier , Galimand Julie , Loundon Natalie , Denoyelle Françoise , Grangeot-Keros Liliane , Leruez-Ville Marianne
Published: September 2007

We compared two protocols for extracting DNA from dried blood spots for cytomegalovirus (CMV) DNA detection and quantification by real-time PCR. Both extraction methods were reliable for the retrospective diagnosis of CMV congenital infection. Quantification of CMV DNA was valuable after normalization of viral loads with albumin gene PCR amplification results.
Evidence for a Multiprotein Gamma-2 Herpesvirus Entry Complex
Authors: Gillet Laurent , Stevenson Philip G.
Published: September 2007

Herpesviruses use multiple virion glycoproteins to enter cells. How these work together is not well understood: some may act separately or they may form a single complex. Murine gammaherpesvirus 68 (MHV-68) gB, gH, gL, and gp150 all participate in entry. gB and gL are involved in binding, gB and gH are conserved fusion proteins, and gp150 inhibits cell binding until glycosaminoglycans are engaged. Here we show that a gH-specific antibody coprecipitates gB and thus that gH and gB are associated in the virion membrane. A gH/gL-specific antibody also coprecipitated gB, implying a tripartite complex of gL/gH/gB, although the gH/gB association did not require gL. The association was also independent of gp150, and gp150 was not demonstrably bound to gB or gH. However, gp150 incorporation into virions was partly gL dependent, suggesting that it too contributes to a single entry complex. gp150
−
and gL
−
gp150
−
mutants bound better than the wild type to B cells and readily colonized B cells in vivo. Thus, gp150 and gL appear to be epithelial cell-adapted accessories of a core gB/gH entry complex. The cell binding revealed by gp150 disruption did not require gL and therefore seemed most likely to involve gB.
Acetylated Histone H3 and H4 Mark the Upregulated LMP2A Promoter of Epstein-Barr Virus in Lymphoid Cells
Authors: Gerle Borbala , Koroknai Anita , Fejer György , Bakos Agnes , Banati Ferenc , Szenthe Kalman , Wolf Hans , Niller Hans Helmut , Minarovits Janos , Salamon Daniel
Published: September 2007

We analyzed the levels of acetylated histones and histone H3 dimethylated on lysine 4 (H3K4me2) at the LMP2A promoter (LMP2Ap) of Epstein-Barr virus in well-characterized type I and type III lymphoid cell line pairs and additionally in the nasopharyngeal carcinoma cell line C666-1 by using chromatin immunoprecipitation. We found that enhanced levels of acetylated histones marked the upregulated LMP2Ap in lymphoid cells. In contrast, in C666-1 cells, the highly DNA-methylated, inactive LMP2Ap was also enriched in acetylated histones and H3K4me2. Our results suggest that the combinatorial effects of DNA methylation, histone acetylation, and H3K4me2 modulate the activity of LMP2Ap.
Atraumatic Oral Spray Immunization with Replication-Deficient Viral Vector Vaccines
Authors: Stahl-Hennig Christiane , Kuate Seraphin , Franz Monika , Suh You S. , Stoiber Heribert , Sauermann Ulrike , Tenner-Racz Klara , Norley Stephen , Park Ki S. , Sung Young C. , Steinman Ralph , Racz Paul , Überla Klaus
Published: September 2007

The development of needle-free vaccines is one of the recently defined “grand challenges in global health” (H. Varmus, R. Klausner, R. Klausner, R. Zerhouni, T. Acharya, A. S. Daar, and P. A. Singer, Science 302:398-399, 2003). To explore whether a natural pathway to the inductive site of the mucosa-associated lymphatic tissue could be exploited for atraumatic immunization purposes, replication-deficient viral vector vaccines were sprayed directly onto the tonsils of rhesus macaques. Tonsillar immunization with viral vector vaccines encoding simian immunodeficiency virus (SIV) antigens induced cellular and humoral immune responses. Viral RNA levels after a stringent SIV challenge were reduced, providing a level of protection similar to that observed after systemic immunization with the same vaccines. Thus, atraumatic oral spray immunization with replication-deficient vectors can overcome the epithelial barrier, deliver the vaccine antigen to the mucosa-associated lymphatic tissue, and avoid induction of tolerance, providing a novel approach to circumvent acceptability problems of syringe and needle vaccines for children and in developing countries.
A Recombinant Herpes Simplex Virus Type 1 Expressing Two Additional Copies of gK Is More Pathogenic than Wild-Type Virus in Two Different Strains of Mice
Authors: Mott Kevin R. , Perng Guey-Chuen , Osorio Yanira , Kousoulas Konstantin G. , Ghiasi Homayon
Published: September 2007

The effect of glycoprotein K (gK) overexpression on herpes simplex virus type 1 (HSV-1) infection in two different strains of mice was evaluated using a recombinant HSV-1 virus that expresses two additional copies of the gK gene in place of the latency-associated transcript (LAT). This mutant virus (HSV-gK3) expressed higher levels of gK than either the wild-type McKrae virus or the parental dLAT2903 virus both in vitro (in cultured cells) and in vivo (in infected mouse corneas and trigeminal ganglia [TG] of BALB/c and C57BL/6 mice). gK transcripts were detected in the TG of both HSV-gK3-infected mouse strains on day 30 postinfection (p.i.), while gB transcripts were detected only in the TG of the HSV-gK3-infected C57BL/6 mice, a finding that suggests that increased gK levels promote chronic infection. C57BL/6 mice infected with HSV-gK3also contained free virus in their TG on day 30 p.i. Both HSV-gK3-infected mouse strains had significantly higher corneal scarring (CS) than did McKrae-infected mice. T-cell depletion studies in C57BL/6 mice suggested that this CS enhancement in the HSV-gK3-infected mice was mediated by a CD8+T-cell response. Taken together, these results strongly suggest that increased gK levels promote eye disease and chronic infection in infected mice.
Crimean-Congo Hemorrhagic Fever Virus Glycoprotein Processing by the Endoprotease SKI-1/S1P Is Critical for Virus Infectivity
Authors: Bergeron Éric , Vincent Martin J. , Nichol Stuart T.
Published: September 2007

Crimean-Congo hemorrhagic fever virus (CCHFV) causes severe human disease. The CCHFV medium RNA encodes a polyprotein which is proteolytically processed to yield the glycoprotein precursors PreGn and PreGc, followed by structural glycoproteins Gn and Gc. Subtilisin kexin isozyme-1/site-1 protease (SKI-1/S1P) plays a central role in Gn processing. Here we show that CCHFV-infected cells deficient in SKI-1/S1P produce no infectious virus, although PreGn and PreGc accumulated normally in the Golgi apparatus, the site of virus assembly. Only nucleoprotein-containing particles which lacked virus glycoproteins (Gn/Gc or PreGn/PreGc) were secreted. Complementation of SKI-1/S1P-deficient cells with a SKI-1/S1P expression vector restored release of infectious virus (>10
6
PFU/ml), confirming that SKI-1/S1P processing is required for incorporation of viral glycoproteins. SKI-1/S1P may represent a promising antiviral target.
Shoot architecture in the VitaceaeThis article is one of a selection of papers presented at the symposium onVitisat the XVII International Botanical Congress held in Vienna, Austria, in 2005.
Authors: Gerrath Jean M. , Posluszny Usher
Published: September 2007

This paper examines the question of how the unique shoot architectural pattern of the Vitaceae, typically with leaf-opposed tendrils or inflorescences in a three-node modular repetitive pattern, can be related to the traditional concepts of monopodial and sympodial shoot development. Based on complete comparative morphological developmental studies of 13 species in six genera, supplemented with observations of 21 other taxa, we have found five shoot architectural patterns in the family. The pattern of shoot architecture is consistent within a species, but there may be more than one pattern present within a genus. Species that lack tendrils, thus exhibiting pattern 1, show sympodial growth. Taxa exhibiting patterns 2, 3, and 4, with tendrils at two of three nodes and with progressively one, two, or three axillary buds within the three-node cycle, grow monopodially, and taxa that exhibit pattern 5, with both tendrils and axillary buds at every node, achieve the pattern via either monopodial or sympodial growth, depending on the species. Although rare in the Vitaceae, pattern 1 is the only one shared with the sister family Leeaceae. We conclude that this was the original shoot architectural pattern, and that the monopodial pattern present in most species today is derived, and unique to the Vitaceae.
Flowering transition in grapevine (Vitis viniferaL.)This review is one of a selection of papers presented at the symposium onVitisat the XVII International Botanical Congress held in Vienna, Austria, 2005.
Authors: Carmona María José , Cubas Pilar , Calonje Myriam , Martínez-Zapater José Miguel
Published: September 2007

The available information on the regulation of flowering transition in model systems, such as Arabidopsis and rice, provides a framework to undertake the study of this process in plant species with different growth strategies. The grapevine ( Vitis vinifera L.) is the most widely cultivated and economically important fruit crop in the world. Understanding the regulation of flowering transition in this species can be relevant for the improvement of yield and quality of the crop. The grapevine is a representative of the family Vitaceae, whose species mostly grow as vines and have evolved climbing organs, tendrils, which are ontogenetically related to the reproductive organs. Here, we summarize the available information on the flowering transition in the grapevine. With this purpose, we first describe the vegetative and reproductive development of the grapevine as well as the reports on the physiology of flowering induction in this species. As well, we review the recent information on the molecular genetics of flowering signal integrator and flower meristem identity genes in the grapevine and compare the process with what is already known in model systems such as Arabidopsis. Finally, we propose a preliminary model to explain the regulation of flower initiation in the grapevine that is useful to identify its differential features and infer future prospects in the understanding of this process.
An equilibrium model for predicting the efficacy of marine protected areas in coastal environments
Authors: Walters Carl J , Hilborn Ray , Parrish Richard
Published: September 2007

Quantitative models of marine protected area (MPA) proposals can be used to compare outcomes given current biological knowledge. We used a model of a linear coastline, with 200 discrete cells each spanning 1.6 km of coast. This model is used to evaluate alternative proposals for marine protected area networks, predicting equilibrium changes in abundances and harvests while accounting for dispersal of larvae and older fish, changes in fecundity with reduced mortality in reserves, impacts of displaced fishing effort on abundances outside reserves, and compensatory (stock–recruitment) changes in postsettlement juvenile survival. The model demonstrates that modest dispersal rates of older fish can substantially reduce abundance within protected areas compared with predictions from models that ignore such dispersal. The strength of compensatory improvements in postsettlement juvenile survival is the most critical factor in determining whether a reserve network can rescue populations from the impacts of severe overharvesting. We use the model to compare specific alternative proposals for protected area networks along the California coast, as mandated through California's Marine Life Protection Act, and show that achieving the goals of the Act depends primarily on the fisheries management regulations outside of protected areas and that the size and configuration of MPAs has little impact.
Estimating abundance of pelagic fishes using gillnet catch data in data-limited fisheries: a Bayesian approach
Authors: Griffiths Shane P , Kuhnert Petra M , Venables William N , Blaber Stephen J.M
Published: September 2007

We describe a Bayesian modelling approach to estimate abundance and biomass of pelagic fishes from gillnet catches in data-limited situations. By making a number of simple assumptions, we use fish sustained swimming speed to calculate the effective area fished by a gillnet in a specified soak time to estimate abundance (fish·km–2) from the number of fish caught. We used catch data from various sampling methods in northern Australia and elicited anecdotal information from experts to build a size distribution of the true population to compensate for size classes that were unlikely to be represented in the catch because of size selectivity of the gear. Our final abundance estimates for various-sized scombrids (0.04–4.17 fish·km–2) and istiophorids (0.004–0.005 fish·km–2) were similar to what has been estimated for similar species in more data-rich situations in tropical regions of the Pacific Ocean. The model is particularly useful in data-limited situations in which abundance or biomass estimates are required for pelagic fish species of low economic importance. These data are often required for ecosystem models (e.g., Ecopath) that are increasingly being considered as potential tools for ecosystem-based fisheries management.
Assessing pH changes since pre-industrial times in 51 low-alkalinity lakes in Nova Scotia, Canada
Authors: Ginn Brian K , Cumming Brian F , Smol John P
Published: September 2007

Diatom-based paleolimnological techniques were used to reconstruct lake acidification trends in 51 low-alkalinity Nova Scotia lakes that spanned gradients of dissolved organic carbon (DOC) concentrations and sulphate deposition. Pre-industrial, diatom-inferred pH values of these lakes were <6.8, with 31 lakes having pre-industrial pH < 6.0 and two lakes having pH < 5.5. Lakes in Kejimkujik National Park documented the greatest pH decline (–0.4 pH unit (±0.2)) since the 19th century, whereas those in northern parts of the province (e.g., Cape Breton Highlands National Park) experienced little or no acidification, with a net mean pH decline = –0.1 pH unit (±0.2). While the sulphate deposition and diatom-inferred pH changes have not been as great as those observed in other acidified areas of northeastern North America (e.g., Adirondack region of New York or New England), Nova Scotia lakes have experienced biological changes toward more acidophilous diatom assemblages, especially in lakes with low pre-industrial pH values (currently with high DOC concentrations) located in Kejimkujik National Park, which receives the highest loading of sulphate deposition in Nova Scotia. However, the generally low pre-industrial pH values inferred for most of the study lakes suggest that many of these lakes were somewhat naturally acidic, but acidified further as a result of atmospheric deposition.
Metabolic rate and tissue reserves in gilthead sea bream (Sparus aurata) under thermal fluctuations and fasting and their capacity for recovery
Authors: Ibarz Antoni , Blasco Josefina , Sala-Rabanal Mònica , Gallardo Ángeles , Redondo Anna , Fernández-Borràs Jaume
Published: September 2007

To differentiate between cold and fasting effects on gilthead sea bream (Sparus aurata) physiology, three conditions (cold-induced fasting at 8 °C, cold group; forced fasting at 18 °C, fasting group, and cyclic thermal fluctuations between 16 °C and 8 °C, fluctuating group) were compared with a control group (feeding at 18 °C). Oxygen consumption rate, plasma lipid fractions, and tissue composition were analysed either during long exposure (5 weeks) or after 20 days of recovery. Sea bream showed strict thermoconformism in metabolic rate and feeding, and all groups, after changes, mobilised perivisceral fat. The fasting group also consumed other tissue reserves sequentially, except nonpolar lipids in liver. In the cold group, this liver lipid fraction increased twofold, but in the fluctuating group, food intake was gradually restored during each short period of higher temperature, and the steatotic livers caused by cold were not seen. During recovery, the fasting group showed the highest growth rate and deposition of reserves, whereas the cold group, although they mobilised liver lipid, did not grow. Appropriate management of the transient short periods of higher temperature may improve recovery from the cold season in gilthead sea bream culture.
The lampricide 3-trifluoromethyl-4-nitrophenol (TFM) interferes with intermediary metabolism and glucose homeostasis, but not with ion balance, in larval sea lamprey (Petromyzon marinus)
Authors: Wilkie Michael P , Holmes John A , Youson John H
Published: September 2007

Although treatment of streams with the lampricide 3-trifluoromethyl-4-nitrophenol (TFM) has been highly effective for sea lamprey (Petromyzon marinus) population control in the Great Lakes, little is known about its mechanism(s) of toxicity. We investigated two hypotheses of TFM toxicity in larval sea lamprey exposed to TFM for 12 h. The first was that TFM interferes with oxidative ATP production by mitochondria, causing depletion of fuel stores in the body. The second was that TFM interferes with gill-mediated ion exchange, which eventually causes circulatory collapse. While exposure of larvae to TFM (2 mg·L–1) did not disturb tissue ATP stores, it led to a sustained 60% reduction in phosphocreatine (PCr) after 6 h. This was accompanied by 6- to 10-fold increases in plasma and tissue lactate, which persisted through 12 h. By 12 h, plasma glucose was nearly depleted in the five surviving lamprey, but TFM caused no appreciable changes in plasma Cl–, haematocrit, haemoglobin, or ammonia concentration. We conclude that TFM-mediated gill damage and ionic failure are not underlying mechanisms of TFM toxicity. Rather, TFM likely interferes with oxidative ATP production, leading to reduced tissue PCr stores and eventually profound hypoglycaemia that starves the nervous system of glucose, causing death.
Evidence for the existence of a native population of sockeye salmon (Oncorhynchus nerka) and subsequent introgression with introduced populations in a Pacific Northwest watershed
Authors: Spies Ingrid B , Anderson Eric C , Naish Kerry , Bentzen Paul
Published: September 2007

The Lake Washington watershed (Washington, USA) has been the recipient of numerous transplantations of nonnative Oncorhynchus nerka (both sockeye salmon and their landlocked form, kokanee) over the past century and currently contains self-sustaining populations of both ecotypes. Microsatellite DNA markers were used to identify native and introduced groups while characterizing population structure. This study confirmed that Baker Lake sockeye transplantations during the 20th century contributed to three current sockeye populations: Cedar River, Issaquah Creek, and Pleasure Point Beach in the Lake Washington watershed. Distinctive allele distributions at two loci, One101 and One114, provide evidence that a fourth Lake Washington sockeye population, Bear Creek, is divergent from other Lake Washington sockeye and may be of substantially native origin despite heavy stocking activity in the watershed over the past century. Data from these loci also suggest the presence of native genes in populations that had been regarded as entirely of introduced origin.