bluuebunny/crossref_metadata_2025 huggingface dataset:
Generation of an adenoviral vaccine vector based on simian adenovirus 21
Authors: Roy Soumitra , Zhi Yan , Kobinger Gary P. , Figueredo Joanita , Calcedo Roberto , Miller James R. , Feldmann Heinz , Wilson James M.
Published: August 2006

Adenoviral vectors can be used to generate potent humoral and cellular immune responses to transgene products. Use of adenoviral vectors based on non-human isolates may allow for their utilization in populations harbouring neutralizing antibodies to common human serotypes. A vector chimera was constructed using simian adenovirus 22 (a serotype belonging to the species Human adenovirus E) and simian adenovirus 21 (a serotype belonging to the species Human adenovirus B) expressing the Ebola (Zaire) virus glycoprotein (Ad C5/C1-ZGP). This chimeric adenovirus vector was used as a model to test its efficacy as a genetic vaccine and comparisons were made to a vector based on the commonly used human adenovirus C serotype 5 (Adhu5-ZGP). Ebola glycoprotein-specific T- and B-cell responses were measured in B10BR mice vaccinated with either Adhu5-ZGP or Ad C5/C1-ZGP vectors. Both vectors resulted in Ebola glycoprotein-specific gamma interferon-expressing T cells, although the Ad C5/C1-ZGP vector appeared to induce lower frequencies with kinetics slower than those elicited by the Adhu5-ZGP vector. The total immunoglobulin G response to Ebola glycoprotein was similar in sera from mice vaccinated with either vector. Two rhesus macaques vaccinated with the Ad C5/C1-ZGP vector were found to mount T-cell and antibody responses to the Ebola glycoprotein. It was found that a single administration of the chimeric Ad C5/C1-ZGP vector protected mice against a lethal challenge with a mouse-adapted strain of the Ebola (Zaire) virus.
Comparative analysis reveals no consistent association between the secondary structure of the 3′-untranslated region of dengue viruses and disease syndrome
Authors: Zhou Yang , Mammen Mammen P. , Klungthong Chonticha , Chinnawirotpisan Piyawan , Vaughn David W. , Nimmannitya Suchitra , Kalayanarooj Siripen , Holmes Edward C. , Zhang Chunlin
Published: August 2006

A comparative analysis was performed of the 3′-untranslated region (UTR) of Dengue virus (DENV) sampled from Bangkok, Thailand, over a 30 year period and representing all four serotypes. Considerable genetic variation was observed both within and among serotypes. Notably, a full-length version of the critical 3′-long stable hairpin structure was absent from some isolates, suggesting the occurrence of complex structural interactions within the 3′-UTR, including the influence of upstream mutations. The Thai sequences were then combined with 61 globally sampled isolates of DENV taken from patients with either dengue fever or severe dengue disease. No consistent association was found between 3′-UTR secondary structure and the clinical outcome of DENV infection, although some evidence for a trend in this direction was observed in DENV-2. It was concluded that the 3′-UTR is not the sole determinant of DENV virulence in nature, although variation in secondary structure may greatly influence viral fitness.
Transmission of Moloney murine leukemia virus (ts-1) by breast milk
Authors: Duggan Joan , Okonta Henry , Chakraborty Joana
Published: August 2006

A murine model has been developed to study maternal transmission of the temperature-sensitive Moloney murine leukemia virus (ts-1). The goal of this study was to confirm early and late mother-to-offspring transmission of the virus and demonstrate transmission via breast milk. A series of six experiments was performed using six groups of BALB/c mice. Group 1 consisted of pups born to ts-1-infected mothers removed at birth to suckle from surrogate uninfected mothers. Groups 2 and 5 consisted of pups born to ts-1-infected mothers that suckled from ts-1-infected mothers (surrogate and biological). Group 3 consisted of non-infected pups removed at birth to suckle from ts-1-infected mothers. Groups 4 and 6 consisted of non-infected pups suckled from non-infected mothers. The combined in utero, intrapartum and breast-milk infection rate was 100 % to the offspring (groups 2 and 5). The in utero to early post-partum group (group 1) had an infection rate of 78 %. Breast milk alone (group 3) resulted in a 97 % infection rate. Control groups (groups 4 and 6) had a 0 % infection rate. The relative frequency of maternal CD4+ cells in peripheral blood mononuclear cells was consistently lower in infected mothers, whilst offspring did not show a significant decrease in CD4+ frequency. Pups infected via breast milk had a lower CD4+ frequency (group 3) than those infected by the uterine and/or intrapartum route (group 1). Breast milk from ts-1-infected mothers appears to be highly infectious for neonatal BALB/c mice.
Permeabilized mammalian cells as an experimental system for nuclear import of geminiviral karyophilic proteins and of synthetic peptides derived from their nuclear localization signal regions
Authors: Kass Gideon , Arad Gabriel , Rosenbluh Joseph , Gafni Yedidya , Graessmann Adolf , Rojas Maria R. , Gilbertson Robert L. , Loyter Abraham
Published: August 2006

The plant-infecting geminiviruses deliver their genome and viral proteins into the host cell nucleus. Members of the familyGeminiviridaepossess either a bipartite genome composed of two ∼2.6 kb DNAs or a monopartite genome of ∼3.0 kb DNA. The bipartite genome ofBean dwarf mosaic virus(BDMV) encodes several karyophilic proteins, among them the capsid protein (CP) and BV1 (nuclear shuttle protein). A CP is also encoded by the monopartite genome ofTomato yellow leaf curl virus(TYLCV). Here, anin vitroassay system was used for direct demonstration of nuclear import of BDMV BV1 and TYLCV CP, as well as synthetic peptides containing their putative nuclear localization signals (NLSs). Full-length recombinant BDMV BV1 and TYLCV CP mediated import of conjugated fluorescently labelled BSA molecules into nuclei of permeabilized mammalian cells. Fluorescently labelled and biotinylated BSA conjugates bearing the synthetic peptides containing aa 3–20 of TYLCV CP (CP-NLS) or aa 84–106 of BDMV BV1 (BV1-NLS) were also imported into the nuclei of permeabilized cells. This import was blocked by the addition of unlabelled BSA–NLS peptide conjugates or excess unlabelled free NLS peptides. The CP- and BV1-NLS peptides also mediated nuclear import of fluorescently labelled BSA molecules into the nuclei of microinjected mesophyll cells ofNicotiana benthamianaleaves, demonstrating their biological function in intact plant tissue. BV1-NLS and CP-NLS were shown to mediate specific binding to importinα, bothin vitroandin vivo. These results are consistent with a common nuclear-import pathway for CP and BV1, probably via importinα.
Lyssavirus infection activates interferon gene expression in the brain
Authors: Johnson Nicholas , McKimmie Clive S. , Mansfield Karen L. , Wakeley Philip R. , Brookes Sharon M. , Fazakerley John K. , Fooks Anthony R.
Published: August 2006

To investigate the innate immune response within the brain to lyssavirus infection, key transcripts indicative of innate defences were measured in a mouse model system. Following infection with Rabies virus, transcript levels for type 1 interferons (IFN-α and -β), the inflammatory mediator interleukin 6 (IL-6) and the antiviral protein Mx1 increased in the brains of mice. Intracranial inoculation resulted in the early detection of virus replication and rapid expression within the brain of the innate immune response genes. Transcripts for type 1 IFNs declined as the disease progressed. Peripheral, extraneural inoculation delayed the host response until virus entered the brain, but then resulted in a large increase in the level of IFN-β, IL-6 and Mx1 transcripts. Induction of this response was also observed following infection with the related European bat lyssaviruses, a group of zoonotic viruses capable of causing fatal, rabies-like disease in mammalian species.
L-SIGN (CD209L) isoforms differently mediate trans-infection of hepatoma cells by hepatitis C virus pseudoparticles
Authors: Falkowska Emilia , Durso Robert J. , Gardner Jason P. , Cormier Emmanuel G. , Arrigale Robert A. , Ogawa Raymond N. , Donovan Gerald P. , Maddon Paul J. , Olson William C. , Dragic Tatjana
Published: August 2006

L-SIGN is a C-type lectin that is expressed on liver sinusoidal endothelial cells. Capture of Hepatitis C virus (HCV) by this receptor results in trans-infection of hepatoma cells. L-SIGN alleles have been identified that encode between three and nine tandem repeats of a 23 residue stretch in the juxtamembrane oligomerization domain. Here, it was shown that these repeat-region isoforms are expressed at the surface of mammalian cells and variably bind HCV envelope glycoprotein E2 and HCV pseudoparticles. Differences in binding were reflected in trans-infection efficiency, which was highest for isoform 7 and lowest for isoform 3. These findings provide a molecular mechanism whereby L-SIGN polymorphism could influence the establishment and progression of HCV infection.
Inhibition of vesicular stomatitis virus infection in epithelial cells by alpha interferon-induced soluble secreted proteins
Authors: Basu Mausumi , Maitra Ratan K. , Xiang Yan , Meng Xiangzhi , Banerjee Amiya K. , Bose Santanu
Published: August 2006

Interferons (IFNs) are potent antiviral cytokines that inhibit infection by a wide spectrum of viruses by activating the Janus kinase/signal transducers and activators of transcription (JAK/STAT) pathway. Several IFN-induced antiviral proteins including 2′,5′-oligoadenylate synthetase, dsRNA-activated protein kinase and Mx play a critical role in conferring the antiviral properties of IFN. However, studies have shown that additional antiviral factors are involved in addition to these proteins during IFN-mediated antiviral action. In an effort to characterize these novel antiviral factors, the antiviral mechanism of alpha IFN (IFN-α) against vesicular stomatitis virus (VSV) was investigated in human lung epithelial A549 cells. These studies demonstrated that soluble secreted antiviral proteins as the constituents of conditioned medium prepared from IFN-α-treated cells reduced VSV infectivity by more than 2 logs, compared with a 4 log inhibition observed following treatment of cells with IFN-α. The antiviral mechanism of these secreted proteins appeared to act at the level of cellular entry of VSV. Interestingly, the IFN-α-induced antiviral proteins were secreted independently of STAT1 (an essential component of the JAK/STAT pathway), demonstrating that the release of such extracellular soluble antiviral proteins from cells may represent an alternative mechanism of the antiviral defence strategy of IFN towards VSV infection.
Gag–Pol bearing a reverse transcriptase drug-resistant mutation influences viral genomic RNA incorporation into human immunodeficiency virus type 1 particles
Authors: Aguiar Renato S. , Pereira Helena S. , Costa Luciana J. , Brindeiro Rodrigo M. , Tanuri Amilcar
Published: August 2006

The unspliced human immunodeficiency virus type 1 (HIV-1) RNA is both the messenger for Gag and Gag–Pol and the viral genomic RNA (vRNA) that is packaged into the virion. Although Gag alone is sufficient for the incorporation of vRNA into virus particles, Gag–Pol molecules play an important role in vRNA dimerization and virion maturation. Here, a cis model for vRNA packaging was demonstrated, in which nascent Gag–Pol molecules were preferentially co-encapsulated with their cognate RNA used as the template. Genome-incorporation frequencies were evaluated for two distinct HIV-1 proviral clones differing in their ability to respond to nevirapine (NVP) treatment in one round of infection. It was shown that, under NVP selection, there was a twofold-higher incorporation of vRNAs and integration of provirus genome carrying NVP resistance when compared with the wild-type counterpart. Although cis incorporation has been already demonstrated for Gag, the novelty of these findings is that newly acquired resistant mutations in Gag–Pol will select their specific genomic RNA during virus replication, thus rapidly increasing the chance of the emergence of resistant viruses during the course of anti-retroviral treatment.
A molecular approach to the identification of cytotoxic T-lymphocyte epitopes within equine herpesvirus 1
Authors: Kydd Julia H. , Davis-Poynter N. J. , Birch J. , Hannant D. , Minke J. , Audonnet J.-C. , Antczak D. F. , Ellis Shirley A.
Published: August 2006

Equine herpesvirus 1 (EHV-1) causes respiratory and neurological disease and abortion in horses. Animals with high frequencies of cytotoxic T lymphocytes (CTL) show reduced severity of respiratory disease and frequency of abortion, probably by CTL-mediated control of cell-associated viraemia. This study aimed to identify CTL epitopes restricted by selected major histocompatibility complex (MHC) class I alleles expressed in the equine leukocyte antigen (ELA) A3 haplotype. Effector CTL were induced from EHV-1-primed ponies and thoroughbreds with characterized MHC class I haplotypes and screened against P815 target cells transfected with selected EHV-1 genes and MHC class I genes. Targets that expressed EHV-1 gene 64 and the MHC B2 gene were lysed by effector CTL in a genetically restricted manner. There was no T-cell recognition of targets expressing either the MHC B2 gene and EHV-1 genes 2, 12, 14, 16, 35, 63 or 69, or the MHC C1 gene and EHV-1 genes 12, 14, 16 or 64. A vaccinia virus vector encoding gene 64 (NYVAC-64) was also investigated. Using lymphocytes from ELA-A3 horses, the recombinant NYVAC-64 virus induced effector CTL that lysed EHV-1-infected target cells; the recombinant virus also supplied a functional peptide that was expressed by target cells and recognized in an MHC-restricted fashion by CTL induced with EHV-1. This construct may therefore be used to determine the antigenicity of EHV-1 gene 64 for other MHC haplotypes. These techniques are broadly applicable to the identification of additional CTL target proteins and their presenting MHC alleles, not only for EHV-1, but for other equine viruses.
An internal ribosome entry site located upstream of the crucifer-infecting tobamovirus coat protein (CP) gene can be used for CP synthesis in vivo
Authors: Dorokhov Yu. L. , Ivanov P. A. , Komarova T. V. , Skulachev M. V. , Atabekov J. G.
Published: August 2006

It was previously shown that, unlike the type member of the genus Tobamovirus (TMV U1), a crucifer-infecting tobamovirus (crTMV) contains a 148 nt internal ribosome entry site (IRES)CP,148
CR upstream of the coat protein (CP) gene. Here, viral vectors with substitutions in the stem–loop (SL) region of CP subgenomic promoters (TMV U1-CP–GFP/SL-mut and crTMV-CP–GFP/SL-mut) were constructed and the levels of CP synthesis in agroinoculation experiments were compared. No CP–GFP (green fluorescent protein) synthesis was detected in Nicotiana benthamiana leaves inoculated with TMV U1-CP–GFP/SL-mut, whereas a small amount of CP–GFP synthesis was obtained in crTMV-CP–GFP/SL-mut-injected leaves. Northern blots proved that both promoters were inactive. It could be hypothesized that IRES-mediated early production of the CP by crTMV is needed for realization of its crucifer-infecting capacity.
Coronaviruses in bent-winged bats (Miniopterus spp.)
Authors: Chu D. K. W. , Poon L. L. M. , Chan K. H. , Chen H. , Guan Y. , Yuen K. Y. , Peiris J. S. M.
Published: August 2006

A novel group 1 coronavirus was previously identified in bent-winged bats (Miniopterus spp.). Here, results are described from our ongoing surveillance of these bats for coronaviruses. These findings show that group 1 coronaviruses are endemic in these bat populations in Hong Kong. Genetic analysis of these viruses indicates that there are at least four different, but closely related, group 1 coronaviruses (bat-CoV 1A, 1B, HKU7 and HKU8) circulating in bent-winged bats. Phylogenetic analysis revealed that these group 1 bat coronaviruses have descended from a common ancestor and that these viruses have been established in these bats for a long period of time. These data provide a better understanding of the emergence and evolution of coronaviruses. Bat-CoV 1A and 1B were detected in apparently healthy Miniopterus magnater and Miniopterus pusillus, respectively, on repeated sampling occasions at a single habitat, suggesting that these viruses have established a persistent infection in these populations.
The Impact of a Program of Prejudice‐Reduction Seminars in South Africa1
Authors: McCool Jr. M. Alan , Du Toit Fanie , Petty Christopher R. , McCauley Clark
Published: August 2006

The influence of weekend‐long prejudice‐reduction seminars on attitudes, knowledge, and behavioral expectations of South African student leaders was assessed quantitatively and qualitatively. Pre–post comparisons indicated increases in perceived stereotyping‐caused suffering, ease of committing cross‐cultural mistakes, and comfort with approaching racially diverse strangers. The seminars did not reduce essentialist thinking, nor the in‐group favoritism found with measures of group identification and comfort approaching strangers. Similarly, they did not affect summary measures of stereotype understanding, perceived inter‐ or intragroup heterogeneity, preferred model of interethnic relations, nor attitudes toward affirmative action. Despite limited evidence of seminar impact, participants evaluated the seminars highly. Qualitative results suggest that opportunities to address racially based misperception of self and in‐group were particularly valued.
Assignment of 117 genes from HSA5 to the porcine IMpRH map and generation of a dense human–pig comparative map
Authors: Shimogiri T. , Kiuchi S. , Hiraiwa H. , Hayashi T. , Takano Y. , Maeda Y. , Yasue H.
Published: August 2006

Twenty‐two and eight significant quantitative trait loci for economically important traits have been located on porcine chromosomes (SSC) 2q and SSC16 respectively, both of which have been shown to correspond to human chromosome 5 (HSA5) by chromosome painting. To provide a comprehensive comparative map for efficient selection of candidate genes, we assigned 117 genes from HSA5 using a porcine radiation hybrid (IMpRH) panel. Sixty‐six genes were assigned to SSC2 and 48 to SSC16. One gene was suggested to link to SSC2 markers and another to SSC6. One gene did not link to any gene, expressed sequence tag or marker in the map, including those in the present investigation. This study demonstrated the following: (1) SSC2q21–q28 corresponds to the region ranging from 74.0 to 148.2 Mb on HSA5q13–q32 and the region from 176.0 to 179.3 Mb on HSA5q35; (2) SSC16 corresponds to the region from 1.4 to 68.7 Mb on HSA5p–q13 and to the region from 150.4 to 169.1 Mb on HSA5q32–q35 and (3) the conserved synteny between HSA5 and SSC2q21–q28 is interrupted by at least two sites and the synteny between HSA5 and SSC16 is also interrupted by at least two sites.
Patient self‐management of anticoagulation therapy: a trial‐based cost‐effectiveness analysis
Authors: Jowett Sue , Bryan Stirling , Murray Ellen , McCahon Deborah , Raftery James , Richard Hobbs F. D. , Fitzmaurice David
Published: August 2006

Demand for anticoagulation management is increasing due to an expansion of clinical indications for therapy. One possible model of care to meet demand is patient self‐management (PSM), beneficial to patients who need control over their condition. This study aimed to determine the cost and cost‐effectiveness of PSM of anticoagulation compared with routine clinic‐based care for patients receiving long‐term anticoagulation. A cost–utility analysis was conducted alongside a randomised controlled trial; 617 patients were recruited and followed up for 12 months. There was no significant difference in mean quality‐adjusted life years (QALYs) between groups – after adjusting for baseline, the mean difference in QALYs was 0·009 (95% CI, −0·012 to 0·030). Overall mean healthcare costs in the PSM arm were significantly higher at £417 (CI £394–£442) compared with £122 (CI £103–£144) in the control arm. Therefore, using a formal cost‐effectiveness analysis, PSM of anticoagulation does not appear to be cost‐effective. However, PSM may have other benefits in relieving pressure on traditional clinic‐based care, and the cost‐effectiveness of this model of care for some subgroups of anticoagulation patients needs to be explored further.
Design of a meso‐scale indoor lysimeter for undisturbed soil to investigate the behaviour of solutes in soil
Authors: Takamatsu T. , Koshikawa M. K. , Watanabe M. , Hou H. , Murata T.
Published: August 2006

Indoor cylindrical titanium lysimeters (80 cm internal diameter × 150 cm height) filled with undisturbed soil were constructed to study the behaviour of solutes in soil. They were equipped with thermometers, tensiometers, ceramic porous cups, percolate reservoirs, and an automatic irrigation system. Soil sampling was conducted using an original drilling technique. Examination of the wetting front and downward migration of Br− in an Andosol monolith showed no artificial sidewall flow.
Application of two surface complexation models to the adsorption of weak organic acids by soil: an additive approach
Authors: Calvet R. , Barriuso E. , Dubus I. G.
Published: August 2006

The description of adsorption of organic acids by soil with models requires many parameters. It is often difficult to obtain their values, and so we might try to test the application of models with published data on soil characteristics. We used two models in our trials, namely the constant capacitance model and the variable surface charge–variable surface potential model. We modelled the sorption data for three weak organic acids [2,4‐D, 2–4‐dichloro‐phenoxy acetic acid; salicylic acid, 2‐hydroxybenzoic acid; and clofencet, 2–4‐(chlorophenyl)‐3‐ethyl‐2,5‐dihydro‐5‐oxopyridazine‐4‐carboxylic acid] in three Cambisols and two Ferralsols. We adopt an additive approach where the five soils were considered to behave as mixtures of goethite and gibbsite. This was done with values taken from the literature on the assumption that the compounds formed monodentate complexes. Variations given by the two models in adsorbed amounts as a result of pH changes were well described for clofencet and 2,4‐D but were less successful for salicylic acid. Simulations of sorption isotherms at various pHs ranging from 5 to 8 matched the experimental data closely for clofencet. Prediction of the adsorption of clofencet and 2,4‐D in a range of Cambisols and Ferralsols at their native pH was generally good. We attribute the somewhat poorer fit observed for salicylic acid to the formation of bidendate complexes. Further improvement to the modelling should involve the formation of bidentate complexes between organic acids and oxide material and the effects of organic matter, particularly in relation to adsorption of non‐ionized compounds.
Physico‐chemical and biological controls on dissolved organic matter in peat aggregate columns
Authors: Stutter M. I. , Lumsdon D. G. , Thoss V.
Published: August 2006

We investigated the importance of physico‐chemical mechanisms responsible for the release of dissolved organic matter (DOM) from a peaty soil. Columns containing peat aggregates (embedded within a sand matrix) provided an experimental system in which both convective and diffusive processes contributed to DOM leaching. The use of aggregated peat avoided the problems associated with traditional batch equilibration experiments in which soil structure is destroyed. Biotic and abiotic processes operating in the columns were manipulated by working with two unsterilized columns (at 5°C and 22°C) and one gamma irradiation‐sterilized column (5°C). Continuous solute flows (< 80 hours) and periods of flow interruption (five interruptions of 6 hours to 384 hours) were applied to the columns (using a 1‐mm NaCl electrolyte) to investigate mechanisms of diffusion‐controlled release of DOM. For all columns, dissolved organic carbon and nitrogen (DOC and DON) effluent concentrations increased after resumption of flow and the maximum concentrations increased with increased flow‐interruption duration. Measurements of effluent UV absorbance (λ= 285 nm) showed that the DOM leached immediately after the flow interruptions contained fewer aromatic moieties of lower molecular weight than the DOM leached after periods of steady flow. The sterilized column had larger DOC and DON effluent concentration spikes than those from the unsterilized column at 5°C (38 mg C dm−3 and 6.5 mg N dm−3 versus 13 mg C dm−3 and 6.5 mg N dm−3 after the 384 hours flow interruption). This result suggested that the concentrations of DOM resulting from physico‐chemical release mechanisms (sterilized column) were attenuated by biological activity (unsterilized columns). Our results indicate that the peat’s microporous structure provides reservoirs of DOM that interact with solute in transport pores via abiotic, rate‐controlled mass transport. Hence, diffusion can influence the quantity and composition of DOM leached from peat in the field depending on intensity and duration of rainfall.
Can taxonomic distinctness assess anthropogenic impacts in inland waters? A case study from a Mediterranean river basin
Authors: ABELLÁN P. , BILTON D. T. , MILLÁN A. , SÁNCHEZ‐FERNÁNDEZ D. , RAMSAY P. M.
Published: August 2006

1. It is increasingly recognised that adequate measures of biodiversity should include information on the ‘relatedness’ of species within ecological assemblages, or the phylogenetic levels at which diversity is expressed. Taxonomic distinctness measures provide a series of indices to achieve this, which are independent of sample size. Taxonomic distinctness has been employed widely in marine systems, where it has been suggested that this index can provide a reliable measure of anthropogenic impact.

2. We tested the behaviour of three related taxonomic distinctiveness indices (Average Taxonomic Distinctness, Δ+; Variation in Taxonomic Distinctness, Λ+; and Total Taxonomic Distinctness, sΔ+) in relation to putative levels of anthropogenic impact in inland waters and their potential utility in environmental monitoring, using an extensive data set for aquatic beetles from the south‐east of the Iberian Peninsula.

3. Taxonomic distinctness measures were not able to identify human disturbance effects and there were no clear relationships between these new biodiversity measures and the disturbance level recorded at individual localities. Furthermore, the taxonomic distinctness measures used were apparently less sensitive to the effects of anthropogenic impact than other diversity metrics, such as species richness and rarity.

4. We conclude that taxonomic distinctness indices may not always perform as well as other metrics in the assessment of environmental quality. In addition, taxonomic distinctness measure should be interpreted with caution, as their performance and ability to detect anthropogenic disturbance may depend on the phylogenetic structure of sampled taxa within a region, and their evolutionary and ecological history.
Net regional ecosystem CO2 exchange from airborne and ground‐based eddy covariance, land‐use maps and weather observations
Authors: MIGLIETTA F. , GIOLI B. , HUTJES R. W. A. , REICHSTEIN M.
Published: August 2006

Measurements of regional net ecosystem exchange (NEE) were made over a period of 21 days in summer 2002 in the South‐Central part of the Netherlands and extrapolated to an area of 13 000 km2 using a combination of flux measurements made by a Sky Arrow ERA research aircraft, half‐hourly eddy covariance data from four towers, half‐hourly weather data recorded by three weather stations and detailed information on regional land use. The combination of this type of information allowed to estimate the net contribution of the terrestrial ecosystems to the overall regional carbon flux and to map dynamically the temporal and spatial variability of the fluxes. A regional carbon budget was calculated for the study period and the contributions of the different land uses to the overall regional flux, were assessed. Ecosystems were, overall, a small source of carbon to the atmosphere equivalent to to 0.23±0.025 g C m−2 day−1. When considered separately, arable and grasslands were a source of, respectively, 0.68±0.022 and 1.28±0.026 g C m−2 day−1. Evergreen and deciduous forests were instead a sink of −1.42±0.015 g C m−2 day−1. During the study period, forests offset approximately 3.5% of anthropogenic carbon emission estimates obtained from inventory data. Lacking of a robust validation, NEE values obtained with this method were compared with independent state of art estimates of the regional carbon balance that were obtained by applying a semi‐empirical model of NEE driven by MODIS satellite fAPAR data. The comparison showed an acceptable matching for the carbon balance of forest that was a sink in both cases, while a much larger difference for arable and grassland was found. Those ecosystems were a sink for satellite‐based estimates while they were a source for the combined aircraft and tower estimates. Possible causes of such differences are discussed and partly addressed. The importance of new methods for determining carbon balance at the regional scale, is outlined.
Climatic controls on the carbon and water balances of a boreal aspen forest, 1994–2003
Authors: BARR ALAN G. , BLACK T. A. , HOGG E. H. , GRIFFIS T. J. , MORGENSTERN K. , KLJUN N. , THEEDE A. , NESIC Z.
Published: August 2006

The carbon and water budgets of boreal and temperate broadleaf forests are sensitive to interannual climatic variability and are likely to respond to climate change. This study analyses 9 years of eddy‐covariance data from the Boreal Ecosystem Research and Monitoring Sites (BERMS) Southern Old Aspen site in central Saskatchewan, Canada and characterizes the primary climatic controls on evapotranspiration, net ecosystem production (FNEP), gross ecosystem photosynthesis (P) and ecosystem respiration (R). The study period was dominated by two climatic extremes: extreme warm and cool springs, which produced marked contrasts in the canopy duration, and a severe, 3‐year drought.

Annual FNEP varied among years from 55 to 367 g C m−2 (mean 172, SD 94). Interannual variability in FNEP was controlled primarily by factors that affected the R/P ratio, which varied between 0.74 and 0.96 (mean 0.87, SD 0.06). Canopy duration enhanced P and FNEP with no apparent effect on R. The fraction of annual photosynthetically active radiation (PAR) that was absorbed by the canopy foliage varied from 38% in late leaf‐emergence years to 51% in early leaf‐emergence years. Photosynthetic light‐use efficiency (mean 0.0275, SD 0.026 mol C mol−1 photons) was relatively constant during nondrought years but declined with drought intensity to a minimum of 0.0228 mol C mol−1 photons during the most severe drought year. The impact of drought on FNEP varied with drought intensity. Years of mild‐to‐moderate drought suppressed R while having little effect on P, so that FNEP was enhanced. Years of severe drought suppressed both R and P, causing either little change or a subtle reduction in FNEP. The analysis produced new insights into the dominance of canopy duration as the most important biophysical control on FNEP.

The results suggested a simple conceptual model for annual FNEP in boreal deciduous forests. When water is not limiting, annual P is controlled by canopy duration via its influence on absorbed PAR at constant light‐use efficiency. Water stress suppresses P, by reducing light‐use efficiency, and R, by limiting growth and/or suppressing microbial respiration. The high photosynthetic light‐use efficiency showed this site to be a highly productive boreal deciduous forest, with properties similar to many temperate deciduous forests.
Estimating parameters in a land‐surface model by applying nonlinear inversion to eddy covariance flux measurements from eight FLUXNET sites
Authors: WANG YING PING , BALDOCCHI DENNIS , LEUNING RAY , FALGE EVA , VESALA TIMO
Published: August 2006

Flux measurements from eight global FLUXNET sites were used to estimate parameters in a process‐based, land‐surface model (CSIRO Biosphere Model (CBM), using nonlinear parameter estimation techniques. The parameters examined were the maximum photosynthetic carboxylation rate () the potential photosynthetic electron transport rate (jmax, 25) of the leaf at the top of the canopy, and basal soil respiration (rs, 25), all at a reference temperature of 25°C. Eddy covariance measurements used in the analysis were from four evergreen forests, three deciduous forests and an oak‐grass savanna. Optimal estimates of model parameters were obtained by minimizing the weighted differences between the observed and predicted flux densities of latent heat, sensible heat and net ecosystem CO2 exchange for each year. Values of maximum carboxylation rates obtained from the flux measurements were in good agreement with independent estimates from leaf gas exchange measurements at all evergreen forest sites. A seasonally varying and jmax, 25 in CBM yielded better predictions of net ecosystem CO2 exchange than a constant and jmax, 25 for all three deciduous forests and one savanna site. Differences in the seasonal variation of and jmax, 25 among the three deciduous forests are related to leaf phenology. At the tree‐grass savanna site, seasonal variation of and jmax, 25 was affected by interactions between soil water and temperature, resulting in and jmax, 25 reaching maximal values before the onset of summer drought at canopy scale. Optimizing the photosynthetic parameters in the model allowed CBM to predict quite well the fluxes of water vapor and CO2 but sensible heat fluxes were systematically underestimated by up to 75 W m−2.
Long‐term CO2 production from deeply weathered soils of a tropical rain forest: evidence for a potential positive feedback to climate warming
Authors: SCHWENDENMANN LUITGARD , VELDKAMP EDZO
Published: August 2006

Currently, it is unknown what role tropical forest soils will play in the future global carbon cycle under higher temperatures. Many tropical forests grow on deeply weathered soils and although it is generally accepted that soil carbon decomposition increases with higher temperatures, it is not known whether subsurface carbon pools are particularly responsive to increasing soil temperatures. Carbon dioxide (CO2) diffusing out of soils is an important flux in the global carbon. Although soil CO2 efflux has been the subject of many studies in recent years, it remains difficult to deduct controls of this flux because of the different sources that produce CO2 and because potential environmental controls like soil temperature and soil moisture often covary. Here, we report results of a 5‐year study in which we measured soil CO2 production on two deeply weathered soil types at different depths in an old‐growth tropical wet forest in Costa Rica. Three sites were developed on old river terraces (old alluvium) and the other three were developed on old lava flows (residual). Annual soil CO2 efflux varied between 2.8–3.6 μmol CO2‐C m−2 s−1 (old alluvium) and 3.4–3.9 μmol CO2‐C m−2 s−1 (residual). More than 75% of the CO2 was produced in the upper 0.5 m (including litter layer) and less than 7% originated from the soil below 1 m depth. This low contribution was explained by the lack of water stress in this tropical wet forest which has resulted in very low root biomass below 2 m depth. In the top 0.5 m CO2 production was positively correlated with both temperature and soil moisture; between 0.6 and 2 m depth CO2 production correlated negatively with soil moisture in one soil and positively with photosynthetically active radiation in the other soil type. Below 2 m soil CO2 production strongly increased with increasing temperature. In combination with reduced tree growth that has been shown for this ecosystem, this would be a strong positive feedback to ecosystem warming.
Release of cell contents and comminution of particles of perennial ryegrass herbage during ingestion by dairy cows fed indoors or grazing
Authors: Boudon A. , Acosta A. , Delagarde R. , Peyraud J.‐L.
Published: August 2006

The effect of feeding indoors fresh perennial ryegrass vs. grazing on ingestive behaviour, release of cell contents and comminution of particles during ingestion, as well as on gas production of ingested boli fermented in vitro, was studied. Indoor feeding and grazing were compared using four dairy cows according to a triple reversal design with six periods. Chemical and morphological composition of the ingested herbage was similar for both indoor feeding and grazing treatments. The intake rate was markedly higher indoors compared with grazing [52·1 vs. 22·9 g dry matter (DM) min−1] with heavier boli and less saliva added per gram of DM intake. The proportions of intracellular nitrogen and chlorophyll released during mastication after ingestion of herbage fed indoors were lower, and the median size of the particles in the boli was larger (5·97 vs. 4·44 mm) compared with grazing. As a result, the rate of gas production in vitro was also lower for herbage fed indoors compared with grazing (0·423 vs. 0·469 mL min−1 g−1 incubated DM). Indoor feeding or grazing may have limited consequences in vivo on the kinetics of availability of nutrients for micro‐organisms in the rumen, because the consequences of the more extensive physical damage suffered by herbage ingested at grazing could be compensated by a lower intake rate.
Life strategies and spatial arrangement of grasses in a Mediterranean ecosystem in Greece
Authors: Dalaka A. , Sgardelis S.
Published: August 2006

The temporal and spatial distribution, and the life strategies, of fifteen grass species in a Mediterranean evergreen sclerophyllous formation at Petralona (Chalkidiki, Greece) were studied in order to identify the relationships between species, and among species and the environment, which allows for the coexistence of species.

The grass species were grouped into (i) early annual species that were characterized by early germination and a relatively long growth period; they did not need excessive resources and were distributed over the entire site, (ii) late annuals that were characterized by late germination and a short growth period; they required resources within this limited period and were competitive in capturing them and so were confined to the most productive sites of the site and (iii) perennial grasses that were characterized by early germination and vegetative reproduction; they were tolerant to nutrient shortages and hence maintained their distribution on the site.

The spatial arrangement of species can be considered as a response to the selective pressures of the seasonal water and resource availability in a Mediterranean environment. This environment posed temporal limitations on the activity of early annual and late annual species, which restricts them in time and space. The perennial species overcame this by being flexible in their resource capture and use, because of their ability to store nutrients.
Performance and environmental effects of forage production on sandy soils. V. Impact of grass understorey, slurry application and mineral N fertilizer on nitrate leaching under maize for silage
Authors: Wachendorf M. , Büchter M. , Volkers K.C. , Bobe J. , Rave G. , Loges R. , Taube F.
Published: August 2006

A field experiment with maize for silage was conducted to assess the effects of mineral nitrogen (N) fertilizer application rates (0, 50, 100, 150 kg ha−1), slurry application rates (0, 20, 40 m3 ha−1) and the use of an understorey with perennial ryegrass on nitrate (NO3)‐leaching losses. Leachate was collected using ceramic suction cups. Soil mineral N (SMN) was determined to a depth of 90 cm at the end of the growing season. Higher levels of N supply with mineral fertilizer or slurry resulted in higher leaching losses. The grass understorey significantly reduced the losses. The amount of N lost to the groundwater was positively related to SMN at the end of the growing season, with leaching losses representing less than 0·45 of SMN on average. Leaching losses were positively related to the N surplus, which was calculated from the difference between N input (N from fertilizer, slurry and atmospheric deposition) and N output (N removed with maize herbage mass and bound in the understorey biomass in spring). In view of the large variation in weather conditions between the experimental years, it is suggested that for the sandy soils in this experiment N‐leaching losses under maize can be estimated satisfactorily from SMN and the calculated N surplus.
Performance and environmental effects of forage production on sandy soils. IV. Impact of slurry application, mineral N fertilizer and grass understorey on yield and nitrogen surplus of maize for silage
Authors: Wachendorf M. , Volkers K. C. , Loges R. , Rave G. , Taube F.
Published: August 2006

A field experiment was conducted from 1998 to 2001 to measure the performance and environmental effects of a maize crop (Zea mais L.) in a continuous production system with and without a grass understorey (Lolium perenne L.), with varied N inputs. The experiment was located on a sandy soil in northern Germany and comprised all combinations of slurry application rate (0, 20, 40 m3 ha−1) and mineral N fertilizer (0, 50, 100, 150 kg N ha−1). Understorey treatments included maize with and without perennial ryegrass. Net energy (NEL) yield of maize increased with mineral N application rate but reached a plateau at high rates. Increase in yield of dry matter because of mineral N fertilizer was lower with increased slurry application rate. Neither slurry and mineral N application nor a grass understorey affected NEL concentration of maize, whereas crude protein (CP) concentration increased with increase in application of slurry and mineral N fertilizer. Nitrogen supply by slurry or mineral fertilizer had no effect on the amount of N in the grass understorey after the harvest of maize. The average amount of N bound annually in the understorey was 60 kg N ha−1. The reduced biomass of the understorey because of enhanced maize competition was compensated for by an increased CP concentration in the grass. The grass understorey affected the NEL yield of maize negatively only at very low levels of N input but increased the N surplus at all levels.
Diurnal and seasonal patterns of leaf gas exchange in bahiagrass (Paspalum notatum Flügge) growing in a subtropical climate
Authors: Ribeiro R. V. , Lyra G. B. , Santiago A. V. , Pereira A. R. , Machado E. C. , Oliveira R. F.
Published: August 2006

The objective of this study was to evaluate the seasonal and diurnal changes in leaf gas exchange in bahiagrass (Paspalum notatum) plants grown in an irrigated lawn. Carbon dioxide assimilation, transpiration, stomatal conductance, leaf temperature and leaf‐to‐air vapour pressure difference were measured during the daylight period from April 2003 to March 2004. The monitored environmental variables were photosynthetic photon flux density, air temperature, air relative humidity, photoperiod and sunshine rate. Factor and cluster analyses were used to select variables and to group months with similar physiological and meteorological characteristics, and three distinct periods were identified: (i) May to July: with low energetic availability, low leaf temperatures and low photosynthetic activity; (ii) September to January: with high energetic availability, high leaf temperatures and high photosynthetic activity; and (iii) April–March–August: a transient period with environmental and physiological characteristics showing intermediate values. The reduced plant development and growth during the winter season was in accordance to the lower photosynthetic activity recorded from June to August, this variable being a potential indicator of reduced phytomass production. The relationships between leaf gas exchange and seasonal growth are discussed.
Scaling up of a mechanistic dynamic model in a GIS environment to model temperate grassland production at the regional scale
Authors: Gimona A. , Birnie R. V. , Sibbald A. R.
Published: August 2006

Regional‐scale ecological processes are mediated by processes occurring at local scales. Spatially explicit models are needed to understand the broad‐scale consequences of a large number of local processes, driven by factors which are heterogeneous at a broad scale. A Geographic Information System (GIS)‐based mechanistic model, which can be used as a flexible tool to investigate the regional‐scale effects of changes in environmental factors on herbage production from aLolium perennesward, was developed and used to investigate the consequences of aggregating driving variables at different resolutions. The model allows rigorous scaling up of previously existing field‐based modelling approaches within a GIS context. The model's mechanistic approach allows flexibility in the simulation of the separate effects of environmental driving variables and of cutting regimes. The driving variables (temperature, solar radiation, available soil moisture and soil nitrogen status) are scaled up using geostatistical techniques. The model is used to evaluate weekly changes in herbage production under environmental conditions, variable both in space and time, under different cutting regimes. It is shown that, in this model, aggregation at 1 km2is a good compromise between accuracy and practical feasibility, and that, while ignoring heterogeneity over many square kilometres can induce large errors, their magnitude and direction also depend on the model response curve to an input variable. The results obtained were consistent with the known trends in influential environmental factors. The programming within a GIS makes the model flexible in its application and, therefore, makes it easy to apply at a variety of scales.
Effects of plant age, experimental nutrient addition and ant occupancy on herbivory in a neotropical myrmecophyte
Authors: TRAGER MATTHEW D. , BRUNA EMILIO M.
Published: August 2006

Variation in antiherbivore defences among individuals within a plant species may be influenced by intrinsic characteristics of the plant, environmental conditions and the interactions between these factors.

We used a long‐term field experiment and a laboratory palatability trial to elucidate the effects of plant age, nutrient availability and ant occupancy on herbivore damage sustained byCordia alliodora, a common neotropical myrmecophyte.

Herbivory in this system was influenced by both plant characteristics and environmental conditions, and the relative importance of these variables changed with plant age.

Five‐year‐old plants had a higher frequency of ant occupation and more workers per domatium than 1‐year‐old plants.

Plant age did not significantly affect herbivory in either field studies or laboratory palatability trials conducted with a specialist herbivore. In the field, however, 1‐year‐old plants tended to have higher levels of herbivory than 5‐year‐old plants.

There was a trend towards lower herbivory in trees that had been fertilized. Additionally, leaves from fertilized trees were significantly less palatable to specialist herbivores.

In 1‐year‐old plants, the abundance of ants in domatia had no effect on herbivory of nearby leaves. In contrast, ant abundance and herbivory were negatively correlated for 5‐year‐old trees, demonstrating that ants provide effective defence only for older plants.

These results suggest that understanding ant‐plant‐herbivore relationships requires examining how biotic and abiotic factors and their interactions change with plant ontogeny. Although our work focused on one particular ant‐plant system, the importance of ontogenetic variation in antiherbivore defence is increasingly recognized as a critical area of study in plant defence theory.