bluuebunny/crossref_metadata_2025 huggingface dataset:
Unusual Cu(I)/Ag(I) coordination of Escherichia coli CusF as revealed by atomic resolution crystallography and X‐ray absorption spectroscopy
Authors: Loftin Isabell R. , Franke Sylvia , Blackburn Ninian J. , McEvoy Megan M.
Published: September 2007

Elevated levels of copper or silver ions in the environment are an immediate threat to many organisms. Escherichia coli is able to resist the toxic effects of these ions through strictly limiting intracellular levels of Cu(I) and Ag(I). The CusCFBA system is one system in E. coli responsible for copper/silver tolerance. A key component of this system is the periplasmic copper/silver‐binding protein, CusF. Here the X‐ray structure and XAS data on the CusF–Ag(I) and CusF–Cu(I) complexes, respectively, are reported. In the CusF–Ag(I) structure, Ag(I) is coordinated by two methionines and a histidine, with a nearby tryptophan capping the metal site. EXAFS measurements on the CusF–Cu(I) complex show a similar environment for Cu(I). The arrangement of ligands effectively sequesters the metal from its periplasmic environment and thus may play a role in protecting the cell from the toxic ion.
Forbidden penta‐peptides
Authors: Tuller Tamir , Chor Benny , Nelson Nathan
Published: September 2007

There are 3,200,000 amino acid sequences of length 5 (penta‐peptides). Statistically, we expect to see a distribution of penta‐peptides that is determined by the frequency of the participating amino acids. We show, however, that not only are there thousands of such penta‐peptides that are absent from all known proteomes, but many of them are coded for multiple times in the non‐coding genomic regions. This suggests a strong selection process that prevents these peptides from being expressed. We also show that the characteristics of these forbidden penta‐peptides vary among different phylogenetic groups (e.g., eukaryotes, prokaryotes, and archaea). Our analysis provides the first steps toward understanding the “grammar” of the forbidden penta‐peptides.
Crystal structure of activin receptor type IIB kinase domain from human at 2.0 Å resolution
Authors: Han Seungil , Loulakis Pat , Griffor Matt , Xie Zhi
Published: September 2007

Activin receptor type IIB (ActRIIB), a type II TGF‐β serine/threonine kinase receptor, is integral to the activin and myostatin signaling pathway. Ligands such as activin and myostatin bind to activin type II receptors (ActRIIA, ActRIIB), and the GS domains of type I receptors are phosphorylated by type II receptors. Myostatin, a negative regulator of skeletal muscle growth, is regarded as a potential therapeutic target and binds to ActRIIB effectively, and to a lesser extent, to ActRIIA. The high‐resolution structure of human ActRIIB kinase domain in complex with adenine establishes the conserved bilobal architecture consistent with all other catalytic kinase domains. The crystal structure reveals that the adenine has a considerably different orientation from that of the adenine moiety of ATP observed in other kinase structures due to the lack of an interaction by ribose‐phosphate moiety and the presence of tautomers with two different protonation states at the N9 nitrogen. Although the Lys217–Glu230 salt bridge is absent, the unphosphorylated activation loop of ActRIIB adopts a conformation similar to that of the fully active form. Unlike the type I TGF‐β receptor, where a partially conserved Ser280 is a gatekeeper residue, the AcRIIB structure possesses Thr265 with a back pocket supported by Phe247. Taken together, these structural features provide a molecular basis for understanding the coupled activity and recognition specificity for human ActRIIB kinase domain and for the rational design of selective inhibitors.
Fast‐growing transgenic common carp mounting compensatory growth
Authors: Fu C. , Li D. , Hu W. , Wang Y. , Zhu Z.
Published: September 2007

Compensatory growth is a phase of accelerated growth apparent when favourable conditions are restored after a period of growth depression. To investigate if F2 common ‘all‐fish’ growth hormone gene transgenic common carp (Cyprinus carpio) could mount compensatory growth, a 9 week study at 29° C was performed. The control group was fed to satiation twice a day throughout the experiment. The other two groups were deprived of feed for 1 or 2 weeks, respectively, and then fed to satiation during the re‐feeding period. At the end of the experiment, the live masses of fish in the deprived groups were still significantly lower than those of the controls. During the re‐feeding period, size‐adjusted mean specific growth rates and mean feed intakes were significantly higher in the deprived fish than in the controls, indicating a partial compensatory growth response in these fish. No significant differences were found in food conversion efficiency between the deprived and control fish during re‐feeding, suggesting that hyperphagia was the mechanism responsible for increased growth rates. The proximate composition of the deprived fish at the end of the experiment was similar to that of the control fish. This study is, to our knowledge, the first to report that fast‐growing transgenic fish can achieve partial compensation of growth following starvation.
Low mitochondrial divergence indicates a rapid expansion across Europe in the weather loach, Misgurnus fossilis (L.)
Authors: Bohlen J. , ŠLechtová V. , Doadrio I. , Ráb P.
Published: September 2007

Several phylogeographic studies using mtDNA sequence data have revealed an expressed geographic structure in nearly every European freshwater fish species studied. The authors present a phylogeographic study of Misgurnus fossilis on the base of 43 specimens from 17 localities across a major part of the known distribution area of M. fossilis. Despite the large geographic distance between the sampling points and their origin from different major European river systems, only eight closely related haplotypes in the sequences of the whole mitochondrial cytochrome b were detected. The most common haplotype I included more than 60% of specimens and occurred in the North Sea basin in northern Germany, in the Danube and Elbe basins in the Czech Republic, in the Nieman basin in Poland and in the Dniester and Vistula basins in the Ukraine. Since the highest number of haplotypes (six out of eight) and the most divergent haplotypes were found in the Danube, the authors tentatively consider the Danube to have acted as a refuge area for Misgurnus during the glaciation maxima in the Pleistocene. From this refuge, the species presumably recolonized Central and Eastern Europe but failed to stretch to Western Europe.
Genetic evidence for asymmetric hybridization between menhadens (Brevoortiaspp.) from peninsular Florida
Authors: Anderson J. D. , Karel W. J.
Published: September 2007

Hybridization between the North American menhadensBrevoortia smithi,Brevoortia tyrannusandBrevoortia patronushas been reported by numerous authors, based primarily on the morphological intermediacy of hybrids relative to each parental type. In this study, genetic characterization of individuals in areas previously designated as hybrid zones validates the presence of F1hybrids. Evidence from microsatellite genotypes indicates thatB. patronusandB. smithiare parental species of hybrids on both sides of the Florida peninsula, and mitochondrial DNA (mtDNA) haplotypes suggest a maternal contribution byB. smithiin each case. Hybrids betweenB. tyrannusandB. smithiwere not identified in this study. The presence ofB. patronuson the Atlantic coast of Florida, coupled with admixture between this species andB. tyrannus, has likely influenced the mixed lineage assortment of mtDNA haplotypes demonstrated in this study and in previous studies.
Linkage variation at the sex‐determining locus within Fraser strain Arctic charr Salvelinus alpinus
Authors: Moghadam H. K. , Ferguson M. M. , Danzmann R. G.
Published: September 2007

The association of genetic markers linked to the sex‐determining locus (SEX) was investigated in five Arctic charr Salvelinus alpinus full sib families, all originating from the Fraser River strain, Labrador, Canada. Two distinct sex‐linkage classes were identified: type I (two families), with previously reported markers on linkage group 4 (AC‐4) linked with SEX; and type II (three families), with two unlinked segments of the AC‐4 linkage group, but with markers in only one cluster associated with SEX. Large differences in recombination rates, pseudolinkage assembly or various chromosomal rearrangements may explain these findings.
RFLP and semi‐multiplex PCR‐based identification of four eel species from the south‐western Indian Ocean region
Authors: Gagnaire P. A. , Tsukamoto K. , Aoyama J. , Minegishi Y. , Valade P. , Berrebi P.
Published: September 2007

To make the assignment of elvers to species more easily attainable and reliable, unpublished and recently published mitochondrial DNA sequences were used to design molecular determination approaches not based on sequencing. Two methods were proposed based on 16SrRNA single nucleotide polymorphism analysis, which improve identification of the four eel species living in the south‐western Indian Ocean region.
Simultaneous formation of haploid, diploid and triploid eggs in diploid–triploid mosaic loaches
Authors: Yoshikawa H. , Morishima K. , Fujimoto T. , Yamaha E. , Arai K.
Published: September 2007

In the loach Misgurnus anguillicaudatus, very few diploid–triploid mosaic individuals, which are generated by accidental incorporation of the sperm nucleus into diploid eggs produced by clonal diploid loach, occur in nature. Ploidy examination of gynogenetic progeny induced by activation with ultraviolet‐irradiated goldfish sperm indicated that diploid–triploid mosaic females laid haploid, diploid and triploid eggs, simultaneously. In addition, triploid eggs exhibited larger egg sizes. Microsatellite genotyping of diploid–triploid mosaics revealed that triploid genotypes of mosaic mothers possessed two alleles specific to the clonal diploid and one allele from normal diploid male. Diploid eggs from a mosaic mother had genotypes absolutely identical to the diploid clone. Most genotypes of triploid eggs were identical to the mosaic mother, and one of the three alleles of the mosaic mother was transmitted to haploid eggs. These results suggested that diploid germ cells, which had a clonal genome, were differentiated into clonal diploid eggs, and triploid and haploid eggs were produced from triploid germ cells in the same ovary of mosaic individuals.
Genetic differentiation in pikeperch (Sander lucioperca): the relative importance of gene flow, drift and common history
Authors: Björklund M. , Aho T. , Larsson L. C.
Published: September 2007

To investigate the relative importance of homogenizing factors, such as gene flow, and diversifying factors, such as drift, genetic variation in pikeperch (Sander lucioperca) in two Fennoscandian regions (North and South) was analysed with microsatellites. Allelic richness and the degree of differentiation were significantly higher in the North (FST= 0·20) than in the South (FST= 0·064). In northern areas, assignments of genotypes were almost exclusively to the population of origin, but in southern areas, the proportion of correct assignments was significantly lower. Most samples exhibited significant heterozygote deficits, and the level of relatedness was higher than expected from randomness. These combined results suggest that there has been more gene flow between populations in southern areas than in northern areas, where the importance of genetic drift has been greater. Effective population sizes were small (c.100) and did not differ between areas. The effect of a common history appears minor, and thus processes such as genetic drift and gene flow have been more influential in shaping the patterns of genetic diversity in this species.
Comparative genomics of transcription factors driving expression of the immunoglobulin heavy chain locus in teleost fish
Authors: Lennard Richard M. L , Bengtén E. , Wilson M. R. , Miller N. W. , Warr G. W. , Hikima J.
Published: September 2007

The immunoglobulin heavy chain locus of teleost fish is driven by an enhancer (Eμ3′) that contains, in all species examined, octamer and E‐box motifs (typically μE5). Thus, the transcription factors known (through experiments in fish) or predicted (from knowledge of their mammalian homologues) to be involved in the function of the enhancer are the octamer‐binding (Oct) transcription factors Oct1 and Oct2, their coactivator BOB.1 and the μE5‐binding E‐proteins (E2A, HEB and E2‐2). Comparative genomic analysis of the genes encoding these transcription factors in teleost fish permits some conclusions to be drawn concerning the fate of these genes following the genome‐wide duplication event that occurred in this lineage. Although problems in the assembly of some regions of the zebrafish genome may complicate the analysis, the pattern that emerges from these studies is that Oct1, Oct2, BOB.1 and E2‐2 are all single‐copy genes in teleosts, whereas in the case of E2A and HEB, two copies of each gene are present. The evolutionary conservation of sequences between related genes is variable, but with the highest similarities always being observed in the domains with ligand‐binding function, whether the ligand is a DNA motif or, as in the case of BOB.1, another protein domain. A major challenge that must be faced is the assignment of precise functions to these diverse transcription factors in teleosts; assumptions drawn by inference from their mammalian homologues will likely be misleading.
Cryptic estuarine gobiid fish larvae (Pisces: Gobiidae) identified as Pseudogobius olorum using allozyme markers
Authors: Close P. G. , Gouws G.
Published: September 2007

Allozyme electrophoresis was used to identify cryptic larvae of potentially four sympatric south‐western Australian estuarine gobiid species: Afurcagobius suppositus, Arenigobius bifrenatus, Favonigobius lateralis and Pseudogobius olorum. Genotypes of six diagnostic loci expressed in 46 unidentified larval gobiids indicated that they were unambiguously P. olorum.
Regression of intestinal adenomas by vaccination with heat shock protein 105‐pulsed bone marrow‐derived dendritic cells in ApcMin/+ mice
Authors: Yokomine Kazunori , Nakatsura Tetsuya , Senju Satoru , Nakagata Naomi , Minohara Motozumi , Kira Jun–ichi , Motomura Yutaka , Kubo Tatsuko , Sasaki Yutaka , Nishimura Yasuharu
Published: September 2007

Heat shock protein (HSP) 105 is overexpressed in various cancers, but is expressed at low levels in many normal tissues, except for the testis. A vaccination with HSP105‐pulsed bone marrow‐derived dendritic cells (BM‐DC) induced antitumor immunity without causing an autoimmune reaction in a mouse model. Because ApcMin/+ mice develop multiple adenomas throughout the intestinal tract by 4 months of age, the mice provide a clinically relevant model of human intestinal tumor. In the present study, we investigated the efficacy of the HSP105‐pulsed BM‐DC vaccine on tumor regression in the ApcMin/+ mouse. Western blot and immunohistochemical analyses revealed that the tumors of the ApcMin/+ mice endogenously overexpressed HSP105. Immunization of the ApcMin/+ mice with a HSP105‐pulsed BM‐DC vaccine at 6, 8, and 10 weeks of age significantly reduced the number of small‐intestinal polyps accompanied by infiltration of both CD4+ and CD8+ T cells in the tumors. Cell depletion experiments proved that both CD4+ and CD8+ T cells play a critical role in the activation of antitumor immunity induced by these vaccinations. These findings indicate that the HSP105‐pulsed BM‐DC vaccine can provide potent immunotherapy for tumors that appear spontaneously as a result of the inactivation of a tumor suppressor gene, such as in the ApcMin/+ mouse model. (Cancer Sci 2007; 98: 1930–1935)
Vector‐based Ape1 small interfering RNA enhances the sensitivity of human osteosarcoma cells to endostatin in vivo
Authors: Wang Dong , Zhong Zhao‐Yang , Li Meng‐Xia , Xiang De‐Bing , Li Zeng‐Peng
Published: September 2007

Osteosarcoma is a highly vascular and extremely destructive malignancy, and the survival of patients with osteosarcoma has not improved significantly in recent years. Antiangiogenic therapy currently holds great potential in conjunction with conventional treatment modalities for osteosarcoma. However, there are examples of gradual loss of response, and perhaps acquired resistance to antiangiogenic drugs. The acquired resistance of antiangiogenesis may be associated with a lot of hypoxia‐response genes. The human apurinic/apyrimidinic endonuclease (Ape1) protein, a bifunctional redox factor and apurinic/apyrimidinic (AP) endonuclease, plays a crucial role in protecting against cell death due to hypoxia. We therefore hypothesized that Ape1 may contribute to the resistance of antiangiogenic therapy. To investigate the effect of Ape1 on the sensitivity of human osteosarcoma cells to endostatin, we constructed an Ape1 small interfering RNA expression vector, pSilenceApe1. Transfection of human osteosarcoma 9901 and HOS cells with pSilenceApe1 resulted in a dose‐dependent loss of Ape1 protein. pSilenceApe1 also significantly suppressed the expression of vascular endothelial growth factor (VEGF) protein in the 9901 cells. Combined treatment with pSilenceApe1 and recombinant human endostatin (rhES) showed potent antiangiogenic effects in the transwell chamber invasion assay. Then, 20 nude mice bearing 9901 xenografts were divided into four groups: the phosphate‐buffered saline treatment control group; the rhES treatment group (1.5 mg/kg, daily); the pSilenceApe1 treatment group (20 µg, once every 3 days); and the combination of rhES and pSilenceApe1 treatment group. pSilenceApe1 significantly suppressed the expression of Ape1 and VEGF protein in the 9901 xenografts. The tumor‐inhibition rate of the pSilenceApe1, rhES, and combination of rhES and pSilenceApe1 treatment groups was 38.23, 35.29, and 62.18%, respectively. Furthermore, a significant decrease in microvessel density with an increase in apoptosis was observed following combined treatment with pSilenceApe1 and rhES, compared with control and either agent alone in 9901 xenografts. These results indicate that Ape1 small interfering RNA could enhance the sensitivity of osteosarcoma cells to endostatin. (Cancer Sci 2007; 98: 1993–2001)
Inhibition of angiogenesis in the treatment of non‐small cell lung cancer
Authors: Keedy Vicki L. , Sandler Alan B.
Published: September 2007

Angiogenesis and its role in the growth and development of metastases has become a topic of increasing importance. In non‐small cell lung cancer (NSCLC), vascular endothelial growth factor (VEGF) plays an important role in angiogenesis, growth of the primary tumor, and development of metastases. In addition, elevated expression in tissue samples is a negative prognostic feature. For these reasons, VEGF is a worthy target for novel therapies. Recent clinical trials have shown that the anti‐VEGF monoclonal antibody bevacizumab adds to the effect of chemotherapy in the metastatic setting. Hypertension and proteinuria are, as expected, commonly seen in this patient population, but the unexpected toxicity of life‐threatening hemoptysis has also been observed. This makes careful patient selection especially important for this class of drugs. Our understanding of the VEGF pathway is increasing, as are the number of available targeted agents. In addition to the monoclonal antibody, bevacizumab, VEGF receptor tyrosine kinase inhibitors, multitargeted kinase inhibitors, and combination VEGF and epidermal growth factor receptor (EGFR) inhibition, are all being evaluated in NSCLC. Small phase I and II trials have suggested modest benefit when used alone; however, we now know that the anti‐angiogenic therapies work best in combination with chemotherapy. The results of ongoing trials using these agents in combination with standard therapy will provide more insight into their potential benefit. As it is known that small tumors require angiogenesis to grow and metastasize, the use of anti‐angiogenic therapies in the adjuvant setting may provide even greater benefit, and increase the potential cure rate in this population of patients. The results of well‐designed phase III trials will be required to truly understand how to best use this class of targeted therapies in resectable and metastatic NSCLC. (Cancer Sci 2007; 98: 1825–1830)
Increased phosphorylation of Akt in triple‐negative breast cancers
Authors: Umemura Shinobu , Yoshida Sei , Ohta Yoshikazu , Naito Kenichiro , Osamura R. Yoshiyuki , Tokuda Yutaka
Published: September 2007

Cells from breast cancers lacking hormone receptors (estrogen receptor [ER], progesterone receptor [PgR]) and human epidermal growth factor receptor (HER) 2 strongly express the cell proliferation marker Ki‐67. However, the mechanisms of and stimulus signals involved in cell proliferation of this type of breast cancer are not well understood. The aim of the present study was to examine the characteristics of signal transduction in triple‐negative (ER‐, PgR‐, and HER2‐negative) breast cancers. For 44 tumor samples, western blotting analysis was conducted to examine the phosphorylation of HER2, external signal‐regulated kinase (ERK)1 and ‐2 and Akt, and the immunohistochemical phenotypes of the samples with respect to ER and HER2 were also assessed. Phosphorylation of HER2 was detected in 4 of 15 immunohistochemically HER2‐positive tumor samples (26.7%). ERK1/2 was more highly phosphorylated in triple‐negative breast cancers. Phosphorylation of Akt kinase was significantly higher in triple‐negative breast cancers. Triple‐negative breast cancers are characterized by increased phosphorylation of Akt kinase. In the present study, we found for the first time that there is a population with a significantly activated Akt pathway in this type of breast cancer. (Cancer Sci 2007; 98: 1889–1892)
Pharmacokinetic modelling of the placental transfer of nelfinavir and its M8 metabolite: a population study using 75 maternal‐cord plasma samples
Authors: Hirt Déborah , Urien Saïk , Jullien Vincent , Firtion Ghislaine , Chappuy Hélène , Rey Elisabeth , Pons Gérard , Mandelbrot Laurent , Treluyer Jean‐Marc
Published: September 2007

What is already known about this subject

• Nelfinavir is an HIV protease inhibitor used in pregnant women, although no ex vivo and few in vivo data are available describing its transfer across the placenta.

What this study adds

• A population pharmacokinetic study was performed on maternal, cord plasma and amniotic fluid samples to characterize the concentration–time courses of nelfinavir and its metabolite M8 in the three compartments and to study the influence of covariates, such as weight and duration of pregnancy, on placental transfer.

• The pharmacokinetics of nelfinavir and M8 were satisfactorily described by a three compartment model. The median nelfinavir fetus : maternal concentration ratio was 25% for maternal concentrations between 0.1 and 2.5 mg l−1, between the 31st and 41st week of gestation, irrespective of bodyweight. This ratio was significantly higher for M8 (a 55% increase).

• To our knowledge this is the first population pharmacokinetic integrated model to describe satisfactorily the maternal‐foetal‐amniotic fluid transfer of a drug.

Aims

A population pharmacokinetic model was developed to characterize the transfer of nelfinavir and its active metabolite M8 from maternal to cord plasma and amniotic fluid.

Methods

Concentration data were obtained from 75 women on the day of delivery and for whom maternal, umbilical plasma and amniotic fluid samples were collected. Data from 53 pregnant, 61 nonpregnant and seven consecutively pregnant and non pregnant women were then added to the database, the contents of which were analyzed using NONMEM.

Results

Nelfinavir and M8 concentrations in maternal plasma, umbilical plasma and amniotic fluid were described by six connected compartments. Mean (% intersubject variability) population estimates were: absorption rate 00.67 h−1, lag time 00.87 h, oral clearance and volume of distribution: 39.5 l h−1 (53%), and 557 l for non pregnant and pregnant women, respectively, and 115 l h−1 (132%) and 1626 l, respectively, on the day of delivery, M8 formation clearance 0.77 l h−1 and M8 elimination rate constant 03.41 h−1 (74%). For nelfinavir and M8, respectively, the mother‐to‐cord parameters were 0.058 l h−1 (34%), and 00.35 h−1 (76%), the cord‐to‐amniotic fluid rate constants were 0.23 and 00.59 h−1, and the elimination rate constants from amniotic fluid were 0.36 and 00.49 h−1. The nelfinavir fetus : maternal concentration ratio was 25% for maternal concentrations between 0.1 and 2.5 mg l−1, between the 31 and 41st week of gestation.

Conclusions

The low transfer of nelfinavir from the placenta is unlikely to protect the fetus from vertical HIV‐1 transmission.
Maternal punishment practices in a rural area of Turkey
Authors: Buldukoglu Kadriye , Kukulu Kamile
Published: September 2007

Objective  We examined a number of maternal characteristics that influence punishment practices in a rural area of Turkey.

Methods  Questionnaires were filled out in face‐to‐face interviews with 539 mothers who agreed to participate in this study.

Results  The majority findings of this study were as follows: all of the mothers had used various forms of punishment on their children; hitting other children was the primary reason for punishment, and hitting was the most common form of punishment used by mothers. Another interesting finding of this study was that mothers did not demonstrate the same responses to their children when they were alone as when others were present. Mothers commonly felt regret in the post‐punishment period.

Conclusion  These findings can be useful in establishing parental educational programming that is directed at decreasing the rates of punishment practices.
The response of an Eastern Amazonian rain forest to drought stress: results and modelling analyses from a throughfall exclusion experiment
Authors: FISHER R. A. , WILLIAMS M. , Da COSTA A. LOLA , MALHI Y. , Da COSTA R. F. , ALMEIDA S. , MEIR P.
Published: September 2007

Warmer and drier climates over Eastern Amazonia have been predicted as a component of climate change during the next 50–100 years. It remains unclear what effect such changes will have on forest–atmosphere exchange of carbon dioxide (CO2) and water, but the cumulative effect is anticipated to produce climatic feedback at both regional and global scales. To allow more detailed study of forest responses to soil drying, a simulated soil drought or ‘throughfall exclusion’ (TFE) experiment was established at a rain forest site in Eastern Amazonia, Brazil, for which time‐series sap flow and soil moisture data were obtained. The experiment excluded 50% of the throughfall from the soil. Sap flow data from the forest plot experiencing normal rainfall showed no limitation of transpiration throughout the two monitored dry seasons. Conversely, data from the TFE showed large dry season declines in transpiration, with tree water use restricted to 20% of that in the control plot at the peak of both dry seasons. The results were examined to evaluate the paradigm that the restriction on transpiration in the dry season was caused by limitation of soil‐to‐root water transport, driven by low soil water potential and high soil‐to‐root hydraulic resistance. This paradigm, embedded in the soil–plant–atmosphere (SPA) model and driven using on‐site measurements, provided a good explanation (R2 > 0.69) of the magnitude and timing of changes in sap flow and soil moisture. This model‐data correspondence represents a substantial improvement compared with other ecosystem models of drought stress tested in Amazonia. Inclusion of deeper rooting should lead to lower sensitivity to drought than the majority of existing models. Modelled annual GPP declined by 13–14% in response to the treatment, compared with estimated declines in transpiration of 30–40%.
Carbon mitigation by the energy crop, Miscanthus
Authors: CLIFTON‐BROWN JOHN C. , BREUER JÖERN , JONES MICHAEL B.
Published: September 2007

Biomass crops mitigate carbon emissions by both fossil fuel substitution and sequestration of carbon in the soil. We grew Miscanthus x giganteus for 16 years at a site in southern Ireland to (i) compare methods of propagation, (ii) compare response to fertilizer application and quantify nutrient offtakes, (iii) measure long‐term annual biomass yields, (iv) estimate carbon sequestration to the soil and (v) quantify the carbon mitigation by the crop. There was no significant difference in the yield between plants established from rhizome cuttings or by micro‐propagation. Annual off‐takes of N and P were easily met by soil reserves, but soil K reserves were low in unfertilized plots. Potassium deficiency was associated with lower harvestable yield. Yields increased for 5 years following establishment but after 10 years showed some decline which could not be accounted for by the climate driven growth model MISCANMOD. Measured yields were normalized to estimate both autumn (at first frost) and spring harvests (15 March of the subsequent year). Average autumn and spring yields over the 15 harvest years were 13.4±1.1 and 9.0±0.7 t DW ha−1 yr−1 respectively. Below ground biomass in February 2002 was 20.6±4.6 t DW ha−1. Miscanthus derived soil organic carbon sequestration detected by a change in 13C signal was 8.9±2.4 t C ha−1 over 15 years. We estimate total carbon mitigation by this crop over 15 years ranged from 5.2 to 7.2 t C ha−1 yr−1 depending on the harvest time.
Monoterpene emissions from rubber trees (Hevea brasiliensis) in a changing landscape and climate: chemical speciation and environmental control
Authors: WANG YONG‐FENG , OWEN SUSAN M. , LI QING‐JUN , PEÑUELAS JOSEP
Published: September 2007

Emissions of biogenic volatile organic compounds (VOCs) have important roles in ecophysiology and atmospheric chemistry at a wide range of spatial and temporal scales. Tropical regions are a major global source of VOC emissions and magnitude and chemical speciation of VOC emissions are highly plant‐species specific. Therefore it is important to study emissions from dominant species in tropical regions undergoing large‐scale land‐use change, for example, rubber plantations in South East Asia. Rubber trees (Hevea brasiliensis) are strong emitters of light‐dependent monoterpenes. Measurements of emissions from leaves were made in the dry season in February 2003 and at the beginning of the wet season in May 2005. Major emitted compounds were sabinene, α‐pinene and β‐pinene, but β‐ocimene and linalool also contributed significantly at low temperature and light. Cis‐ocimene was emitted with a circadian course independent of photosynthetic active radiation (PAR) and temperature changes with a maximum in the middle of the day. Total isoprenoid VOC emission potential at the beginning of the wet season (94 μg gdw−1 h−1) was almost two orders of magnitude higher than measured in the dry season (2 μg g dw−1 h−1). Composition of total emissions changed with increasing temperature or PAR ramps imposed throughout a day. As well as light and temperature, there was evidence that assimilation rate was also a factor contributing to seasonal regulating emission potential of monoterpenes from rubber trees. Results presented here contribute to a better understanding of an important source of biogenic VOC associated with land‐use change in tropical South East Asia.
Prediction of the distribution of Arctic‐nesting pink‐footed geese under a warmer climate scenario
Authors: JENSEN RIKKE A. , MADSEN JESPER , O'CONNELL MARK , WISZ MARY S. , TØMMERVIK HANS , MEHLUM FRIDTJOF
Published: September 2007

Global climate change is expected to shift species ranges polewards, with a risk of range contractions and population declines of especially high‐Arctic species. We built species distribution models for Svalbard‐nesting pink‐footed geese to relate their occurrence to environmental and climatic variables, and used the models to predict their distribution under a warmer climate scenario. The most parsimonious model included mean May temperature, the number of frost‐free months and the proportion of moist and wet moss‐dominated vegetation in the area. The two climate variables are indicators for whether geese can physiologically fulfil the breeding cycle or not and the moss vegetation is an indicator of suitable feeding conditions. Projections of the distribution to warmer climate scenarios propose a large north‐ and eastward expansion of the potential breeding range on Svalbard even at modest temperature increases (1 and 2 °C increase in summer temperature, respectively). Contrary to recent suggestions regarding future distributions of Arctic wildlife, we predict that warming may lead to a further growth in population size of, at least some, Arctic breeding geese.
Developing an empirical model of stand GPP with the LUE approach: analysis of eddy covariance data at five contrasting conifer sites in Europe
Authors: MÄKELÄ ANNIKKI , PULKKINEN MINNA , KOLARI PASI , LAGERGREN FREDRIK , BERBIGIER PAUL , LINDROTH ANDERS , LOUSTAU DENIS , NIKINMAA EERO , VESALA TIMO , HARI PERTTI
Published: September 2007

This paper develops a statistical model for daily gross primary production (GPP) in boreal and temperate coniferous forests. The model applies the light use efficiency (LUE) approach, which estimates the conversion efficiency of daily absorbed photosynthetically active radiation (APAR) into daily GPP as a product of potential LUE and modifying factors. The latter were derived from daily total APAR and daily mean temperature, vapour pressure deficit (VPD) and soil water content (SWC). Modelling data came from five European eddy covariance measurement towers over 2–8 years. The model was tested against independent data from two AmeriFlux stations. The model with the APAR, temperature and VPD modifiers worked well in almost all the site–year combinations, but the SWC modifier only improved the fit in few cases. Geographical variation was found in the modifiers and potential LUE in site‐specific models. When a model was fitted to pooled data, differences between sites could be explained by potential LUE, leaf area and environmental conditions. The test against the AmeriFlux data corroborated this finding. The potential LUE varied from 1.9 to 3.1 g C MJ−1, and a weak correlation was found between foliar nitrogen concentration and potential LUE. Some year‐to‐year variation remained which could be captured by neither the pooled nor the site‐specific models.
Seamounts: identity crisis or split personality?
Authors: McClain Craig R.
Published: September 2007

At present, researchers propose that over 14,000 seamounts exist and, like their terrestrial analogues, function like islands. In addition, seamounts are described as oases, biodiversity hotspots, and lush coral/sponge gardens. Here I discuss the extent to which these tenets regarding seamounts may be inappropriate, suffer from a lack of support, and be over‐generalizations of a broad range of environmental types encountered on seamounts. Ultimately, for seamount science to progress, we need to challenge our conventional wisdom on these habitats and the extent to which all seamounts function in a similar manner.
Regional genetic diversity patterns in Antarctic hairgrass (Deschampsia antarctica Desv.)
Authors: Wouw Mark van de , Dijk Peter van , Huiskes Ad H. L.
Published: September 2007

Aim  To determine patterns in diversity of a major Antarctic plant species, including relationships of Antarctic populations with those outside the Antarctic zone.

Location  Antarctic Peninsula, Maritime Antarctica, sub‐Antarctic islands, Falkland Islands and South America.

Methods  Amplified fragment length polymorphisms (AFLPs) and chloroplast sequences were used to study patterns of genetic diversity in Antarctic hairgrass (Deschampsia antarctica Desv.) and the genetic relationships between populations over its distribution range. Thirty‐eight populations were sampled from a large part of the distribution of D. antarctica, and additionally, herbarium specimens were included for areas from which we could not obtain fresh samples.

Results  A gradient in AFLP diversity was observed going from the Falklands southwards into the Antarctic. This gradient in diversity was also observed within the Antarctic Peninsula: diversity was lower further south. Diversity in the chloroplast genome of D. antarctica was low. Only three chloroplast haplotypes were found, each with a strong regional distribution.

Main conclusions  The phylogenetic construction of AFLP marker frequencies in meta‐populations of D. antarctica supports a stepping‐stone model of colonization, whereby gene flow mainly occurs between neighbouring populations. It is concluded that long‐distance gene flow is very limited in D. antarctica. A very low diversity was found in the sub‐Antarctic islands in the Indian Ocean, indicating that these populations have experienced a recent evolutionary bottleneck.
A pre‐European settlement pollen–climate calibration set for Minnesota, USA: developing tools for palaeoclimatic reconstructions
Authors: Jacques Jeannine‐Marie St. , Cumming Brian F. , Smol John P.
Published: September 2007

Aim The bias in modern North American pollen assemblages by landscape disturbance from Euro‐American settlement has long been overlooked in the construction of pollen–climate transfer functions. Our aim is to examine this problem and to develop an unbiased pre‐settlement pollen–climate transfer function, and to test its performance and inference power in comparison with commonly used techniques.

Location Minnesota, USA, is of palaeoclimatic interest because within the state are located two continental‐scale ecotones, controlled by temperature and available moisture. Shifts of these ecotones can be tracked using palaeoecological techniques.

Methods Using a data set of pre‐settlement pollen assemblages from 133 lakes, which were coupled to climate data from the earliest instrumental records (i.e. 1895–1924), a pre‐settlement pollen–climate data set was developed that lacked the influence of anthropogenic landscape disturbance. A corresponding modern pollen data set (from lake sediment core tops) and a modern climate (i.e. 1961–90) data set were also developed. The two pollen sets were compared to demonstrate the effects of landscape disturbance from human activities. Ordination (redundancy analysis with Monte Carlo permutation tests) and regression techniques (generalized linear modelling) were used to establish the relationships between the early instrumental climate variables and pre‐settlement pollen assemblages and individual taxa, respectively. Transfer functions for the most suitable climate variables (i.e. those forming a minimal set of non‐collinear climate variables that explained the greatest amount of pollen variance) were developed from the pre‐settlement data set using bootstrapping.

Results Comparison of pre‐settlement pollen and modern pollen showed an over‐representation ofAmbrosia, Chenopodiaceae and Poaceae, and an under‐representation of arboreal taxa (e.g.Pinus,Quercus,Ostrya) in the modern assemblages. Not surprisingly, ordination and regression techniques showed a strong relationship between the early instrumental climate variables and pre‐settlement pollen assemblages and taxa. Transfer functions were developed for May and February mean temperature and available moisture. Pre‐settlement transfer functions substantially improved the root mean squared error by 37–72% in comparison with modern transfer functions inferring pre‐settlement conditions, suggesting that the modern transfer functions have poorer predictive abilities.

Main conclusions For climatic reconstructions, there can be a serious distortion of inferences based solely on modern pollen–climate data sets in regions where anthropogenic landscape disturbance has occurred. By using historical climate data, coupled with pre‐disturbance pollen assemblages, robust transfer functions for temperature and effective moisture were developed.
Contrasting population genetic structure for workers and queens in the putatively unicolonial antFormica exsecta
Authors: KÜMMERLI ROLF , KELLER LAURENT
Published: September 2007

The theory of inclusive fitness provides a powerful explanation for reproductive altruism in social insects, whereby workers gain inclusive fitness benefit by rearing the brood of related queens. Some ant species, however, have unicolonial population structures where multiple nests, each containing numerous queens, are interconnected and individuals move freely between nests. In such cases, nestmate relatedness values may often be indistinguishable from zero, which is problematic for inclusive fitness‐based explanations of reproductive altruism. We conducted a detailed population genetic study in the polygynous antFormica exsecta, which has been suggested to form unicolonial populations in its native habitat. Analyses based on adult workers indeed confirmed a genetic structuring consistent with a unicolonial population structure. However, at the population level the genetic structuring inferred from worker pupae was not consistent with a unicolonial population structure, but rather suggested a multicolonial population structure of extended family‐based nests. These contrasting patterns suggest limited queen dispersal and free adult worker dispersal. That workers indeed disperse as adults was confirmed by mark–recapture measures showing consistent worker movement between nests. Together, these findings describe a new form of social organization, which possibly also characterizes other ant species forming unicolonial populations in their native habitats. Moreover, the genetic analyses also revealed that while worker nestmate relatedness was indistinguishable from zero at a small geographical scale, it was significantly positive at the population level. This highlights the need to consider the relevant geographical scale when investigating the role of inclusive fitness as a selective force maintaining reproductive altruism.
Rapid morphological and genetic change in Chicago‐area Peromyscus
Authors: PERGAMS OLIVER R. W. , LACY ROBERT C.
Published: September 2007

We report rapid change of morphology and mitochondrial genes in white‐footed mice (Peromyscus leucopus) in the Chicago (Illinois, USA) region. We sequenced mitochondrial DNA COX2 from 55 museum skins of white‐footed mice caught in the Chicago area since 1855 and from 44 mice recently trapped in the same locations. We found consistent directional genotype replacement at five separate collection locations. We later focused on a single one of these locations (Volo Bog State Natural Area) and sequenced mitochondrial D‐loop control region from 58 museum skins of mice collected in 1903–1976 and 32 mice recently trapped there. We found complete and more recent replacement of D‐loop haplotypes, apparently occurring between 1976 and 2001. We tested whether these genetic changes were mirrored by changes in morphology by comparing 15 external and cranial traits. We found no significant morphological differences between mice collected in 1903–1976; however, mice collected in 2001–2003 showed 9 of 15 measurements to be significantly changed relative to the earlier samples. Recent mice were longer in total length, with broader, longer noses, and longer but shallower skulls1. Discriminant function analysis allowed for 100% correct classification using these traits. Principal components analysis shows variance over time is well distributed across both external and cranial measures. The sequential replacements of haplotypes and the rapid change of morphology can best be explained by replacement of the regional population with immigrants from genetically distinct neighbouring populations, likely facilitated by the large environmental changes occurring over the time period. Replacement with genotypes from external populations may be a common mechanism of evolution of newly adaptive local forms in an increasingly human‐impacted world.
Analysis of Spanish populations ofOphiostoma ulmiandO. novo‐ulmiusing phenotypic characteristics and RAPD markers
Authors: Solla A. , Dacasa M. C. , Nasmith C. , Hubbes M. , Gil L.
Published: September 2007

One hundred and six isolates of the Dutch elm disease (DED) fungiOphiostoma ulmiandOphiostoma novo‐ulmiwere collected from elm trees with symptoms in 15 regions of Spain. Isolates were compared with eight reference strains belonging toO. ulmiand the two subspecies ofO. novo‐ulmi.The purpose of this study was to assign Spanish isolates to species and subspecies of the DED fungi and to analyse the genetic variability within the Spanish populations of these pathogens. Isolates were examined for their growth rates, colony morphologies and fertility responses and by using random amplified polymorphic DNA (RAPD) markers. Six isolates were identified asO. ulmi, 16 asO. novo‐ulmissp.novo‐ulmiand 78 asO. novo‐ulmissp.americana. Nei's and Shannon's diversity indices and theupgmadendrogram from RAPD profiles indicated a high level of variation among isolates, probably reflecting post‐epidemic status of DED in Spain. Although most isolates were separated into three major clusters representing the three taxa of DED fungi in the RAPD analysis, two isolates from central Spain clustered betweenO. novo‐ulmissp.americanaandO. novo‐ulmissp.novo‐ulmi, and four isolates from Mallorca clustered betweenO. ulmiand the group representingO. novo‐ulmissp.novo‐ulmi. Mating tests conducted with these isolates revealed a variety of fertility responses. The novel combinations between molecular profile and fertility reaction suggest that three isolates from Mallorca may be interspecific hybrids of the DED fungi.
Spatial pattern of black spot incidence within citrus trees related to disease severity and pathogen dispersal
Authors: Spósito M. B. , Amorim L. , Bassanezi R. B. , Filho A. Bergamin , Hau B.
Published: September 2007

Guignardia citricarpa, the causal agent of citrus black spot, forms airborne ascospores on decomposing citrus leaves and water‐spread conidia on fruits, leaves and twigs. The spatial pattern of diseased fruit in citrus tree canopies was used to assess the importance of ascospores and conidia in citrus black spot epidemics in São Paulo State, Brazil. The aggregation of diseased fruit in the citrus tree canopy was quantified by the binomial dispersion index (D) and the binary form of Taylor's Power Law for 303 trees in six groves. D was significantly greater than 1 in 251 trees. The intercept of the regression line of Taylor's Power Law was significantly greater than 0 and the slope was not different from 1, implying that diseased fruit was aggregated in the canopy independent of disease incidence. Disease incidence (p) and severity (S) were assessed in 2875 citrus trees. The incidence‐severity relationship was described (R2 = 88·7%) by the model ln(S) = ln(a) + bCLL(p) where CLL = complementary log‐log transformation. The high severity at low incidence observed in many cases is also indicative of low distance spread of G. citricarpa spores. For the same level of disease incidence, some trees had most of the diseased fruit with many lesions and high disease severity, whereas other trees had most of the fruit with few lesions and low disease severity. Aggregation of diseased fruit in the trees suggests that splash‐dispersed conidia have an important role in increasing the disease in citrus trees in Brazil.