bluuebunny/crossref_metadata_2025 huggingface dataset:
Interaction between desialylated hepatitis B virus and asialoglycoprotein receptor on hepatocytes may be indispensable for viral binding and entry
Authors: Owada T. , Matsubayashi K. , Sakata H. , Ihara H. , Sato S. , Ikebuchi K. , Kato T. , Azuma H. , Ikeda H.
Published: December 2005

Summary.  The cellular receptor for hepatitis B virus (HBV) infection has not yet been identified. The purpose of this study was to address the possibility of participation by desialylated HBV and the asialoglycoprotein receptor (ASGP‐R) exclusively expressed on liver parenchymal cells, in infection. Assays for viral binding and entry were performed by culturing a hepatoblastoma cell line, HepG2, and HBV particles derived from the HBV carrier in the presence or absence of neuraminidase (NA). Viral binding and entry were clearly enhanced in the presence of NA, and the enhancement of the binding could be blocked by asialo‐fetuin and ethylenediamine‐tetraacetic acid (EDTA). In addition, covalently closed circular (CCC)‐DNA, as a marker of infectivity, was detected in the presence of NA, but not in its absence. The optimal concentration of NA raised infectivity more than 1000 times. We concluded that this method makes it feasible to evaluate the infectivity of HBV in vitro and that ASGP‐R may be a specific HBV receptor once viral particles are desialylated.
Molecular epidemiology of hepatitis C virus (HCV) in Greece: temporal trends in HCV genotype‐specific incidence and molecular characterization of genotype 4 isolates
Authors: Katsoulidou A. , Sypsa V. , Tassopoulos N. C. , Boletis J. , Karafoulidou A. , Ketikoglou I. , Tsantoulas D. , Vafiadi I. , Hatzis G. , Skoutelis A. , Akriviadis E. , Vasiliadis T. , Kitis G. , Magiorkinis G. , Hatzakis A.
Published: December 2005

Summary.  This study aimed to estimate the overall HCV genotype distribution and to reconstruct the HCV genotype‐specific incidence in Greece during the recent decades. It also focused at the identification of genotype 4 subtype variability in Greek isolates. A total of 1686 chronically infected HCV patients with detectable serum HCV RNA by RT‐PCR, belonging to different risk groups were studied. Amplified products from the 5′‐noncoding region were typed using a commercially available assay based on the reverse hybridization principle. The HCV genotype‐specific incidence was estimated using a previously described back calculation method. HCV genotype 1 was the most prevalent (46.9%) followed by genotype 3 (28.1%), 4 (13.2%), 2 (6.9%) and 5 (0.4%). A high prevalence of genotype 1 (66.3%) in haemophilia patients was recorded whereas HCV genotype 3 was found mainly among patients infected by I.V. drug use (58.2%). Data on the temporal patterns of HCV genotype‐specific incidence in Greece revealed a moderate increase (1.3–1.6 times) for genotypes 1 and 4, and a decrease (1.5 times) for genotype 2 from 1970 to 1990, whereas there was a sharp (13‐fold) increase for genotype 3. The molecular characterization of 41 genotype 4 HCV isolates belonging to various risk groups revealed that, subtype 4a was the most frequently detected (78%). Phylogenetic comparison of the Greek 4a isolates with all HCV‐4a isolates reported worldwide so far revealed a topology which does not discriminate Greek isolates from the others. HCV‐4 does not represent a recent introduction in Greece.
European colonization by the spined loach (Cobitis taenia) from Ponto‐Caspian refugia based on mitochondrial DNA variation
Authors: CULLING MARK A. , JANKO KAREL , BORON ALICJA , VASIL’EV VICTOR P. , CÔTÉ ISABELLE M. , HEWITT GODFREY M.
Published: December 2005

In the last 20 years, new species, asexual reproduction, polyploidy and hybridization have all been reported within the genus Cobitis. An understanding of the current distribution and baseline phylogeographical history of ‘true’ nonhybrid Cobitis species is crucial in order to unravel these discoveries. In the present work, we investigated the phylogeography of the spined loach, Cobitis taenia, using 1126 bp of the mitochondrial cytochrome b gene from 174 individuals collected at 47 sites. In total, 51 haplotypes that differed at 49 positions (4.35%) were detected. We deduce that C. taenia survived European glaciations in at least three refuges in the Ponto‐Caspian area. Two of these refuges each provided a major lineage that recolonized Europe in separate directions: one westward to England and the other spreading north into Russia before moving west. A third (minor) lineage that contributed little to the recolonization of Europe was also revealed — remaining near its Black Sea refuge. However, more recent history was difficult to resolve with colonization from a more western refugium during the last glacial maximum (LGM) a distinct possibility. Nested clade analysis indicates a pattern of restricted gene flow with isolation by distance at the first two levels and overall. Unlike many other European freshwater fish species, the Danube is not part of the current distribution of C. taenia, nor was it used as either a refuge or a source of colonization of Europe. Low genetic diversity within C. taenia suggests that its colonization of Europe is relatively recent. Demographic analyses revealed a history of recent expansion and isolation by distance.
A tale of two siblings: multiple paternity in big brown bats (Eptesicus fuscus) demonstrated using microsatellite markers
Authors: VONHOF M. J. , BARBER D. , FENTON M. B. , STROBECK C.
Published: December 2005

In many bat species, the opportunity for sperm competition or other mechanisms of post‐copulatory paternity biasing is thought to be great, due to the long delay between copulation and fertilization, demonstrated sperm storage capabilities, and observed promiscuity. We present the results of the first study to assess whether litters of big brown bats (Eptesicus fuscus) containing dizygotic twins share the same father. We sampled 26 mother–offspring triads from three colonies in Indiana and Illinois, as well as 299 additional adults (237 females and 62 males) from these colonies and six other maternity colonies in the same area in 1997–1998. All individuals were genotyped at nine highly variable autosomal microsatellite loci and one X‐linked locus. We assessed multiple paternity using autosomal and X‐linked locus exclusions, and using maximum‐likelihood methods. All methods confirmed multiple paternity within litters, and the maximum‐likelihood analyses indicated that almost half of the sampled litters were composed of maternal half‐siblings rather than full‐siblings. Our results highlight the potential importance of post‐copulatory mechanisms of paternity determination in the mating system of big brown bats, and have important implications for gene flow and population structuring in this species.
Rapid parallel evolutionary changes of gene transcription profiles in farmed Atlantic salmon
Authors: ROBERGE CHRISTIAN , EINUM SIGURD , GUDERLEY HELGA , BERNATCHEZ LOUIS
Published: December 2005

Farmed salmon strains have been selected to improve growth rates as well as other traits of commercial interest but the 2 million farmed salmon escaping annually may enhance the risk of extinction of wild populations through genetic and ecological interactions. Here, we compare the transcription profiles of 3557 genes in the progeny of farmed and wild Atlantic salmon from Norway and Canada grown in controlled conditions, and demonstrate that five to seven generations of artificial selection led to heritable changes in gene transcription profiles, the average magnitude of the differences being 25% and 18% for at least 1.4% and 1.7% of the expressed genes in juvenile salmon from Norway and Canada, respectively. Moreover, genes showing significant transcription profile differences in both farmed strains (16%) all exhibited parallel changes. These findings, along with the identification of several genes whose expression profiles were modified through artificial selection, provide new insights into the molecular basis of parallel evolution, and suggest how gene flow from farmed escapees may affect the genetic integrity of wild populations.
Bayesian analyses of admixture in wild and domestic cats (Felis silvestris) using linked microsatellite loci
Authors: LECIS R. , PIERPAOLI M. , BIRÒ Z. S. , SZEMETHY L. , RAGNI B. , VERCILLO F. , RANDI E.
Published: December 2005

Methods recently developed to infer population structure and admixture mostly use individual genotypes described by unlinked neutral markers. However, Hardy–Weinberg and linkage disequilibria among independent markers decline rapidly with admixture time, and the admixture signals could be lost in a few generations. In this study, we aimed to describe genetic admixture in 182 European wild and domestic cats (Felis silvestris), which hybridize sporadically in Italy and extensively in Hungary. Cats were genotyped at 27 microsatellites, including 21 linked loci mapping on five distinct feline linkage groups. Genotypes were analysed with structure 2.1, a Bayesian procedure designed to model admixture linkage disequilibrium, which promises to assess efficiently older admixture events using tightly linked markers. Results showed that domestic and wild cats sampled in Italy were split into two distinct clusters with average proportions of membership Q > 0.90, congruent with prior morphological identifications. In contrast, free‐living cats sampled in Hungary were assigned partly to the domestic and the wild cat clusters, with Q < 0.50. Admixture analyses of individual genotypes identified, respectively, 5/61 (8%), and 16–20/65 (25–31%) hybrids among the Italian wildcats and Hungarian free‐living cats. Similar results were obtained in the past using unlinked loci, although the new linked markers identified additional admixed wildcats in Italy. Linkage analyses confirm that hybridization is limited in Italian, but widespread in Hungarian wildcats, a population that is threatened by cross‐breeding with free‐ranging domestic cats. The total panel of 27 loci performed better than the linked loci alone in the identification of domestic and known hybrid cats, suggesting that a large number of linked plus unlinked markers can improve the results of admixture analyses. Inferred recombination events led to identify the population of origin of chromosomal segments, suggesting that admixture mapping experiments can be designed also in wild populations.
Spatial dynamics of supercolonies of the invasive yellow crazy ant,Anoplolepis gracilipes, on Christmas Island, Indian Ocean
Authors: Abbott K. L.
Published: December 2005

Key to the management of invasive species is an understanding of the scope of an invasion, the rate of proliferation and the rate at which invaded habitats become degraded. This study examines the spatial dynamics of high‐density supercolonies of the invasive yellow crazy ant,Anoplolepis gracilipes, on Christmas Island, Indian Ocean, and the associated impacts at their boundaries. Since the early 1990s,A. gracilipessupercolonies have occupied over 30% of the 10,000 ha of rainforest on Christmas Island. Thirty‐four discrete high‐density supercolonies formed between 1989 and 2003, ranging in size across nearly three orders of magnitude from 0.9 to 787 ha. Supercolonies boundaries are diffuse, and ants were observed in low densities in some cases up to 200 m from the main high‐density supercolony. The 13 boundaries examined were all dynamic over a 10–20 observation month period: nine boundaries expanded, and the maximum rate of spread was 0.5 m day−1. Across boundary transition zones, between high‐density supercolonies and intact rainforest, yellow crazy ants reduced other ant species richness, occupied red crab burrows and killed resident red crabs, which was the trigger for ‘invasional meltdown’ on Christmas Island. The highly variable and unpredictable nature ofA. gracilipesboundaries poses a challenge for incorporation into a predictive framework, as well as for their management.
Regional and local influence of grazing activity on the diversity of a semi‐arid dung beetle community
Authors: Lobo Jorge M. , Hortal Joaquín , Cabrero‐Sañudo Francisco J.
Published: December 2005

This study analyses the effect of resource availability (i.e. sheep dung) on dung beetle communities in an arid region of Central Spain, both at regional and at local scales. A total of 18 sites within 600 km2were sampled for the regional analysis and 16 sites within the 30 km2of an Iberian municipality were sampled for the local analysis. Spatial and environmental characteristics of sampling sites were also compiled at both scales, including measures of grazing activity (livestock density at regional scale, and two counts of rabbit and sheep dung at local scale). At a regional scale, any environmental or spatial variable can help to explain the variation in abundance. However, species richness was related to summer precipitation and composition was related to elevation. At local scale, abundance is not significantly related to any of the environmental variables, but species richness was related to the local amount of sheep dung (27% of variance). The amount of dung in a 2‐km buffer around the site accounts for 27–32% of variance in abundance and 60–65% of variance in species richness. The presence of the flock with the highest sheep density explains 53% of abundance variability and 73% of species richness variance. A cluster analysis of localities identified two main groups, one characterized by a lower abundance and species richness that can be considered a nested subsample of the species‐rich group. The mean and maximum amount of sheep dung in the sites separated by less than 2 km are the only significant explanatory variables able to discriminate both groups.

These results suggest that grazing intensity (and the associated increase in the amount of trophic resources) is a key factor in determining local variation in the diversity and composition of dung beetle assemblages. However, dung beetle assemblages are not spatially independent at the analysed resolution, and the amount of dung in the surroundings seems to be more important for locally collected species than the dung effectively found in the site. Although differences in the availability and quantity of trophic resources among nearby sites could be affecting the population dynamics and dispersion of dung beetles within a locality, sites with larger populations, and greater species numbers would not be able to exercise enough influence as to bring about a complete local faunistic homogenization.
Do body size and diet breadth affect partitioning of species diversity? A test with forest Lepidoptera
Authors: Summerville Keith S. , Wilson Tiffany D. , Veech Joseph A. , Crist Thomas O.
Published: December 2005

Two of the major themes resulting from recent macroecological research are the central roles that body size and niche breadth may play as determinants of species geographical distribution. Unanswered questions, however, linger regarding how similarities in body size or niche breadth affect the allocation of α‐ and β‐diversity across spatial scales. Using data on moth diversity in the eastern deciduous forest of North America, we tested the predictions that smaller‐bodied and diet‐restricted species would have lower levels of α‐diversity within forest stands and greater β‐diversity at higher sampling scales compared to larger or more generalist species. Moths were sampled using a nested sampling design consisting of three hierarchical levels: 20 forest stands, 5 sites and 3 ecoregions. Body size for 492 species was estimated as mean forewing length, and diet breadth was assessed from the published literature. Moth species were then classified according to body size (small or large) or diet breadth (generalist or restricted), and partitioning was conducted on each group. Diversity partitions for large‐ and small‐bodied species yielded similar patterns. When observed diversity components differed from those derived from our null model, a consistent pattern was observed: α‐diversity was greater than expected, β‐diversity among forest stands was less than expected, and β‐diversity among sites and ecoregions was higher than expected. In contrast, diet‐restricted moths contributed significantly less to stand‐level α‐diversity than generalist feeders. Furthermore, specialists contributed to a greater proportion of β‐diversity across scales compared to generalist moths. Because absolute measures of β‐diversity among stands were greater for generalists than for restricted feeders, we suggest that regional β‐diversity of forest moths may be influenced by several possible factors: intraspecific aggregation of diet‐restricted species, local fluctuations in population size of eruptive generalists and small geographical distributions of generalist moths than predicted by the geographical extent of putative host plants
Reconstructing ancestral ecologies: challenges and possible solutions
Authors: Hardy Christopher R.
Published: December 2005

There are several ways to extract information about the evolutionary ecology of clades from their phylogenies. Of these, character state optimization and ‘ancestor reconstruction’ are perhaps the most widely used despite their being fraught with assumptions and potential pitfalls. Requirements forrobustinferences of ancestral traits in general (i.e. those applicable to all types of characters) include accurate and robust phylogenetic hypotheses, complete species‐level sampling and the appropriate choice of optimality criterion. Ecological characters, however, also require careful consideration of methods for accounting for intraspecific variability. Such methods include ‘Presence Coding’ and ‘Polymorphism Coding’ for discrete ecological characters, and ‘Range Coding’ and ‘MaxMin Coding’ for continuously variable characters. Ultimately, however, historical inferences such as these are, as with phylogenetic inference itself, associated with a degree of uncertainty. Statistically based uncertainty estimates are available within the context of model‐based inference (e.g. maximum likelihood and Bayesian); however, these measures are only as reliable as the chosen model is appropriate. Although generally thought to preclude the possibility of measuring relative uncertainty or support for alternative possible reconstructions, certain useful non‐statistical support measures (i.e. ‘Sharkey support’ and ‘Parsimony support’) are applicable to parsimony reconstructions.
What can phylogenetics tell us about speciation in the Cape flora?
Authors: Barraclough Timothy G.
Published: December 2005

The spectacular diversity of the Cape flora has promoted wide speculation on the evolutionary processes behind its origins, but until recently these ideas could not be tested rigorously due to the almost complete absence of a fossil record for the region. Now, molecular phylogenetic approaches, combined with analyses of ecological and biogeographical information, offer the potential to test key hypotheses about speciation of so‐called Cape clades of flowering plants. We outline the main theories and how they might be tested by phylogenetic approaches. One conclusion is that population level studies of particular species complexes are now needed to complement the growing volume of phylogenetic information for Cape clades and to provide better understanding of mechanisms of population divergence in the Cape. Another is that comparisons between Cape and non‐Cape clades are needed to confirm whether speciation is indeed faster in the Cape region. An alternative possibility, that extinction rates are lower, should also be considered in these comparisons. By virtue of the ongoing, coordinated efforts by a global team of botanists, the Cape is now uniquely placed for exploring the origins and assembly of a regional assemblage or biome.
Using phylogeny to investigate the origins of the Cape flora: the importance of taxonomic, gene and genome sampling strategies
Authors: Hawkins J. A.
Published: December 2005

Phylogenetic methods hold great promise for the reconstruction of the transition from precursor to modern flora and the identification of underlying factors which drive the process. The phylogenetic methods presently used to address the question of the origin of the Cape flora of South Africa are considered here. The sampling requirements of each of these methods, which include dating of diversifications using calibrated molecular trees, sister pair comparisons, lineage through time plots and biogeographical optimizations, are reviewed. Sampling of genes, genomes and species are considered. Although increased higher‐level studies and increased sampling are required for robust interpretation, it is clear that much progress is already made. It is argued that despite the remarkable richness of the flora, the Cape flora is a valuable model system to demonstrate the utility of phylogenetic methods in determining the history of a modern flora.
Molecular dating of phylogenetic trees: A brief review of current methods that estimate divergence times
Authors: Rutschmann Frank
Published: December 2005

This article reviews the most common methods used today for estimating divergence times and rates of molecular evolution. The methods are grouped into three main classes: (1) methods that use a molecular clock and one global rate of substitution, (2) methods that correct for rate heterogeneity, and (3) methods that try to incorporate rate heterogeneity. Additionally, links to the most important literature on molecular dating are given, including articles comparing the performance of different methods, papers that investigate problems related to taxon, gene and partition sampling, and literature discussing highly debated issues like calibration strategies and uncertainties, dating precision and the calculation of error estimates.
Investigating the evolution of floras: problems and progress — An introduction
Authors: Linder H. P.
Published: December 2005

The Cape flora of southern Africa is a remarkable hotspot for plant species diversity and endemism. At a meeting in Zurich in 2004 progress in understanding the evolution of this diversity was reviewed. In this symposium, four papers presenting several of the methods used in this investigation were reported. These papers deal with molecular dating methods, the reconstruction of ancestral habitats, with possible speciation scenarios for the Cape flora, and the importance of the correct sampling strategies.
Using niche‐based modelling to assess the impact of climate change on tree functional diversity in Europe
Authors: Thuiller Wilfried , Lavorel Sandra , Sykes Martin T. , Araújo Miguel B.
Published: December 2005

Rapid anthropogenic climate change is already affecting species distributions and ecosystem functioning worldwide. We applied niche‐based models to analyse the impact of climate change on tree species and functional diversity in Europe. Present‐day climate was used to predict the distributions of 122 tree species from different functional types (FT). We then explored projections of future distributions under one climate scenario for 2080, considering two alternative dispersal assumptions: no dispersal and unlimited dispersal. The species‐rich broadleaved deciduous group appeared to play a key role in the future of different European regions. Temperate areas were projected to lose both species richness and functional diversity due to the loss of broadleaved deciduous trees. These were projected to migrate to boreal forests, thereby increasing their species richness and functional diversity. Atlantic areas provided an intermediate case, with a predicted reduction in the numbers of species and occasional predicted gains in functional diversity. This resulted from a loss in species within the broadleaved deciduous FT, but overall maintenance of the group. Our results illustrate the fact that both species‐specific predictions and functional patterns should be examined separately in order to assess the impacts of climate change on biodiversity and gain insights into future ecosystem functioning.
Spider diversity in a tropical habitat gradient in Chiapas, Mexico
Authors: Pinkus‐Rendón Miguel Angel , León‐Cortés Jorge Leonel , Ibarra‐Núñez Guillermo
Published: December 2005

This paper presents an assessment of spider diversity in a complex landscape of southern Mexico. Eighteen different habitats were identified, measured and mapped across this fragmented landscape. Habitat types were characterized by measuring various features, including number of plant forms, tree cover and litter depth. Each month from February to April (dry season) and from June to August 2002 (wet season), spiders were sampled on each habitat by using pitfall traps and direct collection. Correlations between spider diversity and habitat characteristics were carried out to explore the relative contribution of each habitat variable as related to changes in spider composition and richness. In total, 115 spider species were recorded in 18 habitat types, and the mean number and density of species per habitat were 21 (± 3, standard error of mean) and 57 (± 9), respectively. The species recorded represent 41% of the fauna recorded in the Mexican state of Chiapas and 4% of the fauna recorded in Mexico. Relatively pristine habitats (e.g. deciduous forest) contained an important proportion of spider diversity in this fragmented landscape. Epigean spider diversity was significantly correlated with tree cover and with the diversity of plant forms during the rainy season. No correlation was detected between soil spider diversity and the habitat variables measured for any season. The results of this work suggest that in highly fragmented tropical landscapes, some habitat types (e.g. coffee plantations, hedgerows) might play an important role for the persistence of spider populations. The prevalence of relatively stable conditions in some of these habitats can allow spiders species (e.g. Nephila clavipes) to overcome adverse conditions such as a decrease in humidity and dramatic changes in temperature and wind exposure, allowing them to recolonize when favourable conditions return.
Modelling local and long‐distance dispersal of invasive emerald ash borer Agrilus planipennis (Coleoptera) in North America
Authors: Muirhead Jim R. , Leung Brian , van Overdijk Colin , Kelly David W. , Nandakumar Kanavillil , Marchant Kenneth R. , MacIsaac Hugh J.
Published: December 2005

Limiting the damage by non‐indigenous species requires rapid determination of current and potential distributions and vectors of dispersal, and development of appropriate management measures. The emerald ash borer (Agrilus planipennis), a wood‐boring beetle native to South‐East Asia, was first reported in the Great Lakes region during summer 2002. The beetle poses an enormous threat to native ash (Fraxinus) species of North America, as untreated trees in infested areas of Ontario, Michigan and Ohio suffer high mortality. We demonstrate that the borer has spread in North America through a combination of diffusive range extension, associated with local flights, and by long‐distance ‘jump’ dispersal associated with human movement of infested sapling or contaminated firewood. Probability of infestation was inversely related to distance from borer epicentres but positively related to the size of human population centres. At least 9 of 39 populations that were first reported in Michigan during 2004 cannot be accounted for by local diffusion, raising the possibility that other unidentified mechanisms may be contributing to the dispersal of the beetle. In the absence of quarantine, by 2005 all of Michigan's lower peninsula was contained within the boundaries of potential diffusive range expansion. Infested ash saplings also were introduced from Michigan to Maryland during 2003, and subsequently transplanted to five sites in Maryland and Virginia. Quarantine and eradication measures have had mixed results: in the south‐central USA, the species appears on the brink of eradication, whereas its distribution has continued to spread during 2005 in the Great Lakes region despite extensive containment and quarantine measures. Quarantine success in the Great Lakes region is encumbered by multiple dispersal vectors, larger borer population sizes and by the more extensive geographical distribution that was achieved prior to implementation of control measures.
Metformin‐glibenclamide versus metformin plus rosiglitazone in patients with type 2 diabetes inadequately controlled on metformin monotherapy
Authors: Garber A. , Klein E. , Bruce S. , Sankoh S. , Mohideen P.
Published: December 2005

Aim:  This double‐blind study evaluated the efficacy and safety of metformin‐glibenclamide tablets vs. metformin plus rosiglitazone therapy in patients with type 2 diabetes inadequately controlled on metformin monotherapy.

Subjects and methods:  After an open‐label, metformin lead‐in phase, 318 patients were randomly assigned to treatment based on metformin‐glibenclamide 500/2.5 mg tablets (initial daily dose 1000/5 mg) or metformin 500 mg plus rosiglitazone 4 mg (initial daily dose 1000–2000 mg + 4 mg, depending on previous treatment) for 24 weeks. Doses were titrated to achieve the therapeutic glycaemic target. The primary efficacy variable was the change in HbA1C.

Results:  At week 24, metformin‐glibenclamide tablets resulted in significantly greater reductions in HbA1C (−1.5%) and fasting plasma glucose [−2.6 mmol/l (−46 mg/dl)] than metformin plus rosiglitazone [−1.1%, p < 0.001; −2 mmol/l (−36 mg/dl), p = 0.03]. More patients receiving metformin‐glibenclamide attained HbA1C <7.0% than did those in the metformin plus rosiglitazone group (60 vs. 47%) and had fasting plasma glucose levels <7 mmol/l (<126 mg/dl) by week 24 (34 vs. 25%). Both treatments were well tolerated. Frequency of adverse gastrointestinal events was comparable between groups. Four per cent of patients receiving metformin‐glibenclamide withdrew because of symptomatic hypoglycaemia contrasted with 3% of patients receiving metformin plus rosiglitazone who withdrew because of persistent hyperglycaemia. Hypoglycaemic events were mild or moderate in intensity and were easily self‐managed.

Conclusions:  Metformin‐glibenclamide tablets resulted in significantly greater reductions in HbA1C and fasting plasma glucose compared with metformin plus rosiglitazone in patients with type 2 diabetes inadequately controlled on metformin monotherapy.
Mitigation of establishment of Brassica napus transgenes in volunteers using a tandem construct containing a selectively unfit gene
Authors: Al‐Ahmad Hani , Dwyer Jennice , Moloney Maurice , Gressel Jonathan
Published: December 2005

Transgenic oilseed rape (Brassica napus) plants may remain as ‘volunteer’ weeds in following crops, complicating cultivation and contaminating crop yield. Volunteers can become feral as well as act as a genetic bridge for the transfer of transgenes to weedy relatives. Transgenic mitigation using genes that are positive or neutral to the crop, but deleterious to weeds, should prevent volunteer establishment, as previously intimated using a tobacco (Nicotiana tabacum) model. A transgenically mitigated (TM), dwarf, herbicide‐resistant construct using a gibberellic acid‐insensitive (Δgai) gene in the B. napus crop was effective in offsetting the risks of transgene establishment in volunteer populations of B. napus. This may be useful in the absence of herbicide, e.g. when wheat is rotated with oilseed rape. The TM dwarf B. napus plants grown alone had a much higher yield than the non‐transgenics, but were exceedingly unfit in competition with non‐transgenic tall cohorts. The reproductive fitness of TM B. napus was 0% at 2.5‐cm and 4% at 5‐cm spacing between glasshouse‐grown plants relative to non‐transgenic B. napus. Under screen‐house conditions, the reproductive fitness of TM B. napus relative to non‐transgenic B. napus was less than 12%, and the harvest index of the TM plants was less than 40% of that of the non‐transgenic competitors. The data clearly indicate that the Δgai gene greatly enhances the yield in a weed‐free transgenic crop, but the dwarf plants can be eliminated when competing with non‐transgenic cohorts (and presumably other species) when the selective herbicide is not used.
Mitigation using a tandem construct containing a selectively unfit gene precludes establishment of Brassica napus transgenes in hybrids and backcrosses with weedy Brassica rapa
Authors: Al‐Ahmad Hani , Gressel Jonathan
Published: December 2005

Transgenic oilseed rape (Brassica napus) plants can interbreed with nearby weedy Brassica rapa, potentially enhancing the weediness and/or invasiveness of subsequent hybrid offspring. We have previously demonstrated that transgenic mitigation effectively reduces the fitness of the transgenic dwarf and herbicide‐resistant B. napus volunteers. We now report the efficacy of such a tandem construct, including a primary herbicide‐resistant gene and a dwarfing mitigator gene, to preclude the risks of gene establishment in the related weed B. rapa and its backcross progeny. The transgenically mitigated and non‐transgenic B. rapa × B. napus interspecific hybrids and the backcrosses (BC1) with B. rapa were grown alone and in competition with B. rapa weed. The reproductive fitness of hybrid offspring progressively decreased with increased B. rapa genes in the offspring, illustrating the efficacy of the concept. The fitness of F2 interspecific non‐transgenic hybrids was between 50% and 80% of the competing weedy B. rapa, whereas the fitness of the comparable T2 interspecific transgenic hybrids was never more than 2%. The reproductive fitness of the transgenic T2 BC1 mixed with B. rapa was further severely suppressed to 0.9% of that of the competing weed due to dwarfism. Clearly, the mitigation technology works efficiently in a rapeseed crop–weed system under biocontainment‐controlled environments, but field studies should further validate its utility for minimizing the risks of gene flow.
Pod shatter‐resistant Brassica fruit produced by ectopic expression of the FRUITFULL gene
Authors: Østergaard Lars , Kempin Sherry A. , Bies Dawn , Klee Harry J. , Yanofsky Martin F.
Published: December 2005

Arabidopsis has proven to be extremely useful as a reference organism for studies in plant biology, and huge efforts have been employed to unravel various mechanisms of Arabidopsis growth. A major challenge now is to demonstrate that this wealth of knowledge can be used for global agricultural and environmental improvement. Brassica species are closely related to Arabidopsis and represent ideal candidates for model‐to‐crop approaches as they include important crop plants, such as canola. Brassica plants normally disperse their seeds by a pod‐shattering mechanism. Although this mechanism is an advantage in nature, unsynchronized pod shatter constitutes one of the biggest problems for canola farmers. Here, we show that ectopic expression of the Arabidopsis FRUITFULL gene in Brassica juncea is sufficient to produce pod shatter‐resistant Brassica fruit and that the genetic pathway leading to valve margin specification is conserved between Arabidopsis and Brassica. These studies demonstrate a genetic strategy for the control of seed dispersal that should be generally applicable to diverse Brassica crop species to reduce seed loss.
Morphological and habitat evolution in the Cyanobacteria using a compartmentalization approach
Authors: SÁNCHEZ‐BARACALDO P. , HAYES P. K. , BLANK C. E.
Published: December 2005

A phylogenomic approach was used to study the evolution of traits in the Cyanobacteria. A cyanobacterial backbone tree was constructed using multiple concatenated sequences from whole genome sequences. Additional taxa were added using a separate alignment that contained morphological characters, SSU (small subunit) and LSU (large subunit) rDNA, rpoC, rpoD, tufA, and gyrB genes. A compartmentalization approach was then used to construct a robust phylogeny with resolved deep branches. Additional morphological characters (e.g. unicellular or filamentous growth, presence or absence of heterocysts) were coded, mapped onto the backbone cyanobacterial tree, and the ancestral character states inferred. Our analyses show that the earliest cyanobacterial lineages were likely unicellular coccoid/ellipsoidal/short rods that lived in terrestrial/freshwater environments. Later cyanobacterial lineages independently gained the ability to colonize brackish, marine, and hypersaline environments while acquiring a large number of more complex traits: sheath, filamentous growth, nitrogen fixation, thermophily, motility, and use of sulphide as an electron donor. Many of these adaptations would have been important in the appearance of dense microbial mats early in Earth's history. Complex traits such as hormogonia, heterocysts, and akinetes had a single ancestor. Within the Nostocales, hormogonia and heterocysts arose before akinetes.
Spatial variations of methanotrophic consortia at cold methane seeps: implications from a high‐resolution molecular and isotopic approach
Authors: ELVERT M. , HOPMANS E. C. , TREUDE T. , BOETIUS A. , SUESS E.
Published: December 2005

Anaerobic methane‐oxidizing microbial communities in sediments at cold methane seeps are important factors in controlling methane emission to the ocean and atmosphere. Here, we investigated the distribution and carbon isotopic signature of specific biomarkers derived from anaerobic methanotrophic archaea (ANME groups) and sulphate‐reducing bacteria (SRB) responsible for the anaerobic oxidation of methane (AOM) at different cold seep provinces of Hydrate Ridge, Cascadia margin. The special focus was on their relation to in situ cell abundances and methane turnover. In general, maxima in biomarker abundances and minima in carbon isotope signatures correlated with maxima in AOM and sulphate reduction as well as with consortium biomass. We found ANME‐2a/DSS aggregates associated with high abundances of sn‐2,3‐di‐O‐isoprenoidal glycerol ethers (archaeol, sn‐2‐hydroxyarchaeol) and specific bacterial fatty acids (C16:1ω5c, cyC17:0ω5,6) as well as with high methane fluxes (Beggiatoa site). The low to medium flux site (Calyptogena field) was dominated by ANME‐2c/DSS aggregates and contained less of both compound classes but more of AOM‐related glycerol dialkyl glycerol tetraethers (GDGTs). ANME‐1 archaea dominated deeper sediment horizons at the Calyptogena field where sn‐1,2‐di‐O‐alkyl glycerol ethers (DAGEs), archaeol, methyl‐branched fatty acids (ai‐C15:0, i‐C16:0, ai‐C17:0), and diagnostic GDGTs were prevailing. AOM‐specific bacterial and archaeal biomarkers in these sediment strata generally revealed very similar δ13C‐values of around −100. In ANME‐2‐dominated sediment sections, archaeal biomarkers were even more 13C‐depleted (down to −120), whereas bacterial biomarkers were found to be likewise 13C‐depleted as in ANME‐1‐dominated sediment layers (δ13C: −100). The zero flux site (Acharax field), containing only a few numbers of ANME‐2/DSS aggregates, however, provided no specific biomarker pattern. Deeper sediment sections (below 20 cm sediment depth) from Beggiatoa covered areas which included solid layers of methane gas hydrates contained ANME‐2/DSS typical biomarkers showing subsurface peaks combined with negative shifts in carbon isotopic compositions. The maxima were detected just above the hydrate layers, indicating that methane stored in the hydrates may be available for the microbial community. The observed variations in biomarker abundances and 13C‐depletions are indicative of multiple environmental and physiological factors selecting for different AOM consortia (ANME‐2a/DSS, ANME‐2c/DSS, ANME‐1) along horizontal and vertical gradients of cold seep settings.
Archaeal and bacterial communities in geochemically diverse hot springs of Yellowstone National Park, USA
Authors: MEYER‐DOMBARD D. R. , SHOCK E. L. , AMEND J. P.
Published: December 2005

Microbiological and geochemical surveys were conducted at three hot springs (Obsidian Pool, Sylvan Spring, and ‘Bison Pool’) in Yellowstone National Park (Wyoming, USA). Microbial community structure was investigated by polymerase chain reaction (PCR) amplification of 16S rRNA gene sequences from DNA extracted from sediments of each hot spring, followed by molecular cloning. Both bacterial and archaeal DNA was retrieved from all samples. No Euryarchaea were found, but diverse Crenarchaea exist in all three pools, particularly affiliating with deep‐branching, but uncultivated organisms. In addition, cloned DNA affiliating with the Desulphurococcales and Thermoproteales was identified, but the distribution of taxa differs in each hot spring. The bacterial community at all three locations is dominated by members of the Aquificales and Thermodesulfobacteriales, indicating that the ‘knallgas’ reaction (aerobic hydrogen oxidation) may be a central metabolism in these ecosystems. To provide geochemical context for the microbial community structures, energy‐yields for a number of chemolithoautotrophic reactions are provided for >80 sampling sites in Yellowstone, including Obsidian Pool, Sylvan Spring, and ‘Bison Pool’. This energy profile shows that the knallgas reaction is just one of many exergonic reactions in the Yellowstone hot springs, that energy‐yields for certain reactions can vary substantially from one site to the next, and that few of the demonstrated exergonic reactions are known to support microbial metabolism.
Living under an atomic force microscope
Authors: OBST M. , DITTRICH M.
Published: December 2005

An approach for long‐term in vivo investigations on cyanobacterial cell surface changes at high spatial resolution by Atomic Force Microscopy (AFM) was developed in this study.

Until recently, changes of bacterial cell surfaces due to changes of the chemical environment could neither be investigated in situ nor in vivo. However, in vivo investigations give insights into kinetics of cell response to environmental changes and mineral nucleation at the cell's surface. Continuously cultured cyanobacteria of the representative freshwater strain Synechococcus leopoliensis (PCC 7942) were washed and artificially immobilized on poly‐l‐lysine‐coated glass slides. Both immobilization and environmental conditions were optimized in order to facilitate long‐term experiments (> 100 h) with living cells. AFM samples were investigated in situ in two different solutions: Culture medium was used for cultivation experiments and nutrient‐free NaHCO3/CaCl2 solutions (supersaturated with respect to calcite) for long‐term characterizations of the changes in cell surface topography. Cell viability under these conditions was investigated by AFM, TEM and epifluorescence microscopy, independently.

No indications for extended starvation were found within the relevant timescales. Analysing the influence of Ca2+ on the surface of S. leopoliensis, we found significant changes compared to a Ca‐free solution. Few hours after CaCl2 was added to the circumfluent solution, small protuberances were observed on the cell surface.

These are promising results to environmental scientists for a wide range of applications, as cell response to environmental changes can now be monitored online and in vivo at timescales, which are relevant for natural processes. Most especially studies of biomineralization and mineral nucleation on bacterial cell surfaces will profit from this new approach.
The potential significance of microbial Fe(III) reduction during deposition of Precambrian banded iron formations
Authors: KONHAUSER K. O. , NEWMAN D. K. , KAPPLER A.
Published: December 2005

During deposition of late Archean–early Palaeoproterozoic Precambrian banded iron formations (BIFs) the downward flux of ferric hydroxide (Fe(OH)3) and phytoplankton biomass should have facilitated microbial Fe(III) reduction. However, quantifying the significance of such a metabolic pathway in the Precambrian is extremely difficult, considering the post‐depositional alteration of the rocks and the lack of ideal modern analogues. Consequently, we have very few constraints on the Fe cycle at that time, namely (i) the concentration of dissolved Fe(II) in the ocean waters; (ii) by what mechanisms Fe(II) was oxidized (chemical, photochemical or biological, the latter using either O2 or light); (iii) where the ferric hydroxide was precipitated (over the shelf vs. open ocean); (iv) the amount of phytoplankton biomass, which relates to the nutrient status of the surface waters; (v) the relative importance of Fe(III) reduction vs. the other types of metabolic pathways utilized by sea floor microbial communities; and (vi) the proportion of primary vs. diagenetic Fe(II) in BIF. Furthermore, although estimates can be made regarding the quantity of reducing equivalents necessary to account for the diagenetic Fe(II) component in Fe‐rich BIF layers, those same estimates do not offer any insights into the magnitude of Fe(III) actually generated within the water column, and hence, the efficiency of Fe and C recycling prior to burial. Accordingly, in this study, we have attempted to model the ancient Fe cycle, based simply on conservative experimental rates of photosynthetic Fe(II) oxidation in the euphotic zone. We estimate here that under ideal growth conditions, as much as 70% of the biologically formed Fe(III) could have been recycled back into the water column via fermentation and organic carbon oxidation coupled to microbial Fe(III) reduction. By comparing the potential amount of biomass generated phototrophically with the reducing equivalents required for Fe(III) reduction and magnetite formation, we also hypothesize that another anaerobic metabolic pathway might have been utilized in the surface sediment to oxidize the fermentation by‐products. Based on the premise that the deep ocean waters were anoxic, this role could have been fulfilled by methanogens, and maybe even methanotrophs that employed Fe(III) reduction.
ELEVATED ATMOSPHERIC CARBON DIOXIDE INCREASES ORGANIC CARBON FIXATION BY EMILIANIA HUXLEYI (HAPTOPHYTA), UNDER NUTRIENT‐LIMITED HIGH‐LIGHT CONDITIONS1
Authors: Leonardos Nikos , Geider Richard J.
Published: December 2005

Phytoplankton play a key role in determining the partitioning of CO2 between the atmosphere and the ocean on seasonal, interannual, and millennial time scales. The magnitude of biological draw‐down of atmospheric CO2 and C storage in the oceans is affected by concurrent changes in other environmental factors, like nutrient supply. Furthermore, variations in carbon‐to‐nitrogen (C:N) and carbon‐to‐phosphorus (C:P) assimilation ratios modify the oceanic CO2 storage capacity. Here we show that increased atmospheric CO2 concentration enhances CO2 fixation into organic matter by a noncalcifying strain of Emiliania huxleyi (Lohmann) Hay & Mohler only under certain conditions, namely high light and nutrient limitation. Enhanced organic matter production was accompanied by marked deviations of the C:N:P ratio from the canonical stoichiometry of marine particulate matter of 106:16:1 (C:N:P) known as the Redfield ratio. Increased cell organic carbon content, C:N, and C:P were observed at high light when growth was either nitrogen or phosphorus limited. Elevated CO2 led to further increases in the particulate C:N and C:P ratios. Enhanced CO2 uptake by phytoplankton such as E. huxleyi, in response to elevated atmospheric CO2, could increase carbon storage in the nitrogen‐limited regions of the oceans and thus act as a negative feedback on rising atmospheric CO2 levels.