bluuebunny/crossref_metadata_2025 huggingface dataset:
Impact of summer warming on the thermal characteristics of a polymictic lake and consequences for oxygen, nutrients and phytoplankton
Authors: WILHELM SUSANN , ADRIAN RITA
Published: October 2007

1. The impact of long thermal stratification events on some key properties in a polymictic lake was studied by determining the mixing regime of Müggelsee, Germany, using water temperature profiles taken hourly over 4 years. The period included two exceptional summer heatwaves.

2. Long thermal stratification events lasted from about 1 week to 2 months, and exhibited a high variability in thermocline depth and stratification intensity within and between events.

3. During stratification events, hypolimnetic oxygen concentrations strongly decreased while hypolimnetic SRP accumulation increased, depending on the duration and intensity of stratification and on hypolimnetic water temperature.

4. The impact of stratification on the functional phytoplankton composition increased with increasing stratification duration, but was rather different for the heatwaves.

5. Stratification events were followed by strong nutrient pulses into the euphotic zone and intense phytoplankton growth, particularly after the heatwaves. Hence, the influence of the climate extremes counteracted effects of reduced external nutrient loading.
The significance of side‐arm connectivity for carbon dynamics of the River Danube, Austria
Authors: PREINER S. , DROZDOWSKI I. , SCHAGERL M. , SCHIEMER F. , HEIN T.
Published: October 2007

1. Side‐arms connected to the main stem of the river are key areas for biogeochemical cycling in fluvial landscapes, exhibiting high rates of carbon processing.

2. This work focused on quantifying autochthonous and allochthonous carbon pools and, thereby, on comparing transport and transformation processes in a restored side‐arm system of the River Danube (Regelsbrunn). We established a carbon budget and quantified carbon processing from March to September 2003. In addition, data from previous studies during 1997 to 1999 were assessed.

3. Gross primary production (GPP) and community respiration were estimated by diel oxygen time curves and an oxygen mass balance. Plankton primary production was determined to estimate its contribution to GPP under different hydrological conditions.

4. Based on the degree of connectivity, three hydrological phases were differentiated. Most of the organic matter, dominated by allochthonous carbon, was transported in the main channel and through the side‐arm during floods, while at intermediate and low flows (and thus connectivity), transformation processes became more important and autochthonous carbon dominated the carbon pool. The side‐arm system functioned as a sink for particulate matter [total suspended solids and particulate organic carbon (POC)] and a source of dissolved organic carbon (DOC) and chlorophyll‐a.

5. Autochthonous primary production of 4.2 t C day−1in the side‐arm was equivalent to about 20% of the allochthonous inputs of 20 t C day−1(POC and DOC) entering the area at mean flow (1% of the discharge of the main channel). Pelagic photosynthesis was generally high at mean flow (1.3–3.8 g C m−2 day−1), and contributed up to 90% of system productivity. During long stagnant periods at low discharge, the side‐arm was controlled by biological processes and a shift from planktonic to benthic activity occurred (benthic primary production of 0.4–14 g C m−2 day−1).

6. The transformation of the organic matter that passes through the side‐arm under different hydrological conditions, points to the importance of these subsystems in contributing autochthonous carbon to the food web of the main channel.
Differential response of phytoplankton to additions of nitrogen, phosphorus and iron in Lake Tanganyika
Authors: WEVER AAIKE DE , MUYLAERT KOENRAAD , LANGLET DENIS , ALLEMAN LAURENT , DESCY JEAN‐PIERRE , ANDRÉ LUC , COCQUYT CHRISTINE , VYVERMAN WIM
Published: October 2007

1. In order to evaluate limitation of different phytoplankton groups by inorganic nutrients, multiple nutrient enrichment bioassays using the addition of iron (Fe) and the combined addition of nitrogen and phosphorus (NP) were carried out in the north and the south of Lake Tanganyika during the rainy and dry seasons in 2003 and 2004.

2. Nutrient additions resulted in an increase in phytoplankton growth rate relative to control treatments in all experiments. HPLC pigment data and epifluorescence microscopy counts indicated differential stimulation of the dominant phytoplankton groups. Iron additions mainly stimulated prokaryotic picophytoplankton, while enrichments with nitrogen and phosphorus stimulated green algae and in some cases diatoms. Extended incubation (3 days) indicated co‐limitation of Fe and NP, in particular for picocyanobacteria.
Climate change cannot be entirely responsible for soil carbon loss observed in England and Wales, 1978–2003
Authors: SMITH PETE , CHAPMAN STEPHEN J. , SCOTT W. ANDY , BLACK HELAINA I. J. , WATTENBACH MARTIN , MILNE RONNIE , CAMPBELL COLIN D. , LILLY ALLAN , OSTLE NICK , LEVY PETER E. , LUMSDON DAVID G. , MILLARD PETER , TOWERS WILLIE , ZAEHLE SÖNKE , SMITH JO U.
Published: October 2007

We present results from modelling studies, which suggest that, at most, only about 10–20% of recently observed soil carbon losses in England and Wales could possibly be attributable to climate warming. Further, we present reasons why the actual losses of SOC from organic soils in England and Wales might be lower than those reported.
Impacts of bark and foliage harvest on Khaya senegalensis (Meliaceae) reproductive performance in Benin
Authors: Gaoue Orou G. , Ticktin Tamara
Published: October 2007

Increasing concern over the sustainability of harvesting non‐timber forest products (NTFP) has led to a growing literature on the ecological impacts of NTFP extraction. A large proportion of NTFP are harvested for multiple plant parts, but few studies have assessed the impacts of harvesting multi‐use species. In addition, few studies have assessed how harvest effects may vary across space. This information is necessary for designing effective conservation plans for the many NTFP species that are harvested from variable ecological contexts.

This study assessed the impacts of combined bark and foliage harvest on Khaya senegalensis (Meliaceae) reproductive performance in Benin. K. senegalensis bark is an important medicine for malaria, the leaves are pruned by indigenous Fulani herders as a critical source of fodder for their livestock, and the timber is highly prized. Data on reproductive characteristics were collected from 12 populations spread across two ecological regions (Sudanian and Sudano–Guinean). Half the populations had a history of high harvest intensity and half were subject to low/no harvest.

Trees produced more fruit and began fruiting at a significantly smaller size in the drier Sudanian region than in the wetter Sudano–Guinean region. However, pruning decreased fruit production significantly in the Sudanian region but not in the Sudano–Guinean region. Pruning had a significantly greater impact on fruit production in larger trees than in smaller trees. High harvest populations in the Sudano–Guinean region had significantly higher rates of seed production than low harvest populations, although the seeds were significantly lighter. There were no significant effects of debarking or combined debarking and pruning on reproductive performance.

Synthesis and applications. This study illustrates that heavy rates of foliage harvest can decrease rates and patterns of reproduction in K. senegalensis, and that the impacts may vary across environmental contexts. Lowered rates of reproduction may lead to decreases in K. senegalensis population size over the long term. Effective ex situ conservation strategies for K. senegalensis include increasing the availability of its fodder and bark by promoting K. senegalensis plantations programmes involving Fulani harvesters.
Trapping and vaccination of endangered Ethiopian wolves to control an outbreak of rabies
Authors: Knobel D. L. , Fooks A. R. , Brookes S. M. , Randall D. A. , Williams S. D. , Argaw K. , Shiferaw F. , Tallents L. A. , Laurenson M. K.
Published: October 2007

As outbreaks of infectious diseases have emerged as a threat to small populations, conservation managers are increasingly making decisions regarding whether and how to intervene in such situations. Past controversies and lack of knowledge and firm guidelines may inhibit this process. We present data on a vaccination campaign against a rabies outbreak in endangered Ethiopian wolves as a case study of a disease‐control intervention in a threatened population.

Ethiopian wolves on the periphery of the outbreak area were trapped to administer a dose of injectable rabies vaccine and to assess the magnitude and duration of the immune response. The expansion of an established population monitoring programme allowed us to assess the factors influencing the probability of capturing particular animals and to evaluate the overall success of the intervention.

All wolves sampled 1 month after vaccination had protective levels of serum antibody titres. A booster dose administered within 1–6 months appeared to be necessary to maintain these levels. Females were less likely to be trapped than expected, if dispersing females were included in the population. Animals captured in the first trapping session were more likely to be recaptured if the pack was trapped again.

The intervention was successful in halting the spread of the rabies outbreak and had few short‐term impacts on the population of wolves and non‐target species.

Synthesis and applications. Demographic, spatial and behavioural heterogeneities within populations may affect vaccine uptake or delivery and thus the efficacy of vaccine‐based interventions. Managers of populations of threatened species should ensure that disease‐control programmes are carefully designed to maximize information gained on all aspects of an intervention, and thus to evaluate its outcome and impact. Dissemination and discussion of results is crucial in order to apply what has been learnt to similar scenarios in the same or related populations.
Avifaunal changes as a consequence of large‐scale livestock exclusion in the mountains of Central Argentina
Authors: García César , Renison Daniel , Cingolani Ana M. , Fernández‐Juricic Esteban
Published: October 2007

In the high Mountains of Córdoba (Central Argentina) large native herbivores were replaced completely by domestic livestock early in the 20th century. Recently, livestock were excluded in a large portion of the mountains to reduce alarming soil erosion rates, leading to an unnatural situation as the area has a long evolutionary history of large herbivore grazing. Many of the birds living in this area are endemic subspecies. Lack of large herbivore grazing can reduce plant diversity, but the response of birds is unknown.

We surveyed birds in 46 1·8‐ha transects distributed across eight vegetation units under (a) traditional livestock rearing and (b) 4 years of livestock exclusion. We described bird communities per transect using density and richness. The effects of grazing situation and vegetation units on these parameters were analysed by two‐way analysis of variance (anova). Additionally, we analysed bird composition through detrended correspondence analysis (DCA).

Livestock exclusion caused, in all vegetation units, significant reductions in observed bird density and richness when all species were included in the analysis, and when the 12 endemic subspecies were considered separately. An analysis for each guild showed a similar pattern but differences were significant only for richness of insectivorous and granivorous birds. Vegetation units always showed significant differences in bird density and richness, with no significant interactions between vegetation and grazing situations. Community composition described through DCA was different between vegetation units but not between grazing situations. Endemic birds were associated mainly with rocky areas.

Synthesis and applications. In areas where large native herbivores are locally extinct, extensive exclusion of domestic livestock is not recommended where bird conservation is also a priority. Where possible, we suggest reintroducing native large herbivores. Where reintroductions are not feasible, livestock must be excluded only from those sites where it is most necessary, and maintained elsewhere at reduced stocking rates. To mimic past natural grazing regimes more effectively, livestock grazing regimes should incorporate temporal fluctuations at seasonal, yearly and decade scales.
Ecological correlates of vulnerability to fragmentation in Neotropical bats
Authors: Meyer Christoph F. J. , Fründ Jochen , Lizano Willy Pineda , Kalko Elisabeth K.V.
Published: October 2007

In the face of widespread human‐induced habitat fragmentation, identification of those ecological characteristics that render some species more vulnerable to fragmentation than others is vital for understanding, predicting and mitigating the effects of habitat alteration on biodiversity. We compare hypotheses on the causes of interspecific differences in fragmentation sensitivity using distribution and abundance data collected on 23 species of Neotropical bats.

Bats were captured over a 2‐year period on 11 land‐bridge islands in Gatún Lake, Panama, and on the adjacent mainland. We derived a series of explanatory variables from our capture data and from the literature: (1) natural abundance in continuous forest, (2) body mass, (3) trophic level, (4) dietary specialization, (5) vertical stratification, (6) edge‐sensitivity, (7) mobility, (8) wing morphology (aspect ratio and relative wing loading) and (9) ecologically scaled landscape indices (ESLIs). After phylogenetic correction, these variables were used separately and in combination to assess their association with two indices of fragmentation sensitivity, species prevalence (proportion of islands occupied) as well as an index of change in abundance.

Model selection based on Akaike's information criterion identified edge‐sensitivity as the best correlate of vulnerability to fragmentation. Natural abundance and mobility or traits linked to mobility (relative wing loading and ESLI) received limited support as predictors. Vulnerability of gleaning animalivorous bats is probably caused by a combination of these traits.

Synthesis and applications. Our findings emphasize the importance of a local‐scale approach in developing predictive models of species fragmentation sensitivity and indicate that risk assessments of Neotropical bats could be based on species tolerance to habitat edges and mobility‐related traits. We suggest that, in order to be effective, management efforts should aim to minimize the amount of edge‐habitat and reduce the degree of fragment‐matrix contrast. Moreover, if high bat diversity is to be preserved in fragmented Neotropical landscapes, conservation measures regarding reserve design should assure spatial proximity to source populations in larger tracts of continuous forest and a low degree of remnant isolation.
Indicators for biodiversity in agricultural landscapes: a pan‐European study
Authors: Billeter R. , Liira J. , Bailey D. , Bugter R. , Arens P. , Augenstein I. , Aviron S. , Baudry J. , Bukacek R. , Burel F. , Cerny M. , De Blust G. , De Cock R. , Diekötter T. , Dietz H. , Dirksen J. , Dormann C. , Durka W. , Frenzel M. , Hamersky R. , Hendrickx F. , Herzog F. , Klotz S. , Koolstra B. , Lausch A. , Le Coeur D. , Maelfait J. P. , Opdam P. , Roubalova M. , Schermann A. , Schermann N. , Schmidt T. , Schweiger O. , Smulders M.J.M. , Speelmans M. , Simova P. , Verboom J. , Van Wingerden W.K.R.E. , Zobel M. , Edwards P.J.
Published: October 2007

In many European agricultural landscapes, species richness is declining considerably. Studies performed at a very large spatial scale are helpful in understanding the reasons for this decline and as a basis for guiding policy. In a unique, large‐scale study of 25 agricultural landscapes in seven European countries, we investigated relationships between species richness in several taxa, and the links between biodiversity and landscape structure and management.

We estimated the total species richness of vascular plants, birds and five arthropod groups in each 16‐km2 landscape, and recorded various measures of both landscape structure and intensity of agricultural land use. We studied correlations between taxonomic groups and the effects of landscape and land‐use parameters on the number of species in different taxonomic groups. Our statistical approach also accounted for regional variation in species richness unrelated to landscape or land‐use factors.

The results reveal strong geographical trends in species richness in all taxonomic groups. No single species group emerged as a good predictor of all other species groups. Species richness of all groups increased with the area of semi‐natural habitats in the landscape. Species richness of birds and vascular plants was negatively associated with fertilizer use.

Synthesis and applications. We conclude that indicator taxa are unlikely to provide an effective means of predicting biodiversity at a large spatial scale, especially where there is large biogeographical variation in species richness. However, a small list of landscape and land‐use parameters can be used in agricultural landscapes to infer large‐scale patterns of species richness. Our results suggest that to halt the loss of biodiversity in these landscapes, it is important to preserve and, if possible, increase the area of semi‐natural habitat.
Experimental or precautionary? Adaptive management over a range of time horizons
Authors: Hauser Cindy E , Possingham Hugh P
Published: October 2007

Many studies of adaptive harvest management already exist in the literature, but most (if not all) use long, sometimes infinite, time horizons. Such long‐term objectives provide an opportunity to manage experimentally, so that poorly understood dynamics are learned and any returns sacrificed for experimentation are repaid by improved management over the remaining time horizon.

However, a manager is unlikely to weight outcomes in the distant future equally against outcomes in the present. Furthermore, the most appropriate model of system dynamics may not remain constant over the time‐frame required to experiment, learn and improve management. In these cases the use of discounting and/or a finite time horizon fit the manager's assumptions and goals more effectively, and the value of experimentation is likely to be diminished.

In this paper we construct a simple model of a hypothetical population and compare optimal passive and active adaptive harvest strategies over a range of time horizons. This allows us to determine the optimal level of experimentation for short‐, medium‐ and long‐term goals.

We discover that the optimal active adaptive harvest strategy may be precautionary over short to medium time horizons, rather than experimental. That is, an action with known moderate benefits is preferred over an action with uncertain but marginally larger expected benefits. This runs counter to the widespread assumption in the adaptive management literature that incorporating learning into an optimization of management will encourage experimentation.

Synthesis and applications. The general results of this paper have potential application to any environmental management problem where adaptive management might be applied; for example, conservation, pest control, harvesting and management of water flows. We examine adaptive management over a range of finite time horizons to reflect a variety of possible management goals and assumptions. Our simple example demonstrates that in the face of model uncertainty, the management strategy that maximizes benefits does not necessarily include deliberate experimentation and learning. Optimal active adaptive management weighs experimentation against all its potential consequences, and this can yield a precautionary approach.
Environmental and landscape effects on cross‐pollination rates observed at long distance among French oilseed rape Brassica napus commercial fields
Authors: Devaux C. , Klein E. K. , Lavigne C. , Sausse C. , Messéan A.
Published: October 2007

Evaluation of our ability to predict cross‐pollination rates (CPR) at long distance using dispersal functions estimated in experimental set‐ups differing by either their scale or their environmental conditions is crucial to establish appropriate management rules following the release of genetically modified (GM) crops.

From 1998 to 2004 we measured oilseed rape CPR in commercial fields for 44 donor‐recipient couples separated by 220 up to 2000 m, from up to three different pollen donor cultivars in two French oilseed rape production areas. We followed the same sampling and screening designs and tested the effect of region, year, size, cultivar and distance on the observed CPR.

We then compared observed CPR to predictions from six empirical pollen dispersal models based on dispersal kernels that were fitted previously at the local and landscape scales. These predictions allowed us to test the possibility to extrapolate and up‐scale dispersal kernels.

The observed CPR varied from 0% to 0·092%. They were higher in Champagne‐Ardennes, where they depended negatively on distance, than in Bourgogne where they did not depend on distance. CPR also differed among years, being nil for the last 3 successive years, partly because of different environmental conditions and detection issues. CPR depended further on the source cultivars due to differences in pollen production. Dispersal kernels fitted at the local scale lead to systematic and huge underestimation of CPR, when observed. The power‐law kernel fitted at the landscape scale under‐estimated CPR by two orders of magnitude above 400 m but followed the rate of decrease of the observed pollination with distance.

Synthesis and applications. Caution should be taken when extrapolating and up‐scaling dispersal kernels and models because predictions may differ greatly from observations. Models should rely at least upon dispersal kernels estimated from landscape‐scale data obtained in different regions. Models should also integrate several phenomena at the agro‐ecosystem scale including the dispersal by insects and become more mechanistic to account for variations observed among years, environments and distance to borders.
The AraC/XylS regulator TxtR modulates thaxtomin biosynthesis and virulence in Streptomyces scabies
Authors: Joshi Madhumita V. , Bignell Dawn R. D. , Johnson Evan G. , Sparks Jed P. , Gibson Donna M. , Loria Rosemary
Published: October 2007

Streptomyces scabies is the best studied of those streptomycetes that cause an economically important disease known as potato scab. The phytotoxin thaxtomin is made exclusively by these pathogens and is required for virulence. Here we describe regulation of thaxtomin biosynthesis by TxtR, a member of the AraC/XylS family of transcriptional regulators. The txtR gene is imbedded in the thaxtomin biosynthetic pathway and is located on a conserved pathogenicity island in S. scabies, S. turgidiscabies and S. acidiscabies. Thaxtomin biosynthesis was abolished and virulence was almost eliminated in the txtR deletion mutant of S. scabies 87.22. Accumulation of thaxtomin biosynthetic gene (txtA, txtB, txtC, nos) transcripts was reduced compared with the wild‐type S. scabies 87.22. NOS‐dependent nitric oxide production by S. scabies was also reduced in the mutant. The TxtR protein bound cellobiose, an inducer of thaxtomin production, and transcription of txtR and thaxtomin biosynthetic genes was upregulated in response to cellobiose. TxtR is the first example of an AraC/XylS family protein regulated by cellobiose. Together, these data suggest that cellobiose, the smallest oligomer of cellulose, may signal the availability of expanding plant tissue, which is the site of action of thaxtomin.
A partner for the resuscitation‐promoting factors of Mycobacterium tuberculosis
Authors: Hett Erik C. , Chao Michael C. , Steyn Adrie J. , Fortune Sarah M. , Deng Lynn L. , Rubin Eric J.
Published: October 2007

Many cases of active tuberculosis are thought to result from the reactivation of dormant Mycobacterium tuberculosis from a prior infection, yet remarkably little is known about the mechanism by which these non‐sporulating bacteria reactivate. A family of extracellular bacterial proteins, known as resuscitation‐promoting factors (Rpfs), has previously been shown to stimulate growth of dormant mycobacteria. While Rpf proteins are clearly peptidoglycan glycosidases, the mechanism and role of Rpf in mediating reactivation remains unclear. Here we use a yeast two‐hybrid screen to identify potential binding partners of RpfB and report the interaction between RpfB and a putative mycobacterial endopeptidase, which we named Rpf‐interacting protein A (RipA). This interaction was confirmed by in vitro and in vivo co‐precipitation assays. The interacting domains map to the C‐termini of both proteins, near predicted enzymatic domains. We show that RipA is a secreted, cell‐associated protein, found in the same cellular compartment as RpfB. Both RipA and RpfB localize to the septa of actively growing bacteria by fluorescence microscopy. Finally, we demonstrate that RipA is capable of digesting cell wall material and is indeed a peptidoglycan hydrolase. The interaction between these two peptidoglycan hydrolases at the septum suggests a role for the complex in cell division, possibly during reactivation.
Glutathione and Gts1p drive beneficial variability in the cadmium resistances of individual yeast cells
Authors: Smith Matthew C. A. , Sumner Edward R. , Avery Simon V.
Published: October 2007

Phenotypic heterogeneity among individual cells within isogenic populations is widely documented, but its consequences are not well understood. Here, cell‐to‐cell variation in the stress resistance of Saccharomyces cerevisiae, particularly to cadmium, was revealed to depend on the antioxidant glutathione. Heterogeneity was decreased strikingly in gsh1 mutants. Furthermore, cells sorted according to differing reduced‐glutathione (GSH) contents exhibited differing stress resistances. The vacuolar GSH‐conjugate pathway of detoxification was implicated in heterogeneous Cd resistance. Metabolic oscillations (ultradian rhythms) in yeast are known to modulate single‐cell redox and GSH status. Gts1p stabilizes these oscillations and was found to be required for heterogeneous Cd and hydrogen‐peroxide resistance, through the same pathway as Gsh1p. Expression of GTS1 from a constitutive tet‐regulated promoter suppressed oscillations and heterogeneity in GSH content, and resulted in decreased variation in stress resistance. This enabled manipulation of the degree of gene expression noise in cultures. It was shown that cells expressing Gts1p heterogeneously had a competitive advantage over more‐homogeneous cell populations (with the same mean Gts1p expression), under continuous and fluctuating stress conditions. The results establish a novel molecular mechanism for single‐cell heterogeneity, and demonstrate experimentally fitness advantages that depend on deterministic variation in gene expression within cell populations.
The initiation and pattern of spread of histone H4 acetylation parallel the order of transcriptional activation of genes in the aflatoxin cluster
Authors: Roze Ludmila V. , Arthur Anna E. , Hong Sung‐Yong , Chanda Anindya , Linz John E.
Published: October 2007

The 27 genes involved in aflatoxin biosynthesis are clustered within a 70 kb region in the Aspergillus parasiticus genome. Using chromatin immunoprecipitation, we demonstrated a positive correlation between the initiation and spread of histone H4 acetylation in aflatoxin promoters and the onset of accumulation of aflatoxin proteins and aflatoxin. Histone H4 acetylation in the pksA (encodes an ‘early’ biosynthetic pathway enzyme) promoter peaked at 30 h, prior to the increased acetylation in the omtA and ordA (encode ‘late’ enzymes) promoters detected at 40 h. The specific order in which pksA, ver‐1 (encodes a ‘middle’ enzyme) and omtA transcripts accumulated in cells paralleled the pattern of spread of histone H4 acetylation. Binding of AflR, a positive regulator of aflatoxin biosynthesis, to the ordA promoter showed a positive correlation with the spread of histone H4 acetylation. The data suggest that the order of genes within the aflatoxin cluster determines the timing and order of transcriptional activation, and that the site of initiation and spread of histone H4 acetylation mediate this process. Our data indicate that the aflatoxin and adjacent sugar utilization clusters are part of a larger ‘regulatory unit’.
RutR is the uracil/thymine‐sensing master regulator of a set of genes for synthesis and degradation of pyrimidines
Authors: Shimada Tomohiro , Hirao Kiyo , Kori Ayako , Yamamoto Kaneyoshi , Ishihama Akira
Published: October 2007

Using the genomic SELEX, a total of six Escherichia coli DNA fragments have been identified, which formed complexes with transcription factor RutR. The RutR regulon was found to include a large number of genes encoding components for not only degradation of pyrimidines but also transport of glutamate, synthesis of glutamine, synthesis of pyrimidine nucleotides and arginine, and degradation of purines. DNase I footprinting indicated that RutR recognizes a palindromic sequence of TTGACCAnnTGGTCAA. The RutR box in P1 promoter of carAB encoding carbamoyl phosphate synthetase, a key enzyme of pyrimidine synthesis, overlaps with the PepA (CarP) repressor binding site, implying competition between RutR and PepA. Adding either uracil or thymine abolished RutR binding in vitro to the carAB P1 promoter. Accordingly, in the rutR‐deletion mutant or in the presence of uracil, the activation in vivo of carAB P1 promoter was markedly reduced. Northern blot analysis of the RutR target genes indicated that RutR represses the Gad system genes involved in glutamate‐dependent acid resistance and allantoin degradation. Altogether we propose that RutR is the pyrimidine sensor and the master regulator for a large set of the genes involved in the synthesis and degradation of pyrimidines.
GolS controls the response to gold by the hierarchical induction of Salmonella‐specific genes that include a CBA efflux‐coding operon
Authors: Pontel Lucas B. , Audero María E. Pérez , Espariz Martín , Checa Susana K. , Soncini Fernando C.
Published: October 2007

Salmonella employs a specific set of proteins that allows it to detect the presence of gold salts in the environment and to mount the appropriate resistance response. This includes a P‐type ATPase, GolT, and a small cytoplasmic metal binding protein, GolB. Their expression is controlled by a MerR‐like sensor, GolS, which is highly selective for Au ions. Here, we identify a new GolS‐controlled operon named gesABC which codes for a CBA efflux system, and establish its role in Au resistance. GesABC can also mediate drug resistance when induced by Au in a GolS‐dependent manner, in a strain deleted in the main drug transporter acrAB. The GolS‐controlled transcription of gesABC differs from the other GolS‐regulated loci. It is activated by gold, but not induced by copper, even in a strain deleted of the main Cu transporter gene copA, which triggers a substantial GolS‐dependent induction of golTS and golB. We demonstrate that the Au‐dependent induction of gesABC transcription requires higher GolS levels than for the other members of the gol regulon. This correlates with a divergent GolS operator in the gesABC promoter. We propose that the hierarchical induction within the gol regulon allows Salmonella to cope with Au‐contaminated environments.
Nitrosative stress treatment of E. coli targets distinct set of thiol‐containing proteins
Authors: Brandes Nicolas , Rinck Andrea , Leichert Lars Ingo , Jakob Ursula
Published: October 2007

Reactive nitrogen species (RNS) function as powerful antimicrobials in host defence, but so far little is known about their bacterial targets. In this study, we set out to identify Escherichia coli proteins with RNS‐sensitive cysteines. We found that only a very select set of proteins contain cysteines that undergo reversible thiol modifications upon nitric oxide (NO) treatment in vivo. Of the 10 proteins that we identified, six (AtpA, AceF, FabB, GapA, IlvC, TufA) have been shown to harbour functionally important thiol groups and are encoded by genes that are considered essential under our growth conditions. Media supplementation studies suggested that inactivation of AceF and IlvC is, in part, responsible for the observed NO‐induced growth inhibition, indicating that RNS‐mediated modifications play important physiological roles. Interestingly, the majority of RNS‐sensitive E. coli proteins differ from E. coli proteins that harbour H2O2‐sensitive thiol groups, implying that reactive oxygen and nitrogen species affect distinct physiological processes in bacteria. We confirmed this specificity by analysing the activity of one of our target proteins, the small subunit of glutamate synthase. In vivo and in vitro activity studies confirmed that glutamate synthase rapidly inactivates upon NO treatment but is resistant towards other oxidative stressors.
Genetic basis for retention of a critical virulence plasmid of Borrelia burgdorferi
Authors: Jewett Mollie W. , Byram Rebecca , Bestor Aaron , Tilly Kit , Lawrence Kevin , Burtnick Mary N. , Gherardini Frank , Rosa Patricia A.
Published: October 2007

The genome of Borrelia burgdorferi is composed of one linear chromosome and approximately 20 linear and circular plasmids. Although some plasmids are required by B. burgdorferi in vivo, most plasmids are dispensable for growth in vitro. However, circular plasmid (cp) 26 is present in all natural isolates and has never been lost during in vitro growth. This plasmid carries ospC, which is critical for mammalian infection. We previously showed that cp26 encodes essential functions, including the telomere resolvase, ResT, and hence cannot be displaced. Here we identify two additional essential genes on cp26, bbb26 and bbb27, through a systematic attempt to inactivate each open reading frame (ORF). Furthermore, an incompatible plasmid carrying resT, bbb26 and bbb27 could displace cp26. Computational and experimental analyses suggested that both BBB26 and BBB27 are membrane‐associated, periplasmic proteins. These data indicate that bbb26 and bbb27 encode essential but possibly redundant functions and that one or the other of these cp26 genes, in addition to resT, is required for bacterial viability. We conclude that the genetic linkage of critical physiological and virulence functions on cp26 is pertinent to its stable maintenance throughout the evolution of B. burgdorferi.
TECHNICAL ADVANCE: LeafAnalyser: a computational method for rapid and large‐scale analyses of leaf shape variation
Authors: Weight Caroline , Parnham Daniel , Waites Richard
Published: October 2007

A comprehensive understanding of leaf shape is important in many investigations in plant biology. Techniques to assess variation in leaf shape are often time‐consuming, labour‐intensive and prohibited by complex calculation of large data sets. We have developed LeafAnalyser, software that uses image‐processing techniques to greatly simplify the measurement of leaf shape variation. LeafAnalyser places a large number of evenly distributed landmarks along leaf margins and records the position of each automatically. We used LeafAnalyser to analyse the variation in 3000 leaves from 400 plants of Antirrhinum majus. We were able to summarise the major trends in leaf shape variation using a principal components (PC) analysis and assess the changes in size, width and tip‐to‐base asymmetry within our leaf library. We demonstrate how this information can be used to develop a model that describes the range and variation of leaf shape within standard wild‐type lines, and illustrate the shape transformations that occur between leaf nodes. We also show that information from LeafAnalyser can be used to identify novel trends in shape variation, as low‐variance PCs that only affect a subset of position landmarks. These results provide a high‐throughput method to calculate leaf shape variation that allows a large number of leaves to be visualised in higher‐dimensional phenotypic space. To illustrate the applicability of LeafAnalyser we also calculated the leaf shape variation in 300 leaves from Arabidopsis thaliana.
A transcriptional repression motif in the MADS factor AGL15 is involved in recruitment of histone deacetylase complex components
Authors: Hill Kristine , Wang Huai , Perry Sharyn E.
Published: October 2007

AGAMOUS‐like 15 (AGL15) encodes a MADS‐domain transcription factor that is preferentially expressed in the plant embryo. A number of direct downstream targets of AGL15 have been identified, and although some of these target genes are induced in response to AGL15, others are repressed. Additionally, direct target genes have been analyzed that exhibit strong association with AGL15 in vivo, yet in vitro AGL15 binds only weakly. These data suggest that AGL15 may form complexes with other proteins, thus modulating the specificity and function of AGL15 in planta. Here we report that AGL15 interacts with members of the SWI‐independent 3/histone deacetylase (SIN3/HDAC) complex, and that AGL15 target genes are also responsive to an AGL15 interacting protein that is also a member of this complex, SIN3‐associated polypeptide of 18 kDa (SAP18). AGL15 can repress transcription in vivo, and a region essential to this repressive function contains a motif that is conserved among putative orthologs of AGL15. This motif mediates the association of AGL15 with SAP18, thus providing a possible mechanism for the role of AGL15 in regulating gene expression via recruitment of an HDAC complex.
Application of carborundum abrasion for investigating the leaf epidermis: molecular cloning of Catharanthus roseus 16‐hydroxytabersonine‐16‐O‐methyltransferase
Authors: Levac Dylan , Murata Jun , Kim Won S. , De Luca Vincenzo
Published: October 2007

The Madagascar periwinkle (Catharanthus roseus) produces the well‐known and remarkably complex anti‐cancer dimeric alkaloids vinblastine and vincristine that are derived from the coupling of vindoline and catharanthine monomers. This study describes the novel application of a carborundum abrasion (CA) technique for large‐scale isolation of leaf epidermis‐enriched proteins in order to purify to apparent homogeneity 16‐hydroxytabersonine‐16‐O‐methyltransferase (16OMT), which catalyses the second of six steps in the conversion of tabersonine into vindoline, and to clone the gene. Functional expression and biochemical characterization of recombinant 16OMT demonstrated its very narrow substrate specificity and high affinity for 16‐hydroxytabersonine. In addition to allowing the cloning of this gene, the CA technique clearly showed that 16OMT is predominantly expressed in Catharanthus leaf epidermis. The results provide compelling evidence that most of the pathway for vindoline biosynthesis, including the O‐methylation of 16‐hydroxytabersonine, occurs exclusively in the leaf epidermis, with subsequent steps occurring in other leaf cell types.
Evidence for a sorting endosome in Arabidopsis root cells
Authors: Jaillais Yvon , Fobis‐Loisy Isabelle , Miège Christine , Gaude Thierry
Published: October 2007

In eukaryotic cells, the endocytic and secretory pathways are key players in several physiological processes. These pathways are largely inter‐connected in animal and yeast cells through organelles named sorting endosomes. Sorting endosomes are multi‐vesicular compartments that redirect proteins towards various destinations, such as the lysosomes or vacuoles for degradation, the trans‐Golgi network for retrograde transport and the plasma membrane for recycling. In contrast, cross‐talk between the endocytic and secretory pathways has not been clearly established in plants, especially in terms of cargo protein trafficking. Here we show by co‐localization analyses that endosomes labelled with the AtSORTING NEXIN1 (AtSNX1) protein overlap with the pre‐vacuolar compartment in Arabidopsis root cells. In addition, alteration of the routing functions of AtSNX1 endosomes by drug treatments leads to mis‐routing of endocytic and secretory cargo proteins. Based on these results, we propose that the AtSNX1 endosomal compartment represents a sorting endosome in root cells, and that this specialized organelle is conserved throughout eukaryotes.
Subcellular co‐localization of Arabidopsis RTE1 and ETR1 supports a regulatory role for RTE1 in ETR1 ethylene signaling
Authors: Dong Chun‐Hai , Rivarola Maximo , Resnick Josephine S. , Maggin Benjamin D. , Chang Caren
Published: October 2007

Ethylene is an important plant growth regulator perceived by membrane‐bound ethylene receptors. The ETR1 ethylene receptor is positively regulated by a predicted membrane protein, RTE1, based on genetic studies in Arabidopsis. RTE1 homologs exist in plants, animals and protists, but the molecular function of RTE1 is unknown. Here, we examine RTE1 expression and subcellular protein localization in order to gain a better understanding of RTE1 and its function in relation to ETR1. Arabidopsis plants transformed with the RTE1 promoter fused to the β‐glucuronidase (GUS) reporter gene revealed that RTE1 expression partly correlates with previously described sites of ETR1 expression or sites of ethylene response, such as the seedling root, root hairs and apical hook. RTE1 transcript levels are also enhanced by ethylene treatment, and reduced by the inhibition of ethylene signaling. For subcellular localization of RTE1, a functional RTE1 fusion to red fluorescent protein (RFP) was expressed under the control of the native RTE1 promoter. Using fluorescence microscopy, RTE1 was observed primarily at the Golgi apparatus and partially at the endoplasmic reticulum (ER) in stably transformed Arabidopsis protoplasts, roots and root hairs. Next, a functional ETR1 fusion to a 5xMyc epitope tag was expressed under the control of the native ETR1 promoter. Immunohistochemistry of root hairs not only showed ETR1 residing at the ER as previously reported, but revealed substantial localization of ETR1 at the Golgi apparatus. Lastly, we demonstrated the subcellular co‐localization of RTE1 and ETR1. These findings support and enhance the genetic model that RTE1 plays a role in regulating ETR1.
The epidemiology of childhood asthma
Authors: Strachan D. P.
Published: October 2007

Variability is the hallmark of childhood asthma. Conceptually defined as variable airflow obstruction, asthma affects individual children through a variety of clinical manifestations. Particular controversy surrounds the nature of wheezing in early infancy and its relationship to atopic asthma of later onset. Asthma prognosis is also highly variable and only to a limited extent predictable by clinical indicators in early childhood. Long‐term follow‐up studies suggest a complex pattern of remission and relapse as wheezy children are followed through adolescence into adult life. Similarly, the population burden of asthma is highly variable, both over time and between countries. The balance of evidence worldwide suggests a modest but sustained increase in the prevalence of asthma symptoms over the past three decades. Superimposed on this have been larger changes in diagnostic fashion and use of health services for childhood asthma in many countries. There is substantial international variation in the prevalence of asthma symptoms, and marked urban‐rural differences have been reported from several African countries. These contrast with the more uniform distribution of the disease within industrialized countries, reflecting its ubiquity in affluent societies.
The environmental influence on childhood asthma
Authors: Björkstén B.
Published: October 2007

The pathogenesis of allergy depends on the interaction between the time and amount of allergen exposure and the presence of nonspecific “adjuvant” factors in genetically susceptible individuals. There seems to be a period in early life during which the individual is particularly susceptible to sensitization, and there are variations in susceptibility over time. Allergens are almost ubiquitous, but the relative importance of the individual allergens varies between regions. In many temperate regions, house‐dust mites used to be absent but are now more common. This may be due to modern methods of building houses. Differences in the prevalence of a particular allergy cannot explain variations in the prevalence of allergy in general. Various environmental factors that may enhance sensitization include tobacco smoke, NO1, SO2, ozone, and diesel particles. Passive smoking is by far the best established risk factor, particularly in early childhood. The indoor environment probably plays a larger role than outdoor air pollution in the development of allergic disease. The mother is not only a source of genetic information, but also an “environmental factor”, as there is a close immunologic interaction between the mother and her offspring, mediated through the placenta and the breast milk, which may affect the likelihood of allergic disease. The concepts of “lifestyle” and “environment” should be expanded to include, for example, dietary changes, the microbial environment, and extensive traveling, as all the currently suspected risk factors taken together can only explain a small proportion of the geographic differences in and increasing prevalence of allergy. The future search for significant environmental factors should be interdisciplinary and be directed toward areas that have not yet been explored, thus giving “lifestyle” a broader interpretation.
Recognizing early asthma
Authors: Martinez F. D.
Published: October 2007

Asthma symptoms often develop during the first years of life. Longitudinal studies show that at least 40% of children with wheezing lower respiratory illnesses (LRIs) during the first 3 years of life still have wheezing episodes at 6 years of age. Thus, it is important to identify children at risk of developing asthma, and to distinguish these from those in whom early wheezing is likely to be transient. This is complicated, however, by the variable nature of asthma and the lack of specific and sensitive markers. Genetic markers and epidemiologic risk factors for asthma have been identified, but cannot be used to predict the development of asthma in an individual patient. Similarly, infants who subsequently develop asthma in childhood have higher serum immunoglobulin E (IgE) and peripheral eosinophil counts than those who do not develop asthma, but, again, these factors are not sufficiently sensitive and specific to allow identification of children at risk of developing asthma. An algorithm is presented that outlines possible criteria to determine the risk of developing asthma in infants.
Options for bronchodilation in children: can we rely on adult data?
Authors: Verberne A. A. P. H.
Published: October 2007

Bronchodilators, especially β2‐agonists, are effective in relieving asthma symptoms. Therefore, short‐acting β2‐agonists are recommended in all guidelines on a p. r. n. basis, usually in combination with anti‐inflammatory treatment, at least in moderate to severe asthma. Although for adult asthma some concerns have been raised about regular use of short‐acting β2‐agonists, studies in children do not suggest that continuous use results in deterioration of asthma. This question is more relevant to the chronic use of the long‐acting β2‐agonists, salmeterol and formoterol. These drugs may be used instead of antiinflammatory drugs, especially inhaled corticosteroids. Recent studies in adult asthmatics have supported the use of a longacting β2‐agonist in combination with a lower dose of inhaled corticosteroid in preference to a higher dose of inhaled corticosteroid. So far, data in children are less convincing for this therapeutic strategy. It may be that differences in the disease process between adults and children are likely to account for these different responses in treatment regimens. Furthermore, it has to be determined whether treatment should primarily aim at symptom reduction or whether other disease parameters should also be taken into account.