bluuebunny/crossref_metadata_2025 huggingface dataset:
Small heat-shock protein HspL is induced by VirB protein(s) and promotes VirB/D4-mediated DNA transfer in Agrobacterium tumefaciens
Authors: Tsai Yun-Long , Wang Ming-Hsuan , Gao Chan , Klüsener Sonja , Baron Christian , Narberhaus Franz , Lai Erh-Min
Published: September 2009

Agrobacterium tumefaciens is a Gram-negative plant-pathogenic bacterium that causes crown gall disease by transferring and integrating its transferred DNA (T-DNA) into the host genome. We characterized the chromosomally encoded alpha-crystallin-type small heat-shock protein (α-Hsp) HspL, which was induced by the virulence (vir) gene inducer acetosyringone (AS). The transcription of hspL but not three other α-Hsp genes (hspC, hspAT1, hspAT2) was upregulated by AS. Further expression analysis in various vir mutants suggested that AS-induced hspL transcription is not directly activated by the VirG response regulator but rather depends on the expression of VirG-activated virB genes encoding components of the type IV secretion system (T4SS). Among the 11 virB genes encoded by the virB operon, HspL protein levels were reduced in strains with deletions of virB6, virB8 or virB11. VirB protein accumulation but not virB transcription levels were reduced in an hspL deletion mutant early after AS induction, implying that HspL may affect the stability of individual VirB proteins or of the T4S complex directly or indirectly. Tumorigenesis efficiency and the VirB/D4-mediated conjugal transfer of an IncQ plasmid RSF1010 derivative between A. tumefaciens strains were reduced in the absence of HspL. In conclusion, increased HspL abundance is triggered in response to certain VirB protein(s) and plays a role in optimal VirB protein accumulation, VirB/D4-mediated DNA transfer and tumorigenesis.
Enterohaemorrhagic Escherichia coli serogroup O111 inhibits NF-κB-dependent innate responses in a manner independent of a type III secreted OspG orthologue
Authors: Nobe Rika , Nougayrède Jean-Philippe , Taieb Frédéric , Bardiau Marjorie , Cassart Dominique , Navarro-Garcia Fernando , Mainil Jacques , Hayashi Tetsuya , Oswald Eric
Published: September 2009

Enterohaemorrhagic and enteropathogenic Escherichia coli (EHEC and EPEC) inject a repertoire of effector proteins into host cells via a type III secretion system (T3SS) encoded by the locus of enterocyte effacement (LEE). OspG is an effector protein initially identified in Shigella that was shown to inhibit the host innate immune response. In this study, we found ospG homologues in EHEC (mainly of serogroup O111) and in Yersinia enterocolitica. The T3SS encoded by the LEE was able to inject these different OspG homologues into host cells. Infection of HeLa cells with EHEC O111 inhibited the NF-κB-dependent innate immune response via a T3SS-dependent mechanism. However, an EHEC O111 ospG mutant was still able to inhibit NF-κB p65 transfer to the nucleus in infected cells stimulated by tumour necrosis factor α (TNF-α). In addition, no difference in the inflammatory response was observed between wild-type EHEC O111 and the isogenic ospG mutant in the rabbit ligated intestinal loop model. These results suggest that OspG is not the sole effector protein involved in the inactivation of the host innate immune system during EHEC O111 infection.
Analysis of the Pseudomonas putida CA-3 proteome during growth on styrene under nitrogen-limiting and non-limiting conditions
Authors: Nikodinovic-Runic Jasmina , Flanagan Michelle , Hume Aisling R. , Cagney Gerard , O'Connor Kevin E.
Published: September 2009

Pseudomonas putidaCA-3 is a styrene-degrading bacterium capable of accumulating medium-chain-length polyhydroxyalkanoate (mclPHA) when exposed to limiting concentrations of a nitrogen source in the growth medium. Using shotgun proteomics we analysed global proteome expression inP. putidaCA-3 supplied with styrene as the sole carbon and energy source under N-limiting (condition permissive for mclPHA synthesis) and non-limiting (condition non-permissive for mclPHA accumulation) growth conditions in order to provide insight into the molecular response ofP. putidaCA-3 to limitation of nitrogen when grown on styrene. A total of 1761 proteins were identified with high confidence and the detected proteins could be assigned to functional groups including styrene degradation, energy, nucleotide metabolism, protein synthesis, transport, stress response and motility. Proteins involved in the upper and lower styrene degradation pathway were expressed throughout the 48 h growth period under both nitrogen limitation and excess. Proteins involved in polyhydroxyalkanoate (PHA) biosynthesis, nitrogen assimilation and amino acid transport, and outer membrane proteins were upregulated under nitrogen limitation. PHA accumulation and biosynthesis were only expressed under nitrogen limitation. Nitrogen assimilation proteins were detected on average at twofold higher amounts under nitrogen limitation. Expression of the branched-chain amino acid ABC transporter was up to 16-fold higher under nitrogen-limiting conditions. Branched chain amino acid uptake by nitrogen-limited cultures was also higher than that by non-limited cultures. Outer membrane lipoproteins were expressed at twofold higher levels under nitrogen limitation. This was confirmed by Western blotting (immunochemical detection) of cells grown under nitrogen limitation. Our study provides the first global description of protein expression changes during growth of any organism on styrene and accumulating mclPHA (nitrogen-limited growth).
Pumping iron: mechanisms for iron uptake by Campylobacter
Authors: Miller Claire E. , Williams Peter H. , Ketley Julian M.
Published: September 2009

Campylobacter requires iron for successful colonization of the host. In the last 7 years, a wealth of data has been generated allowing detailed molecular characterization of Campylobacter iron-uptake systems. Several exogenous siderophores have been identified as sources of ferric iron for Campylobacter. Ferri-enterochelin uptake requires both the outer-membrane receptor protein CfrA and the inner-membrane ABC transporter system CeuBCDE. Ferrichrome has been shown to support growth of some Campylobacter jejuni strains and the presence of homologues of Escherichia coli fhuABD genes was proposed; the Cj1658–Cj1663 system appears to be involved in the uptake of ferri-rhodotorulic acid. In addition to siderophores, the importance of host iron sources was highlighted by recent studies demonstrating that C. jejuni can exploit haem compounds and the transferrins using ChuABCDZ and Cj0173c–Cj0178, respectively. An additional putative receptor, Cj0444, present in some, but not all, strains has not yet been characterized. Following diffusion through the outer membrane, inner-membrane transport of ferrous iron can occur via the FeoB protein. While it may be assumed that all systems are not essential, there is growing evidence supporting the need for multiple iron-uptake systems for successful host colonization by Campylobacter. In light of this, comparative molecular characterization of iron systems in all Campylobacter strains is necessary to gain further insight into the pathogenesis of members of this genus.
Censusing the mountain gorillas in the Virunga Volcanoes: complete sweep method versus monitoring
Authors: Gray Maryke , McNeilage Alastair , Fawcett Katie , Robbins Martha M. , Ssebide Benard , Mbula Deo , Uwingeli Prosper
Published: September 2009

The mountain gorillas (Gorilla beringei beringei) of the Virunga Volcanoes Range of Rwanda, Uganda, and the Democratic Republic of Congo are one of the most endangered ape populations in the world. Following a dramatic decline during the 1960s, and relative stability in the 1970s, the population steadily increased during the 1980s. Due to political instability and war, a complete census had not been conducted since 1989. Here we compare the results of a complete census using the ‘sweep method’ conducted in 2003 with those from a monitoring program, to estimate the size and distribution of the gorilla population. A total of 360 gorillas were counted from census measurements and known habituated groups. Based on quantitative assessments of the census accuracy, we calculated that an additional 20 gorillas were not counted, leading to an estimated population of 380 individuals, and a 1.15% annual growth rate since 1989. The Ranger Based Monitoring programme yielded similar results. The encouraging results must be viewed with caution, however, because the growth was concentrated almost entirely in one section of the Virungas. Additionally, the distribution of gorilla groups was negatively correlated with the frequency of human disturbances, which highlights the need to continue strengthening conservation efforts.
Sharing natural resources: mountain gorillas and people in the Parc National des Volcans, Rwanda
Authors: Van Gils Hein , Kayijamahe Eugene
Published: September 2009

The compatibility of natural resource use by people and mountain gorillas (Gorilla beringei beringei) within the Parc National des Volcans was studied. The distribution of gorillas was modelled using a Maximum Entropy algorithm. Biophysical predictor variables were trained with daily GPS locations of gorillas during 2006. Elevation, as a climate surrogate, was the best predictor (58%) of the occurrence of gorillas. The mid‐altitudes (2500–3500 m a.s.l.) contained the bulk of the gorilla groups. Incoming solar radiation, as proxy for comfortable nesting sites, was the second best predictor (17%). Vegetation types, as foliage provider, (13%) and slope steepness for providing security (12%) were contributing predictors. The modelled and actual gorilla distributions were together overlaid with people’s resource use in the park. Both people and gorillas were congregated in the areas identified as most suitable for gorillas. However, within these areas spatial segregation was found between human natural resource‐users and gorillas. Therefore, the number of gorillas is likely to be limited by the human natural resource use within the park. A perimeter fence, the introduction of community‐based natural resource management, and a buffer zone are discussed as short‐, medium‐ and long‐term mitigation measures.
Seedling survival in Manilkara butugi Chiov. along a dispersal gradient in Kakamega forest, Kenya
Authors: Wahungu Geoffery M. , Mureu Lucy K. , Wato Yussuf A. , Mureithi Sarah N. , Karanja Geoffery G.
Published: September 2009

The spatial patterns of seedling distribution in Manilkara butugi were studied between December 2004 and April 2005 at Kakamega forest, Kenya. Our objectives were to determine the spatial variation in seedling density in relation to distance from the parent tree and the survivorship patterns of M. butugi seedlings. We hypothesized that seedling density and mortality would be highest beneath the parent tree and would reduce with increasing distance from the parent tree. Line transects, radiating along the four compass directions from mature female M. butugi trees were established, and quadrats marked out at intervals of 5 m in which seedlings were counted. To determine establishment and survivorship, belt transects 5 m × 40 m running along the northerly compass direction were laid and data collected on seedling variables. Seedling density reduced with increasing distance from the parent plant (F = 25.72, df = 3; P < 0.001). Whereas seedling height (F = 14.806, df = 1; P < 0.05) and the number of leaves (F = 12.45, df = 1; P < 0.05) increased with increasing distance from the parent tree, damage to seedlings reduced with increasing distance (F = 27.59, P < 0.05). Our results were consistent with the Janzen–Cornell escape hypothesis and have implications for natural regeneration of M. butugi and to maintenance of species diversity.
The use of breeding sites of Tilapia congica (Thys & van Audenaerde 1960) to delineate conservation sites in the Lake Tumba, Democratic Republic of Congo: toward the conservation of the lake ecosystem
Authors: Inogwabini Bila‐Isia , Dianda Mputu , Lingopa Zanga
Published: September 2009

To guide the zoning process in Lake Tumba, Democratic Republic of Congo, breeding sites of Tilapia congica were studied. Physical metrics measured were: nest depths, exposure to sun rays, distance from the edges, site spreads, and habitat types. Mean nest depth = 0.23 m ± 0.08 (SD), range = 0.04–2.2 m (n = 553 nests); 100% (n = 70 sites) sites were exposed to the sun and the polynomial regression analysis showed 90% sites were within the range 51–250 m from the lake shores (y = −1.7143x2 + 10.371x− 1.8; R2 = 0.597, n = 70 sites), with 60% clumped within the range of 51–150 m, indicating a relationship between nesting sites and the distance from edges. The largest group spread group was 300 m, and among the four breeding sites identified, one was ∼10 km long, meaning a zonal spatial spread ∏ = 300 ha and a core reproduction zone ∏′ = 100 ha. T. congica built 87.30% of their nest in habitats where Hippo grass Vossia cuspidata (48.20%) and Water lily Nympheae stellata (39.10%) dominated. T. congica shared 41.81% of its nesting sites with other fish species, leading to the conclusion that protecting the species habitats would provide the umbrella for the conservation of other species.
Analysis of candidate genes underlying two epistatic quantitative trait loci on SSC12 affecting litter size in pig
Authors: Fernández‐Rodríguez A. , Rodríguez C. , Varona L. , Balcells I. , Noguera J. L. , Óvilo C. , Fernández A. I.
Published: September 2009

The previous results from a genome scan for total number of piglets born and number of piglets born alive in a F2 Iberian by Meishan intercross showed several single and epistatic QTL. One of the most interesting results was obtained for SSC12, where two QTL affecting both traits showed epistatic interaction. In this study, we proposed two genes (SLC9A3R1 and NOS2) as biological and potentially positional candidates underlying these QTL. Both cDNAs were characterized and 23 polymorphisms were detected. A chromosome scan was conducted with 12 markers, plus one SNP in SLC9A3R1 and one in NOS2, covering 110 cM of SSC12. The epistatic QTL (QTL1 at 15 cM and QTL2 at 97 cM) were confirmed, and SLC9A3R1 and NOS2 were mapped around the QTL1 and QTL2 regions respectively. Several SNPs in both genes were tested with standard animal model and marker assisted association tests. The most significant results were obtained with the NOS2 haplotype defined by one missense SNP c.2192C > T (Val to Ala) and a 15 bp duplication at the 3′UTR. This duplication seems to include AU‐rich elements, and could be a target site for miRNA, therefore there are statistical and biological indications to consider this haplotype as the potential causal mutation underlying QTL2. SLC9A3R1 results were not conclusive. Although the interaction between the SNPs was not significant, we cannot reject the possibility of interaction of the NOS2 haplotype with other polymorphisms closely linked to the SL9A3R1 SNPs analysed.
The variant red coat colour phenotype of Holstein cattle maps to BTA27
Authors: Dreger D. L. , Schmutz S. M.
Published: September 2009

The variant red phenotype in Holstein cattle is indistinguishable from the traditional e/e recessive red phenotype caused by a mutation in melanocortin 1 receptor, but is inherited as a dominant trait in relation to black. Co‐segregation analysis in four half‐sib families segregating for variant red was conducted, excluding melanocortin 1 receptor, agouti signalling protein, attractin and melatonin receptor 1A as causative genes. However, variant red co‐segregated with markers in a region of BTA27 that includes beta‐defensin 103 (DEFB103). Two newly identified microsatellites and 5 SNPs 5′ of DEFB103 were used for linkage mapping in four segregating families (LOD = 3.26). One haplotype was inherited in VR cattle in a 6‐generation pedigree.
Immune dysregulation and dyserythropoiesis in the myelodysplastic syndromes
Authors: Alfinito Fiorella , Sica Michela , Luciano Luigiana , Pepa Roberta Della , Palladino Carmela , Ferrara Idalucia , Giani Umberto , Ruggiero Giuseppina , Terrazzano Giuseppe
Published: September 2009

The myelodysplastic syndromes (MDS) are clonal disorders characterised by ineffective haematopoiesis with high risk of leukaemia progression. The relevance of immune‐dysregulation for emergence, dominance and progression of dysplastic clones has been suggested, but valuable criteria to obtain insight into these connections are lacking. This study showed significant increase of CD8 lymphocytes and mature B cells in the bone marrow (BM) compared to peripheral blood (PB) of low risk MDS patients. Different BM levels of Regulatory T cells (Treg) identified two sub‐groups in these patients; only the sub‐group with lower Treg percentage showed BM recruitment of CD8 lymphocytes. Different levels of CD54 on BM CD8 cells revealed two sub‐groups of Intermediate‐1 (Int‐1) patients. The sub‐group with higher CD54 expression on BM CD8 showed high levels of this molecule also on CD4 cells. BM recruitment of CD8 lymphocytes in the low risk group and/or the presence of high CD54 expression on BM CD8 in Int‐1 patients were associated with more pronounced dyserythropoiesis and erythropoietin treatment. Our data shed light on the involvement of immune‐mediated mechanisms in Low and Int‐1 risk MDS patients and suggest that BM versus PB levels of immune effectors could represent useful criteria for a more homogeneous grouping of MDS patients.
Platelet vascular endothelial growth factor is a useful predictor for prognosis in Kawasaki syndrome
Authors: Ueno Kentaro , Nomura Yuichi , Hashiguchi Teruto , Masuda Kiminori , Morita Yasuko , Hazeki Daisuke , Eguchi Taisuke , Maruyama Ikuro , Kawano Yoshifumi
Published: September 2009

Kawasaki syndrome (KS) is an acute febrile vasculitis of childhood. Coronary artery abnormalities (CAA) are a significant problem in KS patients. High dose intravenous immunoglobulin (IVIG) is effective for reducing the occurrence of CAA. Clinical and histopathological findings suggest that vascular endothelial growth factor (VEGF) is involved in CAA. In circulating blood, newly activated platelets are the major source of VEGF, which is released in large amounts in vascular inflammation. The present study analysed 80 KS patients (69 IVIG responders and 11 IVIG non‐responders) and evaluated the role of platelet VEGF in KS vasculitis. Serum VEGF and platelet VEGF levels were significantly higher in KS patients than controls (P < 0·001). Platelet VEGF reflected the reactivity of IVIG treatment and was decreased in responders (P < 0·001), but remained increased in non‐responders (P = 0·01). Platelet VEGF levels, but not serum VEGF levels, before IVIG were significantly correlated with the maximum CAA z‐score (r = 0·524, P = 0·02). Our findings demonstrate that platelet VEGF may reflect the severity of vasculitis related to the pathological development of CAA in KS. Platelet VEGF may be an important feature of KS pathophysiology.
Biotic attrition from tropical forests correcting for truncated temperature niches
Authors: FEELEY KENNETH J. , SILMAN MILES R.
Published: September 2009

Species migration in response to warming temperatures is expected to lead to ‘biotic attrition,’ or loss of local diversity, in areas where the number of species emigrating or going locally extinct exceeds the number immigrating. Biotic attrition is predicted be especially severe in the low‐lying hot tropics since elevated temperatures may surpass the observed tolerances of most extant species. It is possible, however, that the estimated temperature niches of many species are inaccurate and truncated with respect to their true tolerances due to the absence of hotter areas under current global climate. If so, these species will be capable of persisting in some areas where future temperatures exceed current temperatures, reducing rates of biotic attrition. Here, we use natural history collections data to estimate the realized thermal niches of > 2000 plant species from the tropical forests of South America. In accord with the truncation hypothesis, we find that the thermal niches of species from hot lowland areas are several degrees narrower than the thermal niches of species from cooler areas. We estimate rates of biotic attrition for South American tropical forests due to temperature increases ranging from 1 to 5 °C, and under two niche assumptions. The first is that the observed thermal niches truly reflect the plant's tolerances and that the reduction in niche breadth is due to increased specialization. The second is that lowland species have the same mean thermal niche breadth as nonlowland and nonequatorial species. The differences between these two models are dramatic. For example, using observed thermal niches we predict an almost complete loss of plant diversity in most South American tropical forests due to a 5 °C temperature increase, but correcting for possible niche truncation we estimate that most forests will retain > 50–70% of their current species richness. The different predictions highlight the importance of using fundamental vs. realized niches in predicting the responses of species to global climate change.
Ten years of elevated atmospheric carbon dioxide alters soil nitrogen transformations in a sheep‐grazed pasture
Authors: RÜTTING TOBIAS , CLOUGH TIM J. , MÜLLER CHRISTOPH , LIEFFERING MARK , NEWTON PAUL C. D.
Published: September 2009

The increasing concentration of atmospheric carbon dioxide (CO2) is expected to lead to enhanced competition between plants and microorganisms for the available nitrogen (N) in soil. Here, we present novel results from a 15N tracing study conducted with a sheep‐grazed pasture soil that had been under 10 years of CO2 enrichment. Our study aimed to investigate changes in process‐specific gross N transformations in a soil previously exposed to an elevated atmospheric CO2 (eCO2) concentration and to examine indicators for the occurrence of progressive nitrogen limitation (PNL). Our results show that the mineralization–immobilization turnover (MIT) was enhanced under eCO2, which was driven by the mineralization of recalcitrant organic N. The retention of N in the grassland was enhanced by increased dissimilatory NO3− reduction to NH4+ (DNRA) and decreased NH4+ oxidation. Our results indicate that heterotrophic processes become more important under eCO2. We conclude that higher MIT of recalcitrant organic N and enhanced N retention are mechanisms that may alleviate PNL in grazed temperate grassland.
Predicting spatial and temporal patterns of bud‐burst and spring frost risk in north‐west Europe: the implications of local adaptation to climate
Authors: BENNIE JONATHAN , KUBIN EERO , WILTSHIRE ANDREW , HUNTLEY BRIAN , BAXTER ROBERT
Published: September 2009

The timing of spring bud‐burst and leaf development in temperate, boreal and Arctic trees and shrubs fluctuates from year to year, depending on meteorological conditions. Over several generations, the sensitivity of bud‐burst to meteorological conditions is subject to selection pressure. The timing of spring bud‐burst is considered to be under opposing evolutionary pressures; earlier bud‐burst increases the available growing season (capacity adaptation) but later bud‐burst decreases the risk of frost damage to actively growing parts (survival adaptation). The optimum trade‐off between these two forms of adaptation may be considered an evolutionarily stable strategy that maximizes the long‐term ecological fitness of a phenotype under a given climate. Rapid changes in climate, as predicted for this century, are likely to exceed the rate at which trees and shrubs can adapt through evolution or migration. Therefore the response of spring phenology will depend not only on future climatic conditions but also on the limits imposed by adaptation to current and historical climate. Using a dataset of bud‐burst dates from twenty‐nine sites in Finland for downy birch (Betula pubescens Ehrh.), we parameterize a simple thermal time bud‐burst model in which the critical temperature threshold for bud‐burst is a function of recent historical climatic conditions and reflects a trade‐off between capacity and survival adaptation. We validate this approach with independent data from eight independent sites outside Finland, and use the parameterized model to predict the response of bud‐burst to future climate scenarios in north‐west Europe. Current strategies for budburst are predicted to be suboptimal for future climates, with bud‐burst generally occurring earlier than the optimal strategy. Nevertheless, exposure to frost risk is predicted to decrease slightly and the growing season is predicted to increase considerably across most of the region. However, in high‐altitude maritime regions exposure to frost risk following bud‐burst is predicted to increase.
Production and oxidation of methane in a boreal mire after a decade of increased temperature and nitrogen and sulfur deposition
Authors: ERIKSSON TOBIAS , ÖQUIST MATS G. , NILSSON MATS B.
Published: September 2009

Natural wetlands are the single largest source of atmospheric methane (CH4). Both a changed climate and deposition of anthropogenic nitrogen and sulfur can alter the production and oxidation of CH4 respectively and thereby also CH4 exchange. We used a long‐term (12 years) factorial field experiment in a boreal oligotrophic mire to evaluate the effects of greenhouse cover and addition of ammonium nitrate and sodium sulfate on the production and oxidation of CH4 by applying laboratory incubations of samples from five depths in the mire. The rates of CH4 production were measured without amendments and after the addition of either glucose or sulfate. Twelve years of increased nitrogen deposition has changed the mire from a Sphagnum‐dominated plant community to one dominated by sedges and dwarf shrubs. The deposition of nitrogen to the field plots caused increased production of CH4 in incubations without amendments (34%), and also after amendments with glucose (40%) or sulfate (42%). This indicates increased substrate availability (without amendments) but also a greater abundance of methanogens (glucose amendment). The greenhouse cover caused a decrease in CH4 production in incubations without amendments (34%), after glucose amendment (20%) and after sulfate amendment (31%). These responses indicate decreased substrate availability (without amendment) accompanied by the reduced abundance of methanogens (glucose amendment). The field application of sulfur had no effect on CH4 production at the depth where maximal CH4 production occurred. Closer to the mire surface, however, the rate of CH4 production was significantly reduced by 32–45%. These results suggest that the deposition of sulfate has altered the vertical distribution of methanogens and sulfate‐reducing bacteria. The oxidation of CH4 was not significantly affected by any of the long‐term field treatments.
Sugar sweet springtails: on the transcriptional response ofFolsomia candida(Collembola) to desiccation stress
Authors: Timmermans M. J. T. N. , Roelofs D. , Nota B. , Ylstra B. , Holmstrup M.
Published: September 2009

Several species of Collembola survive stressful desiccating conditions by absorbing water vapour from the environment. To obtain insight into the transcriptomic responses underlying this ‘water vapour absorption’ mechanism we subjectedFolsomia candida(Collembola) to transcriptome profiling. We show that ecologically relevant desiccation stress leads to strong time‐dependent transcriptomic changes. Exposure ofF. candidato 98.2% relative humidity over an interval of 174 h resulted in a high number of gene transcripts being differentially expressed (up to 41%;P‐value < 0.05). Additional Gene Ontology analyses suggest that carbohydrate transport, sugar catabolism and cuticle maintenance are biological processes involved in combating desiccation. However, many additional pathways seem to be affected; additional experiments are needed to elucidate which responses are primarily linked to desiccation resistance.
A context‐aware ubiquitous learning environment for language listening and speaking
Authors: Liu T.‐Y.
Published: September 2009

This paper reported the results of a study that aimed to construct a sensor and handheld augmented reality (AR)‐supported ubiquitous learning (u‐learning) environment called the Handheld English Language Learning Organization (HELLO), which is geared towards enhancing students' language learning. The HELLO integrates sensors, AR, ubiquitous computing and information technologies. It is composed of two subsystems: an English learning management system and a u‐learning tool. In order to evaluate the effects of the proposed learning environment on the learning performance of students, a case study on English learning was conducted on a school campus. The participants included high school teachers and students. A learning course entitled ‘My Campus’ was conducted in the class; it included three activities, namely ‘Campus Environment’, ‘Campus Life’ and ‘Campus Story’. The evaluation results showed that the proposed HELLO and the learning activities could improve the students' English listening and speaking skills.
Spatial genetic structure in continuous and fragmented populations of Pinus pinaster Aiton
Authors: DE‐LUCAS A. I. , GONZÁLEZ‐MARTÍNEZ S. C. , VENDRAMIN G. G. , HIDALGO E. , HEUERTZ M.
Published: September 2009

Habitat fragmentation, i.e., the reduction of populations into small isolated remnants, is expected to increase spatial genetic structure (SGS) in plant populations through nonrandom mating, lower population densities and potential aggregation of reproductive individuals. We investigated the effects of population size reduction and genetic isolation on SGS in maritime pine (Pinus pinaster Aiton) using a combined experimental and simulation approach. Maritime pine is a wind‐pollinated conifer which has a scattered distribution in the Iberian Peninsula as a result of forest fires and habitat fragmentation. Five highly polymorphic nuclear microsatellites were genotyped in a total of 394 individuals from two population pairs from the Iberian Peninsula, formed by one continuous and one fragmented population each. In agreement with predictions, SGS was significant and stronger in fragments (Sp = 0.020 and Sp = 0.026) than in continuous populations, where significant SGS was detected for one population only (Sp = 0.010). Simulations suggested that under fat‐tailed dispersal, small population size is a stronger determinant of SGS than genetic isolation, while under normal dispersal, genetic isolation has a stronger effect. SGS was always stronger in real populations than in simulations, except if unrealistically narrow dispersal and/or high variance of reproductive success were modelled (even when accounting for potential overestimation of SGS in real populations as a result of short‐distance sampling). This suggests that factors such as nonrandom mating or selection not considered in the simulations were additionally operating on SGS in Iberian maritime pine populations.
Genetic and biochemical analysis of the serine/threonine protein kinases PknA, PknB, PknG and PknL of Corynebacterium glutamicum: evidence for non‐essentiality and for phosphorylation of OdhI and FtsZ by multiple kinases
Authors: Schultz Christian , Niebisch Axel , Schwaiger Astrid , Viets Ulrike , Metzger Sabine , Bramkamp Marc , Bott Michael
Published: September 2009

We previously showed that the 2‐oxoglutarate dehydrogenase inhibitor protein OdhI of Corynebacterium glutamicum is phosphorylated by PknG at Thr14, but that also additional serine/threonine protein kinases (STPKs) can phosphorylate OdhI. To identify these, a set of three single (ΔpknA, ΔpknB, ΔpknL), five double (ΔpknAG, ΔpknAL, ΔpknBG, ΔpknBL, ΔpknLG) and two triple deletion mutants (ΔpknALG, ΔpknBLG) were constructed. The existence of these mutants shows that PknA, PknB, PknG and PknL are not essential in C. glutamicum. Analysis of the OdhI phosphorylation status in the mutant strains revealed that all four STPKs can contribute to OdhI phosphorylation, with PknG being the most important one. Only mutants in which pknG was deleted showed a strong growth inhibition on agar plates containing glutamine as carbon and nitrogen source. Thr14 and Thr15 of OdhI were shown to be phosphorylated in vivo, either individually or simultaneously, and evidence for up to two additional phosphorylation sites was obtained. Dephosphorylation of OdhI was shown to be catalysed by the phospho‐Ser/Thr protein phosphatase Ppp. Besides OdhI, the cell division protein FtsZ was identified as substrate of PknA, PknB and PknL and of the phosphatase Ppp, suggesting a role of these proteins in cell division.
Paralogous antirepressors acting on the master regulator for biofilm formation in Bacillus subtilis
Authors: Chai Yunrong , Kolter Roberto , Losick Richard
Published: September 2009

Matrix production during biofilm formation by Bacillus subtilis is governed by a gene control circuit at the heart of which are three dedicated regulatory proteins, the antirepressor SinI, the repressor SinR and the downstream regulator SlrR. Matrix production is triggered by the synthesis of SinI, which binds to and inactivates SinR, thereby derepressing genes for matrix production as well as the gene for SlrR. Recently, two additional regulators of matrix genes were identified: SlrA, which was reported to be an activator of SlrR, and YwcC, a repressor of SlrA synthesis (Kobayashi, 2008). We present evidence indicating that SlrA, which is a paralogue of SinI, is like SinI, an antirepressor that binds to, and inactivates, SinR. We also show that SlrA does not activate SlrR for expression of matrix genes. Instead, SlrR binds to, and inhibits the activity of, SlrA. Thus, the YwcC‐SlrA‐SinR‐SlrR pathway is a negative feedback loop in which SlrA indirectly stimulates the synthesis of SlrR, and SlrR, in turn, inhibits the activity of SlrA. Finally, we report that under standard laboratory conditions SlrA makes only a small contribution to the expression of genes for matrix production. We propose that in response to an unknown signal recognized by the YwcC repressor, SlrA transiently boosts matrix production.
Lactobacillus reuteri ingestion and IKCa channel blockade have similar effects on rat colon motility and myenteric neurones
Authors: Wang B. , Mao Y.‐k. , Diorio C. , Wang L. , Huizinga J. D. , Bienenstock J. , Kunze W.
Published: September 2009

Abstract  Background  We have previously shown that ingestion of Lactobacillus reuteri may modulate colonic enteric neuron activity but with unknown effects on colon motility. The aim of the present report was to elucidate the neuronal mechanisms of action of the probiotic by comparing the effects on motility of L. reuteri ingestion with blockade of a specific ionic current in enteric neurons.

Methods  We have used intraluminal pressure recordings from ex vivo rat colon segments and whole cell patch clamp recordings from neurons of rat longitudinal muscle myenteric plexus preparations to investigate the effects of L. reuteri and TRAM‐34 on colon motility and neurophysiology. The effects of daily feeding of 109L. reuteri bacteria or acute application of TRAM‐34 on threshold fluid filling pressure or pulse pressure was measured.

Key Results  Lactobacillus reuteri increased intraluminal fluid filling pressure thresholds for evoking pressure pulses by 51% from 0.47 ± 0.17 hPa; the probiotic also decreased the pulse pressure amplitudes, but not frequency, by 18% from 3.91 ± 0.52 hPa. The intermediate conductance calcium‐dependent potassium (IKCa) channel blocker TRAM‐34 (3 μmol L−1) increased filling threshold pressure by 43% from 0.52 ± 0.22 hPa and reduced pulse pressure amplitude by 40% from 2.63 ± 1.11 hPa; contraction frequency was unaltered. TRAM‐34 (3 μmol L−1) reduced membrane polarization, leak conductance and the slow afterhyperpolarization current in 16/16 myenteric rat colon AH cells but 19/19 S cells were unaffected.

Conclusions & Inferences  The present results are consistent with L. reuteri enhancing tonic inhibition of colon contractile activity by acting via the IKCa channel current in AH cells.
A bioinformatics approach to ascertaining the rarity of HLA alleles
Authors: Middleton D. , Gonzalez F. , Fernandez‐Vina M. , Tiercy J.‐M. , Marsh S. G. E. , Aubrey M. , Bicalho M. G. , Canossi A. , Carter V. , Cate S. , Guerini F. R. , Loiseau P. , Martinetti M. , Moraes M. E. , Morales V. , Perasaari J. , Setterholm M. , Sprague M. , Tavoularis S. , Torres M. , Vidal S. , Witt C. , Wohlwend G. , Yang K. L.
Published: September 2009

A project of the 15th International Histocompatibility Workshop examined the rarity of human leukocyte antigen (HLA) alleles. A section was constructed in the website, www.allelefrequencies.net to contain this data from different sources. A mechanism to search the data was implemented for use by any individual.
Combined split liver and kidney transplantation in a three‐year‐old child with primary hyperoxaluria type 1 and complete thrombosis of the inferior vena cava
Authors: Khan Zahida , Sciveres Marco , Salis Paola , Minervini Marida , Maggione Giuseppe , Cintorino Davide , Riva Silvia , Gridelli Bruno , Emma Francesco , Spada Marco
Published: September 2009

Khan Z, Sciveres M, Salis P, Minervini M, Maggione G, Cintorino D, Riva S, Gridelli B, Emma F, Spada M. Combined split liver and kidney transplantation in a three‐year‐old child with primary hyperoxaluria type 1 and complete thrombosis of the inferior vena cava. Pediatr Transplantation 2011: 15: E64–E70. © 2009 John Wiley & Sons A/S.

Abstract:  PH1 is an inborn error of the metabolism in which a functional deficiency of the liver‐specific peroxisomal enzyme, AGT, causes hyperoxaluria and hyperglycolic aciduria. Infantile PH1 is the most aggressive form of this disease, leading to early nephrocalcinosis, systemic oxalosis, and end‐stage renal failure. Infantile PH1 is rapidly fatal in children unless timely liver‐kidney transplantation is performed to correct both the hepatic enzyme defect and the renal end‐organ damage. The surgical procedure can be further complicated in infants and young children, who are at higher risk for vascular anomalies, such as IVC thrombosis. Although recently a limited number of children with IVC thrombosis have underwent successful kidney transplantation, successful multi‐organ transplantation in a child with complete IVC thrombosis is quite rare. We report here the interesting and technically difficult case of a three‐yr‐old girl with a complete thrombosis of the IVC, who was the recipient of combined split liver and kidney transplantation for infantile PH1. Although initial delayed renal graft function with mild‐to‐moderate acute rejection was observed, the patient rapidly regained renal function after steroid boluses, and was soon hemodialysis‐independent, with good diuresis. Serum and plasma oxalate levels progressively decreased; although, to date they are still above normal. Hepatic and renal function indices were at, or approaching, normal values when the patient was discharged 15‐wk post‐transplant, and the patient continues to do well, with close and frequent follow‐up. This is the first report of a successful double‐organ transplant in a pediatric patient presenting with infantile PH1 complicated by complete IVC thrombosis.
Synergistic and antagonistic interaction between different branches of the immune system is related to melanin‐based coloration in nestling tawny owls
Authors: GASPARINI J. , PIAULT R. , BIZE P. , ROULIN A.
Published: September 2009

When exposed to parasites, hosts often mount energetically expensive immune responses, and this may alter resource allocation between competing life history traits including other components of the immune system. Here, we investigated whether a humoral immune challenge towards a vaccine reduces or enhances the cutaneous immune responses towards an injection of lipopolysaccharid (LPS, innate immunity) and phytohaemagglutinin (PHA, T‐cell immunity) in nestling tawny owls in interaction with the degree of plumage melanin‐based coloration. The humoral immune challenge enhanced the response to LPS similarly in differently coloured nestlings. In contrast, the same humoral immune challenge enhanced immune response to PHA in dark reddish melanic nestlings while reducing it in pale reddish melanic nestlings. Our results highlight that both antagonistic and synergistic interactions can take place among branches of immune system, and that the sign and magnitude of these interactions can vary with immune responses involved and the degree of melanin‐based coloration.
Parent–offspring conflict and selection on egg size in turtles
Authors: JANZEN F. J. , WARNER D. A.
Published: September 2009

The trade‐off between offspring size and number can present a conflict between parents and their offspring. Because egg size is constrained by clutch size, the optimal egg size for offspring fitness may not always be equivalent to that which maximizes parental fitness. We evaluated selection on egg size in three turtle species (Apalone mutica, Chelydra serpentina and Chrysemys picta) to determine if optimal egg sizes differ between offspring and their mothers. Although hatching success was generally greater for larger eggs, the strength and form of selection varied. In most cases, the egg size that maximized offspring fitness was greater than that which maximized maternal fitness. Consistent with optimality theory, mean egg sizes in the populations were more similar to the egg sizes that maximized maternal fitness, rather than offspring fitness. These results provide evidence that selection has maximized maternal fitness to achieve an optimal balance between egg size and number.
Local adaptation of Ruellia nudiflora (Acanthaceae) to biotic counterparts: complex scenarios revealed when two herbivore guilds are considered
Authors: ORTEGÓN‐CAMPOS I. , PARRA‐TABLA V. , ABDALA‐ROBERTS L. , HERRERA C. M.
Published: September 2009

This study evaluated whether the herb Ruellia nudiflora is locally adapted to a specialist insect seed predator (SP) and insect folivores, and if plant local adaptation (LA) to the former is more likely. A reciprocal transplant experiment was conducted using three sites in Yucatan (Mexico) (n = 864 plants). A third of the plants of each origin were placed at each site, and we recorded the following during a 9‐month period: fruit number, leaf damage, and fruits attacked by SP. Results indicated lack of plant LA for all the variables measured. Instead, seed predation was c. 100% greater for native plants at one study site, suggesting insect LA or plant maladaptation; folivory was homogeneous across sites/origins. Based on these results, we discuss differences in the potential each herbivore guild has to promote plant LA, as well as divergent evolutionary outcomes of plant–herbivore interactions across sites.
Comparative susceptibility of pine, spruce and larch to sapstain
Authors: Beal E. , Webber J. F. , Eaton R. A.
Published: September 2009

Summary This study compared the susceptibility of five UK‐grown conifer species to colonization by sapstain fungi in two trials carried out in consecutive years. The conifers consisted of Sitka spruce (Picea sitchensis), Japanese larch (Larix kaempferi), Norway spruce (Picea abies), Scots pine (Pinus sylvestris) and lodgepole pine (Pinus contorta). Freshly cut 1‐m logs were exposed to the available inoculum of sapstain fungi from April to August in a woodland environment in the south east of England. Logs of each species were removed after 1‐, 2‐ and 4‐month exposure and sampled destructively to assess the amount of sapstain. In the second trial, per cent moisture content and concentrations of nitrogen, carbohydrate and phenolic compounds in the sapwood were also measured at the start and end of the trial. After 2 months, only the sapwood of both pine species had significant levels of sapstain; mean values of 37% and 19% for lodgepole pine (year 1 and year 2 respectively) and 12% and 1% for Scots pine. After 4 months, the levels of sapstain in both pine species exceeded 60% in both years. By contrast, very little sapstain developed in the other conifer species with maximum mean values of 10% for Norway spruce, 3.5% for larch and less than 1% for Sitka spruce. Overall, the moisture content of the logs decreased progressively in all species over the length of the trial. However, pine logs tended to retain higher levels of moisture throughout the trial compared with spruce or larch. The relatively higher moisture content of pine sapwood may be closer to the optimal moisture content that sapstain fungi require for infection and colonization, thereby contributing to the increased susceptibility of pine compared with the other conifer species. The pine logs also suffered from some colonization by bark beetles (Ips sexdentatus), which increased the inoculum potential and the opportunity for colonization by sapstain fungi. In addition, particular phenolic compounds in conifer sapwood may play a role in determining the resistance of some species to sapstain. Notably the most resistant species, Sitka spruce, was the only softwood that still retained detectable levels of phenolics in the sapwood to the end of the trial.
Floral Traits and Seed Production of Sorghum A‐, B‐ and R‐lines under Chilling Field Temperatures
Authors: Cisneros‐López M. E. , Mendoza‐Onofre L. E. , Zavaleta‐Mancera H. A. , González‐Hernández V. A. , Córdova‐Téllez L. , Hernández‐Martínez M. , Mora‐Aguilera G.
Published: September 2009

In A‐lines of sorghum (Sorghum bicolor L. Moench), seed production under field conditions with manual pollination is generally lower than that in self‐pollinated B‐lines. This may be associated with floral differences. Six pairs of A/B‐lines and four R‐lines were evaluated during 2005 and 2006 at Montecillo, State of México (2240 m altitude). Rachis length, number of primary branches and fertile flowers per panicle, 100‐seed weight, seed number, seed yield and seed set per panicle were evaluated. In the A‐lines, the pistil characteristics were also measured and in the male‐fertile lines, the size of anthers and the amount and size of viable pollen were recorded. Compared with the A‐ and B‐lines, the R‐lines exhibited significantly higher (P ≤ 0.05) numbers of flowers, seed set and seed yield per panicle and they also produced more pollen grains of larger size and with greater viability during their longer flowering period (FP). Between A‐ and B‐lines, there were differences (P ≤ 0.05) in most of the yield traits, which also interacted with year. The proportion of viable pollen in B‐ and R‐lines (75 %) was not considered to be a factor that might account for their low seed production. Chilling temperatures (3.5–8.4 °C) during the FP could have affected stigma receptivity in the three different line types and thus may have reduced seed set in the male‐fertile lines.