bluuebunny/crossref_metadata_2025_split huggingface dataset:
The zig‐zag‐zig in oomycete–plant interactions
Authors: HEIN INGO , GILROY ELEANOR M. , ARMSTRONG MILES R. , BIRCH PAUL R. J. 
Published: April 2009

SUMMARYIn addition to a range of preformed barriers, plants defend themselves against microbial invasion by detecting conserved, secreted molecules, called pathogen‐associated molecular patterns (PAMPs). PAMP‐triggered immunity (PTI) is the first inducible layer of plant defence that microbial pathogens must navigate by the delivery of effector proteins that act to suppress or otherwise manipulate key components of resistance. Effectors may themselves be targeted by a further layer of defence, effector‐triggered immunity (ETI), as their presence inside or outside host cells may be detected by resistance proteins. This ‘zig‐zag‐zig’ of tightly co‐evolving molecular interactions determines the outcome of attempted infection. In this article, we consider the complex molecular interplay between plants and plant pathogenic oomycetes, drawing on recent literature to illustrate what is known about oomycete PAMPs and elicitors of defence responses, the effectors they utilize to suppress PTI, and the phenomenal molecular ‘battle’ between effector and resistance (R) genes that dictates the establishment or evasion of ETI.
Present‐day stresses in Brunei, NW Borneo: superposition of deltaic and active margin tectonics
Authors: King R. C. , Hillis R. R. , Tingay M. R. P. , Damit A.‐R. 
Published: April 2009

ABSTRACTThe Baram Delta System, Brunei, NW Borneo, is a Tertiary delta system located on an active continental margin. Delta top regions in many Tertiary delta systems (e.g. Niger Delta) are thought to exhibit a normal‐fault stress regime and margin‐parallel maximum horizontal stress orientations. However, unlike in passive margin Tertiary delta systems, two present‐day stress provinces have been previously identified across the Baram Delta System: an inner shelf inverted province with a margin‐normal (NW–SE) maximum horizontal stress orientation and an outer shelf extension province with a margin‐parallel (NE–SW) maximum horizontal stress orientation. Before this study, there were few data constraining the inverted province other than in the vicinity of the Champion Fields. New data from 12 petroleum wells in the western inner shelf and onshore west Brunei presented herein confirm the margin‐normal maximum horizontal stress orientations of the inverted province. A total of 117 borehole breakouts, all documented in shale units, and one drilling‐induced tensile fracture (in a sandstone interval) reveal a mean maximum horizontal stress orientation of 117 with a standard deviation of 19°. This orientation is consistent with contemporary margin‐normal maximum horizontal stress orientations of the inverted province described previously in the vicinity of the Champion Fields that have been linked to basement tectonics of the Crocker–Rajang accretionary complex and associated active margin. However, stress magnitudes calculated using data from these 12 petroleum wells indicate a borderline strike–slip fault to normal fault stress regime for the present day; combined with the absence of seismicity, this suggests that the studied part of the NW Borneo continental margin is currently tectonically quiescent.
T cells and eosinophils in bronchial smooth muscle cell death in asthma
Authors: Solarewicz‐Madejek K. , Basinski T. M. , Crameri R. , Akdis M. , Akkaya A. , Blaser K. , Rabe K. F. , Akdis C. A. , Jutel M. 
Published: April 2009

SummaryBackground
Bronchial smooth muscle cells (SMC) proliferate, express adhesion molecules, secrete cytokines and thus efficiently contribute to the pathogenesis of asthma.Objective
The aim of the study was to investigate whether, and by which mechanism, T cells and eosinophils can cause death of airway SMC.Methods
The T cell‐ and eosinophil‐induced cell death was analysed in primary human bronchial SMC cultures as well as in bronchial biopsy specimens from non‐asthmatic and asthmatic individuals.Results
Bronchial SMC death showed characteristic morphological features of apoptosis in 3–6 days cultures with inflammatory cytokines (IFN‐γ, TNF‐α), soluble death ligands [sFasL, TNF‐related apoptosis‐inducing ligand (TRAIL)] and activated T‐helper type 1 (Th1) and Th2 cell supernatants. The recombinant eosinophil cationic protein induced SMC necrosis within 1 h. Resting SMC expressed the death receptors TNFR1, TNFR2, Fas, TRAILR1, TRAILR2 and membrane FasL as a death‐inducing ligand. IFN‐γ and TNF‐α up‐regulated TNFR1, TNFR2, Fas and membrane FasL on SMC. TNF‐α up‐regulated TRAILR1 and TRAILR2; sFasL up‐regulated TNFR2. The intracellular caspase‐3 activation in SMC was significantly increased by IFN‐γ, sFasL, TRAIL, Th1 and Th2 cell supernatants. Increased expression of TRAIL in asthmatics, but not in non‐asthmatic individuals was demonstrated in situ. The apoptosis receptors TRAILR1 and TRAILR2 were expressed in SMC and epithelial cells both in healthy and asthmatic biopsies. Prominent apoptosis of SMC was observed in fatal asthma, but not intermittent asthma biopses.Conclusion
The demonstration of bronchial SMC death both by apoptosis and necrosis indicates the essential role of T cells and eosinophils in the bronchial tissue injury particularly in the severe asthma.
Age at puberty in male African striped mice: the impact of food, population density and the presence of the father
Authors: Schradin Carsten , Schneider Carola , Yuen Chi Hang 
Published: April 2009

Summary1. The time at which animals enter puberty and become sexually mature is a significant life‐history trait, influencing lifetime reproductive success. Great variation exists both between and within species.2. The proximate mechanisms regulating the time at which a male enters puberty are not well‐understood. Environmental cues are predicted to provide the relevant information on resource availability and opportunities for reproduction. When these are good the onset of puberty begins whereas at other times investment in survival becomes more important.3. Male African striped mice (Rhabdomys pumilio) demonstrate large variation in the age at which they enter puberty, with grassland populations starting at 4 weeks old and semi‐desert populations at over 10 weeks old.4. We predicted that differences in the availability of food, social organization and population density could explain these differences.5. Using data on 170 individual males from 4 years of field studies in a semi‐desert population, we found that males became scrotal at a younger age when no breeding male was present in their group and when food was abundant, while population density had no effect.6. In laboratory experiments we demonstrated that males fed with poor protein food, that regularly encounter larger unfamiliar males (mimicking high population density), and that live in family groups with their father present, become scrotal at a significantly later age, independent of their growth rate.7. Males housed in family groups have lower testosterone but higher corticosterone levels than singly housed males, indicating they are sexually suppressed. When they become scrotal in their family group, their testes are only half as large as those of their singly housed brothers, and they contained significantly less sperm.8. We conclude that male striped mice have a flexible response to the onset of puberty, and that the onset of sexual maturity is dependent on several environmental cues. Our results indicate that there is no threshold body mass, which, when reached, would automatically trigger puberty in male striped mice.9. Male helpers in some species are reproductively suppressed, but ours is the first study that demonstrated the importance of different ecological factors in the timing of puberty in male helpers in a facultative cooperatively breeding species.
Influence of solvent and temperature on extraction of phenolic compounds from grape seed, antioxidant activity and colour of extract
Authors: Bucić‐Kojić Ana , Planinić Mirela , Tomas Srećko , Jakobek Lidija , Šeruga Marijan 
Published: April 2009

SummaryThis study was aimed to investigate the influence of solvent (water and ethanol in concentration: 50%, 70% and 96%) and extraction temperature (25–80) °C on polyphenols extraction of grape seed (Vitis viniferaL. cv. “Frankovka”) cultivated in Eastern Croatia. The best results were reached using 50% ethanol at 80 °C. The most abundant individual polyphenolic compound was catechin which makes the average of 45.11% of the total phenolic content followed by epicatechin (34.45%), procyanidin B2(12.90%), gallic acid (5.34%), gallocatechin (1.58%), epicatechin gallate (1.01%). The antioxidant activity of extracts was determined by DPPH‐method and it was highly dependent on extraction solvent and temperature. The total extractable proanthocyanidins content of extract had the highest positive correlation (r = 0.994) with antioxidant activity, which indicated that these compounds might be the most important antioxidant in examined grape seed extracts. Relationship between phenolic content and colour of extracts was observed.
Natural preservative ingredient from marine alga Ulva lactuca L.
Authors: Abd El‐Baky Hanaa H. , El‐Baz Farouk K. , El‐Baroty Gamal S. 
Published: April 2009

SummaryThe contents of total chlorophyll (T‐Chl), carotenoids and phenolics compounds were quantified in the biomasses of Ulva lactuca grown either in normal or artificial sea water under indoor conditions. The antioxidant and antibacterial activities of U. lactuca crude organic extracts (Ulva‐COEs) were determined. Thirty‐four compounds in Ulva‐COEs were characterised by thin layer chromatography and high‐performance liquid chromatography. The major compounds were chlorophyll a (Chl a) (15.60–30.90%) and b (Chl b) (12.20–14.89%), 9‐cis β‐carotene (13.12–14.47%), α‐carotene (11.44–11.47%) and all‐trans β‐carotene (6.16–29.70%, of total carotenoids).The Ulva‐COEs exhibited remarkable antioxidant activity, with an IC50 (concentration which causes a 50% of DPPH radical scavenging activity) values ranged from 16.5 and 18.7 μg mL−1, which could be compared with the synthetic antioxidants: α‐tocopherol (14.4 μg mL−1), butylated hydroxyanisol (13.1 μg mL−1) and butylated hydroxyltoluene (13.1 μg mL−1). Also, Ulva‐COEs exhibited great potential antibacterial activities against six bacterial strains, with minimal inhibitory concentration values ranged from 0.40 to 0.35 mg mL−1.
Gear‐based fisheries management as a potential adaptive response to climate change and coral mortality
Authors: Cinner Joshua E. , McClanahan Tim R. , Graham Nicholas A. J. , Pratchett Morgan S. , Wilson Shaun K. , Raina Jean‐Baptiste 
Published: April 2009

Summary

Climate change is emerging as one of the greatest threats to coral reef ecosystems. Climate‐induced warming events trigger coral bleaching and mortality, which can indirectly affect coral reef fishes. Managing fisheries across coral mortality events is expected to influence the persistence of species and reef recovery potential. The most common management recommendation has been to prohibit fishing using fisheries closures, but this response often has limited support from resource users.
Here, we explore an alternative of managing fishing gear commonly used in artisanal coral reef fisheries. We examined fisheries landing data from 15 sites in Papua New Guinea and Kenya to explore whether or how specific gears select for: (i) species that depend on coral reefs for feeding or habitat and are likely to be susceptible to the loss of coral, and (ii) different functional groups of fishes.
Only 6% of the fishes targeted by fishers were susceptible to the immediate effects of coral mortality; however, loss of habitat structure following coral mortality is expected to affect 56% of targeted species.
Importantly, 25% of target species had feeding characteristics (i.e. reef scrapers/excavators and grazers) that contribute to the recovery of coral reef ecosystems, and gears differed considerably in catches of these species.
Spear guns and traps target a high proportion of species likely to be affected by bleaching and key for the recovery of corals. These gears are strong candidates for management restrictions in reefs with high coral mortality. In contrast, line fishing catches the lowest proportion of susceptible and recovery‐enabling species and is preferential for increasing recovery rates on coral reefs.
Synthesis and applications. Fisheries managers will require a range of tools to meet the novel challenges posed by climate change. This study presents a way to help reduce the negative impacts of climate change and potentially increase resilience of marine ecosystems by managing fishing gear. Specific gears used by artisanal fishers differentially target fish functional groups. In the coral reefs that we studied, traps and spear guns targeted a high proportion of species highly susceptible to coral mortality and critical to coral reef resilience through their top‐down control. Given that full fisheries closures are not always practical, selectively banning or restricting fishing gears is a potentially powerful tool for reducing the detrimental ecosystem effects of climate change disturbances.
Heterologous hybridization to a complementary DNA microarray reveals the effect of thermal acclimation in the endothermic bluefin tuna (Thunnus orientalis)
Authors: CASTILHO PEDRO C. , BUCKLEY BRADLEY A. , SOMERO GEORGE , BLOCK BARBARA A. 
Published: April 2009

AbstractThe temperature stress that pelagic fishes experience can induce physiological and behavioural changes that leave a signature in gene expression profiles. We used a functional genomics approach to identify genes that were up‐ or down‐regulated following thermal stress in the Pacific bluefin tuna. Following the acclimation period, 113, 81 and 196 genes were found to be differentially expressed between the control (20 °C) and cold (15°) treatment groups, in ventricle, red muscle and white muscle, respectively. The genes whose expression levels were responsive to thermal acclimation varied according to muscle fibre type, perhaps reflecting the tissue‐specific degrees of endothermy characteristic of this species.
Reticulate evolution on a mosaic of soils: diversification of the New Caledonian endemic genus Codia (Cunoniaceae)
Authors: PILLON YOHAN , MUNZINGER JÉRÔME , AMIR HAMID , HOPKINS HELEN C. F. , CHASE MARK W. 
Published: April 2009

AbstractWe reconstructed the evolutionary history of Codia, a plant genus endemic to the New Caledonia biodiversity hotspot in the southwest Pacific, using three single‐copy nuclear genes. It seems likely that more than half of Codia species have a hybrid origin, but in the absence of cytological information, it is not known whether polyploids occur. Adaptation to ultramafic soils is possibly a plesiomorphic character for the entire genus. We found that species of hybrid origin can have some morphological characters absent in putative parental species, that is, they exhibit transgressive phenotypes. There is evidence of considerable range alteration post‐origin in several species because some likely parental species of hybrid taxa no longer co‐occur and are confined to putative rainforest refugia; in some cases, hybrid species do not now co‐occur with either of their parental species. These results have implications for the design of conservation strategies, for example, prioritization of parental species for ex‐situ conservation and preservation of the contact zones between soil types where hybridization is more likely to occur (i.e. conserving the possibility for the process to continue rather than trying to conserve taxa).
From alpha to beta: identification of amino acids required for the N‐acetyllactosamine‐specific lectin‐like activity of bundlin
Authors: Humphries Romney M. , Donnenberg Michael S. , Strecker Jonathan , Kitova Elena , Klassen John S. , Cui Lina , Griener Thomas P. , Mulvey George L. , Armstrong Glen D. 
Published: April 2009

SummaryBundle‐forming pili (BFP) promote the adherence of typical enteropathogenic Escherichia coli (EPEC) to human intestinal epithelial cells. BFP are polymers of bundlin and nine bundlin alleles have been identified in EPEC isolated from diverse sources. These alleles are divided into two main groups, α and β, based on their amino acid sequences. Alpha bundlins are also N‐acetyllactosamine‐ (LacNAc) specific lectins and bind to HEp‐2 cells, whereas β bundlins do not display these characteristics. The four surface‐exposed regions of amino acid sequence heterogeneity between α and β bundlin were therefore investigated as potential LacNAc‐specific carbohydrate‐binding domains in a bundlin. Mutation of one of these domains, 137‐GENNI‐141, in α1 bundlin to that of β bundlin (136‐SPDST‐140) resulted in BFP that no longer bound to LacNAc or HEp‐2 cells. Conversely, mutating the β3 bundlin gene to encode the α bundlin sequence at this domain resulted in the gain of HEp‐2 cell adherence. The importance of this domain in carbohydrate binding is supported by the finding that introducing the mutation GENNI→GENNT altered the α1 bundlin carbohydrate‐binding specificity from LacNAc to the Lewis X glycan sequence.
Dissection of recognition determinants of Escherichia coli	σ32 suggests a composite −10 region with an ‘extended −10’ motif and a core −10 element
Authors: Koo Byoung‐Mo , Rhodius Virgil A. , Campbell Elizabeth A. , Gross Carol A. 
Published: April 2009

Summaryσ32 controls expression of heat shock genes in Escherichia coli and is widely distributed in proteobacteria. The distinguishing feature of σ32 promoters is a long −10 region (CCCCATNT) whose tetra‐C motif is important for promoter activity. Using alanine‐scanning mutagenesis of σ32 and in vivo and in vitro assays, we identified promoter recognition determinants of this motif. The most downstream C (−13) is part of the −10 motif; our work confirms and extends recognition determinants of −13C. Most importantly, our work suggests that the two upstream Cs (−16, −15) constitute an ‘extended −10’ recognition motif that is recognized by K130, a residue universally conserved in β‐ and γ‐proteobacteria. This residue is located in the α‐helix of σDomain 3 that mediates recognition of the extended −10 promoter motif in other σs. K130 is not conserved in α‐ and δ‐/ε‐proteobacteria and we found that σ32 from the α‐proteobacterium Caulobacter crescentus does not need the extended −10 motif for high promoter activity. This result supports the idea that K130 mediates extended −10 recognition. σ32 is the first Group 3 σ shown to use the ‘extended −10’ recognition motif.
Mutational analysis of Escherichia coli	σ28 and its target promoters reveals recognition of a composite −10 region, comprised of an ‘extended −10’ motif and a core −10 element
Authors: Koo Byoung‐Mo , Rhodius Virgil A. , Campbell Elizabeth A. , Gross Carol A. 
Published: April 2009

Summaryσ28 controls the expression of flagella‐related genes and is the most widely distributed alternative σ factor, present in motile Gram‐positive and Gram‐negative bacteria. The distinguishing feature of σ28 promoters is a long −10 region (GCCGATAA). Despite the fact that the upstream GC is highly conserved, previous studies have not indicated a functional role for this motif. Here we examine the functional relevance of the GCCG motif and determine which residues in σ28 participate in its recognition. We find that the GCCG motif is a functionally important composite element. The upstream GC constitutes an extended −10 motif and is recognized by R91, a residue in Domain 3 of σ28. The downstream CG is the upstream edge of −10 region of the promoter; two residues in Region 2.4, D81 and R84, participate in its recognition. Consistent with their role in base‐specific recognition of the promoter, R91, D81 and D84 are universally conserved in σ28 orthologues. σ28 is the second Group 3 σ shown to use an extended −10 region in promoter recognition, raising the possibility that other Group 3 σs will do so as well.
Peptide alarmone signalling triggers an auto‐active bacteriocin necessary for genetic competence
Authors: Perry Julie A. , Jones Marcus B. , Peterson Scott N. , Cvitkovitch Dennis G. , Lévesque Céline M. 
Published: April 2009

SummaryThe induction of genetic competence is a strategy used by bacteria to increase their genetic repertoire under stressful environmental conditions. Recently, Streptococcus pneumoniae has been shown to co‐ordinate the uptake of transforming DNA with fratricide via increased expression of the peptide pheromone responsible for competence induction. Here, we document that environmental stress‐induced expression of the peptide pheromone competence‐stimulating peptide (CSP) in the oral pathogen Streptococcus mutans. We showed that CSP is involved in the stress response and determined the CSP‐induced regulon in S. mutans by microarray analysis. Contrary to pneumococcus, S. mutans responds to increased concentrations of CSP by cell lysis in only a fraction of the population. We have focused on the mechanism of cell lysis and have identified a novel bacteriocin as the ‘death effector’. Most importantly, we showed that this bacteriocin causes cell death via a novel mechanism of action: intracellular action against self. We have also identified the cognate bacteriocin immunity protein, which resides in a separate unlinked genetic locus to allow its differential regulation. The role of the lytic response in S. mutans competence is also discussed. Together, these findings reveal a novel autolytic pathway in S. mutans which may be involved in the dissemination of fitness‐enhancing genes in the oral biofilm.
Ectopic production of VapCs from Enterobacteria inhibits translation and trans‐activates YoeB mRNA interferase
Authors: Winther Kristoffer S. , Gerdes Kenn 
Published: April 2009

SummaryToxin–antitoxin loci have been identified in almost all free‐living prokaryotes, often in high copy numbers. The biological function and molecular targets of the abundant vapBC loci are not yet known. Here we analyse the vapBC loci of Salmonella LT2 and Shigella plasmid pMYSH6000. Both loci encode putative PIN (PilT N‐terminal) domain toxins, and antitoxins that may regulate vapBC transcription. We show that vapBCLT2 and vapBCpMYSH are bona fide TA loci: (i) both VapCs inhibited cell growth very efficiently and were counteracted by the cognate VapBs; (ii) both VapCs inhibited translation; (iii) transcription of the vapBC loci was induced by amino acid starvation and chloramphenicol, consistent with the proposal that VapB is an unstable inhibitor of vapBC transcription; (iv) ectopic expression of both VapCs induced a bacteriostatic condition that could be reversed by the cognate antitoxins. Unexpectedly, induction of vapC in Escherichia coli resulted in mRNA cleavage at stop‐codons. Surprisingly, these cleavages depended on the yefM yoeB locus, indicating cross‐activation between different toxins, that is, VapC activated YoeB mRNA interferase. Activation of YoeB depended on Lon, indicating that Lon degrades YefM antitoxin. Based on these results we present a model that explains activation of YoeB.