bluuebunny/crossref_metadata_2025 huggingface dataset:
Pathways and substrate‐specific regulation of amino acid degradation in Phaeobacter inhibens DSM 17395 (archetype of the marine Roseobacter clade)
Authors: Drüppel Katharina , Hensler Michael , Trautwein Kathleen , Koßmehl Sebastian , Wöhlbrand Lars , Schmidt‐Hohagen Kerstin , Ulbrich Marcus , Bergen Nils , Meier‐Kolthoff Jan P. , Göker Markus , Klenk Hans‐Peter , Schomburg Dietmar , Rabus Ralf
Published: September 2013

Combining omics and enzymatic approaches, catabolic routes of nine selected amino acids (tryptophan, phenylalanine, methionine, leucine, isoleucine, valine, histidine, lysine and threonine) were elucidated in substrate‐adapted cells of Phaeobacter inhibens DSM 17395 (displaying conspicuous morphotypes). The catabolic network [excluding tricarboxylic acid (TCA) cycle] was reconstructed from 71 genes (scattered across the chromosome; one‐third newly assigned), with 69 encoded proteins and 20 specific metabolites identified, and activities of 10 different enzymes determined. For example, Ph. inhibens DSM 17395 does not degrade lysine via the widespread saccharopine pathway but might rather employ two parallel pathways via 5‐aminopentanoate or 2‐aminoadipate. Tryptophan degradation proceeds via kynurenine and 2‐aminobenzoate; the latter is metabolized as known from Azoarcus evansii. Histidine degradation is analogous to the Pseudomonas‐type Hut pathway via N‐formyl‐l‐glutamate. For threonine, only one of the three genome‐predicted degradation pathways (employing threonine 3‐dehydrogenase) is used. Proteins of the individual peripheral degradation sequences in Ph. inhibens DSM 17395 were apparently substrate‐specifically formed contrasting the non‐modulated TCA cycle enzymes. Comparison of genes for the reconstructed amino acid degradation network in Ph. inhibens DSM 17395 across 27 other complete genomes of Roseobacter clade members revealed most of them to be widespread among roseobacters.
Economic impacts of climate change on the Australian dairy sector
Authors: Hanslow Kevin , Gunasekera Don , Cullen Brendan , Newth David
Published: September 2013

We analyse the economic implications of climate‐driven pressures on the pasture‐based dairy sector in Australia. We use an integrated assessment model that includes a climate scenario generator, a climate‐biophysical response framework and an economywide analytical framework. For the climate scenario generator, we use data from the OzClim database of the Commonwealth Scientific and Industrial Research Organisation. For the climate‐biophysical response framework, we use the DairyMod model with inputs of changes in climate variables from OzClim to quantify climate change effects on pasture growth and productivity. For the economywide analytical framework, we use the National Integrated Assessment Model to quantify the economic implications of these effects on the dairy sector. The simulated pattern of regional changes in dairy output is not a simple function of the changes in dairy productivity. Our results show that the relative size of productivity changes across regions affects the relative competitive advantage of dairy‐producing regions. Several factors affect the regional distribution of simulated dairy‐output changes, including substitution among sources of dairy output and competition for inputs like supplementary feed. An increased output in regions with moderate reductions in dairy productivity may occur because the severely climate‐affected regions absorb the greatest loss in output.
Using Google Adwords to recruit family carers of people with dementia
Authors: O'Dwyer Siobhan T , Moyle Wendy
Published: September 2013

Aim

Online advertising is a new frontier in research recruitment and Google Adwords (GA) is one method of online advertising. Only a handful of studies, however, have described its cost and effectiveness and none have focused on older adults. The aim of this paper is to describe a GA campaign used to recruit family carers of people with dementia and provide insight for researchers planning to use GA to recruit other older adults.

Method

A GA campaign was used to recruit family carers of people with dementia to a cross‐sectional study of wellbeing.

Results

The ads were viewed more than 450,000 times in a six‐week period, but only 49 surveys were completed, at a cost of $122 per survey.

Conclusion

GA has promise, but much remains to be understood about how to maximize its potential in ageing research. Recommendations for the design of future GA campaigns are provided.
Thymic Stromal Lymphopoietin Suppresses the Apoptosis of Decidual Gamma‐delta T Cells via Regulation of the Signal Transduction and Activation of Transcription 3/Caspase‐3 Signaling Pathway
Authors: Duan Jie , Jiang Xiao‐Ping , Li Ming‐Qing , Fan Deng‐Xuan , Wang Ying , Li Da‐Jin , Jin Li‐Ping
Published: September 2013

Problem

To investigate whether thymic stromal lymphopoietin (TSLP) regulates the apoptosis of decidual γδ T cells and to elucidate the mechanism.

Method of study

Primary human decidual γδ T cells were treated with TSLP only or TSLP combined with different signaling inhibitors (STAT3, STAT5, AKT, and ERK). The levels of signal transduction and activation of transcription 3 (STAT3) tyrosine phosphorylation and caspase3 expression were determined using Western blot analysis, and the apoptosis of decidual γδ T cells was analyzed by flow cytometry.

Results

The proportions of γδ T cells in the peripheral circulation and in decidual CD3+ cell population in women with normal pregnancy were higher than the proportions of γδ T cells in either non‐pregnant control or miscarriage. Decidual γδ T cells co‐expressed the TSLP receptors (TSLPR) and IL‐7Rα, and the expression of TSLPR in decidual γδ T cells was higher than that in decidual CD8+ and CD4+ T cells. Treatment with TSLP significantly suppressed the apoptosis of decidual γδ T cells and enhanced STAT3 phosphorylation. Moreover, STAT3, and not other inhibitors, completely abrogated the anti‐apoptotic effect and expression of caspase3 in decidual γδ T cells induced by recombinant human TSLP.

Conclusion

These results suggest that TSLP may down‐regulate caspase3 expression through activation of the STAT3 pathway, thereby suppressing the apoptosis of decidual γδ T cells.
Review of calls to an Australian teratogen information service regarding psychotropic medications over a 12‐year period
Authors: Kennedy Debra , Eamus Maya , Hill Majella , Oei Ju Lee
Published: September 2013

Background

Telephone counselling services are increasingly utilised by consumers to obtain contemporary and confidential information about perinatal drug and toxin exposure. The use of such services in regard to psychotropic agents is unknown.

Aim

To determine the frequency and types of calls to a New South Wales (NSW)‐based telephone counselling service regarding perinatal psychotropic agent exposure between 2000 and 2011.

Methods

Retrospective analyses of MotherSafe call data between two epochs: I (2000–2005, n = 46,277) and II (2006–2011, n = 118,587), total 164,864 calls.

Results

25,698 (15.6%) calls were made about psychotropic agents: 16,218 (9.8%) about antidepressants, 3,145 calls (1.9%) about mood stabilisers/antiepileptic agents, 2,878 (1.7%) about benzodiazepines and 3,457 (2.1%) about antipsychotic drugs. Calls regarding psychotropic agents doubled in epoch II (18,231 vs 7,467, epoch I) but decreased as a proportion of total calls (I: 16.1% vs II: 15.4%, P < 0.001). Selective serotonin inhibitors (SSRIs) were the most common drugs of concern (>44% of total psychotropic calls). The proportion of calls regarding particular agents changed significantly between epochs, for example paroxetine (epoch I: 14.8% vs epoch II: 6.7% of all antidepressant calls, P < 0.001) and quetiapine (epoch 1: 10.6% vs epoch II: 34.7% of all antipsychotic calls (P < 0.001). Calls from rural areas of NSW increased from 22.6 to 24.7% (P < 0.001).

Conclusion

Consumer demand for information about the use of psychotropic agents for women of child‐bearing age has increased considerably over the last decade, particularly in rural areas of Australia. This indicates a need to review current existing services, particularly for rural consumers.
Influence of a modified propofol equilibration rate constant (ke0) on the effect‐site concentration at loss and recovery of consciousness with the Marsh model
Authors: Seo J. H. , Goo E. K. , Song I. A. , Park S. H. , Park H. P. , Jeon Y. T. , Hwang J. W.
Published: September 2013

This study compared the predicted effect‐site concentration of propofol at loss and recovery of consciousness when using target‐controlled infusion devices with the same pharmacokinetic model (Marsh) but a different plasma effect‐site equilibration rate constant (ke0), the DiprifusorTM (ke0 0.26 min−1) and Base Primea™ (ke0 1.21 min−1). We studied 60 female patients undergoing minor gynaecological surgery under general anaesthesia. Although the total dose of propofol and time until loss of consciousness were comparable, the effect‐site concentration at loss of consciousness was significantly lower with the Diprifusor than with the Base Primea (1.2 (0.3) μg.ml−1 vs 4.5 (0.9) μg.ml−1, respectively, p < 0.001). The effect‐site concentration at recovery of consciousness was significantly higher with the Diprifusor than with the Base Primea (1.8 (0.4) μg.ml−1 vs 1.5 (0.2) μg.ml−1, respectively, p = 0.01). In conclusion, the effect‐site concentration of propofol differs depending on the ke0, despite the use of the same pharmacokinetic model. Therefore, the ke0 should be considered when predicting loss and recovery of consciousness based on the effect‐site concentration of propofol.
Relationships between flavin‐containing mono‐oxygenase 3 (FMO3) genotype and trimethylaminuria phenotype in a Japanese population
Authors: Shimizu Makiko , Allerston Charles K. , Shephard Elizabeth A. , Yamazaki Hiroshi , Phillips Ian R.
Published: September 2013

Aim

The aim of this study was to investigate relationships between flavin‐containing mono‐oxygenase 3 (FMO3) genotype and phenotype (conversion of odorous trimethylamine into non‐odorous trimethylamine N‐oxide) in a large Japanese cohort suffering from trimethylaminuria.

Methods

Urinary excretion of trimethylamine and trimethylamine N‐oxide was determined for 102 volunteers with self‐reporting symptoms of trimethylaminuria. For each we determined the sequence of the entire coding region, plus 1.3 kb of flanking intronic and 2.5 kb of the upstream region of the FMO3 gene. The affect of upstream variants on transcription was determined with a reporter gene assay.

Results

Seventy‐eight subjects were diagnosed as suffering from trimethylaminuria, based on urinary excretion of <90% of total TMA as TMA N‐oxide. Of these, 13 were classified as severe, 56 as moderate and nine as mild cases, excreting <43%, 48–70% and 73–83% of trimethylamine as trimethylamine N‐oxide, respectively. Twenty‐seven mutations were identified in FMO3, 15 in the coding region, of which eight abolish or severely impair FMO3 activity (Pro70Leu, Cys197fsX, Thr201Lys, Arg205Cys, Met260Val, Trp388Ter, Gln470Ter and Arg500Ter), and 12 in the upstream region. The mutations segregate into 19 haplotypes, including four different combinations of upstream mutations, each of which reduces transcriptional activity in comparison with the ancestral upstream sequence of FMO3.

Conclusions

Comparisons of genotype and phenotype reveal that severe trimethylaminuria is caused by loss of function mutations in FMO3. For moderate and mild cases the situation is more complex, with most resulting from factors other than FMO3 genotype. Our results have implications for the diagnosis and management of the disorder.
Treatment of elderly patients with acute lymphoblastic leukaemia using a paediatric‐based protocol
Authors: Poch Martell Marc , Atenafu Eshetu G. , Minden Mark D. , Schuh Andre C. , Yee Karen W. L. , Schimmer Aaron D. , Gupta Vikas , Brandwein Joseph M.
Published: September 2013

All newly diagnosed patients aged 60–79 years with acute lymphoblastic leukaemia (ALL) receiving induction chemotherapy with a modified paediatric‐based regimen over a 7‐year period were retrospectively analysed (n = 51, median age 65 years). The treatment regimen consisted of induction, central nervous system prophylaxis, seven cycles of intensification and 24 cycles of maintenance. BCR‐ABL1 negative patients received weekly asparaginase during intensification, while BCR‐ABL1+ patients received daily imatinib. Post‐remission therapy was given in an outpatient setting. The complete response rate was 75%, with an induction mortality of 20%; 6% of patients had resistant disease. 37% of patients who achieved a complete remission relapsed. The estimated 5‐year overall survival was 40% for BCR‐ABL1 negative and 47% for BCR‐ABL1+ patients (P = not significant); the 5‐year disease‐free survival was 57% and 39%, respectively (P = NS). The post‐induction phase was generally well tolerated, with 81% able to complete the intensification phase and proceed to maintenance. In conclusion, administration of this modified paediatric‐based protocol is feasible and active for elderly patients with ALL. Survival is superior to most previously reported series in this age group, but remains worse compared to younger patients. Further improvement of the toxicity profile, particularly during induction, is required to improve outcomes.
Incidence of haematological malignancies by ethnic group in England, 2001–7
Authors: Shirley Megan H. , Sayeed Shameq , Barnes Isobel , Finlayson Alexander , Ali Raghib
Published: September 2013

The aetiology of most haematological malignancies is largely unknown. Studies of migrant populations can provide insights into the relative importance of genetic and environmental risk factors for these diseases. This study compares incidence rates in British Indians, Pakistanis, Bangladeshis, Black Africans, Black Caribbeans, Chinese and Whites in England from 2001 to 2007. We analysed 134 302 haematological cancer registrations with ethnicity obtained by linkage to the Hospital Episodes Statistics database. Mid‐year population estimates from 2001 to 2007 were used. Incidence rate ratios adjusted for age, sex and income were calculated, comparing the six ethnic groups to Whites and to each other. Whites had the highest rates for most subtypes. However, Blacks experienced more than double the incidence of plasma cell and mature T‐cell neoplasms compared to other ethnic groups. There were also significant differences in incidence between Indians, Pakistanis and Bangladeshis for Hodgkin lymphoma and mature B‐cell neoplasms and between Black African and Black Caribbeans for mature B‐cell and other lymphoid neoplasms (all P < 0·001). Our results show that the risk of haematological cancers varies greatly by ethnic group, including within those groups that have traditionally been grouped together (South Asians and Blacks) with many of these differences not explicable by known risk factors.
Endometrial stem cell differentiation into smooth muscle cell: a novel approach for bladder tissue engineering in women
Authors: Shoae‐Hassani Alireza , Sharif Shiva , Seifalian Alexander M. , Mortazavi‐Tabatabaei Seyed Abdolreza , Rezaie Sassan , Verdi Javad
Published: September 2013

Objective

To investigate manufacturing smooth muscle cells (SMCs) for regenerative bladder reconstruction from differentiation of endometrial stem cells (EnSCs), as the recent discovery of EnSCs from the lining of women's uteri, opens up the possibility of using these cells for tissue engineering applications, such as building up natural tissue to repair prolapsed pelvic floors as well as building urinary bladder wall.

Materials and Methods

Human EnSCs that were positive for cluster of differentiation 146 (CD146), CD105 and CD90 were isolated and cultured in Dulbecco's modified Eagle/F12 medium supplemented with myogenic growth factors.

The myogenic factors included: transforming growth factor β, platelet‐derived growth factor, hepatocyte growth factor and vascular endothelial growth factor.

Differentiated SMCs on bioabsorbable polyethylene‐glycol and collagen hydrogels were checked for SMC markers by real‐time reverse‐transcriptase polymerase chain reaction (RT‐PCR), western blot (WB) and immunocytochemistry (ICC) analyses.

Results

Histology confirmed the growth of SMCs in the hydrogel matrices.

The myogenic growth factors decreased the proliferation rate of EnSCs, but they differentiated the human EnSCs into SMCs more efficiently on hydrogel matrices and expressed specific SMC markers including α‐smooth muscle actin, desmin, vinculin and calponin in RT‐PCR, WB and ICC experiments.

The survival rate of cultures on the hydrogel‐coated matrices was significantly higher than uncoated cultures.

Conclusions

Human EnSCs were successfully differentiated into SMCs, using hydrogels as scaffold.

EnSCs may be used for autologous bladder wall regeneration without any immunological complications in women.

Currently work is in progress using bioabsorbable nanocomposite materials as EnSC scaffolds for developing urinary bladder wall tissue.
Understanding the parents of children with special needs: collaboration between health, social and education networks
Authors: Tétreault S. , Freeman A. , Carrière M. , Beaupré P. , Gascon H. , Marier Deschênes P.
Published: September 2013

Context

In 2003, Quebec's Ministry of Health and Social Services (MSSS) and the Ministry of Education, Recreation and Sports (MELS) concluded the Agreement for the complementarity of services between the health and social services network and the education network. The objectives of the current investigation were to evaluate the implementation of this Agreement and its impact upon renewal of practices and services, and to investigate the consequences for children with special needs and their families. The specific focus of this article is to describe parents' perspectives regarding the impact of this Agreement upon them and their children.

Methods

Interviews were conducted with 56 parents of children with disabilities, social maladjustment or learning difficulties across the province of Quebec. Data were analysed using content analysis.

Results

Most parents were not directly aware of any contact between school staff and health or social professionals, although discussions might have been held without their knowledge. The intervention plans seemed to be the main vehicle through which some parents perceived collaboration to be occurring. For parents, the impact upon actual practices or collaborative work is either minimal or non‐existent.

Conclusion

School inclusion of children with special needs is a challenge for all societies. The Agreement illustrates the Quebec government's intent to promote an alliance between two complex networks and has the potential to greatly benefit children and their families. However, more concrete action is required in order to realize specific changes regarding work cohesion and service organization for these groups.
Reproducibility of a soil organic carbon fractionation method to derive RothC carbon pools
Authors: Poeplau C. , Don A. , Dondini M. , Leifeld J. , Nemo R. , Schumacher J. , Senapati N. , Wiesmeier M.
Published: September 2013

Fractionation of soil is undertaken to isolate organic carbon with distinct functional properties, such as stability and turnover times. Soil organic carbon (SOC) fractionation helps us to understand better the response of SOC to changes in land use, management or climate. However, fractionation procedures are often poorly defined and there is little information available on their reproducibility in different laboratories. In a ring trial, we assessed the reproducibility of a SOC fractionation method introduced by Zimmermann et al. (2007). The isolated fractions were linked to the model pool sizes of the Rothamsted carbon model (RothC). We found significant differences between six laboratories for all five defined fractions in three different soils with coefficients of variation ranging from 14 to 138%. During ultrasonic dispersion, the output power (energy per unit time) was identified as an important factor controlling the distribution of SOC within these five fractions, while commonly only the output energy is standardized. The amount of water used to wet‐sieve dispersed soil slurry significantly influenced the amount of extracted dissolved organic carbon (DOC). We therefore suggest using a fixed amount of power for ultrasonic dispersion (20 W) and a minimum amount of water for wet sieving (2000 ml). RothC pool sizes were predicted from the measured fractions and compared with RothC equilibrium pool size distributions. This model initialization using measured SOC fractions, however, led to an over‐estimation of stable RothC SOC pools when compared with pool size distributions derived from RothC equilibrium runs under a bare fallow soil model simulation. To improve the isolation of particulate organic matter from stable mineral‐bound organic matter, we suggest that the density should be increased from 1.8 to 2.0 g cm−3 in the density fractionation step. We formulated a modified fractionation procedure, which aims specifically to enhance reproducibility across laboratories and to improve the match of the isolated SOC fractions with RothC's SOC pools.
An experimental study of the regulation of glycolytic oscillations in yeast
Authors: Schrøder Tine D. , Özalp Veli C. , Lunding Anita , Jernshøj Kit D. , Olsen Lars F.
Published: September 2013

We have studied oscillating glycolysis in the strain BY4743 and isogenic strains with deletions of genes encoding enzymes in glycolysis, mitochondrial electron transport and ATP synthesis. We found that deletion of the gene encoding the hexokinase 1 isoform does not affect the oscillations while deletion of the gene encoding the hexokinase 2 isoform results in oscillations with smaller amplitude. The latter is associated with an almost 50% decrease in hexokinase activity. Deletions in the genes encoding the α‐ and β‐subunits of phosphofructokinase abolish the oscillations entirely. This loss in oscillatory activity is associated with a fourfold decrease in phosphofructokinase activity. Deletions of genes encoding subunits of the F1F0 ATPase also inhibit the oscillations in accordance with earlier studies using for example inhibitors. Finally, we identified an apparently new control point involving the mitochondrial cytochrome c oxidase. The latter is difficult to explain as oscillatory activity entails 100% inhibition of this enzyme. The mitochondria of this strain seem to have normal F1F0 ATPase activity. Overall these results support earlier experimental and model studies suggesting that in addition to processes within glycolysis also processes outside this pathway contribute to the control of the oscillatory behaviour.
Incorporating adaptive responses into future projections of coral bleaching
Authors: Logan Cheryl A. , Dunne John P. , Eakin C. Mark , Donner Simon D.
Published: September 2013

Climate warming threatens to increase mass coral bleaching events, and several studies have projected the demise of tropical coral reefs this century. However, recent evidence indicates corals may be able to respond to thermal stress though adaptive processes (e.g., genetic adaptation, acclimatization, and symbiont shuffling). How these mechanisms might influence warming‐induced bleaching remains largely unknown. This study compared how different adaptive processes could affect coral bleaching projections. We used the latest bias‐corrected global sea surface temperature (SST) output from the NOAA/GFDL Earth System Model 2 (ESM2M) for the preindustrial period through 2100 to project coral bleaching trajectories. Initial results showed that, in the absence of adaptive processes, application of a preindustrial climatology to the NOAA Coral Reef Watch bleaching prediction method overpredicts the present‐day bleaching frequency. This suggests that corals may have already responded adaptively to some warming over the industrial period. We then modified the prediction method so that the bleaching threshold either permanently increased in response to thermal history (e.g., simulating directional genetic selection) or temporarily increased for 2–10 years in response to a bleaching event (e.g., simulating symbiont shuffling). A bleaching threshold that changes relative to the preceding 60 years of thermal history reduced the frequency of mass bleaching events by 20–80% compared with the ‘no adaptive response’ prediction model by 2100, depending on the emissions scenario. When both types of adaptive responses were applied, up to 14% more reef cells avoided high‐frequency bleaching by 2100. However, temporary increases in bleaching thresholds alone only delayed the occurrence of high‐frequency bleaching by ca. 10 years in all but the lowest emissions scenario. Future research should test the rate and limit of different adaptive responses for coral species across latitudes and ocean basins to determine if and how much corals can respond to increasing thermal stress.
Vegetation controls on northern high latitude snow‐albedo feedback: observations and CMIP5 model simulations
Authors: Loranty Michael M. , Berner Logan T. , Goetz Scott J. , Jin Yufang , Randerson James T.
Published: September 2013

The snow‐masking effect of vegetation exerts strong control on albedo in northern high latitude ecosystems. Large‐scale changes in the distribution and stature of vegetation in this region will thus have important feedbacks to climate. The snow‐albedo feedback is controlled largely by the contrast between snow‐covered and snow‐free albedo (Δα), which influences predictions of future warming in coupled climate models, despite being poorly constrained at seasonal and century time scales. Here, we compare satellite observations and coupled climate model representations of albedo and tree cover for the boreal and Arctic region. Our analyses reveal consistent declines in albedo with increasing tree cover, occurring south of latitudinal tree line, that are poorly represented in coupled climate models. Observed relationships between albedo and tree cover differ substantially between snow‐covered and snow‐free periods, and among plant functional type. Tree cover in models varies widely but surprisingly does not correlate well with model albedo. Furthermore, our results demonstrate a relationship between tree cover and snow‐albedo feedback that may be used to accurately constrain high latitude albedo feedbacks in coupled climate models under current and future vegetation distributions.
Range expansions across ecoregions: interactions of climate change, physiology and genetic diversity
Authors: Rius Marc , Clusella‐Trullas Susana , McQuaid Christopher D. , Navarro René A. , Griffiths Charles L. , Matthee Conrad A. , von der Heyden Sophie , Turon Xavier
Published: September 2013

Aim

Climate change is expected to drive range shifts among a wide array of organisms. Non‐indigenous species (NIS) provide a unique opportunity to observe the establishment of range boundaries in a way that cannot be directly seen for native species. Recent studies have indicated that climate change facilitates biological invasions at local scales. However, the generality of these effects is unclear, as there is a dearth of comparative studies that assess how rapid environmental change affects species ranges across taxa and biogeographic provinces.

Location

The South African coast and other coastlines across the world.

Methods

We first studied the distribution of shallow‐marine benthic organisms along the South African coastline and analysed the global distribution of NIS. We then obtained DNA sequence data from a suite of co‐occurring NIS from along the studied coastline and compared these data with available genetic information from other regions of the world. Subsequently, we conducted physiological experiments to assess how thermal tolerance was related to species distribution. Finally, we analysed ship‐based seawater temperature records and compared these with past changes in the range size and abundance of NIS. These records were used to estimate shipping intensity and NIS propagule pressure.

Results

We found that NIS with a variety of thermal tolerances and distributions have expanded their ranges and increased in abundance as seawater temperature regimes have changed. We found little interannual variation in shipping transport intensity. Most haplotypes of the studied NIS in South Africa were shared with other regions.

Main conclusions

This study provides empirical evidence that NIS, regardless of their thermal tolerance, range size and genetic variability, are expanding their ranges and increasing in abundance. This trend is uncorrelated with levels of human‐mediated NIS transport but concurrent with changes in seawater temperature, which suggests that climate change fosters the spread and abundance of NIS across multiple spatial scales.
Multiple waves of colonization by monarch flycatchers (Myiagra, Monarchidae) across the Indo‐Pacific and their implications for coexistence and speciation
Authors: Fabre Pierre‐Henri , Moltensen Maria , Fjeldså Jon , Irestedt Martin , Lessard Jean‐Philippe , Jønsson Knud A.
Published: September 2013

Aim

Islands and archipelagos have played an important role in the development of ecological and evolutionary theories. Using a newly compiled molecular phylogeny we infer the biogeographical history of a monarch flycatcher genus,Myiagra, which is distributed across the Indo‐Pacific. We subsequently integrate biogeographical and ecomorphological data to examine the role of dispersal and trait evolution in the build‐up of avian assemblages.

Location

Australia, the Moluccas, New Guinea and Pacific islands.

Methods

We generated a taxonomically densely sampled mitochondrialDNAdataset that included almost all species and subspecies of the reciprocally monophyletic generaMyiagraandArses. We then used maximum likelihoood and Bayesian inference to infer their phylogenetic relationships. To reconstruct their biogeographical history, we first dated the tree topology and then usedLagrangeto infer ancestral geographical areas. Finally, we combined ancestral area reconstructions with information on ecomorphological traits to infer mechanisms underlying community assembly.

Results

We provide the first comprehensive molecular phylogenetic reconstruction forMyiagraandArsesmonarch flycatchers. Our phylogenetic reconstruction reveals a relatively recent diversification from the Miocene associated with several major dispersal events. Ancestral area reconstruction reveals several independent colonizations of the Moluccas, Melanesia, Fiji and the Micronesian islands. Ancestral state reconstruction of ecological traits suggests that the diversity of traits in co‐occurring species of monarch flycatchers results from independent colonization events and ecological niche conservatism rather thanin situdiversification.

Main conclusions

Three waves of colonization, non‐overlapping in time, led to independent speciation events in the Bismarcks, Fiji and the Moluccas, in addition toin situspeciation events on remote islands of Micronesia, the Solomons, Vanuatu and Samoa. Few of these colonizations have led to the co‐occurrence of congenerics or species with similar ecomorphological profiles on the same island. Thus, we suggest that priority effects might prevent new colonizers from establishing themselves if they share high levels of ecological similarity with resident species. We conclude that historical dispersal to and colonization of new islands, combined with ecologically deterministic priority effects, drove the assembly of insular monarch flycatcher communities across the Indo‐Pacific.
Reply to the Commentaries: Of Course, We Do Not Yet Know What it is All About, But Functional Contextualism is a Good Place to Start
Authors: Benson Lisa A. , Sevier Mia , Christensen Andrew
Published: September 2013

In this reply to the commentaries, we note several points of disagreement with Johnson and Greenman on theoretical and empirical grounds. We are particularly surprised by their assumption that attachment has already been established as the key mechanism of change in couple therapy, as our present findings do not support this idea. We also elaborate on Gurman's functional contextualist views and describe why IBCT may be a particularly helpful model for training new couple therapists in a contextualist way.
Seed Treatment with Live or Dead Fusarium verticillioides Equivalently Reduces the Severity of Subsequent Stalk Rot
Authors: Martins Vitor F. , Vaughan Martha M. , Huffaker Alisa , Schmelz Eric A. , Christensen Shawn , Sims James , Benda Nicole D. , Swerbilow Jay , Alborn Hans , Teal Peter E.
Published: September 2013

Fusarium verticillioides is a widely distributed fungus that can associate with maize as a deleterious pathogen and an advantageous endophyte. Here, we show that seed treatment with live F. verticillioides enhances maize resistance to secondary stalk rot infection and further demonstrate that dead F. verticillioides is sufficient to equivalently reduce F. verticillioides biomass. Seed treatment with live or dead F. verticillioides primes maize plants, and upon subsequent stalk infection, terpenoid phytoalexins accumulate faster than control‐treated plants. Seed treatment did not constitutively activate plant defences nor did it impact plant growth. These results suggest that seed treatment with dead F. verticillioides can be used as a ‘vaccination’ method to decrease the severity of stalk rot and potentially pathogen infection throughout the plant.
Trait variability differs between leaf and wood tissues across ecological scales in subtropical forests
Authors: Kang Meng , Chang Scott X. , Yan En‐Rong , Wang Xi‐Hua
Published: September 2013

Question

Revealing how plant traits vary over disparate spatial scales and how ecological processes mediate such variation is important for understanding plant community assembly. However, to what extent does the distribution of trait variation among ecological scales differ between leaf and wood tissues and between physical and chemical traits? What are the consequences of resource competition and/or habitat filtering on the community assembly with respect to differences between leaf and wood traits, and between physical and chemical traits?

Location

Subtropical evergreen broad‐leaved forests in five sites in the Ningbo area (29°41–50′ N, 121°36–52′ E) in eastern China.

Methods

Traits of 96 woody plant species were sampled and variation of ten physical‐ and chemical‐based leaf and wood traits were partitioned across six ecological scales (site, plot, species, individual plant, twigs and leaf age) using a linear mixed model.

Results

From individual plant to site scales, variance partitions were distinct between leaf and wood traits. In leaf tissues, physical and chemical traits showed a consistent pattern, with the majority of variation found among species and individual plants, with little among plots. For wood tissues, the largest variation in physical traits was at the species and individual plant scales, with the largest variation in chemical traits observed at the plot scale. Variance partition was markedly similar within and across species.

Conclusion

Leaf and wood traits vary differently in relation to ecological scale, suggesting that trait variability is tissue‐specific. The large variability of wood traits at the plot scale suggests a strong habitat filtering process. The large variation in leaf traits within plots may reflect niche differentiation across species and the importance of intra‐specific variation that affects species co‐existence. Our study demonstrated that physical and chemical traits may be independent. These decoupled trait axes may increase the dimensionality of niche space and facilitate species co‐existence in forest communities.
Effect of short‐chain fatty acids and acidification on the phasic and tonic motor activity of the human colon
Authors: Jouët P. , Moussata D. , Duboc H. , Boschetti G. , Attar A. , Gorbatchef C. , Sabaté J.‐M. , Coffin B. , Flourié B.
Published: September 2013

Background

The effects of bacterial fermentation on human colonic motor activity could be explained by colonic acidification or short‐chain fatty acid (SCFA) production. We compared in healthy volunteers the colonic motor effects of intracolonic infusion of neutral or acidic saline solutions and then of neutral or acidic solutions containing an SCFA mixture.

Methods

20 healthy volunteers swallowed a probe (with an infusion catheter, 6 perfused catheters and a balloon connected to a barostat) that migrated into the colon. Colonic motor activity was recorded in fasting basal state (1 h), during (3 h) and after (2 h) intracolonic infusion in a random order on two consecutive days of 750 mL of NaCl at pH 7.0 (neutral saline) or 4.5 (acidic saline) in 10 volunteers (first experiment) and of an SCFA mixture (acetic acid 66%, propionic acid 24% and butyric acid 10%; 100 mM) at pH 7.0 or 4.5 in 10 other volunteers (second experiment). We determined for each hour a global motility index (reflecting phasic activity recorded by all catheters), the mean balloon volume (reflecting tonic activity), and the mean number of high‐amplitude‐propagated contractions (HAPCs).

Key Results

Intracolonic infusion of neutral or acidic solutions containing saline or an SCFA mixture did not change the global motility index, the barostat balloon volume, or the HAPC number compared with basal values.

Conclusions & Inferences

Under our experimental conditions, these findings suggest that the stimulation of colonic motor activity induced by carbohydrate fermentation is not explained by the acidification of the colonic contents or the resulting production of SCFAs.
A whole‐genome SNP array (RICE6K) for genomic breeding in rice
Authors: Yu Huihui , Xie Weibo , Li Jing , Zhou Fasong , Zhang Qifa
Published: September 2013

The advances in genotyping technology provide an opportunity to use genomic tools in crop breeding. As compared to field selections performed in conventional breeding programmes, genomics‐based genotype screen can potentially reduce number of breeding cycles and more precisely integrate target genes for particular traits into an ideal genetic background. We developed a whole‐genome single nucleotide polymorphism (SNP) array, RICE6K, based on Infinium technology, using representative SNPs selected from more than four million SNPs identified from resequencing data of more than 500 rice landraces. RICE6K contains 5102 SNP and insertion–deletion (InDel) markers, about 4500 of which were of high quality in the tested rice lines producing highly repeatable results. Forty‐five functional markers that are located inside 28 characterized genes of important traits can be detected using RICE6K. The SNP markers are evenly distributed on the 12 chromosomes of rice with the average density of 12 SNPs per 1 Mb and can provide information for polymorphisms between indica and japonica subspecies as well as varieties within indica and japonica groups. Application tests of RICE6K showed that the array is suitable for rice germplasm fingerprinting, genotyping bulked segregating pools, seed authenticity check and genetic background selection. These results suggest that RICE6K provides an efficient and reliable genotyping tool for rice genomic breeding.
Modeling Uncertainties in Workforce Disruptions from Influenza Pandemics Using Dynamic Input‐Output Analysis
Authors: Haimar Amine El , Santos Joost R.
Published: September 2013

Influenza pandemic is a serious disaster that can pose significant disruptions to the workforce and associated economic sectors. This article examines the impact of influenza pandemic on workforce availability within an interdependent set of economic sectors. We introduce a simulation model based on the dynamic input‐output model to capture the propagation of pandemic consequences through the National Capital Region (NCR). The analysis conducted in this article is based on the 2009 H1N1 pandemic data. Two metrics were used to assess the impacts of the influenza pandemic on the economic sectors: (i) inoperability, which measures the percentage gap between the as‐planned output and the actual output of a sector, and (ii) economic loss, which quantifies the associated monetary value of the degraded output. The inoperability and economic loss metrics generate two different rankings of the critical economic sectors. Results show that most of the critical sectors in terms of inoperability are sectors that are related to hospitals and health‐care providers. On the other hand, most of the sectors that are critically ranked in terms of economic loss are sectors with significant total production outputs in the NCR such as federal government agencies. Therefore, policy recommendations relating to potential mitigation and recovery strategies should take into account the balance between the inoperability and economic loss metrics.
Microbially influenced formation of Mg‐calcite and Ca‐dolomite in the presence of exopolymeric substances produced by sulphate‐reducing bacteria
Authors: Bontognali Tomaso R. R. , McKenzie Judith A. , Warthmann Rolf J. , Vasconcelos Crisogono
Published: September 2013

Some species of sulphate‐reducing bacteria (SRB) are known to mediate the formation of dolomite and Mg‐calcite. However, their exact role in the mineralization process remains elusive. Here, we present the result of a laboratory experiment that was designed to test whether formation of carbonate minerals by SRB can occur in the absence of living cells, through passive mineralization of their exopolymeric substances (EPS). SRB capable of mediating dolomite were cultivated in the laboratory, allowing them to secrete EPS. Microbial activity within the cultures was subsequently inhibited with antibiotics. Only after this step, Ca2+ and Mg2+ were added to the solution and carbonate minerals could form. Mg‐calcite and disordered Ca‐dolomite precipitated in association with EPS. The mol.% of Mg2+ in the crystals increased with longer incubation times. This result demonstrates that organic compounds produced by SRB can mediate the formation of Ca‐Mg carbonates in the absence of an active metabolism.
Vernalization requirement duration in winter wheat is controlled by TaVRN‐A1 at the protein level
Authors: Li Genqiao , Yu Ming , Fang Tilin , Cao Shuanghe , Carver Brett F. , Yan Liuling
Published: September 2013

Winter wheat requires a period of low temperatures to accelerate flowering (vernalization). This requirement could make winter wheat more vulnerable to elevated global temperature via insufficient vernalization. All known vernalization genes are cloned according to qualitative variation in vernalization requirement between spring and winter wheat, but the genes controlling quantitative variation for more or less vernalization requirement among winter wheat cultivars remain unknown. We report here that the gene for the vernalization requirement duration in winter wheat was cloned using a BC1F2:3 population that segregated in a 3:1 ratio of early‐flowering plants and late‐flowering plants after vernalization for 3 weeks. The positional cloning of the gene for vernalization requirement duration demonstrated that this trait is controlled by TaVRN‐A1 at the protein level. The Ala180 in vrn‐A1a, encoded by the dominant allele for 3–week vernalization, was mutated to Val180 in vrn‐A1b, encoded by the recessive allele for 6–week vernalization. Further studies with in vitro protein pull‐down assays and immunoprecipitation analyses indicated that the mutated Val180 in vrn‐A1b protein decreased the ability to bind with TaHOX1 (the first homeobox protein in Triticum aestivum). The direct binding of TaVRN‐A1 and TaHOX1 proteins was confirmed in the nucleus of living plant cells by bimolecular fluorescence complementation (BiFC) analyses. The TaHOX1 gene was found to be upregulated by low temperatures, and to have a significant genetic effect on heading date, suggesting that TaHOX1 functions in the flowering pathway in winter wheat.
Genetic dissection of a TIR‐NB‐LRR locus from the wild North American grapevine species Muscadinia rotundifolia identifies paralogous genes conferring resistance to major fungal and oomycete pathogens in cultivated grapevine
Authors: Feechan Angela , Anderson Claire , Torregrosa Laurent , Jermakow Angelica , Mestre Pere , Wiedemann‐Merdinoglu Sabine , Merdinoglu Didier , Walker Amanda R. , Cadle‐Davidson Lance , Reisch Bruce , Aubourg Sebastien , Bentahar Nadia , Shrestha Bipna , Bouquet Alain , Adam‐Blondon Anne‐Françoise , Thomas Mark R. , Dry Ian B.
Published: September 2013

The most economically important diseases of grapevine cultivation worldwide are caused by the fungal pathogen powdery mildew (Erysiphe necator syn. Uncinula necator) and the oomycete pathogen downy mildew (Plasmopara viticola). Currently, grapegrowers rely heavily on the use of agrochemicals to minimize the potentially devastating impact of these pathogens on grape yield and quality. The wild North American grapevine species Muscadinia rotundifolia was recognized as early as 1889 to be resistant to both powdery and downy mildew. We have now mapped resistance to these two mildew pathogens in M. rotundifolia to a single locus on chromosome 12 that contains a family of seven TIR‐NB‐LRR genes. We further demonstrate that two highly homologous (86% amino acid identity) members of this gene family confer strong resistance to these unrelated pathogens following genetic transformation into susceptible Vitis vinifera winegrape cultivars. These two genes, designated resistance to Uncinula necator (MrRUN1) and resistance to Plasmopara viticola (MrRPV1) are the first resistance genes to be cloned from a grapevine species. Both MrRUN1 and MrRPV1 were found to confer resistance to multiple powdery and downy mildew isolates from France, North America and Australia; however, a single powdery mildew isolate collected from the south‐eastern region of North America, to which M. rotundifolia is native, was capable of breaking MrRUN1‐mediated resistance. Comparisons of gene organization and coding sequences between M. rotundifolia and the cultivated grapevine V. vinifera at the MrRUN1/MrRPV1 locus revealed a high level of synteny, suggesting that the TIR‐NB‐LRR genes at this locus share a common ancestor.
A rice lectin receptor‐like kinase that is involved in innate immune responses also contributes to seed germination
Authors: Cheng Xiaoyan , Wu Yan , Guo Jianping , Du Bo , Chen Rongzhi , Zhu Lili , He Guangcun
Published: September 2013

Seed germination and innate immunity both have significant effects on plant life spans because they control the plant's entry into the ecosystem and provide defenses against various external stresses, respectively. Much ecological evidence has shown that seeds with high vigor are generally more tolerant of various environmental stimuli in the field than those with low vigor. However, there is little genetic evidence linking germination and immunity in plants. Here, we show that the rice lectin receptor‐like kinase OslecRK contributes to both seed germination and plant innate immunity. We demonstrate that knocking down the OslecRK gene depresses the expression of α–amylase genes, reducing seed viability and thereby decreasing the rate of seed germination. Moreover, it also inhibits the expression of defense genes, and so reduces the resistance of rice plants to fungal and bacterial pathogens as well as herbivorous insects. Yeast two‐hybrid and co‐immunoprecipitation experiments revealed that OslecRK interacts with an actin‐depolymerizing factor (ADF) in vivo via its kinase domain. Moreover, the rice adf mutant exhibited a reduced seed germination rate due to the suppression of α–amylase gene expression. This mutant also exhibited depressed immune responses and reduced resistance to biotic stresses. Our results thus provide direct genetic evidence for a common physiological pathway connecting germination and immunity in plants. They also partially explain the common observation that high‐vigor seeds often perform well in the field. The dual effects of OslecRK may be indicative of progressive adaptive evolution in rice.