bluuebunny/crossref_metadata_2025 huggingface dataset:
TheArabidopsis thalianaCheckpoint Kinase WEE1 Protects against Premature Vascular Differentiation during Replication Stress
Authors: Cools Toon , Iantcheva Anelia , Weimer Annika K. , Boens Shannah , Takahashi Naoki , Maes Sara , Van den Daele Hilde , Van Isterdael Gert , Schnittger Arp , De Veylder Lieven
Published: April 2011

A sessile lifestyle forces plants to respond promptly to factors that affect their genomic integrity. Therefore, plants have developed checkpoint mechanisms to arrest cell cycle progression upon the occurrence of DNA stress, allowing the DNA to be repaired before onset of division. Previously, the WEE1 kinase had been demonstrated to be essential for delaying progression through the cell cycle in the presence of replication-inhibitory drugs, such as hydroxyurea. To understand the severe growth arrest of WEE1-deficient plants treated with hydroxyurea, a transcriptomics analysis was performed, indicating prolonged S-phase duration. A role for WEE1 during S phase was substantiated by its specific accumulation in replicating nuclei that suffered from DNA stress. Besides an extended replication phase, WEE1 knockout plants accumulated dead cells that were associated with premature vascular differentiation. Correspondingly, plants without functional WEE1 ectopically expressed the vascular differentiation marker VND7, and their vascular development was aberrant. We conclude that the growth arrest of WEE1-deficient plants is due to an extended cell cycle duration in combination with a premature onset of vascular cell differentiation. The latter implies that the plant WEE1 kinase acquired an indirect developmental function that is important for meristem maintenance upon replication stress.
AaTFL1Confers an Age-Dependent Response to Vernalization in PerennialArabis alpina
Authors: Wang Renhou , Albani Maria C. , Vincent Coral , Bergonzi Sara , Luan Ming , Bai Yan , Kiefer Christiane , Castillo Rosa , Coupland George
Published: April 2011

Flowering of many plants is induced by environmental signals, but these responses can depend on the age of the plant. Exposure of Arabidopsis thaliana to vernalization (winter temperatures) at germination induces flowering, whereas a close perennial relative Arabis alpina only responds if exposed when at least 5 weeks old. We show that vernalization of these older A. alpina plants reduces expression of the floral repressor PEP1 and activates the orthologs of the Arabidopsis flowering genes SOC1 (Aa SOC1) and LFY (Aa LFY). By contrast, when younger plants are vernalized, PEP1 and Aa SOC1 mRNA levels change as in older plants, but Aa LFY is not expressed. We demonstrate that A. alpina TFL1 (Aa TFL1) blocks flowering and prevents Aa LFY expression when young plants are exposed to vernalization. In addition, in older plants, Aa TFL1 increases the duration of vernalization required for Aa LFY expression and flowering. Aa TFL1 has similar functions in axillary shoots, thus ensuring that following a flowering episode vegetative branches are maintained to continue the perennial life cycle. We propose that Aa TFL1 blocks flowering of young plants exposed to vernalization by setting a threshold for a flowering pathway that is increased in activity as the shoot ages, thus contributing to several perennial traits.
Mobile Gibberellin Directly StimulatesArabidopsisHypocotyl Xylem Expansion
Authors: Ragni Laura , Nieminen Kaisa , Pacheco-Villalobos David , Sibout Richard , Schwechheimer Claus , Hardtke Christian S.
Published: April 2011

Secondary growth of the vasculature results in the thickening of plant structures and continuously produces xylem tissue, the major biological carbon sink. Little is known about the developmental control of this quantitative trait, which displays two distinct phases in Arabidopsis thaliana hypocotyls. The later phase of accelerated xylem expansion resembles the secondary growth of trees and is triggered upon flowering by an unknown, shoot-derived signal. We found that flowering-dependent hypocotyl xylem expansion is a general feature of herbaceous plants with a rosette growth habit. Flowering induction is sufficient to trigger xylem expansion in Arabidopsis. By contrast, neither flower formation nor elongation of the main inflorescence is required. Xylem expansion also does not depend on any particular flowering time pathway or absolute age. Through analyses of natural genetic variation, we found that ERECTA acts locally to restrict xylem expansion downstream of the gibberellin (GA) pathway. Investigations of mutant and transgenic plants indicate that GA and its signaling pathway are both necessary and sufficient to directly trigger enhanced xylogenesis. Impaired GA signaling did not affect xylem expansion systemically, suggesting that it acts downstream of the mobile cue. By contrast, the GA effect was graft transmissible, suggesting that GA itself is the mobile shoot-derived signal.
Systems Biology Approach in Chlamydomonas Reveals Connections between Copper Nutrition and Multiple Metabolic Steps
Authors: Castruita Madeli , Casero David , Karpowicz Steven J. , Kropat Janette , Vieler Astrid , Hsieh Scott I. , Yan Weihong , Cokus Shawn , Loo Joseph A. , Benning Christoph , Pellegrini Matteo , Merchant Sabeeha S.
Published: April 2011

In this work, we query the Chlamydomonas reinhardtii copper regulon at a whole-genome level. Our RNA-Seq data simulation and analysis pipeline validated a 2-fold cutoff and 10 RPKM (reads per kilobase of mappable length per million mapped reads) (~1 mRNA per cell) to reveal 63 CRR1 targets plus another 86 copper-responsive genes. Proteomic and immunoblot analyses captured 25% of the corresponding proteins, whose abundance was also dependent on copper nutrition, validating transcriptional regulation as a major control mechanism for copper signaling in Chlamydomonas. The impact of copper deficiency on the expression of several O2-dependent enzymes included steps in lipid modification pathways. Quantitative lipid profiles indicated increased polyunsaturation of fatty acids on thylakoid membrane digalactosyldiglycerides, indicating a global impact of copper deficiency on the photosynthetic apparatus. Discovery of a putative plastid copper chaperone and a membrane protease in the thylakoid suggest a mechanism for blocking copper utilization in the chloroplast. We also found an example of copper sparing in the N assimilation pathway: the replacement of copper amine oxidase by a flavin-dependent backup enzyme. Forty percent of the targets are previously uncharacterized proteins, indicating considerable potential for new discovery in the biology of copper.
Phosphorylation of a WRKY Transcription Factor by Two Pathogen-Responsive MAPKs Drives Phytoalexin Biosynthesis in Arabidopsis
Authors: Mao Guohong , Meng Xiangzong , Liu Yidong , Zheng Zuyu , Chen Zhixiang , Zhang Shuqun
Published: April 2011

Plant sensing of invading pathogens triggers massive metabolic reprogramming, including the induction of secondary antimicrobial compounds known as phytoalexins. We recently reported that MPK3 and MPK6, two pathogen-responsive mitogen-activated protein kinases, play essential roles in the induction of camalexin, the major phytoalexin in Arabidopsis thaliana. In search of the transcription factors downstream of MPK3/MPK6, we found that WRKY33 is required for MPK3/MPK6-induced camalexin biosynthesis. In wrky33 mutants, both gain-of-function MPK3/MPK6- and pathogen-induced camalexin production are compromised, which is associated with the loss of camalexin biosynthetic gene activation. WRKY33 is a pathogen-inducible transcription factor, whose expression is regulated by the MPK3/MPK6 cascade. Chromatin immunoprecipitation assays reveal that WRKY33 binds to its own promoter in vivo, suggesting a potential positive feedback regulatory loop. Furthermore, WRKY33 is a substrate of MPK3/MPK6. Mutation of MPK3/MPK6 phosphorylation sites in WRKY33 compromises its ability to complement the camalexin induction in the wrky33 mutant. Using a phospho-protein mobility shift assay, we demonstrate that WRKY33 is phosphorylated by MPK3/MPK6 in vivo in response to Botrytis cinerea infection. Based on these data, we conclude that WRKY33 functions downstream of MPK3/MPK6 in reprogramming the expression of camalexin biosynthetic genes, which drives the metabolic flow to camalexin production in Arabidopsis challenged by pathogens.
Effects of strong CYP2D6 and 3A4 inhibitors, paroxetine and ketoconazole, on the pharmacokinetics and cardiovascular safety of tamsulosin
Authors: Troost Joachim , Tatami Shinji , Tsuda Yasuhiro , Mattheus Michaela , Mehlburger Ludwig , Wein Martina , Michel Martin C.
Published: April 2011

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• Tamsulosin metabolism involves both CYP2D6 and 3A4. However, data on potential drug–drug interactions between tamsulosin and inhibitors of CYP2D6 and 3A4 are limited and information on potential pharmacodynamic consequences of such pharmacokinetic interactions is missing.

WHAT THIS STUDY ADDS

• This study provides information on the drug–drug interactions of tamsulosin with strong CYP2D6 and strong CYP3A4 inhibitors after single dose administration in healthy subjects.

AIM To determine the effect of the strong CYP2D6 inhibitor paroxetine and strong CYP3A4 inhibitor ketoconazole on the pharmacokinetics and safety (orthostatic challenge) of tamsulosin.

METHODS Two open‐label, randomized, two‐way crossover studies were conducted in healthy male volunteers (extensive CYP2D6 metabolizers).

RESULTS Co‐administration of multiple oral doses of 20 mg paroxetine once daily with a single oral dose of the 0.4 mg tamsulosin HCl capsule increased the adjusted geometric mean (gMean) values of Cmax and AUC(0,∞) of tamsulosin by factors of 1.34 (90% CI 1.21, 1.49) and 1.64 (90% CI 1.44, 1.85), respectively, and increased the terminal half‐life (t1/2) of tamsulosin HCl from 11.4 h to 15.3 h. Co‐administration of multiple oral doses of 400 mg ketoconazole once dailywith a single oral dose of the 0.4 mg tamsulosin increased the gMean values of Cmax and AUC(0,∞) of tamsulosin by a factor of 2.20 (90% CI 1.96, 2.45) and 2.80 (90% CI 2.56, 3.07), respectively. The terminal half‐life was slightly increased from 10.5 h to 11.8 h. These pharmacokinetic changes were not accompanied by clinically significant alterations of haemodynamic responses during orthostatic stress testing.

CONCLUSION The exposure to tamsulosin is increased upon co‐administration of strong CYP2D6 inhibitors and even more so of strong 3A4 inhibitors, but neither PK alteration was accompanied by clinically significant haemodynamic changes during orthostatic stress testing.
The importance of direct patient reporting of suspected adverse drug reactions: a patient perspective
Authors: Anderson Claire , Krska Janet , Murphy Elizabeth , Avery Anthony ,   on behalf of the Yellow Card Study Collaboration
Published: April 2011

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• Little is known about why patients actually report suspected adverse drug reactions to schemes like the Yellow Card Scheme. Greater understanding of the reasons for reporting could be of benefit in marketing strategies aiming to increase the number of reports.

WHAT THIS STUDY ADDS

• Direct patient reporting through the Yellow Card Scheme is viewed as important by those who have used the scheme, in order to provide the patient experience for the benefit of pharmacovigilance, as an independent perspective from those of health professionals.

• Reporters viewed the Yellow Card Scheme as an important opportunity to describe their experiences for the benefit of others and to contribute to pharmacovigilance.

• The Yellow Card Scheme's independence from health professionals was regarded as important, in part to provide the patient perspective to manufacturers and regulators, but also because of dismissive attitudes and under‐reporting by health professionals.

AIM To explore the opinions of patient reporters to the UK Yellow Card Scheme (YCS) on the importance of the scheme.

METHODS Postal questionnaires were distributed on our behalf to all patient reporters submitting a Yellow Card to the Medicines and Healthcare Regulatory Agency (MHRA) between March and December 2008, with one follow‐up reminder to non‐responders. Qualitative analysis was undertaken of responses to an open question asking why respondents felt patient reporting was important. This was followed up by telephone interviews with a purposive sample of selected respondents.

RESULTS There were 1362 evaluable questionnaires returned from 2008 distributed (68%) and 1238 (91%) respondents provided a total of 1802 comments. Twenty‐seven interviews were conducted, which supported and expanded the views expressed in the questionnaire. Four main themes emerged, indicating views that the YCS was of importance to pharmacovigilance in general, manufacturers and licensing authorities, patients and the public and health professionals. Reporters viewed the YCS as an important opportunity to describe their experiences for the benefit of others and to contribute to pharmacovigilance. The scheme's independence from health professionals was regarded as important, in part to provide the patient perspective to manufacturers and regulators, but also because of dismissive attitudes and under‐reporting by health professionals.

CONCLUSION Direct patient reporting through the YCS is viewed as important by those who have used the scheme, in order to provide the patient experience for the benefit of pharmacovigilance, as an independent perspective from those of health professionals.
The association of serum prolactin concentration with inflammatory biomarkers – cross‐sectional findings from the population‐based Study of Health in Pomerania
Authors: Friedrich Nele , Schneider Harald J. , Spielhagen Christin , Markus Marcello Ricardo Paulista , Haring Robin , Grabe Hans J. , Buchfelder Michael , Wallaschofski Henri , Nauck Matthias
Published: April 2011

Objective  Prolactin (PRL) is involved in immune regulation and may contribute to an atherogenic phenotype. Previous results on the association of PRL with inflammatory biomarkers have been conflicting and limited by small patient studies. Therefore, we used data from a large population‐based sample to assess the cross‐sectional associations between serum PRL concentration and high‐sensitivity C‐reactive protein (hsCRP), fibrinogen, interleukin‐6 (IL‐6), and white blood cell (WBC) count.

Design and Population  From the population‐based Study of Health in Pomerania (SHIP), a total of 3744 subjects were available for the present analyses.

Methods and Measurements  PRL and inflammatory biomarkers were measured. Linear and logistic regression models adjusted for age, sex, body‐mass‐index, total cholesterol and glucose were analysed.

Results  Multivariable linear regression models revealed a positive association of PRL with WBC. Multivariable logistic regression analyses showed a significant association of PRL with increased IL‐6 in non‐smokers [highest vs lowest quintile: odds ratio 1·69 (95% confidence interval 1·10–2·58), P = 0·02] and smokers [OR 2·06 (95%‐CI 1·10–3·89), P = 0·02]. Similar results were found for WBC in non‐smokers [highest vs lowest quintile: OR 2·09 (95%‐CI 1·21–3·61), P = 0·01)] but not in smokers. Linear and logistic regression analyses revealed no significant associations of PRL with hsCRP or fibrinogen.

Conclusions  Serum PRL concentrations are associated with inflammatory biomarkers including IL‐6 and WBC, but not hsCRP or fibrinogen. The suggested role of PRL in inflammation needs further investigation in future prospective studies.
An alternative approach for infrared heater control in warming and extreme event experiments in terrestrial ecosystems
Authors: De Boeck Hans J. , Nijs Ivan
Published: April 2011

1. The infrared (IR) heating technique used in terrestrial vegetation warming experiments has been continuously improved over the past two decades, but the temperature control methods applied thus far inadequately reflect natural conditions.

2. Current control methods base the IR radiation administered on measured canopy or air temperatures. However, these temperatures are influenced by stomatal responses of the vegetation, which depend on moisture conditions and therefore also on warming. In nature, drought‐stressed vegetation warms up more than well‐watered vegetation, leading to potential differences in heat stress. Current control methods preclude such differences from developing.

3. We propose an alternative approach to render temperature control independent of plant responses. Theoretical canopy temperatures associated with given (target) air temperatures are calculated, based on reference canopy conductance determined from controls and fluctuating meteorological conditions. The IR radiation needed to attain the theoretical temperature is subsequently applied. Actual canopy and air temperatures are free to deviate from that temperature, as measured temperatures no longer control the heaters’ radiation output.

4. Synthesis. We devised an alternative control method for IR heaters that is independent of plant responses to heating. This is especially critical in extreme event studies, where differences in plant water status, and therefore canopy temperatures, are likely to be exacerbated.
Extreme climatic event‐triggered overstorey vegetation loss increases understorey solar input regionally: primary and secondary ecological implications
Authors: Royer Patrick D. , Cobb Neil S. , Clifford Michael J. , Huang Cho‐Ying , Breshears David D. , Adams Henry D. , Villegas Juan Camilo
Published: April 2011

1. Climate extremes such as drought can trigger large‐scale tree die‐off, reducing overstorey canopy and thereby increasing near‐ground solar radiation. This directly affects biotic and abiotic processes, including plant physiology, reproduction, phenology, soil evaporation and nutrient cycling, which themselves affect understory facilitation, productivity and diversity, and land surface–atmosphere fluxes of energy, carbon and water.

2. Although important, assessing extreme‐event solar radiation responses regionally following die‐off is complex compared with characterizing patch‐scale inputs. Estimating regional‐scale changes requires integration of broad‐scale downward‐looking shading patterns due to canopy and topography with fine‐scale upward‐looking canopy details (e.g. live vs. dead trees, height, diameter, spatial pattern and foliar diffusivity).

3. We quantified increases in near‐ground solar radiation following overstorey loss of piñon pine cover in response to a recent extreme drought event (2002–2003). We evaluated 211 km2 in south‐western USA seasonally and annually using high‐spatial resolution satellite imagery, hemispherical ground photography, GIS (Geographic Information System)‐based solar radiation modelling tools, in situ meteorological data and tree measurements.

4. Overstorey loss due to die‐off produced increases in near‐ground solar radiation regionally each season – up to 28 W m−2, an increase of 9.1%, in summer – while simultaneously decreasing spatial variation. Annually the increase was c. 17 W m−2. Larger increases occurred where initial canopy cover was greater or at higher elevations, by as much as c. 80 W m−2 (a 40% increase).

5. Synthesis. Our results are notable in that they quantify increases regionally in near‐ground solar radiation in response to a climate extreme triggering widespread tree die‐off. The substantial increases quantified are expected to have primary direct effects on processes such as plant physiology, reproduction, phenology, soil evaporation and nutrient cycling, and secondary effects on understory facilitation, productivity and diversity, and land surface–atmosphere fluxes of energy, carbon and water. Consequently, extreme event‐induced changes in near‐ground solar radiation need to be considered by both ecologists and physical scientists in assessing global change impacts. More generally, our results highlight an important but sometimes overlooked aspect of plant ecology – that plants not only respond to their physical environment and other plants, but also directly modify their physical environment from individual plant to regional scales.
Ecotypes of European grass species respond differently to warming and extreme drought
Authors: Beierkuhnlein Carl , Thiel Daniel , Jentsch Anke , Willner Evelin , Kreyling Juergen
Published: April 2011

1. Climate extremes are expected to increase in frequency and magnitude as a consequence of global warming.

2. Managed permanent grasslands cover a large surface in Europe and contribute substantially to agricultural production. These managed plant communities are dominated by perennial clonal species. Their capacity to adapt to rapidly changing environmental conditions may be limited.

3. We hypothesize that those plant populations that have already been exposed to conditions that are expected to occur due to future climate change, particularly conditions that would be ‘extreme’ in the target area, are able to cope better with these conditions.

4. For a common‐garden experiment we selected ecotypes (provenances as supported by accessions in seed banks) of important European grass species: Arrhenatherum elatius, Festuca pratensis, Holcus lanatus and Alopecurus pratensis. Southern target locations of ecotypes (populations) were identified based on climate model projections for the local site in Northern Bavaria, Germany.

5. In a controlled experiment, the plants were exposed to warming and extreme drought. Drought conditions(16–19 days, depending on the species) were imposed starting from the end of May in combination with and without an increase in the average temperature from May to September 2009 (+1.5 K compared with control; +2.5 K compared with ambient conditions outside of the experimental units).

6. Ecotypes and drought manipulation had significant impacts on biomass production and tissue die‐back. Significant interactions between ecotype and drought indicated a different drought tolerance of the ecotypes in some cases. The warming treatment yielded a less significant response. The local ecotype generally did not perform significantly worse than the presumably better‐adapted southern ecotypes.

7. Synthesis. The selection of ecotypes that are adapted to more extreme climatic conditions could be an option for maintaining future ecosystem functioning in temperate managed grasslands, as was indicated by the clear differences between ecotypes in our experiment. Based on our data, however, performance cannot be predicted from climatic origin. Therefore, we recommend enhancing the genetic variability within populations of species in general.
Extrinsic and intrinsic forcing of abrupt ecological change: case studies from the late Quaternary
Authors: Williams John W. , Blois Jessica L. , Shuman Bryan N.
Published: April 2011

1. Abrupt changes and regime shifts are common phenomena in terrestrial ecological records spanning centuries to millennia, thus offering a rich opportunity to study the patterns and drivers of abrupt ecological change.

2. Because Quaternary climate changes also often were abrupt, a critical research question is to distinguish between extrinsic versus intrinsic abrupt ecological changes, i.e. those externally driven by abruptly changing climates, versus those resulting from thresholds, tipping points, and other nonlinear responses of ecological systems to progressive climate change. Extrinsic and intrinsic abrupt ecological changes can be distinguished in part by compiling and analysing regional networks of palaeoecological records.

3. Abrupt ecological changes driven by spatially coherent and abrupt climate changes should manifest as approximately synchronous ecological responses, both among different taxa at a site and among sites. However, the magnitude and direction of response may vary among sites and taxa. Ecological responses to the rapid climatic changes accompanying the last deglaciation offer good model systems for studying extrinsic abrupt change.

4. When abrupt ecological changes are intrinsically driven, the timing and rate of ecological response to climate change will be strongly governed by local biotic and abiotic processes and by stochastic processes such as disturbance events or localized climatic extremes. Consequently, at a regional scale, one should observe ‘temporal mosaics’ of abrupt ecological change, in which the timing and rate of ecological change will vary among species within sites and among sites. These temporal mosaics are analogous to the spatial mosaics observed in ecological systems prone to threshold switches between alternate stable states. The early Holocene aridification of the North American mid‐continent and the middle‐Holocene aridification of North Africa may be good examples of temporal mosaics.

5. Synthesis. Past instances of extrinsic and intrinsic abrupt change are of direct relevance to global‐change ecologists. The former allow study of the capacity of ecological systems to quickly adjust to abrupt climate changes, while the latter offer opportunities to understand the ecological processes causing abrupt local responses to regional climate change, to test tools for predicting critical thresholds, and to develop climate‐adaptation strategies.
A climatically extreme year has large impacts on C4species in tallgrass prairie ecosystems but only minor effects on species richness and other plant functional groups
Authors: Arnone John A. , Jasoni Richard L. , Lucchesi Annmarie J. , Larsen Jessica D. , Leger Elizabeth A. , Sherry Rebecca A. , Luo Yiqi , Schimel David S. , Verburg Paul S.J.
Published: April 2011

1. The occurrence and intensity of climate extremes, such as extremely warm years, are expected to continue to increase with increasing tropospheric radiative forcing caused by anthropogenic greenhouse gas emissions.

2. Responses of terrestrial ecosystem processes and services – such as above‐ground net primary productivity (ANPP) and maintenance of plant species diversity – to these extreme years for multiple years post‐perturbation are poorly understood but can have significant feedback effects on net ecosystem CO2uptake and ecosystem carbon sequestration.

3. We exposed six 12 000‐kg intact natural tallgrass prairie monoliths to an extremely warm year (+4 °C in 2003) in the second year of a 4‐year study (2002–2005) using the EcoCELL whole‐ecosystem controlled‐environment, gas exchange facility. Six control monoliths were not warmed in the second year but were maintained under average field conditions. Natural diel and seasonal patterns in air temperature were maintained in both treatments throughout the study. Thus, with the exception of the second year in the ‘warmed’ treatment, we created 4 years of nearly identical climate in all EcoCELLs.

4. Interannual ANPP (10 cm clipping height) responses of the entire plant community to the extreme year were largely determined by responses of the dominant C4grasses. These included large decreases in ANPP in 2003 followed by complete recovery to levels observed in the control ecosystems in the year following warming. Species richness and productivity of the nitrogen‐fixing plant functional group appeared to play a role in defining overall plant community ANPP, however, even though this richness and productivity could not explain the decrease in community ANPP observed in warmed ecosystems in the second year (2003) of the study or its recovery in the year after (2004). Surprisingly, very few of the 67 species present in plant communities during the 4‐year study responded to the warm year at any time during or after the treatment.

5. Synthesis. Results from this study indicate that as extreme climate years become more prevalent, their immediate and lagged impacts on collective ecosystem processes, such as whole‐community ANPP, may be very pronounced, but effects on component ecosystem processes may be limited to the dominant plant functional group (ANPP).
Climate extremes initiate ecosystem‐regulating functions while maintaining productivity
Authors: Jentsch Anke , Kreyling Juergen , Elmer Michael , Gellesch Ellen , Glaser Bruno , Grant Kerstin , Hein Roman , Lara Marco , Mirzae Heydar , Nadler Stefanie E. , Nagy Laura , Otieno Denis , Pritsch Karin , Rascher Uwe , Schädler Martin , Schloter Michael , Singh Brajesh K. , Stadler Jutta , Walter Julia , Wellstein Camilla , Wöllecke Jens , Beierkuhnlein Carl
Published: April 2011

1. Studying the effects of climate or weather extremes such as drought and heat waves on biodiversity and ecosystem functions is one of the most important facets of climate change research. In particular, primary production is amounting to the common currency in field experiments world‐wide. Rarely, however, are multiple ecosystem functions measured in a single study in order to address general patterns across different categories of responses and to analyse effects of climate extremes on various ecosystem functions.

2. We set up a long‐term field experiment, where we applied recurrent severe drought events annually for five consecutive years to constructed grassland communities in central Europe. The 32 response parameters studied were closely related to ecosystem functions such as primary production, nutrient cycling, carbon fixation, water regulation and community stability.

3. Surprisingly, in the face of severe drought, above‐ and below‐ground primary production of plants remained stable across all years of the drought manipulation.

4. Yet, severe drought significantly reduced below‐ground performance of microbes in soil indicated by reduced soil respiration, microbial biomass and cellulose decomposition rates as well as mycorrhization rates. Furthermore, drought reduced leaf water potential, leaf gas exchange and leaf protein content, while increasing maximum uptake capacity, leaf carbon isotope signature and leaf carbohydrate content. With regard to community stability, drought induced complementary plant–plant interactions and shifts in flower phenology, and decreased invasibility of plant communities and primary consumer abundance.

5. Synthesis. Our results provide the first field‐based experimental evidence that climate extremes initiate plant physiological processes, which may serve to regulate ecosystem productivity. A potential reason for different dynamics in various ecosystem services facing extreme climatic events may lie in the temporal hierarchy of patterns of fast versus slow response. Such data on multiple response parameters within climate change experiments foster the understanding of mechanisms of resilience, of synergisms or decoupling of biogeochemical processes, and of fundamental response dynamics to drought at the ecosystem level including potential tipping points and thresholds of regime shift. Future work is needed to elucidate the role of biodiversity and of biotic interactions in modulating ecosystem response to climate extremes.
The ecological role of climate extremes: current understanding and future prospects
Authors: Smith Melinda D.
Published: April 2011

1. Climate extremes, such as severe drought, heat waves and periods of heavy rainfall, can have profound consequences for ecological systems and for human welfare. Global climate change is expected to increase both the frequency and the intensity of climate extremes and there is an urgent need to understand their ecological consequences.

2. Major challenges for advancing our understanding of the ecological consequences of climate extremes include setting a climatic baseline to facilitate the statistical determination of when climate conditions are extreme, having sufficient knowledge of ecological systems so that extreme ecological responses can be identified, and finally, being able to attribute a climate extreme as the driver of an extreme ecological response, defined as an extreme climatic event (ECE).

3. The papers in this issue represent a cross‐section of the emerging field of climate extremes research, including an examination of the palaeo‐ecological record to assess patterns and drivers of extreme ecological responses in the late Quaternary, experiments in grasslands assessing a range of ecological responses and the role of ecotypic variation in determining responses to climate extremes, and the quantification of the ecological consequences of a recent ECE in the desert Southwest of the USA.

4. Synthesis. The papers in this Special Feature suggest that although the occurrence of ECEs may be common in palaeo‐ecological and observational studies, studies in which climate extremes have been experimentally imposed often do not result in ecological responses outside the bounds of normal variability of a system. Thus, ECEs occur much less frequently than their potential drivers and even less frequently than observational studies suggest. Future research is needed to identify the types and time‐scales of climate extremes that result in ECEs, the potential for interactions among different types of climate changes and extremes, and the role of genetic, species and trait diversity in determining ecological responses and their evolutionary consequences. These research priorities require the development of alternative research approaches to impose realistic climate extremes on a broad range of organisms and ecosystems.
Biological Flora of the British Isles:Epipogium aphyllumSw.
Authors: Taylor Lin , Roberts David L.
Published: April 2011

1. This account provides information on all aspects of the biology ofEpipogium aphyllumSw. that are relevant to understanding its ecological characteristics and behaviour. The main topics are presented within the standard framework of theBiological Flora of the British Isles: distribution, habitat, communities, response to biotic factors, responses to environment, structure and physiology, phenology, reproductive characteristics, herbivores and disease, history and conservation.

2. Epipogium aphyllumis a native mycoheterotrophic herb, with a British distribution that is restricted to a few beech and oak woodlands in the Chilterns and the Welsh Borders. Sightings are scarce, the majority of years passing with no observations in the British Isles. The species extends throughout temperate Eurasia, with concentrations of records in Scandinavia and the foothills of the Alps.

3. Epipogium aphyllumis most commonly found growing in the deep shade of dense woodland; its achlorophyllous nature means that it is entirely dependent on its endomycorrhizal symbiont (Inocybesp.) for nutrition.

4. The biology of reproduction is poorly understood. Sexual reproduction, both entomogamous and autogamous, appears inefficient, as fruiting plants are rare. Vegetative propagation can occur via bulbils attached to the underground stolons.

5. Both the occurrence and timing of flowering are highly unpredictable, the season extending from late May to early October. A wet winter followed by a warm summer is thought to trigger flowering. The rhizome can survive underground undetected for many years.

6. Epipogium aphyllumhas repeatedly been described as Britain’s rarest orchid. Sightings since its first English record in 1854 have been interrupted by periods of decades. A recent observation gap of more than two decades led to suggestions of extirpation, though this assumption has been challenged by statistical modelling and refuted by the discovery of a single depauperate flower on the Welsh Borders in 2009. Primary threats to this species already at the edge of its natural range include deforestation and degradation of its native broadleaf habitat, as well as trampling, herbivory and climate change. As a result, extirpation of the Ghost Orchid from Britain is still likely in the near future.
A functional polymorphism in pre‐microRNA‐196a‐2 contributes to the susceptibility of hepatocellular carcinoma in a Turkish population: a case–control study
Authors: Akkız H. , Bayram S. , Bekar A. , Akgöllü E. , Ülger Y.
Published: April 2011

Summary.  MicroRNAs (miRNAs) are an abundant class of small nonprotein‐coding RNAs with posttranscriptional regulatory functions as tumour suppressors and oncogenes. Aberrant expression and structural alteration of miRNAs are thought to participate in tumourigenesis and cancer development. It has been suggested that the presence of single‐nucleotide polymorphisms in precursor miRNAs (pre‐miRNAs) can alter miRNA processing, expression, and/or binding to target mRNA and represent another type of genetic variability that can contribute to the development of human cancers. Recent studies have indicated that the miR‐196a‐2 rs11614913 (C→T) polymorphism could alter mature miR‐196a‐2 expression and target mRNA binding. To determine the association of the miR‐196a‐2 rs11614913 polymorphism with the risk of hepatocellular carcinoma (HCC) development in a Turkish population, a hospital‐based case–control study was designed consisting of 185 subjects with HCC and 185 cancer‐free control subjects matched for age, gender, smoking and alcohol status. The genotype frequency of the miR‐196a‐2 rs11614913 polymorphism was determined by using a polymerase chain reaction‐restriction fragment length polymorphism (PCR‐RFLP) assay. Our data shows that the CC genotype of the miR‐196a‐2 rs11614913 polymorphism is associated with increased risk of HCC development in this Turkish population (OR = 2.41, 95% CI: 1.30–4.50, P = 0.005). Furthermore, according to stratified analysis, a significant association was observed between the homozygote CC genotype and HCC risk in the subgroups of male gender (OR = 3.12, 95% CI: 1.53–6.34, P = 0.002) and patients with hepatitis B virus (HBV)‐related HCC (OR = 2.88, 95% CI: 1.33–6.22, P = 0.007). Because our results suggest for the first time that the miR‐196a‐2 rs11614913 polymorphism may be a genetic susceptibility factor for HCC (especially in the male gender and HBV‐infected patients) in the Turkish population, further independent studies are required to validate our findings in a larger series, as well as in patients of different ethnic origins.
Whole‐genome array CGH identifies pathogenic copy number variations in fetuses with major malformations and a normal karyotype
Authors: D'Amours G , Kibar Z , Mathonnet G , Fetni R , Tihy F , Désilets V , Nizard S , Michaud JL , Lemyre E
Published: April 2011

D’Amours G, Kibar Z, Mathonnet G, Fetni R, Tihy F, Désilets V, Nizard S, Michaud JL, Lemyre E. Whole‐genome array CGH identifies pathogenic copy number variations in fetuses with major malformations and a normal karyotype.

Despite a wide range of clinical tools, the etiology of mental retardation and multiple congenital malformations remains unknown for many patients. Array‐based comparative genomic hybridization (aCGH) has proven to be a valuable tool in these cases, as its pangenomic coverage allows the identification of chromosomal aberrations that are undetectable by other genetic methods targeting specific genomic regions. Therefore, aCGH is increasingly used in clinical genetics, both in the postnatal and the prenatal settings. While the diagnostic yield in the postnatal population has been established at 10–12%, studies investigating fetuses have reported variable results. We used whole‐genome aCGH to investigate fetuses presenting at least one major malformation detected on ultrasound, but for whom standard genetic analyses (including karyotype) failed to provide a diagnosis. We identified a clinically significant chromosomal aberration in 8.2% of tested fetuses (4/49), and a result of unclear clinical significance in 12.2% of tested fetuses (6/49). Our results document the value of whole‐genome aCGH as a prenatal diagnostic tool and highlight the interpretation difficulties associated with copy number variations of unclear significance.
Hepatic artery reconstruction with the jejunal artery of the Roux‐en‐Y limb in pediatric living donor liver re‐transplantation
Authors: Wakiya T. , Sanada Y. , Mizuta K. , Umehara M. , Urahashi T. , Egami S. , Hishikawa S. , Nakata M. , Hakamada K. , Yasuda Y. , Kawarasaki H.
Published: April 2011

Wakiya T, Sanada Y, Mizuta K, Umehara M, Urahashi T, Egami S, Hishikawa S, Nakata M, Hakamada K, Yasuda Y, Kawarasaki H. Hepatic artery reconstruction with the jejunal artery of the Roux‐en‐Y limb in pediatric living donor liver re‐transplantation.

Abstract:  When re‐anastomosis and re‐transplantation becomes necessary after LDLT, arterial reconstruction can be extremely difficult because of severe inflammation and lack of an adequate artery for reconstruction. Frequently, the recipient’s HA is not in good condition, necessitating an alternative to the HA. In such cases, the recipient’s splenic artery, right gastroepiploic artery or another vessel can be safely used for arterial reconstruction. There have, however, been few reports on using the jejunal artery. Herein, we report our experience with arterial reconstruction using the jejunal artery of the Roux‐en‐Y limb as an alternative to the HA. A three‐yr‐old girl who had developed graft failure due to early HA thrombosis after LDLT required re‐transplantation. At re‐transplantation, an adequate artery for reconstruction was lacking. We reconstructed the artery by using the jejunal artery of the Roux‐en‐Y limb, as we judged it to be the most appropriate alternative. After surgery, stent was deployed because hepatic blood flow had reduced due to kinking of the anastomosed site, and a favorable outcome was obtained. In conclusion, when an alternative to the HA is required, using the jejunal artery is a feasible alternative.
MiR398 and plant stress responses
Authors: Zhu Cheng , Ding Yanfei , Liu Haili
Published: April 2011

Because of their sessile nature, plants are constantly exposed to a multitude of abiotic and biotic stresses. Great progress has been made in elucidating the complex stress response mechanisms in plants. MicroRNAs (miRNAs), recently recognized as important regulators of gene expression at the posttranscriptional level, have been found to be involved in plant stress responses. Most plant miRNAs usually mediate cleavage of their target mRNAs. The observation that some miRNAs are up‐ or downregulated in response to stress implies that miRNAs play vital roles in plant resistance to abiotic and biotic stresses. Manipulation of miRNA‐guided gene regulation may represent a new way to engineer plants with improved stress tolerance. Among stress‐responsive miRNAs, miRNA398 (miR398) is a miRNA proposed to be directly linked to the plant stress regulatory network and regulates plant responses to oxidative stress, water deficit, salt stress, abscisic acid stress, ultraviolet stress, copper and phosphate deficiency, high sucrose and bacterial infection. This review highlights recent progress in understanding the crucial role of miR398 in plant stress responses, and also includes a discussion of miR398‐centered gene regulatory network.
Proteomic analysis of peach endocarp and mesocarp during early fruit development
Authors: Hu Hao , Liu Yong , Shi Guang‐Lu , Liu Yue‐Ping , Wu Rui‐Jie , Yang Ai‐Zhen , Wang Yi‐Ming , Hua Bao‐Guang , Wang You‐Nian
Published: April 2011

The development of the stone and formation of peach (Prunus persica) fruit were explored in this work using a proteomic approach. Sixty‐eight proteins with different expression patterns were identified in both the endocarp and mesocarp during early fruit development (from 28 to 59 days after flowering) and the majority were involved in primary or secondary metabolism. In contrast to most proteins associated with primary metabolism in the endocarp, whose expression is down‐regulated, expression of pyruvate dehydrogenase (PDH) unexpectedly increased exponentially. Moreover, its expression pattern was linearly positively correlated with the exponentially growing lignin content (R = 0.940), which suggests that PDH may play a role in endocarp lignification. Our data also revealed different spatiotemporal expressions of enzymes involved in the lignin and flavonoid pathways that provided proteome‐level evidence to support the hypothesis that these two pathways are competitive during endocarp development. In addition, we observed endocarp‐specific oxidative stress and propose that it may act as a stimulating factor in activating lignification and subsequent programmed cell death in the endocarp.
Environmental metabolomics links genotype to phenotype and predicts genotype abundance in wild plant populations
Authors: Field Katie J. , Lake Janice A.
Published: April 2011

‘The Holy Grail’ of plant ecology is to uncover rules that associate species and traits with environmental constraints, community composition and subsequent ecosystem functioning. These aims have been crystallized in recent years within the context of global climate change and environmental pollution, increasing the urgency of the need to predict how vegetation will respond across spatial scales. We investigated whether genetic diversity is associated with the way in which phenotypic plasticity within plant populations is realized and whether this is related to genotype abundance. We used environmental metabolomics to demonstrate biochemical variation between co‐occurring genotypes of Carex caryophyllea L. A novel combined metabolomic/functional trait analysis was used to test the functionality of this variation in governing plasticity to variation in edaphic conditions, with particular reference to metabolic pathways that play important roles in growth‐related traits. We show that genetic diversity within a wild C. caryophyllea population relates to differences in metabolic composition and functional traits in response to soil nutrient variation, influencing genotype abundance within a community. Our findings highlight the vital role genetic diversity plays within a population in facilitating plant phenotypic plasticity and the potential usefulness of environmental metabolomics to future ecological studies.
Deep sequencing of grapevine flower and berry short RNA library for discovery of novel microRNAs and validation of precise sequences of grapevine microRNAs deposited in miRBase
Authors: Wang Chen , Wang Xicheng , Kibet Nicholas K. , Song Changnian , Zhang Changqing , Li Xiaoying , Han Jian , Fang Jinggui
Published: April 2011

MicroRNAs (miRNAs) are a class of non‐coding RNA molecules which have significant gene regulation roles in organisms. The advent of new high‐throughput sequencing technologies has enabled the discovery of novel miRNAs. Although there are two recent reports on high‐throughput sequencing analysis of small RNA libraries from different organs of two wine grapevine varieties, there was a significant divergence in the number and kinds of miRNAs sequenced in these studies. More sequencing of small RNA libraries is still important for the discovery of novel miRNAs in grapevine. In this study, a total of 130 conserved grapevine Vitis vinifera miRNA (Vv‐miRNA) belonging to 28 Vv‐miRNA families were validated, other 80 unconserved Vv‐miRNAs including 72 novel potential and 8 known but unconserved ones were found. Fifty‐two (52.5%) of these 80 unconserved Vv‐miRNAs exhibited differential poly(A)‐tailed reverse transcriptase‐polymerase chain reaction expression profiles in various grapevine tissues that could further confirm their existence in grapevine, among which 20 were expressed only in grapevine berries, indicating a degree of fruit‐specificity. One hundred thirty target genes for 56 unconserved miRNAs could be predicted. The locations of these potential target genes on grapevine chromosomes and their complementary levels with the corresponding miRNAs were also analyzed. These results point to a regulatory role of miRNAs in grapevine berry development and response to various environments.