bluuebunny/crossref_metadata_2025_split huggingface dataset:
Strategic planning for instream flow restoration: a case study of potential climate change impacts in the central Columbia River basin
Authors: Donley Erin E. , Naiman Robert J. , Marineau Mathieu D. 
Published: July 2012

AbstractWe provide a case study prioritizing instream flow restoration activities by sub‐basin according to the habitat needs of Endangered Species Act (ESA)‐listed salmonids relative to climate change in the central Columbia River basin in Washington State (USA). The objective is to employ scenario analysis to inform and improve existing instream flow restoration projects. We assess the sensitivity of late summer (July, August, and September) flows to the following scenario simulations – singly or in combination: climate change, changes in the quantity of water used for irrigation and possible changes to existing water resource policy. Flows for four sub‐basins were modeled using the Water Evaluation and Planning system (WEAP) under historical and projected conditions of 2020 and 2040 for each scenario. Results indicate that Yakima will be the most flow‐limited sub‐basin with average reductions in streamflow of 41% under climate conditions of 2020 and 56% under 2040 conditions; 1.3–2.5 times greater than those of other sub‐basins. In addition, irrigation plays a key role in the hydrology of the Yakima sub‐basin – with flow reductions ranging from 78% to 90% under severe to extreme (i.e., 20–40%) increases in agricultural water use (2.0–4.4 times the reductions in the other sub‐basins). The Yakima and Okanogan sub‐basins are the most responsive to simulations of flow‐bolstering policy change (providing salmon with first priority water allocation and at biologically relevant flows), as demonstrated by 91–100% target flows attained. The Wenatchee and Methow sub‐basins do not exhibit similar responsiveness to simulated policy changes. Considering climate change only, we conclude that flow restoration should be prioritized first in the Yakima and Wenatchee sub‐basins, and second in the Okanogan and Methow. Considering both climate change and possible policy changes, we recommend that the Yakima sub‐basin receive the highest priority for flow restoration activities to sustain critical instream habitat for ESA‐listed salmonids.
Maize potential yields and yield gaps in the changing climate of northeast China
Authors: Liu Zhijuan , Yang Xiaoguang , Hubbard Kenneth G. , Lin Xiaomao 
Published: July 2012

AbstractNortheast China (NEC) is not only one of the major agricultural production areas in China, but it is also the most susceptible to climate variability. This led us to investigate the impact of climate change on maize potential yield and yield gaps in this region, where maize accounts for about 30% of the nation's production. The APSIM‐Maize model was calibrated and validated for maize phenology and yields. The validated model was then used to estimate potential yields, rain‐fed potential yields, and yield gaps for assessing the climate impacts on maize productivity in NEC. During maize growing seasons from 1981 to 2010, the analysis indicates a warming trend all across NEC, whereas the trends in solar radiation and total precipitation tended to decrease. When the same hybrid was specified in APSIM for all years, a simulated increase of maximum temperature resulted in a negative impact on both potential yield and rain‐fed potential yield. A simulated increase in minimum temperature produced no significant changes in potential or rain‐fed potential yield. However, the increase of minimum temperature was shown to result in a positive impact on the on‐farm yield, consistent with our finding that farmers adopted longer season hybrids for which the increase in minimum temperature provided better conditions for germination, emergence, and grain filling during night time. The gap between potential and rain‐fed potential yields was shown to be larger at locations with lower seasonal precipitation (<500 mm). Our results indicate that regions with the largest yield gaps between rain‐fed potential and on‐farm yields were located in the southeast of NEC. Within NEC, on‐farm maize yields were, on average, only 51% of the potential yields, indicating a large exploitable yield gap, which provides an opportunity to significantly increase production by effective irrigation, fertilization, herbicide, and planting density in NEC.
Recovery of ponderosa pine ecosystem carbon and water fluxes from thinning and stand‐replacing fire
Authors: Dore Sabina , Montes‐Helu Mario , Hart Stephen C. , Hungate Bruce A. , Koch George W. , Moon John B. , Finkral Alex J. , Kolb Thomas E. 
Published: July 2012

AbstractCarbon uptake by forests is a major sink in the global carbon cycle, helping buffer the rising concentration ofCO2in the atmosphere, yet the potential for future carbon uptake by forests is uncertain. Climate warming and drought can reduce forest carbon uptake by reducing photosynthesis, increasing respiration, and by increasing the frequency and intensity of wildfires, leading to large releases of stored carbon. Five years of eddy covariance measurements in a ponderosa pine (Pinus ponderosa)‐dominated ecosystem in northern Arizona showed that an intense wildfire that converted forest into sparse grassland shifted site carbon balance from sink to source for at least 15 years after burning. In contrast, recovery of carbon sink strength after thinning, a management practice used to reduce the likelihood of intense wildfires, was rapid. Comparisons between an undisturbed‐control site and an experimentally thinned site showed that thinning reduced carbon sink strength only for the first two posttreatment years. In the third and fourth posttreatment years, annual carbon sink strength of the thinned site was higher than the undisturbed site because thinning reduced aridity and drought limitation to carbon uptake. As a result, annual maximum gross primary production occurred when temperature was 3 °C higher at the thinned site compared with the undisturbed site. The severe fire consistently reduced annual evapotranspiration (range of 12–30%), whereas effects of thinning were smaller and transient, and could not be detected in the fourth year after thinning. Our results show large and persistent effects of intense fire and minor and short‐lived effects of thinning on southwestern ponderosa pine ecosystem carbon and water exchanges.
Climate, duration, and N placement determine N2O emissions in reduced tillage systems: a meta‐analysis
Authors: van Kessel Chris , Venterea Rodney , Six Johan , Adviento‐Borbe Maria Arlene , Linquist Bruce , van Groenigen Kees Jan 
Published: July 2012

AbstractNo‐tillage and reduced tillage (NT/RT) management practices are being promoted in agroecosystems to reduce erosion, sequester additional soil C and reduce production costs. The impact of NT/RT on N2O emissions, however, has been variable with both increases and decreases in emissions reported. Herein, we quantitatively synthesize studies on the short‐ and long‐term impact of NT/RT on N2O emissions in humid and dry climatic zones with emissions expressed on both an area‐ and crop yield‐scaled basis. A meta‐analysis was conducted on 239 direct comparisons between conventional tillage (CT) and NT/RT. In contrast to earlier studies, averaged across all comparisons, NT/RT did not alter N2O emissions compared with CT. However, NT/RT significantly reduced N2O emissions in experiments >10 years, especially in dry climates. No significant correlation was found between soil texture and the effect of NT/RT on N2O emissions. When fertilizer‐N was placed at ≥5 cm depth, NT/RT significantly reduced area‐scaled N2O emissions, in particular under humid climatic conditions. Compared to CT under dry climatic conditions, yield‐scaled N2O increased significantly (57%) when NT/RT was implemented <10 years, but decreased significantly (27%) after ≥10 years of NT/RT. There was a significant decrease in yield‐scaled N2O emissions in humid climates when fertilizer‐N was placed at ≥5 cm depth. Therefore, in humid climates, deep placement of fertilizer‐N is recommended when implementing NT/RT. In addition, NT/RT practices need to be sustained for a prolonged time, particularly in dry climates, to become an effective mitigation strategy for reducing N2O emissions.
BRG1 and NRG1 form a novel feedback circuit regulating Candida albicans hypha formation and virulence
Authors: Cleary Ian A. , Lazzell Anna L. , Monteagudo Carlos , Thomas Derek P. , Saville Stephen P. 
Published: July 2012

SummaryIn the opportunistic fungal pathogen Candida albicans both cellular morphology and the capacity to cause disease are regulated by the transcriptional repressor Nrg1p. One of the genes repressed by Nrg1p is BRG1, which encodes a putative GATA family transcription factor. Deletion of both copies of this gene prevents hypha formation. We discovered that BRG1 overexpression is sufficient to overcome Nrg1p‐mediated repression and drive the morphogenetic shift from yeast to hyphae even in the absence of environmental stimuli. We further observed that expression of BRG1 influences the stability of the NRG1 transcript, thus controlling filamentation through a feedback loop. Analysis of this phenomenon revealed that BRG1 expression is required for the induction of an antisense NRG1 transcript. This is the first demonstration of a role for mRNA stability in regulating the key C. albicans virulence trait: the ability to form hyphae.
GNA11 and N‐RAS mutations: alternatives for MAPK pathway activating GNAQ mutations in primary melanocytic tumours of the central nervous system
Authors: Gessi M. , Hammes J. , Lauriola L. , Dörner E. , Kirfel J. , Kristiansen G. , zur Muehlen A. , Denkhaus D. , Waha A. , Pietsch T. 
Published: July 2012

M. Gessi, J. Hammes, L. Lauriola, E. Dörner, J. Kirfel, G. Kristiansen, A. zur Muehlen, D. Denkhaus, A. Waha and T. Pietsch (2013) Neuropathology and Applied Neurobiology39, 417–425
GNA11 and N‐RAS mutations: alternatives for MAPK pathway activating GNAQ mutations in primary melanocytic tumours of the central nervous systemAim: Primary melanocytic tumours are uncommon neoplasms of the central nervous system. Although similarities with uveal melanomas have been hypothesized, data on their molecular features are limited. Methods: In this study, we investigated the mutational status of BRAFV600E, KIT, GNAQ, GNA11, N‐RAS and H‐RAS in a series of 19 primary melanocytic tumours of the central nervous system (CNS). Results: We identified six cases harbouring mutations in the hotspot codon 209 of the GNAQ gene and two cases with mutations in the hotspot codon 209 of the GNA11 gene. Two mutations in codon 61 of N‐RAS were also found. In the single strand conformation polymorphism (SSCP) analysis, no shifts corresponding to BRAFV600E mutations or suggesting activating mutations in the KIT gene were observed. Conclusions: In primary melanocytic tumours of the CNS, GNA11 and N‐RAS mutations represent a mechanism of MAPK pathway activation alternative to the common GNAQ mutations. On the other hand, BRAFV600E mutations and activating KIT mutations seem to be absent or very rare in these tumours.
Geochemical evidence for sediment provenance in mudstones and fossil‐poor wackestones (Upper Jurassic, Majorca Island)
Authors: Coimbra Rute , Olóriz Federico 
Published: July 2012

Terra Nova, 24, 437–445, 2012AbstractThe notion that diagenetic imprint on ancient carbonates significantly compromises palaeoenvironmental interpretations is revealed as an oversimplification. The enigmatic case at the core of this research is an extended, homogeneous, macrofossil‐poor deposit showing distinctive dark brown colour and very fine grain size (Aumedrá Fm., Majorca Island). This markedly contrasts with standard ammonitico rosso (AR) facies known from Jurassic epioceanic swells. Geochemical analysis of matrix micrite, carbonate cements and belemnite rostra are used to interpret the Aumedrá carbonates. Stable (Carbon and Oxygen) isotopes and elemental abundance are compared with data from under‐ and overlying deposits, and coeval sections. Conspicuously higher than expected C and O isotope signature, together with strontium enrichment and a typically low iron and manganese concentrations favour a distant, shallower, probably aragonitic sedimentary supply. Modern and ancient examples of carbonate deposition are integrated with possible hydrodynamic conditions justifying transport over the studied area. A potential NE source is envisagedTerra Nova, 00, 1–9, 2012
The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads
Authors: Wang Zhiwen , Hobson Neil , Galindo Leonardo , Zhu Shilin , Shi Daihu , McDill Joshua , Yang Linfeng , Hawkins Simon , Neutelings Godfrey , Datla Raju , Lambert Georgina , Galbraith David W. , Grassa Christopher J. , Geraldes Armando , Cronk Quentin C. , Cullis Christopher , Dash Prasanta K. , Kumar Polumetla A. , Cloutier Sylvie , Sharpe Andrew G. , Wong Gane K.‐S. , Wang Jun , Deyholos Michael K. 
Published: July 2012

SummaryFlax (Linum usitatissimum) is an ancient crop that is widely cultivated as a source of fiber, oil and medicinally relevant compounds. To accelerate crop improvement, we performed whole‐genome shotgun sequencing of the nuclear genome of flax. Seven paired‐end libraries ranging in size from 300 bp to 10 kb were sequenced using an Illumina genome analyzer. A de novo assembly, comprised exclusively of deep‐coverage (approximately 94× raw, approximately 69× filtered) short‐sequence reads (44–100 bp), produced a set of scaffolds with N50 = 694 kb, including contigs with N50 = 20.1 kb. The contig assembly contained 302 Mb of non‐redundant sequence representing an estimated 81% genome coverage. Up to 96% of published flax ESTs aligned to the whole‐genome shotgun scaffolds. However, comparisons with independently sequenced BACs and fosmids showed some mis‐assembly of regions at the genome scale. A total of 43 384 protein‐coding genes were predicted in the whole‐genome shotgun assembly, and up to 93% of published flax ESTs, and 86% of A. thaliana genes aligned to these predicted genes, indicating excellent coverage and accuracy at the gene level. Analysis of the synonymous substitution rates (Ks) observed within duplicate gene pairs was consistent with a recent (5–9 MYA) whole‐genome duplication in flax. Within the predicted proteome, we observed enrichment of many conserved domains (Pfam‐A) that may contribute to the unique properties of this crop, including agglutinin proteins. Together these results show that de novo assembly, based solely on whole‐genome shotgun short‐sequence reads, is an efficient means of obtaining nearly complete genome sequence information for some plant species.
Balearic insular isolation and large continental spread framed the phylogeography of the western Mediterranean Cheirolophus intybaceus s.l. (Asteraceae)
Authors: Garnatje T. , Pérez‐Collazos E. , Pellicer J. , Catalán P. 
Published: July 2012

AbstractRecent Quaternary geological and climate events have shaped the evolutionary histories of plant species in the Mediterranean basin, one of the most important hotspots of biodiversity. Genetic analyses of the western Mediterranean Cheirolophus intybaceus s.l. (Asteraceae) based on AFLP were conducted to establish the relationships between its close species and populations, to reconstruct the phylogeography of the group and to analyse potential unidirectional versus bidirectional dispersals between the Ibero‐Provençal belt and the Balearic Islands. AFLP data revealed two main genetic groups, one constituted by the Balearic populations and Garraf (NE Iberia) and the other formed by the remaining mainland populations that were further sub‐structured into two geographically separated subgroups (SE + E Iberia and NE Iberia + SW France). Genetic diversity and spatial structure analyses suggested a mid‐Pleistocene scenario for the origin of C. intybaceus in southern Iberia, followed by dispersal to the north and a single colonisation event of the Balearic archipelago from the near Dianic NE Iberian area. This hypothesis was supported by paleogeographic data, which showed the existence of terrestrial connections between the continent and the islands during the Middle–Late Pleistocene marine regressions, whereas the more recent single back‐colonisation of the mainland from Mallorca might be explained by several hypotheses, such as long‐distance dispersal mediated by migratory marine birds or sea currents.
Nivalenol and 15‐acetyldeoxynivalenol Chemotypes of Fusarium graminearum Clade Species are Prevalent on Maize throughout China
Authors: Ndoye Mbacke , Zhang Jing‐Bo , Wang Jian‐Hua , Gong An‐Dong , Li He‐Ping , Qu Bo , Li ShaO‐Jun , Liao Yu‐Cai 
Published: July 2012

AbstractFusarium graminearum clade species are among the main causative agents of Gibberella ear rot (GER) in maize and responsible for the various trichothecene mycotoxins accumulated in contaminated maize grains. In this study, a total of 620 isolates from diseased maize ears collected from 59 districts in 19 provinces throughout China, previously identified morphologically as Fusarium graminearum clade, was genetically characterized at the species level based on SCAR (Sequence Characterized Amplified Region) and for their potential capability of mycotoxin production using the genetic chemotyping assay. The results showed that 359 isolates were F. asiaticum (SCAR 5), which consisted of 97% nivalenol (NIV)‐chemotypes, 0.8% 3‐acetyldeoxynivalenol (3‐ADON)‐producing isolates and 2.2% 15‐acetyldeoxynivalenol (15‐ADON) producers, whereas the remaining 261 isolates were identified as F. graminearum sensu stricto (SCAR 1), all of which produced 15‐ADON mycotoxins. This high proportion of NIV producers present in F. asiaticum is different from the chemotype patterns in F. asiaticum populations isolated from wheat and barley, where DON and its acetylated chemotypes were the predominant mycotoxins. Moreover, the majority of NIV producers (59.1%) and all the 3‐ADON‐producing strains were derived from the warmer regions in southern China, whereas most of the 15‐ADON‐producing strains (78.4%) were isolated from the colder regions in northern China. Our study is the first report of NIV chemotypes of F. asiaticum and 15‐ADON chemotypes of F. graminearum sensu stricto that were associated with the GER of maize in China.
Frequency of fungi in respiratory samples from Turkish cystic fibrosis patients
Authors: Güngör Özge , Tamay Zeynep , Güler Nermin , Erturan Zayre 
Published: July 2012

SummaryAn increased isolation of fungi from the respiratory tract of patients with cystic fibrosis (CF) has been reported. The prevalence of different fungi in CF patients from Turkey is not known. Our aim was to determine the frequency of fungi in the respiratory tract of Turkish CF patients. We investigated a total of 184 samples from 48 patients. Samples were inoculated on Medium B+ and CHROMagar Candida. Candida albicans was the predominant yeast isolated [30 patients (62.5%)], followed by C. parapsilosis [6 (12.5%)] and C. dubliniensis 5 (10.4%). Aspergillus fumigatus was the most common filamentous fungus [5 (10.4%)] and non‐fumigatus Aspergillus species were isolated from four (8.3%) patients. Staphylococcus aureus was the most frequently detected bacterium in C. albicans positive samples (53.57%). A. fumigatus and Pseudomonas aeruginosa or S. aureus were detected together in 75% of A. fumigatus positive samples each. No statistically significant relationship was detected between growth of yeast and moulds and age, gender, the use of inhaled corticosteroids or tobramycin. No significant correlation was found between the isolation of C. albicans, A. fumigatus and P. aeruginosa, Stenotrophomonas maltophilia or S. aureus, and the isolation of C. albicans and Haemophilus influenzae. Other factors which may be responsible for the increased isolation of fungi in CF need to be investigated.
Metagenomic analysis of hadopelagic microbial assemblages thriving at the deepest part of Mediterranean Sea, Matapan‐Vavilov Deep
Authors: Smedile Francesco , Messina Enzo , La Cono Violetta , Tsoy Olga , Monticelli Luis S. , Borghini Mireno , Giuliano Laura , Golyshin Peter N. , Mushegian Arcady , Yakimov Michail M. 
Published: July 2012

SummaryThe marine pelagic zone situated > 200 m below the sea level (bls) is the largest marine subsystem, comprising more than two‐thirds of the oceanic volume. At the same time, it is one of the least explored ecosystems on Earth. Few large‐scale environmental genomics studies have been undertaken to examine the phylogenetic diversity and functional gene repertoire of planktonic microbes present in mesopelagic and bathypelagic environments. Here, we present the description of the deep‐sea microbial community thriving at > 4900 m depth in Matapan‐Vavilov Deep (MVD). This canyon is the deepest site of Mediterranean Sea, with a deepest point located at approximately 5270 m, 56 km SW of city Pylos (Greece) in the Ionian Sea (36°34.00N, 21°07.44E). Comparative analysis of whole‐metagenomic data revealed that unlike other deep‐sea metagenomes, the prokaryotic diversity in MVD was extremely poor. The decline in the dark primary production rates, measured at 4908 m depth, was coincident with overwhelming dominance of copiotrophic Alteromonas macleodii‘deep‐ecotype’ AltDE at the expense of other prokaryotes including those potentially involved in both autotrophic and anaplerotic CO2 fixation. We also demonstrate the occurrence in deep‐sea metagenomes of several clustered regularly interspaced short palindromic repeats systems.
The modulator of the general stress response, MgsR, of Bacillus subtilis is subject to multiple and complex control mechanisms
Authors: Reder Alexander , Pöther Dierk‐Christoph , Gerth Ulf , Hecker Michael 
Published: July 2012

SummaryThe alternative sigma factor σB is the master regulator of the general stress regulon that comprises approximately 200 genes whose products confer a comprehensive stress resistance to Bacillus subtilis. The characterization of MgsR (modulator of the general stress response) revealed that the activation and induction of σB are a prerequisite but not sufficient for a full expression of all general stress genes. MgsR is a paralogue of the global regulator of the diamide stress response, Spx, and controls a subregulon of the general stress response. Here we demonstrate that MgsR activity is controlled at multiple levels. These mechanisms include a positive autoregulatory loop on mgsR transcription, a post‐translational redox‐sensitive activation step by an intramolecular disulfide bond formation in response to ethanol stress in vivo, as well as rapid proteolytic degradation of MgsR by the ClpXP and ClpCP proteases. Our results indicate an elaborate regulatory network integrating secondary oxidative stress signals into a σB‐mediated regulatory cascade that is aimed at rapid and finely tuned target gene expression to coordinately fulfil the physiological needs of the cell in the face of multiple environmental changes.