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  • 1
    Online Resource
    Online Resource
    Drosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution
    Oxford University Press (OUP) ; 2015
    In:  G3 Genes|Genomes|Genetics Vol. 5, No. 5 ( 2015-05-01), p. 719-740
    Details
    In: G3 Genes|Genomes|Genetics, Oxford University Press (OUP), Vol. 5, No. 5 ( 2015-05-01), p. 719-740
    Abstract: The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25–50%) than euchromatic reference regions (3–11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11–27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4–3.6 vs. 8.4–8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu.
    Type of Medium: Online Resource
    ISSN: 2160-1836
    URL: Article
    DOI: 10.1534/g3.114.015966
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2015
    detail.hit.zdb_id: 2629978-1
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  • 2
    Online Resource
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    Whether in life or in death: fresh perspectives on how plants affect biogeochemical cycling
    Wiley ; 2015
    In:  Journal of Ecology Vol. 103, No. 6 ( 2015-11), p. 1367-1371
    Details
    In: Journal of Ecology, Wiley, Vol. 103, No. 6 ( 2015-11), p. 1367-1371
    Abstract: Plants have numerous impacts on biogeochemical cycling across both aquatic and terrestrial ecosystems. These effects extend well beyond the critical role of carbon (C) fixation through photosynthesis that provides the basis for ecosystem energy flow. While foliar and root traits of senescent plant material (litter) have been explored in detail in terrestrial ecosystems, there is a resurgence of interest in how plants modulate biogeochemical cycling in ways other than litter quality effects on C and nutrient mineralization. This Special Feature represents a collection of ‘fresh’ perspectives on how plants alone, or in interaction with other organisms, have important and lasting impacts on biogeochemical cycles of C and nutrients in a range of terrestrial and aquatic environments. We begin in the open ocean and then peer from the forest edge before moving into forest understoreys and grasslands to examine the control by live terrestrial plants on ecosystem C and nutrient cycling. Plants directly affect biogeochemical cycling while living through their diversity and composition, nutrient capture and strategies for assimilating C, and by altering the microclimate for decomposition. In addition, how they construct their tissues and alter the abiotic environment has large impacts on the turnover of C and nutrients once plants have senesced or died. From the direct impact of plants, we move onto the influence of plant–insect interactions, which effectively determine changes in plant stoichiometry in grasslands of varying diversity. Finally, looking directly in the soil, it is clear that plant–mycorrhizae interactions are important in modulating the response of litter decomposition to nutrient addition and the nature of C metabolism in the soil. Synthesis . The papers here highlight careful matching between how plants live and their biotic and abiotic contexts. Taken together, it appears that the dynamic, rather than passive, nature of plant responses to variable environments is key in affecting ecosystem level processes of C and nutrient turnover. This Special Feature highlights a diversity of connections between plants and their environment and demonstrates that in both life and death, how plants respond to these changes differs among plant lineages and this diversity will play a central role in determining biogeochemical cycling in the future in aquatic and terrestrial ecosystems.
    Type of Medium: Online Resource
    ISSN: 0022-0477 , 1365-2745
    URL: Issue
    URL: Article
    DOI: 10.1111/jec.2015.103.issue-6
    DOI: 10.1111/1365-2745.12486
    Language: English
    Publisher: Wiley
    Publication Date: 2015
    detail.hit.zdb_id: 3023-5
    detail.hit.zdb_id: 2004136-6
    SSG: 12
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  • 3
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    Online Resource
    Ozone depletion, ultraviolet radiation, climate change and prospects for a sustainable future
    Springer Science and Business Media LLC ; 2019
    In:  Nature Sustainability Vol. 2, No. 7 ( 2019-06-24), p. 569-579
    Details
    In: Nature Sustainability, Springer Science and Business Media LLC, Vol. 2, No. 7 ( 2019-06-24), p. 569-579
    Type of Medium: Online Resource
    ISSN: 2398-9629
    URL: Article
    DOI: 10.1038/s41893-019-0314-2
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2019
    detail.hit.zdb_id: 2917573-2
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  • 4
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    Pine afforestation alters rhizosphere effects and soil nutrient turnover across a precipitation gradient in Patagonia, Argentina
    Springer Science and Business Media LLC ; 2017
    In:  Plant and Soil Vol. 415, No. 1-2 ( 2017-6), p. 449-464
    Details
    In: Plant and Soil, Springer Science and Business Media LLC, Vol. 415, No. 1-2 ( 2017-6), p. 449-464
    Type of Medium: Online Resource
    ISSN: 0032-079X , 1573-5036
    URL: Article
    DOI: 10.1007/s11104-017-3174-4
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2017
    detail.hit.zdb_id: 1478535-3
    detail.hit.zdb_id: 208908-7
    SSG: 12
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  • 5
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    Dysfunctional BMPR2 signaling drives an abnormal endothelial requirement for glutamine in pulmonary arterial hypertension
    Wiley ; 2017
    In:  Pulmonary Circulation Vol. 7, No. 1 ( 2017-01), p. 186-199
    Details
    In: Pulmonary Circulation, Wiley, Vol. 7, No. 1 ( 2017-01), p. 186-199
    Abstract: Pulmonary arterial hypertension (PAH) is increasingly recognized as a systemic disease driven by alteration in the normal functioning of multiple metabolic pathways affecting all of the major carbon substrates, including amino acids. We found that human pulmonary hypertension patients (WHO Group I, PAH) exhibit systemic and pulmonary‐specific alterations in glutamine metabolism, with the diseased pulmonary vasculature taking up significantly more glutamine than that of controls. Using cell culture models and transgenic mice expressing PAH‐causing BMPR2 mutations, we found that the pulmonary endothelium in PAH shunts significantly more glutamine carbon into the tricarboxylic acid (TCA) cycle than wild‐type endothelium. Increased glutamine metabolism through the TCA cycle is required by the endothelium in PAH to survive, to sustain normal energetics, and to manifest the hyperproliferative phenotype characteristic of disease. The strict requirement for glutamine is driven by loss of sirtuin‐3 (SIRT3) activity through covalent modification by reactive products of lipid peroxidation. Using 2‐hydroxybenzylamine, a scavenger of reactive lipid peroxidation products, we were able to preserve SIRT3 function, to normalize glutamine metabolism, and to prevent the development of PAH in BMPR2 mutant mice. In PAH, targeting glutamine metabolism and the mechanisms that underlie glutamine‐driven metabolic reprogramming represent a viable novel avenue for the development of potentially disease‐modifying therapeutics that could be rapidly translated to human studies.
    Type of Medium: Online Resource
    ISSN: 2045-8940 , 2045-8940
    URL: Article
    DOI: 10.1086/690236
    Language: English
    Publisher: Wiley
    Publication Date: 2017
    detail.hit.zdb_id: 2638089-4
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  • 6
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    A World of Cobenefits: Solving the Global Nitrogen Challenge
    American Geophysical Union (AGU) ; 2019
    In:  Earth's Future Vol. 7, No. 8 ( 2019-08), p. 865-872
    Details
    In: Earth's Future, American Geophysical Union (AGU), Vol. 7, No. 8 ( 2019-08), p. 865-872
    Abstract: Global nitrogen solutions generate cobenefits for (i) world hunger, (ii) pollution, (iii) climate change, and (iv) biodiversity We provide the most comprehensive, solutions‐focused strategy for global nitrogen to date We call for an IPCC‐type organization focused on global nitrogen issues and public‐private partnerships to scale solutions
    Type of Medium: Online Resource
    ISSN: 2328-4277 , 2328-4277
    URL: Article
    DOI: 10.1029/2019EF001222
    Language: English
    Publisher: American Geophysical Union (AGU)
    Publication Date: 2019
    detail.hit.zdb_id: 2746403-9
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  • 7
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    Recalculating growth and defense strategies under competition: key roles of photoreceptors and jasmonates
    Oxford University Press (OUP) ; 2019
    In:  Journal of Experimental Botany Vol. 70, No. 13 ( 2019-07-05), p. 3425-3434
    Details
    In: Journal of Experimental Botany, Oxford University Press (OUP), Vol. 70, No. 13 ( 2019-07-05), p. 3425-3434
    Abstract: The growth–defense trade-off in plant biology has gained enormous traction in the last two decades, highlighting the importance of understanding how plants deal with two of the greatest challenges for their survival and reproduction. It has been well established that in response to competition signals perceived by informational photoreceptors, shade-intolerant plants typically activate the shade-avoidance syndrome (SAS). In turn, in response to signals of biotic attack, plants activate a suite of defense responses, many of which are directed to minimize the loss of plant tissue to the attacking agent (broadly defined, the defense syndrome, DS). We argue that components of the SAS, including increased elongation, apical dominance, reduced leaf mass per area (LMA), and allocation to roots, are in direct conflict with configurational changes that plants require to maximize defense. We hypothesize that these configurational trade-offs provide a functional explanation for the suppression of components of the DS in response to competition cues. Based on this premise, we discuss recent advances in the understanding of the mechanisms by which informational photoreceptors, by interacting with jasmonic acid (JA) signaling, help the plant to make intelligent allocation and developmental decisions that optimize its configuration in complex biotic contexts.
    Type of Medium: Online Resource
    ISSN: 0022-0957 , 1460-2431
    URL: Article
    DOI: 10.1093/jxb/erz237
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
    detail.hit.zdb_id: 1466717-4
    SSG: 12
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  • 8
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    Supplemental Information 1: Fig. S1. Tree triangle in a native Patagonian forest.
    PeerJ ; 2018
    In:  PeerJ Vol. 6 ( 2018-05-11), p. e4754-
    Details
    In: PeerJ, PeerJ, Vol. 6 ( 2018-05-11), p. e4754-
    Abstract: Plant–microbial interactions in the litter layer represent one of the most relevant interactions for biogeochemical cycling as litter decomposition is a key first step in carbon and nitrogen turnover. However, our understanding of these interactions in the litter layer remains elusive. In an old-growth mixed Nothofagus forest in Patagonia, we studied the effects of single tree species identity and the mixture of three tree species on the fungal and bacterial composition in the litter layer. We also evaluated the effects of nitrogen (N) addition on these plant–microbial interactions. In addition, we compared the magnitude of stimulation of litter decomposition due to home field advantage (HFA, decomposition occurs more rapidly when litter is placed beneath the plant species from which it had been derived than beneath a different plant species) and N addition that we previously demonstrated in this same forest, and used microbial information to interpret these results. Tree species identity had a strong and significant effect on the composition of fungal communities but not on the bacterial community of the litter layer. The microbial composition of the litter layer under the tree species mixture show an averaged contribution of each single tree species. N addition did not erase the plant species footprint on the fungal community, and neither altered the bacterial community. N addition stimulated litter decomposition as much as HFA for certain tree species, but the mechanisms behind N and HFA stimulation may have differed. Our results suggest that stimulation of decomposition from N addition might have occurred due to increased microbial activity without large changes in microbial community composition, while HFA may have resulted principally from plant species’ effects on the litter fungal community. Together, our results suggest that plant–microbial interactions can be an unconsidered driver of litter decomposition in temperate forests.
    Type of Medium: Online Resource
    ISSN: 2167-8359
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    DOI: 10.7717/peerj.4754
    DOI: 10.7717/peerj.4754/fig-1
    DOI: 10.7717/peerj.4754/fig-2
    DOI: 10.7717/peerj.4754/fig-3
    DOI: 10.7717/peerj.4754/fig-4
    DOI: 10.7717/peerj.4754/supp-1
    Language: English
    Publisher: PeerJ
    Publication Date: 2018
    detail.hit.zdb_id: 2703241-3
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  • 9
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    Online Resource
    Journal of Ecology News: Data Archiving Compliance
    Wiley ; 2016
    In:  Journal of Ecology Vol. 104, No. 1 ( 2016-01), p. 1-3
    Details
    In: Journal of Ecology, Wiley, Vol. 104, No. 1 ( 2016-01), p. 1-3
    Type of Medium: Online Resource
    ISSN: 0022-0477 , 1365-2745
    URL: Issue
    URL: Article
    DOI: 10.1111/jec.2016.104.issue-1
    DOI: 10.1111/1365-2745.12502
    Language: English
    Publisher: Wiley
    Publication Date: 2016
    detail.hit.zdb_id: 3023-5
    detail.hit.zdb_id: 2004136-6
    SSG: 12
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  • 10
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    Photodegradation alleviates the lignin bottleneck for carbon turnover in terrestrial ecosystems
    Proceedings of the National Academy of Sciences ; 2016
    In:  Proceedings of the National Academy of Sciences Vol. 113, No. 16 ( 2016-04-19), p. 4392-4397
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 113, No. 16 ( 2016-04-19), p. 4392-4397
    Abstract: A mechanistic understanding of the controls on carbon storage and losses is essential for our capacity to predict and mitigate human impacts on the global carbon cycle. Plant litter decomposition is an important first step for carbon and nutrient turnover, and litter inputs and losses are essential in determining soil organic matter pools and the carbon balance in terrestrial ecosystems. Photodegradation, the photochemical mineralization of organic matter, has been recently identified as a mechanism for previously unexplained high rates of litter mass loss in arid lands; however, the global significance of this process as a control on carbon cycling in terrestrial ecosystems is not known. Here we show that, across a wide range of plant species, photodegradation enhanced subsequent biotic degradation of leaf litter. Moreover, we demonstrate that the mechanism for this enhancement involves increased accessibility to plant litter carbohydrates for microbial enzymes. Photodegradation of plant litter, driven by UV radiation, and especially visible (blue–green) light, reduced the structural and chemical bottleneck imposed by lignin in secondary cell walls. In leaf litter from woody species, specific interactions with UV radiation obscured facilitative effects of solar radiation on biotic decomposition. The generalized effect of sunlight exposure on subsequent microbial activity, mediated by increased accessibility to cell wall polysaccharides, suggests that photodegradation is quantitatively important in determining rates of mass loss, nutrient release, and the carbon balance in a broad range of terrestrial ecosystems.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.1516157113
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2016
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
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