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  • 1
    Publication Date: 2015-10-28
    Description: Shallow lakes process large amounts of carbon (C) via gross primary production (GPP) and respiration (R), but C fluxes are highly variable among lakes. We used a two-prong approach to determine whether C fluxes differed between two alternative stable states observed in shallow lakes. First, we used a replicated whole-lake experiment where we manipulated fish densities in four experimental lakes to induce shifts from the phytoplankton-dominated state (turbid state) to a submersed macrophyte-dominated state (clear state), and determined whether whole-lake GPP, R, and net aquatic production (NAP) changed in response to the manipulation. We also compared lake metabolism in the four experimental lakes to four lakes in a turbid state and four lakes in a clear state. Second, we used sediment cores from 68 shallow lakes to test whether modern burial rates of organic C differed between lakes in clear and turbid states. Biomanipulation in the experimental lakes reduced abundance of fish and phytoplankton and increased abundance of aquatic invertebrates and submerged macrophytes. However, there was no significant change in GPP, R, or NAP. Similarly, GPP, R, and NAP did not differ among experimental lakes, turbid-state lakes, or clear-state lakes. Lastly, organic C burial in sediments did not differ between lakes in clear vs. turbid states, though variability among sites was high. High light and nutrient availability facilitate rapid transitions between two alternative groups of competing, rapidly growing primary producers in shallow lakes. These characteristics facilitate relatively uniform C fluxes at the ecosystem scale despite substantial differences in community structure.
    Print ISSN: 0024-3590
    Electronic ISSN: 1939-5590
    Topics: Biology , Geosciences , Physics
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  • 2
    Publication Date: 2016-06-10
    Description: Ecological shifts in shallow lakes from clear-water macrophyte-dominated to turbid-water phytoplankton-dominated are generally thought of as rapid short-term transitions. Diatom remains in sediment records from shallow lakes in the Prairie Pothole Region of North America provide new evidence that the long-term ecological stability of these lakes is defined by the legacy of large regime shifts. Here we examine the modern and historical stability of eleven shallow lakes. Currently, four of the lakes are in a clear-water state, three are consistently turbid-water, and four have been observed to change state from year to year (transitional). Lake sediment records spanning the past 150-200 years suggest that: 1) the diatom assemblage is characteristic of either clear or turbid lakes; 2) prior to significant landscape alteration, all of the lakes existed in a regime of a stable clear-water state; 3) lakes that are currently classified as turbid or transitional have experienced one strong regime shift over the past 150-200 years, and have since remained in a regime where turbid-water predominates; and 4) top-down impacts to the lake food web from fish introductions appear to be the dominant driver of strong regime shifts, and not increased nutrient availability. Based on our findings we demonstrate a method that could be used by lake managers to identify lakes that have an ecological history close to the clear-turbid regime threshold; such lakes might more easily be returned to a clear-water state through biomanipulation. The unfortunate reality is that many of these lakes are now part of a managed landscape and will likely require continued intervention. This article is protected by copyright. All rights reserved.
    Print ISSN: 1051-0761
    Electronic ISSN: 1939-5582
    Topics: Biology
    Published by Wiley on behalf of The Ecological Society of America (ESA).
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  • 3
    Publication Date: 2007
    Description: We report the draft genome sequence of the model moss Physcomitrella patens and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments (e.g., flagellar arms); acquisition of genes for tolerating terrestrial stresses (e.g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rensing, Stefan A -- Lang, Daniel -- Zimmer, Andreas D -- Terry, Astrid -- Salamov, Asaf -- Shapiro, Harris -- Nishiyama, Tomoaki -- Perroud, Pierre-Francois -- Lindquist, Erika A -- Kamisugi, Yasuko -- Tanahashi, Takako -- Sakakibara, Keiko -- Fujita, Tomomichi -- Oishi, Kazuko -- Shin-I, Tadasu -- Kuroki, Yoko -- Toyoda, Atsushi -- Suzuki, Yutaka -- Hashimoto, Shin-Ichi -- Yamaguchi, Kazuo -- Sugano, Sumio -- Kohara, Yuji -- Fujiyama, Asao -- Anterola, Aldwin -- Aoki, Setsuyuki -- Ashton, Neil -- Barbazuk, W Brad -- Barker, Elizabeth -- Bennetzen, Jeffrey L -- Blankenship, Robert -- Cho, Sung Hyun -- Dutcher, Susan K -- Estelle, Mark -- Fawcett, Jeffrey A -- Gundlach, Heidrun -- Hanada, Kousuke -- Heyl, Alexander -- Hicks, Karen A -- Hughes, Jon -- Lohr, Martin -- Mayer, Klaus -- Melkozernov, Alexander -- Murata, Takashi -- Nelson, David R -- Pils, Birgit -- Prigge, Michael -- Reiss, Bernd -- Renner, Tanya -- Rombauts, Stephane -- Rushton, Paul J -- Sanderfoot, Anton -- Schween, Gabriele -- Shiu, Shin-Han -- Stueber, Kurt -- Theodoulou, Frederica L -- Tu, Hank -- Van de Peer, Yves -- Verrier, Paul J -- Waters, Elizabeth -- Wood, Andrew -- Yang, Lixing -- Cove, David -- Cuming, Andrew C -- Hasebe, Mitsuyasu -- Lucas, Susan -- Mishler, Brent D -- Reski, Ralf -- Grigoriev, Igor V -- Quatrano, Ralph S -- Boore, Jeffrey L -- BBS/E/C/00004948/Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2008 Jan 4;319(5859):64-9. Epub 2007 Dec 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, D-79104 Freiburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18079367" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Angiosperms/genetics/physiology ; Animals ; Arabidopsis/genetics/physiology ; *Biological Evolution ; Bryopsida/*genetics/physiology ; Chlamydomonas reinhardtii/genetics/physiology ; Computational Biology ; DNA Repair ; Dehydration ; Gene Duplication ; Genes, Plant ; *Genome, Plant ; Metabolic Networks and Pathways/genetics ; Multigene Family ; Oryza/genetics/physiology ; Phylogeny ; Plant Proteins/genetics/physiology ; Repetitive Sequences, Nucleic Acid ; Retroelements ; Sequence Analysis, DNA ; Signal Transduction/genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2011-05-10
    Description: Vascular plants appeared ~410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166216/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166216/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Banks, Jo Ann -- Nishiyama, Tomoaki -- Hasebe, Mitsuyasu -- Bowman, John L -- Gribskov, Michael -- dePamphilis, Claude -- Albert, Victor A -- Aono, Naoki -- Aoyama, Tsuyoshi -- Ambrose, Barbara A -- Ashton, Neil W -- Axtell, Michael J -- Barker, Elizabeth -- Barker, Michael S -- Bennetzen, Jeffrey L -- Bonawitz, Nicholas D -- Chapple, Clint -- Cheng, Chaoyang -- Correa, Luiz Gustavo Guedes -- Dacre, Michael -- DeBarry, Jeremy -- Dreyer, Ingo -- Elias, Marek -- Engstrom, Eric M -- Estelle, Mark -- Feng, Liang -- Finet, Cedric -- Floyd, Sandra K -- Frommer, Wolf B -- Fujita, Tomomichi -- Gramzow, Lydia -- Gutensohn, Michael -- Harholt, Jesper -- Hattori, Mitsuru -- Heyl, Alexander -- Hirai, Tadayoshi -- Hiwatashi, Yuji -- Ishikawa, Masaki -- Iwata, Mineko -- Karol, Kenneth G -- Koehler, Barbara -- Kolukisaoglu, Uener -- Kubo, Minoru -- Kurata, Tetsuya -- Lalonde, Sylvie -- Li, Kejie -- Li, Ying -- Litt, Amy -- Lyons, Eric -- Manning, Gerard -- Maruyama, Takeshi -- Michael, Todd P -- Mikami, Koji -- Miyazaki, Saori -- Morinaga, Shin-ichi -- Murata, Takashi -- Mueller-Roeber, Bernd -- Nelson, David R -- Obara, Mari -- Oguri, Yasuko -- Olmstead, Richard G -- Onodera, Naoko -- Petersen, Bent Larsen -- Pils, Birgit -- Prigge, Michael -- Rensing, Stefan A -- Riano-Pachon, Diego Mauricio -- Roberts, Alison W -- Sato, Yoshikatsu -- Scheller, Henrik Vibe -- Schulz, Burkhard -- Schulz, Christian -- Shakirov, Eugene V -- Shibagaki, Nakako -- Shinohara, Naoki -- Shippen, Dorothy E -- Sorensen, Iben -- Sotooka, Ryo -- Sugimoto, Nagisa -- Sugita, Mamoru -- Sumikawa, Naomi -- Tanurdzic, Milos -- Theissen, Gunter -- Ulvskov, Peter -- Wakazuki, Sachiko -- Weng, Jing-Ke -- Willats, William W G T -- Wipf, Daniel -- Wolf, Paul G -- Yang, Lixing -- Zimmer, Andreas D -- Zhu, Qihui -- Mitros, Therese -- Hellsten, Uffe -- Loque, Dominique -- Otillar, Robert -- Salamov, Asaf -- Schmutz, Jeremy -- Shapiro, Harris -- Lindquist, Erika -- Lucas, Susan -- Rokhsar, Daniel -- Grigoriev, Igor V -- GM065383/GM/NIGMS NIH HHS/ -- GM84051/GM/NIGMS NIH HHS/ -- HG004164/HG/NHGRI NIH HHS/ -- R01 GM043644/GM/NIGMS NIH HHS/ -- R01 GM084051/GM/NIGMS NIH HHS/ -- R01 GM084051-01A1/GM/NIGMS NIH HHS/ -- R01 HG004164/HG/NHGRI NIH HHS/ -- R01 HG004164-02/HG/NHGRI NIH HHS/ -- R01 HG004164-03/HG/NHGRI NIH HHS/ -- R01 HG004164-04/HG/NHGRI NIH HHS/ -- T32 GM007757/GM/NIGMS NIH HHS/ -- T32-HG00035/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2011 May 20;332(6032):960-3. doi: 10.1126/science.1203810. Epub 2011 May 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA. banksj@purdue.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21551031" target="_blank"〉PubMed〈/a〉
    Keywords: Angiosperms/chemistry/genetics ; *Biological Evolution ; Bryopsida/genetics ; Chlamydomonas/chemistry/genetics ; DNA Transposable Elements ; Evolution, Molecular ; Gene Expression Regulation, Plant ; Genes, Plant ; *Genome, Plant ; MicroRNAs/genetics ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/genetics/metabolism ; Proteome/analysis ; RNA Editing ; RNA, Plant/genetics ; Repetitive Sequences, Nucleic Acid ; Selaginellaceae/*genetics/growth & development/metabolism ; Sequence Analysis, DNA
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2013-05-01
    Description: A 3D atomistic model of a plant cellulose synthase (CESA) has remained elusive despite over forty years of experimental effort. Here, we report a computationally predicted 3D structure of 506 amino acids of cotton CESA within the cytosolic region. Comparison of the predicted plant CESA structure with the solved structure...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 6
    Publication Date: 2017-09-06
    Description: Author(s): J. Ruiz-Fuertes, T. Bernert, D. Zimmer, N. Schrodt, M. Koch-Müller, B. Winkler, L. Bayarjargal, C. Popescu, S. MacLeod, and K. Glazyrin The ferroelectric to paraelectric phase transition of multiferroic CaMnTi 2 O 6 has been investigated at high pressures and ambient temperature by second-harmonic generation (SHG), Raman spectroscopy, and powder and single-crystal x-ray diffraction. We have found that CaMnTi 2 O 6 undergoes a pressure-ind... [Phys. Rev. B 96, 094101] Published Tue Sep 05, 2017
    Keywords: Structure, structural phase transitions, mechanical properties, defects
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
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  • 7
    Publication Date: 2017-08-12
    Description: Author(s): D. Zimmer, J. Ruiz-Fuertes, L. Bayarjargal, E. Haussühl, B. Winkler, J. Zhang, C. Q. Jin, V. Milman, E. Alig, and L. Fink The low-temperature behavior of tetragonal copper sulfide, Cu 2 S , was investigated by powder and single-crystal x-ray diffraction, calorimetry, electrical resistance measurements, and ambient temperature optical absorption spectroscopy. The experiments were complemented by density-functional-theory-b... [Phys. Rev. B 96, 054108] Published Fri Aug 11, 2017
    Keywords: Structure, structural phase transitions, mechanical properties, defects
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
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  • 8
    Publication Date: 2018-04-14
    Description: Author(s): D. Zimmer, J. Ruiz-Fuertes, W. Morgenroth, A. Friedrich, L. Bayarjargal, E. Haussühl, D. Santamaría-Pérez, S. Frischkorn, V. Milman, and B. Winkler The high-pressure behavior of monoclinic ( P 2 1 / c ) α -chalcocite, Cu 2 S , was investigated at ambient temperature by single-crystal x-ray diffraction, electrical resistance measurements, and optical absorption spectroscopy up to 16 GPa. The experiments were complemented by density-functional-theory-based... [Phys. Rev. B 97, 134111] Published Fri Apr 13, 2018
    Keywords: Structure, structural phase transitions, mechanical properties, defects
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
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  • 9
    Publication Date: 2017-10-31
    Description: Ecosystems sometimes undergo dramatic shifts between contrasting regimes. Shallow lakes, for instance, can transition between two alternative stable states: a clear state dominated by submerged aquatic vegetation and a turbid state dominated by phytoplankton. Theoretical models suggest that critical nutrient thresholds differentiate three lake types: highly resilient clear lakes, lakes that may switch between clear and turbid states following perturbations, and highly resilient turbid lakes. For effective and efficient management of shallow lakes and other systems, managers need tools to identify critical thresholds and state-dependent relationships between driving variables and key system features. Using shallow lakes as a model system for which alternative stable states have been demonstrated, we developed an integrated framework using Bayesian latent variable regression (BLR) to classify lake states, identify critical total phosphorus (TP) thresholds, and estimate steady state relationships between TP and chlorophyll a (Chla) using cross-sectional data. We evaluated the method using data simulated from a stochastic differential equation model and compared its performance to k -means clustering with regression (KMR). We also applied the framework to data comprising 130 shallow lakes. For simulated datasets, BLR had high state classification rates (median/mean accuracy 〉97%) and accurately estimated TP thresholds and state-dependent TP/Chla relationships. Classification and estimation improved with increasing sample size and decreasing noise levels. Compared to KMR, BLR had higher classification rates and better approximated the TP/Chla steady state relationships and TP thresholds. We fit the BLR model to three different years of empirical shallow lake data, and managers can use the estimated bifurcation diagrams to prioritize lakes for management according to their proximity to thresholds and chance of successful rehabilitation. Our model improves upon previous methods for shallow lakes because it allows classification and regression to occur simultaneously and inform one another, directly estimates TP thresholds and the uncertainty associated with thresholds and state classifications, and enables meaningful constraints to be built into models. The BLR framework is broadly applicable to other ecosystems known to exhibit alternative stable states in which regression can be used to establish relationships between driving variables and state variables. This article is protected by copyright. All rights reserved.
    Print ISSN: 1051-0761
    Electronic ISSN: 1939-5582
    Topics: Biology
    Published by Wiley on behalf of The Ecological Society of America (ESA).
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  • 10
    Publication Date: 2017-03-07
    Description: Animals can be important in modulating ecosystem-level nutrient cycling, although their importance varies greatly among species and ecosystems. Nutrient cycling rates of individual animals represent valuable data for testing the predictions of important frameworks such as the Metabolic Theory of Ecology (MTE) and ecological stoichiometry (ES). They also represent an important set of functional traits that may reflect both environmental and phylogenetic influences. Over the past two decades, studies of animal-mediated nutrient cycling have increased dramatically, especially in aquatic ecosystems. Here we present a global compilation of aquatic animal nutrient excretion rates. The dataset includes 10,534 observations from freshwater and marine animals of N and/or P excretion rates. These observations represent 491 species, including most aquatic phyla. Coverage varies greatly among phyla and other taxonomic levels. The dataset includes information on animal body size, ambient temperature, taxonomic affiliations, and animal body N:P. This data set was used to test predictions of MTE and ES, as described in Vanni and McIntyre (2016; Ecology DOI: 10.1002/ecy.1582). This article is protected by copyright. All rights reserved.
    Print ISSN: 0012-9658
    Electronic ISSN: 1939-9170
    Topics: Biology
    Published by Wiley on behalf of The Ecological Society of America (ESA).
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