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  • 12851.
    Yeo, Sara K.
    et al.
    University of Hawaii.
    Huggett, Megan J.
    University of Hawaii.
    Eiler, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Rappé, Michael S.
    University of Hawaii.
    Coastal Bacterioplankton Community Dynamics in Response to a Natural Disturbance2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 2, p. e56207-Article in journal (Refereed)
    Abstract [en]

    In order to characterize how disturbances to microbial communities are propagated over temporal and spatial scales in aquatic environments, the dynamics of bacterial assemblages throughout a subtropical coastal embayment were investigated via SSU rRNA gene analyses over an 8-month period, which encompassed a large storm event. During non-perturbed conditions, sampling sites clustered into three groups based on their microbial community composition: an offshore oceanic group, a freshwater group, and a distinct and persistent coastal group. Significant differences in measured environmental parameters or in the bacterial community due to the storm event were found only within the coastal cluster of sampling sites, and only at 5 of 12 locations; three of these sites showed a significant response in both environmental and bacterial community characteristics. These responses were most pronounced at sites close to the shoreline. During the storm event, otherwise common bacterioplankton community members such as marine Synechococcus sp. and members of the SAR11 clade of Alphaproteobacteria decreased in relative abundance in the affected coastal zone, whereas several lineages of GammaproteobacteriaBetaproteobacteria, and members of the Roseobacter clade of Alphaproteobacteria increased. The complex spatial patterns in both environmental conditions and microbial community structure related to freshwater runoff and wind convection during the perturbation event leads us to conclude that spatial heterogeneity was an important factor influencing both the dynamics and the resistance of the bacterioplankton communities to disturbances throughout this complex subtropical coastal system. This heterogeneity may play a role in facilitating a rapid rebound of regions harboring distinctly coastal bacterioplankton communities to their pre-disturbed taxonomic composition.

  • 12852.
    Yi, Peng
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Aldahan, Ala
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Possnert, Goran
    Uppsala University, Disciplinary Domain of Science and Technology, För teknisk-naturvetenskapliga fakulteten gemensamma enheter, Tandem Laboratory. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Hou, Xiaolin
    Technical University of Denmark, Risø Campus, Roskilde, Denmark.
    He, Peng
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Biao, Wang
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Depth profiles of I-129 species in the Bothnian Sea2013In: Journal of Radioanalytical and Nuclear Chemistry, ISSN 0236-5731, E-ISSN 1588-2780, Vol. 295, no 2, p. 1459-1463Article in journal (Refereed)
    Abstract [en]

    The Bothnian Sea which is located between Finland and Sweden represents an important source of fresh water to the Baltic Sea. We here present new data on the radioactive isotope I-129 species from water samples collected in December 2009 at different depths in the Bothnian Sea. Concentrations of I-129(-) (iodide) in the Bothnian Sea range from 14 x 10(8) to 32 x 10(8) atoms/L, while (IO3)-I-129 (-) (iodate) concentrations are relatively low and fluctuating at 1 x 10(8) atoms/L. For nutrients data determined in the same samples as I-129, significant correlations could be found between I-129(-) and total P, NO3-N, SiO3-Si, but rather poor with NH4-N. The correlations suggest comparable source pathway of I-129(-) and nutrient parameters, while the source of NH4-N may be different. The small amounts and negligible change of (IO3)-I-129 (-) indicate prevailing extensive reduction of iodate in the Baltic Sea.

  • 12853.
    Yi, Peng
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Aldahan, Ala
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Possnert, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, För teknisk-naturvetenskapliga fakulteten gemensamma enheter, Tandem Laboratory. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Hou, X. L.
    He, Peng
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Wang, Biao
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Seasonal variation of I-129 species in the Baltic Proper2013In: Journal of Radioanalytical and Nuclear Chemistry, ISSN 0236-5731, E-ISSN 1588-2780, Vol. 295, no 3, p. 1797-1801Article in journal (Refereed)
    Abstract [en]

    Iodine speciation plays a significant role in iodine volatilizing into atmosphere from the seas, as well as serving as a biological indicator. Despite this importance, the data on iodine species revealed inconclusive evidence of what factors controlling speciation transformation. We here present new data on profiles of I-129 speciation in the Baltic Proper during November 2009. Along with the two earlier investigations (August 2006 and April 2007), an assessment of seasonal variation of I-129 species is presented. The results show that, due to the anoxic nature of Baltic Proper, presence of (IO3)-I-129 (-) in the Baltic Proper does not follow an obvious seasonal cycle, as the case with I-129(-). Concentrations of I-129(-) in the Baltic Proper exhibit higher values in summer than the other two seasons (spring and winter), which might be associated with degrading of organic matter and release from sediment to water column that is more pronounced during summer. I-129(-) in surface water from the three seasons does not reflect the release function from the reprocessing facilities during the period April 2007 to November 2009. Consequently variability of I-129(-) in surface seawater of the Baltic Proper depends, to some extent, on local physical as well as biochemical conditions.

  • 12854.
    Yi, Peng
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Chen, X. G.
    Aldahan, Ala
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Possnert, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, För teknisk-naturvetenskapliga fakulteten gemensamma enheter, Tandem Laboratory.
    Hou, X. L.
    Yu, Z. B.
    Xiong, D. H.
    Wang, Biao
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Circulation of water masses in the Baltic Proper revealed through iodine isotopes2013In: Applied Geochemistry, ISSN 0883-2927, E-ISSN 1872-9134, Vol. 36, p. 118-124Article in journal (Refereed)
    Abstract [en]

    Tracer technology has been used to understand water circulation in marine systems where the tracer dose is commonly injected into the marine waters through controlled experiments, accidental releases or waste discharges. Anthropogenic discharges of I-129 have been used to trace water circulation in the Arctic and North Atlantic Ocean. Here, I-129, together with I-127, is utilized as a tracer of water pathways and circulation in the Baltic Sea through collection of seawater depth profiles. The results indicate the presence of I-129 signatures which are distinct for each water mass and provide evidence for: (1) inflow water masses through the Drogden Sill that may reach as far as the SW of the Arkona Sea, (2) a portion of North Atlantic water in the bottom of Arkona basin, (3) cyclonic upwelling which breaks through the halocline in a pattern similar to the Baltic haline conveyor belt and (4) more influx of fresher water from the Gulf of Finland and Bothnian Sea in August relative to April. These findings provide advances in labeling and understanding water pathways in the Baltic Sea.

  • 12855.
    Yi, Peng
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Chen, X. G.
    Bao, D. X.
    Qian, R. Z.
    Aldahan, Ala
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Tian, F. Y.
    Possnert, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, För teknisk-naturvetenskapliga fakulteten gemensamma enheter, Tandem Laboratory.
    Bryhn, A. C.
    Gu, T. F.
    Hou, X. L.
    He, Peng
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Yu, Z. B.
    Wang, Biao
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Model simulation of inflow water to the Baltic Sea based on I-1292013In: Applied Radiation and Isotopes, ISSN 0969-8043, E-ISSN 1872-9800, Vol. 82, p. 223-231Article in journal (Refereed)
    Abstract [en]

    The semi-enclosed Baltic Sea represents a vital economic and recreational resource for more than 90 million people inhabiting its coasts. Extensive contamination of this sea by a variety of anthropogenic pollutants has raised the concern of the people in the region. Quantifying seawater inflow is crucial for estimating potential environmental risks as well as to find the best remedial strategy. We present here a model to estimate water inflow from the North Sea to the Baltic Sea by utilizing 1291 as a tracer. The results predicted inflow range of 230-450 km(3)/y with best fit value around 330 km(3)/y from the North Sea to the Baltic Sea during 1980-1999. Despite limited time series data on I-129, the model presented here demonstrates a new management tool for the Baltic Sea to calculate inflow water compared to conventional methods (such as salinity, temperature and hydrographic models). 

  • 12856.
    Yildirim, Ahmet
    et al.
    Siirt Univ, Dept Phys, TR-56100 Siirt, Turkey.
    Wassenaar, Tsjerk A.
    Univ Groningen, Groningen Biomol Sci & Biotechnol Inst, NL-9747 AG Groningen, Netherlands;Univ Groningen, Zernike Inst Adv Mat, NL-9747 AG Groningen, Netherlands.
    Van der Spoel, David
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
    Statistical efficiency of methods for computing free energy of hydration2018In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 149, no 14, article id 144111Article in journal (Refereed)
    Abstract [en]

    The hydration free energy (HFE) is a critical property for predicting and understanding chemical and biological processes in aqueous solution. There are a number of computational methods to derive HFE, generally classified into the equilibrium or non-equilibrium methods, based on the type of calculations used. In the present study, we compute the hydration free energies of 34 small, neutral, organic molecules with experimental HFE between + 2 and 16 kcal/mol. The one-sided non-equilibrium methods Jarzynski Forward (JF) and Backward (JB), the two-sided non-equilibrium methods Jarzynski mean based on the average of JF and JB, Crooks Gaussian Intersection (CGI), and the Bennett Acceptance Ratio (BAR) are compared to the estimates from the two-sided equilibrium method Multistate Bennett Acceptance Ratio (MBAR), which is considered as the reference method for HFE calculations, and experimental data from the literature. Our results show that the estimated hydration free energies from all the methods are consistent with MBAR results, and all methods provide a mean absolute error of similar to 0.8 kcal/mol and root mean square error of similar to 1 kcal for the 34 organic molecules studied. In addition, the results show that one-sided methods JF and JB result in systematic deviations that cannot be corrected entirely. The statistical efficiency epsilon of the different methods can be expressed as the one over the simulation time times the average variance in the HFE. From such an analysis, we conclude that epsilon(MBAR) > epsilon(BAR) approximate to epsilon(CGI) > epsilon(JX), where JX is any of the Jarzynski methods. In other words, the non-equilibrium methods tested here for the prediction of HFE have lower computational efficiency than the MBAR method. 

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  • 12857.
    Yildirim, Ahmet
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics. Siirt Univ, Fac Sci & Art, Dept Phys, TR-56100 Siirt, Turkey..
    Zhang, Jin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics. Zhejiang Univ, Dept Chem, Hangzhou 310027, Peoples R China..
    Manzetti, Sergio
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
    Binding of Pollutants to Biomolecules: A Simulation Study2016In: Chemical Research in Toxicology, ISSN 0893-228X, E-ISSN 1520-5010, Vol. 29, no 10, p. 1679-1688Article in journal (Refereed)
    Abstract [en]

    A number of cases around the world have been reported where animals were found dead or dying with symptoms resembling a thiamine (vitamin B) deficiency, and for some of these, a link to pollutants has been suggested. Here, we investigate whether biomolecules involved in thiamin binding and transport could be blocked by a range of different pollutants. We used in silico docking of five compound classes (25 compounds in total) to each of five targets (prion protein, ECF-type ABC transporter, thi-box riboswitch receptor, thiamin pyrophosphokinase, and YKoF protein) and subsequently performed molecular dynamics (MD) simulations to assess the stability of the complexes. The compound classes were thiamin analogues (control), pesticides, veterinary medicines, polychlorinated biphenyls, and dioxins, all of which are prevalent in the environment to some extent. A few anthropogenic compounds were found to bind the ECF-type ABC transporter, but none binds stably to prion protein. For the riboswitch, most compounds remained in their binding pockets during 50 ns of MD simulation, indicating that RNA provides a promiscuous binding site. In both YKoF and thiamin pyrophosphokinase (TPK), most compounds remain tightly bound. However, TPK biomolecules undergo pollutant-induced conformational changes. Although most compounds are found to bind to some of these targets, a larger data set is needed along with more quantitative methods like free energy perturbation calculations before firm conclusions can be drawn. This study is in part a test bed for large-scale quantitative computational screening of interactions between biological entities and pollutant molecules.

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  • 12858.
    Yin, Chunhua
    et al.
    Univ Sci & Technol Beijing, Sch Chem & Biol Engn, Dept Biol Sci & Engn, Beijing 100083, Peoples R China.
    Cui, Ziheng
    Beijing Univ Chem Technol, Coll Life Sci & Technol, Beijing Key Lab Bioproc, Box 53, Beijing 100029, Peoples R China.
    Jiang, Yang
    Beijing Univ Chem Technol, Coll Life Sci & Technol, Beijing Key Lab Bioproc, Box 53, Beijing 100029, Peoples R China;Penn State Univ, Dept Chem, University Pk, PA 16802 USA.
    Van der Spoel, David
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
    Zhang, Haiyang
    Univ Sci & Technol Beijing, Sch Chem & Biol Engn, Dept Biol Sci & Engn, Beijing 100083, Peoples R China.
    Role of Host-Guest Charge Transfer in Cyclodextrin Complexation: A Computational Study2019In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 123, no 29, p. 17745-17756Article in journal (Refereed)
    Abstract [en]

    Charge transfer (CT) was proposed to play a role in the cyclodextrin (CD) complexation with guest molecules. To elucidate the importance of CT interactions, here we used computational methods of quantum mechanics, docking, and molecular dynamics (MD) to investigate alpha-CD complexes with aromatic guest molecules of nitrobenzene, carboxybenzene, benzoate, 4-nitrophenol, and 4-nitrophenolate. Considering host guest CT in the docking has more of a chance to search reasonable guest orientations relative to alpha-CD matching the experiment, compared to that without CT. The CT interaction enlarges the difference in binding affinities of varied guests, as evidenced from potential of mean force (PMF) MD calculations. Energy decomposition of the total enthalpy and entropy shows the CT influence on the binding reactions in detail and indicates that there are considerable compensating effects of individual contributions from the binding partners and surrounding water. Charge transfer reduces the total dipole of alpha-CD by 9% on average and alters its dipole direction thereby affecting guest association. Gas-phase zeroth-order symmetry-adapted perturbation theory calculations show host guest CT amounts to approximately 6% of the total binding energy. The continuum solvation model based on the quantum mechanical charge density predicts binding energies comparable with the well depth of PMF profiles in explicit water. The abnormal binding strength of alpha-CD with the similar guests can be rationalized in terms of hydrogen bonding, extent of host guest CT, and dipole arrangement of guest relative to host.

  • 12859. Ylla, Irene
    et al.
    Peter, Hannes
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Romani, Anna M.
    Tranvik, Lars J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Different diversity-functioning relationship in lake and stream bacterial communities2013In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 85, no 1, p. 95-103Article in journal (Refereed)
    Abstract [en]

    Biodiversity patterns have been successfully linked to many ecosystem functions, and microbial communities have been suspected to harbour a large amount of functionally redundant taxa. We manipulated the diversity of stream and lake water column bacterial communities and investigated how the reduction in diversity affects the activities of extracellular enzymes involved in dissolved organic carbon degradation. Dissimilar communities established in cultures inoculated with stream or lake bacteria and utilized different organic matter compounds as indicated by the different extracellular enzyme activities. Stream bacterial communities preferentially used plant-derived organic material such as cellulose and hemicellulose. Communities obtained from the lake, where the longer residence time might permit the organic matter to age, efficiently degraded lignin-like material and also showed higher peptide degradation capacities. The results highlight a stronger negative effect of decreasing diversity on ecosystem multifunctionality for stream than for lake bacterial communities. We found a relatively higher multifunctional redundancy in the lake as compared to the stream-derived cultures and suggest that community assembly might shape diversity-functioning relationships in freshwater bacterial communities.

  • 12860. Yom-Tov, Yoram
    et al.
    Roos, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Environmental Toxicology.
    Mortensen, Peter
    Wiig, Øystein
    Yom-Tov, Shlomith
    Heggberget, Thrine M
    Recent changes in body size of the Eurasian otter Lutra lutra in Sweden.2010In: Ambio, ISSN 0044-7447, E-ISSN 1654-7209, Vol. 39, no 7, p. 496-503Article in journal (Refereed)
    Abstract [en]

    We studied geographical and temporal body size trends among 169 adult museum specimens of the Eurasian otter (Lutra lutra) collected in Sweden between 1962 and 2008, whose sex, year of collection, and locality were known. Skull size and body mass increased significantly in relation to the year of collection, and skull size (but not body mass) was significantly and negatively related to latitude, contrasting Bergmann's rule and the trend found for Norwegian otters. Latitudinal differences in body size between the two countries may be due to differences in food availability. The temporal increase in body size among Swedish otters resembled that observed for Norway otters, though Swedish otters are smaller with respect to their Norwegian counterparts. Latitude and year represent a combination of environmental factors, including ambient temperature in the year of collection as well as the number of days of ice coverage. We replaced the above factors with mean annual temperature or the number of days of ice coverage, and found that each of these factors explains a similar proportion of the variation in body size as did latitude and year. We hypothesize that this temporal increase in body size is related to a combination of factors, including reduced energy expenditure resulting from increasing ambient temperature, and increased food availability from longer ice-free periods.

  • 12861. Yoon, Chun Hong
    et al.
    Schwander, Peter
    Abergel, Chantal
    Andersson, Inger
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Aquila, Andrew
    Bajt, Sasa
    Barthelmess, Miriam
    Barty, Anton
    Bogan, Michael J.
    Bostedt, Christoph
    Bozek, John
    Chapman, Henry N.
    Claverie, Jean-Michel
    Coppola, Nicola
    DePonte, Daniel P.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Epp, Sascha W.
    Erk, Benjamin
    Fleckenstein, Holger
    Foucar, Lutz
    Graafsma, Heinz
    Gumprecht, Lars
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hampton, Christina Y.
    Hartmann, Andreas
    Hartmann, Elisabeth
    Hartmann, Robert
    Hauser, Gunter
    Hirsemann, Helmut
    Holl, Peter
    Kassemeyer, Stephan
    Kimmel, Nils
    Kiskinova, Maya
    Liang, Mengning
    Loh, Ne-Te Duane
    Lomb, Lukas
    Maia, Filipe R. N. C.
    Martin, Andrew V.
    Nass, Karol
    Pedersoli, Emanuele
    Reich, Christian
    Rolles, Daniel
    Rudek, Benedikt
    Rudenko, Artem
    Schlichting, Ilme
    Schulz, Joachim
    Seibert, Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seltzer, Virginie
    Shoeman, Robert L.
    Sierra, Raymond G.
    Soltau, Heike
    Starodub, Dmitri
    Steinbrener, Jan
    Stier, Gunter
    Strueder, Lothar
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ullrich, Joachim
    Weidenspointner, Georg
    White, Thomas A.
    Wunderer, Cornelia
    Ourmazd, Abbas
    Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering2011In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 19, no 17, p. 16542-16549Article in journal (Refereed)
    Abstract [en]

    Single-particle experiments using X-ray Free Electron Lasers produce more than 10(5) snapshots per hour, consisting of an admixture of blank shots (no particle intercepted), and exposures of one or more particles. Experimental data sets also often contain unintentional contamination with different species. We present an unsupervised method able to sort experimental snapshots without recourse to templates, specific noise models, or user-directed learning. The results show 90% agreement with manual classification.

  • 12862. Yoon, Chun Hong
    et al.
    Schwander, Peter
    Abergel, Chantal
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Aquila, Andrew
    Bajt, Saša
    Barthelmess, Miriam
    Barty, Anton
    Bogan, Michael J
    Bostedt, Christoph
    Bozek, John
    Chapman, Henry N
    Claverie, Jean-Michel
    Coppola, Nicola
    DePonte, Daniel P
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Epp, Sascha W
    Erk, Benjamin
    Fleckenstein, Holger
    Foucar, Lutz
    Graafsma, Heinz
    Gumprecht, Lars
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Hampton, Christina Y
    Hartmann, Andreas
    Hartmann, Elisabeth
    Hartmann, Robert
    Hauser, Gunter
    Hirsemann, Helmut
    Holl, Peter
    Kassemeyer, Stephan
    Kimmel, Nils
    Kiskinova, Maya
    Liang, Mengning
    Loh, Ne-Te Duane
    Lomb, Lukas
    Maia, Filipe R N C
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Martin, Andrew V
    Nass, Karol
    Pedersoli, Emanuele
    Reich, Christian
    Rolles, Daniel
    Rudek, Benedikt
    Rudenko, Artem
    Schlichting, Ilme
    Schulz, Joachim
    Seibert, Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Seltzer, Virginie
    Shoeman, Robert L
    Sierra, Raymond G
    Soltau, Heike
    Starodub, Dmitri
    Steinbrener, Jan
    Stier, Gunter
    Strüder, Lothar
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Ullrich, Joachim
    Weidenspointner, Georg
    White, Thomas A
    Wunderer, Cornelia
    Ourmazd, Abbas
    Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering.2011In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 19, no 17, p. 15929-15936Article in journal (Refereed)
    Abstract [en]

    Single-particle experiments using X-ray Free Electron Lasers produce more than 10(5) snapshots per hour, consisting of an admixture of blank shots (no particle intercepted), and exposures of one or more particles. Experimental data sets also often contain unintentional contamination with different species. We present an unsupervised method able to sort experimental snapshots without recourse to templates, specific noise models, or user-directed learning. The results show 90% agreement with manual classification.

  • 12863. Yopak, Kara E.
    et al.
    Lisney, Thomas J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal Ecology.
    Darlington, Richard B.
    Collin, Shaun P.
    Montgomery, John C.
    Finlay, Barbara L.
    A conserved pattern of brain scaling from sharks to primates2010In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 107, no 29, p. 12946-12951Article in journal (Refereed)
    Abstract [en]

    Several patterns of brain allometry previously observed in mammals have been found to hold for sharks and related taxa (chondrichthyans) as well. In each clade, the relative size of brain parts, with the notable exception of the olfactory bulbs, is highly predictable from the total brain size. Compared with total brain mass, each part scales with a characteristic slope, which is highest for the telencephalon and cerebellum. In addition, cerebellar foliation reflects both absolute and relative cerebellar size, in a manner analogous to mammalian cortical gyrification. This conserved pattern of brain scaling suggests that the fundamental brain plan that evolved in early vertebrates permits appropriate scaling in response to a range of factors, including phylogeny and ecology, where neural mass may be added and subtracted without compromising basic function.

  • 12864.
    Younesi, Simin
    et al.
    Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran.
    Mehregan, Iraj
    Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran.
    Assadi, Mostafa
    AREEO, Res Inst Forests & Rangelands, POB 13185-116, Tehran, Iran.
    Nejadsattari, Taher
    Islamic Azad Univ, Dept Biol, Sci & Res Branch, Tehran, Iran.
    Lidén, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Dionysia robusta (Primulaceae), a new species from W Iran2016In: Willdenowia, ISSN 0511-9618, E-ISSN 1868-6397, Vol. 46, no 1, p. 105-112Article in journal (Refereed)
    Abstract [en]

    A new species from the W part of the Iranian Zagros Mountains in Ilam province, Dionysia robusta (Primulaceae), is described, illustrated and compared with similar and related species. It differs from these relatives in leaf shape, length and density of glandular hairs, and shape of the calyx. The DNA sequence of the nuclear ribosomal ITS region of D. robusta is most similar to that of D. gaubae.

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  • 12865. Yu, Bao-Zhu
    et al.
    Apitz-Castro, Rafael J.
    Jain, Mahendra K.
    Berg, Otto G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Role of 57-72 loop in the allosteric action of bile salts on pancreatic IB phospholipase A(2): Regulation of fat and cholesterol homeostasis2007In: Biochimica et Biophysica Acta - Biomembranes, ISSN 0005-2736, E-ISSN 1879-2642, Vol. 1768, no 10, p. 2478-2490Article in journal (Refereed)
    Abstract [en]

    Mono- and biphasic kinetic effects of bile salts on the pancreatic IB phospholipase A2 (PLA2) catalyzed interfacial hydrolysis are characterized. This novel phenomenon is modeled as allosteric action of bile salts with PLA2 at the interface. The results and controls also show that these kinetic effects are not due to surface dilution or solubilization or disruption of the bilayer interface where in the mixed-micelles substrate replenishment becomes the rate-limiting step. The PLA2-catalyzed rate of hydrolysis of zwitterionic dimyristoylphosphatidylcholine (DMPC) vesicles depends on the concentration and structure of the bile salt. The sigmoidal rate increase with cholate saturates at 0.06 mole fraction and changes little at the higher mole fractions. Also, with the rate-lowering bile salts (B), such as taurochenodeoxycholate (TCDOC), the initial sigmoidal rate increase at lower mole fraction is followed by nearly complete reversal to the rate at the pre-activation level at higher mole fractions. The rate-lowering effect of TCDOC is not observed with the (62–66)-loop deleted ΔPLA2, or with the Naja venom PLA2 that is evolutionarily devoid of the loop. The rate increase is modeled with the assumption that the binding of PLA2 to DMPC interface is cooperatively promoted by bile salt followed by allosteric kcat-activation of the bound enzyme by the anionic interface. The rate-lowering effect of bile salts is attributed to the formation of a specific catalytically inert EB complex in the interface, which is noticeably different than the 1:1 EB complex in the aqueous phase. The cholate-activated rate of hydrolysis is lowered by hypolidemic ezetimibe and guggul extract which are not interfacial competitive inhibitors of PLA2. We propose that the biphasic modulation of the pancreatic PLA2 activity by bile salts regulates gastrointestinal fat metabolism and cholesterol homeostasis.

  • 12866. Yu, Bao-Zhu
    et al.
    Bai, Shi
    Berg, Otto G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Jain, Mahendra K.
    Allosteric Effect of Amphiphile Binding to Phospholipase A22009In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 48, no 14, p. 3219-3229Article in journal (Refereed)
    Abstract [en]

    In the preceding paper, we showed that the formation of the second premicellar complex of pig pancreatic IB phospholipase A2 (PLA2) can be considered a proxy for interface-activated substrate binding. Here we show that this conclusion is supported by results from premicellar;E-i(#) (i = 1, 2, or 3) complexes with a wide range of mutants of PLA2. Results also show a structural bass-for the correlated functional changes during the formation of E-2(#), and this is interpreted as an allosteric T (inactive) to R (active) transition. For example, the dissociation constant K-2(#) for decylsulfate bound to E-2(#) is lower at lower pH, at higher calcium concentrations, or with an inhibitor bound to the active site. Also, the lower limits of the K-2(#) values are comparable under these conditions. The pH-dependent increase in K-2(#) with a pK(a) of 6.5 is attributed to E71 which participates in the binding of the second calcium which in turn influences the enzyme binding to phosphatidylcholine interface. Most mutants exhibited kinetic and spectroscopic behavior that is comparable to that of native PLA2 and Delta PLA2 with a deleted 62-66 loop. However, the Delta Y52L substitution mutant cannot undergo the calcium-, pH-, or interface-dependent changes. We suggest that the Y52L substitution impairs the R to T transition and also hinders the approach of the Michaelis complex to the transition state. This allosteric change may be mediated by the structural motifs that connect the D48-D99 catalytic diad, the substrate-binding slot, and the residues of the i-face. Our interpretation is that the 57-72 loop and the H48DNCY52 segment of PLA2 are involved in transmitting the effect of the cooperative amphiphile binding to the i-face as a structural change in the active site.

  • 12867. Yu, Bao-Zhu
    et al.
    Kaimal, Rajani
    Bai, Shi
    El Sayed, Khalid A.
    Tatulian, Suren A.
    Apitz, Rafael J.
    Jain, Mahendra K.
    Deng, Ruitang
    Berg, Otto G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Effect of Guggulsterone and Cembranoids of Commiphora mukul on Pancreatic Phospholipase A(2): Role in Hypocholesterolemia2009In: Journal of natural products (Print), ISSN 0163-3864, E-ISSN 1520-6025, Vol. 72, no 1, p. 24-28Article in journal (Refereed)
    Abstract [en]

    Guggulsterone (7) and cembranoids (8-12) from Commiphora mukul stem bark resin guggul were shown to be specific modulators of two independent sites that are also modulated by bile salts (1-6) to control cholesterol absorption and catabolism. Guggulsterone (7) antagonized the chenodeoxycholic acid (3)-activated nuclear farnesoid X receptor (FXR), which regulates cholesterol metabolism in the liver. The cembranoids did not show a noticeable effect on FXR, but lowered the cholate (I)-activated rate of human pancreatic 113 phospholipase A2 (hPLA2), which controls gastrointestinal absorption of fat and cholesterol. Analysis of the data using a kinetic model has suggested an allosteric mechanism for the rate increase of hPLA2 by cholate and also for the rate-lowering effect by certain bile salts or cembranoids on the cholate-activated hPLA2 hydrolysis of phosphatidylcholine vesicles. The allosteric inhibition of PLA2 by certain bile salts and cembranoids showed some structural specificity. Biophysical studies also showed specific interaction of the bile salts with the interface-bound cholate-activated PLA2. Since cholesterol homeostasis in mammals is regulated by FXR in the liver for metabolism and by PLA2 in the intestine for absorption, modulation of PLA2 and FXR by bile acids and selected guggul components suggests novel possibilities for hypolipidemic and hypocholesterolemic therapies.

  • 12868. Yu, Bao-Zhu
    et al.
    Polenova, Tatyana
    Jain, Mahendra Kumar
    Berg, Otto
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Premicellar complexes of sphingomyelinase mediate enzyme exchange for the stationary phase turnover2005In: Biochimica et Biophysica Acta - Biomembranes, ISSN 0005-2736, E-ISSN 1879-2642, Vol. 1712, no 2, p. 137-151Article in journal (Refereed)
    Abstract [en]

    During the steady state reaction progress in the scooting mode with highly processive turnover, Bacillus cereus sphingomyelinase (SMase) remains tightly bound to sphingomyelin (SM) vesicles (Yu et al., Biochim. Biophys. Acta 1583, 121–131, 2002). In this paper, we analyze the kinetics of SMase-catalyzed hydrolysis of SM dispersed in diheptanoylphosphatidyl-choline (DC7PC) micelles. Results show that the resulting decrease in the turnover processivity induces the stationary phase in the reaction progress. The exchange of the bound enzyme (E*) between the vesicle during such reaction progress is mediated via the premicellar complexes (Ei#) of SMase with DC7PC. Biophysical studies indicate that in Ei# monodisperse DC7PC is bound to the interface binding surface (i-face) of SMase that is also involved in its binding to micelles or vesicles. In the presence of magnesium, required for the catalytic turnover, three different complexes of SMase with monodisperse DC7PC (Ei# with i = 1, 2, 3) are sequentially formed with Hill coefficients of 3, 4 and 8, respectively. As a result, during the stationary phase reaction progress, the initial rate is linear for an extended period and all the substrate in the reaction mixture is hydrolyzed at the end of the reaction progress. At low mole fraction (X) of total added SM, exchange is rapid and the processive turnover is limited by the steps of the interfacial turnover cycle without becoming microscopically limited by local substrate depletion or enzyme exchange. At high X, less DC7PC will be monodisperse, Ei# does not form and the turnover becomes limited by slow enzyme exchange. Transferred NOESY enhancement results show that monomeric DC7PC in solution is in a rapid exchange with that bound to Ei# at a rate comparable to that in micelles. Significance of the exchange and equilibrium properties of the Ei# complexes for the interpretation of the stationary phase reaction progress is discussed.

  • 12869.
    Yu, BZ
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology. MOLECULAR EVOLUTION.
    Poi, MJ
    Ramagopal, UA
    Jain, R
    Ramakumar, S
    Berg, OG
    Tsai, MD
    Sekar, K
    Jain, MK
    Structural basis of the anionic interface preference and kcat*-activation of pancreatic phospholipase A22000In: Biochemistry, Vol. 39, p. 12312-12323Article in journal (Refereed)
  • 12870.
    Yu, N
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology.
    Fu, YX
    Sambuughin, N
    Ramsay, M
    Jenkins, T
    Leskinen, E
    Patthy, L
    Jorde, LB
    Kuromori, T
    Li, WH
    Global patterns of human DNA sequence variation in a 10-kb region on chromosome 12001In: MOLECULAR BIOLOGY AND EVOLUTION, Vol. 18, no 2, p. 214-222Article in journal (Refereed)
  • 12871.
    Yu, Sheng-Xiang
    et al.
    State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China.
    Janssens, Steven B.
    Botanic Garden Meise, Nieuwelaan 38, Meise, BE-1860, Belgium.
    Zhu, Xiang-Yun
    State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China.
    Lidén, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Gao, Tian-Gang
    State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China.
    Wang, Wei
    State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China.
    Phylogeny of Impatiens (Balsaminaceae): integrating molecular and morphological evidence into a new classification2016In: Cladistics, ISSN 0748-3007, E-ISSN 1096-0031, Vol. 32, no 2, p. 179-197Article in journal (Refereed)
    Abstract [en]

    Impatiens L. is one of the largest angiosperm genera, containing over 1000 species, and is notorious for its taxonomic difficulty. Here, we present, to our knowledge, the most comprehensive phylogenetic analysis of the genus to date based on a total evidence approach. Forty-six morphological characters, mainly obtained from our own investigations, are combined with sequence data from three genetic regions, including nuclear ribosomal ITS and plastid atpB-rbcL and trnL-F. We include 150 Impatiens species representing all clades recovered by previous phylogenetic analyses as well as three outgroups. Maximum-parsimony and Bayesian inference methods were used to infer phylogenetic relationships. Our analyses concur with previous studies, but in most cases provide stronger support. Impatiens splits into two major clades. For the first time, we report that species with three-colpate pollen and four carpels form a monophyletic group (clade I). Within clade II, seven well-supported subclades are recognized. Within this phylogenetic framework, character evolution is reconstructed, and diagnostic morphological characters for different clades and subclades are identified and discussed. Based on both morphological and molecular evidence, a new classification outline is presented, in which Impatiens is divided into two subgenera, subgen. Clavicarpa and subgen. Impatiens; the latter is further subdivided into seven sections.

  • 12872. Yu, Sheng-Xiang
    et al.
    Lidén, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Han, Bao-Cai
    Zhang, Xiao-Xia
    Impatiens lixianensis, a new species of Balsaminaceae from Sichuan, China2013In: Phytotaxa, ISSN 1179-3155, E-ISSN 1179-3163, Vol. 115, no 1, p. 25-30Article in journal (Refereed)
    Abstract [en]

    Impatiens lixianensis, a new species of Balsaminaceae from Zhegushan, Lixian, Sichuan province, China, is described and illustrated. This species is closely related to I. apsotis in having small white to greenish-white flowers, 2 lateral sepals, and 1-2-flowered short racemes, but differs by its non-crested dorsal petals, a short 2-lobed swollen spur, long-clawed lower petals, and small scale-shaped upper petals. Regarding palynological characters, the lumina of the reticulum in I. lixianensis are smaller and much more granulate than those in I. apsotis.

  • 12873.
    Yu, Wenqiang
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Ginjala, Vasudeva
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Pant, Vinod
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Chernukhin, Igor
    Whitehead, Joanne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Docquier, France
    Farrar, Dawn
    Tavoosidana, Gholamreza
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Mukhopadhyay, Rituparna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Kanduri, Chandrasekhar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Oshimura, Mitsuo
    Feinberg, Andrew P
    Lobanenkov, Victor
    Klenova, Elena
    Rolf Ohlsson, Rolf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Poly(ADP-ribosyl)ation regulates CTCF-dependent chromatin insulation2004In: Nature Genetics, ISSN 1061-4036, E-ISSN 1546-1718, Vol. 36, no 10, p. 1105-1110Article in journal (Refereed)
    Abstract [en]

    Chromatin insulators demarcate expression domains by blocking the cis effects of enhancers or silencers in a position-dependent manner1, 2. We show that the chromatin insulator protein CTCF carries a post-translational modification: poly(ADP-ribosyl)ation. Chromatin immunoprecipitation analysis showed that a poly(ADP-ribosyl)ation mark, which exclusively segregates with the maternal allele of the insulator domain in the H19 imprinting control region, requires the bases that are essential for interaction with CTCF3. Chromatin immunoprecipitation−on−chip analysis documented that the link between CTCF and poly(ADP-ribosyl)ation extended to more than 140 mouse CTCF target sites. An insulator trap assay showed that the insulator function of most of these CTCF target sites is sensitive to 3-aminobenzamide, an inhibitor of poly(ADP-ribose) polymerase activity. We suggest that poly(ADP-ribosyl)ation imparts chromatin insulator properties to CTCF at both imprinted and nonimprinted loci, which has implications for the regulation of expression domains and their demise in pathological lesions.

  • 12874.
    Yu, Yang
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Molecular Mechanisms Underlying Abnormal Placentation in the Mouse2007Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Placental development can be disturbed by various factors, such as mutation of specific genes or maternal diabetes. Our previous work on interspecies hybrid placental dysplasia (IHPD) and two additional models of placental hyperplasia, cloned mice and Esx1 mutants, showed that many genes are deregulated in placental dysplasia. Two of these candidate placentation genes, Cpe and Lhx3, were further studied. We performed in situ hybridization to determine their spatio-temporal expression in the placentas and placental phenotypes were analyzed in mutant mice. Our results showed that the placental phenotype in Cpe mutant mice mimics some IHPD phenotypes. Deregulated expression of Cpe and Cpd, a functionally equivalent gene, prior to the manifestation of the IHPD phenotype, indicated that Cpe and Cpd are potentially causative genes in IHPD. Lhx3 mutants lacked any placental phenotype. Deletion of Lhx3 and Lhx4 together caused an inconsistent placental phenotype which did not affect placental lipid transport function or expression of Lhx3/Lhx4 target genes. Down regulation of Lhx3/Lhx4 did not rescue the placental phenotype of AT24 mice and hence could be excluded as causative genes in IHPD. Analysis of placental development in diabetic mice showed that severe maternal diabetes resulted in fetal intrauterine growth restriction (IUGR) without any change in placental weight and lipid transport function. The diabetic placentas however exhibited abnormal morphology. Gene expression profiling identified some genes that might contribute to diabetic pathology. In another study, it was found that the heterochromatin protein CBX1 is required for normal placentation, as deletion of the gene caused consistent spongiotrophoblast and labyrinthine phenotypes. Gene expression profiling and spatio-temporal expression analysis showed that several genes with known function in placental development were deregulated in the Cbx1 null placenta.

    List of papers
    1. Carboxypeptidase E in the mouse placenta
    Open this publication in new window or tab >>Carboxypeptidase E in the mouse placenta
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    2006 (English)In: Differentiation, ISSN 0301-4681, E-ISSN 1432-0436, Vol. 74, no 9-10, p. 648-660Article in journal (Refereed) Published
    Abstract [en]

    Carboxypeptidase E (CPE) has important functions in processing of endocrine pro-peptides, such as pro-insulin, pro-opiomelanocortin, or pro-gonadotropin-releasing hormone, as evidenced by the hyperpro-insulinemia, obesity, and sterility of Cpe mutant mice. Down-regulation of Cpe in enlarged placentas of interspecific hybrid (interspecies hybrid placental dysplasia (IHPD)) and cloned mice suggested that reduced CPE enzyme and receptor activity could underlie abnormal placental phenotypes. In this study, we have explored the role of Cpe in murine placentation by determining its expression at various stages of gestation, and by phenotypic analysis of Cpe mutant placentas. Our results show that Cpe and Carboxypeptidase D (Cpd), another carboxypeptidase with a very similar function, are strictly co-localized in the mouse placenta from late mid-gestation to term. We also show that absence of CPE causes a sporadic but striking placental phenotype characterized by an increase in giant and glycogen cell numbers and giant cell hypertrophy. Microarray-based transcriptional pro. ling of Cpe mutant placentas identified only a very small number of genes with altered expression, including Dtprp, which belongs to the prolactin gene family. Concordant deregulation of Cpe and Cpd in abnormal placentas of interspecies hybrids before the onset of IHPD phenotype and recapitulation of some phenotypes of IHPD hyperplastic placentas in Cpe mutant placentas suggests that these two genes are causally involved in IHPD and may function as speciation genes in the genus Mus.

    Keywords
    interspecies hybrid placental dysplasia, Cpe, Cpd, fat mutation, trophoblast giant cells
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-94491 (URN)10.1111/j.1432-0436.2006.00093.x (DOI)000242657200016 ()17177860 (PubMedID)
    Available from: 2006-05-08 Created: 2006-05-08 Last updated: 2017-12-14Bibliographically approved
    2. Expression and function of the LIM homeobox containing genes Lhx3 and Lhx4 in the mouse placenta
    Open this publication in new window or tab >>Expression and function of the LIM homeobox containing genes Lhx3 and Lhx4 in the mouse placenta
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    2008 (English)In: Developmental Dynamics, ISSN 1058-8388, E-ISSN 1097-0177, Vol. 237, no 5, p. 1517-1525Article in journal (Refereed) Published
    Abstract [en]

    The LIM homeobox containing genes of the LIM-3 group, Lhx3 and Lhx4, are critical for normal development. Both genes are involved in the formation of the pituitary and the motoneuron system and loss of either gene causes perinatal lethality. Previous studies had shown that Lhx3 is overexpressed in hyperplastic placentas of mouse interspecies hybrids. To determine the role of LHX3 in the mouse placenta, we performed expression and function analyses. Our results show that Lhx3 exhibits specific spatial and temporal expression in the mouse placenta. However, deletion of Lhx3 does not produce a placental phenotype. To test whether this is due to functional substitution by Lhx4, we performed a phenotype analysis of Lhx3-/-; Lhx4-/- double-mutant placentas. A subset of Lhx3-/-; Lhx4-/- placentas exhibited abnormal structure of the labyrinth. However, absence of both LIM-3 genes did not interfere with placental transport nor consistently with expression of target genes such as Gnrhr. Thus, LHX3 and LHX4 appear to be dispensable for placental development and function.

    Keywords
    LIM-homeobox gene, Lhx3, Lhx4, mouse placenta
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-96495 (URN)10.1002/dvdy.21546 (DOI)000255842900027 ()
    Available from: 2007-11-21 Created: 2007-11-21 Last updated: 2017-12-14Bibliographically approved
    3. Influence of murine maternal diabetes on placental morphology, gene expression, and function
    Open this publication in new window or tab >>Influence of murine maternal diabetes on placental morphology, gene expression, and function
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    2008 (English)In: Archives of Physiology and Biochemistry, ISSN 1381-3455, E-ISSN 1744-4160, Vol. 114, no 2, p. 99-110Article in journal (Refereed) Published
    National Category
    Developmental Biology
    Identifiers
    urn:nbn:se:uu:diva-96496 (URN)10.1080/13813450802033776 (DOI)
    Available from: 2007-11-21 Created: 2007-11-21 Last updated: 2017-12-14Bibliographically approved
    4. Loss of the heterochromatin protein-1β encoding gene Cbx1 leads to defective placental development
    Open this publication in new window or tab >>Loss of the heterochromatin protein-1β encoding gene Cbx1 leads to defective placental development
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    (English)Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-96497 (URN)
    Available from: 2007-11-21 Created: 2007-11-21 Last updated: 2010-02-03Bibliographically approved
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  • 12875.
    Yu, Yang
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Shi, Wei
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Bullwinkel, Jörn
    Billur, Mustafa
    Geyer, Rudolf
    Singh, Prim B.
    Fundele, Reinald H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Loss of the heterochromatin protein-1β encoding gene Cbx1 leads to defective placental developmentManuscript (Other academic)
  • 12876.
    Yu, Yang
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Singh, Umashankar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Shi, Wei
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Konno, Toshihiro
    Soares, Michael J.
    Geyer, Rudolf
    Fundele, Reinald H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Influence of murine maternal diabetes on placental morphology, gene expression, and function2008In: Archives of Physiology and Biochemistry, ISSN 1381-3455, E-ISSN 1744-4160, Vol. 114, no 2, p. 99-110Article in journal (Refereed)
  • 12877.
    Yu, Young-Sang
    et al.
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA.;Univ Illinois, Dept Chem, Chicago, IL 60607 USA..
    Farmand, Maryam
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA..
    Kim, Chunjoong
    Univ Illinois, Dept Chem, Chicago, IL 60607 USA.;Chungnam Natl Univ, Dept Mat Sci & Engn, Taejon 305764, Chungnam, South Korea..
    Liu, Yijin
    SLAC Natl Accelerator Lab, Stanford Synchrotron Radiat Lightsource, Menlo Pk, CA 94025 USA..
    Grey, Clare P.
    Univ Cambridge, Dept Chem, Lensfield Rd, Cambridge CB2 1EW, England.;SUNY Stony Brook, Dept Chem, Stony Brook, NY 11794 USA..
    Strobridge, Fiona C.
    Univ Cambridge, Dept Chem, Lensfield Rd, Cambridge CB2 1EW, England..
    Tyliszczak, Tolek
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA..
    Celestre, Rich
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA..
    Denes, Peter
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA..
    Joseph, John
    Lawrence Berkeley Natl Lab, Div Engn, Berkeley, CA 94720 USA..
    Krishnan, Harinarayan
    Lawrence Berkeley Natl Lab, Computat Res Div, Berkeley, CA 94720 USA..
    Maia, Filipe R.N.C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Kilcoyne, A. L. David
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA..
    Marchesini, Stefano
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA..
    Leite, Talita Perciano Costa
    Lawrence Berkeley Natl Lab, Computat Res Div, Berkeley, CA 94720 USA..
    Warwick, Tony
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA..
    Padmore, Howard
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA..
    Cabana, Jordi
    Univ Illinois, Dept Chem, Chicago, IL 60607 USA..
    Shapiro, David A.
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA..
    Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 921Article in journal (Refereed)
    Abstract [en]

    Battery function is determined by the efficiency and reversibility of the electrochemical phase transformations at solid electrodes. The microscopic tools available to study the chemical states of matter with the required spatial resolution and chemical specificity are intrinsically limited when studying complex architectures by their reliance on two-dimensional projections of thick material. Here, we report the development of soft X-ray ptychographic tomography, which resolves chemical states in three dimensions at 11 nm spatial resolution. We study an ensemble of nano-plates of lithium iron phosphate extracted from a battery electrode at 50% state of charge. Using a set of nanoscale tomograms, we quantify the electrochemical state and resolve phase boundaries throughout the volume of individual nanoparticles. These observations reveal multiple reaction points, intra-particle heterogeneity, and size effects that highlight the importance of multi-dimensional analytical tools in providing novel insight to the design of the next generation of high-performance devices.

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  • 12878. Yusuf, Dilmurat
    et al.
    Davis, Andrew M
    Kleywegt, Gerard J
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structural Molecular Biology.
    Schmitt, Stefan
    An alternative method for the evaluation of docking performance: RSR vs RMSD.2008In: Journal of chemical information and modeling, ISSN 1549-9596, Vol. 48, no 7, p. 1411-1422Article in journal (Refereed)
    Abstract [en]

    A new assessment criterion for docking poses is proposed in which experimental electron density is taken into account when evaluating the ability of docking programs to reproduce experimentally observed binding modes. Three docking programs (Gold, Glide, and Fred) were used to generate poses for a set of 88 protein-ligand complexes for which the crystal structure is known. The new criterion is based on the real space R-factor (RSR), which measures how well a group of atoms-in our case the ligand-fits the experimental electron density by comparing that density to the expected density, calculated from the model (i.e., the predicted ligand pose). The RSR-based measure is compared to the traditional criterion, the root-mean-square distance (RMSD) between the docking pose and the binding configuration in the crystallographic model. The results highlight several shortcomings of the RMSD criterion that do not affect the RSR-based measure. Examples illustrate that the RSR-derived approach allows a more meaningful a posteriori assessment of docking methods and results. Practical implications for docking evaluations and for methodological development work in this field are discussed.

  • 12879.
    Yutin, Natalya
    et al.
    NIH, Natl Ctr Biotechnol Informat, Natl Lib Med, Bethesda, MD 20894 USA..
    Bäckstrom, Disa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ettema, Thijs J G
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Krupovic, Mart
    Inst Pasteur, Dept Microbiol, Unite Biol Mol Gene Chez Extremophiles, Paris, France..
    Koonin, Eugene V.
    NIH, Natl Ctr Biotechnol Informat, Natl Lib Med, Bethesda, MD 20894 USA..
    Vast diversity of prokaryotic virus genomes encoding double jelly-roll major capsid proteins uncovered by genomic and metagenomic sequence analysis2018In: Virology Journal, ISSN 1743-422X, E-ISSN 1743-422X, Vol. 15, article id 67Article in journal (Refereed)
    Abstract [en]

    Background: Analysis of metagenomic sequences has become the principal approach for the study of the diversity of viruses. Many recent, extensive metagenomic studies on several classes of viruses have dramatically expanded the visible part of the virosphere, showing that previously undetected viruses, or those that have been considered rare, actually are important components of the global virome.

    Results: We investigated the provenance of viruses related to tail-less bacteriophages of the family Tectiviridae by searching genomic and metagenomics sequence databases for distant homologs of the tectivirus-like Double JellyRoll major capsid proteins (DJR MCP). These searches resulted in the identification of numerous genomes of viruslike elements that are similar in size to tectiviruses (10-15 kilobases) and have diverse gene compositions. By comparison of the gene repertoires, the DJR MCP-encoding genomes were classified into 6 distinct groups that can be predicted to differ in reproduction strategies and host ranges. Only the DJR MCP gene that is present by design is shared by all these genomes, and most also encode a predicted DNA-packaging ATPase; the rest of the genes are present only in subgroups of this unexpectedly diverse collection of DJR MCP-encoding genomes. Only a minority encode a DNA polymerase which is a hallmark of the family Tectiviridae and the putative family "Autolykiviridae". Notably, one of the identified putative DJR MCP viruses encodes a homolog of Cas1 endonuclease, the integrase involved in CRISPR-Cas adaptation and integration of transposon-like elements called casposons. This is the first detected occurrence of Cas1 in a virus. Many of the identified elements are individual contigs flanked by inverted or direct repeats and appear to represent complete, extrachromosomal viral genomes, whereas others are flanked by bacterial genes and thus can be considered as proviruses. These contigs come from metagenomes of widely different environments, some dominated by archaea and others by bacteria, suggesting that collectively, the DJR MCP-encoding elements have a broad host range among prokaryotes.

    Conclusions: The findings reported here greatly expand the known host range of (putative) viruses of bacteria and archaea that encode a DJR MCP. They also demonstrate the extreme diversity of genome architectures in these viruses that encode no universal proteins other than the capsid protein that was used as the marker for their identification. From a supposedly minor group of bacterial and archaeal viruses, these viruses are emerging as a substantial component of the prokaryotic virome.

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  • 12880. Yvon-Durocher, Gabriel
    et al.
    Allen, Andrew P.
    Bastviken, David
    Conrad, Ralf
    Gudasz, Cristian
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    St-Pierre, Annick
    Thanh-Duc, Nguyen
    del Giorgio, Paul A.
    Methane fluxes show consistent temperature dependence across microbial to ecosystem scales2014In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 507, no 7493, p. 488-491Article in journal (Refereed)
    Abstract [en]

    Methane (CH4) is an important greenhouse gas because it has 25 times the global warming potential of carbon dioxide (CO2) by mass over a century(1). Recent calculations suggest that atmospheric CH4 emissions have been responsible for approximately 20% of Earth's warming since pre-industrial times(2). Understanding how CH4 emissions from ecosystems will respond to expected increases in global temperature is therefore fundamental to predicting whether the carbon cycle will mitigate or accelerate climate change. Methanogenesis is the terminal step in the remineralization of organic matter and is carried out by strictly anaerobic Archaea(3). Like most other forms of metabolism, methanogenesis is temperature-dependent(4,5). However, it is not yet known how this physiological response combines with other biotic processes (for example, methanotrophy(6), substrate supply(3,7), microbial community composition(8)) and abiotic processes (for example, water-table depth(9,10)) to determine the temperature dependence of ecosystem-level CH4 emissions. It is also not known whether CH4 emissions at the ecosystem level have a fundamentally different temperature dependence than other key fluxes in the carbon cycle, such as photosynthesis and respiration. Here we use meta-analyses to show that seasonal variations in CH4 emissions from a wide range of ecosystems exhibit an average temperature dependence similar to that of CH4 production derived from pure cultures of methanogens and anaerobic microbial communities. This average temperature dependence (0.96 electron volts (eV)), which corresponds to a 57-fold increase between 0 and 30 degrees C, is considerably higher than previously observed for respiration (approximately 0.65 eV)(11) and photosynthesis (approximately 0.3 eV)(12). As a result, we show that both the emission of CH4 and the ratio of CH4 to CO2 emissions increase markedly with seasonal increases in temperature. Our findings suggest that global warming may have a large impact on the relative contributions of CO2 and CH4 to total greenhouse gas emissions from aquatic ecosystems, terrestrial wetlands and rice paddies.

  • 12881.
    Zaferani, Bahareh
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Evolution of Male Mating Success During Local Adaptation in Seed Beetles2011Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
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    Bahar's master thesis
  • 12882. Zagalska-Neubauer, Magdalena
    et al.
    Babik, Wieslaw
    Stuglik, Michal
    Gustafsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Animal Ecology.
    Cichon, Mariusz
    Radwan, Jacek
    454 sequencing reveals extreme complexity of the class II Major Histocompatibility Complex in the collared flycatcher2010In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 10, no 1, p. 395-Article in journal (Refereed)
    Abstract [en]

    Background: Because of their functional significance, the Major Histocompatibility Complex (MHC) class I and II genes have been the subject of continuous interest in the fields of ecology, evolution and conservation. In some vertebrate groups MHC consists of multiple loci with similar alleles; therefore, the multiple loci must be genotyped simultaneously. In such complex systems, understanding of the evolutionary patterns and their causes has been limited due to challenges posed by genotyping. Results: Here we used 454 amplicon sequencing to characterize MHC class IIB exon 2 variation in the collared flycatcher, an important organism in evolutionary and immuno-ecological studies. On the basis of over 152,000 sequencing reads we identified 194 putative alleles in 237 individuals. We found an extreme complexity of the MHC class IIB in the collared flycatchers, with our estimates pointing to the presence of at least nine expressed loci and a large, though difficult to estimate precisely, number of pseudogene loci. Many similar alleles occurred in the pseudogenes indicating either a series of recent duplications or extensive concerted evolution. The expressed alleles showed unambiguous signals of historical selection and the occurrence of apparent interlocus exchange of alleles. Placing the collared flycatcher's MHC sequences in the context of passerine diversity revealed transspecific MHC class II evolution within the Muscicapidae family. Conclusions: 454 amplicon sequencing is an effective tool for advancing our understanding of the MHC class II structure and evolutionary patterns in Passeriformes. We found a highly dynamic pattern of evolution of MHC class IIB genes with strong signals of selection and pronounced sequence divergence in expressed genes, in contrast to the apparent sequence homogenization in pseudogenes. We show that next generation sequencing offers a universal, affordable method for the characterization and, in perspective, genotyping of MHC systems of virtually any complexity.

  • 12883.
    Zajitschek, Felix
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Monash Univ, Sch Biol Sci, Victoria, Australia.
    Georgolopoulos, Grigorios
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Vourlou, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Ericsson, Maja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Zajitschek, Susanne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Monash Univ, Sch Biol Sci, Victoria, Australia;CSIC, EBD, Donana Biol Stn, Seville, Spain.
    Friberg, Urban
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Linkoping Univ, Genom & Physiol Grp, AVIAN Behav, IFM Biol, Linkoping, Sweden.
    Maklakov, Alexei A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Univ East Anglia, Norwich Res Pk, Sch Biol Sci, Norwich, Norfolk, England.
    Evolution Under Dietary Restriction Decouples Survival From Fecundity in Drosophila melanogaster Females2019In: The journals of gerontology. Series A, Biological sciences and medical sciences, ISSN 1079-5006, E-ISSN 1758-535X, Vol. 74, no 10, p. 1542-1548Article in journal (Refereed)
    Abstract [en]

    One of the key tenets of life-history theory is that reproduction and survival are linked and that they trade-off with each other. When dietary resources are limited, reduced reproduction with a concomitant increase in survival is commonly observed. It is often hypothesized that this dietary restriction effect results from strategically reduced investment in reproduction in favor of somatic maintenance to survive starvation periods until resources become plentiful again. We used experimental evolution to test this "waiting-for-the-good-times" hypothesis, which predicts that selection under sustained dietary restriction will favor increased investment in reproduction at the cost of survival because "good-times" never come. We assayed fecundity and survival of female Drosophila melanogaster fruit flies that had evolved for 50 generations on three different diets varying in protein content-low (classic dietary restriction diet), standard, and high-in a full-factorial design. High-diet females evolved overall increased fecundity but showed reduced survival on low and standard diets. Low-diet females evolved reduced survival on low diet without corresponding increase in reproduction. In general, there was little correspondence between the evolution of survival and fecundity across all dietary regimes. Our results contradict the hypothesis that resource reallocation between fecundity and somatic maintenance underpins life span extension under dietary restriction.

  • 12884.
    Zajitschek, Felix
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Jin, Tuo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Colchero, Fernando
    Maklakov, Alexei A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Aging Differently: Diet- and Sex-Dependent Late-Life Mortality Patterns in Drosophila melanogaster2014In: The journals of gerontology. Series A, Biological sciences and medical sciences, ISSN 1079-5006, E-ISSN 1758-535X, Vol. 69, no 6, p. 666-674Article in journal (Refereed)
    Abstract [en]

    Diet effects on age-dependent mortality patterns are well documented in a large number of animal species, but studies that look at the effects of nutrient availability on late-life mortality plateaus are lacking. Here, we focus on the effect of dietary protein content (low, intermediate, and high) on mortality trajectories in late life in the fruit fly Drosophila melanogaster. According to the two theories that are mainly implicated in explaining the deceleration of mortality rate in late life (the heterogeneity/frailty theory and the Hamiltonian theory), we predict, in general, the occurrence of late-life mortality deceleration under most circumstances, independent of sex and dietary regime. However, the heterogeneity theory of late life is more flexible in allowing no mortality deceleration to occur under certain circumstances compared with the Hamiltonian theory. We applied a novel statistical approach based on Bayesian inference of age-specific mortality rates and found a deceleration of late-life mortality rates on all diets in males but only on the intermediate (standard) diet in females. The difference in mortality rate deceleration between males and females on extreme diets suggests that the existence of mortality plateaus in late life is sex and diet dependent and, therefore, not a universal characteristic of large enough cohorts.

  • 12885.
    Zajitschek, Felix
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal Ecology.
    Lailvaux, Simon P.
    Dessmann, Josephine
    Brooks, Robert
    Diet, sex, and death in field crickets2012In: Ecology and Evolution, ISSN 2045-7758, Vol. 2, no 7, p. 1627-1636Article in journal (Refereed)
    Abstract [en]

    Senescence is shaped by age-dependent trade-offs between fitness components. Because males and females invest different resources in reproduction, the trade-offs behind age-dependent reproductive effort should be resolved differently in the sexes. In this study, we assess the effects of diet (high carbohydrate and low protein vs. equal carbohydrate and protein) and mating (once mated vs. virgin) on lifespan and age-dependent mortality in male and female field crickets (Teleogryllus commodus), and on male calling effort. Females always had higher actuarial ageing rates than males, and we found a clear lifespan cost of mating in females. Mated males, however, lived longer than virgin males, possibly because virgins call more than mated males. The fastest age-dependent increases in mortality were among mated males on the high-carbohydrate diet. Males on a high-carbohydrate diet showed a faster increase in calling effort earlier in life, and a more pronounced pattern of senescence once they reached this peak than did males on a diet with equal amounts of protein and carbohydrates. Our results provide evidence that the cost of mating in this cricket species is both diet and sex-dependent, and that the underlying causes of sex differences in life-history traits such as lifespan and senescence can be complex.