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  • 1
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    Population genomics of domestic and wild yeasts (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-02-13
    Description: Since the completion of the genome sequence of Saccharomyces cerevisiae in 1996 (refs 1, 2), there has been a large increase in complete genome sequences, accompanied by great advances in our understanding of genome evolution. Although little is known about the natural and life histories of yeasts in the wild, there are an increasing number of studies looking at ecological and geographic distributions, population structure and sexual versus asexual reproduction. Less well understood at the whole genome level are the evolutionary processes acting within populations and species that lead to adaptation to different environments, phenotypic differences and reproductive isolation. Here we present one- to fourfold or more coverage of the genome sequences of over seventy isolates of the baker's yeast S. cerevisiae and its closest relative, Saccharomyces paradoxus. We examine variation in gene content, single nucleotide polymorphisms, nucleotide insertions and deletions, copy numbers and transposable elements. We find that phenotypic variation broadly correlates with global genome-wide phylogenetic relationships. S. paradoxus populations are well delineated along geographic boundaries, whereas the variation among worldwide S. cerevisiae isolates shows less differentiation and is comparable to a single S. paradoxus population. Rather than one or two domestication events leading to the extant baker's yeasts, the population structure of S. cerevisiae consists of a few well-defined, geographically isolated lineages and many different mosaics of these lineages, supporting the idea that human influence provided the opportunity for cross-breeding and production of new combinations of pre-existing variations.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2659681/" 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/PMC2659681/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liti, Gianni -- Carter, David M -- Moses, Alan M -- Warringer, Jonas -- Parts, Leopold -- James, Stephen A -- Davey, Robert P -- Roberts, Ian N -- Burt, Austin -- Koufopanou, Vassiliki -- Tsai, Isheng J -- Bergman, Casey M -- Bensasson, Douda -- O'Kelly, Michael J T -- van Oudenaarden, Alexander -- Barton, David B H -- Bailes, Elizabeth -- Nguyen, Alex N -- Jones, Matthew -- Quail, Michael A -- Goodhead, Ian -- Sims, Sarah -- Smith, Frances -- Blomberg, Anders -- Durbin, Richard -- Louis, Edward J -- 067008/Wellcome Trust/United Kingdom -- 084507/Wellcome Trust/United Kingdom -- BB/F015216/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- G10415/Biotechnology and Biological Sciences Research Council/United Kingdom -- Biotechnology and Biological Sciences Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2009 Mar 19;458(7236):337-41. doi: 10.1038/nature07743. Epub 2009 Feb 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Genetics, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19212322" target="_blank"〉PubMed〈/a〉
    Keywords: Genetics, Population ; Genome, Fungal/*genetics ; *Genomics ; Geography ; INDEL Mutation/genetics ; Phenotype ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Saccharomyces/classification/*genetics ; Saccharomyces cerevisiae/*genetics ; Selection, Genetic
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    PI3K and CDK inhibitors induce apoptosis in glioma [Medical Sciences] (2012)
    National Academy of Sciences
    Details
    Publication Date: 2012-08-01
    Description: Malignant glioma, the most common primary brain tumor, is generally incurable. Although phosphatidylinositol-3-kinase (PI3K) signaling features prominently in glioma, inhibitors generally block proliferation rather than induce apoptosis. Starting with an inhibitor of both lipid and protein kinases that induced prominent apoptosis and that failed early clinical development because of its broad target profile and overall toxicity, we identified protein kinase targets, the blockade of which showed selective synthetic lethality when combined with PI3K inhibitors. Prioritizing protein kinase targets for which there are clinical inhibitors, we demonstrate that cyclin-dependent kinase (CDK)1/2 inhibitors, siRNAs against CDK1/2, and the clinical CDK1/2 inhibitor roscovitine all cooperated with the PI3K inhibitor PIK-90, blocking the antiapoptotic protein Survivin and driving cell death. In addition, overexpression of CDKs partially blocked some of the apoptosis caused by PIK-75. Roscovitine and PIK-90, in combination, were well tolerated in vivo and acted in a synthetic-lethal manner to induce apoptosis in human glioblastoma xenografts. We also tested clinical Akt and CDK inhibitors, demonstrating induction of apoptosis in vitro and providing a preclinical rationale to test this combination therapy in patients.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 3
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    Abstract: Integration of Seismic and Surface Geochemistry Data for Evaluation of Hydrocarbon Systems in the Gulf of Mexico (1998)
    American Association of Petroleum Geologists
    Details
    Publication Date: 1998-01-01
    Print ISSN: 0149-1423
    Electronic ISSN: 1943-2674
    Topics: Geosciences
    Published by American Association of Petroleum Geologists
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  • 4
    Electronic Resource
    Electronic Resource
    Chromosomal evolution in Saccharomyces (2000)
    [s.l.] : Macmillian Magazines Ltd.
    Nature 405 (2000), S. 451-454 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] The chromosomal speciation model invokes chromosomal rearrangements as the primary cause of reproductive isolation. In a heterozygous carrier, chromosomes bearing reciprocal translocations mis-segregate at meiosis, resulting in reduced fertility or complete sterility. Thus, chromosomal ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/35013058
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  • 5
    Electronic Resource
    Electronic Resource
    Whole-tree water transport scales with sapwood capacitance in tropical forest canopy trees (2003)
    Oxford, UK : Blackwell Science Ltd
    Plant, cell & environment 26 (2003), S. 0 
    Details
    ISSN: 1365-3040
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: The present study examines the manner in which several whole-tree water transport properties scale with species-specific variation in sapwood water storage capacity. The hypothesis that constraints on relationships between sapwood capacitance and other water relations characteristics lead to predictable scaling relationships between intrinsic capacitance and whole-tree behaviour was investigated. Samples of sapwood from four tropical forest canopy tree species selected to represent a range of wood density, tree size and architecture, and taxonomic diversity were used to generate moisture release curves in thermocouple psychrometer chambers, from which species-specific values of sapwood capacitance were calculated. Sapwood capacitance was then used to scale several whole-tree water transport properties determined from measurements of upper branch and basal sap flow, branch water potential, and axial and radial movement of deuterated water (D2O) injected into the base of the trunk as a tracer. Sapwood capacitance ranged from 83 to 416 kg m−3 MPa−1 among the four species studied and was strongly correlated with minimum branch water potential, soil-to-branch hydraulic conductance, daily utilization of stored water, and axial and radial movement of D2O. The species-independent scaling of several whole-tree water transport properties with sapwood capacitance indicated that substantial convergence in plant function at multiple levels of biological organization was revealed by a simple variable related to a biophysical property of water transport tissue.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1046/j.1365-3040.2003.01039.x
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  • 6
    Electronic Resource
    Electronic Resource
    Dependence of amino acid composition upon nitrogen availability in birch (Betula pendula) (1990)
    Oxford, UK : Blackwell Publishing Ltd
    Physiologia plantarum 80 (1990), S. 0 
    Details
    ISSN: 1399-3054
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Small birch plants (Betula pendula Roth.) were grown at different rates of exponentially increasing nitrogen supply. This resulted in plants with different relative growth rates and different internal nitrogen concentrations. Within a nitrogen treatment, both of these variables remained constant with time.Free amino acids were measured in leaves and roots of the seedlings at two different harvests. At greater nitrogen supply, higher concentrations of total amino acid nitrogen were found in roots and leaves. The ratio of amino acid nitrogen to total nitrogen was low albeit greater at higher nitrogen supply. Higher concentrations of amino acid nitrogen were mainly due to high concentrations of citrulline, glutamine, γ-aminobuitric acid and arginine.Greater leaf concentrations of amino acid nitrogen at higher nitrogen supply may be related lo increased concentrations in the xylem sap and/or may be indicative of small excesses of nitrogen with respect to current nitrogen usage in protein synthesis.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1399-3054.1990.tb05671.x
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  • 7
    Electronic Resource
    Electronic Resource
    Why do leaves and leaf cells of N-limited barley elongate at reduced rates? (1997)
    Springer
    Planta 202 (1997), S. 522-530 
    Details
    ISSN: 1432-2048
    Keywords: Key words: Cell expansion ; Hordeum (leaf growth ; nitrogen) ; Ingestad-nutrient technique ; Nitrogen (leaf growth) ; Water relations (turgor ; osmotic pressure)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. The objective of the present study was to assess whether, in barley, nitrogen supply limits the rate of leaf elongation through a reduction in (relative) cell elongation rate and whether this is attributable to a reduced turgor, a reduced availability of osmolytes or, by implication, changed wall properties. Plants were grown on full-strength Hoagland solution (“Hoagland”-plants), or on N-deficient Hoagland solution while receiving N at a relative addition rate of 16 or 8% N · plant-N−1 · d−1 (“16%-” and “8%-plants”). Hoagland-plants were demand-limited, whereas 16%- and 8%-plants were supply-limited in N. Third leaves were analysed for leaf elongation rate and final epidermal cell length, and, within the basal growing region, for the spatial distribution of relative segmental elongation rates (RSER, pin-pricking method), epidermal cell turgor (cell-pressure probe), osmotic pressure (OP, picolitre osmometry) and water potential (Ψ). During the development of the third leaf, plants grew at relative growth rates (relative increase in fresh weight ) of 18.2, 15.6 and 8.1% · d−1 (Hoagland-, 16%- and 8%-plants, respectively). Final leaf length and leaf elongation rate were highest in Hoagland plants (ca. 34.1 cm and 2.33–2.60 mm · h−1, respectively), intermediate in 16%- plants (31.0 cm and 1.89–1.96 mm · h−1) and lowest in 8%-plants (29.4 cm and 1.41–1.58 mm · h−1). These differences were accompanied by only small differences in final cell length, but large differences in cell-flux rates (146, 187 and 201 cells · cell-file−1 · d−1 in 8%-, 16%- and Hoagland-plants, respectively). The length of the growth zone (32–38 mm) was not much affected by N-levels (and nutrient technique). A decrease in RSER in the growth zone distal to 10 mm produced the significant effect of N-levels on leaf elongation rate. In all treatments, cell turgor was almost constant throughout the growing region, as were cell OP and Ψ in 16%- and 8%-plants. In Hoagland-plants, however, cell OP increased by ca. 0.1 MPa within the zone of highest elongation rates and, as a consequence, cell Ψ decreased simultaneously by 0.1 MPa. Cell Ψ increased considerably where elongation ceased. Within the zone where differences in RSERs were highest between treatments (10–34 mm from base) average turgor was lowest, OP highest and Ψ most negative in Hoagland- compared to 8%- and 16%-plants (P 〈 0.001), but not significantly different between 8%- and 16%-plants.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004250050157
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  • 8
    Electronic Resource
    Electronic Resource
    Net assimilation rate and shoot area development in birch (Betula pendula Roth.) at different steady-state values of nutrition and photon flux density (1992)
    Springer
    Trees 6 (1992), S. 1-6 
    Details
    ISSN: 1432-2285
    Keywords: Nitrogen ; Photon flux density ; Growth ; Betula
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Summary Small birch plants (Betula pendula Roth.) were grown in a climate chamber at different, exponentially increasing rates of nitrogen supply and at different photon flux densities. This resulted in treatments with relative growth rate equal to the relative rate of increase in nitrogen supply and with different equilibrium values of plant nitrogen concentration. Nitrogen productivity (rate of dry matter increase per plant nitrogen) was largely independent of nitrogen supply and was greater at higher photon flux density. Leaf weight ratio, average specific leaf area (and thus leaf area ratio) were all greater at better nitrogen supply and at lower values of photon flux density. The dependencies were such that the ratio of total projected leaf area to plant nitrogen at a given photon flux density was similar at all rates of nitrogen supply. The ratio was greater at lower values of photon flux density. At a given value of photon flux density, net assimilation rate and net photosynthetic rate per shoot area (measured at the growth climate) were only slightly greater at better rates of nitrogen supply. Values were greater at higher photon flux densities. Acclimation of the total leaf area to plant nitrogen ratio and of net assimilation rate was such that nitrogen productivity was largely saturated with respect to photon flux density at values greater than 230 μmol m-2 s-1. At higher photon flux densities, any potential gain in nitrogen productivity associated with higher net assimilation rates was apparently offset by lower ratios of total leaf area to plant nitrogen.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00224491
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  • 9
    Electronic Resource
    Electronic Resource
    Effects of nitrogen supply on the acclimation of photosynthesis to elevated CO2 (1994)
    Springer
    Photosynthesis research 39 (1994), S. 389-400 
    Details
    ISSN: 1573-5079
    Keywords: elevated CO2 ; nitrogen supply ; photosynthesis ; acclimation ; growth
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A common observation in plants grown in elevated CO2 concentration is that the rate of photosynthesis is lower than expected from the dependence of photosynthesis upon CO2 concentration in single leaves of plants grown at present CO2 concentration. Furthermore, it has been suggested that this apparent down regulation of photosynthesis may be larger in leaves of plants at low nitrogen supply than at higher nitrogen supply. However, the available data are rather limited and contradictory. In this paper, particular attention is drawn to the way in which whole plant growth response to N supply constitutes a variable sink strength for carbohydrate usage and how this may affect photosynthesis. The need for further studies of the acclimation of photosynthesis at elevated CO2 in leaves of plants whose N supply has resulted in well-defined growth rate and sink activity is emphasised, and brief consideration is made of how this might be achieved.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00014593
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  • 10
    Electronic Resource
    Electronic Resource
    Nitrogen supply and the control of expansive growth and function in leaves and roots (1993)
    Springer
    Plant and soil 155-156 (1993), S. 195-198 
    Details
    ISSN: 1573-5036
    Keywords: nitrogen supply ; steady-state nutrition
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract In plants which have acclimatized to limiting supplies of nitrogen (steady-state nutrition), leaf expansion (numbers and sizes of leaves and cells) is under tight control. Over a wide range of nitrogen supplies, the control of leaf growth is associated with a narrow band of photosynthetic rate per leaf area (measured at the growth climate) and, at limiting supplies, a carbon uptake which is in excess of immediate carbon usage in structural growth. For every increment of nitrogen absorbed, root extension is greater at limited nitrate supply, but Vmax values (per root dry weight) for nitrate absorption are typically less. However, the capacity of the whole root system for nitrate uptake at limited supply is sufficient to allow for maximum growth, should nitrate supply be increased. It is concluded that a better understanding at the cellular level of the mechanisms which result in a greater inhibition of the expansion of single leaves than of root extension would contribute to an understanding of differences in carbon sink strength among plant organs. This may be a crucial step towards a more physiologically-based appreciation of plant dry matter distribution among organs in plants experiencing different nitrogen supplies.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00025017
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