ALBERT

All Library Books, journals and Electronic Records Telegrafenberg

X
feed icon rss

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
  • 1
    facet.materialart.
    Unknown
    Tree size and light availability increase photochemical instead of non-photochemical capacities of Nothofagus nitida trees growing in an evergreen temperate rain forest (2011)
    Oxford University Press
    Details
    Publication Date: 2011-11-24
    Description: Nothofagus nitida (Phil.) Krasser (Nothofagaceae) regenerates under the canopy in microsites protected from high light. Nonetheless, it is common to find older saplings in clear areas and adults as emergent trees of the Chilean evergreen forest. We hypothesized that this shade to sun transition in N. nitida is supported by an increase in photochemical and non-photochemical energy dissipation capacities of both photosystems in parallel with the increase in plant size and light availability. To dissect the relative contribution of light environment and plant developmental stage to these physiological responses, the photosynthetic performance of both photosystems was studied from the morpho-anatomical to the biochemical level in current-year leaves of N. nitida plants of different heights (ranging from 0.1 to 7 m) growing under contrasting light environments (integrated quantum flux (IQF) 5–40 mol m –2  day –1 ). Tree height (TH) and light environment (IQF) independently increased the saturated electron transport rates of both photosystems, as well as leaf and palisade thickness, but non-photochemical energy flux, photoinhibition susceptibility, state transition capacity, and the contents of D1 and PsbS proteins were not affected by IQF and TH. Spongy mesophyll thickness and palisade cell diameter decreased with IQF and TH. A max , light compensation and saturation points, Rubisco and nitrogen content (area basis) only increased with light environment (IQF), whereas dark respiration ( R d ) decreased slightly and relative chlorophyll content was higher in taller trees. Overall, the independent effects of more illuminated environment and tree height mainly increased the photochemical instead of the non-photochemical energy flux. Regardless of the photochemical increase with TH, carbon assimilation only significantly improved with higher IQF. Therefore it seems that mainly acclimation to the light environment supports the phenotypic transition of N. nitida from shade to sun.
    Print ISSN: 0829-318X
    Electronic ISSN: 1758-4469
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 2
    facet.materialart.
    Unknown
    Novel Papillomaviruses in Free-Ranging Iberian Bats: No Virus-Host Co-evolution, No Strict Host Specificity, and Hints for Recombination (2014)
    Oxford University Press
    Details
    Publication Date: 2014-01-22
    Description: Papillomaviruses (PVs) are widespread pathogens. However, the extent of PV infections in bats remains largely unknown. This work represents the first comprehensive study of PVs in Iberian bats. We identified four novel PVs in the mucosa of free-ranging Eptesicus serotinus (EserPV1, EserPV2, and EserPV3) and Rhinolophus ferrumequinum (RferPV1) individuals and analyzed their phylogenetic relationships within the viral family. We further assessed their prevalence in different populations of E. serotinus and its close relative E. isabellinus . Although it is frequent to read that PVs co-evolve with their host, that PVs are highly species-specific, and that PVs do not usually recombine, our results suggest otherwise. First, strict virus–host co-evolution is rejected by the existence of five, distantly related bat PV lineages and by the lack of congruence between bats and bat PVs phylogenies. Second, the ability of EserPV2 and EserPV3 to infect two different bat species ( E. serotinus and E. isabellinus ) argues against strict host specificity. Finally, the description of a second noncoding region in the RferPV1 genome reinforces the view of an increased susceptibility to recombination in the E2-L2 genomic region. These findings prompt the question of whether the prevailing paradigms regarding PVs evolution should be reconsidered.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 3
    facet.materialart.
    Unknown
    New approaches to modelling cross-sectional area to height allometry in four Mediterranean pine species (2014)
    Oxford University Press
    In: Forestry
    Details
    Publication Date: 2014-04-29
    Description: Crown dynamics affect tree cross-sectional growth by responding to individual traits and stand history and features, i.e. species, stocking, thinning, site quality or climatic conditions. Under this assumption we analysed two simple models that relate cross-sectional growth to the growth of stem length above the cross section in four species of Mediterranean pines. Cross-sectional growth was measured at breast height. The first model (Model 0) has no parameters, and specifies an isometric relationship between cross-sectional area and stem length. The second model (Model α), which was formulated to analyse Model 0, has one parameter. Neither of the two simple models requires knowledge of crown length, though Model 0 derives – under an assumption of constant crown length – from a more general model that relates cross-sectional growth to crown length dynamics. A mixed-effects modelling strategy was selected to fit Model α in order to incorporate fixed effects of species, and random effects to account for factors like ontogeny (tree effect), stand history (plot effect) and climatic conditions (growth period). Results indicate that Model α predicts better than Model 0 when the single parameter is expanded to take into account all these effects and indicate that the constant ratio between cross-sectional area and the length of stem predicted by Model 0 is one possible value within a ratio that changes over time as function of ontogeny, stand history and climatic conditions. On average the ratio is positive, indicating greater cross-sectional growth than height growth showing greater variation in stem formation. Inter-specific analysis indicated a less asymmetric behaviour in competition for pine species growing in water-stress environment
    Print ISSN: 0015-752X
    Electronic ISSN: 1464-3626
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 4
    facet.materialart.
    Unknown
    Vanishing Abelian integrals on zero-dimensional cycles (2013)
    Oxford University Press
    Details
    Publication Date: 2013-12-12
    Description: In this paper, we study conditions for the vanishing of Abelian integrals on families of zero-dimensional cycles. That is, for any rational function f ( z ), characterize all rational functions g ( z ) and zero-sum integers { n i } such that the function t ↦ n i g ( z i ( t )) vanishes identically. Here z i ( t ) are continuously depending roots of f ( z )– t . We introduce a notion of (un)balanced cycles. Our main result is an inductive solution of the problem of vanishing of Abelian integrals when f , g are polynomials on a family of zero-dimensional cycles under the assumption that the family of cycles we consider as well as all the cycles encountered in the inductive process is unbalanced. We also solve the problem on some balanced cycles. The main motivation for our study is the problem of the vanishing of Abelian integrals on single families of one-dimensional cycles. We show that our problem and our main result are sufficiently rich to include some related problems, such as hyper-elliptic integrals on one-cycles, some applications to slow-fast planar systems and the polynomial (and trigonometric) moment problem for the Abel equation. This last problem was recently solved by Pakovich [ Bull. Sci. Math. 133 (2009) 693–732] and Pakovich and Muzychuk [ Proc. London Math. Soc. 99 (2009) 633–657]. Our approach is largely inspired by their work, thought we provide examples of vanishing Abelian integrals on zero-cycles that are not given as a sum of composition terms in contrast to the situation in the solution of the polynomial moment problem.
    Print ISSN: 0024-6115
    Electronic ISSN: 1460-244X
    Topics: Mathematics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 5
    facet.materialart.
    Unknown
    Determinants of expression variability (2014)
    Oxford University Press
    Details
    Publication Date: 2014-04-03
    Description: The amount of tissue-specific expression variability (EV) across individuals is an essential characteristic of a gene and believed to have evolved, in part, under functional constraints. However, the determinants and functional implications of EV are only beginning to be investigated. Our analyses based on multiple expression profiles in 41 primary human tissues show that a gene’s EV is significantly correlated with a number of features pertaining to the genomic, epigenomic, regulatory, polymorphic, functional, structural and network characteristics of the gene. We found that (i) EV of a gene is encoded, in part, by its genomic context and is further influenced by the epigenome; (ii) strong promoters induce less variable expression; (iii) less variable gene loci evolve under purifying selection against copy number polymorphisms; (iv) genes that encode inherently disordered or highly interacting proteins exhibit lower variability; and (v) genes with less variable expression are enriched for house-keeping functions, while genes with highly variable expression tend to function in development and extra-cellular response and are associated with human diseases. Thus, our analysis reveals a number of potential mediators as well as functional and evolutionary correlates of EV, and provides new insights into the inherent variability in eukaryotic gene expression.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 6
    facet.materialart.
    Unknown
    BlindCall: ultra-fast base-calling of high-throughput sequencing data by blind deconvolution (2014)
    Oxford University Press
    Details
    Publication Date: 2014-04-25
    Description: Motivation: Base-calling of sequencing data produced by high-throughput sequencing platforms is a fundamental process in current bioinformatics analysis. However, existing third-party probabilistic or machine-learning methods that significantly improve the accuracy of base-calls on these platforms are impractical for production use due to their computational inefficiency. Results: We directly formulate base-calling as a blind deconvolution problem and implemented BlindCall as an efficient solver to this inverse problem. BlindCall produced base-calls at accuracy comparable to state-of-the-art probabilistic methods while processing data at rates 10 times faster in most cases. The computational complexity of BlindCall scales linearly with read length making it better suited for new long-read sequencing technologies. Availability and Implementation: BlindCall is implemented as a set of Matlab scripts available for download at http://cbcb.umd.edu/~hcorrada/secgen . Contact: hcorrada@umiacs.umd.edu
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 7
    facet.materialart.
    Unknown
    Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays (2014)
    Oxford University Press
    Details
    Publication Date: 2014-05-11
    Description: Motivation: The recently released Infinium HumanMethylation450 array (the ‘450k’ array) provides a high-throughput assay to quantify DNA methylation (DNAm) at ~450 000 loci across a range of genomic features. Although less comprehensive than high-throughput sequencing-based techniques, this product is more cost-effective and promises to be the most widely used DNAm high-throughput measurement technology over the next several years. Results: Here we describe a suite of computational tools that incorporate state-of-the-art statistical techniques for the analysis of DNAm data. The software is structured to easily adapt to future versions of the technology. We include methods for preprocessing, quality assessment and detection of differentially methylated regions from the kilobase to the megabase scale. We show how our software provides a powerful and flexible development platform for future methods. We also illustrate how our methods empower the technology to make discoveries previously thought to be possible only with sequencing-based methods. Availability and implementation: http://bioconductor.org/packages/release/bioc/html/minfi.html . Contact: khansen@jhsph.edu ; rafa@jimmy.harvard.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 8
    facet.materialart.
    Unknown
    The roles of WRN and BLM RecQ helicases in the Alternative Lengthening of Telomeres (2012)
    Oxford University Press
    Details
    Publication Date: 2012-11-25
    Description: Approximately 10% of all cancers, but a higher proportion of sarcomas, use the recombination-based alternative lengthening of telomeres (ALT) to maintain telomeres. Two RecQ helicase genes, BLM and WRN , play important roles in homologous recombination repair and they have been implicated in telomeric recombination activity, but their precise roles in ALT are unclear. Using analysis of sequence variation present in human telomeres, we found that a WRN– ALT+ cell line lacks the class of complex telomere mutations attributed to inter-telomeric recombination in other ALT+ cell lines. This suggests that WRN facilitates inter-telomeric recombination when there are sequence differences between the donor and recipient molecules or that sister-telomere interactions are suppressed in the presence of WRN and this promotes inter-telomeric recombination. Depleting BLM in the WRN– ALT+ cell line increased the mutation frequency at telomeres and at the MS32 minisatellite, which is a marker of ALT. The absence of complex telomere mutations persisted in BLM-depleted clones, and there was a clear increase in sequence homogenization across the telomere and MS32 repeat arrays. These data indicate that BLM suppresses unequal sister chromatid interactions that result in excessive homogenization at MS32 and at telomeres in ALT+ cells.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 9
    facet.materialart.
    Unknown
    Rbg1-Tma46 dimer structure reveals new functional domains and their role in polysome recruitment (2012)
    Oxford University Press
    Details
    Publication Date: 2012-11-25
    Description: Developmentally Regulated GTP-binding (DRG) proteins are highly conserved GTPases that associate with DRG Family Regulatory Proteins (DFRP). The resulting complexes have recently been shown to participate in eukaryotic translation. The structure of the Rbg1 GTPase, a yeast DRG protein, in complex with the C-terminal region of its DFRP partner, Tma46, was solved by X-ray diffraction. These data reveal that DRG proteins are multimodular factors with three additional domains, helix–turn–helix (HTH), S5D2L and TGS, packing against the GTPase platform. Surprisingly, the S5D2L domain is inserted in the middle of the GTPase sequence. In contrast, the region of Tma46 interacting with Rbg1 adopts an extended conformation typical of intrinsically unstructured proteins and contacts the GTPase and TGS domains. Functional analyses demonstrate that the various domains of Rbg1, as well as Tma46, modulate the GTPase activity of Rbg1 and contribute to the function of these proteins in vivo . Dissecting the role of the different domains revealed that the Rbg1 TGS domain is essential for the recruitment of this factor in polysomes, supporting further the implication of these conserved factors in translation.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 10
    facet.materialart.
    Unknown
    The pneumococcal MgaSpn virulence transcriptional regulator generates multimeric complexes on linear double-stranded DNA (2013)
    Oxford University Press
    Details
    Publication Date: 2013-08-09
    Description: The Mga Spn transcriptional regulator contributes to the virulence of Streptococcus pneumoniae . It is thought to be a member of the Mga/AtxA family of global regulators. Mga Spn was shown to activate in vivo the P1623B promoter, which is divergent from the promoter ( Pmga ) of its own gene. This activation required a 70-bp region ( PB activation region) located between both promoters. In this work, we purified an untagged form of the Mga Spn protein, which formed dimers in solution. By gel retardation and footprinting assays, we analysed the binding of Mga Spn to linear double-stranded DNAs. Mga Spn interacted with the PB activation region when it was placed at internal position on the DNA. However, when it was positioned at one DNA end, Mga Spn recognized preferentially the Pmga promoter placed at internal position. In both cases, and on binding to the primary site, Mga Spn spread along the adjacent DNA regions generating multimeric protein–DNA complexes. When both Mga Spn -binding sites were located at internal positions on longer DNAs, electron microscopy experiments demonstrated that the PB activation region was the preferred target. DNA molecules totally or partially covered by Mga Spn were also visualized. Our results suggest that Mga Spn might recognize particular DNA conformations to achieve DNA-binding specificity.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...