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  • 1
    In: G3 Genes|Genomes|Genetics, Oxford University Press (OUP), Vol. 5, No. 5 ( 2015-05-01), p. 719-740
    Abstract: The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25–50%) than euchromatic reference regions (3–11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11–27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4–3.6 vs. 8.4–8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu.
    Type of Medium: Online Resource
    ISSN: 2160-1836
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2015
    detail.hit.zdb_id: 2629978-1
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  • 2
    In: Monthly Notices of the Royal Astronomical Society, Oxford University Press (OUP), Vol. 503, No. 2 ( 2021-03-23), p. 1940-1975
    Abstract: The past decade has seen significant progress in understanding galaxy formation and evolution using large-scale cosmological simulations. While these simulations produce galaxies in overall good agreement with observations, they employ different sub-grid models for galaxies and supermassive black holes (BHs). We investigate the impact of the sub-grid models on the BH mass properties of the Illustris, TNG100, TNG300, Horizon-AGN, EAGLE, and SIMBA simulations, focusing on the MBH − M⋆ relation and the BH mass function. All simulations predict tight MBH − M⋆ relations, and struggle to produce BHs of $M_{\rm BH}\leqslant 10^{7.5}\, \rm M_{\odot }$ in galaxies of $M_{\star }\sim 10^{10.5}\!-\!10^{11.5}\, \rm M_{\odot }$. While the time evolution of the mean MBH − M⋆ relation is mild ($\rm \Delta M_{\rm BH}\leqslant 1\, dex$ for 0 $\leqslant z \leqslant$ 5) for all the simulations, its linearity (shape) and normalization varies from simulation to simulation. The strength of SN feedback has a large impact on the linearity and time evolution for $M_{\star }\leqslant 10^{10.5}\, \rm M_{\odot }$. We find that the low-mass end is a good discriminant of the simulation models, and highlights the need for new observational constraints. At the high-mass end, strong AGN feedback can suppress the time evolution of the relation normalization. Compared with observations of the local Universe, we find an excess of BHs with $M_{\rm BH}\geqslant 10^{9}\, \rm M_{\odot }$ in most of the simulations. The BH mass function is dominated by efficiently accreting BHs ($\log _{10}\, f_{\rm Edd}\geqslant -2$) at high redshifts, and transitions progressively from the high-mass to the low-mass end to be governed by inactive BHs. The transition time and the contribution of active BHs are different among the simulations, and can be used to evaluate models against observations.
    Type of Medium: Online Resource
    ISSN: 0035-8711 , 1365-2966
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 2016084-7
    SSG: 16,12
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  • 3
    In: JNCI: Journal of the National Cancer Institute, Oxford University Press (OUP), Vol. 105, No. 11 ( 2013-4), p. 791-801
    Type of Medium: Online Resource
    ISSN: 0027-8874 , 1460-2105
    RVK:
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2013
    detail.hit.zdb_id: 2992-0
    detail.hit.zdb_id: 1465951-7
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  • 4
    In: Open Forum Infectious Diseases, Oxford University Press (OUP), Vol. 6, No. Supplement_2 ( 2019-10-23), p. S964-S964
    Abstract: The host immune response to influenza vaccination can be affected by prior imprinting to a specific influenza strain based on birth cohort and prior influenza vaccination history. Understanding the underlying immune mechanisms is essential to development of an improved seasonal vaccine and an effective universal influenza vaccine. Methods This is a prospective pilot study, with a total of 20 subjects in either the H3N2 cohort (N = 10, born 1968–1977) or the H1N1 cohort (N = 10, born 1948–1957). Each cohort was further stratified by subjects who have received the influenza vaccine 〈 2 or ≥ 3 of the past 5 years. The FDA-approved quadrivalent 2018–19 influenza vaccine (containing A(H1N1), an A/Michigan/45/2015-like virus; A(H3N2), an A/Singapore/INFIMH-16–0019/2016-like virus; B/Colorado/06/2017-like virus; and B/Phuket/3073/2013-like virus) was administered on Day 1. Demographic information included age, gender, ethnicity, and BMI. HAI titers for each component of the vaccine were obtained at baseline, 29 days post-vaccination, and 180 days post-vaccination. HAI fold-change and HAI geometric mean titers (GMT) were analyzed. Results There was no significant difference between H1N1 or H3N2 HAI fold-change in the H3N2 birth cohort (P = 0.7496) or in the H1N1 birth cohort (P = 0.8237), Figure A. Comparing HAI fold-change for the repeatedly vs. minimally vaccinated groups, there was a significant higher fold change in the minimally vaccinated group (H1N1 HAI (P = 0.002) and H3N2 HAI (P 〈 0.0001), Figure B). GMT was higher at baseline for the repeatedly vaccinated group (H1N1, 70; H3N2, 98; vs. H1N1, 30; H3N2, 21 for the minimally vaccinated group); however, the GMT for the minimally vaccinated group was higher at day 29 (H1N1, 172; H3N2, 184; vs. H1N1, 422; H3N2, 299 for the minimally vaccinated group; Figure C). HAI titers and analysis at day 180 post vaccination are in progress. Conclusion There was no evidence of an imprinting effect by birth cohort for HAI titer magnitudes, even when stratified by vaccination history. There was a significantly higher HAI fold change for individuals who had received minimal influenza vaccinations in the past 5 years at 29 days post-vaccination. Individuals who had repeated vaccinations in the last 5 years had higher HAI GMT at baseline. Disclosures Nadine Rouphael, MD, Merck: I conduct as Emory PI the PNEUMO MERCK study at Emory, Research Grant; Pfizer: I conduct as co-PI the RSV PFIZER study at Emory, Research Grant; Sanofi-Pasteur: I conducted as Emory PI the CDIFFENSE trial at Emory, Research Grant.
    Type of Medium: Online Resource
    ISSN: 2328-8957
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
    detail.hit.zdb_id: 2757767-3
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