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  • 1
    Publication Date: 2015-01-24
    Description: The possibility that alterations in DNA methylation are mechanistic drivers of development, aging and susceptibility to disease is widely acknowledged, but evidence remains patchy or inconclusive. Of particular interest in this regard is the brain, where it has been reported that DNA methylation impacts on neuronal activity, learning and memory, drug addiction and neurodegeneration. Until recently, however, little was known about the ‘landscape’ of the human brain methylome. Here we assay 1.9 million CpGs in each of 43 brain samples representing different individuals and brain regions. The cerebellum was a consistent outlier compared to all other regions, and showed over 16 000 differentially methylated regions (DMRs). Unexpectedly, the sequence characteristics of hypo- and hypermethylated domains in cerebellum were distinct. In contrast, very few DMRs distinguished regions of the cortex, limbic system and brain stem. Inter-individual DMRs were readily detectable in these regions. These results lead to the surprising conclusion that, with the exception of cerebellum, DNA methylation patterns are more homogeneous between different brain regions from the same individual, than they are for a single brain region between different individuals. This finding suggests that DNA sequence composition, not developmental status, is the principal determinant of the human brain DNA methylome.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 2
    Publication Date: 2015-10-02
    Description: We present Spitzer /Infrared Spectrograph (IRS) 5–21 μm spectroscopic maps towards 12 regions in the Andromeda galaxy (M31). These regions include the nucleus, bulge, an active region in the star-forming ring and nine other regions chosen to cover a range of mid-to-far-infrared colours. In line with previous results, polycyclic aromatic hydrocarbon (PAH) feature ratios (6.2 and 7.7 μm features compared to the 11.2 μm feature) measured from our extracted M31 spectra, except the nucleus, strongly correlate. The equivalent widths of the main PAH features, as a function of metallicity and radiation hardness, are consistent with those observed for other nearby spiral and starburst galaxies. Reprocessed data from the ISOCAM instrument on the Infrared Space Observatory agree with the IRS data; early reports of suppressed 6–8 μm features and enhanced 11.3 μm feature intensity and full width at half-maximum apparently resulted from background-subtraction problems. The nucleus does not show any PAH emission but does show strong silicate emission at 9.7 μm. Furthermore, different spectral features (11.3 μm PAH emission, silicate emission and [Ne  iii ] 15.5 μm line emission) have distinct spatial distributions in the nuclear region: the silicate emission is strongest towards the stellar nucleus, while the PAH emission peaks 15 arcsec north of the nucleus. The PAH feature ratios at this position are atypical with strong emission at 11.2 and 15–20 μm but weak emission at 6–8 μm. The nucleus itself is dominated by stellar light giving rise to a strong blue continuum and silicate emission.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 3
    Publication Date: 2012-09-16
    Description: Vertebrates have experienced two rounds of whole-genome duplication (WGD) in the stem lineages of deep nodes within the group and a subsequent duplication event in the stem lineage of the teleosts—a highly diverse group of ray-finned fishes. Here, we present the first full Hox gene sequences for any member of the Acipenseriformes, the American paddlefish, and confirm that an independent WGD occurred in the paddlefish lineage, approximately 42 Ma based on sequences spanning the entire HoxA cluster and eight genes on the HoxD gene cluster. These clusters comprise different HOX loci and maintain conserved synteny relative to bichir, zebrafish, stickleback, and pufferfish, as well as human, mouse, and chick. We also provide a gene genealogy for the duplicated fzd8 gene in paddlefish and present evidence for the first Hox14 gene in any ray-finned fish. Taken together, these data demonstrate that the American paddlefish has an independently duplicated genome. Substitution patterns of the "alpha" paralogs on both the HoxA and HoxD gene clusters suggest transcriptional inactivation consistent with functional diploidization. Further, there are similarities in the pattern of sequence divergence among duplicated Hox genes in paddlefish and teleost lineages, even though they occurred independently approximately 200 Myr apart. We highlight implications on comparative analyses in the study of the "fin-limb transition" as well as gene and genome duplication in bony fishes, which includes all ray-finned fishes as well as the lobe-finned fishes and tetrapod vertebrates.
    Electronic ISSN: 1759-6653
    Topics: Biology
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  • 4
    Publication Date: 2004-08-07
    Description: A deep earthquake swarm in late 2003 at Lake Tahoe, California (Richter magnitude 〈 2.2; depth of 29 to 33 kilometers), was coeval with a transient displacement of 6 millimeters horizontally outward from the swarm and 8 millimeters upward measured at global positioning system station Slide Mountain (SLID) 18 kilometers to the northeast. During the first 23 days of the swarm, hypocentral depths migrated at a rate of 2.4 millimeters per second up-dip along a 40-square-kilometer structure striking north 30 degrees west and dipping 50 degrees to the northeast. SLID's transient velocity of 20 millimeters per year implies a lower bound of 200 nanostrains per year (parts per billion per year) on local strain rates, an order of magnitude greater than the 1996 to 2003 regional rate. The geodetic displacement is too large to be explained by the elastic strain from the cumulative seismic moment of the sequence, suggesting an aseismic forcing mechanism. Aspects of the swarm and SLID displacements are consistent with lower-crustal magma injection under Lake Tahoe.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Smith, Kenneth D -- von Seggern, David -- Blewitt, Geoffrey -- Preston, Leiph -- Anderson, John G -- Wernicke, Brian P -- Davis, James L -- New York, N.Y. -- Science. 2004 Aug 27;305(5688):1277-80. Epub 2004 Aug 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Nevada Seismological Laboratory, University of Nevada, Reno, NV 89557, USA. ken@seismo.unr.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15297623" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2016-11-06
    Description: After approximately two months of swarm-like earthquakes in the Mogul neighborhood of west Reno, NV, seismicity rates and event magnitudes increased over several days culminating in an M w 4.9 dextral strike-slip earthquake on 26 April 2008. Although very shallow, the M w 4.9 mainshock had a different sense of slip than locally mapped dip-slip surface faults. We relocate 7,549 earthquakes, calculate 1,082 focal mechanisms, and statistically cluster the relocated earthquake catalog to understand the character and interaction of active structures throughout the Mogul, NV earthquake sequence. Rapid temporary instrument deployment provides high-resolution coverage of microseismicity, enabling a detailed analysis of swarm behavior and faulting geometry. Relocations reveal an internally clustered sequence in which foreshocks evolved on multiple structures surrounding the eventual mainshock rupture. The relocated seismicity defines a fault-fracture mesh and detailed fault structure from approximately 2-6 km depth on the previously unknown Mogul fault that may be an evolving incipient strike-slip fault zone. The seismicity volume expands before the mainshock, consistent with pore-pressure diffusion, and the aftershock volume is much larger than is typical for an M w 4.9 earthquake. We group events into clusters using space-time-magnitude nearest-neighbor distances between events and develop a cluster criterion through randomization of the relocated catalog. Identified clusters are largely mainshock-aftershock sequences, without evidence for migration, occurring within the diffuse background seismicity. The migration rate of the largest foreshock cluster and simultaneous background events is consistent with it having triggered, or having been triggered by, an aseismic slip event.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 6
    Publication Date: 2017-10-10
    Description: We estimate stress drops for 148 shallow (〈6km) earthquakes in the complex 2008 Mogul, Nevada swarm using EGF-derived spectral ratios. Near-source, temporary broadband seismometers deployed before the M W 4.9 mainshock provide high-quality records of many foreshocks and aftershocks, and an ideal opportunity to investigate uncertainties in corner frequency measurement as well as stress drop (Δσ) variation related to space, time, depth, mechanism, and magnitude. We explore uncertainties related to source model, measurement approach, cross-correlation limit, and frequency bandwidth. P (S) wave Δσ results range from 0.2±0.15 (0.3±0.15) to 36±20 (58±7) MPa, a variation greater than the error range of each individual estimate. Although this variation is not explained simply by any one parameter, spatiotemporal variation along the mainshock fault plane is distinct: coherent clusters of high and low Δσ earthquakes are seen, and high-Δσ foreshocks correlate with an area of reduced aftershock productivity. These observations are best explained by a difference in rheology along the fault plane. Average Δσs of 3.9±1.1 (4.0±1.1) MPa using P (S) are similar to those found for earthquakes in a variety of settings, implying that these shallow, potentially fluid-driven earthquakes do not have systematically lower Δσ than average tectonic earthquakes (~4MPa) and, therefore, have similar (or higher, due to proximity to the surface) expected ground motions compared to typical earthquakes. The unprecedented detail achieved for these shallow, small magnitude earthquakes confirms that Δσ, when measured precisely, is a valuable observation of physically-meaningful fault zone properties and earthquake behavior.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 7
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1979-10-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Smith, K D -- Steinberger, E -- Rodriguez-Rigau, L J -- New York, N.Y. -- Science. 1979 Oct 5;206(4414):96-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/482933" target="_blank"〉PubMed〈/a〉
    Keywords: Birth Weight/*drug effects ; Female ; Humans ; Prednisone/*adverse effects ; Pregnancy
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
    Publication Date: 2012-08-01
    Description: A hydrogeochemical study using high resolution ICP-MS was undertaken at the giant Pebble porphyry Cu-Au-Mo deposit and surrounding mineral occurrences. Surface water and groundwater samples from regional background and the deposit area were collected at 168 sites. Rigorous quality control reveals impressive results at low nanogram per litre (ng/l) levels. Sites with pH values below 5.1 are from ponds in the Pebble West area, where sulphide-bearing rubble crop is thinly covered. Relative to other study area waters, anomalous concentrations of Cu, Cd, K, Ni, Re, the REE, Tl, SO 4 2– and F – are present in water samples from Pebble West. Samples from circum-neutral waters at Pebble East and parts of Pebble West, where cover is much thicker, have anomalous concentrations of Ag, As, In, Mn, Mo, Sb, Th, U, V, and W. Low-level anomalous concentrations for most of these elements were also found in waters surrounding nearby porphyry and skarn mineral occurrences. Many of these elements are present in low ng/l concentration ranges and would not have been detected using traditional quadrupole ICP-MS. Hydrogeochemical exploration paired with high resolution ICP-MS is a powerful new tool in the search for concealed deposits.
    Print ISSN: 1467-7873
    Electronic ISSN: 1467-7873
    Topics: Chemistry and Pharmacology , Geosciences
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  • 9
    Publication Date: 2012-12-01
    Description: Leukocyte telomere length (LTL) is associated with a number of common age-related diseases and is a heritable trait. Previous genome-wide association studies (GWASs) identified two loci on chromosomes 3q26.2 ( TERC ) and 10q24.33 ( OBFC1 ) that are associated with the inter-individual LTL variation. We performed a meta-analysis of 9190 individuals from six independent GWAS and validated our findings in 2226 individuals from four additional studies. We confirmed previously reported associations with OBFC1 (rs9419958 P = 9.1 x 10 –11 ) and with the telomerase RNA component TERC (rs1317082, P = 1.1 x 10 –8 ). We also identified two novel genomic regions associated with LTL variation that map near a conserved telomere maintenance complex component 1 ( CTC1 ; rs3027234, P = 3.6 x 10 –8 ) on chromosome17p13.1 and zinc finger protein 676 ( ZNF676; rs412658, P = 3.3 x 10 –8 ) on 19p12. The minor allele of rs3027234 was associated with both shorter LTL and lower expression of CTC1 . Our findings are consistent with the recent observations that point mutations in CTC1 cause short telomeres in both Arabidopsis and humans affected by a rare Mendelian syndrome. Overall, our results provide novel insights into the genetic architecture of inter-individual LTL variation in the general population.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 10
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Journal of the American Chemical Society 96 (1974), S. 994-998 
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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