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  • 1
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    Comparison of human and mouse transcriptomes [Genetics] (2014)
    National Academy of Sciences
    Details
    Publication Date: 2014-12-03
    Description: Although the similarities between humans and mice are typically highlighted, morphologically and genetically, there are many differences. To better understand these two species on a molecular level, we performed a comparison of the expression profiles of 15 tissues by deep RNA sequencing and examined the similarities and differences in the...
    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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  • 2
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    Regulatory genes control a key morphological and ecological trait transferred between species (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-11-15
    Description: Hybridization between species can lead to introgression of genes from one species to another, providing a potential mechanism for preserving and recombining key traits during evolution. To determine the molecular basis of such transfers, we analyzed a natural polymorphism for flower-head development in Senecio. We show that the polymorphism arose by introgression of a cluster of regulatory genes, the RAY locus, from the diploid species S. squalidus into the tetraploid S. vulgaris. The RAY genes are expressed in the peripheral regions of the inflorescence meristem, where they promote flower asymmetry and lead to an increase in the rate of outcrossing. Our results highlight how key morphological and ecological traits controlled by regulatory genes may be gained, lost, and regained during evolution.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, Minsung -- Cui, Min-Long -- Cubas, Pilar -- Gillies, Amanda -- Lee, Karen -- Chapman, Mark A -- Abbott, Richard J -- Coen, Enrico -- BB-D017742/Biotechnology and Biological Sciences Research Council/United Kingdom -- G10929/Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2008 Nov 14;322(5904):1116-9. doi: 10.1126/science.1164371.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell and Developmental Biology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19008450" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Biological Evolution ; Crosses, Genetic ; Flowers/anatomy & histology/*genetics/growth & development ; *Gene Transfer, Horizontal ; *Genes, Plant ; *Genes, Regulator ; Genotype ; Haplotypes ; *Hybridization, Genetic ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Polymorphism, Genetic ; Selection, Genetic ; Senecio/*genetics/growth & development ; Sequence Analysis, DNA
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Initial genome sequencing and analysis of multiple myeloma (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-03-25
    Description: Multiple myeloma is an incurable malignancy of plasma cells, and its pathogenesis is poorly understood. Here we report the massively parallel sequencing of 38 tumour genomes and their comparison to matched normal DNAs. Several new and unexpected oncogenic mechanisms were suggested by the pattern of somatic mutation across the data set. These include the mutation of genes involved in protein translation (seen in nearly half of the patients), genes involved in histone methylation, and genes involved in blood coagulation. In addition, a broader than anticipated role of NF-kappaB signalling was indicated by mutations in 11 members of the NF-kappaB pathway. Of potential immediate clinical relevance, activating mutations of the kinase BRAF were observed in 4% of patients, suggesting the evaluation of BRAF inhibitors in multiple myeloma clinical trials. These results indicate that cancer genome sequencing of large collections of samples will yield new insights into cancer not anticipated by existing knowledge.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3560292/" 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/PMC3560292/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chapman, Michael A -- Lawrence, Michael S -- Keats, Jonathan J -- Cibulskis, Kristian -- Sougnez, Carrie -- Schinzel, Anna C -- Harview, Christina L -- Brunet, Jean-Philippe -- Ahmann, Gregory J -- Adli, Mazhar -- Anderson, Kenneth C -- Ardlie, Kristin G -- Auclair, Daniel -- Baker, Angela -- Bergsagel, P Leif -- Bernstein, Bradley E -- Drier, Yotam -- Fonseca, Rafael -- Gabriel, Stacey B -- Hofmeister, Craig C -- Jagannath, Sundar -- Jakubowiak, Andrzej J -- Krishnan, Amrita -- Levy, Joan -- Liefeld, Ted -- Lonial, Sagar -- Mahan, Scott -- Mfuko, Bunmi -- Monti, Stefano -- Perkins, Louise M -- Onofrio, Robb -- Pugh, Trevor J -- Rajkumar, S Vincent -- Ramos, Alex H -- Siegel, David S -- Sivachenko, Andrey -- Stewart, A Keith -- Trudel, Suzanne -- Vij, Ravi -- Voet, Douglas -- Winckler, Wendy -- Zimmerman, Todd -- Carpten, John -- Trent, Jeff -- Hahn, William C -- Garraway, Levi A -- Meyerson, Matthew -- Lander, Eric S -- Getz, Gad -- Golub, Todd R -- K12 CA133250/CA/NCI NIH HHS/ -- R01 AG020686/AG/NIA NIH HHS/ -- R01 AG020686-07/AG/NIA NIH HHS/ -- R01 CA133115/CA/NCI NIH HHS/ -- R01 CA133115-04/CA/NCI NIH HHS/ -- R01 CA133966/CA/NCI NIH HHS/ -- R01 CA133966-03/CA/NCI NIH HHS/ -- England -- Nature. 2011 Mar 24;471(7339):467-72. doi: 10.1038/nature09837.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Eli and Edythe L. Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02412, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21430775" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Blood Coagulation/genetics ; CpG Islands/genetics ; DNA Mutational Analysis ; DNA Repair/genetics ; Exons/genetics ; Exosome Multienzyme Ribonuclease Complex ; Genome, Human/*genetics ; Genomics ; Histones/metabolism ; Homeodomain Proteins/genetics ; Homeostasis/genetics ; Humans ; Methylation ; Models, Molecular ; Molecular Sequence Data ; Multiple Myeloma/drug therapy/enzymology/*genetics/metabolism ; Mutation/*genetics ; NF-kappa B/metabolism ; Oncogenes/genetics ; Open Reading Frames/genetics ; Protein Biosynthesis/genetics ; Protein Conformation ; Proto-Oncogene Proteins B-raf/antagonists & inhibitors/genetics/metabolism ; RNA Processing, Post-Transcriptional/genetics ; Ribonucleases/chemistry/genetics ; Signal Transduction/genetics ; Transcription, Genetic/genetics
    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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  • 4
    Electronic Resource
    Electronic Resource
    Human impacts on the Waikato River system, New Zealand (1996)
    Springer
    GeoJournal 40 (1996), S. 85-99 
    Details
    ISSN: 1572-9893
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geography
    Notes: Abstract The Waikato River drains 13% of the North Island. It rises in the Central Volcanic Plateau; the headwaters, including the Tongariro R., drain into oligotrophic Lake Taupo, important for fishing and holidaying. The river flows north from Taupo for 450 km to the sea near Auckland. Human impacts on the river system have been extensive, primarily dating from European colonisation begun in the 1800s. Most of the catchment below L. Taupo has been altered by agricultural development (mainly sheep and cattle rearing); the original forests and swamps have been lost leading to increased nutrient levels, erosion, light intensities, and water temperatures. There is also extensive use of the water for electricity generation. The Tongarino Power Scheme involves impoundment of water, and the diversion of additional water from the Whanganui River and other catchments with consequent effects on their biota. There are 8 hydro-electric dams on the Waikato River below Taupo causing barriers to migratory animals, downstream effects due to impoundments, and alterations to water flow regimes. Impacts of geothermal power stations, and the water-cooled Huntly Power Station in the lower Waikato are more localised. Eutrophication is enhanced by sewage and stormwater discharges, but all wastes now receive some form of treatment. There are only 340,000 people in the catchment and the major industrial pollution comes from meat and dairy processing and forestry. Some natural pollution results from geothermal inputs. Water abstraction and discharges into the river are now closely regulated. Extensive introductions of exotic biota have been made, notably trout, coarse fish, and macrophytes. The native biota has been little-studied and the biological processes operating in the river are poorly understood. It is not possible to assess the relative importance of eutrophication and habitat change, nor to predict the impacts of future changes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00222535
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  • 5
    Electronic Resource
    Electronic Resource
    A preliminary biological study of the effects of pollution on Farmer's Creek and Cox's River, New South Wales (1966)
    Springer
    Hydrobiologia 27 (1966), S. 160-192 
    Details
    ISSN: 1573-5117
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Biological means were used to assess the effect of organic pollution from sewage effluent and mill-washings in Farmer's Creek and Cox's River (New South Wales). The work was largely qualitative and based on monthly collections of plants and animals for a period of a year. Some additional evidence was produced by a quantitative analysis of the growth of algae on immersed slides, numbers of Protozoa, and numerical counts of the macro-fauna on stones, from a single series of observations. It was found that the association of oligochaetes, chironomids, snails, sewage fungus and small growths of Stigeoclonium and diatoms immediately below the outfall was rapidly succeeded by extensive growths of Stigeoclonium, high counts of Protozoa, and an increase in the number of snails. Recovery from the effects of pollution in Farmer's Creek before the confluence of the two streams was marked by the appearance of stoneflies, dragonflies, mayflies, caddis, and riffle beetles, although snails, limpets, and chironomids were the dominant organisms. In the lower reaches of Cox's River most of the wide range of species found in the clean water above the confluence was recorded, and variations between the fauna at the two stations were regarded as habitat differences. It was found however that the nutrients produced by mineralization of the sewage had induced a more extensive growth of algae in Cox's River. No “indicator species” of pollution was found. The results are compared with chemical analyses and show biological associations provide a means of assessing pollution.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00161494
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  • 6
    Electronic Resource
    Electronic Resource
    The effects of recent environmental changes in Lake Waahi on two forms of the common smelt Retropinna retropinna, and other biota (1987)
    Springer
    Water, air & soil pollution 32 (1987), S. 427-443 
    Details
    ISSN: 1573-2932
    Source: Springer Online Journal Archives 1860-2000
    Topics: Energy, Environment Protection, Nuclear Power Engineering
    Notes: Abstract Since 1977 open cast (open pit) coal mining has increased discharge of silt-laden wastes into Lake Waahi, a small shallow lake in the Waikato River system, New Zealand. Phenolic wastes from a coal carbonization factory on the major tributary also have entered the lake in high but variable concentrations since 1974. During and after the summer of 1978–1979 total suspended solids and turbidity were high, the formerly dense macrophyte beds disappeared, the summer phytoplankton community changed from dominance by blue-green algae to diatoms, the eel fishery failed and the black swan population decreased to low levels. The once abundant lake resident form of the common smelt declined drastically between 1975 and 1981 and apparently was extinct by 1983. The migratory form, although abundant until 1981, was scarce by 1983. Low water levels in the outlet stream and the malfunction of a fish pass in the flood control structure located near its mouth may have impeded upstream migration in the spring of 1982. The major cause for the changes in Lake Waahi was the addition of silt; however, the loss of macrophytes may have caused increased toxicity of phenols, particularly to eels, and also promoted continual resuspension of sediments by more effective wind-produced circulation. Remedial measures are considered.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00225127
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  • 7
    Electronic Resource
    Electronic Resource
    Relationships between zooplankton abundance and trophic state in seven New Zealand lakes (1985)
    Springer
    Hydrobiologia 123 (1985), S. 119-136 
    Details
    ISSN: 1573-5117
    Keywords: New Zealand ; zooplankton ; Calamoecia lucasi ; populations ; multivariate analyses ; trophic levels
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The zooplankton communities of seven Rotorua, New Zealand, lakes of different trophic status were studied in 1977–78. They were generally dominated by the calanoid copepod, Calamoecia lucasi. Bosmina meridionalis occurred in all the lakes and Ceriodaphnia dubia in most. Only small numbers of Macrocyclops albidus ever occurred. Rotifers were not studied in detail. Community composition was similar to that in other northern New Zealand lakes. No well defined patterns of seasonal change in abundance were found and the timing of changes, which were of low magnitude, was different in each lake. Clutch sizes in all species were small. Calamoecia population parameters were analysed using multivariate methods and shown to be related to lake trophic level. Population densities were higher in more productive lakes whereas breeding levels were inversely related to indices of trophic status and population abundance. It is suggested that the populations, as in other northern New Zealand lakes, are food-limited, probably as a consequence of a lack of marked climatic seasonality and the absence of major predation pressures. Groupings of the lakes based on the Calamoecia data are in general agreement with those derived from parallel studies of water chemistry, phytoplankton and macrobenthos.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00018974
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  • 8
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    Adiabatic quenches and amplitude excitations [Physics] (2016)
    National Academy of Sciences
    Details
    Publication Date: 2016-08-24
    Description: Spontaneous symmetry breaking occurs in a physical system whenever the ground state does not share the symmetry of the underlying theory, e.g., the Hamiltonian. This mechanism gives rise to massless Nambu–Goldstone modes and massive Anderson–Higgs modes. These modes provide a fundamental understanding of matter in the Universe and appear as...
    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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  • 9
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    Disruption of both nesprin 1 and desmin results in nuclear anchorage defects and fibrosis in skeletal muscle (2014)
    Oxford University Press
    Details
    Publication Date: 2014-10-22
    Description: Proper localization and anchorage of nuclei within skeletal muscle is critical for cellular function. Alterations in nuclear anchoring proteins modify a number of cellular functions including mechanotransduction, nuclear localization, chromatin positioning/compaction and overall organ function. In skeletal muscle, nesprin 1 and desmin are thought to link the nucleus to the cytoskeletal network. Thus, we hypothesize that both of these factors play a key role in skeletal muscle function. To examine this question, we utilized global ablation murine models of nesprin 1, desmin or both nesprin 1 and desmin. Herein, we have created the nesprin-desmin double-knockout (DKO) mouse, eliminating a major fraction of nuclear-cytoskeletal connections and enabling understanding of the importance of nuclear anchorage in skeletal muscle. Globally, DKO mice are marked by decreased lifespan, body weight and muscle strength. With regard to skeletal muscle, DKO myonuclear anchorage was dramatically decreased compared with wild-type, nesprin 1 –/– and desmin –/– mice. Additionally, nuclear-cytoskeletal strain transmission was decreased in DKO skeletal muscle. Finally, loss of nuclear anchorage in DKO mice coincided with a fibrotic response as indicated by increased collagen and extracellular matrix deposition and increased passive mechanical properties of muscle bundles. Overall, our data demonstrate that nesprin 1 and desmin serve redundant roles in nuclear anchorage and that the loss of nuclear anchorage in skeletal muscle results in a pathological response characterized by increased tissue fibrosis and mechanical stiffness.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 10
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    Investigation of Attenuation of the Lg-Wave Amplitude in the Caribbean Region (2015)
    Seismological Society of America (SSA)
    Details
    Publication Date: 2015-04-01
    Description: The focus of this study is to determine the frequency-dependent quality factor function Q ( f ) for the Caribbean region. The analysis considers the Lg portion of 2685 three-component waveforms. Waveforms are selected from 116 earthquakes that occurred between 2006 and 2013 with moment magnitude M w ranging from 4.6 to 7.0. Spectral amplitudes over 12 distinct passbands from 0.1 to 12.8 Hz are calculated only for waveforms with a signal-to-noise ratio of 5 or better. In the regression model, the vertical component and the geometric mean of two horizontal components are used to estimate Q ( f ). A geometrical spreading function with spectral amplitude decay of R –0.5 is used for distances beyond 100 km. The following quality factor functions for the assumed geometrical spreading are obtained: Q H =310 f 0.54 for the horizontal components, and Q V =235 f 0.65 for the vertical components.
    Print ISSN: 0037-1106
    Electronic ISSN: 1943-3573
    Topics: Geosciences , Physics
    Published by Seismological Society of America (SSA)
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