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  • 1
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    Human recombinant arginase enzyme reduces plasma arginine in mouse models of arginase deficiency (2015)
    Oxford University Press
    Details
    Publication Date: 2015-10-23
    Description: Arginase deficiency is caused by deficiency of arginase 1 (ARG1), a urea cycle enzyme that converts arginine to ornithine. Clinical features of arginase deficiency include elevated plasma arginine levels, spastic diplegia, intellectual disability, seizures and growth deficiency. Unlike other urea cycle disorders, recurrent hyperammonemia is typically less severe in this disorder. Normalization of plasma arginine levels is the consensus treatment goal, because elevations of arginine and its metabolites are suspected to contribute to the neurologic features. Using data from patients enrolled in a natural history study conducted by the Urea Cycle Disorders Consortium, we found that 97% of plasma arginine levels in subjects with arginase deficiency were above the normal range despite conventional treatment. Recently, arginine-degrading enzymes have been used to deplete arginine as a therapeutic strategy in cancer. We tested whether one of these enzymes, a pegylated human recombinant arginase 1 (AEB1102), reduces plasma arginine in murine models of arginase deficiency. In neonatal and adult mice with arginase deficiency, AEB1102 reduced the plasma arginine after single and repeated doses. However, survival did not improve likely, because this pegylated enzyme does not enter hepatocytes and does not improve hyperammonemia that accounts for lethality. Although murine models required dosing every 48 h, studies in cynomolgus monkeys indicate that less frequent dosing may be possible in patients. Given that elevated plasma arginine rather than hyperammonemia is the major treatment challenge, we propose that AEB1102 may have therapeutic potential as an arginine-reducing agent in patients with arginase deficiency.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 2
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    Hypomorphic mutations in TRNT1 cause retinitis pigmentosa with erythrocytic microcytosis (2015)
    Oxford University Press
    Details
    Publication Date: 2015-12-25
    Description: Retinitis pigmentosa (RP) is a highly heterogeneous group of disorders characterized by degeneration of the retinal photoreceptor cells and progressive loss of vision. While hundreds of mutations in more than 100 genes have been reported to cause RP, discovering the causative mutations in many patients remains a significant challenge. Exome sequencing in an individual affected with non-syndromic RP revealed two plausibly disease-causing variants in TRNT1 , a gene encoding a nucleotidyltransferase critical for tRNA processing. A total of 727 additional unrelated individuals with molecularly uncharacterized RP were completely screened for TRNT1 coding sequence variants, and a second family was identified with two members who exhibited a phenotype that was remarkably similar to the index patient. Inactivating mutations in TRNT1 have been previously shown to cause a severe congenital syndrome of sideroblastic anemia, B-cell immunodeficiency, recurrent fevers and developmental delay (SIFD). Complete blood counts of all three of our patients revealed red blood cell microcytosis and anisocytosis with only mild anemia. Characterization of TRNT1 in patient-derived cell lines revealed reduced but detectable TRNT1 protein, consistent with partial function. Suppression of trnt1 expression in zebrafish recapitulated several features of the human SIFD syndrome, including anemia and sensory organ defects. When levels of trnt1 were titrated, visual dysfunction was found in the absence of other phenotypes. The visual defects in the trnt1 -knockdown zebrafish were ameliorated by the addition of exogenous human TRNT1 RNA. Our findings indicate that hypomorphic TRNT1 mutations can cause a recessive disease that is almost entirely limited to the retina.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 3
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    TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD (2016)
    American Chemical Society (ACS)
    Details
    Publication Date: 2016-06-02
    Description: Journal of Chemical Information and Modeling DOI: 10.1021/acs.jcim.6b00103
    Topics: Chemistry and Pharmacology
    Published by American Chemical Society (ACS)
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  • 4
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    Climate‐driven reduction of genetic variation in plant phenology alters soil communities and nutrient pools (2019)
    Wiley
    Details
    Publication Date: 2019
    Description: We examined the hypothesis that climate‐driven evolution of plant traits will influence associated soil microbiomes and ecosystem function across the landscape. We show that (a) as mean annual temperature (MAT) increases, genetic and phenotypic variation for bud break phenology decline; (b) soil microbiomes, soil nitrogen (N), and soil carbon (C) vary in response to MAT and conditioning by trees; and (c) with losses of genetic variation due to warming, population‐level regulation of community and ecosystem functions strengthen. These results demonstrate a relationship between the potential evolutionary response of populations and subsequent shifts in ecosystem function along a large temperature gradient. Abstract We examined the hypothesis that climate‐driven evolution of plant traits will influence associated soil microbiomes and ecosystem function across the landscape. Using a foundation tree species, Populus angustifolia, observational and common garden approaches, and a base population genetic collection that spans 17 river systems in the western United States, from AZ to MT, we show that (a) as mean annual temperature (MAT) increases, genetic and phenotypic variation for bud break phenology decline; (b) soil microbiomes, soil nitrogen (N), and soil carbon (C) vary in response to MAT and conditioning by trees; and (c) with losses of genetic variation due to warming, population‐level regulation of community and ecosystem functions strengthen. These results demonstrate a relationship between the potential evolutionary response of populations and subsequent shifts in ecosystem function along a large temperature gradient.
    Print ISSN: 1354-1013
    Electronic ISSN: 1365-2486
    Topics: Biology , Energy, Environment Protection, Nuclear Power Engineering , Geography
    Published by Wiley
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  • 5
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    Genetic variation at the MHC DRB1 locus is similar across Gunnison's prairie dog (Cynomys gunnisoni) colonies regardless of plague history (2016)
    Wiley
    Details
    Publication Date: 2016-03-18
    Description: Yersinia pestis was introduced to North America around 1900 and leads to nearly 100% mortality in prairie dog ( Cynomys spp.) colonies during epizootic events, which suggests this pathogen may exert a strong selective force. We characterized genetic diversity at an MHC class II locus ( DRB1 ) in Gunnison's prairie dog ( C. gunnisoni ) and quantified population genetic structure at the DRB1 versus 12 microsatellite loci in three large Arizona colonies. Two colonies, Seligman (SE) and Espee Ranch (ES), have experienced multiple plague-related die-offs in recent years, whereas plague has never been documented at Aubrey Valley (AV). We found fairly low allelic diversity at the DRB1 locus, with one allele ( DRB1 *01) at high frequency (0.67–0.87) in all colonies. Two other DRB1 alleles appear to be trans-species polymorphisms shared with the black-tailed prairie dog ( C. ludovicianus ), indicating that these alleles have been maintained across evolutionary time frames. Estimates of genetic differentiation were generally lower at the MHC locus ( F ST  = 0.033) than at microsatellite markers ( F ST  = 0.098). The reduced differentiation at DRB1 may indicate that selection has been important for shaping variation at MHC loci, regardless of the presence or absence of plague in recent decades. However, genetic drift has probably also influenced the DRB1 locus because its level of differentiation was not different from that of microsatellites in an F ST outlier analysis. We then compared specific MHC alleles to plague survivorship in 60 C. gunnisoni that had been experimentally infected with Y. pestis . We found that survival was greater in individuals that carried at least one copy of the most common allele ( DRB1 *01) compared to those that did not (60% vs. 20%). Although the sample sizes of these two groups were unbalanced, this result suggests the possibility that this MHC class II locus, or a nearby linked gene, could play a role in plague survival. Yersinia pestis leads to nearly 100% mortality in prairie dog ( Cynomys spp.) colonies during epizootic events and may have exerted a strong selective force over the past 100 years. We investigated the variation at an important immune system gene, the MHC- DRB 1, in three large prairie dog colonies from Arizona. Genetic diversity and differentiation was generally lower at the MHC gene than at microsatellite markers, indicating that selection and past demography have both been important for shaping variation at MHC loci regardless of the presence or absence of plague in recent decades.
    Electronic ISSN: 2045-7758
    Topics: Biology
    Published by Wiley
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  • 6
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    Education. Undergraduate research experiences: impacts and opportunities (2015)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2015-02-07
    Description: Most undergraduates give high ratings to research experiences. Studies report that these experiences improve participation and persistence, often by strengthening students' views of themselves as scientists. Yet, the evidence for these claims is weak. More than half the 60 studies reviewed rely on self-report surveys or interviews. Rather than introducing new images of science, research experiences may reinforce flawed images especially of research practices and conceptual understanding. The most convincing studies show benefits for mentoring and for communicating the nature of science, but the ideas that students learn are often isolated or fragmented rather than integrated and coherent. Rigorous research is needed to identify ways to design research experiences so that they promote integrated understanding. These studies need powerful and generalizable assessments that can document student progress, help distinguish effective and ineffective aspects of the experiences, and illustrate how students interpret the research experiences they encounter. To create research experiences that meet the needs of interested students and make effective use of scarce resources, we encourage systematic, iterative studies with multiple indicators of success.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Linn, Marcia C -- Palmer, Erin -- Baranger, Anne -- Gerard, Elizabeth -- Stone, Elisa -- New York, N.Y. -- Science. 2015 Feb 6;347(6222):1261757. doi: 10.1126/science.1261757.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of California, Berkeley, CA, USA. mclinn@berkeley.edu. ; University of California, Berkeley, CA, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25657254" target="_blank"〉PubMed〈/a〉
    Keywords: *Career Choice ; Curriculum ; *Mentors ; Research/*education ; Students
    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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  • 7
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    Challenges of Integrating Stochastic Dynamics and Cryo-Electron Tomograms in Whole-Cell Simulations (2017)
    American Chemical Society (ACS)
    Details
    Publication Date: 2017-03-31
    Description: The Journal of Physical Chemistry B DOI: 10.1021/acs.jpcb.7b00672
    Electronic ISSN: 1520-5207
    Topics: Chemistry and Pharmacology , Physics
    Published by American Chemical Society (ACS)
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  • 8
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    Ecosystem consequences of plant genetic divergence with colonization of new habitat (2017)
    Wiley
    In: Ecosphere
    Details
    Publication Date: 2017-05-27
    Description: When plants colonize new habitats altered by natural or anthropogenic disturbances, those individuals may encounter biotic and abiotic conditions novel to the species, which can cause plant functional trait divergence. Over time, site-driven adaptation can give rise to population-level genetic variation, with consequences for plant community dynamics and ecosystem processes. We used a series of 3000-yr-old, lava-created forest fragments on the Island of Hawai`i to examine whether disturbance and subsequent colonization can lead to genetically differentiated populations, and where differentiation occurs, if there are ecosystem consequences of trait-driven changes. These fragments are dominated by a single tree species, Metrosideros polymorpha (Myrtaceae) or ʻōhiʻa, which have been actively colonizing the surrounding lava flow created in 1858. To test our ideas about differentiation of genetically determined traits, we (1) created rooted cuttings of ʻōhiʻa individuals sampled from fragment interiors and open lava sites, raised these individuals in a greenhouse, and then used these cuttings to create a common garden where plant growth was monitored for three years; and (2) assessed genetic variation and made Q ST / F ST comparisons using microsatellite repeat markers. Results from the greenhouse showed quantitative trait divergence in plant height and pubescence across plants sampled from fragment interior and matrix sites. Results from the subsequent common garden study confirmed that the matrix environment can select for individuals with 9.1% less shoot production and 17.3% higher leaf pubescence. We found no difference in molecular genetic variation indicating gene flow among the populations. The strongest Q ST level was greater than the F ST estimate, indicating sympatric genetic divergence in growth traits. Tree height was correlated with ecosystem properties such as soil carbon and nitrogen storage, soil carbon turnover rates, and soil phosphatase activity, indicating that selection for growth traits will influence structure, function, and dynamics of developing ecosystems. These data show that divergence can occur on centennial timescales of early colonization.
    Electronic ISSN: 2150-8925
    Topics: Energy, Environment Protection, Nuclear Power Engineering
    Published by Wiley on behalf of The Ecological Society of America (ESA).
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  • 9
    Electronic Resource
    Electronic Resource
    Laboratory Machine for the Continuous Production of Grease (1947)
    s.l. : American Chemical Society
    Industrial & engineering chemistry 39 (1947), S. 506-507 
    Details
    ISSN: 1520-5045
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ie50448a018
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    Paper (German National Licenses)
    Fulltext
  • 10
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    Protein misfolding and the pathogenesis of ABCA4-associated retinal degenerations (2015)
    Oxford University Press
    Details
    Publication Date: 2015-05-09
    Description: Mutations in the ABCA4 gene are a common cause of autosomal recessive retinal degeneration. All mouse models to date are based on knockouts of Abca4 , even though the disease is often caused by missense mutations such as the complex allele L541P;A1038V (PV). We now show that the PV mutation causes severe human disease whereas the V mutation alone causes mild disease. Mutant ABCA4 proteins expressed heterologously in mammalian cells retained normal cellular localization. However, basal and all- trans -retinal-stimulated ATPase activities were reduced substantially for P and PV but only mildly for V. Electron microscopy revealed marked structural changes and misfolding for the P and PV mutants but few changes for the V mutant, consistent with the disease severity difference in patients. We generated Abca4 PV/PV knock-in mice homozygous for the complex PV allele to investigate the effects of this misfolding mutation in vivo . Mutant ABCA4 RNA levels approximated WT ABCA4 RNA levels but, surprisingly, only trace amounts of mutant ABCA4 protein were noted in the retina. RNA sequencing of WT, Abca4 –/– and Abca4 PV/PV mice revealed mild gene expression alterations in the retina and RPE. Similar to Abca4 –/– mice, Abca4 PV/PV mice showed substantial A2E and lipofuscin accumulation in their RPE cells but no retinal degeneration up to 12 months of age. Thus, rapid degradation of this large misfolded mutant protein in mouse retina caused little detectable photoreceptor degeneration. These findings suggest likely differences in the unfolded protein response between murine and human photoreceptors and support development of therapies directed at increasing this capability in patients.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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