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  • 1
    Publication Date: 2014-02-19
    Description: The exploration of protease substrate specificity is generally restricted to naturally occurring amino acids, limiting the degree of conformational space that can be surveyed. We substantially enhanced this by incorporating 102 unnatural amino acids to explore the S1–S4 pockets of human neutrophil elastase. This approach provides hybrid natural and unnatural...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 2
    Publication Date: 2013-05-15
    Description: Macropinocytosis is a highly conserved endocytic process by which extracellular fluid and its contents are internalized into cells through large, heterogeneous vesicles known as macropinosomes. Oncogenic Ras proteins have been shown to stimulate macropinocytosis but the functional contribution of this uptake mechanism to the transformed phenotype remains unknown. Here we show that Ras-transformed cells use macropinocytosis to transport extracellular protein into the cell. The internalized protein undergoes proteolytic degradation, yielding amino acids including glutamine that can enter central carbon metabolism. Accordingly, the dependence of Ras-transformed cells on free extracellular glutamine for growth can be suppressed by the macropinocytic uptake of protein. Consistent with macropinocytosis representing an important route of nutrient uptake in tumours, its pharmacological inhibition compromises the growth of Ras-transformed pancreatic tumour xenografts. These results identify macropinocytosis as a mechanism by which cancer cells support their unique metabolic needs and point to the possible exploitation of this process in the design of anticancer therapies.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3810415/" 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/PMC3810415/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Commisso, Cosimo -- Davidson, Shawn M -- Soydaner-Azeloglu, Rengin G -- Parker, Seth J -- Kamphorst, Jurre J -- Hackett, Sean -- Grabocka, Elda -- Nofal, Michel -- Drebin, Jeffrey A -- Thompson, Craig B -- Rabinowitz, Joshua D -- Metallo, Christian M -- Vander Heiden, Matthew G -- Bar-Sagi, Dafna -- 5 P30CA016087-32/CA/NCI NIH HHS/ -- P01 CA104838/CA/NCI NIH HHS/ -- P01 CA117969/CA/NCI NIH HHS/ -- P01-CA117969/CA/NCI NIH HHS/ -- P30 CA014051/CA/NCI NIH HHS/ -- P30-CA14051-39/CA/NCI NIH HHS/ -- R01 CA055360/CA/NCI NIH HHS/ -- R01 CA105463/CA/NCI NIH HHS/ -- R01 CA163591/CA/NCI NIH HHS/ -- R01CA055360/CA/NCI NIH HHS/ -- Canadian Institutes of Health Research/Canada -- England -- Nature. 2013 May 30;497(7451):633-7. doi: 10.1038/nature12138. Epub 2013 May 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23665962" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acids/*metabolism ; Animals ; Biological Transport ; Carbon/metabolism ; Cell Line, Transformed ; Cell Line, Tumor ; Cell Proliferation ; *Cell Transformation, Neoplastic/genetics ; Disease Models, Animal ; Female ; Glutamine/metabolism ; Mice ; Mice, Nude ; NIH 3T3 Cells ; Oncogene Protein p21(ras)/genetics/*metabolism ; Pancreatic Neoplasms/genetics/*metabolism/*pathology ; *Pinocytosis ; Proteolysis
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2016-04-07
    Description: Cells receive growth and survival stimuli through their attachment to an extracellular matrix (ECM). Overcoming the addiction to ECM-induced signals is required for anchorage-independent growth, a property of most malignant cells. Detachment from ECM is associated with enhanced production of reactive oxygen species (ROS) owing to altered glucose metabolism. Here we identify an unconventional pathway that supports redox homeostasis and growth during adaptation to anchorage independence. We observed that detachment from monolayer culture and growth as anchorage-independent tumour spheroids was accompanied by changes in both glucose and glutamine metabolism. Specifically, oxidation of both nutrients was suppressed in spheroids, whereas reductive formation of citrate from glutamine was enhanced. Reductive glutamine metabolism was highly dependent on cytosolic isocitrate dehydrogenase-1 (IDH1), because the activity was suppressed in cells homozygous null for IDH1 or treated with an IDH1 inhibitor. This activity occurred in absence of hypoxia, a well-known inducer of reductive metabolism. Rather, IDH1 mitigated mitochondrial ROS in spheroids, and suppressing IDH1 reduced spheroid growth through a mechanism requiring mitochondrial ROS. Isotope tracing revealed that in spheroids, isocitrate/citrate produced reductively in the cytosol could enter the mitochondria and participate in oxidative metabolism, including oxidation by IDH2. This generates NADPH in the mitochondria, enabling cells to mitigate mitochondrial ROS and maximize growth. Neither IDH1 nor IDH2 was necessary for monolayer growth, but deleting either one enhanced mitochondrial ROS and reduced spheroid size, as did deletion of the mitochondrial citrate transporter protein. Together, the data indicate that adaptation to anchorage independence requires a fundamental change in citrate metabolism, initiated by IDH1-dependent reductive carboxylation and culminating in suppression of mitochondrial ROS.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4860952/" 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/PMC4860952/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jiang, Lei -- Shestov, Alexander A -- Swain, Pamela -- Yang, Chendong -- Parker, Seth J -- Wang, Qiong A -- Terada, Lance S -- Adams, Nicholas D -- McCabe, Michael T -- Pietrak, Beth -- Schmidt, Stan -- Metallo, Christian M -- Dranka, Brian P -- Schwartz, Benjamin -- DeBerardinis, Ralph J -- R01 CA157996/CA/NCI NIH HHS/ -- R01 CA188652/CA/NCI NIH HHS/ -- R01CA157996/CA/NCI NIH HHS/ -- R01CA188652/CA/NCI NIH HHS/ -- England -- Nature. 2016 Apr 14;532(7598):255-8. doi: 10.1038/nature17393. Epub 2016 Apr 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Children's Medical Center Research Institute, UT Southwestern Medical Center, Dallas, Texas 75390-8502, USA. ; Department of Radiology, University of Pennsylvania School of Medicine, 3620 Hamilton Walk, Philadelphia, Pennsylvania 19104, USA. ; Seahorse Bioscience, 16 Esquire Road, North Billerica, Massachusetts 01862, USA. ; Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA. ; Touchstone Diabetes Center, UT Southwestern Medical Center, Dallas, Texas 75390, USA. ; Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas 75390, USA. ; GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, USA. ; Department of Pediatrics, UT Southwestern Medical Center, Dallas, Texas 75390, USA. ; McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, Texas 75390, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27049945" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Adhesion ; Cell Hypoxia ; Cell Line, Tumor ; Cell Proliferation ; Citric Acid/*metabolism ; Contact Inhibition ; Cytosol/enzymology/metabolism ; Extracellular Matrix/metabolism ; Glucose/metabolism ; Glutamic Acid/metabolism ; Glutamine/metabolism ; *Homeostasis ; Humans ; Isocitrate Dehydrogenase/antagonists & inhibitors/deficiency/genetics/*metabolism ; Isocitrates/metabolism ; Mitochondria/*metabolism ; NADP/biosynthesis ; Neoplasms/enzymology/*metabolism/*pathology ; Oxidation-Reduction ; Oxidative Stress ; Reactive Oxygen Species/*metabolism ; Spheroids, Cellular/metabolism/pathology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
    Electronic Resource
    Electronic Resource
    Springer
    Bulletin of environmental contamination and toxicology 60 (1998), S. 425-432 
    ISSN: 1432-0800
    Source: Springer Online Journal Archives 1860-2000
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Medicine
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    Springer
    Entomologia experimentalis et applicata 54 (1990), S. 237-244 
    ISSN: 1570-7458
    Keywords: Rhopalosiphum padi ; aphids ; morphs ; intermediate morph ; gynoparae ; alate exules ; host selection ; suction traps
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Description / Table of Contents: Résumé Des femelles de R. padi L. ont été capturées vivantes dans des pièges a succion en 1986–88. Les ailés exules et les gynopares ont été identifiés par le morphe de leurs descendants. Les gynopares ont remplacé généralement les ailés exules en septembre, ce qui montre que la majorité de la population est holocyclique même dans le sud de l'Angleterre où l'hôte primaire, Prunus padus L., est rare. Cependant, quelques ailés exules se maintiennent pendant l'automne montrant qu'une partie de la population est anholocyclique. Au cours de l'automne, on observe un morphe intermédiaire entre les ailés exules et les gynopares. Les exules ailés et les gynopares préfèrent respectivement l'orge et P. padus, sur lesquels ils s'installent et produisent des larves; les gynopares étaient moins sélectifs que les exules, peut-être par suite d'une rupture physiologique incomplète de leur préférence pour l'orge sur laquelle ils se développent rendant moins impérative leur attraction par P. padus sur lequel leur cycle sexuel est complet. Les individus intermédiaires préfèrent s'établir sur P. padus, mais leur larves virginipares et ovipares sont produites respectivement sur oreg et sur P. padus. Les morphes intermédiaires maintenus en jours courts (L12/N12) ont donné surtout des virginipares aptères les mâles apparaissant à la fin de leur vie; des intermédiaires sont apparus occasionnellement parmi les aptères. Les intermédiaires seraient une composante programmée de la structure polymorphe et contribueraient à la fois à l'apparition des fractions holocyclique et anholocyclique de la population.
    Notes: Abstract Alate female Rhopalosiphum padi (L.) were trapped alive in suction traps in autumn, 1986–1988. Alate exules and gynoparae were identified by the morph of their offspring. Gynoparae largely replaced alate exules in September indicating that most of the population were holocyclic even in southern England where the primary host, Prunus padus L., is scarce. However, a few alate exules occurred throughout the autumn indicating that a proportion of the population is anholocyclic. A morph intermediate between alate exules and gynoparae occurred at low frequency throughout the autumn. Alate exules and gynoparae preferred barley and P. padus, respectively, on which to settle and larviposit; gynoparae were less selective than exules possibly due to an incomplete physiological switch from a preference for Gramineae to P. padus on which the sexual cycle is completed. Intermediate individuals preferred to settle on P. padus, but their virginoparous and oviparous nymphs were produced on barley and P. padus respectively. Intermediate morphs maintained under continuous short day conditions (L12 : D12) produced mainly apterous virginoparae with males occurring at the end of their reproductive live; intermediates occurred occasionally amongst the apterae. It is proposed that intermediates are a programmed component of the morph structure and have the potential to contribute to both the holocyclic and anholocyclic portions of the population.
    Type of Medium: Electronic Resource
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  • 6
    Publication Date: 2012-04-23
    Description: Groundwater in Chalk catchments is a major resource that also helps support internationally important habitats and ecosystems. Its dual porosity and dual permeability properties, coupled with large-scale structural features (such as hard rock layers and marls), produce a highly complex hydrogeological system. Recent impacts from groundwater flooding as well as vulnerability to drought have raised questions over the ability of traditional approaches to model these aquifers. Current work on near-surface hydrological processes has highlighted the importance of the soil and weathered zone for controlling recharge rates. In addition, karst-like features, sedimentary deposits and valley bottom processes govern stream–aquifer interaction and present a challenge in their representation in any modelling system. Methods that have, and are being, developed to incorporate these features, and their use in modelling Chalk catchments, are described. These are required in order to address major challenges, such as groundwater flooding and drought impacts, both of which could become more frequent and intense as a result of climate change.
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  • 7
    Publication Date: 1994-12-01
    Print ISSN: 0818-9641
    Electronic ISSN: 1440-1711
    Topics: Biology , Medicine
    Published by Wiley
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  • 8
    Publication Date: 2015-12-19
    Description: Author(s): D. Smalley, H. Iwasaki, P. Navrátil, R. Roth, J. Langhammer, V. M. Bader, D. Bazin, J. S. Berryman, C. M. Campbell, J. Dohet-Eraly, P. Fallon, A. Gade, C. Langer, A. Lemasson, C. Loelius, A. O. Macchiavelli, C. Morse, J. Parker, S. Quaglioni, F. Recchia, S. R. Stroberg, D. Weisshaar, K. Whitmore, and K. Wimmer We studied transition rates for the lowest 1 / 2 + and 5 / 2 + excited states of C 17 through lifetime measurements with the GRETINA array using the recoil-distance method. The present measurements provide a model-independent determination of transition strengths giving the values of B ( M 1 ; 1 / 2 + → 3 / 2 g . s . + ) = 1 . … [Phys. Rev. C 92, 064314] Published Fri Dec 18, 2015
    Keywords: Nuclear Structure
    Print ISSN: 0556-2813
    Electronic ISSN: 1089-490X
    Topics: Physics
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  • 9
    Publication Date: 2015-02-26
    Description: Cytosolic accumulation of TAR DNA binding protein 43 (TDP-43) is a major neuropathological feature of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). However, the mechanisms involved in TDP-43 accumulation remain largely unknown. Previously, we reported that inhibitors of cyclin-dependent kinases (CDKs) prevented cytosolic stress granule accumulation of TDP-43, correlating with depletion of heterogeneous ribonucleoprotein (hnRNP) K from stress granules. In the present study, we further investigated the relationship between TDP-43 and hnRNP K and their control by CDKs. Inhibition of CDK2 abrogated the accumulation of TDP-43 into stress granules. Phosphorylated CDK2 co-localized with accumulated TDP-43 and phosphorylated hnRNP K in stress granules. Inhibition of CDK2 phosphorylation blocked phosphorylation of hnRNP K, preventing its incorporation into stress granules. Due to interaction between hnRNP K with TDP-43, the loss of hnRNP K from stress granules prevented accumulation of TDP-43. Mutation of Ser216 and Ser284 phosphorylation sites on hnRNP K inhibited hnRNP K- and TDP-43-positive stress granule formation in transfected cells. The interaction between hnRNP K and TDP-43 was further confirmed by the loss of TDP-43 accumulation following siRNA-mediated inhibition of hnRNP K expression. A substantial decrease of CDK2 and hnRNP K expression in spinal cord motor neurons in ALS patients demonstrates a potential key role for these proteins in ALS and TDP-43 accumulation, indicating that further investigation of the association between hnRNP K and TDP-43 is warranted. Understanding how kinase activity modulates TDP-43 accumulation may provide new pharmacological targets for disease intervention.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 10
    Publication Date: 2015-01-16
    Description: Many regulatory mechanisms require a high degree of specificity in protein-DNA binding. Nucleotide sequence does not provide an answer to the question of why a protein binds only to a small subset of the many putative binding sites in the genome that share the same core motif. Whereas higher-order effects, such as chromatin accessibility, cooperativity and cofactors, have been described, DNA shape recently gained attention as another feature that fine-tunes the DNA binding specificities of some transcription factor families. Our G enome B rowser for DNA shape annotations (GBshape; freely available at http://rohslab.cmb.usc.edu/GBshape/ ) provides minor groove width, propeller twist, roll, helix twist and hydroxyl radical cleavage predictions for the entire genomes of 94 organisms. Additional genomes can easily be added using the GBshape framework. GBshape can be used to visualize DNA shape annotations qualitatively in a genome browser track format, and to download quantitative values of DNA shape features as a function of genomic position at nucleotide resolution. As biological applications, we illustrate the periodicity of DNA shape features that are present in nucleosome-occupied sequences from human, fly and worm, and we demonstrate structural similarities between transcription start sites in the genomes of four Drosophila species.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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