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  • Male  (4)
  • Molecular Sequence Data  (3)
  • *Seawater  (2)
  • American Association for the Advancement of Science (AAAS)  (9)
  • Elsevier
  • Institute of Physics
  • Wiley
  • 2010-2014  (9)
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  • 1
    Publication Date: 2011-08-13
    Description: Estimates suggest that only one-tenth of the true fungal diversity has been described. Among numerous fungal lineages known only from environmental DNA sequences, Soil Clone Group 1 is the most ubiquitous. These globally distributed fungi may dominate below-ground fungal communities, but their placement in the fungal tree of life has been uncertain. Here, we report cultures of this group and describe the class, Archaeorhizomycetes, phylogenetically placed within subphylum Taphrinomycotina in the Ascomycota. Archaeorhizomycetes comprises hundreds of cryptically reproducing filamentous species that do not form recognizable mycorrhizal structures and have saprotrophic potential, yet are omnipresent in roots and rhizosphere soil and show ecosystem and host root habitat specificity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rosling, Anna -- Cox, Filipa -- Cruz-Martinez, Karelyn -- Ihrmark, Katarina -- Grelet, Gwen-Aelle -- Lindahl, Bjorn D -- Menkis, Audrius -- James, Timothy Y -- New York, N.Y. -- Science. 2011 Aug 12;333(6044):876-9. doi: 10.1126/science.1206958.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Forest Mycology and Pathology, Uppsala BioCentre, SLU, Box 7026, 750 07 Uppsala, Sweden. anna.rosling@slu.se〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21836015" target="_blank"〉PubMed〈/a〉
    Keywords: *Ascomycota/classification/genetics/growth & development/isolation & purification ; Coniferophyta/microbiology ; *Ecosystem ; Genes, Fungal ; Genes, rRNA ; Meristem/*microbiology ; Molecular Sequence Data ; *Mycorrhizae/classification/genetics ; Phylogeny ; Rhizosphere ; *Soil Microbiology
    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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  • 2
    Publication Date: 2011-02-12
    Description: Splicing of mammalian precursor transfer RNA (tRNA) molecules involves two enzymatic steps. First, intron removal by the tRNA splicing endonuclease generates separate 5' and 3' exons. In animals, the second step predominantly entails direct exon ligation by an elusive RNA ligase. Using activity-guided purification of tRNA ligase from HeLa cell extracts, we identified HSPC117, a member of the UPF0027 (RtcB) family, as the essential subunit of a tRNA ligase complex. RNA interference-mediated depletion of HSPC117 inhibited maturation of intron-containing pre-tRNA both in vitro and in living cells. The high sequence conservation of HSPC117/RtcB proteins is suggestive of RNA ligase roles of this protein family in various organisms.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Popow, Johannes -- Englert, Markus -- Weitzer, Stefan -- Schleiffer, Alexander -- Mierzwa, Beata -- Mechtler, Karl -- Trowitzsch, Simon -- Will, Cindy L -- Luhrmann, Reinhard -- Soll, Dieter -- Martinez, Javier -- New York, N.Y. -- Science. 2011 Feb 11;331(6018):760-4. doi: 10.1126/science.1197847.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), A-1030 Vienna, Austria.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21311021" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Exons ; HeLa Cells ; Humans ; Introns ; Molecular Sequence Data ; Proteins/*chemistry/isolation & purification/*metabolism ; RNA Interference ; RNA Ligase (ATP)/*chemistry/isolation & purification/*metabolism ; RNA Precursors/*metabolism ; *RNA Splicing ; RNA, Transfer/*metabolism ; Spliceosomes/metabolism
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    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2010-05-15
    Description: It is predicted that climate change will cause species extinctions and distributional shifts in coming decades, but data to validate these predictions are relatively scarce. Here, we compare recent and historical surveys for 48 Mexican lizard species at 200 sites. Since 1975, 12% of local populations have gone extinct. We verified physiological models of extinction risk with observed local extinctions and extended projections worldwide. Since 1975, we estimate that 4% of local populations have gone extinct worldwide, but by 2080 local extinctions are projected to reach 39% worldwide, and species extinctions may reach 20%. Global extinction projections were validated with local extinctions observed from 1975 to 2009 for regional biotas on four other continents, suggesting that lizards have already crossed a threshold for extinctions caused by climate change.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sinervo, Barry -- Mendez-de-la-Cruz, Fausto -- Miles, Donald B -- Heulin, Benoit -- Bastiaans, Elizabeth -- Villagran-Santa Cruz, Maricela -- Lara-Resendiz, Rafael -- Martinez-Mendez, Norberto -- Calderon-Espinosa, Martha Lucia -- Meza-Lazaro, Rubi Nelsi -- Gadsden, Hector -- Avila, Luciano Javier -- Morando, Mariana -- De la Riva, Ignacio J -- Victoriano Sepulveda, Pedro -- Rocha, Carlos Frederico Duarte -- Ibarguengoytia, Nora -- Aguilar Puntriano, Cesar -- Massot, Manuel -- Lepetz, Virginie -- Oksanen, Tuula A -- Chapple, David G -- Bauer, Aaron M -- Branch, William R -- Clobert, Jean -- Sites, Jack W Jr -- New York, N.Y. -- Science. 2010 May 14;328(5980):894-9. doi: 10.1126/science.1184695.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA. lizardrps@gmail.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20466932" target="_blank"〉PubMed〈/a〉
    Keywords: Acclimatization ; Animals ; *Biodiversity ; Biological Evolution ; Body Temperature ; *Climate Change ; *Ecosystem ; *Extinction, Biological ; Female ; Forecasting ; Geography ; Global Warming ; *Lizards/genetics/physiology ; Male ; Mexico ; Models, Biological ; Phylogeny ; Population Dynamics ; Reproduction ; Seasons ; Selection, Genetic ; Temperature
    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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  • 4
    Publication Date: 2011-09-03
    Description: Recent studies suggest that unidentified prokaryotes fix inorganic carbon at globally significant rates in the immense dark ocean. Using single-cell sorting and whole-genome amplification of prokaryotes from two subtropical gyres, we obtained genomic DNA from 738 cells representing most cosmopolitan lineages. Multiple cells of Deltaproteobacteria cluster SAR324, Gammaproteobacteria clusters ARCTIC96BD-19 and Agg47, and some Oceanospirillales from the lower mesopelagic contained ribulose-1,5-bisphosphate carboxylase-oxygenase and sulfur oxidation genes. These results corroborated community DNA and RNA profiling from diverse geographic regions. The SAR324 genomes also suggested C(1) metabolism and a particle-associated life-style. Microautoradiography and fluorescence in situ hybridization confirmed bicarbonate uptake and particle association of SAR324 cells. Our study suggests potential chemolithoautotrophy in several uncultured Proteobacteria lineages that are ubiquitous in the dark oxygenated ocean and provides new perspective on carbon cycling in the ocean's largest habitat.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Swan, Brandon K -- Martinez-Garcia, Manuel -- Preston, Christina M -- Sczyrba, Alexander -- Woyke, Tanja -- Lamy, Dominique -- Reinthaler, Thomas -- Poulton, Nicole J -- Masland, E Dashiell P -- Gomez, Monica Lluesma -- Sieracki, Michael E -- DeLong, Edward F -- Herndl, Gerhard J -- Stepanauskas, Ramunas -- New York, N.Y. -- Science. 2011 Sep 2;333(6047):1296-300. doi: 10.1126/science.1203690.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Bigelow Laboratory for Ocean Sciences, 180 McKown Point Road, Post Office Box 475, West Boothbay Harbor, ME 04575, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21885783" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/genetics/metabolism ; Carbon Cycle ; Carbon Dioxide/metabolism ; *Chemoautotrophic Growth ; Darkness ; Deltaproteobacteria/classification/genetics/growth & development/*metabolism ; Gammaproteobacteria/classification/genetics/growth & development/*metabolism ; Genes, Bacterial ; Genome, Bacterial ; Metagenome ; Molecular Sequence Data ; Oceans and Seas ; Oxidation-Reduction ; Phylogeny ; Ribulose-Bisphosphate Carboxylase/genetics ; Seawater/*microbiology ; Sulfur/metabolism ; Sulfur Compounds/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2011-06-02
    Description: The retrovirus XMRV (xenotropic murine leukemia virus-related virus) has been detected in human prostate tumors and in blood samples from patients with chronic fatigue syndrome, but these findings have not been replicated. We hypothesized that an understanding of when and how XMRV first arose might help explain the discrepant results. We studied human prostate cancer cell lines CWR22Rv1 and CWR-R1, which produce XMRV virtually identical to the viruses recently found in patient samples, as well as their progenitor human prostate tumor xenograft (CWR22) that had been passaged in mice. We detected XMRV infection in the two cell lines and in the later passage xenografts, but not in the early passages. In particular, we found that the host mice contained two proviruses, PreXMRV-1 and PreXMRV-2, which share 99.92% identity with XMRV over 〉3.2-kilobase stretches of their genomes. We conclude that XMRV was not present in the original CWR22 tumor but was generated by recombination of two proviruses during tumor passaging in mice. The probability that an identical recombinant was generated independently is negligible (~10(-12)); our results suggest that the association of XMRV with human disease is due to contamination of human samples with virus originating from this recombination event.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3278917/" 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/PMC3278917/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Paprotka, Tobias -- Delviks-Frankenberry, Krista A -- Cingoz, Oya -- Martinez, Anthony -- Kung, Hsing-Jien -- Tepper, Clifford G -- Hu, Wei-Shau -- Fivash, Matthew J Jr -- Coffin, John M -- Pathak, Vinay K -- P30 CA093373/CA/NCI NIH HHS/ -- R01CA150197/CA/NCI NIH HHS/ -- R37 CA 089441/CA/NCI NIH HHS/ -- R37 CA089441/CA/NCI NIH HHS/ -- R37 CA089441-11/CA/NCI NIH HHS/ -- ZIA BC011339-02/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2011 Jul 1;333(6038):97-101. doi: 10.1126/science.1205292. Epub 2011 May 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Viral Mutation Section, HIV Drug Resistance Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21628392" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line, Tumor/*virology ; DNA Contamination ; DNA, Viral/analysis ; Endogenous Retroviruses/genetics ; Fatigue Syndrome, Chronic/virology ; Gammaretrovirus/*genetics ; Genes, env ; Genes, gag ; Humans ; Male ; Mice ; Mice, Nude ; Neoplasm Transplantation ; Polymerase Chain Reaction ; Prostatic Neoplasms/*virology ; Proviruses/genetics/isolation & purification ; *Recombination, Genetic ; Transplantation, Heterologous ; Xenotropic murine leukemia virus-related virus/*genetics/*isolation & ; purification
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  • 6
    Publication Date: 2011-08-20
    Description: Most cancer cells are characterized by aneuploidy, an abnormal number of chromosomes. We have identified a clue to the mechanistic origins of aneuploidy through integrative genomic analyses of human tumors. A diverse range of tumor types were found to harbor deletions or inactivating mutations of STAG2, a gene encoding a subunit of the cohesin complex, which regulates the separation of sister chromatids during cell division. Because STAG2 is on the X chromosome, its inactivation requires only a single mutational event. Studying a near-diploid human cell line with a stable karyotype, we found that targeted inactivation of STAG2 led to chromatid cohesion defects and aneuploidy, whereas in two aneuploid human glioblastoma cell lines, targeted correction of the endogenous mutant alleles of STAG2 led to enhanced chromosomal stability. Thus, genetic disruption of cohesin is a cause of aneuploidy in human cancer.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3374335/" 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/PMC3374335/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Solomon, David A -- Kim, Taeyeon -- Diaz-Martinez, Laura A -- Fair, Joshlean -- Elkahloun, Abdel G -- Harris, Brent T -- Toretsky, Jeffrey A -- Rosenberg, Steven A -- Shukla, Neerav -- Ladanyi, Marc -- Samuels, Yardena -- James, C David -- Yu, Hongtao -- Kim, Jung-Sik -- Waldman, Todd -- CA097257/CA/NCI NIH HHS/ -- R01 CA133662/CA/NCI NIH HHS/ -- R01 CA138212/CA/NCI NIH HHS/ -- R01 CA169345/CA/NCI NIH HHS/ -- R01CA115699/CA/NCI NIH HHS/ -- R21CA143282/CA/NCI NIH HHS/ -- Z01 HG200337-01/Intramural NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Aug 19;333(6045):1039-43. doi: 10.1126/science.1203619.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, DC 20057, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21852505" target="_blank"〉PubMed〈/a〉
    Keywords: *Aneuploidy ; Antigens, Nuclear/*genetics/*physiology ; Cell Cycle ; Cell Line ; Cell Line, Tumor ; Chromatids/physiology ; *Chromosomal Instability ; Chromosomes, Human, X/genetics ; Female ; Gene Deletion ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Gene Silencing ; Gene Targeting ; Glioblastoma/*genetics ; Humans ; Karyotyping ; Male ; Melanoma/genetics ; Mutation ; Neoplasms/*genetics ; Polymorphism, Single Nucleotide ; Sarcoma, Ewing/genetics
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 2014-01-25
    Description: Dust deposition in the Southern Ocean constitutes a critical modulator of past global climate variability, but how it has varied temporally and geographically is underdetermined. Here, we present data sets of glacial-interglacial dust-supply cycles from the largest Southern Ocean sector, the polar South Pacific, indicating three times higher dust deposition during glacial periods than during interglacials for the past million years. Although the most likely dust source for the South Pacific is Australia and New Zealand, the glacial-interglacial pattern and timing of lithogenic sediment deposition is similar to dust records from Antarctica and the South Atlantic dominated by Patagonian sources. These similarities imply large-scale common climate forcings, such as latitudinal shifts of the southern westerlies and regionally enhanced glaciogenic dust mobilization in New Zealand and Patagonia.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lamy, F -- Gersonde, R -- Winckler, G -- Esper, O -- Jaeschke, A -- Kuhn, G -- Ullermann, J -- Martinez-Garcia, A -- Lambert, F -- Kilian, R -- New York, N.Y. -- Science. 2014 Jan 24;343(6169):403-7. doi: 10.1126/science.1245424.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Alfred-Wegener-Institut (AWI) Helmholtz-Zentrum fur Polar- und Meeresforschung, Bremerhaven, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24458637" target="_blank"〉PubMed〈/a〉
    Keywords: Climate Change ; *Dust ; *Geologic Sediments ; *Ice Cover ; New Zealand ; Pacific Ocean ; *Seawater
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
    Publication Date: 2014-12-20
    Description: During the last interglacial period, global temperatures were ~2 degrees C warmer than at present and sea level was 6 to 8 meters higher. Southern Ocean sediments reveal a spike in authigenic uranium 127,000 years ago, within the last interglacial, reflecting decreased oxygenation of deep water by Antarctic Bottom Water (AABW). Unlike ice age reductions in AABW, the interglacial stagnation event appears decoupled from open ocean conditions and may have resulted from coastal freshening due to mass loss from the Antarctic ice sheet. AABW reduction coincided with increased North Atlantic Deep Water (NADW) formation, and the subsequent reinvigoration in AABW coincided with reduced NADW formation. Thus, alternation of deep water formation between the Antarctic and the North Atlantic, believed to characterize ice ages, apparently also occurs in warm climates.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hayes, Christopher T -- Martinez-Garcia, Alfredo -- Hasenfratz, Adam P -- Jaccard, Samuel L -- Hodell, David A -- Sigman, Daniel M -- Haug, Gerald H -- Anderson, Robert F -- New York, N.Y. -- Science. 2014 Dec 19;346(6216):1514-7. doi: 10.1126/science.1256620.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02142, USA. Lamont-Doherty Earth Observatory of Columbia University, Palisades, NY 10964, USA. cthayes@mit.edu. ; Geological Institute, ETH Zurich, 8092 Zurich, Switzerland. ; Institute of Geological Sciences and Oeschger Centre for Climate Change Research, University of Bern, 3012 Bern, Switzerland. ; Department of Earth Sciences, University of Cambridge, Cambridge CB2 3EQ, UK. ; Department of Geosciences, Princeton University, Princeton, NJ 08544, USA. ; Lamont-Doherty Earth Observatory of Columbia University, Palisades, NY 10964, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25525246" target="_blank"〉PubMed〈/a〉
    Keywords: Atlantic Ocean ; Climate Change ; *Ice Cover ; Oxygen/analysis ; Salinity ; *Seawater
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
    Publication Date: 2014-05-09
    Description: Throughout life, new neurons are continuously added to the dentate gyrus. As this continuous addition remodels hippocampal circuits, computational models predict that neurogenesis leads to degradation or forgetting of established memories. Consistent with this, increasing neurogenesis after the formation of a memory was sufficient to induce forgetting in adult mice. By contrast, during infancy, when hippocampal neurogenesis levels are high and freshly generated memories tend to be rapidly forgotten (infantile amnesia), decreasing neurogenesis after memory formation mitigated forgetting. In precocial species, including guinea pigs and degus, most granule cells are generated prenatally. Consistent with reduced levels of postnatal hippocampal neurogenesis, infant guinea pigs and degus did not exhibit forgetting. However, increasing neurogenesis after memory formation induced infantile amnesia in these species.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Akers, Katherine G -- Martinez-Canabal, Alonso -- Restivo, Leonardo -- Yiu, Adelaide P -- De Cristofaro, Antonietta -- Hsiang, Hwa-Lin Liz -- Wheeler, Anne L -- Guskjolen, Axel -- Niibori, Yosuke -- Shoji, Hirotaka -- Ohira, Koji -- Richards, Blake A -- Miyakawa, Tsuyoshi -- Josselyn, Sheena A -- Frankland, Paul W -- MOP74650/Canadian Institutes of Health Research/Canada -- MOP86762/Canadian Institutes of Health Research/Canada -- New York, N.Y. -- Science. 2014 May 9;344(6184):598-602. doi: 10.1126/science.1248903.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, M5G 1X8, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24812394" target="_blank"〉PubMed〈/a〉
    Keywords: Amnesia/*pathology/*physiopathology ; Animals ; Dentate Gyrus/cytology ; Female ; Guinea Pigs ; Hippocampus/*cytology ; Male ; *Memory ; Mice ; Mice, Inbred C57BL ; *Neurogenesis ; Neurons/cytology
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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