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  • 1
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    Expression, functionality and localization of apurinic/apyrimidinic endonucleases in replicative and non-replicative forms of Trypanosoma cruzi (2013)
    Wiley
    Details
    Publication Date: 2013-10-01
    Description: Trypanosoma cruzi is the etiological agent of Chagas disease. The parasite has to overcome oxidative damage by ROS/RNS all along its life cycle to survive and to establish a chronic infection. We propose that T. cruzi is able to survive, among other mechanisms of detoxification, by repair of its damaged DNA through activation of the DNA base excision repair (BER) pathway. BER is highly conserved in eukaryotes with apurinic/apirimidinic endonucleases (APEs) playing a fundamental role. Previous results showed that T. cruzi exposed to hydrogen peroxide and peroxinitrite significantly decreases its viability when co-incubated with methoxyamine, an AP endonuclease inhibitor. In this work the localization, expression and functionality of two T. cruzi APEs (TcAP1, Homo sapiens APE1 orthologous and TcAP2, orthologous to Homo sapiens APE2 and to Schizosaccaromyces pombe Apn2p) were determined. These enzymes are present and active in the two replicative parasite forms (epimastigotes and amastigotes) as well as in the non-replicative, infective trypomastigotes. TcAP1 and TcAP2 are located in the nucleus of epimastigotes and their expression is constitutive. Epimastigote AP endonucleases as well as recombinant TcAP1 and TcAP2 are inhibited by methoxyamine. Overexpression of TcAP1 increases epimastigotes viability when they are exposed to acute ROS/RNS attack. This protective effect is more evident when parasites are submitted to persistent ROS/RNS exposition, mimicking nature conditions. Our results confirm that the BER pathway is involved in T. cruzi resistance to DNA oxidative damage and points to the participation of DNA AP endonucleases in parasite survival. J. Cell. Biochem. © 2013 Wiley Periodicals, Inc.
    Electronic ISSN: 0091-7419
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Published by Wiley
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  • 2
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    Latitudinal variation in soil nematode communities under climate warming‐related range‐expanding and native plants (2019)
    Wiley
    Details
    Publication Date: 2019
    Description: In Europe, we explored latitudinal community shifts for nematodes—abundant soil organisms that include root herbivores—in the rhizospheres of climate change‐driven range‐expanding plant species. We sampled nematode communities of several range‐expanding plant species along their expansion trajectory and compared these nematode communities with those of related plant species that are native along the entire expansion gradient. We show that nematode communities change with latitude, but that the strength of nematode community shifts strongly depends on range‐expanding plant species. Abstract Current climate change has led to latitudinal and altitudinal range expansions of numerous species. During such range expansions, plant species are expected to experience changes in interactions with other organisms, especially with belowground biota that have a limited dispersal capacity. Nematodes form a key component of the belowground food web as they include bacterivores, fungivores, omnivores and root herbivores. However, their community composition under climate change‐driven intracontinental range‐expanding plants has been studied almost exclusively under controlled conditions, whereas little is known about actual patterns in the field. Here, we use novel molecular sequencing techniques combined with morphological quantification in order to examine nematode communities in the rhizospheres of four range‐expanding and four congeneric native species along a 2,000 km latitudinal transect from South‐Eastern to North‐Western Europe. We tested the hypotheses that latitudinal shifts in nematode community composition are stronger in range‐expanding plant species than in congeneric natives and that in their new range, range‐expanding plant species accumulate fewest root‐feeding nematodes. Our results show latitudinal variation in nematode community composition of both range expanders and native plant species, while operational taxonomic unit richness remained the same across ranges. Therefore, range‐expanding plant species face different nematode communities at higher latitudes, but this is also the case for widespread native plant species. Only one of the four range‐expanding plant species showed a stronger shift in nematode community composition than its congeneric native and accumulated fewer root‐feeding nematodes in its new range. We conclude that variation in nematode community composition with increasing latitude occurs for both range‐expanding and native plant species and that some range‐expanding plant species may become released from root‐feeding nematodes in the new range.
    Print ISSN: 1354-1013
    Electronic ISSN: 1365-2486
    Topics: Biology , Energy, Environment Protection, Nuclear Power Engineering , Geography
    Published by Wiley
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  • 3
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    Accelerated Diversification of Nonhuman Primate Malarias in Southeast Asia: Adaptive Radiation or Geographic Speciation? (2015)
    Oxford University Press
    Details
    Publication Date: 2015-01-20
    Description: Although parasitic organisms are found worldwide, the relative importance of host specificity and geographic isolation for parasite speciation has been explored in only a few systems. Here, we study Plasmodium parasites known to infect Asian nonhuman primates, a monophyletic group that includes the lineage leading to the human parasite Plasmodium vivax and several species used as laboratory models in malaria research. We analyze the available data together with new samples from three sympatric primate species from Borneo: The Bornean orangutan and the long-tailed and the pig-tailed macaques . We find several species of malaria parasites, including three putatively new species in this biodiversity hotspot. Among those newly discovered lineages, we report two sympatric parasites in orangutans. We find no differences in the sets of malaria species infecting each macaque species indicating that these species show no host specificity. Finally, phylogenetic analysis of these data suggests that the malaria parasites infecting Southeast Asian macaques and their relatives are speciating three to four times more rapidly than those with other mammalian hosts such as lemurs and African apes. We estimate that these events took place in approximately a 3–4-Ma period. Based on the genetic and phenotypic diversity of the macaque malarias, we hypothesize that the diversification of this group of parasites has been facilitated by the diversity, geographic distributions, and demographic histories of their primate hosts.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    Consistent effects of nitrogen amendments on soil microbial communities and processes across biomes (2012)
    Wiley
    Details
    Publication Date: 2012-04-15
    Description: Ecosystems worldwide are receiving increasing amounts of reactive nitrogen (N) via anthropogenic activities with the added N having potentially important impacts on microbially mediated belowground carbon dynamics. However, a comprehensive understanding of how elevated N availability affects soil microbial processes and community dynamics remains incomplete. The mechanisms responsible for the observed responses are poorly resolved and we do not know if soil microbial communities respond in a similar manner across ecosystems. We collected 28 soils from a broad range of ecosystems in North America, amended soils with inorganic N, and incubated the soils under controlled conditions for 1 year. Consistent across nearly all soils, N addition decreased microbial respiration rates, with an average decrease of 11% over the year-long incubation, and decreased microbial biomass by 35%. High-throughput pyrosequencing showed that N addition consistently altered bacterial community composition, increasing the relative abundance of Actinobacteria and Firmicutes , and decreasing the relative abundance of Acidobacteria and Verrucomicrobia . Further, N-amended soils consistently had lower activities in a broad suite of extracellular enzymes and had decreased temperature sensitivity, suggesting a shift to the preferential decomposition of more labile C pools. The observed trends held across strong gradients in climate and soil characteristics, indicating that the soil microbial responses to N addition are likely controlled by similar wide-spread mechanisms. Our results support the hypothesis that N addition depresses soil microbial activity by shifting the metabolic capabilities of soil bacterial communities, yielding communities that are less capable of decomposing more recalcitrant soil carbon pools and leading to a potential increase in soil carbon sequestration rates.
    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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    Evidence for middle Eocene and younger land emergence in central Panama: Implications for Isthmus closure (2012)
    Geological Society of America (GSA)
    Details
    Publication Date: 2012-05-01
    Description: The rise of the Isthmus of Panama, linked to a number of climatic, paleoceanographic, and biological events, has been studied mostly from indirect, often distal, geochemical and biotic evidence. We have upgraded existing geologic mapping in central Panama with more than 2000 field stations, over 40 petrographic analyses, and more than 30 new geochronological and thermochronological analyses. This data set suggests that the isthmus was an uninterrupted chain above sea level from late Eocene until at least late Miocene times. The basement complex of central Panama is a folded-faulted, ∼3-km-thick arc sequence, intruded by granitoid bodies and onlapped by mildly deformed upper Eocene and Oligocene strata. Six U/Pb zircon ages in the granitoids—along with published geochronological data—reveal intense late Paleocene to middle Eocene magmatism (58–39 Ma), a temporary cessation of magmatic activity between 38 and 27 Ma, and renewed magmatism between 25 and 15 Ma in a position ∼75 km south of the former magmatic axis. Thermochronological analyses in zircon (eight U-Th/He ages), and in apatite crystals (four U-Th/He ages and nine fission-track ages) obtained from a subset of 58–54 Ma granitoid bodies record a concordant Lutetian-age (47–42 Ma) cooling from ∼200 °C to ∼70 °C in ∼5 m.y., and cooling below ∼40 °C between 12 and 9 Ma. Cooling is linked to exhumation by an angular unconformity that separates the deformed basement complex below from mildly deformed, upper Eocene to Oligocene terrestrial to shallow-marine strata above. Exhumation and erosion of the basement complex are independently confirmed by lower Miocene strata that have a detrital zircon signature that closely follows the central Panama basement complex age distribution. These results greatly restrict the width and depth of the strait separating southern Central America from South America, and challenge the widely accepted notion that the Central American Seaway closed in late Pliocene time, when the ice age began.
    Print ISSN: 0016-7606
    Electronic ISSN: 1943-2674
    Topics: Geosciences
    Published by Geological Society of America (GSA)
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  • 6
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    Latitudinal variation in soil nematode communities under climate warming‐related range‐expanding and native plants (2019)
    Wiley
    Details
    Publication Date: 2019
    Description: In Europe, we explored latitudinal community shifts for nematodes—abundant soil organisms that include root herbivores—in the rhizospheres of climate change‐driven range‐expanding plant species. We sampled nematode communities of several range‐expanding plant species along their expansion trajectory and compared these nematode communities with those of related plant species that are native along the entire expansion gradient. We show that nematode communities change with latitude, but that the strength of nematode community shifts strongly depends on range‐expanding plant species. Abstract Current climate change has led to latitudinal and altitudinal range expansions of numerous species. During such range expansions, plant species are expected to experience changes in interactions with other organisms, especially with belowground biota that have a limited dispersal capacity. Nematodes form a key component of the belowground food web as they include bacterivores, fungivores, omnivores and root herbivores. However, their community composition under climate change‐driven intracontinental range‐expanding plants has been studied almost exclusively under controlled conditions, whereas little is known about actual patterns in the field. Here, we use novel molecular sequencing techniques combined with morphological quantification in order to examine nematode communities in the rhizospheres of four range‐expanding and four congeneric native species along a 2,000 km latitudinal transect from South‐Eastern to North‐Western Europe. We tested the hypotheses that latitudinal shifts in nematode community composition are stronger in range‐expanding plant species than in congeneric natives and that in their new range, range‐expanding plant species accumulate fewest root‐feeding nematodes. Our results show latitudinal variation in nematode community composition of both range expanders and native plant species, while operational taxonomic unit richness remained the same across ranges. Therefore, range‐expanding plant species face different nematode communities at higher latitudes, but this is also the case for widespread native plant species. Only one of the four range‐expanding plant species showed a stronger shift in nematode community composition than its congeneric native and accumulated fewer root‐feeding nematodes in its new range. We conclude that variation in nematode community composition with increasing latitude occurs for both range‐expanding and native plant species and that some range‐expanding plant species may become released from root‐feeding nematodes in the new range.
    Print ISSN: 1354-1013
    Electronic ISSN: 1365-2486
    Topics: Biology , Energy, Environment Protection, Nuclear Power Engineering , Geography
    Published by Wiley
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  • 7
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    Consistent effects of nitrogen amendments on soil microbial communities and processes across biomes (2012)
    Wiley
    Details
    Publication Date: 2012-01-12
    Description: Ecosystems worldwide are receiving increasing amounts of reactive nitrogen (N) via anthropogenic activities with the added N having potentially important impacts on microbially-mediated belowground carbon dynamics. However, a comprehensive understanding of how elevated N availability affects soil microbial processes and community dynamics remains incomplete. The mechanisms responsible for the observed responses are poorly resolved and we do not know if soil microbial communities respond in a similar manner across ecosystems. We collected 28 soils from a broad range of ecosystems in North America, amended soils with inorganic N, and incubated the soils under controlled conditions for one year. Consistent across nearly all soils, N addition decreased microbial respiration rates, with an average decrease of 11% over the year-long incubation, and decreased microbial biomass by 35%. High-throughput pyrosequencing showed that N addition consistently altered bacterial community composition, increasing the relative abundance of Actinobacteria and Firmicutes , and decreasing the relative abundance of Acidobacteria and Verrucomicrobia . Further, N-amended soils consistently had lower activities in a broad suite of extracellular enzymes and had decreased temperature sensitivity, suggesting a shift to the preferential decomposition of more labile C pools. The observed trends held across strong gradients in climate and soil characteristics, indicating that the soil microbial responses to N addition are likely controlled by similar wide-spread mechanisms. Our results support the hypothesis that N addition depresses soil microbial activity by shifting the metabolic capabilities of soil bacterial communities, yielding communities that are less capable of decomposing more recalcitrant soil carbon pools and leading to a potential increase in soil carbon sequestration rates.
    Print ISSN: 1354-1013
    Electronic ISSN: 1365-2486
    Topics: Biology , Energy, Environment Protection, Nuclear Power Engineering , Geography
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  • 8
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    Analysis of BH3-only proteins upregulated in response to oxygen/glucose deprivation in cortical neurons identifies Bmf but not Noxa as potential mediator of neuronal injury (2014)
    Springer Nature
    Details
    Publication Date: 2014-10-10
    Description: Analysis of BH3-only proteins upregulated in response to oxygen/glucose deprivation in cortical neurons identifies Bmf but not Noxa as potential mediator of neuronal injury Cell Death and Disease 5, e1456 (October 2014). doi:10.1038/cddis.2014.426 Authors: S Pfeiffer, U Anilkumar, G Chen, S Ramírez-Peinado, J Galindo-Moreno, C Muñoz-Pinedo & J H M Prehn
    Electronic ISSN: 2041-4889
    Topics: Biology , Medicine
    Published by Springer Nature
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  • 9
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    Are there links between responses of soil microbes and ecosystem functioning to elevated CO2, N deposition and warming? A global perspective (2014)
    Wiley
    Details
    Publication Date: 2014-11-02
    Description: In recent years there has been an increase in research to understand how global changes’ impacts on soil biota translate into altered ecosystem functioning. However, results vary between global change effects, soil taxa and ecosystem processes studied, and a synthesis of relationships is lacking. Therefore, here we initiate such a synthesis to assess whether the effect size of global change drivers (elevated CO 2 , N deposition and warming) on soil microbial abundance is related with the effect size of these drivers on ecosystem functioning (plant biomass, soil C cycle and soil N cycle) using meta-analysis and structural equation modeling. For N deposition and warming, the global change effect size on soil microbes was positively associated with the global change effect size on ecosystem functioning, and these relationships were consistent across taxa and ecosystem processes. However, for elevated CO 2 , such links were more taxon and ecosystem process specific. For example, fungal abundance responses to elevated CO 2 were positively correlated with those of plant biomass but negatively with those of the N cycle. Our results go beyond previous assessments of the sensitivity of soil microbes and ecosystem processes to global change, and demonstrate the existence of general links between the responses of soil microbial abundance and ecosystem functioning. Further we identify critical areas for future research, specifically altered precipitation, soil fauna, soil community composition, and litter decomposition, that are need to better quantify the ecosystem consequences of global change impacts on soil biodiversity. This article is protected by copyright. All rights reserved.
    Print ISSN: 1354-1013
    Electronic ISSN: 1365-2486
    Topics: Biology , Energy, Environment Protection, Nuclear Power Engineering , Geography
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  • 10
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    IAPP-driven metabolic reprogramming induces regression of p53-deficient tumours in vivo (2014)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2014-11-20
    Description: TP53 is commonly altered in human cancer, and Tp53 reactivation suppresses tumours in vivo in mice (TP53 and Tp53 are also known as p53). This strategy has proven difficult to implement therapeutically, and here we examine an alternative strategy by manipulating the p53 family members, Tp63 and Tp73 (also known as p63 and p73, respectively). The acidic transactivation-domain-bearing (TA) isoforms of p63 and p73 structurally and functionally resemble p53, whereas the DeltaN isoforms (lacking the acidic transactivation domain) of p63 and p73 are frequently overexpressed in cancer and act primarily in a dominant-negative fashion against p53, TAp63 and TAp73 to inhibit their tumour-suppressive functions. The p53 family interacts extensively in cellular processes that promote tumour suppression, such as apoptosis and autophagy, thus a clear understanding of this interplay in cancer is needed to treat tumours with alterations in the p53 pathway. Here we show that deletion of the DeltaN isoforms of p63 or p73 leads to metabolic reprogramming and regression of p53-deficient tumours through upregulation of IAPP, the gene that encodes amylin, a 37-amino-acid peptide co-secreted with insulin by the beta cells of the pancreas. We found that IAPP is causally involved in this tumour regression and that amylin functions through the calcitonin receptor (CalcR) and receptor activity modifying protein 3 (RAMP3) to inhibit glycolysis and induce reactive oxygen species and apoptosis. Pramlintide, a synthetic analogue of amylin that is currently used to treat type 1 and type 2 diabetes, caused rapid tumour regression in p53-deficient thymic lymphomas, representing a novel strategy to target p53-deficient cancers.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4312210/" 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/PMC4312210/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Venkatanarayan, Avinashnarayan -- Raulji, Payal -- Norton, William -- Chakravarti, Deepavali -- Coarfa, Cristian -- Su, Xiaohua -- Sandur, Santosh K -- Ramirez, Marc S -- Lee, Jaehuk -- Kingsley, Charles V -- Sananikone, Eliot F -- Rajapakshe, Kimal -- Naff, Katherine -- Parker-Thornburg, Jan -- Bankson, James A -- Tsai, Kenneth Y -- Gunaratne, Preethi H -- Flores, Elsa R -- CA-16672/CA/NCI NIH HHS/ -- P30 CA016672/CA/NCI NIH HHS/ -- P50CA136411/CA/NCI NIH HHS/ -- R01 CA134796/CA/NCI NIH HHS/ -- R01 CA160394/CA/NCI NIH HHS/ -- R01CA134796/CA/NCI NIH HHS/ -- R01CA160394/CA/NCI NIH HHS/ -- England -- Nature. 2015 Jan 29;517(7536):626-30. doi: 10.1038/nature13910. Epub 2014 Nov 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA [2] Department of Translational Molecular Pathology, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA [3] Graduate School of Biomedical Sciences, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA [4] Metastasis Research Center, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA. ; 1] Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA [2] Department of Translational Molecular Pathology, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA. ; Department of Veterinary Medicine and Surgery, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA. ; Department of Molecular and Cellular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, USA. ; 1] Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA [2] Department of Translational Molecular Pathology, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA [3] Metastasis Research Center, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA. ; 1] Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA [2] Department of Translational Molecular Pathology, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA [3] Metastasis Research Center, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA [4] Radiation Biology &Health Sciences Division, Bhabha Atomic Research Center, Mumbai 400085, India. ; Department of Imaging Physics, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA. ; Department of Genetics, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA. ; 1] Department of Translational Molecular Pathology, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA [2] Department of Dermatology, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA. ; Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25409149" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line, Tumor ; Cell Transformation, Neoplastic/genetics/pathology ; DNA-Binding Proteins/genetics/metabolism ; Female ; Genes, Tumor Suppressor ; Humans ; Islet Amyloid Polypeptide/*metabolism/pharmacology/secretion/therapeutic use ; Lymphoma/drug therapy/genetics/*metabolism/*pathology ; Male ; Mice ; Nuclear Proteins/genetics/metabolism ; Phosphoproteins/genetics/metabolism ; Receptor Activity-Modifying Protein 3/metabolism ; Receptors, Calcitonin/metabolism ; Thymus Gland/metabolism/pathology ; Trans-Activators/genetics/metabolism ; Tumor Suppressor Protein p53/*deficiency/genetics ; Tumor Suppressor Proteins/genetics/metabolism
    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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