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  • 1
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    Self-organization is a dynamic and lineage-intrinsic property of mammary epithelial cells [Cell Biology] (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-02-23
    Description: Loss of organization is a principle feature of cancers; therefore it is important to understand how normal adult multilineage tissues, such as bilayered secretory epithelia, establish and maintain their architectures. The self-organization process that drives heterogeneous mixtures of cells to form organized tissues is well studied in embryology and with mammalian cell lines that were abnormal or engineered. Here we used a micropatterning approach that confined cells to a cylindrical geometry combined with an algorithm to quantify changes of cellular distribution over time to measure the ability of different cell types to self-organize relative to each other. Using normal human mammary epithelial cells enriched into pools of the two principal lineages, luminal and myoepithelial cells, we demonstrated that bilayered organization in mammary epithelium was driven mainly by lineage-specific differential E-cadherin expression, but that P-cadherin contributed specifically to organization of the myoepithelial layer. Disruption of the actomyosin network or of adherens junction proteins resulted in either prevention of bilayer formation or loss of preformed bilayers, consistent with continual sampling of the local microenvironment by cadherins. Together these data show that self-organization is an innate and reversible property of communities of normal adult human mammary epithelial cells.
    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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    Excitonic effects in intraband quantum dot spectroscopy: Formation of bound continuum excitons (2014)
    American Physical Society (APS)
    Details
    Publication Date: 2014-09-13
    Description: Author(s): Sandra C. Kuhn and Marten Richter We study intraband spectra, resulting from intraband transitions between the bound ground state of a semiconductor quantum dot and unbound continuum states in the host medium. The influence of excitonic coupling on these intraband absorption spectra and the formation of special excitons are discusse... [Phys. Rev. B 90, 125308] Published Fri Sep 12, 2014
    Keywords: Semiconductors II: surfaces, interfaces, microstructures, and related topics
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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  • 3
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    Plant and Animal Glycolate Oxidases Have a Common Eukaryotic Ancestor and Convergently Duplicated to Evolve Long-Chain 2-Hydroxy Acid Oxidases (2014)
    Oxford University Press
    Details
    Publication Date: 2014-04-23
    Description: Glycolate oxidase (GOX) is a crucial enzyme of plant photorespiration. The encoding gene is thought to have originated from endosymbiotic gene transfer between the eukaryotic host and the cyanobacterial endosymbiont at the base of plantae. However, animals also possess GOX activities. Plant and animal GOX belong to the gene family of (L)-2-hydroxyacid-oxidases ((L)-2-HAOX). We find that all (L)-2-HAOX proteins in animals and archaeplastida go back to one ancestral eukaryotic sequence; the sole exceptions are green algae of the chlorophyta lineage. Chlorophyta replaced the ancestral eukaryotic (L)-2-HAOX with a bacterial ortholog, a lactate oxidase that may have been obtained through the primary endosymbiosis at the base of plantae; independent losses of this gene may explain its absence in other algal lineages (glaucophyta, rhodophyta, and charophyta). We also show that in addition to GOX, plants possess (L)-2-HAOX proteins with different specificities for medium- and long-chain hydroxyacids (lHAOX), likely involved in fatty acid and protein catabolism. Vertebrates possess lHAOX proteins acting on similar substrates as plant lHAOX; however, the existence of GOX and lHAOX subfamilies in both plants and animals is not due to shared ancestry but is the result of convergent evolution in the two most complex eukaryotic lineages. On the basis of targeting sequences and predicted substrate specificities, we conclude that the biological role of plantae (L)-2-HAOX in photorespiration evolved by co-opting an existing peroxisomal protein.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    Synthesis, properties, and biological activity of boranophosphate analogs of the mRNA cap: versatile tools for manipulation of therapeutically relevant cap-dependent processes (2014)
    Oxford University Press
    Details
    Publication Date: 2014-09-17
    Description: Modified mRNA cap analogs aid in the study of mRNA-related processes and may enable creation of novel therapeutic interventions. We report the synthesis and properties of 11 dinucleotide cap analogs bearing a single boranophosphate modification at either the α-, β- or -position of the 5',5'-triphosphate chain. The compounds can potentially serve either as inhibitors of translation in cancer cells or reagents for increasing expression of therapeutic proteins in vivo from exogenous mRNAs. The BH 3 -analogs were tested as substrates and binding partners for two major cytoplasmic cap-binding proteins, DcpS, a decapping pyrophosphatase, and eIF4E, a translation initiation factor. The susceptibility to DcpS was different between BH 3 -analogs and the corresponding analogs containing S instead of BH 3 (S-analogs). Depending on its placement, the boranophosphate group weakened the interaction with DcpS but stabilized the interaction with eIF4E. The first of the properties makes the BH 3 -analogs more stable and the second, more potent as inhibitors of protein biosynthesis. Protein expression in dendritic cells was 2.2- and 1.7-fold higher for mRNAs capped with m 2 7,2'- O Gpp BH3 pG D1 and m 2 7,2'- O Gpp BH3 pG D2, respectively, than for in vitro transcribed mRNA capped with m 2 7,3'- O GpppG. Higher expression of cancer antigens would make mRNAs containing m 2 7,2'- O Gpp BH3 pG D1 and m 2 7,2'- O Gpp BH3 pG D2 favorable for anticancer immunization.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    The cells and peripheral representation of sodium taste in mice (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-01-29
    Description: Salt taste in mammals can trigger two divergent behavioural responses. In general, concentrated saline solutions elicit robust behavioural aversion, whereas low concentrations of NaCl are typically attractive, particularly after sodium depletion. Notably, the attractive salt pathway is selectively responsive to sodium and inhibited by amiloride, whereas the aversive one functions as a non-selective detector for a wide range of salts. Because amiloride is a potent inhibitor of the epithelial sodium channel (ENaC), ENaC has been proposed to function as a component of the salt-taste-receptor system. Previously, we showed that four of the five basic taste qualities-sweet, sour, bitter and umami-are mediated by separate taste-receptor cells (TRCs) each tuned to a single taste modality, and wired to elicit stereotypical behavioural responses. Here we show that sodium sensing is also mediated by a dedicated population of TRCs. These taste cells express the epithelial sodium channel ENaC, and mediate behavioural attraction to NaCl. We genetically engineered mice lacking ENaCalpha in TRCs, and produced animals exhibiting a complete loss of salt attraction and sodium taste responses. Together, these studies substantiate independent cellular substrates for all five basic taste qualities, and validate the essential role of ENaC for sodium taste in mice.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2849629/" 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/PMC2849629/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chandrashekar, Jayaram -- Kuhn, Christina -- Oka, Yuki -- Yarmolinsky, David A -- Hummler, Edith -- Ryba, Nicholas J P -- Zuker, Charles S -- R01 DC003160/DC/NIDCD NIH HHS/ -- R01 DC003160-05/DC/NIDCD NIH HHS/ -- Z01 DE000561-13/Intramural NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2010 Mar 11;464(7286):297-301. doi: 10.1038/nature08783. Epub 2010 Jan 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Neurobiology, University of California at San Diego, La Jolla, California 92093-0649, USA〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20107438" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Behavior/physiology ; Epithelial Sodium Channels/genetics/metabolism ; Mice ; Mice, Transgenic ; Sodium/*physiology ; Taste/*genetics ; Taste Buds/cytology/metabolism/*physiology
    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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  • 6
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    All-optical approach to determine the spatial shape of nanoscale electron wave functions using intraband spectroscopy (2014)
    American Physical Society (APS)
    Details
    Publication Date: 2014-05-30
    Description: Author(s): Sandra C. Kuhn, Andreas Knorr, Marten Richter, Nina Owschimikow, Mirco Kolarczik, Yücel I. Kaptan, and Ulrike Woggon A spectroscopic pump-probe method to determine the spatial shape of bound quantum states in semiconductor quantum dots is proposed. The method uses intraband transitions between the bound states and unbound continuum states in the host medium. The developed theoretical scheme is applicable to quantu... [Phys. Rev. B 89, 201414] Published Thu May 29, 2014
    Keywords: Surface physics, nanoscale physics, low-dimensional systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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  • 7
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    Infectious cytosolic protein aggregates [Cell Biology] (2013)
    National Academy of Sciences
    Details
    Publication Date: 2013-04-10
    Description: Prions are self-templating protein conformers that replicate by recruitment and conversion of homotypic proteins into growing protein aggregates. Originally identified as causative agents of transmissible spongiform encephalopathies, increasing evidence now suggests that prion-like phenomena are more common in nature than previously anticipated. In contrast to fungal prions that replicate in...
    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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  • 8
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    Porosity and density of the AND-1B sediment core, McMurdo Sound region, Antarctica: Field consolidation enhanced by grounded ice (2013)
    Geological Society of America (GSA)
    In: Geosphere
    Details
    Publication Date: 2013-06-01
    Description: A study of density and porosity is presented for the 1285-m-long AND-1B core recovered from a flexural moat in the McMurdo Sound (Antarctica) in order to interpret sediment consolidation in an ice-proximal location on the Antarctic shelf. Various lithologies imply environmental changes from open marine to subglacial, and are numerically expressed in high-resolution whole-core wet-bulk density (WBD). Grain density data interpolated from discrete samples range from 2.14 to 3.85 g/cm 3 and are used to calculate porosity from WBD in order to avoid the 5%–15% overestimation and underestimation of porosities obtained by standard methods. The trend of porosity extends from 0.5 near the top (Pleistocene) to 0.2 at the bottom (Miocene). Porosity fluctuations in different lithologies are superimposed with 0.2–0.3 in sequences younger than ca. 1 Ma and 0.5–0.8 in Pliocene diatomites. The AND-1B porosities and void ratios of Pliocene diatomites and Pleistocene mudstones exhibit a large negative offset compared to modern lithological analogs and their consolidation trends. This offset cannot be explained in terms of the effective stress at the AND-1B site. The effective stress ranges from 0 to 4000 kPa in the upper 600 m, and reaches 13,000 kPa at the base of the AND-1B hole. We suggest an excess of effective overburden stress of ~1700 and ~6000 kPa to explain porosities in Pliocene diatomites and Pleistocene mudstones, respectively. This is interpreted as glacial preconsolidation by subsequently grounded ice sheets under subpolar to polar, followed by colder polar types of glaciations. Information on Miocene consolidation is sparse due to alteration by diagenesis.
    Electronic ISSN: 1553-040X
    Topics: Geosciences
    Published by Geological Society of America (GSA)
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  • 9
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    eggNOG v4.0: nested orthology inference across 3686 organisms (2013)
    Oxford University Press
    Details
    Publication Date: 2013-12-29
    Description: With the increasing availability of various ‘omics data, high-quality orthology assignment is crucial for evolutionary and functional genomics studies. We here present the fourth version of the eggNOG database (available at http://eggnog.embl.de ) that derives nonsupervised orthologous groups (NOGs) from complete genomes, and then applies a comprehensive characterization and analysis pipeline to the resulting gene families. Compared with the previous version, we have more than tripled the underlying species set to cover 3686 organisms, keeping track with genome project completions while prioritizing the inclusion of high-quality genomes to minimize error propagation from incomplete proteome sets. Major technological advances include (i) a robust and scalable procedure for the identification and inclusion of high-quality genomes, (ii) provision of orthologous groups for 107 different taxonomic levels compared with 41 in eggNOGv3, (iii) identification and annotation of particularly closely related orthologous groups, facilitating analysis of related gene families, (iv) improvements of the clustering and functional annotation approach, (v) adoption of a revised tree building procedure based on the multiple alignments generated during the process and (vi) implementation of quality control procedures throughout the entire pipeline. As in previous versions, eggNOGv4 provides multiple sequence alignments and maximum-likelihood trees, as well as broad functional annotation. Users can access the complete database of orthologous groups via a web interface, as well as through bulk download.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 10
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    Centrality determination of Pb-Pb collisions atsNN=2.76TeV with ALICE (2013)
    American Physical Society
    Details
    Publication Date: 2013-10-15
    Print ISSN: 0556-2813
    Electronic ISSN: 1089-490X
    Topics: Physics
    Published by American Physical Society
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