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  • 1
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    A Comprehensive Transcriptomic and Proteomic Analysis of Hydra Head Regeneration (2015)
    Oxford University Press
    Details
    Publication Date: 2015-07-18
    Description: The cnidarian freshwater polyp Hydra sp. exhibits an unparalleled regeneration capacity in the animal kingdom. Using an integrative transcriptomic and stable isotope labeling by amino acids in cell culture proteomic/phosphoproteomic approach, we studied stem cell-based regeneration in Hydra polyps. As major contributors to head regeneration, we identified diverse signaling pathways adopted for the regeneration response as well as enriched novel genes. Our global analysis reveals two distinct molecular cascades: an early injury response and a subsequent, signaling driven patterning of the regenerating tissue. A key factor of the initial injury response is a general stabilization of proteins and a net upregulation of transcripts, which is followed by a subsequent activation cascade of signaling molecules including Wnts and transforming growth factor (TGF) beta-related factors. We observed moderate overlap between the factors contributing to proteomic and transcriptomic responses suggesting a decoupled regulation between the transcriptional and translational levels. Our data also indicate that interstitial stem cells and their derivatives (e.g., neurons) have no major role in Hydra head regeneration. Remarkably, we found an enrichment of evolutionarily more recent genes in the early regeneration response, whereas conserved genes are more enriched in the late phase. In addition, genes specific to the early injury response were enriched in transposon insertions. Genetic dynamicity and taxon-specific factors might therefore play a hitherto underestimated role in Hydra regeneration.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Full microtremor H/V(z, f) inversion for shallow subsurface characterization (2015)
    Oxford University Press
    Details
    Publication Date: 2015-05-01
    Description: The H/V spectral ratio has emerged as a single station method within the seismic ambient noise analysis field by its capability to quickly estimate the frequency of resonance at a site and through inversion the average profile information. Although it is easy to compute from experimental data, its counter theoretical part is not obvious when building a forward model which can help in reconstructing the derived H/V spectrum. This has led to the simplified assumption that the noise wavefield is mainly composed of Rayleigh waves and the derived H/V often used without further correction. Furthermore, only the right (and left) flank around the H/V peak frequency is considered in the inversion for the subsurface 1-D shear wave velocity profile. A new theoretical approach for the interpretation of the H/V spectral ratio has been presented by Sánchez-Sesma et al. In this paper, the fundamental idea behind their theory is presented as it applies to receivers at depth. A smooth H/V( z , f ) spectral curve on a broad frequency range is obtained by considering a fine integration step which is in turn time consuming. We show that for practical purposes and in the context of inversion, this can be considerably optimized by using a coarse integration step combined with the smoothing of the corresponding directional energy density (DED) spectrum. Further analysis shows that the obtained H/V( z , f ) spectrum computed by the mean of the imaginary part of Green's function method could also be recovered using the reflectivity method for a medium well illuminated by seismic sources. Inversion of synthetic H/V( z , f ) spectral curve is performed for a single layer over a half space. The striking results allow to potentially use the new theory as a forward computation of the H/V( z , f ) to fully invert the experimental H/V spectral ratio at the corresponding depth for the shear velocity profile ( Vs ) and additionally the compressional velocity profile ( Vp ) using receivers both at the surface and in depth. We use seismic ambient noise data in the frequency range of 0.2–50 Hz recorded at two selected sites in Germany where borehole information is also available. The obtained 1-D Vs and Vp profiles are correlated with geological log information. Results from shallow geophysical experiment are also used for comparison.
    Keywords: Seismology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 3
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    Expression of MTAP Inhibits Tumor-Related Phenotypes in HT1080 Cells via a Mechanism Unrelated to Its Enzymatic Function (2015)
    Genetics Society of America (GSA)
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    Publication Date: 2015-01-13
    Description: Methylthioadenosine Phosphorylase ( MTAP ) is a tumor suppressor gene that is frequently deleted in human cancers and encodes an enzyme responsible for the catabolism of the polyamine byproduct 5'deoxy-5'-methylthioadenosine (MTA). To elucidate the mechanism by which MTAP inhibits tumor formation, we have reintroduced MTAP into MTAP -deleted HT1080 fibrosarcoma cells. Expression of MTAP resulted in a variety of phenotypes, including decreased colony formation in soft-agar, decreased migration, decreased in vitro invasion, increased matrix metalloproteinase production, and reduced ability to form tumors in severe combined immunodeficiency mice. Microarray analysis showed that MTAP affected the expression of genes involved in a variety of processes, including cell adhesion, extracellular matrix interaction, and cell signaling. Treatment of MTAP -expressing cells with a potent inhibitor of MTAP’s enzymatic activity (MT-DADMe-ImmA) did not result in a MTAP – phenotype. This finding suggests that MTAP ’s tumor suppressor function is not the same as its known enzymatic function. To confirm this, we introduced a catalytically inactive version of MTAP , D220A, into HT1080 cells and found that this mutant was fully capable of reversing the soft agar colony formation, migration, and matrix metalloproteinase phenotypes. Our results show that MTAP affects cellular phenotypes in HT1080 cells in a manner that is independent of its known enzymatic activity.
    Electronic ISSN: 2160-1836
    Topics: Biology
    Published by Genetics Society of America (GSA)
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  • 4
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    Type III restriction endonuclease EcoP15I is a heterotrimeric complex containing one Res subunit with several DNA-binding regions and ATPase activity (2012)
    Oxford University Press
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    Publication Date: 2012-04-24
    Description: For efficient DNA cleavage, the Type III restriction endonuclease EcoP15I communicates with two inversely oriented recognition sites in an ATP-dependent process. EcoP15I consists of methylation (Mod) and restriction (Res) subunits forming a multifunctional enzyme complex able to methylate or to cleave DNA. In this study, we determined by different analytical methods that EcoP15I contains a single Res subunit in a Mod 2 Res stoichiometry. The Res subunit comprises a translocase (Tr) domain carrying functional motifs of superfamily 2 helicases and an endonuclease domain with a PD..D/EXK motif. We show that the isolated Tr domain retains ATP-hydrolyzing activity and binds single- and double-stranded DNA in a sequence-independent manner. To localize the regions of DNA binding, we screened peptide arrays representing the entire Res sequence for their ability to interact with DNA. We discovered four DNA-binding regions in the Tr domain and two DNA-binding regions in the endonuclease domain. Modelling of the Tr domain shows that these multiple DNA-binding regions are located on the surface, free to interact with DNA. Interestingly, the positions of the DNA-binding regions are conserved among other Type III restriction endonucleases.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    Comparing bark thickness: testing methods with bark–stem data from two South African fire-prone biomes (2014)
    Wiley
    Details
    Publication Date: 2014-03-13
    Description: Aims Bark thickness–stem diameter relationships are non-linear above a stem diameter threshold in many woody species, which makes relative bark thickness measures dependent on the range of stem diameters that are sampled. This influences the appropriateness of different methods for comparing fire responses of woody plants across studies. Here we develop a framework for bark thickness comparisons by evaluating relative bark thickness estimates and bark thickness predictions obtained from linear and curved models fitted to raw and log-transformed bark–stem data. We use this framework to contrast bark thickness among fynbos and savanna plant functional groups. Location Fynbos (17 species) and savanna (21 species) systems in South Africa. Methods The linear subset of bark–stem data was identified using a three-step procedure. Linear regressions (with and without an intercept) and curved models (allometric and modified exponential models) were fitted to the linear subset and complete raw bark–stem data set, respectively. In addition, linear regression models were fitted to the log-transformed complete bark–stem data set. Regression slopes and bark thickness predictions obtained from these different approaches were compared, to determine which method provides the most robust metric for comparing bark thickness. Bark thickness was compared among fynbos resprouter guilds and acacias from low- and high-fire savannas. Results The slope of the regression model fitted to the linear subset of raw bark–stem data provides a reliable metric for general comparisons of relative bark thickness. Bark thickness predictions from the curved and log models were comparable at 20-cm stem diameter, but the log model underestimated bark thickness at 5 cm for certain species. Relative bark thickness was significantly higher in: (1) fynbos fire resisters and epicormic resprouters than in non-resprouters; and (2) acacias from high- vs low-fire savannas. Conclusions The slope of the regression model fitted to the linear subset of raw bark–stem data is a useful metric for bark thickness comparisons across studies, and compares favourably with bark thickness predictions derived from models fitted to the complete bark–stem data set. Fynbos and savanna trends support the proposition that relative bark thickness reflects differences in woody plant responses to fire and indicate the modal fire regime of ecosystems. There has been a recent proliferation of studies on bark thickness, notably as a fire resistance trait. However, cross-study comparisons of relative bark thickness are severely limited by an overlooked dependence of this metric on the shape of the bark thickness-stem diameter relationship. We provide a method to address this issue, and also explore alternative measures for bark thickness comparisons.
    Print ISSN: 1100-9233
    Electronic ISSN: 1654-1103
    Topics: Biology
    Published by Wiley on behalf of The International Association for Vegetation Science (IAVS).
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  • 6
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    Comparison of postseismic afterslip models with aftershock seismicity for three subduction-zone earthquakes: Nias 2005, Maule 2010 and Tohoku 2011 (2014)
    Oxford University Press
    Details
    Publication Date: 2014-09-07
    Description: We focus on the relation between seismic and total postseismic afterslip following the Maule M w 8.8 earthquake on 2010 February 27 in central Chile. First, we calculate the cumulative slip released by aftershock seismicity. We do this by summing up the aftershock regions and slip estimated from scaling relations. Comparing the cumulative seismic slip with afterslip models we show that seismic slip of individual aftershocks exceeds locally the inverted afterslip model from geodetic constraints. As the afterslip model implicitly contains the displacements from the aftershocks, this reflects the tendency of afterslip models to smear out the actual slip pattern. However, it also suggests that locally slip for a number of the larger aftershocks exceeds the aseismic slip in spite of the fact that the total equivalent moment of the afterslip exceeds the cumulative moment of aftershocks by a large factor. This effect, seen weakly for the Maule 2010 and also for the Tohoku 2011 earthquake, can be explained by taking into account the uncertainties of the seismicity and afterslip models. In spite of uncertainties, the hypocentral region of the Nias 2005 earthquake is suggested to release a large fraction of moment almost purely seismically. Therefore, these aftershocks are not driven solely by the afterslip but instead their slip areas have probably been stressed by interseismic loading and the mainshock rupture. In a second step, we divide the megathrust of the Maule 2010 rupture into discrete cells and count the number of aftershocks that occur within 50 km of the centre of each cell as a function of time. We then compare this number to a time-dependent afterslip model by defining the ‘afterslip to aftershock ratio’ (ASAR) for each cell as the slope of the best fitting line when the afterslip at time t is plotted against aftershock count. Although we find a linear relation between afterslip and aftershocks for most cells, there is significant variability in ASAR in both the downdip and along-strike directions of the megathrust. We compare the spatial distribution of ASAR with the spatial distribution of seismic coupling, coseismic slip and Bouguer gravity anomaly, and in each case we find no significant correlation.
    Keywords: Seismology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 7
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    Dissociation of CH4 at high pressures and temperatures: diamond formation in giant planet interiors? (1999)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1999-10-03
    Description: Experiments using laser-heated diamond anvil cells show that methane (CH4) breaks down to form diamond at pressures between 10 and 50 gigapascals and temperatures of about 2000 to 3000 kelvin. Infrared absorption and Raman spectroscopy, along with x-ray diffraction, indicate the presence of polymeric hydrocarbons in addition to the diamond, which is in agreement with theoretical predictions. Dissociation of CH4 at high pressures and temperatures can influence the energy budgets of planets containing substantial amounts of CH4, water, and ammonia, such as Uranus and Neptune.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Benedetti, L R -- Nguyen, J H -- Caldwell, W A -- Liu, H -- Kruger, M -- Jeanloz, R -- New York, N.Y. -- Science. 1999 Oct 1;286(5437):100-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics, Department of Geology and Geophysics, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10506552" target="_blank"〉PubMed〈/a〉
    Keywords: Diamond/*chemistry ; Evolution, Planetary ; Hot Temperature ; Hydrocarbons/chemistry ; Methane/*chemistry ; *Neptune ; Pressure ; Spectroscopy, Fourier Transform Infrared ; Spectrum Analysis, Raman ; *Uranus ; X-Ray Diffraction
    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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  • 8
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    Biodiversity assessment and conservation strategies (1998)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1998-04-08
    Description: The efficient representation of all species in conservation planning is problematic. Often, species distribution is assessed by dividing the land into a grid; complementary sets of grids, in which each taxon is represented at least once, are then sought. To determine if this approach provides useful surrogate information, species and higher taxon data for South African plants and animals were analyzed. Complementary species sets did not coincide and overlapped little with higher taxon sets. Survey extent and taxonomic knowledge did not affect this overlap. Thus, the assumptions of surrogacy, on which so much conservation planning is based, are not supported.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉van Jaarsveld AS -- Freitag -- Chown -- Muller -- Koch -- Hull -- Bellamy -- Kruger -- Endrody-Younga -- Mansell -- Scholtz -- New York, N.Y. -- Science. 1998 Mar 27;279(5359):2106-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉A. S. van Jaarsveld, S. Freitag, S. L. Chown, C. Muller, S. Kock, H. Hull, C. H. Scholtz, Department of Zoology and Entomology, University of Pretoria, Pretoria 0002, South Africa. C. Bellamy, M. Kruger, S. Endrody-Younga, Transvaal Museum〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9516111" target="_blank"〉PubMed〈/a〉
    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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  • 9
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    Genetic compensation induced by deleterious mutations but not gene knockdowns (2015)
    Nature Publishing Group (NPG)
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    Publication Date: 2015-07-15
    Description: Cells sense their environment and adapt to it by fine-tuning their transcriptome. Wired into this network of gene expression control are mechanisms to compensate for gene dosage. The increasing use of reverse genetics in zebrafish, and other model systems, has revealed profound differences between the phenotypes caused by genetic mutations and those caused by gene knockdowns at many loci, an observation previously reported in mouse and Arabidopsis. To identify the reasons underlying the phenotypic differences between mutants and knockdowns, we generated mutations in zebrafish egfl7, an endothelial extracellular matrix gene of therapeutic interest, as well as in vegfaa. Here we show that egfl7 mutants do not show any obvious phenotypes while animals injected with egfl7 morpholino (morphants) exhibit severe vascular defects. We further observe that egfl7 mutants are less sensitive than their wild-type siblings to Egfl7 knockdown, arguing against residual protein function in the mutants or significant off-target effects of the morpholinos when used at a moderate dose. Comparing egfl7 mutant and morphant proteomes and transcriptomes, we identify a set of proteins and genes that are upregulated in mutants but not in morphants. Among them are extracellular matrix genes that can rescue egfl7 morphants, indicating that they could be compensating for the loss of Egfl7 function in the phenotypically wild-type egfl7 mutants. Moreover, egfl7 CRISPR interference, which obstructs transcript elongation and causes severe vascular defects, does not cause the upregulation of these genes. Similarly, vegfaa mutants but not morphants show an upregulation of vegfab. Taken together, these data reveal the activation of a compensatory network to buffer against deleterious mutations, which was not observed after translational or transcriptional knockdown.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rossi, Andrea -- Kontarakis, Zacharias -- Gerri, Claudia -- Nolte, Hendrik -- Holper, Soraya -- Kruger, Marcus -- Stainier, Didier Y R -- England -- Nature. 2015 Aug 13;524(7564):230-3. doi: 10.1038/nature14580. Epub 2015 Jul 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26168398" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; Brain/metabolism/pathology ; CRISPR-Cas Systems/genetics ; *Gene Knockdown Techniques ; Larva/genetics ; Membrane Glycoproteins/genetics ; Morpholinos/genetics ; Mutation/*genetics ; *Phenotype ; Proteome/analysis ; *RNA Interference ; Suppression, Genetic/*genetics ; Transcriptome/genetics ; Up-Regulation/*genetics ; Vascular Endothelial Growth Factor A/genetics ; Zebrafish/embryology/*genetics/metabolism ; Zebrafish Proteins/genetics
    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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  • 10
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    Hirschsprung disease is linked to defects in neural crest stem cell function (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-08-16
    Description: Genes associated with Hirschsprung disease, a failure to form enteric ganglia in the hindgut, were highly up-regulated in gut neural crest stem cells relative to whole-fetus RNA. One of these genes, the glial cell line-derived neurotrophic factor (GDNF) receptor Ret, was necessary for neural crest stem cell migration in the gut. GDNF promoted the migration of neural crest stem cells in culture but did not affect their survival or proliferation. Gene expression profiling, combined with reverse genetics and analyses of stem cell function, suggests that Hirschsprung disease is caused by defects in neural crest stem cell function.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2614078/" 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/PMC2614078/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Iwashita, Toshihide -- Kruger, Genevieve M -- Pardal, Ricardo -- Kiel, Mark J -- Morrison, Sean J -- CA46592/CA/NCI NIH HHS/ -- DK58771/DK/NIDDK NIH HHS/ -- NIH5P60-DK20572/DK/NIDDK NIH HHS/ -- P30 AR48310/AR/NIAMS NIH HHS/ -- P60-AR20557/AR/NIAMS NIH HHS/ -- R01 NS040750/NS/NINDS NIH HHS/ -- R01 NS040750-01/NS/NINDS NIH HHS/ -- R01 NS40750-01/NS/NINDS NIH HHS/ -- R21 HD40760-02/HD/NICHD NIH HHS/ -- New York, N.Y. -- Science. 2003 Aug 15;301(5635):972-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109-0934, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12920301" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Differentiation ; Cell Division ; Cell Movement ; Cell Separation ; Cell Survival ; Cells, Cultured ; Digestive System/cytology/*embryology/innervation/metabolism ; Fetus/metabolism ; Gene Expression Profiling ; *Gene Expression Regulation, Developmental ; Glial Cell Line-Derived Neurotrophic Factor ; Glial Cell Line-Derived Neurotrophic Factor Receptors ; Hirschsprung Disease/*etiology/genetics ; Mice ; Multipotent Stem Cells/*physiology ; Nerve Growth Factors/genetics/metabolism/pharmacology ; Neural Crest/*cytology/physiology ; Oligonucleotide Array Sequence Analysis ; Proto-Oncogene Proteins/*genetics/metabolism ; Proto-Oncogene Proteins c-ret ; Rats ; Rats, Sprague-Dawley ; Receptor Protein-Tyrosine Kinases/*genetics/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Signal Transduction ; Up-Regulation
    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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