1. Postnatal dynamics of Zeb2 expression in rat brain : analysis of novel 3′ UTR sequence reveals a miR-9 interacting siteKlara Kropivšek, Jasmine Pickford, David A. Carter, 2014, original scientific article Abstract: ZEB2 is a transcription factor with established roles in neurogenesis but no defined function in postnatal brain despite extensive neuronal expression in telencephalic structures. Multiple, incompletely annotated transcripts derive from the Zeb2 locus; the purpose of the present study was to structurally characterize rat brain Zeb2 transcripts with respect to 3′ untranslated (UTR) sequence in order to understand Zeb2 transcript regulation including possible interactions with regulatory molecules such as neuronal miRNAs. We cloned a 5054-nucleotide Zeb2 3′ UTR that is included in the most abundant Zeb2 transcript in neonatal rat brain. Unique features of the distal 3′ UTR region included a number of brain-specific miRNA target sites; a highly conserved miR-9 target site at 3′ UTR position 4097 was selected for functional verification in transfection experiments. Parallel analysis of Zeb2 transcript, ZEB2 protein and miR-9 levels across postnatal brain cortical development revealed a significant accumulation of ZEB2 protein levels only between postnatal days P2 and P5 that was associated with an acute loss of postnatal miR-9 expression in cortex. These studies demonstrate novel features of Zeb2 gene expression in postnatal rat brain and highlight the importance of full transcript annotation for identifying the complement of potential transcript-interacting regulators.
Keywords: transcription factor, RNA, untranslated region, miRNA, brain, rat
Published in RUNG: 11.11.2024; Views: 216; Downloads: 3
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2. HERMES : gamma-ray burst and gravitational wave counterpart hunterGiancarlo Ghirlanda, L. Nava, O. Salafia, F. Fiore, R. Campana, R. Salvaterra, A. Sanna, Dejan Gačnik, Andreja Gomboc, David Selčan, 2024, original scientific article Keywords: astronomija, satelit HERMES, izbruhi sevanja gama
Published in RUNG: 07.10.2024; Views: 441; Downloads: 5
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3. Processing feature assignment in Bulgarian : lecture at the Beyond Agreement Workshop, Geneve, 20. 6. 2024Danil Khristov, Penka Stateva, Julie Franck, Dávid György, Arthur Stepanov, 2024, unpublished conference contribution Keywords: Sentence processing, psycholinguistics, memory, feature assignment, Bulgarian
Published in RUNG: 26.06.2024; Views: 990; Downloads: 2
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4. Rubin Observatory LSST transients and variable stars roadmapKelly M. Hambleton, Federica B. Bianco, Rachel Street, Keaton Bell, David Buckley, Melissa Lynn Graham, Nina Hernitschek, Michael B. Lund, Katja Bricman, Andreja Gomboc, 2023, original scientific article Keywords: observatorij Vere Rubin, astrofizikalni tranzienti, spremenljivi izvori
Published in RUNG: 08.11.2023; Views: 1969; Downloads: 8
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5. A framework for evaluating the performance of SMLM cluster analysis algorithmsDaniel J. Nieves, Jeremy A. Pike, Florian Levet, David J. Williamson, Mohammed Baragilly, Sandra Oloketuyi, Ario De Marco, Juliette Griffié, Daniel Sage, Edward A. K. Cohen, 2023, original scientific article Keywords: super resolution microscopy, functionalized nanobodies
Published in RUNG: 22.02.2023; Views: 1890; Downloads: 0
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6. Observation of the Cumbre Vieja volcano plume above the Observatorio del Roque de los Muchachos with the Barcelona Raman LIDARMiha Živec, Otger Ballester, Oscar Blanch, Juan Boix, Paolo G. Calisse, Anna Campoy Ordaz, Michele Doro, Lluis Font, Rafael Garcia, Markus Gaug, Roger Grau, Manel Martinez, David Roman, Samo Stanič, Santiago Ubach Ramírez, Marko Zavrtanik, 2022, published scientific conference contribution Keywords: lidar, remote sensing, CTA, CTAO, Cumbre Vieja, atmospheric monitoring, volcano
Published in RUNG: 13.02.2023; Views: 1909; Downloads: 22
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7. Classification of gamma-ray targets for velocity-dependent and subhalo-boosted dark-matter annihilationThomas Lacroix, Gaetán Facchinetti, Judit Pérez Romero, Martin Stref, Julien Lavalle, David Maurin, Miguel Sánchez-Conde, original scientific article Abstract: Gamma-ray observations have long been used to constrain the properties of dark matter (DM), with a strong focus on weakly interacting massive particles annihilating through velocity-independent processes. However, in the absence of clear-cut observational evidence for the simplest candidates, the interest of the community in more complex DM scenarios involving a velocity-dependent cross-section has been growing steadily over the past few years. We present the first systematic study of velocity-dependent DM annihilation (in particular p-wave annihilation and Sommerfeld enhancement) in a variety of astrophysical objects, not only including the well-studied Milky Way dwarf satellite galaxies, but nearby dwarf irregular galaxies and local galaxy clusters as well. Particular attention is given to the interplay between velocity dependence and DM halo substructure. Uncertainties related to halo mass, phase-space and substructure modelling are also discussed in this velocity-dependent context. We show that, for s-wave annihilation, extremely large subhalo boost factors are to be expected, up to 10^11 in clusters and up to 10^6–10^7 in dwarf galaxies where subhalos are usually assumed not to play an important role. Boost factors for p-wave annihilation are smaller but can still reach 10^3 in clusters. The angular extension of the DM signal is also significantly impacted, with e.g. the cluster typical emission radius increasing by a factor of order 10 in the s-wave case. We also compute the signal contrast of the objects in our sample with respect to annihilation happening in the Milky Way halo. Overall, we find that the hierarchy between the brightest considered targets depends on the specific details of the assumed particle-physics model.
Keywords: dark matter theory, dwarf galaxies, galaxy clusters, gamma-ray theory
Published in RUNG: 27.01.2023; Views: 2042; Downloads: 0
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8. The molecular toolbox of ectomycorrhizal-driven phosphate mineral weatheringChristina Paparokidou, Leake Jonathan R., Rolfe Stephen A., Beerling David J., 2022, published scientific conference contribution abstract Abstract: Ectomycorrhizal fungi (EMF) form symbiotic partnerships with tree roots and are able to
chemically weather inorganic phosphorus (Pi)-rich minerals, supplying Pi to their host in
return for photosynthates. The fungal-driven nutrient cycling from mineral weathering
plays a pivotal role in ecosystems and crops productivity, as well as geochemical cycles.
The aim of the study presented in this thesis is to unravel the molecular mechanisms by
which the EM fungus Paxillus involutus weathers the Pi-rich mineral hydroxyapatite
(HAP), either non-symbiotically or in symbiosis with its host tree Pinus sylvestris.
Development of an artificial system to study P. involutus responses to varying
concentration of Pi led to the identification of five high-affinity Pi transporter genes, of
which the expression varies in an inversely proportional manner to Pi availability. Using
the same system, whole-transcriptomic data from fungal hyphae unravelled the molecular
basis of the EMF ability in Pi uptake at the global gene scale, revealing that EM symbiosis
can directly affect Pi-responsive fungal genes such as the Pi transporter PiPT4. A second
artificial system was used to study HAP solubilisation driven by P. involutus, which was
confirmed by EDX spectroscopy data showing depletion of Pi from the HAP crystals,
along with secondary minerals formation. Whole-transcriptomic analysis revealed that EM
symbiosis induces a different set of HAP weathering genes in P. involutus hyphae,
compared to the fungus growing non-symbiotically, including the specific expression of
organic acid metabolic genes, which resulted in enhanced HAP solubilisation.
Metabolomic analysis led to the identification of multiple secreted metabolites enriched in
the presence of HAP in P. involutus systems grown non-symbiotically or in symbiosis with
P. sylvestris seedlings. The analysis also led to the identification of putative novel fungal
weathering agents. Results from transcriptomic and metabolomic analyses were
ultimately combined in a model of HAP weathering by P. involutus.
Keywords: Paxillus involutus, Pinus Sylvestris, ectomycorrhizal symbiosis, mineral weathering, hydroxyapatite, RNA-seq, SEM-EDS, UPLC-Q-TOF-MS
Published in RUNG: 18.01.2023; Views: 1987; Downloads: 0
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9. Light-Induced Magnetization at the NanoscaleJonas Wätzel, Primož Rebernik Ribič, Marcello Coreno, Miltcho Danailov, Christian David, Alexander Demidovich, Michele Di Fraia, Luca Giannessi, Klavs Hansen, Špela Krušič, Michele Manfredda, Michael Meyer, Andrej Mihelič, Najmeh Mirian, Oksana Plekan, Barbara Ressel, Benedikt Rosner, Alberto Simoncig, Simone Spampinati, Matija Stupar, Matjaž Žitnik, Marco Zangrando, Carlo Callegari, Jamal Berakdar, Giovanni De Ninno, 2022, original scientific article Keywords: FEL, orbital angular momentum, magnetisation
Published in RUNG: 16.01.2023; Views: 1803; Downloads: 0
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