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The future heavy-ion experiment CBM (FAIR/GSI, Darmstadt, Germany) will focus on the measurements of very rare probes, which require the experiment to operate under extreme interaction rates of up to 10 MHz. Due to high multiplicity of charged particles in heavy-ion collisions, this will lead to the data rates of up to 1 TB/s. In order to meet the modern achievable archival rate, this data ow has to be reduced online by more than two orders of magnitude.
The rare observables are featured with complicated trigger signatures and require full event topology reconstruction to be performed online. The huge data rates together with the absence of simple hardware triggers make traditional latency limited trigger architectures typical for conventional experiments inapplicable for the case of CBM. Instead, CBM will employ a novel data acquisition concept with autonomous, self-triggered front-end electronics.
While in conventional experiments with event-by-event processing the association of detector hits with corresponding physical event is known a priori, it is not true for the CBM experiment, where the reconstruction algorithms should be modified in order to process non-event-associated data. At the highest interaction rates the time difference between hits belonging to the same collision will be larger than the average time difference between two consecutive collisions. Thus, events will overlap in time. Due to a possible overlap of events one needs to analyze time-slices rather than isolated events.
The time-stamped data will be shipped and collected into a readout buffer in a form of a time-slice of a certain length. The time-slice data will be delivered to a large computer farm, where the archival decision will be obtained after performing online reconstruction. In this case association of hit information with physical events must be performed in software and requires full online event reconstruction not only in space, but also in time, so-called 4-dimensional (4D) track reconstruction.
Within the scope of this work the 4D track finder algorithm for online reconstruction has been developed. The 4D CA track finder is able to reproduce performance and speed of the traditional event-based algorithm. The 4D CA track finder is both vectorized (using SIMD instructions) and parallelized (between CPU cores). The algorithm shows strong scalability on many-core systems. The speed-up factor of 10.1 has been achieved on a CPU with 10 hyper-threaded physical cores.
The 4D CA track finder algorithm is ready for the time-slice-based reconstruction in the CBM experiment.
The Facility for Antiproton and Ion Research (FAIR) at GSI Darmstadt will provide unprecedented intensities of protons and heavy ions up to uranium at energies of up to 29 GeV for protons and 2.7 GeV/u for Uranium 28+. To achieve high intensities in the synchrotron accelerators, high beam currents have to be provided by the injector linear accelerators. High current heavy ion beams are provided by the Universal Linear Accelerator (UNILAC), which in its current state will not be able to provide the required FAIR beam currents. This thesis deals with the development of upgrades for the UNILAC to ensure its high current capability. The first improvement is a matching section (MEBT) for the interface between the RFQ and the IH-DTL of the existing high current injector HSI at the UNILAC. With this new MEBT section, particle losses are eliminated and the overall beam quality is improved. As a second improvement, a complete replacement of the existing Alvarez-DTL is presented. A combination of efficient IH-type cavities and KONUS beam dynamics results in a reduction of the linac length from about 60 m (Alvarez) to just 23 m (new IH-DTL) while providing the same energy and fulfilling FAIR requirements of a high beam current and beam quality. This thesis contains a detailed beam dynamics design of the new linac including some fundamental investigations of the KONUS beam dynamics concept. A cross-check of the beam dynamics design was performed with two independent multi-particle simulation codes. Detailed error studies were conducted to investigate the influence of manufacturing, alignment and operating errors on the beam dynamics performance. Additionally, all five linac cavities were designed, optimized, and their RF parameters including power requirements calculated to provide a comprehensive linac design.
In this thesis, we study some features of the quantum chromodynamics (QCD) phase diagram at purely imaginary chemical potential using lattice techniques. This is one of the possible methodologies to get insights about the situation at finite density, where the sign problem prevents direct investigations from first principles.
We focus, in particular, on the Roberge-Weiss plane, where the phase structure with two degenerate flavours is studied both in the light and in the heavy quark mass limit. On the lattice, any result is affected by cut-off effects and so are the positions of the two tricritical points m_{tric}^{1,2} separating the second-order intermediate mass region from the first-order triple light and heavy mass regions. Therefore, changing the lattice spacing 'a', the values of m_{tric}^1 and m_{tric}^2 will change. In order to find their position in the continuum limit – i.e. for 'a' going to 0 – they have to be located on finer and finer lattices. Typically, in lattice QCD (LQCD) simulations, the temperature T is tuned through the bare coupling β, on which 'a' depends, while keeping Nt fixed. Hence, it is common to implicitly refer to how fine the lattice is just mentioning its temporal extent.
Using both Wilson and staggered fermions, we simulate Nf=2 QCD on Nt=6 lattices, varying the quark bare mass from the chiral (m_{u,d} going to 0) to the quenched (m_{u,d} going to infinity) limit. For each quark mass, a thorough finite scaling analysis is carried out, taking advantage of two different but consistent methods. In this way we identify the order of the phase transition locating, then, the position of the tricritical points. In order to convert our measurements to physical units we fix the scale measuring the lattice spacing as well as the pion mass corresponding to the quark bare mass used. This allows a comparison between different discretisation, getting a first idea of how serious are cut-off effects.
To be able to make a comparison between two different discretisations, we added an RHMC algorithm with staggered fermions to the CL2QCD software, a GPU code based on OpenCL, which we released in 2014. A considerable part of our work has been invested in ameliorating and optimising CL2QCD, as well as in developing new analysis tools regularly used next to it. Just to mention one, the multiple histogram method has been implemented in a completely general way and we took advantage of it in order to obtain more precise results. Finally, in order to efficiently handle and monitor the hundreds of simulations that are typically concurrently run in finite temperature LQCD, a completely new Bash library of tools has been developed. We plan to release it as a byproduct of CL2QCD in the near future.
Ultrafast protein dynamics are of great interest for understanding the molecular basis of biochemical function. One method to study structural changes with highest time-resolution starting in the femtosecond regime is 2D-IR spectroscopy. However its application to investigate protein dynamics both with high temporal and spatial resolution is currently limited to few biological systems with intrinsic chromophores. Spectral congestion, the contribution of many similar oscillators to the same signals, makes it difficult to draw conclusions about local structural dynamics in most other proteins.
The aim of this thesis is to extend the application of 2D-IR spectroscopy to a wider range of proteins by introducing unnatural amino acids (UAAs) with azide or nitrile groups as site-specific vibrational probes, which absorb in the free spectral window between 1800 to 3000 cm-1 by using methods from chemical biology.
In a comparative experimental study using FTIR and 2D-IR spectroscopy of single amino acids azidohomoalanine (Aha), a methionine analogue, was identified as preferred label. To demonstrate the application potential of UAAs as site-specific probes, Aha was then incorporated into different positions in a small globular protein. By using both FTIR and ultrafast 2D-IR it was shown, that indeed the local microenvironment as well as conformational fluctuations on picosecond timescale could be monitored with high spatial information. The azide moiety shows a shift of its absorption frequency depending on the polarity of its surrounding. Using this approach, different subensembles for the protein conformations with more polar and less polar environment around the vibrational probe can be distinguished.
A second major application of site-specific labels is the study of vibrational energy transfer processes (VET), predicted to be relevant for allosteric communication in protein domains such as the PDZ domain. VET can be tracked with high spatial resolution using time-resolved IR spectroscopy by exciting a localized vibrational mode and probing separate modes in a two-colour 2D-IR experiment. To extend this kind of experiment to proteins, a specific donor-acceptor pair of two UAAs was introduced. It uses an azulene moiety as donor that can be excited in the visible range but deposits the excess energy by internal conversion into the vibrational modes of the ground state. In small peptides this VET pair was applied successfully, showing a distance-dependent energy transfer induced signal for VET through covalent bonds. These findings bare great promise for the direct observation of vibrational energy flow in proteins in real-time.
Overall this thesis is the basis for extending the usability of 2D-IR spectroscopy to study structural dynamics in a wide range of proteins systems both with high temporal and spatial resolution.
In this doctoral thesis the transformation from relativistic hydrodynamics to transport and vice versa is studied. Approximations made by hybrid (hydrodynamics + transport) simulations of relativistic heavy ion collisions are discussed and their reliability is assessed at intermediate collision energies. A new method to simulate heavy ion collisions is suggested, based on the forced thermalization in high-density regions.
Multicellular organisms require that cells adhere to each other. This cell-cell adhesion is indispensable for the formation and the integrity of epithelial structures, tissues and organs. Mammals have developed four different cell-cell adhesion structures, the adhering junctions, which ensure the tight contact between cells but are also important platforms for communication and exchange in tissues. Two of these adhering junctions are cadherin based, the belt-like adherens junctions and the spot-like desmosomes. Both structures have in common that they are composed of single membrane spanning proteins, the cadherins, which accomplish adhesion in a calcium-dependent manner. The intracellular parts of classical as well as desmosomal cadherins bind to different adaptor proteins of the armadillo-protein family and others which build a protein plaque underneath the membrane and link the cadherins to the actin or intermediate filament cytoskeleton.
Desmosomes are of special importance for tissues that have to withstand mechanical stress. Although they are essential to stabilize tissues they have to be highly flexible and dynamic structures, as processes like wound healing or tissue remodeling require that adhesive interactions can be modulated. The molecular dynamics within desmosomes are not jet understood in detail, but it is assumed that two different membrane associated pools of desmosomal cadherins exist in cells. Cadherins that are incorporated in mature desmosomes are part of the junctional pool, whereas cadherins that are not associated with firm desmosomes and the intermediate filament cytoskeleton belong to the non-junctional pool. Lateral movements between the two pools results in a dynamic equilibrium and allows for example the exchange of old cadherins. Little is known about the breakdown of desmosomal cadherins. Several studies found that desmosome assembly or endocytosis are cholesterol dependent processes and claimed that membrane microdomains play a role in the regulation of desmosome dynamics. Moreover, membrane rafts may be involved in the pathomechanism of the desmosome associated disease pemphigus, were autoantibodies bind to the cadherin desmoglein-3 and trigger its internalization which results in a loss of adhesion in skin cells.
Membrane rafts are cholesterol dependent nanoscale structures of cellular membranes that are able to regulate the distribution of proteins within the plasma membrane and thus form platforms for cell signaling and membrane trafficking. Flotillins are proteins that are associated with membrane rafts and are reported to be involved in processes like endocytosis, endosomal sorting and a multitude of different signaling events. We could recently show that the membrane raft associated proteins flotillin-1 and flotillin-2 bind directly to the armadillo protein y-catenin which can be part of both, the adherens junction and the desmosome. The aim of this study was to eluciadate a possible role of flotillins in the regulation of desmosomes.
HaCaT keratinocytes were chosen as the main cell system for this study and at first the association of desmosomal components with flotillins was analyzed in detail. It was found that flotillins are clearly associated with desmosomal proteins. They colocalize with desmoglein-3 at cell borders and precipitate the other desmogleins. Further binding assays revealed that both flotillins bind to all desmogleins and the long isoforms of the second class of desmosomal cadherins, the desmocollins. The interaction is a direct one and was mapped to the ICS sequence within the cadherins. This close association rendered the question whether flotillins are functionally implicated in desmosome regulation. To address this issue, stable flotillin knockdown HaCaT cells were analyzed in detail. The molecular morphology of desmoglein-3, desmoglein-1 and two plaque proteins was clearly altered in the absence of flotillins. The membrane staining of all tested desmosomal proteins was derailed and disordered. Furthermoore, the loss of flotillins had an impact on the adhesive capacity of HaCaT keratinocytes. The cell-cell adhesion was weakened in the absence of flotillins, which was monitored by an increased fragmentation of knockdown cells in a cell dissociation assay.
In order to find out the mechanism by which flotillins influence the membrane morphology and the adhesiveness in keratinocytes, the association of desmosomal proteins with membrane microdomains was examined, at first. A predominant part of desmoglein-3 is associated with membrane rafts in HaCaT keratinocytes, whereas only a minor part of desmoglein-1 is found there. However, the raft-association of none of the examined proteins was altered in the absence of flotillins. Furthermore, flotillin depletion did not change the distribution of desmogleins with the two different cadherin pools. Less desmoglein-3 is found in the junctional pool of the flotillin depleted cells compared to the control cells, but this is due to an overall diminished desmoglein-3 protein level in these cells.
Flotillins are involved in endocytic processes but their exact role there is under debate. The endocytic uptake of desmosomal cadherins requires intact membrane rafts, but the precise mechanism is still unknown. A possible involvement of flotillins on the endocytosis of desmoglein-3 was addressed next. It is known that the internalization of desmoglein-2 is dependent on the GTPase dynamin, arguing for an involvement of dynamin in the endocytosis of desmoglein-3 as well. When dynamin and thus desmoglein-3 endocytosis was inhibited using chemical compounds, the mislocalization of desmoglein-3 that was observed in flotillin knockdown cells was restored. This suggest that inhibition of desmoglein-3 endocytosis enhances the amount and/or availability of desmoglein-3 at the plasma membrane, which then normalizes the morphological alterations caused by a knockdown of flotillins. Furthermore the morphological alterations in the flotillin knockdown HaCaT cells were found to be similar to the localization of desmoglein-3 that was observed upon treatment of keratinocytes with PV IgG These structures have been described before as linear arrays and are assumed to be sites of endocytic uptake. This strengthens the idea that enhanced desmoglein-3 internalization takes place in the absence of flotillins, which then results in a weakened adhesion.
Altogether this study revealed flotillins as novel players in desmosome mediated cell-cell adhesion processes. By binding to desmosomal cadherins and desmosomal plaque proteins, flotillins stabilize desmosomes at the plasma membrane and are required for a proper cell-cell adhesion.
In light of the global sea-level rise and climate change of the 21th century, it is important to look back into the recent past in order to understand what the future might hold. A multi-proxy data set was compiled to evaluate the influence of geomorphological and environmental factors, such as antecedent topography, subsidence, sea level and climate, on reef, sand apron and lagoon development in modern carbonate platforms through the Holocene. Therefore, a combination of remote sensing and morphological data from 122 modern carbonate platforms and atolls in the Atlantic, Indian and Pacific Oceans were conducted, along with a case study from the oceanic (Darwinian) barrier-reef system of Bora Bora, French Polynesia, South Pacific.
The influence of antecedent topography and platform size as factors controlling Holocene sand apron development and extension in modern atolls and carbonate platforms is hypothesized. Antecedent topography describes the elevation and relief of the underlying Pleistocene topography (karst) and determines the distance from the sea floor to the rising postglacial sea level. Maximum lagoon depth and marginal reef thickness, when available in literature, were used as proxies for antecedent topography. Sand apron proportions of 122 atolls and carbonate platforms from the Atlantic, Indian and Pacific Oceans were quantified and correlated to maximum lagoon depth, total platform area and marginal reef thickness. This study shows that sand apron proportions increase with decreasing lagoon depths. Sand apron proportions also increase with decreasing platform area. The interaction of antecedent topography and Holocene sea-level rise is responsible for variations in accommodation space and at least determines the extension of the lateral expansion of sand aprons. In general, sand apron formation started when marginal reefs approached relative sea level. Spatial and regional variations in sea-level history let sand apron formation start earlier in the Indo-Pacific region (transgressive-regressive) than in the Western Atlantic Ocean (transgressive).
The influence of sea level, antecedent topography and subsidence of a volcanic island on late Quaternary reef development was evaluated based on six rotary core transects on the barrier and fringing reefs of Bora Bora. This study was designed to revalue the Darwinian model, the subsidence theory of reef development, which genetically connects fringing reef, barrier reef and atoll development by continuous subsidence of the volcanic basement. Postglacial sea-level rise, and to a minor degree subsidence, were identified as major factors controlling Holocene reef development in that they have created accommodation space and controlled reef architecture. Antecedent topography was also an important factor because the Holocene barrier reef is located on a Pleistocene barrier reef forming a topographic high. Pleistocene soil and basalt formed the pedestal of the fringing reef. Uranium-Thorium dating shows that barrier and fringing reefs developed contemporaneously during the Holocene.
In the barrier–reef lagoon of Bora Bora, the influence of environmental factors, such as sea level and climate, tsunamis and tropical cyclones controlling Holocene sediment dynamics was evaluated based on sedimentological, paleontological, geochronological and geochemical data. The lagoonal succession comprises mixed carbonate-siliciclastic sediments overlying peat and Pleistocene soil. The multi-proxy data set shows variations in grain-size, total organic carbon (proxy for primary productivity), Ca and Cl element intensities (proxies for carbonate availability and lagoonal salinity) during the mid-late Holocene. These patterns could result from event sedimentation during storms and correlate to event deposits found in nearby Tahaa, probably induced by elevated cyclone activity. Accordingly, elevated erosion and runoff from the volcanic island and lower lagoonal salinity would be a result of rainfall during repeated cyclone landfall. However, Ti/Ca and Fe/Ca ratios as proxies for terrigenous sediment delivery peaked out in the early Holocene and declined since the mid-Holocene. Benthic foraminifera assemblages do not indicate reef-to-lagoon transport. Alternatively, higher and sustained hydrodynamic energy is probably induced by stronger trade winds and a higher-than-present sea level during the mid-late Holocene. The increase in mid-late Holocene sediment dynamics within the back-reef lagoon is supposed to display sediment-load shedding of sand aprons due to the oversteepening of slopes at sand apron/lagoon edges during their progradation rather than an increase in tropical storm activity during that time.
The influence of sea-level and climate changes on sediment import, composition and distribution in the Bora Bora lagoon during the Holocene is validated. Lagoonal facies succession comprises siderite-rich marly wackestones, foraminifera-siderite wackestones, mollusk-foraminifera marly packstones and mollusk-rich wackestones during the early-mid Holocene, and mudstones since the mid-late Holocene. During the early Holocene, enhanced weathering and iron input from the volcanic island due to wetter climate conditions led to the formation of siderite within the lagoonal sediments. The geochemical composition of these siderites shows that precipitation was driven by microbial activity and iron reduction in the presence of dissolved bicarbonate. Chemical substitutions at grain margins illustrate changes in the oxidation state and probably reflect changes in pore water chemistry due to sea-level rise and climate change (rainfall). In the late Holocene, sediment transport into the lagoon is hampered by motus on the windward side of the lagoon, which led to early submarine lithification within the lagoon.
Gepulste dipolare EPR-Spektroskopie ist eine wertvolle Methode, um Abstände von 1.5 bis 10 nm zwischen zwei Spinmarkern zu messen. Diese Information kann für Strukturbestimmungen hilfreich sein, wo traditionelle Methoden wie Kristallstrukturanalyse und NMR nicht angewendet werden können. Zusätzlich ist es möglich, Änderungen in Konformation und Flexibilität zu verfolgen. Für diese Studien haben sich stabile Nitroxidradikale als Spinmarker etabliert. Diese werden spezifisch durch die site-directed spin labelling Methode (SDSL) kovalent an das zu untersuchende Biomolekül gebunden. In den letzten Jahren wurden weitere Spinmarker für Abstandsbestimmungen mittels EPR-Spektroskopie entwickelt. Besonders interessant sind Triarylmethylradikale (im Folgenden abgekürzt als Trityl) und paramagnetische Metallzentren.
Im Vergleich zu Nitroxidradikalen hat das Tritylradikal einige Vorteile: Eine höhere Stabilität in einer reduzierenden Umgebung wie im Inneren von Zellen, längere Elektronenspin-Relaxationszeiten bei Raumtemperatur und ein schmaleres EPR-Spektrum. Deswegen ist dieses organische Radikal ein alternativer Spinmarker, der besonders gut für die Forschung von Biomolekülen in einer nativen Umgebung unter physiologischen Bedingungen geeignet ist. Auch paramagnetische Metallzentren sind weniger reduktionsempfindlich als Nitroxidradikale. Zusätzlich sind diese Spinmarker interessant in biologischen Fragestellungen. Zum Beispiel besitzen zahlreiche Enzyme paramagnetische Manganzentren als Cofaktoren. Zudem kann Magnesium, ein wesentlicher Cofaktor in Enzymen, Nukleinsäuren und Nukleotid-Bindungsdomänen der G- und Membranproteine, oft durch das paramagnetische Mangan ersetzt werden. Um Abstandsmessungen an Biomolekülen, die nur ein Metallzentrum besitzen, durchzuführen, können zusätzliche Spinmarker in Form eines Nitroxid-, Tritylradikals oder eines anderen paramagnetischen Metallkomplexes mithilfe der SDSL-Methode kovalent gebunden werden.
Nitroxidradikale, Tritylradikale und Metallzentren haben deutlich unterschiedliche EPR-spektroskopische Eigenschaften, welche oft als orthogonale Spinmarker bezeichnet werden. Solche Spinmarker sind nützlich für die Untersuchung von verschiedenen Untereinheiten bei makromolekularen Komplexen. Somit können die intramolekularen Abstände innerhalb einer Untereinheit sowie intermolekularen Abstände zwischen den unterschiedlichen Untereinheiten mit nur einer einzigen Probe bestimmt werden. Zusätzlich können die orthogonalen Marker sehr effektiv genutzt werden, um Metallzentren in Biomolekülen mithilfe der Trilateration-Strategie genau zu lokalisieren.
Die hier vorliegende Doktorarbeit beschäftigt sich mit der Nutzung dieser neuen Spinmarker für Abstandsmessungen. Solche Spinmarker sind noch kaum erforscht, obwohl sie für biologische Anwendungen eine große Rolle spielen könnten.
Das erste Ziel dieser Doktorarbeit war eine Studie über Tritylradikale mithilfe der dipolaren EPR-Spektroskopie. Zu diesem Zweck wurden sowohl double quantum coherence (DQC) und single frequency technique for refocussing dipolar couplings (SIFTER) Experimente als auch Hochfrequenz pulsed electron electron double resonance (PELDOR) Experimente mit einem Trityl-Modellsystem durchgeführt. Dabei wurden die Besonderheiten der unterschiedlichen dipolaren Spektroskopiemethoden mit diesem Spinmarker untersucht, um die Empfindlichkeit und Robustheit für die Abstandsmessungen zu optimieren.
Das zweite Ziel war eine Studie über den Einfluss der Hochspin-Multiplizität des Mangans auf die Abstandsbestimmungen. Für diesen Zweck wurde zuerst ein Modellsystem mit einem orthogonalen Mn2+ Ion und Nitroxidradikal mithilfe der PELDOR-Spektroskopie untersucht. Anschließend wurde ein weiteres Modellsystem mit zwei Mn2+-Ionen untersucht, um PELDOR und relaxation-induced dipolar modulation enhancement (RIDME) Experimente bezüglich ihrer Empfindlichkeit und Robustheit sowie Genauigkeit der Datenanalyse zu optimieren.
Das Trityl-Modellsystem wurde in der Arbeitsgruppe von Prof. Sigurdsson synthetisiert. Die EPR Messungen wurden bei zwei verschiedenen Mikrowellenfrequenzen (34 und 180 GHz) durchgeführt. Es wurde gezeigt, dass die Auswahl der optimalen Methode von den EPR-spektroskopischen Eigenschaften des Systems bei den jeweiligen Mikrowellenfrequenzen abhängig ist. Das EPR-Spektrum des Trityls ist bei 34 GHz so schmal, dass das ganze Spektrum von einem üblichen Mikrowellenpuls angeregt werden kann. In diesem Fall sind die DQC und SIFTER Experimente am besten geeignet. Der mit diesen Methoden bestimmte Abstand von 4.9 nm ist in guter Übereinstimmung mit Werten aus der Literatur. Es wurde festgestellt, dass die SIFTER Messung eine höhere Empfindlichkeit als DQC besitzt, da das Signal-zu-Rausch Verhältnis um den Faktor vier größer ist. Außerdem ist die SIFTER-Methode experimentell weniger anspruchsvoll, da ein deutlich kürzerer Phasenzyklus für die Mikrowellenpulse benötigt wird. ...
In the dentate gyrus (DG) of the mammalian hippocampus, neurogenesis continues to take place throughout an organism’s life. Adult neurogenesis includes proliferation and differentiation of neural stem cells into dentate granule cells (GCs) that mature and integrate into the existing cellular network. This thesis work presents a novel approach that enables longitudinal examination of living postnatally generated GCs in their endogenous niche by using retroviral (RV) labeling in organotypic entorhino-hippocampal slice cultures (OTCs). Older GCs were fluorescence-labeled with an adeno-associated virus controlled by the synapsin 1 promoter (AAV-Syn). The combination of time-lapse imaging and 3-D reconstruction of newborn developing GCs and older, more mature GCs enabled comparative analyses of dendritic growth and cellular dynamics as well as investigations of spine formation and the establishment of synaptic contacts.
Postnatal neurogenesis was studied in the mouse and rat DG in vivo by analysis of the distribution of chemical neuronal maturation markers doublecortin (DCX) and calbindin in combination with the GC marker Prox1 between P7 and P42. The marker expression patterns at different time points indicated that the number of mature GCs increased gradually over time and that young, immature GCs were added to the inner layers of the granule cell layer (GCL), as is the case in the adult brain. The most substantial shift in GC maturation took place between P7 and P14, though GCs in the rat DG matured faster (i.e. by ~5 days) than GCs in the mouse. Immunocytochemical in vitro analysis in OTCs at DIV 7, 14, and 28 exhibited a distribution of marker expression over time that was comparable to in vivo, though the number of DCX-expressing GCs was low at DIV 28, indicating a considerable decrease in neurogenesis rate over time in the OTC. Nevertheless, RV-labeling of newborn GCs at DIV 0 yielded successful visualization and enabled time-lapse imaging of complete developing GCs up to 4 weeks after mitosis. During the second week of development, newborn GCs exhibited a high level of structural dynamics, including extension and retraction of dendritic segments. In the third week, newborn GCs displayed high dendritic complexity which was followed by pronounced dendritic pruning. Finally, a phase of structural stabilization and local refinement could be observed during the fourth week. Older AAV-Syn-labeled GCs did not exhibit such dynamic structural remodeling. Anterograde tracing of entorhinal projection fibers using the biotinylated dextran amine Mini Ruby showed innervation of the outer molecular layer (OML) by entorhinal axons at early time points, i.e. DIV 8 when newborn GCs started to extend dendrites into the ML, as well as at DIV 20 when RV-labeled GCs exhibited elaborate dendritic trees with processes in the OML intermingling with entorhinal fibers. This shows that newborn GCs in the OTC grow into an area of existing entorhinal axon terminals, which is highly similar to the situation in the adult brain. Hence, the results show that postnatal neurogenesis can be studied effectively in the OTC system as a model of adult neurogenesis. The first appearance of spine-like protrusions in newborn GCs was observed two weeks post RV injection. Ultrastructural electron-microscopic images revealed that spines established synaptic contacts with axonal boutons. These findings suggest that newborn GCs are successfully integrated into the existing cellular circuitry in the OTC system. The high level of structural flexibility found in this study might be a necessary requisite of new neurons for successful dendritic maturation and functional integration into a neuronal network. Thus, live imaging of postnatally born GCs in the OTC appears as a useful novel approach to elucidate the mechanisms that affect cellular dynamics of neurogenesis.
Heat stress transcription factors (Hsfs) play essential role in heat stress response and thermotolerance by controlling the transcriptional activation of heat stress response (HSR) genes including molecular chaperones. Plant Hsf families show a striking multiplicity, with more than 20 members in the many plant species. Among Hsfs, HsfA1s act as the master regulators of heat stress (HS) response and HsfA2 becomes one of the most abundant Hsfs during HS. Using transgenic plans with suppressed expression of HsfA2 we have shown that this Hsf is involved in acquired thermotolerance of S. lycopersicum cv Moneymaker as HsfA2 is required for high expression and maintenance of increased levels of Hsps during repeated cycles of HS treatment.
Interestingly, HsfA2 undergoes temperature-dependent alternative splicing (AS) which results in the generation of seven transcript variants. Three of these transcripts (HsfA2-Iα-γ), generated due to alternative splicing of a second, newly identified intron encode for the full length protein involved in acquired thermotolerance. Another 3 transcripts (HsfA2-IIIα-γ) are generated due to alternative splicing in intron 1, leading in all cases to a premature termination codon and targeting of these transcripts for degradation via the non-sense mRNA decay mechanism (NMD).
Interestingly, excision of intron 2, results into the generation of a second previously unreported protein isoform, annotated as HsfA2-II. HsfA2-II shows similar transcriptional activity to the full-length protein HsfA2-I in the presence of HsfA1a but lacks the nuclear export signal (NES) required for nucleocytoplasmic shuttling which allows efficient nuclear retention and stimulation of transcription of HS-induced genes. Furthermore, stability assays showed that HsfA2-II exhibits lower protein stability compared to HsfA2-I.
The presence of a second intron and the generation of a second protein isoform we identified in other Solanaceae species as well. Remarkably, we observed major differences in the splicing efficiency of HsfA2 intron 2 among different tomato species. Several wild tomato accessions exhibit higher splicing efficiency that favors the generation of HsfA2-II, while in these species the splice variant HsfA2-Iγ is absent. This natural variation in splicing efficiency specifically occurring at temperatures around 37.5oC is associated with the presence of 3 intronic polymorphisms. In the case of wild species these polymorphisms seemingly restrict the binding of RS2Z36, identified as a putative splicing silencer for HsfA2 intron 2.
Tomato accessions with the polymorphic “wild” HsfA2 show enhanced thermotolerance against a direct severe heat stress incident due to the stronger increase of Hsps and other stress induced genes. Introgression of the “wild” S. pennellii HsfA2 locus into the cultivar M82, resulted in enhanced seedling thermotolerance highlighting the potential use of the polymorphic HsfA2 for breeding.
We conclude that alterations in the splicing efficiency of HsfA2 have contributed to the adaption of tomato species to different environments and these differences might be directly related to natural variation in their thermotolerance.