Episodi
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Organisms respond to changes in their environment affecting their physiological or
ecological optimum by reactions called stress responses. These stress responses may
enable the organism to survive by counteracting the consequences of the environ-
mental change, the stressor, and usually consist of plastic alterations of traits related
to physiology, behaviour, or morphology. In the ecological model species Daphnia,
the waterflea, stressors like predators or parasites are known to have an important
role in adaptive evolution and have been therefore studied in great detail. However,
although various aspects of stress responses in Daphnia have been analysed, molecu-
lar mechanisms underlying these traits are not well understood so far. For studying
unknown molecular mechanisms, untargeted ‘omics’ approaches are especially suit-
able, as they may identify undescribed key players and processes.
Recently, ‘omics’ approaches became available for Daphnia. Daphnia is a cosmo-
politan distributed fresh water crustacean and has been in research focus for a long
time because of its central role in the limnic food web. Furthermore, the responses of
this organism to a variety of stressors have been intensively studied e.g. to hypoxic
conditions, temperature changes, ecotoxicological relevant substances, parasites or
predation. Of these environmental factors, especially predation and interactions with
parasites have gained much attention, as both are known to have great influence on
the structure of Daphnia populations.
In the work presented in this thesis, I characterised the stress responses of Daphnia
using proteomic approaches. Proteomics is particularly well suited to analyse bio-
logical systems, as proteins are the main effector of nearly all biological processes.
However, performing Daphnia proteomics is a challenging task due to high proteolytic activity in the samples, which most probably originate from proteases located
in the gut of Daphnia, and are not inhibited by proteomics standard sample pre-
paration protocols. Therefore, before performing successful proteomic approaches,
I had to optimise the sample preparation step to inhibit proteolytic activity in Daph-
nia samples. After succeeding with this task, I was able to analyse stress responses of
Daphnia to well-studied stressors like predation and parasites. Furthermore, I stud-
ied their response to microgravity exposure, a stressor not well analysed in Daphnia
so far.
My work on proteins involved in predator-induced phenotypic plasticity is de-
scribed in chapter 2 and 3. Daphnia is a textbook example for this phenomenon and is
known to show a multitude of inducible defences. For my analysis, I used the system
of Daphnia magna and its predator Triops cancriformis. D. magna is known to change its
morphology and to increase the stability of its carapace when exposed to the pred-
ator, which has been shown to serve as an efficient protection against T. cancriformis
predation. In chapter 2, I used a proteomic approach to study predator-induced traits
in late-stage D. magna embryos. D. magna neonates are known to be defended against
Triops immediately after the release from the brood pouch, if mothers were exposed
to the predator. Therefore, the formation of the defensive traits most probably oc-
curs during embryonic development. Furthermore, embryos should have reduced
protease abundances, as they do not feed inside the brood pouch until release. To
study proteins differing in abundance between D. magna exposed to the predator
and a control group, I applied a proteomic 2D-DIGE approach, which is a gel based
method and therefore enables visual monitoring of protein sample quality. I found
differences in traits directly associated with known defences like cuticle proteins and
chitin-modifying enzymes most probably involved in carapace stability. In addition,
enzymes of the energy metabolism and the yolk protein vitellogenin indicated alterations in energy demand. In chapter 3, I present a subsequent study supporting
these results. Here, I analysed responses of adult D. magna to Triops predation at
the proteome level using an optimised sample preparation procedure, which was
able to generate adult protein samples thereby inhibiting proteolysis. Furthermore,
I established a different proteomic approach using a mass-spectrometry based label-
free quantification, in which I integrated additional genotypes of D. magna to create a
more comprehensive analysis. With this approach, I was able to confirm the results of
the embryo study, as similar biological processes indicated by cuticle proteins and vi-
tellogenins were involved. Furthermore, additional calcium-binding cuticle proteins
and chitin-modifying enzymes and proteins involved in other processes, e.g. protein
biosynthesis, could be assigned. Interestingly, I also found evidence for proteins in-
volved in a general or a genotype dependent response, with one genotype, which is
known to share its habitat with Triops, showing the most distinct responses.
Genotype dependent changes in the proteome were also detectable in the study
which I present in chapter 4. Here, I analysed molecular mechanisms underlying
host-parasite interactions using the well characterised system of D. magna and the
bacterial endoparasite Pasteuria ramosa. P. ramosa is known to castrate and kill their
host and the infection success is known to depend strongly on the host’s and the para-
site’s genotype. I applied a similar proteomic approach as in chapter 3 using label-
free quantification, but contrastingly, I did not use whole animal samples but only
the freshly shed cuticle. It has been shown, that the genotypic specificity of P. ramosa
infection is related to the parasite’s successful attachment to the cuticle of the host
and is therefore most probably caused by differences in cuticle composition. Hence,
I analysed exuvia proteomes of two different genotypes known to be either suscept-
ible to P. ramosa or not. Furthermore, I compared exuvia proteomes of susceptible
Daphnia exposed to P. ramosa to a control group for finding proteins involved in the infection process and in the stress response of the host. The proteomes of the different
genotypes showed indeed very interesting abundance alterations, connected either to
cuticle proteins or matrix metalloproteinases (MMPs). Additionally, the cuticle pro-
teins more abundant in the susceptible genotype showed a remarkable increase in
predicted glycosylation sites, supporting the hypothesis that P. ramosa attaches to the
host’s cuticle by using surface collagen-like proteins to bind to glycosylated cuticle
proteins. Most interestingly, in all replicates of the susceptible genotype exposed to
P. ramosa, such a collagen-like protein was found in high abundances. Another group
of proteins found in higher abundance in the non-susceptible genotype, the MMPs,
are also connected to this topic, as they may have collagenolytic characteristics and
therefore could interfere with parasite infection. Furthermore, the data indicate that
parasite infection may lead to retarded moulting in Daphnia, as moulting is known to
reduce the infection success.
Contrastingly to the work presented so far, the study described in chapter 5 invest-
igated the protein response of Daphnia to a stressor not well studied on other levels,
namely microgravity. As gravity is the only environmental parameter which has not
changed since life on earth began, organisms usually do not encounter alterations of
gravity on earth and cannot adapt to this kind of change. Daphnia has been part of
one mission to space, however, responses of the animals to microgravity are not well
described so far. In addition, as Daphnia are an interesting candidate organisms for
aquatic modules of biological life support systems (BLSS), more information on their
response to microgravity is necessary. For this reason, proteomics is an interesting ap-
proach, as biological processes not detectable at the morphological or physiological
level may become apparent. Therefore, a ground-based method, a 2D-clinostat, was
used to simulate microgravity, as studies under real microgravity conditions in space
need high technical complexity and financial investment. Subsequently, a proteomic 2D-DIGE approach was applied to compare adult Daphnia exposed to microgravity to
a control group. Daphnia showed a strong response to microgravity with abundance
alterations in proteins related to the cytoskeleton, protein folding and energy meta-
bolism. Most interestingly, this response is very similar to the reactions of a broad
range of other organisms to microgravity exposure, indicating that the response to
altered gravity conditions in Daphnia follows a general concept.
Altogether, the work of my thesis showed a variety of examples of how a proteomic
approach may increase the knowledge on stress responses in an organisms not well-
established in proteomics. I described both, the analysis of molecular mechanisms
underlying well-known traits and the detection of proteins involved in a response not
well characterised. Furthermore, I gave examples for highly genotype dependent and
also more general stress responses. Therefore, this thesis improves our understanding
of the interactions between genotype, phenotype and environment and, moreover,
offers interesting starting points for studying the molecular mechanisms underlying
stress responses of Daphnia in more detail. -
Episodi mancanti?
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Eye movements are important to aid vision, and they serve two main functions: to stabilize a moving visual target on the retina and to stabilize gaze during own body movements. Six types of eye movements have been evolved fulfilling this function: saccades, smooth pursuit, vestibulo-ocular reflex, optokinetic response, convergence and gaze holding. In all vertebrates the eyes are moved by six pairs of extraocular muscles that enable horizontal, vertical and rotatory eye movements. The motoneurons of these muscles are located in the oculomotor (nIII), trochlear (nIV) and abducens (nVI) nucleus in the brainstem. Motoneurons of the lateral rectus muscle (LR) in nVI and of the medial rectus muscle (MR) in nIII provide horizontal eye movements, those of inferior oblique (IO) and superior rectus muscle (SR) in nIII upward eye movements. Motoneurons of the superior oblique (SO) and the inferior rectus muscle (IR) in nIII convey downward eye movements. Recently, it was shown that each extraocular muscle is controlled by two motoneuronal groups:
1. Motoneurons of singly innervated muscle fibers (SIF) that lie within the boundaries of motonuclei providing a fast muscle contraction (twitch) and 2. motoneurons of multiply innervated muscle fibers (MIF) in the periphery of motonuclei providing a tonic muscle contraction (non-twitch). Tract-tracing studies indicate that both motoneuronal groups receive premotor inputs from different brainstem areas. A current hypothesis suggests that pathways controlling twitch motoneurons serve to generate eye movements, whereas the non-twitch system is involved in gaze holding. Lesions of inputs to the twitch motoneuron system may lead to supranuclear gaze palsies, whereas impairment of the non-twitch motoneuron system may result in gaze holding deficits, like nystagmus, or strabismus. Up to date only limited data are available about the histochemical characteristics including transmitters to the SIF- (twitch) and MIF (non-twitch) motoneurons.
The present study was undertaken to investigate the histochemical profile of inputs to motoneuronal groups of individual eye muscles mediating horizontal and vertical eye movements including the inputs to MIF- and SIF motoneurons. The MIF motoneurons of the IR and MR are located in the periphery dorsolateral to nIII, close to the Edinger-Westphal nucleus (EW), which is known to contain preganglionic cholinergic neurons. Other scientists have found that the EW is composed of urocortin-positive neurons involved in food intake or stress. In order to delineate these different cell populations within the supraoculomotor area dorsal to nIII, a comparative study in different mammals was conducted to locate the cholinergic preganglionic neurons and urocortin-positive neurons. Only then, it became obvious that the cytoarchitecturally defined EW labels different cell populations in different species. In rat, ferret and human the cytoarchitecturally defined EW is composed of urocortin-positive neurons. Only in monkey the EW contains cholinergic preganglionic neurons, which lie close to the MIF-motoneurons of MR and IR in the C-group.
In monkey, I performed a systematic study on the histochemical profile and transmitter inputs to the different motoneuron subgroups, including MIF- and SIF motoneurons. Brainstem sections containing prelabelled motoneurons were immunostained for the calcium-binding protein calretinin (CR), gamma-aminobutyric acid (GABA) or glutamate decarboxylase (GAD), glycine transporter 2, glycine receptor 1, and the vesicular glutamate transporters (vGlut) 1 and 2.
The study on the histochemical profile of the motoneuron inputs revealed three main results: 1.The inhibitory control of SIF motoneurons for horizontal and vertical eye movements differs. Unlike previous studies in the primate a considerable GABAergic input was found to all SIF motoneuronal groups, but a glycinergic input was confined to motoneurons of the MR mediating horizontal eye movements. 2. The excitatory inputs to motoneurons for upgaze and downgaze differ in their histochemistry. A striking finding was that CR-positive nerve endings were confined to the motoneurons of muscles involved in upgaze, e.g. SR, IO and the levator palpebrae, which elevates the upper eyelid and acts in synchrony with the SR. Since double-immunoflourescence labelling with anti-GAD did not reveal any colocalization of GAD and CR, the CR-input to upgaze motoneurons is considered as excitatory. 3. The histochemistry of MIF- and SIF motoneurons differs only for vGlut1. Whereas SIF- and MIF motoneurons of individual eye muscles do not differ in their GABAergic, glycinergic and vGlut2 input, vGlut1 containing terminals were covering the supraoculomotor area and targeting only MR MIF motoneurons. It is reasonable to assume that the vGlut1 input affects the near response system in the supraoculomotor area, which houses the preganglionic neurons in the EW mediating pupillary constriction and accommodation and the MR MIF motoneurones involved in vergence.
The histochemical data in monkey enabled the localization of the corresponding motoneuronal subgroups of individual eye muscles in human with the development of an updated nIII map.
Taken together the present work provides new data on the histochemical properties of premotor inputs to motoneuronal groups of the twitch- and non-twitch eye muscle systems in primates. Especially the selective association of CR in premotor upgaze pathways may open the possibility for a targeted research of this system in human post-mortem studies of clinical cases with impairment of upward eye movements, such as progressive supranuclear palsy (PSP) or Niemann-Pick disease (NPC). -
Desmosomen sind spezialisierte Haftstrukturen, die die Stabilisierung des Zellverbundes gegenüber Zug- und Scherkräften gewährleisten. Dazu binden desmosomale Cadherine extrazellulär an Haftmoleküle benachbarter Zellen und sind intrazellulär unter anderem über Desmoplakin (DP) und Plakoglobin (PG) an Keratinfilamenten verankert. Insbesondere für das desmosomale Cadherin Desmoglein 3 (Dsg3), das sowohl innerhalb als auch außerhalb der Desmosomen vorkommt, wurde eine wichtige Bedeutung als Adhäsionsprotein in Keratinozyten nachgewiesen. Trotz ihrer Funktion, Widerstand gegen hohe mechanische Belastungen zu vermitteln, sind Desmosomen dynamische Strukturen, die einem stetigen Umbau unterliegen. Die Notwendigkeit einer genauen Regulierung des desmosomalen Auf- und Abbaus wird durch das Vorkommen zahlreicher vererbbarer und autoimmuner Erkrankungen unterstrichen. In der vorliegenden Arbeit wurden Mechanismen, die der geordneten Assemblierung der Desmosomen und der Disassemblierung nach Störung der desmosomalen Zell-Zell-Haftung unterliegen, untersucht.
Im ersten Teil der vorliegenden Studien standen die Vorgänge der Desmosomenbildung in humanen Keratinozyten im Fokus. Adhärenskontakte und deren Zusammenwirken mit Actinfilamenten spielen eine wichtige Rolle in der Ausbildung der Desmosomen. Für die Actin-Bindeproteine Adducin und Cortactin wurde durch siRNA-Interferenzstudien eine essentielle Funktion für die Vermittlung der desmosomalen Zell-Zell-Haftung nachgewiesen. Die siRNA-induzierte Depletion von Adducin verursachte eine Reduktion der zytoskelettal-gebundenen Dsg3-Moleküle, was mit einer reduzierten Membranmobiltät korrelierte. Für Cortactin wurde eine direkte Interaktion mit Dsg3 mittels zweier unabhängiger molekularbiologischer Methoden nachgewiesen. Dies deutet auf eine direkte Rolle des Cortactins in der Regulierung der Desmosomen hin. Die siRNA-induzierte Depletion von E-Cadherin führte zum Verlust der membranständigen Lokalisation von Dsg3 und zu einer verminderten Verankerung der Dsg3-Moleküle innerhalb der zytoskelettalen Proteinfraktion. Es wurde ein Signalkomplex aus extradesmosomalen Dsg3, E-Cadherin und der Tyrosinkinase Src identifiziert, dessen Stabilität durch Src reguliert wurde. Hierbei wurden Dsg3 und E-Cadherin an Tyrosinresten durch Src phosphoryliert, deren Aktivität sowohl für die Inkorporation von Dsg3 in die Desmosomen als auch für die Reifung der Desmosomen zu stabilen Haftkontakten essentiell war.
Im zweiten Teil der vorliegenden Arbeit wurden die Prozesse der desmosomalen Disassemblierung nach Inkubation mit Pemphigus vulgaris-Autoantikörpern (PV-IgG) analysiert.PV ist eine etablierte Modellerkrankung zur Untersuchung der Desmosomen-vermittelten Zelladhäsion in Keratinozyten. Die Bindung der gegen Dsg1 und Dsg3 gerichteten PV-IgGs induziert eine Reduktion der Dsg3-Proteinmengen und eine Aktivierung verschiedener Signalwege, u.a. von RhoA und PKC. Da diese Signalwege ebenfalls Adducin regulieren und PV-IgGs eine Umorganisierung des Actin-Zytoskeletts verursachen, die durch exogene Aktivierung von RhoA verhindert wird, wurde das Zusammenspiel von PV-IgGs, RhoA und Adducin untersucht. Die protektive Wirkung der RhoA-Aktivierung auf die Zell-Zell-Haftung und die Verteilung von Dsg3 nach Applikation der PV-IgGs war sowohl von der Expression als auch von der Phosphorylierung von Adducin an Serin726 abhängig. Interessanterweise verursachten PV-IgGs über den Ca2+-Einstrom und über PKC, unabhangig von RhoA, eine schnelle Phosphorylierung von Adducin an Serin726. Die durch den Ca2+-Einstrom- und PKC-vermittelte Phosphorylierung von Adducin könnte somit einen Rettungsmechanismus der Keratinozyten darstellen, der in Reaktion auf die PV-IgG-Bindung einsetzt und die desmosomale Assemblierung induziert. Ferner wurde die reduzierte Verankerung der Keratinfilamente an Desmosomen, ein weiteres Merkmal der PV-Pathogenese, mit der Aktivität von PKC korreliert. Keratinfilamente, die einer dynamischen Regulierung durch p38MAPK unterliegen, lösen sich in Reaktion auf PV-IgGs von den Desmosomen und akkumulieren perinukleär. Dieses Phänomen der Zytokeratin-Retraktion wurde durch Inkubation mit Tandempeptid (TP), das die Transinteraktion von Desmogleinen stärkt, verhindert.
Zusammenfassend liefern die in dieser Arbeit gewonnenen Daten neue Erkenntnisse über die Mechanismen des desmosomalen Umsatzes. Adducin und E-Cadherin nehmen eine essentielle Rolle in der Ausbildung und Aufrechterhaltung der desmosomalen Haftstrukturen ein. Untersuchungen der pathogenen Effekte der PV-IgGs unterstreichen die hohe Relevanz eines intakten Actin- und Keratin-Stützgerüsts für die interzelluläre Haftung von Keratinozyten. Diese Befunde könnten in Zukunft auch von medizinischer Relevanz für die Therapie von Pemphigus-Patienten sein. -
Childhood abuse is one of the major risk factors for the development of adult
psychopathology though the response to childhood abuse and other types of early
life adversities is not uniform. Genetic predisposition modulates the exposure to
environmental factors in form of gene by environment interaction. This has been
shown for FKBP5, a modulator of the stress hormone axis, with certain alleles in
FKBP5 conferring a higher risk towards PTSD in adulthood in response to childhood
abuse. This thesis investigates the potential molecular mechanism behind this gene
by environment interaction and delineates an allele-specific demethylation
mechanism in response to childhood abuse. In addition, data on genome-wide gene
expression and DNA methylation profiles in peripheral blood in response to
childhood abuse is presented providing evidence for the hypothesis that childhood
trauma leads to a different molecular trajectory towards adult psychopathology
compared to adult traumatization. The data presented here contribute to our
understanding of the molecular mechanisms underlying gene by environment
interactions in psychiatry and the pathophysiology of trauma- and stress-induced
psychiatric disorders. -
Super-resolution fluorescence microscopy performed via 3D structured illumination microscopy (3D-SIM) features an 8-fold volumetric resolution improvement over conventional microscopy and is well established on flat, adherent cells. However, blastomeres in mammalian embryos are non-adherent, round and large. Scanning whole mount mammalian embryos with 3D-SIM is prone to failure due to non-adherent embryos moving during scanning and a large distance to the cover glass. The biggest challenge and achievement of this doctorate thesis was the development of a novel method to perform 3D-SIM on mammalian embryos (“3D structured illumination microscopy of mammalian embryos and spermatozoa” published in BMC Developmental Biology). The development and fine-tuning of this method took over two years due to the time-intense generation of embryos and the subsequent two day long embryo staining, embedding and scanning with steps that required novel techniques such as micromanipulation which was not associated with sample preparation prior to this protocol. Problem identification was time-intensive since each of the numerous steps necessary could negatively affect the image quality. This method was fine-tuned during three studies. The first study “Reprogramming of fibroblast nuclei in cloned bovine embryos involves major structural remodeling with both striking similarities and differences to nuclear phenotypes of in vitro fertilized embryos” (published in Nucleus) investigates the profound changes of nuclear architecture during cattle preimplantation development of embryos generated by somatic cell nuclear transfer (SCNT) and in vitro fertilization (IVF). Fibroblast nuclei in embryos generated by SCNT go through similar changes in nuclear architecture as embryos generated by IVF. In both embryo types the occurrence of a large, chromatin-free lacuna in the center of nuclei around major embryonic genome activation (EGA) was noted. Similarly, the chromosome territory-interchromatin compartment (CT-IC) model applied to both types of embryos, featuring a lacuna or not, with an enrichment of RNA polymerase II and H3K4me3, a histone modification for transcriptionally competent chromatin, in less concentrated chromatin and an enrichment of H3K9me3, a transcriptionally restrictive histone modification, in more concentrated chromatin. However, large, highly concentrated H3K4me3 and H3K9me3 clusters were noted in both embryo types at chromatin concentrations that did not fit to the model. The chromatin-free lacunas were highly enriched in newly synthesized mRNA.
The second study “Remodeling of the Nuclear Envelope and Lamina during Bovine Preimplantation Development and Its Functional Implications” (published in PLOS ONE) presents the changes of the nuclear envelope and lamina during bovine preimplantation development. Before major EGA, chromatin-free areas of the nuclear periphery were also free of nuclear pore complexes (NPCs), whereas after major EGA, the entire nuclear periphery was equipped with at least a fine layer of chromatin and associated NPCs. Three types of nuclear invaginations were predominant at different stages. The most common invagination was lamin B and NUP153 positive and was most prominent between the 2-cell and 8-cell stages until the onset of major EGA. Lamin B positive, but NUP153 negative invaginations were most prominent during stages with large nuclear volume and surface reductions. The least common invagination was lamin B negative but NUP153 positive and occurred almost exclusively at the morula stage. RNA-Seq and 3D-SIM data showed large deposits of spliced NUP153 mRNA and cytoplasmic NUP153 protein clusters until shortly after major EGA. NUP153 association with chromatin was initiated at metaphase.
The third study “Stage-dependent remodeling of the nuclear envelope and lamina during rabbit early embryonic development” (published in the Journal of Reproduction and Development) demonstrated that rabbit embryonic nuclei feature a nuclear invagination type containing a large volume of cytoplasm that provides cytoplasmic proximity to nucleoli in addition to the small volume invaginations that were previously observed in bovine nuclei. The underlying mechanism for these two invaginations must differ from each other since small volume invaginations were frequently emanating from large volume invaginations emanating from the nuclear border but large volume invaginations were never emanating from small volume invaginations emanating from the nuclear border. Abundance of import/export competent invaginations featuring NPCs peaked at the 4-cell stage, which is the last stage before a drastic nuclear volume decline and also the last stage before major EGA is initiated at the 8- to 16-cell stage. Import/export incompetent invaginations positive for lamin B but not NUP153 peaked at the 2-cell stage. This was the stage with the largest variability in nuclear volumes. This may hint at an interphase nuclear surface reduction mechanism.
Additionally, previously generated but unpublished 3D-FISH data about the localization changes of a stably inserted reporter gene upon activation in cloned bovine embryos was analyzed and documented in the study “Positional changes of a pluripotency marker gene during structural reorganization of fibroblast nuclei in cloned early bovine embryos” (published in Nucleus). This study showed that the stably inserted OCT-4 reporter gene “GOF” in bovine fetal fibroblasts was initially moved towards the nuclear interior in day 2 bovine embryos generated by SCNT of bovine fetal fibroblasts. However, in day 4 SCNT embryos the localization of GOF had moved towards the periphery while it was still activated. Its carrier chromosome territory did not significantly move differently compared with the non-carrier homolog. Constant proximity of GOF to its carrier chromosome territory ruled out a movement by giant loops.
In cooperation with the Department of Histology and Embryology of the Ege University (Izmir, Turkey) the destructive effects of cryopreservation on blastomere integrity were analyzed in the study “Ultra-Structural Alterations in In Vitro Produced Four-Cell Bovine Embryos Following Controlled Slow Freezing or Vitrification” (published in Anatomia, Histologia, Embryologia). The cryopreservation method slow freezing caused more damage to blastomeres and to the zona pellucida than its fast freezing alternative vitrification. This was most likely caused by ice crystal formation and the longer exposure to the toxic side effects of cryoprotectants before freezing was complete. -
Eukaryotic genomes make use of nucleosomes to considerably reduce their packaging volumes. As a consequence, the underlying DNA is rendered inaccessible. Cells make use of ATP-dependent remodeling factors to disrupt histone-DNA contacts and bring about access to the DNA. ACF1 is the largest regulatory subunit of two nucleosome remodeling factors, namely ACF and CHRAC. These complexes assemble, slide or evenly space nucleosomes on DNA with an ability to sense the linker lengths. However, roles of ACF1 in organizing nucleosomes in vivo and their physiological consequences are largely unclear. To understand the roles of ACF1 on chromatin organization, I compared nucleosome occupancy and transcription profiles in wild-type and ACF1-deficient Drosophila embryos. To further investigate and corroborate these chromatin changes, I performed genomewide mapping of ACF1 using chromatin immunoprecipitation.
Nucleosome occupancy was mapped by subjecting DNA obtained from MNase-digested chromatin to deep sequencing and the occupancies were analyzed using advanced analog signal processing methods. We found discontinuous and discrete patches of regularly positioned nucleosomes in wild-type tissue, referred to as ‘regularity regions’. These regions span actively transcribing and silent chromatin domains and show associated variation in the linker lengths across them. A subset of these regions located at sides remote from the transcriptional start sites loses regularity upon ACF1 deletion and show presence of a novel DNA sequence motif. Analyzing nucleosome periodicity by autocorrelation function revealed that nucleosome linker length is longer in ACF1-deficient embryos. Despite profound quantifiable changes in the chromatin organization the RNA expression analyses did not show any major changes.
Genomewide localization of ACF1 was studied using by chromatin immunoprecipitation. We observed a strong enrichment of ACF1 along active promoter regions, coinciding strikingly well with another remodeling factor, RSF-1. However, careful analyses using mutant tissues for both proteins demonstrated that the observed enrichments were in fact false positive. We define 3100 genomic sites as false positive ‘Phantom Peaks’ that tend to enrich in the ChIP-seq experiments. By comparing publicly accessible profiles and the Phantom regions, we showed that several ChIP-seq profiles of the epigenetic regulators show strong enrichment along the Phantom Peaks.
In conclusion, we identify regions of regularly organized nucleosomes across the genome and show that a subset localized in silent chromatin regions is affected by ACF1 deletion. Moreover, we identified a class of false positive ChIP-seq peaks at active promoters. This list of Phantom Peaks can be used to assess potential false positive signal in a ChIP-seq profile, especially when mutant tissue is not available as a control. -
Das größte Problem für HIV-infizierte Personen ist die Tatsache, dass die Infektion nicht „geheilt“ werden kann und die Betroffenen ihr Leben lang infiziert bleiben. Deshalb erfordert die HIV Infektion die dauerhafte Anwendung von Therapien, die das Virus an der Replikation hindern und damit die „Viruslast“ im Körper möglichst gering halten. Die optimale Bekämpfung der HIV-Infektion wären Wirkstoffkombinationen die sowohl die Produktion des Virus durch persistent infizierte Reservoirs als auch die Neuinfektion von HIV-Zielzellen unterbinden.
Interessanterweise sind einige zelluläre Faktoren bekannt, die in die HIV-Replikation eingreifen und der HIV-Produktion entgegenwirken können. Ein Beispiel für solche HIV-Restriktionsfaktoren sind die Risp/ Fam21 Proteine, die mit dem HIV Rev Protein interagieren und so vermutlich seine regulatorische Funktion hemmen können. Frühere Untersuchungen an persistent HIV-infizierten Astrozyten belegten einen Zusammenhang zwischen der Expressionsstärke von Risp/ Fam21 und der Hemmung der HIV Produktion in diesen Zellen. In dieser Arbeit wurde mit Hilfe der quantitativen PCR Analyse gezeigt, dass risp/ fam21 Gene in unterschiedlichen Stärken in menschlichen Zellen exprimiert werden. Zur Modulation der Risp/ Fam21 Expression in diesen als auch anderen für HIV relevanten Zellen wurde ein lentivirales Vektorsystem etabliert. In akut infizierten T-Zellen wurde kein Einfluss der Risp/ Fam21-Modulation auf die HIV-Infektion gefunden, was die Theorie nahelegt, dass Risp/ Fam21 Proteine nur in persistent infizierten Zellen wie den o.g. Astrozyten eine Aktivität zeigen könnten.
Um neue Inhibitoren der akuten HIV-Infektion gesunder Zellen zu identifizieren, wurde die medizinische Heilpflanze Cistus incanus (Ci) im Hinblick auf ihre anti-HIV Aktivität getestet. Bei dieser Pflanze handelt es sich um eine sehr polyphenolreiche Pflanze und Polyphenole stellen eine interessante Klasse an HIV-Inhibitoren dar. In der vorliegenden Arbeit wurde gezeigt, dass Präparate aus Ci die Infektion von Zellen hemmen, indem sie spezifisch an die Virusoberfläche binden und die Anheftung der Viren an die Zielzellen verhindern. Präparate aus Ci inhibieren ein sehr breites Spektrum an verschiedenen HIV-Laborstämmen und –Patientenisolaten. -
Diese Arbeit beschäftigt sich mit der Expression des astrozytenspezifischen Enzyms Glutaminsynthetase in Ergänzung zum gliaspezifischen Marker Repo, um Gliazellen, die mit der embryonalen Entwicklung des Zentralkomplexes in Schistocerca gregaria assoziiert sind, zellulär und molekular zu charakterisieren. Der Zentralkomplex ist ein modulares System neuropiler Strukturen im Mittelhirn aller Insekten, und ist in vielen Verhaltensvorgängen wie Laufen, Fliegen, Stridulation und Ernährung involviert. In der Heuschrecke entwickeln sich die Neuropile des Zentralkomplexes im Laufe der Embryogenese und sind zum Zeitpunkt des Schlüpfens funktionsfähig. Trotz großer Kenntnisse neuronaler Aspekte über die Entwicklung des Zentralkomplexes verbleibt die Funktion der Gliazellen unklar.
In dieser Arbeit wurde das Expressionsmuster des astrozytenspezifischen Enzyms Glutaminsynthetase (GS) und des gliaspezifischen Homöobox Gens reversed polarity (repo) in Kombination mit der negativen Expression des neuron-spezifischen Markers Meerrettich Peroxidase (HRP) zur Identifizierung glialer Zellen benutzt.
Doppelfärbungen zeigen, dass alle GS-positiven Zellen, die mit dem Zentralkomplex assoziiert sind, gleichzeitig Repo-positiv sind. Zum ersten Mal konnte ich durch diese Kombination nicht nur Zellkörper, sondern auch Projektionen (Gliapodien) der Gliazellen sichtbar machen. Während der Embryogenese, also noch vor der Entwicklung des Zentralkomplexes, formen Gliazellen eine zusammenhängende Population, die aus der Pars intercerebralis in die Region der Faserbündel einwandert. Anschließend verteilen sich die Gliazellen neu und umhüllen jedes der einzelnen Module des Zentralkomplexes. Innerhalb der einzelnen Neuropile des Zentralkomplexes sind keine glialen Zellkörper zu finden. Rekonstruktionen einzelner Zellen zeigen Populationen von Gliazellen, die ausgedehnte umhüllende Projektionen um die Neuropile des Zentralkomplexes, wie den Zentralkörper, senden, während eine andere Population von Gliazellen säulenartige Verzweigungen in den Zentralkörper hinein projiziert. Solche Verzweigungen in den Modulen des Zentralkomplexes sind erst nach Fertigstellung der Neuroarchitektur zu erkennen. Daher kann man annehmen, dass diese Verzweigungen auf ein zuvor entstandenes Gerüst von Neuronen oder Tracheen projizieren. Höchstwahrscheinlich sind diese Gliaprojektionen in die Transmitterregulation innerhalb des Neuropils involviert.
Da Gliazellen weitreichende Projektionen (Gliapodien) in und um die Mittelhirnneuropile senden, wurden in gefrorenen Hirnschnitten intrazelluläre Injektionen durchgeführt um zu erforschen, ob diese Gliazellen ein zelluläres Netzwerk via Zellkopplung im Verlauf der Embryogenese bilden. Färbungen individueller Zellen, die an vier unterschiedlichen Injektionsstellen um den Zentralkörper lokalisiert sind, zeigen eine Population gekoppelter Zellen, deren Anzahl und räumliche Verteilung stereotypisch für jeden der Injektionspunkte ist. Darüber hinaus sind sie sowohl bei 70%igem wie auch bei einem embryonalen Entwicklungsstand von 100% miteinander vergleichbar. Anschließende immunhistochemische Experimente bestätigen, dass es sich bei den gekoppelten Zellen um astrozytenähnliche Gliazellen handelt. Durch Hinzufügen von n-Heptanol in das Puffermedium wurde die Zellkopplung verhindert. Da die Zellkopplung auch ohne direkten intersomalen Kontakt auftritt, könnten die erheblichen Verzweigungen der Gliapodien, die sich im Laufe der Embryogenese ausbreiten, involviert sein. Durch die Datenerhebung aller Injektionspunkte kann darauf geschlossen werden, dass die Gliazellen, welche den Zentralkörper umrunden, ein Netzwerk gekoppelter Gliazellen bilden, das als Positionierungssystem der sich entwickelnden Neuropile des Zentralkomplexes dient. -
The CHO-K1 cell line is the most common expression system for therapeutic proteins in the pharmaceutical industry. Due to the nature of economics, the cell lines and the vector design are subject to constant change to increase product quality and quantity. During the cultivation, the production cell lines are susceptible to decreasing productivity over time. Often the loss of production can be associated with a reduction of copy number and the silencing of transgenes. During cell line development, the most promising cell lines are cultivated in large batch culture. Consequently, the loss of a stable production cell line can be very cost-intensive. For this reason I developed different strategies to avoid a reduced productivity. Instability of production cell lines can be predicted by the degree of CpG methylation of the driving promoter. Considering that the DNA methylation is at the end of an epigenetic cascade and associated with the maintenance of the repressive state, I investigated the upstream signals of histone modifications with the assumption to obtain a higher predictive power of production instability. For this reason I performed a chromatin immunoprecipitation of the histone modifications H3K9me3 and H3K27me3 as repressive signals and H3ac as well as H3K4me3 as active marks. The accumulations of those signals were measured close to the hCMV-MIE at the beginning of the cultivation and were then compared with the loss of productivity over two month. I found that the degree of the H3 acetylation (H3ac) correlated best with the production stability. Furthermore I was able to identify an H3ac threshold to exclude most of the unstable producers.
In the second project I aimed to improve the vector design by considering epigenetic mechanisms. To this end I designed on the one hand a target-oriented histone acetyltransferase to enforce an open and active chromatin status at the transgene. On the other hand I point-mutated methylation-susceptible CpGs within the hCMV-MIE to impede the maintenance of inactive heterochromatin formation. Remarkably, the C to G mutation located 179 bp upstream of transcription start site resulted in very stable antibody producing cell lines. In addition, the examination of cell pools expressing eGFP showed that G-179 promoter variants were less prone to a general methylation and gene amplification, which illustrates the dominating effect in epigenetic mechanisms of one single CpG.
The last project was performed to localize stable integration sites within the CHO-K1 genome. In so doing I could show that the transfection leads predominantly to integration into inactive regions. Furthermore I identified promising integration sites with a high potential to induce stable expression. However, those results are preliminary and must be viewed with caution. Further examination needs to be done to confirm these results.
Considering the results of all three projects, I propose that the interplay of metabolic burden and selection pressure at an early time point of cultivation plays an important role in cell line development. Small alterations of selection pressure can lead to a decisive change of cell properties. Therefore, stable cells are less susceptible than weak producers. The increase of selection pressure leads to compensatory effect by gene amplification in the instable cell lines. The resulting adjustment of productivity masks the truly stable cells, which precludes the selection of the right cell lines. For this reason the selection pressure, the copy number as well as the growth rate should be considered to minimize repressive effects. - Mostra di più
