Refine
Has Fulltext
- yes (11)
Is part of the Bibliography
- yes (11) (remove)
Year of publication
Document Type
Language
- English (11) (remove)
Keywords
- Genetik (11) (remove)
How genomic and ecological traits shape island biodiversity - insights from individual-based models
(2020)
Life on oceanic islands provides a playground and comparably easy\-/studied basis
for the understanding of biodiversity in general. Island biota feature many
fascinating patterns: endemic species, species radiations and species with
peculiar trait syndromes. However, classic and current island biogeography
theory does not yet consider all the factors necessary to explain many of these
patterns. In response to this, there is currently a shift in island biogeography
research to systematically consider species traits and thus gain a more
functional perspective. Despite this recent development, a set of species
characteristics remains largely ignored in island biogeography, namely genomic
traits. Evidence suggests that genomic factors could explain many of the
speciation and adaptation patterns found in nature and thus may be highly
informative to explain the fascinating and iconic phenomena known for oceanic
islands, including species radiations and susceptibility to biotic invasions.
Unfortunately, the current lack of comprehensive meaningful data makes studying
these factors challenging. Even with paleontological data and space-for-time
rationales, data is bound to be incomplete due to the very environmental
processes taking place on oceanic islands, such as land slides and volcanism,
and lacks causal information due to the focus on correlative approaches. As
promising alternative, integrative mechanistic models can explicitly consider
essential underlying eco\-/evolutionary mechanisms. In fact, these models have
shown to be applicable to a variety of different systems and study questions.
In this thesis, I therefore examined present mechanistic island models to
identify how they might be used to address some of the current open questions in
island biodiversity research. Since none of the models simultaneously considered
speciation and adaptation at a genomic level, I developed a new genome- and
niche-explicit, individual-based model. I used this model to address three
different phenomena of island biodiversity: environmental variation, insular
species radiations and species invasions.
Using only a single model I could show that small-bodied species with flexible
genomes are successful under environmental variation, that a complex combination
of dispersal abilities, reproductive strategies and genomic traits affect the
occurrence of species radiations and that invasions are primarily driven by the
intensity of introductions and the trait characteristics of invasive
species. This highlights how the consideration of functional traits can promote
the understanding of some of the understudied phenomena in island biodiversity.
The results presented in this thesis exemplify the generality of integrative
models which are built on first principles. Thus, by applying such models to
various complex study questions, they are able to unveil multiple biodiversity
dynamics and patterns. The combination of several models such as the one I
developed to an eco\-/evolutionary model ensemble could further help to identify
fundamental eco\-/evolutionary principles. I conclude the thesis with an outlook
on how to use and extend my developed model to investigate geomorphological
dynamics in archipelagos and to allow dynamic genomes, which would further
increase the model's generality.
The etiology of anxiety disorders is multifactorial with contributions from both
genetic and environmental factors. Several susceptibility genes of anxiety disorders or
anxiety-related intermediate phenotypes have been identified, including the
serotonin transporter gene (5-HTT) and the neuropeptide S receptor gene (NPSR1),
which have been shown to modulate responses to distal and acute stress experiences.
For instance, gene-environment interaction (GxE) studies have provided evidence
that both 5-HTT and NPSR1 interact with environmental stress, particularly
traumatic experiences during childhood, in the moderation of anxiety traits, and
both 5-HTT and NPSR1 have been implicated in hypothalamic-pituitary-adrenal
(HPA) axis reactivity – an intermediate phenotype of mental disorders – in response
to acute stress exposure. The first part of this thesis aimed to address the interplay of
variations in both 5-HTT and NPSR1 genes and distal stress experiences, i.e.
childhood trauma, in the moderation of anxiety-related traits, extended by
investigation of the potentially protective effect of positive influences, i.e. elements of
successful coping such as general self-efficacy (GSE), on a GxE risk constellation by
introducing GSE as an indicator of coping ability (“C”) as an additional dimension in
a GxExC approach conferring – or buffering – vulnerability to anxiety. Increased
anxiety was observed in 5-HTTLPR/rs25531 LALA genotype and NSPR1 rs324981 AA
genotype carriers, respectively, with a history of childhood maltreatment but only in
the absence of a person’s ability to cope with adversity, whereas a dose-dependent
effect on anxiety traits as a function of maltreatment experiences irrespective of
coping characteristics was observed in the presence of at least one 5-HTT S/LG or
NSPR1 T allele, respectively. The second part of this thesis addressed the respective
impact of 5-HTT and NPSR1 variants on the neuroendocrine, i.e. salivary cortisol
response to acute psychosocial stress by applying the Maastricht Acute Stress Test
(MAST). A direct effect of NPSR1 – but not 5-HTT – on the modulation of acute
stress reactivity could be discerned, with carriers of the more active NPSR1 T allele
Summary
III
displaying significantly higher overall salivary cortisol levels in response to the MAST
compared to AA genotype carriers.
In summary, study 1 observed a moderating effect of GSE in interaction with
childhood maltreatment and 5-HTT and NPSR1, respectively, in an extended GxExC
model of anxiety risk, which may serve to inform targeted preventive interventions
mitigating GxE risk constellations and to improve therapeutic interventions by
strengthening coping ability as a protective mechanism to promote resilient
functioning. In study 2, a modulation of HPA axis function, considered to be an
endophenotype of stress-related mental disorders, by NPSR1 gene variation could be
discerned, suggesting neuroendocrine stress reactivity as an important potential
intermediate phenotype of anxiety given findings linking NPSR1 to dimensional and
categorical anxiety. Results from both studies may converge within the framework of
a multi-level model of anxiety risk, integrating neurobiological, neuroendocrine,
environmental, and psychological factors that act together in a highly complex
manner towards increasing or decreasing anxiety risk.
Sustained anxiety is considered as a chronic and future-oriented state of apprehension that does not belong to a specific object. It is discussed as an important characteristic of anxiety disorders including panic disorder, generalized anxiety disorder (GAD) and posttraumatic stress disorder (PTSD). Experimentally, sustained anxiety can be induced by contextual fear conditioning in which aversive events are unpredictably presented and therefore the whole context becomes associated with the threat. This thesis aimed at investigating important mechanisms in the development and maintenance of sustained anxiety: (1) facilitated acquisition and resistant extinction of contextual anxiety due to genetic risk factors (Study 1), and (2) the return of contextual anxiety after successful extinction using a new reinstatement paradigm (Study 2). To this end, two contextual fear conditioning studies were conducted in virtual reality (VR). During acquisition one virtual office was paired with unpredictable mildly painful electric stimuli (unconditioned stimulus, US), thus becoming the anxiety context (CXT+). Another virtual office was never paired with any US, thus becoming the safety context (CXT-). Extinction was conducted 24 h later, i.e. no US was presented, and extinction recall was tested another 24 h later on Day 3. In both studies context-evoked anxiety was measured on three different response levels: behavioral (anxiety-potentiated startle reflex), physiological (skin conductance level), and verbal (explicit ratings). In Study 1, participants were stratified for 5-HTTLPR (S+ risk allele vs. LL no risk allele) and NPSR1 rs324981 (T+ risk allele vs. AA no risk allele) polymorphisms, resulting in four combined genotype groups with 20 participants each: S+/T+, S+/LL, LL/T+, and LL/AA. Results showed that acquisition of anxiety-potentiated startle was influenced by a gene × gene interaction: only carriers of both risk alleles (S+ carriers of the 5-HTTLPR and T+ carriers of the NPSR1 polymorphism) exhibited significantly higher startle magnitudes in CXT+ compared to CXT-. However, extinction recall as measured with anxiety-potentiated startle was not affected by any genotype. Interestingly, the explicit anxiety level, i.e. valence and anxiety ratings, was only influenced by the NPSR1 genotype, in a way that no risk allele carriers (AA) reported higher anxiety and more negative valence in response to CXT+ compared to CXT-, whereas risk allele carriers (T+) did not. Study 2 adopted nearly the same paradigm with the modification that one group (reinstatement group) received one unsignaled US at the beginning of the experimental session on Day 3 before seeing CXT+ and CXT-. The second group served as a control group and received no US, but was immediately exposed to CXT+ and CXT-. Results showed a return of anxiety on the implicit and explicit level (higher startle responses and anxiety ratings in response to CXT+ compared to CXT-) in the reinstatement group only. Most important, the return of contextual anxiety in the reinstatement group was associated with a change of state anxiety and mood from extinction to test, that is the more anxiety and negative mood participants experienced before the reinstatement procedure, the higher their return of anxiety was. In sum, results of Study 1 showed that facilitated contextual fear conditioning on an implicit behavioral level (startle response) could be regarded as an endophenotype for anxiety disorders, which can contribute to our understanding of the etiology of anxiety disorders. Results of Study 2 imply that anxiety and negative mood after extinction could be an important facilitator for the return of anxiety. Furthermore, the present VR-based contextual fear conditioning paradigm seems to be an ideal tool to experimentally study mechanisms underlying the acquisition and the return of anxiety. Future studies could investigate clinical samples and extend the VR paradigm to evolutionary-relevant contexts (e.g., heights, darkness, open spaces).
The synaptonemal complex (SC) is a proteinaceous, meiosis-specific structure that is highly conserved in evolution. During meiosis, the SC mediates synapsis of homologous chromosomes. It is essential for proper recombination and segregation of homologous chromosomes, and therefore for genome haploidization. Mutations in human SC genes can cause infertility. In order to gain a better understanding of the process of SC assembly in a model system that would be relevant for humans, we are investigating meiosis in mice. Here, we report on a newly identified component of the murine SC, which we named SYCE3. SYCE3 is strongly conserved among mammals and localizes to the central element (CE) of the SC. By generating a Syce3 knockout mouse, we found that SYCE3 is required for fertility in both sexes. Loss of SYCE3 blocks synapsis initiation and results in meiotic arrest. In the absence of SYCE3, initiation of meiotic recombination appears to be normal, but its progression is severely impaired resulting in complete absence of MLH1 foci, which are presumed markers of crossovers in wild-type meiocytes. In the process of SC assembly, SYCE3 is required downstream of transverse filament protein SYCP1, but upstream of the other previously described CE–specific proteins. We conclude that SYCE3 enables chromosome loading of the other CE–specific proteins, which in turn would promote synapsis between homologous chromosomes.
The present work investigated the neural mechanisms underlying cognitive inhibition/thought suppression in Anderson’s and Green’s Think/No-Think paradigm (TNT), as well as different variables influencing these mechanisms at the cognitive, the neurophysiological, the electrophysiological and the molecular level. Neurophysiological data collected with fNIRS and fMRI have added up to the existing evidence of a fronto-hippocampal network interacting during the inhibition of unwanted thoughts. Some evidence has been presented suggesting that by means of external stimulation of the right dlPFC through iTBS thought suppression might be improved, providing further evidence for an implication of this region in the TNT. A combination of fNIRS with ERP has delivered evidence of a dissociation of early condition-independent attentional and later suppression-specific processes within the dlPFC, both contributing to suppression performance. Due to inconsistencies in the previous literature it was considered how stimulus valence would influence thought suppression by manipulating the emotional content of the to-be-suppressed stimuli. Findings of the current work regarding the ability to suppress negative word or picture stimuli have, however, been inconclusive as well. It has been hypothesized that performance in the TNT might depend on the combination of valence conditions included in the paradigm. Alternatively, it has been suggested that inconsistent findings regarding the suppression of negative stimuli or suppression at all might be due to certain personality traits and/or genetic variables, found in the present work to contribute to thought inhibition in the TNT. Rumination has been shown to be a valid predictor of thought suppression performance. Increased ruminative tendencies led to worse suppression performance which, in the present work, has been linked to less effective recruitment of the dlPFC and in turn less effective down-regulation of hippocampal activity during suppression trials. Trait anxiety has also been shown to interrupt thought suppression despite higher, however, inefficient recruitment of the dlPFC. Complementing the findings regarding ruminative tendencies and decreased thought inhibition a functional polymorphism in the KCNJ6 gene, encompassing a G-to-A transition, has been shown to disrupt thought suppression despite increased activation of the dlPFC. Through the investigation of thought suppression at different levels, the current work adds further evidence to the idea that the TNT reflects an executive control mechanism, which is sensitive to alterations in stimulus valence to some extent, neurophysiological functioning as indicated by its sensitivity to iTBS, functional modulations at the molecular level and personality traits, such as rumination and trait anxiety.
In our analysis I was interested in the gene duplications, with focus on in-paralogs. In-paralogs are gene duplicates which arose after species split. Here I analysed the in-paralogs quantitatively, as well as qualitatively. For quantitative analysis genomes of 21 species were taken. Most of them have vastly different lifestyles with maximum evolutionary distance between them 1100 million years. Species included mammals, fish, insects and worm, plus some other chordates. All the species were pairwised analysed by the Inparanoid software, and in-paralogs matrix were built representing number of in-paralogs in all vs. all manner. Based on the in-paralogs matrix I tried to reconstruct the evolutionary tree using in-paralog numbers as evolutionary distance. If all 21 species were used the resulting tree was very far from real one: a lot of species were misplaced. However if the number was reduced to 12, all of the species were placed correctly with only difference being wrong insect and fish clusters switched. Then to in-paralogs matrix the neighbour-net algorithm was applied. The resulting "net" tree showed the species with fast or slow duplications rates compared to the others. We could identify species with very high or very low duplications frequencies and it correlates with known occurrences of the whole genome duplications. As the next step I built the graphs for every single species showing the correlation between their in-paralogs number and evolutionary distance. As we have 21 species, graph for every species is built using 20 points. Coordinates of the points are set using the evolutionary distance to that particular species and in-paralogs number. In mammals with increasing the distance from speciation the in-paralogs number also increased, however not in linear fashion. In fish and insects the graph close to zero is just the same in mammals' case. However, after reaching the evolutionary distances more than 800 million years the number of inparalogs is beginning to decrease. We also made a simulation of gene duplications for all 21 species and all the splits according to the fossil and molecular clock data from literature. In our simulation duplication frequency was minimal closer to the past and maximum in the near-present time. Resulting curves had the same shape the experimental data ones. In case of fish and insect for simulation the duplication rate coefficient even had to be set negative in order to repeat experimental curve shape. To the duplication rate coefficient in our simulation contribute 2 criteria: gene duplications and gene losses. As gene duplication is stochastical process it should always be a constant. So the changing in the coefficient should be solely explained by the increasing gene loss of old genes. The processes are explained by the evolution model with high gene duplication and loss ratio. The drop in number of in-paralogs is probably due to the BLAST algorithm. It is observed in comparing highly divergent species and BLAST cannot find the orthologs so precisely anymore. In the second part of my work I concentrated more on the specific function of inparalogs. Because such analysis is time-consuming it could be done on the limited number species. Here I used three insects: Drosophila melanogaster (fruit y), Anopheles gambiae (mosquito) and Apis mellifera (honeybee). After Inparnoid analyses and I listed the cluster of orthologs. Functional analyses of all listed genes were done using GO annotations and also KEGG PATHWAY database. We found, that the gene duplication pattern is unique for each species and that this uniqueness is rejected through the differences in functional classes of duplicated genes. The preferences for some classes reject the evolutionary trends of the last 350 million years and allow assumptions on the role of those genes duplications in the lifestyle of species. Furthermore, the observed gene duplications allowed me to find connections between genomic changes and their phenotypic manifestations. For example I found duplications within carbohydrate metabolism rejecting feed pattern adaptation, within photo- and olfactory-receptors indicating sensing adaptation and within troponin indicating adaptations in the development. Despite these species specific differences, found high correlations between the independently duplicated genes between the species. This might hint for a "pool" of genes preferentially duplicated. Taken together, the observed duplication patterns reject the adaptational process and provide us another link to the field of genomic zoology.
As one of the disciplines of systems biology, proteomics is central to enabling the elucidation of protein function within the cell; furthermore, the question of how to deduce protein structure and function from the genetic readout has gained new significance. This problem is of particular relevance for proteins engaged in cell signalling. In dealing with this question, I shall critically comment on the reliability and predictability of transmission and translation of the genetic blue print into the phenotype, the protein. Based on this information, I will then evaluate the intentions and goals of today’s proteomics and gene-networking and appraise their chances of success. Some of the themes commented on in this publication are explored in greater detail with particular emphasis on the historical roots of concepts and techniques in my forthcoming book, published in German: Von Molekülen zu Zellen. 100 Jahre experimentelle Biologie. Betrachtungen eines Biochemikers
Vertebrate and invertebrate visual systems exhibit similarities in early stages of visual processing. For instance, in the human brain, the modalities of color, form and motion are separately processed in parallel neuronal pathways. This basic property is also found in the fly Drosophila melanogaster which has a similar division in color- sensitive and (color blind) motion-sensitive pathways that are determined by two distinct subsets of photoreceptors (the R1-6 and the R7/8 system, respectively). Flies have a highly organized visual system that is characterized by its repetitive, retinotopic organization of four neuropils: the lamina, the medulla, the lobula and the lobula plate. Each of these consists of columns which contain the same set of neurons. In the lamina, axon bundles of six photoreceptors R1-6 that are directed towards the same point in space form columnar structures called cartridges. These are the visual sampling units and are associated with four types of first-order interneuron that receive common input from R1-6: L1, L2, L3 and the amacrine cells (amc, together with their postsynaptic partner T1). They constitute parallel pathways that have been studied in detail at the anatomical level. Little is known, however, about their functional role in processing behaviorally relevant information, e.g. for gaze stabilization, visual course control or the fixation of objects. The availability of a variety of neurogenetic tools for structure-function analysis in Drosophila allowed first steps into the genetic dissection of the neuronal circuitry mediating motion and position detection. In this respect, the choice of the effector turned out to be crucial. Surprisingly, it was found that the clostridial tetanus neurotoxin failed to block mature Drosophila photoreceptor synapses, but caused irreversible damage when expressed during their development. Therefore, the dominant-negative shibire allele shits1 which turned out to be better suited was used for blocking lamina interneurons and thereby analyzing the necessity of the respective pathways. To determine whether the latter were also sufficient for the same behavioral task, the inverse strategy was developed, based on the fact that lamina interneurons express histamine receptors encoded by the ort gene. The specific rescue of ort function in defined channels in an otherwise mutant background allowed studying their sufficiency in a given task. Combining these neurogenetic methods with the optomotor response and object induced orientation behavior as behavioral measures, the aim of the present thesis was to answer the following questions: (a) Which pathways feed into elementary motion detectors and which ones are necessary and/or sufficient for the detection of directional motion? (b) Do pathways exist which specifically mediate responses to unidirectional motion? (c) Which pathways are necessary and/or sufficient for object induced orientation behavior? Some basic properties of the visual circuitry were revealed: The two central cartridge pathways, represented by the large monopolar cells L1 and L2, are key players in motion detection. Under a broad range of stimulatory conditions, the two subsystems are redundant and are able to process motion independently of each other. To detect an impairment when only one of the pathways is intact, one has to drive the system to its operational limits. At low signal to noise ratios, i.e. at low pattern contrast or low background illumination, the L2 pathway has a higher sensitivity. At intermediate pattern contrast, both pathways are specialized in mediating responses to unidirectional motion of opposite stimulus direction. In contrast, neither the L3, nor the amc/T1 pathway is necessary or sufficient for motion detection. While the former may provide position information for orientation, the latter has a modulatory role at intermediate pattern contrast. Orientation behavior turned out to be even more robust than motion vision and may utilize a less sophisticated mechanism, as it does not require a nonlinear comparison of signals from neighboring visual sampling units. The position of objects is processed in several redundant pathways, involving both receptor subsystems. The fixation of objects does not generally require motion vision. However, motion detection improves the fixation of landmarks, especially when these are narrow or have a reduced contrast.
In the context of this thesis, I investigated the molecular causes and functional consequences of genetic instability using a human inherited disease, Fanconi anemia. FA patients display a highly variable clinical phenotype, including congenital abnormalities, progressive bone marrow failure and a high cancer risk. The FA cellular phenotype is characterized by spontaneous and inducible chromosomal instability, and a typical S/G2 phase arrest after exposure to DNA-damaging agents. So far, 13 genes have been identified, whose biallelic (or, in the case of X-linked FANCB, hemizygous) mutations cause this multisystem disorder. The FA proteins interact in a multiprotein network, instrumental and essential in the cellular response to DNA damage. A more comprehensive summary of Fanconi anemia and its myriad clinical, cellular and molecular manifestations is provided in the introduction section of this thesis. The results of my experimental work are presented as published papers and manuscripts ready to be submitted. In the first publication, I investigated the connection between FA genes and bladder tumors. The question I tried to answer was whether a disruption of the FA/BRCA pathway may be a frequent and possibly causal event in bladder cancer, explaining the hypersensitivity of these cells to DNA-crosslinking agents. On the basis of my experimental data I arrived at the conclusion that disruption of the FA/BRCA pathway might be detrimental rather than advantageous for the majority tumor types by rendering them vulnerable towards DNA damaging agents and oxidative stress. The second publication deals with the gene coding for the core complex protein FANCE and tries to answer the question why FANCE is so rarely affected among FA-patients. The conclusion from these studies is that like FANCF, FANCE functions as a probable adaptor protein with a high tolerance towards amino acid substitutions which would explain the relative rareness of FA-E patients. I have also investigated the FANCL gene whose product functions as the catalytic subunit of the E3 ligase. The third publication addresses this issue by providing the first comprehensive description of genetic alterations and phenotypic manifestations in a series of three FA-L patients. The results of my study show that genetic alterations of FANCL are compatible with survival, these alterations may include large deletions such as so far common only in the FANCA gene, FA-L phenotypes can be mild to severe, and FANCL belongs to the group of FA genes that may undergo somatic reversion. The central protein of the FA/BRCA network, FANCD2, is the subject of the fourth publication presented in this thesis. Most importantly, we were able to show that there are no biallelic null mutations in FANCD2. Correspondingly, residual protein of both FANCD2-isotypes (FANCD2-S and FANCD2-L) was present in all available patient cell lines. This suggests that complete abrogation of the FANCD2 protein cannot be tolerated and causes early embryonic lethality. There are at least three FA proteins that are not required for the posttranslational modification of FANCD2. One of these proteins is the 5’-3’ helicase BRIP1 (BRCA1-interacting protein 1), a protein that interacts directly with the breast cancer susceptibility protein BRCA1. I participated in the identification of BRIP1 as the FA protein FANCJ. This discovery is described in the fifth publication of this thesis. The newly discovered protein BRIP1/FANCJ seems to act as one of the mediators of genomic maintenance downstream of FANCD2. Another protein identified downstream of FANCD2 is PALB2. PALB2 was originally discovered as “partner and localizer of BRCA2”. In a candidate gene approach we tested patients with early childhood cancers but without mutations in BRCA2 for mutations in PALB2 (publication 6). PALB2 was identified as a novel FA gene and designated FANCN. FA-N patients are very severely affected. The last publication included in my thesis describes the identification of the FA gene FANCI as the second monoubiquitinated member of the FA/BRCA pathway (publication 7). We identified biallelic mutations in KIAA1794 in four FA patients, thus proving the genuine FA-nature of this candidate sequence. The general discussion provides a synopsis of the results and conclusions of my work with the state of art of FA research.