Comparative DNA sequence and methylation analyses of orthologous genes in humans and non-human primates: Genetic and epigenetic footprints of evolution

Welche genetische Unterschiede machen uns verschieden von unseren nächsten Verwandten, den Schimpansen, und andererseits so ähnlich zu den Schimpansen? Was wir untersuchen und auch verstehen wollen, ist die komplexe Beziehung zwischen den multiplen genetischen und epigenetischen Unterschieden, deren Interaktion mit diversen Umwelt- und Kulturfaktoren in den beobachteten phänotypischen Unterschieden resultieren. Um aufzuklären, ob chromosomale Rearrangements zur Divergenz zwischen Mensch und Schimpanse beigetragen haben und welche selektiven Kräfte ihre Evolution geprägt haben, habe ich die kodierenden Sequenzen von 2 Mb umfassenden, die perizentrischen Inversionsbruchpunkte flankierenden Regionen auf den Chromosomen 1, 4, 5, 9, 12, 17 und 18 untersucht. Als Kontrolle dienten dabei 4 Mb umfassende kollineare Regionen auf den rearrangierten Chromosomen, welche mindestens 10 Mb von den Bruchpunktregionen entfernt lagen. Dabei konnte ich in den Bruchpunkten flankierenden Regionen im Vergleich zu den Kontrollregionen keine höhere Proteinevolutionsrate feststellen. Meine Ergebnisse unterstützen nicht die chromosomale Speziationshypothese für Mensch und Schimpanse, da der Anteil der positiv selektierten Gene (5,1% in den Bruchpunkten flankierenden Regionen und 7% in den Kontrollregionen) in beiden Regionen ähnlich war. Durch den Vergleich der Anzahl der positiv und negativ selektierten Gene per Chromosom konnte ich feststellen, dass Chromosom 9 die meisten und Chromosom 5 die wenigsten positiv selektierten Gene in den Bruchpunkt flankierenden Regionen und Kontrollregionen enthalten. Die Anzahl der negativ selektierten Gene (68) war dabei viel höher als die Anzahl der positiv selektierten Gene (17). Eine bioinformatische Analyse von publizierten Microarray-Expressionsdaten (Affymetrix Chip U95 und U133v2) ergab 31 Gene, die zwischen Mensch und Schimpanse differentiell exprimiert sind. Durch Untersuchung des dN/dS-Verhältnisses dieser 31 Gene konnte ich 7 Gene als negativ selektiert und nur 1 Gen als positiv selektiert identifizieren. Dieser Befund steht im Einklang mit dem Konzept, dass Genexpressionslevel unter stabilisierender Selektion evolvieren. Die meisten positiv selektierten Gene spielen überdies eine Rolle bei der Fortpflanzung. Viele dieser Speziesunterschiede resultieren eher aus Änderungen in der Genregulation als aus strukturellen Änderungen der Genprodukte. Man nimmt an, dass die meisten Unterschiede in der Genregulation sich auf transkriptioneller Ebene manifestieren. Im Rahmen dieser Arbeit wurden die Unterschiede in der DNA-Methylierung zwischen Mensch und Schimpanse untersucht. Dazu wurden die Methylierungsmuster der Promotor-CpG-Inseln von 12 Genen im Cortex von Menschen und Schimpansen mittels klassischer Bisulfit-Sequenzierung und Bisulfit-Pyrosequenzierung analysiert. Die Kandidatengene wurden wegen ihrer differentiellen Expressionsmuster zwischen Mensch und Schimpanse sowie wegen Ihrer Assoziation mit menschlichen Krankheiten oder dem genomischen Imprinting ausgewählt. Mit Ausnahme einiger individueller Positionen zeigte die Mehrzahl der analysierten Gene keine hohe intra- oder interspezifische Variation der DNA-Methylierung zwischen den beiden Spezies. Nur bei einem Gen, CCRK, waren deutliche intraspezifische und interspezifische Unterschiede im Grad der DNA-Methylierung festzustellen. Die differentiell methylierten CpG-Positionen lagen innerhalb eines repetitiven Alu-Sg1-Elements. Die Untersuchung des CCRK-Gens liefert eine umfassende Analyse der intra- und interspezifischen Variabilität der DNA-Methylierung einer Alu-Insertion in eine regulatorische Region. Die beobachteten Speziesunterschiede deuten darauf hin, dass die Methylierungsmuster des CCRK-Gens wahrscheinlich in Adaption an spezifische Anforderungen zur Feinabstimmung der CCRK-Regulation unter positiver Selektion evolvieren. Der Promotor des CCRK-Gens ist anfällig für epigenetische Modifikationen durch DNA-Methylierung, welche zu komplexen Transkriptionsmustern führen können. Durch ihre genomische Mobilität, ihren hohen CpG-Anteil und ihren Einfluss auf die Genexpression sind Alu-Insertionen exzellente Kandidaten für die Förderung von Veränderungen während der Entwicklungsregulation von Primatengenen. Der Vergleich der intra- und interspezifischen Methylierung von spezifischen Alu-Insertionen in anderen Genen und Geweben stellt eine erfolgversprechende Strategie dar.

Serumfreie Collagen-Monolayer- und Sandwich-Kulturen primärer Hepatozyten als ein wertvolles Modell zur Detektion von Toxizität und Arzneimittelwechselwirkungen in vitro

In dieser Arbeit wurden Zellkulturen primärer Hepatozyten von Ratte und Mensch hinsichtlich ihrer Eignung untersucht Speziesunterschiede der toxischen Wirkung und des Metabolismus von Substanzen darzustellen und inwieweit die in vitro-Ergebnisse in vivo vergleichbar bzw. übertragbar sind. Des Weiteren wurde ein Zellkulturmodell entwickelt, das eine Kultivierung von primären Hepatozyten aus Ratte, Mensch und Maus über einen Zeitraum von mindestens einer bis zwei Wochen erlaubt.rnrnDie Zellkulturen primärer Hepatozyten von Ratte und Mensch zeigten deutliche Unterschiede in der substanzinduzierten Veränderung der Genexpression nach Behandlung mit den, vor allem für den Menschen, lebertoxischen Substanzen Diclofenac und Troglitazon. Diese Unterschiede traten hauptsächlich in der Induktion fremdstoffmetabolisierender Enzyme sowie deren transkriptionsregulierenden Kernrezeptoren in den humanen Hepatozyten auf. Ebenso war eine verstärkte Stressantwort zu beobachten.rnDeutliche Speziesunterschiede konnten ebenso in der Wirkung der Arzneimittelentwicklungssubstanz EMD 392949 auf die Aktivität bzw. Genexpression von Cytochrom P450 Enzymen sowie deren Regulatoren nachgewiesen werden. Des Weiteren konnte hier eine sehr gute Übereinstimmung der Ergebnisse aus den Zellkulturen primärer Ratten- bzw. Humanhepatozyten mit jenen aus in vivo-Experimenten mit Ratten bzw. Affen (Macaca fascicularis) beobachtet werden, was die Aussagekraft der Primärkulturen verdeutlichte.rnDie große Übereinstimmung zwischen Enzymaktivität und Genexpression in der Induktion fremdstoffmetabolisierender Enzyme konnte durch die Behandlung mit einer Reihe speziesspezifischer Induktoren in Zellkulturen primärer Ratten- bzw. Humanhepatozyten bestätigt werden; vor allem nach dem von der amerikanischen Arzneimittelzulassungsbehörde (FDA, Food and Drug Administartion) vorgeschlagenen Bewertungsschema zur Untersuchung der CYP-Induktion.rnrnDie Lebensdauer sowie der Differenzierungsgrad von primären Hepatozyten in Kultur sind stark abhängig von den Zellkulturbedingungen. Durch diese Arbeit konnte gezeigt werden, dass spezifische Eigenschaften von Rattenleberzellen durch Kultivierung in einem Sandwich aus zwei hydratisierten Collagengelschichten und unter serumfreien Bedingungen für einen Zeitraum von mindestens zwei Wochen aufrechterhalten werden können. Dieses Kulturmodel konnte auf Primärhepatozyten von Mensch und Maus übertragen werden und erweitert die möglichen Anwendungen hin zu einer Behandlung über einen längeren Zeitraum und der Untersuchung von subchronischen Effekten.rn

Incretin receptors in non-neoplastic and neoplastic thyroid C cells in rodents and humans: relevance for incretin-based diabetes therapy

While incretins are of great interest for the therapy of diabetes 2, the focus has recently been brought to the thyroid, since rodents treated with glucagon-like peptide-1 (GLP-1) analogs were found to occasionally develop medullary thyroid carcinomas. Incretin receptors for GLP-1 and glucose-dependent insulinotropic polypeptide (GIP) were therefore measured in various rodent and human thyroid conditions. In vitro GLP-1 and GIP receptor autoradiography were performed in normal thyroids, C-cell hyperplasia and medullary thyroid carcinomas in rodents. Receptor incidence and density were assessed and compared with the receptor expression in human thyroids, medullary thyroid carcinomas, and TT cells. GLP-1 receptors are expressed in C cells of normal rat and mice thyroids. Their density is markedly increased in rat C-cell hyperplasia and medullary thyroid carcinomas, where their incidence amounts to 100%. GIP receptors are neither detected in normal rodent thyroids nor in C-cell hyperplasia, but are present in all rat medullary thyroid carcinomas. No GLP-1 or GIP receptors are detected in normal human thyroids. Whereas only 27% of all human medullary thyroid carcinomas express GLP-1 receptors, up to 89% express GIP receptors in a high density. TT cells lack GLP-1 receptors but express GIP receptors. GLP-1 receptors are frequently expressed in non-neoplastic and neoplastic C cells in rodents while they are rarely detected in human C-cell neoplasia, suggesting species differences. Conversely, GIP receptors appear to be massively overexpressed in neoplastic C cells in both species. The presence of incretin receptors in thyroid C cell lesions suggests that this organ should be monitored before and during incretin-based therapy of diabetes.

Feature Versus Spatial Strategies by Orangutans (Pongo abelii) and Human Children (Homo sapiens) in a Cross-Dimensional Task

Despite the fact that photographic stimuli are used across experimental contexts with both human and nonhuman subjects, the nature of individuals' perceptions of these stimuli is still not well understood. In the present experiments, we tested whether three orangutans and 36 human children could use photographic information presented on a computer screen to solve a perceptually corresponding problem in the physical domain. Furthermore, we tested the cues that aided in this process by pitting featural information against spatial position in a series of probe trials. We found that many of the children and one orangutan were successfully able to use the information cross-dimensionally; however, the other two orangutans and almost a quarter of the children failed to acquire the task. Species differences emerged with respect to ease of task acquisition. More striking, however, were the differences in cues that participants used to solve the task: Whereas the orangutan used a spatial strategy, the majority of children used a feature one. Possible reasons for these differences are discussed from both evolutionary and developmental perspectives. The novel results found here underscore the need for further testing in this area to design appropriate experimental paradigms in future comparative research settings.

Toll-like receptors in domestic animals

Toll-like receptors are pattern recognition receptors with which hosts recognize pathogen-associated molecular patterns (PAMP). This recognition process is translated rapidly into a meaningful defense reaction. This form of innate host defense is preserved in the animal kingdom: invertebrates heavily depend on it; higher vertebrates also have an adaptive immune system. Both adaptive and innate immune systems are intertwined in that the former also depends on an intact innate recognition and response system. Members of the TLR system cover recognition of parasitic, bacterial or viral germs. Due to the constraints imposed by the necessity to recognize PAMP and to interact with downstream signaling molecules, the TLR system is relatively conserved in evolution. Nevertheless, subtle species differences have been reported for several mammalian TLR members. Examples of this will be given. In all mammalian species investigated, part of the coding sequence is available for the most important TLR members, thus allowing study of expression of these TLR members in various tissues by reverse-transcription polymerase chain reaction in its classical (RT-PCR) and quantitative real time RT-PCR (qRT-PCR) form. In some species, the whole coding sequences of the most important or even all TLR members are known. This allows construction of cDNA and transfection of common host cells, thus permitting functional studies. Extensive investigations were devoted to the study of non-synonymous single nucleotide polymorphisms. In a few cases, expression of a given amino acid in the extracellular (ligand-binding) portion of TLR members could be associated with infectious diseases. This will be discussed below.

Moving beyond a descriptive aquatic toxicology: the value of biological process and trait information

In order to improve the ability to link chemical exposure to toxicological and ecological effects, aquatic toxicology will have to move from observing what chemical concentrations induce adverse effects to more explanatory approaches, that are concepts which build on knowledge of biological processes and pathways leading from exposure to adverse effects, as well as on knowledge on stressor vulnerability as given by the genetic, physiological and ecological (e.g., life history) traits of biota. Developing aquatic toxicology in this direction faces a number of challenges, including (i) taking into account species differences in toxicant responses on the basis of the evolutionarily developed diversity of phenotypic vulnerability to environmental stressors, (ii) utilizing diversified biological response profiles to serve as biological read across for prioritizing chemicals, categorizing them according to modes of action, and for guiding targeted toxicity evaluation; (iii) prediction of ecological consequences of toxic exposure from knowledge of how biological processes and phenotypic traits lead to effect propagation across the levels of biological hierarchy; and (iv) the search for concepts to assess the cumulative impact of multiple stressors. An underlying theme in these challenges is that, in addition to the question of what the chemical does to the biological receptor, we should give increasing emphasis to the question how the biological receptor handles the chemicals, i.e., through which pathways the initial chemical-biological interaction extends to the adverse effects, how this extension is modulated by adaptive or compensatory processes as well as by phenotypic traits of the biological receptor.

Exploration Of Survival Traits In The White-Nose Syndrome-Affected Big Brown Bat (Eptesicus Fuscus)

The widespread mortality of hibernating bats is associated with the emerging infectious disease white-nose syndrome (WNS), and has provoked a strong interest in understanding which bats will survive, and why? The ability of infected bats to resist WNS may depend upon variation in the expression of different characteristics. In a captive colony of big brown bats, I sought to characterize the phenotypic variability, repeatability, and survivability for several key ¿survival¿ traits, including: torpor patterns, microclimate preferences, and wound healing capacity. Torpor patterns were profiled using temperature sensitive dataloggers throughout the hibernation season, while microclimate preferences were quantified by using temperature-graded boxes and thermal imaging. In order to assess wound healing capacity, small wing biopsies were obtained from each bat and healing progress was tracked for one month. Individuals exhibited a wide range of phenotypes that were significantly influenced by sex and body condition. Repeatability estimates suggest that there is not a strong genetic basis for the observed variation in torpor patterns or microclimate preferences. Certain phenotypes (e.g., BMI) were associated with an increased probability of overwinter survivorship, which suggests a basis for intra-species differences in WNS susceptibility. The results from this project provide novel insight into what we know about ¿who will survive,¿ and will influence the direction and implementation of future conservation and mitigation strategies.

Fenofibrate metabolism in the cynomolgus monkey using ultraperformance liquid chromatography-quadrupole time-of-flight mass spectrometry-based metabolomics

Fenofibrate, widely used for the treatment of dyslipidemia, activates the nuclear receptor, peroxisome proliferator-activated receptor alpha. However, liver toxicity, including liver cancer, occurs in rodents treated with fibrate drugs. Marked species differences occur in response to fibrate drugs, especially between rodents and humans, the latter of which are resistant to fibrate-induced cancer. Fenofibrate metabolism, which also shows species differences, has not been fully determined in humans and surrogate primates. In the present study, the metabolism of fenofibrate was investigated in cynomolgus monkeys by ultraperformance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QTOFMS)-based metabolomics. Urine samples were collected before and after oral doses of fenofibrate. The samples were analyzed in both positive-ion and negative-ion modes by UPLC-QTOFMS, and after data deconvolution, the resulting data matrices were subjected to multivariate data analysis. Pattern recognition was performed on the retention time, mass/charge ratio, and other metabolite-related variables. Synthesized or purchased authentic compounds were used for metabolite identification and structure elucidation by liquid chromatographytandem mass spectrometry. Several metabolites were identified, including fenofibric acid, reduced fenofibric acid, fenofibric acid ester glucuronide, reduced fenofibric acid ester glucuronide, and compound X. Another two metabolites (compound B and compound AR), not previously reported in other species, were characterized in cynomolgus monkeys. More importantly, previously unknown metabolites, fenofibric acid taurine conjugate and reduced fenofibric acid taurine conjugate were identified, revealing a previously unrecognized conjugation pathway for fenofibrate.

Divergent selection and phenotypic plasticity during incipient speciation in Lake Victoria cichlid fish

Divergent selection acting on several different traits that cause multidimensional shifts are supposed to promote speciation, but the outcome of this process is highly dependent on the balance between the strength of selection vs. gene flow. Here, we studied a pair of sister species of Lake Victoria cichlids at a location where they hybridize and tested the hypothesis that divergent selection acting on several traits can maintain phenotypic differentiation despite gene flow. To explore the possible role of selection we tested for correlations between phenotypes and environment and compared phenotypic divergence (P-ST) with that based on neutral markers (F-ST). We found indications for disruptive selection acting on male breeding colour and divergent selection acting on several morphological traits. By performing common garden experiments we also separated the environmental and heritable components of divergence and found evidence for phenotypic plasticity in some morphological traits contributing to species differences.

Epigenetic diversity increases the productivity and stability of plant populations

Biological diversity within species can be an important driver of population and ecosystem functioning. Until now, such within-species diversity effects have been attributed to underlying variation in DNA sequence. However, within-species differences, and thus potentially functional biodiversity, can also be created by epigenetic variation. Here, we show that epigenetic diversity increases the productivity and stability of plant populations. Epigenetically diverse populations of Arabidopsis thaliana produce up to 40% more biomass than epigenetically uniform populations. The positive epigenetic diversity effects are strongest when populations are grown together with competitors and infected with pathogens, and they seem to be partly driven by complementarity among epigenotypes. Our study has two implications: first, we may need to re-evaluate previous within-species diversity studies where some effects could reflect epigenetic diversity; second, we need to incorporate epigenetics into basic ecological research, by quantifying natural epigenetic diversity and testing for its ecological consequences across many different species.

Litter breakdown and mineralization in a central African rain forest dominated by ectomycorrhizal trees

Based on litter mass and litterfall data, decomposition rates for leaves were found to be fast (k = 3.3) and the turnover times short (3.6 mo) on the low-nutrient sandy soils of Korup. Leaf litter of four ectomycorrhizal tree species (Berlinia bracteosa, Didelotia africana, Microberlinia bisulcata and Tetraberlinia bifoliolata) and of three non-ectomycorrhizal species (Cola verticillata, Oubanguia alata and Strephonema pseudocola) from Korup were left to decompose in 2-mm mesh bags on the forest floor in three plots of each of two forest types forest of low (LEM) and high (HEM) abundance of ectomycorrhizal (caesalp) trees. The litter of the ectomycorrhizal species decayed at a significantly slower rate than that of the non-ectomycorrhizal species, although the former were richer in P and N concentrations of the start. Disappearance rates of the litter layer showed a similar trend. Ectomycorrhizal species immobilized less N, but mineralized more P, than non-ectomycorrhizal species. Differences between species groups in K, Mg and Ca mineralization were negligible. Effect of forest type was clear only for Mg: mineralization of Mg was faster in the HEM than LEM plots, a pattern repeated across all species. This difference was attributed to a much more prolific fine root mat in the HEM than LEM forest. The relatively fast release of P from the litter of the ectomycorrhizal species suggests that the mat must allow an efficient uptake to maintain P in the forest ecosystem.

Concentrations of metals and POPs in liver tissue of wild sea bird chicks from the Norwegian arctic region

Lysosomal membrane stability, lipofuscin (LF), malondialdehyde (MDA), neutral lipid (NL) levels, as well as halogenated organic compounds (HOCs), Cr, Cd, Pb and Fe concentrations were analyzed in liver of black-legged kittiwake (BK), herring gull (HG), and northern fulmar (NF) chicks. There were significant species differences in the levels of NL, LF and lysosomal membrane stability. These parameters were not associated with the respective HOC concentrations. LF accumulation was associated with increasing Cr, Cd and Pb concentrations. HG presented the lowest lysosomal membrane stability and the highest. LF and NL levels, which indicated impaired lysosomes in HG compared to NF and BK. Lipid peroxidation was associated with HOC and Fe2+ levels. Specific HOCs showed positive and significant correlations with MDA levels in HG. The study indicates that contaminant exposure can affect lysosomal and lipid associated parameters in seabird chicks even at low exposure levels. These parameters may be suitable markers of contaminant induced stress in arctic seabirds.

(Table 1) Antioxidant concentrations in liver of wild sea bird chicks from the Norwegian arctic region

The efficiency of antioxidant defenses and relationship with body burden of metal and organic contaminants has not been previously investigated in arctic seabirds, neither in chicks nor in adults. The objective of this study was to compare such defenses in chicks from three species, Black-legged kittiwake (Rissa tridactyla), Northern fulmar (Fulmarus glacialis), and Herring gull (Larus argentatus), and the relationship with tissue concentrations of essential metals such as selenium and iron and halogenated organic compounds, represented by polychlorinated biphenyl (PCB). The results showed significant species-specific differences in the antioxidant responses which also corresponded with metal and PCB levels in different ways. The capability to neutralize hydroxyl radicals (TOSC-HO°) and the activities of catalase and Se-dependent glutathione peroxidases (GPX) clearly increased in species with the higher levels of metals and PCBs, while the opposite trend was observed for Se-independent GPX, TOSC against peroxyl radicals (ROO°) and peroxynitrite (ONOOH). Less clear relationships were obtained for glutathione levels, GSH/GSSG ratio, glutathione reductase and superoxide dismutase. The results showed differences in antioxidant efficiency between the species, and some of these defenses exhibited dose-response-like relationships with measured levels of selenium, iron and XPCBs. PCBs, selenium and iron levels were positively related to the responses of antioxidants with potential to reduce HO°/H2O2 (Se-dependent GPX, CAT and TOSC against HO°). However, direct causal relationships between antioxidant responses and contaminant concentrations could not be shown on individual level. Varying levels of metals and contaminants due to different diet and age were probably the main explanations for the species differences in antioxidant defense.