PhD Students Presentations
Credits picture: UCPH
Ane Elise Schrøder
Natural History Museum of Denmark, Section for Vertebrate Zoology and Geology
The deep past of Denmark – The origins of modern teleost fishes
The fish fossils of the Fur Formation are likely to hold clues that are central to our understanding of the evolution of fish. The infraclass Teleostei is the largest group of all living vertebrates. With an estimated 27,000 species, the Teleostei is the most abundant and largest group of actinopterygians. The group comprises approximately 96 % of all living fish species, and they inhabit freshwater and marine environments, ranging from polar to tropical oceans to alkaline hot springs, deep-sea trenches to high latitude mountain lakes. The diversification of teleost fish appears to occur quite late (after the mass extinction event ~66 million years ago). The reasons and timing of the diversification of teleosts are not well understood and are now only beginning to be explored. The earliest Eocene (Ypresian, ~55 Ma) Fur Formation of northwestern Jutland, Denmark is in this context a yet untapped asset with its wealth of exquisitely preserved, complete fish fossils. Until now, the Fur Formation has been appreciated primarily within Denmark when, indeed, the paleontological and geobiological value is of global interest. The foci of this project are taxonomy, taphonomy, geochemistry, and phylogeny of and around these early and well-preserved fish fossils. Additionally, the results will be part of the preparations, and included in the applications, to make the Fur Formation a UNESCO World Heritage site. The results will also form the basis of new exhibitions implemented at Museum Mors, Fur Museum and the Natural History Museum of Denmark.
Natural History Museum of Denmark, Section for Citizen Science
Citizen Science and DNA metabarcoding as a tool to survey flying insect diversity
Recent studies report declines in biomass, abundance and diversity of terrestrial insect groups; however, broad-scale studies on insects are rare.
In this study, we employed rooftop-mounted car nets in a citizen science project (‘InsectMobile’) to allow for large scale geographic sampling of flying insects. Citizen scientist sampled insects during June 2018 and 2019 along ~300 predefined routes under specific weather conditions, collecting more than 1200 bulk insect samples. Sample biomass is obtained before non-destructive DNA extraction and tagged PCR amplification with three universal insect primer pairs. We assess land cover and land use effects on insect biomass and evaluate the car net sampling method alongside DNA metabarcoding as a tool to survey flying insect diversity.
We find drastic declines in insect biomass with increasing urbanization and biomass increases with increasing farmland cover but is still lower than in semi-natural areas. Based on half of the collected material we have detected 319 new species occurrences for Denmark belonging to the insect orders Diptera, Coleoptera, Hemiptera, Hymenoptera and Psocoptera. Further work will compare DNA-derived insect diversity to land cover-, bird fauna-, and biodiversity data.
Credits picture: UCPH
Christian Parsbæk Pedersen
Section for Biomolecular Sciences
The determinants of ligand binding for the endogenous retroviral protein Arc
The activity-regulated cytoskeleton-associated protein (Arc) is a domesticated retroviral protein, which is highly expressed in neuronal dendrites. Arc regulates synaptic plasticity – a process associated with memory formation – by interacting with the cellular machinery responsible for the internalization of neuronal receptors. It has recently been discovered that Arc has preserved its intrinsic structural property required to form protein capsid throughout evolution as Arc may self-assemble in vivo and transfer its own mRNA from one neuron to another. The specificity of ligand recognition of Arc remains uncharacterized and a consensus motif of only two residues has been proposed. This short motif, however, does not explain the specificity of Arc and the interplay between the different regulatory modes thus remains unknown.
We have solved the structure and characterized the slow dynamics of the monomeric capsid domain of Arc and investigated the interactions of Arc with the transmembrane AMPAR regulatory protein γ2 (TARPγ2) and N-methyl-D-aspartate (NMDA)-type glutamate receptors. Our results indicate that Arcs interaction with the NMDA receptor subunits inhibits its self-assembly. Furthermore, we have characterized the binding affinity to peptides found in the clathrin-mediated endocytosis pathway. The preliminary results indicate that the length of the peptide affects the affinity of binding indicating that the flanking regions of the motif greatly impacts the binding.
Elise Nagel Ebstrup
Section For Functional Genomics
Autophagy regulation of developmental responses
What triggers a fully differentiated cell in a multicellular organism to dedifferentiate and behave like a stem cell? And what cellular machines are involved? While forced expression of certain genes can drive such reprograming, answers to these questions remain elusive. Such reprogramming is widespread and is most likely orchestrated by conserved programs independent of tissue and species. My unreported discoveries indicate that a conserved metabolic process (autophagy) mediate the efficiency of reprogramming in the model plant Arabidopsis by controlling the levels of ARF7, a master regulator of totipotency. I found that Autophagy deficient mutants accumulate ARF7 and display deregulated reprogramming. Moreover, ARF7 interacts with the autophagic cargo receptor NBR1 and nbr1 mutants exhibit developmental defects caused by increased ARF7 accumulation. I thus used plants as a model to answer questions about how autophagy contributes to somatic reprogramming and developments to pave the way for new strategies in regenerative research.
Section for Computational and RNA Biology
Phosphorylation of Argonaute1 regulate gene expression
Small RNA is a class of non coding RNA molecule with a size of 21-25nt. They play an essential rule in fine tuning gene regulation. Among them, 22 nt miRNAs target mRNA by base pairing after loading into Argonaute to perform translational repression or cleave target mRNA. Argonaute functions centrally in RNA induced silencing complex (RISC) by holding miRNA, mRNA and other factors. Phosphorylation is one of the most common post translational modifications of proteins, and Argonaute is no exception. C terminal phosphorylation cluster, T1000/s1001/s1003/s1005 s1008 is a very conserved phosphorylation cluster between human, plants and other organism. By constructing phospho-dead and phospho-mimic Argoanute, we investigated and inferred that phosphorylation of Argonaute affects target mRNA binding without disturbing miRNA binding. One reason could be that the C terminal phosphorylation cluster located in the proximity of miRNA binding site with Argoanute, possibly causes conformational change of Argoanute to influence mRNA binding.
Natural History Museum of Denmark, Section for Entomology
Taxonomy, Phylogeography and Myrmecophily of the spider genus Mastigusa (Araneae, Hahniidae)
This little known genus of small spiders (3-4 mm of body length) distributed in Europe, North Africa and Near East are fascinating for several reasons. The extreme morphology of their genitalia is unique, having no equal among all the other known spiders. A long and confused taxonomic history led to us not being totally sure at the moment about the phylogenetic relationships of this genus and about how many species it should actually contain. The ecology of this spiders, at last, is quite peculiar; this spiders are in fact myrmecophilic, living in close association with ants and spending all their life cycle inside ant nests. My study focuses on all this aspects related to the genus Mastigusa with an interdisciplinary approach. The main goals are a better understanding of the evolutionary relationships of this genus and its taxonomy, by the use of morphological comparative analysis and molecular tools, understanding how the genetic variability is distributed among different European populations and finding clues about the mechanisms undergoing the little known relationships that this spiders have with ants, using comparative chemical analyses and behavioral tests.
Section for Ecology and Evolution
One individual, many genomes. Detecting single-cell mutations across the human body
The life of a human individual starts when a zygote, bearing a single genome, undergoes multiple rounds of mitotic divisions and cellular differentiation to give rise to the trillions of cells that altogether, form an adult individual. Every cell, from a neuron to an immune cell, have a replica of the original genome of the zygote. Yet, the genome of every cell is constantly exposed to DNA replication errors and mutagens that transform the genome of every cell into a unique entity. In the end, these somatic mutations have the potential to alter the way cells execute their vital functions and increase the chances to develop certain diseases such as cancer.
Modern single cell DNA sequencing provide the ability to determine the genome sequence of every cell. However, the DNA purification and amplification processes introduce biases that prohibit the detection of somatic mutations. During my pitch talk, I will present a new computational method that estimates and corrects these biases, which in turn permit the detection of somatic mutations in single cells.
Section for Terrestrial Ecology
Joint effects of insect herbivory and long-term in situ warming on plant volatile emissions in a Subarctic tundra
Climate change is expected to increase insect abundance and diversity in the Arctic ecosystems. Insect herbivory is a major biotic stress that increases volatile organic compound (VOC) emissions and alters VOC composition. Climate warming is directly and indirectly affecting the emissions of VOCs from the vegetation. Ongoing changes in both climatic conditions and insect herbivore pressure are likely to be crucial determinants of future VOC emissions in the Arctic ecosystems. However, it is still unclear how insect herbivory is affecting high latitude ecosystems that are experiencing faster climatic changes than the rest of the planet.
In this study we assessed how 30 years of in situ experimental manipulation of temperature and light availability in interaction with insect herbivory affect VOC emissions from dwarf birch (Betula nana L.) in Subarctic tundra.
We show that short-term insect herbivory and warming alone increased and modified the VOC emissions from dwarf birch. Furthermore, the effects of insect herbivory were further amplified when in interaction with warming, but not in interaction with light availability. These results suggest that with climate warming and higher insect herbivore pressure, we could expect higher VOC emissions from Arctic ecosystems.
Natural History Museum of Denmark, Research section
Dynamics and factors driving gut microbiomes of Passerine birds
Despite the important roles played by gut microbiomes, we do not see tight associations between gut bacterial community similarities and the host avian phylogeny. In my PhD, I am investigating the factors driving avian gut microbial community compositions to improve our understanding of this lack of association. First, I have investigated the importance of diet on gut microbiome structure in Parus major (Great tits) through diet manipulation, showing that gut microbiomes are highly malleable to dietary changes. Secondly, I am investigating the association between natural diets (identified through metabarcoding) of birds from Papua New Guinea to understand associations between individual diets and gut microbiomes in nature. Finally, I am investigating the effects of habitat and gut morphology on passerine microbiomes in Papua New Guinean birds to explore their impact on the structure and heterogeneity of microbiomes.
Lucas Leon Peralta Ogorek
Section for Freshwater Biology
Roots in amour – protective trait of the barrier to radial oxygen loss
Climate change has resulted in more frequent and severe flooding events. Too much water results in soil waterlogging that leads to soil anoxia because gas diffusion is greatly constrained in water compared to in air. The root barrier to radial O2 loss (ROL) is a key trait enabling waterlogging tolerance by restricting O2 diffusion from wetland plant roots to the anoxic soil so that O2 is retained within the root tissue. However, the role of the ROL barrier in restricting radial diffusion of other gases was unknown and therefore I assessed its capacity to restrict diffusion H2 (biologically inert), and H2S (a known phytotoxin produced in anoxic soils). H2 and H2S microelectrodes were used to measure concentrations externally and in the root cortex. Gas concentrations were manipulated to visualize the radial diffusion restriction imposed by the barrier to ROL using steep gradients. The results show that the barrier slows radial diffusion into the root for both H2 and H2S. I conclude that the barrier to ROL has a secondary beneficial trait during waterlogging as it restricts radial intrusion of toxic H2S.
Credits picture: UCPH
Lucas van Duin
Section for Computational and RNA Biology
Transcriptional decomposition of population scale expression data
The amount of transcription at genomic loci may be determined by two classes of mechanisms: Those that act on single genes, for example hormone receptors acting as transcription factors, and those that act on multiple genes within a genomic neighbourhood, influenced by local three-dimensional chromatin architectures. We infer the magnitude of these two components along the genome, using a Bayesian hierarchical model on transcriptional data. In our previous paper, this transcriptional decomposition approach accurately revealed chromatin compartments and boundaries of active topologically associating domains (Rennie et al., 2018). In addition, it was shown to lead to better prediction of enhancer- promoter interactions than correlation-based methods. Here, we apply transcriptional decomposition to the GEUVADIS data set (Lappalainen et al., 2013), which contains RNA-Seq data of 456 individuals from the 1000 genomes project, to determine if differences in the PD component can be used to infer individual variation in chromatin architecture. We identify regions showing distinct component differences across different populations and link them to genetic variants observed in these regions. Overall, our work provides yet unobserved insights into the link between transcription, three-dimensional architectures and genetic variation across large groups of individuals.
Section for Ecology and Evolution
Pedigree-based estimation of germline mutation rate
Germline mutations are the source of every evolutionary adaptation. Next-Generation Sequencing has allowed pedigree-based methods to estimate per generation germline mutation rates by comparing whole genome sequences of parents and offspring. My Ph.D. project was divided into 3 chapters that I will briefly present here. First, I established a pipeline for estimating the germline mutation rate of a large pedigree of Rhesus macaque (Macaca mulatta). Secondly, I applied this pipeline to 69 species of vertebrate to explore variation between species. Finally, I organized a worldwide competition between different research groups, called the ‘mutationathon’, to reach a consensus methodology to estimate mutation rates from pedigree samples.
Section for Cell and Neurobiology
Organismal and cellular growth control by hormonal and nutritional signals
Growth control is fundamentally important for normal biological development. Nutrient availability is a key factor in regulating growth both at the cellular and systemic levels. The conserved Target of Rapamycin (TOR) kinase is the main cellular nutrient censor, which controls cell-autonomous growth in multicellular. Insulin and insulin-like growth factors are the main long-range hormonal signal by which control growth systemically in response to nutritional status. Dysregulation of these pathways is frequently linked to cancers. Cholesterol is emerging as a key factor fueling the growth and aggressiveness of many cancers, yet the mechanisms by which this nutrient promotes cell growth are poorly understood. Recently we have identified an unexpected role for cholesterol in promoting cellular and organismal growth during Drosophila development, likely through a novel TOR-dependent cholesterol-sensing mechanism. By manipulating cholesterol- and TOR-related genes and dietary cholesterol levels, we are able to further study cellular cholesterol-sensing mechanisms and cholesterol-modulated TOR activity that regulate cellular and organismal growth. These are areas of great scientific and medical interest, because they will provide a basis for understanding the link between cholesterol and growth control in development, cancer, and metabolic disorders.
Nataly Olivia Allasi Canales
Natural History Museum of Denmark, Section for Botany
Paleogenomic and chemical diversity of Cinchona bark collections
Have you ever wonder what makes gin and tonic bitter? It’s quinine! A chemical produced in the bark of Cinchona trees, which is original from the Andes, just like me. Once it was found that Cinchona bark could treat malaria, the quest for the best bark started. My PhD project aims is to bring back to life plant museum collections by exploring its genomic and chemical diversity. In spite of the economic and pharmaceutical importance of this tree, taxonomic issues have prevented to elucidate the evolutionary history of the Cinchona genus and the potential relation with its chemical diversity. Furthermore, with the advent of palaeogenomics, it is possible to obtain, analyse and authenticate DNA from historical samples. This PhD project is centred on historical Cinchona barks as a model of wood museomics. The first chapter is on the chemical analysis of historically annotated bark collections. The second chapter was conceived to assembled the chloroplast and mitochondrial reference genomes of Cinchona pubescens. The third chapter was developed to find the best approach to obtain quality DNA and analyse the data produced. Finally, after we built the necessary genomic tools, the fourth chapter focuses on tracing Cinchona plantations to their native forests in the Andes. With the results, we hope to trace the genetic changes across time and space. And to potentially identify varieties or species within this genus that can lead us to potential new drugs.
Ole Bjørn Brodnicke
Section for Marine Biology
Climate change impacts on coral reef crypto benthic fauna
Healthy coral reefs harbour a staggering diversity of fishes. However, 50% of these are rarely seen and surveyed, as many species are small, camouflaged and hidden. These unseen, elusive ‘crypto benthic’ fishes have been shown to be pivotal in sustaining the high productivity of coral reefs. The benthic interstitial meiofauna face the same underestimations. We therefore develop molecular tools (barcoding and eDNA) to more accurately survey the diversity of the crypto benthic fauna on the Maldivian coral reefs. Development of eDNA methods targeting the elusive crypto benthic fauna in collaboration with local governmental stakeholders extends the toolbox available to local and international marine biologists and conservationists at lower cost, higher accuracy and reduced effort. Furthermore, through population connectivity analyses, we assess local and regional extinction risks of target taxa due to climate change induced reef degradation. In conclusion, we pave the way for improved, more standardized biodiversity indexes to characterize, monitor, and compare coral reefs worldwide while establishing climate change impacts on the diversity of Maldivian coral reefs.
Oscar Alberto Rojas Castillo
Section for Freshwater Biology
Assessing the impacts of land use change driven by the expansion of oil palm plantations on the stream biodiversity and ecosystem functions in northern Guatemala
Oil palm has expanded 96% of its territory in the last two decades with expectations of spreading furthermore. Species loss, freshwater pollution, and decreased ecosystem functions are consequences of this tropical agriculture. It is crucial to assess the impacts of this practice on tropical ecosystems. In this regard, most studies have assessed terrestrial species, while freshwater biota, especially plankton, has been dramatically less studied. In Guatemala, the palm-oil industry has been accused of massive fish killings and water-quality deterioration. However, further research is needed to determine its consequences on freshwater ecosystems. We aimed to evaluate these impacts by contrasting freshwater ecosystem functions (litter-decomposition, biomass, water quality, water temperature, and silica’s transportation) and biota (macroinvertebrates, periphyton, and bacteria) in forests, cattle, and oil palm streams from Guatemala (6th world’s greatest palm-oil producer). Litter-decomposition will be assessed through litter bags (by macroinvertebrates) and tea-bags (by bacteria), periphyton biomass through carbon dry-weight from clay tiles placed in the streams, water quality (physical and chemical parameters), temperature (data-loggers), silica content (silica transportation) and biota (direct sampling and bacteria metabarcoding) in strategic points in the streams. We expect detecting and describing important differences in biota and ecosystem function based on land-use and identify solutions.