6th Annual NORBIS Conferen – PhD student talks, schedule and abstracts
10:30-10:50 Christian Schulz, NTNU, “Beer in the NMR – Who left fingerprints?” – in person
10:50-11:10 Olena Meleshko, NTNU, “Studying the implications of gene flow for species diversification using phylogenomics in peatmoss” – online
11:10-11:30 Snorre Sulheim, NTNU/SINTEF, “Construction of secondary metabolite pathways from BGCs” – in person
11:30-11:50 Ferenc Kagan, UiB, “Comparative study of maternal genes within Ecdysozoa using transcriptomics” – in person
10:45-11:05 Alexandra Jonsson, UiO, “Mechanisms of protective immunity in Atlantic cod” – in person
11:05-11:25 Kristine Løkås Haftorn, UiO, “An EPIC predictor of gestational age shows excellent precision in newborns conceived by assisted reproductive technologies” – online
11:25-11:45 Sowmya Ramachandran, NU, “Imagine having two types of ribosomes!” – in person
11:45-12:05 William John Hatchett, NU, “The evolution of sex biased gene expression in Fucus species” – in person
12:05-12:25 Yousri Abdelmutalab Ahmed Abdelhafiz, NU, “Breeding strategy-dependent changes in the composition of bacterial communities in Nile tilapia” – online
Talk 1 – Tuesday 3rd at 10:30-10:50
Title: Beer in the NMR – Who left fingerprints?
Beer is one of the most important beverages in the world. Besides “generic” types such as Lager, Ale, or Stout various regions offer specialties, also including a variety of additional ingredients such as fruits, herbs, or spices. Additionally unique beer styles such as Indian Pale Ale (IPA), Sour Beer, or Weißbier broaden the marked. The ingredients are similar for all of them: Water, malt, hops – and yeast. Within the last years the Norwegian yeast community “kveik” was rediscovered. It was evolved by local farms using always the same equipment in a beer. Consequently the kveik is a community of multiple yeast and bacteria strains used in fermenting – at high temperatures. Ale and lager (single) strains are limited to low temperature ranges (5° to 21°C) via the production of off-flavors. Kveik can ferment a beer at 38° to 40°C and thus finish fermentation within 3 days. Due to the various kveik communities on farms all over Norway their taste profile differs significantly. Here we present an NMR based methodology to prepare samples for fingerprint based analysis of several single industrial yeast strains in comparison with Norwegian kveik at different temperatures.
Talk: 2 – Tuesday 3rd at 10:50-11:20
Title: Studying the implications of gene flow for species diversification using phylogenomics in peatmoss
Department of Natural History, NTNU University Museum
The relative importance of gene flow for species diversification remains an open question in evolution and speciation research. Answering this question is especially challenging in rapidly radiated groups, in which intensive incomplete lineage sorting (ILS) substantially hinders the identification and quantification of gene flow. Here, we use the rapidly radiated, actively hybridizing, ecologically diverse, and carbon storing genus of peatmoss (Sphagnum) to reconstruct the species phylogeny, quantify interspecific introgression and differentiate between the gene flow and ILS signals. In order to do this, we applied diverse phylogenomic methods to whole nuclear, chloroplast and mitochondrial genomes from 12 peatmoss species sampled on different geographical scales. We demonstrate cytonuclear as well as genome-wide phylogenetic discordance, which is associated with deeper nodes in the phylogeny and is best explained by extensive ILS, due to rapid radiation of the genus, rather than by post-speciation gene flow. Despite that interspecific hybridization is common in the genus, our tests for introgression suggest minimal recent gene flow among the species and support the idea of ancient introgression among the ancestral lineages with subsequent ILS. Our findings contribute to understanding of complex speciation processes in actively hybridizing, rapidly radiated species groups and support the suggested earlier idea of universality of evolutionary processes among land plants.
Talk: 3 – Tuesday 3rd at 11:20-11:40
Title: Automatic reconstruction of metabolic pathways from annotated biosynthetic gene clusters
Department of Biotechnology and Food Science, NTNU
Department of Biotechnology and nanomedicine, SINTEF Industry
Natural products are an immense source of bioactive small molecules of medical and agricultural importance. The biosynthetic pathways responsible for producing these molecules are often encoded by biosynthetic gene clusters (BGCs) that can be identified and functionally annotated based on their genome sequence. Using their functional annotation, (dis)similarity to known BGCs, bioactivity assays etc. one can prioritize candidates for further research and development. Production of the target compound in the native strain is often inconvenient, and heterologous expression in an optimized host strain has emerged as the preferable path forward. Genome-scale metabolic models are routinely used to guide strain development, but large-scale the incorporation and testing of heterologous production in this framework is hampered by the amount of manual work required to translate annotated BGCs to metabolic pathways. To this end, we have developed a pipeline for the automated reconstruction of pathways encoded by polyketide synthases and non-ribosomal peptide synthases. To demonstrate its value, we simulate heterologous production and predict optimal gene knockout strategy for more than 1,000 BGCs in a Streptomyces coelicolor host model.
Talk: 4 – Tuesday 3rd at 11:40-12:00
Title: Comparative study of maternal genes within Ecdysozoa using transcriptomics
University of Bergen
Maternal effector genes are expressed during oogenesis by the mother and their transcripts are loaded in the oocytes. Previous studies have shed light on the role of maternal genes in orchestrating the early development of the embryo. Historically they have been heavily investigated in model species with some attempts to draw conclusions about their evolution. There are contradicting results in the scientific literature with some studies pointing towards conservation of maternal genes while some studies claim a high divergence of maternal genes. With my project I want to contribute results to this debate by investigating the evolution of maternal genes withing the clade of Ecdysozoa using diverese transcriptomic approaches.
Talk: 5 – Wednesday 4th 10:45-11:05
Title: Mechanisms of protective immunity in Atlantic cod
University of Oslo
The Atlantic cod (Gadus morhua) is a large, cold-adapted teleost that represents an important species for the commercial fisheries in Norway and Northern Europe. However, Atlantic cod and other codfishes (gadiforms) have not yet proven successful as an aquaculture species for several reasons including susceptibility to disease. About 100 million years ago, gadiforms selectively lost the major histocompatibility complex (MHC) II, CD4+ T cells and invariant chain, important molecules for adaptive immunity in vertebrates, rendering them poor subjects for vaccination1,3. These features are essential for producing specific antibody response and long-lasting memory against pathogens upon immunization, nevertheless, Atlantic cod is not particularly susceptible to infectious diseases in its natural environment. It remains to be understood how the immune system in codfishes are able to efficiently fight diseases without the classical adaptive immunity. This knowledge will reveal novel principles of immune regulation in Atlantic cod and aid in improving fisheries management by development of efficient vaccination strategies, disease control and food safety for aquaculture and wild stock.
Talk: 6 – Wednesday 4th 11:05-11:25
Title: An EPIC predictor of gestational age shows excellent precision in newborns conceived by assisted reproductive technologies
Kristine Løkås Haftorn
University of Oslo
Introduction: Gestational age is a useful proxy for assessing developmental maturity and can be estimated from DNA methylation data. Earlier predictors of epigenetic gestational age were based on the Illumina HumanMethylation 27K or 450K arrays, which have been replaced by the Illumina MethylationEPIC array. For children conceived by assisted reproductive technologies (ART), the exact time when the embryo is transferred back to the uterus is known, making DNA methylation data from ART-births valuable for developing and validating gestational age clocks.
Aims: Our first aim was to build an epigenetic gestational age clock based on the EPIC array and compare its performance to previously published gestational age clocks. Our second aim was to test our clock in ART newborns with known embryo transfer date, and investigate whether ART and non-ART newborns differed in epigenetic gestational age acceleration.
Methods: This study was based on data from the Norwegian Mother, Father and Child Cohort Study and the Medical Birth Registry of Norway. We built an epigenetic gestational age clock using Lasso regression trained on 755 non-ART newborns. The predicted gestational age was compared to ultrasound-based gestational age in 200 non-ART and 838 ART newborns using MM-type robust regression. The performance of the clock was compared to previous clocks in 148 newborns from the Prediction and Prevention of Preeclampsia and Intrauterine Growth Restrictions (PREDO) cohort. Results: The clock predicted embryo transfer date-based gestational age accurately, and performed significantly better than previous clocks. However, we observed a similar performance when restricting the analysis to only those CpGs that are present on both 450K and EPIC, indicating that the additional CpGs on EPIC do not enhance the prediction of gestational age. Further, we did not find any significant difference in gestational age acceleration between ART and non-ART newborns (p=0.385). Conclusions: Our EPIC-based gestational age predictor showed remarkable precision in ART newborns and outperformed previously published gestational age clocks. As more datasets are being generated on the EPIC array, our clock will be valuable in studies of gestational age, neonatal development, and disease.
Talk: 7 – Wednesday 4th 11:45-12:05
Title: Imagine having two types of ribosomes!
RiboMeth-seq is a great method to qualitatively and quantitatively study 2’-O-Me modifications in rRNA. Since there have been indications of the presence of two types of rRNA during zebrafish development (early-type and late-type), we applied RiboMeth-seq to 4 different developmental stages of zebrafish and validated the methylated sites by finding their cognate SNORDs. We observed two different types of rRNA which were substantially different in sequence with a total of 98 high-confidence sites and that zebrafish rRNA was methylated at 10 additional sites which have not been described in other vertebrates. Interestingly, we also found a methylated site specific to late-type rRNA. Not all sites were fully methylated and the methylation at a subset of sites fluctuated between different developmental stages, especially in the zebrafish novel sites. The late-type rRNA more closely resembles human and mice rRNA and therefore we propose that the early-type is a specialized form which may be an adaptation to specific features of development.
Talk: 8 – Wednesday 4th 11:45-12:05
Title: The evolution of sex-biased genes in Fucus species
William John Hatchett
Sex-dependent variations within species, otherwise known as sexual dimorphism, has stimulated research at the ecological, behavioural and molecular levels. The majority of the genome is identical between males and females, with the most distinct genetic variation found on sex chromosomes or associated with gamete production. However, it has been shown that the majority of variation within species is a result of sex-biased gene (SBG) expression. SBG expression has been documented across a wide number of different organisms and generally, male-biased genes are more abundant, highly expressed and show higher divergence rates than female-biased genes. The genus Fucus provides a unique model to study the evolution of SBGs as it presents two lineages that have independently evolved monoecious and dioecious modes of reproduction, allowing us to compare the evolution of SBGs between two lineages. Using high throughput transcriptomics, we were able to identify genes that are differentially expressed between males and females and between vegetative and reproductive tissues. We found a common pattern between the two dioecious species with males having a higher number of SBGs and a higher level expression. dN/dS analysis on all SBGs showed that male biased genes are under higher selective pressure than female biased genes. This conforms with the global trend for SBG expression with males having a higher number of SBGs, higher level of expression and higher selection pressure. In addition we found that males from both dioecious species shared more 1 – 1 SBG orthologs with one another and the monoecious species than with the females. This suggests that dioecy has evolved analogous in the two lineages and was driven by male-biased genes.
Talk: 9 – Wednesday 4th 12:05-12:25
Title: Breeding strategy-dependent changes in the composition of bacterial communities in Nile tilapia
Yousri Abdelmutalab Ahmed Abdelhafiz
In industrial animal production, breeding strategies are essential to produce offspring of better quality and vitality. Here, we report for the first time the influence of mating strategy, inbreeding or outbreeding, on the mouth and intestine bacterial communities in Nile tilapia (Oreochromis niloticus). Employing a 16S rRNA gene sequencing technique, we found a significant difference between the diversities of the bacterial communities of the inbred and outbred groups. The core microbiota composition in the groups was not affected but their abundance varied between the two groups. Inter-individual variation in the intestine of the inbred group was limited compared to the outbred group. Furthermore, beneficial and opportunistic bacteria were abundant in the intestine of the inbred and outbred groups, respectively. The inbred group which has less inter-individual microbiome variability could be a better choice for controlled studies that examine the maternal transfer of microbiome to offspring.