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| 3. |
- Jonker, R.M., et al.
(författare)
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Genetic consequences of breaking migratory traditions in barnacle geese Branta leucopsis
- 2013
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Ingår i: Molecular Ecology. - : John Wiley & Sons. - 0962-1083 .- 1365-294X. ; 22:23, s. 5835-5847
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Tidskriftsartikel (refereegranskat)abstract
- Cultural transmission of migratory traditions enables species to deal with their environment based on experiences from earlier generations. Also, it allows a more adequate and rapid response to rapidly changing environments. When individuals break with their migratory traditions, new population structures can emerge that may affect gene flow. Recently, the migratory traditions of the Barnacle Goose Branta leucopsis changed, and new populations differing in migratory distance emerged. Here, we investigate the population genetic structure of the Barnacle Goose to evaluate the consequences of altered migratory traditions. We used a set of 358 single nucleotide polymorphism (SNP) markers to genotype 418 individuals from breeding populations in Greenland, Spitsbergen, Russia, Sweden and the Netherlands, the latter two being newly emerged populations. We used discriminant analysis of principal components, FST, linkage disequilibrium and a comparison of geneflow models using MIGRATE-N to show that there is significant population structure, but that relatively many pairs of SNPs are in linkage disequilibrium, suggesting recent admixture between these populations. Despite the assumed traditions of migration within populations, we also show that genetic exchange occurs between all populations. The newly established nonmigratory population in the Netherlands is characterized by high emigration into other populations, which suggests more exploratory behaviour, possibly as a result of shortened parental care. These results suggest that migratory traditions in populations are subject to change in geese and that such changes have population genetic consequences. We argue that the emergence of nonmigration probably resulted from developmental plasticity.
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| 4. |
- Moeller, Steffen, et al.
(författare)
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Community-driven development for computational biology at Sprints, Hackathons and Codefests
- 2014
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Ingår i: BMC Bioinformatics. - 1471-2105. ; 15, s. S7-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Computational biology comprises a wide range of technologies and approaches. Multiple technologies can be combined to create more powerful workflows if the individuals contributing the data or providing tools for its interpretation can find mutual understanding and consensus. Much conversation and joint investigation are required in order to identify and implement the best approaches. Traditionally, scientific conferences feature talks presenting novel technologies or insights, followed up by informal discussions during coffee breaks. In multi-institution collaborations, in order to reach agreement on implementation details or to transfer deeper insights in a technology and practical skills, a representative of one group typically visits the other. However, this does not scale well when the number of technologies or research groups is large. Conferences have responded to this issue by introducing Birds-of-a-Feather (BoF) sessions, which offer an opportunity for individuals with common interests to intensify their interaction. However, parallel BoF sessions often make it hard for participants to join multiple BoFs and find common ground between the different technologies, and BoFs are generally too short to allow time for participants to program together. Results: This report summarises our experience with computational biology Codefests, Hackathons and Sprints, which are interactive developer meetings. They are structured to reduce the limitations of traditional scientific meetings described above by strengthening the interaction among peers and letting the participants determine the schedule and topics. These meetings are commonly run as loosely scheduled unconferences (self-organized identification of participants and topics for meetings) over at least two days, with early introductory talks to welcome and organize contributors, followed by intensive collaborative coding sessions. We summarise some prominent achievements of those meetings and describe differences in how these are organised, how their audience is addressed, and their outreach to their respective communities. Conclusions: Hackathons, Codefests and Sprints share a stimulating atmosphere that encourages participants to jointly brainstorm and tackle problems of shared interest in a self-driven proactive environment, as well as providing an opportunity for new participants to get involved in collaborative projects.
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- Muntean, Stela Andrea
(författare)
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Molecular-dynamics simulations of polymeric surfaces for biomolecular applications
- 2013
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In-vitro diagnostics plays a very important role in the present healthcare system. It consists of a large variety of medical devices designed to diagnose a medical condition by measuring a target molecule in a sample, such as blood or urine. In vitro is the latin term for in glass and refers here to the fact that the samples are investigated outside the living organism. The range of target molecules is very broad, spanning from salts to small molecules, proteins, nucleic acids and cells. An important segment in this range is the measurement of macromolecules, such as biomarker proteins or nucleic acids, in biological samples. Biosensors are compact systems for rapid detection of biological molecules. The first commercial biosensor was introduced in 1975 for glucose analysis by the Yellow Springs Instrument Company, based on the pioneering work of Clark and Lyons. Since that time, biosensors are becoming more integrated, more sensitive, smaller, faster and cheaper and are becoming available for more and more classes of biomarkers. The immunoassays can be performed nowadays in devices with very different formats, from the high-throughput parallel analysis on well-plates to integrated point-of-care biosensors using lab-on-a-chip technology. The solid phase in these devices is very often a polymeric glass. Polymeric glasses, such as polystyrene, are easy to process and can be produced at low costs, which makes them suitable for disposable cartridges in lab-on-a-chip devices. An important process in the immunoassays is the physisorption of the macromolecules to the polymeric solid phase, such as the non-specific binding of molecules from the biological sample onto the polymeric carrier. This process plays a very important role in the limit of detection, which is given by specific binding (signal) over non-specific binding (background). Therefore, the understanding of the non-specific binding of macromolecules to polymeric surfaces is crucial for the improvement of the sensitivity in these devices. The scope of this thesis is to gain fundamental knowledge on the physisorption of proteins onto polymeric surfaces and to understand how to model this process in atomistic details. The goal of this work is to model the interaction between myoglobin and polystyrene surfaces, within a clean buffer. Computer simulations provide detailed informations about the nature of the non-specific interactions between the biomolecule and the polymeric substrate, at molecular and atomic scales. The high level of detail obtained from simulations on a smaller scale is complementary to the experimental results obtained at a larger scale. The polymeric substrate is in our case modeled by an atactic amorphous polystyrene thin film. We would like to explore the possibility of changing the properties of the polymeric substrate, to prevent non-specific interaction, by chemical modification induced by oxidation. Pure polystyrene is a hydrophobic material. We tune the hydrophilicity of its surface by adding oxygen atoms to the phenyl rings of the polystyrene chain. This addition of oxygen is a way to mimic the oxidation of polystyrene surfaces that is performed in experiments. We represent the buffer solution in simulations by explicit water molecules described at atomistic level, to which we add Na+ and Cl- ions to reproduce the salt concentration in the experimentally used buffer solution. We chose myoglobin as model biomolecule because it is a relatively small globular protein, well studied in the past and represents a good candidate for practical applications. The first question we intend to answer is to which extent the model used to represent the polystyrene chains is important for the macroscopic properties of the polystyrene films and in particular to their interaction with the water molecules. To tackle this issue, we chose two representations of the polystyrene chains: the united atoms representations on one hand, in which only the heavy atoms are modeled explicitly and the hydrogen atoms are collapsed on the carbon atoms to which they are covalently bonded, and the dummy-hydrogens atoms representation on the other hand, in which the hydrogen atoms are modeled as interaction sites with no mass and with a positive partial electrical charge. The results of these simulations are presented in Chapter 3. We begin our systematic study on the interacting species in a biomedical device by characterizing the atactic amorphous polystyrene substrate. In Chapter 4 we present the results of molecular-dynamics simulations of polystyrene surfaces with controlled degree of oxidation. The variations in degree of oxidation at the surface, ranging from 0% to 24%, correspond to different degrees of hydrophilicity of the polystyrene surface, from hydrophobic to hydrophilic. We study the influence of the oxidation on the roughness of the film, both in vacuum and in water environment. We compare our results with experimental results from AFM measurements obtained by our collaborators. We also analyze the ordering of the molecular segments in non-oxidized and oxidized polystyrene at the interface with vacuum and with water. The structure of the water interface near polystyrene surfaces with different hydrophilicity is analyzed as well. Since the interaction between proteins and polymeric surfaces is a water-mediated process, it is very important to know how water behaves near these surfaces. In Chapter 5 we discuss the dynamics of water near non-oxidized (hydrophobic) and oxidized (hydrophilic) polystyrene surfaces, both in united-atoms and dummy-hydrogen atoms representations. We discuss the orientational dynamics of water molecules and its dependence on the distance from the interface. Furthermore, the translational diffusion of water molecules is briefly discussed. In Chapter 6 we study the nature of non-specific adsorption of myoglobin, as model protein, to hydrophobic and hydrophilic polystyrene surfaces. We investigate the importance of the orientation of the protein in the process of adsorption. We also discuss the influence of the hydrophilicity of the surface on the strength of adsorption of the protein. We conclude this thesis by Chapter 7, in which our main results are summarized. In addition, we give there an outlook on further interesting questions.
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| 6. |
- Prins, M. J., et al.
(författare)
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Biomass pyrolysis in a heated-grid reactor: Visualization of carbon monoxide and formaldehyde using Laser-Induced Fluorescence
- 2011
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Ingår i: Journal of Analytical and Applied Pyrolysis. - : Elsevier BV. - 1873-250X .- 0165-2370. ; 92:2, s. 280-286
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Tidskriftsartikel (refereegranskat)abstract
- The development of improved biomass pyrolysis models is vital for more accurate modelling and design of biomass conversion equipment. Such improved models must be based on reliable experimental data: biomass should be pyrolyzed at high heating rates and the reaction products should be measured using an on-line, non-intrusive method. Therefore, a heated grid reactor with heating rate of 300-600 K/s was used to study pyrolysis of biomass at temperatures in the range of 500-700 degrees C. The formation of formaldehyde and carbon monoxide from wood at high heating rates was successfully visualized using Laser-Induced Fluorescence (LIF). A thin vertical laser line or sheet was present directly above the biomass lying on the heated grid. Two-photon excitation at 230 nm was applied to induce fluorescence of carbon monoxide present in the volatiles, whereas excitation of formaldehyde was done at 355 nm. Visualization of these compounds shows that the release rises strongly with temperature; this typically happens on a timescale in the order of seconds. In principle, the method described allows for the determination of truly primary products. Future research is recommended, aimed at quantifying the concentrations measured by LIE. Care must be taken to calibrate for quenching of the fluorescence signal. Avoiding secondary reactions taking place in the gas phase is another experimental challenge. (C) 2011 Elsevier B.V. All rights reserved.
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| 7. |
- Kraus, Robert H. S., et al.
(författare)
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Genome wide SNP discovery, analysis and evaluation in mallard (Anas platyrhynchos)
- 2011
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Ingår i: BMC Genomics. - 1471-2164 .- 1471-2164. ; 12, s. 150-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Next generation sequencing technologies allow to obtain at low cost the genomic sequence information that currently lacks for most economically and ecologically important organisms. For the mallard duck genomic data is limited. The mallard is, besides a species of large agricultural and societal importance, also the focal species when it comes to long distance dispersal of Avian Influenza. For large scale identification of SNPs we performed Illumina sequencing of wild mallard DNA and compared our data with ongoing genome and EST sequencing of domesticated conspecifics. This is the first study of its kind for waterfowl. Results: More than one billion base pairs of sequence information were generated resulting in a 16x coverage of a reduced representation library of the mallard genome. Sequence reads were aligned to a draft domesticated duck reference genome and allowed for the detection of over 122,000 SNPs within our mallard sequence dataset. In addition, almost 62,000 nucleotide positions on the domesticated duck reference showed a different nucleotide compared to wild mallard. Approximately 20,000 SNPs identified within our data were shared with SNPs identified in the sequenced domestic duck or in EST sequencing projects. The shared SNPs were considered to be highly reliable and were used to benchmark non-shared SNPs for quality. Genotyping of a representative sample of 364 SNPs resulted in a SNP conversion rate of 99.7%. The correlation of the minor allele count and observed minor allele frequency in the SNP discovery pool was 0.72. Conclusion: We identified almost 150,000 SNPs in wild mallards that will likely yield good results in genotyping. Of these, similar to 101,000 SNPs were detected within our wild mallard sequences and similar to 49,000 were detected between wild and domesticated duck data. In the similar to 101,000 SNPs we found a subset of similar to 20,000 SNPs shared between wild mallards and the sequenced domesticated duck suggesting a low genetic divergence. Comparison of quality metrics between the total SNP set (122,000 + 62,000 = 184,000 SNPs) and the validated subset shows similar characteristics for both sets. This indicates that we have detected a large amount (similar to 150,000) of accurately inferred mallard SNPs, which will benefit bird evolutionary studies, ecological studies (e. g. disentangling migratory connectivity) and industrial breeding programs.
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| 8. |
- Kraus, Robert H. S., et al.
(författare)
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Genome wide SNP discovery, analysis and evaluation in mallard (Anas platyrhynchos)
- 2011
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Ingår i: BMC Genomics. - : BioMed Central Ltd.. - 1471-2164. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- Background: Next generation sequencing technologies allow to obtain at low cost the genomic sequence information that currently lacks for most economically and ecologically important organisms. For the mallard duck genomic data is limited. The mallard is, besides a species of large agricultural and societal importance, also the focal species when it comes to long distance dispersal of Avian Influenza. For large scale identification of SNPs we performed Illumina sequencing of wild mallard DNA and compared our data with ongoing genome and EST sequencing of domesticated conspecifics. This is the first study of its kind for waterfowl. Results: More than one billion base pairs of sequence information were generated resulting in a 16x coverage of a reduced representation library of the mallard genome. Sequence reads were aligned to a draft domesticated duck reference genome and allowed for the detection of over 122,000 SNPs within our mallard sequence dataset. In addition, almost 62,000 nucleotide positions on the domesticated duck reference showed a different nucleotide compared to wild mallard. Approximately 20,000 SNPs identified within our data were shared with SNPs identified in the sequenced domestic duck or in EST sequencing projects. The shared SNPs were considered to be highly reliable and were used to benchmark non-shared SNPs for quality. Genotyping of a representative sample of 364 SNPs resulted in a SNP conversion rate of 99.7%. The correlation of the minor allele count and observed minor allele frequency in the SNP discovery pool was 0.72. Conclusion: We identified almost 150,000 SNPs in wild mallards that will likely yield good results in genotyping. Of these, similar to 101,000 SNPs were detected within our wild mallard sequences and similar to 49,000 were detected between wild and domesticated duck data. In the similar to 101,000 SNPs we found a subset of similar to 20,000 SNPs shared between wild mallards and the sequenced domesticated duck suggesting a low genetic divergence. Comparison of quality metrics between the total SNP set (122,000 + 62,000 = 184,000 SNPs) and the validated subset shows similar characteristics for both sets. This indicates that we have detected a large amount (similar to 150,000) of accurately inferred mallard SNPs, which will benefit bird evolutionary studies, ecological studies (e. g. disentangling migratory connectivity) and industrial breeding programs.
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| 9. |
- Tenow, Olle, et al.
(författare)
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Geometrid outbreak waves travel across Europe
- 2013
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Ingår i: Journal of Animal Ecology. - : Wiley. - 0021-8790 .- 1365-2656. ; 82:1, s. 84-95
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Tidskriftsartikel (refereegranskat)abstract
- We show that the population ecology of the 9- to 10-year cyclic, broadleaf-defoliating winter moth (Operophtera brumata) and other early-season geometrids cannot be fully understood on a local scale unless population behaviour is known on a European scale. Qualitative and quantitative data on O. brumata outbreaks were obtained from published sources and previously unpublished material provided by authors of this article. Data cover six decades from the 1950s to the first decade of twenty-first century and most European countries, giving new information fundamental for the understanding of the population ecology of O. brumata. Analyses on epicentral, regional and continental scales show that in each decade, a wave of O. brumata outbreaks travelled across Europe. On average, the waves moved unidirectionally ESE-WNW, that is, toward the Scandes and the Atlantic. When one wave reached the Atlantic coast after 9-10 years, the next one started in East Europe to travel the same c. 3000 km distance. The average wave speed and wavelength was 330 km year-1 and 3135 km, respectively, the high speed being incongruous with sedentary geometrid populations. A mapping of the wave of the 1990s revealed that this wave travelled in a straight E-W direction. It therefore passed the Scandes diagonally first in the north on its way westward. Within the frame of the Scandes, this caused the illusion that the wave moved N-S. In analogy, outbreaks described previously as moving S-N or occurring contemporaneously along the Scandes were probably the result of continental-scale waves meeting the Scandes obliquely from the south or in parallel. In the steppe zone of eastern-most and south-east Europe, outbreaks of the winter moth did not participate in the waves. Here, broadleaved stands are small and widely separated. This makes the zone hostile to short-distance dispersal between O. brumata subpopulations and prevents synchronization within meta-populations. We hypothesize that hostile boundary models, involving reciprocal host-herbivore-enemy reactions at the transition between the steppe and the broadleaved forest zones, offer the best explanation to the origin of outbreak waves. These results have theoretical and practical implications and indicate that multidisciplinary, continentally coordinated studies are essential for an understanding of the spatio-temporal behaviour of cyclic animal populations.
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