| 1. |
- Engstedt, Olof, 1980-
(författare)
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Anadromous Pike in the Baltic Sea
- 2011
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The pike (Esox lucius) is a major predator and top-down regulator in the Baltic Sea where it exists in two sympatric forms. One spawn in streams and rivers and the other one spawn in the sea. During the last decades, the habitats for both of these forms have developed in a negative way. In some freshwater systems, up to 90 % of the water areas have disappeared, mainly through drainage and straightening of watercourses for agricultural purposes. In the sea, reproduction habitats decrease due to construction of harbours and human activities that create disturbances. The perhaps largest single factor negatively affecting recruitment of pike in the sea is the eutrophication. Bottoms are overgrown with filamentous algae and shallow bays are covered with dense Phragmites belts decreasing the habitats suitable for spawning. Further on, a predator on egg and fish larvae, the three-spined stickleback (Gasterosteus aculeatus) has increased in abundance. It is difficult to restore and enhance pike production in the sea and probably the only economically viable alternative is to make restorations in freshwater. However, there is a limited knowledge about the freshwater spawning pike in the Baltic Sea. Thus in this thesis I, together with my coauthors, set out with an aim to increase the knowledge base regarding anadromous pike behaviour.We found that pike of natal freshwater origin were common in the Baltic Sea. Through Sr:Ca studies in otoliths, about 45 % of the pike were interpreted to be of freshwater origin. The majority of the pike had emigrated out of freshwater at a length below 6 cm. These results indicate that freshwater recruitment is successful, contrasting the vast areas available for spawning in the sea. This creates incitements that restoration measures in these watercourses could have a significant effect on the pike population in the Baltic Sea.Further, in four streams running out in the Baltic Sea, more than three thousand pike were marked to study spawning migration. About 30-40 % returned to the same river the subsequent year. Most of the pike used the lower parts of the stream for spawning. The homing of pike to a watercourse indicate that freshwater pike in the Baltic Sea consist of specific populations and this is crucial information when taking decisions on fish restoration measures.Three wetlands adjacent to streams were restored for pike production. The most successful restoration involved minimal digging, with flooded grasslands providing optimal conditions for spawning. The first spawning season after restoration increased the pike production hundredfold.In conclusion, the anadromous pike are numerous in the Baltic Sea. To compensate for the decline in pike populations in the sea, “pike-factories” created along the coastline are probably the most justifiable option.
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| 2. |
- Bernes, Claes, et al.
(författare)
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What is the influence on water quality in temperate eutrophic lakes of a reduction of planktivorous and benthivorous fish? : A systematic review protocol
- 2013
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Ingår i: Environmental Evidence. - : BioMed Central (BMC). - 2047-2382. ; 2:1
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Forskningsöversikt (refereegranskat)abstract
- Background: In lakes that have become eutrophic due to sewage discharges or nutrient runoff from land, problems such as algal blooms and oxygen deficiency often persist even when nutrient supplies have been reduced. One reason is that phosphorus stored in the sediments can exchange with the water. There are indications that the high abundance of phytoplankton, turbid water and lack of submerged vegetation seen in many eutrophic lakes may represent a semi-stable state. For that reason, a shift back to more natural clear-water conditions could be difficult to achieve. In some cases, though, temporary mitigation of eutrophication-related problems has been accomplished through biomanipulation: stocks of zooplanktivorous fish have been reduced by intensive fishing, leading to increased populations of phytoplankton-feeding zooplankton. Moreover, reduction of benthivorous fish may result in lower phosphorus fluxes from the sediments. An alternative to reducing the dominance of planktivores and benthivores by fishing is to stock lakes with piscivorous fish. These two approaches have often been used in combination. The implementation of the EU Water Framework Directive has recently led to more stringent demands for measures against eutrophication, and a systematic review could clarify whether biomanipulation is efficient as a measure of that kind. Methods: The review will examine primary field studies of how large-scale biomanipulation has affected water quality and community structure in eutrophic lakes or reservoirs in temperate regions. Such studies can be based on comparison between conditions before and after manipulation, on comparison between treated and nontreated water bodies, or both. Relevant outcomes include Secchi depth, concentrations of oxygen, nutrients, suspended solids and chlorophyll, abundance and composition of phytoplankton, zooplankton and fish, and coverage of submerged macrophytes.
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| 3. |
- Eriksson, Katarina, et al.
(författare)
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Vaginal retention of locally administered clindamycin
- 2011
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Ingår i: Acta Pathologica, Microbiologica et Immunologica Scandinavica (APMIS). - : John Wiley & Sons. - 0903-4641 .- 1600-0463. ; 119:6, s. 373-376
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Tidskriftsartikel (refereegranskat)abstract
- Since bacterial vaginosis (BV) is characterized by a lack of, or very few, lactobacilli and high numbers of small, mostly anaerobic bacteria, an obvious treatment modality would be eradication of the BV-associated bacterial flora followed by reintroduction of lactobacilli vaginally. As probiotic treatment with lactobacilli is one tool for improving the cure rate when treating BV, it is necessary to know the length of time after treatment that clindamycin can be found in the vagina and if this could interfere with the growth of the probiotic lactobacilli. We evaluated the vaginal concentration of clindamycin in 12 women for 8 days to obtain data on the concentration of clindamycin in the vagina after intravaginal treatment with the drug. The participants were examined five times between two menstrual periods: before treatment, the day after treatment was finished, and 3, 5 and 8 days post-treatment. The first day post-treatment clindamycin 0.46 x 10-3 to 8.4 x 10-3 g/g vaginal fluid (median 2.87 x 10-3) was found. Thereafter, the concentration of clindamycin decreased rapidly. In 10 patients clindamycin was found after 3 days. A very low concentration was still present 5 days after treatment in four patients. After 8 days no clindamycin was found. Clindamycin is rapidly eliminated from the vagina, within 3-8 days, after local administration. Our results indicate that treatment with probiotic lactobacilli could be problematic if carried out within 5 days after cessation of clindamycin treatment.
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| 4. |
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| 5. |
- Peciulyte, Ausra, 1986, et al.
(författare)
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Morphology and enzyme production of Trichoderma reesei Rut C-30 are affected by the physical and structural characteristics of cellulosic substrates
- 2014
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1087-1845 .- 1096-0937. ; 72, s. 64-72
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Tidskriftsartikel (refereegranskat)abstract
- The industrial production of cellulolytic enzymes is dominated by the filamentous fungus Trichoderma reesei (anamorph of Hypocrea jecorina). In order to develop optimal enzymatic cocktail, it is of importance to understand the natural regulation of the enzyme profile as response to the growth substrate. The influence of the complexity of cellulose on enzyme production by the microorganisms is not understood. In the present study we attempted to understand how different physical and structural properties of cellulose-rich substrates affected the levels and profiles of extracellular enzymes produced by T. reesei. Enzyme production by T. reesei Rut C-30 was studied in submerged cultures on five different cellulose-rich substrates, namely, commercial cellulose Avicel (R) and industrial-like cellulosic pulp substrates which consist mainly of cellulose, but also contain residual hemicellulose and lignin. In order to evaluate the hydrolysis of the substrates by the fungal enzymes, the spatial polymer distributions were characterised by cross-polarisation magic angle spinning carbon-13 nuclear magnetic resonance (CP/MAS C-13-NMR) in combination with spectral fitting. Proteins in culture supernatants at early and late stages of enzyme production were labeled by Tandem Mass Tags (TMT) and protein profiles were analysed by liquid chromatography-tandem mass spectrometry. The data have been deposited to the ProteomeXchange with identifier PXD001304. In total 124 proteins were identified and quantified in the culture supernatants, including cellulases, hemicellulases, other glycoside hydrolases, lignin-degrading enzymes, auxiliary activity 9 (AA9) family (formerly GH61), supporting activities of proteins and enzymes acting on cellulose, proteases, intracellular proteins and several hypothetical proteins. Surprisingly, substantial differences in the enzyme profiles were found even though there were minor differences in the chemical composition between the cellulose-rich substrates.
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| 6. |
- Pronk, Sander, et al.
(författare)
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GROMACS 4.5 : a high-throughput and highly parallel open source molecular simulation toolkit
- 2013
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 29:7, s. 845-854
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Tidskriftsartikel (refereegranskat)abstract
- Motivation: Molecular simulation has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation of, for instance, many conformers or mutants of biomolecules with or without a range of ligands. At the same time, advances in performance and scaling now make it possible to model complex biomolecular interaction and function in a manner directly testable by experiment. These applications share a need for fast and efficient software that can be deployed on massive scale in clusters, web servers, distributed computing or cloud resources. Results: Here, we present a range of new simulation algorithms and features developed during the past 4 years, leading up to the GROMACS 4.5 software package. The software now automatically handles wide classes of biomolecules, such as proteins, nucleic acids and lipids, and comes with all commonly used force fields for these molecules built-in. GROMACS supports several implicit solvent models, as well as new free-energy algorithms, and the software now uses multithreading for efficient parallelization even on low-end systems, including windows-based workstations. Together with hand-tuned assembly kernels and state-of-the-art parallelization, this provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations.
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| 7. |
- Yakovleva, Maria, et al.
(författare)
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A novel combined thermometric and amperometric biosensor for lactose determination based on immobilised cellobiose dehydrogenase.
- 2012
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Ingår i: Biosensors & Bioelectronics. - : Elsevier BV. - 1873-4235 .- 0956-5663. ; 31, s. 251-256
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Tidskriftsartikel (refereegranskat)abstract
- A novel method for lactose determination in milk is proposed. It is based on oxidation of lactose by cellobiose dehydrogenase (CDH) from the basidiomycete Phanerochaete chrysosporium, immobilised in an enzyme reactor. The reactor was prepared by cross-linking CDH onto aminopropyl-silanised controlled pore glass (CPG) beads using glutaraldehyde. The combined biosensor worked in flow injection analysis (FIA) mode and was developed for simultaneous monitoring of the thermometric signal associated with the enzymatic oxidation of lactose using p-benzoquinone as electron acceptor and the electrochemically generated current associated with the oxidation of the hydroquinone formed. A highly reproducible linear response for lactose was obtained between 0.05mM and 30mM. For a set of more than 500 samples an R.S.D. of less than 10% was achieved. The assay time was ca. 2min per sample. The sensor was applied for the determination of lactose in dairy milk samples (milk with a fat content of 1.5% or 3% and also "lactose free" milk). No sample preparation except dilution with buffer was needed. The proposed method is rapid, suitable for repeated use and allows the possibility to compare results from two different detection methods, thus providing a built-in quality assurance. Some differences in the response observed between the methods indicate that the dual approach can be useful in mechanistic studies of redox enzymes. In addition, a dual system opens up interesting possibilities for studies of enzyme properties and mechanisms.
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| 8. |
- Larsson, Per, 1972-, et al.
(författare)
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Algorithm improvements for molecular dynamics simulations
- 2011
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Ingår i: Wiley Interdisciplinary Reviews. Computational Molecular Science. - : Wiley. - 1759-0884 .- 1759-0876. ; 1:1, s. 93-108
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Tidskriftsartikel (refereegranskat)abstract
- High-performance implementations of molecular dynamics (MD) simulations play an important role in the study of macromolecules. Recent advances in both hardware and simulation software have extended the accessible time scales significantly, but the more complex algorithms used in many codes today occasionally make it difficult to understand the program flow and data structures without at least some knowledge about the underlying ideas used to improve performance. In this review, we discuss some of the currently most important areas of algorithm improvement to accelerate MD, including floating-point maths, techniques to accelerate nonbonded interactions, and methods to allow multiple or extended time steps. There is also a strong trend of increased parallelization on different levels, including both distributed memory domain decomposition, stream processing algorithms running, e. g., on graphics processing units hardware, and last but not least techniques to decouple simulations to enable massive parallelism on next-generation supercomputers or distributed computing. We describe some of the impacts these algorithms are having in current performance, and also how we believe they can be combined in the future.
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| 9. |
- Larsson, Per, et al.
(författare)
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From Side Chains Rattling on Picoseconds to Ensemble Simulations of Protein Folding
- 2014
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Ingår i: Israel Journal of Chemistry. - : Wiley. - 0021-2148. ; 54:8-9, s. 1274-1285
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Forskningsöversikt (refereegranskat)abstract
- Simulations of biological macromolecules have evolved tremendously since the discoveries of the 1970s. The field has moved from simple simulations in vacuo on picosecond scales to milliseconds of accurate sampling of large proteins, and it has become a standard tool in biochemistry and biophysics, rather than a dedicated theoretical one. This is partly due to increasing computational power, but it would not have been possible without huge research efforts invested in new algorithms and software. Here, we illustrate some of this development, both past and future challenges, and in particular, discuss how the recent introduction of modern ensemble methods is breaking the trend of ever-longer simulations to instead focus on throughput and sampling. This has not only helped simulations become much more accurate, but it provides statistical error estimates, which are critical, as simulations are increasingly used to predict properties that have not yet been measured experimentally.
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| 10. |
- Bjelkmar, Pär, 1980-, et al.
(författare)
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Implementation of the CHARMM Force Field in GROMACS : Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models
- 2010
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Ingår i: Journal of Chemical Theory and Computation. - Washington : American Chemical Society. - 1549-9618 .- 1549-9626. ; 6:2, s. 459-466
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Tidskriftsartikel (refereegranskat)abstract
- CHARMM27 is a widespread and popular force field for biomolecular simulation, and several recent algorithms such as implicit solvent models have been developed specifically for it. We have here implemented the CHARMM force field and all necessary extended functional forms in the GROMACS molecular simulation package, to make CHARMM-specific features available and to test them in combination with techniques for extended time steps, to make all major force fields available for comparison studies in GROMACS, and to test various solvent model optimizations, in particular the effect of Lennard-Jones interactions on hydrogens. The implementation has full support both for CHARMM-specific features such as multiple potentials over the same dihedral angle and the grid-based energy correction map on the , ψ protein backbone dihedrals, as well as all GROMACS features such as virtual hydrogen interaction sites that enable 5 fs time steps. The medium-to-long time effects of both the correction maps and virtual sites have been tested by performing a series of 100 ns simulations using different models for water representation, including comparisons between CHARMM and traditional TIP3P. Including the correction maps improves sampling of near native-state conformations in our systems, and to some extent it is even able to refine distorted protein conformations. Finally, we show that this accuracy is largely maintained with a new implicit solvent implementation that works with virtual interaction sites, which enables performance in excess of 250 ns/day for a 900-atom protein on a quad-core desktop computer.
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