376 research outputs found
Conserved and variable correlated mutations in the plant MADS protein network
No full textAbstract Background Plant MADS domain proteins are involved in a variety of developmental processes for which their ability to form various interactions is a key requisite. However, not much is known about the structure of these proteins or their complexes, whereas such knowledge would be valuable for a better understanding of their function. Here, we analyze those proteins and the complexes they form using a correlated mutation approach in combination with available structural, bioinformatics and experimental data. Results Correlated mutations are affected by several types of noise, which is difficult to disentangle from the real signal. In our analysis of the MADS domain proteins, we apply for the first time a correlated mutation analysis to a family of interacting proteins. This provides a unique way to investigate the amount of signal that is present in correlated mutations because it allows direct comparison of mutations in various family members and assessing their conservation. We show that correlated mutations in general are conserved within the various family members, and if not, the variability at the respective positions is less in the proteins in which the correlated mutation does not occur. Also, intermolecular correlated mutation signals for interacting pairs of proteins display clear overlap with other bioinformatics data, which is not the case for non-interacting protein pairs, an observation which validates the intermolecular correlated mutations. Having validated the correlated mutation results, we apply them to infer the structural organization of the MADS domain proteins. Conclusion Our analysis enables understanding of the structural organization of the MADS domain proteins, including support for predicted helices based on correlated mutation patterns, and evidence for a specific interaction site in those proteins.</p
Does Migration Make You Happy?:A Longitudinal Study of Internal Migration and Subjective Well-Being
No full textThe majority of quantitative studies on the consequences of internal migration focus almost exclusively on the labour-market outcomes and the material well-being of migrants. We investigate whether individuals who migrate within the UK become happier after the move than they were before, and whether the effect is permanent or transient. Using life-satisfaction responses from twelve waves of the British Household Panel Survey and employing a fixed-effects model, we derive a temporal pattern of migrants’ subjective well-being around the time of the migration event. Our findings make an original contribution by revealing that, on average, migration is preceded by a period when individuals experience a significant decline in happiness for a variety of reasons, including changes in personal living arrangements. Migration itself causes a boost in happiness, and brings people back to their initial levels. The research contributes, therefore, to advancing an understanding of migration in relation to set-point theory. Perhaps surprisingly, long-distance migrants are at least as happy as short-distance migrants despite the higher social and psychological costs involved. The findings of this paper add to the pressure to retheorize migration within a conceptual framework that accounts for social well-being from a life-course perspective
Does Migration Make You Happy?:A Longitudinal Study of Internal Migration and Subjective Well-Being
No full textThe majority of modelling studies on consequences of internal migration focus almost exclusively on the labour market outcomes and the material well-being of migrants. We investigate whether individuals who migrate within the UK become happier after the move than they were before it and whether the effect is permanent or transient. Using life satisfaction responses from 12 waves of the British Household Panel Survey (BHPS) and employing a fixed-effects model, we derive a temporal pattern of migrants’ subjective wellbeing (SWB) around the time of the migration event. Our findings make an original contribution by revealing for the first time that, on average, migration is preceded by a period when individuals experience a significant decline in happiness. The boost that is received through migration appears to bring people back to their initial level of happiness. As opposed to labour market outcomes of migration, SWB outcomes do not differ significantly between men and women. Perhaps surprisingly, long-distance migrants are at least as happy as short-distance migrants despite the higher social costs that are involved.OTB Research Institute for the Built Environmen
PRI-CAT: a web-tool for the analysis, storage and visualization of plant ChIP-seq experiments.
No full textAlthough several tools for the analysis of ChIP-seq data have been published recently, there is a growing demand, in particular in the plant research community, for computational resources with which such data can be processed, analyzed, stored, visualized and integrated within a single, user-friendly environment. To accommodate this demand, we have developed PRI-CAT (Plant Research International ChIP-seq analysis tool), a web-based workflow tool for the management and analysis of ChIP-seq experiments. PRI-CAT is currently focused on Arabidopsis, but will be extended with other plant species in the near future. Users can directly submit their sequencing data to PRI-CAT for automated analysis. A QuickLoad server compatible with genome browsers is implemented for the storage and visualization of DNA-binding maps. Submitted datasets and results can be made publicly available through PRI-CAT, a feature that will enable community-based integrative analysis and visualization of ChIP-seq experiments. Secondary analysis of data can be performed with the aid of GALAXY, an external framework for tool and data integration. PRI-CAT is freely available at http://www.ab.wur.nl/pricat. No login is required
Method of separating a particle mixture using a biphasic system
No full textAbstract of GB 2363999 (A) A method of separating a particle mixture comprising first and second types of particle which differ chemically from each other, using a biphasic fluid system comprising a relatively dense first fluid and a relatively less dense second fluid, said fluids being substantially insoluble in each other. The particles PM to be separated and the two fluids are introduced into a separation chamber 10; the content of said chamber is allowed to settle to form an interface between said fluids; particles at the bulk interface are separated from particles near the bottom of the separation chamber - part of the settled material is discharged from 10 as a first stream H1 (denser fluid enriched with second-type of particles) into separation chamber 20, part of inter-phase material discharged as second stream L1 (less dense fluid enriched with first-type of particles) into separation chamber 30. The method is characterised in that:at least the first fluid is a liquid; each particle can be found at the interface between said fluids in the absence of said other particle; the amount of particle mixture introduced into the separation chamber is chosen such that the ratio between the surface area of an interface formed when only the two fluids are present in the separation chamber while at rest and the smallest area occupied by the particles while in contact with a flat surface is & 1.Applied Science
Assessing the contribution of alternative splicing to proteome diversity in <it>Arabidopsis thaliana </it>using proteomics data
No full textAbstract Background Large-scale analyses of genomics and transcriptomics data have revealed that alternative splicing (AS) substantially increases the complexity of the transcriptome in higher eukaryotes. However, the extent to which this complexity is reflected at the level of the proteome remains unclear. On the basis of a lack of conservation of AS between species, we previously concluded that AS does not frequently serve as a mechanism that enables the production of multiple functional proteins from a single gene. Following this conclusion, we hypothesized that the extent to which AS events contribute to the proteome diversity in Arabidopsis thaliana would be lower than expected on the basis of transcriptomics data. Here, we test this hypothesis by analyzing two large-scale proteomics datasets from Arabidopsis thaliana. Results A total of only 60 AS events could be confirmed using the proteomics data. However, for about 60% of the loci that, based on transcriptomics data, were predicted to produce multiple protein isoforms through AS, no isoform-specific peptides were found. We therefore performed in silico AS detection experiments to assess how well AS events were represented in the experimental datasets. The results of these in silico experiments indicated that the low number of confirmed AS events was the consequence of a limited sampling depth rather than in vivo under-representation of AS events in these datasets. Conclusion Although the impact of AS on the functional properties of the proteome remains to be uncovered, the results of this study indicate that AS-induced diversity at the transcriptome level is also expressed at the proteome level.</p
High-Speed Data Path for a Laser Communication Terminal: Building a 100 Mbit/s Laser Communication Terminal for CubeSats
No full textIn the recent years the satellite industry has progressed on the subject of optical communication for use in space. With recorded speeds over 5 Gb/s it has shown to be an alternative for radio communication. In the CubeSat market this technology is new, underdeveloped, and could lead to new missions that were not possible before. As such, TNO and Hyperion joined forces to create the CubeCAT LCT (Laser Communication Terminal). The core part of this LCT is the high-speed digital data path, which was not implemented. This thesis discusses the design, implementation, and verification of the high-speed data path of the CubeCAT LCT (Laser Communication Terminal) that has a targeted speed of 100 Mb/s, with a future upgrade path to 1 Gb/s. The CubeCAT module consists of multiple modules, of which the DMU (Data Management Unit) hosts the high-speed data path. As the DMU was not implemented, a design for the DMU is proposed in this thesis. For this design multiple architectures, interconnects, and components where considered. The proposed design is based on an Hyperion CP400.85 microprocessor connected to a Lattice ECP5-5G FPGA, together with extra external memory and external storage. Then, an implementation of the high-speed data path was made that is based on a QSPI link between the microprocessor and the FPGA. This implementation is based on streaming the data from the microprocessor to the FPGA, in which the data is encoded according to the TNO3k FEC (Forward Error Correction) scheme. After encoding, the data is outputted as an LVDS signal to the laser output. The implementation of the high-speed data path was verified by simulation and on a development setup. This was done by first verifying all submodules, with focus on the QSPI link and the TNO3k encoder, and then as a whole system. All submodule tests were successful, with a note to the verification of the QSPI link. It was found that the development setup was limited to a SPI frequency of 41.50 MHz due to signal integrity issues. During the system test it was found that the there was a lack of LVDS test material. As such the LVDS output was replaced by a UART output. With this output the whole system has been validated for a QSPI link speed of 119.2 Mb/s and an internal FPGA speed of 3.2 Gb/s. The system, with LVDS output, is estimated to consume 1 watts of power. With the validation of the whole system, the high-speed data path of the CubeCAT LCT has been implemented. The design of the DMU allows for a later, 1 Gb/s upgrade of the high-speed data path.CubeCATComputer Engineerin
Microwave TM010 cavities as versatile 4D electron optical elements
No full textThe realization of high quality ultrashort pulsed beams requires ultrafast time-dependent electron optics. We present derivations of closed expressions both for the longitudinal and transverse focusing powers of resonant microwave TM010 cavities. The derived expressions are validated by particle tracking simulations using realistic cavity fields. For small field amplitudes, in which case the weak lens approximation holds, the focusing powers obtained from simulations are in good agreement with the derived expressions. Furthermore, the required phase and temperature stability for synchronization of electron bunches generated by femtosecond photoemission are discussed
Emission of Cryptosporidium and Giardia by farm animals
No full textIn this study, the relative contributions of the pathogenic protozoa Cryptosporidium and Giardia by manure of farm animals in The Netherlands to the total yearly environmental load was studied. Manure of veal calves forms a very large source of Cryptosporidium (1.5 m 10 square 16 oocysts per year) and of Giardia (2.8 m 10 square 15 cysts per year). The contribution of manure from dairy cattle to the emission of protozoa into the environment is uncertain. Manure of commercial egg layers forms a large source of Cryptosporidium. However, the species may be Cryptosporidium baileyi, which is not zoonotic, but the species has not been confirmed. The contribution of wastewater from slaughterhouses for cattle, pigs and poultry to discharges of Cryptosporidium and Giardia into surface water has been found to be negligible. Based on emission via slurry from calves, a high emission of Cryptosporidium and Giardia by veal calves was calculated. Although manure of veal calves form a large source of Cryptosporidium and Giardia, their actual contribution to the load to surface water is still unknown.Het hier gepresenteerde deelonderzoek richt zich op de relatieve bijdrage van verschillende populaties landbouwhuisdieren via mest en afvalwater aan de totale emissie van Cryptosporidium en Giardia in Nederland. Vleeskalveren vormen per jaar in Nederland via hun mest een grote emissiebron van beide protozoa, namelijk naar schatting 1,5 m 10 tot de zestinede macht oocysten van Cryptosporidium en 2,8 m 10 tot de vijftiende macht cysten van Giardia. In mest van melkkoeien zijn ook Giardia-cysten aangetoond, maar deze emissiebron is onvoldoende gekwantificeerd. Cryptosporidium werd in mest van melkkoeien niet aangetoond. Cryptosporidium en Giardia zijn niet in mest van vleeskuikens aangetoond, derhalve levert deze mest waarschijnlijk geen bijdrage van betekenis. Legkippen vormen een belangrijke emissiebron voor Cryptosporidium. Echter, dit zou Cryptosporidium baileyi, welke niet zoonotisch is, kunnen zijn, maar de species is in deze studie niet getypeerd. Giardia werd in mest van legkippen niet aangetoond. Slachthuisafvalwater van runderen, varkens en pluimvee levert geen bijdrage van betekenis aan de lozing van Cryptosporidium en Giardia op het oppervlaktewater. Op basis van het onderzoek aan kalvergier werd een hoge emissie van Cryptosporidium en Giardia door vleeskalveren berekend. Hoewel emissie van Cryptosporidium en Giardia vooral via de mest van vleeskalveren aanzienlijk is, kan nog niets worden gezegd over de werkelijke bijdrage aan de lozing van deze protozoa op het oppervlaktewater
Emission of Cryptosporidium and Giardia by farm animals
No full textHet hier gepresenteerde deelonderzoek richt zich op de relatieve bijdrage van verschillende populaties landbouwhuisdieren via mest en afvalwater aan de totale emissie van Cryptosporidium en Giardia in Nederland. Vleeskalveren vormen per jaar in Nederland via hun mest een grote emissiebron van beide protozoa, namelijk naar schatting 1,5 m 10 tot de zestinede macht oocysten van Cryptosporidium en 2,8 m 10 tot de vijftiende macht cysten van Giardia. In mest van melkkoeien zijn ook Giardia-cysten aangetoond, maar deze emissiebron is onvoldoende gekwantificeerd. Cryptosporidium werd in mest van melkkoeien niet aangetoond. Cryptosporidium en Giardia zijn niet in mest van vleeskuikens aangetoond, derhalve levert deze mest waarschijnlijk geen bijdrage van betekenis. Legkippen vormen een belangrijke emissiebron voor Cryptosporidium. Echter, dit zou Cryptosporidium baileyi, welke niet zoonotisch is, kunnen zijn, maar de species is in deze studie niet getypeerd. Giardia werd in mest van legkippen niet aangetoond. Slachthuisafvalwater van runderen, varkens en pluimvee levert geen bijdrage van betekenis aan de lozing van Cryptosporidium en Giardia op het oppervlaktewater. Op basis van het onderzoek aan kalvergier werd een hoge emissie van Cryptosporidium en Giardia door vleeskalveren berekend. Hoewel emissie van Cryptosporidium en Giardia vooral via de mest van vleeskalveren aanzienlijk is, kan nog niets worden gezegd over de werkelijke bijdrage aan de lozing van deze protozoa op het oppervlaktewater.In this study, the relative contributions of the pathogenic protozoa Cryptosporidium and Giardia by manure of farm animals in The Netherlands to the total yearly environmental load was studied. Manure of veal calves forms a very large source of Cryptosporidium (1.5 m 10 square 16 oocysts per year) and of Giardia (2.8 m 10 square 15 cysts per year). The contribution of manure from dairy cattle to the emission of protozoa into the environment is uncertain. Manure of commercial egg layers forms a large source of Cryptosporidium. However, the species may be Cryptosporidium baileyi, which is not zoonotic, but the species has not been confirmed. The contribution of wastewater from slaughterhouses for cattle, pigs and poultry to discharges of Cryptosporidium and Giardia into surface water has been found to be negligible. Based on emission via slurry from calves, a high emission of Cryptosporidium and Giardia by veal calves was calculated. Although manure of veal calves form a large source of Cryptosporidium and Giardia, their actual contribution to the load to surface water is still unknown.DGM-DW
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