83 research outputs found
On metabolic networks and multi-omics integration
No full text<p>Cellular metabolism is a highly complex chemical system, involving thousands of interacting metabolites and reactions. The traditional approach to understanding metabolism has been that of reductionism; by isolating and carefully measuring the involved components, the goal has been to understand the whole as the sum of its parts. This reductionist approach has successfully identified most of the components of metabolism but, unfortunately, it fails to capture the long-range and complex interactions that are essential for the functionality. Systems biology is an emerging research field which uses high-throughput data generation and mathematical modelling in order to apply a holistic, or network-centric, view on metabolism. One type of modelling framework, which is in line with this thinking, is genome-scale metabolic modelling. These models, called GEMs, represent very valuable resources, but their applications have been limited due to the large manual effort required to reconstruct them. In this project, we have developed algorithms and software for streamlining the reconstruction process, as well as for novel applications of GEMs. More specifically, we here present: the RAVEN Toolbox, a software suite for automated reconstruction and quality control; the INIT algorithm, an algorithm for inferring GEMs for human cell types; an algorithm which integrates fluxomics and transcriptomics data in order to identify transcriptionally controlled metabolic reactions.</p>
<p>The methods and software were used in a number of case studies to address real biological questions. These studies were: 1) Metabolic engineering of <i>Saccharomyces cerevisiae</i> for succinic acid overproduction. The predictions from the modelling were successfully validated experimentally. 2) Study of metabolic regulation in <i>S. cerevisiae</i>. This led to the identification of a small number of transcription factors and enzymes which were predicted to be controlling central parts of metabolism. 3). Penicillin production in <i>Penicillium chrysogenum</i>. This led to the reconstruction of the first GEM for <i>P. chrysogenum</i>, an important resource in itself, and to identification of metabolic engineering targets for more efficient production of penicillin. 4) Human cancer metabolism. This led to the identification of metabolic subnetworks which were predicted to be significantly more active in cancers, and to identification of potential drug targets for treatment. 5) Lipid metabolism in obesity. This led to new insights into the large-scale metabolic rearrangements associated with obesity, and to identification of possible therapeutic strategies. 6) Metabolism in non-alcoholic fatty liver disease. This led to the identification of serine deficiency as a central aspect of the disease, and to proposed therapeutic strategies for remedying it.</p>
<p>The work put forward in this thesis has resulted in improvements on several important aspects of genome-scale metabolic modelling, and it has shown how the framework can be applied to gain novel biological insights. As such, it can contribute to further increase the role of the framework in modelling of human health and disease.</p
Optimerad rendering av fluid meshes
No full textSimuleringen av vätskor är idag en viktig del inom både film-, spel- och reklamindustrin. Detta kräver dock mycket av hårdvaran vilket saktar ner processen att rendera markant. I detta projekt forskades det inom optimering av renderingstekniker för att göra det lättare att rendera fram kvalitativa resultat när man använder sig av fluids i program för 3D-grafik. Arbetet innehåller en undersökning där testpersoner bedömt ett antal renderingar samt de optimerade inställningar som används till renderin
On metabolic networks and multi-omics integration [Elektronisk resurs]
No full textCellular metabolism is a highly complex chemical system, involving thousands of interacting metabolites and reactions. The traditional approach to understanding metabolism has been that of reductionism; by isolating and carefully measuring the involved components, the goal has been to understand the whole as the sum of its parts. This reductionist approach has successfully identified most of the components of metabolism but, unfortunately, it fails to capture the long-range and complex interactions that are essential for the functionality. Systems biology is an emerging research field which uses high-throughput data generation and mathematical modelling in order to apply a holistic, or network-centric, view on metabolism. One type of modelling framework, which is in line with this thinking, is genome-scale metabolic modelling. These models, called GEMs, represent very valuable resources, but their applications have been limited due to the large manual effort required to reconstruct them. In this project, we have developed algorithms and software for streamlining the reconstruction process, as well as for novel applications of GEMs. More specifically, we here present: the RAVEN Toolbox, a software suite for automated reconstruction and quality control; the INIT algorithm, an algorithm for inferring GEMs for human cell types; an algorithm which integrates fluxomics and transcriptomics data in order to identify transcriptionally controlled metabolic reactions.The methods and software were used in a number of case studies to address real biological questions. These studies were: 1) Metabolic engineering of Saccharomyces cerevisiae for succinic acid overproduction. The predictions from the modelling were successfully validated experimentally. 2) Study of metabolic regulation in S. cerevisiae. This led to the identification of a small number of transcription factors and enzymes which were predicted to be controlling central parts of metabolism. 3). Penicillin production in Penicillium chrysogenum. This led to the reconstruction of the first GEM for P. chrysogenum, an important resource in itself, and to identification of metabolic engineering targets for more efficient production of penicillin. 4) Human cancer metabolism. This led to the identification of metabolic subnetworks which were predicted to be significantly more active in cancers, and to identification of potential drug targets for treatment. 5) Lipid metabolism in obesity. This led to new insights into the large-scale metabolic rearrangements associated with obesity, and to identification of possible therapeutic strategies. 6) Metabolism in non-alcoholic fatty liver disease. This led to the identification of serine deficiency as a central aspect of the disease, and to proposed therapeutic strategies for remedying it.The work put forward in this thesis has resulted in improvements on several important aspects of genome-scale metabolic modelling, and it has shown how the framework can be applied to gain novel biological insights. As such, it can contribute to further increase the role of the framework in modelling of human health and disease
Dan Andersson
No full textSpecial feature issue on the Swedish author Dan Andersson, with articles by Anders Hallengren, Nisse Munck, Lars Furuland, Lars Järnemo (2), Gösta Ågren, Inge Mattsson, Arne Säll, and Bure Holmbäck.</p
Suppression of cation intermixing highly boosts the performance of core-shell lanthanide upconversion nanoparticles
No full textThis folder contains all raw data underlying the results presented in a manuscript, submitted to Journal of American Chemistry Society, and entitled:
Suppression of cation intermixing highly boosts the performance of core-shell lanthanide upconversion nanoparticles
Authored by:
Fuhua Huang2,3, Niusha Bagheri1, Li Wang *2,3, Hans Ågren*2,3, Jinglai Zhang*2,3, Jerker Widengren1, Haichun Liu*1
1 Department of Applied Physics, KTH Royal Institute of Technology, S-10691, Stockholm, Sweden
2 College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan 475004, P. R. China
3 Henan Center for Outstanding Overseas Scientists, Henan University, Kaifeng 475004, P. R. China
*Corresponding author: E-mail: [email protected]
Data files containing the raw data and the results of the analysis are grouped according to the order of the figures in the manuscript.
ABSTRACT
Lanthanide upconversion nanoparticles (UCNPs) have been extensively explored as biomarkers, energy transducers and information carriers in wide-ranging applications in areas from healthcare and energy to information technology. In boosting the brightness and enriching the functionalities of UCNPs, core-shell structural engineering has been well established as an important approach. Despite its importance, a strong limiting issue has been identified, namely cation intermixing in the interfacial region of the synthesized core-shell nanoparticles. Currently there still exists confusion regarding this destructive phenomenon and there is still a lack of facile means to reach a delicate control of it. By means of a new set of experiments, we provide in this work a clear picture for the physical mechanism of cation intermixing occurring in core-shell UCNPs, i.e. partial or substantial core nanoparticle dissolution followed by epitaxial growth of the outer layer and ripening of the entire particle. Based on this picture, we provide an easy but effective approach to tackle this issue that enables producing UCNPs with highly boosted optical properties.
*Corresponding authors.
E-mail addresses:[email protected] (H. Liu), [email protected] (H. Ågren), [email protected] (L. Wang), [email protected] (J. Zhang
Närvarodetektering i pool
No full textThis Bechelor thesis is written on behalf of Verisure Innovation AB in Mamö, Sweden. The authors were studying Bachelors of Sience in Electrical Engineering with focus on automation at Lunds Tekniska Högskola, Campus Helsingborg. The main goal of the thesis was to develop a prototype of an alarmsystem for domestic swimming pools. The system was supposed to sound an alarm if a human being or animal were to fall in to the pool. If the prototype was a success the company could decide later if they wanted to proceed with the development of the product and add it to their product catalog. The first thing that was done was to study what kind of sensors, and thereby also which physical phenomena that could be used. After this a short survey of available pool alarms were conducted, the advantages and disadvantages of the products were analyzed. Two alarms were selected and tested to determine their functionality. The developed device consisted of the parts; the sensors, the hardware and the detection algorithm. The sensors that were chosen where piezotranducers, the hardware was composed of two amplifiers and a developmentboard from STmicroelectronics with a ARM-Cortex M4 processor. The software was developed in an onlinecompiler, “mbed” The software controlled the signals that were sent to and received by the sensors; the received signals were first digitalized in an ADC and later run through a detection algorithm to determine if the device should sound the alarm
Fastq files for the NBIS Tools for Reproducible Research course
No full textBackup in case SRA Tools doesn't work
(In)visible bodies : An Anthropological Study on Systematic Ableism, Embodiment, and Identity
No full textUppsala is the fourth biggest city in Sweden and is known for having a rich cultural life, beautiful landscapes, and a long history. Because of how Uppsala is built, infrastructure and urban planning limit people with mobility restrictions from being able to access shops, and well-visited locations due to the absence of accessibility adjustments or poorly constructed routes. This ethnographic study takes a phenomenological approach to emphasize the experiences and perspectives of those affected by mobility restrictions and those who feel peripheral in society in multiple areas, ranging from infrastructure to social stigma due to a society built upon systematic ableism. The thesis thus explores the body as a symbol and the experience of being (in)visible. The physical body's presence is acknowledged while the stigma of being disabled, and the social and environmental barriers one encounters when navigating public areas designed for normative bodies, remain invisible.Keywords: Embodiment, ableism, impairments, identity, agency
(In)visible bodies : An Anthropological Study on Systematic Ableism, Embodiment, and Identity
No full textUppsala is the fourth biggest city in Sweden and is known for having a rich cultural life, beautiful landscapes, and a long history. Because of how Uppsala is built, infrastructure and urban planning limit people with mobility restrictions from being able to access shops, and well-visited locations due to the absence of accessibility adjustments or poorly constructed routes. This ethnographic study takes a phenomenological approach to emphasize the experiences and perspectives of those affected by mobility restrictions and those who feel peripheral in society in multiple areas, ranging from infrastructure to social stigma due to a society built upon systematic ableism. The thesis thus explores the body as a symbol and the experience of being (in)visible. The physical body's presence is acknowledged while the stigma of being disabled, and the social and environmental barriers one encounters when navigating public areas designed for normative bodies, remain invisible.Keywords: Embodiment, ableism, impairments, identity, agency
Slides for NBIS Tools for Reproducible Research (Stockholm, March 2018)
No full textSlides for NBIS Tools for Reproducible Research (Stockholm, March 2018
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