189 research outputs found
An integrated model quantitatively describing metabolism, growth and cell cycle in budding yeast
No full textComputational models are expected to increase understanding of how complex biological functions arise from the interactions of large numbers of gene products and biologically active low molecular weight molecules. Recent studies underline the need to develop quantitative models of the whole cell in order to tackle this challenge and to accelerate biological discoveries. In this work we describe three major functions of a yeast cell: Metabolism, Growth and Cycle, through two coarse grain models, MeGro (Metabolism + Growth) and GroCy (Growth + Cycle). GroCy effectively recapitulates major phenotypic properties of cells grown in glucose and ethanol supplement media. MeGro can act as a parameter generator for GroCy. The resulting iMeGroCy integrated model can be used as a scaffold for molecularly detailed models of yeast functions.</p
WortelLab/EvoCoexistenceFluctuations: Publication version for "Evolutionary coexistence in a fluctuating environment by specialization on resource level"
No full textCode to generate all images and analyses for the paper "Evolutionary coexistence in a fluctuating environment by specialization on resource level" published in the Journal of Evolutionary Biology in 2023
Emancipation in the net : theatre spectators and the "agency" of network
No full textIn a lecture given during the 49th Counterpoint Review of Small Theatrical Forms in Szczecin, Meike Wagner focuses on the emancipation of the theater viewer and the “agency of the Web.” The author's point of departure are some of Jacques Rancière's theses concerning the viewer as a “storyteller” and a “translator,” as well as a theory of the Internet by Bruno Latour. Using these concepts, Wagner performs an insightful analysis of the audience protests at Covent Garden in 1809 (the Old Price Riots) and the Situation Rooms project (2013) by the Rimini Protokoll group. The author considers the course and efficiency of the emancipation process in institutionalized theaters open to this sort of initiative, or the contrary, those which block the viewers' striving toward freedom
Scholarly Rights and Responsibilities in the Digital Age
No full textThis panel discussion session was about author and creator rights from the faculty and graduate student perspective. John Willinsky is a Khosla Family Professor of Education at Stanford University, as well a part-time professor in the UBC Faculty of Education. Reilly Yeo has an MA in comparative politics from McGill University and is currently pursuing an academic career in literature, in addition to her role as a Strategic Consultant with OpenMedia.ca and coordinating social media for the Red Tent campaign. She is a specialist in online communications on complex issues. Meike Wernicke is an SFU graduate with an M.A. in French linguistics currently pursuing a doctoral degree in the Department of Language and Literacy Education at UBC. Her research focuses on multi- and plurilingualism, French language education in Canada, and language teacher professional development. Meike heads the German Department at Capilano University and teaches in the French language MEd cohort program at UBC. This session took place on October 20, 2010 in the Lillooet Room of the Irving K. Barber Learning Centre at the University of British Columbia.Education, Faculty ofOther UBCNon UBCLanguage and Literacy Education (LLED), Department ofUnreviewedOthe
Evolutionary coexistence in a fluctuating environment by specialization on resource level
No full textMicrobial communities in fluctuating environments, such as oceans or the human gut, contain a wealth of diversity. This diversity contributes to the stability of communities and the functions they have in their hosts and ecosystems. To improve stability and increase production of beneficial compounds, we need to understand the underlying mechanisms causing this diversity. When nutrient levels fluctuate over time, one possibly relevant mechanism is coexistence between specialists on low and specialists on high nutrient levels. The relevance of this process is supported by the observations of coexistence in the laboratory, and by simple models, which show that negative frequency dependence of two such specialists can stabilize coexistence. However, as microbial populations are often large and fast growing, they evolve rapidly. Our aim is to determine what happens when species can evolve; whether evolutionary branching can create diversity or whether evolution will destabilize coexistence. We derive an analytical expression of the invasion fitness in fluctuating environments and use adaptive dynamics techniques to find that evolutionarily stable coexistence requires a special type of trade-off between growth at low and high nutrients. We do not find support for the necessary evolutionary trade-off in data available for the bacterium Escherichia coli and the yeast Saccharomyces cerevisiae on glucose. However, this type of data is scarce and might exist for other species or in different conditions. Moreover, we do find evidence for evolutionarily stable coexistence of the two species together. Since we find this coexistence in the scarce data that are available, we predict that specialization on resource level is a relevant mechanism for species diversity in microbial communities in fluctuating environments in natural settings
Eco-evolutionary Red Queen dynamics regulate biodiversity in a metabolite-driven microbial system
No full textThe Red Queen Hypothesis proposes that perpetual co-evolution among organisms can result from purely biotic drivers. After more than four decades, there is no satisfactory understanding as to which mechanisms trigger Red Queen dynamics or their implications for ecosystem features such as biodiversity. One reason for such a knowledge gap is that typical models are complicated theories where limit cycles represent an idealized Red Queen, and therefore cannot be used to devise experimental setups. Here, we bridge this gap by introducing a simple model for microbial systems able to show Red Queen dynamics. We explore diverse biotic sources that can drive the emergence of the Red Queen and that have the potential to be found in nature or to be replicated in the laboratory. Our model enables an analytical understanding of how Red Queen dynamics emerge in our setup, and the translation of model terms and phenomenology into general underlying mechanisms. We observe, for example, that in our system the Red Queen offers opportunities for the increase of biodiversity by facilitating challenging conditions for intraspecific dominance, whereas stasis tends to homogenize the system. Our results can be used to design and engineer experimental microbial systems showing Red Queen dynamics
Metabolic shifts: A fitness perspective for microbial cell factories
No full textPerformance of industrial microorganisms as cell factories is limited by the capacity to channel nutrients to desired products, of which optimal production usually requires careful manipulation of process conditions, or strain improvement. The focus in process improvement is often on understanding and manipulating the regulation of metabolism. Nonetheless, one encounters situations where organisms are remarkably resilient to further optimization or their properties become unstable. Therefore it is important to understand the origin of these apparent limitations to find whether and how they can be improved. We argue that by considering fitness effects of regulation, a more generic explanation for certain behaviour can be obtained. In this view, apparent process limitations arise from trade-offs that cells faced as they evolved to improve fitness. A deeper understanding of such trade-offs using a systems biology approach can ultimately enhance performance of cell factories.BiotechnologyApplied Science
Reuse of scrap wood: in a building product
No full textClimate is changing. The average temperature on earth is rising due to excessive emissions of greenhouse gasses such as CO2. In the meantime the economy is a linear economy where a produced from exhaustive materials are consumed and turned into waste. In order to fight climate change and exhaust the earth less the greenhouse gas emissions need to decrease and less waste needs to be produced. The government has set goals to have a circular economy by 2050. A circular economy means the elimination of waste, instead all materials are reused and recycled to its final potential and new materials come from renewable sources.One commonly used renewable material in the built in environment is wood. Besides, wood sequesters CO2, has a low environmental impact and can be reused and recycled. When more wood is used and forests keep growing, more CO2 is sequestered, especially when it is substituted for product that emit a lot of CO2. Wood can so contribute to the overall decrease in CO2 emissions.But at the moment there is also a huge waste production of wood, with a annually production of 1,8 Mton waste wood, of which 435 kton is scrap wood (waste wood from the construction and demolition industry) (Sloopcheck, 2021). Most is incinerated or otherwise recycled. Only a small portion is reused. In order to contribute to the circular economy goals scrap wood should therefore be reused and recycled. This thesis aims to research why the portion of reusing scrap wood is so small and tries to find a suitable building product to show that scrap wood can and should be reused. The suitable building product is CLT, due to the used lamellae consisting of varying dimensions, mechanical properties and possibly wood species. This research shows that scrap wood can be implemented into scrap wood, although the portion of scrap wood into a panel depends on the availability of certain required properties. The substitution of scrap wood in CLT panels always results in extra CO2 savings, and therefore the reuse of scrap wood into CLT panels can contribute to reducing CO2 emissions.Architecture, Urbanism and Building Sciences | Building Technology | Sustainable Desig
Designing SeaBubble docks: A handbook for guidance on the design process for a SeaBubble dock
No full textThe project that is performed is for the master thesis of the master study ‘Integrated Product Design’ at the faculty of Industrial Design Engineering at the TU Delft. The final product is a handbook that functions as a tool to create a dock for SeaBubbles, and it is developed for the company Advier. The process started with exploring the scope. The scope can be split up in three directions: the business direction in which the company Advier and its stakeholders is analysed. It becomes clear that Advier will give the handbook to a design agency that will create the actual dock design. The second direction is the analysis of the location. The network is situated in the area of Dordrecht, also known as Drechtsteden. The effect of the weather and tide on this area is analysed and the conclusion is drawn that the design of the dock must deal with changing water levels. The third direction focuses on the SeaBubble, in which the SeaBubble for seven passengers and twelve passengers are presented. The reservation system is mapped out and shows that the SeaBubble will define its route on the demand, in between it is possible that the SeaBubble will change its route. This has a large impact on the passenger journey. In the passenger journey, two types of passengers are presented: a prepared and an unprepared passenger. The prepared passenger has bought a ticket at home, while the unprepared passenger must buy a ticket at the dock. From this point in the process, the focus will be on the experience of the passenger. By creating a building that fulfils the needs of the passenger when the passenger is being guided, is waiting, and is boarding, the experience of the passenger will be good. The next part that is being analysed is the elements that is needed for guiding, waiting and boarding. For guiding, first the crowd flow is analysed. Based on this crowd flow, a general layout of the building is created for the location of ticket vending machines, waiting areas and potential one-way systems. Secondly, the needed information is analysed and tested in an online 3D environment. The location and the initial way of communication for several information elements is determined. For waiting, literature is analysed, and people are interviewed and observed. The passengers will find distraction on a smartphone or while enjoying the view, having a seat is preferred. For creating a comfortable boarding experience, two supports are needed in an area with even floor and no gaps. By getting inspired from the results, different configurations of docks were created. By determining the principles behind the configurations, the design choices are mapped out. These design choices are structured with a morphological map and explained in the handbook, which is the final product of this master thesis. After finalising the handbook, interviews were held with the client and an architect to evaluate the final product.Integrated Product Desig
Low affinity uniporter carrier proteins can increase net substrate uptake rate by reducing efflux
No full textMany organisms have several similar transporters with different affinities for the same substrate. Typically, high-affinity transporters are expressed when substrate is scarce and low-affinity ones when it is abundant. The benefit of using low instead of high-affinity transporters remains unclear, especially when additional nutrient sensors are present. Here, we investigate two hypotheses. It was previously hypothesized that there is a trade-off between the affinity and the catalytic efficiency of transporters, and we find some but no definitive support for it. Additionally, we propose that for uptake by facilitated diffusion, at saturating substrate concentrations, lowering the affinity enhances the net uptake rate by reducing substrate efflux. As a consequence, there exists an optimal, external-substrate-concentration dependent transporter affinity. A computational model of Saccharomyces cerevisiae glycolysis shows that using the low affinity HXT3 transporter instead of the high affinity HXT6 enhances the steady-state flux by 36%. We tried to test this hypothesis with yeast strains expressing a single glucose transporter modified to have either a high or a low affinity. However, due to the intimate link between glucose perception and metabolism, direct experimental proof for this hypothesis remained inconclusive. Still, our theoretical results provide a novel reason for the presence of low-affinity transport systems
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