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Exact Biology in Progress

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Displaying theses 1-10 of 26 total
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E.S. Deutekom
Bachelor programme: Bio-exact August 9th, 2012
Institute: SILS Research group: Biosystems Data Analysis Graduation thesis Supervisor: Age K. Smilde
The NutriGUI, a Graphical User Interface for Nutrikinetics
The NutriGUI is a Graphical User Interface which incorporates Nutrikinetics. A Graphical User interface is a program, where students can interactively use buttons and sliders to make their own scientific data. Students will then be able to evaluate this data and learn the concepts of Nutrikinetics. Nutrikinetics investigates the disposition of food compounds in the human body and this is important to understand how food works inside the body.
picture that illustrates the research done
Scientific abstract (docx 14K)   Full text (pdf 2748K)

R. de Leeuw
Bachelor programme: Bio-exact August 1st, 2012
Institute: SILS Research group: Epigenetic regulation of gene expression Graduation thesis Supervisor: Paul Fransz
Obtaining recombinant mammalian cell lines with continuous and high protein expression levels
It is an interesting challenge to produce a recombinant protein in mammalian cell lines. In this research, this is done by creating a stringent selection system and augmenting DNA elements that are known to enhance protein expression.
picture that illustrates the research done
Scientific abstract (docx 14K)   For more info or full text, mail to:

W.W. Woud
Bachelor programme: Bio-exact July 4th, 2012
Institute: SILS Research group: Mass spectrometry of biomacromolecules Graduation thesis Supervisor: Chris de Koster
A mathematical model for estimating anaerobic synthesis rate constants for Escherichia coli proteins.
The aim of my research was to build a mathematical model which can be used to estimate reaction rate constants of both synthesis and degradation as well as half-lifes of given proteins. The mathematical model has been created using the computer program MatLab® and uses a proteomic data set as input. Whilst our model can be used to estimate both reaction rate constants and half-lifes, my paper will only discuss the part of the model which estimates the anaerobic reaction rate constants.
picture that illustrates the research done
Scientific abstract   Full text (doc 497K)

F.A.M.C. Mayr
Bachelor programme: Bio-exact August 22nd, 2011
Institute: SILS Research group: Microarray Department Graduation thesis Supervisor: Martijs Jonker
photo of the author
Transcriptome analysis of short read Illumina RNA sequencing: investigating baseline variability in gene expression levels and splice variants among human brain and Lymphoblastoid samples
Understanding baseline variability in gene expression levels and splice variants is essential for interpreting many studies. Although recent advances in RNA sequencing enable the analyses of transcript variation at unprecedented resolution, not much effort has been done to assess baseline variation between individuals. Biological variability in gene expression has been shown not to be eliminated by sequencing technology and we show the same accounts to splice variation. We analyzed RNA-seq data from two studies using sufficient biological variants (replicates). We find for the Cerebellum tissue samples (brain) little differential expression of genes and splice variants. Also we find ~75% of the differentially expressed genes are differentially expressed by one of the samples. Although these can be biologically functional, they can also possibly represent baseline variance of the Cerebellum cells. In contrast to Cerebellum cells, we find many differentially expressed genes and a large variation in differentially expressed splice variants for Lymphoblastoid cell-line samples (lymph nodes). We find three samples of the pool of samples to be very much alike and could be annotated as a subgroup. As Lymphoblastoid cells are stem-cell like that differentiate into three subgroups (B lymphocytes, T lymphocytes and Natural Killer cells). Our results enforce significant use of biological replicates. The desired saturation level, which is partial to sample type, should be taken into account before deciding the sequencing depth.
picture that illustrates the research done
Scientific abstract (doc 31K)   Full text (pdf 866K)

M. Hijdra
Master programme: Communicatieve en Educatieve variant (CE) July 1st, 2011
Institute: Other Research group: none Literature thesis Supervisor: P.P.M. Molenaar
Studie over de overgang naar de 2e fase voor het vak biologie op VWO niveau, Aanbevelingen op onderwijskundig en competentiegericht niveau
In this study my research was about the transition of the lower classes in hoghschool to the higher classes. (VWO - Biology). Some recommendation were made for improvement of students results
picture that illustrates the research done
Scientific abstract   For more info or full text, mail to:

K.R. Schoofs
Bachelor programme: Bio-exact June 27th, 2011
Institute: SILS Research group: Nuclear Organization Group Graduation thesis Supervisor: Mariliis Tark-Dame and Roel van Driel
Chromatin folding in the interphase nucleus observed using fluorescence in situ hybridization
Human chromosomes are not randomly distributed in the cell nucleus, but there is some sort of organization. Chromatin organization plays an important role in gene activity: the way it is folded can activate or repress certain genes. The principles of this folding are not fully understood yet, because the chromatin fibre cannot be visualized and followed directly. Indirect methods like 3C have been used to investigate chromatin-chromatin interactions and models of human loci have been proposed. Although 3C and derivatives are able to give insight into the folding, it is using millions of cells resulting in averaged model of many cells. Therefore, FISH has the advantage of visualizing one single cell at the time. In this study, the main principles of chromatin organization are studied with FISH. Five probes from chromosome 1 have been chosen from an region of low gene density to study chromatin folding. The probes were labeled directly with fluorophore in order to make them visible under the microscope. The aim was to visualize all probes simultaneously. Initially, the FISH protocol did not work, so the procedure has been optimized by experimenting with the three main steps of FISH: permeabilization, denaturing time and the washing. Eventually, harsher permeabilization conditions and a longer denaturing time have been used to visualize three probes at the same time.
picture that illustrates the research done
Scientific abstract (docx 11K)   For more info or full text, mail to:

F.S. Peters
Bachelor programme: Bio-exact June 4th, 2011
Institute: Other Research group: Nederlands Kanker Instituut Graduation thesis Supervisor: Waseem Akhtar
The development of a tethering system to study the direct effects of long non-coding RNAs on gene expression and chromatin structure
A tethering system is established to recruit lncRNAs to specific places in the genome and then effects on gene expression can be studied. It is done by cloning different plasmids and transfecting these in mouse embryonic stem cells. Gene expression levels are measured by RT-qPCR;.
picture that illustrates the research done
Scientific abstract (doc 30K)   For more info or full text, mail to:

M. Hijdra
Master programme: Communicatieve en Educatieve variant (CE) April 22nd, 2011
Institute: Other Research group: none Graduation thesis Supervisor: E. Joling
Master thesis VeenLanden College, Mijdrecht
In this thesis i wrote about my development as a teacher during my internship at the highschool: VeenLanden College. I proved why i am worthy of being a teacher
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Scientific abstract   For more info or full text, mail to:

G. Schutten
Bachelor programme: Bio-exact September 30th, 2010
Institute: SILS Research group: Molecular Microbial Physiology Graduation thesis Supervisor: Klaas Jan Hellingwerf
Cyanobacteria, How to survive the night
A study about the concentrations of Glycogen under different day/night cycles, and what the influence of PixD on these concentrations is.
picture that illustrates the research done
Scientific abstract (pdf 729K)   Full text (pdf 729K)

Karen van Meeteren
Bachelor programme: Bio-exact August 17th, 2010
Institute: AMSTEL Research group: AMSTEL Graduation thesis Supervisor: Dr. N. Brouwer
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Peer feedback in Higher Science Education
In science research, review between peers (colleagues in the same area of interest) is commonly used to check papers that will be published in science journals. In higher education this is called peer feedback in which students assess each other’s reports or presentations. In this research we looked at how many lecturers actually use peer feedback in their education, what the quality is of peer feedback, how serious students handle peer feedback, what they actually do with the received peer feedback and if there is any effect on their study success and behavior.
picture that illustrates the research done
Scientific abstract (pdf 22K)   Full text (pdf 1206K)

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