Dissertations / Theses: 'Biological Science'

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Shih, Yu-Keng. "Identifying Protein Functions and Biological Systems through Exploring Biological Networks." The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1388676152.

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Holden, Matthew Alexander. "Studies in biological surface science: microfluidics, photopatterning and artificial bilayers." Diss., Texas A&M University, 2004. http://hdl.handle.net/1969.1/458.

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Herein is presented the collective experimental record of research performed in the Laboratory for Biological Surface Science. These investigations are generally classified under the category of bioanalytical surface science and include the following projects. Chapters III and IV describe the creation of a microfluidic device capable of generating fixed arrays of concentration gradients. Experimental results were matched with computational fluid dynamics simulations to predict analyte distributions in these systems. Chapters V and VI demonstrate the discovery and utility of photobleaching fluorophores for micropatterning applications. Bleached fluorophores were found to rapidly attach to electron rich surfaces and this property was used to pattern enzymes inside microfluidic channels in situ. Finally, Chapter VII exhibits a method by which solid supported lipid bilayers can be dried and preserved by specifically bound proteins. The intrinsic property of lateral lipid mobility was maintained during this process and a mechanism by which the protein protects the bilayer was suggested.

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Fattah, Zahra Ali. "Applications of bipolar electrochemistry : from materials science to biological systems." Phd thesis, Université Sciences et Technologies - Bordeaux I, 2013. http://tel.archives-ouvertes.fr/tel-00917770.

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Bipolar electrochemistry deals with the exposure of an isolated conducting substrate that has no direct connection with a power supply except via an electric field. Therefore it can be considered as a "wireless technique". The polarization of the substrate with respect to the surrounding medium generates a potential difference between its opposite ends which can support localized electrochemical oxidation reduction reactions and break the surface symmetry of the substrate. The method was applied in the present thesis to materials science and biological systems. In the frame of designing asymmetric particles, also called "Janus" particles, bipolar electrochemistry was adapted for the bulk preparation of these objects. Conductive substrates with different nature, sizes and shapes have been modified with various materials such as metals, ionic and inorganic compounds using this approach. Moreover, a control over the deposit topology could be achieved for substrates at different length scales. Bipolar electrodeposition is also a good tool for investigating the generation of different metal morphologies. Further developments in the bipolar setup allowed us to use the technology for microstructuration of conductive objects. Furthermore the concept has shown to be very useful in the field of the induced motion of particles. The asymmetric objects that have been prepared by bipolar electrodeposition were employed as microswimmers which could show both translational and rotational motion. The application of electric fields in the bipolar setup can be used for the direct generation of motion of isotropic objects through bubble generation. A levitation motion of objects combined with light emission was possible using this concept. Finally, bipolar electrochemistry was also used for studying the intrinsic conductivity of biological molecules (DNA), which is of great importance in the nanotechnology.

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Shepard, Pamela Ann. "The Use of Part-Time Faculty in Associate Degree Nursing, Social Science, and Biological Science Programs." Thesis, University of North Texas, 1990. https://digital.library.unt.edu/ark:/67531/metadc332403/.

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This study surveyed the opinions of academic administrators of associate degree nursing programs, community college social science programs, and community college biological science programs regarding major benefits and concerns associated with the employment of part-time faculty. This study found that most part-time social science faculty teach in the classroom, half participate in non-teaching faculty activities, and most are paid a contract amount per course or credit hour. Part-time biological science faculty differed only in that most teach a combination of classroom and lab/practicum. Part-time nursing faculty differed in all three areas. Most part-time nursing faculty teach in lab or practicum settings, most participate in more non-teaching activities than other part-time faculty, and most are paid an hourly wage. However, the benefits and concerns associated with the employment of part-time nursing faculty were not significantly different from those identified by academic administrators of the other programs with one exception. Academic administrators felt that part-time nursing faculty expose students to the latest technologies in specialty areas and part-time social science faculty do not. The benefits cited by the respondents, that were in addition to the benefits most frequently cited in the literature, include increased interaction with the community and the ability to "try out" prospective full-time faculty. The concerns cited by respondents, that were in addition to the concerns most frequently cited in the literature, include the inability to find qualified part-time faculty to fill available positions and the concern that the employment of part-time faculty causes resentment among full-time faculty. The results from this study indicate that the literature pertaining to the benefits and concerns associated with the employment of social science and biological science part-time faculty in community colleges can be used to develop policies regarding part-time faculty in associate degree nursing programs.

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Barsotti, Robert J. Jr. "Nanomanufacturing for biological sensing applications." Thesis, Massachusetts Institute of Technology, 2007. http://hdl.handle.net/1721.1/38588.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Materials Science and Engineering, 2007.
"February 2007."
Includes bibliographical references (leaves 219-226).
Over the past 10-15 years, there have been tremendous research efforts in the synthesis of nanomaterials with unique electronic properties. Much less work, however, has focused on the incorporation of the nanomaterials into electronic devices. In order for nanomaterials to have a technological impact in electronic devices, nanomanufacturing techniques must be established for the reliable and reproducible creation of devices with nanomaterials as the active component. In this thesis, the incorporation of 3-20 nm diameter ligand coated gold nanoparticles into an electronic device is studied. Ligand coated nanoparticles provide great control over their solubility and electronic properties through the choice of protecting ligand molecule. The use of an isolated nanoparticle in electronic devices presents two major difficulties which are studied in detail in this work. In order to use the electrical properties of a single particle or a few particles, insulating gaps in metallic electrodes must be fabricated with dimensions of 5-50 nm. Several methods including direct patterning with electron beam lithography, physical methods of gap formation, and electrical methods of gap formation are described, studied and evaluated for use in nanomanufacturing.
(cont.) A second major challenge is the specific assembly of nanoparticles into the nanogaps. The use of chemically directed assembly to pattern particles on templates generated by Dip Pen Nanolithography is described using several different surface chemistries. An electrical based method, dielectrophoresis, is found to be better suited for assembly of particles into the gaps and the forces which affect assembly are studied in detail. Electrical characterizations of networks of 10-200 nanoparticles are studied as a function of protecting ligand molecule. Preliminary results on the use of nanomanufactured devices consisting of gold nanoparticles-oglionucleotide conjugates bridging a nano-gap for DNA sensing are presented.
by Robert J. Barsotti, Jr.
Ph.D.

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SCARDONI, Giovanni. "Computational Analysis of Biological networks." Doctoral thesis, Università degli Studi di Verona, 2010. http://hdl.handle.net/11562/343983.

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Caratterizzare, descrivere ed estrarre informazioni da un network, è sicuramente uno dei principali obbiettivi della scienza, dato che lo studio dei network interessa differenti campi della ricerca, come la biologia, l'economia, le scienze sociali, l'informatica e così via. Ciò che si vuole è riuscire ad estrarre le proprietà fondamentali dei network e comprenderne la funzionalità. Questa tesi riguarda sia l'analisi topologica che l' analisi dinamica dei network biologici, anche se i risultati possono essere applicati a diversi campi. Per quanto riguarda l'analisi topologica viene utilizzato un approccio orientato ai nodi, utilizzando le centralità per individuare i nodi più rilevanti e integrando tali risultati con dati da laboratorio. Viene inoltre descritto CentiScaPe, un software implementato per effettuare tale tipo di analisi. Vengono inoltre introdotti i concetti di "interference" e "robustness" che permettono di comprendere come un network si riarrangia in seguito alla rimozione o all'aggiunta di nodi. Per quanto riguarda l'analisi dinamica, si mostra come l'abstract interpretation può essere utilizzata nella simulazione di pathways per ottenere i risultati di migliaia di simulazioni in breve tempo e come possibile soluzione del problema della stima dei parametri mancanti.
This thesis, treating both topological and dynamic points of view, concerns several aspects of biological networks analysis. Regarding the topological analysis of biological networks, the main contribution is the node-oriented point of view of the analysis. It means that instead of concentrating on global properties of the networks, we analyze them in order to extract properties of single nodes. An excellent method to face this problem is to use node centralities. Node centralities allow to identify nodes in a network having a relevant role in the network structure. This can not be enough if we are dealing with a biological network, since the role of a protein depends also on its biological activity that can be detected with lab experiments. Our approach is to integrate centralities analysis and data from biological experiments. A protocol of analysis have been produced, and the CentiScaPe tool for computing network centralities and integrating topological analysis with biological data have been designed and implemented. CentiScaPe have been applied to a human kino-phosphatome network and according to our protocol, kinases and phosphatases with highest centralities values have been extracted creating a new subnetwork of most central kinases and phosphatases. A lab experiment established which of this proteins presented high activation level and through CentiScaPe the proteins with both high centrality values and high activation level have been easily identified. The notion of node centralities interference have also been introduced to deal with central role of nodes in a biological network. It allow to identify which are the nodes that are more affected by the remotion of a particular node measuring the variation on their centralities values when such a node is removed from the network. The application of node centralities interference to the human kino-phosphatome revealed that different proteins affect centralities values of different nodes. Similarly to node centralities interference, the notion of centrality robustness of a node is introduced. This notion reveals if the central role of a node depends on other particular nodes in the network or if the node is ``robust'' in the sense that even if we remove or add other nodes the central role of the node remains almost unchanged. The dynamic aspects of biological networks analysis have been treated from an abstract interpretation point of view. Abstract interpretation is a powerful framework for the analysis of software and is excellent in deriving numerical properties of programs. Dealing with pathways, abstract interpretation have been adapted to the analysis of pathways simulation. Intervals domain and constants domain have been succesfully used to automatically extract information about reactants concentration. The intervals domain allow to determine the range of concentration of the proteins, and the constants domain have been used to know if a protein concentration become constant after a certain time. The other domain of analysis used is the congruences domain that, if applied to pathways simulation can easily identify regular oscillating behaviour in reactants concentration. The use of abstract interpretation allows to execute thousands of simulation and to completely and automatically characterize the behaviour of the pathways. In such a way it can be used also to solve the problem of parameters estimation where missing parameters can be detected with a brute force algorithm combined with the abstract interpretation analysis. The abstract interpretation approach have been succesfully applied to the mitotic oscillator pathway, characterizing the behaviour of the pathway depending on some reactants. To help the analysis of relation between reactants in the network, the notions of variables interference and variables abstract interference have been introduced and adapted to biological pathways simulation. They allow to find relations between properties of different reactants of the pathway. Using the abstract interference techniques we can say, for instance, which range of concentration of a protein can induce an oscillating behaviour of the pathway.

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Booth, Austin Greeley. "Essays on Biological Individuality." Thesis, Harvard University, 2014. http://nrs.harvard.edu/urn-3:HUL.InstRepos:13070056.

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Much of biology, especially evolutionary theory, makes assumptions about the individuality of living things. A population, for example, is made up of individuals. Those individuals sometimes reproduce, creating new individuals. The very use of these concepts requires that living individuals can be distinguished both synchronically and diachronically. There are many examples in nature, however, in which a living system is present, but it is not clear how to understand that system's individuality. Plants, fungi, colonial marine invertebrates, insect colonies, and symbiosis are all classic cases that have puzzled biologists interested in understanding their population structure and evolution. Scientific exploration of these issues has connections with traditional philosophical terrain, particularly the ontology of persistence and the nature of individuality broadly construed. A biologically informed philosophical literature has arisen in recent years, aimed at understanding the nature of biological individuality and its role in biological theorizing. My dissertation makes two kinds of contributions to this current literature. One contribution is theoretical, reframing our thinking about biological individuality. I distinguish between two categories of individuality and argue that they play different roles in theorizing about nature. One important kind of individual is that of the organism, understood as an entity that persists through space and time, takes in and processes resources from the environment, and maintains physiological autonomy. Another important kind of individual is that of the evolutionary individual, understood as an entity that has the capacity to participate in processes of natural selection. Distinguishing between these two types of individuality has theoretical utility, keeping clear the distinctive kinds of biological processes that individuals engage in. The other contribution of my dissertation involves detailed natural historical analysis of three kinds of problem cases. Using the framework articulated earlier in the dissertation, I assess the individuality of symbioses between larger organisms and their microbial associates, mushroom-producing fungi, and the classic case of ant colonies. The combined result of the assessments is a hierarchical pluralism about biological individuality.
Philosophy

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Murrel, Benjamin. "Improved models of biological sequence evolution." Thesis, Stellenbosch : Stellenbosch University, 2012. http://hdl.handle.net/10019.1/71870.

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Thesis (PhD)--Stellenbosch University, 2012.
ENGLISH ABSTRACT: Computational molecular evolution is a field that attempts to characterize how genetic sequences evolve over phylogenetic trees – the branching processes that describe the patterns of genetic inheritance in living organisms. It has a long history of developing progressively more sophisticated stochastic models of evolution. Through a probabilist’s lens, this can be seen as a search for more appropriate ways to parameterize discrete state continuous time Markov chains to better encode biological reality, matching the historical processes that created empirical data sets, and creating useful tools that allow biologists to test specific hypotheses about the evolution of the organisms or the genes that interest them. This dissertation is an attempt to fill some of the gaps that persist in the literature, solving what we see as existing open problems. The overarching theme of this work is how to better model variation in the action of natural selection at multiple levels: across genes, between sites, and over time. Through four published journal articles and a fifth in preparation, we present amino acid and codon models that improve upon existing approaches, providing better descriptions of the process of natural selection and better tools to detect adaptive evolution.
AFRIKAANSE OPSOMMING: Komputasionele molekulêre evolusie is ’n navorsingsarea wat poog om die evolusie van genetiese sekwensies oor filogenetiese bome – die vertakkende prosesse wat die patrone van genetiese oorerwing in lewende organismes beskryf – te karakteriseer. Dit het ’n lang geskiedenis waartydens al hoe meer gesofistikeerde waarskynlikheidsmodelle van evolusie ontwikkel is. Deur die lens van waarskynlikheidsleer kan hierdie proses gesien word as ’n soektog na meer gepasde metodes om diskrete-toestand kontinuë-tyd Markov kettings te parametriseer ten einde biologiese realiteit beter te enkodeer – op so ’n manier dat die historiese prosesse wat tot die vorming van biologiese sekwensies gelei het nageboots word, en dat nuttige metodes geskep word wat bioloë toelaat om spesifieke hipotesisse met betrekking tot die evolusie van belanghebbende organismes of gene te toets. Hierdie proefskrif is ’n poging om sommige van die gapings wat in die literatuur bestaan in te vul en bestaande oop probleme op te los. Die oorkoepelende tema is verbeterde modellering van variasie in die werking van natuurlike seleksie op verskeie vlakke: variasie van geen tot geen, variasie tussen posisies in gene en variasie oor tyd. Deur middel van vier gepubliseerde joernaalartikels en ’n vyfde artikel in voorbereiding, bied ons aminosuur- en kodon-modelle aan wat verbeter op bestaande benaderings – hierdie modelle verskaf beter beskrywings van die proses van natuurlike seleksie sowel as beter metodes om gevalle van aanpassing in evolusie te vind.

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Cramer, Karla B. "Impact of constructivism via the biological sciences curriculum study (BSCS) 5E model on student science achievement and attitude." Montana State University, 2012. http://etd.lib.montana.edu/etd/2012/cramer/CramerK0812.pdf.

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The investigation involved implementing constructivist instruction via the Biological Sciences Curriculum Study 5E Instructional Model to determine its' impact on student achievement and attitude. The study included 68 seventh grade Life Science students of average to above average achievement at a community based K-12 school in Florence, Montana. Treatment was implemented during a six week biome unit in which student achievement was assessed through the Evaluation Association Measured Academic Progress and summative assessments. Student attitude was evaluated through the Test of Science Related Attitudes and learning preference surveys, pre- and post-treatment. The effectiveness of constructivism approach to instruction on achievement via the BSCS 5E Instructional Model in the science classroom was not conclusively supported by data.

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Liu, Hui Qing 1957. "Fingerprinting biological materials." Thesis, The University of Arizona, 1992. http://hdl.handle.net/10150/291369.

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A study for non-destructive measurement and analysis of agricultural products was undertaken. Some enhancements were made to a spectrophotometer, DK-2A to meet the requirements of low uniform error band when using the factor analysis method. The instrument was modified by adding an integrating sphere, optical transducer, and electronic interface linked to a computer. The instrument was calibrated using targets traceable to NITS standards of BaSO₄ with mixtures of Carbon Black. This gave a range of known reflectance and provided consistent and reproducible data every 5 nm wavelengths between 350 nm and 800 nm. The spectral wavelength bands of the different biological materials were studied with target factor analysis. Target factors were applied in biological materials to characterize the important spectral properties. Pigment of foods, chlorophyll, carotenoid and myoglobin were separated from the spectral response of oranges, apples and meat. Their respective spectral signatures were determined.

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Norville, Julie Erin 1980. "Modular design of biological systems." Thesis, Massachusetts Institute of Technology, 2011. http://hdl.handle.net/1721.1/71484.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, February 2012.
"February 2012." Cataloged from PDF version of thesis.
Includes bibliographical references (p. [153]-191).
The focus of my research is the development of technology for building compound biological systems from simpler pieces. I designed BioScaffold parts, a family of variable regions that can be inserted into a DNA sequence so that at a later time another set of pieces can be substituted for each variable. The variable regions are selective so that a particular piece can be targeted to each region. I have used this technique to assemble protein domains, tune the expression levels of proteins and remove BioBrick scars. BioScaffold parts can be used in combination with BioBrick Standard Biological Parts to create and store devices with tunable components. I developed simplified methods to produce and examine SbpA, a protein that can either self associate into two-dimensional crystals or bring together fused enzymes when divalent cations such as calcium are added to the protein monomers. My fast and easy purification protocol allows SbpA to be produced under non-denaturing conditions as well as examination of the native state of the protein monomers before crystallization. The absence of a white precipitate when calcium is added to SbpA monomers concentrated to 1 mg/ml provides a simple visual screen that indicates that the protein has failed to crystallize. I also developed a protocol to embed SbpA crystallized on lipid monolayers in trehalose for electron microscopy, allowing creation of a 7 Å resolution map for SbpA. I created a cells-on-paper system to compose, isolate, and subsequently destack and examine different cell types grown in sheets of ordinary filter paper and maintained in a humidified incubation chamber. I found that E coli diluted in LB broth and then applied to filter paper grew at rates similar to the same culture spotted on agar plates. Track etch membranes could be used to isolate different cell types, while still allowing chemical communication between the layers. Use of plasmids that contain fluorescent proteins allowed the behaviour of cells to be tracked using a scanner after destacking of the layers. The cells-on-paper system can be used both to test and construct modular synthetic systems composed of bacterial ensembles and to create and examine the behavior of compositions of cell types typically found in biofilms.
by Julie Erin Norville.
Ph.D.

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Burrows, Andrea C. "A social study of women in contemporary biological sciences." Diss., This resource online, 1991. http://scholar.lib.vt.edu/theses/available/etd-07282008-135540/.

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Cotton-Barratt, Rebecca. "Modelling biological form in evolution." Thesis, University of Warwick, 2013. http://wrap.warwick.ac.uk/70973/.

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How are processes working at the individual level, the species level and the macro-ecological level connected? This thesis explores the theoretical and structural constraints on biological evolution. It does this by developing an evolutionary program to model biological form. This development was necessary as the existing models of evolution are poorly suited to modelling morphological constraint. The model of biological form developed in this thesis uses graphs to abstractly represent organisms and the relationships of their internal structure. We show that by increasing the number of degrees of freedom, or by increasing the ruggedness of the fitness landscape, higher levels of diversity are supported - particularly when there is strong directional selection. We explore whether meta-regulation is bounded in the model by using an analytical framework. We show that there is no analytical steady state, but that one can be induced in the model by selection effects. We find that a mixed strategy between increasing object complexity and increasing hierarchical complexity maximises the average degree of a vertex. This agrees with the evolutionary history of meta-regulation. We claim that the macro-ecological response to environmental perturbation is determined by both the characteristic time scale of mutation and the time scale of the environmental change. We show that for high amplitude changes the system can adapt provide the mutation time scale is smaller than the environmental change. We also show that low amplitude environmental changes cause rapid turnovers in species' diversity. Finally, we show that mass extinctions can be the result of species' interactions and background rates of extinction, and do not need large external perturbations to occur. This, combined with the results above, suggests that many of the trends seen over geologically long time periods can be explained as a result of the interacting processes at the individual and species level.

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Wala, Zingfa Jantur. "Birds and people: studies based on citizen science and census data of Greater Gauteng, South Africa." Doctoral thesis, University of Cape Town, 2018. http://hdl.handle.net/11427/29541.

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Global human population growth has been predicted to grow exponentially, to a point where it exceeds the capacity of available resources to sustain it. The consequences that such exponential increase will have on the environment has also been the focus of several research. The spatial pattern of human population has reveal uneven pattern of human population with the urban areas being subject of increased influx of human population from the rural areas in search of better economic factors. The United Nations in 2007 revealed that at least half of the world’s 6.6 billion human population was living in urban areas. This number is expected to increase to over 60% of the world's population by the end of 2050. Most of this population growth is occurring in developing countries. While the health, security and town planning amongst other consequences of this global explosion in urbanization have been well-studied and documented, the impact which urbanization is having and will have on the ecosystem and on biodiversity, especially at regional and local scales has remained an a field of knowledge that has continued to evolve especially given the variable patterns and drivers of urbanization in different regions of the world as well as the different environmental factors and biodiversity in these regions. Biodiversity monitoring has been shown to be crucial to conservation goals aimed at accessing the state and condition of biodiversity. The Second South African Bird Atlas Project (SABAP2) is a citizen science atlas project which commenced in 2007. Over a decade, SABAP2 has produced a rich source of data, capturing bird distributions in South Africa. This makes SABAP2 a powerful tool for monitoring observed changes in bird communities and by extension biodiversity through time. I examined the effect that urbanization is having on the avian biodiversity in South Africa, one of the most urbanized countries in Africa. My research was focused on the 576 pentads in the four one-degree grid cells (25S 27E, 25S 28E, 26S 27E and 26E 28E) centered on the Gauteng province, referred to as Greater Gauteng region. In addition to being very urbanized, Greater Gauteng is also the most populated area in the country, and is home to 30% of the country’s 51 million people. The region is the most atlased SABAP2 region in the country, with each pentad having a minimum of 11 full-protocol SABAP2 checklists. It thus provide opportunities for the development of tools to monitor the temporal dynamics of bird communities. The first chapter is the general introduction where I did an extensive literature review of the research subject and gave an overview of the data chapters that make up the thesis. In the second chapter, I examined spatial patterns of urbanization and avian biodiversity. I assess avian species composition in the urban and rural areas of Greater Gauteng. I categorized bird data from SABAP2 for Greater Gauteng Urban and Rural subgroups. The dataset for this chapter had 700 bird species. 644 showed no range preference for either urban or rural areas. Five species showed a preference for rural areas while 51 species showed a preference for urban areas. The higher species richness recorded in urban pentads highlights the often overlooked benefits of biodiversity conservation efforts in urban areas such as green spaces and parks, gardens and water bodies. This chapter highlights the need for conservation efforts to be targeted at birds and other biodiversity in urban spaces. It is also raises the need to further promote policies aimed at having conservation efforts incorporated into town planning. In the third and fourth chapters, I used data from SABAP2 to investigate how different protected areas such as Important Bird Areas (IBAs) are to their surrounding areas by demonstrating how different the Devon Grasslands (Chapter 3) and Suikerbosrand Nature Reserve (Chapter 4) IBAs are to their immediate surrounding areas in terms of avian species richness and assemblage. Atlas data from the pentads covering these two IBAs were compared with data from the surrounding pentads. Both IBAs stand out as having more bird species than their immediate surroundings. The simple yet effective method used in this chapters can be applied in identifying potential sites for biodiversity conservation. In the fifth chapter, using a variation of the Shannon-Weiner species diversity index which is known to reach an asymptote rapidly even while species richness keeps increasing, to investigate patterns of spatial distribution of species richness and proportional diversity in Greater Gauteng. The chapter provides insights into pentads with the richest bird communities and also provides a method which can be applied to citizen science data such as SABAP2 to discover areas where particular groups of species, such as waterbirds and threatened species, are concentrated in the region. The sixth chapter examines the relationship between reporting rates of birds and human population in Greater Gauteng. With Greater Gauteng being the most populated region in South Africa, it presented an ideal situation to investigate patterns of correlation between human population and the reporting rates of bird species in the region. Based on the results obtained, the species were grouped into 18 groups categorized by the relationship pattern revealed by species reporting rates and human population. The Seventh chapter follows a similar pattern with chapter six. However, chapter seven, examines patterns between a socio-economic index, mean income per person, and the reporting rates of birds in Greater Gauteng. The eighth chapter is the conclusion. It gives a synthesis of the thesis and presents the implications for conservation of avian biodiversity in Greater Gauteng. Overall, this thesis highlights the contribution of citizen science can make to research. It also makes for a strong case showing fundamental importance of large volumes of data such as SABAP2 data, and the useful information that can be harnessed from this data. The conservation-relevant studies in the chapters of this thesis are a result of the spatial distribution patterns of the avifauna revealed by SABAP2 data from Greater Gauteng. It showed how we can detect changes in species abundance, richness and composition in a pentad or in any area, a method we can extend further to detect when bird species are starting to decline or drop out of the species list for a pentad. The results reported in this thesis provides a rich field of study for future research, especially in the field of urban ecology.

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Xu, Keyuan. "Stochastic modeling of biological sequence evolution." Thesis, Massachusetts Institute of Technology, 2005. http://hdl.handle.net/1721.1/32113.

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Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2005.
This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Includes bibliographical references (leaves 81-86).
Markov models of sequence evolution are a fundamental building block for making inferences in biological research. This thesis reviews several major techniques developed to estimate parameters of Markov models of sequence evolution and presents a new approach for evaluating and comparing estimation techniques. Current methods for evaluating estimation techniques require sequence data from populations with well-known phylogenetic relationships. Such data is not always available since phylogenetic relationships can never be known with certainty. We propose generating sequence data for the purpose of estimation technique evaluation by simulating sequence evolution in a controlled setting. Our elementary simulator uses a Markov model and a binary branching process, which dynamically builds a phylogenetic tree from an initial seed sequence. The sequences at the leaves of the tree can then be used as input to estimation techniques. We demonstrate our evaluation approach on Arvestad and Bruno's estimation method, and show how our approach can reveal performance variations empirically. The results of our simulation can be used as a guide towards improving estimation techniques.
by Keyuan Xu.
M.Eng.

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West, H. K. "Competing divalent cations in biological systems." Thesis, University of Worcester, 2001. http://eprints.worc.ac.uk/7188/.

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Gao, Si Zhu 1975. "A survey of tree models in biological applications /." Thesis, McGill University, 2006. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=97956.

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We present a survey of mathematical models explored in computational biology. Of particular interest are random tree models. The survey is intended to give an overview of the models used in this burgeoning field. We limited ourselves mainly to definitions and provide the key references.

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Wu, Daniel Duanqing Hu Xiaohua. "The structure and function of biological networks /." Philadelphia, Pa. : Drexel University, 2010. http://hdl.handle.net/1860/3327.

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Jennings, Arthur John. "Practical work in school secondary science and the curriculum influence of its assessment, with particular reference to biological science." Thesis, University College London (University of London), 1995. http://discovery.ucl.ac.uk/10020245/.

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Practical work in secondary school science has long held a prominent position. With particular reference to biology this thesis, which is essentially a reflective study, examines the way practical science has developed over the last fifty years. Major curriculum revisions are considered in the light of both changing educational insights and societal expectations during this half century which has seen remarkable changes affecting all aspects of life. The primary focus, however, concerns the influence of practical assessment on the teaching of biology. In a chronological sequence the transition of biology is traced from its position as a minority curriculum subject with a predominantly descriptive approach suitable for its morphological and taxonomic emphasis to its place within balanced science for all pupils of compulsory school age. The struggle of biology to emerge as a rigorous school science and the adaptation of biology curricula to accommodate a biosocial synthesis fitting to a society that has become increasingly environmentally aware forms an important strand through the account. Always, though, the effect of examinations and what is examinable has affected teaching priorities and teaching approaches. Therefore this thesis looks at pivotal curriculum and examination changes and seeks to evaluate the match of examinations to curriculum goals. The conclusion is made that practical examinations have frequently served curriculum aims, especially at times of syllabus revision but during periods of relative curriculum and examination stability practical assessment has sometimes exerted a constraining influence. Despite all the changes in science education during the past fifty years practical science has maintained its high profile. Whilst the stated aims of practical work have taken different emphases at different times there is evidence that teachers have persistently lacked clarity about its precise purpose. Despite modem rhetoric about 'doing science' and the national curriculum thrust towards investigations teachers still cling to very general beliefs about the value of practical science even though there is a significant change in disposition towards more investigatory science.

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King, Lance E. "Competing discourses in science education policy a discourse analysis of the tensions surrounding biological evolution in Florida's science standards /." Tallahassee, Florida : Florida State University, 2009. http://etd.lib.fsu.edu/theses/available/etd-05052009-121505/.

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Thesis (M.S.)--Florida State University, 2009.
Advisor: Sherry A. Southerland, Florida State University, College of Education, School of Teacher Education. Title and description from dissertation home page (viewed on Oct. 27, 2009). Document formatted into pages; contains viii, 113 pages. Includes bibliographical references.

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21

Reblitz-Richardson, Orion Aubrey 1976. "Architecture for biological model and database networking." Thesis, Massachusetts Institute of Technology, 2000. http://hdl.handle.net/1721.1/86495.

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Thesis (S.B. and M.Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2000.
Includes bibliographical references (leaves 73-75).
by Orion Aubrey Reblitz-Richardson.
S.B.and M.Eng.

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22

Hee, Michael Richard. "Biological imaging with low coherence optical interferometry." Thesis, Massachusetts Institute of Technology, 1992. http://hdl.handle.net/1721.1/12928.

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23

Scelfo, Tony (Tony W. ). "Data visualization of biological microscopy image analyses." Thesis, Massachusetts Institute of Technology, 2006. http://hdl.handle.net/1721.1/37073.

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Thesis (M. Eng. and S.B.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2006.
Includes bibliographical references.
The Open Microscopy Environment (OME) provides biologists with a framework to store, analyze and manipulate large sets of image data. Current microscopes are capable of generating large numbers of images and when coupled with automated analysis routines, researchers are able to generate intractable sets of data. I have developed an extension to the OME toolkit, named the LoViewer, which allows researchers to quickly identify clusters of images based on relationships between analytically measured parameters. By identifying unique subsets of data, researchers are able to make use of the rest of the OME client software to view interesting images in high resolution, classify them into category groups and apply further analysis routines. The design of the LoViewer itself and its integration with the rest of the OME toolkit will be discussed in detail in body of this thesis.
by Tony Scelfo.
M.Eng.and S.B.

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24

Tsankov, Alex. "Communication between layers in biological transcriptional networks." Thesis, Massachusetts Institute of Technology, 2005. http://hdl.handle.net/1721.1/33208.

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Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, June 2005.
This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
"May 2005."
Includes bibliographical references (leaves 87-89).
Chromatin-immunoprecipitation experiments in combination with microarrays (known as ChIP-chip) have recently allowed biologists to map where proteins bind in the yeast genome. The combinatorial binding of different proteins at or near a gene controls the transcription (copying) of a gene and the production of the functional RNA or protein that the gene encodes. Therefore, ChIP-chip data provides powerful insight on how genes and gene products (i.e., proteins, RNA) interact and regulate one another in the underlying network of the cell. Much of the current work in modeling yeast transcriptional networks focuses on the regulatory effect of a class of proteins known as transcription factors (TF). However, other sets of factors also influence transcription, including histone modifications and states (HS), histone modifiers (HM) and remodelers, nuclear processing (NP), and nuclear transport (NT) proteins. In order to gain a holistic understanding of the non-linear process of transcription, our work examines the communication between all five forementioned classes (or layers) of regulators. We use vastly available rich-media ChIP-chip data for various proteins within the five classes to model a multi-layered transcriptional network of the yeast species Saccharomyces cerevisiae.
(cont.) Following the introduction in Chapter 1, Chapter 2 describes the non-trivial process of incorporating the different sources of data into a coherent set and normalizing the heterogeneous data to improve biological accuracy. Using the normalized data, Chapter 3 finds biologically meaningful pairwise statistics between proteins, including filtered correlation coefficient, and mutual information p-values. It then combines the p-values of the two complementary approaches in order to increase the reliability of our predictions. Chapter 4 uncovers group-wise relationships between proteins using a novel semi-supervised clustering algorithm that preserves information about elements of a cluster in order to better capture group-wise dependencies. Throughout the theoretical analysis, we confirm various known biological processes and uncover several novel hypotheses. Based on the developed methodology, Chapter 5 builds a multi-layered transcriptional network and quantifies the communication between levels in biological transcriptional networks.
by Alex Tsankov.
S.M.

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25

Patke, Usha. "Inquiry-based laboratory investigations and student performance on standardized tests in biological science." Thesis, Walden University, 2013. http://pqdtopen.proquest.com/#viewpdf?dispub=3600291.

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Achievement data from the 3rd International Mathematics and Sciences Study and Program for International Student Assessment in science have indicated that Black students from economically disadvantaged families underachieve at alarming rates in comparison to White and economically advantaged peer groups. The study site was a predominately Black, urban school district experiencing underachievement. The purpose of this correlational study was to examine the relationship between students’ use of inquiry-based laboratory investigations and their performance on the Biology End of Course Test, as well as to examine the relationship while partialling out the effects of student gender. Constructivist theory formed the theoretical foundation of the study. Students’ perceived levels of experience with inquiry-based laboratory investigations were measured using the Laboratory Program Variable Inventory (LPVI) survey. LPVI scores of 256 students were correlated with test scores and were examined by student gender. The Pearson correlation coefficient revealed a small direct correlation between students’ experience in inquiry-based laboratory investigation classes and standardized test scores on the Biology EOCT. A partial correlational analysis indicated that the correlation remained after controlling for gender. This study may prompt a change from teacher-centered to student-centered pedagogy at the local site in order to increase academic achievement for all students. The results of this study may also influence administrators and policy makers to initiate local, state, or nationwide curricular development. A change in curriculum may promote social change as students become more competent, and more able, to succeed in life beyond secondary school.

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Kinchin, Ian M. "The active use of concept mapping to promote meaningful learning in biological science." Thesis, University of Surrey, 2000. http://epubs.surrey.ac.uk/908/.

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27

Stadler, Max. "Assembling life : models, the cell, and the reformations of biological science, 1920-1960." Thesis, Imperial College London, 2010. http://hdl.handle.net/10044/1/11920.

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28

Patke, Usha. "Inquiry-based laboratory investigations and student performance on standardized tests in biological science." ScholarWorks, 2011. https://scholarworks.waldenu.edu/dissertations/1089.

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Achievement data from the 3rd International Mathematics and Sciences Study and Program for International Student Assessment in science have indicated that Black students from economically disadvantaged families underachieve at alarming rates in comparison to White and economically advantaged peer groups. The study site was a predominately Black, urban school district experiencing underachievement. The purpose of this correlational study was to examine the relationship between students' use of inquiry-based laboratory investigations and their performance on the Biology End of Course Test, as well as to examine the relationship while partialling out the effects of student gender. Constructivist theory formed the theoretical foundation of the study. Students' perceived levels of experience with inquiry-based laboratory investigations were measured using the Laboratory Program Variable Inventory (LPVI) survey. LPVI scores of 256 students were correlated with test scores and were examined by student gender. The Pearson correlation coefficient revealed a small direct correlation between students' experience in inquiry-based laboratory investigation classes and standardized test scores on the Biology EOCT. A partial correlational analysis indicated that the correlation remained after controlling for gender. This study may prompt a change from teacher-centered to student-centered pedagogy at the local site in order to increase academic achievement for all students. The results of this study may also influence administrators and policy makers to initiate local, state, or nationwide curricular development. A change in curriculum may promote social change as students become more competent, and more able, to succeed in life beyond secondary school.

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29

Su, Wei. "Motif Mining On Structured And Semi-structured Biological Data." Case Western Reserve University School of Graduate Studies / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=case1365089538.

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30

Ensair, Hend Assiad M. "The biology of Boopsoidea inornata (Castelnau, 1861) and life history comparisons within the Sparidae." Doctoral thesis, Faculty of Science, 2019. http://hdl.handle.net/11427/31412.

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South African marine ichthyofauna has remarkable diversity across a range of biogeographic zones from cold-temperate to subtropical. Two families stand out here, both with high diversity and high rates of endemism to the region, namely Sparidae and Clinidae. The Sparidae are of greater interest because of their commercial importance, and conversely, their conservation status. Several are listed as threatened by the IUCN. The Sparidae is also the family with the greatest plasticity in life history characteristics of any vertebrate family, as they include gonochorism, rudimentary hermaphrodites, and both kinds of sequential hermaphrodites. Life history characteristics are known determinants of the resilience of fish species to fishing, and more generally of their response, either positive or negative, to any form of disturbance. Life history characteristics of most of the species of Sparidae, in South Africa and worldwide, have been studied, particularly those of commercial and conservation importance. Omissions include those that are small, with little commercial importance. This is an oversight, as there is much to be learned about life history strategies by studying the full spectrum of variation in the family, and particularly those variants which produce numerically, and therefore ecologically, significant population sizes. In this thesis, I study the life history and parasite community of one of South Africa’s most abundant seabreams in separate chapters. In the last chapter I take a fresh perspective on life history variation among fishes, by comparing four sympatric seabreams to describe the several dimensions along which life history trade-offs can occur without the confounding influences of environment and phylogeny. Boopsoidea inornata (Castelnau, 1861) is endemic to South Africa. Eight hundred and seventeen fishes were sampled from four locations: False Bay, Struisbaai, Goukamma and Port Elizabeth from 2012 to 2014. They ranged in size from 130 to 310 mm fork length. The diet of B. inornata was investigated in False Bay and Struisbaai using Prey-Specific Index of Relative Importance (%PSIRI). B. inornata is an omnivore, with a preference towards small sand- and reef-dwelling prey and has only limited intake of algae and small fish. Age and growth were assessed using sectioned otoliths. A clear seasonal pattern of band formations deduced from the frequency of opaque margins show that B. inornata lay down one opaque and one transparent band per year. B. inornata is a small species (L∞= 222.7 mm) with high longevity (tmax= 37). It is a rudimentary hermaphrodite. The ovaries hold up to 8000 vitellogenic eggs, which equates to an average 19 eggs per gram of body mass. This value is low compared with other seabream species. B. inornata females spawn repeatedly during the year, although there is more spawning activity in spring, than in other months. The sex ratio is heavily skewed towards females (1:3.35). The presence of post-ovulatory follicles together with hydrated oocytes indicates that the species is an indeterminate batch spawner. Length at 50% maturity was calculated based on gonads collected throughout the spawning season. Females mature at 178 mm FL, compared to 185 mm FL for males. Female GSI greatly exceeds male GSI, and, together with the sex ratio, suggests a polygamous mating system. One hundred and fifty B. inornata were collected from False Bay, Struisbaai, Goukamma and Port Elizabeth to investigate associated parasite assemblages. Eighty six percent of the sample was infected by parasites. Parasites infecting B. inornata have never before been recorded. Nineteen parasite taxa were found infecting B. inornata across all localities and included myxozoan, monogenean, digenean, cestode, nematode, copepod and isopod representatives. Three species of digenean metacercaria showed high prevalence of infection in B. inornata across all four localities. These included a Stephanostomum sp. infecting the gill arches of 61%, and two unidentified digeneans. The unidentified digenean metacercariae- 2 was found in the kidneys and musculature of 59% of the total sample and the unidentified digenean metacercariae-1 was found infecting the hearts of 47% of the total sample. Overall parasite assemblages were significantly different amongst all localities, with no significant difference in parasite assemblages among size classes, age classes or sex within localities. Fish life history is affected by environmental and biological factors but is also constrained by phylogenetic influences on morphology and physiology. In an attempt to expose the nature and extent of life history trade-offs, I compared four closely related and sympatric seabreams, namely Spondyliosoma emarginatum, Pachymetopon blochii, Rhabdosargus globiceps and Boopsoidea inornata. I contend that only by eliminating or reducing as far as possible the effect of environment, habitat and phylogeny can we expose real trade-offs. Samples of each species were obtained in every season from the south-western Cape, South Africa, to obtain measures of total length, mass, gonadosomatic index and condition. S. emarginatum is a nest-guarding, short-lived, protogynous hermaphrodite. P. blochii is a resident, group-spawner, engaging in sperm competition. R. globiceps is a moderately long-lived migrant with a sex ratio of 1:1, that also engages in sperm competition over a short spawning season. B. inornata is a polygamous, long-lived resident with low annual fecundity, but a protracted spawning season. Although all four species are periodic strategists, life history trade-offs exist between several sets of variables, namely semelparity vs iteroparity, age-at-maturity vs maximum size, annual fecundity vs longevity, length of spawning season vs parental care, and length of spawning season vs migration. The efficiency of the sequential hermaphrodite strategy which allows every fish to spawn as a female until they are large enough to act as a male makes one question the rarity of this strategy. I argue that halving of the female life-span compromises the periodic strategy, and that hermaphroditism is at odds with migration. The latter rests on the assumption that the migrant social structure is based on cooperation, for feeding, defence and navigating in schools, whereas the hermaphrodite social structure is based on aggression and dominance hierarchies which requires residency and territoriality. No clear adaptive reason for the divergence among the sympatric species can be identified, although competition among the young is a candidate. This comparison reveals a wide range of options available to seabreams and shows how disparate life histories can be equally adaptive under identical conditions. More generally I have shown how a variety of life-history traits, such as migration, sex-ratio, reproductive strategy and somatic growth form interact to define a life-history.

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31

Botha, Thomas Petrus Arnoldus. "The Burrowing Barnacles (Cirripedia, Acrothoracica) of South Africa." Master's thesis, Faculty of Science, 2019. http://hdl.handle.net/11427/31090.

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The Acrothoracica of South Africa are reviewed for the first time, 50 years after the last publication on this group appeared. A new host category for acrothoracicans is described in Chapter 1, as Weltneria spinosa was collected from coralline red algae. This finding was not an isolated event, as this species was found inhabiting four different species of coralline algae across a range of sites up to 900 km apart. These are the first unequivocal records of living acrothoracicans burrowing into coralline red algae. Further inspections of coralline algae in this and other regions will likely reveal many more new host records and possibly new acrothoracican species. In Chapter 2 a systematic account and key to all known South African acrothoracicans are given, with each description accompanied by scanning electron microscopy, light microscopy and a distribution map. The number of known South African acrothoracicans is increased from four to eight species, as three new records and two undescribed species are added to the fauna, while one existing record is determined to be a nomen nudum. Chapter 3 examines patterns of distribution and host specificity. All species except one saw a range extension, some of which were > 500 km, while all species had additional hosts described. The species with the most hosts was W. spinosa, which was reported from 13 hosts that included gastropods, chitons and coralline red algae. South Africa thus now includes 11.27% of the world’s acrothoracican species, with 62.50% of these endemic. Moreover, 75% of South African acrothoracicans were endemic to specific provinces. However, these values are likely to change substantially as more sites are sampled both within the region and in neighbouring countries. In conclusion this dissertation shows that South Africa has more acrothoracican species, occupying more hosts across wider distributional ranges than previously thought. Although this study serves as a valuable baseline it should be expanded on through future sampling, specifically focusing on areas (Delagoa, Namaqua and offshore bioregions) and hosts (especially corals) not yet sampled in South Africa.

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32

Smith, Megan. "Population genetics of South African Protea L. (Proteaceae) species associated with various pollinator guilds." Master's thesis, Faculty of Science, 2019. http://hdl.handle.net/11427/31267.

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South Africa hosts plant species with a large variety of floral traits associated with different pollinator guilds. Suites of specialised floral traits associated with particular pollinators are known as pollination systems or syndromes. However, it is often uncertain how these pollination systems affect gene flow between plant populations, mating system outcome, and subsequent genetic health of plant species. Genetic variability is an important aspect in understanding the long-term survival of a species because excessive homozygosity, as a result of high amounts of inbreeding, may restrict a species’ long-term local adaptive potential. The African genus, Protea, is an ideal study system for exploring the evolution and maintenance of mating systems, because the pollination system for many species have been confirmed by pollinator exclusion experiments. The genus has several pollination systems including birds, insects and non-flying mammals. Comparative estimates of pollinators’ outcrossing abilities are rare and confined to bird and insect guilds. Furthermore, 10 microsatellite markers have been developed for the genus, but have not been used to assess the outcrossing abilities of various pollinators. This study thus had two aims: Firstly, to use microsattelite markers to estimate the outcrossing rates and subsequent genetic diversity of Protea species primarily pollinated by either birds (P. laurifolia and P. roupelliae), insects (P. caffra and P. simplex) or non-flying mammals (P. amplexicaulis and P. humiflora). Secondly, I aimed to understand how birds and non-flying mammal pollinators affect population connectivity and gene dispersal. This was done by comparing indirect estimates of gene flow in the therophilous, P. amplexicaulis, and ornithophilous, P. laurifolia. These estimates included population differentiation (G”st) between subpopulations and spatial genetic structuring within metapopulations of each species. I expected that less vagile pollinators, such NMP’s (non-flying mammal pollinators), would contribute the least to gene flow and cause high selfing rates and low genetic diversity within therophilous populations. Contrastingly, flying pollinators would be able to travel longer distances resulting in more genetic connectivity between plant populations. The high energetic demands and interplant movements of flying animals were predicted to result in high outcrossing rates in ornithophilous and entomophilous species. Non-flying mammal-pollinated (NMP) Protea species had high (> 0.8) and non-significantly different (p > 0.05) outcrossing rates relative to species pollinated by flying animals. Similarly, hand pollen supplementation experiments also revealed that small mammals were effective pollen vectors since P. amplexicualis individuals were not pollen limited. High multilocus outcrossing rates (> 0.80) may have resulted in all sampled Protea species exhibiting high levels of heterozygosity (> 0.7) and low levels of inbreeding. However, some of the outcrossing events were between kin (approximately 14 %), giving evidence for biparental inbreeding. Furthermore, the relationship between geographic distance and genetic distance was significant for sampled P. amplexicaulis individuals. In contrast, sampled P. laurifolia individuals were genetically similar across the landscape. This pattern was reflected in fine-scale (> 500 m) spatial genetic structuring in a sampled metapopulaton of P. amplexicaulis and a homogeneous distribution of P. laurifolia genotypes. Restricted gene dispersal recorded for P. amplexicaulis in this study may have been a result of the high levels of biparental inbreeding. It was not clear whether poor gene flow was primarily a result of restricted pollen dispersal created by NMP’s or restricted seed dispersal. Nevertheless, continuous limited gene dispersal between NMP populations may result in allopatric speciation over time. This provides a hypothesized reason as to why many of the therophilous Protea species are located in small and isolated populations. Additionally, there is a concern that restricted population size in combination with poor gene flow may lead to increased levels of inbreeding over time. This study provided the first evidence for localised gene dispersal, but high outcrossing rates, in NMP proteas.

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33

Adaramola, Rhoda Fiyinfoluwa. "Relationship between Aspalathus linearis (Burm. F.) R. Dahlgren (rooibos) growth and soil moisture in a glasshouse and in the DSSAT-CSM crop model." Master's thesis, Faculty of Science, 2021. http://hdl.handle.net/11427/33623.

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Climate change and drought pose a major threat to agriculture and water resources globally and for rooibos (Aspalathus linearis (Burm. F.) R. Dahlgren) production in the Western Cape province of South Africa. Rooibos is adapted to the coarse, nutrient poor, acidic, well-drained, deep sandy soil of the Fynbos biome. The region has a Mediterranean climate, which is characterised by wet cold winters, with an average annual rainfall of about 375 mm, and dry summers. The growth of rooibos peaks in the summer months, implying a reliance on soil moisture. The current study aims to investigate the relationship between rooibos growth and soil moisture. The objectives of the study were: 1) to determine the effect of soil moisture on growth and evapotranspiration in rooibos under glasshouse conditions, 2) to adapt the CROPGRO model in DSSAT to simulate the shoot biomass yield of rooibos, using the rooibos CROPGRO model, 3) to investigate the effect of rooibos growth on soil moisture, and 4) to determine the effect of different levels of mulching and irrigation on rooibos yield and soil moisture. Some of the results obtained in the glasshouse study in Objective 1 and observational field data from the literature were used in the adaptation of the CROPGRO model. The glasshouse study was carried out at the University of Cape Town, using soils from Clanwilliam and Citrusdal sites to grow rooibos seedling for 16 weeks in pots before exposing them to drought treatments. The pots were arranged on trays in the glasshouse using a completely randomized design. Two drought treatments were used: moderate drought stress (MDS), set at 20% FC, and severe drought stress (SDS), during which watering was completely withdrawn, were applied to 10 pots per treatment per site. Data on plant growth, root morphology, evapotranspiration, soil moisture, chlorophyll fluorescence and leaves to determine chlorophyll and carotenoid concentration were collected from the plants in the glasshouse after 10 days of these drought treatments. The SDS plants were re-watered for 8 weeks for recovery, and together with the MDS and control plants were transferred into a growth chamber for measurement of gas exchange parameters and biomass. The CROPGRO model in DSSAT was adapted for rooibos by changing some parameters in a pigeon pea (Cajanus cajan L. Millspaugh) CROPGRO model. The adapted rooibos model was used to set up an experiment that compared the cumulative evapotranspiration and soil moisture from the rooibos field and bare soil under rainfed conditions. Also, in a simulation experiments, the model was used to determine the effect of three levels of mulching by means of wheat residue at 8000 kg/ha, 4000 kg/ ha and 2000 kg/ha and drip irrigation at 25.4mm and at 12.5mm once a week from December to March, both separately and in combination, on rooibos shoot biomass and soil moisture. The results from the glasshouse study showed a 40% decrease in biomass under MDS conditions for 12 weeks, while SDS plants could not survive beyond 10 days in the glasshouse. Root morphological features changed under severe drought stress, resulting in longer and thinner roots relative to the control plants. The reduced biomass accumulation under drought conditions was followed by reduced photosynthesis, stomata conductance, transpiration, and concentration of chlorophyll and carotenoids. Changes in both maximum quantum efficiency of photosystem II (Fv/Fm) and fluorescence quantum yield (Fq'/Fm') were observed in the later stages of the SDS plants (days 9 and 10) compared to the control plants but were unaltered in the MDS plants. The soil moisture correlated negatively with evapotranspiration and stomata conductance in control plants, while these relationships were absent in MDS plants. Changes in temperature in the glasshouse correlated positively with stomata conductance and transpiration in the control plants, but these correlations were also absent in MDS plants. However, changes in temperature correlated negatively with soil moisture in both the control plants and the MDS treated plants. The CROPGRO model in DSSAT was successfully adapted to simulate shoot biomass in rooibos under field conditions and the rooibos model had an agreement of 94% with observational shoot biomass under field conditions. Furthermore, the model simulated cumulative evapotranspiration in rooibos plants in the field, with an agreement of 56%. The simulated experiments showed that cumulative evapotranspiration from the rooibos field was 33% higher than that of bare soil, and showed that rooibos plants extract moisture from deep soil layers to a depth of about 2 m. Furthermore, rooibos growth in deep soil, and in mulched or irrigated treatments, produced higher shoot biomass than control plants. In deep soil, the simulated irrigated rooibos plants, which received 25.4 mm water weekly from December to March, produced a higher biomass yield than only rainfed or mulched plants. However, the combined treatments of mulching at 8000 or 4000 kg/ha and irrigation at 12.5 mm was similar to irrigation at 25.4mm. The average extractable soil moisture was greater in deep soil for all the treatments and control plants compared to shallow soil. Overall, the rooibos crop model shows that an increased supply of soil moisture enhances the production of biomass yield in rooibos in the field. Also, rooibos extracts moisture from a deeper soil layer, which enables it to hydrate its leaves and to transpire during the summer period for better growth and biomass production. Water loss through evapotranspiration was high in rooibos fields, and thus mulching of the plants would be beneficial for increased biomass production. However, even better rooibos yields were obtained when mulching was combined with irrigation. The glasshouse experiments showed a yield decrease of rooibos biomass by about 40% when the moisture supply was reduced by about 50% of the adequate conditions. The thinner and longer roots of rooibos, among other drought tolerance traits, most likely enable it to cope with low rainfall and drought conditions, which are prevalent in the Cederberg region of the Western Cape. The production of rooibos in the farms is prone to water loss through evapotranspiration, and thus soil moisture conservation technologies such as mulching would greatly enhance its biomass yield.

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Aarthy, T. "Limonoid biosynthesis in azadirachta indica: characterization of pathway genes and analysis of labeled metabolites through stable isotope feeding." Thesis(Ph.D.), CSIR-National Chemical Laboratory, Pune, 2019. http://dspace.ncl.res.in:8080/xmlui/handle/20.500.12252/4584.

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Due to their immobile nature, plants have evolved and adapted to different environmental stresses by effective synthesis, storage and emission of secondary metabolites in the necessary time and space. These secondary metabolites or natural products are of immense fortitude to mankind due to its different kind of ameliorating property on human health ailments. Neem tree, one of the Indian medicinal plant well-known and being used for its healing property from ancient past is of profound interest and hence, the study of its biosynthetic pathway, understanding its localization, regulation etc., will pave the way to design an efficient way of treating human diseases as a natural means of medicament. The thesis entitled, “Limonoid biosynthesis in Azadirachta indica: Characterization of pathway genes and analysis of labeled metabolites through stable isotope feeding” is concerned with the study of biosynthesis of limonoids and other secondary metabolites and their localization in neem. Neem tree is known for its bountiful and diverse natural products conferring numerous medicinal and agricultural uses for mankind1. Among these plenty of natural products, most of them belong to triterpenoid (limonoids)2. More than 150 limonoids have been isolated and characterized from neem so far and each of them has been studied for its biological activities3. Azadirachtin, one of the highly complex limonoid had been studied widely for its excellent anti-feedant, insecticidal property, with no proven harmful effects on vertebrates and are found to be an unsurpassable natural product identified hitherto for its efficiency. The successful chemical synthesis of this complex molecule was accomplished after 22 years of efforts by Ley et al.4, 5. Azadirachtin and other bioactive limonoids are highest in the fruits of neem tree. There is an indispensable requisite for metabolic engineering of this pathway in heterologous system. Therefore, the study of azadirachtin biosynthetic pathway is highly essential to harness the biosynthetic capacity of the tree for its medicinal properties. Following are the main goals of the thesis, To identify and characterize the organelles/ intra-cellular compartments involved in the storage of limonoids in different tissues. • To trace the flow of carbon in limonoid skeleton through stable isotope feeding experiments. • To study the expression level of the genes involved in isoprene biosynthetic pathway and to characterize the putative candidate genes associated with limonoid biosynthesis. Development of in vitro cultures of neem, limonoid profiling and study of organelles and cells involved in limonoid storage In our laboratory, we have identified previously, the tissue and developmental stage specific differential distribution and abundance of ring intact (basic) and C-seco limonoids in different neem tissues6. This incredible and impressive abundance of limonoids in fruit and leaf tissues actuated us to look for the specialized cells involved in accumulating limonoids and also the development of neem plantlets, in vitro callus from kernel and callus derived suspension system to study limonoid biosynthesis. C-seco limonoid group exists as major limonoid synthesized in the in vitro plantlets and also callus and suspension cells. In the present study, histochemical analysis of different tissues has been carried out to study the limonoid localization in cellular and subcellular compartments. It suggested that laticifers are rich in basic limonoids and oil bodies are found to be the major source of C-seco-limonoids in pericarp and kernel of neem fruit respectively, whereas limonoids exist in abundance in idioblast vacuoles in pericarp and leaf tissues. Average number of idioblasts per mm2 of tissue was comparatively high in pericarp to that of leaf, which matched with the abundance of limonoids in these tissues respectively Ex vivo tracer study of limonoid biosynthesis in Azadirachta indica Neem tree serves as a cornucopia for triterpenoids called limonoids that are of profound interest to humans due to their diverse biological activities. A well-known potent anti-feedant, highly complex molecule, azadirachtin and many other biologically active limonoids are distributed in different tissues of neem7. The biosynthetic machinery that plant cell employs for the production remains unexplored for this wonder tree. Herein, we report the tracing of limonoid biosynthetic pathway through feeding experiments using 13C labeled isotopologues of glucose in neem cell suspension. In order to identify the signature fragment of azadirachtin A generated through ESI-MS, fragments generated from MS/MS of azadirachtin derivatives such as azadirachtin B, H, 3-deacetylazadirachtin A, epi-azadirachtin D, vepaol were studied comparatively at different normalized collision energies. The plausible fragmentation pathway for azadirachtin A has been proposed showing the structure-fragment relationship. This helped in tandem mass spectrometry (MS/MS) analyses of labeled limonoid.extract,which lead to the identification of signature isoprenoid units involved in azadirachtin and other limonoid biosynthesis (Figure 2). Therefore, the isoprene units contributed for limonoid skeleton biosynthesis are found to be formed through mevalonate (MVA) pathway (Figure 3). Study of the role of MVA and MEP pathway in limonoid biosynthesis and characterization of pathway genes To study the role of MVA and MEP pathway towards limonoid biosynthesis, chemical inhibition of the pathways along with concomitant 13C Glc labeling was carried out. Treatment of cell suspension with mevinolin, a specific inhibitor for MVA pathway, resulted in drastic decrease in limonoid levels whereas their biosynthesis was unaffected with fosmidomycin mediated plastidial methylerythritol 4-phosphate (MEP) pathway inhibition (Figure 4). This was also conspicuous, as the expression level of genes encoding for the rate-limiting enzyme of MVA pathway, 3-hydroxy-3-methyl-glutaryl-coenzyme A reductase (HMGR) was comparatively higher to that of deoxyxylulose-phosphate synthase (DXS) of MEP pathway in different tissues and also in the in vitro grown cells as evident from real-time PCR analysis (Figure 5). This chapter also deals with the cloning of putative acyltransferase genes in neem. Neem limonoids being triterpenoids are biosynthesized from the triterpene intermediate squalene, which en route to 2,3 oxidosqualene leading to cyclized triterpene intermediate which further modifies to form protolimonoids. Limonoids further undergoes numerous functionalizations such as redox reactions, hydroxylation, acetylation, tigloylation etc. to form several limonoids in multistep pathway, which are yet to be elucidated. In order to understand limonoid diversity in neem, putative acyltransferase ORFs were selected from neem transcriptome for cloning. The selected acyltransferases matched with BAHD family of plant acetyltransferases, which transfers group from CoA to natural products. The two full-length ORFs were cloned into bacterial and yeast vector systems and characterization of the expressed protein to understand its function with limonoids and/ other terpene or non-terpene alcohols as substrates.
AcSIR

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35

Walker, Michael John. "Safeguarding food : advances in forensic measurement science and the regulation of allergens, additives and authenticity." Thesis, Kingston University, 2016. http://eprints.kingston.ac.uk/37907/.

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This commentary reports on work published between 2005 and 2015 forming a record of a varied career building technical competence alongside strategic skills in the analytical chemistry and molecular biology of food. The unifying theme is practice based problem solving in the scientific regulation and enforcement of food safety and authenticity. The work demonstrates advances in sound, forensically robust, measurement science addressing problems arising from food additives, food authenticity and food allergens. In particular the mature discipline that underpins the regulation and enforcement of food additives is shown to be needed for the management of food allergens. The background to food regulation and enforcement is described alongside technical appeals in the official food control system to develop societally meaningful food surveillance, supported by a sustainable UK based official food control infrastructure (Public Analyst service) at the interface between science and the law. For food additives, publication of previously un-collated results informs regulatory practice and demonstrates the value of scientific collaboration between both jurisdictions on the island of Ireland. A definitive strategy is reported for the chemical analysis and risk assessment of ‘jelly mini-cups’ in which gel forming additives have caused choking fatalities and solutions to problems in the analysis of two illegal toxic additives, morpholine and dimethyl yellow are described. For food allergens the portfolio includes the first study to assess in quantitative terms the level of risk to peanut allergic consumers in take-away catering, leading to better training and similar work on coeliac disease and the availability of ‘gluten-free’ food. Systematic assessment of food allergen analysis and a programme of analytical improvement to support allergen risk assessment and risk management are discussed. A narrative account of an allergen related food sabotage incident and the subsequent Crown Court case and previously uncollated reports of court-sanctions for allergen noncompliances, severe incidents and deaths make key policy and practice recommendations for improvement in these areas. Page 7 of 162 In the study of food authenticity a critical review describes the nitrogen content of important species in the food supply chain as a proxy in the quantitative estimation of high value flesh foods in compound products. An exemplar study follows determining previously unavailable nitrogen factor data for farmed salmon and salmon frame mince. A critical survey of the up skilling of the UK Official Food Control System in DNA food authenticity techniques and major historical and contemporary reviews of food fraud (butter and horsemeat) support substantial policy and analytical recommendations. Many threats to our food supply can be assessed and managed only with the assistance of measurement science. Integrating elements of chemico-legal practice including lessons learned from ‘referee analyses’ and metrology in chemistry this commentary concludes with a synthesis describing major changes in the UK scientific food control system stemming from the author’s involvement in the ‘Elliott Review’ and recommendations for an international programme of work on food allergen analysis with interconnected learning for the benefit of the analytical and regulatory communities and society at large.

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Chen, Weiqi. "Active module identification in biological networks." Thesis, University of Birmingham, 2018. http://etheses.bham.ac.uk//id/eprint/8542/.

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This thesis addresses the problem of active module identification in biological networks. Active module identification is a research topic in network biology that aims to identify regions in network showing striking changes in activity. It is often associated with a given cellular response and expected to reveal dynamic and process-specific information. The key research questions for this thesis are the practical formulations of active module identification problem,the design of effective, efficient and robust algorithms to identify active modules, and the right way to interpret identified active module. This thesis contributes by proposing three different algorithm frameworks to address the research question from three different aspects. It first explores an integrated approach of combining both gene differential expression and differential correlation, formulates it as a multi-objective problem, and solves it on both simulated data and real world data. Then the thesis investigates a novel approach that brings in prior knowledge of biological process, and balances between pure data-driven search and prior information guidance. Finally, the thesis presents a brand new framework of identifying active module and topological communities simultaneously using evolutionary multitasking, accompanied with a series of task-specific algorithm designs and improvements, and provides a new way of integrating topological information to help the interpretation of active module.

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Leeson-Schatz, Joseph. "The technological narrative of biological evolution." Diss., Online access via UMI:, 2009.

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Tunstall, Lucy Victoria. "Synthesis and biological evaluation of three novel antimalarial series." Thesis, Keele University, 2018. http://eprints.keele.ac.uk/5150/.

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This research explored the optimisation of three novel antimalarial series based on the MMV compound leads shown below. Extensive research began to optimise these potent hits through exploration of multiple functional group substitutions on two or more sites of the core structure (shown above). The highest activity tetrahydro-β-carboline analogue discovered during this research was LVT30 (IC50=1μM) which possesses an absent C3 interaction and a p-trifluoromethyl R2 substitution. Meanwhile, of the spirocyclic subset of derivatives, a high nanomolar activity compound was generated LVT86 (IC50=960 nM), possessing a butyl R1 chain and a m-trifluoromethyl R2 group and future work will include optimisation of this analogues pharmacokinetic properties. The most fruitful subseries of this project was a catalogue of 2-iminobenzimidazole compounds. In an attempt to optimise activity and increase potency, exploration involved variation of all three R positions and as a result, generated the most potent derivative over all three series. Compound LVTa95 possesses an inhibitory concentration of 33.4 nM and exhibits: a pentane R1 group, 2,4-dichloro R2 substitution and a hydroxy R3 group. As this compound existed as enantiomers, they were subsequently separated, and it was found both stereoisomers had similar activity.

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Bell, Alexander Charlton. "Formal computational models of biological systems." Thesis, University of Sheffield, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.301423.

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Kumlin, Terese. "Social science students’ perceptions of motivational methods and approaches in science class." Thesis, Malmö högskola, Fakulteten för lärande och samhälle (LS), 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:mau:diva-36394.

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How to motivate students effectively is a question teachers have asked for thousands ofyears. In my teaching program at Malmö University, a variety of teaching methods andapproaches, that also increase motivation, have come into focus. These include:teaching at the right level, using a variety of teaching methods, seeing every student,being enthusiastic about the material, using formative evaluation, connecting lessons tostudents’ everyday life, and adapting classes to students’ interests. The aim of this studyis to find out how secondary students in a social science program perceive teachingmethods and approaches aimed at increasing motivation, and determine which methodsthey perceive as most/least effective. The study used both qualitative and quantitativemethods. 23 upper-secondary students from a class at a school in southern Swedenwere interviewed in four focus groups, where participants were purposefully sampled.10 of these students were also asked to complete a questionnaire ranking the teachingmethods and approaches on a scale of 1-7 (where 1 was most effective at increasingmotivation and 7 least effective), and the mean values of these scores were used in theanalysis. A phenomenological approach and content analysis were used to code andanalyze the data. Students perceived all of the motivational methods to be effective, themost effective being teaching lessons at the right level, followed by using a variety ofteaching methods, with mean values of 1.9 and 3.2, respectively. Adapting lessons tostudents’ interests and connecting them to everyday life were the least effective, withmean values of 5.6 and 5.7, respectively. The categories of teachers having a positiveattitude towards the material and the students, and seeing every student, had the samemean value, 3.8, while formative evaluation had a mean value of 3.9. When trying tomotivate students, it would thus appear more effective to make sure that lessons aretaught at the right level and that teachers vary the lessons, than to adapt lessons tostudents’ interests or connect the material to everyday life. While this was a small studyand the findings cannot be generalized to school populations, they are of high interestfor the researcher.

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Koblentz, Gregory D. "Pathogens as weapons : the international security implications of biological warfare." Thesis, Massachusetts Institute of Technology, 2004. http://hdl.handle.net/1721.1/28498.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Political Science, 2004.
Includes bibliographical references (p. 183-222).
This dissertation assesses the international security implications of biological weapons and the strategic consequences of their proliferation. It examines the impact of biological weapons on four key areas of concern for international security: proliferation, deterrence, civil-military relations, and threat assessment. The dissertation draws upon a range of theories from the field of security studies and a wealth of newly available information regarding the biological weapons programs of Iraq, the former Soviet Union, the United States, United Kingdom, and South Africa. My analysis yields four major findings. First, it is extremely difficult to prevent the spread of biological warfare capabilities to actors that want them and these actors tend to be motivated by a desire to challenge the status quo. Contrary to conventional wisdom, biological weapons have utility across the spectrum of conflict and are well suited to supporting asymmetric strategies against stronger opponents. Second, biological weapons do not confer the deterrent benefits associated with nuclear weapons and will undermine reliance on deterrence as a security strategy. Biological weapons are not suitable as strategic deterrents due to the uncertainty regarding their effects, the availability of defenses and the reliance of these weapons on secrecy and surprise for their effectiveness. The accessibility of these weapons to a diverse range of actors, including terrorists, and the ease of clandestine attacks undermines the effectiveness of deterrence as a security strategy. Third, civilian oversight of biological warfare programs is hindered by the intense secrecy that shrouds these programs. This lack of supervision leads to abuse and corruption by
(cont.) program managers, impedes adherence to international agreements, and increases the risk of such programs becoming the source of materials for terrorists. Fourth, states tend to have flawed assessments of their opponent's biological warfare capabilities and intentions. The result of such flawed assessments may be worst-case planning and overreaction to a perceived threat or complacency and continued vulnerability to attack. Biological. weapons will continue to exert a destabilizing influence on international security until defenses against these weapons are improved, governments can reliably detect biological weapons activities, the proliferation of biological weapons materials and expertise is staunched, and the norms against their possession and use are strengthened.
by Gregory D. Koblentz.
Ph.D.

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Nadeau, Phillip Michel. "Ultra-low energy electronics for synthetic biological sensors." Thesis, Massachusetts Institute of Technology, 2016. http://hdl.handle.net/1721.1/107288.

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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2016.
This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student-submitted PDF version of thesis.
Includes bibliographical references (pages 143-151).
Advances in microelectronics have contributed to the wide availability of wearable sensor nodes for vital signs monitoring. Without additional pieces however, electronics by themselves can perform only basic detection tasks. This work explores the "functionalization" of low-power low-cost microelectronics with equally inexpensive genetically engineered whole-cell microbial sensors to aid in sensing the chemical domain. The driving application is an ingestible sensor for bleeding detection in the gastrointestinal tract. First, we present in vivo measurements of energy-harvesting in the gastrointestinal tract in order to set a power budget for the proposed ingestible sensor. The harvester is based on metal electrodes that react with the stomach contents to generate energy. Here we demonstrate 0.23 [mu]W of average power per mm2 of electrode area delivered to a load for a mean of 6.1 days. Next, we present the design of an ultra-low energy relaxation oscillator. The oscillator can be used as a slow clock source for waking the ingestible sensor from sleep mode and for running slow analog measurements. The core oscillator uses an 18-transistor 3-stage architecture designed to minimize short circuit current and consumes only switching energy across a wide range of Vdd. At 0.6 V, the oscillator system consumes 230 fJ/cycle and can operate across a wide range of low frequencies from 18 Hz to 1000 Hz. Finally, we present the design of an ultra-low energy readout system for genetically engineered whole-cell biosensors. A time-based threshold-crossing scheme is used to quantify the low-intensity bioluminescence incident on the phototransistor detector. The system includes a 900 MHz transmitter, controller, and support electronics on the chip in order to demonstrate molecule-to-wireless-bits sensing on a nanowatt power budget. With the continued expansion of the Internet of Things, the concepts in this thesis can be used to further enhance the capabilities of low-cost microelectronics in the area of vital signs and physiological monitoring. By conferring the ability to sense small molecules using a synthetic biology foundation, new types of low-cost diagnostics can be envisioned for connected health monitoring.
by Phillip Michel Nadeau.
Ph. D.

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Creager, Douglas A. (Douglas Adam) 1979. "A modular architecture for biological microscope image analysis." Thesis, Massachusetts Institute of Technology, 2003. http://hdl.handle.net/1721.1/87398.

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Mellen, Jeffrey C. (Jeffrey Clark) 1981. "Visualization and management of large biological imaging datasets." Thesis, Massachusetts Institute of Technology, 2004. http://hdl.handle.net/1721.1/28451.

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Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2004.
Includes bibliographical references (p. 83).
The Open Microscopy Environment (OME) image browser enables biologists to quickly analyze, manipulate and modify large imaging datasets. The browser includes a variety of features that facilitate image classification, annotation, visualization, and organization. The browser displays image metadata using a variety of techniques, including visual cues, context-sensitive overlays, and color-coding. The application explicitly supports visualization of screening datasets, but also supports multidimensional images, as well as standalone images. When integrated with the rest of the applications of the OME client software, the browser allows users to view images in greater resolution, analyze multiple dimensions, and in future releases will support analysis routines.
by Jeffrey C. Mellen.
M.Eng.

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45

Stanescu, Ana. "Semi-supervised learning for biological sequence classification." Diss., Kansas State University, 2015. http://hdl.handle.net/2097/35810.

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Doctor of Philosophy
Department of Computing and Information Sciences
Doina Caragea
Successful advances in biochemical technologies have led to inexpensive, time-efficient production of massive volumes of data, DNA and protein sequences. As a result, numerous computational methods for genome annotation have emerged, including machine learning and statistical analysis approaches that practically and efficiently analyze and interpret data. Traditional machine learning approaches to genome annotation typically rely on large amounts of labeled data in order to build quality classifiers. The process of labeling data can be expensive and time consuming, as it requires domain knowledge and expert involvement. Semi-supervised learning approaches that can make use of unlabeled data, in addition to small amounts of labeled data, can help reduce the costs associated with labeling. In this context, we focus on semi-supervised learning approaches for biological sequence classification. Although an attractive concept, semi-supervised learning does not invariably work as intended. Since the assumptions made by learning algorithms cannot be easily verified without considerable domain knowledge or data exploration, semi-supervised learning is not always "safe" to use. Advantageous utilization of the unlabeled data is problem dependent, and more research is needed to identify algorithms that can be used to increase the effectiveness of semi-supervised learning, in general, and for bioinformatics problems, in particular. At a high level, we aim to identify semi-supervised algorithms and data representations that can be used to learn effective classifiers for genome annotation tasks such as cassette exon identification, splice site identification, and protein localization. In addition, one specific challenge that we address is the "data imbalance" problem, which is prevalent in many domains, including bioinformatics. The data imbalance phenomenon arises when one of the classes to be predicted is underrepresented in the data because instances belonging to that class are rare (noteworthy cases) or difficult to obtain. Ironically, minority classes are typically the most important to learn, because they may be associated with special cases, as in the case of splice site prediction. We propose two main techniques to deal with the data imbalance problem, namely a technique based on "dynamic balancing" (augmenting the originally labeled data only with positive instances during the semi-supervised iterations of the algorithms) and another technique based on ensemble approaches. The results show that with limited amounts of labeled data, semisupervised approaches can successfully leverage the unlabeled data, thereby surpassing their completely supervised counterparts. A type of semi-supervised learning, known as "transductive" learning aims to classify the unlabeled data without generalizing to new, previously not encountered instances. Theoretically, this aspect makes transductive learning particularly suitable for the task of genome annotation, in which an entirely sequenced genome is typically available, sometimes accompanied by limited annotation. We study and evaluate various transductive approaches (such as transductive support vector machines and graph based approaches) and sequence representations for the problems of cassette exon identification. The results obtained demonstrate the effectiveness of transductive algorithms in sequence annotation tasks.

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Seier, Edith, and Karl H. Joplin. "Introduction to STATISTICS in a Biological Context." Digital Commons @ East Tennessee State University, 2011. http://amzn.com/1463613377.

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47

Campos, Joana Monteiro de. "TRIB2 in human AML : a biological and clinical investigation." Thesis, University of Glasgow, 2016. http://theses.gla.ac.uk/7499/.

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Acute myeloid leukemia (AML) involves the proliferation, abnormal survival and arrest of cells at a very early stage of myeloid cell differentiation. The biological and clinical heterogeneity of this disease complicates treatment and highlights the significance of understanding the underlying causes of AML, which may constitute potential therapeutic targets, as well as offer prognostic information. Tribbles homolog 2 (Trib2) is a potent murine oncogene capable of inducing transplantable AML with complete penetrance. The pathogenicity of Trib2 is attributed to its ability to induce proteasomal degradation of the full length isoform of the transcription factor CCAAT/enhancer-binding protein alpha (C/EBPα p42). The role of TRIB2 in human AML cells, however, has not been systematically investigated or targeted. Across human cancers, TRIB2 oncogenic activity was found to be associated with its elevated expression. In the context of AML, TRIB2 overexpression was suggested to be associated with the large and heterogeneous subset of cytogenetically normal AML patients. Based upon the observation that overexpression of TRIB2 has a role in cellular transformation, the effect of modulating its expression in human AML was examined in a human AML cell line that expresses high levels of TRIB2, U937 cells. Specific suppression of TRIB2 led to impaired cell growth, as a consequence of both an increase in apoptosis and a decrease in cell proliferation. Consistent with these in vitro results, TRIB2 silencing strongly reduced progression of the U937 in vivo xenografts, accompanied by detection of a lower spleen weight when compared with mice transplanted with TRIB2- expressing control cells. Gene expression analysis suggested that TRIB2 modulates apoptosis and cell-cycle sensitivity by influencing the expression of a subset of genes known to have implications on these phenotypes. Furthermore, TRIB2 was found to be expressed in a significant subset of AML patient samples analysed. To investigate whether increased expression of this gene could be afforded prognostic significance, primary AML cells with dichotomized levels of TRIB2 transcripts were evaluated in terms of their xenoengraftment potential, an assay reported to correlate with disease aggressiveness observed in humans. A small cohort of analysed samples with higher TRIB2 expression did not associate with preferential leukaemic cell engraftment in highly immune-deficient mice, hence, not predicting for an adverse prognosis. However, further experiments including a larger cohort of well characterized AML patients would be needed to clarify TRIB2 significance in the diagnostic setting. Collectively, these data support a functional role for TRIB2 in the maintenance of the oncogenic properties of human AML cells and suggest TRIB2 can be considered a rational therapeutic target. Proteasome inhibition has emerged as an attractive target for the development of novel anti-cancer therapies and results from translational research and clinical trials support the idea that proteasome inhibitors should be considered in the treatment of AML. The present study argued that proteasome inhibition would effectively inhibit the function of TRIB2 by abrogating C/EBPα p42 protein degradation and that it would be an effective pharmacological targeting strategy in TRIB2-positive AMLs. Here, a number of cell models expressing high levels of TRIB2 were successfully targeted by treatment with proteasome inhibitors, as demonstrated by multiple measurements that included increased cytotoxicity, inhibition of clonogenic growth and anti-AML activity in vivo. Mechanistically, it was shown that block of the TRIB2 degradative function led to an increase of C/EBPα p42 and that response was specific to the TRIB2-C/EBPα axis. Specificity was addressed by a panel of experiments showing that U937 cells (express detectable levels of endogenous TRIB2 and C/EBPα) treated with the proteasome inhibitor bortezomib (Brtz) displayed a higher cytotoxic response upon TRIB2 overexpression and that ectopic expression of C/EBPα rescued cell death. Additionally, in C/EBPα-negative leukaemia cells, K562 and Kasumi 1, Brtz-induced toxicity was not increased following TRIB2 overexpression supporting the specificity of the compound on the TRIB2-C/EBPα axis. Together these findings provide pre-clinical evidence that TRIB2- expressing AML cells can be pharmacologically targeted with proteasome inhibition due, in part, to blockage of the TRIB2 proteolytic function on C/EBPα p42. A large body of evidence indicates that AML arises through the stepwise acquisition of genetic and epigenetic changes. Mass spectrometry data has identified an interaction between TRIB2 and the epigenetic regulator Protein Arginine Methyltransferase 5 (PRMT5). Following assessment of TRIB2‟s role in AML cell survival and effective targeting of the TRIB2-C/EBPα degradation pathway, a putative TRIB2/PRMT5 cooperation was investigated in order to gain a deeper understanding of the molecular network in which TRIB2 acts as a potent myeloid oncogene. First, a microarray data set was interrogated for PRMT5 expression levels and the primary enzyme responsible for symmetric dimethylation was found to be transcribed at significantly higher levels in AML patients when compared to healthy controls. Next, depletion of PRMT5 in the U937 cell line was shown to reduce the transformative phenotype in the high expressing TRIB2 AML cells, which suggests that PRMT5 and TRIB2 may cooperate to maintain the leukaemogenic potential. Importantly, PRMT5 was identified as a TRIB2-interacting protein by means of a protein tagging approach to purify TRIB2 complexes from 293T cells. These findings trigger further research aimed at understanding the underlying mechanism and the functional significance of this interplay. In summary, the present study provides experimental evidence that TRIB2 has an important oncogenic role in human AML maintenance and, importantly in such a molecularly heterogeneous disease, provides the rational basis to consider proteasome inhibition as an effective targeting strategy for AML patients with high TRIB2 expression. Finally, the identification of PRMT5 as a TRIB2-interacting protein opens a new level of regulation to consider in AML. This work may contribute to our further understanding and therapeutic strategies in acute leukaemias.

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Lee, Yun Jung Ph D. Massachusetts Institute of Technology. "Nanostructured electrodes for lithium ion batteries using biological scaffolds." Thesis, Massachusetts Institute of Technology, 2009. http://hdl.handle.net/1721.1/54578.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Materials Science and Engineering, 2009.
Cataloged from PDF version of thesis.
Includes bibliographical references (p. 134-139).
Without doubt, energy and environment are becoming central issues for the future. In this regard, not only device performance but also environmentally sustainable ways of making energy device is important. To meet these needs, a M13 virus based biological toolkit was utilized in this work for controlling nanostructures of lithium ion battery electrodes which is a critical process in developing electrodes materials for high power applications. The M13 biological toolkit provides specificity, versatility and multifunctionality for controlling nanostructure of the materials using basic biological principles. The versatile E4 virus template could nucleate active cathode materials at low temperature by an environmentally benign method. High power lithium ion battery cathode materials were fabricated using genetically programmed multifunctional virus as a versatile scaffold for the synthesis and assembly of materials. A novel strategy for specifically attaching electrochemically active materials to conducting carbon nanotubes networks through biological molecular recognition was developed by manipulating the two-genes of the M13 virus. Viral amorphous iron phosphates cathodes achieved remarkable and otherwise impossible high power performance using this multifunctional virus. This environmentally benign low temperature biological scaffold could facilitate new types of electrode materials by activating a class of materials that have been excluded because of their extremely low electronic conductivity. Architecting nanostructures was further extended to activate noble metal alloy nanowires as anodes for lithium ion batteries by alleviating mechanical stress.
(cont.) By demonstrating electrochemical activity of noble metal alloy nanowires with various compositions, the M13 biological toolkit extended its utility for the study on the basic electrochemical property of materials.
by Yun Jung Lee.
Ph.D.

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49

Eren, Kemal. "Application of biclustering algorithms to biological data." The Ohio State University, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=osu1332533492.

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Cowman, Tyler. "Compression and Version Control of Biological Networks." Case Western Reserve University School of Graduate Studies / OhioLINK, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=case160701146645758.

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Dissertations / Theses on the topic 'Biological Science'

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