Masters Degrees (Biochemistry)

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A critical analysis of research done to identify conceptual difficulties in acid-base chemistry.
(2009) Halstead, Sheelagh Edith.; Anderson, Trevor Ryan.
The literature review shows that student alternative conceptions or misconceptions are important for teaching and learning. Causes of such student difficulties may include the counter-intuitive nature of some chemistry concepts or to instruction itself. However, over 30 years research into student conceptual difficulties has had little impact on teaching and learning chemistry. In this study, a critical analysis and synthesis of published research into student conceptions in acid-base chemistry was carried out in the naturalist nomothetic paradigm using a constructivist framework. Historical models which were included were an operational macroscopic model and the theoretical Arrhenius and Brønsted models. Firstly, a comprehensive search strategy with defined inclusion/exclusion criteria identified 42 suitable reports which were mostly peer-reviewed. The identified research was not limited to Anglophone countries although Africa and South America were underrepresented and research among secondary students predominated. Then a critique of the research showed it was of variable quality and often poorly reported. An outcome was a set of guidelines for research into student conceptions. The variable quality and reporting of research then also necessitated a four-level framework to reflect the stability of descriptions of student difficulties. A new method for synthesis of descriptions of student conceptual difficulties was developed which entailed mapping qualitative data on the difficulties, which had been extracted from research publications, to propositional knowledge statements derived in this study. This was an iterative process which simultaneously honed descriptions of difficulties and illuminated propositional knowledge implicated in them. The second major outcome was synthesized descriptions of 10 student difficulties with acid-base species, 26 difficulties with acid-base properties and 17 difficulties concerning terminology and symbolism particular to acid-base chemistry. Some conceptions were also found to have been mis-reported as ‘misconceptions’. The difficulties could be broadly due to student conceptions concerning acid-base models, or students not relating empirical observations to theoretical models or their poor understanding of underlying chemical principles. Some difficulties were found to have been over-researched, while further work was needed to clarify the nature some difficulties with conceptions of bases, acid-base reactions, and symbolism used in acid-base chemistry. The third major outcome from the synthesis was 218 propositional knowledge statements which were shown to be suitable for teaching high-school students, avoided hybrid historical models and were acceptable to expert chemists. These propositional statements were integrated as a set of 11 concept maps. The maps showed the hierarchy and interconnectedness of concepts as well as the propositional links which had been implicated in the difficulties. Furthermore the concept maps indicated critical concepts where teaching in each topic should focus as well as cross-linked concepts that can be used to integrate different aspects of the topic. Accordingly they contribute to PCK in the acidbase topic as they represent the fine-grained yet well integrated conceptual knowledge characteristic of a teacher with highly developed PCK.
Microbiology honours students' conceptual development during a beer brewing teaching learning sequence (TLS)
(2010) Tekane, Rethabile Reginalda.; Anderson, Trevor Ryan.; Hunter, Charles Haig.
Brewing is defined as “the combined processes of preparing beverages from the infusion of sound grains that have undergone sprouting, and the subsequent fermentation of the sugary solution produced, by yeast-whereby a proportion of the carbohydrate is converted to ethanol and carbon-dioxide.” It is a complex process that requires knowledge of concepts from disciplines such as biochemistry, chemistry, engineering, microbiology and physics. The micro-brewery apparatus at the University of KwaZulu-Natal is used by the discipline of microbiology as part of a brewing exercise to introduce students to industrial microbiology with the aim of developing their conceptual understanding of the process. So far, though, no research has been conducted in order to fully establish the effectiveness of this exercise in developing such understanding of the brewing process. The aim, therefore, of this study was to investigate the effectiveness of a micro-brewing Teaching-Learning Sequence (TLS) that incorporates the micro-brewery, for promoting students‟ understanding of the scientific concepts of relevance to the brewing process. The following research questions were addressed: 1) What concepts are essential for understanding the process of beer brewing? 2) Did those students with sound conceptions develop deeper understanding during the TLS? 3) Did students show any conceptual difficulties with the brewing concepts? 4) Did any remediation of such difficulties occur during the TLS? 5) Did students show retention of (mis)understanding two months after the brewing practical? 6) What were students‟ attitudes and motivational levels like during the brewing practical? 7) How well did students rate their experiences of the whole TLS? 8) How well did students‟ motivational levels and their rating of the TLS correlate with any changes in understanding? The study involved ten microbiology honours students subjected to a TLS which consisted of: i) three brewing lectures aimed at introducing students to the brewing process; ii) pre- & post tests including concept mapping tasks aimed at addressing research questions 2, 3 & 4; iii) a brewing practical aimed at facilitating students‟ development of mental models and conceptual understanding of the brewing process and their motivation and attitude to this exercise (addressing question 6 & 8); iv) a group discussion which involved a group tasting session and the evaluation and discussion of each group‟s final beer product; v) semi-structured interviews to establish the source (s) of students‟ difficulties and their retention of knowledge or difficulties (questions 2, 4, & 5 addressed); and vi) an evaluation questionnaire aimed at obtaining student opinion of the TLS (addressing question 7). The data obtained was analyzed via inductive analysis. The results revealed the following brewing difficulties: i) belief that glycolysis reactions are non-consecutively linked chemical reactions which are independent of one another; ii) confusion that whirl-pooling cools the wort; and iii) belief that the final specific gravity value is a measure of the amount of sugars converted to ethanol. Comparison between the pre- & post test responses indicated that some students‟ (B, D & K) conceptual understanding including integrated knowledge of the brewing process improved during the TLS and their brewing difficulties were remediated. In contrast, other students‟ (A, C, E, G, H, J & I) conceptual understanding did not improve during the TLS and their brewing difficulties were not remediated. There was also a positive correlation between student attitudes and motivation towards the brewing practical and the quality of their learning outcomes. Students (B, D & K) who showed high motivational levels and cognitively and physically took part in the TLS showed improved conceptual understanding of the brewing process and retention of knowledge, while those showing low motivational levels did not improve. Furthermore, there are students (G, H & J) who showed high motivational levels during the TLS but their conceptual understanding of the brewing process did not improve. The results obtained suggest that the TLS, based on the micro-brewery apparatus, was at least partially effective in facilitating the development of students‟ conceptual understanding and visualization of the brewing process and the remediation of some of their difficulties, which in some case correlated well with their motivational levels and attitudes towards the brewing exercise. More research is however required to fully confirm the usefulness of such TLSs in brewing education.
Nickel accumulation and tolerance in Berkheya coddii and its application in phytoremediation.
(1998) Slatter, Kerry.; Anderson, Trevor Ryan.
As pollution becomes an ever-increasing threat to the global environment pressure is being placed upon industry to "clean-up" its act, both in terms of reducing the possibility of new pollution and cleaning up already contaminated areas. It was with this in mind that Amplats embarked on a phytoremediation project to decontaminate nickel-polluted soils at one of their mine sites in Rustenburg, using the nickel hyperaccumulating plant, Berkheya coddii, which is endemic to the serpentine areas near Barberton, Mpumalanga. Besides the applied aspects pertaining to the development of the phytoremediation process we were also interested in more academic aspects concerning the transport and storage of nickel within the plant tissues. In order that the progress of nickel could be followed through the plant, a radio-tracer of ⁶³nickel was placed in the soil and its movement within the plant followed by analysing the plant material, at set intervals, using a liquid scintillation counter. From these studies it was found that the nickel appeared to be transported from the roots to the leaves of the plant via the xylem. It appeared that the nickel was not confined to the leaf to which it was initially transported and so movement of nickel within the phloem also appears to occur in B. coddii. As nickel is generally toxic to most plants, hyperaccumulators contain elements that nullify the toxic effect of nickel. In the case of Berkheya coddii it is thought that the accumulated nickel is bound to malate to form a harmless nickel complex. With this in mind an assay for L-malic acid was developed in order that any effect on L-malic acid, caused by growing Berkheya coddii on soils containing various concentrations of nickel, could be determined. This method also enabled comparisons of L-malic acid concentrations to be made between hyperaccumulators and non-hyperaccumulators of various plant species. From the L-malic acid comparisons it was found that the nickel concentration within soils affected the levels of L-malic acid within B. coddii and that the levels of L-malic acid within B. coddii were greater than that of a closely related non-hyperaccumulator, suggesting that L-malic acid is indeed involved in the hyperaccumulation mechanism within B. coddii. B. coddii was chosen as the tool in nickel phytoremediation at Rustenburg Base Metal Refineries as it was found to accumulate up to 2.5% nickel in the dry biomass, it grows rapidly and has a large above-ground biomass with a well developed root system, and it is perennial and so does not need to be planted each season. Earlier work had shown that the nickel levels in the roots were comparatively low (up to 0.3% nickel in the dry material) and thus, for ease of harvesting and to ensure the continued vegetative growth of the plant on the planted sites, it was decided that the leaves and stems of the plants would be harvested at the end of each growing season. The plant was also found to accumulate low levels (0.006 - 0.3 %) of precious metals, including platinum, palladium and rhodium, within its above ground biomass, making it attractive for the remediation of certain soils that contain low levels of these metals. Before B. coddii could be introduced to the Rustenburg area a comparison of the climatic and soil conditions of Barberton, the area to which B. coddii is endemic, and Rustenburg needed to be made to ensure that the plant would be able to survive the new conditions. These comparisons showed that Rustenburg receives on average, 484 mm less rain per year than Barberton, indicating that irrigation was required when the Rustenburg sites were planted out with B. coddii, in order to reduce water stress. Rustenburg was also found to be, on average, 4.6°C warmer than Barberton, but as B. coddii growth responds to wet/dry seasons, as opposed to hot/cold seasons, it was not felt that this temperature difference would have a negative effect on the growth of the plants. The soil comparisons showed the contaminated Rustenburg sites to be serpentine-like in nature, with respect to Barberton, again giving confidence that the plant would adapt to the conditions occurring at the contaminated sites. However, to ensure optimal growth, nutrient experiments were also performed on B. coddii to ascertain the ideal macronutrient concentrations required, without inhibiting nickel uptake. These trials indicated that the individual addition of 250 mg/l ammonium nitrate, 600 mg/l calcium phosphate, 2 000 mg/l calcium chloride, 600 mg/l potassium chloride and 250 mg/l magnesium sulphate enhanced plant growth and nickel uptake, suggesting that, for phytoremediation purposes, these nutrients should be added to the medium in which the plants are growing. The growth-cycle of naturally occurring B. coddii plants in Barberton was also studied in order that seedlings could be germinated, in greenhouses, at the correct time of year so that the plants could be sown as the naturally occurring plants were germinating. From this information the seeds of the plants could be collected at the correct time of year and the above ground biomass harvested when the nickel concentrations were at their highest. It was found that the plants began to germinate as the first rains fell, which was generally at the beginning of September, and plant maturity was reached at about five months, after which flowers were produced. Seeds were produced from the flowers and these matured and were wind-dispersed one month to six weeks after full bloom, usually during February. The plants then started to die back and dry out and dormancy was reached about nine months after germination, generally in about mid- to late- May. It was found that the nickel concentration was at its highest about one month after the plants had begun to dry out and thus it was decided that the above ground biomass would usually be harvested at the end of April each season, in order to achieve maximum nickel recovery. Finally, in order that the plant's potential for use in phytoremediation could be fully assessed, field trials at the contaminated sites in Rustenburg were performed. Germination procedures were developed for the mass production of B. coddii and it was found that, although fully formed plants could be propagated in tissue culture, it was cheaper and faster to germinate the seeds in speedling trays, containing a zeolite germination mix, in greenhouses. It was also found that the seeds had a low germination rate, due to dehydration of the embryos and thus, in order to obtain the number of plants required, four to five times the amount of seeds needed to be sown. The two-month-old seedlings were transferred to potting bags, containing a mixture of potting soil and RBMR soil, and grown up in the greenhouse for a further three months. This growth period allowed B. coddii to adapt to the RBMR soil and also ensured that the plants were relatively healthy when transplanted into three prepared sites at RBMR. The plants were allowed to grow for the entire season after which the above ground biomass, comprising the leaves and stems, was harvested, dried and then ashed in an ashing vessel designed by the author, with the help of Mr K Ehlers. The ashed material was acid-leached with aqua regia in order that the base metals (mainly nickel) and precious metals could be removed from the silicates and carbonised material. The acid solution was then neutralised, causing the base metals (mainly nickel) and precious metals to be precipitated. This precipitate was then smelted with a flux in order that nickel buttons could be formed. Thus, from all the phytoremediation trials it was found that this process is highly successful in employing B. coddii for the clean-up of nickel-contaminated sites. This constitutes the first time that such a complete phytoremediation process has ever been successfully developed with B. coddii as the phytoremediation tool. It also appears to be the first time that phytoremediation has been performed "commercially" to produce a saleable metal product. The success of this project has stimulated Amplats to continue with, and expand it, to include more studies on phytoremediation as well as in the biomining of certain areas containing very low levels of precious metals which, with conventional techniques, were previously not worth mining.
Students' use of diagrams for the visualisation of biochemical processes.
(2003) Hull, Tracy Lee.; Grayson, Diane J.; Anderson, Trevor Ryan.
Research into the usefulness of scientific diagrams as teaching and learning tools has revealed their great effectiveness in reinforcing and replacing text; summarizing, clarifying, grouping and comparing information; illustrating abstract concepts and spatial relations between concepts; and aiding understanding and integration of knowledge. However, these advantages are not always realised as diagram effectiveness depends on the student's cognitive ability, visual literacy and prior knowledge. In biochemistry, flow diagrams are used as tools for the visualisation of biochemical processes, the abstract nature of which presents problems to students, probably because the depicted content is beyond their perceptual experience. In this study, we define visualisation as the entire process from the perception of an external representation (e.g. diagram), its internal processing, and the expression of a mental model of the represented content. Therefore, visualisation incorporates reasoning processes and interactions with a student's conceptual knowledge, in their construction of a mental model. Students' visualisation difficulties, in terms of conceptual and reasoning difficulties, have been well researched in areas such as physics and chemistry, but neglected in biochemistry, especially with respect to the use of diagrams as visualisation tools. Thus the aim of this study was to investigate students' use of diagrams for the visualisation of biochemical processes, and to identify the nature, and potential sources of students' conceptual, reasoning and diagram-related difficulties revealed during the visualisation process. The study groups ranged from 27 to 95 biochemistry students from the University of Natal and 2 to 13 local and international experts. Propositional knowledge was obtained from textbooks and from a questionnaire to experts. Data on student visualisation of biochemical processes was obtained from their responses to written and interview probes as well as student-generated diagrams. All data was subjected to inductive analysis according to McMillan and Schumacher (1993) and any difficulties that emerged were classified at levels 1- 3 on the framework of Grayson et al. (2001). The possible sources of difficulties were considered in terms of a model by Schonborn et al. (2003 & 2002). The results revealed the following major findings. The meaning of linear, cyclic and cascade biochemical processes was partially resolved by means of an extensive list of generic and distinguishing functional features obtained from experts. Attempts to clarify propositional knowledge of the complement system revealed a deficiency in our understanding of the functional relationship between the complement pathways and highlighted the need for further experimental laboratory work. Several students literally interpreted diagrams of the functional characteristics of biochemical processes (e.g. cyclic) as the spatial arrangement of the intermediates within cells (e.g. occur in "circles"), although in some cases, their verbal responses revealed that they did not hold this difficulty suggesting that they might hold more than one internal model of the process. Some students also showed difficulty using textbook diagrams to visualise the chemistry of glycolytic and complement reactions. In this regard, besides students' conceptual knowledge and reasoning ability, a major source of these difficulties included misleading symbolism and visiospatial characteristics in the diagrams, suggesting the need for improvement of diagram design through the use of clearer symbolism, the standardization of conventions, and improvement of visiospatial properties of diagrams. The results constituted further empirical evidence for the model of Schonbom et al. (2003 & 2002) and led to the proposal of a model of visualisation aimed at clarifying the highly complex and cognitive processes involved in individuals' visualisation of biochemical processes in living systems.

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Browsing Masters Degrees (Biochemistry) by Author "Anderson, Trevor Ryan."