Biochemistry

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Assessment of lysine damage during food processing.
(1985) Anderson, Trevor Ryan.; Quicke, George Venn.
The fluorodinitrobenzene (FONB), succinic anhydride (SA), dansyl chloride (DAN), dye-binding lysine (OBL), total lysine (TL), ninhydrin (NIN) and Tetrahymena lysine (TET) methods were compared for their ability to assess available lysine in soyaprotein heated in the absence or presence of glucose, lactose or xylose and in formaldehyde-treated lactalbumin. The reactive lysine methods showed comparable sensitivity to lysine damage in soyaprotein heated in the absence of sugar, the results indicating the presence of acid labile isopeptides and unidentified acid stable derivatives. Results for soyaprotein heated with glucose, lactose or xylose showed that the type of sugar and the extent of heat treatment has a strong influence on the progress of the Maillard reaction. Furthermore since fructoselysine (F-L) and lactulosyl-lysine (L-L) are colourless up to 30% loss of available lysine can occur without any change in product colour. The FONB method is the most sensitive for mildly damaged glucose-soya samples followed by DAN or OBL, SA and TL whereas for mildly damaged lactose-soya samples the order is OBL, FONB, SA, TL and DAN. For severely damaged samples the DAN or SA methods were the most sensitive followed by OBL, FONB and TL. Formylation of lactalbumin occurred more readily at higher formaldehyde concentrations. Exposure time had less effect while pH (5 and 9) had no effect. Methylene derivatives reached maximum levels sooner than the methylol compounds. Lysine and tyrosine but not histidine formed methylene bridges while tyrosine was found to condense with free formaldehyde during acid hydrolysis raising questions as to the interpretation of similar studies reported in the literature. The FONB, OBL and DAN methods were all very sensitive to this type of damage with the NIN and TL methods being less sensitive and the SA method being completely unsuitable. The TET assay is unsuitable for 'early' Maillard damage since at low sample-N levels growth is stimulated by its ability to utilise unavailable F-L and L-L while at higher N-levels growth is inhibited. No single method is most suitable for all types of damage. Furthermore, all except DAN and DBL are either too long, rather complicated, require expensive equipment or involve the use of dangerous chemicals. The DAN method appears promising but the problem of converting arbitrary fluorescence units to lysine values needs to be overcome. The DBL is recommended for routine analysis since it is simple, economical and highly sensitive to all lysine damage provided care is taken to optimise dye-binding for each type of material analysed.
Biochemistry students' difficulties with the symbolic and visual language used in molecular biology.
(2007) Gupthar, Abindra Supersad.; Anderson, Trevor Ryan.
This study reports on recurring difficulties experienced by undergraduate students with respect to understanding and interpretation of certain symbolism, nomenclature, terminology, shorthand notation, models and other visual representations employed in the field of Molecular Biology to communicate information. Based on teaching experience and guidelines set out by a four-level methodological framework, data on various topic-related difficulties was obtained by inductive analyses of students’ written responses to specifically designed, free-response and focused probes. In addition, interviews, think-aloud exercises and student-generated diagrams were also used to collect information. Both unanticipated and recurring difficulties were compared with scientifically correct propositional knowledge, categorized and subsequently classified. Students were adept at providing the meaning of the symbol “Δ” in various scientific contexts; however, some failed to recognize its use to depict the deletion of a leucine biosynthesis gene in the form, Δ leu. “Hazard to leucine”, “change to leucine” and “abbreviation for isoleucine” were some of the erroneous interpretations of this polysemic symbol. Investigations on these definitions suggest a constructivist approach to knowledge construction and the inappropriate transfer of knowledge from prior mental schemata. The symbol, “::”, was poorly differentiated by students in its use to indicate gene integration or transposition and in tandem gene fusion. Idiosyncratic perceptions emerged suggesting that it is, for example, a proteinaceous component linking genes in a chromosome or the centromere itself associated with the mitotic spindle or “electrons” between genes in the same way that it is symbolically shown in Lewis dot diagrams which illustrate covalent bonding between atoms. In an oligonucleotide shorthand notation, some students used valency to differentiate the phosphite trivalent form of the phosphorus atom from the pentavalent phosphodiester group, yet the concept of valency was poorly understood. By virtue of the visual form of a shorthand notation of the 3,5 phosphodiester link in DNA, the valency was incorrectly read. VSEPR theory and the Octet Rule were misunderstood or forgotten when trying to explain the valency of the phosphorus atom in synthetic oligonucleotide intermediates. Plasmid functional domains were generally well-understood although restriction mapping appeared to be a cognitively demanding task. Rote learning and substitution of definitions were evident in the explanation of promoter and operator functions. The concept of gene expression posed difficulties to many students who believed that genes contain the entity they encode. Transcription and translation of in tandem gene fusions were poorly explained by some students as was the effect of plasmid conformation on transformation and gene expression. With regard to the selection of transformants or the hybridoma, some students could not engage in reasoning or lateral thinking as protoconcepts and domain-specific information were poorly understood. A failure to integrate and reason with factual information on phenotypic traits, media components and biochemical pathways were evident in written and oral presentations. DNA-strand nomenclature and associated function were problematic to some students as they failed to differentiate coding strand from template strand and were prone to interchange the labelling of these. A substitution of labels with those characterizing DNA replication intermediates demonstrated erroneous information transfer. DNA replication models posed difficulties integrating molecular mechanisms and detail with line drawings, coupled with inaccurate illustrations of sequential replication features. Finally, a remediation model is presented, demonstrating a shift in assessment score dispersion from a range of 0 - 4.5 to 4 - 9 when learners are guided metacognitively to work with domain-specific or critical knowledge from an information bank. The present work shows that varied forms of symbolism can present students with complex learning difficulties as the underlying information depicted by these is understood in a superficial way. It is imperative that future studies be focused on the standardization of symbol use, perhaps governed by convention that determines the manner in which threshold information is disseminated on symbol use, coupled by innovative teaching strategies which facilitate an improved understanding of the use of symbolic representations in Molecular Biology. As Molecular Biology advances, it is likely that experts will continue to use new and diverse forms of symbolic representations to explain their findings. The explanation of futuristic Science is likely to develop a symbolic language that will impose great teaching challenges and unimaginable learning difficulties to new generation teachers and learners, respectively.
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.
The development of assays for atractyloside and its localisation in rat tissue.
(1991) Bye, Sandra Noel.; Dutton, Michael Francis.; Anderson, Trevor Ryan.
An extract of the tuber of Callilepis laureola is regarded as the source of a powerful therapeutic agent, known as Impila. Its use is associated with fatal hepatic and renal necrosis, the renal toxin being atractyloside (ATR). The aims of this study were threefold. Firstly, to generate a model set of biological specimens (urine, serum, liver and kidney) from rats dosed with 5-25 mg ATR/kg bwt. Secondly, to develop a competitive ELISA and HPLC method for the diagnosis of ATR poisoning employing the model specimens as test samples. Thirdly, to localise the target organs, cells and organelles of ATR, in vivo. The HPLC method necessitated the systematic development of the derivatisation of ATR with 9-anthryldiazomethane, sample clean up employing hexane, methanolic hydrochloric acid and a silica minicolumn, as well as the chromatographic conditions. Optimal resolution was obtained with a 3.9 x 150 mm NovaPak reverse phase column, fluorescence detection (excitation = 365 nm, emission = 425 nm) and a solvent system of MeOH:1M ammonium acetate:1M glacial acetic acid:water (38:2:2:58). This method has a detection limit of 0.001 ng ATR, shows a mean recovery of 89% and detected approximately 6.7 ug ATR/g wet weight of tuber tissue. The toxin was also detected in some of the urine samples at levels of about 200 pg/ml, but not in the serum. The production of antibodies to ATR for use in the ELISA and immunocytochemical investigations required the investigation of the conjugation procedure, carrier type, host species and immunization protocol. Optimal antibody yield, specificity and affinity was obtained with an acid-treated Salmonella minnesota bacterial carrier conjugated to ATR by carbodiimide, although there were indications of class switch inhibition and Tlymphocyte suppression by ATR. The development of the ELISA yielded a protocol involving the coating with a bovine serum albumin-ATR conjugate, blocking with bovine serum albumin, incubating the primary antibody at 4°C and detection with a secondary antibody-alkaline phosphate conjugate. This method detected ATR in both urine and serum from ATR-dosed rats and shows a detection limit of 10 ng. Since the less sensitive ELISA detected ATR in samples where the HPLC did not, this suggested that ATR is biotransformed in vivo, such that its retention time on a reverse phase column is affected, but not its epitope determinants. The results of the organ function assays demonstrated that, when administered intra-peritoneally, ATR is not hepatotoxic, but is a powerful nephrotoxin, targeting for the microvilli of the brush border of the proximal tubules, and compromising glomerular permselectivity and distal tubular function. In addition, this toxin inhibits proline transport in the proximal tubule, and therefore probably affects protein biosynthesis. Renal regeneration is noted 3 days post-dosing, as demonstrated by calcium excretion. Immunocytochemistry was optimised on tuber tissue and necessitated the intracellular fixation of the toxin, using carbodiimide, to prevent leaching out of the ATR. The toxin was encapsulated in vesicles in the tuber tissue. Atractyloside was also located in the kidney of ATR-treated rats, up to 72 hours after exposure, targeting the microvilli of the proximal tubule brush border, the mitochondrial cristae and specific sites on the Golgi apparatus membrane. Microvilli disruption and mitochondrial swelling was noted within 24 hours after exposure to the toxin while after 72 hours, loss of mitochondrial integrity was observed. The development of these diagnostic assays for ATR have provided the means to monitor the levels of this toxin in plant extracts and mammalian body fluids. Future work should include the identification of the hepatotoxin associated with Impila, the effects of the route of administration on the toxicity of this remedy and furthermore, the identification of a suitable antidote, which could include the use of duramycin and stevioside. The association between compounds blocking the ADP/ATP antiporter in the c-state and Reye's syndrome should also provide an interesting area of research.
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.
The presentation and interpretation of arrow symbolism in biology diagrams at secondary-level.
(2006) Du Plessis, Lynn.; Anderson, Trevor Ryan.
The literature contains conflicting ideas about the effectiveness of diagrams, and their constituent symbolism as teaching and learning tools. In addition, only limited research has been specifically conducted on the presentation and interpretation of arrow symbolism used in biology diagrams, let alone on the nature, source and remediation of student difficulties caused by arrows. On the basis of this limited research and 30 years of experience of teaching biology at secondary-level, the author suspected that students might have difficulties interpreting arrow symbolism in diagrams used as explanatory tools and decided to thoroughly investigate this issue. The hypothesis, 'Secondary-level students have difficulty with the use of arrow symbolism in biology diagrams' was formulated and the following broad research questions defined to address the hypothesis: 1. How much of a problem is arrow symbolism in diagrams? 2. How effectively is arrow symbolism used in diagrams to promote the communication of intended ideas? 3. To what extent does the design of arrow symbolism in diagrams influence students ' interpretation and difficulties? 4. How can the emerging empirical data and ideas from literature be combined to illustrate the process of interpretation of arrow symbolism? 5. What measures can be suggested for improving the presentation and interpretation of arrow symbolism in biology diagrams at secondary-level? To address Research question 1, a content analysis of all arrow symbolism in seven popular secondary-level biology textbooks was undertaken. This revealed a wide diversity of arrow styles, spatial organisations, purposes and meanings that could be confusing to students. These results suggested the need for an evaluation of the effectiveness of arrow symbolism (Research question 2). As there was no definitive set of guidelines available for specifically evaluating arrows, general guidelines from the literature on diagrams were used to develop a set of 10 criteria, to evaluate the syntactic, semantic and pragmatic dimensions of arrow symbolism, which were validated by selected educators, students and a graphic design expert. Application of the criteria (which constituted expert opinion) to the arrow symbolism used in 614 realistic, stylised and abstract diagram types, revealed a relatively high incidence (30%) of inappropriately presented arrow designs that could mislead students. To establish whether this problem could be the cause of student difficulties, and to thereby address Research question 3, a stylised and an abstract diagram were selected and evaluated according to the criteria. The results of the evaluation were compared to the responses given by 174 students to a range of written and interview probes and student modified diagrams. In this way, student performance was correlated with expert opinion. The results confirmed that students experience a wide range of difficulties (26 categories) when interpreting arrow symbolism, with some (12 categories) being attributable to inappropriately presented arrow symbolism and others (14 categories) to student-related processing skills and strategies at both surface- and deeper-levels of reasoning. To address question 4, the emerging empirical data from the evaluation and student studies was combined with a wide range of literature, to inform the development of a 3-level, non-tiered model of the process of interpretation of arrow symbolism in diagrams. As this model emphasised the importance of both arrow presentation in diagrams and arrow interpretation by students, it could be used as an effective explanatory tool as well as a predictive tool to identify sources of difficulty with the use of arrow symbolism. This model was, in turn, used to inform the compilation of a range of guidelines for improving the presentation and interpretation of arrow symbolism, and so target Research question 5. These, and other guidelines grounded in the data and relevant literature, were suggested for all role players, including students, educators, textbook writers, graphic artists and researchers, to use as remedial tools. Future research should focus on the implementation of these guidelines and studying their effectiveness for improving the presentation and interpretation of diagrams with arrow and other types of symbolism.
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.
Using student difficulties to identify and model factors influencing the ability to interpret external representations of IgG-antigen binding.
(2005) Schonborn, Konrad Janek.; Anderson, Trevor Ryan.; Grayson, Diane J.
Scientific external representations (ERs), such as diagrams, images, pictures, graphs and animations are considered to be powerful teaching and learning tools, because they assist learners in constructing mental models of phenomena, which allows for the comprehension and integration of scientific concepts. Sometimes, however, students experience difficulties with the interpretation of ERs, which· has a negative effect on their learning of science, including biochemistry. Unfortunately, many educators are not aware of such student difficulties and make the wrong assumption that what they, as experts, consider to be an educationally sound ER will necessarily promote sound learning and understanding among novices. On the contrary, research has shown that learners who engage in the molecular biosciences can experience considerable problems interpreting, visualising, reasoning and learning with ERs of biochemical structures and processes, which are both abstract and often represented by confusing computer-generated symbols and man-made markings. The aim of this study was three-fold. Firstly, to identify and classify students' conceptual and reasoning difficulties with a selection of textbook ERs representing· IgG structure and function. Secondly, to use these difficulties to identify sources of the difficulties and, therefore, factors influencing students' ability to interpret the ERs. Thirdly, to develop a model of these factors and investigate the practical applications of the model, including guidelines for improving ER design and the teaching and learning with ERs. The study was conducted at the University of KwaZulu-Natal, South Africa and involved a total of 166 second and third-year biochemistry students. The research aims were addressed using a postpositivistic approach consisting of inductive and qualitative research methods. Data was collected from students by means of written probes, audio- and video-taped clinical interviews, and student-generated diagrams. Analysis of the data revealed three general categories of student difficulties, with the interpretation of three textbook ERs depicting antibody structure and interaction with antigen, termed the process-type (P), the structural-type (S) and DNA-related (D) difficulties. Included in the three general categories of difficulty were seventeen sub-categories that were each classified on the four-level research framework of Grayson et al. (2001) according to how much information we had about the nature of each difficulty and, therefore, whether they required further research. The incidences of the classified difficulties ranged from 3 to 70%, across the student populations and across all three ERs. Based on the evidence of the difficulties, potential sources of the classified difficulties were isolated. Consideration of the nature of the sources of the exposed difficulties indicated that at least three factors play a major role in students' ability to interpret ERs in biochemistry. The three factors are: students' ability to reason with an ER and with their own conceptual knowledge (R), students' understanding (or lack thereof) of the concepts of relevance to the ER (C), and the mode in which the desired phenomenon is represented by the ER (M). A novel three-phase single interview technique (3P-SIT) was designed to explicitly investigate the nature of the above three factors. Application of 3P-SIT to a range of abstract to realistic ERs of antibody structure and interaction with antigen revealed that the instrument was extremely useful for generating data corresponding to the three factors. In addition analysis of the 3P-SIT data showed evidence for the influence of one factor on another during students' ER interpretation, leading to the identification of a further four interactive factors, namely the reasoning-mode (R-M), reasoning conceptual (R-C), conceptual-mode (C-M) and conceptual-reasoning-mode (C-R-M) factors. The Justi and Gilbert (2002) modelling process was employed to develop a model of the seven identified factors. Empirical data generated using 3P-SIT allowed the formulation and validation of operational definitions for the seven factors and the expression of the model as a Venn diagram. Consideration of the implications of the model yielded at least seven practical applications of the model, including its use for: establishing whether sound or unsound interpretation, learning and visualisation of an ER has occurred; identifying the nature and source of any difficulties; determining which of the factors of the model are positively or negatively influencing interpretation; establishing what approaches to ER design and teaching and learning with ERs will optimise the interpretation and learning process; and, generally framing and guiding researchers', educators' and authors' thinking about the nature of students' difficulties with the interpretation of both static and animated ERs in any scientific context. In addition, the study demonstrated how each factor of the expressed model can be used to inform the design of strategies for remediating or preventing students' difficulties with the interpretation of scientific ERs, a target for future research.

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Browsing Biochemistry by Author "Anderson, Trevor Ryan."