6 research outputs found
Doctoral writing for publication at a leading African university: Publication patterns and pedagogies
Writing-for-publication is a practice that doctoral students should acquire for integration into international research culture. Publication rates and forms of pedagogy supporting the development of publication skills for doctoral students, however, remain inadequate worldwide. Limited data of doctoral student publication from African universities is available in terms of publication patterns and pedagogies. To gain insight into publication pedagogies, a top-publishing science department at a leading African university was studied. A literature search was performed to find journal articles linked to dissertations and the numbers and timing of publication were documented. Supervisors and graduates from the sample were interviewed to uncover educational strategies employed to support doctoral student publication. Results indicate that the majority of the students published. Departmental culture and a pedagogy of collaboration were highlighted as aspects encouraging students to publish. These results indicate that, with appropriate educational strategies, PhD students can be prolific publishers and thereby become integrated into research cultures
Transcriptome characterization of the South African abalone Haliotis midae using sequencing-by-synthesis
<p>Abstract</p> <p>Background</p> <p>Worldwide, the genus <it>Haliotis </it>is represented by 56 extant species and several of these are commercially cultured. Among the six abalone species found in South Africa, <it>Haliotis midae </it>is the only aquacultured species. Despite its economic importance, genomic sequence resources for <it>H. midae</it>, and for abalone in general, are still scarce. Next generation sequencing technologies provide a fast and efficient tool to generate large sequence collections that can be used to characterize the transcriptome and identify expressed genes associated with economically important traits like growth and disease resistance.</p> <p>Results</p> <p>More than 25 million short reads generated by the Illumina Genome Analyzer were <it>de novo </it>assembled in 22,761 contigs with an average size of 260 bp. With a stringent <it>E</it>-value threshold of 10<sup>-10</sup>, 3,841 contigs (16.8%) had a BLAST homologous match against the Genbank non-redundant (NR) protein database. Most of these sequences were annotated using the gene ontology (GO) and eukaryotic orthologous groups of proteins (KOG) databases and assigned to various functional categories. According to annotation results, many gene families involved in immune response were identified. Thousands of simple sequence repeats (SSR) and single nucleotide polymorphisms (SNP) were detected. Setting stringent parameters to ensure a high probability of amplification, 420 primer pairs in 181 contigs containing SSR loci were designed.</p> <p>Conclusion</p> <p>This data represents the most comprehensive genomic resource for the South African abalone <it>H. midae </it>to date. The amount of assembled sequences demonstrated the utility of the Illumina sequencing technology in the transcriptome characterization of a non-model species. It allowed the development of several markers and the identification of promising candidate genes for future studies on population and functional genomics in <it>H. midae </it>and in other abalone species.</p
Growth-related gene expression in haliotis midae
Thesis (PhD (Genetics))--University of Stellenbosch, 2010.Includes bibliography.ENGLISH ABSTRACT: The slow growth rate of Haliotis midae impedes the optimal commercial production of this most
profitable South African aquaculture species. To date, no comprehensive effort has been made to
identify genes associated with growth variation in farmed H. midae. The aim of this study was therefore
to investigate growth variation in H. midae and to identify and quantify the expression of selected
growth-related genes. Towards this aim, molecular methodologies and cell cultures were combined as a
time-efficient and economical way of studying abalone transcriptomics and cell biology.
Modern Illumina sequencing-by-synthesis technology and subsequent sequence annotation were used
to elucidate differential gene expression between two sibling groups of abalone demonstrating
significant growth variation. Following transcriptome sequencing, genes involved in growth and
metabolism, previously unknown in H. midae, were identified. The expression of selected target genes
involved in growth was subsequently analyzed by quantitative real-time PCR (qPCR).
The feasibility of primary cell cultures for H. midae was furthermore investigated by targeting embryo,
larval and haemolymph tissues for the initiation of primary cell culture. Larval cells and haemocytes
could be successfully maintained in vitro for limited periods. Primary haemocyte cultures demonstrated
to be a suitable in vitro system for studying gene expression and were subsequently used for RNA
extraction and qPCR, to evaluate differential growth induced by bovine insulin and epidermal growth
factor (EGF).
Gene expression was thus quantified in fast and slow growing abalone and in in vitro primary
haemocyte cultures treated with different growth stimulating factors. The results obtained from
transcriptome analysis and qPCR revealed significant differences in gene expression between large and
small abalone, and between treated and untreated haemocyte cell cultures. Throughout in vivo and in
vitro qPCR experiments, the up-regulation of genes involved in the insulin signaling pathway provides
evidence for the involvement of insulin in enhanced growth rate for various H. midae tissues.
Besides the regulation of target genes, valuable knowledge was also gained in terms of reference genes,
during qPCR experimentation. By quantifying the stable expression of two genes (8629, ribosomal
protein S9 and 12621, ornithine decarboxylase) in various tissues and under various conditions, suitable
reference genes, that can also be used in future H. midae qPCR studies, were identified.
By providing evidence at the transcriptional level for the involvement of insulin, insulin-like growth
factors (IGFs) and insulin-like growth factor binding proteins (IGFBPs) in improved growth rate of H.
midae, the relevance of investigating ways to stimulate insulin/IGF release in aquaculture species was
again emphasized. As nutritional administration remains the most probable route of introducing agents that can stimulate the release of insulin-related peptides, continuous endeavours to stimulate abalone
growth through a nutritional approach is encouraged.
This is the first time next generation sequencing is used towards the large scale transcriptome
sequencing of any haliotid species and also the first time a comprehensive investigation is launched
towards the establishment of primary cell cultures for H. midae. A considerable amount of sequence
data was furthermore annotated for the first time in H. midae. The results obtained here provide a
foundation for future genetic studies exploring ways to optimise the commercial production of H.
midae.AFRIKAANSE OPSOMMING: Die stadige groeitempo van Haliotis midae belemmer die optimale kommersiele produksie van hierdie
mees winsgewende Suid-Afrikaanse akwakultuur spesie. Tot op hede is geen omvattende poging
aangewend om gene verwant aan groeivariasie in H. midae te identifiseer nie. Die doel van hierdie
studie was dus om groeivariasie in H. midae te ondersoek en om spesifieke groei-gekoppelde gene te
identifiseer en hul uitdrukking te kwantifiseer. Ter bereiking van hierdie doel is molekulêre metodes en
selkulture gekombineer as 'n en tydsbesparende en ekonomiese manier om perlemoen transkriptomika en
selbiologie te bestudeer.
Moderne Illumina volgordebepaling-deur-sintese tegnologie en daaropvolgende annotasie is gebruik
om verskille in geenuitdrukking tussen naby-verwante groepe perlemoen, wat noemenswaardige
groeivariasie vertoon, toe te lig. Na afloop van die transkriptoom volgordebepaling is gene betrokke by
groei en metabolisme, vantevore onbekend in H. midae, geïdentifiseer. Die uitdrukking van uitgesoekte
teikengene betrokke by groei is vervolgens ge-analiseer deur kwantitatiewe "real-time PCR" (qPCR). die lewensvatbaarheid van 'n primêre selkulture vir H. midae is ook ondersoek deur embrio, larwe en
hemolimf weefsels te teiken vir die daarstelling van primêre selkulture. Larweselle en hemosiete kon in
vitro suksesvol onderhou word vir beperkte periodes. Primêre hemosietkulture het geblyk 'n gepaste in
vitro sisteem te wees om geenuitdrukking te bestudeer en dit is vervolgens gebruik vir RNS ekstraksie
en qPCR, om differensiële groei, geïnduseer deur insulien en epidermale groeifaktor (EGF), te evalueer.
Geenuitdrukking is dus gekwantifiseer in vinnig- en stadiggroeiende perlemoen en in in vitro primêre
hemosiet selkulture wat behandel is met verskillende groei stimulante. Die resultate wat verkry is van
transkriptoomanalise en qPCR het noemenswaardige verskille in geenuitdrukking tussen groot en klein
perlemoen, en tussen behandelde en onbehandelde hemosiet selkulture uitgelig. Die op-regulering van
gene betrokke by die insulien sein-padweg, tydens in vivo en in vitro qPCR eksperimente, bied getuienis
vir die betrokkenheid van insulien in die verhoogde groeitempo van verskeie H. midae weefsels.
Benewens die regulering van teikengene is waardevolle kennis ook ingewin in terme van
verwysingsgene tydens qPCR eksperimentering. Deur die stabiele uitdrukking van twee gene (8629,
ribosomale proteien S9 en 12621, ornitien dekarboksilase) te kwantifiseer in verskeie weefsels en onder
verskeie kondisies is gepaste verwysingsgene, wat ook in toekomstige H. midae qPCR eksperimente
aangewend kan word, geïdentifiseer.
Deur getuienis vir die betrokkenheid van insulien, insuliensoortige groeifaktor en insuliensoortige
groeifaktor-bindingsproteïene by verbeterde groei van H. midae op transkripsievlak te bied, is die
toepaslikheid van bestudering van maniere om insulienvrystelling in akwakultuurspesies te stimuleer, beklemtoon. Aangesien voeding die mees waarskynlike roete is om middele wat insuliensoortige
peptiedvrystelling stimuleer daar te stel, word vogehoue pogings om perlemoengroei deur die regte
voeding te stimuleer, aangemoedig.
Hierdie is die eerste studie wat volgende generasie volgordebepaling (“next generation sequencing”)
gebruik vir die grootskaalse transkriptoom volgordebepaling van enige haliotied spesie. Dit is ook die
eerste keer dat ‘n omvattende ondersoek geloods word na die daarstelling van primêre selkulture vir H.midae. ‘n Aansienlike hoeveelheid volgorde data is ook vir die eerste keer geannoteer in H. midae. Die
resultate wat hier verkry is bied ‘n basis vir toekomstige genetiese studies wat maniere ondersoek om
die kommersiële produksie van perlemoen te optimiseer
An Intervention to Improve Academic Literacies in a First Year University Biology Course
In South Africa there are many students, especially those from previously underrepresented groups at university, who successfully gain access to university but do not succeed in completing their degree either within the prescribed time or at all. One of the barriers to student success at university is the difficulty these students have in accessing the literacy practices of the disciplines. Therefore, within a first year biology course at a South African University, an intervention that focused on the academic literacy practices in biology was introduced. The intervention was designed around the assignment of writing a lab report. This paper describes this intervention and how it impacted on one student’s journey from learning science at school to learning science at university. A literacy history interview and ‘talk around text’ interviews were used to assess the student’s experience of the intervention. Comparison of the student’s first and final drafts of the report revealed changes in the style and format of his writing. These changes in his report writing as well as in his attitude and motivation for writing the report were facilitated by a better understanding of the expectations of writing in university biology. This understanding was mediated largely through the modelling and deconstruction of the expected genre. This highlights not only the importance of providing first year students with examples of the genres they are expected to be writing but also the facilitation of their engagement with these new genres. Without these kinds of intervention many students are unlikely to gain access to disciplinary ways of learning and writing, which ultimately may lead to their exclusion from university
Investigating the establishment of primary cell culture from different abalone (Haliotis midae) tissues
The abalone, Haliotis midae, is the most valuable commodity in South African aquaculture. The increasing demand for marine shellfish has stimulated research on the biology and physiology of target species in order to improve knowledge on growth, nutritional requirements and pathogen identification. The slow growth rate and long generation time of abalone restrict efficient design of in vivo experiments. Therefore, in vitro systems present an attractive alternative for short term experimentation. The use of marine invertebrate cell cultures as a standardised and controlled system to study growth, endocrinology and disease contributes to the understanding of the biology of economically important molluscs. This paper investigates the suitability of two different H. midae tissues, larval and haemocyte, for establishing primary cell cultures. Cell cultures are assessed in terms of culture initiation, cell yield, longevity and susceptibility to contamination. Haliotis midae haemocytes are shown to be a more feasible tissue for primary cell culture as it could be maintained without contamination more readily than larval cell cultures. The usefulness of short term primary haemocyte cultures is demonstrated here with a growth factor trial. Haemocyte cultures can furthermore be used to relate phenotypic changes at the cellular level to changes in gene expression at the molecular level