The School of Biotechnology and Biomolecular Sciences at UNSW

Undergraduate Scholarships

BABS Faculty Vacation Research Scholarships (FVRS) 2009 – 2010

FVRS Applications close on 9 October 2009.

The School of Biotechnology and Biomolecular Sciences (BABS) at the University of New South Wales has a unique strength in combining fundamental biological and biomolecular sciences with a strong applied biotechnology and medical focus. The School facilitates collaborative research efforts across discipline boundaries for fundamental discoveries, generation of commercial opportunities and clinical research.

BABS has strengths in many areas of biological sciences, with key strengths in environmental microbiology, genetics and cellular biology and a developing strength in molecular medicine. BABS also has strengths in technology development in the areas of functional genomics and many facets of biotechnology. All areas of biology in the School are underpinned by a strength in genomics.

Would you like the opportunity to experience the real world of scientific research first-hand? Students in stages 2 and 3 of their undergraduate program, in science or a related discipline are invited to join a BABS research team and participate in ongoing research. Each Scholarship is valued at $3,600 for a 6 week research project. Applicants must be Australian/New Zealand residents.

Interested in Applying? Contact project supervisors of your project choice to discuss project requirements! When you have decided on your project preferences, please submit an application form by Friday, 9th October 2009. NOTE: If you identify a BABS supervisor that you are interested in but they do not have a project listed on our website we encourage students to approach these supervisors to see if they would be interested in offering any summer vacation projects.

PROJECTS

Supervisor Name: Dr May Thandar Aung-Htut

Contacts: Email – m.aung-htut@unsw.edu.au, Phone – 9385 1810, Office – Room 207, Level 2, Biological Sciences Building.

Name of Project: Characterisation of Glo1 and Gre3 proteins

Short Description: Reactive aldehydes are found to be implicated in ageing and diseases. We have identified two proteins Glo1p and Gre3p which are important in detoxification of a reactive aldehyde methyglyoxyal, a product generated during glycolysis. Further analysis such as enzymatic activity and substrate specificity are needed to be performed. Experimental procedures includes molecular techniques such as PCR, protein purification and enzymatic assay.

Time when project is available: FROM: December TO: February

Student preferences: N/A

Any other conditions: N/A

Supervisor Name: Dr Brendan Burns

Contacts: Email – brendan.burns@unsw.edu.au, Phone – 9385 3659, Office – Room 354A, Level 3, Biological Sciences Building.

Name of Project: Rocking the cradle of life

Short Description: Stromatolites represent a model for studying the origins and evolution life on our planet. They are geobiological structures composed of complex and diverse microbial communities. The study of microorganisms associated with these formations may also be applied to the existence of extraterrestrial life, particularly with the discovery of unique biosignatures. Students will examine novel archaea for their mechanisms of cell signalling that facilitate community communication and other unique physiologies, which allow adaptation to extreme habitats and permit the formation and persistence of these evolutionarily significant systems.

Time when project is available: FROM: early Jan TO: mid Feb

Student preferences: Experience in microbiology and molecular genetics, including sterile technique and pipetting.

Any other conditions: N/A

Supervisor Name: Dr Joyce Chiu and Prof. Ian Dawes

Contacts: Email – j.chiu@unsw.edu.au, i.dawes@unsw.edu.au Phone – 9385 2031, Office – Room 207, Level 2, Biological Sciences Building.

Name of Project: Oxidative stress signalling and regulation of cell division in budding yeast

Short Description: Budding yeast is an excellent model to study oxidative stress responses in eukaryotic cells since many molecular mechanisms are conserved from yeast to human. This project aims to identify how a yeast cell division cycle transcription factor responds to oxidative damage. It employs protein expression of the yeast transcription factor in yeast genetic mutant defective of oxidative stress to dissect the complexity of the stress signalling system and cell division regulation in eukaryotic cells. Techniques include yeast genetic manipulation, protein expression, denaturing gel electrophoresis, and immunoblotting of yeast proteins.

Time when project is available: FROM: January to mid-February 2010

Student preferences: Molecular Biology

Any other conditions: N/A

Supervisor Name: Prof. Rick Cavicchioli

Contacts: Email – r.cavicchioli@unsw.edu.au, Phone – 9385 3516, Office – Room 309, Level 3, Biological Sciences Building.

Name of Project: Environmental Microbial Genomics, Extremophiles and Global Ecosystem Health

Short Description: The Cavicchioli group has a range of programs that examine microbial adaptation at the level of cellular responses, evolution and the impact of microorganisms on whole environmental ecosystems. Our interests cover microorganisms from Antarctica, the Southern Ocean, Heard Island and acid mine drainage sites in the Hunter Valley, to mention a few. In addition to addressing fundamental aspects of biology, we perform commercially orientated research, such as that addressing the use of enzymes from extremophiles to find improved methods of cleaning water recycling membrane filters. Student projects can be based in genomics/proteomics (including metagenomics/metaproteomics), microbial ecology, microbial physiology, bioinformatics, biochemistry/biophyics of proteins; in essence, whatever is required to address a large number of biological questions of interest. Projects provide scope for exposure to on-going Honours and PhD students, postdoctoral fellows, local and overseas collaborators, and a host of whizz-bang research equipment.

Time when project is available: FROM: December 3rd TO: February 22nd

Student preferences: 3rd year preferably, or highly inspired and capable 2nd year; experience as per topics described

Any other conditions: Strong interest in performing research with the group (e.g. Honours, MPhil, PhD, etc)

Supervisor Name: Dr Michelle Gehringer

Contacts: Email – mgehringer@unsw.edu.au, Phone – 9385 3382, Office – Room 357A, Laboratory: 344, Level 3, Biological Sciences Building.

Name of Project: Assessing the effect of the cyanobacterial hepatotoxin, nodularin, on the growth of wheat.

Short Description: The cyanobacterial toxins, microcystin and nodularin are known to cause severe liver toxicosis in humans and animals. Microcystin produced by toxic blooms in irrigation waters has been demonstrated to induce oxidative stress in crop plants accompanied by plant stunting and lower yields. The effects of nodularin produced in the rhizosphere of crops has not been investigated. The aim of this project is to identify the effects of nodularin production in the rhizosphere of various crop plants in a sterile soil free culture system. Our laboratory has isolated nodularin producing cyanobacteria from soils around Australia. We have also established a soil free culture system in place to specifically assess the interaction of cyanobacteria and crop plants. Wheat, mustard and alfalfa seedlings will be grown in the presence of nodularin and nodularin producing bacteria and assessed by measuring plant root length, leaf length, oxidative stress and photosynthetic efficiency. The potential also exists to conduct either enzymatic or molecular assays to assess oxidative stress levels in plants exposed to nodularin. Information obtained in this study will contribute significantly to our knowledge of the rhizosphere of crop plants in Australia and the potential risks of nodularin producing cyanobacteria in agricultural soils.

Time when project is available: From: 3rd December To: 22nd February

Student preferences: Basic knowledge of sterile techniques and culturing of bacteria is essential. This project would suit someone majoring in Microbiology and Botany or interested in the applications of bacteria in the agricultural industry or someone wanting to acquire either enzymology or molecular experience.

Any other conditions: N/A

Supervisor Name: Dr Michelle Gehringer

Contacts: Email – mgehringer@unsw.edu.au, Phone – 9385 3382, Office – Room 357A, Laboratory: 344, Level 3, Biological Sciences Building.

Name of Project: Assessing the potential plant growth promoting activities of cyanobacteria on wheat.

Short Description: One of the greatest expenses to farmers is that of chemical fertilisation. With the raising costs of fertilisers and a move to more sustainable agricultural sources of nitrogen there has been increased interest into developing a biofertiliser for wheat. Cyanobacteria are known to be capable of forming symbiotic associations with plants. Our laboratory has isolated nitrogen fixing symbiotic Nostoc sp. of cyanobacteria from the roots of the Australian cycad genus, Macrozamia. The aim of this project is to identify which of these isolates are capable of associating with wheat roots in a sterile soil free culture system, and assess their nitrogen fixation efficiencies. The wheat seedlings will be cultured in the presence of the cyanobacterial species. Measuring root length, root and shoot dry weight and photosynthetic efficiencies will assess the potential benefits to wheat plant growth. Nitrogen fixation rates of free living and associated cyanobacteria will be assessed using the acetylene reduction assay. The potential exists to assess nitrogen fixation using molecular tools such as real time PCR. This project will make a significant contribution to the development of a biofertiliser for Australian bread wheat varieties.

Time when project is available: From: 3rd December To: 22nd February

Student preferences: Basic knowledge of sterile techniques and culturing of bacteria is essential. This project would suit someone majoring in Microbiology and Botany or interested in the applications of bacteria in the agricultural industry or someone wanting to acquire either enzymology or molecular experience.

Any other conditions: N/A

Supervisor Name: A/Prof. Ruiting Lan

Contacts: Email – r.lan@unsw.edu.au, Phone – 9385 2095, Office – Room 301B, Level 3, Biological Sciences Building.

Name of Project: developing a novel molecular method for epidemiological typing of Shigella

Short Description: Shigellosis (bacillary dysentery) is a severe human disease caused by Gram-negative bacterium Shigella. It is a major diarrheal disease with 165 million cases and 1 million deaths worldwide annually, the majority of which occur in developing countries and involve children less than five years old. The project will identify and apply molecular markers found from genome comparisons to typing for understanding molecular epidemiology of Shigella.

Time when project is available: FROM: Dec 2009 TO: Feb 2010

Student preferences: Preference will be given to student who has done 3rd year Bacteria and disease or equivalent and majoring in medical microbiology.

Any other conditions: None

Supervisor Name: A/Prof. Ruiting Lan

Contacts: Email – r.lan@unsw.edu.au, Phone – 9385 2095, Office – Room 301B, Level 3, Biological Sciences Building.

Name of Project: Assembling a genome from next generation sequencing data

Short Description: Next generation sequencing technologies such as Solexa produces billions of bases in one run and have greatly changed the way genomes are sequenced. However the large amount of data of short reads also presents challenges on how to assemble a genome together. This project will analyse Solexa genome sequencing data and assemble a genome using existing programs as well as writing some scripts for data processing.

Time when project is available: FROM: Dec 2009 TO: Feb 2010

Student preferences: Students studying for a Bioinformatic degree with an interest in honours research in genomics are particularly encouraged to apply. Require skills in perl scripting.

Any other conditions: None

Supervisor Name: Dr Chris Marquis

Contacts: Email – c.marquis@unsw.edu.au, Phone – 9385 3898, Office – Room S131, Samuels Building.

Name of Project: Recombinant yeast bioprocessing

Short Description: We are developing a method to harvest and process 25L recombinant yeast fermentations using constant volume cross-flow diafiltration. The model system used will involve undertaking a 5 and a 25L fed-batch fermentation producing a recombinant human cytokine of therapeutic potential, followed by two filtration processes: first to separate yeast biomass from supernatant, followed by concentration using ultrafiltration. Mass balancing on the cytokine will be undertaking to evaluate product losses in the process. We will also evaluate methods of filter regeneration.

Time when project is available: FROM: 2nd week Jan TO: mid-late Feb

Student preferences: Student interested in recombinant proteins, bioprocessing. Someone who would like to use some equipment that is larger than a pipettor!

Any other conditions: Biotechnology student may prefer this project, however, open to all

Supervisor Name: Prof. Hazel Mitchell

Contacts: Email – h.mitchell@unsw.edu.au, Phone – 9385 2040, Office – Room 301A, Level 3, Biological Sciences Building.

Name of Project: Phylogenetic analyses of Helicobacter pylori detected in intestinal biopsies

Short Description: Helicobacter pylori is found in the gastric mucous layer or adhering to the epithelial lining of the human stomach, and is one of the most prevalent infections in humans (approximately 15.4% in Australia). The ongoing presence of H. pylori causes a lifelong inflammatory response, responsible for the continuous production of species that cause cellular damage. This, in turn, is associated with the development of gastritis, ulcers and gastric cancers in humans. A recent study in our laboratory resulted in the detection of H. pylori DNA from intestinal biopsy samples obtained from children that were negative for gastric H. pylori. Using a genus-specific PCR combined with sequencing analyses, H. pylori has been shown to be present in 14.2% of children negative for gastric H. pylori (n = 162). Although the culture of H. pylori from gastric biopsies has become common practice, previous attempts at culturing the organism from the intestine have been unsuccessful. With the improvement of isolation techniques, our laboratory has been able to isolate related organisms such as Campylobacter and Arcobacter spp. but to date no Helicobacter spp have been isolated.

Preliminary phylogenetic analyses of 5 H. pylori DNA sequences from intestinal biopsies indicated that intestinal H. pylori DNA sequences clustered with extragastric sequences from the hepatobiliary system; although, one of the five intestinal isolates clustered within the gastric group. These results suggest that H. pylori may have slowly adapted towards the colonisation of the intestinal tract.

Given the considerable percentage of H. pylori detected from the intestinal tract of children and the potential divergence of the gastric and intestinal strains, further characterisation of these extragastric species is required. Polymerase chain reactions and sequencing analyses will be performed on intestinal biopsies, and H. pylori sequences will be subjected to more comprehensive phylogenetic analyses. In addition, culture of H. pylori from intestinal biopsies using several types of isolation techniques will be undertaken.

Time when project is available: FROM: 16th November TO: January

Student preferences: Students majoring in Microbiology and Immunology

Any other conditions: N/A

Supervisor Name: Prof. Brett Neilan

Contacts: : Email – b.neilan@unsw.edu.au, Phone – 9385 3235, Office – Room 344, Level 3, Biological Sciences Building.

Name of Project: Characterisation of the methyltransferase, McyJ encoded within the microcystin biosynthesis gene cluster

Short Description: Cyanobacteria (or blue-green algae) are known to produce a wide range of biologically active secondary metabolites, many of which are toxic to humans. The liver toxin, microcystin is a cyclic heptapeptide that contains several unusual amino acids, including the polyketide moiety known as adda (3-amino-9-methoxy-2,6,8-trimethyl-10-phenyl-4,6-decadienoic acid). The most toxic isoforms of microcystin contain an O-methylation on adda, putatively due to the activity of the O-methyltransferase, McyJ. O-methylations feature widely in secondary metabolite structures and can contribute to the stability and biological activity of such compounds.

The aim of this project is to investigate the activity and regulation of McyJ and thereby gain insight into the mechanisms controlling the preferential biosynthesis of certain microcystin isoforms in nature. These aims shall be addressed via the over-expression and biochemical analysis of the recombinant McyJ enzyme. The activity of the purified enzyme shall also be tested against a range of other cyclic compounds in order to address its potential applications in novel drug design.

Time when project is available: From: 3rd December To: 22nd February

Student preferences: A good grasp on molecular biological concepts and basic practical techniques is essential. Familiarity with protein biochemistry would be beneficial, but not essential.

Any other conditions: N/A

Supervisor Name: Dr Gabriel Perrone

Contacts: Email – g.perrone@unsw.edu.au Phone – 9385 1832, Office – Room 201, Level 2, Biological Sciences Building.

Name of Project: How do cells regulate redox environment at the cellular and organellar level?

Short Description: The development of redox-sensitive green fluorescent protein (roGFP) has provided a significant leap forward in terms of assessing cellular redox state in a dynamic ‘real-time’ and non-invasive manner. roGFP probes can also be targeting to specific organelles or compartments. This project aims to exploit roGFP, to indentify the genetic and environmental factors affecting redox homeostasis in cells and cellular compartments. The project will exploit the power and versatility of the model eukaryote organism Saccharomyces cerevisiae (baker’s yeast). The approach will involve genetically engineering roGFP to target the probe to specific compartments including the mitochondrial matrix, endoplasmic reticulum, peroxisome and nucleus. The redox environment of the cytosol and/or organelle will then be assessed by measuring the response of the probe in wild-type and mutant cells of the genome-wide yeast deletion collection. The yeast deletion collection (~4600 mutants) is a very powerful tool that can be exploited to assess the effect of changes in cellular processes or metabolic pathways on a given trait, in this case compartmental redox, on a genome-wide scale. For a limited number of mutants, hand selected based on their putative role in redox, or mutants discovered through genome-wide screening as ‘mutants of interest’, the dynamic (short-term) response to changes in redox will also be studied more intensely. For these selected mutants a range of growth/stress conditions including exposure of cells oxidants, selected drugs and nutrients.

Time when project is available: FROM: December 2009 TO: February 2010

Student preferences: N/A

Any other conditions: N/A

Supervisor Name: Dr Noel Whitaker

Contacts: Email – n.whitaker@unsw.edu.au, Phone – 9385 2041, Office – Room 214B, Level 2, Biological Sciences Building.

Name of Project: Involvement of viruses in human cancers

Short Description: Our lab is interested in the potential causal involvement of various viruses (especially HPV, EBV, MMTV) in human cancers (especially breast cancer and prostate cancer). We have built up a cancer tissue bank of suitable cancer tissues (fixed archival and fresh frozen) as well as relevant cell lines. We use many molecular techniques (e.g. PCR, in situ PCR, in situ hybdridisation, immunohistochemistry) and tissue culture techniques (including siRNA and shRNA) detect the presence and evidence for a causal role of viruses in these cancers. For a description, see http://www.babs.unsw.edu.au/directory.php?personnelID=32

Time when project is available: FROM: Jan, 2010 TO: March, 2010

Student preferences: These techniques are quite finicky and would suit current 3rd year students with good laboratory techniques (i.e. have done courses with significant amount of laboratory work).

Any other conditions: N/A

Supervisor Name: Prof. Marc Wilkins

Contacts: Email – m.wilkins@unsw.edu.au, Phone – 9385 3633, Office – Room 263C, Level 2, Biological Sciences Building.

Name of Project: Understanding redundancy in the methylation network of yeast

Short Description: Protein methylation is a post-translational modification which is poorly understood. We have recently shown that it is widespread in the proteome, although its function in many cases remains unknown. Network analysis of methylated proteins, and their modifying enzymes, has suggested that there is redundancy in the cell’s methylation system. In other words, the knockout of some methyltransferases is likely to be of little effect as other methyltransferases can provide the same function. This project will generate double knockouts of lysine methyltransferases in yeast, and analyse the effect of these knockouts with western blotting and / or tandem mass spectrometry. It will involve the techniques of PCR, cell transformation and screening, nucleic acid and protein electrophoresis, western blotting and immunodetection and / or tandem mass spectrometry. The results will help us understand which enzymes are in fact redundant and which act by themselves in the yeast methylation network.

Time when project is available: FROM: start of January 2010 TO: end of February 2010

Project can be up to 8 weeks (additional funding will be provided from the Wilkins lab).

Student preferences: 3rd year student, with background in molecular biology (nucleic acids and proteins)

Any other conditions: No other special conditions.

FVRS - To apply: Click Here (Application form and/or Apply Online).

FVRS Applications close on 9 October 2009.

BABS Talented Student Scholarship for Outstanding Achievement in Year 1

The School of Biotechnology and Biomolecular Sciences offers a Talented Student Scholarship of $1000 for the second year student who performed best in their first year. The conditions are that:

• You must have completed Year 1 of Biotechnology (program 3052), Science (program 3970), Advanced Science (programs 3972 or 3990) or Medical Science (program 3991) as a full-time student at UNSW with a WAM >75.
• You must also be a full-time student in one of these programs and enrolled in all four of BIOC2101, BIOC2201, MICR2201 and MICR2011.
• Anyone who is already receiving a scholarship for their study at UNSW is not eligible.

Applications in the form of a copy of your full academic transcript and a brief covering letter should be submitted to the student office. If there is more than one eligible applicant, the Scholarship will be awarded to the student with the highest WAM. Further detailed information about the conditions for the award of the Talented Student Scholarship can be obtained from the BABS Student Office.

BABS Talented Student Scholarship for Outstanding Achievement in Year 2

The School of Biotechnology and Biomolecular Sciences offers a Talented Student Scholarship of $1000 for the third year student who performed best in their second year. The conditions are that:

• You must have completed Year 2 of Biotechnology (program 3052), Science (program 3970), Advanced Science (programs 3972 or 3990) or Medical Science (program 3991) as a full-time student  and have completed at least three of BIOC2101, BIOC2201, MICR2201 and MICR2011 last year with a WAM >75.
• You must also be a full-time student in one of these programs, enrolled in at least 6 BABS courses (BIOC, MICR or BIOT course codes) and on track to meet all the requirements for an Honours year in BABS.
• Anyone who is already receiving a scholarship for their study at UNSW is not eligible.

Applications in the form of a copy of your full academic transcript and a brief covering letter should be submitted to the student office. If there is more than one eligible applicant, the Scholarship will be awarded to the student with the highest WAM. Further detailed information about the conditions for the award of the Talented Student Scholarship can be obtained from the BABS Student Office.

BABS Talented Student Scholarship for Outstanding Achievement in Year 3

The School of Biotechnology and Biomolecular Sciences offers a Talented Student Scholarship of $1000 for the Honours year student who performed best in their third year. The conditions are that:

• You must have completed Year 3 of Biotechnology (program 3052), Science (program 3970), Advanced Science (programs 3972 or 3990) or Medical Science (program 3991) as a full-time student and have completed at least 6 BABS courses (BIOC, MICR or BIOT course codes) with a WAM >75
• You  must also be a full-time BABS Honours student.
• Anyone who is already receiving a scholarship for their study at UNSW is not eligible.

Applications in the form of a copy of your full academic transcript and a brief covering letter should be submitted to the student office. If there is more than one eligible applicant, the Scholarship will be awarded to the student with the highest WAM. Further detailed information about the conditions for the award of the Talented Student Scholarship can be obtained from the BABS Student Office.