Intern projects
Last updated: 05/08/22
Separating signal from noise - benchmarking machine learning methods to identify biology from big data!
Project title: | Separating signal from noise - benchmarking machine learning methods to identify biology from big data! |
Project duration, hours of engagement & delivery mode | Project Duration: 8-10 weeks; 30-36hrs per week. COVID-19 considerations: Project can be completed remotely if required. |
Description: | The promise of big data is to reveal compelling insights into medical biology. But a major challenge for realizing this goal is the intractable presence of noise. This project focuses on benchmarking different kinds of bioinformatics methods to understand the optimal ways to handle noise in the data to obtain concrete results in biology. |
Expected outcomes and deliverables: | This is a wonderful opportunity to gain hands on experience in computational biology and bioinformatics research. It is also the chance to develop key employability skills in data science, quantitative modelling, teamwork, communication and project management. At a minimum, the student will be expected to produce a report at the end of the project that may lead to a publication and/or software package. |
Suitable for: | We are looking for students with any background in statistics, data science, computer science, mathematics, genetics, molecular & cell biology who are excited to be part of biomedical research! This project is most suited to a 3rd or 4th year student who may be considering Honours or a PhD project in the future. |
Primary Supervisor: | A/Prof Jessica Mar |
Further info: | Please contact me for further information at j.mar@uq.edu.au. |
Understanding the role of transcriptional noise in ageing
Project title: | Understanding the role of transcriptional noise in ageing. |
Project duration, hours of engagement & delivery mode | Project Duration: 8-10 weeks; 30-36hrs per week.
COVID-19 considerations: Project can be completed remotely if required. |
Description: | Aging is a process that affects every human body. While we are gradually recognizing the different pathways involved in the aging process, one open question relates to the distribution of noisy or variable expression across the transcriptome. Do genes get more variable during the aging process that results in de-regulation, or do certain genes get too stable and static as cells age? We posit that it’s a combination of the two, and where these too-noisy, too-static genes are distributed within a pathway is the key to predicting the healthy agers from the poor ones. This project aims to develop models that quantify the noise occurring in gene expression as single cells age and develop statistical classifiers that predict healthy aging profiles. |
Expected outcomes and deliverables: | This is a wonderful opportunity to gain hands on experience in computational biology and bioinformatics research. It is also the chance to develop key employability skills in data science, quantitative modelling, teamwork, communication, and project management. At a minimum, the student will be expected to produce a report at the end of the project that may lead to a publication and/or software package. |
Suitable for: | We are looking for students with any background in statistics, data science, computer science, mathematics, genetics, molecular & cell biology who are excited to be part of biomedical research! This project is most suited to a 3rd or 4th year student who may be considering Honours or a PhD project in the future. |
Primary Supervisor: | A/Prof Jessica Mar |
Further info: | Please contact me for further information at j.mar@uq.edu.au. |
Bioengineering yeast as innovative bio nano technologies for detection of infectious diseases
Project title: | Bioengineering yeast as innovative bio nano technologies for detection of infectious diseases |
Project duration, hours of engagement & delivery mode | 10 weeks , 20-36hrs/week, majority on site |
Description: | There is a critical need to keep pace with emerging Sars Cov2 virus (SCV2) variants to be prepared for future pandemic threats by developing novel rapid response point of care diagnostic technologies which are cheap, easily manufactured on scale and with equivalent detection sensitivity to current laboratory-based methods. There is also a need for improved assays to delineate between respiratory pathogens given that symptoms are very similar, for example influenza, SCV2 and the common cold. Our research program focuses on the development of innovative bio nano reagents, including yeast nanofragments termed nanoyeast, for the rapid and sensitive detection of infectious diseases, with specific focus on respiratory viruses including coronaviruses (Sars Cov1 and 2, MERs), influenza A and B, Respiratory Syncytial Virus A and B, adenoviruses and rhinoviruses The goal of this project is to develop innovative bio nano reagents specific for respiratory viruses, characterise the functional and structural properties of the reagents and apply them in bio nano diagnostic platforms for detection of viral pathogens. This includes testing of the reagents against clinical virus samples from patients with collaborators. The project will utilise approaches in molecular biology, protein bioengineering, nanotechnology, bioassay development and diagnostics. |
Expected outcomes and deliverables: | Participants will gain expertise in lab skills focused on molecular biology, bionanomaterials, protein bioengineering, protein expression and function. Participants will also gain skills in the development of diagnostic assays and an understanding of the clinical and translational relevance of reagents that they will develop. In addition, the participants will be involved in the research team, involved in brainstorming on other projects, and involved in research outputs including potential for publications and presentation of research findings. Outcomes of the project also have potential to lead into additional research progression for the participant (RHD project) |
Suitable for: | The project is open for applications for 3rd to 4th year students with a passion for biotechnology, molecular biology, viral diagnostics, and protein biology. Some experience in molecular biology or biochemistry labs would be great. |
Primary Supervisor: | Dr Christopher Howard |
Further info: | Please contact Dr Chris Howard at c.howard2@uq.edu.au for more details about this project. |
Solar rechargeable Zinc-Bromine Flow Batteries
Project title: | Solar rechargeable Zinc-Bromine Flow Batteries |
Project duration, hours of engagement & delivery mode | This is an 8–10-week project for postgraduate coursework or honours students, who are interested to work on developing next generation battery technologies. Hours of engagement will be between 30-36 hrs per week Applicant will be required on-site for the project. |
Description: | This project aims to develop a new solar rechargeable Zinc-Bromine flow battery for better utilization of the abundant yet intermittently available sunlight. The key design is to create a solar-driven photoelectrochemical process to convert the discharged electrode materials back to their charged states and realise the direct storage of solar energy. Expected outcomes include new solar driven rechargeable technology and photoelectrode materials, as well as new knowledge generated from collaborations across materials science, photoelectrochemistry and nanotechnology disciplines. |
Expected outcomes and deliverables: | In this project, scholars will gain skills in battery materials synthesis, battery device fabrication, testing and data collection and analysis, be involved in specific tasks, and have an opportunity to generate publications from their research. Students may also be asked to produce a report or oral presentation at the end of their project. |
Suitable for: | This project is open to applications from students with a background in physical chemistry, materials engineering, chemical engineering, electrochemistry, and for 3rd – 4th year students only. |
Primary Supervisor: | Dr Bin Luo |
Further info: | Please contact Dr Bin Luo at b.luo1@uq.edu.au for more details about this project. |
Establishing a semi-automated DNA assembly platform for synthetic biology
Project title: | Establishing a semi-automated DNA assembly platform for synthetic biology |
Project duration, hours of engagement & delivery mode | Project duration: 6-10 weeks and 20-36 hrs per week This project is lab based and requires on-site attendance. A remote working arrangement is not possible. |
Description: | This project will be part of efforts at the AIBN to establish a biofoundry and will aim to automate DNA assembly routines on a liquid handling robot. Multi-part DNA assembly is the physical starting point for many projects in synthetic biology. The ability to explore a genetic design space by building libraries of DNA constructs is essential for creating programmed biological systems and shall here be enabled through automation of the DNA assembly process. Such automation shall enable larger builds using less researcher time, while increasing the accessible design space. Specifically, this project shall establish Biopart Assembly Standard for Idempotent Cloning (BASIC), a low-cost DNA assembly method on the liquid handling robot Opentron OT-2. The workflow shall first be tested by expressing fluorescent proteins (easy readout, 6 weeks project) and then be applied to assemble a synthetic version of the hydrogenase-encoding hox operon (9 genes) from Cupriavidus necator, relevant for a research on hydrogen-assisted microbial bioproduction (10 weeks project). |
Expected outcomes and deliverables: | Scholars may gain skills in the use of a liquid handling robots, process automation and high-throughput cloning. Students may be asked to produce a report at the end of their project to be used as a reference for automated cloning in the lab. Publication of follow-up work using the synthetic hox operon will guarantee co-authorship. |
Suitable for: | This project is open to applications from students with a background in bioprocess engineering with knowledge of advanced cloning techniques and a strong interest in automation, including the use of the Python programming language. |
Primary Supervisors: | Dr Birgitta Ebert, Daniel Bergen (M. Sc.) |
Further info: | In case of questions, please contact Birgitta Ebert: birgitta.ebert@uq.edu.au |
Engineering the endoplasmic reticulum for overproduction of triterpenoids in yeast
Project title: | Engineering the endoplasmic reticulum for overproduction of triterpenoids in yeast |
Project duration, hours of engagement & delivery mode | Project duration: 6-10 weeks and 20-36 hrs per week This project is lab-based and requires on-site attendance; a remote working arrangement is not possible. |
Description: | This project is part of a larger program on establishing a yeast platform for plant-derived natural products biomanufacturing. A major bottleneck in this undertaking is the availability of subcellular membranes to anchor membrane-associated plant enzymes. In this project, we are interested in the production of triterpenoids, a major natural product class with species that find application as vaccine adjuvants, anti-cancer drugs, cosmetics, or food supplements. The synthesis occurs in the Endoplasmic Reticulum (ER) membrane, whose proliferation shall be targeted here to improve production. It builds on a proof-of-concept study of a previous student project that established rational and random techniques for ER proliferation. Identified targets shall be introduced into the yeast Saccharomyces cerevisiae engineered for triterpenoid production and the effect of ER proliferation on production be evaluated. |
Expected outcomes and deliverables: | Scholars may gain skills in synthetic biology and yeast metabolic engineering, fluorescent microscopy analyses (visualization of ER structures) and microbial fermentations (shake-flask scale). The student is expected to produce a report or oral presentation at the end of their project and present and discuss their project in lab meetings. Depending on the outcome, there will be an opportunity for the student to engage in publishing the work. |
Suitable for: | This project is open to applications from advanced students with a background in molecular biotechnology. |
Primary Supervisor: | Dr. Birgitta Ebert, Yutong Han (M. Sc.) |
Further info: | Questions? Please don’t hesitate to get in touch: birgitta.ebert@uq.edu.au |
Engineered nano-carrier for agrichemical encapsulation
Project title: | Engineered nano-carrier for agrichemical encapsulation |
Project duration, hours of engagement & delivery mode | Project duration: 8 weeks Hours of engagement: 36 hrs per week The applicant will be required on-site for the project. |
Description: | Agrochemicals are widely used in crop protection and livestock industry with a huge global market of > $ 200 billion. The short effective duration in field conditions is the major obstacle of the application of sensitive agrochemicals. This project aims to use an engineered nano-carrier to protect the agrochemical molecules and address the challenge. Agrochemical nanoformulations (e.g., pesticide or fertilizer amendment agent) will be fabricated by nanoparticle encapsulation for enhanced stability. |
Expected outcomes and deliverables: | Scholars will gain knowledge of engineered nanoparticle design and related agricultural applications. Scholars will gain the skills of nanoparticle synthesis, structure characterization, drug encapsulation and simulated field tests. Scholars will be asked to produce a report and oral presentation in the group meeting at the end of the project. |
Suitable for: | This project is open to applications from students with a background in chemistry, chemical engineering, agricultural science, or other related backgrounds This project is suitable for 4th year undergraduate, honours or Master by coursework students. |
Primary Supervisor: | Dr Jun Zhang, j.zhang11@uq.edu.au |
Further info: | n/a |
Dendritic spine actin dysfunction in autism spectrum disorder
Project title: | Dendritic spine actin dysfunction in autism spectrum disorder |
Project duration, hours of engagement & delivery mode | Project total duration of the project is 8 weeks (28.11.2022-23.12.2022 and 09.01.2023-03.02.2023). Hours of engagement on-site are 20 hrs per week. |
Description: | Autism spectrum disorder (ASD) comprises a group of neurological conditions characterized by repetitive behaviours and social deficits. ASD has a strong genetic component (SFARI), with multiple susceptibility genes converging on cellular pathways intersecting the glutamatergic synapses, dendritic spine maturation and synaptic transmission. The actin cytoskeleton plays a key role in dendritic spine maturation (immature “thin”, “stubby” and mature “mushroom” spines) and, along with ionotropic AMPA glutamate receptor (AMPAR) clustering, is essential for synaptic plasticity. Interestingly, many of the ASD-susceptibility genes are actin cytoskeleton regulators (Joensuu et al. 2018: Dendritic spine actin cytoskeleton in autism spectrum disorder, Prog Neuropsychopharmacol Biol Psychiatry 84:362-381), and ASD patients have been reported to have altered spine morphology and density (increased numbers of “thin” spines), as well as abnormal glutamatergic function, suggesting that AMPAR organization in the spines relies on proper dendritic morphology. Recent research from our collaborators has revealed that one of the ASD-susceptibility genes, the actin cross-linking protein α-actinin-4 (ACTN4), controls the formation of “mushroom” spines, and that the human ASD-associated missense mutation M554V in ACTN4 increases the density of “thin” spines, possibly due to mislocalization of the protein (Hluschenko et al., 2018: ASD-Associated De Novo Mutations in Five Actin Regulators Show Both Shared and Distinct Defects in Dendritic Spines and Inhibitory Synapses in Cultured Hippocampal Neurons, Front Cell Neurosci. 12: 217). Taken that actin cytoskeleton is critical for spine maturation and nanoclustering of plasma membrane receptors, we hypothesize that the ACTN4 M554V-mutation causes changes in the dendritic actin cytoskeleton leading to “thin” spine morphology, which affects AMPAR mobility. The aim of this project is to study how the ACTN4 M554V-mutation affects AMPAR organization in the spines in cultured hippocampal neurons. |
Expected outcomes and deliverables: | Student will study postsynaptic morphology and AMPAR mobility using different imaging techniques (immunofluorescence staining using confocal imaging, and super-resolution uPAINT imaging). The applicant can expect to learn how to prepare, acquire and quantify immunofluorescent stainings, and how to track and interpret single molecule super-resolution data in vitro in primary neuronal cultures. |
Suitable for: | This project is open to applications from students with a background in cell biology or neurobiology. Prior experience on imaging would be beneficial. |
Primary Supervisor: | Dr Merja Joensuu |
Further info: | If you have any questions or would like to discuss the project in more detail, please contact Dr Joensuu via email m.joensuu@uq.edu.au |
Enhancing DNA transfection in macrophages
Project title: | Enhancing DNA transfection in macrophages |
Project duration, hours of engagement & delivery mode | Project duration: 10 weeks Hours of engagement: 36 hours per week Delivery mode: On campus |
Description: | Background: The delivery of DNA molecules into macrophages has widespread applications, however the hard-to-transfect nature of macrophages is the bottleneck. Strategies that can enhance macrophage delivery and transfection efficiency is highly desired. Aim: The aim of the project is to develop of calcium modified spiky silica nanoparticles for enhancing DNA transfection in macrophages. Hypothesis: It is hypothesized that calcium modification can enhance DNA transfection compared to non-modified spiky silica nanoparticles. Approach: 1. Synthesis of spiky silica nanoparticles and calcium modified spiky silica nanoparticles, further conjugated with PEI. 2. Characterisation of nanoparticles. 3. DNA loading and release tests. 4. DNA transfection tests in macrophages. |
Expected outcomes and deliverables: | This is a side project of an ARC linkage project. Through this summer project, the student will receive training such as nanoparticle synthesis, characterization and cell culture techniques. These skillsets are useful for future research in gene therapy and DNA vaccines. |
Suitable for: | The project is open to honour students only with a background in biological or genetics background. |
Primary Supervisor: | Chengzhong (Michael) Yu |
Further info: | Email: c.yu@uq.edu.au Please contact before submitting the applications. |
Enhancing mRNA delivery into dendritic cells
Project title: | Enhancing mRNA delivery into dendritic cells
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Project duration, hours of engagement & delivery mode | 10 weeks (36 hrs per week) and the applicant will be required on-site for the project |
Description: | The delivery of mRNA into dendritic cells is challenging, but important in applications such as vaccine development. The aim of this project is to prepare nanoparticles with tunable structures and to study their mRNA delivery performance in dendritic cells. |
Expected outcomes and deliverables: | This is a side project of an ARC discovery project. Scholars may gain skills in nanomaterial synthesis, characterization, in vitro cell culture study, data collection and analysis. These skillsets are useful for future research in gene therapy and mRNA vaccine development. |
Suitable for: | The project is open to honour students only with a background in biological or genetics background. |
Primary Supervisor: | Chengzhong (Michael) Yu |
Further info: | Email: c.yu@uq.edu.au Please contact before submitting the applications. |
A multifunctional 3D Printing technique for Magnetic resonance imaging (MRI)-guided regenerative medicine
Project title: | A multifunctional 3D Printing technique for Magnetic resonance imaging (MRI)-guided regenerative medicine |
Project duration, hours of engagement & delivery mode | 6 weeks and the applicant will be required on-site (30-36 hours per week) for the project. |
Description: | 3D printing technology has provided a promising tool for manufacturing customized scaffolds in tissue engineering and regenerative medicine applications. However, effective imaging methods are required to observe the process of scaffold-induced tissue regeneration. Nowadays, nanoparticles hold significant advances in tissue regeneration, disease diagnosis, and therapy owing to their unique properties. For instance, magnetic iron oxide nanoparticles are promising multifunctional agents for enhanced MRI signals, tumour photothermal therapy, proliferation, and differentiation of cells. This idea of the project is that integrate iron oxide nanoparticles into stereolithography 3D printing to fabricate novel implants for MIR-guided bone regeneration. It will involve 3D printing, nanoparticle synthesis, material characterization, and medical imaging. This project would suit students keen on learning and understanding the functions of nanoparticles in 3D printing and exploiting new biomedical applications of 3D printing techniques。 |
Expected outcomes and deliverables: | Scholars may gain skills in experimental design, data recording, operation of instruments, be involved in specific tasks, or have an opportunity to generate publications from their research. Students may also be asked to produce a report or oral presentation at the end of their project. Please note that the project might vary depending on circumstances. |
Suitable for: | This project is open to applications from 3rd - 4th-year students with a background in Biochemistry & Molecular Biology, Biomedical Science, Genetics, Biophysics, Bioinformatics, Chemical Sciences, Chemical Engineering, Materials Engineering, and other related fields. |
Primary Supervisor: | Dr. Ruirui Qiao |
Further info: | Please contact Dr. Ruirui Qiao (r.qiao@uq.edu.au) for any matters |
Lead-free halide perovskites for high-performance optoelectronics
Project title: | Lead-free halide perovskites for high-performance optoelectronics |
Project duration: | 10 weeks |
Description: | Halide perovskites have been emerging as a promising family of semiconductors for a wide range of optoelectronic/electronic applications, including solar cells, transistors, lasers, photocatalysis, memory devices, photodetectors, X-ray detectors. Currently, the best-performing halide perovskites contain toxic lead, which causes additional concern on further large-scale deployment. This project will be addressing this critical issue by designing high-performance lead-free halide perovskite semiconductors and demonstrate their applications in renewable energy generation and conversion areas. Aim of the project: Design and synthesis of lead-free halide perovskite semiconductors, focusing on single crystals and thin-films. Demonstrate their applications in solar energy conversion and other optoelectronic devices. |
Expected outcomes and deliverables: | The applicants will learn how to synthesize semiconductor single crystal and thin films. In addition, basic semiconductor characterization techniques will be used for studying the electronic and optoelectronic properties of the as-prepared semiconductors. By the end of the project, the synthesized semiconductors will be applied in solar energy conversion and other optoelectronic devices. Students will be expected to produce a report and oral presentation at the end of their project. |
Suitable for: | This project is open to applications from students with a background in chemical engineering, material engineering or mechanical engineering 3-4 year students. |
Primary Supervisor: | Dr. Miaoqiang Lyu |
Further info: | Please contact the supervisor prior to submitting an application (m.lyu@uq.edu.au ). Further information: |
How does phospholipid chirality and saturation position impact cell membrane properties?
Project title: | How does phospholipid chirality and saturation position impact cell membrane properties? |
Project duration, hours of engagement & delivery mode | The project is for 8 weeks for ~30hrs per weeks and the applicant will be required on-site for the project. The student must be prepared to commence on the 5 December 2022. |
Description: | The integrity of every cell relies on the properties of the phospholipid bilayer that surrounds it. The precise chemistry of each phospholipid in the membrane determines the overall properties of the membrane, such as its thickness, fluidity, and curvature. These properties are important for cellular function. Recent studies have shown that diseases such as cancer change phospholipid chirality and unsaturation positions. This project will use computational techniques (molecular dynamics simulations) to examine the effect of phospholipid chirality on the properties and dynamic behaviour model membranes. No prior computational experience is necessary; students must be willing to learn how to use molecular dynamics software. Students will be required to participate in regular group meetings. |
Expected outcomes and deliverables: | Students will gain experience in computational chemistry, working in a multidisciplinary team, project management and communication skills. They will learn how to interpret and analyse experimental datasets for modelling and data visualisation. They will have the opportunity to engage with collaborators from different backgrounds. Depending on their progress, they may have an opportunity to generate publications from their research. Students may also be asked to produce a report or oral presentation at the end of their project. |
Suitable for: | This project is open to applications from students who have completed their 2nd or 3rd year of undergraduate studies, with a background in chemistry, chemical biology, biophysics and biochemistry. |
Primary Supervisor: | Megan O’Mara |
Further info: | Please contact me by email to discuss further m.omara@uq.edu.au |
Isolation and characterization of cancer cell-derived extracellular vesicles
Project title: | Isolation and characterization of cancer cell-derived extracellular vesicles |
Project duration, hours of engagement & delivery mode |
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Description: | Extracellular vesicles (EVs) are nanoparticles that are naturally produced and released by cells. EVs are loaded and decorated with various signalling molecules that play important roles in intercellular communication throughout the body, including at distant sites. In the context of cancer, EVs produced by cancer cells send messages to other cells, which may corrupt them and facilitate tumour progression. This project aims to isolate and characterise EVs of high quality and yield produced by various cancer cells in vitro. Additionally, the effects of exposing non-cancerous cells to cancer cell-derived EVs will be assessed. |
Expected outcomes and deliverables: | The applicant can expect to gain skills in teamwork, tissue culture, molecular biology techniques, approaches to isolate EVs from biological samples, nanoparticle/EV characterization techniques, experimental research design and planning, and data collection and analysis. Students will be expected to actively participate in experimental planning, analysis, and discussion of results, as well as deliver a final report presenting the methodology and results of their research in a scientific manuscript format. The student may have opportunities to generate publications from their research and to present their findings at scientific conferences. |
Suitable for: | This project is open to applications from motivated UQ-enrolled students who are interested in pursuing a research career (e.g., intend to graduate with an Honours or a Master's degree or apply for a PhD in the future). This is a multidisciplinary project, and no specific background knowledge is required. Desirable qualities include self-motivation, flexibility to learn topics outside of your original field, and good time management. |
Supervisors:
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Further info: | If you are interested, please send an email to Dr. Jenifer Pendiuk Goncalves (j.pendiukgoncalves@uq.edu.au) containing your CV and a motivation letter. Please note: you will also need to submit an official application form via the Summer Research Program website. |
Understanding the immunomodulatory effects of cancer cell-derived extracellular vesicles
Project title: | Understanding the immunomodulatory effects of cancer cell-derived extracellular vesicles |
Project duration, hours of engagement & delivery mode |
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Description: | Extracellular vesicles (EVs) are nanoparticles that are naturally produced and released by cells. EVs are loaded and decorated with various signalling molecules that play important roles in intercellular communication throughout the body, including at distant sites. In the context of cancer, EVs produced by cancer cells send messages to other cells, which may corrupt them and facilitate tumour progression. One potential effect of EVs is to suppress immune responses that were supposed to fight the cancer. This project aims to investigate the effects of exposing immune cells to cancer cell-derived EVs. |
Expected outcomes and deliverables: | The applicant can expect to gain skills in teamwork, tissue culture, molecular biology techniques, immune-oncology, microscopy, experimental research design and planning, and data collection and analysis. Students will be expected to actively participate in experimental planning, analysis, and discussion of results, as well as deliver a final report presenting the methodology and results of their research in a scientific manuscript format. The student may have opportunities to generate publications from their research and to present their findings at scientific conferences. |
Suitable for: | This project is open to applications from motivated UQ-enrolled students who are interested in pursuing a research career (e.g., intend to graduate with an Honours or a Master's degree or apply for a PhD in the future). For this short-time project to be successfully developed, we expect the student to have background knowledge and experience in EVs isolation (from cell culture media), handling, and characterization. If you don’t, please consider our other project titled “Isolation and characterization of cancer cell-derived extracellular vesicles”. Other desirable qualities include self-motivation, flexibility to learn topics outside of your original field, and good time management. |
Supervisors:
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Further info: | If you are interested, please send an email to Dr. Jenifer Pendiuk Goncalves (j.pendiukgoncalves@uq.edu.au) containing your CV and a motivation letter. Please note: you will also need to submit an official application form via the Summer Research Program website. |