2017 Projects

PROJECT DESCRIPTIONS

  1. Postdoctoral fellow Dr. Laura Bilenker – PCIGR (UBC)
  2. Ph.D. candidate Evelyn Frères – PCIGR (UBC)
  3. MSc. candidate Stephen Kinsey – Verheyen Lab (SFU)
  4. Ph.D. candidate Rhy McMillan – PCIGR (UBC)
  5. Ph.D. candidate Nichole Moerhuis – PCIGR (UBC)
  6. Ph.D. candidate Catherine Wu – Hancock Lab (UBC)

How can we use the chemical composition of rocks to learn about early life?
Post-doctoral fellow Dr. Laura Bilenker

Geoscientists can use the chemical compositions of rocks to understand the processes that affected them throughout their lifetimes. These processes can include interaction with magma, interaction with seawater, interaction with small organisms, and more. My current research focuses on using unique seafloor rocks to understand how different elements move when seawater interacts with the seafloor. Their chemical composition today is like a fingerprint of these interactions. My study site is a 4000-meter-tall underwater mountain called Atlantis Massif, which is crowned at its peak by the Lost City Hydrothermal Field. Lost City is home to an entire ecosystem that thrives in extreme conditions (very hot, acidic) that are similar to where the first life on Earth may have begun. We may be able to find the fingerprint of similar present-day organisms preserved in the chemistry of the Atlantis Massif rocks. And if so, this could tell us about the first organisms that lived on the early Earth, and maybe even provide a new tool to investigate the possibility of extraterrestrial life in rocks from meteorites or Mars.

Learning outcomes
After completing this project you will know how to:

  • Prepare rock samples for chemical analysis by using crushing equipment.
  • Work in both an extremely clean laboratory and a “dirtier” geological lab environment.
  • Measure the concentrations of elements and/or isotopes in rocks by using a mass spectrometer.
  • Analyze geochemical data (element concentrations and/or isotope compositions)
  • Determine whether the geochemical data are indeed a fingerprint of life in these rocks.

Why do errors in geochemical measurement occur and how can they be resolved?
Ph.D. Candidate Evelyn Frères

My research is focused on developing methods to improve accuracy and precision in isotopic measurements. A lot of information can be obtained in geochemistry if you can measure the exact concentration of chemical elements and isotopes in different types of rocks and minerals. Even though the instruments that are used to take this type of measurements are incredibly robust and advanced, the numbers we get can still deviate from their “true” value. This can be troublesome and lead to wrong conclusions in geochemical studies. My job is to try to understand the reasons why the measured results we get differ from their standard value, and to develop solutions for these problems. This is a more technical project, that encompasses a lot of data analysis and interpretation. Students with strong interest in chemistry and/or a strong chemistry background would be great candidates for this project.

Learning outcomes
After this project you will learn:

  • Mass spectrometers work and how they are operated (more specifically MC-ICP-MS instruments)
  • What is mass fractionation, why it is important and how it can affect geochemical studies
  • What data can be obtained from it, how to process and interpret it
  • Clean laboratory procedures

Keywords
Chemistry, geochemistry, instrumentation, mass fractionation, mass spectrometry


Investigating the oncogenic potential, and binding targets of various homeodomain interacting protein kinases (Hipks)
M.Sc Student Stephen Kinsey

The homeodomain interacting protein kinase (Hipk) is a protein that normally performs important regulatory roles for cell signaling pathways. However, overproduction of the protein has been correlated to uncontrollable cell growth, epithelial-to-mesenchymal transition, and metastasis, all hallmarks of cancer. This information, combined with the observation of Hipk overproduction in triple-negative breast cancer has led the Verheyen lab to propose that Hipk is a potential oncogene. I plan to investigate the tumor formation and migration ability of cells that are genetically modified to have upregulated levels of Hipk in different tissue types.

In addition to the Hipk cancer model, I am interested in quantifying the binding and kinase activity of the Hipk protein. Quantitative binding and kinetic data has not yet been collected for Hipk, and obtaining this information would allow for a more directed approach to identifying pathways influenced by Hipk.

Working with me on this project will provide you with an understanding of basic research principles, and will introduce you both basic and advanced techniques required for research in developmental genetics. Taking the level of education of the mentees into consideration, I will begin by familiarizing successful applicants with basic genetics principals and techniques, before moving on to dissections, staining and microscopy work. Depending on the progression of the research, you may also be involved with quantifying tumors in genetically modified flies. Preference will be given to students with strong interest in gaining research experience in genetics and/or cell biology.

Learning outcomes
After completing this project, you will have learned how to:

  • Use single channel micropipettes and serological pipettes
  • Use a dissecting microscope
  • Perform plasmid transformations and extractions from coli
  • Identify markers on genetically modified flies
  • Perform dissections of larval fly organs
  • Staining of larval fly organs for epifluorescence microscopy
  • Use an epifluorescence microscope
  • Perform tumor quantification of genetically modified flies
  • Work in a fume hood

Keywords
Drosophila, genetics, biochemistry, cell Biology, cancer


What and how can we learn from prehistoric samples using chemical and isotopic analyses? Are the bones we find in their original context?
Ph.D. Candidate Rhy McMillan

‘When,’ ‘where,’ and ‘who’ are fundamental questions that are integral to understanding our human past. Unfortunately, investigating the artifacts and remains left behind by our ancient ancestors is the closest that we can ever come to directly observing or interacting with them. Previously unattainable details of their lives (e.g., diet, mobility, time since death) are now accessible by chemical and isotopic analyses of their bones and teeth. The proposed research will expand the breadth of information that can be acquired from prehistoric remains by designing and refining novel geochemical methods. Three analytical approaches will be developed for: (1) identifying erosional reworking in bone assemblages from Scladina Cave, Belgium, (2) evaluating prehistoric human mobility on the Northwest Coast (NWC) of British Columbia, and (3) establishing the sex of prehistoric individuals from fragmentary remains.

For one of these projects, we will prepare samples for geochemical analyses and, time permitting, conduct the actual analyses and evaluate and interpret the resulting data. If it is not possible to run the analyses within the timeframe of the internship, we will also work together to interpret geochemical data collected from bones and teeth during prior analytical sessions. Your contributions to the project will result in acknowledgements in publish papers or in my thesis, and provide you with a wide skill set that will be applicable in many different lab settings. We will work together to document your experiences either in a report or presentation format so that you can share with your colleagues/peers and have a tangible take-away that can be used to boost your CV.

Learning outcomes
By the end of the internship, you will be able to:

  • Analyse the morphology and taphonomic alteration of bone and teeth samples with light microscopy
  • Prepare bone and teeth samples for geochemical analyses
  • Work safely and effectively in a laboratory setting
  • Interpret geochemical data of bones and teeth for applications in archaeology and anthropology
  • Synthesize your experience and the work you conducted during the internship in a scientific report or presentation

 Keywords
Archaeology, paleoanthropology, bones, isotopes, trace elements, geochemistry


How do we use minerals to understand the temporal evolution of Vancouver’s mountains?
PhD. Candidate Nichole Moerhuis

Vancouver’s distinctive mountains are part of the Coast Plutonic Complex, a suite of granitic rocks stretching extending 1000km from Vancouver’s North Shore mountains to southeastern Alaska parallel to the coast. However, the crystallization ages of many of these local landmarks remain unknown. This project seeks to resolve the temporal relationships between Cyprus Mountain granitic rocks and establish their position in the regional stratigraphy of the Coast Plutonic Complex. Over the week, students will experience every stage of processing and analysis required to turn a rock hand sample into a concentrated mineral separate, and then establish the crystallization age for this magmatic rock.

Learning outcomes
After completing this project you will learn how to:

  • Use mechanical and magnetic separation techniques to isolate minerals
  • View samples with a scanning electron microscope
  • Analyze minerals for U-Pb using a laser ablation inductively-coupled plasma mass spectrometer (LA-ICP-MS)
  • Process data using Iolite data reduction software
  • Discuss significance of data collected

Keywords
Geology, mineral dating, granite, Cyprus Mountain, mass spectrometry


How do innate defense regulator (IDR) peptides work to dampen harmful inflammation?Ph.D. candidate Catherine Wu

Inflammation is a vital part of the body’s first line of defense, aimed at protecting against foreign invaders, eliminating damaged cells, and initiating tissue repair. Ideally, inflammation is self-limiting, which means inflammatory responses are dampened after the removal of harmful stimuli at the site of injury by white blood cells. However, failure to control the inflammatory reactions can lead to various diseases such as atherosclerosis (heart disease) and rheumatoid arthritis.

Peptides are short chains of amino acids that play essential biological roles as hormones, antibiotics and toxins. Host-defense peptides (HDPs) are positively charged peptides naturally produced by plants, animals and microorganisms. In living organisms, HDPs can selectively modulate immune-cell functions. Innate defense regulator (IDR) peptides are synthetic HDP derivatives with enhanced ability to modulate immunity. IDR peptides can suppress excessive inflammation without compromising the ability of immune system to fight infections.

This research project aims to study the anti-inflammatory activities of IDR peptides using mouse macrophage cell line (RAW264.7). Bacterial surface molecules will be used to stimulate inflammatory responses in RAW264.7 cells. The suppressive effect of IDR peptides on the production of different pro-inflammatory mediators will be quantified by biochemical techniques.

This project provides an understanding of basic research principles and an introduction to lab techniques used in immunological research. Learning cell culture can be challenging, but the student will be guided step by step to make sure all the procedures are carried out safely and correctly. Preference will be given to students with strong interest in gaining research experience in immunological studies.

Learning outcomes
After completing this project you will learn how to:

  • Use single channel and multichannel micropipettes
  • Use a light microscope
  • Use a hemocytometer
  • Make different media and buffers
  • Work in a biosafety cabinet
  • Grow, maintain and passage cell line
  • Measure cell viability (Lactate dehydrogenase assay)
  • Quantify the production of pro-inflammatory molecules (Enzyme-linked immunosorbent assay)
  • Analyze and plot experimental data

Keywords
Immunology, inflammatory response, cell lines


Click here for application (opening December 1, 2016)

If you have questions, please send us an email at megan.chan@stemfellowship.org and cheryl.cheung@stemfellowship.org