Available Student Projects

Students coming into my lab can claim and develop one of the proposed projects below. Because I have a broad range of research interests, some projects might be more suitable for students who want to learn laboratory and analysis techniques, while others are better suited for aspiring field biologists. I have highlighted in boldface the main methods and techniques you can learn from each project – this should help you decide which one is best suited for your interests and career plans.

Have an idea of your own? Great! Email me at karolina.fucikova[at]gmail.com to set up a meeting with me. We will discuss what the best way might be to pursue your research ideas and make sure it is feasible to accomplish your goals within a reasonable time frame.

Research for credit – If you are interested in research for credit, the 3cr independent study courses (BIO490 and BIO491) may be a good route for you. Be sure to review the requirements – you will be expected to dedicate an average of 10 hours a week to this course, plus attending a weekly journal club. In addition, it is required that you present the results of your research at the spring Undergraduate Symposium or in the Natural Sciences seminar series. Honors students typically take HON300 and HON444 – Honors Seminar and Capstone – to develop and conduct a research project.

Summer research experience – a limited number of paid 10-week fellowships is available to students every year. If you are interested in summer research in my lab, be sure to express your interest to me well in advance (mid-spring semester at least). Honors students may be eligible for summer research funding through the Assumption College Honors Program – again, contact me well in advance to make sure I can meet the deadline to submit an application to the Honors Program. Less intensive unpaid opportunities may also be available during the semester.

 

Morphological and Genetic Diversity of Trentepohlia in New England.

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Trentepohlia umbrina from Connecticut

Trentepohlia is a genus of green algae that often grow in conspicuous reddish films on tree bark. In New England, this alga is common but it is unclear whether it represents one or multiple species. Previous studies have indicated that there may be many more species of Trentepohlia than are currently recognized, some of which may be morphologically cryptic (visually indistinguishable from others), but genetically distinct.

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A film of Trentepohlia growing on oak bark (RI)

 

This project will involve collecting samples from representative localities across New England, preparing herbarium specimens, microscopic observations, isolating pure cultures, and DNA barcoding (lab work and phylogenetic analysis). A great opportunity for someone who wants to learn a range of widely applicable lab and field techniques. The project can be taken a step further by adding a pigment analysis (if you’re into chemistry).

 

 


High Throughput Sequencing vs. Traditional Assessment of Algal Biodiversity in New England Wetlands

(ideal for a team of 2 or more students)

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Wetlands often harbor astounding biodiversity – but much of this diversity is hidden to the naked eye. Among the thousands of microorganismal species, algae are the most charismatic (true, I have a bit of a bias here) and as primary producers represent a vital component of the wetland food web.

Traditionally, microalgal species have been identified using a light microscope. Because many algae have distinct morphologies, this approach is still useful, but requires considerable taxonomic expertise and experience (it takes time to learn to recognize different species, or even to look them up in the literature). Over the past decade or so, it became very clear that there are many species that cannot be morphologically distinguished (and are therefore cryptic), but still represent genetically and evolutionarily distinct entities. To identify such species, DNA barcoding can be used, but this approach requires isolating them into pure cultures first, which can be tricky.

High-throughput DNA sequencing now offers a way to assess species diversity in a sample without culturing or even looking at the content with a microscope. By extracting DNA from an environmental sample and sequencing the same gene from every organism present in that sample, this approach yields a snapshot of the genetic diversity present in the sampled habitat. However, it can be difficult to link particular sequences to known species (because we did not actually see which sequence came from which organism).

For this project, a group of students will collect samples from one or more wetlands, analyze part of the sample using microscopy (and potentially also culturing and barcoding), extract DNA from a second part of the sample and prepare it for high-throughput sequencing (which will be done off-site), bioinformatically analyze the sequencing data, and compare the results of the two approaches.

 


Assessment of Algal Biodiversity in New England Soils

(ideal for a team of 2 or more students)

 

 

Similar to the wetland project outlined above, but the study of soil algae involves some specific challenges – we cannot simply see the biodiversity in a soil sample directly using a microscope. Instead, a multi-step isolation and cultivation process is required, using micronutrient-enriched and antibiotic- and antifungal-infused culture media.

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Currently underway (in a very early stage) is a project examining soils from a 12-mile North-South transect (Wapack Trail, southern NH). Depending on the findings, anEast-West transect (a powerline intersecting with the Wapack) study would be an interesting addition.


Characterization of Mitochondrial and Chloroplast Genomes of Selected Green Algae

Mychonastes_homosphaeraGenomes of algae are still largely unexplored and new discoveries about the molecular biology and evolution of these organisms are made every year based on newly sequenced genomes. Organellar (chloroplast and mitochondrial) genomes are typically encoded on fairly small circular molecules (chromosomes) and contain a small number of genes compared to the nuclear genome.

The involved student(s) will extract genomic DNA from selected algal cultures and prepare this DNA for off-site sequencing. The student will analyze the resulting data using bioinformatic methods including sequence assembly, gene and intron annotation, synteny analysis, and phylogenetic analysis.

 


 

Searching for Evidence of Sexual Reproduction in the Green Algal Class Trebouxiophyceae

(ideal for a team of 2 or more students)

Algae from the ancient and diverse green algal class Trebouxiophyceae have long been considered mostly asexual. However, recent survey of published and new data including genomic evidence of sexual reproduction revealed that sex may be much more common in Trebouxiophyceae than previously thought. Building on these findings, the proposed project will look for further evidence of sex in Trebouxiophyceae by testing additional representatives within major subgroups of the class.

The student(s) will conduct culturing experiments, exposing the algal strains to a range of conditions (nutrient levels, light levels, temperature) to determine whether sexual reproduction can be triggered by particular conditions. The results will be observed using microscopy. Further, we will test for genomic evidence of past recombination using bioinformatic and phylogenetic methods.