What do you get when you put a project manager with an electrical & electronics engineering degree, and a biochemist together in a lab? It sounds like the beginning of a bad joke, but nothing is further from the truth. Sometimes unusual interdisciplinary collaborations can turn out to be very productive.
This is exactly what happened when Shivangi Dubey, a BU employee in the IT Department, reached out to Dr. John Kyndt at the Science Department, and expressed that she had an interest in working on some real-life science projects. Together they started working on some of the ongoing project of bacterial genome sequencing at the BU Science Labs.
The collaboration turned out to be fruitful very fast. “Shivangi showed an honest interest and curiosity in the project and was very driven to accomplish results” says Dr. Kyndt. “From the start she described herself as a science enthusiast and a constant leaner. That made it real easy to teach her basic lab and bioinformatic skills”.
In less than two months after the start of the project, the team was able to publish a new article on the genome analysis of an unusual bacterial species. The publication was just released online in Microbiology Resource Announcements this week: Genome Sequence of the Unusual Purple Photosynthetic Bacterium Phaeovibrio sulfidiphilus, Only Distantly Related to Rhodospirillaceae, Reveals Unique Genes for Respiratory Nitrate Reduction and Glycerol Metabolism
Not only did they complete the genome of this species, the genomic analysis and comparisons also revealed the genetic reason behind the strict anaerobic nature of this bacteria and revealed unique metabolic pathways that will be the basis for further physiological studies.
“It all started when a research article on “Photoactive Proteins” by Dr. Kyndt caught my attention and out of curiosity I reached out to Dr. Kyndt to learn more about his research. He not only addressed my curiosity but also provided me an opportunity to learn from him and partner with him in his next research project. Dr. Kyndt has been very supportive and provided guidance throughout this research. I look forward to many more such opportunities to learn from him” Shivangi.
In an effort of continuous education, both Shivangi and Dr. Kyndt are currently taken an online course in Bacterial Bioinformatics, and are hoping to complete their Certificate in Bioinformatics from the University of Virginia in a couple of weeks.
The giant phototrophic bacterium Thiospirillum jenense was first discovered in 1838. Its large size (up to 100μm), spiral shape, orange-brown color, and formation of sulfur globules visible under the light microscope, made it an interesting study object for several renowned microbiologists throughout the 20th century.
Although a very intriguing organism, it was proven to be extremely difficult to cultivate in the lab and even to date, no pure culture has been obtained. For a long time, the only source of this bacterium was a pond in former East Germany where it grew April to July, and bacterial cultures had to be smuggled across the then closed borders to West Germany. For more than five decades, the problems in cultivation of Tsp. jenense and later also the missing availability of cultures, have disabled further detailed studies.
Even though the growth and phototactic behavior was studied, nothing was known about the molecular genetics of this intriguing species, not even 16S rRNA sequences, so no complete taxonomic classification could be performed. Up until now.
Illumina-based sequencing was performed at Bellevue University on an enriched sample of Thiospirillum jenense, obtained from Dr. Johannes Imhoff from the GEOMAR Ocean Research Center in Kiel (Germany). Genome sequencing and metagenomic binning analysis now provided the full genome of Thiospirillum jenense which was published just this week in Archives of Microbiology. It showed the unique placement of this species amongst the purple sulfur bacteria and, in addition, potentially resolved some of the genetic reasons behind the challenges of cultivating Tsp. jenense that have been limiting further experiments in the past.
One key component appears to be lack of a high-affinity oxidase (FixNOP), which presumably renders the cells highly sensitive to oxygen damage. In addition, the two sequenced contaminant species, Rhodopseudomonas palustris and a new species Rhodoferax jenense, might help with removal of oxygen in the cultures. These results likely explain the difficulties with obtaining pure cultures of Tsp. jenense as described in the paper, and opens up the doors for new cultivation methods.
Having genomic and genetic data available for Tsp. jenense has widened our understanding of the microbial diversity and will undoubtedly help to further identify similarly unique species in environmental samples, where they play an important role in the sulfur cycle and other nutrient recycling in the environment.
With the recent growth in Natural Science courses and rapid development of the sustainability outdoor lab, the time was ripe to expand on the biology instructors for the science department.
Dr. Sarah Gaughan has a Ph.D. in Natural Resources (from UNL) and a background in aquatic ecology, fishes and genome sequencing. Her research has been focused on applying novel techniques to facilitate conservation of native species. She also focuses on population management and finding new ways to control invasive species.
This provides a perfect fit for the growing science program and at the same time expands the experience and knowledge of the overall science faculty at BU. Having someone with a diverse ecology background will not only be beneficial for the outdoor lab projects, but also opens up the possibility for students that have an interest in environmental biology and ecology research projects or careers.
Dr. Gaughan will be teaching a variety of natural science courses for the general education but will also be available to mentor students in various research projects in the Biology or Sustainability program throughout the year.
To find out more about Dr. Gaughan’s research projects please check out our Faculty and Staff page, or feel free to contact her directly (email@example.com) if you have any environmental or ecology questions or project suggestions.
Welcome to the science team Sarah!
During the entire month of May the BU Library has their display around the theme of Sustainability and featuring the development of the new Sustainability Learning lab.
While the library is practicing social distancing, the library is open and provides a great opportunity to refresh your knowledge on native gardens, greenhouses, biofuels and solar and wind energy. Besides a large selection of books on these topics, the display also highlights some tips on how to set up a native garden and provides some more background on the use of algal ponds for biofuels. You might even come away with some ideas and inspiration to set up some renewable energy yourself or start some small-scale sustainable farming at home!
The main inspiration for this display comes from the new outdoor Sustainability Learning lab that is currently being constructed behind the Joe Dennis Learning Center. This lab will be a 7000 square foot indoor/outdoor educational and research area, consisting of a greenhouse (1,600 square foot), algae pond, wind and solar energy generating stations, and a native plants garden. The lab will give students a unique hands-on opportunity to study various aspects of biology, environmental science and sustainability. The garden of native Nebraska plants was already started last October and some blooms are already sprouting up! (check out our @scienceondisplay on Instagram for updates). This is just the beginning of a three year innovative project. Most of the construction will be occurring in the Summer and Fall of 2020 when the greenhouse is built. In the second phase, the algae pond and the solar and wind generation stations will be installed.
If you can’t make it to the BU Library but still would like more information and resources on the various aspects of sustainability and on the outdoor learning lab, you can also visit the virtual Library Libguide page, where you can find lots of links to library books and ebooks on native plant gardens, net-zero greenhouses (including an interesting historical overview), and renewable energy from solar, wind or biofuels.
Both the library display and Libguide were created and are maintained by Margie McCandless, Reference Support Specialist at the Freeman Lozier Library at Bellevue University.
We all know how challenging the current COVID-19 pandemic is, and hopefully everyone is doing their part in social distancing and working online. However, imagine if your job is taking you directly in contact with coronavirus patients, makes you work overtime hours with not being able to go to the grocery store until around closing hours, all while you are still taking your college classes online.
That is exactly what is happening to Erica Morillo, who is currently taking Microbiology at Bellevue University, while working at Albany Medical Center hospital in New York. She normally works in the cath lab, but early on in the pandemic they increased that workload because they knew patients would not be able to come in for non-emergency cardiac treatments. Now they have the staff spread out in different departments and working with coronavirus patients where needed. They are still doing critical cardiac procedures, but once those are done they focus on assisting in caring for COVID patients being transferred from NYC to their hospital.
“And it is insane right now, I work 10hr shifts, 4 days a week plus call. We still have been carrying out emergent cardiac procedures, but have to gown up and wear additional PPE like N-95 masks, goggles and face shields” says Erica.
“Our hospital has in place a system to protect ourselves as we care for these patients, but we have had to reuse our PPE materials which undergo a decontamination process.”
Through all this, Erica is trying to keep up with the microbiology course assignments and is using a laboratory kit at home to complete the labs from Hands on Labs. In a way this turned out to be a well-suited time to take a microbiology course where students learn all about working under sterile conditions and details about the growth and lifecycle of infectious microorganisms.
As if all of that wasn’t enough, currently Erica’s father is being treated for COVID-19 infection and has been battling with high fever and reduced lung capacity for the past two weeks. He is in NYC in the Bronx, NY. “So that has been stressful as well as convincing my family about protecting themselves and not going anywhere unnecessary” Erica states.
It is amazing to hear the stories of our students and their dedications and we are proud of how everyone is contributing in unprecedented ways to slow down the spread of COVID-19, while applying their course materials in real life. We wish Erica and her family the best of luck and are grateful to have her at the forefront of battling this pandemic!