Category Archives: award

Identification antibiotic resistance in the microbial communities of a Fairbanks permafrost gradient

IMG_20160405_190655Undergraduate researcher Maddie McCarthy was recently awarded a BLaST Undergraduate Research Experience. Maddie will have a completely funded summer of research ahead of her. She’ll be digging into the soil microbial communities of the Fairbanks Permafrost Experimental Station. Continue reading Identification antibiotic resistance in the microbial communities of a Fairbanks permafrost gradient

Does permafrost thaw alter methane cycling via a shift in the microbial community composition?

Undergraduate researcher Alex Wynne was recently awarded an URSA Summer Research Project. This includes funds for his project and a stipend for the summer. He’ll use next-generation sequencing to characterize the relative abundances of methanogens and methane oxidizers found within a permafrost thaw gradient. By analyzing the relative amount of methane related microbes associated with each disturbance treatment, he will deduce how the thawing of permafrost may contribute to the net amount of greenhouse gases being released into the atmosphere.

Honor Program Award

Honors Program, Piacenza Award
Sarah Hartman nominated Devin Drown for the Piacenza Award

Today, Devin was awarded the Robert Piacenza Award for Excellence in Teaching by the Honors Program here at the University of Alaska Fairbanks.  In her nominating statement, Sarah says

Dr. Drown is directly involved with students’ mastery of the material. He will converse with us one on on, comes to lab, and offers thoughtful feedback on in class exercises. He expects a lot…but he also offers a lot with a positive, engaging teaching style.

 

Testing the Effects of the Alaskan Microbiome

Undergraduate researcher Jackson Drew was recently awarded an URSA Spring Project Award. He’ll now be completely funded to complete a pilot project related to microbiome engineering. Having grown up in Interior Alaska, Jackson is keenly aware of how climate warming is inducing rapid large-scale shifts in plant communities in the boreal biome. His research will measure the effects of soil microbes on plant growth as a means of elucidating plant-microbe interactions.

Using Nanopore Sequencing to Explore Genomics

I found out today that URSA has generously provided me funds to explore using the MinION nanopore sequencer (Oxford Nanopore Technologies) for undergraduate research. Funds from this proposal will facilitate independent undergraduate genomic research opportunities using bleeding edge technology and a simplified workflow. The MinION at just 87 grams and half the size of an iPhone is so portable that it will visit the International Space Station as a proof of concept in remote collection of DNA sequence data. This device can provide opportunities for student researchers to generate their own low cost DNA sequence data (as little as $500 / experiment). In the near future, the machine will allow for the direct acquisition of data from biological samples (including saliva and blood) without lengthy time consuming steps. There are current applications identifying viral pathogens in near real-time.

In the future, students will design their own independent research projects that integrates this technology. This resource could support projects that propose environmental microbial community profiling and bacterial or even eukaryotic whole genome sequencing to just name a few opportunities. Additionally, the equipment can be integrated into fieldwork (e.g. Toolik) or works at remote campuses. The proposed research presents an opportunity for undergraduates to learn the methods and techniques of collecting and analyzing genomic data using bleeding edge technology. By providing training in the methods of genomic analysis, we are better preparing future Alaskans to generate and interpret data in the genomics era.

INBRE Pilot Proposal funded

The news finally came through this past week that my first Alaska INBRE Pilot grant was awarded. The goal of the proposed research is to develop a general evolutionary theory to understand host-symbiont interactions. This is an important missing component of current investigations of the human microbiome and its interpretation in regard to human health. In terms of human pathogens, we may better understand the conditions for disease emergence as well as those that favor increases and decreases in disease virulence.

INBRE_2015_Retreat

Human Microbiome curriculum development

This past month, the Alaska IDeA Network of Biomedical Research Excellence (INBRE) program put out a call for  curriculum proposals. INBRE is supported by a grant from the National Institutes of Health. An objective of the Alaska INBRE Research Training Core is to expand curricula in biomedical and health areas across the University of Alaska system. I worked with Dr. Mary Beth Leigh on a proposal that was just funded. This summer we will be developing a new course to be offered at UAF in the near future. Below is a short description.

Overview: It is now widely recognized that humans are host to a diverse assemblage of microbes (Blaser 2014b). This associated microbiota impacts the behavior, physiology and fitness of their host. The goal is to develop a new course that will broadly explore the biology of host-associated microbiomes. In the process, we will address humans as hosts and include model and non-model systems as tools for research in this complex field. This course will cover research questions on the ecology and evolution of host-associated microbiomes. Additionally, we will explore research methods and tools used to collect and analyze microbiome data.

Relevance to biomedical research: Understanding the role of the human microbiome is an important missing component of current investigations of the human health, so much so that the NIH started the Human Microbiome Project (HMP) in 2007. The HMP developed tools and initial datasets during the initial phase. Now that phase two is wrapping up, we have access to integrated datasets of both microbial communities and host properties. There is growing evidence that human health and disease are significantly impacted by host-associated microbes. The human microbiome is linked to a vast array of health concerns including: asthma and allergies (Reibman et al. 2008), cancer (Marchesi et al. 2011), malnutrition and obesity (Tilg and Kaser 2011), and autism and depression (Mulle et al. 2013). Some even argue that changes in health practices may have exacerbated these effects (e.g. increasing use of antibiotics) (Blaser 2014a).