Research: Applied Biological Sciences

Environmental Planning and Management

Dahl's research involves pragmatic field work strategies for environmental planners in wildlife management. This involves evaluating and improving species action plans, assessing current studies, and informing wildlife planners to help improve the science that will be underpinned in the field. Limited population data are available for certain rabbits and hares in the United States, and current research involves the population status of these leporid species. Instructor Dahl has also had the opportunity to work with the planning and management of koalas and wallabies in Australia and, in the future, plans to work with some of our larger South Dakota fauna, such as mountain lions.

Direct and Indirect Effects of Radiation on Cellular Responses


Dr. DeVeaux investigates the molecular and genetic basis of prokaryotic resistence to extreme stress, including high doses of ionizing radiation. Current work includes determining the role of highly conserved single-stranded binding protein Replication Protein A in survival after extreme DNA damage, in the model Archaeon Halobacterium salinarum and the eubacterium Deinococcus radiodurans.

Biosealants – Biologically-Inspired Nanomaterials

The concept of developing a biosealant in structural remediation is based on a unique microbial metabolic process, microbiologically-induced calcium carbonate precipitation (MICCP). A common soil microorganism, Sporosarcina pasteurii, can induce CaCO3 precipitation in the surroundings in response to environmental cues such as high pH and available nutrients and minerals. This biomolecule, microbial calcite, was introduced as a smart nanomaterial in self-healing concrete its effects on the concrete performance were evaluated with regard to surface crack remediation and durability enhancement. Furthermore, this type of mineral cementation has shown a great potential to aggregate loose soil particles, preventing surface erosion and furthermore plugging the permeable channels on the soil surface. In addition to concrete remediation, microbial calcite has been employed in a wide array of applications for soil improvement by reducing liquefaction potential, strengthening mechanical properties, and controlling fugitive dusts. Currently, we are carrying out an industry-funded research project using microbial calcite for the control of fugitive dusts and closely examining its potential as a dust suppressant.

Geomicrobiology at Homestake DUSEL

The main objective of the research is to identify prokaryotic and eukaryotic microbial community structures and their metabolic diversity.  Archiving this information is also critical as the current dewatering program proceeds and, subsequently, the ecological conditions in the mine continue to change, thus affecting subsequent changes in the microbial diversity. If too much time passes between drainage of an area and sampling, then the baseline data pertaining to the microbiota presence or absence will be forever lost and is not retrievable. Through culture-independent and culture-dependent techniques, we explore a wide range of the Homestake samples identifying their evolutionary lineage and metabolic novelty in terms of their scientific and economic values. Especially, bioprospecting is emphasized on their metabolites such as novel antibiotics and high-quality lignocelluolytic enzymes. Findings of this research will provide critical baseline information on not only ecological succession of the mine geosphere but also its impact on microbial community dynamics. This research is currently being carried out with active participation of three PhD/CBE and two undergraduate students at SD Mines and in close collaboration with Dr. C.M. Anderson, BHSU.

Development of Efficient Biocatalysts in Bioenergy Production

The long-term goal of this research is to effectively convert lignocellulosic biomass to ethanol. Its supporting objective is to develop an economically and environmentally sustainable biocatalyst capable of producing ethanol from agricultural and forestry-based lignocellulosic biomass through simultaneous saccharification and fermentation (SSF). In close collaboration with USDA-NCAUR, ARS, Peoria, IL, we are developing recombinant biocatalysts, Saccharomyces strains, which can degrade lignocellulosic waste into ethanol. Specifically, industrial yeast strains tolerant to high ethanol concentrations and expressing the lignocellulolytic genes will be developed for a seamless process of biofuel production. The source of these enzyme genes will be extremophiles from Homestake Gold Mine, South Dakota. Specific objectives of this research are to characterize the biochemical and molecular properties of the best cellulase activities from the DUSEL thermophiles; clone and express thermostable cellulases from extremophiles in a robust Saccharomyces strain using an automated workcell; and perform SSF to produce bioethanol from lignocellulosic waste including corn-stover, prairie grass, switchgrass, pine woodchips, and pretreated biomass. In industrial application, these thermostable cellulases and yeasts will be recycled in pretreatment, which will lower the cost of lignocellulose deconstruction and also increase the efficiency of bioethanol production.

Extremophilic Bioprocessing

A continuous decrease in fossil fuel reserves warrants the urgent need for the development of alternative fuel sources. Lignocellulosic biomass has long been recognized as a potential sustainable source of biofuels such as bioethanol, biodiesel, biobutanol, and biogas. The Energy Independence and Security Act of 2007 and Biomass Multi-Year Program Plan (2009) declared the need for >36 billion gallons per year of biofuel production. To meet these demands, it is critical that a proportion of non-food biomass including lignocellulosic waste materials should be transformed into biofuels.

The literature suggests that current strategies of lignocellulose processing cannot be used to produce biofuels in a sustainable and economical way until we overcome:  high production costs of lignocellulose deconstruction enzymes; the very slow enzymatic hydrolysis kinetics of sugar-release from lignocellulose; and the low yields of sugars from lignocellulose (incomplete hydrolysis). These issues need a significant fundamental as well as applied research input and are currently being addressed by the research group at SD Mines. For example, one method to increase lignocellulose hydrolysis rates is to use enzymes and microorganisms naturally adapted to environments of extreme temperatures. High temperature processes offer faster, more effective and reliable conversion of substrates to commodity chemicals due to the increased solubility and hydrolysis of lignocelluloses as well as a lower risk of contamination.

This research group has been working on extremophiles isolated from the deepest mine in North America, the Homestake Gold Mine (7,800 feet deep, also known as Deep Underground Science and Engineering Laboratory DUSEL), a Local Compost Facility, and Hot Springs State Park in Thermopolis, WY, for lignocellulose conversion under thermophilic (≥60oC) conditions. The Homestake Mine is located in the heart of the Black Hills in South Dakota, within one-hour driving distance from SD Mines. The mine was active for 125 years until its closure in 2001. Microbial communities in the geographically isolated deep biosphere of the mine have survived under nutrient-limited, extreme environmental conditions, leading their evolutionary lineage to be distinct from the surface microorganisms. However, during active mining operations over 125 years, surface microbes and lignocellulosic substrates were introduced into the extreme environments of the mine. Interactions between introduced and existing microorganisms through horizontal genetic transfer might have resulted in alteration in the gene sequences, becoming “the novel genes”. We hypothesized that genetically distinct microbes including extremophiles with diverse, novel metabolic activities might be present in the biofilms, decaying timbers, and soils of the Homestake Mine. This hypothesis is well-supported and at present we have unique thermophiles producing lignocellulose-degrading enzymes growing in the presence of cellulose as the source of carbon and energy.  (See Dr. Sani’s Home page for more details.)

We have been working on “Hydrogen Production from Lignocellulose using Extremophiles”.  Hydrogen, due to its ability to be converted into electrical energy in fuel cells, has gained much interest as a viable biofuel. We are developing an efficient and cost-effective consolidated biohydrogen production process which will include production of thermostable enzymes (cellulases and xylanases from thermophilic bacteria), hydrolysis, and fermentation of lignocellulosic materials in a single reactor at 60°C.

Uranium Biotransformation

Another area of research involves “Bioremediation and biotransformation of hazardous environmental contaminants including uranium”. With over 30 peer-reviewed published articles, my scientific contributions in this area of research include quantifying rates of microbial transformation of toxic heavy metals and radioactive elements and developing better methods for in situ detoxification of toxic metals. For example, uranium (U) contamination commonly exists in surface and ground water, soil, and sediment at many sites worldwide. A promising strategy for in-situ remediation of U is via biostimulation of iron- and sulfate-reducing native bacterial species, which mediate the reduction of soluble U(VI) leading to its precipitation as uraninite (UO2). Uraninite is generally regarded as the most desirable product of bioreduction because of its low solubility under reducing conditions. Our group’s recent results, however, show that a significant mass fraction of bioreduced U (35-60%) exists as a mobile phase and raises several fundamental questions regarding long-term U reclamation stewardship. For example, what is the fraction of uraninite existing as soluble, suspension, or as co-partitioned phases? What fraction of uraninite is associated with periplasmic and cytoplasmic regions of bacterial cells; surfaces of cells; and colloids (e.g., iron oxides/sulfide particles)? Furthermore, for geologic and redox conditions common to U mining areas of the western US, what are the biogeochemical controls associated with uraninite distribution within the mobile and immobile (mineral) phases? We are trying to answer these fundamental questions. The impact of the research will result in an improved understanding of the fate and transport of bioreduced U in U-reducing microbial ecosystems.

DNA Structure and Function


  • DNA structure and supercoiling: The Sinden lab studies DNA, alternative conformation of DNA, and DNA supercoiling. Alternative conformations of DNA include cruciforms, left-handed Z-DNA, intramolecular triplex DNA, unwound DNA structures, and G-quadruplex structures. In 1995 we discovered a new alternative DNA structure called slipped-strand DNA. We have shown that many of these structures exist in the chromosomes of living bacterial cells. We work to understand the biological roles and consequences of these alternative DNA conformations in mammalian cells.
  • Molecular mechanisms of spontaneous and genotoxicant-induced mutation: A second area of research interest involves understanding the molecular mechanisms of mutagenesis. An exciting correlation exists between DNA sequences that form alternative structures and mutations that cause cancer and human genetic disease. That is – mutations do not really occur randomly, rather they are often templated by the DNA sequence itself. In other words, certain DNA sequences (DNA repeats) are their own worst enemy. These DNA sequences are prone to, or better perhaps, programmed for, self-directed mutation. We work to understand these molecular mechanisms of spontaneous mutagenesis that involve alternative DNA conformations. In addition, we have shown that many types of mutations occur preferentially on either the leading or lagging strand during replication. Currently, we are investigating the genetic instability of DNA sequences that form four-stranded, G-quadruplex structures. These sequences are associated with genetic instabilities associated with cancer.
  • DNA repeat instability associated with human genetic neurodegenerative disease: A third area of interest involves understanding the molecular basis of certain human genetic diseases. This area of research integrates the above two focus areas: DNA structure and spontaneous mutagenesis. Currently, more than 40 human genetic neurodegenerative diseases are caused by the massive expansion of (CTG)n•(CAG)n, (CGG)n•(CCG)n, (GAA)n•(TTC)n, (CCTG)n•(CAGG)n, or (ATTCT)n•(AGAAT)n DNA repeats. All these DNA repeats form one or more alternative DNA conformations, including hairpins, slipped strand DNA, parallel DNA, triplex DNA, and unwound structures, which are likely involved in their genomic instability (i.e., expansion or deletion mutations). We have developed genetic assays for studying the deletion of DNA repeats in a model bacterial system. A goal of our laboratory is to understand the molecular basis for the expansion (and deletion) mutations and to find a therapeutic approach for reducing repeat length. We are currently investigating the role of tryptanthrins and coralyne derivatives as chemicals that may stabilize intramolecular triplex DNA and lead to increased rates of deletion of the Friedreich Ataxia  (GAA)n•(TTC)n repeats. With such an approach, one may be able to prevent or delay onset of repeat expansion diseases.