SURE 2019

BuG ReMeDEE - SURE (Summer Undergrad Research Experience)

Project # 1: Genome-to-Phenome approaches for high throughput screening of high-performance electrodes  (Mentor: Venkata Gadhamshetty, Ph.D.)

Background: Surface properties of electrode materials exert a critical role in determining the biofilm phenotypes in bioelectrochemical systems. All of the electrode surfaces are characterized by heterogeneous surface properties to an extent, either on a micro- or nano-scale, and will influence the local adhesion forces on adhering microbes. The complex interaction between surfaces and microbes will therefore impact the adaptive responses of electrochemically active biofilms.

Objectives: (i) To find out the influence of surface properties on adhesive forces, gene expression, and production of matrix composition; (ii) phenotypic heterogeneity in response to electrochemical properties; (iii) surface modification strategies to precisely control biofilm phenotypes (electrochemical current; adhesion; and extracellular electron transfer)

Outcomes: High throughput strategy for screening an array of emerging electrode materials; (ii) Correlation between surface properties, electrochemical parameters, and gene expression   

Techniques/ tools involved:  DC and AC electrochemistry methods; surface characterization; microbiology and gene expression studies

Gadhamshetty's Bio


Project # 2: Identification of transition state in enzyme-substrate catalysis

Background: Transition state corresponding to the highest potential energy along the reaction coordinates. The concept of a transition state defines the rates at which chemical reactions occur. Transition state structures can be determined by searching for first-order potential energy surface of the chemical species i.e. enzyme and substrate. Identification of these species will be carried out using the computational tools and software.

Objectives: (i) To find out the active site of the enzyme; (ii) Labeling of key amino acids involved in substrate binding & catalysis; (iii) Determination of energy levels of different intermediates; (iv) Evaluation of probable transition-state complex

Outcomes: (i) Basic screening strategy involved in screening of transition state; (ii) Generalized mechanism of energy calculation of different biological compounds, specifically amino acids

Techniques/ tools involved: Protein threading; CHIMERA; MUSCLES

Project # 3: Engineering a Novel Methanotroph for Enhanced Biopolymers (Mentors: Rajesh Sani, Ph.D. & David R. Salem, Ph.D.)

Background: Polyhydroxyalkanoates (PHAs) are a family of biodegradable thermoplastic polyesters produced by microorganisms. They have a great demand in biomedical and industrial sectors, but current biosynthesis methods suffer from poor structural properties, low yield, and high cost. Application of methanotrophs to produce PHAs by oxidizing biogas (methane) can turn out to be a transformative concept because of its double fold advantage of producing the biopolymers simultaneously by tackling the issue of Global Warming (see Figure).

Project 3.1 SURE

Objectives: (i) Regulation control over biopolymer production in an unexplored bacterium; (ii) Improvement in substrate (methane) uptake for enhanced biopolymer production; and (iii) Biopolymer property enhancement

Outcomes: (i) The SURE student will generate mutants of a methanotroph which will convert methane into PHA at greater rates. (ii) Bioplastic which could replace synthetic plastic.

Techniques/ tools involved: Genome to phenome molecular techniques including genetic engineer/genome editing, various spectroscopic techniques, and Bioinformatics using BIOVIA Discovery Studio

Sani's Lab


Project # 4: Rules of life of polyhydroxyalkanoates-producing biofilms (Mentors: David R. Salem, Ph.D. & Rajesh Sani, Ph.D.)

Background:  Research in biopolymers as substitutes for fossil fuel-based synthetic plastics presents a topical research and development field worldwide to develop a circular bio-economy. Recent research focus has been concentrated on the utilization of inexpensive lignocellulose biomass (LCB) materials for polyhydroxyalkanoates (PHA) production. Literature suggests that during the process of degrading LCB into its monomeric components, some portions of lignin and hemicellulose do undergo further reactions, forming byproducts, including volatile organic acids and aromatic compounds. These compounds are inhibitory at low or moderate concentrations to most PHA-accumulating microorganisms and drastically affect the cell growth and PHA production.

In nature, biofilms allow sessile cells to live in a coordinated, more permanent manner that favors their proliferation. They have also been known to confer tolerance to antimicrobial agents (disinfectants and antibiotics) by reducing diffusion of toxic compounds, and these protective benefits of biofilms depend on their inherent structure (matrix), and on the gene expression patterns of sessile cells. However, mechanistic and experimental insights are scare in the literature; For example (1) can PHA produces grow as biofilms in the presence of toxic compounds released during LCB biodegradation? (2) Can those biofilms accumulate greater yields of PHA?

Project 4 SURE 2019

Objectives: (i) Grow a PHA-producing biofilms on 2D material; (ii) Study transcriptomic profiles of freely growing planktonic cells vs sessile biofilm cells to test the hypothesis whether biofilms could be a better alternative for PHA production than planktonic cells.

Outcomes:  The SURE student i) will grow PHA-producing biofilms on 2D materials and (ii) discover genes which are expressed in inhibitor-tolerant biofilms.



Project #5: Role of biofilms and porosity in methane filtering within African termite mounds (Mentor: Bret Lingwall, Ph.D.)

Background: Several species of African termites produce large amounts of methane as they ferment fungi and woody plants in their guts as part of their digestion. Due to the massive numbers of organisms on a large African mound colony, there are massive amounts of methane produced. However, the termite mound is able to filter, or scrub, much of this methane from the air before the greenhouse gas can escape into the atmosphere. This methane filtering is performed by a complex interaction between a biofilm lining tunnels within the mound and the surface of the mound, which has unique pore structures. By studying the genotype and phenotype of the biofilm at micro- to nano scales, the complex interaction between porous surface and biofilm can be studied to help us develop new materials for methane filtering.

Objectives: (i) Find out the influence of surface properties on adhesive forces between microbes and material, (ii) find out the genotype and phenotype of the biofilms, and (iii) determine the penetration depth of the biofilm into the porous material surface.

Outcomes: (i) a basic screening strategy for biofilms in porous media, (ii) understand the ability of the bio-filter to scrub methane from moist warm air, and (iii) generalized method for calculating methane removal from the natural filter system.

Techniques/tools involved: Micro-CT scanning, DNA sequencing, surface characterization, microscopy and spectroscopy, mercury intrusion porosity characterization, and microbiology.

Lingwall's Bio


Project #6: Pseudomonas aeruginosa biofilm rheology (Mentor: Travis W. Walker, Ph.D.)

Background: Bacterial biofilms are one of the most intractable problems facing industries ranging from petroleum to the healthcare industry. This matrix of EPS (extracellular polymer substances) provides a diffusion barrier against antimicrobial agents and provides a protective microenvironment where bacterial cultures can thrive. Pseudomonas aeruginosa is an environmental bacteria that is known for its ability to produce alginate-incased biofilm. It can cause major problems in the medical field as an opportunistic pathogen causing recurrent infections in cystic fibrosis (CF) patients and acute infections in burn victims. P. aeruginosa is known to be virulent against other pathogens, and in CF patients experiencing respiratory distress, it is usually the dominant strain. The rheology of a P. aeruginosa biofilm can reveal the mechanical properties that give this biofilm its characteristic resistance to environmental stresses such as antibiotics. We find that P. aeruginosa (PAO1) biofilm is viscoelastic, showing predominantly gel-like behavior, which is likely responsible for P. aeruginosa biofilm robustness in the presence of outside stresses such as pH, temperature, DO (dissolved oxygen), and antibiotics. We are interested in characterizing the rheology of clinically relevant strains of P. aeruginosa biofilm and expanding to other clinically or industrially relevant biofilm cultures.

Objective(s): (i) Develop rheological techniques to characterize biofilm; (2) Characterize clinically relevant strains of P. aeruginosa biofilm; (iii) Determine mechanical and structural changes as a function of environmental conditions

Outcomes(s): (i) Detailed procedure for reproducible characterization of mechanical properties; (ii) Baseline for comparison for PAO1; (iii) Robustness of biofilm as a function of growth conditions

Techniques / Tools Involved: Rheometry, Microscopy

Walker's Bio


Project # 7: Understanding the microbial physiology under microgravity conditions in a rotating bioreactor (Mentor: Travis W. Walker, Ph.D.)

Background: Growth of cells have been performed in stagnant broth for ages.  This technique has been proven inefficient, as the cells tend to flocculate and settle, leading to deficiency and non-uniformity in nutrient supply to the cells. Rotating bioreactors were developed by NASA to solve these problems, as the environments exhibit “microgravity,” and the cells remain suspended in the fluid.  Using spherical particles as a surrogate, studies have been completed on rotating reactors, both by experiment and by numerical modeling, to investigate the forces on the cells that influence their movements under these conditions.  Further, investigations have been completed into how nutrient transport to the cells are being influenced by the rotation speed of the reactors.  However, detailed investigations are still needed, as many questions remain.  In this work, we are performing detailed experiments and simulations to character the behavior of cells under a wide range of gravitational forces, rotation speeds, and cell morphologies to predict the growth of the cells in the rotating reactor.

Objective(s): (i) Develop codes (in C environment) that would mimic a rotating bioreactor using fundamental transport phenomena; (ii) Characterize cells based on the orbit formed under conditions like gravity and rotating speed of reactor

Outcomes(s): (i) Trajectories of cells under range of values of gravity, rotating speed, and morphology; (ii) Regions of pseudo-stability for cell in rotating reactor; (iii) Detailed forces influencing the path of the cell in a rotating reactor

Techniques / Tools Involved: Stokesian Dynamics Simulations

Walker's Bio


Project # 8: Antibiotic resistance of bacteria in water (Rapid creek) (Mentor: Lisa Kunza, Ph.D.)

Background: Antibiotic resistance has become a hot topic in clinical research.  As bacteria gain antibiotic resistance and combat the pharmaceuticals that are designed to kill them, human health risk increases.  In addition, it becomes more costly to treat illnesses that were once easily treated with antibiotics.  Bacterial infections with antibiotic resistance become much more dangerous and can lead to disability or even be fatal.  Although these bacteria are somewhat common in the clinical setting, it is less clear their distribution in the environment.

Objective(s): (i) Collect bacteria from multiple locations within Rapid Creek, SD; (ii) test for antibiotic resistance of bacteria in Rapid Creek, SD; (iii) examine the gene expression of these organisms.

Outcome(s): (i) protocols for isolating and testing for antibiotic resistance; (ii) distribution of antibiotic resistance in Rapid Creek; (iii) report indicating areas with greater potential human health risk.

Techniques/ Tools Involved: Ecotoxicity analysis

Kunza's lab