Biochemical and Biomolecular Engineering Commons^™

Asm And A Culture Of Sharing, Caring, And Fun In Education, David J. Westenberg

Biological Sciences Faculty Research & Creative Works

One doesn't always equate a professional scientific society with sharing, caring, and fun, but in this age of public distrust, public engagement with science and active student learning are ways to regain trust. ASM holds a leadership position in promoting and recognizing the value of education in the future of our profession and is there to support your educational journey. From K12 outreach and public engagement, to professional development, to presenting and publishing scholarship of teaching and learning, ASM has been at the forefront of biology education. Under the leadership of visionary directors such as Amy Chang and now Irene …

Biosensors For Biomedicine, Drake O'Leary

Miners Solving for Tomorrow Research Conference

This project investigated the use of engineered bacterial reporter systems to detect cellular stress responses associated with antibiotic activity. While constructs were successfully introduced and tested against known antibiotics, the reporter consistently produced a blue signal across conditions, limiting the ability to distinguish specific stress responses. This suggests issues such as leaky expression, insufficient regulatory control, or lack of specificity in the reporter design. Although results were inconclusive, this work highlights key challenges in developing reliable biosensors and provides a foundation for future optimization. Improving signal specificity and reducing background expression will be critical for enabling accurate characterization of antibiotic …

Isolated Bacillus Licheniformis Sp01 From Daqing Oilfield In Reducing Chromium(Iii) Crosslinked Polymer Residue And Enhancing Oil Recovery, Xiao Hui

Student Works (2020-2029)

After polymer gel formation, the residual partially hydrolyzed polyacrylamide (HPAM) and the crosslinker (Cr3+) caused plugging and decreased oil recovery. Microorganisms can degrade HPAM to address the issues, but Cr³⁺ inhibits the process and reduces oil recovery. This study explores the underexamined biodegradation of HPAM and improved oil recovery in the presence of Cr³⁺, offering new perspectives for microbial enhanced oil recovery (MEOR) after polymer gel formation. HPAM and crude oil were innovatively used as the sole nitrogen(N) and carbon(C) sources to isolate the best-growing strain from Daqing Oilfield produced water, identified as Bacillus licheniformis SP01. The oil displacement potential …

A Comprehensive Overview Of Chronic Wound Infections And Current Treatment Methods, Sarah Fakher, David J. Westenberg

Biological Sciences Faculty Research & Creative Works

Chronic wound infections pose significant healthcare challenges due to persistent biofilms, antibiotic resistance, and impaired healing pathways. These wounds are characterized by prolonged inflammation, microbial colonization, and disrupted tissue regeneration, leading to substantial morbidity and healthcare costs. This article reviews current knowledge on chronic wound types, their pathophysiology, and the mechanisms underlying biofilm formation to examine the latest advancements in antimicrobial-based strategies aimed at addressing these challenges. It highlights how diverse materials and technologies have been engineered to improve infection management, enhance tissue regeneration, and overcome the limitations of traditional treatments as well as advances that leverage innovations such as …

Metabolite Analysis To Understand Factors Limiting Microbial Fermentation At High Substrate Concentrations, Bishal D. Sharma

Dartmouth College Ph.D Dissertations

Clostridium thermocellum, a thermophilic anaerobic bacterium, holds promise as a biocatalyst for conversion of lignocellulosic biomass into biofuels. This microbe has been subjected to various metabolic engineering strategies, including the deletion of genes encoding secondary fermentation products such as H₂, formate, acetate, and lactate, as well as the expression of heterologous genes to redirect carbon flux toward ethanol production. Despite these efforts, achieving economically viable ethanol titers remains a challenge. We hypothesized that studying how intracellular metabolite concentrations change as fermentation stops could reveal metabolic bottlenecks or regulatory mechanisms limiting ethanol production at high titers. However, metabolomics studies at …

The Antibiofilm Efficacy Of Copper And Zinc-Enhanced Borate Bioactive Glasses On Polymicrobial Biofilms, Sarah Fakher, David J. Westenberg

Biological Sciences Faculty Research & Creative Works

Healthcare-acquired infections (HAIs) are a significant global challenge driven by biofilm-forming pathogens. Polymicrobial biofilms, involving interactions between multiple microbial species, exacerbate treatment difficulties due to their enhanced resistance to antimicrobial therapies. Borate bioactive glasses (BBGs) are an emerging class of biomaterials that have attracted significant interest in infection control. The incorporation of copper and zinc into the BBG matrix can effectively disrupt biofilm formation and bacterial colonization. This study investigates the antibiofilm efficacy of copper and zinc-doped BBGs against polymicrobial biofilms formed by S. epidermidis, E. coli, and P. aeruginosa. Using static and dynamic biofilm models, BBGs were applied through …

Boosting The Power Performance Of Microbial Fuel Cells By Using Dual Nanomaterial-Modified Carbon Felt Electrodes, Krishna Thapa, Wenyan Liu, Yuwei Zhang, David J. Westenberg, Yishu Zhou, Risheng Wang

Chemistry Faculty Research & Creative Works

Innovative design enhancements to microbial fuel cells (MFCs) are pivotal for improving their viability as renewable energy sources. This study introduces a dual approach to electrode modification, integrating polyaniline (PANI) and gold nanoparticles (AuNPs) on carbon felt (CF) anodes coupled with a unique cathode composed of DNA origami and chitosan. The synergistic effect of PANI and AuNPs significantly increases the hydrophilicity and conductivity of the anode, leading to a considerable surge in power density. Concurrently, the biocompatible DNA origami and chitosan-functionalized cathode facilitates efficient electron transfer without relying on conventional catalysts. Together, these modifications yield a 52.42% increase in the …

Optimizing The Expression Of Polyethylene Terephtalate Hydrolase-Encoding Synthetic Gene In Escherichia Coli Arctic Express (De3), Jocelyn Nataniel, Maria Ulfah, Dini Achnafani, Niknik Nurhayati, Gabriela Christy Sabbathini, Sri Rezeki Wulandari, Abinawanto Abinawanto, Is Helianti

Makara Journal of Science

The waste of polyethylene terephthalate (PET) plastic waste in Indonesia is a pressing concern due to its slow degradation and potential environmental damage. One promising solution is to utilize polyethylene terephthalate hydrolase from Ideonella sakaiensis (IsPETase), an enzyme that specifically degrades PET. However, inducing the expression of IsPETase synthetic gene in Escherichia coli BL21 (DE3) has been challenging because much of it remains insoluble. This study aimed to express IsPETase in E. coli Arctic Express (DE3) and optimize the conditions to enhance its production. First, pET22b(+)pelB-IsPETase was inserted into E. coli Arctic Express (DE3). The …

In Vitro Assessment Of The Anti-Biofilm Effectiveness Of Copper And Zinc Enhanced Borate Bioactive Glass Using Processed Microscopic Images, Sarah Fakher, David J. Westenberg

Biological Sciences Faculty Research & Creative Works

The escalating burden of nosocomial infections presents a formidable challenge to healthcare systems worldwide, leading to increased morbidity, prolonged hospital stays, and elevated healthcare costs. These infections are often resistant to conventional antibiotic therapies due to their association with biofilms which contribute to the persistence and resistance of pathogens. In addressing the challenge of biofilm-associated nosocomial infections, borate bioactive glasses (BBGs) have emerged as promising biomaterials. Doping these glasses with antimicrobial metals could potentially harness their antibacterial properties to prevent biofilm formation. This study undertakes a rigorous evaluation of the anti-biofilm efficacy of copper and zinc-doped BBGs by employing processed …

Borate-Based Bioactive Glasses Properties: Clinical And Biomedical Applications, Sarah Fakher, David J. Westenberg

Biological Sciences Faculty Research & Creative Works

Borate bioactive glasses (BBGs) constitute the recently produced bioactive glasses (BGs) in the domain of bioactive materials, offering enhanced functionalities over conventional silicate and phosphate BGs. This advancement is primarily characterized by BBGs' rapid yet controllable degradation rates, superior bioactivity, and the ability to swiftly form a hydroxyapatite layer (HAP) upon interaction with physiological fluids. A distinguishing feature of BBGs lies in their customizability; doping with therapeutic metal ions tailors their bioactivity towards specific physiological responses, including promoting angiogenesis, antibacterial activity, and osteogenesis. This versatility of BBGs' applications extends to bone regeneration, wound healing, drug delivery systems, and potentially nerve …

Determination Of Spore Viability In Concrete Across Several Factors Using Most Probable Number, Samuel Boyer

Williams Honors College, Honors Research Projects

To determine the lowest concentration of spore added to polyurethane-cement composite (PUCCO) particles that can still germinate after curing in concrete. This research project is a small addition to the larger research project being undertaken by Mirza Mohammed Rashiduzzaman for his Masters. The larger project involves the use of fungal spores added in concrete to act as a self-healing component when cracks form in the concrete structure over time. These spores are suspended in a protective oil and loaded into small, hardened sponge-like PUCCO cubes to act as growth points when water and air can reach the PUCCO in the …

The Effect Of Nanoconfined Liquid Properties On The Water-Responsive Behavior Of Bacterial Cell Walls, Seungri Kim

Dissertations and Theses

Water-responsive (WR) materials have the ability to mechanically swell and shrink in response to changes in relative humidity (RH). These WR materials are used by many biological systems to perform essential tasks; for example, pinecones use WR materials to release their seeds in dry environments, and wheat awns open and close to propel seeds into the soil, driven by daily RH changes. The WR actuation of some biomaterials is extremely powerful, for example Bacillus subtilis cell walls display record-high actuation energy and power densities of 72 MJ m^-3 and 9.1 MW m^-3, surpassing those of all existing …

A Novel Application Of Spinning Disk Technology To Collect Plasma From Whole Blood Prior To Quantifying Plasma Rna, Naomi Rapier-Sharman, Mae-Lynn L. Hutchinson, Carlos M. Moreno, Abraham Quaye, Brian D. Poole, K. Scott Weber, William G. Pitt, Brett E. Pickett

Faculty Publications

The spinning disk technology has previously been utilized to isolate bacterial components from blood in hours instead of days. We hypothesized that this platform could be applied as an alternative approach to isolating plasma RNA from a whole blood sample. We consequently tested the efficacy of the spinning disk technology to extract plasma from whole blood upstream of RNA isolation and analysis. To do so, we collected plasma using either the spinning disk or the typical two-spin centrifuge method. We found that the spinning disk method results in significantly more hemolysis during collection than the conventional two-spin centrifuge method. However, …

Effects Of Continuous In Situ Low-Dose Ionizing Radiation On Microorganisms, Molly E. Wintenberg

All Dissertations

Precise detection and monitoring of nuclear fuel cycle, enrichment, and weapon development activities are critical for supporting warfighter preparation in chemical, biological, radiological, nuclear, and explosives (CBRNE) operations, clandestine activities, and nuclear compliance. A biological sensing system could serve as an alternative to traditional detection methods by using organic material naturally present in the environment to discreetly detect residual trace nuclear material. Microorganisms provide an optimal platform for an alternative sensing system; however, their response to low levels of ionizing radiation is poorly characterized. Combining the power of next-generation sequencing and transcriptomic analysis, this dissertation takes an approach to obtain …

Metabolic Network Analysis Of Filamentous Cyanobacteria, Daniel Alexis Norena-Caro

LSU Doctoral Dissertations

Cyanobacteria were the first organisms to use oxygenic photosynthesis, converting CO₂ into useful organic chemicals. However, the chemical industry has historically relied on fossil raw materials to produce organic precursors, which has contributed to global warming. Thus, cyanobacteria have emerged as sustainable stakeholders for biotechnological production. The filamentous cyanobacterium Anabaena sp. UTEX 2576 can metabolize multiple sources of Nitrogen and was studied as a platform for biotechnological production of high-value chemicals (i.e., pigments, antioxidants, vitamins and secondary metabolites). From a Chemical engineering perspective, the biomass generation in this organism was thoroughly studied by interpreting the cell as a microbial …

Biomethane Production From Distillery Wastewater, Zachary Christman

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Distillery wastewater treatment is a great ecological problem, for example, India produces 2.7 billion liters of alcohol that results in 40 billion liters of wastewater. However, this material can be seen as a resource since 11 million cubic meters of biogas at 60% methane could be produced in addition to cleaning the water. The distillery has two options of what to do with the biogas. The first is to use the biogas to fuel the distillery making the production plant more energy efficient and removing some of the need to buy natural gas. The other is to upgrade the biogas …

Iron-Containing Nanoparticles For The Treatment Of Chrionic Biofilm Infections In Cystic Fibrosis, Leisha M. A. Martin

Nanoscience and Microsystems ETDs

Cystic fibrosis (CF) is the most common genetic disease resulting in the morbidity and mortality of Caucasian children and adults worldwide. Due to a genetic mutation resulting in malfunction of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) protein, CF patients produce highly viscous mucus in their respiratory tract. This leads to impairment of the mucociliary clearance of inhaled microbes. In addition to reduced microbial clearance, anoxic environmental conditions in the lungs promote biofilm-mode growth of the pathogenic bacterial species Pseudomonas aeruginosa. Chronic infections of P. aeruginosa begin in early childhood and typically persist until respiratory failure and death result. The …

Noninvasive Measurement Of Electrical Events Associated With A Single Chlorovirus Infection Of A Microalgal Cell, Seung-Woo Lee, Eun-Hee Lee, Gerhard Thiel, James L. Van Etten, Ravi Saraf

Department of Chemical and Biomolecular Engineering: Faculty Publications

Chlorovirus Paramecium bursaria chlorella virus 1 (PBCV-1) contains a viral-encoded K⁺ channel imbedded in its internal membrane, which triggers host plasma membrane depolarization during virus infection. This early stage of infection was monitored at high resolution by recording the cell membrane depolarization of a single Chlorella cell during infection by a single PBCV-1 particle. The measurement was achieved by depositing the cells onto a network of one-dimensional necklaces of Au nanoparticles, which spanned two electrodes 70 μm apart. The nanoparticle necklace array has been shown to behave as a single-electron device at room temperature. The resulting electrochemical field-effect transistor …

Production And Harvest Of Microalgae In Wastewater Raceways With Resource Recycling, Alexander Colin Roberts

Master's Theses

Microalgae can be grown on municipal wastewater media to both treat the wastewater and produce feedstock for algae biofuel production. However the reliability of treatment must be demonstrated, as well as high areal algae productivity on recycled wastewater media and efficient sedimentation harvesting. This processes was studied at pilot scale in the present research.

A pilot facility was operated with nine CO₂-supplemented raceway ponds, each with a 33-m² surface area and a 0.3-m depth, continuously from March 6, 2013 through September 24, 2014. The ponds were operated as three sets of triplicates with two sets continuously fed …

A Novel Synthetic Yeast For Enzymatic Biodigester Pretreatment, Tianyu Tan, Mark S. Aronson, Arren Liu, Jill H. Osterhus, Melissa Robins, Suraj Mohan, Erich Leazer, Bowman Clark, Alexa Petrucciani, Katherine Lowery, James Welch, Casey Martin, Helena Lysandrou, Michael E. Scharf, Jenna Rickus

The Summer Undergraduate Research Fellowship (SURF) Symposium

Lignin, a complex organic polymer, is a major roadblock to the efficiency of biofuel conversion as it both physically blocks carbohydrate substrates and poisons biomass degrading enzymes, even if broken down to monomer units. A pretreatment process is often applied to separate the lignin from biomass prior to biofuel conversion. However, contemporary methods of pretreatment require large amounts of energy, which may be economically uncompelling or unfeasible. Taking inspiration from several genes that have been isolated from termites and fungi which translate to enzymes that degrade lignin, we want to establish a novel “enzymatic pretreatment” system where microbes secrete these …

Integrated Nanoscale Imaging And Spatial Recognition Of Biomolecules On Surfaces, Congzhou Wang

Theses and Dissertations

Biomolecules on cell surfaces play critical roles in diverse biological and physiological processes. However, conventional bulk scale techniques are unable to clarify the density and distribution of specific biomolecules in situ on single, living cell surfaces at the micro or nanoscale. In this work, a single cell analysis technique based on Atomic Force Microscopy (AFM) is developed to spatially identify biomolecules and characterize nanomechanical properties on single cell surfaces. The unique advantage of these AFM-based techniques lies in the ability to operate in situ (in a non-destructive fashion) and in real time, under physiological conditions or controlled micro-environments.

First, AFM-based …

Comparing Virus Ultrafiltration Of Bacteriophages With Filtration Of Minute Virus Of Mice, Kent Smith

Graduate Theses and Dissertations

Industrial production of protein therapeutics demand rigorous testing and clearance of viruses. The U.S. Food and Drug Administration dictate the purity of pharmaceuticals with regards to viral contamination. As this testing is time consuming and expensive using mammalian cells and viruses, bacteriophages may provide a faster and cheaper alternative for membrane filtration processes. We used ultrafiltration membranes to filter protein solutions with viruses. Two bacteriophages were tested against membranes with two different pore sizes. These membranes were then tested by inverting the membrane's orientation. Flux measurements and log virus removal data were taken. Flux and log virus removal were seen …

Inactivation Of Bacterial Opportunistic Skin Pathogens By Nonthermal Dc-Operated Afterglow Atmospheric Plasma, L. C. Heller, C. M. Edelblute, A. M. Mattson, X. Hao, J. F. Kolb

Bioelectrics Publications

AIMS: Multidrug-resistant opportunistic pathogens are clinically significant and require the development of new antimicrobial methods. In this study, Acinetobacter baumannii, Pseudomonas aeruginosa and Staphylococcus aureus cells were exposed to atmospheric plasma on agar plates and in vitro on porcine skin for the purpose of testing bacterial inactivation.

METHODS AND RESULTS: Microbial inactivation at varying exposure durations was tested using a nonthermal plasma jet generated with a DC voltage from ambient air. The observed reduction in colony forming units was quantified as log₁₀ reductions.

CONCLUSIONS: Direct plasma exposure significantly inactivated seeded bacterial cells by approx. 6 log_{10 …}

Investigation Of Bacillus Subtilis As A Biopesticide Against Botrytis Cinerea, Kenneth K. Ng

Master's Theses

The objective of this thesis was to investigate BiOWiSH^TM-Aqua, a commercial dry solid formulation containing a consortium of bacteria and yeast, as a biopesticide for treatment of Botrytis cinerea, a gray mold that affects strawberries. BiOWiSH^TM-Aqua was compared with another commercial product specifically used as a fungicide and bacteriocide, Serenade® Garden Disease Control Spray (concentrated Bacillus subtilis strain QST 713). Both laboratory tests as well as in vivo lab tests were conducted. BiOWiSH^TM-Aqua results varied widely from plate to plate, regardless of experimental conditions. In some of these plates, inhibition zones were observed …

Rapid Diagnosis Of Tuberculosis In A Peripheral Setting, Elsje Pienaar

Department of Chemical and Biomolecular Engineering: Dissertations, Theses, and Student Research

Tuberculosis is an ancient and worldwide epidemic affecting millions of people in mainly the developing world, killing almost 2 million people in 2008. Current diagnostic techniques are outdated and have proven insufficient to control the disease. Smear microscopy has poor sensitivity and culture is slow to yield results. Modern diagnostic techniques are making great strides in shortening time to result but are restricted by two qualities: 1) prohibitively high costs prevent implementation in resource poor areas, and 2) equipment and technician requirements limit application to centralized laboratories. There exists a divide between new technologies and the people that need them …

Response Surface Optimization Of Crystal Violet Decolorization By Pellets Of Pyncnoporus Sanguineus., Siti Suhana Sulaiman

Student Works (2010-2019)

Ligninolytic enzymes of white-rot fungi have broad specificities and have been implicated in transformation and mineralization of organo-pollutant with chemical structure similar to lignin e.g. synthetic dyes. This study was carried out to optimize selected parameters for decolorization of Crystal violet by Pycnoporus sanguineus in shake flasks. The parameters studied were initial dye concentration (ppm), agitation speed (rpm) and process time. They were optimized using response surface methodology (RSM). Subsequent to the optimization, the decolorization process was scaled up in stirred tank reactor (STR). Effect of different geometry of impellers on the decolorization process was studied. Curved blade and angled …

Temperature Influence And Heat Management Requirements Of Microalgae Cultivation In Photobioreactors, Thomas Hagen Mehlitz

Master's Theses

Microalgae are considered one of the most promising feedstocks for biofuel production for the future. The most efficient way to produce vast amounts of algal biomass is the use of closed tubular photobioreactors (PBR). The heat requirement for a given system is a major concern since the best algae growth rates are obtained between 25-30 °C, depending on the specific strain. A procedure to determine temperature influence on algal growth rates was developed for a lab-scale PBR system using the species Chlorella. A maximum growth rate of 1.44 doublings per day at 29 °C (optimal temperature) was determined. In addition, …

Microbial Cellulose Utilization: Fundamentals And Biotechnology, Lee R. Lynd, Paul J. Weimer, Willem H. Van Zyl, Isak S. Pretorius

Dartmouth Scholarship

Fundamental features of microbial cellulose utilization are examined at successively higher levels of aggregation encompassing the structure and composition of cellulosic biomass, taxonomic diversity, cellulase enzyme systems, molecular biology of cellulase enzymes, physiology of cellulolytic microorganisms, ecological aspects of cellulase-degrading communities, and rate-limiting factors in nature. The methodological basis for studying microbial cellulose utilization is considered relative to quantification of cells and enzymes in the presence of solid substrates as well as apparatus and analysis for cellulose-grown continuous cultures. Quantitative description of cellulose hydrolysis is addressed with respect to adsorption of cellulase enzymes, rates of enzymatic hydrolysis, bioenergetics of microbial …

Isolation, Screening And Characterisation Of Lactic Acid Bacteria Isolated From Local Food Sources, Ahmad Faris Mohd. Adnan

Student Works (2000-2009)

126 bacterial isolates were isolated from several local food sources. Out of these, 55 isolates were subsequently identified as lactic acid bacteria i.e. they were gram-positive and catalase negative. These 55 isolates were put through gel plug test to distinguish between homofermentative and heterofermentative isolates. 16 of the 55 lactic acid bacteria isolates were found to be homofermentative. From the 16 homofermentative isolates, seven were chosen on the basis of origin and sugars used in the enrichment process for preliminary physiological characterisation. Several conditions were chosen such as variable temperature, lactic acid tolerance, NaCl concentration and initial pH These serve …

Production Of Polyhydroaxyalkanoate (Pha) From Palm Oil By Pseudomonas Oleovorans And Indigenous Bacterial Isolate, Pseudomonas Sp., Zazali Alias

Student Works (2000-2009)

In this study, the yield of biomass and polyhydroxyalkanoate  (PHA) of Pseudomonas oleovorans grown in batch and fed-batch cultivations were compared. When oleic acid (QA) (0.5% w/v) was used as carbon source, a significant increase in biomass.and PHA content were observed through fedbatch cultivation. The biomass and PHA content obtained from batch cultivation were 1.45±0.19 g/I and 2.50±0.77 % cell dry weight (CDW) respectively, while in the fed-batch cultivation, the biomass and PHA content increased significantly to 3.35±0.78 g/I and 32.72±0.30 %CDW respectively.  When saponified palm olein (SPO) (0.5% w/v) was used as a carbon source, the batch cultivation yielded …