Biomedical Engineering and Bioengineering Commons^™

Protocol To Engineer Nanofilms Embedded Lipid Nanoparticles For Controlled And Targeted Drug Delivery (Nectar), Rashi Porwal, Stephen L. Hayward, Srivatsan Kidambi

Department of Chemical and Biomolecular Engineering: Faculty Publications

We present a protocol to engineer a substrate-mediated delivery platform comprising hyaluronic acid-coated lipid nanoparticles (HALNPs) embedded into polyelectrolyte multilayer (PEM) films. This platform allows controlled spatiotemporal release of lipid nanoparticles (LNP) by embedding them within the polyelectrolyte multilayer films matrix. HALNP conjugate with antibodies also adds the ability for targeted delivery. The use of LNP enables this platform to encapsulate both hydrophobic and hydrophilic drugs. This platform can easily be reproduced and utilized for various biomedical drug delivery applications. For complete details on the use and execution of this protocol, please refer to Hayward et al. (2015, 2016a, 2016b), …

Genome Structure And Evolutionary History Of Frankincense Producing Boswellia Sacra, Abdul Latif Khan, Ahmed Al-Harrasi, Jin-Peng Wang, Sajjad Asaf, Jean-Jack Riethoven, Tariq Shehzad, Chia-Sin Liew, Xiao-Ming Song, Daniel P. Schachtman, Chao Liu, Ji-Gao Yu, Zhi-Kang Zhang, Fan-Bo Meng, Jia-Qing Yuan, Chen-Dan Wei, He Guo, Xuewen Wang, Ahmed Al-Rawahi, In-Jung Lee, Jeffrey L. Bennetzen, Xi-Yin Wang

Nebraska Center for Biotechnology: Faculty and Staff Publications

Boswellia sacra Flueck (family Burseraceae) tree is wounded to produce frankincense. We report its de novo assembled genome (667.8 Mb) comprising 18,564 high-confidence protein-encoding genes. Comparing conserved single-copy genes across eudicots suggest >97% gene space assembly of B. sacra genome. Evolutionary history shows B. sacra gene-duplications derived from recent paralogous events and retained from ancient hexaploidy shared with other eudicots. The genome indicated a major expansion of Gypsy retroelements in last 2 million years. The B. sacra genetic diversity showed four clades intermixed with a primary genotype—dominating most resin-productive trees. Further, the stemtranscriptome revealed that wounding concurrently activates phytohormones signaling, …

Characterizing Isoform Switching Events In Esophageal Adenocarcinoma, Yun Zhang, Katherine M. Weh, Connor L. Howard, Jean-Jack Riethoven, Jennifer L. Clarke, Kiran H. Lagisetty, Jules Lin, Rishindra M. Reddy, Andrew C. Chang, David G. Beer, Laura A. Kresty

Nebraska Center for Biotechnology: Faculty and Staff Publications

Isoform switching events with predicted functional consequences are common in many cancers, but characterization of switching events in esophageal adenocarcinoma (EAC) is lacking. Next-generation sequencing was used to detect levels of RNA transcripts and identify specific isoforms in treatment- naïve esophageal tissues ranging from premalignant Barrett’s esophagus (BE), BE with low- or high-grade dysplasia (BE.LGD, BE.HGD), and EAC. Samples were stratified by histopathology and TP53 mutation status, identifying significant isoform switching events with predicted functional consequences. Comparing BE.LGD with BE.HGD, a histopathology linked to cancer progression, isoform switching events were identified in 75 genes including KRAS, RNF128, and WRAP53. Stratification …

The Third International Hackathon For Applying Insights Into Large-Scale Genomic Composition To Use Cases In A Wide Range Of Organisms, Kimberly Walker, Divya Kalra, Rebecca Lowdon, Guangyi Chen, Fritz J. Sedlazeck, Ben Busby, Chia-Sin Liew, Et Al.

Nebraska Center for Biotechnology: Faculty and Staff Publications

In October 2021, 59 scientists from 14 countries and 13 U.S. states collaborated virtually in the Third Annual Baylor College of Medicine & DNANexus Structural Variation hackathon. The goal of the hackathon was to advance research on structural variants (SVs) by prototyping and iterating on open-source software. This led to nine hackathon projects focused on diverse genomics research interests, including various SV discovery and genotyping methods, SV sequence reconstruction, and clinically relevant structural variation, including SARS-CoV-2 variants. Repositories for the projects that participated in the hackathon are available at https://github.com/collaborativebioinformatics.

Comparison Effect On Biogas Production From Vegetable And Fruit Waste With Rumen Digesta Through Co-Digestion Process, Anika Tasnim, Muhammad Rashed Al Mamun, Md Anwar Hossen, Md Towfiqur Rahman, Md Janibul Alam Soeb

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Biogas is the best renewable energy as it can be produced from any biomass for example any plant or living organism. The purpose of this research was to produce biomethane from co-digestion of vegetable and fruit waste with rumen digesta through anaerobic digestion process. In this research, two trials of experiment were conducted. Each trial has three different sample with different mixing ratios. Raw materials used in the experiment was rumen digesta of goat and cow, potato, capsicum, cucumbers, onions, radish, cauliflower, carrot, leafy vegetables, apple, banana, and papaya. In each sample, 1200 gram of raw materials were used. Hydraulic …

Substrate Delivery Of Embedded Liposomes, Srivatsan Kidambi, Stephen L. Hayward

Department of Chemical and Biomolecular Engineering: Faculty Publications

This invention relates to compositions useful for localized and sustained release of therapeutic agents, and more particularly to functionalized liposomes embedded in a poly electrolyte multilayer. Methods of preparing the compositions, methods of treating diseases, devices, and pharmaceutical compositions comprising the compositions are also provided.

Development And Characterization Of A Decellularized Neuroinhibitory Scaffold Containing Matrix Bound Nanovesicles, Logan Piening

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

Chronic low back pain (LBP) is a leading cause of disability but treatments for LBP are limited. Degeneration of the intervertebral disc leads to loss of neuroinhibitory sulfated glycosaminoglycans (sGAGs) which allows nerves from dorsal root ganglia (DRG) to grow into the core of the disc, leading to pain. Current treatments for LBP involve drugs that do not target the source of the pain and lack long term efficacy or use invasive surgeries with high complication rates. Treatment with a decellularized tissue scaffold that contains neuroinhibitory components may inhibit nerve growth and prevent disc-associated LBP. Here, a decellularized nucleus pulposus …

Novel Approaches For Enhancing Cell Survival And Function In Vivo, Ou Wang

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

FDA has approved several cell-based therapeutics and hundreds of cell therapy clinical trials are ongoing. Cells will be a significant type of medicine after small molecule and protein drugs. However, several obstacles need to be addressed to achieve the widespread use of cellular therapeutics. The first challenge is the low efficacy of cell transplantation due to low retention, survival, integration, and function of cells in vivo. The second challenge is producing a massive number of cells for clinical treatment with cost-effectively and reproducibly technologies.

In this thesis, we proposed and investigated two approaches to address these challenges. To begin …

Phenolic, Carotenoid And Saccharide Compositions Of Vietnamese Camellia Sinensis Teas And Herbal Teas, Danh C. Vu, Sophie Alvarez

Nebraska Center for Biotechnology: Faculty and Staff Publications

Tea (Camellia sinensis) and herbal tea have been recognized as rich sources of bioactive constituents with the ability to exert antioxidant actions. The aims of this study were to analyze phenolic, carotenoid and saccharide contents in a set of Vietnamese tea and herbal tea and compare the results with those of green and black teas marketed in the U.S. In total, 27 phenolics, six carotenoids and chlorophylls, and three saccharides were quantitatively identified. Catechins, quercetin glycosides and chlorogenic acid were the predominating phenolics in the teas, with the concentrations following the order: jasmine/green teas > oolong tea > black tea. …

Expedited Pcr With Stirring, Hendrik Viljoen

Department of Chemical and Biomolecular Engineering: Faculty Publications

Disclosed are an apparatus and methods for rapid amplification of nucleic acids. More particularly, the present dis closure relates to an apparatus for mixing a reaction solution during amplification of nucleic acids and to methods for amplifying nucleic acids. Also disclosed are methods for lysing cells in a sample and amplifying nucleic acids.

Expedited Pcr With Stirring, Hendrik J. Viljoen

Department of Chemical and Biomolecular Engineering: Faculty Publications

Disclosed are an apparatus and methods for rapid amplifi cation of nucleic acids . More particularly , the present dis closure relates to an apparatus for mixing a reaction solution during amplification of nucleic acids and to methods for amplifying nucleic acids . Also disclosed are methods for lysing cells in a sample and amplifying nucleic acids .

Defining The Innate Immune Responses For Sars-Cov-2-Human Macrophage Interactions, Mai M. Abdelmoaty, Pravin Yeapuri, Jatin Machhi, Katherine E. Olson, Farah Shahjin, Vikas Kumar, You Zhou, Jingjing Liang, Kabita Pandey, Arpan Acharya, Siddappa N. Byrareddy, R. Lee Mosley, Howard E. Gendelman

Nebraska Center for Biotechnology: Faculty and Staff Publications

Host innate immune response follows severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, and it is the driver of the acute respiratory distress syndrome (ARDS) amongst other inflammatory end-organ morbidities. Such life-threatening coronavirus disease 2019 (COVID-19) is heralded by virus-induced activation of mononuclear phagocytes (MPs; monocytes, macrophages, and dendritic cells). MPs play substantial roles in aberrant immune secretory activities affecting profound systemic inflammation and end-organ malfunctions. All follow the presence of persistent viral components and virions without evidence of viral replication. To elucidate SARS-CoV- 2-MP interactions we investigated transcriptomic and proteomic profiles of human monocyte-derived macrophages. While expression of the …

A Single Cell Pair Mechanical Interrogation Platform To Study Cell–Cell Adhesion Mechanics, Amir Monemianesfahani

Department of Mechanical and Materials Engineering: Dissertations, Theses, and Student Research

Cell-cell adhesion complexes are macromolecular adhesive organelles that integrate cells into tissues. Perturbations of the cell-cell adhesion structure or relatedmechanotransduction pathways lead to pathological conditions such as skin and heart diseases, arthritis, and cancer. Mechanical stretching has been used to stimulate the mechanotransduction process originating from the cell-cell adhesion and cell-extracellular matrix (ECM) complexes. The current techniques, however, have limitations on their ability to measure the cell-cell adhesion force directly and quantitatively. These methods use a monolayer of cells, which makes it impossible to quantify the forces within a single cell-cell adhesion complex. Other methods using single cells or cell …

Efficient Polyhydroxyalkanoate Production By Rhodopseudomonas Palustris From Lignocellulosic Biomass, Brandi Brown

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

Polyhydroxyalkanoates (PHAs) are biopolymers produced by bacteria with the potential to replace conventional plastics. However, the relatively high production costs of PHAs are keeping them from market acceptance, with approximately half of the production costs derived from the feedstock. Thus, engineering a microbe for PHA production from cheaper and renewable carbon sources is necessary to promote the valorization of PHAs. Lignocellulosic biomass is considered to be one of the most economic carbon sources in the world, and is thus an attractive candidate for cheaper production of bioplastics. Rhodopseudomonas palustris CGA009 is a metabolically robust bacterium capable of catabolizing lignin breakdown …

Development Of An Intraperitoneal Catheter Placement Device For Use On The Battlefield, Riley Reynolds

Department of Mechanical and Materials Engineering: Dissertations, Theses, and Student Research

The objective of this project was to simplify peritoneal cavity access so an Airforce field medic can safely infuse oxygen microbubbles (OMBs) into the intraperitoneal space for the emergency treatment of hypoxia due to lung damage. To solve this problem, we created an intraperitoneal catheter placement device for use on the battlefield. The three common methods and some of the most common devices for peritoneal cavity access were reviewed. Injury frequencies for each of the three methods were analyzed. The results showed that each of the access techniques gives a similar rate of iatrogenic injury.

The battlefield conditions where the …

Preclinical Development Of Single Walled Carbon Nanotube-Based Optical Biosensors, Eric M. Hofferber

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

High resolution, long-term monitoring of key biological analytes would improve patient outcomes by providing earlier detection of disease states and improved efficacy of treatment. One class of biosensors that have gained much attention in recent years are optical biosensors. Optical probes are attractive biosensors due to their noninvasive nature of detection, as certain light can pass through tissue, water, and blood. Single walled carbon nanotubes (SWNT) are a specific type of optical biosensor that fluoresce in the near infrared range of the electromagnetic spectrum and offer unparalleled spatial and temporal resolution. SWNT have been applied as biosensors in vitro, …

Quantitative Pcr Of Small Nucleic Acids: Size Matters, Jay Min Lim, Rahul Tevatia, Ravi Saraf

Department of Chemical and Biomolecular Engineering: Faculty Publications

Quantitative dysregulation in small nucleic acids (NA), such as microRNA (miRNA), extracted from minimally invasive biopsies, such as, blood, stool, urine, nose, throat, are promising biomarker for diseases diagnosis and management. We quantify the effect of the extra step of poly(A) ligation for cDNA synthesis and small size of the NA on the limit of quantification (LOQ) of quantitative PCR (qPCR), the gold standard to measure copy number. It was discovered that for small NA, the cycle threshold, Ct that is proportional to −log[c], where [c] is the concentration of the target NA exhibits a sharp transition. The results indicate …

Development Of An Internet Of Things (Iot) Enabled Novel Wireless Multi Sensor Network For Infield Crop Monitoring, Nipuna Chamara

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

Multispectral imaging systems on satellite, aerial, and ground platforms are used commonly to monitor in-field crops in precision agriculture by farmers and researchers. Limited spatial and temporal resolution and weather dependence of the data collection are two main disadvantages of these methods. In-field sensor networks can continuously monitor environmental and plant physiological parameters by leveraging low-power computation and long-range communication technologies. We built and tested a novel sensor network equipped with soil moisture, multispectral and RGB imaging sensors in an experimental soybean field at Eastern Nebraska Research and Extension Center, NE, USA. 10 down-looking and 1 up-looking sensor node were …

Co2 Biocapture By Scenedesmus Sp. Grown In Industrial Wastewater, Itzel Y. López-Pacheco, Eduardo Israel Castillo-Vacas, Lizbeth Castañeda-Hernández, Angie Gradiz-Menjivar, Laura Isabel Rodas-Zuluaga, Carlos Castillo-Zacarías, Juan Eduardo Sosa-Hernández, Damià Barceló, Hafiz M.N. Iqbal, Roberto Parra-Saldívar

Panhandle Research and Extension Center

Greenhouse gases (GHG) emissions are widely related to climate change, triggering several environmental problems of global concern and producing environmental, social, and economic negative impacts. Therefore, global research seeks to mitigate greenhouse gas emissions. On the other hand, the use of wastes under a circular economy scheme generates subproducts from the range of high to medium-value, representing away to help sustainable development. Therefore, the use of wastewater as a culture medium to grow microalgae strains that biocapture environmental CO₂, is a proposal with high potential to reduce the GHG presence in the environment. In this work, Scenedesmus sp. …

Lipid Droplet Membrane Proteome Remodeling Parallels Ethanol-Induced Hepatic Steatosis And Its Resolution, Carol A. Casey, Terrence M. Donohue Jr., Jacy L. Kubik, Vikas Kumar, Michael J. Naldrett, Nicholas T. Woods, Cole P. Frisbie, Mark A. Mcniven, Paul G. Thomes

Nebraska Center for Biotechnology: Faculty and Staff Publications

Abstract Lipid droplets (LDs) are composed of neutral lipids enclosed in a phospholipid monolayer, which harbors membrane-associated proteins that regulate LD functions. Despite the crucial role of LDs in lipid metabolism, remodeling of LD protein composition in disease contexts, such as steatosis, remains poorly understood. We hypothesized that chronic ethanol consumption, subsequent abstinence from ethanol, or fasting differentially affects the LD membrane proteome content and that these changes influence how LDs interact with other intracellular organelles. Here, male Wistar rats were pair-fed liquid control or ethanol diets for 6 weeks, and then, randomly chosen animals from both groups were either …

Two-Dimensional & Three-Dimensional Microarray Cell Culture Using Elastomeric Assembly Substrates, Angel Olivera-Torres

Honors Program: Senior Projects (Public)

Tissue engineering and regenerative medicine represent the collection of all engineering disciplines brought together for the common goal of developing novel ways of growing tissues and organs in the laboratory. Efforts have made it possible to replicate or induce growth of 2D structures in the human body like skin, but the clinical need for on-demand solid organs has yet to be met due to lack of understanding of the variables responsible for organogenesis. Cell-colony heterogeneity, 3D-cellular architecture, bioactive molecules, and crosstalk communication between parenchymal cell populations need to be further investigated, and high-throughput technologies can rapidly increase the rate at …

Sensitray: An Integrated Measuring Device For Monitoring Children’S Mealtime Dietary Intake, Hunter S. Guru, Anthony D. Weng, Santosh Pitla, Dipti Dev

Department of Child, Youth, and Family Studies: Faculty Publications

Childhood nutrition establishes consumption norms that affect an individual’s health over the course of their lives. However, early nutrition interventions to establish such norms are uncommon owing to the various inefficiencies associated with current methods of measuring childhood nutrition. Here, we present an IoT measuring device, called the SensiTray, which accurately tracks mealtime intake in a child-friendly and cost-effective fashion. Principal technologies underlying the SensiTray (including mass-sensing technologies, microcontrollers) are identified and analyzed, along with other design choices. Operation of the SensiTray is explained with special attention given to SensiTray software peripherals and algorithms. Preliminary testing consisted of static and …

Designing A Week-Long Biomedical Engineering Summer Camp To Increase Young Students’ Interest And Self-Efficacy In Stem, Kayla Ney

Honors Program: Senior Projects (Public)

In order to combat the negative feelings many young students have towards STEM, I designed a week-long summer camp that teaches students about biomedical engineering as well as collaboration, communication, and confidence with STEM subjects. This work includes a literature review outlining what STEM is and current issues in STEM education, including disinterest in STEM and attrition in STEM degree programs. The literature review outlines current methods and ideas being utilized to combat these issues, namely, inclusive pedagogical strategies, and how some of these concepts can be applied to the summer camp. The curriculum document included outlines each activity, its …

Functional Characterization Of Petiolule-Like Pulvinus (Plp) Gene In Abscission Zone Development In Medicago Truncatula And Its Application To Genetic Improvement Of Alfalfa, Juan Du, Shaoyun Lu, Maofeng Chai, Chuanen Zhou, Liang Sun, Yuhong Tang, Jin Nakashima, Jaydeep Kolape, Zhaozhu Wen, Marjan Behzadirad, Tianxiu Zhong, Juan Sun, Yunwei Zhang, Zeng-Yu Wang

Nebraska Center for Biotechnology: Faculty and Staff Publications

Alfalfa (Medicago sativa L.) is one of the most important forage crops throughout the world. Maximizing leaf retention during the haymaking process is critical for achieving superior hay quality and maintaining biomass yield. Leaf abscission process affects leaf retention. Previous studies have largely focused on the molecular mechanisms of floral organ, pedicel and seed abscission but scarcely touched on leaf and petiole abscission. This study focuses on leaf and petiole abscission in the model legume Medicago truncatula and its closely related commercial species alfalfa. By analysing the petiolule-like pulvinus (plp) mutant in M. truncatula at phenotypic level …

Optimizing Athletic Throwing Power For Increased Training Efficiency, Ian Ghanavati, Curtis Tomasevicz

UCARE: Research Products

A summary on the investigation of the mechanics of weighted baseball pitching.

• The demand for higher pitch velocity has increased at all levels of competitive play within baseball • Weighted baseball training programs are a common way to increase pitch velocity • The efficacy and safety of weighted ball throwing is not fully understood • The aim of this study is to further investigate the mechanics of pitching under and overweight balls in order to better understand their role in athletic training

Synthetic Lethality In Pediatric Brain Cancer Cells By Optimized Plga Nanoparticles And Drug Combinations, Megan Ruckman, Megan Otte, Forrest Kievit

UCARE: Research Products

Here we test drugs effectiveness to inhibit various DNA repair pathways with the purpose of sensitizing cancer cells to radiotherapy. We work on optimizing delivery of DNA repair pathway inhibiting drugs by the use of PLGA nanoparticles.

Inducing Increased Bioplastic Production In R. Palustris Cga009, Cameron Gilley, Dylan Hoppner, Brandi J. Brown

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

PHA’s (polyhydroxyalkanoates) are important bio polymers in different industries such as petroleum, medicine, and nano technology. In the microorganisms in which they are produced, they serve as an energy storage material by storing both carbon and usable electrons. This is useful in environments where the organisms are nutrient starved. PHA’s have a practical use especially in the medical field as bio-plastics because they are biodegradable and bio-compatible. Rhodopseudomonas. palustris, a common soil bacterium, is notable for its uncommon metabolic flexibility. Its diverse metabolism means that it can fix CO 2 and grow on many lignin based monomers in both aerobic …

Quantification Of Phenotypic Change Resulting In Sensitization Of Primary Sensory Neurons Due To Oxidative Stress, Adan Redwine, Sarah M. Romereim, Rebecca A. Wachs

UCARE: Research Products

84% of the population will suffer from low back pain at some point in their lives, and 39% of the cases may be related to pain originating from the intervertebral disc (IVD) also known as discogenic pain. Age or injury can cause progressive degeneration of the IVD, and this can allow innervation by nociceptive (pain-sensing) neurons from the dorsal root ganglion (DRG) into the inner IVD.⁶ Long-term exposure to pain-inducing stimuli can cause nociceptor sensitization, manifested as increased pain sensation in response to non-painful or painful stimuli.⁷ Sensitization results in the nociceptors responding more strongly to a stimulus, …

“Gobabygo!” Rehab Engineering To Make Children Mobile, Connor Albin, Chase M. Pfeifer

UCARE: Research Products

GoBabyGo! is a project to give children with movement difficulties a chance to move on their own. GoBabyGo! conducts community builds of modified ride-on-cars for these children and grants them mobility. Once issue is that once children have cars, there is no feedback to improve future builds. This project "“GoBabyGo!” – Rehab Engineering to Make Children Mobile," wishes to collect quantifiable data on how these cars are being used and how they can be improved. This project aims to do this by collecting surveys from caretakers and through a programmed module to be installed in cars. The installed car module …

Mechanobiology Of Breast Cancer Cells, Shea Thompson

UCARE: Research Products

Mechanobiology Cells response to mechanical loading Mechanical loading includes Shear flow, Stretching, Compression

How does shear flow effect breast cancer cell migration in a three dimensional space?

By going through the engineering cycle, I was able to successfully convert the Parallel Flow Chamber into a Three Dimensional Flow Chamber. At this point, I have no results due to the COVID-19 outbreak.

Future Research Understanding how breast cancer migrates is essential to preventing the spread of cancer. While other chemical means have been investigated, mechanotransduction is relatively unexplored. Next step: Mechanobiology of breast cancer cells moving through a maze Cells have …