Biomedical Engineering and Bioengineering Commons^™

Cross-Species Complementation Reveals Conserved Functions For Early Flowering 3 Between Monocots And Dicots, He Huang, Malia A. Gehan, Sarah E. Huss, Sohpie Alvarez, Cesar Lizarraga, Ellen L. Gruebbling, John Gierer, Michael J. Naldrett, Rebacca K. Bindbeutel, Bradley S. Evans, Todd C. Mockler, Dmitri A. Nusinow

Nebraska Center for Biotechnology: Faculty and Staff Publications

Plant responses to the environment are shaped by external stimuli and internal signaling pathways. In both the model plant Arabidopsis thaliana (Arabidopsis) and crop species, circadian clock factors are critical for growth, flowering, and circadian rhythms. Outside of Arabidopsis, however, little is known about the molecular function of clock gene products. Therefore, we sought to compare the function of Brachypodium distachyon (Brachypodium) and Setaria viridis (Setaria) orthologs of EARLY FLOWERING 3, a key clock gene in Arabidopsis. To identify both cycling genes and putative ELF3 functional orthologs in Setaria, a …

Rapid Thermocycler System For Rapid Amplification Of Nucleic Acids And Related Methods, Joel R. Termaat, Scoltt E. Whitney, Hendrik J. Viljoen, Matthew R. Kreifels

Department of Chemical and Biomolecular Engineering: Patents

A thermo cycling device and method of operating a thermocycler instrument, the instrument including a sample holder, at least one thermal cycling element, and at least one first and second temperature sensors, for causing the sample holder containing the at least one sample to undergo polymerase chain reaction amplification by repeated cycling between at least a denaturation heating stage and an aunealing cooling stage. The first temperature corresponding with the temperature of the sample holder is monitored using the at least one first temperature sensor, and a second temperature corresponding with the temperature external of the sample holder is monitored …

Frequency Sensitive Mechanism In Low-Intensity Ultrasound Enhanced Bioeffects, April D. Miller, Abdoulkadri Chama, Tobias M. Louw, Anuradha Subramanian, Hendrik J. Viljoen

Department of Chemical and Biomolecular Engineering: Faculty Publications

This study presents two novel theoretical models to elucidate frequency sensitive nuclear mechanisms in low-intensity ultrasound enhanced bioeffects. In contrast to the typical 1.5 MHz pulsed ultrasound regime, our group previously experimentally confirmed that ultrasound stimulation of anchored chondrocytes at resonant frequency maximized gene expression of load inducible genes which are regulatory markers for cellular response to external stimuli. However, ERK phosphorylation displayed no frequency dependency, suggesting that the biochemical mechanisms involved in enhanced gene expression is downstream of ERK phosphorylation. To elucidate such underlying mechanisms, this study presents a theoretical model of an anchored cell, representing an in vitro …

Stretch Control Of Adipocyte Insulin Signaling, Tasneem Bouzid

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

Obesity and related metabolic disorders have reached global epidemic proportions in recent decades. Excess and hypertrophic adipose tissue has been implicated in the development of various pathological diseases and disorders including Type-2 diabetes mellitus (Type-2 DM). In addition to serving as energy storage for the body, evidence also suggests that adipose tissue behaves as an endocrine organ capable of secreting bioactive cytokines known as adipokines, which mediate insulin signaling pathways in various tissues. Physical exercise has been demonstrated to positively affect insulin signaling activities potentially through increasing the secretion of insulin sensitizing adipokines and/or decreasing the secretion of pro-inflammatory insulin …

A Tunable, Three-Dimensional In Vitro Culture Model Of Growth Plate Cartilage Using Alginate Hydrogel Scaffolds, Alek G. Erickson, Taylor D. Laughlin, Sarah Romereim, Catherine Sargus-Patino, Angela K. Pannier, Andrew T. Dudley

Biological Systems Engineering: Papers and Publications

Defining the final size and geometry of engineered tissues through precise control of the scalar and vector components of tissue growth is a necessary benchmark for regenerative medicine, but it has proved to be a significant challenge for tissue engineers. The growth plate cartilage that promotes elongation of the long bones is a good model system for studying morphogenetic mechanisms because cartilage is composed of a single cell type, the chondrocyte; chondrocytes are readily maintained in culture; and growth trajectory is predominately in a single vector. In this cartilage, growth is generated via a differentiation program that is spatially and …

Design And Validation Of An In Vivo Long-Term Attachment Capsule Robot, Wanchuan Xie

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

The invention of capsule endoscopy (CE) made the non-invasive monitoring of the entire small bowel possible and became the primary means for diagnosing small bowel pathology. In the last decade, capsule robots have been transformed from diagnostic devices into a widely studied biomedical platform with the potential for active locomotion, drug delivery and therapeutic capabilities. To perform accurate on-site drug release and therapy, it is necessary for a capsule robot to be able to attach to the intestinal tissue and maintain its position long-term. Design challenges derive from the task of long-term mucosal adhesion which requires firm, quick-response attachment without …

Development Of Peritoneal Microbubble Oxygenation As An Extrapulmonary Treatment For Hypoxia, Nathan Legband

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

Patients affected by a respiratory disease or injury experience a substantially impaired respiratory system and as a consequence are unable to obtain a sufficient amount of oxygen. Hypoxia can quickly result in developing permanent tissue damage or death. Currently, the medical methods of treating hypoxia are mechanical ventilation or extracorporeal membrane oxygenation. However, these treatments are ineffective in certain cases and possess significant additional risks including barotrauma, infection, hemorrhage, and thrombosis.

The extrapulmonary method of peritoneal oxygenation has been investigated by other research groups as a potential alternative to providing supplemental oxygen in hypoxic animals. In peritoneal oxygenation, the peritoneum, …

A Novel Biochamberfor Modeling Of Atherosclerotic Arteries: In-Vitro Capabilities And Applications, Iman Salafian, Angelos Karagiannis, Benjamin S. Terry, Yiannis S. Chatzizisis

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

Atherosclerosis is a chronic disease that involves the lipid accumulation and inflammation of the arterial wall [1,2]. Despite great efforts,its pathophysiology has not been fully elucidated. Existent drugs can reduce its progression but there are no available drugs to prevent its complications [3,4]. Atherosclerosis remains the leading global cause of death[5].

The purpose of this work is to design and build a customized biochamber which can be used for the following studies:

•Study the pathophysiology of atherosclerosis in vitro & ex vivo

•Investigate the mechanisms of atherosclerotic plaque disruption

•Examine the direct effect of different anti-atherosclerotic drugs on lesions

•Use …

Chemical And Physical Priming Of Human Mesenchymal Stem Cells To Alter Nonviral Gene Delivery Outcomes, Tyler Kozisek, Andrew Hamann, Amy Mantz, Mathias Schubert, Eva Schubert, Angela K. Pannier

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

Human Mesenchymal Stem Cells: Human mesenchymal stem cells (hMSCs) are a multipotent cell, meaning they are able to differentiate into a more mature cell type, such as osteocytes, chondrocytes, and adipocytes, that are found in numerous tissues in the human body, such as bone marrow, fat, and muscle. Since hMSCs can be derived from adult human tissues, they do not have the same ethical concern associated with them as other stem cells, such as embryonic stem cells. Due to hMSCs multipotency and ease of obtaining, they have become one of the most widely researched stem cell types in areas such …

Chitosan Nanoparticle Modifications For Improved Gene Delivery In An Oral Dna Vaccine Application, Austin Helmink

Honors Theses

Vaccines represent one of the most significant medical innovations of the 20^th century, resulting in the eradication or near eradication of a handful of deadly diseases. However, many infectious diseases remain resistant to effective vaccination, largely due to a lack full immune activation by traditional protein-based vaccines. A promising alternative vaccination strategy is the emerging development of DNA vaccines, which rely upon the delivery of exogenous genetic material to host cells encoding for a viral or bacterial antigen in order to induce a robust immune response by closely mimicking live infection. The delivery of genetic material requires a carrier …

Energy-Water Reduction And Wastewater Reclamation In A Fluid Milk Processing Facility, Carlyrain Adams, Yulie E. Meneses, Bing Wang, Curtis Weller

Department of Food Science and Technology: Dissertations, Theses, and Student Research

The energy-water nexus is the inseparable connection linking water and energy. We are faced with a unique opportunity to co-manage these resources, as conservation of one is directly linked to the conservation of its counterpart. Therefore, immediately facing this critical challenge, will lead to tangible impacts on the water and energy crisis our food system is faced with. Determining the role of water and energy in the food industry has proved to be the starting point for reducing the distance between process productivity and resource efficiency. Therefore, this research focuses on determining opportunities for water-energy optimization and wastewater reduction and …

Repair And Regeneration Of Chondral Defects: An In Vitro Study Demonstrating Feasibility And Mechanism Under Low Intensity Ultrasound, Neety Sahu, Anuradha Subramanian

Department of Chemical and Biomolecular Engineering: Theses and Student Research

Holistic repair of damaged cartilage remains an unsolved biomedical problem. Current methods that employ microfracture (MF) or autologous chondrocyte implantation (ACT) or tissue engineered strategies yield inferior repaired cartilage (Fig. 1). Lack of chondroinductive factors at the site of injury, in vivo, has been identified as a factor that limits repair. Clinically amenable strategies that can improve repair are desired. A novel clinically translatable repair strategy based on low-intensity-ultrasound (US) is proposed (Fig.2). Differently from all approaches that use US, our approach employs US at the cell resonant frequency where bioeffects are maximized. We have shown that US impacts the …

Genetic Code Expansion In Biochemical Investigations And Biomedical Applications, Nanxi Wang

Department of Chemistry: Dissertations, Theses, and Student Research

Genetic code expansion provides a powerful tool for site-specific incorporation of unnatural amino acids (unAAs) with novel biochemical and physiological properties into proteins in live cells and organisms. To achieve this, a nonsense codon suppression system, which consists of an orthogonal aminoacyl-tRNA synthetase (aaRS) and tRNA pair that specifically decodes a nonsense codon (e.g., amber codon and quadruplet codon) with an unAA but do not “cross talk” with their endogenous counterparts, was established. This Ph.D. thesis presents our efforts on evolution and application of nonsense codon suppression systems for biochemical and biomedical investigations.

In Chapter 1, a brief overview of …

Evolutionary History Of Chemosensory-Related Gene Families Across The Arthropoda, Seong-Il Eyun, Ho Young Soh, Marijan Posavi, James B. Munro, Daniel S.T. Hughes, Shwetha C. Murali, Jiaxin Qu, Shannon Dugan, Sandra L. Lee, Hsu Chao, Huyen Dinh, Yi Han, Harshavardhan Doddapaneni, Kim C. Worley, Donna M. Muzny, Eun-Ok Park, Joana C. Silva, Richard A. Gibbs, Stephen Richards, Carol Eunmi Lee

Nebraska Center for Biotechnology: Faculty and Staff Publications

Chemosensory-related gene (CRG) families have been studied extensively in insects, but their evolutionary history across the Arthropoda had remained relatively unexplored. Here, we address current hypotheses and prior conclusions on CRG family evolution using a more comprehensive data set. In particular, odorant receptors were hypothesized to have proliferated during terrestrial colonization by insects (hexapods), but their association with other pancrustacean clades and with independent terrestrial colonizations in other arthropod subphyla have been unclear. We also examine hypotheses on which arthropod CRG family is most ancient. Thus, we reconstructed phylogenies of CRGs, including those from new arthropod genomes and transcriptomes, and …

Theoretically Proposed Optimal Frequency For Ultrasound Induced Cartilage Restoration, April D. Miller, Anuradha Subramanian, Hendrik J. Viljoen

Department of Chemical and Biomolecular Engineering: Faculty Publications

Background: Matching the frequency of the driving force to that of the system’s natural frequency of vibration results in greater amplitude response. Thus we hypothesize that applying ultrasound at the chondrocyte’s resonant frequency will result in greater deformation than applying similar ultrasound power at a frequency outside of the resonant bandwidth. Based on this resonant hypothesis, our group previously confirmed theoretically and experimentally that ultrasound stimulation of suspended chondrocytes at resonance (5 MHz) maximized gene expression of load inducible genes. However, this study was based on suspended chondrocytes. The resonant frequency of a chondrocyte does not only depend on the …

Sugar Versus Lipid For Sustainable Biofuels, Yaşar Demirel

Yaşar Demirel Publications

Introduction

First‐generation biofuels, namely, ethanol and biodiesel, have led to far reaching impact on the peoples’ life world‐wide.[1] However, they inter-fere with the food supply chain and may not be sustainable although some of the biomass are converted to biofuels after those biomasses have met the human needs. Still, the first‐generation–based biofuels have proved that sugar and lipid platforms can be an answer to energy security and global warming concerns without the need for new infrastructure for feedstock delivery as well as for biomass‐to‐biofuel conversion tech-nologies. At the same time, we are discovering and assessing the long‐term environmental im-plications on …

Phylogenomic Analysis Of Copepoda (Arthropoda, Crustacea) Reveals Unexpected Similarities With Earlier Proposed Morphological Phylogenies, Seong-Il Eyun

Nebraska Center for Biotechnology: Faculty and Staff Publications

Background: Copepods play a critical role in marine ecosystems but have been poorly investigated in phylogenetic studies. Morphological evidence supports the monophyly of copepods, whereas interordinal relationships continue to be debated. In particular, the phylogenetic position of the order Harpacticoida is still ambiguous and inconsistent among studies. Until now, a small number of molecular studies have been done using only a limited number or even partial genes and thus there is so far no consensus at the order-level.

Results: This study attempted to resolve phylogenetic relationships among and within four major copepod orders including Harpacticoida and the phylogenetic position of …

A Method For Measuring The Attachment Strength Of The Cestode Hymenolepis Diminuta To The Rat Intestine, Wanchuan Xie, Gábor R. Rácz, Benjamin S. Terry, Scott Lyell Gardner

Scott L. Gardner Publications

A unique adaptation of many internal parasites of mammals is their ability to stay in the intestine for extended periods of time and resist the normal peristaltic movements and forces that push and expel material. To better understand parasite adhesion behavior and replicate their attachment method in medical devices, an experiment was designed and performed using the rat tapeworm, Hymenolepis diminuta. The experiment employed a tensile test machine and a digital scale and was designed to calculate the attachment strength of the scolex to the mucosa through the change of the value of the digital scale during the tensile …

A Comprehensive Dosimetric Study On Switching From A Type-B To A Type-C Dose Algorithm For Modern Lung Sbrt, Christina Zhou, Nathan Bennion, Rongtao Ma, Xiaoying Liang, Shuo Wang, Kristina Zvolanek, Megan Hyun, Xiaobo Li, Sumin Zhou, Weining Zhen, Chi Lin, Andrew Wahl, Dandan Zheng

Biological Systems Engineering: Papers and Publications

Background: Type-C dose algorithms provide more accurate dosimetry for lung SBRT treatment planning. However, because current dosimetric protocols were developed based on conventional algorithms, its applicability for the new generation algorithms needs to be determined. Previous studies on this issue used small sample sizes and reached discordant conclusions. Our study assessed dose calculation of a Type-C algorithm with current dosimetric protocols in a large patient cohort, in order to demonstrate the dosimetric impacts and necessary treatment planning steps of switching from a Type-B to a Type-C dose algorithm for lung SBRT planning.

Methods: Fifty-two lung SBRT patients were included, each …