Biotechnology Commons^™

Effects Of Soil Type And Diversity On Soil Respiration And Litter Decomposition In A Perennial Biofuel Production System, Jordan Young

Annual Graduate Student Symposium

For my master's thesis, I researched soil respiration and litter decomposition at the Cedar River Ecological Research Site. Respiration and decomposition are important processes in the understanding of carbon sequestration, which is one of the main benefits of using biofuels. Cellulosic biofuels can be produced from a wide diversity of plants on a wide range of soil types, and these factors can influence the rate of carbon sequestration, so I investigated the effects of plant diversity and soil type in the context of perennial biofuel production.

Using Technology To Serve The Agricultural Community In The Western Cape Province Of South Africa, Pavarni Naidoo, Lise Sandenbergh, Maud Bonato, Johann Strauss, Mike Wallace, Andre Roux, Shaheed Martin, Ilse Trautmann, Schalk Cloete

Professional Agricultural Workers Journal

Abstract

The Western Cape Department of Agriculture has a team of agricultural experts using novel approaches to address the challenges faced by South African agriculture. The objective of this paper is to describe some of the innovative research and technologies, and methods of technology transfer, used to better serve the agricultural community. The spectrum of technologies implemented includes new research on breeding (biotechnology); new approaches to conservation agriculture; remote sensing satellite and spatial information for improved decision making, such as the spatial intelligence project and FruitLook; Agricultural Integrated Management System; and technology to manage and disseminate information, such as smart …

Plantbot Genetics Presents: The Moth Project, Augustana College, Rock Island Illinois

2015-2016

PlantBot Genetics Inc. presents an engaging overview of second shift pollinators such as the moth, along with recent advances in self-pollinating robo-plants. The Moth Project highlights inspired responses to the decline of the honeybee and the hope that Moths and PlantBots will step in and save the day.

As consumers, we no longer know the real price of our food. Present food distribution systems are so complicated that it is unrealistic to expect consumers will make responsible choices based on the knowledge at hand. We encourage people to think more about their food, where it comes from, and where it …

Anti-Breast Cancer Effect Of Rhus Coriaria Extract, Khawlah Najib Athamneh

Theses

Plants have been shown to be an excellent source of new drugs, including anticancer agents. Rhus coriaria, commonly known as sumac, a plant that is known to possess different therapeutic values including anti-oxidant and anti-microbial activities. Here, we investigated the anti-cancer effect of R. coriaria on triple negative MDA-MB-231 cell line. We demonstrated that Rhus coriaria ethanolic extract (RCE) inhibits the proliferation of MDA-MB-231 cell line in a time- and concentration dependent manner. RCE induced senescence and cell cycle arrest at G1 phase. Moreover, no proliferative recovery was detected after RCE removal. Annexin V staining and PARP cleavage analysis revealed …

Moisture Sensing Sprinkler System, Lewis University

Sustainability

No abstract provided.

Implementing Efficient Laminar-Flow Showerheads, Lewis University

Sustainability

No abstract provided.

A Comparative Study Of Aromatic Pollutants Degradation Using Two Different Peroxidases, Aysha Hamad Muftah Ai Neyadi

Theses

Enzyme based degradation of organic pollutants is a promising new remediation approach due to the promiscuous nature of the technique, the wide range of available enzymes, and the scalability of the process. Oxidoreductases, specifically, peroxidases are the most popular class of enzymes that have been used for the degradation of organic pollutants. It is generously assumed that all peroxidases behave similarly and produce similar degradation products. Our main objective was to test the hypothesis that related peroxidases may act differentially towards the degradation of aromatic pollutants. Therefore, in this study, we have carried out detailed degradation studies on three model …

Anti-Metastatic And Anti-Tumor Growth Effects Of Carnosol On Breast Cancer, Halima Ali Mohammed Salem Al Samri

Theses

Our lab has previously showed that carnosol, a naturally occurring polyphenol, exhibits anti-cancer activity by promoting cell cycle arrest at G2 phase, and induces reactive oxygen species (ROS) dependent apoptosis and beclin-1 independent autophagy in triple negative breast cancer (TNBC) cell line (MDA-MB-231). Here, we extended our study by investigating the potential effect of carnosol on migration, invasion and tumor growth of these cells. Our findings demonstrated that carnosol, at non-cytotoxic concentrations, exerted a potent anti-metastatic and anti-tumor growth activity against the highly invasive TNBC cell line, MBA-MB-231. Carnosol inhibited the migration and invasion of MDA-MB-231 cells. Moreover, carnosol suppressed …

A Model Of Blood Pressure, Heart Rate, And Vaso-Vagal Responses Produced By Vestibulo-Sympathetic Activation, Theodore Raphan, Bernard Cohen, Yongqing Xiang, Sergei B. Yakushin

Publications and Research

Blood Pressure (BP), comprised of recurrent systoles and diastoles, is controlled by central mechanisms to maintain blood flow. Periodic behavior of BP was modeled to study how peak amplitudes and frequencies of the systoles are modulated by vestibular activation. The model was implemented as a relaxation oscillator, driven by a central signal related to Desired BP. Relaxation oscillations were maintained by a second order system comprising two integrators and a threshold element in the feedback loop. The output signal related to BP was generated as a nonlinear function of the derivative of the first state variable, which is a summation …

Bio-Piracy: Creating Proprietary Rights In Plant Genetic Resources, James O. Odek

Journal of Intellectual Property Law

No abstract provided.

Attention Strongly Modulates Reliability Of Neural Responses To Naturalistic Narrative Stimuli, Jason J. Ki, Simon P. Kelly, Lucas C. Parra

Publications and Research

Attentional engagement is a major determinant of how effectively we gather information through our senses. Alongside the sheer growth in the amount and variety of information content that we are presented with through modern media, there is increased variability in the degree to which we “absorb” that information. Traditional research on attention has illuminated the basic principles of sensory selection to isolated features or locations, but it provides little insight into the neural underpinnings of our attentional engagement with modern naturalistic content. Here, we show inhumansubjects that the reliability of an individual’s neural responses with respect to a larger group …

Drought Responsive Gene Expression Regulatory Divergence Between Upland And Lowland Ecotypes Of A Perennial C4 Grass, John T. Lovell, Scott Schwartz, David B. Lowry, Eugene V. Shakirov, Jason E. Bonnette, Xiaoyu Weng, Mei Wang, Jenifer Johnson, Avinash Sreedasyam, Christopher Plott, Jerry Jenkins, Jeremy Schmutz, Thomas E. Juenger

Biological Sciences Faculty Research

Climatic adaptation is an example of a genotype-by-environment interaction (G×E) of fitness. Selection upon gene expression regulatory variation can contribute to adaptive phenotypic diversity; however, surprisingly few studies have examined how genome-wide patterns of gene expression G×E are manifested in response to environmental stress and other selective agents that cause climatic adaptation. Here, we characterize drought-responsive expression divergence between upland (drought-adapted) and lowland (mesic) ecotypes of the perennial C₄ grass, Panicum hallii, in natural field conditions. Overall, we find that cis-regulatory elements contributed to gene expression divergence across 47% of genes, 7.2% of which exhibit drought-responsive G×E. …

Session C-5: Biotech Basics, Elizabeth Martinez, Emily Hood Ferrin

Professional Learning Day

The field of biotechnology is rapidly expanding. What is biotech? What are the applications? How is biotech studied? These topics will be explored as participants engage in hands-on lessons developed at an appropriate level for middle school students. Activities may be used to introduce students to the world of biotech.

Genesis And Growth Of Extracellular Vesicle-Derived Microcalcification In Atherosclerotic Plaques, Joshua D. Hutcheson, Claudia Goettsch, Sergio Bertazzo, Natalia Maldonado, Jessica L. Ruiz, Wilson Goh, Katsumi Yabusaki, Tyler Faits, Carlijn Bouten, Gregory Franck, Thibaut Quillard, Peter Libby, Masanori Aikawa, Sheldon Weinbaum, Elena Aikawa

Publications and Research

Clinical evidence links arterial calcification and cardiovascular risk. Finite-element modelling of the stress distribution within atherosclerotic plaques has suggested that subcellular microcalcifications in the fibrous cap may promote material failure of the plaque, but that large calcifications can stabilize it. Yet the physicochemical mechanisms underlying such mineral formation and growth in atheromata remain unknown. Here, by using three-dimensional collagen hydrogels that mimic structural features of the atherosclerotic fibrous cap, and high-resolution microscopic and spectroscopic analyses of both the hydrogels and of calcified human plaques, we demonstrate that calcific mineral formation and maturation results from a series of events involving the …

Methods For Detecting Microbial Methane Production And Consumption By Gas Chromatography, Jared T. Aldridge, Jennie L. Catlett, Megan L. Smith, Nicole R. Buan

Department of Biochemistry: Faculty Publications

Methane is an energy-dense fuel but is also a greenhouse gas 25 times more detrimental to the environment than CO2. Methane can be produced abiotically by serpentinization, chemically by Sabatier or Fisher-Tropsh chemistry, or biotically by microbes (Berndt et al., 1996; Horita and Berndt, 1999; Dry, 2002; Wolfe, 1982; Thauer, 1998; Metcalf et al., 2002). Methanogens are anaerobic archaea that grow by producing methane gas as a metabolic byproduct (Wolfe, 1982; Thauer, 1998). Our lab has developed and optimized three different gas chromatograph-utilizing assays to characterize methanogen metabolism (Catlett et al., 2015). Here we describe the end point and kinetic …

Engineered Protein Polymer-Gold Nanoparticle Hybrid Materials For Small Molecule Delivery, Min Dai, Ja Frezzo, E Sharma, R Chen, N Singh, C Yuvienco, E Caglar, S Xiao, A Saxena, Jk Montclare

Publications and Research

We have fabricated protein polymer-gold nanoparticle (P-GNP) nanocomposites that exhibit enhanced binding and delivery properties of the small hydrophobic molecule drug, curcumin, to the model breast cancer cell line, MCF-7. These hybrid biomaterials are constructed via in situ GNP templated-synthesis with genetically engineered histidine tags. The P-GNP nanocomposites exhibit enhanced small molecule loading, sustained release and increased uptake by MCF-7 cells. When compared to the proteins polymers alone, the P-GNPs demonstrate a greater than 7-fold increase in curcumin binding, a nearly 50% slower release profile and more than 2-fold increase in cellular uptake of curcumin. These results suggest that P-GNP …

Comparing Apples And Oranges?: Next Generation Sequencing And Its Impact On Microbiome Analysis, Adam G. Clooney, Fiona Fouhy, Roy D. Sleator, Aisling O'Driscoll, Stanton Catherine, Paul D. Cotter, Marcus J. Claesson

Department of Biological Sciences Publications

Rapid advancements in sequencing technologies along with falling costs present widespread opportunities for microbiome studies across a vast and diverse array of environments. These impressive technological developments have been accompanied by a considerable growth in the number of methodological variables, including sampling, storage, DNA extraction, primer pairs, sequencing technology, chemistry version, read length, insert size, and analysis pipelines, amongst others. This increase in variability threatens to compromise both the reproducibility and the comparability of studies conducted. Here we perform the first reported study comparing both amplicon and shotgun sequencing for the three leading next-generation sequencing technologies. These were applied to …

Stabilin-1 And Stabilin-2 Are Specific Receptors For The Cellular Internalization Of Phosphorothioate-Modified Antisense Oligonucleotides (Asos) In The Liver, Colton M. Miller, Aaron J. Donnerr, Emma E. Blank, Andrew W. Egger, Brianna M. Kellar, Michael E. Østergaard, Punit P. Seth, Edward N. Harris

Department of Biochemistry: Faculty Publications

Phosphorothioate (PS)-modified antisense oligonucleotides (ASOs) have been extensively investigated over the past three decades as pharmacological and therapeutic agents. One second generation ASO, Kynamro^TM, was recently approved by the FDA for the treatment of homozygous familial hypercholesterolemia and over 35 second generation PS ASOs are at various stages of clinical development. In this report, we show that the Stabilin class of scavenger receptors, which were not previously thought to bind DNA, do bind and internalize PS ASOs. With the use of primary cells from mouse and rat livers and recombinant cell lines each expressing Stabilin-1 and each isoform …

Dna Sequencing Activity, Sarah O'Leary-Driscoll

Sequencing & Genome Mining

This activity is meant to introduce students to basic DNA sequencing techniques. Using a hands-on approach helps them understand the fundamentals of what is happening in the lab, and the questions that accompany the activity can lead to more in depth discussions about sequencing, and the development of the next generation sequencing techniques.

Screening Of Synthetic Chemical Agents “Chromenes” With Potent Anti-Breast Cancer Activity, Aysha Hamad Zaher Saeed Al Meqbali

Theses

Cancer is the second leading cause of death worldwide. Conventional therapies cause serious side effects and, at best, merely extend the patient’s lifespan by a few years. Cancer control may therefore benefit from the potential that resides in alternative therapies. There is thus an increasing demand to utilize alternative concepts or approaches to the prevention of cancer. The principal aim of this research is to screen and identify new synthetic compounds “chromenes”, with high efficiency, for breast cancer therapy. In this study, we have screened four newly designed and synthesized chromenes (C1, C15, C28 and C29) for their potential anticancer …

Hydrodynamic Loading In Concomitance With Exogenous Cytokine Stimulation Modulates Differentiation Of Bovine Mesenchymal Stem Cells Towards Osteochondral Lineages, Stephen M. Goldman, Gilda A. Barabino

Publications and Research

Background: Mesenchymal stem cells (MSCs) are viewed as a having significant potential for tissue engineering and regenerative medicine therapies. Clinical implementation of MSCs, however, demands that their preparation be stable and reproducible. Given that environmental and bioprocessing parameters such as substrate stiffness, seeding densities, culture medium composition, and mechanical loading can result in undirected differentiation of the MSC population, the objective of this study was to systematically investigate how hydrodynamic loading influences the differentiation of bone marrow-derived mesenchymal stem cells (MSCs) towards the osteochondral lineages both in the presence and absence of exogenous, inductive factors.

Methods: Expanded bovine MSCs were …

Utilization Of The Clinical Laboratory For The Implementation Of Concussion Biomarkers In Collegiate Football And The Necessity Of Personalized And Predictive Athlete Specific Reference Intervals, Stefanie Podlog (Nee Schulte), Natalie N. Rasmussen, Joseph W. Mcbeth, Patrick Q. Richards, Eric Yochem, David J. Petron, Frederick G. Strathmann

Athletic Training Collection

Background: A continued interest in concussion biomarkers makes the eventual implementation of identified biomarkers into routine concussion assessment an eventual reality. We sought to develop and test an interdisciplinary approach that could be used to integrate blood-based biomarkers into the established concussion management program for a collegiate football team.

Methods: We used a CLIA-certified laboratory for all testing and chose biomarkers where clinically validated testing was available as would be required for results used in clinical decision making. We summarized the existing methods and results for concussion assessment across an entire season to identify and demonstrate the challenges with the …

Genome-Wide Transcriptomic And Proteomic Analyses Of Bollworm-Infested Developing Cotton Bolls Revealed The Genes And Pathways Involved In The Insect Pest Defence Mechanism, Saravanan Kumar, Kanakachari Mogilicherla, Dhandapani Gurusamy, Krishan Kumar, Prabhakaran Narayanasamy, Padmalatha Kethireddy Venkata, Amolkumar Solanke, Savita Gamanagatti, Vamadevaiah Hiremath, Ishwarappa S. Katageri, Sadhu Leelavathi, Polumetla Ananda Kumar, Vanga Siva Reddy

Entomology Faculty Publications

Cotton bollworm, Helicoverpa armigera, is a major insect pest that feeds on cotton bolls causing extensive damage leading to crop and productivity loss. In spite of such a major impact, cotton plant response to bollworm infection is yet to be witnessed. In this context, we have studied the genome-wide response of cotton bolls infested with bollworm using transcriptomic and proteomic approaches. Further, we have validated this data using semi-quantitative real-time PCR. Comparative analyses have revealed that 39% of the transcriptome and 35% of the proteome were differentially regulated during bollworm infestation. Around 36% of significantly regulated transcripts and 45% …

Biological Lignocellulose Solubilization: Comparative Evaluation Of Biocatalysts And Enhancement Via Cotreatment, Julie M. D. Paye, Anna Guseva, Sarah K. Hammer, Erica Gjersing

Dartmouth Scholarship

Feedstock recalcitrance is the most important barrier impeding cost-effective production of cellulosic biofuels. Pioneer commercial cellulosic ethanol facilities employ thermochemical pretreatment and addition of fungal cellulase, reflecting the main research emphasis in the field. However, it has been suggested that it may be possible to process cellulosic biomass without thermochemical pretreatment using thermophilic, cellulolytic bacteria. To further explore this idea, we examine the ability of various biocatalysts to solubilize autoclaved but otherwise unpretreated cellulosic biomass under controlled but not industrial conditions.

Development Of A Low-Cost Arduino-Based Sonde For Coastal Applications, Grant Lockridge, Brian Dzwonkowski, Reid Nelson, Sean P. Powers

University Faculty and Staff Publications

This project addresses the need for an expansion in the monitoring of marine environments by providing a detailed description of a low cost, robust, user friendly sonde, built on Arduino Mega 2560 (Mega) and Arduino Uno (Uno) platforms. The sonde can be made without specialized tools or training and can be easily modified to meet individual application requirements. The platform allows for internal logging of multiple parameters of which conductivity, temperature, and GPS position are demonstrated. Two design configurations for different coastal hydrographic applications are highlighted to show the robust and versatile nature of this sensor platform. The initial sonde …

Nitrogenase Femoco Investigated By Spatially Resolved Anomalous Dispersion Refinement, Thomas Spatzal, Julia Schlesier, Eva-Maria Burger, Daniel Sippel, Limei Zhang, Susana L.A. Andrade, Douglas C. Rees, Oliver Einsle

Department of Biochemistry: Faculty Publications

The [Mo:7Fe:9S:C] iron-molybdenum cofactor (FeMoco) of nitrogenase is the largest known metal cluster and catalyses the 6-electron reduction of dinitrogen to ammonium in biological nitrogen fixation. Only recently its atomic structure was clarified, while its reactivity and electronic structure remain under debate. Here we show that for its resting S 1⁄4 3/2 state the common iron oxidation state assignments must be reconsidered. By a spatially resolved refinement of the anomalous scattering contributions of the 7 Fe atoms of FeMoco, we conclude that three irons (Fe1/3/7) are more reduced than the other four (Fe2/4/5/6). Our data are in agreement with the …

Vo-Ohpic Treatment Reduces Cardiac Remodeling In Doxorubicin-Induced Cardiomyopathy, Taylor Johnson

Electronic Theses and Dissertations

Doxorubicin (Doxo) is one of multiple anthracycline drugs used to effectively treat various forms of cancer. Unfortunately, Doxo treatment, as a side effect, induces cardiomyopathy and subsequent heart failure. We have previously demonstrated that transplanted embryonic stem (ES) cells and their conditioned medium (CM) modulate the PTEN pathway and reduce apoptosis, fibrosis and hypertrophy in a Doxo induced cardiomyopathy (DIC) model. However, mechanisms of inhibited apoptosis mediated through PTEN pathway are completely unknown. Therefore, we used VO-OHpic (VO), a potent PTEN inhibitor to understand the mechanism of apoptosis as well as its effect on cardiac remodeling in DIC. Animals were …

The Role Of Type-I Interferon In Limiting Spread And Killing Of An Oncolytic Rna Virus In Prostate Cells, Kritika Kedarinath

Electronic Theses and Dissertations

Prostate cancer is the second most prevalent cancer amongst men and there is an urgent need to address viable therapeutic options for its treatment. Development of viruses which target and kill cancer cells has gained momentum due to the first FDA approved oncolytic virus for treating human cancer patients. Our previous work with the RNA virus, Parainfluenza Virus 5 (PIV5), has led to the generation of mutants that are potential candidates for oncolytic viruses: 1) the hyperfusogenic (P/V/F) mutant has a mutated P/V and fusion gene which activates anti-viral responses and causes massive cell-cell fusion respectively, and 2) the Leader …

Malondialdehyde (Mda) And Glutathione Peroxidase (Gpx) Are Elevated In Crohns Disease-Associated With Mycobacterium Avium Subspecies Paratuberculosis (Map), Ahmad Qasem

Electronic Theses and Dissertations

Inflamed tissue in Crohn’s disease (CD) are continuously producing toxic oxygen metabolites leading to cellular injury and apoptosis. Here, we are evaluating the role of Mycobacterium avium subspecies paratuberculosis (MAP) in oxidative stress in CD by evaluation of lipid peroxidation and antioxidant defense activity. Specifically, we measured malondialdehyde (MDA) level and selenium-dependent glutathione peroxidase (GPx) activity in the plasma from patients and cattle infected with MAP. The level of MAP antibodies in bovine sera was determined by IDEXX kit whereas detection of MAP DNA was performed by IS900-based nPCR. A total of 42 cattle (21 infected with MAP and 21 …

Manufacturing Barriers To Biologics Competition And Innovation, W. Nicholson Price Ii, Arti K. Rai

Faculty Scholarship

As finding breakthrough small-molecule drugs gets harder, drug companies are increasingly turning to “large molecule” biologics. Although biologics represent many of the most promising new therapies for previously intractable diseases, they are extremely expensive. Moreover, the pathway for generic-type competition set up by Congress in 2010 is unlikely to yield significant cost savings.

In this Article, we provide a fresh diagnosis of, and prescription for, this major public policy problem. We argue that the key cause is pervasive trade secrecy in the complex area of biologics manufacturing. Under the current regime, this trade secrecy, combined with certain features of FDA …