Biotechnology Commons^™

Polyglycine Acts As A Rejection Signal For Protein Transport At The Chloroplast Envelope, Joshua K. Endow, Agostinho Gomes Rocha, Amy J. Baldwin, Rebecca L. Roston, Toshio Yamaguchi, Hironari Kamikubo, Kentaro Inoue

Department of Biochemistry: Faculty Publications

PolyGly is present in many proteins in various organisms. One example is found in a transmembrane β-barrel protein, translocon at the outer-envelope-membrane of chloroplasts 75 (Toc75). Toc75 requires its N-terminal extension (t75) for proper localization. t75 comprises signals for chloroplast import (n75) and envelope sorting (c75) in tandem. n75 and c75 are removed by stromal processing peptidase and plastidic type I signal peptidase 1, respectively. PolyGly is present within c75 and its deletion or substitution causes mistargeting of Toc75 to the stroma. Here we have examined the properties of polyGly-dependent protein targeting using two soluble passenger proteins, the mature portion …

Mutation In Atg5 Reduces Autophagy And Leads To Ataxia With Developmental Delay, Myungjin Kim, Erin Sandford, Damian Gatica, Yu Qiu, Xu Liu, Yumei Zheng, Brenda A. Schulman, Jishu Xu, Ian Semple, Seung-Hyun Ro, Boyoung Kim, R. Nehir Mavioglu, Aslihan Tolun, Andras Jipa, Szabolcs Takats, Manuela Karpati, Jun Z. Li, Zuhal Yapici, Gabor Juhasz, Jun Hee Lee, Daniel J. Klionsky, Margit Burmeister

Department of Biochemistry: Faculty Publications

Autophagy is required for the homeostasis of cellular material and is proposed to be involved in many aspects of health. Defects in the autophagy pathway have been observed in neurodegenerative disorders; however, no genetically-inherited pathogenic mutations in any of the core autophagy-related (ATG) genes have been reported in human patients to date. We identified a homozygous missense mutation, changing a conserved amino acid, in ATG5 in two siblings with congenital ataxia, mental retardation, and developmental delay. The subjects’ cells display a decrease in autophagy flux and defects in conjugation of ATG12 to ATG5. The homologous mutation in yeast …

Can Chilling Tolerance Of C4 Photosynthesis In Miscanthus Be Transferred To Sugarcane?, Katarzyna Glowacka, Aasifuddin Ahmed, Shailendra Sharma, Tom Abbott, Jack C. Comstock, Stephen P. Long, Erik J. Sacks

Department of Biochemistry: Faculty Publications

The goal of this study was to investigate whether chilling tolerance of C₄ photosynthesis in Miscanthus can be transferred to sugarcane by hybridization. Net leaf CO₂ uptake (A_sat) and the maximum operating efficiency of photosystem II (Ф_PSII) were measured in warm conditions (25 °C/20 °C), and then during and following a chilling treatment of 10 °C/5 °C for 11 day in controlled environment chambers. Two of three hybrids (miscanes), ‘US 84-1058’ and ‘US 87-1019’, did not differ significantly from the chilling tolerant M. xgiganteus ‘Illinois’ (Mxg), for A_sat, and Φ …

Novel Acyltranserases And Methods Of Using, Edgar B. Cahoon, Umidjon Iskandarov, Hae Jin Kim, Jillian Collins-Silva

Department of Biochemistry: Faculty Publications

Provided herein are novel acyltransferases and methods of using Such novel acyltransferases in making medium-chain fatty acids.

High-Throughput Mutation, Selection, And Phenotype Screening Of Mutant Methanogenic Archaea, Mary E. Walter, Alicia Ortiz, Casey Sondgeroth, Nathan M. Sindt, Nikolas Duszenko, Jennie L. Catlett, You Zhou, Shah R. Valloppilly, Christopher Anderson, Samodha Fernando, Nicole R. Buan

Department of Biochemistry: Faculty Publications

Bacterial and archaeal genomes can contain 30% or more hypothetical genes with no predicted function. Phylogenetically deep-branching microbes, such as methane-producing archaea (methanogens), contain up to 50% genes with unknown function. In order to formulate hypotheses about the function of hypothetical gene functions in the strict anaerobe, Methanosarcina acetivorans, we have developed high-throughput anaerobic techniques to UV mutagenize, screen, and select for mutant strains in 96-well plates. Using these approaches we have isolated 10 mutant strains that exhibit a variety of physiological changes including increased or decreased growth rate relative to the parent strain when cells use methanol and/or …

Mutual Information Upper Bound Of Molecular Communication Based On Cell Metabolism, Massimiliano Pierobon, Zahmeeth Sakkaff, Jennie L. Catlett, Nicole R. Buan

Department of Biochemistry: Faculty Publications

Synthetic biology is providing novel tools to engineer cells and access the basis of their molecular information processing, including their communication channels based on chemical reactions and molecule exchange. Molecular communication is a discipline in communication engineering that studies these types of communications and ways to exploit them for novel purposes, such as the development of ubiquitous and heterogeneous communication networks to interconnect biological cells with nano and biotechnology-enabled devices, i.e., the Internet of Bio-Nano Things. One major problem in synthetic biology stands in the development of reliable techniques to control the engineered cells from the external environment. In this …

Pch1 Integrates Circadian And Light- Signaling Pathways To Control Photoperiod-Responsive Growth In Arabidopsis, He Huang, Chan Yul Yoo, Rebecca Bindbeutel, Jessica Goldsworthy, Allison Tielking, Sophie Alvarez, Michael J. Naldrett, Bradley S. Evans, Meng Chen, Dmitri A. Nusinow

Nebraska Center for Biotechnology: Faculty and Staff Publications

Plants react to seasonal change in day length through altering physiology and development. Factors that function to harmonize growth with photoperiod are poorly understood. Here we characterize a new protein that associates with both circadian clock and photoreceptor components, named PHOTOPERIODIC CONTROL OF HYPOCOTYL1 (PCH1). pch1 seedlings have overly elongated hypocotyls specifically under short days while constitutive expression of PCH1 shortens hypocotyls independent of day length. PCH1 peaks at dusk, binds phytochrome B (phyB) in a red light-dependent manner, and co-localizes with phyB into photobodies. PCH1 is necessary and sufficient to promote the biogenesis of large photobodies to maintain an …

Probing The Plant Cell Wall With Herbicides: A Chemical Genetics Approach, Chad B. Brabham

Theses and Dissertations--Plant and Soil Sciences

The primary cell wall is a highly organized multi-layered matrix of polysaccharides (cellulose, hemi-cellulose, and pectin). The ability of the rigid cell wall to sufficiently loosen to allow growth is a complex process that differs considerably between grasses monocots and dicots. Cellulose is the major structural component required for anisotropic cell expansion and is synthesized by CELLULOSE SYNTHASE A (CesA) proteins. Here, our objectives were two-fold: 1) dissect cell walls and cellulose biosynthesis in dicots and grasses using chemical biology and reverse genetic approaches 2) characterize and classify the inhibitory mechanisms of cellulose biosynthesis inhibitors (CBIs). A reverse genetics TILLING …

Bmp-7 Inhibits P38 And Jnk Pathways And Increases M2 Macrophage Differentiation To Reduce Atherosclerosis In Apolipoprotein E-/- Mice, Heidi Shoulders

Electronic Theses and Dissertations

We have previously shown that treating atherosclerosis with bone morphogenetic protein-7 (BMP-7) affects the presence of macrophage subtypes in vitro, however it remains unknown whether BMP-7 treatment affects development and progression of atherosclerosis in vivo at an early and mid-stage of the disease. We therefore performed a Day 5 (D5) and Day 28 (D28) study to examine BMP-7's potential to affect monocyte differentiation. Atherosclerotic plaque formation was developed using our standard method and ApoE-/- mice were sacrificed at D5 and D28 post-surgery. Treatment animals received intravenous injections of BMP-7 at 200µg/kg of bodyweight. Hematoxylin and Eosin morphological stain shows that …

The Development Of Motuporamine Derivatives And An Investigation Into Their Biological Properties, Kristen Skruber

Electronic Theses and Dissertations

This project investigates the synthesis of a class of compounds derived from a marine-based natural product and probes how iterative changes to its structure affect its derivatives' biological efficacy. The compound class of interest are the motuporamines which were isolated from the sea sponge Xestospongia exigua collected off the coast of Motupore island in Papua, New Guinea. The compounds for this project are predicated upon dihydromotuporamine C (Motu33), the compound that has been shown to be both cytotoxic to MDA-MB231 breast carcinoma cells and has antimetastatic efficacy. The motuporamine scaffold contains a large fifteen-membered saturated macrocycle and an appended polyamine …

Neurological Profile Of Older Apoe-Pon1 Double Knockout Mice, Connie Mitra

Electronic Theses and Dissertations

Atherosclerosis is a cardiovascular disease where plaques made up of lipids in the form of cholesterol ester build up in the carotid and innominate arteries that supply blood to the brain. Accumulation of the plaques limit the flow of blood and nutrients to the brain, leading to diminished oxygen supply, increased oxidative stress and cell death. All these have been implicated in Alzheimer's disease (AD). Alzheimer's disease, a chronic, progressive, age related neurodegenerative disorder is the most common form of dementia in the elderly accounting for 60-80% of the cases. Clinically, Alzheimer's disease is characterized by loss of memory, damage …

Could Dietary Peroxidized Lipids Provoke An Intestinal Inflammatory Response?, Mitsushita Doomra

Electronic Theses and Dissertations

Inflammatory Bowel Disease and Crohn's disease represent chronic intestinal inflammatory diseases. It is suspected that bacterial infection is one of the causes of gut inflammation. Studies from others as well as from our laboratory have indicated that peroxidized lipids and their decomposition products are pro-inflammatory. As we consume considerable amounts of dietary oxidized lipids (arising from deep frying of vegetable oils), we hypothesize that dietary peroxidized lipids may also lead to intestinal inflammation. To test this hypothesis, intestine from C57BL/6J mice were collected and used in this study. The intestinal epithelial tissue as well as intestinal lymphoid tissues [Peyer's Patches …

A Review Of Natural And Engineered Enzymes Involved In Bioethanol Production, Ines Cuesta Urena

Graduate Student Theses, Dissertations, & Professional Papers

Alternative petroleum-derived fuels, such as biofuels, is another form to decrease the dependence of non-renewable energy. The most promising alternative energy is cellulosic ethanol because of the abundance of cellulose and the overall lack of concern for the food-versus-fuel dilemma.

In order to produce ethanol from cellulosic materials, pretreatment is required to “open” the lignocellulosic matrix and make cellulose more susceptible to enzymatic degradation. Enzymatic hydrolysis of lignocellulose is an important area of research due to the absence of negative effects in downstream processes in comparison with acid hydrolysis. Both natural enzymes and engineered enzymes can be used in the …

Controlling Microbial Safety Challenges Of Meat Using High Voltage Atmospheric Cold Plasma, Lu Han, Dana Ziuzina, Caitlin Marie Heslin, Daniela Boehm, Apurva Patange, David Millan-Sango, Vasilis Valdramidis, Patrick J. Cullen, Paula Bourke

Articles

Atmospheric cold plasma (ACP) is a non-thermal technology, effective against a wide range of pathogenic microorganisms. Inactivation efficacy results from plasma generated reactive species. These may interact with any organic components in a test matrix including the target microorganism, thus food components may exert a protective effect against the antimicrobial mode of action. The effect of an in-package high voltage ACP process applied in conjunction with common meat processing MAP gas compositions as well as bacteria type and meat model media composition have been investigated to determine the applicability of this technology for decontamination of safety challenges associated with meat …

Genetic Diversity And Population Structure Of Brassica Oleracea Germplasm In Ireland Using Ssr Markers, Mohamed El-Esawi, Paula Bourke, Renee Malone, Kieran Germaine

Articles

The most economically important Brassica oleracea species is endangered in Ireland, with no prior reported genetic characterization studies. This study assesses the genetic diversity, population structure and relationships of B. oleracea germplasm in Ireland using microsatellite (SSRs) markers. A total of 118 individuals from 25 accessions of Irish B. oleracea were genotyped. The SSR loci used revealed a total of 47 alleles. The observed heterozygosity (0.699) was higher than the expected one (0.417). Moreover, the average values of fixation indices (F) were negative, indicating excess of heterozygotes in all accessions. Polymorphic information content (PIC) values of SSR loci ranged from …

Atmospheric Cold Plasma Interactions With Modified Atmosphere Packaging Inducer Gases For Safe Food Preservation., Lu Han, Daniela Boehm, Vladimir Milosavljević, Ester Amias, Patrick J. Cullen, Paula Bourke

Articles

Diverse microbiological challenges and pervasive microbial resistance drive technological development in food processing, where increasing process complexity and consumer demand for less processed goods leads to strong demand for effective decontamination. Atmospheric cold plasma (ACP) has wide potential for decontamination application in the food sector. We investigated the effect of Modified Atmosphere Packaging (MAP) gas mixtures on reactive species generated, their efficacy and mechanism of inactivation against Escherichia coli, Listeria monocytogenes and Staphylococcus aureus. Oxygen levels in the applied working gas had positive interactive effects on ROS generation, in-package inactivation efficacy in conjunction with post-treatment storage time. …

Effects Of Oil Palm (Elais Guineensis) Fruit Extracts On Glucose Uptake Activity Of Muscle, Adipose And Liver Cells, Faez S, Muhajir H, Amin I, Zainah A

ASEAN Journal on Science and Technology for Development

The effect of oil palm (Elaeis guineensis) fruit aqueous extract (OPF) on glucose uptake activity of three different cell lines was investigated. The cell lines were incubated with different concentrations of OPF to evaluate the stimulatory effect of OPF towards glucose uptake activity of L6 myotubes, 3T3F442A adipocytes and Chang liver cell line. The glucose uptake activities of all tested cells were enhanced in the presence of OPF extract (basal condition). Nevertheless in combination of OPF extract and 100 nM insulin, the glucose uptake activity was only significantly enhanced in L6 myotubes and 3T3F442A adipocytes cell lines. The extracts enhanced …

A Novel Transcription Factor In Arabidopsis Thaliana Abiotic Stress Response, Achira S. Weerathunga Arachchilage

LSU New Orleans Theses and Dissertations

Plants respond to environmental stress by altering their gene expression. Under stress conditions some genes are activated and some genes are repressed. Even though a lot of work has been done to understand mechanisms of gene activation under abiotic stress very little information is available on how stress responsive genes are kept repressed under normal growth conditions. Recent work has revealed that plants use transcriptional repression as common mechanism of gene repression. Transcriptional repression is achieved by recruitment co-repressor complexes to the target genes. Recent studies have revealed that the co-repressor LUH complexes with SLK1 and SLK2 to silence Arabidopsis …

Design And Testing Of Novel Anthrax Vaccines Utilizing A Tobacco Mosaic Virus Expression System, Ryan C. Mccomb

KGI Theses and Dissertations

Anthrax is a potentially fatal disease caused by the bacteria Bacillus anthracis. Infection and disease occur after spores gain entry into the body, germinate into vegetative bacteria, and produce toxin. Bacillus anthracis spores have been engineered as bioweapons and have been used repeatedly in warfare and terrorism to inflict casualties in military and civilian populations. Currently, only one vaccine has been approved for prevention of anthrax in the United States. This vaccine is an undefined product that is difficult to produce, requires a long vaccination schedule, and is reactogenic. Efforts to make an improved anthrax vaccine are being pursued. …

The Importance Of Physicochemical Characteristics And Nonlinear Classifiers In Determining Hiv-1 Protease Specificity, Timmy Manning, Paul Walsh

Department of Biological Sciences Publications

This paper reviews recent research relating to the application of bioinformatics approaches to determining HIV-1 protease specificity, outlines outstanding issues, and presents a new approach to addressing these issues. Leading machine learning theory for the problem currently suggests that the direct encoding of the physicochemical properties of the amino acid substrates is not required for optimal performance. A number of amino acid encoding approaches which incorporate potentially relevant physicochemical properties of the substrate are identified, and are evaluated using a nonlinear task decomposition based neuroevolution algorithm. The results are evaluated, and compared against a recent benchmark set on a nonlinear …