Biotechnology Commons^™

Plant Probiotic Bacteria Bacillus And Paraburkholderia Improve Growth, Yield And Content Of Antioxidants In Strawberry Fruit, Mosaddiqur Rahman, Abdullah As Sabir, Julakha Akter Mukrta, Mohibul Alam Khan, Mohammed Mohi-Ud-Din, Giashuddin Miah, Mahfuzur Rahman, M. Tofazzal Islam

Faculty & Staff Scholarship

Strawberry is an excellent source of natural antioxidants with high capacity of scavenging free radicals.

This study evaluated the effects of two plant probiotic bacteria, Bacillus amylolequefaciens BChi1 and Paraburkholderia fungorum BRRh-4 on growth, fruit yield and antioxidant contents in strawberry fruits. Root dipping of seedlings (plug plants) followed by spray applications of both probiotic bacteria in the field on foliage significantly increased fruit yield (up to 48%) over non-treated control. Enhanced fruit yield likely to be linked with higher root and shoot growth, individual and total fruit weight/plant and production of phytohormone by the probiotic bacteria applied on plants. …

Optimisation Of Ion Exchange Chromatography Purification Protocols For A Staphylococcal Peptidoglycan Degrading Hydrolase Enzyme, Fiona Maher

Theses

Bacteriophage (phage) are the most abundant biological entities on earth and were first discovered by d’Herelle in 1917. They are found wherever their hosts live and, like all viruses they do not have the ability to make their own protein. Therefore, in order to reproduce, phage must invade and infect bacterial cells. This project focused on the optimisation of Ion Exchange Chromatography purification protocols for a staphylococcal peptidoglycan degrading hydrolase enzyme (CHAPk). The project objective was to obtain the greatest yield of enzyme from the growth of the E.coU XL 1-Blue expression system into which the vector pQE60 was previously …

Cancerdiscover: An Integrative Pipeline For Cancer Biomarker And Cancer Class Prediction From High-Throughput Sequencing Data, Akram Mohammed, Greyson Biegert, Jiri Adamec, Tomáš Helikar

Department of Biochemistry: Faculty Publications

Accurate identification of cancer biomarkers and classification of cancer type and subtype from High Throughput Sequencing (HTS) data is a challenging problem because it requires manual processing of raw HTS data from various sequencing platforms, quality control, and normalization, which are both tedious and timeconsuming. Machine learning techniques for cancer class prediction and biomarker discovery can hasten cancer detection and significantly improve prognosis. To date, great research efforts have been taken for cancer biomarker identification and cancer class prediction. However, currently available tools and pipelines lack flexibility in data preprocessing, running multiple feature selection methods and learning algorithms, therefore, developing …

Endosomal Escape Of Antisense Oligonucleotides Internalized By Stabilin Receptors Is Regulated By Rab5c And Eea1 During Endosomal Maturation, Colton M. Miller, W. Brad Wan, Punit P. Seth, Edward N. Harris

Department of Biochemistry: Faculty Publications

Second-generation (Gen 2) Antisense oligonucleotides (ASOs) show increased nuclease stability and affinity for their RNA targets, which has translated to improved potency and therapeutic index in the clinic. Gen 2 ASOs are typically modified using the phosphorothioate (PS) backbone modification, which enhances ASO interactions with plasma, cell surface, and intracellular proteins. This facilitates ASO distribution to peripheral tissues and also promotes cellular uptake after injection into animals. Previous work identified that Stabilin receptors specifically internalize PS-ASOs in the sinusoidal endothelial cells of the liver and the spleen. By modulating expression of specific proteins involved in the trafficking and maturation of …

3-O Sulfation Of Heparin Leads To Hepatotropism And Longer Circulatory Half-Life, Colton M. Miller, Yongmei Xu, Katrina M. Kudrna, Blake E. Hass, Brianna M. Kellar, Andrew W. Egger, Jian Liu, Edward N. Harris

Department of Biochemistry: Faculty Publications

Introduction: Heparins are common blood anticoagulants that are critical for many surgical and biomedical procedures used in modern medicine. In contrast to natural heparin derived from porcine gut mucosa, synthetic heparins are homogenous by mass, polymer length, and chemistry.

Materials & methods: Stable cell lines expressing the human and mouse Stabilin receptors were used to evaluate endocytosis of natural and synthetic heparin. We chemoenzymatically produced synthetic heparin consisting of 12 sugars (dodecamers) containing 14 sulfate groups resulting in a non-3-O sulfated structure (n12mer). Half of the n12mer was modified with a 3-O sulfate on a single GlcNS sugar producing the …

Editorial: Structure And Function Of Chloroplasts, Rebecca L. Roston, Juliette Jouhet, Fei Yu, Hongbo Gao

Department of Biochemistry: Faculty Publications

The primary energy resource of life on earth is the sun, whose energy is captured in the form of usable carbons by a process called photosynthesis. Photosynthesis occurs within a cellular organelle adapted to that purpose, called the chloroplast. Chloroplasts are unique metabolic and sensory organelles restricted to plants, algae, and a few protists. In this special topic, we aimed to gather new research, hypotheses, and reviews that would help us to better understand the important role of chloroplasts in all photosynthetic organisms. We were fortunate enough to have submissions from many talented chloroplast researchers. This topic contains a total …

Identification Of Genes Encoding Enzymes Catalyzing The Early Steps Of Carrot Polyacetylene Biosynthesis, Lucas Busta, Won Cheol Yim, Evan William Labrant, Peng Wang, Lindsey Grimes, Kiah Malyszka, John C. Cushman, Patricia Santos, Dylan K. Kosma, Edgar B. Cahoon

Department of Biochemistry: Faculty Publications

Polyacetylenic lipids accumulate in various Apiaceae species after pathogen attack, suggesting that these compounds are naturally occurring pesticides and potentially valuable resources for crop improvement. These compounds also promote human health and slow tumor growth. Even though polyacetylenic lipids were discovered decades ago, the biosynthetic pathway underlying their production is largely unknown. To begin filling this gap and ultimately enable polyacetylene engineering, we studied polyacetylenes and their biosynthesis in the major Apiaceae crop carrot (Daucus carota subsp. sativus). Using gas chromatography and mass spectrometry, we identified three known polyacetylenes and assigned provisional structures to two novel polyacetylenes. We …

Non-Targeted Colonization By The Endomycorrhizal Fungus, Serendipita Vermifera, In Three Weeds Typically Co-Occurring With Switchgrass, Prasun Ray, Yingqing Guo, Jaydeep Kolape

Nebraska Center for Biotechnology: Faculty and Staff Publications

Serendipita vermifera (=Sebacina vermifera; isolate MAFF305830) is a mycorrhizal fungus originally isolated from the roots of an Australian orchid that we have previously shown to be beneficial in enhancing biomass yield and drought tolerance in switchgrass, an important bioenergy crop for cellulosic ethanol production in the United States. However, almost nothing is known about how this root-associated fungus proliferates and grows through the soil matrix. Such information is critical to evaluate the possibility of non-target effects, such as unintended spread to weedy plants growing near a colonized switchgrass plant in a field environment. A microcosm experiment was conducted …

A Role For A Predicted E. Coli Inner Membrane Lipoprotein In Cell Envelope Integrity, Charlie Chung

Dissertations and Theses

One of the distinct characteristics of Gram-negative bacteria such as Escherichia coli is the possession of a double-membraned cell envelope. The outer membrane provides an additional layer of protection against hydrophobic molecules including antibiotics, contributing to the multidrug resistance crisis. The Gram-negative membrane is composed of phospholipids, glycolipids, and proteins. A large portion of the bacterial cellular proteome is composed of membrane proteins. Despite this, the functions of several membrane proteins are as yet undefined. Therefore, defining the physiological roles of uncharacterized membrane proteins is expected to provide us with insights into the biology of the Gram-negative cell envelope and …

Collective Chemotaxis Of Retinal Neural Cells From Drosophila Melanogaster In Controlled Microenvironments, Stephanie Zhang

Dissertations and Theses

More than 172 million people are influenced by a retinal disorder that stems from either age-related or developmental causes. Of those, 1.5 million people endure a developmental retinal disorder. In the developing retina, neural cells undergo a series of highly complicated differentiation and migration process. A main cause of these diseases is abnormal collective migration of neural progenitors hindering the retinogenesis process. However, our grasp of collective migration and signaling molecules, critical to the developing retina, is incompletely understood. Understanding the molecular mechanisms, such as the fibroblast growth factor pathway, that regulate glial and neuronal migration provides decisive insights in …

Pg-Vtv Biogenesis Requires Atp To Facilitate Phosphorylation Of Syntaxin 17, Anika Saxena

Electronic Theses and Dissertations

The uptake of cytotoxic free fatty acids (FFA) and their conversion to physiologically expedient triglycerides (TAG) which are later on assimilated to very low density lipoproteins (VLDL) is of utmost value among the multifarious tasks performed by the liver. Inflated concentration of VLDL in the blood stream directly correlates with the reinforcement of atherosclerosis. VLDL is synthesized in the hepatic endoplasmic reticulum (ER) and transported to the Golgi where it encounters several alterations. It is then enclosed in distinct post-Golgi VLDL transport vesicles (PG-VTVs) and released into the blood. The data generated in our lab has proved the requirement of …

Deciphering The Role Of Adrenergic Hormones In Embryonic Cardiac Calcium Signaling And Metabolism, Jessica Peoples

Electronic Theses and Dissertations

The adrenergic hormones norepinephrine (NE) and epinephrine (EPI) are critical regulators of mammalian cardiovascular physiology. NE and EPI mediate stress responses to enhance cardiovascular function, however dysregulation of adrenergic signaling leads to heart failure, congenital heart malformations, and sudden cardiac death. Adrenergic hormone-expressing cells were found in the early embryonic heart, and NE has been determined essential for embryonic cardiac development. Despite extensive work in adults, the regulatory roles and adrenergic targets of these hormones during embryonic cardiac development have not yet been fully determined. Prior transcriptomic studies from our lab showed that expression of signal transduction and metabolic genes …

Characterization Of Neural Cells Derived From Reelin-Deficient Schizophrenic Patient Ips Cells, Nicole Roberts

Electronic Theses and Dissertations

Reelin is a large, extracellular glycoprotein that binds to several membrane receptors on neural stem cells (HNSCs), neural progenitor cells (NPCs), and neuroblasts of mammals to direct their migration. Previously, our lab established the presence of Reelin increased migration of wild-type fetal-derived HNSC's, both in vitro and in vivo. In addition, we demonstrated that Reelin protein treatment also increases the formation of radial glia via Notch-1 signaling, in vitro. Radial glia are precursors to NPCs, as well as a scaffold for neuroblast migration during cortical lamination. Reelin has long been associated with Schizophrenia (SZ). Because post-mortem brains are limited to …

Role Of Lipid Peroxide Derived Dicarboxylic Acids In Atherosclerotic Calcification, Aladdin Riad

Electronic Theses and Dissertations

Cardiovascular diseases, including atherosclerosis, are the leading cause of death in the United States. Atherosclerotic lesions are formed by deposition of lipids in the intima of arteries. Upon exposure to oxidative stresses, low-density lipoprotein (LDL) is converted to highly atherogenic oxidized LDL (ox-LDL) particles, contributing to disease development and progression. Advanced disease stages may result in calcification of lesions. This calcification process is important, as it has been shown to be associated with stable plaques that are less prone to rupture. Calcification is present in lipid rich domains of lesions, however neither the composition of the mineralized calcium deposits nor …

Embryonic Stem Cell-Derived Exosomes Inhibit Doxorubicin-Induced Pyroptosis In Cell Culture Models, Zahra Tavakoli Dargani

Electronic Theses and Dissertations

Doxorubicin (Dox) is a potent chemotherapeutic drug used for the treatment of various cancers. Unfortunately, its use is limited as Dox induces adverse cardiotoxicity (DIC) and muscle toxicity (DIMT), which are mediated through oxidative stress, ER stress, and inflammation. However, it remains unknown whether Dox induces an inflammation mediated cell death, called “pyroptosis”. The current study is designed to determine whether Dox induces pyroptosis in cardiac and muscle cell culture models. Moreover, the protective effects of embryonic stem cell-derived exosomes (ES-Exos) in inhibiting pyroptosis will also be determined. For this purpose, we designed two different cell culture models using H9c2 …

Knowledge And Attitudes Regarding The Recent Zika Outbreak Among A Sample Of South Florida Residents, Mohamed Elakkari

Electronic Theses and Dissertations

South Florida has had the largest number of U.S. Zika infection cases during the recent outbreak. This study aimed at assessing South Floridians' basic knowledge, perceptions of the seriousness and susceptibility to Zika infection, their information sources and needs, as well as their attitudes towards the protective measures proposed by the CDC. We also wanted to assess whether any of those factors have affected the frequency of participants' undertaking of the protective behaviors. To this end, we designed an online questionnaire and surveyed the responses of five hundred South Floridians (Age=18-78 years). We found significant gaps in participants' knowledge about …

Agri 115: Biotechnology – Food, Health And Environment, A Peer Review Of Teaching Project Benchmark Portfolio, Leah Sandall

UNL Faculty Course Portfolios

No abstract provided.

Characterization Of Recombinant Glycogen Debranching Enzyme From Corynebacterium Glutamicum And Application For Resistant Starch Production, Chay Sirirattanachatchawan

Chulalongkorn University Theses and Dissertations (Chula ETD)

Glycogen debranching enzyme (EC 2.4.1.25/EC 3.2.1.33) catalyzes a hydrolysis of α-1,6 glycosidic bond and a transfer α-1,4 glucan from donor molecules to acceptor molecules. The objectives of this research are to characterize a glycogen debranching enzyme from Corynebacterium glutamicum (CgGDE) and optimize resistant starch (RS) type 3 production using recombinant CgGDE. Recombinant CgGDE was expressed in Escherichia coli BL21 (DE3) and successfully purified by DEAE FFTM column. The calculated molecular weight of CgGDE was approximately 95 kDa and the protein existed as a trimer as analyzed by size exclusion chromatography. CgGDE showed the highest activity on amylopectin followed by glycogen, …

Optimization Of Protein Hydrolysate Preparation From Split Gill Mushroom Schizophyllum Commune, Aunchalee Wongaem

Chulalongkorn University Theses and Dissertations (Chula ETD)

The optimum conditions for hydrolysate production from split gill mushroom protein using the microbial protease, Alcalase were investigated. The study was conducted using central composite design and response surface methodology. Three independent factors: hydrolysis temperature (45, 50, and 55 °C); hydrolysis time (60, 120, and 180 min); and enzyme to substrate ratio (2%, 4%, and 6% w/v) were varied, while the pH was fixed at pH 8. These three factors had a significant effect on the DH and ABTS radical-scavenging activity (p < 0.05). The optimum conditions obtained from experiments were: enzyme to substrate ratio 2%; hydrolysis time 161.4 min; and temperature 55 °C. The coefficient of determination (R2) of total protein and the IC50 value for ABTS radical-scavenging activity were 0.972 and 0.205 µg/mL, respectively, and the DH value was 50.882%. The hydrolysate was fractionated by molecular weight (MW) cut-off membranes (10, 5, 3, and 0.65 kDa). The < 0.65 kDa fraction had the highest radical scavenging ability (IC50 = 0.026 ± 0.004 µg/mL). The MW < 0.65 kDa fraction was separated by reversed-phase HPLC to yield four subfractions (F1–5). The F4 subfraction showed the highest maximum ABTS radical-scavenging activity and was selected for further analysis by quadrupole-time-of-flight-electron spin induction–mass spectrometry-based. Five antioxidant peptides were identified. In addition, the MW< 0.65 kDa fraction protected against oxidation-induced DNA damage in pBR322, pKS, and pUC19 plasmids. Furthermore, the MW < 0.65 kDa fraction, exhibited cellular antioxidant activity in a human intestinal cancer cell line (HT-29), which was dependent on the peptide concentration. These results suggested that split gill mushroom protein hydrolysate is a good source of bioactive peptides and has potential as a natural antioxidant in food production and cosmetic products.

Reaction Mechanisms Of Substrate And Inhibitor With Ns2b/Ns3 Serine Protease Of Zika Virus By Mm And Qm/Mm Simulations, Bodee Nutho

Chulalongkorn University Theses and Dissertations (Chula ETD)

Zika virus (ZIKV) infection has become a public health concern worldwide. The recent epidemiological data have revealed a possible association of ZIKV infection with neurological manifestations in both newborn children and adults. Currently, there is no anti-ZIKV drug or vaccine available for preventing or controlling ZIKV infection. An attractive drug target for ZIKV treatment is NS2B/NS3 serine protease that plays a crucial role to cleave the peptide bond during the viral replication process. Initially, the ZIKV NS2B/NS3 serine protease in complex with four peptide substrates were studied to investigate the binding recognition and protein-substrate interactions using conventional molecular dynamics (MD) …