Biotechnology Commons^™

Grand Design For Merapi Irrigation Channel System Using Watershed And River Region Approaches Based On Community Development In Yogyakarta, Indonesia, Suprayogi Slamet, Gunawan Totok, Murti Sigit Heru, Prihantarto Wikan Jaya, Alatas Masrur

ASEAN Journal on Science and Technology for Development

This paper proposes a grand design for Merapi Irrigation Channel, an irrigation channel system spanning from Turi to Cangkringan District in Yogyakarta, Indonesia. This design is based on Geographic Information System research to assess the feasibility of the system from two aspects, namely geophysics using site selection approaches (watershed and river region) and community aspirations, analyze potential water resource availability to support its sustainability, and construct a grand design. Primary data acquired from IKONOS image interpretation were used to collect geophysical and ?eld data for parameter mapping, and spatial data were modeled using Geographic Information System technology to determine paths, …

Students Interest And Thoughts On Stem, Chrisitine Girtain

STEM Month

I am Juan Sebastian Bohorquez Mora, I am a sophomore student at Toms River High School North. I am interested in biofuels because I believe they are a good option to replace fossil fuels. I am also interested in duckweed because biofuels are made out of crops, and people need to eat those crops. That’s when duckweed comes in and it can be used as a feedstock for ethanol production which is a biofuel. Bioethanol is a type of biofuel and it is derived from the corn’s starch. Instead of making ethanol from the corn’s starch, we can use duckweed …

Diversity Of Bacteriophage In Burkholderia Species, Abigail Price

Honors Projects

Bacteriophages are viruses that infect and replicate within bacteria and offer the potential of a therapeutic alternative to chronic infections that do not respond to antibiotic-based therapies. B. vietnamiensis is one of a number of Burkholderia species involved with chronic drug resistant infections in the lungs of individuals with compromised respiratory systems, as found in those with chronic obstructive pulmonary disease and, most especially, are of particular significance in patients with cystic fibrosis. The diversity of the Burkholderia species is explored by using online databases and looking at bacteriophage or phage-encoding viruses found in B. vietnamiensis. The open reading frames …

The Synthesis And Purification Methodology Of An Intermolecular Pyrophosphate Sensor: Applications For The Quantitative Polymerase Chain Reaction, Ethan Gevedon

Honors Projects

The optimized synthesis and purification methodology for an intermolecular pyrophosphate sensor scaffold molecule was performed: high performance liquid chromatography afforded the scaffold in excellent purity and yield. The applications of the sensor assembly in the quantitative polymerase chain reaction were discussed, and preliminary results show that

Generating Improved Rna Localization Reporters Using The U1hp-U1a System, Ryan Dannemiller, Rebecca Adams Phd

[Archive] Belmont University Research Symposium (BURS)

Generating Improved RNA Localization Reporters Using the U1hp-U1A System

Ryan Dannemiller, Rebecca Adams, PhD. Belmont University, Nashville, TN.

Messenger mRNA (mRNA) is genetic material that is used to bridge between DNA in the nucleus and protein-making machinery in the cytoplasm of eukaryotic cells. The processes of transcription and translation are physically separated, so the localization of mRNA dictates whether the encoded protein can be generated. In order to observe the localization of specific transcripts in response to stimuli, tools are needed to track location of mRNA. For example, in response to heat shock and ethanol stress, most mRNA is retained …

Europium-Doped Cerium Oxide Nanoparticles For Microglial Aβ Clearance And Homeostasis, Jatin Machhi, Pravin Yeapuri, Milica Markovic, Milankumar Patel, Wenhui Yan, Yaman Lu, Jacob D. Cohen, Mahmudul Hasan, Mai Mohamed Abdelmoaty, You Zhou, Huangui Xiong, Xinglong Wang, R. Lee Mosley, Howard E. Gendelman, Bhavesh D. Kevadiya

Nebraska Center for Biotechnology: Faculty and Staff Publications

Alzheimer’s disease (AD) is the most common neurodegenerative disorder. Pathologically, it is characterized by the deposition of amyloid beta (Aβ) plaques and presence of neurofibrillary tangles. These drive microglia neuroinflammation and consequent neurodegeneration. While the means to affect Aβ plaque accumulation was achieved how it affects disease outcomes remains uncertain. Cerium oxide (CeO₂) reduces Aβ plaques, oxidative stress, inflammation, and Alzheimer’s disease (AD) signs and symptoms. Specifically, CeO₂ nanoparticles (CeO₂NPs) induces free radical scavenging and cell protective intracellular signaling. This can ameliorate the pathobiology of an AD-affected brain. In order to investigate, CeO₂NPs …

Annual Faculty Research Symposium 2022, Oakwood University

Proceedings

No abstract provided.

Characterization Of Erinacine-A, Justice Brakache

Symposium of Student Scholars

The wood-rot fungus known as the lion’s mane mushroom (H. erinaceus) has a long history of usage in ancient eastern medicine, noted for its health-boosting properties, particularly to neurological health. Claims include this mushroom’s ability to stimulate nerve growth as well as prevent the progression of neurodegenerative diseases such as dementia. Recent studies on the subject have shown promising data supporting these anecdotal claims, proving the ability of extracts from this mushroom to stimulate nerve growth factor (NGF) in human cells, among other beneficial findings. This study seeks to assess the effectiveness of the diterpenoid erinacine-A, present in H. …

Improving Photosynthetic Efficiency In Microalgae Through The Genetic Engineering Of Energy Sensors And Photoreceptors, Taylor L. Britton

Biology ETDs

Through photosynthesis microalgae can convert sunlight, water, and CO₂ into chemical energy that can be used to generate carbon neutral biofuels and biomass. With an ever-increasing demand and need for petroleum substitutes it is imperative that we improve the output of industrial-relevant crops such as microalgae. One important way of improving output in algae is by understanding the roles that stress and energy conversion is regulated in these organisms. Photosynthetic organisms fundamentally depend on light- and sugar-driven metabolic and signaling networks, which integrate environmental cues to govern and sustain growth and survival. SnRKs (SNF1-related protein kinases) and the photoreceptor …

Healthcare Simulation: A Key To The Future Of Medical Education - A Review, Omair Ayaz, Faisal Wasim Ismail

Medical College Documents

Aim: Simulation originates from its application in the military and aviation. It is implemented at various levels of healthcare education and certification today. However, its use remains unevenly distributed across the globe due to misconception regarding its cost and complexity and to lack of evidence for its consistency and validity. Implementation may also be hindered by an array of factors unique to the locale and its norms. Resource-poor settings may benefit from diverting external funds for short-term simulation projects towards collaboration with local experts and local material sourcing to reduce the overall cost and achieve long-term benefits. The recent shift …

Als-Associated Kif5a Mutations Abolish Autoinhibition Resulting In A Toxic Gain Of Function, Desiree M. Barron, Adam R. Fenton, Sara Saez-Atienzar, Anthony Giampetruzzi, Aparna Sreeram, Shankaracharya, Pamela J. Keagle, Victoria R. Doocy, Nathan J. Smith, Eric W. Danielson, Megan Andresano, Mary C. Mccormack, Jaqueline Garcia, Valérie Bercier, Ludo Van Den Bosch, Jonathan R. Brent, Claudia Fallini, Brian J. Traynor, Erica L.F. Holzbaur, John E. Landers

Biochemistry -- Faculty Publications

Understandingthepathogenicmechanismsof diseasemutations is critical toadvancingtreatments.ALS-associated mutations in the gene encoding the microtubulemotor KIF5A result in skipping of exon 27 (KIF5ADExon27) and the encoding of a protein with a novel 39 amino acid residue C-terminal sequence. Here, we report that expression of ALS-linked mutant KIF5A results in dysregulated motor activity, cellular mislocalization, altered axonal transport, and decreased neuronal survival. Single-molecule analysis revealed that the altered C terminus of mutant KIF5A results in a constitutively active state. Furthermore,mutant KIF5A possesses altered protein and RNA interactions and its expression results in altered gene expression/splicing. Taken together, our data support the hypothesis that causative …

Developing An Electroporation Method For Transforming Streptomyces Nymphaeiformis, Heather Knott, Stephen Baron

Honors Projects

Streptomyces species are notoriously difficult to transform. Streptomyces nymphaeiformis is no different, so a method of electroporation was used to attempt to transform the cells. Multiple growth stages were used in order to alter the degree of development of the cell wall. The procedure did not kill the cells, but the cells were not transformed. Due to the lack of transformation with S. nymphaeiformis, transformation was attempted on two other Streptomyces strains, S. lividans and S. coelicolor. Neither was successfully transformed to thiostrepton (tsr) resistance, nor did they grow on a plate lacking thiostrepton. One possibility for the …

Comparative Modeling And Evolutionary Comparison Of Serine Protease, A Timber Rattlesnake Venom Protein, Qawer Ayaz

Theses

The aim of this study is to create a homology model of VG35 serine protease and evaluate the evolutionary comparison of secondary structure on basis of protein model using YASARA. This method was furthermore used to predict the potential epitopes which can help in the investigation of future studies.

The VG35 was used to run a BLAST search which gave most resembled serine protease of different species which was then translated and modeled in YASARA. The modeled protein data was then used to determine the secondary structure. This was then used for evolutionary comparison of all proteins to VG35. Then …

A Computational Assessment Of The Allosteric Modulation Of Gabaa Receptor, Abdel Rahman Atef Aly

Theses

γ-aminobutyric acid (GABA) type A receptor (GABA_AR) is a pentameric ligand gated ion channel and a member of the Cys-loop superfamily. It is targeted by several clinically significant allosteric modulators. The role of individual subunits of the receptor has been very extensively studied. However, the exact molecular pathway upon which the receptor is activated remains elusive. The main objective of this study was to probe the molecular activation pathway for the orthosteric GABA and to understand how two of the most well-established positive (PAM) and negative (NAM) allosteric modulators tend to modulate the receptor. Three independent long scale …

Synthesis Of A Streptavidin-Conjugated Agarose Resin For Purification Of Biotin-Tagged Biomolecules, Sydney Thomas

Senior Theses

Streptavidin, a bacteria-derived protein, and the small molecule biotin display extremely high-affinity binding. Researchers have taken advantage of this uniquely strong interaction in a myriad of detection, labeling, and purification techniques, one of which is affinity chromatography. Streptavidin can be immobilized onto a solid support, and this streptavidin-conjugated material can be used to capture biotin-tagged molecules with exceedingly high strength and specificity. In this project, a protocol was developed for synthesizing an agarose-based streptavidin resin for use as an affinity chromatography medium. Additionally, two fluorescence-based assays were developed for quantifying the amount of streptavidin conjugated to each resin and for …

Rna Sequencing Reveals That Cyp3a5 Sirna Treatment Induces Cell Cycle Blockade And Senescence In Mdapca2b Human Prostate Cancer Cells, Jeetesh Sharma

Annual Research Symposium

No abstract provided.

The Design, Construction, And Testing Of A Recombinant Dna Vaccine For Brucella Abortus And Brucella Melitensis, Stephanie Lynn Korle

LSU Doctoral Dissertations

Brucella spp. are a bacterium that cause brucellosis, a zoonotic disease, which is commonly seen in cattle, sheep, goats, swine, and canines. Brucellosis is a problem worldwide, although it is eradicated in some countries (Garin-Bastuji et al. 1998). The reason for designing recombinant DNA (rDNA) vaccines opposed to utilizing the live-attenuated vaccines on the market is that they cannot be given to pregnant animals without potentially causing abortion, while an rDNA vaccine should be safe for pregnant animals since it does not contain viable bacteria. Also, there are no serological tests that can accurately distinguish between an animal vaccinated …

Reduction Of Stabilin-2 Contributes To A Protection Against Atherosclerosisstabilin, Yukako Kayashima1*,, Conner A. Clanton, Amanda M. Lewis, Xinghui Sun, Sylvia Hiller, Phillip Huynh, Jennifer Wilder, John Hagaman, Feng Li, Nobuyo Maeda-Smithies, Edward N. Harris

Department of Biochemistry: Faculty Publications

We have previously identified a novel atherosclerosis quantitative trait locus (QTL), Arch atherosclerosis 5 (Aath5), on mouse chromosome 10 by three-way QTL analyses between Apoe^−/− mice on a DBA/2J, 129S6 and C57BL/6J background. The DBA/2J haplotype at the Aath5 locus was associated with smaller plaque size. One of the candidate genes underlying Aath5 was Stabilin-2 (Stab2), which encodes a clearance receptor for hyaluronan (HA) predominantly expressed in liver sinusoidal endothelial cells (LSECs). However, the role of Stab2 in atherosclerosis is unknown. A congenic line of Apoe^−/− mice carrying Aath5 covering the Stab2^DBA allele …

Reduction Of Stabilin-2 Contributes To A Protection Against Atherosclerosis, Yukako Kayashima, Connor A. Clanton, Amanda M. Lewis, Xinghui Sun, Sylvia Hiller, Phillip Huynh, Jennifer Wilder, John Hagaman, Feng Li, Nobuyo Maeda-Smithies, Ed Harris

Department of Biochemistry: Faculty Publications

We have previously identified a novel atherosclerosis quantitative trait locus (QTL), Arch atherosclerosis 5 (Aath5), on mouse chromosome 10 by three-way QTL analyses between Apoe^−/− mice on a DBA/2J, 129S6 and C57BL/6J background. The DBA/2J haplotype at the Aath5 locus was associated with smaller plaque size. One of the candidate genes underlying Aath5 was Stabilin-2 (Stab2), which encodes a clearance receptor for hyaluronan (HA) predominantly expressed in liver sinusoidal endothelial cells (LSECs). However, the role of Stab2 in atherosclerosis is unknown. A congenic line of Apoe^−/− mice carrying Aath5 covering the Stab2 …

Characterization Of SccMec Instability In Methicillin-Resistant Staphylococcus Aureus Affecting Adjacent Chromosomal Regions, Including The Gene For Staphylococcal Protein A (Spa), Isabella A. Tickler, Fred C. Tenover, C. R. Scharn, R. V. Goering

Biology Faculty Publications

Staphylococcal cassette chromosome mec (SCCmec) represents a sequence of clear clinical and diagnostic importance in staphylococci. At a minimum the chromosomal cassette contains the mecA gene encoding PBP2a but frequently also includes additional antibiotic resistance genes (e.g., ermA and aadC; macrolide and aminoglycoside resistance, respectively). Certain regions within SCCmec elements are hot spots for sequence instability due to cassette-specific recombinases and a variety of internal mobile elements. SCCmec changes may affect not only cassette stability but the integrity of adjacent chromosomal sequences (e.g., the staphylococcal protein A gene; spa). We investigated SCCmec stability …

A Glass Bead Semi‑Hydroponic System For Intact Maize Root Exudate Analysis And Phenotyping, Martha G. Lopez-Guerrero, Peng Wang, Felicia Phares4, Daniel P. Schachtman, Sophie Alvarez, Karin Van Dijk

Department of Biochemistry: Faculty Publications

Background: Although there have been numerous studies describing plant growth systems for root exudate collection, a common limitation is that these systems require disruption of the plant root system to facilitate exudate collection. Here, we present a newly designed semi-hydroponic system that uses glass beads as solid support to simulate soil impedance, which combined with drip irrigation, facilitates growth of healthy maize plants, collection and analysis of root exudates, and phenotyping of the roots with minimal growth disturbance or root damage.

Results: This system was used to collect root exudates from seven maize genotypes using water or 1 mM CaCl …

Disruption Of Claudin-Made Tight Junction Barriers By Clostridium Perfringens Enterotoxin: Insights From Structural Biology, Chinemerem P. Ogbu, Sourav Roy, Alex J. Vecchio

Department of Biochemistry: Faculty Publications

Claudins are a family of integral membrane proteins that enable epithelial cell/cell interactions by localizing to and driving the formation of tight junctions. Via claudin self-assembly within the membranes of adjoining cells, their extracellular domains interact, forming barriers to the paracellular transport of small molecules and ions. The bacterium Clostridium perfringens causes prevalent gastrointestinal disorders in mammals by employing an enterotoxin (CpE) that targets claudins. CpE binds to claudins at or near tight junctions in the gut and disrupts their barrier function, potentially by disabling their assembly or via cell signaling means—the mechanism(s) remain unclear. CpE ultimately destroys claudin-expressing cells …

Sesamum Indicum Diet Prevents Hyperlipidemia In Experimental Rats, Muinat M. Adeyanju, Idris A. Saheed, Oluwaseun I. Oyelekan, Taiwo A. Dele-Osibanjo, Ayodeji A. Adelegan, Adekunle J. Raimi, Samuel O. Olalekan, Olugbenga S. Alabi, Khadijat M. Alli

Department of Biochemistry: Faculty Publications

Cardiovascular diseases and metabolic complications caused by hyperlipidemia are the leading cause of death globally. In this study, the hypolipidemic potency of Sesamum indicum (SI) seeds was investigated. Of the thirty-five (35) male rats used in the study, five (5) were randomly selected for baseline measurements and thirty (30) were fed high fat diet (HFD) for four (4) weeks before random assignment into three (3) groups. The experimental group was treated with 50% SI seed, the positive control group was given a hypolipidemic drug, atorvastatin (5 mg/kg/day) while the untreated group served as the negative control. With SI administration, the …

A Chromosome-Scale Assembly Of The Djulis (Chenopodium Formosanum) Genome, An Emerging Orphan Crop From Taiwan, Peter J. Maughan, Eric N. Jellen, John Sproul, Karol Krak, Tzu-Yun Huang, Tzu Che Lin, Beatriz Navarro Dominguez, Yung-Fen Huang, Kate Jaggi, David E. Jarvis

Library/Life Sciences Undergraduate Poster Competition 2022

Djulis (Chenopodium formosanum Koidz.) is a semi-domesticated Taiwanese native crop. It is a BCD-genome hexaploid (2n = 6x = 54) relative of the Andean-native allotetraploid (AABB) quinoa (C. quinoa). Djulis has been grown in a relatively small area by aboriginal Taiwanese, who use it primarily as a fermentation starter to produce ritual alcoholic beverages. Djulis’ seed protein, like that of quinoa, is complete in terms of its human dietary essential amino acid profile; the seed also offers a wide variety of nutritionally important vitamins and minerals. These nutritional attributes have attracted international attention as a novel, healthy grain option. We …

Effects Of Methyl Salicylate (Mesa) On The Physiology And Biochemical Characteristics Of Rice Under Salinity Stress At Seedling Stage, Thu Ha Thi Pham, Truong Minh Tuan, Pham Thi Thu Hien, Tran Thi My Hiep, Chau Thi Da

The Philippine Agricultural Scientist

Salt stress negatively affects crop survival, growth, development, and yield. Methyl salicylate (MeSA) is synthesized from salicylic acid (SA) which is a volatile organic compound that is responsible for inducing defense mechanisms in plants and also has a protective role in stress sensitivity. The objective of this study was to examine the effect of different concentrations of methyl salicylate (MeSA) on the physiological and biochemical characteristics of two rice varieties GRIS4 (G1) and GRIS5 (G2) under salt stress at the seedling stage. Five hundred seeds of each variety were treated with different doses of MeSA (0, 0.1, 0.5, and 1.0 …

Morpho-Physiological Responses Of Wheat To Silicon And Bio-Fertilizer Under Water-Deficit Conditions, Mehrdad Arab-Aval, Hamid Reza Ganjali

The Philippine Agricultural Scientist

Recently, the use of silicon and bio-fertilizer has become important worldwide to improve the physicochemical characteristics of soil. Thus, they are used as an alternative approach to cope with the water-deficit stress on wheat plant. In this regard, a split-plot factorial experiment based on randomized complete block design with three replications was conducted during 2017 and 2018 at Sistan and Baluchestan Research Station, Iran. In the present study, treatments included water-deficit stress (irrigation after 60, 120, and 180 mm of evaporation from Class A pan) as the main plot, as well as the application of silicic acid (Si) foliar nutrition …

Carbapenemase-Producing Pseudomonas Aeruginosa – An Emerging Challenge, Fred C. Tenover, David P. Nicolau, Christian M. Gill

Biology Faculty Publications

Carbapenem-resistant Pseudomonas aeruginosa (CR-PA) is a major healthcare-associated pathogen worldwide. In the United States, 10–30% of P. aeruginosa isolates are carbapenem-resistant, while globally the percentage varies considerably. A subset of carbapenem-resistant P. aeruginosa isolates harbour carbapenemases, although due in part to limited screening for these enzymes in clinical laboratories, the actual percentage is unknown. Carbapenemase-mediated carbapenem resistance in P. aeruginosa is a significant concern as it greatly limits the choice of anti-infective strategies, although detecting carbapenemase-producing P. aeruginosa in the clinical laboratory can be challenging. Such organisms also have been associated with nosocomial spread requiring infection prevention interventions. The carbapenemases …

Effect Of Rehmannia Glutinosa Libosch Extract On Proliferation And Cardiogenic Pre-Differentiation Of Human Mesenchymal Stem Cells, Huu Dat Nguyen, Len Ho Thi, Xuan Bach Ho, Van Anh Cao, Duy Minh Le Hoang

BioMedicine

Background: Vietnamese medicine tried and tested certain bioactive compounds from plants to increase the rate of tissue immunomodulation, regeneration, and differentiation. Although there are many research papers discovered about phytochemicals of Rehmannia glutinosa Libosch and differentiation induction potential of some substances purified from this herbal, it finds difficult to seek research that investigated the effect of Rehmannia glutinosa Libosch extract on proliferation and cardiogenic differentiation of mesenchymal stem cells, even though it has commonly been used for a long time because of its function as a restorative and as a critical role in cardiovascular treatment in traditional.

Results: Our …

Role Of Specialized Pro-Resolving Mediators In Reducing Neuroinflammation In Neurodegenerative Disorders, Jana Ponce, Arzu Ulu, Corrine Hanson, Erin Cameron-Smith, Jenna Wuebker, John Bertoni, Alfred Fisher, Ka-Chun Siu, Vivien Marmelat, Jiri Adamec, Danish Bhatti

Department of Biochemistry: Faculty Publications

Alzheimer’s disease (AD) and Parkinson’s disease (PD) are neurodegenerative disorders that affect millions of individuals worldwide. As incidence of these conditions increases with age, there will undoubtedly be an increased prevalence of cases in the near future. Neuroinflammation is a hallmark in the development and progression of neurodegenerative diseases and prevention or resolution of chronic neuroinflammation may represent a novel approach to treatment. The present review highlights the potential of the anti-inflammatory and pro-resolving effects of polyunsaturated fatty acid (PUFA)- derived mediators (Specialized Pro-resolving Mediators—SPM) in neurodegenerative disorders. PUFA-derived SPM are biosynthesized in response to chemicals produced from acute inflammatory …

Characterization Of Testis-Derived Mesenchymal Cells And The Hunt For Universal Stemness Markers, Myret Ghabriel

Theses and Dissertations

Mesenchymal stromal/stem cells (MSCs) are multipotent cells residing in multiple tissues with the capacity for self-renewal and differentiation into various cell types. Due to the myriad sources of MSCs the International Society for Cellular Therapy (ISCT) proposed certain criteria for their characterization. Here, we isolate adult MSCs from mouse testes and demonstrate that these testis-derived MSCs (tMSCs) follow some of the ISCT’s criteria. tMSCs expressed the MSCs surface markers CD44, CD73, and CD29 and lacked the expression of the hematopoietic cell marker CD45. Moreover, the cells displayed the capacity for self-renewal and in vitro differentiation into adipocytes. Since the isolation …