Biotechnology Commons^™

Phenotype Bias Determines How Natural Rna Structures Occupy The Morphospace Of All Possible Shapes, Fatme Ghaddar, Dr Kamaludin Dingle, Dr Petr Sulc, Prof Ard A. Louis

Undergraduate Research Symposium

The relative prominence of developmental bias versus natural selection is a long standing controversy in evolutionary biology. Here we demonstrate quantitatively that developmental bias is the primary explanation for the occupation of the morphospace of RNA secondary structure (SS) shapes. By using the RNAshapes method to define coarse-grained SS classes, we can measure the frequencies that non-coding RNA SS shapes appear in nature. Our main findings are firstly that only the most frequent structures appear in nature; the vast majority of possible structures in the morphospace have not yet been explored. Secondly, and perhaps more surprisingly, these frequencies are accurately …

Seaweed Polysaccharide In Food Contact Materials (Active Packaging, Intelligent Packaging, Edible Films, And Coatings), Kalpani Y. Perera, Shubham Sharma, Amit K. Jaiswal, Swarna Jaiswal

Articles

Food contact materials (FCMs) are materials that come in contact with food products such as food packaging which play a significant role in the food quality and safety. Plastic, which is a major food packaging material, harms the eco-system, wildlife, and the environment. As a result, numerous researches have been in progress on alternative polymers, which has similar properties as plastic but is also environmentally friendly (biodegradable). In recent years, the utilization of seaweed polysaccharides has piqued interest due to its biodegradability, non-toxicity, antioxidant capabilities, and excellent film formation ability. However, it has a number of drawbacks such as low …

Anti-Angiogenic Effects Of Chemotherapeutic Agents And Their Enhancement With Ot-515 And S-Nach, Shimaa Adel Heikal

Theses and Dissertations

Chemotherapeutic agents have been used for the treatment of numerous types of tumors with great success. Cisplatin and Doxorubicin are among the well-known chemotherapeutic drugs that showed efficacy against various types of cancers. However, cell resistance and major side effects like chemotherapy-induced peripheral neuropathy (CIPN) are limiting factors in using these compounds. Using a combination or adjuvant compounds with anti-angiogenic effects is one of the strategies suggested to decrease resistance or ameliorate chemotherapeutic toxicity. The present study investigated the anti-angiogenic effects of Cisplatin and Doxorubicin alone and combined with Sulfated non-anticoagulant heparin (S-NACH), a low molecular weight heparin LMWH that …

Optimization Of Ethanol Production From Enzymatically Saccharified Biomass Of Acid-Pretreated Rice Straw, Muzammal Mateen Azhar, Qurban Ali, Arif Malik, Elham Khalili, Muhammad Arshad Javed, Shinawar Waseem Ali, Muhammad Saleem Haidar

The Philippine Agricultural Scientist

The substrate of rice (Oryza sativa) straw employed in this study was procured from local market and stored in polyethene bags until needed. The study was conducted to find out the effects of process optimization of ethanol production from enzymatically saccharified biomass of acid-pretreated rice straw. The results indicated that acid pretreatment has reduced lignin content about 50%. Resultantly, pretreatment raised cellulose contents up to 52% making it suitable for enzymatic saccharification. Optimization of saccharification illustrated that parameters such as biomass, enzyme concentration, temperature, incubation time and agitation indeed affected the action of cellulase on pretreated biomass releasing …

Spectral Lights Based Treatment Enhanced Biomass Accumulation And Secondary Metabolites Production In Callus Culture Of Citrus Reticulata, Faiza Anum, Naveed Iqbal Raja, Tahira Sultana, Abeer Kazmi, Amir Ali, Bushra Qayyum, Anza Afzal, Aneela Nijibat, Zia-Ur-Rehman Mashwani, Abeer Kazmi

The Philippine Agricultural Scientist

Citrus reticulata is a common fruit, belongs to the family Rutaceae. It contains terpenes, phenolics, flavonoids, and vitamin C in conjugation with sugars, amino acids, minerals, organic acids and other biologically important compounds. Application of light elicitation strategies in in vitro plant cultures is acquiring more interest for their potential in feasible biomass accumulation and therapeutically important secondary metabolites production. The present study was designed to investigate the effects of different monochromatic lights (white, red, blue, green, and yellow) on the proliferation and secondary metabolites accumulation in callus cultures of Citrus reticulata raised in response to treatment with AgNPs and …

Tools And Strategies For The Patterning Of Bioactive Molecules And Macromolecules, Daniel J. Valles

Dissertations, Theses, and Capstone Projects

Hypersurface Photolithography (HP) is a printing method for fabricating structures and patterns composed of soft materials bound to solid surfaces and with ~1 micrometer resolution in the x, y, and z dimensions. This platform leverages benign, low intensity light to perform photochemical surface reactions with spatial and temporal control of irradiation, and, as a result, is particularly useful for patterning delicate organic and biological material. In particular, surface- initiated controlled radical polymerizations can be leveraged to create arbitrary polymer and block- copolymer brush patterns. Chapter 1 will review the advances in instrumentation architectures from our group that have made these …

Biocontrol Of Foodborne Pathogens Using Bacteriophages, Dzhuliya Ignatova, Erion Hogan, Simone Dakare, Jean Lu

Symposium of Student Scholars

Biocontrol of Foodborne Pathogens Using Bacteriophages

Dzhuliya Ignatova, Erion Hogan, Simone Dakare, and Jean Lu

Department of Molecular and Cellular Biology

Abstract

Salmonella and Shigella are two important groups of foodborne bacterial pathogens. Salmonella cause an illness called salmonellosis while Shigella cause shigellosis (bacillary dysentery). The most common symptoms of these illnesses are abdominal cramps, diarrhea, and fever. Shigella can also cause bloody diarrhea. It was estimated that each year Salmonella cause 93.8 million cases of gastroenteritis and 155,000 deaths globally. Shigella causes 164.7 million cases and 1.1 million deaths throughout the world yearly. People get these illnesses mainly by …

Complimenting A Chlamydomonas Reinhardtii Mutation Using Cell Penetrating Peptides, Matthew Mckenzie

Symposium of Student Scholars

Complimenting a Chlamydomonas reinhardtii Mutation Using Cell Penetrating Peptides

Matthew McKenzie and Jennifer L. Cooper

Chlamydomonas reinhardtii is a photosynthetic model organism most notable for its easily manipulatable genetics. C. reinhardtii uses flagella to swim and optimize its growth conditions in the light. We plan to use cell penetrating peptides (CPPs) to compliment C. reinhardtii that is affected with the IFT46 mutation. Cell penetrating peptides are short peptides that can move across a cell membrane. The novel CPP that we are using is called TaT-CaM. It consists of the trans-activator of transcription (TaT) and the calmodulin domain (CaM) that binds …

Harnessing Multi-Label Classification Approaches For Economic Phenomena Categorization, Nofriani, Budi Kurniawan Novianto

ASEAN Journal on Science and Technology for Development

One fashion to report a country’s economic state is by compiling economic phenomena from several sources. The collected data may be explored based on their sentiments and economic categories. This research attempted to perform and analyze multiple approaches to multi-label text classification in addition to providing sentiment analysis on the economic phenomena. The sentiment and single-label category classification was performed utilizing the logistic regression model. Meanwhile, the multi-label category classification was fulfilled using a combination of logistic regression, support vector machines, k-nearest neighbor, naïve Bayes, and decision trees as base classifiers, with binary relevance, classifier chain, and label power set …

Constructing An Imaginary Wall In The Ocean: A Technical Cartography Study On The Delimitation Of Maritime Boundaries In The Provinces Of South Sumatra And Bangka Belitung Islands Based On Gis, Kurniawan Agung, Khakhim Nurul, Slamet Hardjo Karen, Iwan Santoso Agus, Setiyo Pranowo Widodo

ASEAN Journal on Science and Technology for Development

Marine management areas in Indonesia can be claimed 12 nautical miles from the coastline by regional governments, according to Law 23 of 2014. However, in reality, there are many provinces whose distances to other provinces are fewer than 2 × 12 nautical miles, necessitating that they be delimited fairly and proportionally. The provinces of South Sumatra and Bangka Belitung Islands are such an example. The absence of clear boundaries drawn on the national map of Indonesia was the fundamental problem and focus of this study, owing to the need for delimitation of regional sea boundaries. The delimitation method used to …

Structural And Electrical Properties Of Silica Materials From Rice Husks, Casnan, Purnawan, Noor Erliza, Hardjomidjojo Hartrisari, Irzaman, Rohaeti Eti, Kurniawan Aditya

ASEAN Journal on Science and Technology for Development

This study aimed to analyze the structural and electrical properties of silica from rice husks recovered by the process of ashing on a medium-scale furnace with a capacity of 15 kg. Rice husks were burned at a heating rate of 1.5°C/min to a temperature of 900°C, where the temperature was retained for 1 hour each at 400°C and 900°C. The methodology of this research was conducted through the process of ashing, extraction of silica, and characterization of its structural electrical properties. The silica extracted from rice husk ash had a relatively low water content by the low absorption intensity of …

The Effect Of Raw Mesocarp Fibre Inclusion On The Durability Properties Of Lightweight Foamed Concrete, Othuman Mydin Md Azree

ASEAN Journal on Science and Technology for Development

Researchers around the globe have recognised the potential need for lightweight, reliable, easy to use, affordable, and even more sustainable building materials. One of the vanguard proposals has been the procurement, development and use of alternative, non-conventional local building materials, which includes the possibility of utilising lightweight foamed concrete (LFC). LFC is excellent under compression but poor in tensile stress, as it produces multiple microcracks. LFC cannot withstand the tensile stress induced by applied forces without additional reinforcing elements. This research was conducted to examine the potential utilisation of oil palm mesocarp fibre-reinforced (OPMF) LFC in terms of its durability. …

Down The Iron Path: Mitochondrial Iron Homeostasis And Beyond, Jonathan Dietz, Jennifer L. Fox, Oleh Khalimonchuk

Department of Biochemistry: Faculty Publications

Cellular iron homeostasis and mitochondrial iron homeostasis are interdependent. Mitochondria must import iron to form iron–sulfur clusters and heme, and to incorporate these cofactors along with iron ions into mitochondrial proteins that support essential functions, including cellular respiration. In turn, mitochondria supply the cell with heme and enable the biogenesis of cytosolic and nuclear proteins containing iron–sulfur clusters. Impairment in cellular or mitochondrial iron homeostasis is deleterious and can result in numerous human diseases. Due to its reactivity, iron is stored and trafficked through the body, intracellularly, and within mitochondria via carefully orchestrated processes. Here, we focus on describing the …

Insights Into Halophilic Microbial Adaptation: Analysis Of Integrons And Associated Genomic Structures And Characterization Of A Nitrilase In Hypersaline Environments, Sarah Sonbol

Theses and Dissertations

Hypersaline environments are extreme habitats that can be exploited as biotechnological resources. Here, we characterized a nitrilase (NitraS-ATII) isolated from Atlantis II Deep brine pool. It showed higher thermal stability and heavy metal tolerance compared to a closely related nitrilase.

We also studied integrons in halophiles and hypersaline environments. Integrons are genetic platforms in which an integron integrase (IntI) mediates the excision and integration of gene cassettes at specific recombination sites. In order to search for integrons in halophiles and hypersaline metagenomes, we used a PCR-based approach, in addition to different bioinformatics tools, mainly IntegronFinder.

We found that integrons and …

Pancreatic Cancer: Novel Therapy, Research Tools, And Educational Outreach, Ayrianne J. Crawford

Theses & Dissertations

Since the 1980’s, legislatures have invested immense effort into strategies to capitalize on the United States’ global lead in basic and translational research. This is largely motivated by the discrepancy the US faces in converting its world leading research discoveries and innovations into commercial products, relative to other countries. This truncated productivity leaves the US out of substantial GDP growth and reduces public access to new innovations. Proponents of government and university owned patents reason that enhanced public private partnerships narrow the gap between the technology transfer of basic research discoveries and accessible commercial products.

With these concepts of technology …

Can A Biotechnology Book Based On Science, Technology, Engineering, Art, And Mathematics-Local Wisdom Improve Students’ Biotechnology Literacy In The Coastal Area Of Jember-Indonesia?, Anjar Putro Utomo

International Programs

The importance of Biotechnology in any field specifically in agriculture encourages students to become literate about this content in their school particularly Indonesia since Indonesia still lacks laboratory activities and appropriate approach in order to teach this content. Therefore, this study aims Science, Technology, Engineering, Art, and Mathematics-Local Wisdom to develop a Biotechnology book based on (STEAM-LW) approach with R&D (research and development) method to tackle the problem. As a result, the book gained a very valid result with 94.79% as well as a significant response from students with average of 91.39%. Additionally, N-gain test revealed that there was a …

Unbiased Automated Quantitation Of Ros Signals In Live Retinal Neurons Of Drosophila Using Fiji/Imagej, Prajakta Deshpande, Neha Gogia, Anuradha Venkatakrishnan Chimata, Amit Singh

Biology Faculty Publications

Numerous imaging modules are utilized to study changes that occur during cellular processes. Besides qualitative (immunohistochemical) or semiquantitative (Western blot) approaches, direct quantitation method(s) for detecting and analyzing signal intensities for disease(s) biomarkers are lacking. Thus, there is a need to develop method(s) to quantitate specific signals and eliminate noise during live tissue imaging. An increase in reactive oxygen species (ROS) such as superoxide (O2•-) radicals results in oxidative damage of biomolecules, which leads to oxidative stress. This can be detected by dihydroethidium staining in live tissue(s), which does not rely on fixation and helps prevent stress on tissues. However, …

Hec-Hms Model For Urban Flood Analysis In Belik River, Yogyakarta, Indonesia, Suprayogi Slamet, Rifai, Latifah Reviana

ASEAN Journal on Science and Technology for Development

The rapid development of Yogyakarta has made city development increase. This construction continues to expand the reach of impervious surfaces. As a result, surface runoff and maximum discharge have increased, overflowing up to urban drainage. This study aimed to analyze the maximum discharge of the watershed based on design storms with 2, 5, 10, and 25-year return periods, used for flood control considerations. The urban flood was modelled using HEC-HMS. The results showed that the contribution of discharge flow in each segment is influenced by the dominance of land use, in which the segment dominated by dense settlements has a …

A Multi-Approach And Multi-Scale Platform To Model Cd4+ T Cells Responding To Infections, Kenneth Y. Wertheim, Bhanwar Lal Puniya, Alyssa La Fleur, Ab Rauf Shah, Matteo Barberis, Tomáš Helikar

Department of Biochemistry: Faculty Publications

Immune responses rely on a complex adaptive system in which the body and infections interact at multiple scales and in different compartments. We developed a modular model of CD4+ T cells, which uses four modeling approaches to integrate processes at three spatial scales in different tissues. In each cell, signal transduction and gene regulation are described by a logical model, metabolism by constraint-based models. Cell population dynamics are described by an agent-based model and systemic cytokine concentrations by ordinary differential equations. A Monte Carlo simulation algorithm allows information to flow efficiently between the four modules by separating the time scales. …

Characterization Of The Growth Factor Receptor Network Oncogenes In Lung Cancer, Ashley Duche

Pharmaceutical Sciences (MS) Theses

Lung cancer remains the leading cause of cancer related deaths worldwide, reportedly contributing to 1.8 million of the 10.0 million mortalities documented in the year 2020. Although advancements have been made in therapeutics and diagnostic methods, formulation of effective treatments and development of drug resistance continues to be a challenge. These challenges arise from our lack of understanding of intricate signaling pathways, such as the Growth Factor Receptor Network (GFRN), which contributes to complex lung tumor heterogeneity allowing for drug resistance development. In this study, gene expression signatures of six GFRN oncogenes overexpressed in human mammary epithelial cells (HMECs) were …

Marker-Assisted Selection To Determine The Introgression Of Rpv-3 Mediated Downy Mildew Resistance In 'Chambourcin' X 'Caberenet Sauvignon' Grapevine Population, Kavya Sri Tummala

Graduate Theses/Dissertations

Downy mildew caused by the fungus, Plasmopara viticola in the grapes is one of the major diseases affecting crop yield throughout the world. Breeding grapes via conventional methods for the downy mildew resistance will take approximately 25-30 years to fully evaluate and release new cultivars. Because of the long breeding cycle in woody plant species like grape, developing DNA markers linked to genes or quantitative trait loci (QTLs) for horticultural traits can greatly accelerate the breeding process and allow a much more accurate selection of progeny. This study aims to determine the presence of resistance in the 267 F1 genotypes …

Characterization Of The Bacterial Microbiome Of Exotic Tick Species Collected From Migratory Birds, Raima Sen

Master's Theses

Migratory birds often serve as natural/accidental hosts to ectoparasites like ticks (predominantly immature stages) and are known reservoirs of several pathogens transmitted by ticks. Parasitizing these birds, exotic tick species often hitch rides to non-native ecological niches, bringing along tick-borne pathogens. This study aims to profile the bacteriome of exotic tick species flying in and out of the US from the Neo-tropical South. A total of 421 tick samples comprised of several different tick species were collected off migratory songbirds at sites north of the Gulf of Mexico (Louisiana State). A 16S rRNA metagenomic multiplexed sequencing approach was used to …

Development Of High Value Oil Traits Using The Model Oilseed Crop Camelina Sativa, Evan Updike

Department of Biochemistry: Dissertations, Theses, and Student Research

Plant oils are an important source of food, fuel, and feed in our society today. The oil found in the seeds of plants is composed almost entirely of triacylglycerol (TAG) molecules, which consist of three fatty acids esterified to a glycerol backbone. As crude oil supplies decline, vegetable oils are gaining traction as a renewable substitute to petroleum-based materials in fuels, lubricants, and specialty oleochemicals. However, as it currently stands vegetable oils do not possess the properties necessary to fill the void of a petroleum free world.

To address this problem, plant biotechnologists have done extensive work on genetic engineering …

Investigation Into The Evolution Of Heterogeneity Within Secondary Replicons And Their Maintenance In Genus Variovorax, Christopher Ne Ville

Electronic Theses, Projects, and Dissertations

Approximately 10% of all bacterial genomes sequenced thus far contain a secondary replicon. This considerable genetic reservoir contains many potentially mobilizable elements, allowing for the formation of many unique secondary replicons. This property of bacterial populations vastly increases the genomic diversity available to species that effectively take up and maintain these replicons. Members of the genus Variovorax have extensive heterogeneity in genome architecture, including sequenced isolates containing plasmids, megaplasmids, and chromids. Using available Illumina data on the NCBI database, we have completed these assemblies using 3^rd generation sequencing methods on 17 members of this genus. We have sequenced, assembled, …

Mycoremediation And Fungi-Assisted Phytoremediation Of Heavy Metal Contaminated Landfills Soil, Auwalu Hassan

Student Works (2020-2029)

The research is aimed to study the bioremediation of heavy metal landfill leachate contaminated soil using consortia of indigenous filamentous fungi and indigenous plants. Thirteen identified fungal isolates were used to formulate the consortia for mycoremediation. The mycoremediation was carried out in three phases, namely laboratory trial 1 using five consortia, laboratory trial 2 with varied concentrations of inoculum, and field application. The fungi-assisted phytoremediation was carried out in two phases: laboratory trials using Alocasia calidora, Prosopis juliflora, and Jatropha sp. and field trial using A. calidora. The analyses conducted included soil physicochemical and biological parameters, Fourier-transform infrared spectroscopy (FTIR) …

Characterization Of Sabp2-Interacting Proteins (Sip) 428: An Nad+-Dependent Deacetylase Enzyme In Plant Abiotic Stress Signaling, Oviavo Nohoesu

Electronic Theses and Dissertations

Abiotic stress leads to a change in the water content of plants. Salinity and osmotic stress affect both the morphology and physiology of plants. Plants have therefore responded to these environmental changes by adapting and tolerating them. The SABP2-interacting proteins (SIP) 428-silenced RNAi transgenic tobacco lines were subjected to various abiotic stresses (salinity, osmotic, and drought). The effect of SIP428-silencing on the tobacco plants subjected to these abiotic stresses was monitored. The results from the root growth data show that the sip428-silenced lines exhibit enhanced tolerance to the stressors compared to the wild-type plants. Interestingly, results of the relative chlorophyll …

Euadb: A Resource For Covid-19 Test Development And Comparison, Alyssa Woronik, Henry W. Shaffer, Karin Kiontke, Jon M. Laurent, Ronald Zambrano, Mariah Daley, Jef D. Boeke, David H. Fitch

Biology Faculty Publications

Due to the sheer number of COVID-19 (coronavirus disease 2019) cases there is a need for increased world-wide SARS-CoV-2 testing capability that is both efficient and effective. Having open and easy access to detailed information about these tests, their sensitivity, the types of samples they use, etc. would be highly useful to ensure their reproducibility, to help clients compare and decide which tests would be best suited for their applications, and to avoid costs of reinventing similar or identical tests. Additionally, this resource would provide a means of comparing the many innovative diagnostic tools that are currently being developed in …

Common Spatial Pattern Detection Of Concept Semantic Relatedness Using Combined Event-Related Potentials And Frequency Spectrum Features, Michael Doyel

Graduate Theses - Biology & Biomedical Engineering

No abstract provided.

Overcoming Obstacles In Protein Expression In The Yeast Pichia Pastoris: Interviews Of Leaders In The Pichia Field, Zoe Ingram, Abha Patkar, Dahoon Oh, Kevin K. Zhang, Christina Chung, Joan Lin-Cereghino, Geoff P. Lin-Cereghino

Pacific Journal of Health

The yeast Pichia pastoris (also known as Komagataella pastoris) has been used for over 30 years to produce thousands of valuable, heterologous proteins, such as insulin to treat diabetes and antibodies to prevent migraine headaches. Despite its success, there are some common, stubborn problems encountered by research scientists when they try to use the yeast to produce their recombinant proteins. In order to provide those working in this field with strategies to overcome these common obstacles, nine experts in P. pastoris protein expression field were interviewed to create a written review and video (https://www.youtube.com/watch?v=FyC9xXVLyD0). This review describes …

Comparative Genomics Methods And Applications, Emily N. Alden

Biomedical Sciences ETDs

Virtually all fields of biology have benefited from the advancements in comparative genomics technologies, specifically in the study of evolution. In this dissertation I develop and use comparative genomic technologies to investigate the novel SARS-CoV-2 virus, assembly the first genome of the black lace domestic angelfish and identify germline genetic variants associated with altered breast cancer-specific survival. Our genome tiling array for the novel coronavirus presents a rapid and cost-effective method to sequence the entire viral genome and can be used to track the rapid evolution of viral variants in the population. The domestic angelfish is a member of the …