Biotechnology Commons^™

Mushrooom Production Without Solid Substrates, Alexander Baena, Marshall Porterfield

Graduate Industrial Research Symposium

Novel biotechnological approaches are needed to enhance renewable food production and waste recycling capabilities in resource-constrained environments. Edible mushrooms possess nutritious profiles and represent emerging opportunities to develop circular bioproduction by transforming waste organic materials into food and high-value products. However, traditional mushroom cultivation methods utilizing solid substrates have technical limitations like 1) uneven nutrient diffusion, 2) constant sterilization needs, 3) numerous intermediate steps that are energy and time-demanding, and 4) waste production from bags and jars. This work introduces an innovative hydroponic fungal cultivation system called Mycoponics™ using bioengineered ceramic materials. This liquid-nutrient-based technique optimizes fungal metabolism and facilitates …

A Machine Learning Model Of Perturb-Seq Data For Use In Space Flight Gene Expression Profile Analysis, Liam F. Johnson, James Casaletto, Lauren Sanders, Sylvain Costes

Graduate Industrial Research Symposium

The genetic perturbations caused by spaceflight on biological systems tend to have a system-wide effect which is often difficult to deconvolute it into individual signals with specific points of origin. Single cell multi-omic data can provide a profile of the perturbational effects, but does not necessarily indicate the initial point of interference within the network. The objective of this project is to take advantage of large scale and genome-wide perturbational datasets by using them to train a tuned machine learning model that is capable of predicting the effects of unseen perturbations in new data. Perturb-Seq datasets are large libraries of …

Antioxidant Properties Of Kombucha Beverage Infused With Ganoderma Lucidum And Green Tea From Camellia Sinensis (L.) Kuntze With Several Fermentation Times, Rizki Rabeca Elfirta, Pamungkas Rizki Ferdian, Iwan Saskiawan, Tri Hadi Handayani, Kayla Faza Gustafri Mandalika, Rini Riffiani, Kasirah Kasirah, Ukhradiya Magharaniq Safira Purwanto

Karbala International Journal of Modern Science

Kombucha is a functional beverage produced through the fermentation of infused tea or Camelia sinensis (L.) Kuntze (CS) by a symbiotic culture of bacteria and yeast. Apparently, the substrate of kombucha can be substituted to enhance its functional properties. Ganoderma lucidum (GL) is a potential substrate reported to have health benefits. This study aims to evaluate antioxidant properties by comparing different formulations and fermentation times. The formulations prepared in the present study varied in the compositions of GL and CS substrates, namely F1 (100% GL), F2 (75% GL: 25% CS), F3 (50% GL: 50% CS), F4 (25% GL: 75% CS), …

Integrative Genomic Insights Into Coral Resilience: Adaptive And Acclimatory Responses To Seasonal Environmental Shifts, Tasnim Ghanim

Theses and Dissertations

Coral reefs, critical to marine biodiversity and coastal protection, face escalating threats from climate change-related phenomena such as ocean warming. This warming is leading to widespread thermal stress that contributes to coral bleaching and infectious disease in corals, leading to the disruption of marine ecosystems and the economies that depend on them. Focusing on the brain coral Platygyra daedalea, known for its thermal resilience in the Persian Arabian Gulf—a region that exemplifies the extreme stressors of climate change—our study aims to dissect the genetic, transcriptomic, and microbiological underpinnings of coral survival in high-temperature environments predicted for the end of …

Vitamin E Biofortification: Enhancement Of Seed Tocopherol Concentrations By Altered Chlorophyll Metabolism, Ping Qin, Peng Chen, Yuanwei Zhou, Wei Zhang, Yunyun Zhang, Jingjing Xu, Lu Gan, Yingnan Liu, Jill Romer, Peter Dörmann, Edgar B. Cahoon, Chunyu Zhang

Department of Biochemistry: Faculty Publications

Homogentisate Phytyltransferase (HPT) catalyzes condensation of homogentisate (HGA) and phytyl diphosphate (PDP) to produce tocopherols, but can also synthesize tocotrienols using geranylgeranyl diphosphate (GGDP) in plants engineered for deregulated HGA synthesis. In contrast to prior tocotrienol biofortification efforts, engineering enhanced tocopherol concentrations in green oilseeds has proven more challenging due to the integral role of chlorophyll metabolism in supplying the PDP substrate. This study show that RNAi suppression of CHLSYN coupled with HPT overexpression increases tocopherol concentrations by >two-fold in Arabidopsis seeds. We obtained additional increases in seed tocopherol concentrations by engineering increased HGA production via overexpression of …

Panorama Of Human Embryo-Derived Cells In Biomedicine And Progress In Their Research And Regulation, Jianchao Gao, Yaojin Peng, Wei Wei, Shuang Lu, Chenyan Gao

Bulletin of Chinese Academy of Sciences (Chinese Version)

Since the establishment of the first human diploid cell line derived from aborted fetal tissue in the 1960s, human embryoderived cells have been widely used in biomedical field and significantly contributes to improving human health. In recent years, human pluripotent stem cells, including human embryonic stem cells (hESCs), have shown great therapeutic potential in regenerative medicine, and thus received great attention from governments and the public. However, due to various factors such as history, culture, religious beliefs, ethics and morality, research and application involving human embryo-derived cells have been controversial worldwide. This study explores the history and progress of human …

Investigating The Phytochemicals In Sargassum (Brown Algae) Against The Therapeutic Targets Of Oral Squamous Cell Carcinoma Metastasized From Breast: An Approach, Mahema S

Annual Research Symposium

ABSTRACT:

Purpose: Oral metastases are relatively rare. In women, the most common oral metastases originate from breast cancer, the most diagnosed malignancy, and the second leading cause of death. Sargassum is a genus of brown algae which exhibits its natural therapeutic potential with anticancer properties. This study aimed to identify a therapeutic target for OSCC metastasized from breast cancer through network pharmacology and to evaluate potent phytochemicals against the identified target.

Methods: DEGs associated with OSCC and breast cancer were obtained from the Gene Expression Omnibus. The upregulated DEGs were then intersected to identify common targets between OSCC and BC. …

Interplay Of Periodontal Bacterial Metabolites In The Progression Of Coronary Artery Disease: A System Biological Approach, Janakiraman V

Annual Research Symposium

Purpose:

The purpose of this study is to investigate the intricate relationship between periodontal disease (PD) and coronary artery disease (CAD), as evidenced by epidemiological associations. Metalloproteinase inhibitor (TIMP1) plays a pivotal role in cellular signaling, differentiation, cell death, and migration by binding to target metalloproteinases, forming complexes with other molecules (collagenases) to inactivate them. However, the expression of TIMP1 is reduced in both PD and CAD, leading to an upregulation of other metalloproteinases. This research explores the hypothesis that metabolites released from (Porphyromonas gingivalis), a prevalent bacterium in atherosclerotic patients, may inhibit TIMP1, thereby influencing CAD progression. …

Mechanistic And Engineering Studies Of Lov Photoreceptors In Yeast, Matthew M. Cleere

Dissertations, Theses, and Capstone Projects

A variety of cellular biosensors have evolved which can translate electromagnetic radiation from the environment into biological functions. Light-Oxygen-Voltage (LOV) domains in particular, are a group of photoreceptors that respond to blue wavelengths of light and can become a cellular photoswitch by converting this stimulus through their attached effector domains. For instance, the Helix-Turn-Helix (HTH) DNA-binding activity of the bacterial transcription factor EL222 and the Regulator of G-protein Signaling (RGS) in the fungal membrane associating protein BcLOV4 are both induced by blue-light sensing LOV domains. While previous work has provided the field with a structural characterization of LOV proteins in …

Us Public Opinion About The Safety Of Gene Editing In The Agriculture And Medical Fields And The Amount Of Evidence Needed To Improve Opinions, Brandon R. Mcfadden, Joy N. Rumble, Kathryn A. Stofer, Kevin M. Folta

Agricultural Economics and Agribusiness Faculty Publications and Presentations

Introduction: Implementation of gene editing in agriculture and medicine hinges on public acceptance. The objectives of this study were to explore U.S. public opinion about gene editing in agricultural and medical fields and to provide more insight into the relationship between opinions about the safety of gene editing and the potential impact of evidence to improve opinions about safety.

Methods: Data were from two samples of U.S. respondents: 1,442 respondents in 2021 and 3,125 respondents in 2022. Survey respondents provided their opinions about the safety of gene editing in the agricultural and medical fields and answered questions about the number …

Investigation Of Alzheimer’S Amyloid-Β Protein Aggregation With A New Fluorescent Dye., Emma Alberty

Undergraduate Research Symposium

Alzheimer’s Disease (AD) is the most common form of dementia characterized by the impairment of at least two brain functions such as memory loss and judgement. AD is a progressive illness that can last as many as 20 years. AD is largely considered to be caused by the formation of extracellular amyloid plaques and intracellular neurofibrillary tangles. A better understanding of the structure and function of these plaques may lead to clearer understanding of the disease. To analyze amyloid plaques, aggregation assays are often used. During these assays we begin with monomer and place the sample in biological conditions to …

Chromosome‑Level Assembly And Analysis Of Camelina Neglecta: A Novel Diploid Model For Camelina Biotechnology Research, Shuo Wang, Rostislav Y. Blume, Zhi‑Wei Zhou, Shaoping Lu, Tara J. Nazarenus, Yaroslav B. Blume, Weibo Xie, Edgar B. Cahoon, Ling‑Ling Chen, Liang Guo

Department of Biochemistry: Faculty Publications

Camelina neglecta is a new diploid Brassicaceae species, which has great research value because of its close relationship with the hexaploid oilseed crop Camelina sativa. Here, we report a chromosome-level assembly of C. neglecta with a total length of 210 Mb. By adopting PacBio sequencing and Hi-C technology, the C. neglecta genome was assembled into 6 chromosomes with scaffold N50 of 29.62 Mb. C. neglecta has undergone the whole-genome triplication (γ) shared among eudicots and two whole-genome duplications (α and β) shared by crucifers, but it has not undergone a specific whole-genome duplication event. By synteny analysis …

Metabolic Collaboration Between Cells In The Tumor Microenvironment Has A Negligible Effect On Tumor Growth, Johan Gustafsson, Fariba Roshanzamir, Anders Hagnestål, Sagar M. Patel, Oseeyi I. Daudu, Donald F. Becker, Jonathan L. Robinson, Jens Nielsen

Department of Biochemistry: Faculty Publications

The tumor microenvironment is composed of a complex mixture of different cell types interacting under conditions of nutrient deprivation, but the metabolism therein is not fully understood due to difficulties in measuring metabolic fluxes and exchange of metabolites between different cell types in vivo. Genome-scale metabolic modeling enables estimation of such exchange fluxes as well as an opportunity to gain insight into the metabolic behavior of individual cell types. Here, we estimated the availability of nutrients and oxygen within the tumor microenvironment using concentration measurements from blood together with a metabolite diffusion model. In addition, we developed an approach …

Emerging Roles Of Cullin-Ring Ubiquitin Ligases In Cardiac Development, Josue Zambrano-Carrasco, Jianqiu Zou, Wenjuan Wang, Xinghui Sun, Jie Li, Huabo Su

Department of Biochemistry: Faculty Publications

Heart development is a spatiotemporally regulated process that extends from the embryonic phase to postnatal stages. Disruption of this highly orchestrated process can lead to congenital heart disease or predispose the heart to cardiomyopathy or heart failure. Consequently, gaining an in-depth understanding of the molecular mechanisms governing cardiac development holds considerable promise for the development of innovative therapies for various cardiac ailments. While significant progress in uncovering novel transcriptional and epigenetic regulators of heart development has been made, the exploration of post-translational mechanisms that influence this process has lagged. Culling-RING E3 ubiquitin ligases (CRLs), the largest family of ubiquitin ligases, …

Augusta: From Rna-Seq To Gene Regulatory Networks And Boolean Models, Jana Musilova, Zdenek Vafek, Bhanwar Lal Puniya, Ralf Zimmer, Tomáš Helikar, Karel Sedlar

Department of Biochemistry: Faculty Publications

Computational models of gene regulations help to understand regulatory mechanisms and are extensively used in a wide range of areas, e.g., biotechnology or medicine, with significant benefits. Unfortunately, there are only a few computational gene regulatory models of whole genomes allowing static and dynamic analysis due to the lack of sophisticated tools for their reconstruction. Here, we describe Augusta, an open-source Python package for Gene Regulatory Network (GRN) and Boolean Network (BN) inference from the high-throughput gene expression data. Augusta can reconstruct genome-wide models suitable for static and dynamic analyses. Augusta uses a unique approach where the first estimation of …

Development And Evaluation Of A Mitochondrial Dna Marker For The Detection Of Rattus Rattus And Rattus Norvegicus Fecal Contamination, A'Aden Redhead

Graduate Research Showcase

No abstract provided.

The Antagonist Effect Of Pichia Kluyveri Against The Aflatoxigenic Aspergillus Flavus, Wafa Masoud

Journal of the Arab American University مجلة الجامعة العربية الامريكية للبحوث

Aspergillus flavus is one of the main fungi that are known to produce Aflatoxin B1 (AFB1). AFB1 has been detected in many food products and reported to be a carcinogenic. Using a biocontrol agent against A. flavus can safely eliminate or reduce the occurrence of AFB1 in food. Therefore, the effects of four yeast strains of Pichia kluyveri on the growth and spore germination of A. flavus were studied. In addition, the effect of exposure of A. flavus to the yeast’s headspace, as well as the effects of different headspace concentrations of 2-phenyl ethyl acetate and ethyl acetate, on the …

On-Site Estimation Of Total Sugars In Flavored Milk Using A Glucometer, Erwin Oliver V. Fundador, Karyn Thea E. Rivera, Kriza Faye A. Calumba, Noreen Grace V. Fundador

ASEAN Journal on Science and Technology for Development

Sugar has been linked to obesity and chronic diseases. Unfortunately some "healthy products," such as flavored milk, contain high sugar. In the Philippines, such an issue is made worse by local brands not putting nutritional labels on their products. Thus, a cheap, home-based method to measure total sugars should be beneficial. In this paper, we have shown that after incubation with invertase and lactase, a glucometer can be used to measure total sugars in flavored milk on-site. All experiments except the weighing of invertase and lactose were done in a home setting for actual proof of concept. The total sugar …

Molecular Identification To Verify The Existence Of Helicotylenchus Dihystera In Coffee Plants At East Java, Indonesia, Ankardiansyah Pandu Pradana, Toyoshi Yoshiga

ASEAN Journal on Science and Technology for Development

Spiral nematodes Helicotylenchus sp. are known to infect a variety of plants, including coffee. This is in line with the studies and surveys of nematodes in Indonesia. However, to date, there has been no study reporting the nematode with molecular analysis. In this study, we surveyed the nematodes in Arabica coffee plantations in Bondowoso regency – Indonesia. These spiral nematodes were collected in DESS solution for morphological, morphometric and molecular analysis. The morphometric analysis was carried out under an Olympus BH-2 compound microscope with an attached calibrated Toupcam M20 camera. The molecular analysis was performed on the total DNA from …

Species Distribution Modelling Using Bioclimatic Variables On Critically Endangered Endemic Species (Macrocephalon Maleo) In Sulawesi, Septianto Aldiansyah, Khalil Abdul Wahid

ASEAN Journal on Science and Technology for Development

The island of Sulawesi isolates migratory fauna from Asia and Australia and creates animal combinations such as the Maleo (Macrocephalon Maleo). The Maleo population is experiencing a downward trend due to habitat fragmentation, deforestation and threats by humans. This study aims to model the potential distribution of Maleo using several famous current and future models as a result of climate change throughout the island of Sulawesi, not only in its natural habitat, but beyond its natural habitat. Bioclimatic variables and in situ attendance data were used in this study. The method used is Maximum Entropy by evaluating the GLM, SVM …