Biotechnology Commons^™

Innovation In Bioinformatics: Recent Tools, Database And Involvement Of Artificial Intelligence, Aziz Ahmed, Mohd Shuaib, Abdulbasid Banga, Rizwan Ahmad

Indonesian Journal of Medical Chemistry and Bioinformatics

Bioinformatics has evolved in recent years into a crucial subject and a well-liked research area that is interconnected with many approaches and disciplines. The capacity of bioinformatics and its approaches to tackle challenging biological problems and promote research and development. There are various tools and database which are used in bioinformatics. AI is the capacity of a computational system to carry out various activities associated with intellectual beings and as a computer system's imitation of human intelligence processes. The bioinformatics applications with artificial intelligence have the capacity to annotate the data in the direction of logical conclusions. By combining AI …

Novel Role And Mechanisms Of Brd4 In Mediating Mesothelial To Mesenchymal Transition And Pleural Fibrosis, Felix Kankam

Biotechnology Theses

Pleural fibrosis is characterized by myofibroblast accumulation and increased expression of collagen and other extracellular matrices due to injury to the pleura and remodeling. Mesothelial to mesenchymal transition (MesoMT) is an important pathological event that contributes to the pool of myofibroblasts although its regulation remains incompletely understood. Recent research has reported the role of BRD4, a member of the bromodomain extra terminal domain (BET) family, in developing fibrosis in the heart and the lungs. One recent study showed that MEOX1 is a downstream target of BRD4 and mediated cardiac fibroblast activation. Our joint work also demonstrated that NOX4 is implicated …

Descspim: An Affordable And Easy-To-Build Light-Sheet Microscope Optimized For Tissue Clearing Techniques, Kohei Otomo, Takaki Omura, Yuki Nozawa, Steven J. Edwards, Yukihiko Sato, Yuri Saito, Shigehiro Yagishita, Hitoshi Uchida, Yuki Watakabe, Kiyotada Naitou, Rin Yanai, Naruhiko Sahara, Satoshi Takagi, Ryohei Katayama, Yusuke Iwata, Toshiro Shiokawa, Yoku Hayakawa, Kensuke Otsuka, Haruko Watanabe-Takano, Yuka Haneda, Shigetomo Fukuhara, Miku Fujiwara, Takenobu Nii, Chikara Meno, Naoki Takeshita, Kenta Yashiro, Juan Marcelo Rosales Rocabado, Masaru Kaku, Tatsuya Yamada, Yumiko Oishi, Hiroyuki Koike, Yinglan Cheng, Keisuke Sekine, Jun-Ichiro Koga, Kaori Sugiyama, Kenichi Kimura, Fuyuki Karube, Hyeree Kim, Ichiro Manabe, Tomomi Nemoto, Kazuki Tainaka, Akinobu Hamada, Hjalmar Brismar, Etsuo A. Susaki

Department of Biochemistry: Faculty Publications

Despite widespread adoption of tissue clearing techniques in recent years, poor access to suitable light-sheet fluorescence microscopes remains a major obstacle for biomedical end-users. Here, we present descSPIM (desktopequipped SPIM for cleared specimens), a low-cost ($20,000–50,000), lowexpertise (one-day installation by a non-expert), yet practical do-it-yourself light-sheet microscope as a solution for this bottleneck. Even the most fundamental configuration of descSPIM enables multi-color imaging of whole mouse brains and a cancer cell line-derived xenograft tumor mass for the visualization of neurocircuitry, assessment of drug distribution, and pathological examination by false-colored hematoxylin and eosin staining in a threedimensional manner. Academically open-sourced (https://github.com/dbsbjuntendo/ …

Multifaceted Roles Of Meg3 In Cellular Senescence And Atherosclerosis, Xiao Cheng, Mohamed Sham Shihabudeen Haider Ali, Vijaya Bhaskar Baki, Matthew Moran, Huabo Su, Xinghui Sun

Department of Biochemistry: Faculty Publications

Background and aims: Long noncoding RNAs are involved in the pathogenesis of atherosclerosis. As long non-coding RNAs maternally expressed gene 3 (Meg3) prevents cellular senescence of hepatic vascular endothelium and obesity-induced insulin resistance, we decided to examine its role in cellular senescence and atherosclerosis.

Methods and Results: By analyzing our data and human and mouse data from the Gene Expression Omnibus database, we found that Meg3 expression was reduced in humans and mice with cardiovascular disease, indicating its potential role in atherosclerosis. In Ldlr^−/− mice fed a Western diet for 12 weeks, Meg3 silencing by chemically modified …

Unveiling The Nexus Of Cellular Quality Control: Exploring The Interplay Between Ribosome-Associated Protein Quality Control And Mitochondrial Quality Control Pathways, Foozhan Tahmasebinia

Biological Sciences Theses and Dissertations

In eukaryotic cells, the intricate interplay between cellular quality control mechanisms is crucial for maintaining homeostasis and safeguarding the integrity of vital processes, spanning from macromolecule synthesis to the renewal of entire cellular organelles.

Disruption of these networks can lead to severe diseases such as metabolic disorders, underscoring the interconnected nature and feedback control mechanisms inherent in biological systems, including cellular quality control systems. This interconnectedness extends to the intricate communication between organelles, enabling coordinated functioning and adaptation to changing cellular conditions, particularly in response to stressors.

While the exact mechanisms governing these communications within cellular quality control systems remain …

Uncovering Novel Small Regulatory Rna In Protostome, Sweta Khanal

Dissertations

Small RNAs play pivotal roles in post-transcriptional gene regulation across diverse phylum of protostomes. In this study, we investigate the functional significance of atypical miRNAs, mirtron miR-1017 in Drosophila. Through ectopic expression in neuronal cells, we demonstrate that miR-1017 extends lifespan by targeting its host transcript, acetylcholine receptor Dα2, and influencing its splicing. This novel trans-regulatory function suggests a mechanism for mirtron evolution, highlighting the interplay between splicing and post-transcriptional regulation. Additionally, we profile small RNA populations in the polychaete developmental model Capitella teleta, shedding light on the small RNA landscape in annelid worms. Our analysis reveals a rich …

Utilizing Biomimicry To Design Sustainable Architecture, Virginia Hammond

Architecture Undergraduate Honors Theses

Nature has an integral relationship with architecture and serves as a sustainable role model and inspiration for designers. The process of biomimicry in architecture has the potential to produce more sustainable design solutions and foster a connection between humans and nature. Existing biomimetic design projects have varying strengths and weaknesses as examples of the process. Utilizing guidelines and references from key leaders in biomimetic design consultancy (Biomimicry 3.8), selected case studies are assessed for their ability to demonstrate the benefits of this design strategy. Using these evaluations, the case studies are diagrammed and critiqued to determine how new projects could …

Transcriptomic Profiling Of Engineered Human Gene Integration In The Mouse Genome Following In Vitro Gene Editing, Ethan Potts, Made Harumi Padmaswari, Christopher Nelson

Biomedical Engineering Undergraduate Honors Theses

Gene replacement is a promising method of therapy for genetic diseases. However, safety and efficacy are areas that need more research. This experiment aims to use RNA sequencing and bioinformatic techniques to provide answers to these questions and provide direction to future studies to develop a gene replacement therapeutic. C2C12 mouse myoblast cells were transfected with a vector containing a CRISPR-Cas9 system and the Human Factor IX (hF9) gene in order to hijack target genes and integrate the hF9 gene. The two target genes, myoglobin (Mb) and creatine kinase (Ckm), were chosen for their high rate of expression and low …

Qualitative Assessment Of Human Embryonic- And Induced Pluripotent Stem Cell Derived Neural Stem Cells Under Cgmp Methods, Michelle Hernandez

Electronic Theses, Projects, and Dissertations

Neural stem cell therapies represent a promising tool for the development of regenerative medicine and are being tested in clinical trials for several neurological disorders. However, the clinical applicability of stem cell therapies is dependent on the implementation of current good manufacturing practices (cGMPs) to ensure the quality, safety, and consistency that stem cell products need to meet FDA regulatory requirements. As such, there is a need for a shift to xeno-free methodologies so experimental conditions are cGMP compliant. The purpose of this study is to test a GMP compatible production method to generate multipotent neural stem cells (NSCs) from …

Determining The Impacts Of Corn Silage Mixing Ratios On Hydrogen Production From Beef Cattle Manure, Katya Faber-Quimby

Honors Program: Senior Projects (Public)

With global warming becoming an increasingly serious threat and a growing population requiring additional energy resources, interest in the production of clean energy from the agricultural sector has surged in popularity. Biohydrogen, also known as green hydrogen, is H₂ that has been produced using renewable energy, such as from agricultural byproducts or waste materials. It presents a promising alternative to nonrenewable resources due to its high potential for energy storage and lack of carbon emissions when used. Cattle manure has been explored as a resource for the production of biohydrogen. Selecting for hydrogen-producing microbes in the manure serves the …

Bootstrapping For Estimating The Conservative Kill Ratio Of The Surrogate To The Pathogen For Use In Thermal Process Validation At The Industrial Scale, Arshpreet Kaur Khattra, Surabhi Wason, Kevin Thompson, Andy Mauromostakos, Jeyamkondan Subbiah, Jennifer C. Acuff

Food Science Faculty Publications and Presentations

A surrogate is commonly used for process validations. The industry often uses the target log cycle reduction for the test (LCR_Test) microorganism (surrogate) to be equal to the desired log cycle reduction for the target (LCR_Target) microorganism (pathogen). When the surrogate is too conservative with far greater resistance than the pathogen, the food may be overprocessed with quality and cost consequences. In aseptic processing, the Institute for Thermal Processing Specialists recommends using relative resistance (D_Target)/(D_Test) to calculate LCR_Test (product of LCR_Target and relative resistance). This method uses the mean values …

Locally Injectable Peptide Hydrogel For Conversion Of Temozolomide And Codelivery Of Sirna In Glioblastoma Multiforme Treatment, Megan Pitz

All Dissertations

Traditional treatment methods for glioblastoma multiforme (GBM) are largely unsuccessful, with a 5-year survival rate of 5.6%. Temozolomide (TMZ), the only chemotherapy FDA-approved for GBM treatment, is a hydrophobic prodrug that is stable in an acidic pH and begins converting to its active form at a physiological pH of 7.4. However, complete conversion of TMZ is observed only at a higher pH, and only about 30% of administered TMZ reaches the central nervous system. Therefore, there is a need for new treatment methods that maximize TMZ delivery to and efficacy at the tumor site. Self-assembling peptides are a unique class …

Broadening The Application Range Of Cell-Free Protein Expression Systems, Matthew Becker

All Theses

Centralized protein manufacturing platforms make the delivery of needed therapies to places with limited infrastructure almost impossible. Cell-free protein expression systems, systems that utilize protein production machinery extracted from cells, offer these communities a viable protein expression platform that is robust and easily deliverable to the place of need. Much work in cell-free system engineering looks to increase the hardiness of cell-free system (CFS) components, like the extract and reaction buffer, needed to carry transcription and translation of gene therapeutic targets forward. Freeze- and air-drying of extract, reaction buffer, or both with certain additives, like sugar molecules, has been proposed …

Biosensor-Enhanced Organ-On-A-Chip Models For Investigating Glioblastoma Tumor Microenvironment Dynamics, Gayathree Thenuwara, Bilal Javed, Baljit Singh, Furong Tian

Articles

Glioblastoma, an aggressive primary brain tumor, poses a significant challenge owing to its dynamic and intricate tumor microenvironment. This review investigates the innovative integration of biosensor-enhanced organ-on-a-chip (OOC) models as a novel strategy for an in-depth exploration of glioblastoma tumor microenvironment dynamics. In recent years, the transformative approach of incorporating biosensors into OOC platforms has enabled real-time monitoring and analysis of cellular behaviors within a controlled microenvironment. Conventional in vitro and in vivo models exhibit inherent limitations in accurately replicating the complex nature of glioblastoma progression. This review addresses the existing research gap by pioneering the integration of biosensor-enhanced OOC …

Investigating Vital Neutrophil Extracellular Trap Pathogen Response In Neutropenic Individuals, Ryan Illig

Thinking Matters Symposium

Neutrophils, also called polymorphonuclear leukocytes (PMNs), constitute the majority of innate immune cells. These cells possess a complex arsenal of functions that allow them to detect and eliminate a broad spectrum of pathogens. Neutropenia is characterized by decreased levels of neutrophils in the bloodstream, typically falling below the normal range. Moderate to severe neutropenia can increase the risk of pathogenic infections and without treatment can be life-threatening. Although the concentration of neutrophils in neutropenic individuals is decreased, upon activation, neutrophils still release neutrophil extracellular traps (NETs). NETs are pivotal in combating a spectrum of pathogens through their non-selective nature. Overreactive …

Amplon: Amplifying Dna With Multiarm Priming And Looping Optimization Of Nucleic Acid, Mert Tunca Doganay, Ethan Roman, Andrea M. Hujer, Robert A. Bonomo, Mohamed S. Draz

Faculty Scholarship

Nucleic acid amplification, the bedrock of biotechnology and molecular diagnostics, surges in applications—especially isothermal approaches—heightening the demand for advanced and precisely engineered methods. Here, a novel approach for amplifying DNA with multiarm priming and looping optimization of nucleic acid (AMPLON) is presented. AMPLON relies on a novel polymeric material with unique set of multiarm polyethylene glycol–DNA primers for efficient DNA amplification under isothermal conditions. Each arm carries single-stranded DNA complementing the sense or antisense sequence of the target DNA. The amplification reaction begins with antisense arms binding to the target DNA, forming a template for sense-carrying arms to direct multiarm …

Annotation Of Hypothetical Genes In Lactococcus Lactis Ssp. Il403, Jennifer A. Tangires

Student Scholar Showcase

The human gastrointestinal tract (GIT) harnesses various microbial organisms involved in almost all processes of physiological homeostasis, among these are lactic acid bacteria (LAB). These bacteria, almost all of which belong to the order Lactobacillales, are able to produce lactic acid, and play an important role in food preservation because they produce bacteriocins. Bacteriocins are antimicrobial proteins that are used to fight off related bacteria in their environment that are competing for the same resources. This study focuses on a specific LAB strain, Lactococcus lactis ssp. IL1403 where 21.9% of its predicted genes have not yet been assigned a function. …

Increasing The Phytoremediation Efficiency Of Heavy Metal-Contaminated Soils In The Uae Using Endophytic Actinobacteria For Sustainable Agriculture, Archana Mathew Mathai

Thesis/ Dissertation Defenses

Pollution caused by heavy metals (HMs) is a major environmental concern worldwide. Human actions, agriculture practices and industrial activities can cause the release of HMs into the environment. Soil contamination with HMs may have negative effects on crops, thus disrupting the food chain and posing risks to human health. Lead (Pb) is a common pollutant found in soils when at high concentrations. Conventional land remediation techniques depending on chemical and mechanical methods are quite expensive and would lead to long-term deterioration of the ecosystems. Phytoremediation can serve as an alternative, eco-friendly approach to restore the lands for agricultural purposes. Hyperaccumulator …

The Effect Of Tryptone And Tomato Juice Addition On The Growth Performance Of Strawberry (Fragaria Ananassa) Explant Under In Vitro Condition, Zulfa Ulinnuha, Etik Wukir Tini, Noor Farid, Dhianing Shalatin

Jurnal Kultivasi

Strawberries are a fruit commodity that has high economic value. The obstacle in strawberry production is the lack of high-quality seed availability with disease-free properties. Tissue culture offers a promising solution to increase both the quantity and quality of strawberry seeds. This study aims to assess the effect of different concentrations of tomato juice and tryptone on the growth of strawberry explants under in vitro growing condition. The research was conducted at the Plant Breeding Laboratory, Faculty of Agriculture, Universitas Jenderal Soedirman, from December 2022 to May 2023. The study employed a Completely Randomized Design (CRD) with two factors. The …

In Vitro Multiplication Of Strawberry In Various Types And Concentrations Of Cytokinins And Auxins, Erni Suminar, Vira Rahmawati, Sumadi, Anne Nuraini

Jurnal Kultivasi

Growth regulator is one of the important factors in the success of plant propagation by tissue culture. 6-Benzylaminopurine (BAP) is one of the most widely used cytokinin because it is more stable, less expensive and more effective. Thidiazuron (TDZ) can increase the action of other cytokinins, either exogenous cytokinin or endogenous cytokinin. 1-Naphthaleneacetic acid (NAA) belongs to the more stable auxin group, because it is not easily decomposed and oxidized by enzymes released by plants. This study aimed to obtain the best types and concentrations of BAP, TDZ, and NAA for the in vitro multiplication of strawberry explant. The experiment …