Biotechnology Commons^™

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

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 …

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

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 …

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

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 …

Role Of Simulation In Open Varicose Veins Surgery: A Systematic Review, Muhammad Ammar Pirzada, Fareed Ahmed Shaikh, Shoaib Badini, Nadeem Ahmed Siddiqui

Department of Surgery

Objective: To assess the types and effectiveness of simulators present for open varicose vein surgery.
Methods: The systematic review was conducted at The Aga Khan University Hospital Karachi and comprised studies published from 1st January 2000 to 30th June 2020 related to open varicose vein surgical procedures done on simulators. Databases searched were PubMed, Medline, Google Scholar, Cochrane and Scopus using appropriate key words. The primary outcome of the review was to assess the effectiveness of different types of simulators used for varicose vein surgery.
Results: Of the 286 articles found, 6(2%) were included. A variety of simulators ranging from …

Innovations In Surgery Between The Past And Future: A Narrative Review Of Targeted Literature, Obada Hasan, Ahmed Ayaz, Laiba Masood, Abdul Mannan Baig, Naveed Baloch

Medical College Documents

Innovation is the introduction of a new method or technology designed to change the way things are done. History is full of remarkable innovations in surgery over the years as surgeons have always been innovating and pioneering latest techniques and equipment that can benefit the mankind. Though persistent, progress has been far from uniform. Despite all the bells and whistles that these innovations bring to the table, the little acknowledged fact is that they are only accessible to a very small proportion of the global population. Five billion people on this planet do not even have access to an operating …

Two Heads Are Better Than One: Current Landscape Of Integrating Qsp And Machine Learning, Tongli Zhang, Ioannis P. Androulakis, Peter Bonate, Limei Cheng, Tomáš Helikar, Jaimit Parikh, Christopher Rackauckas, Kalyanasundaram Subramanian, Carolyn R. Cho

Biochemistry -- Faculty Publications

Quantitative systems pharmacology (QSP) modeling is applied to address essential questions in drug development, such as the mechanism of action of a therapeutic agent and the progression of disease. Meanwhile, machine learning (ML) approaches also contribute to answering these questions via the analysis of multi-layer ‘omics’ data such as gene expression, proteomics, metabolomics, and high-throughput imaging. Furthermore, ML approaches can also be applied to aspects of QSP modeling. Both approaches are powerful tools and there is considerable interest in integrating QSP modeling and ML. So far, a few successful implementations have been carried out from which we have learned about …

Selective Gsk3Β Inhibition Mediates An Nrf2-Independent Anti-Inflammatory Microglial Response, Mohamed H. Yousef

Theses and Dissertations

Glycogen Synthase Kinase 3 (GSK3) is associated with the proinflammatory phenotype of microglia and has been shown to act in concert with Nuclear factor kappa B (NF-κB). . GSK3 is also a suppressor of Nuclear factor erythroid 2-related factor 2 (Nrf2), the principal regulator of redox homeostasis. Agreeing with the oxidative paradigm of aging, Nrf2 is often deregulated in parainflammatory and neurodegenerative diseases. In this study, we aimed to explore a multimodal disease-modifying utility of GSK3 inhibition, beyond neuronal proteopathologies, Furthermore, we aimed to underscore the difference in therapeutic value between the two GSK3 paralogs by isoform-selective chemical inhibition.

The …

A Predictive Model For Geographical Location Using Microbiome Composition And Covid-19 Based Analysis, Ahmed Adel Aboushanab

Theses and Dissertations

The human microbiome is a main contributor for the health and welfare of the human body. It is affected by many factors like diet and hygiene. These factors differ between different populations. Testing the population-microbiome differences using healthy samples from different countries is the first objective of this study. This data was then used in training and testing machine learning models (Random Forest and L2-logistic Regression Classifiers) for the prediction of the geographical location based on the microbiome data. Random Forest Classifier had the highest accuracy. Feature importance analysis showed that the data for Proteobacteria, Actinobacteria, and Bacteroidetes improved the …

Investigation Of A Carbon Monoxide Dehydrogenase From An Uncultured Archaeon, Luke Moore

Dissertations, Master's Theses and Master's Reports

The Nickel based Carbon Monoxide Dehydrogenase (CODH) is an anaerobic metalloenzyme responsible for the reversible conversion of CO and water into CO2 and 2 protons and 2 electrons. This enzyme has importance in the environment as one of Earth’s first carbon fixation pathways, and for human uses as a potential source of biofuels and other commodity chemicals. CODH enzymes are present in a wide array of taxa, many of which are uncultured. In this study we express and purify the catalytic subunit (CooS) of the anaerobic CODH from an uncultured Hydrothermarchaeota JdFR-17 co-expressed with the nickel insertion accessory protein (CooC) …

Cpf1-Based Crispr Genome Editing In The Cyanobacterium N. Punctiforme, Soohan Woo

University of the Pacific Theses and Dissertations

CRISPR systems have been growing in their utility and their application throughout the biological field as researchers continue to grow in their understanding of the relatively novel genome editing technology. However, despite the potential of CRISPR as a genome editing tool, the complexity of applying this technology to a specific organism calls for custom modifications to the system to improve its success rate. In this project, a CRISPR-Cpf1 system that can be effectively employed in the cyanobacterium Nostoc punctiforme was designed, with a focus on the hormogonium development of this species. Multiple plasmids containing the CRISPR system and targeting different …

Characterizing Isoform Switching Events In Esophageal Adenocarcinoma, Yun Zhang, Katherine M. Weh, Connor L. Howard, Jean-Jack Riethoven, Jennifer L. Clarke, Kiran H. Lagisetty, Jules Lin, Rishindra M. Reddy, Andrew C. Chang, David G. Beer, Laura A. Kresty

Papers from the Nebraska Center for Biotechnology

Isoform switching events with predicted functional consequences are common in many cancers, but characterization of switching events in esophageal adenocarcinoma (EAC) is lacking. Next-generation sequencing was used to detect levels of RNA transcripts and identify specific isoforms in treatment- naïve esophageal tissues ranging from premalignant Barrett’s esophagus (BE), BE with low- or high-grade dysplasia (BE.LGD, BE.HGD), and EAC. Samples were stratified by histopathology and TP53 mutation status, identifying significant isoform switching events with predicted functional consequences. Comparing BE.LGD with BE.HGD, a histopathology linked to cancer progression, isoform switching events were identified in 75 genes including KRAS, RNF128, and WRAP53. Stratification …

Genome Structure And Evolutionary History Of Frankincense Producing Boswellia Sacra, Abdul Latif Khan, Ahmed Al-Harrasi, Jin-Peng Wang, Sajjad Asaf, Jean-Jack Riethoven, Tariq Shehzad, Chia-Sin Liew, Xiao-Ming Song, Daniel P. Schachtman, Chao Liu, Ji-Gao Yu, Zhi-Kang Zhang, Fan-Bo Meng, Jia-Qing Yuan, Chen-Dan Wei, He Guo, Xuewen Wang, Ahmed Al-Rawahi, In-Jung Lee, Jeffrey L. Bennetzen, Xi-Yin Wang

Papers from the Nebraska Center for Biotechnology

Boswellia sacra Flueck (family Burseraceae) tree is wounded to produce frankincense. We report its de novo assembled genome (667.8 Mb) comprising 18,564 high-confidence protein-encoding genes. Comparing conserved single-copy genes across eudicots suggest >97% gene space assembly of B. sacra genome. Evolutionary history shows B. sacra gene-duplications derived from recent paralogous events and retained from ancient hexaploidy shared with other eudicots. The genome indicated a major expansion of Gypsy retroelements in last 2 million years. The B. sacra genetic diversity showed four clades intermixed with a primary genotype—dominating most resin-productive trees. Further, the stemtranscriptome revealed that wounding concurrently activates phytohormones signaling, …

Spatially Controlled Monolayers For Electrically Switchable Biomolecule Detection, Eduard Lukhmanov

Theses, Dissertations and Capstones

The development of biosensors that are low-waste, highly stable, and possess an ability to be interchanged between capturing and non-capturing configurations is promising for the biodetector field. Stable packing and attachment of the sensor, the ability to create an interchangeable detecting probe of interest relatively easily, and dynamic control of the probe via a reversible bias can provide for that. With the set goals to control all those properties, DNA-dendron conjugate molecules were designed, synthesized in solution, purified, and utilized to make self-assembled monolayers of single-stranded DNA on gold. To be able to manipulate the conjugates’ sensing qualities in the …

3d Bioprinted Structures From Cells Of Non-Epithelial Mesodermal And Endodermal Lineage Using A Custom Accessible 3d Bioprinting Platform, Xavier-Lewis Palmer, Annette Berkin, Patrick C. Sachs, Robert D. Bruno

College of Engineering & Technology (Batten) Posters

Prior work within our lab has demonstrated the ability to print both murine and human mammary organoids and tumoroids in vitro that can also be reliably transplanted into a murine host for translational studies. Peripherally, this bioprinting system has also been used for 3D printing neurons, stem cells, cancer cells, and a primary cell line rich with fibroblasts, but each of these efforts were with cells of ectodermal lineage. Thus, the system's capacity for use on cells of other origins had been untested. To address this, we have now developed protocols for cells of endodermal and non-epithelial mesodermal/mesenchymal lineage. In …

Monitoring And Modelling The Dynamics Of The Cellular Glycolysis Pathway: A Review And Future Perspectives, Nitin Patil, Hugh Byrne, Orla L. Howe, Paul A. Cahill

Articles

Background

The dynamics of the cellular glycolysis pathway underpin cellular function and dysfunction, and therefore ultimately health, disease, diagnostic and therapeutic strategies. Evolving our understanding of this fundamental process and its dynamics remains critical.

Scope of review

This paper reviews the medical relevance of glycolytic pathway in depth and explores the current state of the art for monitoring and modelling the dynamics of the process. The future perspectives of label free, vibrational microspectroscopic techniques to overcome the limitations of the current approaches are considered.

Major conclusions

Vibrational microspectroscopic techniques can potentially operate in the niche area of limitations of other …

Advancing Competency In Managing Risk And Knowledge: Steps Toward Operationalisation Of The Risk-Knowledge Infinity Cycle (Rki Cycle) - Part 1: Improving Effectiveness Of Risk-Based Decision Making (Rbdm), Martin Lipa, Paige Kane, Anne Green

Articles

To date, literature on the Risk-Knowledge Infinity Cycle (RKI Cycle) has mainly been theoretical. This paper series intent is to focus on the operationalisation of the RKI Cycle by describing a series of steps – the “How to” – for RKI Cycle deployment, to help move the RKI Cycle from theory to practice. The first paper in this series focuses on how the RKI Cycle can support effective Risk-Based Decision Making (RBDM).

Rna Interference For Emerald Ash Borer Suppression: Ecotoxicological Assessment And Delivery Methods, Flavia Pampolini

Theses and Dissertations--Entomology

The emerald ash borer (EAB), Agrilus planipennis (Coleoptera: Buprestidae), is a highly invasive phloem-feeding insect native to Asia. It has killed millions of ash trees (Fraxinus spp.) since its accidental introduction into North America, causing profound economic and ecological impacts. RNA interference (RNAi) or double-stranded RNA (dsRNA)-mediated gene silencing is an emerging biotechnology that is developing as an innovative tool for pest management. Exogenous dsRNA triggers the RNAi pathway, silences genes, and disrupts protein function, causing insect mortality. RNAi has proven effective in reducing target gene expression and causing mortality in EAB; however, two aspects stand as barriers …

Functionalization Of Chitosan Based Microparticles For In Vitro 3d Culture Of Human Liver Cells, William Imes

Williams Honors College, Honors Research Projects

Previous work involving 3D culture of human liver cells with fluorinated chitosan based microparticles has shown that their incorporation provides needed structural cues that the culture of cells alone does not provide, such as increased gas transport. However, using bare microparticles to grow large 3D cellular structures is not practical as they tend to collapse before any meaningful research can be done on them. It is proposed that this is because of the lack of extracellular matrix (ECM)components within pure cell culture in vitro, which in their absence cannot adequately facilitate biochemical communication and adhesion between cells. It is …