Biotechnology Commons^™

Preclinical Assessment Of Psychoplastogens For Treatment Of Psychiatric Symptoms And Neuroplasticity Deficits In Huntington Disease, Nicholas Skiados

Electronic Theses and Dissertations, 2020-2023

Huntington disease (HD) is a neurodegenerative disorder caused by a CAG trinucleotide repeat expansion in the huntingtin (HTT) gene. HD manifests as a triad of psychiatric, cognitive, and motor symptoms, the latter of which defines symptomatic onset of the disease. Psychiatric symptoms including aggression and depression often emerge decades prior to motor symptom onset. Psychiatric disorders are closely linked with dysregulated neural plasticity, the ability of the brain to form new synaptic connections. Neural plasticity is impaired in HD, potentially playing a role in psychiatric symptoms. However, the association between plasticity and psychopathology in HD has yet to be thoroughly …

Genetic Control Of Photoprotection And Photosystem Ii Operating Efficiency In Plants, Seema Sahay, Marcin Grzybowski, James Schnable, Katarzyna Głowacka

Department of Biochemistry: Faculty Publications

• Photoprotection against excess light via nonphotochemical quenching (NPQ) is indispensable for plant survival. However, slow NPQ relaxation under low light conditions can decrease yield of field-grown crops up to 40%.

• Using semi-high-throughput assay, we quantified the kinetics of NPQ and photosystem II operating efficiency (ΦPSII) in a replicated field trial of more than 700 maize (Zea mays) genotypes across 2 yr. Parametrized kinetics data were used to conduct genome-wide association studies.

• For six candidate genes involved in NPQ and ΦPSII kinetics in maize the loss of function alleles of orthologous genes in Arabidopsis (Arabidopsis thaliana) …

Plastic Recognition And Electrogenic Uniport Translocation Of 1st-, 2nd-, And 3rd-Row Transition And Post-Transition Metals By Primary-Active Transmembrane P1b-2-Type Atpase Pumps, Sameera S. Abeyrathna, Nisansala S. Abeyrathna, Priyanka Basak, Gordon W. Irvine, Limei Zhang, Gabriele Meloni

Department of Biochemistry: Faculty Publications

Transmembrane P-type ATPase pumps catalyze the extrusion of transition metal ions across cellular lipid membranes to maintain essential cellular metal homeostasis and detoxify toxic metals. Zn()-pumps of the P-type subclass, in addition to Zn , select diverse metals (Pb, Cdand Hg) at their transmembrane binding site and feature promiscuous metal-dependent ATP hydrolysis in the presence of these metals. Yet, a comprehensive understanding of the transport of these metals, their relative translocation rates, and transport mechanism remain elusive. We developed a platform for the characterization of primary-active Zn()-pumps in proteoliposomes to study metal selectivity, translocation events and transport mechanism in real-time, …

Genome-Wide Investigation Of Snrk2 Gene Family In Two Jute Species: Corchorus Olitorius And Corchorus Capsularis, Borhan Ahmed, Fakhrul Hasan, Anika Tabassum, Rasel Ahmed, Rajnee Hassan, Ruhul Amin, Mobashwer Alam

Department of Biochemistry: Faculty Publications

Background Sucrose non-fermenting-1 (SNF1)-related protein kinase 2 (SnRK2), a plant-specifc serine/threonine kinase family, is associated with metabolic responses, including abscisic acid signaling under biotic and abiotic stresses. So far, no information on a genome-wide investigation and stress-mediated expression profling of jute SnRK2 is available. Recent whole-genome sequencing of two Corchorus species prompted to identify and characterize this SnRK2 gene family.

Result We identifed seven SnRK2 genes of each of Corchorus olitorius (Co) and C. capsularis (Cc) genomes, with similar physico-molecular properties and sub-group patterns of other models and related crops. In both species, the SnRK2 gene …

Structural Basis Of Dna Binding By The Whib-Like Transcription Factor Whib3 In Mycobacterium Tuberculosis, Tao Wan, Magdaléna Horová, Vimmy Khetrapal, Shanren Li, Camden Jones, Andrew Schacht, Xinghui Sun, Limei Zhang

Department of Biochemistry: Faculty Publications

Mycobacterium tuberculosis (Mtb) WhiB3 is an iron–sulfur cluster-containing transcription factor belonging to a subclass of the WhiB-Like (Wbl) family that is widely distributed in the phylum Actinobacteria. WhiB3 plays a crucial role in the survival and pathogenesis of Mtb. It binds to the conserved region 4 of the principal sigma factor (σ^A₄) in the RNA polymerase holoenzyme to regulate gene expression like other known Wbl proteins in Mtb. However, the structural basis of how WhiB3 coordinates with σ^A₄ to bind DNA and regulate transcription is unclear. Here we determined crystal structures …

Factors Influencing Instructors’ Adoption And Continued Use Of Computing Science Technologies: A Case Study In The Context Of Cell Collective, Changsoo Song, Resa M. Helikar, Wendy M. Smith, Tomáš Helikar

Department of Biochemistry: Faculty Publications

Acquiring computational modeling and simulation skills has become ever more critical for students in life sciences courses at the secondary and tertiary levels. Many modeling and simulation tools have been created to help instructors nurture those skills in their classrooms. Understanding the factors that may motivate instructors to use such tools is crucial to improve students’ learning, especially for having authentic modeling and simulation learning experiences. This study designed and tested a decomposed technology acceptance model in which the perceived usefulness and perceived ease of use constructs are split between the teaching and learning sides of the technology to examine …

Akkermansia Muciniphila And Its Membrane Protein Ameliorates Intestinal Inflammatory Stress And Promotes Epithelial Wound Healing Via Crebh And Mir‑143/145, Henry Wade, Kaichao Pan, Qihua Duan, Szczepan Kaluzny, Ekta Pandey, Linda Fatumoju, Viswanathan Saraswathi, Rongxue Wu, Edward N. Harris, Qiaozhu Su

Department of Biochemistry: Faculty Publications

Background The intestinal epithelial barrier is the interface for interaction between gut microbiota and host metabolic systems. Akkermansia muciniphila (A. muciniphila) is a key player in the colonic microbiota that resides in the mucus layer, whose abundance is selectively decreased in the faecal microbiota of inflammatory bowel disease (IBD) patients. This study aims to investigate the regulatory mechanism among A. muciniphila, a transcription factor cAMPresponsive element-binding protein H (CREBH), and microRNA-143/145 (miR-143/145) in intestinal inflammatory stress, gut barrier integrity and epithelial regeneration.

Methods A novel mouse model with increased colonization of A muciniphila in the intestine of CREBH knockout …

Advancements In Computational Modelling Of Biological Systems: Seventh Annual Sysmod Meeting, Bhanwar Lal Puniya, Andreas Dräger

Department of Biochemistry: Faculty Publications

The Computational Modelling of Systems Biology (SysMod) Community of Special Interest (COSI) convenes annually at the Intelligent Systems for Molecular Biology (ISMB) conference to facilitate knowledge dissemination and exchange of research findings on systems modelling from interdisciplinary domains. The SysMod meeting 2022 was held in a hybrid mode in Madison, Wisconsin, spanning a 1-day duration centred on modelling techniques, applications, and single-cell technology implementations. The meeting showcased innovative approaches to modelling biological systems using cell-specific and multiscale modelling, multiomics data integration, and novel tools to develop systems models using single-cell and multiomics technology. The meeting also recognized outstanding research by …

Fusarium Graminearum Effector Fgnls1 Targets Plant Nuclei To Induce Wheat Head Blight, Guixia Hao, Todd A. Naumann, Hui Chen, Guihua Bai, Susan Mccormick, Hye-Seon Kim, Bin Tian, Harold N. Trick, Michael J. Naldrett, Robert Proctor

Nebraska Center for Biotechnology: Faculty and Staff Publications

Fusarium head blight (FHB) caused by Fusarium graminearum is one of the most devastating diseases of wheat and barley worldwide. Effectors suppress host immunity and promote disease development. The genome of F. graminearum contains hundreds of effectors with unknown function. Therefore, investigations of the functions of these effectors will facilitate developing novel strategies to enhance wheat resistance to FHB. We characterized a F. graminearum effector, FgNls1, containing a signal peptide and multiple eukaryotic nuclear localization signals. A fusion protein of green fluorescent protein and FgNls1 accumulated in plant cell nucleiwhen transiently expressed in Nicotiana benthamiana. FgNls1 suppressed …

The Role Of Myocardin In The Progression Of Non-Small Cell Lung Cancer, Soromidayo Akinsiku

Biotechnology Theses

Lung cancer is the leading cause of cancer-related mortality in the world and NSCLC accounts for 85% of all lung cancer cases. The mainstay of treatment for patients with stage I, II and IIIA NSCLC is surgery, followed by post-operative cisplatin-based chemotherapy. Additional adjuvant therapy involving targeted tyrosine kinase inhibitors has been in use, however even for the targeted therapy, resistance eventually develops. Therefore, there is a need for identifying novel targets for this life-threatening disease. Given that preliminary studies in Ikebe lab revealed that myocardin knockdown significantly promoted caspase-3 degradation, in this study, using myocardin siRNA, we investigated the …

Biomechanics Of Mantis Prey Capture, Danielle S. Taylor

Honors Theses

Mantis species have a variety of different morphologies, so do the extreme forms of mantis limbs trade prey catching capability for camouflage? We hypothesize that some extreme forms of mantis limbs that are associated with cryptic species may be associated with a tradeoff of the capability of those limbs. Previous research has developed 2D morphologies of several hundred species of mantises. We are creating a 3D morphology by using micro dissection, micro CT imaging to construct our 3D biomechanical model. We found the attachment points of the ligaments and muscles from a Tenodera forearm and have constructed a 2D biomechanical …

Efficient Text Bounding Box Identification Using Mask R-Cnn: Case Of Thai Documents, Phanthakan Kiatphaisansophon

Chulalongkorn University Theses and Dissertations (Chula ETD)

Text detection is a fundamental task in computer vision, particularly for Optical Character Recognition (OCR) application. This research focuses on text detection part of the OCR. Our previous text detection model, CRAFT (Character-Region Awareness For Text detection) has shown promising outcomes in bounding box identification. Nevertheless, it encounters issues associated with post-processing and multiline text. The post-processing related to the necessity to reconfigure the model when new documents are introduced, resulting in inefficiencies and complexities. Also the CRAFT model tends to blend bounding boxes from consecutive lines, introducing errors and impacting the accuracy in the text recognition part of the …

Expression Of Predicted Salt Tolerant Gene In Rice Oryza Sativa L. And Characterization Of Osbtbz1 Gene, Triono Bagus Saputro

Chulalongkorn University Theses and Dissertations (Chula ETD)

Rice (Oryza sativa L.) holds significant importance as a primary food source globally. In Asia, the production of rice plays a crucial role in enhancing food security. Salinity poses a substantial constraint on plants like rice, leading to a reduction in their growth and overall productivity. The advancement of transcriptomics in agriculture has provided a powerful tool for understanding the molecular processes in crops, contributing to the development of more resilient, productive, and sustainable agricultural systems. The transcriptomic approach in rice using two rice lines with close genetic relationships, but different salt tolerance ability, CSSL16 and KDML105 combined with single …

On Evaluation Of The Indian Standard Topography Factor For Design Wind Speed On Escarpments, Abdul Haseeb Wani, Rajendra Kumar Varma, Ashok Kumar Ahuja

ASEAN Journal on Science and Technology for Development

Standards on wind loads of various countries give wind loading map of respective country in which basic wind speeds are mentioned. Design wind speeds for designing buildings and other structures are evaluated by the structural designers from these basic wind speed values by incorporating many factors. One of these factors taken into consideration is for the local topography effect such as escarpments and hills. Standards on wind loads including Indian Standard give certain recommendations for the same. However, the steps involved in evaluating relevant modification factor for local topography as given in Indian Standard on Wind Loads are many. An …

Liquid Waste Treatment For Sustainable Tapioca Industry: A Comparison Between Biogas And Liquid Sugar, Lilik Sulistyowati, Novi Andareswari, Rifqi Rahmat Hidayatullah, Nurul Amri Komarudin, Yuni Yolanda

ASEAN Journal on Science and Technology for Development

There have been many studies examining the processing of tapioca wastewater. However, most studies have only researched at a laboratory scale without considering whether the treatment is appropriate. The study's purpose is to compare the processing technology of biogas and liquid sugar using technical, environmental, social, and cost-benefit analysis criteria to determine the appropriate technology to be applied. Literature study, observation, and interviews were used to determine the characteristics of each criterion. Cost-benefit analysis is calculated using the R/C Ratio. Furthermore, priority determination is carried out using the Exponential Comparison Method (MPE) using assessments from environmental and industrial experts on …

Disintegration Evaluation Of Mudrock Fragment Through Wet-Dry Cycle By Quantitative Indices, Misbahudin Misbahudin, Dian Yesy Fatimah, Elfarino Trizani

ASEAN Journal on Science and Technology for Development

The disintegration of mudrock during moisture content change caused severe cases in several engineering works in Indonesia. One interesting site is Hambalang, Bogor Regency, West Java Province. The wetting and drying cycle is the easiest and fastest test to evaluate disintegration. After undergoing the process, samples of mudrocks disintegrate into smaller fragments. This paper evaluated the characteristics of the slaked material of mudrock by quantitative indices. The mudrock evaluated in this study underwent rapid disintegration in a short period, indicated by megascopic description and quantitative indices. In addition, evolutionary disintegration up to eight cycles has the same characteristics as the …

Analysis Of Biologically Effective Dose For Retroactive Yttrium-90 Trans-Arterial Radioembolization Treatment Optimization, Mj Lindsey

CMC Senior Theses

Trans-arterial radioembolization (TARE) is a protracted modality of radiation therapy where radionuclides labeled with Yttrium-90 (⁹⁰Y) are inserted inside a patient's hepatic artery to treat hepatocellular carcinoma (HCC). While TARE has been shown to be a clinically effective and safe treatment, there is little understanding of the radiobiological relationship between absorbed dose and tissue response, and thus there is no dosimetric standard for treatment planning. The Biologically Effective Dose (BED) formalism, derived from the Linear-Quadratic model of radiobiology, is used to weigh the absorbed dose by the time pattern of delivery. BED is a virtual dose that can …

Revolutionary Advances In The Treatment Of Genetic Disease, Emma Kaitlyn Carrigan

Honors Theses and Capstones

No abstract provided.

Role Of Histone Deacetylases In Regulation Of Macrophage Phagocytosis Of Mycobacterium Tuberculosis, Benjamin Esiesimua

Biotechnology Theses

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a global health emergency. Macrophages are critical in protection against TB by phagocytosis of Mtb. Although histone deacetylases (HDACs), are critical in macrophage differentiations, their roles in macrophage phagocytosis of Mtb remain unexplored. To explore this, I first established human monocyte derived macrophages (MDMs) phagocytosis of red zymosan beads. MDM phagocytosed zymosan beads at 37°C in a dose dependent manner in contrast to suppressed phagocytosis by the MDMs incubated with beads at 4°C or in the presence of cytochalasin D, actin polymerization inhibitor. Incubation of MDMs with 11 zinc-dependent HDAC inhibitors did …

Development Of Novel Detection Methods For Food Safety Using State-Of-The-Art Technology Platforms, Prae Noppakuadrittidej

Chulalongkorn University Theses and Dissertations (Chula ETD)

Foodborne illness is a significant global public health concern, impacting both the economy and human health. These illnesses are caused by bacteria, viruses, parasites, toxins, and chemicals. This research developed two technology platforms for Bacillus cereus and tropane alkaloid compounds detections. First, traditional detection methods for B. cereus have limitations in long analysis time, and dependence on analysis and interpretation by skilled personnel. Therefore, this study introduces a robust detection method using peptide nucleic acids (PNAs) bearing with a prolyl-2-aminocyclopentanecarboxylic acid (ACPC) backbone as probes in a bead array method. PNAs with groEL, motB, and 16S rRNA sequences were covalently …