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Cell-Based Experimental Evidence To The Anti-Covid-19 Potential Of Ashwagandha And Honeybee Propolis Ingredients, Renu Wadhwa, Durai Sundar, Yoshiyuki Ishida, Keiji Terao, Sunil C. Kaul 2023 National Institute of Advanced Industrial Science & Technology (AIST)

Cell-Based Experimental Evidence To The Anti-Covid-19 Potential Of Ashwagandha And Honeybee Propolis Ingredients, Renu Wadhwa, Durai Sundar, Yoshiyuki Ishida, Keiji Terao, Sunil C. Kaul

Research Symposium

Background: The COVID-19 pandemic emerged in December 2019 by a novel strain of SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) has led to new endeavours in repurposing of existing drugs, anti-COVID-19 vaccine and drug development. Natural products, due to their general safety and wider availability, have attracted research and public attention. In this study, we report anti-COVID potential of compounds from honeybee propolis and Ayurvedic herb, Ashwagandha. Effect of active ingredients was studied on human cell surface receptors (ACE-2:Angiotensin Converting Enzyme-2/Spike protein and TMPRSS2:Transmembrane Protease Serine 2), critical for virus infection and virus main protease (Mpro, essential for virus replication), …


Pro-Apoptosis Activity Of Pogostemon Cablin Benth. Against Nasopharyngeal Carcinoma Through The Bcl-2 Inhibition Signaling Pathway: A Computational Investigation, Aigia Syahraini, Essy Harnelly, Feri Eko Hermanto 2023 Department of Biology, Faculty of Mathematics and Sciences, Universitas Syiah Kuala, Banda Aceh 23111, Indonesia

Pro-Apoptosis Activity Of Pogostemon Cablin Benth. Against Nasopharyngeal Carcinoma Through The Bcl-2 Inhibition Signaling Pathway: A Computational Investigation, Aigia Syahraini, Essy Harnelly, Feri Eko Hermanto

Makara Journal of Science

Resistance to chemotherapy and radiotherapy frequently emerges in the later stage of nasopharyngeal carcinoma (NPC) tumorigenesis. The decreased response of NPC to radiotherapy and chemotherapy occurs owing to the inhibition of cancer cell apoptosis by the B-cell lymphoma-2 (BCL-2) protein. Thus, inhibiting BCL-2 protein may become a powerful approach to eliminate NPC through apoptosis regulation. Meanwhile, Pogostemon cablin is reported to exhibit anticancer properties, but there are limited studies on its use for NPC treatment. The objective of this study is to investigate the potential bioactive compounds in P. cablin as anti-apoptosis BCL-2 protein inhibitors using in-silico approach. Natural compounds …


The Use Of Prognostic Markers To Predict Disease Progression And Clinical Outcome In Monoclonal Gammopathy Of Undetermined Significance, Smouldering Multiple Myeloma And Multiple Myeloma., Róisín C. McMonagle 2023 Cork Institute of Technology

The Use Of Prognostic Markers To Predict Disease Progression And Clinical Outcome In Monoclonal Gammopathy Of Undetermined Significance, Smouldering Multiple Myeloma And Multiple Myeloma., Róisín C. Mcmonagle

International Undergraduate Journal of Health Sciences

Multiple Myeloma (MM) is an incurable plasma cell malignancy with a complex and incompletely understood molecular pathogenesis. Monoclonal Gammopathy of Undetermined Significance (MGUS) and Smouldering Multiple Myeloma (SMM) precede MM, with variable risks and rates of disease progression. The continuing high relapse and death rate in MM cases has prompted research into more accurate prognostic markers to predict progression from MGUS and SMM to MM, as well as identify MM cases with aggressive disease, in order to begin early, targeted and effective therapeutic intervention. Many studies have focused on utilising current markers more effectively, including M-protein, serum-free light chain ratio, …


Drug Repurposing Using Gene Expression Data Mining, Yue Qiu 2023 The Graduate Center, City University of New York

Drug Repurposing Using Gene Expression Data Mining, Yue Qiu

Dissertations, Theses, and Capstone Projects

The conventional drug discovery process that employs the "one disease, one target, one drug'' paradigm is expensive, time-consuming, and has a high rate of failure for multi-genic complex diseases. An alternative approach to drug discovery is to repurpose an existing drug that has been used to treat some medical conditions. Drug repurposing is considered a promising method due to its accelerated the process of drug discovery and lower overall cost and risk.

Drug-perturbed gene expression profiles are powerful phenotype readouts of biological systems, and they have been widely used in drug repurposing studies. However, the existing drug-perturbed gene expression datasets …


State-Of-The-Art Approaches For Sequencing, Assembling And Annotating Naphthenic Acid Degrading Bacterial Metagenomes, Henry H. Say 2023 Western University

State-Of-The-Art Approaches For Sequencing, Assembling And Annotating Naphthenic Acid Degrading Bacterial Metagenomes, Henry H. Say

Electronic Thesis and Dissertation Repository

Naphthenic acids (NAs) are the main toxic component of oil refinery wastewater and require special processes to be removed. Harnessing bacterial biodegradation for NA removal has the potential to be effective, yet NA-degrading bacteria and pathways are poorly understood and uncharacterized. To improve our understanding of NA degradation, I characterize the metagenomes of novel NA-degrading bacterial communities seeded in NA-enriched granulated activated carbon (GAC) filters. I demonstrate methods that maximize the throughput of extraction, sequencing, and annotation of novel metagenomes - producing 72 MAGs and other 5432 circular contigs - 226 of which were putative phages. I also include state-of-the-art …


Generative Ai-Assisted Pathway Analysis And Interpretation Of Rna-Seq Experiment Data, Junguk Hur 2023 University of North Dakota

Generative Ai-Assisted Pathway Analysis And Interpretation Of Rna-Seq Experiment Data, Junguk Hur

AI Assignment Library

No abstract provided.


Predicting Marine Teleost Responses To Ocean Warming And Pollution, Akila Harishchandra 2023 University of Maine

Predicting Marine Teleost Responses To Ocean Warming And Pollution, Akila Harishchandra

Electronic Theses and Dissertations

Ocean warming and pollution are two detrimental anthropogenic factors causing rapid marine ecosystem degradation recorded in the past decades. These factors alter the marine environment intolerable for many marine species, forcing them to either adapt or shift their contemporary habitat ranges to reduce the extinction risk embedded with environmental degradation. Estimating marine species’ habitat range shifts, and their potential for developing adaptive mechanisms are critical for ecosystem conservation and management, human health risk assessment, and climate change vulnerability assessments. Given that, for the first chapter of this thesis, we focused on developing a species distribution model (SDM) integrating marine species …


Evolution Of Overlapping Reading Frames In Virus Genomes, Laura Muñoz Baena 2023 Western University

Evolution Of Overlapping Reading Frames In Virus Genomes, Laura Muñoz Baena

Electronic Thesis and Dissertation Repository

Viruses are formidable pathogens that represent the majority of biological entities in our planet, and their genomes are a source of interesting enigmas. One feature in which virus genomes are usually rich, is the presence of overlapping reading frames (OvRFs) — portions of the genome where the same nucleotide sequence encodes more than one protein. OvRFs are hypothesized to be used by viruses to encode proteins more compactly and to regulate transcription. In addition, OvRFs might be a source of gene novelty, facilitating the creation of new open reading frames (ORF) within the transcriptional context of existing ones.

To characterize …


Mutation-Induced Changes In The Stability, B-Cell Epitope, And Antigenicity Of The Sars-Cov-2 Variant Spike Protein: A Comparative Computational Stud, Nira Meirita Wijayanti, Muhammad Hermawan Widyananda, Lailil Muflikhah, Nashi Widodo 2023 Biology Department, Faculty of mathematics and Natural Sciences, Brawijaya University, Malang, Indonesia

Mutation-Induced Changes In The Stability, B-Cell Epitope, And Antigenicity Of The Sars-Cov-2 Variant Spike Protein: A Comparative Computational Stud, Nira Meirita Wijayanti, Muhammad Hermawan Widyananda, Lailil Muflikhah, Nashi Widodo

Karbala International Journal of Modern Science

The spike (S) protein is a major antigenicity site that targets neutralizing antibodies and drugs. The growing number of S protein mutations has become a severe problem for developing effective vaccines. Here, we investigated four severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants that were the most infectious and widespread during the COVID-19 pandemic to determine the trends and patterns of mutation-induced changes in the stability, B-cell epitope, and antigenicity of the SARS-CoV-2 S protein. The data showed that the Beta and Gamma variants had three mutations on the receptor-binding domain (RBD), which is the specific site on the S …


Genome-Scale Methylation Analysis In Blood And Tumor Identifies Immune Profile, Age Acceleration, And Dna Methylation Alterations Associated With Bladder Cancer Outcomes, Ji-Qing Chen 2023 Dartmouth College

Genome-Scale Methylation Analysis In Blood And Tumor Identifies Immune Profile, Age Acceleration, And Dna Methylation Alterations Associated With Bladder Cancer Outcomes, Ji-Qing Chen

Dartmouth College Ph.D Dissertations

Bladder cancer patients receive frequent screening due to the high tumor recurrence rate (more than 60%). Nowadays, the conventional monitoring method relies on cystoscopy which is highly invasive and increases patient morbidity and burden to the health care system with frequent follow-up. As a result, it is urgent to explore novel markers related to the outcomes of bladder cancer. Immune profiles have been associated with cancer outcomes and may have the potential to be biomarkers for outcomes management. However, little work has been conducted to investigate the associations of immune cell profiles with bladder cancer outcomes. Here, I utilized the …


Examining The Different Soil Horizons Of White Oak Mountain, Tn And Their Effect On The Soil Microbial Community, Ji Won Moon, Timothy D. Trott 2023 Southern Adventist University

Examining The Different Soil Horizons Of White Oak Mountain, Tn And Their Effect On The Soil Microbial Community, Ji Won Moon, Timothy D. Trott

Research in Biology

Soil microorganisms participate in the diverse interaction within virtually all ecosystems, consequently affecting the associated human and animal population. Identifying how edaphic variables alter the functional and taxonomic diversity of the soil microbial community requires an examination of total microbial soil diversity and abundance. This research study examined the effect of soil depth and horizon on the soil microbial community composition of White Oak Mountain. The soil microbial community was characterized by 16S/18S/ITS rDNA amplicon sequencing of the DNA extract of six samples from the three major soil types identified: HcE, MoE, and uMvC. OTU clustering analysis and both alpha …


The Impact Of Soil Disturbance On Soil Bacterial Community Composition, Marie A. Rodriguez, MarK Peach, Timothy D. Trott 2023 Southern Adventist University

The Impact Of Soil Disturbance On Soil Bacterial Community Composition, Marie A. Rodriguez, Mark Peach, Timothy D. Trott

Research in Biology

Soil bacterial communities are an important part of terrestrial ecosystems due to their roles in biogeochemical cycling processes. Consequently, understanding how soil disturbance affects the soil bacterial diversity is vital to understanding the entire ecosystem. In this study we examined the effects of soil disturbance (by mining) on the soil bacterial community composition from three sites on Bauxite Ridge in Southeast Tennessee compared to three undisturbed sites in a nearby location. The soil bacterial community was analyzed by 16S rDNA amplicon sequencing of total DNA extracted from the soil samples collected from each of the six sites. Characterization of the …


Visual Complexity Of The Time-Frequency Image Pinpoints The Epileptogenic Zone: An Unsupervised Deep-Learning Tool To Analyze Interictal Intracranial Eeg, Sarvagya Gupta 2023 University of Massachusetts Boston

Visual Complexity Of The Time-Frequency Image Pinpoints The Epileptogenic Zone: An Unsupervised Deep-Learning Tool To Analyze Interictal Intracranial Eeg, Sarvagya Gupta

Graduate Masters Theses

Epilepsy, a prevalent neurological disorder characterized by recurrent seizures, continues to pose significant challenges in diagnosis and treatment, particularly among children. Despite substantial advancements in medical technology and treatment modalities, localization of the part of brain that causes seizures (Epileptogenic Zone) remains a difficult task. Intracranial EEG (iEEG) is often used to estimate the epileptogenic zone (EZ) in children with drugresistant epilepsy (DRE) and target it during surgery. Conventionally, iEEG signals are inspected in the time domain by human experts aiming to locate epileptiform activity.

Visual scrutiny of the iEEG time-frequency (TF) images can be an alternative way to review …


Growth Of Purple Sulfur Bacteria Allochromatium Vinosum On Solid Phase Metal Sulfides As Sulfur And Electron Sources, Hugo Alarcon 2023 University of Texas at El Paso

Growth Of Purple Sulfur Bacteria Allochromatium Vinosum On Solid Phase Metal Sulfides As Sulfur And Electron Sources, Hugo Alarcon

Open Access Theses & Dissertations

Purple sulfur bacteria (PSB) are photosynthetic microorganisms known for their vital roles in geochemical cycles, especially the sulfur cycle, within anoxic photic environments. PSB are also key contributors to the nitrogen, carbon, and oxygen cycles. This study focuses on the autotrophic growth of Allochromatium vinosum, a model strain of PSB, that utilize solid-phase metal sulfides (MS) as both sulfur and electron donors. Through characterizing the growth profiles of A. vinosum on pyrite (FeS2), nickel sulfide (NiS), and iron monosulfide (FeS) nanoparticles, respectively, and investigating the bacteria-MS interaction mechanisms, this work expands our current knowledge of the metabolic capabilities and flexibility …


Novel Insights Into Oligodendrocyte Biology From Developmental Myelination Studies In Autophagy Deficient Mice And Analysis Of Oligodendrocyte Translatome Response To Contusive Spinal Cord Injury., Michael David Forston 2023 University of Louisville

Novel Insights Into Oligodendrocyte Biology From Developmental Myelination Studies In Autophagy Deficient Mice And Analysis Of Oligodendrocyte Translatome Response To Contusive Spinal Cord Injury., Michael David Forston

Electronic Theses and Dissertations

Loss of myelin causes severe neurological disorders and functional deficits in white matter injuries (WMI) such as traumatic spinal cord injury (SCI). This dissertation is focused on autophagy in OL development and the OL translatome after SCI. Chapter I describes the history of myelin, OL development, and their involvement in neurodegenerative diseases and SCI. The proteostasis network, in particular autophagy, and its contributions to white matter pathology is discussed. It concludes examining advantages and disadvantages of unbiased omics tools, like RiboTag, to study transcriptional/translational landscapes after SCI. Chapter II focuses on autophagy in OPC/OL differentiation, survival, and proper myelination in …


Merging Clinical And Genomic Data In Patients With Acute Leukemia For Downstream Analysis, Amanda Bataycan 2023 University of Texas at El Paso

Merging Clinical And Genomic Data In Patients With Acute Leukemia For Downstream Analysis, Amanda Bataycan

Open Access Theses & Dissertations

The purpose of this study is to integrate multiple sources of information from patients with acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL) to construct organized datasets that would enable downstream bioinformatics and statistical analyses of the patientsâ?? survival status and overall survival times in relation to their demographic, clinical, and genomic mutation profiles. With NIH Genomic Data Commons as the primary data resource and cBioPortal as the access portal, datasets on 149 and 603 unique patients with AML and ALL, respectively, were obtained. Python scripts were written to compile individual patientsâ?? single nucleotide variant (SNV) data files into …


Modeling The Egyptian Goose (Alopochen Aegyptiaca) Invasion; And Future Concerns, Percival Matzinger Marshall 2023 University of Arkansas-Fayetteville

Modeling The Egyptian Goose (Alopochen Aegyptiaca) Invasion; And Future Concerns, Percival Matzinger Marshall

Graduate Theses and Dissertations

In an increasingly interconnected world, the ecological and financial cost of invasive species is expected to continue to climb through the movement of exotic biota. Understanding the driving forces behind how a species invades, what environments promote their establishment, and what impacts they are likely to have on the invaded environment are all critical for management. Waterfowl, order Anseriformes, are one such category of invasive species of concern due to their popularity of accidental introduction, ease of movement, and propensity to affect both terrestrial and aquatic ecosystems. The Egyptian Goose (Alopochen aegyptiaca) is a native to the African continent that …


Computational Analysis Of Antibody Binding Mechanisms To The Omicron Rbd Of Sars-Cov-2 Spike Protein: Identification Of Epitopes And Hotspots For Developing Effective Therapeutic Strategies, Mohammed Alshahrani 2023 Chapman University

Computational Analysis Of Antibody Binding Mechanisms To The Omicron Rbd Of Sars-Cov-2 Spike Protein: Identification Of Epitopes And Hotspots For Developing Effective Therapeutic Strategies, Mohammed Alshahrani

Computational and Data Sciences (PhD) Dissertations

The advent of the Omicron strain of SARS-CoV-2 has elicited apprehension regarding its potential influence on the effectiveness of current vaccines and antibody treatments. The present investigation involved the implementation of mutational scanning analyses to examine the impact of Omicron mutations on the binding affinity of four categories of antibodies that target the Omicron receptor binding domain (RBD) of the Spike protein. The study demonstrates that the Omicron variant harbors 23 unique mutations across the RBD regions I, II, III, and IV. Of these mutations, seven are shared between RBD regions I and II, while three are shared among RBD …


Effects Of Physical Characteristics Of Placebos On Exercise Performance, Owen Sipes 2023 Old Dominion University

Effects Of Physical Characteristics Of Placebos On Exercise Performance, Owen Sipes

Human Movement Sciences Theses & Dissertations

Previous research has shown that placebos can impact medical conditions such as irritable bowel syndrome and depression as well as elicit analgesic effects and improvements in certain exercise performances. These placebo responses occur from a variety of alterations to the placebo itself or through verbal suggestion of how helpful the placebo will be. This study aimed to observe whether changing the color and quantity of capsules can induce improvements in both vertical jump and hand grip strength. This deceptive, parallel study consisted of 28 participants, with a mean age of 24.9 (±4.3) years old, that were randomly assigned to receive …


Annotation Of Non-Model Species’ Genomes, Taiya Jarva 2023 The University of Southern Mississippi

Annotation Of Non-Model Species’ Genomes, Taiya Jarva

Master's Theses

The innovations in high throughput sequencing technologies in recent decades has allowed unprecedented examination and characterization of the genetic make-up of both model and non-model species, which has led to a surge in the use of genomics in fields which were previously considered unfeasible. These advances have greatly expanded the realm of possibilities in the fields of ecology and conservation. It is now possible to the identification of large cohorts of genetic markers, including single nucleotide polymorphisms (SNPs) and larger structural variants, as well as signatures of selection and local adaptation. Markers can be used to identify species, define population …


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