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An In Silico Study Of The Cathepsin L Inhibitory Activity Of Bioactive Compounds In Stachytarpheta Jamaicensis As A Covid-19 Drug Therapy, Juliyatin Putri Utami, Nia Kurnianingsih, Mohammad Reza Faisal 2022 Department of Biomedicine, Faculty of Dentistry, Universitas Lambung Mangkurat, Banjarmasin, 70123 Indonesia

An In Silico Study Of The Cathepsin L Inhibitory Activity Of Bioactive Compounds In Stachytarpheta Jamaicensis As A Covid-19 Drug Therapy, Juliyatin Putri Utami, Nia Kurnianingsih, Mohammad Reza Faisal

Makara Journal of Science

Inhibition of cathepsin L (Cat L) can be considered a target for COVID-19 treatment. Starchytapheta jamaicensis is a plant from the Verbenaceae family that is commonly used for medicinal purposes. This study aims to analyze the inhibitory activities of compounds of Stachytarpheta jamaicensis toward Cat L by computational docking analysis. Ten compounds contained in the extracts (i.e., α-spinasterol, apigenin, luteolol-7-glucuronide, friedelin, hispidulin, chlorogenic acid, ipolamiide, geraniol, hentriacontane, and γ-aminobutyric acid) were selected as ligands; decanoyl-arg-val-lys-arg-chloromethylketone and oxocarbazate were used as the reference. Computational docking analysis was performed using Autodock Vina integrated into PyRx 8.0 and visualized using the Discovery Studio …


Meta-Analysis Of Transcriptomic Datasets For The Investigation Of Differential Expression In Hantavirus-Infected Human Tissue, John Krapohl 2022 Roseman University of Health Sciences

Meta-Analysis Of Transcriptomic Datasets For The Investigation Of Differential Expression In Hantavirus-Infected Human Tissue, John Krapohl

Annual Research Symposium

No abstract provided.


The Design, Construction, And Testing Of A Recombinant Dna Vaccine For Brucella Abortus And Brucella Melitensis, Stephanie Lynn Korle 2022 Louisiana State University and Agricultural and Mechanical College

The Design, Construction, And Testing Of A Recombinant Dna Vaccine For Brucella Abortus And Brucella Melitensis, Stephanie Lynn Korle

LSU Doctoral Dissertations

Brucella spp. are a bacterium that cause brucellosis, a zoonotic disease, which is commonly seen in cattle, sheep, goats, swine, and canines. Brucellosis is a problem worldwide, although it is eradicated in some countries (Garin-Bastuji et al. 1998). The reason for designing recombinant DNA (rDNA) vaccines opposed to utilizing the live-attenuated vaccines on the market is that they cannot be given to pregnant animals without potentially causing abortion, while an rDNA vaccine should be safe for pregnant animals since it does not contain viable bacteria. Also, there are no serological tests that can accurately distinguish between an animal vaccinated …


Deepreal: A Deep Learning Powered Multi-Scalemodeling Framework For Predicting Out-Of-Distributionligand-Induced Gpcr Activity, Tian Cai, Kyra Alyssa Abbu, Yang Liu, Lei Xie 2022 CUNY Graduate Center

Deepreal: A Deep Learning Powered Multi-Scalemodeling Framework For Predicting Out-Of-Distributionligand-Induced Gpcr Activity, Tian Cai, Kyra Alyssa Abbu, Yang Liu, Lei Xie

Publications and Research

Motivation Drug discovery has witnessed intensive exploration of predictive modeling of drug–target physical interactions over two decades. However, a critical knowledge gap needs to be filled for correlating drug–target interactions with clinical outcomes: predicting genome-wide receptor activities or function selectivity, especially agonist versus antagonist, induced by novel chemicals. Two major obstacles compound the difficulty on this task: known data of receptor activity is far too scarce to train a robust model in light of genome-scale applications, and real-world applications need to deploy a model on data from various shifted distributions.

Results To address these challenges, we have developed an end-to-end …


Cell-Free Dna Methylation Signatures In Cancer Detection And Classification, Jinyong Huang 2022 University of South Florida

Cell-Free Dna Methylation Signatures In Cancer Detection And Classification, Jinyong Huang

USF Tampa Graduate Theses and Dissertations

Early detection of cancer is believed as one of the best solutions to improve the therapeutic outcomes and overall survival of cancer patients. Analysis of circulating nucleic acids in bodily fluids, referred to as “liquid biopsies”, is rapidly gaining prominence for this purpose. Cell-free DNA (cfDNA) methylation has emerged as a promising biomarker for early cancer detection, tumor type classification, and treatment response monitoring. Currently, most cfDNA methylation profiling technologies are based on bisulfite conversion, while enrichment-based methods such as cfMeDIP-seq are beginning to show potential. To expand the use of enrichment-based methods in cfDNA methylation profiling, here, we report …


Characterization Of Streptomyces Nymphaeiformis Sp. Nov., And Its Taxonomic Relatedness To Other Polyhydroxybutyrate-Degrading Streptomycetes, Gary R. Hix, Muhammad S. Khan, Mikayla T. Miller, Elisha C. Napier, Allison L. O'Brien, Roger P. White, Stephen F. Baron Ph.D. 2022 Bridgewater College

Characterization Of Streptomyces Nymphaeiformis Sp. Nov., And Its Taxonomic Relatedness To Other Polyhydroxybutyrate-Degrading Streptomycetes, Gary R. Hix, Muhammad S. Khan, Mikayla T. Miller, Elisha C. Napier, Allison L. O'Brien, Roger P. White, Stephen F. Baron Ph.D.

Biology Faculty Scholarship

A polyhydroxybutyrate (PHB)-degrading actinomycete, strain SFB5AT, was identified as a species of Streptomyces based on its membrane fatty acid profile and the presence of LL-diaminopimelic acid in the cell wall. It formed sporulating mycelia on most agar media, but flat or wrinkled, moist colonies on trypticase soy agar. Spores were smooth, cylindrical, and borne on long, straight to flexuous chains. It produced a light brown diffusible pigment, but not melanin. Comparison of genomic digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values indicated that strain SFB5AT was related to Streptomyces litmocidini JCM 4394T , Streptomyces …


Ingredient Classification Using Food Ontology, Ricky Flores 2022 University of Nebraska at Omaha

Ingredient Classification Using Food Ontology, Ricky Flores

UNO Student Research and Creative Activity Fair

A food label provides some of the most crucial information for a food product. The food label is a key resource for many health-conscious consumers for understanding ingredients. It is also vital for individuals to avoid food allergens or help patients follow dietary recommendations. While the food labels in the United States are regulated by the Food and Drug Administration (FDA) many labels contain additional information or statements that are not regulated. Moreover, the food label may be complex or contain terminology that the layperson may not understand. Evidence has indicated that consumers often find nutrition labels confusing, especially when …


Eeg As Successful Diagnostic Tool For Immune Effector Cell Associated Neurotoxicity Syndrome, Daniel Jones, Christine Eckhardt, Haoqi Sun, Ryan Tesh, Brandon Westover 2022 Brigham Young University - Provo

Eeg As Successful Diagnostic Tool For Immune Effector Cell Associated Neurotoxicity Syndrome, Daniel Jones, Christine Eckhardt, Haoqi Sun, Ryan Tesh, Brandon Westover

Library/Life Sciences Undergraduate Poster Competition 2022

CAR T cell therapy was first proven effective in 20131 for the treatment of certain cancer s . However, its widespread adoption is still hindered by side effects like immune effector cell associated neurotoxicity syndrome (ICANS). Current research aims to better predict, diagnose, and treat ICANS so that CAR T cell therapy can be more widely applied. Although prior studies have attempted to identify an objective biomarker of ICANS2 , current practice relies on clinical assessment to diagnose ICANS. We hypothesize that qualitative features of the EEG may be utilized to develop a physiological grading system of the …


Survey Of Visual Opsin Evolution Across Caddisflies (Insecta: Trichoptera), Ashlynn Powell, Jacqueline Heckenhauer, Steffen Pauls, Paul Frandsen 2022 Brigham Young University

Survey Of Visual Opsin Evolution Across Caddisflies (Insecta: Trichoptera), Ashlynn Powell, Jacqueline Heckenhauer, Steffen Pauls, Paul Frandsen

Library/Life Sciences Undergraduate Poster Competition 2022

Caddisflies are a highly diverse order of aquatic insects. As eggs, larvae, and pupae, they occupy freshwater habitats, while as adults, they are generally aerial and terrestrial1. Such varied environments call for a flexible and complex visual system. Visual systems are controlled by light-sensing molecules called opsins, which are categorized by the wavelength of light they are most sensitive to2. In insects, these categories are:

  • Long wavelength (LW)
  • Short wavelength (SW)
  • Ultraviolet wavelength (UV)

Adaptive duplication of opsin genes is the primary mechanism of evolution that allows for greater visual capacity3. While opsins have …


Male And Female Victims Experience Different Types Of Sexual Assault, Carolyn Allen, Samuel Payne, Julie Valentine 2022 Brigham Young University - Provo

Male And Female Victims Experience Different Types Of Sexual Assault, Carolyn Allen, Samuel Payne, Julie Valentine

Library/Life Sciences Undergraduate Poster Competition 2022

Intro:

  • Sexual assault kits (SAKs) contain forensic evidence and are collected following an assault
  • Most research on SAK processing has been done with combined male and female assaults
  • 10% of victims are male
  • There is lots of research on female victims, but very little research on male victims


Does Bathing After Sexual Assault Or Time Elapsed Have A Greater Effect On The Development Of Codis Eligible Dna Profiles?, Emily Black, Sam Payne, Julie Valentine, Leslie Miles 2022 Brigham Young University - Provo

Does Bathing After Sexual Assault Or Time Elapsed Have A Greater Effect On The Development Of Codis Eligible Dna Profiles?, Emily Black, Sam Payne, Julie Valentine, Leslie Miles

Library/Life Sciences Undergraduate Poster Competition 2022

Which has a greater effect on the development of CODIS eligible DNA profiles from SAKs – bathing/showering status of the victim or time between the assault and examination?


Transposon- And Genome Dynamics In The Fungal Genus Neurospora: Insights From Nearly Gapless Genome Assemblies, Diem Nguyen, Valentina Peona, Per Unneberg, Alexander Suh, Patric Jern, Hanna Johannesson 2022 Uppsala University

Transposon- And Genome Dynamics In The Fungal Genus Neurospora: Insights From Nearly Gapless Genome Assemblies, Diem Nguyen, Valentina Peona, Per Unneberg, Alexander Suh, Patric Jern, Hanna Johannesson

Fungal Genetics Reports

A large portion of nuclear DNA is composed of transposable element (TE) sequences, whose transposition is controlled by diverse host defense strategies in order to maintain genomic integrity. One such strategy is the fungal-specific Repeat-Induced Point mutation (RIP) that hyper-mutates repetitive DNA sequences. While RIP is found across Fungi, it has been shown to vary in efficiency. The filamentous ascomycete Neurospora crassa has been a pioneer in the study of RIP, but data on TEs and RIP from other species in the genus is limited. In this study, we investigated 18 nearly gapless genome assemblies of ten Neurospora species, which …


Phylogenomic Discordance Suggests Polytomies Along The Backbone Of The Large Genus Solanum, Edeline Gagnon, Rebeccca Hilgenhof, Andrés Orejuela, Angela J. McDonnell, Gaurav Sablok, Xavier Aubriot, Leandro Giacomin, Yuri Gouvêa, Thamyris Bragionis, João Renato Stehmann, Lynn Bohs, Steven Dodsworth, Christopher T. Martine, Péter Poczai, Sandra Knapp, Tiina Särkinen 2022 Chicago Botanic Garden

Phylogenomic Discordance Suggests Polytomies Along The Backbone Of The Large Genus Solanum, Edeline Gagnon, Rebeccca Hilgenhof, Andrés Orejuela, Angela J. Mcdonnell, Gaurav Sablok, Xavier Aubriot, Leandro Giacomin, Yuri Gouvêa, Thamyris Bragionis, João Renato Stehmann, Lynn Bohs, Steven Dodsworth, Christopher T. Martine, Péter Poczai, Sandra Knapp, Tiina Särkinen

Faculty Journal Articles

Premise of the study

Evolutionary studies require solid phylogenetic frameworks, but increased volumes of phylogenomic data have revealed incongruent topologies among gene trees in many organisms both between and within genomes. Some of these incongruences indicate polytomies that may remain impossible to resolve. Here we investigate the degree of gene-tree discordance in Solanum, one of the largest flowering plant genera that includes the cultivated potato, tomato, and eggplant, as well as 24 minor crop plants.

Methods

A densely sampled species-level phylogeny of Solanum is built using unpublished and publicly available Sanger sequences comprising 60% of all accepted species (742 spp.) …


The Low Abundance Of Cpg In The Sars-Cov-2 Genome Is Not An Evolutionarily Signature Of Zap, Ali Afrasiabi, Hamid Alinejad-Rokny, Azad Khosh, Mostafa Rahnama, Nigel Lovell, Zhenming Xu, Diako Ebrahimi 2022 UNSW Sydney, Australia

The Low Abundance Of Cpg In The Sars-Cov-2 Genome Is Not An Evolutionarily Signature Of Zap, Ali Afrasiabi, Hamid Alinejad-Rokny, Azad Khosh, Mostafa Rahnama, Nigel Lovell, Zhenming Xu, Diako Ebrahimi

Plant Pathology Faculty Publications

The zinc finger antiviral protein (ZAP) is known to restrict viral replication by binding to the CpG rich regions of viral RNA, and subsequently inducing viral RNA degradation. This enzyme has recently been shown to be capable of restricting SARS-CoV-2. These data have led to the hypothesis that the low abundance of CpG in the SARS-CoV-2 genome is due to an evolutionary pressure exerted by the host ZAP. To investigate this hypothesis, we performed a detailed analysis of many coronavirus sequences and ZAP RNA binding preference data. Our analyses showed neither evidence for an evolutionary pressure acting specifically on CpG …


Long-Read Sequencing Of The Zebrafish Genome Reorganizes Genomic Architecture, Yelena Chernyavskaya, Xiaofei Zhang, Jinze Liu, Jessica S. Blackburn 2022 University of Kentucky

Long-Read Sequencing Of The Zebrafish Genome Reorganizes Genomic Architecture, Yelena Chernyavskaya, Xiaofei Zhang, Jinze Liu, Jessica S. Blackburn

Molecular and Cellular Biochemistry Faculty Publications

BACKGROUND: Nanopore sequencing technology has revolutionized the field of genome biology with its ability to generate extra-long reads that can resolve regions of the genome that were previously inaccessible to short-read sequencing platforms. Over 50% of the zebrafish genome consists of difficult to map, highly repetitive, low complexity elements that pose inherent problems for short-read sequencers and assemblers.

RESULTS: We used long-read nanopore sequencing to generate a de novo assembly of the zebrafish genome and compared our assembly to the current reference genome, GRCz11. The new assembly identified 1697 novel insertions and deletions over one kilobase in length and placed …


The Online Ordering Behaviors Among Participants In The Oklahoma Women, Infants, And Children Program: A Cross-Sectional Analysis, Qi Zhang, Kayoung Park, Junzhou Zhang, Chuanyi Tang 2022 Old Dominion University

The Online Ordering Behaviors Among Participants In The Oklahoma Women, Infants, And Children Program: A Cross-Sectional Analysis, Qi Zhang, Kayoung Park, Junzhou Zhang, Chuanyi Tang

Department of Marketing Faculty Scholarship and Creative Works

The Special Supplemental Nutrition Program for Women, Infants, and Children (WIC) is a nutrition assistance program in the United States (U.S.). Participants in the program redeem their prescribed food benefits in WIC-authorized grocery stores. Online ordering is an innovative method being pilot-tested in some stores to facilitate WIC participants’ food benefit redemption, which has become especially important in the COVID-19 pandemic. The present research aimed to examine the online ordering (OO) behaviors among 726 WIC households who adopted WIC OO in a grocery chain, XYZ (anonymous) store, in Oklahoma (OK). These households represented approximately 5% of WIC households who redeemed …


Orfanid: A Web-Based Search Engine For The Discovery And Identification Of Orphan And Taxonomically Restricted Genes, Richard S. Gunasekera, Komal K.B. Raja, Suresh Hewapathirana, Thushara Galbadage, Emanuel Tundrea, Vinodh Gunasekera, Paul A. Nelson 2022 Biola University

Orfanid: A Web-Based Search Engine For The Discovery And Identification Of Orphan And Taxonomically Restricted Genes, Richard S. Gunasekera, Komal K.B. Raja, Suresh Hewapathirana, Thushara Galbadage, Emanuel Tundrea, Vinodh Gunasekera, Paul A. Nelson

Faculty Articles & Research

With the multiplicity of genomes sequenced today, it has been shown that significant percentages of genes in any given taxon do not possess orthologous sequences in other taxa. These sequences are typically designated as orphans/ORFans when found as singletons in one species only or taxonomically restricted genes (TRGs) when found at higher taxonomic ranks. Quantitative and collective studies of these genes are necessary for understanding their biological origins. Currently, orphan gene identifying software is limited, and those previously available are either not functional, are limited in their database search range, or are very complex algorithmically. Thus, an interested researcher studying …


Classification Of Breast Cancer Nottingham Prognostic Index Using High-Dimensional Embedding And Convolutional Neural Networks, Li Zhou 2022 University of Windsor

Classification Of Breast Cancer Nottingham Prognostic Index Using High-Dimensional Embedding And Convolutional Neural Networks, Li Zhou

Electronic Theses and Dissertations

This work builds a prediction model for multi-omics breast cancer Nottingham Prognostics Index (NPI) classes. Rapid development in next-generation sequencing led to the ability to measure different biological indicators called multi-omics data. The availability of multi-omics data sparked the challenge of integrating and analyzing these various biological measures to understand the progression of the diseases. High-dimensional embedding techniques are used to present the features in the lower dimension, that is a 2-dimensional map. This thesis presents a supervised learning method used to predict breast cancer NPI. The objectives of this research are (i) build a diagnosis system for breast cancer …


An In Silico Approach To Investigate The Structural And Biochemical Basis Of The Rna Binding Functions Of Nucleolin, Avdar San 2022 The Graduate Center, City University of New York

An In Silico Approach To Investigate The Structural And Biochemical Basis Of The Rna Binding Functions Of Nucleolin, Avdar San

Dissertations, Theses, and Capstone Projects

Nucleolin (NCL) is a stress responsive multifunctional nucleolar protein and accounts for 10% of the total nucleolar protein content. NCL belongs to the class of RNA binding proteins (RBPs) that regulate many important cellular processes through their interactions with different RNA molecules. The dysregulation of RBPs and the RNA metabolism pathways they intersect is a known driver of tumorigenesis. NCL regulates ribosome biogenesis, chromatin remodeling, microRNA processing, and gene expression on multiple levels. The RNA-protein interactions of NCL are primarily driven by its four RNA binding domains (RBDs). NCL is known to interact with a growing list of primary-miRNA (pri-miRNA) …


A Predictive Model For Geographical Location Using Microbiome Composition And Covid-19 Based Analysis, Ahmed Adel Aboushanab 2022 American University in Cairo

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 …


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