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Regulation Of Protein Synthesis In Arabidopsis Thaliana Through A Bioinformatic And Mathematical Lens, Ricardo Andres Urquidi Camacho 2023 University of Tennessee, Knoxville

Regulation Of Protein Synthesis In Arabidopsis Thaliana Through A Bioinformatic And Mathematical Lens, Ricardo Andres Urquidi Camacho

Doctoral Dissertations

Organisms exist under constantly varying environmental and internal conditions, which necessitate the differential regulation of gene expression. To synthesize proteins, the ribosome translates the information encoded in the nucleotide sequence of an mRNA into the final, functional amino acid sequence. Knockouts of ribosomal proteins lead to lethality. One such protein is the ribosomal protein 6 of the small subunit (eS6/RPS6). We confirmed that the knockout of either one of two eS6 paralogs in Arabidopsis leads to stunted growth and chlorosis. Here, these phenotypes have been further characterized in seedlings by precisely quantifying the ribosome loading of mRNAs as well as …


Multi-Omics Reveals Largely Distinct Transcript- And Protein-Level Responses To The Environment In An Intertidal Mussel, Lani U. Gleason, Florian J. Fekete, Richelle L. Tanner, W. Wesley Dowd 2023 California State University, Sacramento

Multi-Omics Reveals Largely Distinct Transcript- And Protein-Level Responses To The Environment In An Intertidal Mussel, Lani U. Gleason, Florian J. Fekete, Richelle L. Tanner, W. Wesley Dowd

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Organismal responses to stressful environments are influenced by numerous transcript- and protein-level mechanisms, and the relationships between expression changes at these levels are not always straightforward. Here, we used paired transcriptomic and proteomic datasets from two previous studies from gill of the California mussel, Mytilus californianus, to explore how simultaneous transcript and protein abundance patterns may diverge under different environmental scenarios. Field-acclimatized mussels were sampled from two disparate intertidal sites; individuals from one site were subjected to three further treatments (common garden, low-intertidal or high-intertidal outplant) that vary in temperature and feeding time. Assessing 1519 genes shared between …


Multiple Light Signaling Pathways Control Solar Tracking In Sunflowers, Christopher J. Brooks, Hagop S. Atamian, Stacey L. Harmer 2023 University of California, Davis

Multiple Light Signaling Pathways Control Solar Tracking In Sunflowers, Christopher J. Brooks, Hagop S. Atamian, Stacey L. Harmer

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Sunflowers are famous for their ability to track the sun throughout the day and then reorient at night to face east the following morning. This occurs by differential growth patterns, with the east sides of stems growing more during the day and the west sides of stems growing more at night. This process, termed heliotropism, is generally believed to be a specialized form of phototropism; however, the underlying mechanism is unknown. To better understand heliotropism, we compared gene expression patterns in plants undergoing phototropism in a controlled environment and in plants initiating and maintaining heliotropic growth in the field. We …


Molecular Mimicry Of Noda Genes By An N-Acetylmuramoyl-L-Alanine Amidases Gene In A Nodule Forming Staphylococcus Cohnii [Research Note], Aberathne Herath Mudiyanselage Nadeeshani Ruwandika Aberathne, Wedage Methsala Madurangi Wedage, Dilantha Gunawardana 2023 Department of Botany, University of Sri Jayewardenepura, Sri Lanka

Molecular Mimicry Of Noda Genes By An N-Acetylmuramoyl-L-Alanine Amidases Gene In A Nodule Forming Staphylococcus Cohnii [Research Note], Aberathne Herath Mudiyanselage Nadeeshani Ruwandika Aberathne, Wedage Methsala Madurangi Wedage, Dilantha Gunawardana

The Philippine Agricultural Scientist

A rare, nodule-forming, Gram-positive bacterium (Sub4) was isolated from the forage and cover crop Pueraria phaseoloides, which aligned at 99.26% sequence identity to a partial 16S rDNA sequence of Staphylococcus cohnii sp. This was the first record of a strain/species of Staphylococcus capable of independent, unassisted nodule formation in a legume host. When a nodA gene was sought by PCR using a pair of gene-specific primers synthesized using a related (Firmicutes) Paenibacillus sp. nodA gene, the reaction yielded a PCR product of similar size but a distinct identity. The resulting ~400bp PCR product coded for a likely N-acetylmuramoyl-L-alanine amidase …


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 …


The Pros Of Changing Trna Identity, Michael Ibba 2023 Chapman University

The Pros Of Changing Trna Identity, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The notion that errors in protein synthesis are universally harmful to the cell has been questioned by findings that suggest such mistakes may sometimes be beneficial. However, how often these beneficial mistakes arise from programmed changes in gene expression as opposed to reduced accuracy of the translation machinery is still unclear. A new study published in JBC shows that some bacteria have beneficially evolved the ability to mistranslate specific parts of the genetic code, a trait that allows improved antibiotic resistance.


Diversity And Dispersal Among Eastern Continental Divide Headwater Stream Fishes In Gwinnett County, Georgia., James E. Russell, Molly M. Botting, Ryan M. Davenport, Emilee J. Story, Mark Patterson 2023 Georgia Gwinnett College

Diversity And Dispersal Among Eastern Continental Divide Headwater Stream Fishes In Gwinnett County, Georgia., James E. Russell, Molly M. Botting, Ryan M. Davenport, Emilee J. Story, Mark Patterson

Georgia Journal of Science

The eastern continental divide that bisects Georgia runs through Gwinnett County, separating headwater streams of the western Chattahoochee River watershed from headwater streams of the eastern Ocmulgee and Oconee River watersheds. This landscape feature was used to test hypotheses regarding headwater habitat, fish diversity and gene flow. Headwater habitats are dominant components of river network ecosystems delivering vital ecosystem services and biodiversity. Three headwater streams, one in the Chattahoochee watershed and two in the Oconee watershed, on Gwinnett County Park property, were sampled for differences in physical and chemical properties and fish inter- and intraspecific diversity. Our results suggest the …


Assessment Of The First Presentations Of Common Variable Immunodeficiency In A Large Cohort Of Patients, Hossein Esmaeilzadeh, Armita Jokar-Derisi, Amir Hossein Hassani, Reza Yazdani, Samaneh Delavari, Hassan Abolhassani, Negar Mortazavi, Aida Askarisarvestani 2023 Thomas Jefferson University

Assessment Of The First Presentations Of Common Variable Immunodeficiency In A Large Cohort Of Patients, Hossein Esmaeilzadeh, Armita Jokar-Derisi, Amir Hossein Hassani, Reza Yazdani, Samaneh Delavari, Hassan Abolhassani, Negar Mortazavi, Aida Askarisarvestani

Department of Neurology Faculty Papers

BACKGROUND: Common Variable Immunodeficiency (CVID) is a primary immunodeficiency syndrome resulting in recurrent infections, autoimmunity, and granulomatous manifestations.

METHODS AND MATERIALS: This retrospective study was conducted on an Iranian national registry of immunodeficient patients from 2010 to 2021. The frequency of first presentations of CVID and its association with sex, age of onset, and family history of CVID was evaluated.

RESULTS: A total of 383 patients entered the study, 164 of whom were female, and the rest were male. The mean age of the patients was 25.3 ± 14.5 years. The most frequent first presentations of CVID were pneumonia (36.8%) …


Mining Sars-Cov-2 Phylogenetic Trees To Estimate Circulating Infections And Patterns Of Migration, Erin V. Brintnell 2023 The University of Western Ontario

Mining Sars-Cov-2 Phylogenetic Trees To Estimate Circulating Infections And Patterns Of Migration, Erin V. Brintnell

Electronic Thesis and Dissertation Repository

The SARS-CoV-2 pandemic led to the formation of very large databases of genomic viral data. These databases contain information on transmission dynamics, emergence and evolution of SARS-CoV-2. However, extracting this information from sequences is difficult, as most methods of analyzing viral genomes were developed for smaller data sets. Therefore, my objective was to develop new fast estimators of the number of infections (I) and the rate of migration based on simple features of SARS-CoV-2 phylogenies.

I simulated pathogen evolution using a susceptible-exposed-infectious-recovered (SEIR) model of pathogen spread, reconstructing evolution using CoVizu. For simulations of I, I varied the total number …


A Foundational Population Genetics Investigation Of The Sexual Systems Of Solanum (Solanaceae) In The Australian Monsoon Tropics Suggests Dioecious Taxa May Benefit From Increased Genetic Admixture Via Obligate Outcrossing, Jason T. Cantley, Ingrid E. Jordon-Thaden, Morgan Roche, Daniel S. Hayes, Stephamie Kate, Christopher T. Martine 2023 San Francisco State University

A Foundational Population Genetics Investigation Of The Sexual Systems Of Solanum (Solanaceae) In The Australian Monsoon Tropics Suggests Dioecious Taxa May Benefit From Increased Genetic Admixture Via Obligate Outcrossing, Jason T. Cantley, Ingrid E. Jordon-Thaden, Morgan Roche, Daniel S. Hayes, Stephamie Kate, Christopher T. Martine

Faculty Journal Articles

Solanum section Leptostemonum is an ideal lineage to test the theoretical framework regarding proposed evolutionary benefits of outcrossing sexual systems in comparison to cosexuality. Theoretically, non-cosexual taxa should support more genetic diversity within populations, experience less inbreeding, and have less genetic structure due to a restricted ability to self-fertilize. However, many confounding factors present challenges for a confident inference that inherent differences in sexual systems influence observed genetic patterns among populations. This study provides a foundational baseline of the population genetics of several species of different sexual systems with the aim of generating hypotheses of any factor—including sexual system—that influences …


Embracing Ai/Ml In Genetic Counseling: A Nationwide Survey On Program Leaderships’ Perspectives And Curriculum Integration, Kyla Holmes 2023 Claremont Colleges

Embracing Ai/Ml In Genetic Counseling: A Nationwide Survey On Program Leaderships’ Perspectives And Curriculum Integration, Kyla Holmes

KGI Theses and Dissertations

This study aimed to examine the attitudes and preparedness of genetic counseling program directors and faculty leadership in incorporating artificial intelligence and machine learning (AI/ML) into their curricula and its effect on core competency proficiency. AI/ML has been instrumental in creating and maintaining vital analytical tools and models employed by genetic counselors (GCs). However, research on the attitudes of faculty leadership in charge of training future GCs is limited. A nationwide survey conducted between November 2022 and February 2023 gathered 15 respondents holding diverse academic positions in genetic counseling program curriculum development. The majority of respondents had encountered AI/ML in …


Epigenetics In Forensic Science, Reagan Faunce 2023 Bowling Green State University

Epigenetics In Forensic Science, Reagan Faunce

Honors Projects

DNA methylation can be useful for forensic scientists because it can be used to differentiate between the DNA of identical twins, determine the age of a contributor of a DNA sample, and help us understand the actions and tendencies of violent criminals. Research shows that DNA methylation changes over time and can be caused by traumatic events, suggesting that methylation increases with age. Prior studies of DNA methylation at the promoters of the EDARADD, TOM1L1, and NPTX2 genes have been able to predict age within 5.2 years and a study of the ASPA, EDARADD, PDE4C, and ELOVL2 genes predicted age …


Physiological And Transcriptomic Responses Of Two Artemisia Californica Populations To Drought: Implications For Restoring Drought-Resilient Native Communities, Hagop S. Atamian Dr., Jennifer L. Funk 2023 Chapman University

Physiological And Transcriptomic Responses Of Two Artemisia Californica Populations To Drought: Implications For Restoring Drought-Resilient Native Communities, Hagop S. Atamian Dr., Jennifer L. Funk

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

As climate change brings drier and more variable rainfall patterns to many arid and semi-arid regions, land managers must re-assemble appropriate plant communities for these conditions. Transcriptome sequencing can elucidate the molecular mechanisms underlying plant responses to changing environmental conditions, potentially enhancing our ability to screen suitable genotypes and species for restoration. We examined physiological and morphological traits and transcriptome sequences of coastal and inland populations of California sagebrush (Artemisia californica), a critical shrub used to restore coastal sage scrub vegetation communities, grown under low and high rainfall environments. The populations are located approximately 36 km apart but …


The Status Of Invasive Dusky Slug (Arion) Species In The Upper Great Lakes: A Molecular Approach, Olivia W. Hall 2023 Northern Michigan University

The Status Of Invasive Dusky Slug (Arion) Species In The Upper Great Lakes: A Molecular Approach, Olivia W. Hall

All NMU Master's Theses

I update the distribution of two cryptic slug species, Arion fuscus and Arion subfuscus, in the Upper Great Lakes of the United States using molecular identification methods. Arion fuscus has not previously been reported in the literature in this region, and Arion subfuscus has previously been reported as abundant. However, all previous distribution studies were determined using visual identification tools, which can result in misidentification between cryptic species. To molecularly re-examine these distribution maps, I used a mitochondrial ribosomal subunit 16S PCR amplification and subsequent SSpI and MfeI restriction enzyme digest to identify slug specimens. I collected slugs in …


Evaluation Of An Adaptive Sampling Approach To Characterize Microbes Associated With Pneumonia In White-Tailed Deer, Claire Nowak 2023 University of Maine - Main

Evaluation Of An Adaptive Sampling Approach To Characterize Microbes Associated With Pneumonia In White-Tailed Deer, Claire Nowak

Honors College

Infectious diseases have a tremendous global impact, adversely affecting the health and well-being of humans, domestic livestock, and wildlife. Consequently, pathogen surveillance in wild animals is essential for managing the risk of disease transmission to humans and domesticated animals, as well as for understanding host-pathogen interactions. However, pathogen detection methods are often focused on one to a few pathogen species, which limits our understanding of the distributions and effects of multiple co-infecting pathogens on host individuals and populations. In this study, I employed a metagenomic sequencing approach to (1) characterize the microbial community in a white-tailed deer (Odocoileus virginianus …


Be-03 Effects Of Dietary Iron On Taxonomic Composition And Function Of The Zebrafish Gut Microbiome, Megan D. Whisonant, Jeremiah L. Jackson, Sam L. Evans, Stuart Gordon Ph.D. 2023 Presbyterian College

Be-03 Effects Of Dietary Iron On Taxonomic Composition And Function Of The Zebrafish Gut Microbiome, Megan D. Whisonant, Jeremiah L. Jackson, Sam L. Evans, Stuart Gordon Ph.D.

SC Upstate Research Symposium

A healthy gut microbiota is essential to promote host health and well-being, therefore, effects of dietary components on the gut microbiome are important to investigate as the gastrointestinal tract can be a major route of infection. Iron—an essential component of heme and iron-sulfur proteins—plays a central role in many biological activities, including oxygen transport and cellular respiration.

In particular, the iron homeostasis system is one of the best characterized due to iron's causative relationship with iron-deficiency anemia. Dietary iron supplementation is a commonly used treatment for iron deficiency anemia; however, the known direct impacts of iron on the gut microbiome …


Presentation Of Paired P- And Q-Arm Mosaic Deletions On Chromosome 18 Associated With Neuropsychiatric Symptoms, Jackson Nielsen, Laura Minor, John Dougherty Jr., Paige Moore, Kailee Edwards, Brandon Burrell, Jameson Williams, John A. Kriak, David W. Sant, Kyle B. Bills 2023 Noorda College of Osteopathic Medicine

Presentation Of Paired P- And Q-Arm Mosaic Deletions On Chromosome 18 Associated With Neuropsychiatric Symptoms, Jackson Nielsen, Laura Minor, John Dougherty Jr., Paige Moore, Kailee Edwards, Brandon Burrell, Jameson Williams, John A. Kriak, David W. Sant, Kyle B. Bills

Annual Research Symposium

No abstract provided.


American Eel (Anguilla Rostrata) And Other Fishes As Surveyed By Environmental Dna In The Bronx River And Hudson River Watershed, Sam C. Chin 2023 The Graduate Center, City University of New York

American Eel (Anguilla Rostrata) And Other Fishes As Surveyed By Environmental Dna In The Bronx River And Hudson River Watershed, Sam C. Chin

Dissertations, Theses, and Capstone Projects

Mounting an effective response to the threats faced by freshwater fish may require expansions to aquatic biomonitoring in excess of what is feasible using the capture-based survey techniques currently relied upon by natural resource managers. Methods for analyzing environmental DNA (eDNA) are emerging as a minimally invasive and cost-effective approach for surveying fish and other organisms. By detecting taxon-specific DNA sequences recovered from environmental samples (e.g. water, sediment), eDNA methods are able to infer species presence from samples that can be collected rapidly with simple equipment. In many cases, eDNA detection rates of fish species have been shown to meet …


Rhetorics Of Species Revivalism And Biotechnology – A Roundtable Dialogue, Eva Kasprzycka, Charlotte Wrigley, Adam Searle, Richard Twine 2023 University of British Columbia

Rhetorics Of Species Revivalism And Biotechnology – A Roundtable Dialogue, Eva Kasprzycka, Charlotte Wrigley, Adam Searle, Richard Twine

Animal Studies Journal

This informal dialogue contextualises and explores contemporary practices of nonhuman animal gene-modification in de-extinction projects. Looking at recent developments in biotechnology’s role in de-extinction sciences and industries, these interdisciplinary scholars scrutinise the neoliberal impetus driving ‘species revivalism’ in the wake of the Capitalocene. Critical examinations of species integrity, cryo-preservation, techno-optimism, rewilding initiatives and projects aimed at restoring extinct animals such as the woolly mammoth and bucardo are used to map some of the necessary restructuring of conservation policies and enterprises that could secure viably sustainable – and just – futures for nonhuman animals at risk of extinction. The authors question …


Effects Of Depth, Distance To Shore, And Water Velocity On Organismal And Extra-Organismal Environmental Dna Concentrations In A Large River, Dylan Keel 2023 Humboldt State University

Effects Of Depth, Distance To Shore, And Water Velocity On Organismal And Extra-Organismal Environmental Dna Concentrations In A Large River, Dylan Keel

Cal Poly Humboldt theses and projects

Environmental DNA (eDNA) is a sensitive tool for detection of aquatic species and concentrations of eDNA in water samples have been useful for estimating abundance. This study evaluated the effects of depth, distance to shore, and water velocity on the concentration of organismal and extra-organismal eDNA concentrations in the Klamath River, California (basin area ≅ 40,000 km2). At each of six river cross sections 32 water samples were collected, including surface samples and depth samples evenly distributed across the cross section, and eDNA concentrations were determined for the parasite Ceratonova shasta and Chinook salmon, Oncorhynchus tshawytscha, using …


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