Genetics and Genomics Commons^™

Morphological And Molecular Identification Of Saurida Spp. (Teleostei: Synodontidae) From Saudi Arabia And Indonesia, Muhammad Browijoyo Santanumurti, Suciyono Suciyono, Mohamed Ahmed Abu El-Regal

Makara Journal of Science

Saurida is a unique fishery commodity because it is difficult to differentiate visually. They can be only effectively con-served once accurately identified. This study aimed to determine the morphology and molecular characteristics of Sau-rida spp. from Banyuwangi (Indonesia) and Jizan (Saudi Arabia). Meristic and morphometric analysis was performed for morphological identification, whereas COI gene analysis was performed for molecular identification. Morphological analysis was performed to identify Saurida in this study, such as S. tumbil (Jizan, Saudi Arabia) and S. micropectoralis (Banyuwangi, Indonesia). S. tumbil did not have dark brown spots on the lateral line and upper caudal fin, whereas S. …

Gene-Environment Interactions In Non-Alcoholic Fatty Liver Disease: Insights From Mexican American Populations, Eron G. Manusov, Vincent P. Diego, Marcio Almeida, Jacob Galan, Auwal A. Bala, Marco Arriaga, Natasha Garcia-Rodriguez, Renee Hernandez, Satish Kumar, John Blangero, Sarah Williams-Blangero

School of Medicine Publications

Nonalcoholic Fatty Liver Disease (NAFLD) is a prevalent and complex condition influenced by both genetic and environmental factors. This chapter explores the genotype-by-environment interactions that contribute to the development and progression of NAFLD in the Mexican American population. Using advanced genetic epidemiology and bioinformatics approaches, we investigated how specific genetic variants interact with environmental factors such as depression, acculturation stress, and social determinants of health, to influence NAFLD risk and severity. Our findings reveal significant genotype-by-environment interactions for key NAFLD-related traits, including HbA1c, AST/ALT ratio, and steatosis-controlled attenuation parameter (CAP). We also discuss the application of cutting-edge proteomic and transcriptomic …

Presence Of The Ade Multidrug Systems And Response To Triclosan Exposure In Acinetobacter Baumannii From Animal Origins, Sirawit Pagdepanichkit, Rungtip Chuanchuen

The Thai Journal of Veterinary Medicine

Thirty Acinetobacter baumannii from animal origins were obtained from 210 animal carcasses submitted for post-mortem examination, including dogs (n=112), cats (n=45), rabbits (n=17), birds (n=15), pigs (n=7) and exotic animals (n=14). All the isolates were evaluated for antimicrobial susceptibility with absence and presence of efflux inhibitors i.e. reserpine and carbonyl cyanide m-chlorophenylhydrazone (CCCP) and expression profile of important six multidrug efflux systems (i.e. AdeABC, AdeDE, AdeFGH, AdeIJK, AbeM and AmvA). Fifteen isolates expressing different Ade multidrug efflux pumps were selected for determining transcription levels and regulatory mutations. A continuous in vitro exposure experiment with benzalkonium chloride, chlorhexidine and triclosan …

Comparing Multivalent Cross-Linked Sodium Alginate/ Montmorillonite Beads Containing Curcumin Or Cayenne Pepper As Drug Carriers And Their Antimicrobial Resistance, Shionainn Traynor, Shubham Sharma

SURE Journal: Science Undergraduate Research Experience Journal

The aim of the following work was to investigate and compare curcumin and cayenne pepper in microbeads composed of sodium alginate (SA) crosslinked with montmorillonite (MMT) to act as drug carriers and their antimicrobial resistance. The microbeads were prepared through ion-exchange in multivalent solutions of CaCl₂, MgCl₂ and AlCl₃. The microbeads were characterized by Scanning Electron Microscopy (SEM), Energy Dispersive X-ray analysis (EDX) and the time required for intercalation of curcumin and cayenne pepper with MMT. Simulated intestinal fluid (pH 7.3) and gastric fluid (pH 1.2) at 37°C were used for comparison in swelling studies. …

Investigation Into The Effect Of Aspartame On The Expression Of P53 And Bax In Mouse Stomach Tissue, Angelique Cheryl, Aoife Mac Cooey

SURE Journal: Science Undergraduate Research Experience Journal

Introduction: The recent reclassification of aspartame as a Group 2B hazard by the International Agency for Research on Cancer, along with studies suggesting links to cancer, has raised concerns and prompted further investigation. Evidence suggests that aspartame exposure may alter p53 and BAX gene expression, affecting apoptosis in cancer cells. This study aims to examine how aspartame exposure affects p53 and BAX gene expression in normal mouse stomach tissue, shedding light on cellular stress and apoptosis mechanisms.

Methods: Mice were sacrificed, and stomach tissue was excised and divided into control and treatment groups. RNA extraction was carried out in the …

Editorial - Sure Journal Vol 6, Anne M. Friel, Eva Campion, Sinead Loughran

SURE Journal: Science Undergraduate Research Experience Journal

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Next Generation Sequencing Based Profiling Of Genes In Patients With Syndromic Forms Of Retinitis Pigmentosa, Harshavardhini G

Theses and Dissertations

India is one of the largest populations in the world and is estimated to have a high prevalence of Retinitis Pigmentosa (RP). RP is clinically and genetically heterogenous, characterized initially as night blindness, leading to complete vision loss due to retinal degeneration. RP can occur in non-syndromic or syndromic forms, affecting other organs as observed in Bardet Biedl Syndrome (BBS) and Usher syndrome (USH).

BBS is characterized by RP, polydactyly, obesity, renal anomalies and learning difficulties. USH is characterized by RP and sensorineural hearing loss (SNHL), with variable presence of vestibular dysfunction. Nextgeneration sequencing (NGS) has become a cost-effective technology …

Testing Vivo-Morpholino Mediated Gene Knockdown Of Stat6, Spi1b, And Hnf4Α In Adult Threespine Stickleback, Stella Dipippo

Honors Scholar Theses

The fibrotic immune response to the cestode parasite, Schistocephalus solidus, varies among threespine stickleback populations. Fibrosis suppresses parasite growth but has costly effects on the fish. Previous genomic studies in stickleback have suggested potential roles of Spi1b, STAT6, and HNF4α in modulating fibrosis severity, but there is presently no evidence for this in-vivo. We used antisense vivo-morpholino oligonucleotides (MOs) to attempt to knockdown the expression of each gene in the liver, spleen, and intestine of adult stickleback. Vivo-MOs have been proven effective in other species of teleost fish, as well as in mice and humans, but …

A Kinetic Model For Compound Heterozygous Pathogenic Variants In Tyrosyl-Trna Synthetase Gene Yars2-Associated Neonatal Phenotype, Thomas W Christian, Sunita Maharjan, Sitao Yin, Yuka Yamaki, Isao Masuda, Fenglin Li, Colleen Muraresku, Sheila Clever, Rebecca Ganetzky, Ya-Ming Hou

Department of Biochemistry and Molecular Biology Faculty Papers

Human genetic disorders are often caused by mutations of compound heterozygosity, where each allele of the mutant gene harbors a different genetic lesion. However, studies of such mutations are hampered due to the lack of an appropriate model. Here we describe a kinetic model of compound heterozygous variants in an obligate enzyme dimer that contains one mutation in one monomer and the other mutation in the second monomer. This enzyme is encoded by human YARS2 for mitochondrial tyrosyl-tRNA synthetase (mt-TyrRS), which aminoacylates tyrosine to mt-tRNA^Tyr. YARS2 is a member of the genes for mt-aminoacyl-tRNA synthetases, where pathogenic mutations …

Gonadal Absence Of Pig-1: Exploration Of Pig-1 In The Gonad Of Caenorhabditis Elegans, Winston S. Bennah

Undergraduate Theses

Caenorhabditis elegans are model organisms frequently studied to better understand biological processes. They have short life spans and produce a large number of progeny. Additionally, many of their molecular development processes can be found in human, providing insight into cell death and cell fate. In this project, our research aims to create a triple mutant strain to test the importance of the pig-1 gene in the gonad of C. elegans. This strain carries the following alleles: ckb-3::degron; him-8; gfp::pig-1. The pig-1 gene has been previously studied in neuroblast cells in C. elegans and is required for …

Assessing Spatial Distribution And Quantification Of Native Trees In Saskatchewan's Prairie Landscape Using Remote Sensing Techniques, Elham Shafeian, Bryan J. Mood, Kenneth W. Belcher, Colin P. Laroque

Aspen Bibliography

The importance of trees in non-forest landscapes has been the focus of only a few studies. However, these trees provide many important ecosystem services. In this study, we mapped and quantified these trees using Sentinel-2 (S2) and very high-resolution (VHR) Google satellite imagery without any field campaigns. We performed a Random Forest (RF) classification to map the spatial distribution of native trees in different scenarios. The optimal model showed an overall accuracy and kappa of 0.99 and 0.98, respectively. We mapped 40,500 km² of tree cover, including native tree cover (approximately 29,565 km²≈10.5%), excluding plantations, regional and …

The Effect Of Knockdown Of Gene Kit On Sox18 Gene Expression Through The Jak2/Stat3 Signaling Pathway Within An Ewing Sarcoma Cell, Samantha Aragon, Cristina Herrera, Felicity Rodriguez, Riley Smith, Terry Jo Shackleford

Cell and Molecular Methods

Ewing sarcoma is an aggressive cancer that affects children & adolescents. Common treatments include surgery, radiation, and chemotherapy, yet individuals have a poor survival rate and often develop side effects from treatment, including fertility issues, secondary cancer, heart problems, and growth abnormalities.1SOX18 is a gene identified to aid in cell proliferation and cell differentiation, leading to the development of several cancers, such as gastric, bladder, and lung cancer.2,3 SOX18 resides in the JAK2/STAT3 pathway as a regulator, along with another gene named KIT that instigates the formation of the cell signaling pathway.4KIT is a transmembrane tyrosine kinase, which instigates cell …

The Effects Of Ewing Sarcoma Through The Overexpression And Knockdown Of Transcription Factors Sox18 And Stat1, Victoria Castillo, Melany Cervantes, Nicole Robles, Terry Jo Shackleford

Cell and Molecular Methods

SOX18, a transcription factor with a DNA-binding HMG domain, plays a critical role in regulatory processes linked to cancer progression. Exhibiting oncogenic properties, SOX18 has been linked to various cancers, where it promotes tumor growth by enhancing cell invasion, uncontrolled proliferation, and resistance to apoptosis through dysregulated signaling pathways. STAT1, a protein crucial for immune system regulation, is prominently expressed in immune-associated tissues like the lymph nodes, and bone marrow, suggesting it could play a role in tumor growth. Ewing Sarcoma (EWS), an aggressive cancer that targets bone and soft tissue, carries a high mortality rate of 90% without treatment …

Transcription And 3d Chromatin Organization Interplay At Sub-Kilobase Scale, Hannah Harris

Theses & Dissertations

Nuclear compartments are prominent features of 3D chromatin organization, but sequencing depth limitations have impeded investigation at ultra fine-scale. CTCF loops are generally studied at a finer scale, but the impact of looping on proximal interactions remains enigmatic. Here, we critically examine nuclear compartments and CTCF loop-proximal interactions using a combination of in situ Hi-C at unparalleled depth, algorithm development, and biophysical modeling. Producing a large Hi-C map with 33 billion contacts in conjunction with an algorithm for performing principal component analysis on sparse, super massive matrices (POSSUMM), we resolve compartments to 500 bp. Our results demonstrate that essentially all …

Transcriptional Regulation In The Absence Of Inositol Trisphosphate Receptor Calcium Signaling, Michael Young, David M. Booth, David Smith, Marco Tigano, György Hajnóczky, Suresh K. Joseph

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

The activation of IP3 receptor (IP3R) Ca2+ channels generates agonist-mediated Ca2+ signals that are critical for the regulation of a wide range of biological processes. It is therefore surprising that CRISPR induced loss of all three IP3R isoforms (TKO) in HEK293 and HeLa cell lines yields cells that can survive, grow and divide, albeit more slowly than wild-type cells. In an effort to understand the adaptive mechanisms involved, we have examined the activity of key Ca2+ dependent transcription factors (NFAT, CREB and AP-1) and signaling pathways using luciferase-reporter assays, phosphoprotein immunoblots and whole genome transcriptomic studies. In addition, the diacylglycerol …

Single-Molecule Studies Reveal The Off-Pathway Early Paused State Intermediates As A Target Of Streptolydigin Inhibition Of Rna Polymerase And Its Dramatic Enhancement By Gre Factors, Anatolii Arseniev, Mikhail Panfilov, Georgii Pobegalov, Alina Potyseva, Polina Pavlinova, Maria Yakunina, Jookyung Lee, Sergei Borukhov, Konstantin Severinov, Mikhail Khodorkovskii

Rowan-Virtua School of Osteopathic Medicine Departmental Research

Antibiotic streptolydigin (Stl) inhibits bacterial transcription by blocking the trigger loop folding in the active center of RNA polymerase (RNAP), which is essential for catalysis. We use acoustic force spectroscopy to characterize the dynamics of transcription elongation in ternary elongation complexes (ECs) of RNAP in the presence of Stl at a single-molecule level. We found that Stl induces long-lived stochastic pauses while the instantaneous velocity of transcription between the pauses is unaffected. Stl enhances the short-lived pauses associated with an off-pathway early paused state intermediates of the RNAP nucleotide addition cycle. Unexpectedly, we found that transcript cleavage factors GreA and …

Unilateral Tongue Atrophy In Smad3: A Case Report, Gloria Galloway

Nursing & Health Sciences Research Journal

Background: Mothers Against Decapentaplegic Homolog 3 (SMAD3) is a disorder of the protein encoded at locus 15q22.33 and involved in the transcription of growth factor-beta (TGF) signalling. In this disorder, SMAD3 encoding is impaired, resulting in a connective tissue disorder with multisystem involvement (Bertoli-Avella et al., 2015; Dulac et al., 2019). This case is the first to describe unilateral tongue atrophy as an initial presentation of SMAD3, thereby providing an important contribution to the literature. Clinical History and Exam: A 43-year-old patient described a 1–2-week history in which he noted that half of his tongue had wasted away, and he …

Bap1: Genotype-Phenotype Correlation, Variant Classification, And Treatment Efficacy, Elizabeth Hobbs

All Dissertations

BRCA1-associated protein 1 (BAP1) is a tumor suppressor gene located on chromosome 3p21.3 and encodes a deubiquitinase enzyme (DUB) involved in DNA repair, cell cycle and metabolism, and apoptosis. BAP1 pathogenic germline variants are primarily associated with a familial cancer syndrome, Tumor Predisposition Syndrome 1 (TPDS1), but new missense variants have been linked to a neurodevelopmental disorder known as Kury-Isidor Syndrome (KURIS). Patients with TPDS1 variants have an increased risk for developing cancers, such as uveal and cutaneous melanomas, mesothelioma, and renal cell carcinoma, at an earlier age with lower thresholds for environmental exposures, mainly UV rays and asbestos, compared …

Characterizing Mechanisms Of Dna Repair And Genome Stability, Joshua Turner

All Dissertations

Every day our cells are bombarded with DNA lesions that threaten the stability of our genome. To help maintain genomic integrity our cells evolved to have a network of enzymes dedicated to repairing DNA lesions. Upon encountering a site of DNA damage, a cell recruits enzymes that remodel the stalled replication fork by reannealing the newly synthesized DNA together known as fork regression. Loss of fork regression activity has been shown to promote replication stress resistance after induced DNA damage. In this thesis, I discuss the role F-Box Helicase 1 (FBH1) plays in fork regression and how FBH1 promotes the …

Advancing Substance Use Disorder Treatment Using Genomics And Metabolomics, Lindsey Contella

All Dissertations

Advancing our understanding of genetic, metabolic, and environmental factors in substance use disorder (SUD) could lead to more effective therapies. In 2022, 16.5% of the U.S. population was diagnosed with SUD, yet current treatments lack efficacy for all patients, making a precision medicine approach crucial. This dissertation explores SUD's relationship with tryptophan (TRP) metabolism through the kynurenine pathway (KP) as a potential therapeutic target. Chapter I reviews current knowledge on SUD and KP. Chapter II identifies how SUD alters KP metabolite concentrations, identifying a reduced concentration of the neuroprotective metabolite, kynurenic acid (KA) and elevated concentrations of the neurotoxic metabolite, …