Genetics and Genomics Commons^™

Mutations In Several Auxin Biosynthesis Genes And Their Effects On Plant Phenotypes In Arabidopsis, Gabriela Hernandez, Lauren Huebner, Bethany Karlin Zolman

Undergraduate Research Symposium

Auxins are important hormones in plants that regulate growth and development. Disruptions in the auxin biosynthesis pathway result in morphological changes in phenotypes in the model plant Arabidopsis thaliana, including differences in root and leaf formation. Mutations in the Tryptophan Aminotransferase of Arabidopsis (TAA1) and YUCCA (YUC4) genes interfere with the plant's ability to synthesize Indole-3-acetic acid (IAA), the primary auxin involved in plant development. IBR1 and IBR3 act in the multistep conversion of indole-3-butyric acid (IBA) to IAA. ILL2, IAR3, and ILR1 hydrolyze IAA-amino acid conjugates into free IAA. The goal of …

Otoliths Of South-Western Australian Fish: A Photographic Catalogue, Chris Dowling, Kim Smith, Elaine Lek, Joshua Brown

Fisheries Research Reports

Due to the species-specific nature of otoliths and given they are often the only part of the fish preserved when fish die, otolith catalogues can be used in numerous applications, such as diet studies in fish eating animals, including pinnipeds, fish and sea birds; archaeological purposes such as reconstructing indigenous people’s diets from otoliths found in middens or evolutionary history of fish species by comparing fossilized otoliths. Given the unique mixture of subtropical and temperate fish, including many endemic species that occur off the southwest corner of WA having a catalogue for this area is extremely important for people working …

Effects Of Copper Oxide (Cuo) And Zinc Oxide (Zno) Nano And Bulk Forms To Soil Fungal Community [Research Note], Jonathan Jaime Guerrero, Teresita Dalisay, Nolissa Organo, Ireneo Pangga

The Philippine Agricultural Scientist

The effects of copper oxide (CuO) and zinc oxide (ZnO) in bulk and nano forms on soil fungal community was determined. Lipa clay loam soil collected from the University of the Philippines Los Baños were placed in polypropylene bags and amended with 300 mg/L of CuO or ZnO in either forms. Colony-forming units (CFU) as well as average well color development (AWCD), functional richness and stress index were determined on day 1, 8 and 15 via indirect viable plate count method and community – level physiological profiling (CLPP). Fungal isolates from the same soil samples were likewise identified and tested …

Efficacy Study Of Selected Maize (Zea Mays L.) Genotypes Against The Asian Corn Borer, Ostrinia Furnacalis (Guenée), Yoryncita Marfori, Merdelyn Caasi-Lit, Tonette Laude

The Philippine Agricultural Scientist

Laboratory and screen house studies were conducted to assess the efficacy of selected twenty-six maize varieties against Asian corn borer (ACB), Ostrinia furnacalis (Guenée). Hierarchical tree based on resistance parameters clearly revealed that the twenty-six maize varieties are best classified into three groups, viz. resistant, intermediate, and susceptible. In laboratory test, the varieties RCS2, RCS4, RCS5, 'IPB Var13', Bt2, Bt3, and Bt4 were consistently identified as highly resistant. Further examinations in stalk feeding assay showed that the resistant varieties had sharp decline in larval survival (LS) on the 2^nd to the 5^th day of larval feeding in …

Spectral Lights Based Treatment Enhanced Biomass Accumulation And Secondary Metabolites Production In Callus Culture Of Citrus Reticulata, Faiza Anum, Naveed Iqbal Raja, Tahira Sultana, Abeer Kazmi, Amir Ali, Bushra Qayyum, Anza Afzal, Aneela Nijibat, Zia-Ur-Rehman Mashwani, Abeer Kazmi

The Philippine Agricultural Scientist

Citrus reticulata is a common fruit, belongs to the family Rutaceae. It contains terpenes, phenolics, flavonoids, and vitamin C in conjugation with sugars, amino acids, minerals, organic acids and other biologically important compounds. Application of light elicitation strategies in in vitro plant cultures is acquiring more interest for their potential in feasible biomass accumulation and therapeutically important secondary metabolites production. The present study was designed to investigate the effects of different monochromatic lights (white, red, blue, green, and yellow) on the proliferation and secondary metabolites accumulation in callus cultures of Citrus reticulata raised in response to treatment with AgNPs and …

Assesment Of Antibiotic Resistant Gene Expression In Clinical Isolates Of Pseudomonas Aeruginosa, Dustin Esmond

Biology Theses

Increasing prevalence of nosocomial infections by antimicrobial resistant pathogens resulting in higher mortality rates and financial burden is of great concern. Pseudomonas aeruginosa represents one of six highly virulent “ESKAPE” pathogens that exhibit considerable intrinsic drug resistance as well as mechanisms for acquiring further resistance. As many of these mechanisms are regulated through gene expression, we sought to identify regulatory strategies and patterns at play in 23 clinical isolates collected from Baku, Azerbaijan and Tyler, Texas, USA. Real-time quantitative polymerase chain reaction was performed on six gene targets implicated in resistance and contrasted with antibiotic phenotypes. We found AmpC cephalosporinase …

Genetic Diversity And Population Structure Of Sugarcane (Saccharum Officinarum L.) Collected From Seven Philippine Regions For Use As Breeding Stocks For Crop Improvement, Jan Leandro Acedera, Jhun Laurence Rasco, Jemimah Banganan, Antonio Lalusin

The Philippine Agricultural Scientist

Selection of parents for hybridization relies on the information on their genetic relationship and diversity which are essential in any breeding program. This study aimed to estimate the extent of genetic diversity and population structure of 76 sugarcane accessions from seven regions in the Philippines using 57 morphological characters and 50 microsatellite markers. The sugarcane collections exhibited moderate to high diversity with mean of H’ = 0.72 for qualitative and H’ = 0.75 for quantitative morphological characters, respectively. This is corroborated by the analysis of variance (ANOVA) of agronomic parameters, except for stalk length. Unweighted Pair Group Method with Arithmetic …

Informed Consent: Foundations And Applications, Joanna Smolenski

Dissertations, Theses, and Capstone Projects

Since its advent in the 20th century, informed consent has become a cornerstone of ethical healthcare, and obtaining it a core obligation in medical contexts. In my dissertation, I aim to examine the theoretical underpinnings of informed consent and identify what values it is taken to protect. I will suggest that the fundamental motivation behind informed consent rests in something I’ll call bodily self-sovereignty, which I argue involves a coupling of two groups of values: autonomy and non-domination on the one hand, and self-ownership and personal integrity on the other. I will then go on to consider two 'case …

Exome Sequence Association Study Of Levels And Longitudinal Change Of Cardiovascular Risk Factor Phenotypes In European Americans And African Americans From The Atherosclerosis Risk In Communities Study, Elena V Feofanova, Elise Lim, Han Chen, Minjae Lee, Ching-Ti Liu, L Adrienne Cupples, Eric Boerwinkle

Faculty, Staff and Student Publications

Cardiovascular disease (CVD) is responsible for 31% of all deaths worldwide. Among CVD risk factors are age, race, increased systolic blood pressure (BP), and dyslipidemia. Both BP and blood lipids levels change with age, with a dose-dependent relationship between the cumulative exposure to hyperlipidemia and the risk of CVD. We performed an exome sequence association study using longitudinal data with up to 7805 European Americans (EAs) and 3171 African Americans (AAs) from the Atherosclerosis Risk in Communities (ARIC) study. We assessed associations of common (minor allele frequency > 5%) nonsynonymous and splice-site variants and gene-based sets of rare variants with levels …

Investigation Of Notch Signaling In Cone Fate Specification In Vertebrate Retina, Xueqing Chen

Dissertations, Theses, and Capstone Projects

In the vertebrate retina, cone photoreceptors are crucial for high acuity color vision. Several retinal diseases lead to loss of cones and there is a need to identify the normal developmental genesis of these cells to inform the development of stem cell-based therapies. Cone genesis has previously been shown to be repressed by Notch signaling, however, the mechanism by which Notch signaling controls cone fate determination is still unclear. It has been identified that cone photoreceptors are formed from multipotent retinal progenitor cells (RPCs) that first generate genetically-defined, restricted RPCs with limited mitotic and fate potential to preferentially form cones …

The Slit-Binding Ig1 Domain Is Required For Multiple Axon Guidance Activities Of Drosophila Robo2, Lafreda J. Howard, Marie C. Reichert, Timonthy A. Evans

Biological Sciences Faculty Publications and Presentations

Drosophila Robo2 is a member of the evolutionarily conserved Roundabout (Robo) family of axon guidance receptors. Robo receptors signal midline repulsion in response to Slit ligands, which bind to the N-terminal Ig1 domain in most family members. In the Drosophila embryonic ventral nerve cord, Robo1 and Robo2 signal Slit-dependent midline repulsion, while Robo2 also regulates the medial-lateral position of longitudinal axon pathways and acts non-autonomously to promote midline crossing of commissural axons. While Robo2 signals midline repulsion in response to Slit, it is less clear whether Robo2's other activities are also Slit-dependent. To determine which of Robo2's axon guidance roles …

Student Perceptions Of Authoring A Publication Stemming From A Course-Based Undergraduate Research Experience (Cure), Ashley N. Turner, Anil K. Challa, Katelyn M. Cooper

Research, Publications & Creative Work

Course-based undergraduate research experiences (CUREs) engage students in authentic research experiences in a course format and can sometimes result in the publication of that research. However, little is known about student-author perceptions of CURE publications. In this study, we examined how students perceive they benefit from authoring a CURE publication and what they believe is required for authorship of a manuscript in a peer-reviewed journal. All 16 students who were enrolled in a molecular genetics CURE during their first year of college participated in semistructured interviews during their fourth year. At the time of the interviews, students had been authors …

Neurological Gene Jus Is Associated With Aging-Related Muscle Loss In The Fly Model Of Sarcopenia., Soobin An

Symposium of Student Scholars

Sarcopenia is a health condition in the elderly that is associated with degradation of muscle size, mass, and function. It can cause physical disability and, in extreme cases, death. The genetic aspect of sarcopenia is still not well understood. To shed light on sarcopenia mechanisms, we investigated muscle loss in aging fruit flies, Drosophila melanogaster. Our hypothesis was that aging-dependent muscle degradation can be affected by suboptimal functioning of the central nervous system (CNS). We used RNA interference and tissue-specific genetic drivers to induce a selective knockdown (KD) of the julius seizure gene (jus), which is associated …

In Silico Identification Of A Streptococcus Phage From An Unpasteurized Dairy Product

Symposium of Student Scholars

This study aimed to identify novel phages from a West African dairy product, nunu, to better understand the uncharacterized virosphere of a food microbiome. Nunu is a yogurt-like product from spontaneous fermentation of unpasteurized cow milk without a standardized starter culture. Phages and their bacterial hosts make up a microbiome, where their collective metagenome can be studied in silico, or computationally, after next generation sequencing (NGS). The targeted dataset for our study can be found in the Sequence Read Archives under the accession number of ERX2041567. This study utilized several bioinformatics software tools with customized settings: Kraken2, MetaVelvet, Edena, NCBI-BLAST, …

In Silico Isolation Of A Novel Phage For Food Safety Applications Against Pathogenic E. Coli, Daisy Mcgrath

Symposium of Student Scholars

With the advent of next-generation sequencing (NGS) on metagenomes, the elucidation of all genetic material from microbiomes has prompted a renewed interest towards uncultivated members of the virosphere. We describe the discovery of a novel phage from a metagenomic dataset on the West African fermented dairy product, nunu, with a custom bioinformatics workflow to potentially serve as a biocontrol agent against pathogenic E. coli. Initial dataset of ERR2014814 from NCBI was first subjected to Kraken2 to extract novel sequencing reads for further de novo assembly into contigs by MetaVelvet. Resultant contigs served as potential partial phage genomes, then searched …

Examining Effects Of The Dna Regulator Lrp On Quorum Sensing Gene Expression In Pseudomonas Aeruginosa, Bradley Lumsden

Symposium of Student Scholars

Pseudomonas aeruginosa is an opportunistic human pathogen that has the capacity to express multiple virulence factors that are regulated through an extensive quorum sensing network. Three major quorum sensing systems have been identified in Pseudomonas species: the acyl homoserine lactones of las and rhl, and the Pseudomonas Quinolone Signal (PQS). We seek to investigate the involvement of a global regulator, Lrp with the expression of these three networks. Specifically, we will compare expression levels of las, rhl, and pqs in wild type P. aeruginosa (MPAO1) with an lrp transposon insertion mutant using quantitative PCR. Through this comparative …

Towards The Identification Of The Soil Fungal Microbiome Community Associated With Longleaf Pine, Joshua Inneh, Grace Krueger, Ian Thomasson, Fletcher Moon, Geoffrey Eger

Symposium of Student Scholars

This project is part of a larger study looking at the restoration of the Longleaf Pine (LLP) ecosystem in certain Wildlife Management Areas (WMA) in Northwest Georgia. Our long-term aim is to look for potential associations between the aboveground and belowground community structures as the complex system of feedback mechanisms between the soil microbiome, the rhizosphere, and the plant communities is not yet understood.

Soil samples were collected from a total of six plots in the Sheffield WMA located in Paulding County. The samples were collected from north or south facing hillside plots except for in the savanna sites (an …

A Reevaluation Of The Phylogeography Of The Chattahoochee Slimy Salamander (Plethodon Chattahoochee) Using Next-Generation Genomic Data, Jadin Cross

Symposium of Student Scholars

The Plethodon glutinosus species complex is a group of large-bodied, lungless salamanders that are widespread across the eastern United States. Species in this group are morphologically cryptic and were originally delimited using allozyme data, but in most cases, the extent of contemporary gene flow between named taxa has not be rigorously evaluated. The Appalachian Mountains of northern Georgia are home to several members of this group—including P. glutinosus, P. teyahalee, P. chlorobryonis, and P. chattahoochee. P. chattahoochee has been found to be especially cryptic both morphologically and genetically as both intraspecific genetic variation and species boundaries within …

The Evolutionary Origins Of Autism Associated Genes And Their Role In Great Ape Socio-Communication, Azeeza Abdulrauf, Martin Hudson, Susan M.E. Smith, Jared P. Taglialatela

Symposium of Student Scholars

Single nucleotide polymorphisms (SNPs) play a major role in socio-communicative behavior. For this study, the focus is on autism associated OXTR, AVPR1A, and FOXP2 SNPs, and the role they play in great apes. Prior research on the OXTR, AVPR1A, and FOXP2 SNPs show that they affect behavior skills such as understanding and controlling emotion, understanding the emotions of others, and communications skills. Great apes, such as bonobos, chimpanzees, and gorillas are the model, since they are our closest relatives in the animal kingdom capable of understanding complex communication. Each gene has at least two SNPS that are investigated in the …

Foe To Friend: Parallel Domestication Of Ophiocordyceps From Fungal Parasite To Beneficial Symbiont In Cicadas, Jason Vailionis, Eric Rl Gordon, Chris Simon

University Scholar Projects

Nutritional symbioses are integral to the survival and diversity of many insects. The majority of herbivorous insects in the order Hemiptera possess stable, inherited symbionts that produce essential amino acids and vitamins. However, instability has been observed in cicadas, with one bacterial symbiont, Hodgkinia cicadicola, being repeatedly replaced by a new fungal symbiont, Ophiocordyceps. The fungal symbionts are thought to be derived from parasitic Ophiocordyceps species, but little is known about these parasitic ancestors or how the transition from parasite to mutualist occurs. We used a combination of targeted amplified genes and metagenomic sequencing to investigate the evolution …

Higher Entropy Observed In Sars-Cov-2 Genomes From The First Covid-19 Wave In Pakistan, Najia Karim Ghanchi, Asghar Nasir, Kiran I. Masood, Syed Hani Abidi, Syed Faisal Mahmood, Akber Kanji, Safina Abdul Razzak, Waqasuddin Khan, Saba Shahid, Maliha Yameen, Ali Raza, Javaria Ashraf, Zeeshan Ansar Ahmed, Mohammad Buksh Dharejo, Nazneen Islam, Zahra Hasan, Rumina Hasan

Department of Pathology and Laboratory Medicine

Background: We investigated the genome diversity of SARS-CoV-2 associated with the early COVID-19 period to investigate evolution of the virus in Pakistan.
Materials and methods: We studied ninety SARS-CoV-2 strains isolated between March and October 2020. Whole genome sequences from our laboratory and available genomes were used to investigate phylogeny, genetic variantion and mutation rates of SARS-CoV-2 strains in Pakistan. Site specific entropy analysis compared mutation rates between strains isolated before and after June 2020.
Results: In March, strains belonging to L, S, V and GH clades were observed but by October, only L and GH strains were present. The …

Vitamin D Modulates Rett Syndrome Phenotypes And Underlying Cellular Pathways In An Mecp2-Mutant Mouse Model, Mayara De Cassia Ribeiro

Dissertations - ALL

Rett syndrome (RTT) is a progressive and severe X-linked neurodevelopmental disorder caused by mutations in the transcriptional regulator MECP2. There is currently no effective treatment for RTT. Female RTT patients develop relatively normally during the first 6-18 months of life, after which they undergo a period of rapid regression, losing the ability to talk, walk and purposefully use their hands, in addition to suffering from deceleration of head growth, and onset of repetitive, autistic behaviors. RTT symptoms can be partially reversed by the re-expression of Mecp2 in adult mice, suggesting the potential for post-symptomatic therapeutic intervention. Among the many dysfunctions …

Multivariate Analysis Of 1.5 Million People Identifies Genetic Associations With Traits Related To Self-Regulation And Addiction, Richard Karlsson Linnér, Travis T. Mallard, Peter B. Barr, Sandra Sanchez-Roige, James W. Madole, Morgan N. Driver, Holly E. Poore, Ronald De Vlaming, Andrew D. Grotzinger, Mark Z. Kos

School of Medicine Publications

Behaviors and disorders related to self-regulation, such as substance use, antisocial behavior and attention-deficit/hyperactivity disorder, are collectively referred to as externalizing and have shared genetic liability. We applied a multivariate approach that leverages genetic correlations among externalizing traits for genome-wide association analyses. By pooling data from ~1.5 million people, our approach is statistically more powerful than single-trait analyses and identifies more than 500 genetic loci. The loci were enriched for genes expressed in the brain and related to nervous system development. A polygenic score constructed from our results predicts a range of behavioral and medical outcomes that were not part …

Insights Into Halophilic Microbial Adaptation: Analysis Of Integrons And Associated Genomic Structures And Characterization Of A Nitrilase In Hypersaline Environments, Sarah Sonbol

Theses and Dissertations

Hypersaline environments are extreme habitats that can be exploited as biotechnological resources. Here, we characterized a nitrilase (NitraS-ATII) isolated from Atlantis II Deep brine pool. It showed higher thermal stability and heavy metal tolerance compared to a closely related nitrilase.

We also studied integrons in halophiles and hypersaline environments. Integrons are genetic platforms in which an integron integrase (IntI) mediates the excision and integration of gene cassettes at specific recombination sites. In order to search for integrons in halophiles and hypersaline metagenomes, we used a PCR-based approach, in addition to different bioinformatics tools, mainly IntegronFinder.

We found that integrons and …

Primary Industries Development Research Highlights 2021, Department Of Primary Industries And Regional Development, Tim Scanlon

Books & book chapters

The Primary Industries Development Research Highlights 2021 showcases the breadth and depth of the Department of Primary Industries and Regional Development’s research and development activities over the past several years.

Stories featured in Research Highlights 2021 stem from about 60 (of 140) current and recently-completed projects undertaken by the Department of Primary Industries and Regional Development’s (DPIRD) 1100 scientists, technical experts and economists throughout the State.

Explore our Research Highlights 2021.

The publication demonstrates the innovative and applicable research that DPIRD and its collaborators and investment partners deliver to Western Australia.

Download the Research Highlights 2021 here. Alternatively, …

Atg8 Is Conserved Between Saccharomyces Cerevisiae And Psychrophilic, Polar-Collected Fungi, B. J. Ivory, H. M. Smith, E. Cabrera, M. R. Robinson, J. T. Sparks, A. Solem, J. I. Ishihara, H. Takahashi, M. Tsuji, V. A. Segarra

Osteopathic Medicine, Jerry M. Wallace School of

No abstract provided.

Artificial Image Objects For Classification Of Schizophrenia With Gwas-Selected Snvs And Convolutional Neural Network, Xiangning Chen, Daniel G. Chen, Zhongming Zhao, Justin Zhan, Changrong Ji, Jingchun Chen

School of Medicine Faculty Research

In this article, we propose a new approach to analyze large genomics data. We considered individual genetic variants as pixels in an image and transformed a collection of variants into an artificial image object (AIO), which could be classified as a regular image by CNN algorithms. Using schizophrenia as a case study, we demonstrate the principles and their applications with 3 datasets. With 4,096 SNVs, the CNN models achieved an accuracy of 0.678 ± 0.007 and an AUC of 0.738 ± 0.008 for the diagnosis phenotype. With 44,100 SNVs, the models achieved class-specific accuracies of 0.806 ± 0.032 and 0.820 …

Gene Expression Profiling Of Mapk Pathway Inhibitor Resistance In Cutaneous Melanoma: Can Bioinformatics Be Used To Select Better Melanoma Cell Lines?, Stephen Luebker

Theses & Dissertations

Melanoma is the deadliest form of skin cancer, and incidence has continued to increase. Half of all melanomas have a BRAF V600E mutation and respond to MAPK pathway inhibitors, including BRAF inhibitor therapy or BRAF/MEK inhibitor combination therapy, but nearly all patients develop treatment resistance. Melanoma cell lines produce variable results as models of MAPK pathway inhibitor resistance. To better understand how the genomic similarity of a melanoma cell line to patient-derived tumors affects resistance mechanisms, differences in DNA mutations and copy-number alterations were compared between melanoma cell lines profiled by the Cancer Cell Line Encyclopedia and cutaneous melanoma tumors …

Determining The Novel Pathogen Neodothiora Populina As The Causal Agent Of The Aspen Running Canker Disease In Alaska, Loretta M. Winton, Gerard C. Adams, Roger W. Ruess

Aspen Bibliography

Neodothiora populina Crous, G.C. Adams & Winton was determined to be a new pathogen of trembling aspen (Populus tremuloides) growing in Alaska, based on completion of Koch’s Postulates in replicated forest and growth chamber inoculation trials. The pathogen is responsible for severe damage and widespread rapid mortality of sapling to mature aspen (≥ 80 years) in the boreal forests of interior Alaska, due to large diffuse annual (1–2 years) cankers. Isolation of the pathogen was challenging, and identification based on cultural characters was difficult. Fruiting bodies were not found on wild diseased trees, but erumpent pycnidia were found …

Role Of A Cryptic Trna Gene Operon In Survival Under Translational Stress, Javier Santamaría-Gómez, Miguel Ángel Rubio, Rocío López-Igual, Ana B. Romero-Losada, Fernando M. Delgado-Chaves, Roque Bru-Martínez, Francisco J. Romero-Campero, Antonio Herrero, Michael Ibba, Jesús A. G. Ochoa De Alda, Ignacio Luque

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

As compared to eukaryotes, bacteria have a reduced tRNA gene set encoding between 30 and 220 tRNAs. Although in most bacterial phyla tRNA genes are dispersed in the genome, many species from distinct phyla also show genes forming arrays. Here, we show that two types of arrays with distinct evolutionary origins exist. This work focuses on long tRNA gene arrays (L-arrays) that encompass up to 43 genes, which disseminate by horizontal gene transfer and contribute supernumerary tRNA genes to the host. Although in the few cases previously studied these arrays were reported to be poorly transcribed, here we show that …