Genetics and Genomics Commons^™

Predicting Synchronized Gene Coexpression Patterns From Fibration Symmetries In Gene Regulatory Networks In Bacteria, Ian Leifer, Mishael Sánchez‑Pérez, Cecilia Ishida, Hernán A. Makse

Publications and Research

Background: Gene regulatory networks coordinate the expression of genes across physiological states and ensure a synchronized expression of genes in cellular subsystems, critical for the coherent functioning of cells. Here we address the question whether it is possible to predict gene synchronization from network structure alone. We have recently shown that synchronized gene expression can be predicted from symmetries in the gene regulatory networks described by the concept of symmetry fibrations. We showed that symmetry fibrations partition the genes into groups called fibers based on the symmetries of their ’input trees’, the set of paths in the network through which …

Genetic Relationships In The Toxin-Producing Fungal Endophyte, Alternaria Oxytropis Using Polyketide Synthase And Non-Ribosomal Peptide Synthase Genes, Rebecca Creamer, Deana Baucom Hille, Marwa Neyaz, Tesneem Nusayr, Christopher L. Schardl, Daniel Cook

Plant Pathology Faculty Publications

The legume Oxytropis sericea hosts a fungal endophyte, Alternaria oxytropis, which produces secondary metabolites (SM), including the toxin swainsonine. Polyketide synthase (PKS) and non-ribosomal peptide synthase (NRPS) enzymes are associated with biosynthesis of fungal SM. To better understand the origins of the SM, an unannotated genome of A. oxytropis was assessed for protein sequences similar to known PKS and NRPS enzymes of fungi. Contigs exhibiting identity with known genes were analyzed at nucleotide and protein levels using available databases. Software were used to identify PKS and NRPS domains and predict identity and function. Confirmation of sequence for selected gene …

Novel Scalable And Simplified System To Generate Microglia-Containing Cerebral Organoids From Human Induced Pluripotent Stem Cells, Brittany Bodnar, Yongang Zhang, Jinbiao Liu, Yuan Lin, Peng Wang, Zhengyu Wei, Sami Saribas, Yuanjun Zhu, Fang Li, Xu Wang, Wenli Yang, Qingsheng Li, Wen-Zhe Ho, Wenhui Hu

Nebraska Center for Virology: Faculty Publications

Human cerebral organoid (CO) is a three-dimensional (3D) cell culture system that recapitulates the developing human brain. While CO has proved an invaluable tool for studying neurological disorders in a more clinically relevant matter, there have still been several shortcomings including CO variability and reproducibility as well as lack of or underrepresentation of certain cell types typically found in the brain. As the technology to generate COs has continued to improve, more efficient and streamlined protocols have addressed some of these issues. Here we present a novel scalable and simplified system to generate microglia-containing CO (MCO). We characterize the cell …

Diversity And Host Specificity Of Nycteribiid Bat Flies (Diptera: Nycteribiidae) In Kenya, Taylor Verrett

Masters Theses & Specialist Projects

Bat flies (Diptera: Nycteribiidae and Streblidae) are hematophagous ectoparasites of bats distributed globally. Members of Nycteribiidae are morphologically constrained relative to streblids, and are united by their lack of wings, dorso-ventrally compressed bodies, and a primary distribution across the Eastern hemisphere. Bats are principal reservoirs of infectious diseases, including viral zoonoses of important consideration to human health, but the overall high host specificity of bat flies has largely been thought to curb their potential as inter-specific vectors of bat-borne pathogens. However, nycteribiid diversity and host associations remain critically understudied in some geographic regions, and rare examples of nycteribiid bat flies …

Determining The Causal Link Of Honey Bee Gut Microbial Composition On Behavioral Maturation, Thi Lan Anh Nguyen, Cassondra L. Vernier, Gene E. Robinson

PRECS student projects

Emerging studies have supported the association between gut microbiome and host behaviors. However, it is unclear whether changes in the gut microbiome cause changes in host behaviors or vice versa. The European honey bee, Apis mellifera, is an excellent animal model for identifying the causal link between microbiome and behavioral changes over the lifetime of the host as the honey bee gut contains a simple microbiome composed of only nine bacterial taxa clusters. In honey bees, division of labor occurs through behavioral maturation where age determines what task a bee does. For example, older bees forage while younger bees perform …

The Effects Of Forest Management Practices On Wild Bee Abundance And Functional Traits, Harvey Vela, Marissa H. Chase, Alexandra Harmon-Threatt

PRECS student projects

Both wild and managed bees are in decline due to the combined and interactive effects of anthropogenic disturbances such as habitat loss and pesticide use. This is concerning because bees are important not only for the pollination of agricultural lands, but also for plants in both natural and managed landscapes. North America is home to about 4000 native species of bees, all of which can be further classified by various characteristics such as body size, nesting strategy, diet breadth, and sociality. These traits are considered functional traits because they can impact the function – pollination – bees contribute to an …

Mapping Traits In A Soybean Recombinant Inbred Line Population, Gabriela Ortiz, Chris Montes, Lisa Ainsworth

PRECS student projects

What is SoyFACE?

• Soybean Free Air Concentration Enrichment
• Field conditions mimic the future's atmosphere, temperature, and soil
• Connect physiological responses of crops under these conditions to their genes (aka mapping)

What is a recombinant inbred line population?

Method for mapping traits

• Two parents with variance in a certain trait (in this case, response to elevated carbon dioxide)
• The parents used: HS93-4118 and Loda
• Allows understanding of what regions (quantitative trait loci) respond to atmospheric change

Gems Student: Biofilm Production In Rhizobia Influences Clover Drought Response, Faith Smith, Kevin Ricks, Anthony Yannarell

PRECS student projects

Rhizobia serve as model system for examining how phenotypic changes in rhizobia influence the plant. Rhizobium-legume symbioses result in the formation of nodules on the root systems of host plants. Compositional and functional changes in microbial communities facilitate the host plants’ response to environmental stressors (i.e.; drought stress). Physiological effects of soil moisture on microbial communities result in specialized communities that can tolerate much low soil-moisture habitats while others are limited to high soil-moisture environments. This suggests microbial communities can assist in maintaining plant fitness when exposed to nonideal environmental conditions.

Can In Vitro Phenotypes Of Fusarium Graminearum Indicate In Planta Aggressiveness?, Harrison Hall, Santiago Mideros

PRECS student projects

What is Fusarium graminearum and what does it do? Fusarium graminearum (F. graminearum), causes Fusarium Head Blight (FHB) in wheat and barley. FHB results in crop destruction and toxins that are harmful for human and animal consumption. There are several populations of F. graminearum present in North America and rates of in planta aggressiveness and toxin levels vary by Population. Visually, it is difficult to determine the aggression or toxin levels of an infection. However, it may be possible to determine this through in vitro growth. By using in vitro growth, it may be possible to determine in planta aggressiveness …

Effects Of Color Polymorphism And Lighting Environments On Male Bluefin Killifish Behavior, Elijah Davis, Ratna Karatgi, Becky Fuller

PRECS student projects

Polymorphism occurs when multiple, discrete phenotypes exist for a trait within the same species. Polyphenism, a form of phenotypic plasticity, occurs when the environment in which animals develop determines which discrete, morph is expressed. Color polymorphism occurs in male killifish anal fins where red, yellow, and blue color morphs are observed. Populations are found in both spring and swamp habitats. A polyphenism is present where males develop blue anal fins when raised in tea-stained water, which mimics swamps. My goal was to determine whether this plasticity is adaptive. Do blue males have an advantage in swamp water? Previous research involving …

Behavioral Plasticity In Response To Environmental Cues In Poison Frog Tadpoles, Samta Oza, Lisa Surber, Eva K. Fischer

PRECS student projects

Behavioral plasticity is the ability of an organism to detect cues in their environment and respond by modifying behavior. In the wild, dyeing poison frog (Dendrobates tinctorius) tadpoles are delivered by their dads to pools that vary in predation risk, resource availability, con-and hetero-specific density. Conspecific density is especially important as these tadpoles are aggressive and often cannibalistic. Behavioral plasticity in response to environmental cues may help tadpoles to compete for resources and survival.

Bioinformatics Protocol For Assessing Contamination Level And Quality On Genomics Data Of Ensifer Meliloti, Soohyun Lee, Mario Ceròn Romero, Katy Heath

PRECS student projects

Nitrogen (N) fixing bacteria have a symbiotic relationship with host plants. The legume plants provide sugar, a product of its photosynthesis, to rhizobacteria. Rhizobacteria, one of the various N fixing bacteria, utilize the sugar for its energy source needed for conversion of N2into NH4+. The rhizobacteria would provide fixed nitrogen to legume plant for its growth in exchange of energy source. There are various symbiotic relationships between microbes and plants, and the Heath Lab is especially interested in relationship between rhizobacteria and legume plants. Various genomic methods to study rhizobacteria require sequence data in Heath Lab. However, there is high …

Evaluating The Efficiency In The Application Of Transformation And Crispr/Cas9 Gene-Editing Technique On Pumpkins, Min Rung (Nicole) Hsu, Maria Malvino, Sarah R. Hind

PRECS student projects

With the simplicity of a unique genome engineering mechanism, CRISPR/Cas9 gene-editing technique has amazed scholars with its effectiveness and efficiency in manipulating gene sequences.[1] As this advanced technique develops, its applications on different species arise as prominent subjects yet to be determined. Due to the great economic value of pumpkins and the need for examining CRISPR/Cas9 gene-editing efficiency, Casperita pumpkin (Cucurbita pepo) is chosen as the subject to be investigated on. Through introducing CRISPR/Cas9 system —for modifying phytoene desaturase (PDS) gene— into pumpkin seeds with Agrobacterium-mediated transformation, we regenerate transgenic pumpkins and expect to observe albino leaves in the transformed …

Sometimes, When It Rains It Pours: How Does Flooding Alter Plant-Herbivore Relationships?, Lauren R. Urie, Erinn Dady, Esther N. Ngumbi

PRECS student projects

Flooding, an under-studied abiotic stressor, creates hostile soil conditions, including hypoxia, which hinder the growth and development of plants. Plants respond to abiotic and biotic stressors. A common response is the production of volatile organic compounds (VOCs), which modulate stress responses and mediate plant and insect interactions. Flooding causes significant losses in crops of agricultural and economic importance including tomato. Understanding how flooding impacts plant growth, plant chemistry, caterpillar performance and chemical mediated plant-herbivore interactions will create fundamental knowledge to an emerging challenge brought about by climate change and inform pest management decisions post flooding events. This study investigated how …

Gems Student: Can Improved Diet Quality Alleviate Harmful Effects Of Pesticides And Viruses In Honey Bees?, Brittney Bailey, Ed Hsieh, Adam Dolezal

PRECS student projects

This study investigates interacting effects of viruses and pesticides within honey bees and how improved diet quality can mitigate these effects. This experiment allows a multivariate problem which exists in natural conditions of the honey bee community to be observed in a controlled cage bioassay. • The virus used in this study is the Israeli acute-paralysis virus (IAPV). Neonicotinoid thiamethoxam is the pesticide used in both trials shown in the ‘Results’ section. This experiment has not begun the use of the pyrethroid at this time.

The Genetics Of Aggression In Unique Three-Spined Stickleback Populations, Megan Tucker, Colby Behrens, Alison M. Bell

PRECS student projects

No abstract provided.

The Differences Of Prokaryotic Pan-Genome Analysis On Complete Genomes And Simulated Metagenome-Assembled Genomes, Tang Li

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Metagenomic assembly is often used in microbiome research. In metagenomic assembly, contigs are binned based on the shared nucleotide composition. These contig bins are called metagenome-assembled genomes (MAGs), each representing a unique bacterial genome recovered from metagenome sequencing. Hundreds of thousands of high-quality MAGs of various ecological environments have been published since 2017, and increasingly more MAGs are being used in pan-genome analyses where unculturable species or species without reference genomes are studied in microbiome research. However, compared to the traditional pan-genome analysis that uses isolate genomes (from a pure strain isolated from a mixed bacterial population), it is not …

Sensitive And Specific Detection Of Sars-Cov-2 In Saliva Using Reverse Transcriptase Loop-Mediated Isothermal Amplification, Casey Juntila

All NMU Master's Theses

A novel coronavirus called SARS-CoV-2 has caused the emergency release of the most well-known molecular assay, the CDC N1 RT-PCR assay, causing reports of poor analytical performance resulting in false-negative results (20, 26), and inconsistent testing kits received (23, 32). An immediate and dire need for a rapid and reliable SARS-CoV-2 testing workflow specifically designed for a university setting is the purpose this project is aiming and intended to fulfill. The workflow design uses a less invasive saliva sample for rapid screening using colorimetric RT-LAMP detection of three SARS-CoV-2 gene regions for Orf1ab, envelope, and nucleocapsid. Purified SARS-CoV-2 genomic RNA …

Evaluation Of Horizontal Gene Transfer Between Genetically Engineered Cyanobacteria And Gram-Negative Bacteria, Andriana Chrysovalanti Zourou

Chemistry & Biochemistry Theses & Dissertations

As the world population is increasing and societies become more technology driven, there is an imperative to develop ‘green energy’ sources to protect our planet. Cyanobacteria that have been genetically engineered to produce organic compounds that may be burnt as fuels show great potential, as they are an environmentally friendly and self-renewable, net carbon-neutral option. However, there are potential risks in the development and use of genetically modified organisms (GMOs). We need to understand in advance the risks that GMOs may pose to our environment and to animal and human health. This will enable experimental procedures, containment strategies and policies …

Genetic Variability In Fusarium Oxysporum F. Sp. Vasinfectum Causing Damping-Off Of Cotton (Gossypium Barbadense L.) Seedlings [Research Note], Reda Helmy Sammour, Salah Abdel Moemen, Eman Elagamy

The Philippine Agricultural Scientist

The genetic variability of Fusarium oxysporum f. sp. vasinfectum isolates from Gossypium barbadense L. seedlings were assessed using pathogenicity, mycelial compatibility, and RAPD analyses. The results showed that the disease incidence percentages and compatibility percentages considerably varied, extending from 33.2 to 86.6 % and 6 to 60 %, respectively in North Egypt and from 33.3 to 66.6 % and 0.0 to 20% in South Egypt. It also showed that the isolates ISO-8 and ISO-19 had the lowest disease incidence (33.2%) as compared with isolate ISO-5 (86.6%). Results of the mycelial compatibility had a reversible relationship with disease incidence percentage. Cluster …