Genetics and Genomics Commons^™

Whole Plastome Sequencing Within Silene Section Psammophilae Reveals Mainland Hybridization And Divergence With The Balearic Island Populations, José Carlos Del Valle, Inés Casimiro-Soriguer, Mᵃ Luisa Buide, Eduardo Narbona, Justen B. Whittall

Biology

Reconstructing the phylogenetic relationships within Caryophyllaceae tribe Sileneae has been obscured by hybridization and incomplete lineage sorting. Silene is the largest genus in the Caryophyllaceae, and unraveling its evolutionary history has been particularly challenging. In order to infer the phylogenetic relationships among the five species in Silene section Psammophilae, we have performed a genome skimming approach to acquire the complete plastid genome (cpDNA), nuclear ribosomal cistron (nrDNA), and partial mitochondrial genome (mtDNA). We have included 26 populations, representing the range of each species' distribution. This section includes five morphologically similar species endemic to the Iberian Peninsula and Balearic Islands …

Multi-Ancestry Sleep-By-Snp Interaction Analysis In 126,926 Individuals Reveals Lipid Loci Stratified By Sleep Duration, Raymond Noordam, Maxime M. Bos, Heming Wang, Thomas W. Winkler, Amy R. Bentley, Tuomas O. Kilpeläinen, Paul S. De Vries, Yun Ju Sung, Karen Schwander, Brian E. Cade, Alisa Manning, Hugues Aschard, Michael R. Brown, Han Chen, Nora Franceschini, Solomon K. Musani, Melissa Richard, Dina Vojinovic, Stella Aslibekyan, Traci M. Bartz, Donna K. Arnett

Epidemiology and Environmental Health Faculty Publications

Both short and long sleep are associated with an adverse lipid profile, likely through different biological pathways. To elucidate the biology of sleep-associated adverse lipid profile, we conduct multi-ancestry genome-wide sleep-SNP interaction analyses on three lipid traits (HDL-c, LDL-c and triglycerides). In the total study sample (discovery + replication) of 126,926 individuals from 5 different ancestry groups, when considering either long or short total sleep time interactions in joint analyses, we identify 49 previously unreported lipid loci, and 10 additional previously unreported lipid loci in a restricted sample of European-ancestry cohorts. In addition, we identify new gene-sleep interactions for known …

Genome-Wide Variation In Potyviruses, Deepti Nigam, Katherine Latourrette, Pedro F.N. Souza, Hernan Garcia Ruiz

Nebraska Center for Virology: Faculty Publications

Potyviruses (family Potyviridae, genus Potyvirus) are the result of an initial radiation event that occurred 6,600 years ago. The genus currently consists of 167 species that infect monocots or dicots, including domesticated and wild plants. Potyviruses are transmitted in a non-persistent way by more than 200 species of aphids. As indicated by their wide host range, worldwide distribution, and diversity of their vectors, potyviruses have an outstanding capacity to adapt to new hosts and environments. However, factors that confer adaptability are poorly understood. Viral RNA-dependent RNA polymerases introduce nucleotide substitutions that generate genetic diversity. We hypothesized that selection imposed by …

Macrophage-Associated Wound Healing Contributes To African Green Monkey Siv Pathogenesis Control, Fredrik Barrenas, Kevin Raehtz, Cuiling Xu, Lynn Law, Richard R. Green, Guido Silvestri, Steven E. Bosinger, Andrew Nishida, Qingsheng Li, Wuxun Lu, Jianshui Zhang, Matthew J. Thomas, Jean Chang, Elise Smith, Jeffrey M. Weiss, Reem A. Dawoud, George H. Richter, Anita Trichel, Dongzhu Ma, Xinxia Peng, Jan Komorowski, Cristian Apetrei, Ivona Pandrea, Michael Gale Jr.

Nebraska Center for Virology: Faculty Publications

Natural hosts of simian immunodeficiency virus (SIV) avoid AIDS despite lifelong infection. Here, we examined how this outcome is achieved by comparing a natural SIV host, African green monkey (AGM) to an AIDS susceptible species, rhesus macaque (RM). To asses gene expression profiles from acutely SIV infected AGMs and RMs, we developed a systems biology approach termed Conserved Gene Signature Analysis (CGSA), which compared RNA sequencing data from rectal AGM and RM tissues to various other species. We found that AGMs rapidly activate, and then maintain, evolutionarily conserved regenerative wound healing mechanisms in mucosal tissue. The wound healing protein fibronectin …

Immune Gene Diversity And Populations Structure Of Reticulated Flatwoods Salamander (Ambystoma Bishopi), Steven Tyler Williams

LSU Master's Theses

Reticulated flatwoods salamander (Ambystoma bishopi) populations began decreasing dramatically in the late 1900s. Contemporary populations are small, isolated, and may be susceptible to inbreeding and reduced adaptive potential because of low genetic variation. Genetic variation at immune genes is especially important as it influences disease susceptibility and adaptation to emerging infectious pathogens, a central conservation concern for declining amphibians. Connectivity between isolated populations is also vital to maintain genetic diversity and avoid inbreeding. I collected tissue samples from across the extant range of this salamander to examine genetic variation and population structure in: immune genes broadly (immunome), the …

Inferred Function And Dynamics Of Microbial Communities From The Northern Gulf Of Mexico, Deepesh Tourani

HCNSO Student Theses and Dissertations

Microbial communities, or microbiomes, are the major drivers of global biogeochemical cycles, acting as primary producers and decomposers across the water column in the oceans. Thus, they reflect changes in physicochemical properties and nutrient composition of the ocean. However, this correlation between ecological changes and the function of marine microbiomes is poorly understood. Large-scale oceanic events such as the bottom-water oxygen-depleted zone (i.e., “dead zone”) and the Deepwater Horizon oil spill in the Gulf of Mexico (GoM) render the ecosystem fragile. These events decrease survival rates of pelagic and coastal macrofauna and affect the biodiversity of the region. As part …

Aberrant Epigenomic Modulation Of Glucocorticoid Receptor Gene (Nr3c1) In Early Life Stress And Major Depressive Disorder Correlation: Systematic Review And Quantitative Evidence Synthesis, Laurens Holmes Jr., Emily Shutman, Chinacherem Chinaka, Kerti Deepika, Lavisha Palaez, Kirk W. Dabney

Community & Environmental Health Faculty Publications

Early life stress (ELS) induced by psychological trauma, child maltreatment, maternal separation, and domestic violence predisposes to psycho-behavioral pathologies during adulthood, namely major depressive disorder (MDD), anxiety, and bipolar affective disorder. While environmental data are available in illustrating this association, data remain to be established on the epigenomic underpinning of the nexus between ELS and MDD predisposition. Specifically, despite the observed aberrant epigenomic modulation of the NR3C1, a glucocorticoid receptor gene, in early social adversity and social threats in animal and human models, reliable scientific data for intervention mapping in reducing social adversity and improving human health is required. We …

Implication Of Spiritual Network Support System In Epigenomic Modulation And Health Trajectory, Laurens Holmes Jr., Chinacherem Chinaka, Hikma Elmi, Kerti Deepika, Lavisha Palaez, Michael Enwere, Olumuyiwa T. Akinola, Kirk W. Dabnet

Community & Environmental Health Faculty Publications

With challenges in understanding the multifactorial etiologies of disease and individual treatment effect heterogeneities over the past four decades, much has been acquired on how physical, chemical and social environments a ffect human health, predisposing certain subpopulations to adverse health outcomes, especially the socio-environmentally disadvantaged (SED). Current translational data on gene and adverse environment interaction have revealed how adverse gene-environment interaction, termed aberrant epigenomic modulation, translates into impaired gene expression via messenger ribonucleic acid (mRNA) dysregulation, reflecting abnormal protein synthesis and hence dysfunctional cellular differentiation and maturation. The environmental influence on gene expression observed in most literature includes physical, chemical, …

Dynamics Of Trophoblast Differentiation In Peri-Implantation–Stage Human Embryos, Rachel C. West, Hao Ming, Deirdre M. Logsdon, Jiangwen Sun, Sandeep K. Rajput, Rebecca A. Kile, William B. Schoolcraft, R. Michael Roberts, Rebecca L. Krisher, Zongliang Jiang, Ye Yuan

Computer Science Faculty Publications

Single-cell RNA sequencing of cells from cultured human blastocysts has enabled us to define the transcriptomic landscape of placental trophoblast (TB) that surrounds the epiblast and associated embryonic tissues during the enigmatic day 8 (D8) to D12 peri-implantation period before the villous placenta forms. We analyzed the transcriptomes of 3 early placental cell types, cytoTB (CTB), syncytioTB (STB), and migratoryTB (MTB), picked manually from cultured embryos dissociated with trypsin and were able to follow sublineages that emerged from proliferating CTB at the periphery of the conceptus. A unique form of CTB with some features of STB was detectable at D8, …

Multiple Cytosolic Dna Sensors Bind Plasmid Dna After Transfection, Nina Semenova, Masa Bosnjak, Katarina Znidar, Maja Cemazar, Loree Heller

Bioelectrics Publications

Mammalian cells express a variety of nucleic acid sensors as one of the first lines of defense against infection. Despite extensive progress in the study of sensor signaling pathways during the last decade, the detailed mechanisms remain unclear. In our previous studies, we reported increased type I interferon expression and the upregulation of several proposed cytosolic DNA sensors after transfection of several tumor cell types with plasmid DNA (pDNA). In the present study, we sought to reveal the early events in the cytosolic sensing of this nucleic acid in a myoblast cell line. We demonstrated that DNA-dependent activator of interferon …

Genome-Wide Identification Of Short 2',3'-Cyclic Phosphate-Containing Rnas And Their Regulation In Aging., Megumi Shigematsu, Keisuke Morichika, Takuya Kawamura, Shozo Honda, Yohei Kirino

Computational Medicine Center Faculty Papers

RNA molecules generated by ribonuclease cleavage sometimes harbor a 2',3'-cyclic phosphate (cP) at their 3'-ends. Those cP-containing RNAs (cP-RNAs) form a hidden layer of transcriptome because standard RNA-seq cannot capture them as a result of cP's prevention of an adapter ligation reaction. Here we provide genome-wide analyses of short cP-RNA transcriptome across multiple mouse tissues. Using cP-RNA-seq that can exclusively sequence cP-RNAs, we identified numerous novel cP-RNA species which are mainly derived from cytoplasmic tRNAs, mRNAs, and rRNAs. Determination of the processing sites of substrate RNAs for cP-RNA generation revealed highly-specific RNA cleavage events between cytidine and adenosine in cP-RNA …

Rasp 4: Ancestral State Reconstruction Tool For Multiple Genes And Characters, Yan Yu, Christopher Blair, Xingjin He

Publications and Research

With the continual progress of sequencing techniques, genome-scale data are increasingly used in phylogenetic studies. With more data from throughout the genome, the relationship between genes and different kinds of characters is receiving more attention. Here, we present version 4 of RASP, a software to reconstruct ancestral states through phylogenetic trees. RASP can apply generalized statistical ancestral reconstruction methods to phylogenies, explore the phylogenetic signal of characters to particular trees, calculate distances between trees, and cluster trees into groups. RASP 4 has an improved graphic user interface and is freely available from http://mnh.scu.edu.cn/soft/blog/RASP (program) and https://github.com/sculab/RASP (source code).

4d Electron Microscopy Of T Cell Activation., Yue Lu, Byung-Kuk Yoo, Alphonsus H C Ng, Jungwoo Kim, Sinchul Yeom, Jau Tang, Milo M Lin, Ahmed H Zewail, James R Heath

Articles, Abstracts, and Reports

T cells can be controllably stimulated through antigen-specific or nonspecific protocols. Accompanying functional hallmarks of T cell activation can include cytoskeletal reorganization, cell size increase, and cytokine secretion. Photon-induced near-field electron microscopy (PINEM) is used to image and quantify evanescent electric fields at the surface of T cells as a function of various stimulation conditions. While PINEM signal strength scales with multiple of the biophysical changes associated with T cell functional activation, it mostly strongly correlates with antigen-engagement of the T cell receptors, even under conditions that do not lead to functional T cell activation. PINEM image analysis suggests that …

Magnetosome Gene Duplication As An Important Driver In The Evolution Of Magnetotaxis In The Alphaproteobacteria, Haijian Du, Wenyan Zhang, Wensi Zhang, Weijia Zhang, Hongmiao Pan, Yongxin Pan, Dennis A. Bazylinski, Long-Fei Wu, Tian Xiao, Wei Lin

Life Sciences Faculty Research

The evolution of microbial magnetoreception (or magnetotaxis) is of great interest in the fields of microbiology, evolutionary biology, biophysics, geomicrobiology, and geochemistry. Current genomic data from magnetotactic bacteria (MTB), the only prokaryotes known to be capable of sensing the Earth’s geomagnetic field, suggests an ancient origin of magnetotaxis in the domain Bacteria. Vertical inheritance, followed by multiple independent magnetosome gene cluster loss, is considered to be one of the major forces that drove the evolution of magnetotaxis at or above the class or phylum level, although the evolutionary trajectories at lower taxonomic ranks (e.g., within the class level) remain largely …

Correction To: Transcriptome Analyses Of Tumor-Adjacent Somatic Tissues Reveal Genes Co-Expressed With Transposable Elements, Micky Chung, G. M. Jonaid, Sophia Quinton, Austin Ross, Corinne E. Sexton, Adrian Alberto, Cody Clymer, Daphnie Churchill, Omar Navarro Leija, Mira V. Han

Life Sciences Faculty Research

Following publication of the original article [1], the authors reported errors in Table 2 wherein all “KZFP” in the gene names should be changed to “ZNF”.

Specific Effects Of Antitumor Active Norspermidine On The Structure And Function Of Dna, Takashi Nishio, Yuko Yoshikawa, Chwen-Yang Shew, Naoki Umezawa, Tsunehiko Higuchi, Kenichi Yoshikawa

Publications and Research

We compared the effects of trivalent polyamines, spermidine (SPD) and norspermidine (NSPD), a chemical homologue of SPD, on the structure of DNA and gene expression. The chemical structures of SPD and NSPD are different only with the number of methylene groups between amine groups,[N-3-N-4-N] and [N-3-N-3-N], respectively. SPD plays vital roles in cell function and survival, including in mammals. On the other hand, NSPD has antitumor activity and is found in some species of plants, bacteria and algae, but not in humans. We found that both polyamines exhibit biphasic effect; enhancement and inhibition on in vitro gene expression, where SPD …

Characterization And Amplification Of Retrotransposable Elements Platy-1 And Alu In The Cebidae Lineage Of Platyrrhine Primates, Jessica Storer

LSU Doctoral Dissertations

Alu mobile elements are much more than “junk DNA”. Inherent properties such as high copy number, small ~300 bp size, and their nearly homoplasy-free nature make these elements particularly useful in resolving primate phylogenies. In addition, shared sequence features and identity with the Alu element allow for discovery of new SINE retrotransposons, such as the Platyrrhine-limited Platy-1 element. Building on previous research of subfamily analysis, the Platy-1 and Alu elements can be used not only to explore the controversial New World monkey (NWM) phylogeny, but also the mode and tempo of their amplification in different primate genera and species.

Chapter …

A Genome-Wide Assessment Of The Ancestral Neural Crest Gene Regulatory Network, Dorit Hockman, Vanessa Chong-Morrison, Stephen A. Green, Daria Gavriouchkina, Ivan Candido-Ferreira, Irving T. C. Ling, Ruth M. Williams, Chris T. Amemiya, Jeramiah J. Smith, Marianne E. Bronner, Tatjana Sauka-Spengler

Biology Faculty Publications

The neural crest (NC) is an embryonic cell population that contributes to key vertebrate-specific features including the craniofacial skeleton and peripheral nervous system. Here we examine the transcriptional and epigenomic profiles of NC cells in the sea lamprey, in order to gain insight into the ancestral state of the NC gene regulatory network (GRN). Transcriptome analyses identify clusters of co-regulated genes during NC specification and migration that show high conservation across vertebrates but also identify transcription factors (TFs) and cell-adhesion molecules not previously implicated in NC migration. ATAC-seq analysis uncovers an ensemble of cis-regulatory elements, including enhancers of Tfap2B, …

Nuclear Tau, P53 And Pin1 Regulate Parn-Mediated Deadenylation And Gene Expression, Jorge Baquero, Sophia Varriano, Martha Ordonez, Pawel Kuczaj, Michael R. Murphy, Gamage Aruggoda, Devon Lundine, Viktoriya Morozova, Ali Elhadi Makki, Alejandra Del C. Alonso, Frida E. Kleiman

Publications and Research

While nuclear tau plays a role in DNA damage response (DDR) and chromosome relaxation, the mechanisms behind these functions are not fully understood. Here, we show that tau forms complex(es) with factors involved in nuclear mRNA processing such as tumor suppressor p53 and poly(A)-specific ribonuclease (PARN) deadenylase. Tau induces PARN activity in different cellular models during DDR, and this activation is further increased by p53 and inhibited by tau phosphorylation at residues implicated in neurological disorders. Tau’s binding factor Pin1, a mitotic regulator overexpressed in cancer and depleted in Alzheimer’s disease (AD), also plays a role in the activation of …

Increased Interactions And Engulfment Of Dendrites By Microglia Precede Purkinje Cell Degeneration In A Mouse Model Of Niemann Pick Type-C., Larisa Kavetsky, Kayla K Green, Bridget R Boyle, Fawad A K Yousufzai, Zachary M Padron, Sierra E Melli, Victoria L Kuhnel, Harriet M Jackson, Rosa E Blanco, Gareth R Howell, Ileana Soto Reyes

College of Science & Mathematics Departmental Research

Niemann Pick Type-C disease (NPC) is an inherited lysosomal storage disease (LSD) caused by pathogenic variants in the Npc1 or Npc2 genes that lead to the accumulation of cholesterol and lipids in lysosomes. NPC1 deficiency causes neurodegeneration, dementia and early death. Cerebellar Purkinje cells (PCs) are particularly hypersensitive to NPC1 deficiency and degenerate earlier than other neurons in the brain. Activation of microglia is an important contributor to PCs degeneration in NPC. However, the mechanisms by which activated microglia promote PCs degeneration in NPC are not completely understood. Here, we are demonstrating that in the Npc1nmf164 mouse cerebellum, microglia …

The Impact Of Moyamoya Disease And, Ming-Jen Lee, Shannon Fallen, Yong Zhou, David Baxter, Kelsey Scherler, Meng-Fai Kuo, Kai Wang

Articles, Abstracts, and Reports

Moyamoya disease (MMD) is a rare cerebrovascular disorder characterized by occlusion of bilateral internal carotid and intracerebral arteries with the compensatory growth of fragile small vessels. MMD patients develop recurrent infarctions in the basal ganglia and subcortical regions. Symptoms include transient ischemic attack or stroke, seizures, and headaches, which may occur suddenly or in a stepwise progression. Mutations in Ring Finger Protein 213 (

Dose Effects Of Recombinant Adenovirus Immunization In Rodents, Eric A. Weaver

Nebraska Center for Virology: Faculty Publications

Recombinant adenovirus type 5 (rAd) has been used as a vaccine platform against many infectious diseases and has been shown to be an effective vaccine vector. The dose of the vaccine varies significantly from study to study, making it very diffcult to compare immune responses and vaccine effcacy. This study determined the immune correlates induced by serial dilutions of rAd vaccines delivered intramuscularly (IM) and intranasally (IN) to mice and rats. When immunized IM, mice had substantially higher antibody responses at the higher vaccine doses, whereas, the IN immunized mice showed a lower response to the higher rAd vaccine doses. …

Sdrap: An Annotation Pipeline For Highly Scrambled Genomes, Jasper Braun

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Network Structure And Dynamics Of Biological Systems, Deena R. Schmidt

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Loop Homology Of Bi-Secondary Structures, Andrei Bura

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Quantifying Pollen Traits To Build A Mathematical Model Of Pollen Competition - A Biologist's Perspective, Rob Swanson, Alex Capaldi

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Topology And Dynamics Of Gene Regulatory Networks: A Meta-Analysis, Claus Kadelka

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Optimizing Hydroxyproline-O-Glycan Engineering In Tobacco Transient Protein Expression: Fish Il-22 And Enhanced Green Fluorescent Protein (Egfp), Cristofer Calvo

Student Theses and Dissertations

Despite the advantages of plant-produced recombinant proteins, the most important bottleneck that limits the commercialization is the low protein yields. Plants have a unique type of O-glycosylation that has potential to enhance the stability and solubility of recombinant proteins. Specifically, target gene sequences are fused with a sequence to code for hydroxyproline-O-glycosylated peptide (HypGP) tags. We targeted the expression of a very unstable rainbow trout interleukin 22 (rtIL-22) and a readily-monitored enhanced green fluorescent protein (EGFP). The HypGP-tagged rIL-22 accumulation in planta was significantly enhanced over the untagged protein and showed increase stability. Changes in gene expression of the marker …

Ornithological Expeditions To Sarawak, Malaysian Borneo, 2007-2017, Frederick H. Sheldon, Haw Chuan Lim, Phred M. Benham, Matthew L. Brady, Clare E. Brown, Ryan C. Burner, Vivien L. Chua, John C. Mittermeier, Subir B. Shakya, Paul Van Els, Mustafa Abdul Rahman, Dency F. Gawin, Zahirunisa Abdul Rahim, Luisa Duya Setia, Robert Moyle

Occasional Papers of the Museum of Natural Science, Louisiana State University

Louisiana State University, the University of Kansas, and the Universiti Malaysia Sarawak undertook collaborative research on the evolution and ecology of Bornean birds starting in 2005. This collaboration included a series of expeditions from 2007–2017 to collect and study birds at >30 sites in Sarawak, Malaysian Borneo. Here we provide information on the study-sites and summarize the main discoveries resulting from the collaboration.

Importance Of Tree-And Species-Level Interactions With Wildfire, Climate, And Soils In Interior Alaska: Implications For Forest Change Under A Warming Climate, Adrianna C. Foster, Amanda H. Armstrong, Jacquelyn K. Shuman, Herman H. Shugart, Brendan M. Rogers, Michelle C. Mack, Scott J. Goetz, K. Jon Ranson

Aspen Bibliography

The boreal zone of Alaska is dominated by interactions between disturbances, vegetation, and soils. These interactions are likely to change in the future through increasing permafrost thaw, more frequent and intense wildfires, and vegetation change from drought and competition. We utilize an individual tree-based vegetation model, the University of Virginia Forest Model Enhanced (UVAFME), to estimate current and future forest conditions across sites within interior Alaska. We updated UVAFME for application within interior Alaska, including improved simulation of permafrost dynamics, litter decay, nutrient dynamics, fire mortality, and postfire regrowth. Following these updates, UVAFME output on species-specific biomass and stem density …