Biology Commons^™

Random Genetic Drift And Selective Pressures Shaping The Blattabacterium Genome, Austin Alleman, Kate L. Hertweck, Srini Kambhampati

Biology Faculty Publications and Presentations

Estimates suggest that at least half of all extant insect genera harbor obligate bacterial mutualists. Whereas an endosymbiotic relationship imparts many benefits upon host and symbiont alike, the intracellular lifestyle has profound effects on the bacterial genome. The obligate endosymbiont genome is a product of opposing forces: genes important to host survival are maintained through physiological constraint, contrasted by the fixation of deleterious mutations and genome erosion through random genetic drift. The obligate cockroach endosymbiont, Blattabacterium – providing nutritional augmentation to its host in the form of amino acid synthesis – displays radical genome alterations when compared to its most …

Small Noncoding Rna Profiles Along Alternative Developmental Trajectories In An Annual Killifish, Amie L. Romney, Jason E. Podrabsky

Biology Faculty Publications and Presentations

Embryonic development of Austrofundulus limnaeus can occur along two phenotypic trajectories that are physiologically and biochemically distinct. Phenotype appears to be influenced by maternal provisioning based on the observation that young females produce predominately non-diapausing embryos and older females produce mostly diapausing embryos. Embryonic incubation temperature can override this pattern and alter trajectory. We hypothesized that temperature-induced phenotypic plasticity may be regulated by post-transcriptional modification via noncoding RNAs. As a first step to exploring this possibility, RNA-seq was used to generate transcriptomic profiles of small noncoding RNAs in embryos developing along the two alternative trajectories. We find distinct profiles of …

Genetic Testing: Should I Get Tested For Alzheimer’S Risk?, Troy Rohn

Biology Faculty Publications and Presentations

Genetic testing is available to people who want to know if they carry a variant of a gene that confers susceptibility for Alzheimer’s. But knowing whether to get tested is hard.

Displacement Of The Transcription Factor B Reader Domain During Transcription Initiation, Stefan Dexl, Robert Reichelt, Katharina Kraatz, Sarah Schulz, Dina Grohmann, Michael S. Bartlett, Michael Thomm

Biology Faculty Publications and Presentations

Transcription initiation by archaeal RNA polymerase (RNAP) and eukaryotic RNAP II requires the general transcription factor (TF) B/ IIB. Structural analyses of eukaryotic transcription initiation complexes locate the B-reader domain of TFIIB in close proximity to the active site of RNAP II. Here, we present the first crosslinking mapping data that describe the dynamic transitions of an archaeal TFB to provide evidence for structural rearrangements within the transcription complex during transition from initiation to early elongation phase of transcription. Using a highly specific UV-inducible crosslinking system based on the unnatural amino acid para-benzoyl-phenylalanine allowed us to analyze contacts of …

Sputum Detection Of Predisposing Genetic Mutations In Women With Pulmonary Nontuberculous Mycobacterial Disease, Julie V. Philley, Kate L. Hertweck, Anbarasu Kannan, Barbara A. Brown-Elliott, Richard J. Wallace, Anna Kurdowska, Harrison Ndetan, Karan P. Singh, Edmund J. Miller, David E. Griffith, Santanu Dasgupta

Biology Faculty Publications and Presentations

Nontuberculous mycobacterial lung disease (NTM), including Mycobacterium avium complex (MAC), is a growing health problem in North America and worldwide. Little is known about the molecular alterations occurring in the tissue microenvironment during NTM pathogenesis. Utilizing next generation sequencing, we sequenced sputum and matched lymphocyte DNA in 15 MAC patients for a panel of 19 genes known to harbor cancer susceptibility associated mutations. Thirteen of 15 NTM subjects had a diagnosis of breast cancer (BCa) before or after NTM infection. Thirty three percent (4/12) of these NTM-BCa cases exhibited at least 3 somatic mutations in sputa compared to matched lymphocytes. …

Resolving The Anomaly Of Lomatium Anomalum: Discovery Of A New Species In Southwestern Idaho (U.S.A.), Lomatium Andrusianum (Apiaceae), Mckayla Stevens, Donald H. Mansfield, James F. Smith, Mary Ann E. Feist

Biology Faculty Publications and Presentations

Apparent polyphyly within the unresolved clade of Lomatium (Apiaceae) containing L. triternatum, L. anomalum, L. thompsonii, and L. packardiae suggests conflict among current taxonomic classification schemes. To recover this clade and more clearly define species boundaries, we examined populations of L. anomalum from three geographic regions in Idaho and adjacent Oregon. Using phylogenetic, morphological, and ecological data, we conclude that the L. anomalum complex currently circumscribes multiple species. Phylogenetic analysis of the nuclear ribosomal ITS and ETS, and cpDNA rpl32-trnLUAG, rps-16 intron, trnD-trnT, ndhA intron, and psbA-trnH recovered populations from the Boise foothills as a distinct, monophyletic clade. Principal …

Follow The Rain? Environmental Drivers Of Tyrannus Migration Across The New World, Maggie P. Macpherson, Alex E. Jahn, Michael T. Murphy, Daniel H. Kim, Victor R. Cueto, Diego T. Tuero, Elliot D. Hill

Biology Faculty Publications and Presentations

Predictable seasonal changes in resources are thought to drive the timing of annual animal migrations; however, we currently understand little about which environmental cues or resources are tracked by different migratory bird species across the planet. Understanding which environmental cues or resources birds track in multiple migratory systems is a prerequisite to developing generalizable conservation plans for migratory birds in a changing global environment. Within the New World, climatic differences experienced by Nearctic–Neotropical migratory (NNM; i.e. breed in North America and spend the nonbreeding period in the Neotropics) and Neotropical austral migratory (NAM; i.e. breed and spend the nonbreeding period …

The Evolution Of Anti-Bat Sensory Illusions In Moths, Juliette J. Rubin, Chris A. Hamilton, Christopher J.W. Mcclure, Brad A. Chadwell, Akito Y. Kawahara, Jesse R. Barber

Biology Faculty Publications and Presentations

Prey transmit sensory illusions to redirect predatory strikes, creating a discrepancy between what a predator perceives and reality. We use the acoustic arms race between bats and moths to investigate the evolution and function of a sensory illusion. The spinning hindwing tails of silk moths (Saturniidae) divert bat attack by reflecting sonar to create a misleading echoic target. We characterized geometric morphometrics of moth hindwings across silk moths, mapped these traits onto a new, robust phylogeny, and found that elaborated hindwing structures have converged on four adaptive shape peaks. To test the mechanism underlying these anti-bat traits, we pit bats …

Effects Of Mowing And Tebuthiuron On The Nutritional Quality Of Wyoming Big Sagebrush, Kurt T. Smith, Jennifer S. Forbey, Jeffrey L. Black

Biology Faculty Publications and Presentations

Wyoming big sagebrush (Artemisia tridentata Nutt. ssp. wyomingensis Beetle & Young) is the most abundant and widely distributed subspecies of big sagebrush and has been treated through chemical application, mechanical treatments, and prescribed burning in efforts thought to improve habitat conditions for species such as greater sage-grouse (Centrocercus urophasianus) and mule deer (Odocoileus hemionus). Although the response of structural attributes of sagebrush communities to treatments is well understood, there is a need to identify how treatments influence the quality of sagebrush as winter food for wildlife. Our purpose was to identify how mowing and tebuthiuron …

Modification Of Diet And Foraging Range By Harvester Ants In Response To Altered Seed Availability, Ian C. Robertson, Matthew S. Schmasow

Biology Faculty Publications and Presentations

Food collection is a critical component of an individual’s life, and for eusocial insects, the colony that individual foragers support and maintain. Changes to the distribution and composition of food types in the environment are expected influence diet selection if the economics of foraging are altered. For seed-harvesting ants, the abundance and composition of seed types available on the ground typically shows a high degree of spatial and temporal variability, and not all types of seed are equally valued by foragers. We evaluated the response of Owyhee harvester ants (Pogonomyrmex salinus) to reductions in the availability of Sandberg …

Assembly And Analysis Of Unmapped Genome Sequence Reads Reveal Novel Sequence And Variation In Dogs, Lindsay Adrian Holden, Meharji Arumilli, Marjo K. Hytönen, Sruthi Hundi, Jarkko Salojärvi, Kim H. Brown, Hannes Lohi

Biology Faculty Publications and Presentations

Dogs are excellent animal models for human disease. They have extensive veterinary histories, pedigrees, and a unique genetic system due to breeding practices. Despite these advantages, one factor limiting their usefulness is the canine genome reference (CGR) which was assembled using a single purebred Boxer. Although a common practice, this results in many high-quality reads remaining unmapped. To address this whole-genome sequence data from three breeds, Border Collie (n = 26), Bearded Collie (n = 7), and Entlebucher Sennenhund (n = 8), were analyzed to identify novel, non- CGR genomic contigs using the previously validated pseudo-de novo assembly pipeline. We …

Comparative Genetic And Genomic Analysis Of The Novel Fusellovirus Sulfolobus Spindle-Shaped Virus 10, David Andrew Goodman, Kenneth M. Stedman

Biology Faculty Publications and Presentations

Viruses that infect thermophilic Archaea are unique in both their structure and genetic makeup. The lemon-shaped fuselloviruses—which infect members of the order Sulfolobales, growing optimally at 80 C and pH 3—are some of the most ubiquitous and best studied viruses of the thermoacidophilic Archaea. Nonetheless, much remains to be learned about these viruses. In order to investigate fusellovirus evolution, we have isolated and characterized a novel fusellovirus, Sulfolobus spindle-shaped virus 10 (formerly SSV-L1). Comparative genomic analyses highlight significant similarity with both SSV8 and SSV9, as well as conservation of promoter elements within the Fuselloviridae. SSV10 encodes five ORFs with no …

Osm Potentiates Preintravasation Events, Increases Ctc Counts, And Promotes Breast Cancer Metastasis To The Lung, Ken Tawara, Celeste Bolin, Jordan Koncinsky, Sujatha Kadaba, Hunter Covert, Caleb Sutherland, Laura Bond, Cheryl L. Jorcyk

Biology Faculty Publications and Presentations

Background: Systemic and chronic inflammatory conditions in patients with breast cancer have been associated with reduced patient survival and increased breast cancer aggressiveness. This paper characterizes the role of an inflammatory cytokine, oncostatin M (OSM), in the preintravasation aspects of breast cancer metastasis.

Methods: OSM expression levels in human breast cancer tissue samples were assessed using tissue microarrays, and expression patterns based on clinical stage were assessed. To determine the in vivo role of OSM in breast cancer metastasis to the lung, we used three orthotopic breast cancer mouse models, including a syngeneic 4T1.2 mouse mammary cancer model, the MDA-MB-231 …

Dietary Partitioning Of Toxic Leaves And Fibrous Stems Differs Between Sympatric Specialist And Generalist Mammalian Herbivores, M. M. Crowell, L. A. Shipley, J. S. Forbey, J. L. Rachlow, R. G. Kelsey

Biology Faculty Publications and Presentations

Dietary specialists often reside in habitats that provide a high and predictable abundance of their primary food, which is usually difficult for other herbivores to consume because of high levels of plant toxins or structural impediments. Therefore, sympatric specialist and generalist herbivores may partition food resources within and among plants. We compared how a dietary specialist (pygmy rabbit, Brachylagus idahoensis) and generalist (mountain cottontail, Sylvilagus nuttallii) used sagebrush as a food resource during winter across 3 field sites in Idaho, USA, and in controlled feeding trials with captive rabbits. The proportion of sagebrush consumed by both rabbit species …

Sexually Dimorphic Patterns Of Cell Proliferation In The Brain Are Linked To Seasonal Life-History Transitions In Red-Sided Garter Snakes, Deborah Lutterschmidt, Ashley R. Lucas, Ritta A. Karam, Vicky T. Nguyen, Meghann R. Rasmussen

Biology Faculty Publications and Presentations

Seasonal rhythms in physiology and behavior are widespread across diverse taxonomic groups and may be mediated by seasonal changes in neurogenesis, including cell proliferation, migration, and differentiation. We examined if cell proliferation in the brain is associated with the seasonal life-history transition from spring breeding to migration and summer foraging in a free-ranging population of red-sided garter snakes (Thamnophis sirtalis) in Manitoba, Canada. We used the thymidine analog 5-bromo-2′-deoxyuridine (BrdU) to label newly proliferated cells within the brain of adult snakes collected from the den during the mating season or from a road located along their migratory route. …

Dicer1 Syndrome: Dicer1 Mutations In Rare Cancers, Jake C. Robertson, Cheryl L. Jorcyk, Julia Thom Oxford

Biology Faculty Publications and Presentations

DICER1 syndrome is a rare genetic disorder that predisposes individuals to multiple cancer types. Through mutations of the gene encoding the endoribonuclease, Dicer, DICER1 syndrome disrupts the biogenesis and processing of miRNAs with subsequent disruption in control of gene expression. Since the first description of DICER1 syndrome, case reports have documented novel germline mutations of the DICER1 gene in patients with cancers as well as second site mutations that alter the function of the Dicer protein expressed. Here, we present a review of mutations in the DICER1 gene, the respective protein sequence changes, and clinical manifestations of DICER1 syndrome. Directions …

Group Characteristics Influence Distribution Patterns Of Off-Road Vehicle Recreation Within A Complex Trail System In Southwest Idaho, Eric Frey, Kathryn Demps, Ben Pauli, Julie A. Heath

Biology Faculty Publications and Presentations

Recreation on public lands is growing and is increasingly recognized as an ecosystem service providing improved health, connection to nature, and social time while also disturbing and degrading ecosystems. Human impacts must be managed, but often managers have little information about the factors that affect recreation patterns. We combined data from global positioning system receivers to record off-road vehicle (ORV) travel with a pretrip survey to determine how group characteristics, site experience, site knowledge, and motivation are associated with ORV trip patterns on public lands in southwest Idaho. Spatial and temporal extent and distribution could summarize most variation in ORV …

Gymnosperms On The Edge, Félix Forest, Justin Moat, Elisabeth Baloch, Neil A. Brummitt, Steve P. Bachman, Steffi Ickert-Bond, Peter M. Hollingsworth, Aaron Liston, Damon P. Little, Sarah Mathews, Hardeep Rai, Catarina Rydin, Dennis W. Stevenson, Philip Thomas, Sven Buerki

Biology Faculty Publications and Presentations

Driven by limited resources and a sense of urgency, the prioritization of species for conservation has been a persistent concern in conservation science. Gymnosperms (comprising ginkgo, conifers, cycads, and gnetophytes) are one of the most threatened groups of living organisms, with 40% of the species at high risk of extinction, about twice as many as the most recent estimates for all plants (i.e. 21.4%). This high proportion of species facing extinction highlights the urgent action required to secure their future through an objective prioritization approach. The Evolutionary Distinct and Globally Endangered (EDGE) method rapidly ranks species based on their evolutionary …

Taxonomy Based On Science Is Necessary For Global Conservation, Scott A. Thomson, Richard L. Pyle, Shane T. Ahyong, Miguel Alonso-Zarazaga, Joe Ammirati, Luis A. Ruedas, Multiple Additional Authors

Biology Faculty Publications and Presentations

Taxonomy is a scientific discipline that has provided the universal naming and classification system of biodiversity for centuries and continues effectively to accommodate new knowledge. A recent publication by Garnett and Christidis (Garnett ST, Christidis L. Taxonomy anarchy hampers conservation. Nature. 2017; 546(7656):25±27. https://doi.org/10.1038/546025a) expressed concerns regarding the difficulty that taxonomic changes represent for conservation efforts and proposed the establishment of a system to govern taxonomic changes. Their proposal to "restrict the freedom of taxonomic action" through governing subcommittees that would "review taxonomic papers for compliance" and their assertion that "the scientific community's failure to govern taxonomy threatens the …

Allele Frequencies Of 15 Str Loci (Identifiler™ Kit) In Basque-Americans, Jason Besecker, Gianluca Peri, Michael Davis, Josu Zubizarreta, Greg Hampikian

Biology Faculty Publications and Presentations

Individuals with Basque ancestry form a historically and culturally important minority of the population of the western United States. Allele frequencies for the 15 autosomal STRs in the AmpFlSTR^® Identifiler^® PCR Amplification Kit (Applied Biosystems) from 156 unrelated self-identified Basque individuals born in the United States are presented. Allele frequencies were used to calculate parameters commonly used in genetics and forensics including power of discrimination (PD), power of exclusion (PE), polymorphic information content (PIC), and expected heterozygosity (He). The sample population was also compared with the European Basque population and the major American ethnicities.

Ten Simple Rules For Collaborative Lesson Development, Gabriel A. Devenyi, Remi Emonet, Rayna M. Harris, Kate L. Hertweck, Damien Irving, Ian Milligan, Greg Wilson

Biology Faculty Publications and Presentations

Lessons take significant effort to build and even more to maintain. Most academics do this work on their own, but leveraging a community approach can make educational resource development more sustainable, robust, and responsive. Treating lessons as a community resource to be updated, adapted, and improved incrementally can free up valuable time while increasing quality.

Draft Genome Sequence Of A Dictyoglomus Sp. From An Enrichment Culture Of A New Zealand Geothermal Spring, Anna-Louise Reysenbach, John A. Donaho, John F. Kelley, Emily St. John, Christina Turner, Mircea Podar, Matthew B. Stott

Biology Faculty Publications and Presentations

A draft genome of a novel Dictyoglomus sp., NZ13-RE01, was obtained from a New Zealand hot spring enrichment culture. The 1,927,012-bp genome is similar in both size and G+C content to other Dictyoglomus spp. Like its relatives, Dictyoglomus sp. NZ13-RE01 encodes many genes involved in complex carbohydrate metabolism.

Beyond The Matrix: The Many Non-Ecm Ligands For Integrins, Bryce Lafoya, Jordan A. Munroe, Alison Miyamoto, Michael A. Detweiler, Jacob J. Crow, Tana Gazdik, Allan R. Albig

Biology Faculty Publications and Presentations

The traditional view of integrins portrays these highly conserved cell surface receptors as mediators of cellular attachment to the extracellular matrix (ECM), and to a lesser degree, as coordinators of leukocyte adhesion to the endothelium. These canonical activities are indispensable; however, there is also a wide variety of integrin functions mediated by non-ECM ligands that transcend the traditional roles of integrins. Some of these unorthodox roles involve cell-cell interactions and are engaged to support immune functions such as leukocyte transmigration, recognition of opsonization factors, and stimulation of neutrophil extracellular traps. Other cell-cell interactions mediated by integrins include hematopoietic stem cell …

Draft Genome Sequence Of A Novel Thermofilum Sp. Strain From A New Zealand Hot Spring Enrichment Culture, Anna-Louise Reysenbach, John A. Donaho, Todd M. Hinsch, John F. Kelley, Kathleen Kouba, Mircea Podar, Matthew B. Stott

Biology Faculty Publications and Presentations

A draft genome of a new Thermofilum sp. strain was obtained from an enrichment culture metagenome. Like its relatives, Thermofilum sp. strain NZ13 is adapted to organic-rich thermal environments and has to depend on other organisms and the environment for some key amino acids, purines, and cofactors.

Replication Rapidly Recovers And Continues In The Presence Of Hydroxyurea In Escherichia Coli, Samvel A. Nazaretyan, Neda Savic, Michael Sadek, Brandy J. Hackert, Justin Courcelle, Charmain T. Courcelle

Biology Faculty Publications and Presentations

In both prokaryotes and eukaryotes, hydroxyurea is suggested to inhibit DNA replication by inactivating ribonucleotide reductase and depleting deoxyribonucleoside triphosphate pools. In this study, we show that the inhibition of replication in Escherichia coli is transient even at concentrations of 0.1 M hydroxyurea and that replication rapidly recovers and continues in its presence. The recovery of replication does not require the alternative ribonucleotide reductases, NrdEF and NrdDG, or translesion DNA polymerases, Pol II, Pol IV, or Pol V. Ribonucleotides are incorporated at higher frequencies during replication in the presence of hydroxyurea. However, these do not contribute significantly to the observed …

A Comparison Of Resveratrol And Other Polyphenolic Compounds On Notch Activation And Endothelial Cell Activity, Bryce Lafoya, Jordan A. Munroe, Allan R. Albig

Biology Faculty Publications and Presentations

Resveratrol is a polyphenolic compound produced by plants which makes its way into the human diet through plant-based foods. It has been shown to provide many health benefits, helping to ward of age-related diseases and promoting cardiovascular health. Additionally, resveratrol is a potent activator of the Notch signaling pathway. While resveratrol receives the most attention as a polyphenolic nutraceutical, other compounds with similar structures may be more potent regulators of specific cellular processes. Here, we compare resveratrol, apigenin, chrysin, genistein, luteolin, myricetin, piceatannol, pterostilbene, and quercetin for their ability to regulate Notch signaling. In addition, we compare the ability of …

Assessing Patterns Of Barn Owl Tyto Alba Occupancy From Call Broadcast Surveys, Tempe Regan, Christopher J.W. Mcclure, James R. Belthoff

Biology Faculty Publications and Presentations

Owing to habitat loss, changes in farming practices, urbanization, and high mortality through vehicle collisions, barn owls Tyto alba are a species of conservation concern in portions of their range. This species can be secretive and difficult to survey, particularly away from breeding sites, so factors related to barn owl occurrence often remain unknown. We conducted nighttime broadcast surveys for barn owls during the early- and post-breeding seasons and used an occupancy modeling framework to understand how factors related to landcover, landscape features, and human development related to occupancy in southern Idaho, USA. We also assessed the effectiveness of using …

Constitutive Map-Kinase Activation Suppresses Germline Apoptosis In Nth-1 Dna Glycosylase Deficient C. Elegans, Henok Kassahun, Tamina Sengupta, Alfonso Schiavi, Suzanne Estes, Silvia Maglioni, Hanne K. Skjeldam, Katarzyna Arczewska, Nicole L. Brockway, Lars Eide, Natascia Ventura, Hilde Nilsen

Biology Faculty Publications and Presentations

Oxidation of DNA bases, an inevitable consequence of oxidative stress, requires the base excision repair (BER) pathway for repair. Caenorhabditis elegans is a well-established model to study phenotypic consequences and cellular responses to oxidative stress. To better understand how BER affects phenotypes associated with oxidative stress, we characterised the C. elegans nth-1 mutant, which lack the only DNA glycosylase dedicated to repair of oxidative DNA base damage, the NTH-1 DNA glycosylase. We show that nth-1 mutants have mitochondrial dysfunction characterised by lower mitochondrial DNA copy number, reduced mitochondrial membrane potential, and increased steady-state levels of reactive oxygen species. Consistently, nth-1 …

Lyttr Regulatory Systems: A Potential New Class Of Prokaryotic Sensory System, Zhengzhong Zou, Hua Qin, Amanda E. Brenner, Rahul Raghavan, Jess A. Millar, Qiang Gu, Zhoujie Xie, Jens Kreth, Justin Merritt

Biology Faculty Publications and Presentations

The most commonly studied prokaryotic sensory signal transduction systems include the one-component systems, phosphosignaling systems, extracytoplasmic function (ECF) sigma factor systems, and the various types of second messenger systems. Recently, we described the regulatory role of two separate sensory systems in Streptococcus mutans that jointly control bacteriocin gene expression, natural competence development, as well as a cell death pathway, yet they do not function via any of the currently recognized signal transduction paradigms. These systems, which we refer to as LytTR Regulatory Systems (LRS), minimally consist of two proteins, a transcription regulator from the LytTR Family and a transmembrane protein …

Quantitative Effects Of Soil Salinity On The Symbiosis Of Wild Lima Bean (Phaseolus Lunatus L.) And Bradyrhizobium In Costa Rica, Daniel J. Ballhorn, Emily R. Wolfe, Jess Tyler, Wren Ronan, Scott Sands-Gouner, Curran Shaw, Mehmet Ali Balkan, Stefanie Kautz

Biology Faculty Publications and Presentations

Global climate change and local anthropogenic activities are increasing soil salinization with permanent negative effects on agricultural and ecosystem productivity. While salt stress is known to affect plant performance, its effects on the association with key microbial plant symbionts, such as legume-associated nitrogen-fixing rhizobia, are less understood. In this field study conducted in Costa Rica (Puntarenas), we used sympatrically-occurring wild lima bean (Phaseolus lunatus L.) and Bradyrhizobium to quantify biomass production of unfertilized rhizobial (R+) and fertilized rhizobia-free (R-) plants at different levels of experimentally manipulated salinity in native soil. In response to salt stress, nodulation was significantly reduced even …