Biology Commons^™

The Triggering Receptor Expressed On Myeloid Cells 2: “Trem-Ming” The Inflammatory Component Associated With Alzheimer's Disease, Troy T. Rohn

Biology Faculty Publications and Presentations

Alzheimer's disease (AD) is an age-related neurodegenerative disorder characterized by a progressive loss of memory and cognitive skills. Although much attention has been devoted concerning the contribution of the microscopic lesions, senile plaques, and neurofibrillary tangles to the disease process, inflammation has long been suspected to play a major role in the etiology of AD. Recently, a novel variant in the gene encoding the triggering receptor expressed on myeloid cells 2 (TREM2) has been identified that has refocused the spotlight back onto inflammation as a major contributing factor in AD. Variants in TREM2 triple one's risk of developing late-onset AD. …

Phytochemistry Predicts Habitat Selection By An Avian Herbivore At Multiple Spatial Scales, Graham G. Frye, John W. Connelly, David D. Musil, Jennifer S. Forbey

Biology Faculty Publications and Presentations

Animal habitat selection is a process that functions at multiple, hierarchically structured spatial scales. Thus multi-scale analyses should be the basis for inferences about factors driving the habitat selection process. Vertebrate herbivores forage selectively on the basis of phytochemistry, but few studies have investigated the influence of selective foraging (i.e., fine-scale habitat selection) on habitat selection at larger scales. We tested the hypothesis that phytochemistry is integral to the habitat selection process for vertebrate herbivores. We predicted that habitats selected at three spatial scales would be characterized by higher nutrient concentrations and lower concentrations of plant secondary metabolites (PSMs) than …

Matrix Gla Protein Reinforces Angiogenic Resolution, Bikram Sharma, Allan R. Albig

Biology Faculty Publications and Presentations

Matrix Gla Protein (MGP) is an ECM molecule commonly associated with dysfunctions of large blood vessels such as arteriosclerosis and atherosclerosis. However, the exact role of MGP in the microvasculature is not clear. Utilizing a mouse MGP knockout model we found that MGP suppresses angiogenic sprouting from mouse aorta restricts microvascular density in cardiac and skeletal muscle, and is an endogenous inhibitor of tumor angiogenesis. Similarly, morpholino based knockdown of MGP in zebrafish embryos caused a progressive loss of luminal structures in intersegmental vessels, a phenotype reminiscent of Dll4/Notch inhibition. Accordingly, MGP suppressed Notch-dependent Hes-1 promoter activity and expression of …

Caspase-Cleaved Glial Fibrillary Acidic Protein Within Cerebellar White Matter Of The Alzheimer's Disease Brain, Troy T. Rohn, Lindsey W. Catlin, Wayne W. Poon

Biology Faculty Publications and Presentations

Although the cerebellum is generally thought of as an area spared of Alzheimer's disease (AD) pathology, recent evidence suggests that balance and mobility dysfunction may be magnified in affected individuals. In the present study, we sought to determine the degree of pathological changes within the cerebellum utilizing an antibody that specifically detects caspase-cleaved GFAP within degenerating astrocytes. Compared to control subjects, application of this antibody, termed the GFAP caspase-cleavage product (GFAPccp) antibody, revealed widespread labeling in cerebellar white matter with little staining observed in grey matter. Staining was observed within damaged astrocytes, was often localized near blood vessels and co-localized …

Nullomer Derived Anticancer Peptides (Nullops): Differential Lethal Effects On Normal And Cancer Cells In Vitro, Abdelkrim Alileche, Jayita Goswami, William Bourland, Mike Davis, Greg Hampikian

Biology Faculty Publications and Presentations

We demonstrate the first use of the nullomer (absent sequences) approach to drug discovery and development. Nullomers are the shortest absent sequences determined in a species, or group of species. By identifying the shortest absent peptide sequences from the NCBI databases, we screened several potential anti-cancer peptides. In order to improve cell penetration and solubility we added short poly arginine tails (5Rs), and initially solubilized the peptides in1M trehalose. The results for one of the absent sequences 9R (RRRRRNWMWC), and its scrambled version 9S1R (RRRRRWCMNW) are reported here. We refer to these peptides derived from nullomers as PolyArgNulloPs. A control …

When Dna Won't Work, Rick Visser, Greg Hampikian

Biology Faculty Publications and Presentations

Within the criminal justice system, DNA (deoxyribonucleic acid) evidence has often been heralded as the gold standard of forensic science. In a 2009 U.S. Supreme Court decision, Chief Justice Roberts wrote that "DNA testing has an unparalleled ability both to exonerate the wrongly convicted and to identify the guilty. It has the potential to significantly improve both the criminal justice system and police investigative practices." The phrases “unparalleled ability” and “significantly improve” reflect the high standard that DNA has attained in both forensic science and the entire criminal justice system.

Forensic DNA technology has a major advantage over other forensic …

Phylogeny Of A Neotropical Clade In The Gesneriaceae: More Tales Of Convergent Evolution, John L. Clark, Minde M. Funke, Aaron M. Duffy, James F. Smith

Biology Faculty Publications and Presentations

The Gesneriaceae is a family known for convergent evolution of complex floral forms. As a result, defining genera and resolving evolutionary relationships among such genera using morphological data alone has been challenging and often does not accurately reflect monophyletic lineages. The tribe Episcieae is the most diverse within Neotropical Gesneriaceae in terms of its number of species and morphological diversity. As a result, defining genera using floral characters has been historically troublesome. Here we investigate relationships among genera of the tribe using an array of chloroplast DNA, nuclear ribosomal genes, and low-copy nuclear genes to provide resolution for the monophyly …

Identification Of An Amino-Terminal Fragment Of Apolipoprotein E4 That Localizes To Neurofibrillary Tangles Of The Alzheimer’S Disease Brain, Troy T. Rohn, Lindsey W. Catlin, Kendra G. Coonse, Jeffrey W. Habig

Biology Faculty Publications and Presentations

Although the risk factor for harboring the apolipoprotein E4 (apoE4) allele in late-onset Alzheimer’s disease (AD) is well known, the mechanism by which apoE4 contributes to AD pathogenesis has yet to be clarified. Preferential cleavage of the ApoE4 isoform relative to other polymorphic forms appears to be significant, as the resulting fragments are associated with hallmarks of AD. To examine the possible role of apoE4 proteolysis in AD, we designed a site-directed antibody directed at position D172, which would yield a predicted amino-terminal fragment previously identified in AD brain extracts. Western blot analysis utilizing this novel antibody, termed the amino-terminal …

Landscape Of Transcription In Human Cells, Jainab Khatun

Biology Faculty Publications and Presentations

Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic subcellular localizations are also poorly understood. Because RNA represents the direct output of the genetic information encoded by genomes and a significant proportion of a cell’s regulatory capabilities are focused on its synthesis, processing, transport, modification and translation, the generation of such a catalogue is crucial for understanding genome function. Here we report evidence that three-quarters of the human genome is capable of being transcribed, …

An Integrated Encyclopedia Of Dna Elements In The Human Genome, Jainab Khatun

Biology Faculty Publications and Presentations

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence …

Oncostatin M Promotes Mammary Tumor Metastasis To Bone And Osteolytic Bone Degradation, Celeste Bolin, Ken Tawara, Caleb Sutherland, Jeff Redshaw, Patrick S. Aranda, Jim Moselhy, Robin Anderson, Cheryl Jorcyk

Biology Faculty Publications and Presentations

Oncostatin M (OSM) is an interleukin-6 (IL-6) family cytokine that has been implicated in a number of biological processes including inflammation, hematopoiesis, immune responses, development, and bone homeostasis. Recent evidence suggests that OSM may promote breast tumor invasion and metastasis. We investigated the role of OSM in the formation of bone metastases in vivo using the 4T1.2 mouse mammary tumor model in which OSM expression was knocked down using shRNA (4T1.2-OSM). 4T1.2-OSM cells were injected orthotopically into Balb/c mice, resulting in a greater than 97% decrease in spontaneous metastasis to bone compared to control cells. Intratibial injection of these same …

Long Noncoding Rnas Are Rarely Translated In Two Human Cell Lines, Jainab Khatun, Brian Risk, Morgan Giddings

Biology Faculty Publications and Presentations

Data from the Encyclopedia of DNA Elements (ENCODE) project show over 9640 human genome loci classified as long noncoding RNAs (lncRNAs), yet only ~100 have been deeply characterized to determine their role in the cell. To measure the protein-coding output from these RNAs, we jointly analyzed two recent data sets produced in the ENCODE project: tandem mass spectrometry (MS/MS) data mapping expressed peptides to their encoding genomic loci, and RNA-seq data generated by ENCODE in long polyA+ and polyA– fractions in the cell lines K562 and GM12878. We used the machinelearning algorithm RuleFit3 to regress the peptide data against RNA …

Predicting Occupancy Of Wintering Migratory Birds: Is Microhabitat Information Necessary?, Christopher J. W. Mcclure, Brian W. Rolek, Geoffrey E. Hill

Biology Faculty Publications and Presentations

Information regarding microhabitat, here defined as small-scale vegetation structure, is often useful in predicting use of habitat by birds. Quantifying microhabitat, however, is expensive and labor intensive compared to assessment of habitat at a larger scale, possibly from remotely sensed imagery. To assess the importance of microhabitat information in constructing predictive models of habitat occupancy, we compared occupancy models built on the basis of macro- and microhabitat together and separately. We based our models on counts of wintering migratory bird species and vegetation surveys within Tuskegee National Forest, Alabama, completed during winter 2009. Models built from macrohabitat data only outperformed …

The Effect Of Human Activities And Their Associated Noise On Ungulate Behavior, Casey L. Brown, Amanda R. Hardy, Jesse R. Barber, Kurt M. Fristrup, Kevin R. Crooks, Lisa M. Angeloni

Biology Faculty Publications and Presentations

Background: The effect of anthropogenic noise on terrestrial wildlife is a relatively new area of study with broad ranging management implications. Noise has been identified as a disturbance that has the potential to induce behavioral responses in animals similar to those associated with predation risk. This study investigated potential impacts of a variety of human activities and their associated noise on the behavior of elk (Cervus elaphus) and pronghorn (Antilocapra americana) along a transportation corridor in Grand Teton National Park.

Methodology/Principal Findings: We conducted roadside scan surveys and focal observations of ungulate behavior while concurrently recording …

Morphology And Phylogeny Of A New Woodruffiid Ciliate, Etoschophrya Inornata Sp. N. (Ciliophora, Colpodea, Platyophryida), With An Account On Evolution Of Platyophryids, William A. Bourland, Greg Hampikian, Peter Vďačný

Biology Faculty Publications and Presentations

We studied the morphology, morphometry, resting cysts and molecular phylogeny of a new woodruffiid ciliate, Etoschophrya inornata, from ephemeral puddles and two lacustrine habitats in Idaho, North-west USA. Up to now, the genus Etoschophrya has included a single species, Etoschophrya oscillatoriophaga, from which our new form is distinguished by (i) the absence of interkinetal cortical granules and, consequently, the absence of extrusible red material in methyl green-pyronin stains, (ii) usually ≥5 adoral membranelles vs. usually four, (iii) greater length and length/width ratio, (iv) prominent cortical furrows vs. inconspicuous and (v) adaptation to non-saline semi-terrestrial and lacustrine habitats in …

Shorter Migration Distances Associated With Higher Winter Temperatures Suggest A Mechanism For Advancing Nesting Phenology Of American Kestrels Falco Sparverius, Julie A. Heath, Karen Steenhof, Mark A. Foster

Biology Faculty Publications and Presentations

Global climate change has affected avian migration patterns and nesting phenology. Changes in one phase of a bird's cycle will most likely affect other stages, but few studies focus simultaneously on multiple life-history events. We used western North American ringing records and Christmas Bird Counts to examine whether changes in migration patterns were concordant with advancing American kestrel Falco sparverius nesting phenology. Consistent with previous findings, male kestrels migrated shorter distances than female kestrels, and kestrels nesting in southern latitudes migrated shorter distances than kestrels nesting in more northern areas. In addition, kestrel migration distance decreased significantly from 1960 to …

Novel Mouse Mammary Cell Lines For In Vivo Bioluminescence Imaging (Bli) Of Bone Metastasis, Celeste Bolin, Caleb Sutherland, Ken Tawara, Jim Moselhy, Cheryl Jorcyk

Biology Faculty Publications and Presentations

Background

Tumor cell lines that can be tracked in vivo during tumorigenesis and metastasis provide vital tools for studying the specific cellular mechanisms that mediate these processes as well as investigating therapeutic targets to inhibit them. The goal of this study was to engineer imageable mouse mammary tumor cell lines with discrete propensities to metastasize to bone in vivo. Two novel luciferase expressing cell lines were developed and characterized for use in the study of breast cancer metastasis to bone in a syngeneic mouse model.

Results

The 4T1.2 luc3 and 66c14 luc2 cell lines were shown to have high …

Nuclear Ribosomal Internal Transcribed Spacer (Its) Region As A Universal Dna Barcode Marker For Fungi, Eric Tretter, Yan Wang, Eric M. Johnson, Merlin M. White

Biology Faculty Publications and Presentations

Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding …

The Y-Str Genetic Diversity Of An Idaho Basque Population, With Comparison To European Basques And Us Caucasians, Josu Zubizarreta, Michael C. Davis, Greg Hampikian

Biology Faculty Publications and Presentations

Fifty unrelated Basque males from southwest Idaho were typed for the 17 Y-STR loci in the Yfiler multiplex kit (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, YGATA_H4.1 and DYS385a/b). A total of 42 haplotypes were identified, with no more than two individuals sharing a single haplotype. The haplotype diversity (HD) was 0.9935, and gene diversity (D) over loci was 0.457 ± 0.137. The Idaho Basque population was compared to the source population from the Basque autonomous region of Northern Spain and Southern France, as well as a US Caucasian population. The haplotype diversity …

Environmental Regulation Of Dormancy Loss In Seeds Of Lomatium Dissectum, Melissa Dawn Scholten

Boise State University Theses and Dissertations

Lomatium dissectum (Nutt.) Mathias & Constance is a perennial plant found across much of western North America. For disturbed lands within this range, there is interest in using L. dissectum in restoration. A problem in the propagation of L. dissectum is that at the time of dispersal the seeds are dormant. Thus, prior to usage in restoration projects the type of dormancy and the procedures necessary to release dormancy in these seeds must be determined. Determining the type of dormancy and the treatments necessary to break dormancy in L. dissectum seeds was the primary focus of this study. To approach …

Parathyroid Hormone-Related Protein Is Not Required For Normal Ductal Or Alveolar Development In The Post-Natal Mammary Gland, Kata Boras-Granic, Joshua Vanhouten, Minoti Hiremath, John Wysolmerski

Biology Faculty Publications and Presentations

PTHrP is necessary for the formation of the embryonic mammary gland and, in its absence, the embryonic mammary bud fails to form the neonatal duct system. In addition, PTHrP is produced by the breast during lactation and contributes to the regulation of maternal calcium homeostasis during milk production. In this study, we examined the role of PTHrP during post-natal mammary development. Using a PTHrP-lacZ transgenic mouse, we surveyed the expression of PTHrP in the developing post-natal mouse mammary gland. We found that PTHrP expression is restricted to the basal cells of the gland during pubertal development and becomes expressed in …

Mucosal Immunization With A Staphylococcus Aureus Isda-Cholera Toxin A2/B Chimera Induces Antigen-Specific Th2-Type Responses In Mice, Britni M. Arlian, Juliette Tinker

Biology Faculty Publications and Presentations

Staphylococcus aureus is a leading cause of opportunistic infection worldwide and a significant public health threat. The iron-regulated surface determinant A (IsdA) adhesin is essential for S. aureus colonization on human nasal epithelial cells and plays an important role in iron acquisition and resistance to human skin defenses. Here we investigated the murine immune response to intranasal administration of a cholera toxin (CT) A₂/B chimera containing IsdA. Plasmids were constructed to express the IsdA-CTA₂/B chimera and control proteins in E. coli. Proper construction of the chimera was verified by SDS-PAGE, western blot, GM1 ELISA, and …

Effects Of Developmental Conditions On Nestling American Kestrel (Falco Sparverius) Corticosterone Concentrations, Erin H. Strasser, Julie A. Heath

Biology Faculty Publications and Presentations

How nestling birds respond to stressful situations may constitute an important survival component that has lasting developmental effects on the hypothalamic pituitary adrenal (HPA) axis. As birds are exposed to increasing amounts of potential anthropogenic stressors through land use change, understanding how these factors contribute to HPA development is important. We examined whether conditions experienced during the nestling stage affected free-living American Kestrel (Falco sparverius) HPA activity prior to fledging. Kestrels experienced varying levels of human disturbance around their nest and we classified this environmental exposure as high or low environmental human disturbance based on traffic patterns and …

Depletion Of Beclin-1 Due To Proteolytic Cleavage By Caspases In The Alzheimer's Disease Brain, Troy T. Rohn, Ellen Wirawan, Raquel J. Brown, Jordan R. Harris, Eliezer Masliah, Peter Vandenabeele

Biology Faculty Publications and Presentations

The Beclin-1 protein is essential for the initiation of autophagy and recent studies suggest this function may be compromised in Alzheimer’s disease (AD). In addition, in vitro studies have supported a loss of function of Beclin-1 due to proteolytic modification by caspases. In the present study we examined whether caspase-cleavage of Beclin-1 occurs in the AD brain by designing a site-directed caspase-cleavage antibody based upon a known cleavage site within the protein at position D149. We confirmed that Beclin-1 is an excellent substrate for caspase-3 and demonstrate cleavage led to the formation of a 35 kDa C-terminal fragment labeled by …

Propagule Pressure And Introduction Pathways Of Bromus Tectorum (Cheatgrass; Poaceae) In The Central United States, Temsha D. Huttanus, Richard N. Mack, Stephen J. Novak

Biology Faculty Publications and Presentations

An introduced species' propagule pressure strongly influences the genetic diversity and evolutionary potential of its descendants and even the likelihood of biological invasion. We examined population genetic consequences arising from introduction of the invasive annual grass Bromus tectorum into the central United States (U.S.). The origin and frequency of introductions were investigated by assembling allozyme diversity data from 60 widely spaced populations. At least five introduction events contributed to the grass’s genetic diversity in the central U.S. Populations in this region have fewer alleles (30 vs. 43) and polymorphic loci (5 vs. 13) than native populations, evidence of a genetic …

The Effects Of Neonatal Handling On Adrenocortical Responsiveness, Morphological Development And Corticosterone Binding Globulin In Nestling American Kestrels (Falco Sparverius), Buddy A. Whitman, Creagh W. Breuner, Alfred M. Dufty

Biology Faculty Publications and Presentations

Early developmental experiences play an important role in development of the adult phenotype. We investigated the effects of neonatal handling on the hypothalamic-pituitary-adrenal axis in a free-living avian species, the American kestrel (Falco sparverius). In the handled group (H), kestrel chicks were handled for 15 min/day from hatching until 26 days of age, after which time blood samples were collected for analysis of adrenal responsiveness and corticosterone binding globulin (CBG) levels. The non-handled control group (NH) was left undisturbed until 26 days of age when blood samples were collected and analyzed as above. Handled and NH kestrels did not differ …

Immunolocalization Of Influenza A Virus And Markers Of Inflammation In The Human Parkinson’S Disease Brain, Troy T. Rohn, Lindsey W. Catlin

Biology Faculty Publications and Presentations

Although much is known regarding the molecular mechanisms leading to neuronal cell loss in Parkinson’s disease (PD), the initiating event has not been identified. Prevailing theories including a chemical insult or infectious agent have been postulated as possible triggers, leading to neuroinflammation. We present immunohistochemical data indicating the presence of influenza A virus within the substantia nigra pars compacta (SNpc) from postmortem PD brain sections. Influenza A virus labeling was identified within neuromelanin granules as well as on tissue macrophages in the SNpc. Further supporting a role for neuroinflammation in PD was the identification of T-lymphocytes that colocalized with an …

Passive Immunization Reduces Behavioral And Neuropathological Deficits In An Alpha-Synuclein Transgenic Model Of Lewy Body Disease, Troy Rohn

Biology Faculty Publications and Presentations

Dementia with Lewy bodies (DLB) and Parkinson's Disease (PD) are common causes of motor and cognitive deficits and are associated with the abnormal accumulation of alpha-synuclein (α-syn). This study investigated whether passive immunization with a novel monoclonal α-syn antibody (9E4) against the C-terminus (CT) of α-syn was able to cross into the CNS and ameliorate the deficits associated with α-syn accumulation. In this study we demonstrate that 9E4 was effective at reducing behavioral deficits in the water maze, moreover, immunization with 9E4 reduced the accumulation of calpain-cleaved α-syn in axons and synapses and the associated neurodegenerative deficits. In vivo studies …

A User's Guide To The Encyclopedia Of Dna Elements (Encode), Morgan Giddings, Brian Risk

Biology Faculty Publications and Presentations

The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results …

New World Origins Of Southwest Pacific Gesneriaceae: Multiple Movements Across And Within The South Pacific, Vincent L. Woo, Minde M. Funke, James F. Smith, Peter J. Lockhart, Philip J. Garnock-Jones

Biology Faculty Publications and Presentations

Coronanthereae is a tribe of ~20 species with a suite of unique morphological characters and a disjunct geographic distribution in the Southern Hemisphere. Three species are found in southern South America and the remainder in the southwest Pacific. It has been suggested, because of this distribution and disjunction, that Coronanthereae represents a relictual Gondwanan group from which the two major lineages in the family, the Old World Cyrtandroideae and the New World Gesnerioideae, originated. We tested this hypothesis by using phylogenetic analyses of nuclear and chloroplast DNA sequences, ancestral-area reconstruction, and molecular dating. The tribe is placed within the mostly …