Digital Commons Network^™

Decoding The Genome With An Integrative Analysis Tool: Combinatorial Crm Decoder, Keunsoo Kang, Joomyeong Kim, Jae Hoon Chung, Daeyoup Lee

Faculty Publications

The identification of genome-wide cis-regulatory modules (CRMs) and characterization of their associated epigenetic features are fundamental steps toward the understanding of gene regulatory networks. Although integrative analysis of available genome-wide information can provide new biological insights, the lack of novel methodologies has become a major bottleneck. Here, we present a comprehensive analysis tool called combinatorial CRM decoder (CCD), which utilizes the publicly available information to identify and characterize genome-wide CRMs in a species of interest. CCD first defines a set of the epigenetic features which is significantly associated with a set of known CRMs as a code called 'trace code', …

Participational Agency, Stephen C. Yanchar

Faculty Publications

Participational agency is presented as a conceptual account of human action, volition, and possibility. Rooted in hermeneutic and narrative traditions, this view differs from other theorizing about agency (and most psychological theorizing in general) in that it makes no effort to explain human action by virtue of reified constructs. As an alternative to traditional theorizing in this area, participational agency is defined as meaningful engagement in the world and treats the experienced meaningfulness of practical human activity as its central feature. The concept of meaningful engagement is clarified through the presentation of four related themes—situated participation, existential concern, dispositional action, …

Bioactive Properties And Clinical Safety Of A Novel Milk Protein Peptide, Richard B. Kreider, Mike Iosia, Matt Cooke, Geoffrey M. Hudson, Chris Rasmussen, Helen Chen, Olof Mollstedt, Men-Hwei Tsai

Faculty Publications

Background: Milk protein fractions and peptides have been shown to have bioactive properties. This preliminary study examined the potential mechanisms of action and clinical safety of novel milk protein peptide ( MP).

Findings: A novel MP mixture inhibits the tyrosine kinase activity of epidermal growth factor receptor ( EGFR), vascular endothelial growth factor receptor 2 (VEGFR2), and insulin receptor (IR) with IC(50) of 9.85 mu M, 7.7 mu M, and 6.18 mu M respectively. In vitro, this multi-kinase inhibitor causes apoptosis in HT-29 colon cancer cells, and in a C. elegans worm study, showed a weak but significant …

Socially Induced Ovulation Synchrony And Its Effect On Seabird Population Dynamics, Shandelle M. Henson, J. M. Cushing, James L. Hayward

Faculty Publications

Spontaneous oscillator synchrony is a form of self-organization in which populations of interacting oscillators ultimately cycle together. This phenomenon occurs in a wide range of physical and biological systems. In rats and humans, oestrous/menstrual cycles synchronize through social stimulation with pheromones acting as synchronizing signals. In previous work, we showed that glaucous-winged gulls (Larus glaucescens) can lay eggs synchronously on an every-other-day schedule, and that synchrony increases with colony density. We posed a discrete-time mathematical model for reproduction during the breeding season based on the hypothesis that pre-ovulatory luteinizing hormone surges synchronize by means of visual, auditory and/or olfactory cues. …

Separation Of River Network–Scale Nitrogen Removal Among The Main Channel And Two Transient Storage Compartments, Robert J. Stewart, Wilfred M. Wollheim, Michael N. Gooseff, Martin A. Briggs, Jennifer M. Jacobs, Bruce J. Peterson, Charles S. Hopkinson

Faculty Publications

Transient storage (TS) zones are important areas of dissolved inorganic nitrogen (DIN) processing in rivers. We assessed sensitivities regarding the relative impact that the main channel (MC), surface TS (STS), and hyporheic TS (HTS) have on network denitrification using a model applied to the Ipswich River in Massachusetts, United States. STS and HTS connectivity and size were parameterized using the results of in situ solute tracer studies in first‐ through fifth‐order reaches. DIN removal was simulated in all compartments for every river grid cell using reactivity derived from Lotic Intersite Nitrogen Experiment (LINX2) studies, hydraulic characteristics, and simulated discharge. Model …

Foreign Language Houses: Identities In Transition, Wendy Baker, Jennifer Brown, Dan P. Dewey, Rob A. Martinsen

Faculty Publications

This study examined the lived experience of students participating in foreign language houses to improve their skills in Russian, French, or Japanese. American students residing in apartments with other language learners and a nativespeaking resident facilitator were required to speak with one another exclusively in the target language and participate in activities such as preparing and eating dinner together. Data sources for the study included interviews, observations, and video recordings. The data, which were analyzed qualitatively, revealed that the central experience of living in the foreign language house was the creation of a livable community and that use of the …

Direct Anthelmintic Effects Of Cereus Jamacaru (Cactaceae) On Trichostrongylid Nematodes Of Sheep: In Vivo Studies, A. F. Vatta, C. Kandu-Lelo, I. O. Ademola, J. N. Eloff

Faculty Publications

Following claims of anthelmintic activity of Cereus jamacaru DC (Cactaceae) by a commercial farmer, in vivo studies were conducted to determine the possible direct anthelmintic effects of the plant on ovine gastrointestinal nematodes. Eighteen sheep were infected with 4000 Haemonchus contortus and 6000 Trichostrongylus colubriformis larvae given in three divided doses over a period of three days. Once the infections were patent, the sheep were allocated to three groups and were drenched once a week for six weeks with fresh blended C. jamacaru plant material at a single (32.3. g/sheep) or double dose (64.6. g/sheep) or they remained as undrenched …

Intraspecific Aflatoxin Inhibition In Aspergillus Flavus Is Thigmoregulated, Independent Of Vegetative Compatibility Group And Is Strain Dependent, Changwei Huang, Archana Jha, Rebecca Sweany, Catherine Derobertis, Kenneth E. Damann

Faculty Publications

Biological control of preharvest aflatoxin contamination by atoxigenic stains of Aspergillus flavus has been demonstrated in several crops. The assumption is that some form of competition suppresses the fungus's ability to infect or produce aflatoxin when challenged. Intraspecific aflatoxin inhibition was demonstrated by others. This work investigates the mechanistic basis of that phenomenon. A toxigenic and atoxigenic isolate of A. flavus which exhibited intraspecific aflatoxin inhibition when grown together in suspended disc culture were not inhibited when grown in a filter insert-plate well system separated by a.4 or 3 μm membrane. Toxigenic and atoxigenic conidial mixtures (50:50) placed on both …

A Preliminary Report On Disordered Speech With Deep Brain Stimulation In Individuals With Parkinson's Disease, Christopher Dromey, Suzy Bjarnason

Faculty Publications

Deep brain stimulation (DBS) of the subthalamic nucleus (STN) has proven effective in treating the major motor symptoms of advanced Parkinson's disease (PD). The aim of this study was to learn which laryngeal and articulatory acoustic features changed in patients who were reported to have worse speech with stimulation. Six volunteers with PD who had bilateral STN electrodes were recorded with DBS turned on or off. Perceptual ratings reflected poorer speech performance with DBS on. Acoustic measures of articulation (corner vowel formants, diphthong slopes, and a spirantization index) and phonation (perturbation, long-term average spectrum) as well as verbal fluency scores …

The Third Covenant: People, Animals, And Land In The Jewish And Christian Scriptures, David Dillard-Wright

Faculty Publications

No abstract provided.

Inhibition Of Neutrophil Apoptosis By Pai-1, Jaroslaw W. Zmijewski, Hong Beom Bae, Jessy S. Deshane, Cynthia B. Peterson, David D. Chaplin, Edward Abraham

Faculty Publications

Increased circulating and tissue levels of plasminogen activator inhibitor 1 (PAI-1) are often present in severe inflammatory states associated with neutrophil activation and accumulation and correlate with poor clinical outcome from many of these conditions. The mechanisms by which PAI-1 contributes to inflammation have not been fully delineated. In the present experiments, we found that addition of PAI-1 to neutrophil cultures diminished the rate of spontaneous and TNFrelated apoptosis-inducing ligand-induced apoptotic cell death. The effects of PAI-1 on cell viability were associated with activation of antiapoptotic signaling pathways, including upregulation of PKB/Akt, Mcl-1, and Bcl-xL. Although urokinase-plasminogen activator receptor, lipoprotein …

Role Of Ph In A Nitric Oxide-Dependent Increase In Cytosolic Cl - In Retinal Amacrine Cells, Emily Mcmains, Evanna Gleason

Faculty Publications

Nitric oxide (NO) synthase-expressing neurons are found throughout the vertebrate retina. Previous work by our laboratory has shown that NO can transiently convert inhibitory GABAergic synapses onto cultured retinal amacrine cells into excitatory synapses by releasing Cl - from an internal store in the postsynaptic cell. The mechanism underlying this Cl -release is currently unknown. Because transport of Cl - across internal membranes can be coupled to proton flux, we asked whether protons could be involved in the NO-dependent release of internal Cl -. Using pH imaging and whole cell voltage-clamp recording, we addressed the relationship between cytosolic pH and …

Identification Of Cytochrome P450 2c2 Protein Complexes In Mouse Liver, Bin Li, Peter Yau, Byron Kemper

Faculty Publications

Interactions of microsomal cytochromes P450 (CYPs) with other proteins in the microsomal membrane are important for their function. In addition to their redox partners, CYPs have been reported to interact with other proteins not directly involved in their enzymatic function. In this study, proteins were identified that interact with CYP2C2 in vivo in mouse liver. Flag-tagged CYP2C2 was expressed exogenously in mouse liver and was affinity purified, along with associated proteins which were identified by MS and confirmed by Western blotting. Over 20 proteins reproducibly copurified with CYP2C2. The heterogeneous sedimentation velocity of CYP2C2 and associated proteins by centrifugation in …

Some Low Homogenization Pressures Improve Certain Probiotic Characteristics Of Yogurt Culture Bacteria And Lactobacillus Acidophilus La-K1, T. Muramalla, K. J. Aryana

Faculty Publications

Lactobacillus delbrueckii ssp. bulgaricus, Streptococcus salivarius ssp. thermophilus, and Lactobacillus acidophilus are dairy cultures widely used in the manufacture of cultured dairy products. Commonly used homogenization pressures in the dairy industry are 13.80 MPa or less. It is not known whether low homogenization pressures can stimulate bacteria to improve their probiotic characteristics. Objectives were to determine the effect of homogenization at 0, 3.45, 6.90, 10.34, and 13.80 MPa on acid tolerance, bile tolerance, protease activity, and growth of L. delbrueckii ssp. bulgaricus LB-12, S. salivarius ssp. thermophilus ST-M5, and L. acidophilus LA-K. The cultures were individually inoculated in cool autoclaved …

Dietary Whey Protein Decreases Food Intake And Body Fat In Rats, June Zhou, Michael J. Keenan, Jack N. Losso, Anne M. Raggio, Li Shen, Kathleen L. Mccutcheon, Richard T. Tulley, Marc R. Blackman, Roy J. Martin

Faculty Publications

We investigated the effects of dietary whey protein on food intake, body fat, and body weight gain in rats. Adult (11-12 week) male Sprague-Dawley rats were divided into three dietary treatment groups for a 10-week study: control. Whey protein (HP-W), or high-protein content control (HP-S). Albumin was used as the basic protein source for all three diets. HP-W and HP-S diets contained an additional 24% (wt/wt) whey or isoflavone-free soy protein, respectively. Food intake, body weight, body fat, respiratory quotient (RQ), plasma cholecystokinin (CCK), glucagon like peptide-1 (GLP-1), peptide YY (PYY), and leptin were measured during and/or at the end …

Register Of The Camp Floyd Field School Records, J. Michael Hunter

Faculty Publications

The Brigham Young University Field School of Archaeology excavated part of Camp Floyd during the 1980s. College credit was offered to both university and high school students for participating in the field work. This Register contains an inventory of 4 boxes of materials from 1982 to 1992, including field school correspondence, field notes, laboratory notes, historical research notes, photos, copy orders, flyers, student information, budgets, artifact records, newspapers articles, journal articles, historical records such as enlistments, deaths, and supply inventories. The materials inventoried are housed in the Camp Floyd State Park Museum at Camp Floyd Stagecoach Inn State Park, 18035 …

Up-Regulation Of P-Glycoprotein Reduces Intracellular Accumulation Of Beta Amyloid: Investigation Of P-Glycoprotein As A Novel Therapeutic Target For Alzheimer's Disease, Alaa H. Abuznait, Courtney Cain, Drury Ingram, David Burk, Amal Kaddoumi

Faculty Publications

Objectives: Several studies have suggested the efflux transporter P-glycoprotein (P-gp) to play a role in the etiology of Alzheimer's disease through the clearance of amyloid beta (Aβ) from the brain. In this study, we aimed to investigate the possibility of P-gp as a potential therapeutic target for Alzheimer's disease by examining the impact of P-gp up-regulation on the clearance of Aβ, a neuropathological hallmark of Alzheimer's disease. Methods: Uptake studies for 125I-radiolabelled Aβ 1-40, and fluorescent immunostaining technique for P-gp and fluorescent imaging of Aβ 1-40 were carried out in LS-180 cells following treatment with drugs known to induce P-gp …

Spatial Ecology Of The Palm-Leaf Skeletonizer, Homaledra Sabelella (Lepidoptera: Coleophoridae), James T. Cronin

Faculty Publications

Understanding the processes that determine the distribution of populations is a fundamental goal in ecology. In this study, I determined the relative contribution of space and the biotic and abiotic environment to the distribution of the palm-leaf skeletonizer Homaledra sabalella (PLS; Lepidoptera: Coleophoridae) among patchily distributed dwarf palmettos (Sabal minor; Arecaceae). Based on surveys conducted at two sites in the Sherburne Wildlife Management Area, Louisiana, I found that the distribution of the PLS was primarily related to local environmental conditions - number of PLS increased with palmetto height, was greater in dry versus wet habitats, and varied in an inconsistent …

Alterations In The Transciptome And Antibiotic Susceptibility Of Staphylococcus Aureus Grown In The Presence Of Diclofenac, James T. Riordan, Joanne M. Dupre, Stephanie A. Cantore-Matyi, Atul Kumar-Singh, Yang Song, Shahrear Zaman, Sonia Horan, Nada S. Helal, Vijayaraj Nagarajan, Mohamed O. Elasri, Brian J. Wilkinson, John E. Gustafson

Faculty Publications

Background

Diclofenac is a non-steroidal anti-inflammatory drug (NSAID) which has been shown to increase the susceptibility of various bacteria to antimicrobials and demonstrated to have broad antimicrobial activity. This study describes transcriptome alterations in S. aureus strain COL grown with diclofenac and characterizes the effects of this NSAID on antibiotic susceptibility in laboratory, clinical and diclofenac reduced-susceptibility (Dc^RS) S. aureus strains.

Methods

Transcriptional alterations in response to growth with diclofenac were measured using S. aureus gene expression microarrays and quantitative real-time PCR. Antimicrobial susceptibility was determined by agar diffusion MICs and gradient plate analysis. Ciprofloxacin accumulation was measured …

Progressive Cenozoic Cooling And The Demise Of Antarctica's Last Refugium, John B. Anderson, Sophie Warny, Rosemary A. Askin, Julia S. Wellner, Steven M. Bohaty, Alexandra E. Kirshner, Daniel N. Livsey, Alexander R. Simms, Tyler R. Smith, Werner Ehrmann, Lawrence A. Lawver, David Barbeau, Sherwood W. Wise, Denise K. Kulhenek, Fred M. Weaver, Wojciech Majewski

Faculty Publications

The Antarctic Peninsula is considered to be the last region of Antarctica to have been fully glaciated as a result of Cenozoic climatic cooling. As such, it was likely the last refugium for plants and animals that had inhabited the continent since it separated from the Gondwana supercontinent. Drill cores and seismic data acquired during two cruises (SHALDRIL I and II) in the northernmost Peninsula region yield a record that, when combined with existing data, indicates progressive cooling and associated changes in terrestrial vegetation over the course of the past 37 million years. Mountain glaciation began in the latest Eocene …

Luther On Translating The Bible, Mary Jane Haemig

Faculty Publications

Martin Luther—reformer, theologian, exegete, pastor, teacher, and counselor—was also a skilled translator. His defense of his translation of Rom 3:28 (“by faith alone”) and of several psalms provides insight into the principles that guided his translation and continue to inform the difficult and necessary work of translation.

Oncolytic Herpes Simplex Virus 1 Encoding 15-Prostaglandin Dehydrogenase Mitigates Immune Suppression And Reduces Ectopic Primary And Metastatic Breast Cancer In Mice, Jason D. Walker, Inder Sehgal, Konstantin G. Kousoulas

Faculty Publications

Oncolytic herpes simplex virus 1 (HSV-1) viruses armed with immunomodulatory transgenes have shown potential for enhanced antitumor therapy by overcoming tumor-based immune suppression and promoting antitumor effector cell development. Previously, we reported that the new oncolytic HSV-1 virus, OncSyn (OS), engineered to fuse tumor cells, prevented tumor growth and metastasis to distal organs in the 4T1/BALB/c immunocompetent breast cancer mouse model, suggesting the elicitation of antitumor immune responses (Israyelyan et al., Hum. Gen. Ther. 18:5, 2007, and Israyelyan et al., Virol. J. 5:68, 2008). The OSV virus was constructed by deleting the OS viral host shutoff gene (vhs; UL41) to …

Regulation Of The Edwardsiella Ictaluri Type Iii Secretion System By Ph And Phosphate Concentration Through Esra, Esrb, And Esrc, Matthew L. Rogge, Ronald L. Thune

Faculty Publications

A recently described Edwardsiella ictaluri type III secretion system (T3SS) with functional similarity to the Salmonella pathogenicity island 2 T3SS is required for replication in channel catfish head-kidney-derived macrophages (HKDM) and virulence in channel catfish. Quantitative PCR and Western blotting identified low pH and phosphate limitation as conducive to expression of the E. ictaluri T3SS, growth conditions that mimic the phagosomal environment. Mutagenesis studies demonstrated that expression is under the control of the EsrAB two-component regulatory system. EsrB also induces upregulation of the AraC-type regulatory protein EsrC, which enhances expression of the EscB/EseG chaperone/effector operon in concert with EsrB and …

Acquisition Of Rickettsia Felis By Cat Fleas During Feeding, Kathryn E. Reif, Michael T. Kearney, Lane D. Foil, Kevin R. Macaluso

Faculty Publications

Evidence for horizontal routes of transmission for Rickettsia felis has come from detection of R. felis infection in vertebrates and multiple blood-feeding arthropods; however, infection of cat fleas, Ctenocephalides felis, during blood feeding has not been demonstrated. In this study, the ability of cat fleas to acquire R. felis through an infectious blood meal with subsequent vertical transmission was examined. Utilizing an artificial feeding system, Rickettsia-naive fleas were exposed to R. felis-infected blood meals and monitored for subsequent infection at weekly intervals for 4 weeks. At 7 days postexposure (dpe) ∼52% of fleas successfully acquired rickettsiae and R. felis DNA; …

Altered Gene Expression And Spongiotrophoblast Differentiation In Placenta From A Mouse Model Of Diabetes In Pregnancy, J. M. Salbaum, C. Kruger, X. Zhang, N. Arbour Delahaye, G. Pavlinkova, D. H. Burk, C. Kappen

Faculty Publications

Aims/hypothesis: Pregnancies complicated by diabetes have a higher risk of adverse outcomes for mothers and children, including predisposition to disease later in life, e.g. metabolic syndrome and hypertension. We hypothesised that adverse outcomes from diabetic pregnancies may be linked to compromised placental function, and sought to identify cellular and molecular abnormalities in diabetic placenta. Methods: Using a mouse model of diabetic pregnancy, placental gene expression was assayed at mid-gestation and cellular composition analysed at various stages. Genome-wide expression profiling was validated by quantitative PCR and tissue localisation studies were performed to identify cellular correlates of altered gene expression in diabetic …

Transcriptional Profiles Uncover Aspergillus Flavus-Induced Resistance In Maize Kernels, Meng Luo, Robert L. Brown, Zhi Yuan Chen, Abebe Menkir, Jiujiang Yu, Deepak Bhatnagar

Faculty Publications

Aflatoxin contamination caused by the opportunistic pathogen A. flavus is a major concern in maize production prior to harvest and through storage. Previous studies have highlighted the constitutive production of proteins involved in maize kernel resistance against A. flavus' infection. However, little is known about induced resistance nor about defense gene expression and regulation in kernels. In this study, maize oligonucleotide arrays and a pair of closely-related maize lines varying in aflatoxin accumulation were used to reveal the gene expression network in imbibed mature kernels in response to A. flavus' challenge. Inoculated kernels were incubated 72 h via the laboratory-based …

Christian's Aren't Perfect ...: Christ's Ministry In The Heavenly Sanctuary, Felix H. Cortez

Faculty Publications

No abstract provided.

Serum Igf-1 Concentrations Change With Soy And Seaweed Supplements In Healthy Postmenopausal American Women, Jane Teas, Mohammad R. Irhimeh, Susan Druker, Thomas G. Hurley, James R. Hébert, Todd M. Savarese, Mindy S. Kurzer

Faculty Publications

Insulin-like growth factor 1 (IGF-1) is an anabolic hormone important for growth and development. However, high-circulating serum concentrations in adults are associated with increased risk of postmenopausal breast cancer. Nutritional status and specific foods influence serum IGF-1 concentrations. Breast cancer incidence is typically low in Asian countries where soy is commonly consumed. Paradoxically, soy supplement trials in American women have reported significant increases in IGF-1. Seaweed also is consumed regularly in Asian countries where breast cancer risk is low. We investigated the possibility that seaweed could modify soy-associated increases in IGF-1 in American women. Thirty healthy postmenopausal women (mean age …

"Christians Aren’T Perfect Just Forgiven": A Second Look To Christ’S Ministry In The Heavenly Sanctuary, Felix H. Cortez

Faculty Publications

No abstract provided.

Infectivity Period Of Mice Inoculated With Human Adenoviruses, Rashmi Krishnapuram, Heather Kirk-Ballard, Aamri Zuberi, Nikhil V. Dhurandhar

Faculty Publications

Due to non-productive infections, mice are not a good model to study some human adenoviruses. However, mice provide an excellent model to study the metabolic effects of human adenovirus, Ad36. Research interest in Ad36 is increasing rapidly, and consequently an increase in the use of mice as a model is anticipated. However, little is known about the transmission potential of Ad36 from infected mice to other laboratory animals or personnel. While underestimating the infectivity could promote inadvertent spread of Ad36, overstating it could drain valuable laboratory resources and animals. Therefore, we determined the duration of infectivity in female C57BL/6J mice …