Systems Biology Commons^™

Spatiotemporal Dynamics Of Nitrogen And Carbon Biogeochemistry In A Wetland-Stream Sequence, Patrick E. Hurley

Graduate Student Theses, Dissertations, & Professional Papers

Studies of aquatic ecosystems often segregate streams from the influential ponds, lakes, and wetland zones that act as important transitions between terrestrial and fluvial systems. Across the aquatic landscape, these zones interact to form linked ecosystems that function as discrete nutrient processing domains, shifting biogeochemical signals due to spatial and temporal variability in hydrologic and biologic controls. Using a mass-balance approach, we profiled nutrient dynamics along a 23-km wetland-stream sequence over three seasons. Hydrologic, morphologic, and biologic conditions, as well as landscape attributes, were quantified to determine potential controls on biogeochemical cycling in a tributary of the Upper Clark Fork …

Life History Of The Coastal Tailed Frog (Ascaphus Truei) Across An Elevational Gradient, Adrian Daniel Macedo

Cal Poly Humboldt theses and projects

The life history of a species is described in terms of its growth, longevity, and reproduction. Unsurprisingly, life history traits are known to vary in many taxa across environmental gradients. In the case of amphibians, species at high elevations and latitudes tend to have shorter breeding seasons, shorter activity periods, longer larval periods, reach sexual maturity at older ages, and produce fewer and larger clutches per year.

The Coastal Tailed Frog (Ascaphus truei) is an ideal species for the study of geographic variation in life history because it ranges across most of the Pacific Northwest from northern California …

Quantifying Signpost Usage By Captive Male White-Tailed Deer, Cassie L. Auxt, Eric S. Michel, Jonathan A. Jenks

The Prairie Naturalist

White-tailed deer (Odocoileus virginianus) use rubbing of signpost structures to communicate during the breeding season. Rubbing of signpost structures allows deer to communicate via visual and chemical cues, which allows them to establish dominance hierarchies and maintain hierarchal status throughout the breeding season (Moore and Marchinton 1974, Miller et al. 1981, Hewitt 2011). Once a living tree is rubbed, the exposed light-colored sapwood creates a stark contrast in wooded areas, increasing visibility and further enticing deer to investigate the structure (Oehler et al. 1995). Anatomically, the tubular apocrine sudoriferous glands of white-tailed deer are located at the antler …

Comparative Analysis Of Zebrafish And Planarian Model Systems For Developmental Neurotoxicity Screens Using An 87-Compound Library, D. Hagstrom, L. Truong, S. Zhang, R. Tanguay, Eva-Maria S. Collins

Biology Faculty Works

There is a clear need to establish and validate new methodologies to more quickly and efficiently screen chemicals for potential toxic effects, particularly on development. The emergence of alternative animal systems for rapid toxicology screens presents valuable opportunities to evaluate how systems complement each other. In this article, we compare a chemical library of 87-compounds in two such systems, developing zebrafish and freshwater planarians, by screening for developmental neurotoxic effects. We show that the systems’ toxicological profiles are complementary to each other, with zebrafish yielding more detailed morphological endpoints and planarians more behavioral endpoints. Overall, zebrafish was more sensitive to …

Context Is Everything: An Investigation Of Spanish River Carbonatite And Its Effects On Soil-Plant-Microorganism Systems, James Mc Jones

Theses and Dissertations (Comprehensive)

With growing concerns about agricultural sustainability and food security, the use of rock fertilizers and agrominerals is receiving renewed interest. A wide variety of geological resources have been proposed as crop nutrient sources, with silicate rocks the predominant focus. Carbonatite rocks are known to weather more readily than silicate rocks; yet, they have received relatively little attention as it is thought their high Ca and Mg contents hinder effective nutrient release. However, there is strong evidence that the nutrients within carbonatite rocks are easily accessible to plants, and that these rocks have noticable effects on crop plant growth. Here I …

The International Conference On Intelligent Biology And Medicine (Icibm) 2018: Bioinformatics Towards Translational Applications, Xiaoming Liu, Lei Xie, Zhijin Wu, Kai Wang, Zhongming Zhao, Jianhuan Ruan, Degui Zhi

Publications and Research

The 2018 International Conference on Intelligent Biology and Medicine (ICIBM 2018) was held on June 10–12, 2018, in Los Angeles, California, USA. The conference consisted of a total of eleven scientific sessions, four tutorials, one poster session, four keynote talks and four eminent scholar talks, which covered a wild range of aspects of bioinformatics, medical informatics, systems biology and intelligent computing. Here, we summarize nine research articles selected for publishing in BMC Bioinformatics.

Micrat: A Novel Algorithm For Inferring Gene Regulatory Networks Using Time Series Gene Expression Data, Bei Yang, Yaohui Xu, Andrew Maxwell, Wonryull Koh, Ping Gong, Chaoyang Zhang

Faculty Publications

Background: Reconstruction of gene regulatory networks (GRNs), also known as reverse engineering of GRNs, aims to infer the potential regulation relationships between genes. With the development of biotechnology, such as gene chip microarray and RNA-sequencing, the high-throughput data generated provide us with more opportunities to infer the gene-gene interaction relationships using gene expression data and hence understand the underlying mechanism of biological processes. Gene regulatory networks are known to exhibit a multiplicity of interaction mechanisms which include functional and non-functional, and linear and non-linear relationships. Meanwhile, the regulatory interactions between genes and gene products are not spontaneous since various …

Review: Canids Of The World: Wolves, Wild Dogs, Foxes, Jackals, Coyotes, And Their Relatives. José R. Castelló., Jonathan (Jon) Way

The Prairie Naturalist

Canids of the World is one of those reads where just when you think that something cannot be beat, this book comes out. What I mean by that is that I have read many works on wolves and other canids, most recently Nate Blakeslee’s American Wolf (Way 2017), and I have enjoyed and been enthralled with many of them. But Canids of the World may take the cake for being the most impressive book available on canids. For a modest price of just under $30.00, you can own a book that has over 600 amazing high-resolution glossy photographs of every …

New Breeding Record And Location For Wilson’S Phalarope (Phalaropus Tricolor) In The Nebraska Great Plains, Usa, Madison O. Sutton, Nico Arcilla

The Prairie Naturalist

Wilson’s phalarope (Phalaropus tricolor; Scolopacidae) is a migratory shorebird that relies on interior wetlands for foraging and breeding (Colwell and Jehl 1994, van Gils et al. 2018). Its global population status is unclear (Colwell and Jehl 1994, Lesterhuis and Clay 2010), and is variously listed as declining (Morrison et al. 2006, van Gils et al. 2018), increasing (Andres 2009, BirdLife International 2018), and exhibiting a long-term decline but recent stability (Sauer et al. 2011, Andres et al. 2012). Its global population estimate of 1.5 million birds has not been updated for 30 years, since 1988 (Colwell and Jehl 1994, Lesterhuis …

Metabolic Gas Emissions From Prairie Soil Containing Foraging Termites, Charles E. Konemann, B.M. Kard, Tom A. Royer, Mark E. Payton

The Prairie Naturalist

Differences in subterranean termite metabolic gas emissions are readily observed in laboratory experiments. However, in natural field ecosystems a primary difficulty in measuring subterranean termite gases is non-homogeneous distribution of foraging termites in soil. Our field experiment was designed to aggregate foragers of the 'eastern subterranean termite', Reticulitermes flavipes Kollar (EST), in one of four flux chamber configurations placed on a tallgrass prairie throughout 2014 and 2015. We used differently configured flux chambers to measure metabolic gas emissions from soil with or without foraging termites on The Joseph H. Williams Tallgrass Prairie Preserve (TGPP) in north-central Oklahoma. Foraging termitesaggregated in …

Comparison Of Northern Flying And Red Squirrel Phylogenies With Focus On The Insular United States, Alyssa M. Kiesow, Hugh B. Britten

The Prairie Naturalist

Northern flying squirrel (Glaucomys sabrinus) and red squirrel (Tamiasciurus hudsonicus) populations are endemic to northern North America, including the Black Hills. The Black Hills populations are considered disjunct from other populations within their range. We examined insular populations to determine whether arboreal squirrels in the Black Hills each represent a unique population. We trapped and collected ear samples from northern flying and red squirrels in the Black Hills and in areas of Montana, Wyoming, Idaho, Utah, Minnesota, and Wisconsin to infer population phylogenies with special consideration of the Black Hills population. Microsatellite loci and two mtDNA sequences were used for …

Preparing An Effective Poster Presentation, Christopher N. Jacques

The Prairie Naturalist

Greetings GPNSS members! By the time you read this editorial, many of have been experiencing the fury unleashed by ‘Old Man Winter’ and may find yourself counting the days until warmer spring temperatures return once again to the Great Plains. Until then, just a couple more months of bitter cold temperatures, strong winds, and blowing and drifting snow. But not to worry, winter also provides the cold weather enthusiasts among us a chance to enjoy a range of outdoor recreational opportunities, a chance to reflect on the previous year in review, exciting professional and personal opportunities ushered in by the …

Review: Edges And Rushes Of Minnesota: The Complete Guide To Species Identification, Welby R. Smith; Photography By Richard Haug, Edward S. Dekeyser

The Prairie Naturalist

Even the most seasoned individual with a plant identification background can relate to the difficulty of identifying sedges and rushes to the species level. Historically, one has had to rely on dichotomous keys to identify a sedge or rush species in the field. After hours of frustration, a person ends up collecting the plant and, if lucky, bringing the collection back to a herbarium where it can be compared to known specimens. I have been collecting and identifying sedge and rush species for over 25 years, and author Welby Smith along with photographer Richard Haug have published what I believe …

The Prairie Naturalist: The Journal Of The Great Plains Natural Science Society Volume 50 No. 2

The Prairie Naturalist

TABLE OF CONTENTS

43 EDITOR’S NOTE

RESEARCH ARTICLES

46 Metabolic Gas Emissions from Prairie Soil Containing Foraging Termites Charles E. Konemann, B. M. Kard, Tom A. Royer, and Mark. E. Payton

59 Comparison of northern flying and red squirrel phylogenies with focus on the insular United States Alyssa M. Kiesow, and Hugh B. Britten

NOTES

70 Two-Headed White-Tailed Deer Fetus

72 Red-Bellied Snake (Storeria occipitomacilata) Copulation in South Dakota

74 New Breeding Record and Location for Wilson's Phalarope (Phalaropus tricolor) in the Nebraska Great Plains, USA

BOOK REVIEWS

76 Sedges and Rushes of Minnesota: The Complete Guide to Species Identification. …

Red-Bellied Snake (Storeria Occipitomaculata) Copulation In South Dakota, Drew R. Davis

The Prairie Naturalist

Storeria occipitomaculata is a small, terrestrial species of snake that occurs across much of eastern North America (Ernst and Barbour 1989, Ernst 2002, Ernst and Ernst 2003). Due to this widespread distribution, S. occipitomaculata faces varied climates that likely result in regional differences in reproductive phenology. Much of what is known about the reproductive ecology of S. occipitomaculata has been documented from the southeastern portion of its range in North America (South Carolina: Semlitsch and Moran 1984, North Carolina: Willson and Dorcas 2004), though Blanchard (1937) studied a population from northern Michigan. The exact reproductive timing in this …

The Mayfly Newsletter, Donna J. Giberson

The Mayfly Newsletter

The Mayfly Newsletter is the official newsletter of the Permanent Committee of the International Conferences on Ephemeroptera.

Lakeshore Modification Reduces Secondary Production Of Macroinvertebrates In Littoral But Not Deeper Zones, Marlene Pätzig, Yvonne Vadeboncoeur, Mario Brauns

Biological Sciences Faculty Publications

Littoral macroinvertebrates are an integral component of lake food webs, but their productivity may be affected by shoreline alteration. We hypothesized that human modification of lake shores simplifies habitat diversity, which, in turn, affects littoral macroinvertebrate production and patterns of depth–production relationships. Furthermore, we expected that lakeshore modification would favor nonnative species, potentially compensating for negative effects of lakeshore modification on production of native taxa. To test these ideas, we estimated benthic macroinvertebrate production in the upper littoral, middle littoral, and profundal zones of a large lowland lake (Lake Scharmützelsee) in Northeast Germany. We collected samples between April and November …

Notes: Two-Headed White-Tailed Deer Fetus, William F. Jensen, Daniel M. Grove, Ryan J. Herigstad, William J. Haase

The Prairie Naturalist

On 6 April 2018 a female white-tailed deer (Odocoileus virginianus dakotensis) was hit and killed by a vehicle along HWY 1806 in rural Morton County, North Dakota, USA (N46o 38.617; W100o 42.901). Based upon dental eruption and wear (Severinghaus 1949), the female was estimated to be a >4.5 years-of-age. A male fetus with parapagus diprosopus (i.e., shared face) apparently was expelled from the adult female, and a domestic canine (Canis lupus familiaris) carried the fetus to a private residence. The resident contacted the North Dakota Game and Fish Department (NDGFD) to turn in the fetus. On 10 April 2018, NDGFD …

Epidermal Growth Factor-Like Ligands Regulate Dimer Selection., Jamie S. Rush

Electronic Theses and Dissertations

There are thirteen known endogenous EGF-like ligands. We previously reported that Betacellulin (BTC) increases ligand-mediated corneal wound healing more than Epidermal Growth Factor (EGF) [Peterson et al. (2014) IOVS 55(5):2870-80], although the molecular reason for this is unknown. Despite being better at promoting wound healing via enhanced cell migration, BTC has reduced receptor affinity and weaker induction of EGFR phosphorylation. These data indicate that BTC’s response is not due to enhanced affinity or EGFR-kinase activity. Receptor phosphorylation and proximity ligation assays indicate that BTC treatment significantly increases ErbB3 phosphorylation and EGFR:ErbB3 heterodimers. BTC traffics EGFR at a faster rate than …

Integrating Node Embeddings And Biological Annotations For Genes To Predict Disease-Gene Associations, Sezin Kircali Ata, Le Ou-Yang, Yuan Fang, Chee-Keong Kwoh, Min Wu, Xiao-Li Li

Research Collection School Of Computing and Information Systems

Background: Predicting disease causative genes (or simply, disease genes) has played critical roles in understandingthe genetic basis of human diseases and further providing disease treatment guidelines. While various computationalmethods have been proposed for disease gene prediction, with the recent increasing availability of biologicalinformation for genes, it is highly motivated to leverage these valuable data sources and extract useful information foraccurately predicting disease genes. Results: We present an integrative framework called N2VKO to predict disease genes. Firstly, we learn the nodeembeddings from protein-protein interaction (PPI) network for genes by adapting the well-known representationlearning method node2vec. Secondly, we combine the learned node …