Digital Commons Network^™

Effects Of Nitrogen And Phosphorus Fertilization On Soil Carbon Fractions In Alpine Meadows On The Qinghai-Tibetan Plateau, Jin Hua Li, Yu Jie Yang, Bo Wen Li, Wen Jin Li, Gang Wang, Johannes M. H. Knops

School of Biological Sciences: Faculty Publications

In grassland ecosystems, N and P fertilization often increase plant productivity, but there is no concensus if fertilization affects soil C fractions. We tested effects of N, P and N+P fertilization at 5, 10, 15 g m^-2 yr^-1 (N₅, N₁₀, N₁₅, P₅, P₁₀, P₁₅, N₅P₅, N₁₀P₁₀, and N₁₅P₁₅) compared to unfertilized control on soil C, soil microbial biomass and functional diversity at the 0– 20 cm and 20–40 cm depth in an alpine meadow …

Immunity Of The Saccharomyces Cerevisiae Ssy5 Mrna To Nonsense-Mediated Mrna Decay, Jesseeca Obenoskey, Dakota R. Lane, Audrey L. Atkin, Bessie W. Kebaara

School of Biological Sciences: Faculty Publications

The nonsense-mediated mRNA decay (NMD) pathway is a specialized pathway that triggers the rapid degradation of select mRNAs. Initially, identified as a pathway that degrades mRNAs with premature termination codons, NMD is now recognized as a pathway that also regulates some natural mRNAs. Since natural mRNAs do not typically contain premature termination codons, these mRNAs contain features that target them to NMD. In Saccharomyces cerevisiae mRNAs with a typically long 3’UTRs are usually degraded by NMD, however in some conditions a constitutively expressed SSY5 mRNA with multiple NMD targeting signals including an atypically long 3’-UTR is an exception. We investigated …

Genome-Wide Gene Expression Effects Of Sex Chromosome Imprinting In Drosophila, Bernardo Lemos, Alan T. Branco, Pan-Pan Jiang, Daniel L. Hartl, Colin D. Meiklejohn

School of Biological Sciences: Faculty Publications

Imprinting is well-documented in both plant and animal species. In Drosophila, the Y chromosome is differently modified when transmitted through the male and female germlines. Here, we report genome-wide gene expression effects resulting from reversed parent-of-origin of the X and Y chromosomes. We found that hundreds of genes are differentially expressed between adult male Drosophila melanogaster that differ in the maternal and paternal origin of the sex chromosomes. Many of the differentially regulated genes are expressed specifically in testis and midgut cells, suggesting that sex chromosome imprinting might globally impact gene expression in these tissues. In contrast, we observed much …

Atx1/Atcompass And The H3k4me3 Marks: How Do They Activate Arabidopsis Genes?, Michael E. Fromm, Zoya Avramova

School of Biological Sciences: Faculty Publications

Despite the proven correlation between gene transcriptional activity and the levels of tri-methyl marks on histone 3 lysine4 (H3K4me3) of their nucleosomes, whether H3K4me3 contributes to, or “registers,” activated transcription is still controversial. Other questions of broad relevance are whether histone-modifying proteins are involved in the recruitment of Pol II and the general transcription machinery and whether they have roles other than their enzyme activities. We address these questions as well as the roles of the ARABIDOPSIS HOMOLOG OF TRITHORAX1 (ATX1), of the COMPASS-related (AtCOMPASS) protein complex, and of their product, H3K4me3, at ATX1-dependent genes. We suggest that the ambiguity …

Role Of An Archaeal Pita Transporter In The Copper And Arsenic Resistance Of Metallosphaera Sedula, An Extreme Thermoacidophile, Samuel Mccarthy, Chenbing Al, Garrett Wheaton, Rahul Tevatla, Valerie Eckrich, Robert Kelly, Paul H. Blum

School of Biological Sciences: Faculty Publications

Thermoacidophilic archaea, such as Metallosphaera sedula, are lithoautotrophs that occupy metal-rich environments. In previous studies, an M. sedula mutant lacking the primary copper efflux transporter, CopA, became copper sensitive. In contrast, the basis for supranormal copper resistance remained unclear in the spontaneous M. sedula mutant, CuR1. Here, transcriptomic

analysis of copper-shocked cultures indicated that CuR1 had a unique regulatory response to metal challenge corresponding to the upregulation of 55 genes. Genome resequencing identified 17 confirmed mutations unique to CuR1 that were likely to change gene function. Of these, 12 mapped to genes with annotated function associated with transcription, metabolism, …

Identification And Codon Reading Properties Of 5-Cyanomethyl Uridine, A New Modified Nucleoside Found In The Anticodon Wobble Position Of Mutant Haloarchaeal Isoleucine Trnas, Debabrata Mandal, Caroline Köhrer, Dan Su, Ramesh Babu, Clement T.Y. Chan, Yuchen Liu, Dieter Söll, Paul H. Blum, Masayasu Kuwahara, Peter C. Dedon, Uttam L. Rajbhandary

School of Biological Sciences: Faculty Publications

Most archaea and bacteria use a modified C in the anticodon wobble position of isoleucine tRNA to base pair with A but not with G of the mRNA. This allows the tRNA to read the isoleucine codon AUA without also reading the methionine codon AUG. To understand why a modified C, and not U or modified U, is used to base pair with A, we mutated the C34 in the anticodon of Haloarcula marismortui isoleucine tRNA (tRNA₂^Ile) to U, expressed the mutant tRNA in Haloferax volcanii, and purified and analyzed the tRNA. Ribosome binding experiments show that …

Endogenous Aba Extraction And Measurement From Arabidopsis Leaves, Ning Liu, Yong Ding, Michael Fromm, Zoya Avramova

School of Biological Sciences: Faculty Publications

The endogenous messenger, the phytohormone abscisic acid (ABA) plays a major role in plant’s adaption to drought, salinity, cold and other abiotic stresses. In addition to abiotic stress signaling, ABA is involved also in developmental regulation and in responses to diverse biotic stresses. Dehydration stress results in a strong increase in endogenous ABA levels, which can be perceived by RCAR/PYR1/PYL receptors, initiating the ABA signaling pathway to coordinate the genome-wide gene expression, and plants adaptive physiological responses. ABA biosynthesis triggered by environmental cues as well as developmental signals occurs predominantly in vascular parenchyma cells. The measurement of ABA content in …

Aba Signaling Is Necessary But Not Sufficient For Rd29b Transcriptional Memory During Successive Dehydration Stresses In Arabidopsis Thaliana, Laetitia Virlouvet, Yong Ding, Hiroaki Fujii, Zoya Avramova, Michael Fromm

School of Biological Sciences: Faculty Publications

Plants subjected to a prior dehydration stress were seen to have altered transcriptional responses during a subsequent dehydration stress for up to 5 days after the initial stress. The abscisic acid (ABA) inducible RD29B gene of Arabidopsis thaliana was strongly induced after the first stress and displayed transcriptional memory with transcript levels nine-fold higher during the second dehydration stress. These increased transcript levels were due to an increased rate of transcription and are associated with an altered chromatin template during the recovery interval between the dehydration stresses. Here we use a combination of promoter deletion/substitutions, mutants in the trans-acting …

Quorum Sensing Activity And Control Of Yeast-Mycelium Dimorphism In Ophiostoma Floccosum, Alexander Berrocal, Claudia Oviedo, Kenneth W. Nickerson, José Navarrete

School of Biological Sciences: Faculty Publications

Quorum sensing (QS) activity in Ophiostoma fungi has not been described. We have examined the growth conditions on the control of dimorphism in Ophiostoma floccosum, an attractive biocontrol agent against blue-stain fungi, and its relationship with QS activity. In a defined culture medium with l-proline as the N source, a high inoculum size (10⁷ c.f.u. ml^-1) was the principal factor that promoted yeast-like growth. Inoculum size effect can be explained by the secretion of a QS molecule(s) (QSMs) responsible for inducing yeast morphology. QSM candidates were extracted from spent medium and their structure was determined by GC–MS. …

An Assembly Of Proteins And Lipid Domains Regulates Transport Of Phosphatidylserine To Phosphatidylserine Decarboxylase 2 In Saccharomyces Cerevisiae, Wayne R. Riekhof, Wen-I Wu, Jennifer L. Jones, Mrinalini Nikrad, Mallory M. Chan, Christopher J. R. Loewen, Dennis R. Voelker

School of Biological Sciences: Faculty Publications

Background: The machinery for interorganelle phosphatidylserine (PtdSer) transport is poorly defined at the molecular level.

Results: Molecular interaction studies identify specific protein-protein and protein-lipid interactions in PtdSer transport.

Conclusion: A protein and lipid interaction network defines key participants in PS transport to the locus of PtdSer-decarboxylase 2.

Significance: This study identifies important molecular participants involved in non-vesicular phospholipid traffic.

The Importance Of Rare Species: A Trait-Based Assessment Of Rare Species Contributions To Functional Diversity And Possible Ecosystem Function In Tall-Grass Prairies, Meha Jain, Dan F.B. Flynn, Case M. Prager, Georgia M. Hart, Caroline M. Devan, Farshid S. Ahrestani, Matthew I. Palmer, Daniel E. Bunker, Johannes M. H. Knops, Claire F. Jouseau, Shahid Naeem

School of Biological Sciences: Faculty Publications

The majority of species in ecosystems are rare, but the ecosystem consequences of losing rare species are poorly known. To understand how rare species may influence ecosystem functioning, this study quantifies the contribution of species based on their relative level of rarity to community functional diversity using a trait-based approach. Given that rarity can be defined in several different ways, we use four different definitions of rarity: abundance (mean and maximum), geographic range, and habitat specificity. We find that rarer species contribute to functional diversity when rarity is defined by maximum abundance, geographic range, and habitat specificity. However, rarer species …

Nocturnal Homing In The Tropical Amblypygid Phrynus Pseudoparvulus (Class Arachnida, Order Amblypygi), Eileen Hebets, E.J. Gering, Verner P. Bingman, Daniel D. Wiegmann

Eileen Hebets Publications

Arthropods are renowned for their navigational capabilities, with numerous examples known from insects and crustaceans. Early studies of amblypygids (Class Arachnida, Order Amblypygi) also suggest complex nocturnal navigation, despite their apparent lack of visual adaptations to the low-light conditions of a tropical understory. In a series of two studies, we use the tropical amblypygid, Phrynus pseudoparvulus, to assess their nocturnal homing ability. Our first experiment displaced and tracked resident and nonresident individuals. Resident individuals, displaced up to 4.5 m from their home refuges and released onto their home tree, were more likely to return to their previously occupied refuge than …

Why American Higher Education Needs Parasitologists, John J. Janovy Jr.

John J. Janovy, Jr. Publications

Addresses four topics that characterize the discipline of parasitology and are largely missing from our national conversation in the United States about education, especially at the college and university level. Those topics are the production of transferable skills; our perceptions of the world, especially the natural world; access to reasonably difficult problems in natural settings; and intellectual epidemiology, or the movement of ideas, innovations, and cultural items through populations. These topics have been a part of the author's discussions with fellow parasitologists for at least half a century, beginning with his choice to pursue a graduate degree under the supervision …

Detection Of Predator Cues Alters Mating Tactics In Male Wolf Spiders, Dustin J. Wilgers, Daniel Wickwire, Eileen Hebets

Eileen Hebets Publications

Males of the wolf spider, Rabidosa punctulata, exhibit condition-dependent alternative mating tactics, whereby small, poor condition males engage in multimodal courtship while large, good condition males adopt a direct mount tactic that forgoes courtship. This study explores the possibility that tactic-specific costs can help explain this unintuitive pattern of mating tactic expression. Specifically, we hypothesize that courtship signaling is costly with respect to eavesdropping by predators and that males can alter their tactic expression based upon the perceived environmental predation risk. We test this by first examining the risk of predation associated with different mating tactics. We use a …

Demographic Variation And Habitat Specialization Of Tree Species In A Diverse Tropical Forest Of Cameroon, David Kenfack, George B. Chuyong, Richard Condit, Sabrina E. Russo, Duncan W. Thomas

School of Biological Sciences: Faculty Publications

Background: Many tree species in tropical forests have distributions tracking local ridge-slope-valley topography. Previous work in a 50-ha plot in Korup National Park, Cameroon, demonstrated that 272 species, or 63% of those tested, were significantly associated with topography.

Methods: We used two censuses of 329,000 trees ≥1 cm dbh to examine demographic variation at this site that would account for those observed habitat preferences. We tested two predictions. First, within a given topographic habitat, species specializing on that habitat (‘residents’) should outperform species that are specialists of other habitats (‘foreigners’). Second, across different topographic habitats, species should perform best …

Bridging Physics And Biology Teaching Through Modeling, Anne-Marie Hoskinson, Brian A. Couch, Benjamin M. Zwickl, Kathleen A. Hinko, Marcos D. Caballero

School of Biological Sciences: Faculty Publications

As the frontiers of biology become increasingly interdisciplinary, the physics education community has engaged in ongoing efforts to make physics classes more relevant to life science majors. These efforts are complicated by the many apparent differences between these fields, including the types of systems that each studies, the behavior of those systems, the kinds of measurements that each makes, and the role of mathematics in each field. Nonetheless, physics and biology are both sciences that rely on observations and measurements to construct models of the natural world. In this article, we propose that efforts to bridge the teaching of these …

The Roles Of Cis- And Trans-Regulation In The Evolution Of Regulatory Incompatibilities And Sexually Dimorphic Gene Expression, Colin D. Meiklejohn, Joseph D. Coolon, Daniel L. Hartl, Patricia J. Wittkopp

School of Biological Sciences: Faculty Publications

Evolutionary changes in gene expression underlie many aspects of phenotypic diversity within and among species. Understanding the genetic basis for evolved changes in gene expression is therefore an important component of a comprehensive understanding of the genetic basis of phenotypic evolution. Using interspecific introgression hybrids, we examined the genetic basis for divergence in genome-wide patterns of gene expression between Drosophila simulans and Drosophila mauritiana. We find that cis-regulatory and trans-regulatory divergences differ significantly in patterns of genetic architecture and evolution. The effects of cis-regulatory divergence are approximately additive in heterozygotes, quantitatively different between males and females, …

Effect Of Prey Richness On A Consumer’S Intrinsic Growth Rate, Brian J. Darby, Michael A. Herman

School of Biological Sciences: Faculty Publications

The intrinsic growth rate of nonselective microbivores increases asymptotically with increasing prey biomass, but we do not know how intrinsic growth rate is affected by prey richness. The objective of this experiment was to determine the effect of prey richness on the growth kinetics of nematode predators while grazing on mixed bacterial lawns. We found that the intrinsic growth rate of Caenorhabditis elegans in laboratory culture increased asymptotically with prey richness. The mechanism of this pattern was primarily due to the best available prey species in the mixture: the intrinsic growth rate of the consumer feeding on a mixture of …

Construction Of A Live-Attenuated Hiv-1 Vaccine Through Genetic Code Expansion, Nanxi Wang, Yue Li, Wei Niu, Ming Sun, Ronald Cerny, Qingsheng Li, Jiantao Guo

Qingsheng Li Publications

A safe and effective vaccine against human immunodeficiency virus type 1 (HIV-1) is urgently needed to combat the worldwide AIDS pandemic, but still remains elusive. The fact that uncontrolled replication of an attenuated vaccine can lead to regaining of its virulence creates safety concerns precluding many vaccines from clinical application. We introduce a novel approach to control HIV-1 replication, which entails the manipulation of essential HIV-1 protein biosynthesis through unnatural amino acid (UAA*)-mediated suppression of genome-encoded blank codon. We successfully demonstrate that HIV-1 replication can be precisely turned on and off in vitro.

Includes supporting information.

Serial Cervicovaginal Exposures With Replication-Deficient Sivsm Induce Higher Dendritic Cell (Pdc) And Cd4+ T-Cell Infiltrates Not Associated With Prevention But A More Severe Sivmac251 Infection Of Rhesus Macaques, Shaheed A. Abdulhaqq, Melween I. Martinez, Guobin Kang, Andrea S. Foulkes, Idia V. Rodriguez, Stephanie M. Nichols, Meredith Hunter, Carlos A. Sariol, Lynnette A. Ruiz, Brian N. Ross, Xiangfan Yin, David W. Speicher, Ashley T. Haase, Preston A. Marx, Qingsheng Li, Edmundo N. Kraiselburd, Luis J. Montaner

Qingsheng Li Publications

Objective: Intravaginal exposure to simian immunodeficiency virus (SIV) acutely recruits interferon-alpha (IFN-α) producing plasmacytoid dendritic cells (pDC) and CD4+ T-lymphocyte tar-gets to the endocervix of nonhuman primates. We tested the impact of repeated cervicovaginal ex-posures to noninfectious, defective SIV particles over 72 hours on a subsequent cervicovaginal challenge with replication competent SIV. Methods: Thirty-four female Indian Rhesus macaques were given a 3-day twice-daily vaginal exposures to either SIVsmB7, a replication deficient derivative of SIVsmH3 produced by a T lymphoblast CEMx174 cell clone (n = 16), or to CEM supernatant controls (n = 18). On the fourth day, animals were either …

The Globin Gene Repertoire Of Lampreys: Convergent Evolution Of Hemoglobin And Myoglobin In Jawed And Jawless Vertebrates, Kim Schwarze, Kevin L. Campbell, Thomas Hankeln, Jay F. Storz, Federico G. Hoffmann, Thorsten Burmester

Jay F. Storz Publications

Agnathans (jawless vertebrates) occupy a key phylogenetic position for illuminating the evolution of vertebrate anatomy and physiology. Evaluation of the agnathan globin gene repertoire can thus aid efforts to reconstruct the origin and evolution of the globin genes of vertebrates, a superfamily that includes the well-known model proteins hemoglobin and myoglobin. Here, we report a comprehensive analysis of the genome of the sea lamprey (Petromyzon marinus) which revealed 23 intact globin genes and two hemoglobin pseudogenes. Analyses of the genome of the Arctic lamprey (Lethenteron camtschaticum) identified 18 full length and five partial globin gene sequences. …

Repeated Evolution Of Chimeric Fusion Genes In The Β-Globin Gene Family Of Laurasiatherian Mammals, Michael J. Gaudry, Jay F. Storz, Gary Tyler Butts, Kevin L. Campbell, Federico G. Hoffmann

Jay F. Storz Publications

The evolutionary fate of chimeric fusion genes may be strongly influenced by their recombinational mode of origin and the nature of functional divergence between the parental genes. In the β-globin gene family of placental mammals, the two postnatally expressed δ- and β-globin genes (HBD and HBB, respectively) have a propensity for recombinational exchange via gene conversion and unequal crossing-over. In the latter case, there are good reasons to expect differences in retention rates for the reciprocal HBB/HBD and HBD/ HBB fusion genes due to thalassemia pathologies associated with the HBD/HBB “Lepore” deletion mutant in humans.Here,were port a comparative …

Design Of Pso Based Robust Blood Glucose Control In Diabetic Patients, Hazem I.

Iraqi Journal of Computers, Communications, Control and Systems Engineering

In this paper, the design of robust blood glucose controller in diabetes using H-infinity technique is presented. The Particle Swarm Optimization (PSO) method is used to tune the specific structure controller parameters subject to H-infinity constraints. The Bergman model is used to represent the artificial pancreas. This model is one of the more widely used models of the effect of insulin infusion and glucose inputs on the blood glucose concentration. The results show the effectiveness of the designed controller in controlling the behavior of glucose deviation to a sudden rise in the blood glucose. The proposed controller can effectively attenuate …

Investigating The Guidance Feature Of Searching In The Genetic Algorithm, Laith Jasim, Mohamed Jasim Mohamed

Iraqi Journal of Computers, Communications, Control and Systems Engineering

There is an argument about the optimization capability of the Genetic Algorithm (GA) and whether its approach of search is guided or random. Although it has its own criticism, Schema theorem was the main effort for explaining the way a GA works, and justifying that the GA search is guided. After that, Schema theorem efforts continued for analyzing and justifying GA optimization approach with no complete analytic proof so far. In this paper a different approach, namely a statistical approach, is used to test and justify guidance feature in the Genetic Algorithm when it is used for optimization purposes. Different …

Proposed Integrated Wire/Wireless Network Intrusion Detection System, Soukaena Hassan

Iraqi Journal of Computers, Communications, Control and Systems Engineering

This research proposes “Integrated Network Intrusion Detection System (INIDS)” which is NIDS for wire/wireless networks. INIDN consider features of the three layers; transport and Internet layers for wire and data link layer for wireless. The proposal is a Data Mining (DM)-based INIDS, which trained over a labeled wire and wireless datasets (each transaction labeled normal, intrusion name or unknown), INIDS is a hybrid IDS (anomaly and misuse). INIDS, train and construct two separated proposed models these are, Wire-NIDS and Wireless-NIDS then integrate the two models to build the final INIDS. Wire-NIDS use NSL-KDD dataset; use Principle Component Analysis (PCA) as …

Lte Based E-Health Monitoring System, Muayad Sadik

Iraqi Journal of Computers, Communications, Control and Systems Engineering

Recently, the on-line health monitoring have been considered in the research to obtain pragmatic e-health systems with low cost and high efficiency. In this paper, a mobile e-health system is proposed based on an algorithm over long terms eVolution (LTE) technology that can be called as fourth generation (4G). This system controls the receiving of the transmitted health data from the patients under supervision and replies the responses of the considered algorithm. The responded signals include the required actions that should be performed by the patient and the hospital. The proposed system utilizes the LTE based mobile networks for the …

Static Stability Analysis Of Hexagonal Hexapod Robot For The Periodic Gaits, Firas A., Hind Z. Khaleel

Iraqi Journal of Computers, Communications, Control and Systems Engineering

Hexagonal hexapod robot is a flexible mechanical robot with six legs. It has the ability to walk over terrain. The hexapod robot likes insect so it has the same periodic gaits. These gaits are tripod, wave and ripple gaits. Hexapod robot needs to stay statically stable at all the times during each gait in order not to fall with three or more legs continuously contacts with the ground. The safety static stability walking can be indicated by the stability margin. In this paper we based on the forward, inverse kinematics for each hexapod’s leg to simulate the hexapod robot model …

Collective Robotics Search Using Particle System, Ahmed Ibraheem

Iraqi Journal of Computers, Communications, Control and Systems Engineering

This work introduces the implementation of particle system to be simulated to work as a group of unmanned mobile robots (swarm robots). These robots are able to locate a specified target in the predefined environment with high efficiency when driven by an optimized Particle Swarm Optimization (PSO) algorithm. The application of the particle system to the mobile robots to search for a target in the environment is called Collective Robotics Search (CRS) problem. The main benefit of this application is to eVolve better solutions than using single robot through the collective interaction of all robots between them to achieve the …

Native Insect Herbivory Limits Population Growth Rate Of A Non-Native Thistle, James O. Eckberg, Brigitte Tenhumberg, Svata M. Louda

Brigitte Tenhumberg Papers

The influence of native fauna on non-native plant population growth, size, and distribution is not well documented. Previous studies have shown that native insects associated with tall thistle (Cirsium altissimum) also feed on the leaves, stems, and flower heads of the Eurasian congener Cirsium vulgare, thus limiting individual plant performance. In this study, we tested the effects of insect herbivores on the population growth rate of C. vulgare. We experimentally initiated invasions by adding seeds at four unoccupied grassland sites in eastern Nebraska, USA, and recorded plant establishment, survival, and reproduction. Cumulative foliage and floral herbivory …

Comparison Of The Wing Polyphenic Response Of Pea Aphids (Acyrthosiphon Pisum) To Crowding And Predator Cues, Swapna R. Purandare, Brigitte Tenhumberg, Jennifer A. Brisson

Brigitte Tenhumberg Papers

1. Pea aphids (Acyrthosiphon pisum Harris; Hemiptera: Aphididae) exhibit transgenerational wing polyphenism, in which unwinged females produce genetically identical winged offspring in response to environmental cues such as overcrowding and predation risk that indicate poor habitat quality.

2. Laboratory experiments were carried out to explore the intensity of the wing polyphenic response of pea aphids exposed to cues from ladybird predators and crowding, and their response was compared with pea aphids that were not exposed to any cues (control).

3. The study used cues from two different ladybird species—Coccinella septempunctata L. (Coleoptera: Coccinellidae) and Hippodamia convergens Guérin-Méneville (Coleoptera: …