Digital Commons Network^™

Source And Transport Of Terrigenous Organic Matter In The Upper Yukon River: Evidence From Isotope (��C-13, Δc-14, And ��N-15) Composition Of Dissolved, Colloidal, And Particulate Phases, Laodong Guo, Robie W. Macdonald

Faculty Publications

Natural organic matter was collected from the upper Yukon River and size fractionated into the (LMW-DOC), colloidal (COC, 1 kDa to 0.45 mu m) and particulate organic carbon (POC, > 0.45 mu m) phases for characterization of elemental (C and N) and isotopic (C-13, C-14 and N-15) composition to examine their sources and transport. Concentrations of total organic carbon (TOC) decreased from 3010 mu M in mid-May to 608 mu M in September, accompanying an increase in river water delta O-18 from the snowmelt to summer and early fall. COC was the predominant OC species, comprising, on average, 63 +/- 8% …

Recently Integrated Alu Retrotransposons Are Essentially Neutral Residents Of The Human Genome, Richard Cordaux, Jungnam Lee, Liv Dinoso, Mark A. Batzer

Faculty Publications

Alu elements represent the largest family of human mobile elements in copy number. A controversial issue with implications for both Alu biology and human genome evolution is whether selective pressures are affecting Alu elements on a large scale. To address this issue, we analyzed the genomic distribution of the three youngest known human Alu subfamilies (Ya5a2, Ya8 and Yb9) in conjunction with their insertion polymorphism status in the human population, since selection can only act on polymorphic elements. Our results indicate that: (i) polymorphic and fixed recently integrated Alu elements are found in genomic regions whose GC contents are statistically …

Estimating The Retrotransposition Rate Of Human Alu Elements, Richard Cordaux, Dale J. Hedges, Scott W. Herke, Mark A. Batzer

Faculty Publications

Mobile elements such as Alu repeats have substantially altered the architecture of the human genome, and de novo mobile element insertions sometimes cause genetic disorders. Previous estimates for the retrotransposition rate (RR) of Alu elements in humans of one new insertion every ∼100-125 births were developed prior to the sequencing of the human and chimpanzee genomes. Here, we used two independent methods (based on the new genomic data and on disease-causing de novo Alu insertions) to generate refined Alu RR estimates in humans. Both methods consistently yielded RR on the order of one new Alu insertion every ∼20 births, despite …

Birth Of A Chimeric Primate Gene By Capture Of The Transposase Gene From A Mobile Element, Richard Cordaux, Swalpa Udit, Mark A. Batzer, Cédric Feschotte

Faculty Publications

The emergence of new genes and functions is of central importance to the evolution of species. The contribution of various types of duplications to genetic innovation has been extensively investigated. Less understood is the creation of new genes by recycling of coding material from selfish mobile genetic elements. To investigate this process, we reconstructed the evolutionary history of SETMAR, a new primate chimeric gene resulting from fusion of a SET histone methyltransferase gene to the transposase gene of a mobile element. We show that the transposase gene was recruited as part of SETMAR 40-58 million years ago, after the insertion …

Summer Transport Estimates Of The Kamchatka Current Derived As A Variational Inverse Of Hydrophysical And Surface Drifter Data, G.G. Panteleev, P. Stabeno, V.A. Luchin, Dmitri A. Nechaev, M. Ikeda

Faculty Publications

The quasistationary summer Bering Sea circulation is reconstructed as a variational inverse of the hydrographic and atmospheric climatologies, transport estimates through the Bering Strait, and surface drifter data. Our results indicate the splitting of the Kamchatka Current in the vicinity of the Shirshov Ridge. This branching is in agreement with independent ARGO drifter observations. It was also found, that transport of the Kamchatka Current gradually increases downstream from 14 Sv in the Olyutorsky Gulf to 24 Sv in the Kamchatka Strait, which is twice higher than previous estimates.

A Time-Resolved Vibrational Spectroscopy Glimpse Into The Oxygen-Evolving Complex Of Photosynthesis, Terry M. Bricker

Faculty Publications

No abstract provided.

Nitric Oxide Transiently Converts Synaptic Inhibition To Excitation In Retinal Amacrine Cells, Brian Hoffpauir, Emily Mcmains, Evanna Gleason

Faculty Publications

Nitric oxide (NO) is generated by multiple cell types in the vertebrate retina, including amacrine cells. We investigate the role of NO in the modulation of synaptic function using a culture system containing identified retinal amacrine cells. We find that moderate concentrations of NO alter GABAA receptor function to produce an enhancement of the GABA-gated current. Higher concentrations of NO also enhance GABA-gated currents, but this enhancement is primarily due to a substantial positive shift in the reversal potential of the current. Several pieces of evidence, including a similar effect on glycine-gated currents, indicate that the positive shift is due …

Small-Scale Fuel Variation Alters Fire Intensity And Shrub Abundance In A Pine Savanna, Jarrod M. Thaxton, William J. Platt

Faculty Publications

Small-scale variation in fire intensity and effects may be an important source of environmental heterogeneity in frequently burned plant communities. We hypothesized that variation in fire intensity resulting from local differences in fuel loads produces heterogeneity in pine savanna ground cover by altering shrub abundance. To test this hypothesis, we experimentally manipulated prefire fuel loads to mimic naturally occurring fuel-load heterogeneity associated with branch falls, needle fall near large pines, and animal disturbances in a frequently burned longleaf pine (Pinus palustris) savanna in Louisiana, USA. We applied one of four fuel treatments (unaltered control, fine-fuel removal, fine-fuel addition, wood addition) …

Lipid Trafficking To The Outer Membrane Of Gram-Negative Bacteria, William T. Doerrler

Faculty Publications

The envelope of Gram-negative bacteria is composed of two distinct lipid membranes: an inner membrane and outer membrane. The outer membrane is an asymmetric bilayer with an inner leaflet of phospholipids and an outer leaflet of lipopolysaccharide. Most of the steps of lipid synthesis occur within the cytoplasmic compartment of the cell. Lipids must then be transported across the inner membrane and delivered to the outer membrane. These topological features combined with the ability to apply the tools of biochemistry and genetics make the Gram-negative envelope a fascinating model for the study of lipid trafficking. In addition, as lipopolysaccharide is …

The Shoot-Specific Expression Of Γ-Glutamylcysteine Synthetase Directs The Long-Distance Transport Of Thiol-Peptides To Roots Conferring Tolerance To Mercury And Arsenic, Yujing Li, Om Parkash Dankher, Laura Carreira, Aaron P. Smith, Richard B. Meagher

Faculty Publications

Thiol-peptides synthesized as intermediates in phytochelatin (PC) biosynthesis confer cellular tolerance to toxic elements like arsenic, mercury and cadmium, but little is known about their long-distance transport between plant organs. A modified bacterial γ-glutamylcysteine synthetase (ECS) gene, S1pt::ECS, was expressed in the shoots of the ECS-deficient, heavy-metal-sensitive cad2-1 mutant of Arabidopsis (Arabidopsis thaliana). S1pt::ECS directed strong ECS protein expression in the shoots, but no ECS was detected in the roots of transgenic plant lines. The S1pt::ECS gene restored full mercury tolerance and partial cadmium tolerance to the mutant and enhanced arsenate tolerance significantly beyond wild-type levels. After arsenic treatment, the …

Comparing Tropical Forest Tree Size Distributions With The Predictions Of Metabolic Ecology And Equilibrium Models, Helene C. Muller-Landau, Richard S. Condit, Kyle E. Harms, Christian O. Marks, Sean C. Thomas, Sarayudh Bunyavejchewin, George Chuyong, Leonardo Co, Stuart Davies, Robin Foster, Savitri Gunatilleke, Nimal Gunatilleke, Terese Hart, Stephen P. Hubbell, Akira Itoh, Abd Rahman Kassim, David Kenfack, James V. Lafrankie, Daniel Lagunzad, Hua Seng Lee, Elizabeth Losos, Jean Remy Makana, Tatsuhiro Ohkubo, Cristian Samper, Raman Sukumar, I. Fang Sun, M. N. Nur Supardi, Sylvester Tan, Duncan Thomas, Jill Thompson, Renato Valencia, Martha Isabel Vallejo, Gorky Villa Muñoz

Faculty Publications

Tropical forests vary substantially in the densities of trees of different sizes and thus in above-ground biomass and carbon stores. However, these tree size distributions show fundamental similarities suggestive of underlying general principles. The theory of metabolic ecology predicts that tree abundances will scale as the -2 power of diameter. Demographic equilibrium theory explains tree abundances in terms of the scaling of growth and mortality. We use demographic equilibrium theory to derive analytic predictions for tree size distributions corresponding to different growth and mortality functions. We test both sets of predictions using data from 14 large-scale tropical forest plots encompassing …

Testing Metabolic Ecology Theory For Allometric Scaling Of Tree Size, Growth And Mortality In Tropical Forests, Helene C. Muller-Landau, Richard S. Condit, Jerome Chave, Sean C. Thomas, Stephanie A. Bohlman, Sarayudh Bunyavejchewin, Stuart Davies, Robin Foster, Savitri Gunatilleke, Nimal Gunatilleke, Kyle E. Harms, Terese Hart, Stephen P. Hubbell, Akira Itoh, Abd Rahman Kassim, James V. Lafrankie, Hua Seng Lee, Elizabeth Losos, Jean Remy Makana, Tatsuhiro Ohkubo, Raman Sukumar, I. Fang Sun, M. N. Nur Supardi, Sylvester Tan, Jill Thompson, Renato Valencia, Gorky Villa Muñoz, Christopher Wills, Takuo Yamakura, George Chuyong, Handanakere Shivaramaiah Dattaraja, Shameema Esufali, Pamela Hall

Faculty Publications

The theory of metabolic ecology predicts specific relationships among tree stem diameter, biomass, height, growth and mortality. As demographic rates are important to estimates of carbon fluxes in forests, this theory might offer important insights into the global carbon budget, and deserves careful assessment. We assembled data from 10 old-growth tropical forests encompassing censuses of 367 ha and > 1.7 million trees to test the theory's predictions. We also developed a set of alternative predictions that retained some assumptions of metabolic ecology while also considering how availability of a key limiting resource, light, changes with tree size. Our results show that …

A Comprehensive Catalog Of Human Krab-Associated Zinc Finger Genes: Insights Into The Evolutionary History Of A Large Family Of Transcriptional Repressors, Stuart Huntley, Daniel M. Baggott, Aaron T. Hamilton, Mary Tran-Gyamfi, Shan Yang, Joomyeong Kim, Laurie Gordon, Elbert Branscomb, Lisa Stubbs

Faculty Publications

Krüppel-type zinc finger (ZNF) motifs are prevalent components of transcription factor proteins in all eukaryotes. KRAB-ZNF proteins, in which a potent repressor domain is attached to a tandem array of DNA-binding zinc-finger motifs, are specific to tetrapod vertebrates and represent the largest class of ZNF proteins in mammals. To define the full repertoire of human KRAB-ZNF proteins, we searched the genome sequence for key motifs and then constructed and manually curated gene models incorporating those sequences. The resulting gene catalog contains 423 KRAB-ZNF protein-coding loci, yielding alternative transcripts that altogether predict at least 742 structurally distinct proteins. Active rounds of …

Modelling Responses Of Pine Savannas To Climate Change And Large-Scale Disturbance, Brian Beckage, Louis J. Gross, William J. Platt

Faculty Publications

Global warming can potentially influence ecological communities through altered disturbance regimes in addition to increased temperatures. We investigate the response of pine savannas in the southeastern United States to global warming using a simple Lotka-Volterra competition model together with predicted changes to fire and hurricane disturbance regimes with global climate change. In the southeastern United States, decreased frequency of both fires and hurricanes with global warming will shift pine savannas toward a forested state. A CO2 fertilization effect that increases the growth rate of tree populations will also push southeastern landscapes from open savannas towards closed forests. Transient dynamics associated …

Natural Disturbances And The Physiognomy Of Pine Savannas: A Phenomenological Model, Frank S. Gilliam, William J. Platt, Robert K. Peet

Faculty Publications

Question: The decline of the Pinus palustris ecosystems has resulted from anthropogenic influences, such as conversion to pine plantation forestry, agriculture and land development, all of which are closely related to increases in human populations. Other effects, however, have arisen from alterations in disturbance regimes that maintain the structure and function of these ecosystems. How have alterations of the disturbance regime altered the physiognomy of 'old-growth' stands, and what are the implications for ecosystem conservation and restoration? Methods: In contrast to models that emphasize close interactions among the vertically complex strata, we develop a conceptual phenomenological model for the physiognomic …

Conservation And Restoration Of The Pinus Palustris Ecosystem, Frank S. Gilliam, William J. Platt

Faculty Publications

The well-documented decline of the Pinus palustris ecosystem has resulted from several anthropogenic influences, such as forest clearing (e.g. pine plantation forestry, agriculture) and urban development, both of which are closely related to increases in human populations. Other impacts have arisen from alterations in disturbance regimes responsible for maintaining the structure and function of these ecosystems. Restoration and management of degraded pine savanna ecosystems is critical. Identification of ecological processes that determine the structure and function of the intact system are important because successful restoration efforts should be based on sound scientific understanding. In this paper, we introduce this special …

Pine Savanna Overstorey Influences On Ground-Cover Biodiversity, William J. Platt, Susan M. Carr, Matthew Reilly, Jean Fahr

Faculty Publications

Question: Does the overstorey of pine savannas influence plant species biodiversity in the ground cover? Location: Camp Whispering Pines (30°41' N; 90°29' W), eastern Louisiana (USA). Methods: We used ecologically sensitive restoration logging to remove patches of Pinus palustris (longleaf pine) in a second-growth loess plain Pinus palustris savanna managed using frequent lightning season fires. Five years later, we measured numbers of vascular plant species and transmitted light in replicated 100-m2 plots. Treatments involved three different overstorey conditions: no overstorey for 5 years, no overstorey for several decades, and overstorey pines present for decades. Results: Both recent and long-term openings …

Characterization Of A Branchial Epithelial Calcium Channel (Ecac) In Freshwater Rainbow Trout (Oncorhynchus Mykiss), A. Shahsavarani, B. Mcneill, F. Galvez, C. M. Wood, G. G. Goss, P. P. Hwang, S. F. Perry

Faculty Publications

The entry of calcium (Ca2+) through an apical membrane epithelial calcium channel (ECaC) is thought to a key step in piscine branchial Ca2+ uptake. In mammals, ECaC is a member of the transient receptor potential (TRP) gene family of which two sub-families have been identified, TRPV5 and TPRV6. In the present study we have identified a single rainbow trout (Oncorhynchus mykiss) ECaC (rtECaC) that is similar to the mammalian TRPV5 and TRPV6. Phylogenetic analysis of the protein sequence suggests that an ancestral form of the mammalian genes diverged from those in the lower vertebrates prior to the gene duplication event …

Sauria Sines: Novel Short Interspersed Retroposable Elements That Are Widespread In Reptile Genomes, Oliver Piskurek, Christopher C. Austin, Norihiro Okada

Faculty Publications

SINEs are short interspersed retrotransposable elements that invade new genomic sites. Their retrotransposition depends on reverse transcriptase and endonuclease activities encoded by partner LINEs (long interspersed elements). Recent genomic research has demonstrated that retroposons account for at least 40% of the human genome. Hitherto, more than 30 families of SINEs have been characterized in mammalian genomes, comprising ∼4600 extant species; the distribution and extent of SINEs in reptilian genomes, however, are poorly documented. With more than 7400 species of lizards and snakes, Squamata constitutes the largest and most diverse group of living reptiles. We have discovered and characterized a novel …

Comparing The Direct And Community-Mediated Effects Of Disturbance On Plant Population Dynamics: Flooding, Herbivory And Mimulus Guttatus, Bret D. Elderd, Dan F. Doak

Faculty Publications

Competition, trophic interactions and abiotic disturbances play important roles in governing plant population dynamics, yet few studies have addressed their relative contributions or interacting effects. We used Life Table Response Experiment (LTRE) analysis, coupled with stochastic analyses, to examine how a major abiotic disturbance, flooding, influences the fitness and population growth of a common riparian plant, Mimulus guttatus, and how this effect compares and interacts with that exerted by herbivory. We also extended LTRE analysis to include nested factors, which enabled us to examine differences across experimental sites. These spatial contributions to changes in population growth rate, λ, were compared …

Mid-Season Prediction Of Wheat-Grain Yield Potential Using Plant, Soil, And Sensor Measurements, K. Girma, K. L. Martin, R. H. Anderson, D. B. Arnall, K. D. Brixey, M. A. Casillas, B. Chung, B. C. Dobey, S. K. Kamenidou, S. K. Kariuki, E. E. Katsalirou, J. C. Morris, J. Q. Moss, C. T. Rohla, B. J. Sudbury, B. S. Tubana, W. R. Raun

Faculty Publications

The components that define cereal-grain yield potential have not been well defined. The objective of this study was to collect many differing biological measurements from a long-term winter wheat (Triticum aestivum L.) study in an attempt to better define yield potential. Four treatments were sampled that annually received 0, 45, 90, and 135 kg N ha-1 at fixed rates of phosphorus (P) (30 kg ha-1) and potassium (K) (37 kg ha -1). Mid-season measurements of leaf color, chlorophyll, normalized difference vegetative index (NDVI), plant height, canopy temperature, tiller density, plant density, soil moisture, soil NH4-N, NO3-N, organic carbon (C), total …

Resisting Deep Capture: The Commercial Speech Doctrine And Junk-Food Advertising To Children, David Yosifon

Faculty Publications

The present Article is more precisely dedicated to analyzing, from a critical realist perspective, the wisdom and constitutional viability of one possible policy response to the obesity crisis: a ban on junk-food advertising to children.

This Article seeks not only to show that an effective junk-food advertising ban could pass constitutional scrutiny, but also to demonstrate, through the rigor of a constitutional analysis, the wisdom of such an approach to this substantial social problem. Simultaneously, my purpose is to show, in the context of a difficult First Amendment question, that the critical realist approach to legal theory is capable of …

Vittatispora, A New Melanosporaceous Genus From Indian Soil, Preeti Chaudhary, Jinx Campbell, David L. Hawksworth, Kedarnath N. Sastry

Faculty Publications

Vittatispora coorgii gen. sp. nov., isolated from soil in India, is described and illustrated. The fungus has morphological characteristics of the genera Melanospora, Sphaerodes and Syspastospora. The most striking feature is the presence of a thick hyaline ridge along the vertical axis of the lemonshaped ascospores wall. Perithecia also have a long neck composed of adhering hyphae, similar to that of Syspatospora. Phylogenetic studies on the 28S rDNA indicate it is closely related to Melanospora and Sphaerodes and belongs in the Ceratostomataceae. The new genus is based on the distinctive morphology and phylogenetic analyses. The fungus grew in culture only …

Phylogeny And Androecial Evolution In Schisandraceae, Inferred From Sequences Of Nuclear Ribosomal Dna Its And Chloroplast Dna TrnL-F Regions, Zhong Liu, Gang Hao, Yi-Bo Luo, Leonard B. Thien, Samuel W. Rosso, An-Ming Lu, Zhi-Duan Chen

Faculty Publications

Sequences of nuclear ribosomal DNA ITS and chloroplast trnL‐F regions were used to construct a phylogeny of Schisandraceae. The results show that there are two major clades in Schisandraceae. One is composed entirely of Schisandra species; the other contains a mixture of Schisandra and Kadsura species. Molecular data place Smith’s sect. Sphaerostema of Schisandra prominently within Kadsura, and thus neither Schisandra nor Kadsura is monophyletic, refuting the traditional division of the family into two genera based on morphological characters of mature fruits. The sister relationship between S. glabra (North America) and S. bicolor (China) and the monophyly of …

Mechanisms Imposing The Vbeta Bias Of V14a Natural Killer T Cells And Consequences For Microbial Glycolipid Recognition, Paul B. Savage, Dasten G. Wei, Shane A. Curran, Luc Teyton, Albert Bendelac

Faculty Publications

Mouse and human natural killer T (NKT) cells recognize a restricted set of glycosphingolipids presented by CD1d molecules, including self iGb3 and microbial alpha-glycuronosylceramides. The importance of the canonical Valpha 14-Jalpha18 TCR alphachain for antigen recognition by NKT cells is well recognized, but the mechanisms underlying the Vbeta8, Vbeta7, and Vbeta2 bias in mouse have not been explored. To study the influences of thymic selection and the constraints of pairing with Valpha 14-Jalpha 18, we have created a population of mature T cells expressing Valpha 14-Jalpha 18 TCRalpha chain in CD1d-deficient mice and studied its recognition properties in vitro and …

Design Of Compact Polymer Mach-Zender Interferometer And Ring Resonator With Air Trench Structures, Seunghyun Kim, Jianhua Jiang, Gregory P. Nordin

Faculty Publications

We discuss the design of a compact ring resonator (RR) and Mach-Zehnder interferometer (MZI) in a low-refractive-index-contrast waveguide material system through the use of air trenches. A narrow air trench at the intersection of one input and two output waveguides can function as a high-efficiency splitter, while wider air trenches operate as waveguide bends. We first discuss the design of individual splitters and bends and then show how they can be used to realize a compact MZI and RR. The RR has a footprint of only 70 X 100 um, and its optical efficiency at the drop wavelengths is 86%. …

Extensive Individual Variation In L1 Retrotransposition Capability Contributes To Human Genetic Diversity, Maria Del Carmen Seleme, Melissa R. Vetter, Richard Cordaux, Laurel Bastone, Mark A. Batzer, Haig H. Kazazian

Faculty Publications

Despite being scarce in the human genome, active L1 retrotrans-posons continue to play a significant role in its evolution. Because of their recent expansion, many L1s are not fixed in humans, and, when present, their mobilization potential can vary among individuals. Previously, we showed that the great majority of retrotransposition events in humans are caused by highly active, or hot. L1s. Here, in four populations of diverse geographic origins (160 haploid genomes), we investigated the degree of sequence poly-morphism of three hot L1s and the extent of individual variation in mobilization capability of their allelic variants. For each locus, we …

Phylogenetic And Ecological Determinants Of The Neotropical Dawn Chorus, Karl S. Berg, Robb T. Brumfield, Victor Apanius

Faculty Publications

The concentration of avian song at first light (i.e. the dawn chorus) is widely appreciated, but has an enigmatic functional significance. One widely accepted explanation is that birds are active at dawn, but light levels are not yet adequate for foraging. In forest communities, the onset to singing should thus be predictable from the species' foraging strata, which is ultimately related to ambient light level. To test this, we collected data from a tropical forest of Ecuador involving 57 species from 27 families of birds. Time of first song was a repeatable, species-specific trait, and the majority of resident birds, …

Antarctic Climate Cooling And Response Of Diatoms In Glacial Meltwater Streams, Rhea M.M. Esposito, S. L. Horn, D. M. Mcknight, M. J. Cox, M. C. Grant, S. A. Spaulding, P. T. Doran, K. D. Cozzetto

Faculty Publications

To understand biotic responses to an Antarctic cooling trend diatom samples from glacial meltwater streams in the McMurdo Dry Valleys, the largest ice-free area in Antarctica. Diatoms are abundant in these streams, and 24 of 40 species have only been found in the Antarctic. The percentage of these Antarctic diatom species increased with decreasing annual stream flow and increasing harshness of the stream habitat. The species diversity of assemblages reached a maximum when the Antarctic species accounted for 40-60% of relative diatom abundance. Decreased solar radiation and air-temperatures reduce annual stream flow, raising the dominance of these Antarctic species to …

Erratum: "Hard Sphere Radial Distribution Function Again", Andrij Trokhymchuk, Douglas Henderson, Ivo Nezbeda, Jan Jirsak

Faculty Publications

Some misprints have been found for parameters given by Eqs. 29 and 30 and the relevant equations in the Appendix.