Life Sciences Commons^™

Identification Of Regulatory Elements Using A Feature Selection Method, Sunduz Keles, Mark J. Van Der Laan, Michael B. Eisen

U.C. Berkeley Division of Biostatistics Working Paper Series

Many methods have been described to identify regulatory motifs in the transcription control regions of genes that exhibit similar patterns of gene expression across a variety of experimental conditions. Here we focus on a single experimental condition, and utilize gene expression data to identify sequence motifs associated with genes that are activated under this experimental condition. We use a linear model with two way interactions to model gene expression as a function of sequence features (words) present in presumptive transcription control regions. The most relevant features are selected by a feature selection method called stepwise selection with monte carlo cross …

Vitis Aestivalis F.Michx., John E. Ebinger

Specimens by Name

No abstract provided.

Familiarity Facilitates Social Learning Of Foraging Behaviour In The Guppy, Will Swaney, Jeremy Kendal, Hannah Capon, Culum Brown, Kevin N. Laland

Sentience Collection

Previous studies have shown that guppies, Poecilia reticulata, can learn the route to a food source by shoaling with knowledgeable conspecifics, and prefer to shoal with experienced foragers and familiar fish. We tested the hypothesis that guppies would learn more effectively from (1) familiar than unfamiliar demonstrators and (2) well-trained than poorly trained demonstrators. Demonstrator fish were given experience in swimming a route to a food source and then introduced into shoals of untrained observer guppies; the spread of this foraging skill was recorded over 15 trials. The demonstrators were either familiar or unfamiliar to the observers and either well …

The Effect Of Response Contingencies On Scale Model Task Performance By Chimpanzees (Pan Troglodytes), Valerie A. Kuhlmeier, Sarah T. Boysen

Sentience Collection

The effects of modified procedures on chimpanzees' (Pan troglodytes) performance in a scale model comprehension task were examined. Seven chimpanzees that previously participated in a task in which they searched an enclosure for a hidden item after watching an experimenter hide a miniature item in the analogous location in a scale model were retested under procedures incorporating response costs. In Experiment 1, chimpanzees were trained under procedures that rewarded only item retrievals occurring on the 1st search attempt. During test trials, 6 chimpanzees performed above chance, including 4 that were previously unsuccessful under the original procedures (V. A. Kuhlmeier, S. …

The Invasion Of Western Waters By Non-Native Species: Threats To The West, Western Regional Panel On Aquatic Nuisance Species

All U.S. Government Documents (Utah Regional Depository)

The waters of western North America are being transformed by invasive aquatic plants, fish, and other animals from around the world. These plants and animals, which have been introduced both intentionally and accidentally by humans, can irrevocably alter our native ecosystems. While they may be harmless in their own waters, once brought into a new ecosystem where their native predators do not exist, they can harm native species by eating their food, preying on them, transmitting diseases to which the natives have no defenses, or (like many invasive aquatic plants) simply outgrowing them. Not all non-native species cause serious problems, …

Western Rangeland Noxious Weeds: Collecting, Sharing And Using Information, U.S. Department Of The Interior, Usda, Charles Valentine Riley Memorial Foundation

All U.S. Government Documents (Utah Regional Depository)

Western rangeland weeds such as yellow starthistle, leafy spurge, Canada thistle and Russian knapweed are causing tremendous losses to agricultural industries including both crop and livestock production. Concurrently, many public lands managed by federal agencies are being steadily invaded. As a result, these lands held in the public trust are experiencing reductions in commodity yields, recreational opportunities, biodiversity and ecosystem function. Consequently, every state in the West has noxious weed management programs that endeavor to enhance the financial and technical resources available for weed management and to assist in coordination across the diverse public and private land ownership mosaic common …

An Accelerated Feeding Study For Dairy Beef Steers, D. R. Zobell

All Archived Publications

A large number of Holstein bull (steer) calves are produced by the dairy industry. Producers who purchase these calves should understand that depending on the production strategy employed, the economic outcome could be quite broad. Dairy beef calves that are intensively managed, using aggressive feeding strategies to achieve high levels of efficiency, increase the opportunity for profitability.

Preface: Proceedings Of The National Coral Reef Institute's International Conference On Scientific Aspects Of Coral Reef Assessment, Monitoring And Restoration, James Darwin Thomas

Marine & Environmental Sciences Faculty Proceedings, Presentations, Speeches, Lectures

No abstract provided.

Structure Of The Rgrgs Domain Of P115rhogef, Zhe Chen, Clark D. Wells, Paul C. Sternweis, Stephen R. Sprang

Biological Sciences Faculty Publications

p115RhoGEF, a guanine nucleotide exchange factor for Rho GTPase, is also a GTPase activating protein (GAP) for G₁₂ and G₁₃ heterotrimeric Gα subunits. Near its N-terminus, p115RhoGEF contains a domain (rgRGS) with remote sequence identity to RGS (regulators of G protein signaling) domains. The rgRGS domain is necessary but not sufficient for the GAP activity of p115RhoGEF. The 1.9 Å resolution crystal structure of the rgRGS domain shows structural similarity to RGS domains but possesses a C-terminal extension that folds into a layer of helices that pack against the hydrophobic core of the domain. Mutagenesis experiments show that …

Mutations In Sid2, A Novel Gene In Saccharomyces Cerevisiae, Cause Synthetic Lethality With Sic1 Deletion And May Cause A Defect During S Phase, Matthew D. Jacobson , '97, Claudia C. Muñoz , '99, Kirstin S. Knox , '99, Beth E. Williams , '01, Lenette L. Lu , '02, Frederick Cross , '78, Elizabeth Ann Vallen

Biology Faculty Works

SIC1 encodes a nonessential B-type cyclin/CDK inhibitor that functions at the G1/S transition and the exit from mitosis. To understand more completely the regulation of these transitions, Mutations causing synthetic lethality with sic1 Delta were isolated. In this screen, we identified a novel gene, SID2, which encodes an essential protein that appear., to be required for DNA replication or repair. sid2-1 sic1 Delta strains and sid2-21 temperature-sensitive strains arrest preanaphase as large-budded cells with a single nucleus, a short spindle, and an similar to 2C DNA content. RAD9, which is necessary for the DNA damage checkpoint, is required for the …

Applying Habitat Equivalency Analysis For Coral Reef Damage Assessment And Restoration, J. Walter Milon, Richard E. Dodge (Editor)

Marine & Environmental Sciences Faculty Articles

Quantifying economic damages and restoration measures for injuries to coral reefs has been a difficult task. In the U.S., habitat equivalency analysis (HEA) has emerged as a novel tool that combines biological and economic information to identify replacement habitats of an appropriate scale to substitute for the interim losses resulting from coral reef injuries. This article provides a review of the basic principles underlying HEA and a discussion of important considerations in applying HEA. These considerations include: how to describe coral reef functions and related human uses, recovery rates of coral reef organisms at injured sites with natural and active …

Site-Dependent Differences In Artificial Reef Function: Implications For Coral Reef Restoration, Robin L. Sherman, David S. Gilliam, Richard E. Spieler

Marine & Environmental Sciences Faculty Articles

There is an increasing use of artificial structure in coral reef restoration (for references, see Spieler et al., this volume). Often artificial reef structures are chosen for a restoration project simply because they were used elsewhere. However, it is questionable whether the results obtained at one restoration site can be extrapolated to another. In recent years, several studies have examined the effect of artificial reef site selection on formation of associated fish, algae, and/or invertebrate assemblages (Alevizon et al., 1985; Blinova et al., 1994; Bombace et al., 1994; Caley and St. John, 1996; Chang, 1985; Haughton and Aiken, 1989; Hixon …

Artificial Substrate And Coral Reef Restoration: What Do We Need To Know To Know What We Need, Richard E. Spieler, David S. Gilliam, Robin L. Sherman

Marine & Environmental Sciences Faculty Articles

To use artificial substrate effectively in coral reef restoration certain basic knowledge is required: (1) what is the artificial substrate expected to accomplish relative to the goals of the restoration effort and (2) what are the expected interactions of the selected substrate’s composition, texture, orientation, and design with the damaged environment and the biota of interest. Whereas the first point is usually clear, at least in general terms, the second is not. In this review, we examine: the functions of artificial substrate in restoration and some of the physical (i.e., composition; surface texture; color and chemistry; and design in terms …

Mapping And Monitoring Of Coral Communities And Their Spatial Patterns Using A Surface-Based Video Method From A Vessel, Bernhard Riegl, Jan L. Korrubel, Charles Martin

Marine & Environmental Sciences Faculty Articles

No Abstract Provided.

Degradation Of Reef Structure, Coral And Fish Communities In The Red Sea By Ship Groundings And Dynamite Fisheries, Bernhard Riegl

Marine & Environmental Sciences Faculty Articles

Reef degradation was investigated on 66 Egyptian Red Sea reefs—60 reefs for dynamite damage (using line transects) and six ship grounding sites (using 1 m sample squares). Ship groundings and dynamite fishing caused similar damage, reduction of the reef to rubble (65% of reefs were dynamited, mostly leeward, 58%). Changes in coral (line transect study) and fish communities (point count study) in impacted sites were documented. On impacted reefs, coral cover decreased, bare substratum and rubble increased, and fish dominance shifted away from Pomacentridae. Oceanographic conditions result in a stable pattern of coral communities (windward Acropora, leeward Porites). …

The Use Of Landmarks By Clark's Nutcrackers: First Tests Of A New Model, Alan Kamil, Aleida J. Goodyear, Ken Cheng

Papers in Behavior in Biological Sciences

Animals use many different mechanisms to navigate in space. The characteristics of the mechanism employed are usually well-suited to the demands of each particular navigational problem. For example, desert ants navigating in a relatively featureless environment use path integration, birds homing or migrating over long distances use compasses of various sorts, salmon returning to their natal stream home on olfactory cues. The study of navigation requires the study of many different taxa confronting different problems. One interesting case 1 involves scatter-hoarding species that use memory to relocate their hidden food. Such animals face the problem of remembering many locations simultaneously. …

Forage News [2001-09], Department Of Plant And Soil Sciences, University Of Kentucky

Forage News

• Sign-Up Now for the Kentucky Grazing School
• Novel Endophyte Varieties
• KFGC Award Nominations Deadline October 15
• Roundup Ready Alfalfa, When?
• Seeding Cool Season Grasses
• Stockpiling
• Kentucky Grazing Conference
• Annual Ryegrass Variety Information Supplied to County Agent Offices
• Regional Grazing Conference
• Endophyte Infected Perennial Ryegrass and Horse Farms
• Upcoming Events

A Bird On The Shoreline, Shelly Clark

Nebraska Bird Review

A Bird on the Shoreline

My daughter tells me she doesn't believe in God.

Her words pour onto the supper table like milk spilling.

In measured silence

she waits for what I will say.

The evening news mumbles in the background,

dog scratching at the door.

I look out the window to September sky opening

its dark blue skirt of night. I tell her

the Piping plovers will be leaving soon, if they haven't already.

Asking her, do you remember the first time we saw them through binoculars,

on the broad sandbar new McConaughy?

You were eight or nine.

How …

Masthead From Nebraska Bird Review September 2001

Nebraska Bird Review

The Nebraska Bird Reyiew (http://rip.physics.unk.edu/NOU/) is published quarterly by the Nebraska Ornithologists' Union, Inc., as its official journal, and is sent to members not in arrears of dues. Annual subscription rates (on a calendar-year basis only): $14.00 in the United States; $18.00 for all foreign countries, payable in advance. Single copies are $4.00 each, postpaid, in the United States, and $5.00 elsewhere. Send orders for back issues to Mary Prichard, NOU Librarian, University of Nebraska State Museum, Lincoln, NE 68588-0514.

Memberships in NOU (on a calendar year basis only): Active, $15.00; Sustaining, $25.00; Student, $10.00; Family Active, $20.00; Family Sustaining, …

Nou Spring Meeting Bird Count, 18 To 20 May, Camp Calvin Crest (Fremont)

Nebraska Bird Review

NOU Spring Meeting Bird Count

18 to 20 May, Camp Calvin Crest (Fremont)

Summer Field Report, June And July 2001, W. Ross Silcock

Nebraska Bird Review

Jaeger at Lake McConaughy; the continuing advance of the Eurasian Collared-Dove; possible breeding or hybridization with Eurasian Collared-Dove of White-winged Dove at Kearney; a resurgence of Black-billed Cuckoos; breeding of Long-eared Owl in Knox County; hummingbirds (including Calliope) in the Panhandle; and interesting information on the Red Crossbills on the Pine Ridge.

First Records Of The Neotropic Genus Dilopharius Townes (Hymenoptera: Ichneumonidae: Ichneumoninae) In Florida, Charles C. Porter

Insecta Mundi

Dilopharius Townes (1966) ranges from the southern United States to Argentina. Its only described species is D. otomitus (Cresson 1868), previously known from Mexico and south Texas, but now recorded for the first time from Florida.

This is a medium sized ichneumonid (fore wing 5-10 mm long) recognizable as follows: mandible broad, lower tooth a little shorter than upper; occipital carina joins base of mandible; scutellum nearly flat, with a strong, percurrent lateral carina; propodeum with broadly triangular apico-latera1 crests; female gaster short and broad; second tergite with coarse punctures, thyridia broad, space between them not much greater than width …

A Taxonomic Study Of The Genus Atheas Champion (Heteroptera: Tingidae), Laura Torres Miller

Insecta Mundi

The genus Atheas Champion is revised. A key to all 14 species cataloged in the genus is included. Species occurring in Mexico are redefined and illustrated. Descriptions of species not occurring in Mexico are also provided. Host plant information has been included, when available.

A New Key To The Species Of The Genus Cradytes Casey (Insecta: Coleoptera: Melyridae), Jonathan R. Mawdsley

Insecta Mundi

A new key is presented to separate adults of the four currently-recognized species of the genus Cradytes Casey (Insecta: Coleoptera: Melyridae): C. longicollis Casey, C. serricollis (LeConte), C. serrulatus (LeConte), and C. ursinus Blaisdell. The inaccurate statements in an earlier key to species of Cradytes are discussed.

Tres Nuevos Registros De Cóccidos (Hemíptera: Coccoidea: Coccidae) Para Cuba, Nereida Mestre Novoa, Avas B. Hamon, Pedro Herrara Oliver

Insecta Mundi

Resumen: La mayoría de las especies de "guaguas" blandas presentes en Cuba han sido estudiadas por su relación con las plantas de interés económico, sin embargo, en los sistemas naturales la fauna de estos insectos es casi desconocida. En este trabajo se dan a conocer tres nuevos registros de cóccidos para Cuba, recolectados en ecosistemas naturales, los cuales corresponden a Coccus capparidis (Green, 1904), Saissetia miranda (Cockerell & Parrot, 1899) y Toumeyella liriodendri (Gmelin, 1790), y se relacionan sus plantas hospedantes con nuevos registros para estas especies.

Abstract:Most of the soft scales present in Cuba have been studied because …

The Metabolic Basis Of Life History Variation: Genetic And Phenotypic Differences In Lipid Reserves Among Life History Morphs Of The Wing-Polymorphic Cricket, Gryllus Firmus, Anthony J. Zera, A. Larsen

Anthony Zera Publications

The flight-capable morph of the wing-polymorphic cricket, Gryllus firmus, accumulated a substantially greater quantity of total lipid and triglyceride, compared with the obligately flightless morph, during the first five days of adulthood. Increased lipid accumulation in the flight-capable morph was genetically based, and was produced when ovarian growth is substantially reduced in that morph. Temporal changes in lipid levels suggest that the higher triglyceride reserves in the flight-capable morph fed a high-nutrient diet were produced by elevated lipid biosynthesis. By contrast, on a low-nutrient or high carbohydrate diet, increased lipid levels in the flight-capable morph appeared to result primarily …

Endangered Species Bulletin, September 2001 - Vol. Xxvi No. 1

Endangered Species Bulletin

In this issue:
4 Incentives for Conservation on Private Lands
6 Preventative Medicine for Species at Risk
8 Partners for Fish and Wildlife
10 Landowners Help Karner Blues
13 Working Together for Riparian Conservation
16 A Safe Harbor for the Red-cockaded Woodpecker
19 Stewardship on the Plains
22 A Partnerships to Restore the Aplomado Falcon
24 New Habitat Conservation Plan Grants
26 A Private Effort to Conserve Biological Diversity
30 Rare Woodpeckers Reintroduced to North Florida
32 Training Courses Highlight Partnerships
34 Partnering with Plants
36 “Working the Sturge”

The International Lepidoptera Survey Newsletter, September 2001, International Lepidoptera Survey, Ron Gatrelle, Harry Pavulaan, Norbert G. Kondla

International Lepidoptera Survey Newsletter

Contents

Thorybes clarification by Ron Gatrelle (pages 1-2)

TC-ISBN Taxonomically Correct - Index of Scientific Butterfly Names: Why do we need yet another North American names list? by Harry Pavulaan (pages 3-6)

The Taxonomic Report, preview

Mitoura grynea smilacis aberrants by Ron Gatrelle (page 8)

Research request: Agriades aquilo? by Norbert G. Kondla (page 9)

New Vistas For Developmental Biology, Scott F. Gilbert, R. Tuan

Biology Faculty Works

No abstract provided.

Inferring And Testing Hypotheses Of Cladistic Character Dependence By Using Character Compatibility, F. Robin O’Keefe, Peter J. Wagner

Biological Sciences Faculty Research

The notion that two characters evolve independently is of interest for two reasons. First, theories of biological integration often predict that change in one character requires complementary change in another. Second, character independence is a basic assumption of most phylogenetic inference methods, and dependent characters might confound attempts at phylogenetic inference. Previously proposed tests of correlated character evolution require a model phylogeny and therefore assume that nonphylogenetic correlation has a negligible effect on initial tree construction. This paper develops “tree-free” methods for testing the independence of cladistic characters. These methods can test the character independence model as a hypothesis before …