Life Sciences Commons^™

Global Change, Global Trade, And The Next Wave Of Plant Invasions, Bethany A. Bradley, Dana M. Blumenthal, Regan Early, Edwin D. Grosholz, Joshua J. Lawler, Luke P. Miller, Cascade J.B. Sorte, Carla M. D'Antonio, Jeffrey M. Diez, Jeffrey S. Dukes, Ines Ibanez, Julian D. Olden

Faculty Publications, Biological Sciences

Many non-native plants in the US have become problematic invaders of native and managed ecosystems, but a new generation of invasive species may be at our doorstep. Here, we review trends in the horticultural trade and invasion patterns of previously introduced species and show that novel species introductions from emerging horticultural trade partners are likely to rapidly increase invasion risk. At the same time, climate change and water restrictions are increasing demand for new types of species adapted to warm and dry environments. This confluence of forces could expose the US to a range of new invasive species, including many …

Communicator, Dec. 2011, San Jose State University, Department Of Kinesiology

Communicator (Kinesiology)

Volume 24, Issue 2

University Scholar Series: Brandon White, Brandon White

University Scholar Series

Use and Applications of HeLa Cells in Science and Biotechnology

On October 26, 2011, Dr. Brandon White spoke in the University Scholar Series hosted by Provost Gerry Selter at the Dr. Martin Luther King, Jr. Library. Brandon White is an Assistant Professor in Biological Sciences at SJSU, teaching courses in molecular biology, molecular biological techniques, and cell biology. His research focuses on Notch signaling and identification, and characterization of natural products involved in cell death of cancer cells. In this seminar, Dr. Brandon White discusses the use and applications of HeLa cells in science and biotechnology.

Establishing Lower Developmental Thresholds For A Common Blowfly: For Use In Estimating Elapsed Time Since Death Using Entomologyical Methods, Gail S. Anderson, Jodie-A. Warren

Faculty Research, Scholarly, and Creative Activity

Forensic entomology is a science used to estimate a post-mortem interval (PMI). Larvae develop at predictable rates and the time interval for this development can be used to estimate the PMI. Environmental temperatures are not constant and fluctuate with the photoperiod. In early and late insect seasons, temperatures can drop to below threshold temperatures where development essentially ceases. Threshold temperatures differ for different species and should be determined by raising insects at the extremely low temperatures. The lower threshold temperature for Protophormia terraenovae for egg hatch is 10.3°C ; for first instar larvae to molt to second instar larvae it …

Communicator, Sept. 2011, San Jose State University, Department Of Kinesiology

Communicator (Kinesiology)

Volume 24, Issue 1

Rumbling In The Benthos: Acoustic Ecology Of The California Mantis Shrimp Hemisquilla Californiensis, E. Staaterman, C. Clark, A. Gallagher, M. Devries, T. Claverie, S. Patek

Faculty Publications, Biological Sciences

Although much research has focused on acoustic mapping and exploration of the benthic environment, little is known about the acoustic ecology of benthic organisms, particularly benthic crustaceans. Through the use of a coupled audio–video system, a hydrophone array, and an autonomous recording unit, we tested several hypotheses about the field acoustics of a benthic marine crustacean, Hemisquilla califor­niensis. Living in muddy burrows in southern California, these large mantis shrimp produce low frequency ‘rumbles’ through muscle vibrations. First, we tested whether acoustic signals are similar in the field and in the laboratory, and discovered that field-produced rumbles are more acoustically and …

In Search Of An Uncultured Human-Associated Tm7 Bacterium In The Environment, Jorge Dinis, David Barton, Jamsheed Ghadiri, Deepa Surendar, Kavitha Reddy, Fernando Velasquez, Carol Chaffee, Mei-Chong Lee, Helen Gavrilova, Hazel Ozuna, Samuel Smits, Cleber Ouverney

Faculty Publications, Biological Sciences

We have identified an environmental bacterium in the Candidate Division TM7 with ≥98.5% 16S rDNA gene homology to a group of TM7 bacteria associated with the human oral cavity and skin. The environmental TM7 bacterium (referred to as TM7a-like) was readily detectable in wastewater with molecular techniques over two years of sampling. We present the first images of TM7a-like cells through FISH technique and the first images of any TM7 as viable cells through the STARFISH technique. In situ quantification showed TM7 concentration in wastewater up to five times greater than in human oral sites. We speculate that upon further …

Efficient Unfolding Pattern Recognition In Single Molecule Force Spectroscopy Data, Bill Andreopoulos, Dirk Labudde

Faculty Publications, Computer Science

BackgroundSingle-molecule force spectroscopy (SMFS) is a technique that measures the force necessary to unfold a protein. SMFS experiments generate Force-Distance (F-D) curves. A statistical analysis of a set of F-D curves reveals different unfolding pathways. Information on protein structure, conformation, functional states, and inter- and intra-molecular interactions can be derived.ResultsIn the present work, we propose a pattern recognition algorithm and apply our algorithm to datasets from SMFS experiments on the membrane protein bacterioRhodopsin (bR). We discuss the unfolding pathways found in bR, which are characterised by main peaks and side peaks. A main peak is the result of the pairwise …

Importance Of Behavior And Morphological Traits For Controlling Body Temperature In Littorinid Snails, Luke Miller, Mark Denny

Faculty Publications, Biological Sciences

For organisms living in the intertidal zone, temperature is an important selective agent that can shape species distributions and drive phenotypic variation among populations. Littorinid snails, which occupy the upper limits of rocky shores and estuaries worldwide, often experience extreme high temperatures and prolonged aerial emersion during low tides, yet their robust physiology—coupled with morphological and behavioral traits—permits these gastropods to persist and exert strong grazing control over algal communities. We use a mechanistic heat-budget model to compare the effects of behavioral and morphological traits on the body temperatures of five species of littorinid snails under natural weather conditions. Model …

Point-Of-Purchase Nutrition Information Influences Food-Purchasing Behaviors Of College Students: A Pilot Study, Marjorie Freedman, Rachel Conners

Faculty Publications

The goal of point-of-purchase (POP) nutrition information is to help consumers make informed, healthful choices. Despite limited evaluation, these population-based approaches are being advocated to replace traditional, more expensive, individual behavior-change strategies. Few studies have examined the effect of POP information on buying patterns of college students, a group with high obesity rates and poor eating habits. This quasi-experimental pilot project sought to determine whether the “Eat Smart” POP program affected food-purchasing habits of multiethnic college students shopping at an on-campus convenience store. Baseline sales data of foods in the cereal, soup, cracker, and bread categories were collected for 6 …

Drosophila Model For Fetal Alcohol Syndrome Disorders: Role For The Insulin Pathway, Rachael L. French, K D. Mcclure, U Heberlein

Faculty Publications, Biological Sciences

Prenatal exposure to ethanol in humans results in a wide range of developmental abnormalities, including growth deficiency, developmental delay, reduced brain size, permanent neurobehavioral abnormalities and fetal death. Here we describe the use of Drosophila melanogaster as a model for exploring the effects of ethanol exposure on development and behavior. We show that developmental ethanol exposure causes reduced viability, developmental delay and reduced adult body size. We find that flies reared on ethanol-containing food have smaller brains and imaginal discs, which is due to reduced cell division rather than increased apoptosis. Additionally, we show that, as in mammals, flies reared …

Drosophila Model For Fetal Alcohol Syndrome Disorders: Role For The Insulin Pathway, Rachael L. French, K D. Mcclure, U Heberlein

Rachael L. French

Prenatal exposure to ethanol in humans results in a wide range of developmental abnormalities, including growth deficiency, developmental delay, reduced brain size, permanent neurobehavioral abnormalities and fetal death. Here we describe the use of Drosophila melanogaster as a model for exploring the effects of ethanol exposure on development and behavior. We show that developmental ethanol exposure causes reduced viability, developmental delay and reduced adult body size. We find that flies reared on ethanol-containing food have smaller brains and imaginal discs, which is due to reduced cell division rather than increased apoptosis. Additionally, we show that, as in mammals, flies reared …

White Potatoes, Including French Fries, Contribute Shortfall Nutrients To Children's And Adolescents' Diets, Marjorie Freedman, Debra Keast

Faculty Publications

To test the hypothesis that white potatoes (WP), oven-baked fries (OBF), and french fries (FF) contribute important nutrients within energy needs to children's and adolescents' diets, secondary analysis of 24-hour dietary recall data from the National Health and Nutrition Examination Survey 2003-2006 was conducted. Potato content of survey foods was determined using US Department of Agriculture recipe databases (Standard Reference (SR)-Link files). Nutrient content of potatoes was determined by linking SR codes to US Department of Agriculture food composition data. Daily nutrient intakes from potatoes were determined by applying the composition database to respondent's recall data. Sample-weighted data were analyzed; …

Communicator, April 2011, San Jose State University, Department Of Kinesiology

Communicator (Kinesiology)

Volume 23, Issue 4

Geographic Variation In Temperature Tolerance As An Indicator Of Potential Population Responses To Climate Change, Cascade J.B. Sorte, Sierra J. Jones, Luke P. Miller

Faculty Publications, Biological Sciences

The temperature tolerances of individuals in geographically separated populations of a single species can be used as indicators of each population's potential to persist or become extinct in response to climate change. We evaluated the population-level variation in temperature tolerance in populations of several marine invertebrate taxa, including bryozoans, tunicates, bivalves, and gastropods, separated by distances of < 200 km to > 5000 km. We then combined physiological thermotolerance data with current temperature data and climate change predictions to predict which of these populations may be most vulnerable to future changes. In a trans-continental comparison of four subtidal epibenthic species, we show that populations on …

Ab Initio Protein Structure Prediction Algorithms, Maciej Kicinski

Master's Projects

Genes that encode novel proteins are constantly being discovered and added to databases, but the speed with which their structures are being determined is not keeping up with this rate of discovery. Currently, homology and threading methods perform the best for protein structure prediction, but they are not appropriate to use for all proteins. Still, the best way to determine a protein's structure is through biological experimentation. This research looks into possible methods and relations that pertain to ab initio protein structure prediction. The study includes the use of positional and transitional probabilities of amino acids obtained from a non-redundant …

Rna Secondary Structure Prediction Tool, Meenakshee Mali

Master's Projects

Ribonucleic Acid (RNA) is one of the major macromolecules essential to all forms of life. Apart from the important role played in protein synthesis, it performs several important functions such as gene regulation, catalyst of biochemical reactions and modification of other RNAs. In some viruses, instead of DNA, RNA serves as the carrier of genetic information. RNA is an interesting subject of research in the scientific community. It has lead to important biological discoveries. One of the major problems researchers are trying to solve is the RNA structure prediction problem. It has been found that the structure of RNA is …

Communicator, Feb. 2011, San Jose State University, Department Of Kinesiology

Communicator (Kinesiology)

Volume 23, Issue 3

Synthesis Of Knowledge Of Extreme Fire Behavior: Volume I For Fire Managers, Paul Werth, Brian Potter, Craig Clements, Mark Finney, Scott Goodrick, Martin Alexander, Miguel Cruz, Jason Forthofer, Sara Mcallister

Faculty Publications, Meteorology and Climate Science

The National Wildfire Coordinating Group definition of extreme fire behavior (EFB) indicates a level of fire behavior characteristics that ordinarily precludes methods of direct control action. One or more of the following is usually involved: high rate of spread, prolific crowning/ spotting, presence of fire whirls, and strong convection column. Predictability is difficult because such fires often exercise some degree of influence on their environment and behave erratically, sometimes dangerously. Alternate terms include “blow up” and “fire storm.” Fire managers examining fires over the last 100 years have come to understand many of the factors necessary for EFB development. This …

A Bulk Water-Dependent Desolvation Energy Model For Analyzing The Effects Of Secondary Solutes On Biological Equilibria, Daryl K. Eggers

Faculty Publications, Chemistry

A new phenomenological model for interpreting the effects of solutes on biological equilibria is presented. The model attributes changes in equilibria to differences in the desolvation energy of the reacting species that, in turn, reflect changes in the free energy of the bulk water upon addition of secondary solutes. The desolvation approach differs notably from that of other solute models by treating the free energy of bulk water as a variable and by not ascribing the observed shifts in reaction equilibria to accumulation or depletion of solutes next to the surfaces of the reacting species. On the contrary, the partitioning …

Point-Of-Selection Nutrition Information Influences Choice Of Portion Size In An All-You-Can-Eat University Dining Hall, Marjorie Freedman

Faculty Publications

There is limited information about point-of-selection nutrition information on food choices in all-you-can-eat university dining halls, where food cost is controlled. This pilot study examined effects of point-of-selection nutrition information (pictures of different portion sizes with corresponding nutrition information) on students' choice of French fries and salad dressing and portion size of French fries. Point-of-selection nutrition information significantly decreased percentage consuming “large” portions of French fries (p < 0.05) but had a limited effect on salad dressing choice. Surveys indicated that >99% of respondents (n = 359) recalled point-of-selection nutrition information; more females used point-of-selection nutrition information to determine portion size. Additional studies are needed to support these promising results.

Freshman Orientation Sessions Can Teach Incoming Students About Healthful Lifestyles, Marjorie Freedman, Jennifer Waldrop

Faculty Publications

Currently, 32% of college students are overweight or obese (body mass index ≥ 25),which is likely because many adolescents enter college with an elevated body mass index. Further, the transition from high school to college is associated with weight gain.On their own for the first time, freshmen have greater independence in all aspects of their lives. Increased independence, in turn, often results in changes in types of food and beverages consumed, and in overall eating and exercise patterns—changes that often affect weight gain. Although the popular media continues to perpetuate the “Freshman 15” myth, a recent meta-analysis reported freshmen gain, …

Commentary: Selecting Synaptic Partners: Grasping The Role Of Unc- 6/Netrin, Q L. Ch'ng

Faculty Publications, Biological Sciences

Forming synaptic connections of the appropriate strength between specific neurons is crucial for constructing neural circuits to control behavior. A recent paper in Neural Development describes the use of a synapse-specific label in Caenorhabditis elegans to implicate local UNC-6/netrin signaling in this developmental process. Thus, as well as their well known roles in cell migration and axon guidance, UNC-6/netrin signals distinguish an appropriate synaptic partner from other potential targets.

Lichens Of Callahan Mine, A Copper And Zinc-Enriched Superfund Site In Brooksville, Maine, U.S.A., N Rajakaruna, T B. Harris, S Clayden, A Dibble, F S. Olday

Faculty Publications, Biological Sciences

Metal-enriched habitats often harbor physiologically distinct biotas able to tolerate and accumulate toxic metals. Plants and lichens that accumulate metals have served as effective indicators of ecosystem pollution. Whereas the diversity of metal-tolerant lichens has been well documented globally, the literature of metal-tolerant lichen communities for eastern North America is limited. We examined the lichen flora of the Callahan Mine, a Cu-, Pb-, and Zn-enriched superfund site in Brooksville, Hancock County, Maine, U.S.A. Through collections along transects across metal-contaminated areas of the mine, we documented 76 species of lichens and related fungi. Fifty species were saxicolous, 26 were terricolous. Forty-three …

A Preliminary Study Of The Vegetation Of Vernal Pools Of Acadia National Park, Mount Desert Island, B Ciccotelli, T B. Harris, B Connery, N Rajakaruna

Faculty Publications, Biological Sciences

We conducted a preliminary floristic study of six vernal pools in Acadia National Park on Mount Desert Island, Maine. Plant species were recorded on three sampling dates from April to October, 2008. Sixty-five vascular plant species from 26 families were recorded. Of these, 27 are considered occasional or uncommon in Acadia National Park. Thirteen species are new reports for vernal pools in the northeastern United States. This represents the first published study of the vernal pool flora of Acadia National Park

Ecological Strategies In California Chaparral: Interacting Effects Of Soils, Climate, And Fire On Specific Leaf Area, B L. Anacker, N Rajakaruna, D D. Ackerly, S P. Harrison, J E. Keeley, M C. Vasey

Faculty Publications, Biological Sciences

Background: High values of specific leaf area (SLA) are generally associated with high maximal growth rates in resource-rich conditions, such as mesic climates and fertile soils. However, fire may complicate this relationship since its frequency varies with both climate and soil fertility, and fire frequency selects for regeneration strategies (resprouting versus seeding) that are not independent of resource-acquisition strategies. Shared ancestry is also expected to affect the distribution of resource-use and regeneration traits. Aims: We examined climate, soil, and fire as drivers of community-level variation in a key functional trait, SLA, in chaparral in California. Methods: We quantified the phylogenetic, …

A Conserved Juxtacrine Signal Regulates Synaptic Partner Recognition In C. Elegans, J R. Park, P L. Knezevich, W Wung, S N. O'Hanlon, A Goyal, K L. Benedetti, B J. Barsi-Rhyne, M Raman, N Mock, M Bremer, Miri Vanhoven

Faculty Publications, Biological Sciences

Forming synaptic connections of the appropriate strength between specific neurons is crucial for constructing neural circuits to control behavior. A recent paper in Neural Development describes the use of a synapse-specific label in Caenorhabditis elegans to implicate local UNC-6/netrin signaling in this developmental process. Thus, as well as their well known roles in cell migration and axon guidance, UNC-6/netrin signals distinguish an appropriate synaptic partner from other potential targets.

The Effects Of Kettlebell Training On Aerobic Capacity, Jonathan Asher Falatic

Master's Theses

The purpose of this study was to determine the effects of a kettlebell training program on aerobic capacity. Seventeen female NCAA Division I collegiate soccer players (age 19.7 +1.0 years, height 166.1 +6.4 cm, weight 64.2 +8.2 kg) completed a graded exercise test to determine maximal oxygen consumption (VO₂max). Participants were placed into a kettlebell intervention (KB) group (n = 9) or a circuit weight training control (CWT) group (n = 8). Participants in the KB group completed a kettlebell snatch test to determine individual snatch repetitions. Both groups trained 3 days per week for 4 weeks in …

Commentary: Selecting Synaptic Partners: Grasping The Role Of Unc- 6/Netrin, Q L. Ch'ng

Miri VanHoven

Forming synaptic connections of the appropriate strength between specific neurons is crucial for constructing neural circuits to control behavior. A recent paper in Neural Development describes the use of a synapse-specific label in Caenorhabditis elegans to implicate local UNC-6/netrin signaling in this developmental process. Thus, as well as their well known roles in cell migration and axon guidance, UNC-6/netrin signals distinguish an appropriate synaptic partner from other potential targets.

Contemporary And Historical Separation Of Transequatorial Migration Between Genetically Distinct Seabird Populations, M J. Rayner, M E. Hauber, T E. Steeves, H A. Lawrence, D R. Thompson, P M. Sagar, S J. Bury, R A. Phillips, T J. Landers, L Ranjard, Scott A. Shaffer

Scott A. Shaffer

Pelagic seabirds are highly mobile, reducing the likelihood of allopatric speciation where disruption of gene flow between populations is caused by physically insurmountable, extrinsic barriers. Spatial segregation during the non-breeding season appears to provide an intrinsic barrier to gene flow among seabird populations that otherwise occupy nearby or overlapping regions during breeding, but how this is achieved remains unclear. Here we show that the two genetically distinct populations of Cook's petrel (Pterodroma cookii) exhibit transequatorial separation of non-breeding ranges at contemporary (ca. 2–3 yrs) and historical (ca. 100 yrs) time scales. Segregation during the non-breeding season per se appears as …