Biology Commons^™

Removal Of Pcr Inhibitors From Soil Dna By Chemical Flocculation, Michael D. Braid, Laura M. Daniels, Christopher L. Kitts

Biological Sciences

Extracting high-purity DNA directly from soil has become essential for the study of microorganisms in environmental samples. However, many soils contain compounds that inhibit enzymes involved in manipulating DNA. In this study, chemical flocculation using multivalent cations was investigated as a potential method for eliminating soil-based inhibitors during the extraction process. The addition of AlNH4(SO4)2 during extraction significantly reduced the co-purification of PCR inhibitors with minimal loss of DNA yield.

Evolution And Plasticity Of Photosynthetic Thermal Tolerance, Specific Leaf Area And Leaf Size: Congeneric Species From Desert And Coastal Environments, Charles A. Knight, David D. Ackerly

Biological Sciences

• We examined whether increased high temperature photosynthetic thermal tolerance (PT), reduced specific leaf area (SLA) and reduced leaf size represent correlated and convergent adaptations for recently diverged Encelia, Salvia, Atriplex and Eriogonumcongeneric species pairs from contrasting thermal and water environments (the Mojave Desert and coastal California). We also studied whether variation in PT is associated with inducible small heat shock protein expression (sHsp).

• Traits were measured in a common environment (CE) and in the field to partition effects of phenotypic plasticity and genetic divergence.

• We found little evidence for convergent adaptation of PT (CE measurements). Field …

When Does A Reproducing Female Viper (Vipera Aspis) ‘Decide’ On Her Litter Size?, Olivier Lourdais, Xavier Bonnet, Richard Shine, Emily N. Taylor

Biological Sciences

Some organisms rely on stored energy to fuel reproductive expenditure (capital breeders) whereas others use energy gained during the reproductive bout itself (income breeders). Most species occupy intermediate positions on this continuum, but few experimental data are available on the timescale over which food intake can affect fecundity. Mark–recapture studies of free-ranging female aspic vipers Vipera aspis have suggested that reproductive output relies not only on the energy in fat bodies accumulated in previous years, but also on food intake immediately before ovulation. A simple experiment was conducted to test this hypothesis, maintaining female snakes in captivity throughout the vitellogenic …

Small Heat Shock Protein Responses Of A Closely Related Pair Of Desert And Coastal Encelia, Charles A. Knight, David D. Ackerly

Biological Sciences

Evolutionary variation for accumulation of small heat shock protein (sHsp) may contribute to thermal niche differentiation between species. Here we examine temperature and time-course-dependent variation for sHsp accumulation in a recently diverged pair of Encelia raised in a common environment: Encelia farinosa, common in the Mojave desert, and Encelia californica, which is found along the cool coastal bluffs of southern North America. Both species exhibit peak sHsp accumulation at 42^oC. Encelia californica accumulated greater levels of sHsp at temperatures below 42^oC, while E. farinosa had greater levels above 42^oC. Encelia farinosa accumulates …

Assessment Of Fungal Diversity Using Terminal Restriction Fragment (Trf) Pattern Analysis: Comparison Of 18s And Its Ribosomal Regions, N. S. Lord, Christopher W. Kaplan, P. Shank, Christopher L. Kitts, Susan L. Elrod

Biological Sciences

Assessment of fungal diversity in environmental samples is currently a challenge. Several recently developed molecular methods offer new avenues for determining the presence and diversity of fungi in complex microbial communities. Terminal restriction fragment (TRF) pattern analysis was tested as a method for assessing the fungal molecular diversity of a terrestrial microbial community. Community DNA was isolated from sand samples taken from a pilot-scale petroleum-contaminated land treatment unit. PCR amplification was carried out using primers, one of which was fluorescently labeled, designed to hybridize to conserved sequences in the fungal ribosomal small subunit (18S) or the internal transcribed spacer ITS1–5.8S–ITS2 …

Nearshore Physical Processes And Bio-Optical Properties In The New York Bight, G. C. Chang, T. D. Dickey, Oscar M. Schofield, A. D. Weidemann, E. Boss, W. S. Pegau, Mark A. Moline, Scott M. Glenn

Biological Sciences

Temporal and spatial variability of physical, biological, and optical properties on scales of minutes to months and meters to ~50 km are examined using an extensive data set collected on the New York Bight continental shelf during the Hyperspectral Coastal Ocean Dynamics Experiment. Measurements from a midshelf mooring and bottom tripod (~25 km offshore, 24 m water depth) and two nearshore profiling nodes (~5 km offshore, 15 m water depth) are utilized to quantify and correlate midshelf and nearshore variability. Towed shipboard undulating profilers and a high-frequency radar (CODAR) array provide complementary spatial data. We show that phytoplankton and dissolved …

Reduced Reproductive Effort In Male Field Crickets Infested With Parasitoid Fly Larvae, Gita R. Kolluru, Marlene Zuk, Mark A. Chappell

Biological Sciences

Some populations of the field cricket Teleogryllus oceanicus are parasitized by the phonotactic fly Ormia ochracea. Flies locate crickets by their song and deposit larvae onto them. The larvae develop inside the cricket for 1 week before killing the host upon emergence. The reproductive compensation hypothesis predicts that parasitized crickets should increase their reproductive effort during the initial stages of infestation to offset the loss of fitness resulting from their shortened life span. An alternative hypothesis predicts that parasitized crickets will decrease reproduction, either because they are unable to reproduce or because selection acting on the parasitoid favors decreased …

The Heat-Shock Response: Its Variation, Regulation And Ecological Importance In Intertidal Gastropods (Genus Tegula), Lars Tomanek

Biological Sciences

The enhanced synthesis of heat-shock proteins (hsps), called the heat-shock (or stress) response, is activated when environmental stress denatures proteins. Hsp synthesis is activated at the upper temperatures of an organism's thermal range and is therefore thought to be critical for enhancing thermal tolerance limits in ectothermic animals. Here I show that the two temperate sister species T. brunnea and T. montereyi that occupy the subtidal and low-intertidal zone differ from the low- to mid-intertidal T. funebralis (and the subtropical mid-intertidal T. rugosa) in (i) heat tolerance, (ii) the onset temperature of their main hsp, hsp70 (70 kDa), (iii) …

Discovering Lactic Acid Bacteria By Genomics, Todd Klaenhammer, Eric Altermann, Fabrizio Arigoni, Alexander Bolotin, Fred Breidt, Jeffrey Broadbent, Raul J. Cano, Stephane Chaillou, Josef Deutscher, Mike Gasson, Maarten Van De Guchte, Jean Guzzo, Axel Hartke, Trevor Hawkins, Pascal Hols, Robert Hutkins, Michiel Kleerebezem, Jan Kok, Oscar Kuipers, Mark Lubbers, Emmanuelle Maguin, Larry Mckay, David Mills, Arjen Nauta, Ross Overbeek, Herman Pel, David Pridmore, Milton Saier, Douwe Van Sinderen, Alexei Sorokin, James Steele, Daniel O'Sullivan, Willem De Vos, Bart Weimer, Monique Zagorec, Roland Siezen

Biological Sciences

This review summarizes a collection of lactic acid bacteria that are now undergoing genomic sequencing and analysis. Summaries are presented on twenty different species, with each overview discussing the organisms fundamental and practical significance, environmental habitat, and its role in fermentation, bioprocessing, or probiotics. For those projects where genome sequence data were available by March 2002, summaries include a listing of key statistics and interesting genomic features. These efforts will revolutionize our molecular view of Gram-positive bacteria, as up to 15 genomes from the low GC content lactic acid bacteria are expected to be available in the public domain by …

Effects Of Temperature, Epinephrine And Ca2+ On The Hearts Of Yellowfin Tuna (Thunnus Albacares), Jason M. Blank, Jeffery M. Morrissette, Peter S. Davie, Barbara A. Block

Biological Sciences

Tuna are endothermic fish with high metabolic rates, cardiac outputs and aerobic capacities. While tuna warm their skeletal muscle, viscera, brain and eyes, their hearts remain near ambient temperature, raising the possibility that cardiac performance may limit their thermal niches. We used an in situ perfused heart preparation to investigate the effects of acute temperature change and the effects of epinephrine and extracellular Ca²⁺ on cardiac function in yellowfin tuna (Thunnus albacares). Heart rate showed a strong temperature-dependence, ranging from 20 beats min^-1 at 10 °C to 109 beats min^-1 at 25 °C. Maximal stroke …

Litr, A New Transcriptional Activator In Vibrio Fischeri, Regulates Luminescence And Symbiotic Light Organ Colonization, Pat Fidopiastis, Carol M. Miyamoto, Michael G. Jobling, Edward A. Meighen, Edward G. Ruby

Biological Sciences

Vibrio fischeri is the bacterial symbiont within the light-emitting organ of the sepiolid squid Euprymna scolopes . Upon colonizing juvenile squids, bacterial symbionts grow on host-supplied nutrients, while providing a bioluminescence that the host uses during its nocturnal activities. Mutant bacterial strains that are unable to emit light have been shown to be defective in normal colonization. A 606 bp open reading frame was cloned from V. fischeri that encoded a protein, which we named LitR, that had about 60% identity to four related regulator proteins: Vibrio cholerae HapR, Vibrio harveyi LuxR, Vibrio parahaemolyticus OpaR and Vibrio vulnificus SmcR. When …

Predicting Plant Invasion With Modeling, Scott J. Steinmaus

Biological Sciences

No abstract provided.

Chaperones As Buffering Agents?, Thomas Mitchell-Olds, Charles A. Knight

Biological Sciences

No abstract provided.

Comparative Phenotypic, Molecular, And Virulence Characterization Of Vibrio Parahaemolyticus O3:K6 Isolates, P.S. Marie Yeung, Micaela C. Hayes, Angelo Depaola, Charles A. Kaysner, Laura Kornstein

Biological Sciences

Historically, Vibrio parahaemolyticus infections have been characterizedby sporadic cases caused by multiple, diverse serotypes. However,since 1996, V. parahaemolyticus serotype O3:K6 strains havebeen associated with several large-scale outbreaks of illness,suggesting the emergence of a "new" group of organisms withenhanced virulence. We have applied three different molecularsubtyping techniques to identify an appropriate method for differentiatingO3:K6 isolates from other serotypes. Pulsed-field gel electrophoresis(PFGE) following NotI digestion differentiated seven closelyrelated subtypes among O3:K6 and related strains, which weredistinct from PFGE patterns for non-O3:K6 isolates. Ribotypingand tdh sequencing were less discriminatory than PFGE, but furtherconfirmed close genetic relationships among recent O3:K6 isolates.In vitro adherence …

The Production Of Communication Signals At The Air–Water And Water–Substrate Boundaries, Sean C. Lema, John T. Kelly

Biological Sciences

The 2 interfaces of the aquatic environment, the boundary between air–water and water–substrate, have distinctive physical characteristics that facilitate the production of communication signals. Recent evidence suggests that animals living on or near these boundaries use the interface to generate signals in 2 ways: (a) by producing a signal that propagates along the interface or (b) by producing a signal at the interface that is transmitted and detected within 1 of the component media. By examining the diversity of behaviors used to produce signals at these boundaries, the authors illustrate how human perception of these environments may cause researchers to …

Species-Specific Identification Of Commercial Probiotic Strains, Marie Yeung, M. E. Sanders, Christopher L. Kitts, Raul Cano, Phillip S. Tong

Biological Sciences

Products containing probiotic bacteria are gaining popularity, increasing the importance of their accurate speciation. Unfortunately, studies have suggested that improper labeling of probiotic species is common in commercial products. Species identification of a bank of commercial probiotic strains was attempted using partial 16S rDNA sequencing, carbohydrate fermentation analysis, and cellular fatty acid methyl ester analysis. Results from partial 16S rDNA sequencing indicated discrepancies between species designations for 26 out of 58 strains tested, including two ATCC Lactobacillus strains. When considering only the commercial strains obtained directly from the manufacturers, 14 of 29 strains carried species designations different from those obtained …

The Long-Term Ecosystem Observatory: An Integrated Coastal Observatory, Oscar Schofield, Trisha Bergmann, Paul Bissett, J. Frederick Grassle, Dale B. Haidvogel, Josh Kohut, Mark A. Moline, Scott M. Glenn

Biological Sciences

An integrated ocean observatory has been developed and operated in the coastal waters off the central coast of New Jersey, USA. One major goal for the Long-term Ecosystem Observatory (LEO) is to develop a real-time capability for rapid environmental assessment and physical/biological forecasting in coastal waters. To this end, observational data are collected from satellites, aircrafts, ships, fixed/relocatable moorings and autonomous underwater vehicles. The majority of the data are available in real-time allowing for adaptive sampling of episodic events and are assimilated into ocean forecast models. In this observationally rich environment, model forecast errors are dominated by uncertainties in the …

A New Auv Platform For Studying Near Shore Bioluminescence Structure, Mark A. Moline, S. Blackwell, J. Case, S. Glenn, J. Kohut, O. Schofield, M. Purcell, C. Vonalt

Biological Sciences

Peaks in bioluminescence are often associated with small spatial features including frontal boundaries, vertical thin-layers, and convergence/divergence zones.^1,2 Due to the highly variable nature of these features in the near shore environment, accurate assessment of bioluminescence potential is dependent upon the application of appropriate platforms and the use of these platforms at relevant time and space scales. Both traditional shipboard profiling techniques and moored vertical profiling instrumentation fail to adequately provide the appropriate spatial resolution to explain the dynamics of near shore bioluminescence. In an effort to resolve the mechanisms underlying the temporal and spatial variation in near shore …

Interspecific- And Acclimation-Induced Variation In Levels Of Heat-Shock Proteins 70 (Hsp70) And 90 (Hsp90) And Heat-Shock Transcription Factor-1 (Hsf1) In Congeneric Marine Snails (Genus Tegula): Implications For Regulation Of Hsp Gene Expression, Lars Tomanek, George N. Somero

Biological Sciences

In our previous studies of heat-shock protein (hsp) expression in congeneric marine gastropods of the genus Tegula, we observed interspecific and acclimation-induced variation in the temperatures at which heat-shock gene expression is induced (T_on). To investigate the factors responsible for these inter- and intraspecific differences in T_on, we tested the predictions of the ‘cellular thermometer’ model for the transcriptional regulation of hsp expression. According to this model, hsps not active in chaperoning unfolded proteins bind to a transcription factor, heat-shock factor-1 (HSF1), thereby reducing the levels of free HSF1 that are available to bind …

Occam's Razor & The Nature Of Scientific Theories, William D. Stansfield

Biological Sciences

No abstract provided.

An Ecological And Evolutionary Analysis Of Photosynthetic Thermotolerance Using The Temperature-Dependent Increase In Fluorescence, Charles A. Knight, David D. Ackerly

Biological Sciences

The hypothesis that species inhabiting warmer regions have greater photosynthetic tolerance of high temperatures was tested using the temperature-dependent increase in fluorescence (T-F_o). Congeneric species pairs of Atriplex, Salvia, Encelia, and Eriogonum with desert versus coastal distributions were studied in a common environment and in the field. In addition, 21 species with contrasting microclimate distributions were studied at a field site in a northern California chaparral community. The average July maximum temperature within the current distributions of species was quantified using a geographic information system. Four parameters (T_crit, T_S20, …

Leaf Size, Specific Leaf Area And Microhabitat Distribution Of Chaparral Woody Plants: Contrasting Patterns In Species Level And Community Level Analyses, D. D. Ackerly, Charles A. Knight, S. B. Weiss, K. Barton, K. P. Starmer

Biological Sciences

We examined variation in leaf size and specific leaf area (SLA) in relation to the distribution of 22 chaparral shrub species on small-scale gradients of aspect and elevation. Potential incident solar radiation (insolation) was estimated from a geographic information system to quantify microclimate affinities of these species across north- and south-facing slopes. At the community level, leaf size and SLA both declined with increasing insolation, based on average trait values for the species found in plots along the gradient. However, leaf size and SLA were not significantly correlated across species, suggesting that these two traits are decoupled and associated with …

Variation In Nuclear Dna Content Across Environmental Gradients: A Quantile Regression Analysis, Charles A. Knight, David D. Ackerly

Biological Sciences

The nuclear DNA content of angiosperms varies by several orders of magnitude. Previous studies suggest that variation in 2C DNA content (i.e. the amount of DNA in G1 phase nuclei, also referred to as the 2C-value) is correlated with environmental factors, but there are conflicting reports in the literature concerning the nature of these relationships. We examined variation in 2C DNA content for 401 species in the ecologically diverse California flora in relation to the mean July maximum temperature, January minimum temperature, and annual precipitation within the geographical ranges of these species. Species with small 2C-values predominate in all environments. …

Two New Species Of Pectis (Asteraceae: Tageteae) From South America, David J. Keil

Biological Sciences

Pectis hassleri and P. pumila are new species, the former from the Gran Chaco area of Paraguay and the latter from southwester Encuador and northwestern Peru. Pectis hassleri differs from P. odorata by leaves that are glandular-punctaoten the adaxial as well as the abaxial surfaces, by longer and wider ligules of the ray florets, and by ray pappi of awns and shorter bristles. Pectis pumila differs from the closely related P. arida by its wider leaves and by its sessile or subsessile capitula with campanulatein volucresa nd obovatep hyllaries.A hexaploid chromosome count of 2n = 361 is newly reported for …

Antimicrobial Activity Of Plants Collected From Serpentine Outcrops In Sri Lanka, Nishanta Rajakaruna, Cory S. Harris, G. H. N. Towers

Biological Sciences

Thirty-two plant species collected from serpentine (ultramafic) soils in Sri Lanka were screened for antimicrobial properties against three Gram-positive and two Gramnegative bacteria, a non-acid fast bacterium, and the yeast, Candida albicans. Methanol extracts of 29 species belonging to 12 families were active against at least one microorganism. Activity against the Gram-positive and non-acid fast bacteria was common, however, only two taxa, Lantana camara L. (Verbenaceae) and a species of Phyllanthus L. (Euphorbiaceae), were active against the Gram-negative bacterium Pseudomonas aeruginosa. None of the species was active against the other Gram-negative bacterium, Escherichia coli, or C. albicans. Photoactivity was observed …

Longitudinal Variation In Muscle Protein Expression And Contraction Kinetics Of Largemouth Bass Axial Muscle, Tierney M. Thys, Jason M. Blank, David J. Coughlin, Fred Schachat

Biological Sciences

The present study investigates muscle protein expression in largemouth bass Micropterus salmoides through intra- and intermyomeric comparisons of white muscle. Using denaturing SDS-polyacrylamide gel electrophoresis, muscle protein expression in the arm and cone regions of sequential myomeres was compared for three bass. Low percentage (4.75 %) polyacrylamide-SDS gels and cyanogen bromide (CNBr) peptide mapping revealed no obvious intramyomeric differences between the myosin heavy chains of the arm and cone regions. Electrophoresis of myofibrils and muscle homogenates on higher percentage gels also failed to demonstrate any significant differences between arm and cone regions in either the myosin light chains or any …

Mf-Ea-705Α & Mf-Ea-705Β, New Metabolites From Microbial Fermentation Of A Streptomyces Sp., Asfia Qureshi, Jacob B. Mauger, Raul J. Cano, Jorge L. Galazzo, May D. Lee

Biological Sciences

No abstract provided.

Effects Of Artisanal Fishing On Marine Communities In The Galápagos Islands, Benjamin I. Ruttenberg

Biological Sciences

The Galápagos Islands harbor some of the least impacted marine ecosystems in the tropics, but there are indications that local artisanal fishing is affecting exploited marine communities. To quantify these effects, I sampled communities of fishes and sea urchins at a number of heavily fished and lightly fished sites throughout the central islands of the archipelago. Sites were selected based on information collected as part of a local fisheries monitoring study and standardized across a number of abiotic factors. Abundance and biomass of the primary target species were significantly lower in the heavily fished sites than in the lightly fished …

Re-Evaluating Nadph-Diaphorase Histochemistry As An Indicator Of Nitric Oxide Synthase: An Examination Of The Olfactory System Of Coho Salmon (Oncorhynchus Kisutch), Sean C. Lema, Gabrielle A. Nevitt

Biological Sciences

The NADPH-diaphorase (NADPH-d) histochemical technique is commonly used to localize the nitric oxide (NO)-producing enzyme NO synthase (NOS) in neural tissues. In the olfactory tissues of vertebrates, however, NADPH-d staining can be present without the detection of NOS by other methods. We used pharmacological controls to determine whether NADPH-d staining was indicative of NOS in olfactory tissues from coho salmon (Oncorhynchus kisutch). We also compared NADPH-d staining with immunoreactivity to NOS. NADPH-d staining localized to the olfactory epithelium and to the glomerular layer of the olfactory bulb. Two NOS inhibitors, _L-N-nitroarginine and _L-N-methyl-_L-arginine, failed …

Whence Meiosis?, Anne M. Villeneuve, Kenneth J. Hillers

Biological Sciences

Sexual reproduction predominates among eukaryotic organisms on our planet. While debate continues over why this should be so, burgeoning genomic and functional information now allows us to begin to think reasonably about some of the events that may have occurred to make sex possible in the first place.