Biology Commons^™

Complete Genome Sequence Of The Probiotic Lactic Acid Bacterium Lactobacillus Acidophilus Ncfm, Eric Altermann, W. Michael Russell, M. Andrea Azcarate- Peril, Rodolphe Barrangou, B. Logan Buck, Olivia Mcauliffe, Nicole Souther, Alleson Dobson, Tri Duong, Michael Callanan, Sonja Lick, Alice Hamrick, Raul J. Cano, Todd R. Klaenhammer

Biological Sciences

Lactobacillus acidophilus NCFM is a probiotic bacterium that has been produced commercially since 1972. The complete genome is 1,993,564 nt and devoid of plasmids. The average GC content is 34.71% with 1,864 predicted ORFs, of which 72.5% were functionally classified. Nine phage-related integrases were predicted, but no complete prophages were found. However, three unique regions designated as potential autonomous units (PAUs) were identified. These units resemble a unique structure and bear characteristics of both plasmids and phages. Analysis of the three PAUs revealed the presence of two R/M systems and a prophage maintenance system killer protein. A spacers interspersed direct …

The Relationship Between Pelagic Larval Duration And Range Size In Tropical Reef Fishes: A Synthetic Analysis, Sarah E. Lester, Benjamin I. Ruttenberg

Biological Sciences

We address the conflict in earlier results regarding the relationship between dispersal potential and range size. We examine all published pelagic larval duration data for tropical reef fishes. Larval duration is a convenient surrogate for dispersal potential in marine species that are sedentary as adults and that therefore only experience significant dispersal during their larval phase. Such extensive quantitative dispersal data are only available for fishes and thus we use a unique dataset to examine the relationship between dispersal potential and range size. We find that dispersal potential and range size are positively correlated only in the largest ocean basin, …

Hybrid Xerogel Films As Novel Coatings For Antifouling And Fouling Release, Ying Tang, John A. Finlay, Gregory L. Kowalke, Anne E. Meyer, Frank V. Bright, Maureen E. Callow, James A. Callow, Dean E. Wendt, Michael R. Detty

Biological Sciences

Hybrid sol-gel-derived xerogel films prepared from 45/55 (mol ratio) n-propyltrimethoxysilane (C3-TMOS)/tetramethylorthosilane (TMOS), 2/98 (mol ratio) bis[3-(trimethoxysilyl)propyl]-ethylenediamine (enTMOS)/tetraethylorthosilane (TEOS), 50/50 (mol ratio) n-octyltriethoxysilane (C8-TEOS)/TMOS, and 50/50 (mol ratio) 3,3,3-trifluoropropyltrimethoxysilane (TFP-TMOS)/TMOS were found to inhibit settlement of zoospores of the marine fouling alga Ulva (syn. Enteromorpha) relative to settlement on acid-washed glass and give greater release of settled zoospores relative to glass upon exposure to pressure from a water jet. The more hydrophobic 50/50 C8-TEOS/TMOS xerogel films had the lowest critical surface tension by comprehensive contact angle analysis and gave significantly greater release of 8-day Ulva sporeling biomass after exposure to …

Relationship Between Habitat Distribution, Growth Rate, And Plasticity In Congeneric Larval Dragonflies, S. J. Mccauley

Biological Sciences

The relationship between habitat distribution, growth rate, and plasticity was examined in the larvae of three species of dragonfly in the genus Libellula L., 1758. Growth rates were compared under three conditions: in the absence of predation risk, in the presence of sunfish (Lepomis macrochirus Rafinesque, 1819; Pisciformes: Centrachidae), and in the presence of invertebrate predators. I assessed how the habitat distributions of the three species of dragonfly, specifically how commonly they occur with fish, were related to growth rates and to the level of growth plasticity under different levels of perceived predation risk. There was a negative relationship …

The Bell Family Legacies, William D. Stansfield

Biological Sciences

No abstract provided.

Use Of Cover And Response To Cover Type Edges By Female Sierra Nevada Red Foxes In Winter, John F. Benson, John D. Perrine, Richard T. Golightly Jr., Reginald H. Barrett

Biological Sciences

Red foxes (Vulpes vulpes) use a variety of habitats across their range, including semiarid deserts, tundra, boreal forests, farmland, and urban areas (Larivière and Pasitschniak-Arts 1996). Within these habitats there is much variation in the use of different cover types among populations of red foxes (Jones and Theberge 1982, Halpin and Bissonette 1988, Theberge and Wedeles 1989, St-Georges et al. 1995). In Maine, red foxes used coniferous stands and open areas more than expected (Halpin and Bissonette 1988). In British Columbia, red foxes used shrub communities more than expected and open areas less than expected (Jones and Theberge 1982). In …

Correct Author Citation For Cirsium Eatonii Var. Eriocephalum (Asteraceae: Cardueae), David J. Keil

Biological Sciences

No abstract provided.

Integration Of Flowering Signals In Winter-Annual Arabidopsis, Scott D. Michaels, Edward Himelblau, Sang Yeol Kim, Fritz M. Schomburg, Richard M. Amasino

Biological Sciences

Photoperiod is the primary environmental factor affecting flowering time in rapid-cycling accessions of Arabidopsis (Arabidopsis thaliana). Winter-annual Arabidopsis, in contrast, have both a photoperiod and a vernalization requirement for rapid flowering. In winter annuals, high levels of the floral inhibitor FLC (FLOWERING LOCUS C) suppress flowering prior to vernalization. FLC acts to delay flowering, in part, by suppressing expression of the floral promoter SOC1 (SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1). Vernalization leads to a permanent epigenetic suppression of FLC. To investigate how winter-annual accessions integrate signals from the photoperiod and vernalization pathways, we have …

The Effects Of Resource Availability On Alternative Mating Tactics In Guppies (Poecilia Reticulata), Gita R. Kolluru, Gregory F. Grether

Biological Sciences

Food availability can influence the optimal allocation of time and energy among alternative behaviors such as foraging, courting, and competing for mates. If populations differ consistently in food availability, selection may cause geographic divergence in allocation strategies. At the opposite extreme, a norm of reaction may evolve such that food intake influences the allocation strategy of individuals in the same way in all populations. Between these two extremes, food intake reaction norms may diverge genetically among populations. For example, at sites where food is scarce, selection may strengthen the effect of food intake on behavior, whereas at sites with abundant …

The Large Genome Constraint Hypothesis: Evolution, Ecology And Phenotype, Charles A. Knight, Nicole A. Molinari, Dmitri A. Petrov

Biological Sciences

• Background and Aims If large genomes are truly saturated with unnecessary ‘junk’ DNA, it would seem natural that there would be costs associated with accumulation and replication of this excess DNA. Here we examine the available evidence to support this hypothesis, which we term the ‘large genome constraint’. We examine the large genome constraint at three scales: evolution, ecology, and the plant phenotype.

• Scope In evolution, we tested the hypothesis that plant lineages with large genomes are diversifying more slowly. We found that genera with large genomes are less likely to be highly specious – suggesting a large …

Does Intracellular Metabolite Diffusion Limit Post-Contractile Recovery In Burst Locomotor Muscle?, Stephen T. Kinsey, Pragyansri Pathi, Kristin M. Hardy, Amanda Jordan, Bruce R. Locke

Biological Sciences

Post-metamorphic growth in the blue crab entails an increase in body mass that spans several orders of magnitude. The muscles that power burst swimming in these animals grow hypertrophically, such that small crabs have fiber diameters that are typical of most cells (600μm). Thus, as the animals grow, their muscle fibers cross and greatly exceed the surface area to volume ratio (SA:V) and intracellular diffusion distance threshold that is adhered to by most cells. Large fiber size should not impact burst contractile function, but post-contractile recovery may be limited by low SA:V and excessive intracellular diffusion distances. A number of …

Episodic Physical Forcing And The Structure Of Phytoplankton Communities In The Coastal Waters Of New Jersey, Mark A. Moline, Shelley M. Blackwell, Robert Chant, Matthew J. Oliver, Trisha Bergmann, Scott Glenn, Oscar M.E. Schofield

Biological Sciences

The high variability in physical, biological, and chemical properties in coastal waters have limited our ability to sample the appropriate timescale and space scale to resolve physical forcing of the ecosystem. To improve our understanding, a multiplatform adaptive sampling program at the Long-term Ecosystem Observatory(LEO-15) off the coast of New Jersey examined the relationship between episodic summertime upwelling and downwelling events and the corresponding dynamics in bulk phytoplankton biomass and community structure. Inherent and apparent optical properties were concurrently measured to evaluate the use of optics to improve future sampling coverage in coastal regions. Results indicate peak chlorophyll biomass tracked …

Exogenous Vasotocin Alters Aggression During Agonistic Exchanges In Male Amargosa River Pupfish (Cyprinodon Nevadensis Amargosae), Sean C. Lema, Gabrielle A. Nevitt

Biological Sciences

Pupfishes in the Death Valley region have rapidly differentiated in social behaviors since their isolation in a series of desert streams, springs, and marshes less than 20,000 years ago. These habitats can show dramatic fluctuations in ecological conditions, and pupfish must cope with the changes by plastic physiological and behavioral responses. Recently, we showed differences among some Death Valley populations in brain expression of arginine vasotocin (AVT). As AVT regulates both hydromineral balance and social behaviors in other taxa, these population differences may indicate adaptive changes in osmoregulatory and/or behavioral processes. To test whether AVT is relevant for behavioral shifts …

Identification And Phenotypic Characterization Of The Cell-Division Protein Cdpa, Eric Altermann, B. Logan Buck, Raul Cano, Todd R. Klaenhammer

Biological Sciences

Analysis of the automated computer annotation of the early draft phase genome of Lactobacillus acidophilus NCFM revealed the previously discovered S-layer gene slpA and an additional partial ORF with weak similarities to S-layer proteins. The entire gene was sequenced to reveal a 1799-bp gene coding for 599 amino acids with a calculated molecular mass of 64.8 kDa. No transcription or translation signals could be determined in close proximity to the 5′-region. However, a strong putative terminator with a free energy of −16.84 kcal/mol was identified directly downstream of the gene. A PSI-Blast analysis showed similarities to members of S-layer proteins, …

Application Of Genotypic And Phenotypic Analyses To Commercial Probiotic Strain Identity And Relatedness, P. S. M. Yeung, Christopher L. Kitts, Phillip S. Tong, M. E. Sanders

Biological Sciences

Aims: The objective of this study was to generate strain-specific genomic patterns of a bank of 67 commercial and reference probiotic strains, with a focus on probiotic lactobacilli.
Methods and Results: Pulsed-field gel electrophoresis (PFGE) was used as the primary method for strain differentiation. This method was compared with carbohydrate fermentation analysis. To supplement visual comparison, PFGE patterns were analysed quantitatively by cluster analysis using unweighted pair group method with arithmetic averages. SmaI, NotI and XbaI were found to effectively generate clear and easy-to-interpret PFGE patterns of a range of probiotic strains. Some probiotic strains from different sources shared highly …

Sex Differences In Metabolic Rates In Field Crickets And Their Dipteran Parasitoids, Gita R. Kolluru, Mark A. Chappell, Marlene Zuk

Biological Sciences

Sex differences in metabolic rate (MR) can result from dimorphism in the performance of energetically demanding activities. Male crickets (Teleogryllus oceanicus) engage in costly calling and aggressive activity not performed by females. Consistent with this difference, we found higher maximal MR, factorial scope, and fat content in males than females. T. oceanicus song is also costly because it attracts the parasitoid fly Ormia ochracea. Parasitized crickets had reduced maximal MR consistent with a metabolic cost to harboring larvae. This cost was greater for females, either because females invest more heavily into reproduction at the expense of metabolic …

Alteration Of The Food Web Along The Antarctic Peninsula In Response To A Regional Warming Trend, Mark A. Moline, Herve Claustre, Thomas K. Frazer, Oscar Schofield, Maria Vernet

Biological Sciences

In the nearshore coastal waters along the Antarctic Peninsula, a recurrent shift in phytoplankton community structure, from diatoms to cryptophytes, has been documented. The shift was observed in consecutive years (1991–1996) during the austral summer and was correlated in time and space with glacial melt-water runoff and reduced surface water salinities. Elevated temperatures along the Peninsula will increase the extent of coastal melt-water zones and the seasonal prevalence of cryptophytes. This is significant because a change from diatoms to cryptophytes represents a marked shift in the size distribution of the phytoplankton community, which will, in turn, impact the zooplankton assemblage. …

Application Of Genotypic And Phenotypic Analyses To Commerical Probiotic Strain Identity And Relatedness, P.S.M. Yeung, C. L. Kitts, R. Cano, P. Tong

Biological Sciences

Aims: The objective of this study was to generate strain-specific genomic patterns of a bank of 67 commercial and reference probiotic strains, with a focus on probiotic lactobacilli.

Methods and Results: Pulsed-field gel electrophoresis (PFGE) was used as the primary method for strain differentiation. This method was compared with carbohydrate fermentation analysis. To supplement visual comparison, PFGE patterns were analysed quantitatively by cluster analysis using unweighted pair group method with arithmetic averages. SmaI, NotI and XbaI were found to effectively generate clear and easy-to-interpret PFGE patterns of a range of probiotic strains. Some probiotic strains from different sources …

Evidence That Thyroid Hormone Induces Olfactory Cellular Proliferation In Salmon During A Sensitive Period For Imprinting, Sean C. Lema, Gabrielle A. Nevitt

Biological Sciences

Salmon have long been known to imprint and home to natal stream odors, yet the mechanisms driving olfactory imprinting remain obscure. The timing of imprinting is associated with elevations in plasma thyroid hormone levels, with possible effects on growth and proliferation of the peripheral olfactory system. Here, we begin to test this idea by determining whether experimentally elevated plasma levels of 3,5,3′-triiodothyronine (T₃) influence cell proliferation as detected by the 5-bromo-2′-deoxyuridine (BrdU) cell birth-dating technique in the olfactory epithelium of juvenile coho salmon (Oncorhynchus kisutch). We also explore how natural fluctuations in thyroxine (T₄) …

Complete Genomic Sequence Of Bacteriophage B3, A Mu-Like Phage Of Pseudomonas Aeruginosa, Michael D. Braid, Jennifer L. Silhavy, Christopher L. Kitts, Raul J. Cano, Martha M. Howe

Biological Sciences

Bacteriophage B3 is a transposable phage of Pseudomonas aeruginosa. In this report, we present the complete DNA sequence and annotation of the B3 genome. DNA sequence analysis revealed that the B3 genome is 38,439 bp long with a G+C content of 63.3%. The genome contains 59 proposed open reading frames (ORFs) organized into at least three operons. Of these ORFs, the predicted proteins from 41 ORFs (68%) display significant similarity to other phage or bacterial proteins. Many of the predicted B3 proteins are homologous to those encoded by the early genes and head genes of Mu and Mu-like prophages found …

Identification And Inactivation Of Genetic Loci Involved With Lactobacillus Acidophilus Acid Tolerance, M. Andrea Azcarate-Peril, Eric Altermann, Rebecca L. Hoover- Fitzula, Raul J. Cano, Todd R. Klaenhammer

Biological Sciences

Amino acid decarboxylation-antiporter reactions are one of themost important systems for maintaining intracellular pH betweenphysiological limits under acid stress. We analyzed the Lactobacillusacidophilus NCFM complete genome sequence and selected fouropen reading frames with similarities to genes involved withdecarboxylation reactions involved in acid tolerance in severalmicroorganisms. Putative genes encoding an ornithine decarboxylase,an amino acid permease, a glutamate -aminobutyrate antiporter,and a transcriptional regulator were disrupted by insertionalinactivation. The ability of L. acidophilus to survive low-pHconditions, such as those encountered in the stomach or fermenteddairy foods, was investigated and compared to the abilitiesof early- and late-stationary-phase cells of the mutants bychallenging them with …

Deriving In Situ Phytoplankton Absorption For Bio-Optical Productivity Models In Turbid Waters, Christina Orrico, Matthew J. Oliver, Oscar Schofield, Trisha Bergmann, Scott Glenn, Mark A. Moline

Biological Sciences

As part of Hyperspectral Coupled Ocean Dynamics Experiment, a high-resolution hydrographic and bio-optical data set was collected from two cabled profilers at the Long-Term Ecosystem Observatory (LEO). Upwelling-and downwelling-favorable winds and a buoyant plume from the Hudson River induced large changes in hydrographic and optical structure of the water column. An absorption inversion model estimated the relative abundance of phytoplankton, colored dissolved organic matter (CDOM) and detritus, as well as the spectral exponential slopes of CDOM and detritus from in situ WET Labs nine-wavelength absorption/attenuation meter (ac-9) absorption data. Derived optical weights were proportional to the parameter concentrations and allowed …

Watercolors In The Coastal Zone: What Can We See?, Oscar Schofield, Robert A. Arnone, W. Paul Bissett, Tommy D. Dickey, Curtis O. Davis, Zoe Finkel, Matthew Oliver, Mark A. Moline

Biological Sciences

No abstract provided.

The New Age Of Hyperspectral Oceanography, Grace Chang, Kevin Mahoney, Amanda Briggs-Whitmire, David Kohler, Curtis Mobley, Marlon Lewis, Mark A. Moline, Emmanuel Boss, Minsu Kim, William Philpot, Tommy Dickey

Biological Sciences

No abstract provided.

Diploid And Polyploid Cytotype Distribution In Melampodium Cinereum And M. Leucanthum (Asteraceae, Heliantheae), Tod F. Stuessy, Hanna Weiss-Schneeweiss, David J. Keil

Biological Sciences

Previous chromosomal studies within Melampodium (Asteraceae, Heliantheae) of Mexico and Central America have documented chromosome numbers n = 9, 10, 11, 12, 18, 20, 23, 25 ± 1, 27, 30, and 33. Some species also have been shown to exhibit infra-and interpopulational polyploidy. The presence of cytotype mixtures is especially pronounced in the white-rayed complex, which occurs in the southwestern United States and adjacent Mexico. This group includes M. cinereum (n = 10 and 20), M. leucanthum (n = 10 and 20), and M. argophyllum (n = 30). Cytotype distribution has been newly analyzed in 415 plants from 152 populations …

Variability In Spectral Backscatter Estimated From Satellites And Its Relation To In Situ Measurements In Optically Complex Coastal Waters, Mark A. Moline, Robert Arnone, Trisha Bergmann, Scott Glenn, Matthew J. Oliver, Cristina Orrico, Oscar Schofield, Sasha Tozzi

Biological Sciences

A large database of in situ bio-optical measurements was collected at the Long-term Ecosystem Observatory off the southern coast of New Jersey, USA. In part, the research effort focused on reconciling in situ estimates with satellite-derived estimates of the inherent optical properties (IOP). At 442 nm, in situ absorption values ranged from less than 0.2 to over 1.5 inverse metres. Satellite estimates of backscatter ranged from 0.002 to 0.03 inverse metres at 442 nm and showed significant variability in time and space during July 1999, reflecting the recurrent high frequency events that characterize the region—wind-mixing, storms and coastal upwelling. Despite …

Micrococcus Luteus - Survival In Amber, C. L. Greenblatt, J. Baum, B. Y. Klein, S. Nachshon, V. Koltunov, R. J. Cano

Biological Sciences

A growing body of evidence now supports the isolation of microorganisms from ancient materials. However, questions about the stringency of extraction methods and the genetic relatedness of isolated organisms to their closest living relatives continue to challenge the authenticity of these ancient life forms. Previous studies have successfully isolated a number of spore-forming bacteria from organic and inorganic deposits of considerable age whose survival is explained by their ability to enter suspended animation for extended periods of time. However, despite a number of putative reports, the isolation of non-spore-forming bacteria and an explanation for their survival have remained enigmatic. Here …

Variability In Measured And Modelled Remote Sensing Reflectance For Coastal Waters At Leo-5, Sasha Tozzi, Oscar Schofield, Trisha Bergmann, Mark A. Moline, Robert Arnone

Biological Sciences

A large database of in situ bio-optical measurements were collected at the LEO-15 (Long-term Ecosystem Observatory) off the southern coast of New Jersey, USA. The data were used to quantify the impact of coastal upwelling on near-shore bulk apparent (AOP) and inherent (IOP) optical properties. There was good qualitative agreement between the AOPs and IOPs in space and time. The measured IOPs were used as inputs to the Hydrolight radiative transfer model (RTE). Estimated spectral AOPs from the RTE were strongly correlated (generally R²>0.80) to measured AOPs. If optical closure between in-water measurements was achieved then the RTE …

Bayesian Statistics For Biological Data: Pedigree Analysis, William D. Stansfield, Matthew A. Carlton

Biological Sciences

No abstract provided.

Fossil Tuna Vertebrae Punctured By Istiophorid Billfishes, Vincent P. Schneider, Harry L. Fierstine

Biological Sciences

No abstract provided.