The use of multibeam sonar mapping techniques to refine population estimates of the endangered white abalone (Haliotis sorenseni)

Multibeam sonar mapping techniques provide detailed benthic habitat information that can be combined with the data on species-specific habitat preferences to provide highly accurate calculations of populations in a particular area. The amount of suitable habitat available for the endangered white abalone (Haliotis sorenseni) was quantified to aid in obtaining an accurate estimate of the number of remaining individuals at two offshore banks and one island site off the coast of southern California. Habitat was mapped by using multibeam sonar survey techniques and categorized by using rugosity and topographic position analysis. Abalone densities were evaluated by using a remotely operated vehicle and video transect methods. The total amount of suitable habitat at these three sites was far greater than that previously estimated. Therefore, although present estimates of white abalone densities are several orders of magnitude lower than historic estimates, the total population is likely larger than previously reported because of the additional amount of habitat surveyed in this study

Physicochemical Aspects of Metal Nanoparticle Preparation

Physicochemical properties, including optical properties or catalytic activity, and biological properties of metal nanoparticles are considerably influenced by their diameter. Therefore, a tailored synthesis of metal nanoparticles represents a key topic in the field of nanotechnology, and the number of research papers, concerning this topic, has been annually growing with an arithmetic progression. Metal nanoparticles are most frequently prepared via chemical reduction of metals in ionic form from their solutions. Using this synthetic approach, tailored parameters of the particles can be achieved via the adjustment of numerous factors: difference of potentials of the metal redox system and the reducing agent redox system, pH of the reaction mixture, and its temperature. The influence of these three factors on the diameter of the prepared metal nanoparticles will be discussed in the following chapter with respect to general laws and based on numerous examples from research practice

Substrate Effects of Noble Metal Nanostructures Prepared by Sputtering

Cathode sputtering is a well-established technique for preparation of metal nanostructures. However, the substrate properties are very important in this process. On glass substrates, there is a difficulty with poor adhesion of the metal layers, but thanks to this, metal nanostructures can be produced using solid state dewetting process. Thin metal films on polymer substrates are strongly influenced by the surface properties of the polymers, which originate in the method of their preparation. A recent focus is direct sputtering of metal nanoparticles (NPs) into liquid substrates and their characterizations and applications. Polyethylene glycol (PEG) is one of the most commonly used liquid, which provides “stealth” character to nanostructures. Recent results in this area are reviewed in this chapter. PEGylated NPs could find application in drug delivery systems, therapy, imaging, biosensing, and tissue regeneration

Effects of Epistasis and Pleiotropy on Fitness Landscapes

The factors that influence genetic architecture shape the structure of the fitness landscape, and therefore play a large role in the evolutionary dynamics. Here the NK model is used to investigate how epistasis and pleiotropy -- key components of genetic architecture -- affect the structure of the fitness landscape, and how they affect the ability of evolving populations to adapt despite the difficulty of crossing valleys present in rugged landscapes. Populations are seen to make use of epistatic interactions and pleiotropy to attain higher fitness, and are not inhibited by the fact that valleys have to be crossed to reach peaks of higher fitness.Comment: 10 pages, 6 figures. To appear in "Origin of Life and Evolutionary Mechanisms" (P. Pontarotti, ed.). Evolutionary Biology: 16th Meeting 2012, Springer-Verla

The Valley-of-Death: Reciprocal sign epistasis constrains adaptive trajectories in a constant, nutrient limiting environment

The fitness landscape is a powerful metaphor for describing the relationship between genotype and phenotype for a population under selection. However, empirical data as to the topography of fitness landscapes are limited, owing to difficulties in measuring fitness for large numbers of genotypes under any condition. We previously reported a case of reciprocal sign epistasis (RSE), where two mutations individually increased yeast fitness in a glucose-limited environment, but reduced fitness when combined, suggesting the existence of two peaks on the fitness landscape. We sought to determine whether a ridge connected these peaks so that populations founded by one mutant could reach the peak created by the other, avoiding the low-fitness Valley-of-Death between them. Sequencing clones after 250 generations of further evolution provided no evidence for such a ridge, but did reveal many presumptive beneficial mutations, adding to a growing body of evidence that clonal interference pervades evolving microbial populations

Bioinformatic approaches for the genetic and phenotypic characterization of a Saccharomyces cerevisiae wine yeast collection

The objective of the present study was to compare genetic and phenotypic variation of 103 Saccharomyces cerevisiae strains isolated from winemaking environments. We used bioinformatics approaches to identify genetically similary strains with specific phenotypes and to estimate a strain's biotechnological potential. 
A S. cerevisiae collection, comprising 440 strains that were obtained from winemaking environments in Portugal has been constituted during the last years. All strains were genetically characterized by a set of eleven highly polymorphic microsatellites and showed unique allelic combinations. Using neural networks, a subset of 103 genetically most diverse strains was chosen for phenotypic analysis, that included growth in synthetic must media at various temperatures, utilization of carbon sources (glucose, ribose, arabinose, xylose, saccharose, galactose, rafinose, maltose, glycerol, potassium acetate and pyruvic acid), growth in ethanol containing media, evaluation of osmotic and oxidative stress resistance, H2S production and utilization of different nitrogen sources. Using supervised data mining approaches we have found that genotype represented with presence/absence of eleven microsatellites relates well with geographical location (performance evaluation using leave-out-out technique resulted in high performance scores; e.g., area under ROC curve was above 0.8 for a number of standard machine learning approaches tested). To find relations between phenotypes and genotypes, we used a two-step approach which first hierarchically clusters the strains according to their phenotype, and then tests if the resulting sub-clusters are identifiable using strain’s genetic data. Several groups of strains with similar phenotype profiles and common features in genotype were identified this way, and they are subject to further investigations. 

Financially supported by the programs POCI 2010 (FEDER/FCT, POCTI/AGR/56102/2004) and AGRO (ENOSAFE, Nº 762).
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Synthesis, characterisation and antifungal activity of chemically and fungal-produced silver nanoparticles against Trichophyton rubrum

Aims To characterise and explore the potential in extracellular biosynthesis of silver nanoparticles (AgNPs) by Penicillium chrysogenum and Aspergillus oryzae and to investigate the antifungal effect of chemically vs. biologically synthesised AgNPs comparing with conventional antifungal drugs against Trichophyton rubrum. Methods and Results Chemically synthesised AgNPs (Chem-AgNPs) coated with polyvinylpyrrolidone (PVP) were synthesised by chemical reduction method with glucose in PVP aqueous solution. Biologically synthesised AgNPs (Bio-AgNPs) were produced from the extracellular cell-free filtrate of Penicillium chrysogenum MUM 03.22 and Aspergillus oryzae MUM 97.19. Among the commercial antifungal drugs terbinafine exhibited the lower MIC range values of 0.063 to 0.25 μg ml-1 for the clinical strains. Chem-AgNPs exhibited antifungal activity against all T. rubrum strains. Bio-AgNPs produced by the fungal cell-free filtrate of P. chrysogenum showed an antifungal activity higher than fluconazole but less than terbinafine, itraconazole and Chem-AgNPs. Conclusion The synthesis parameters in future works should be carefully studied to take full advantage of all the potential of filamentous fungi in the synthesis of AgNPs. Significance and Impact of the study: Bio-AgNPs could be used as antifungal agents, namely against dermatophytesThe authors thank Pedro Martins (Physics Department of University of Minho) for help in XRD analysis. The authors thank to SDBSWeb: http://sdbs.db.aist.go.jp (Japanese National Institute of Advanced Industrial Science and Technology). The authors thank the FCT Strategic Project PEst-OE/EQB/LA0023/2013. Nicolina Dias acknowledges the project 'Consolidating Research Expertise and Resources on Cellular and Molecular Biotechnology at CEB/IBB', RECI/BBB-EBI/0179/2012

Acoustic detection and quantification of benthic egg beds of the squid Loligo opalescens in Monterey Bay, California

Author Posting. © Acoustical Society of America, 2006. This article is posted here by permission of Acoustical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Acoustical Society of America 119 (2006): 844-856, doi:10.1121/1.2149840.The squid Loligo opalescens is a key species in the nearshore pelagic community of California, supporting the most valuable state marine fishery, yet the stock biomass is unknown. In southern Monterey Bay, extensive beds occur on a flat, sandy bottom, water depths 20–60 m, thus sidescan sonar is a prima-facie candidate for use in rapid, synoptic, and noninvasive surveying. The present study describes development of an acoustic method to detect, identify, and quantify squid egg beds by means of high-frequency sidescan-sonar imagery. Verification of the method has been undertaken with a video camera carried on a remotely operated vehicle. It has been established that sidescan sonar images can be used to predict the presence or absence of squid egg beds. The lower size limit of detectability of an isolated egg bed is about 0.5 m with a 400-kHz sidescan sonar used with a 50-m range when towed at 3 knots. It is possible to estimate the abundance of eggs in a region of interest by computing the cumulative area covered by the egg beds according to the sidescan sonar image. In a selected quadrat one arc second on each side, the estimated number of eggs was 36.5 million.funding from the National Sea Grant, Essential Fish Habitat Program, Sea Grant Project No. NA16RG2273

Computational models reveal genotype-phenotype associations in Saccharomyces cerevisiae

Genome sequencing is essential to understand individual variation and to study the mechanisms that explain relations between genotype and phenotype. The accumulated knowledge from large-scale genome sequencing projects of Saccharomyces cerevisiae isolates is being used to study the mechanisms that explain such relations. Our objective was to undertake genetic characterization of 172 S. cerevisiae strains from different geographical origins and technological groups, using 11 polymorphic microsatellites, and computationally relate these data with the results of 30 phenotypic tests. Genetic characterization revealed 280 alleles, with the microsatellite ScAAT1 contributing most to intrastrain variability, together with alleles 20, 9 and 16 from the microsatellites ScAAT4, ScAAT5 and ScAAT6. These microsatellite allelic profiles are characteristic for both the phenotype and origin of yeast strains. We confirm the strength of these associations by construction and cross-validation of computational models that can predict the technological application and origin of a strain from the microsatellite allelic profile. Associations between microsatellites and specific phenotypes were scored using information gain ratios, and significant findings were confirmed by permutation tests and estimation of false discovery rates. The phenotypes associated with higher number of alleles were the capacity to resist to sulphur dioxide (tested by the capacity to grow in the presence of potassium bisulphite) and the presence of galactosidase activity. Our study demonstrates the utility of computational modelling to estimate a strain technological group and phenotype from microsatellite allelic combinations as tools for preliminary yeast strain selection. Copyright (C) 2014 John Wiley & Sons, Ltd.Ricardo Franco-Duarte and Ines Mendes are the recipients of fellowships from the Portuguese Science Foundation (FCT; Grant Nos SFRH/BD/74798/2010 and SFRH/BD/48591/2008, respectively) and Joao Drumonde-Neves is the recipient of a fellowship from the Azores Government (Grant No. M3.1.2/F/006/2008; DRCT). Financial support was obtained from FEDER funds through the programme COMPETE and by national funds through FCT by Project Nos FCOMP-01-0124-008775 (PTDC/AGR-ALI/103392/2008) and PTDC/AGR-ALI/121062/2010. Lan Umek and Blaz Zupan acknowledge financial support from the Slovene Research Agency (Grant No. P2-0209). The authors would like also to thank all the researchers who kindly provided yeast strains: Gianni Liti, Institute of Genetics, UK; Laura Carreto, CESAM and Biology Department, Portugal; Goto Yamamoto, NRIB, Japan; Cletus Kurtzman, Microbial Properties Research, USA; Rogelio Brandao, Laboratorio de Fisologia e Bioquimica de Microorganismos, Brazil; and Huseyin Erten, Cukurova University, Turkey.info:eu-repo/semantics/publishedVersio

The influence of anthropogenic nitrogen loading and meteorological conditions on the dynamics and toxicity of Alexandrium fundyense blooms in a New York (USA) estuary

Author Posting. © The Author(s), 2010. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Harmful Algae 9 (2010): 402-412, doi:10.1016/j.hal.2010.02.003.The goal of this two-year study was to explore the role of nutrients and climatic conditions in promoting reoccurring Alexandrium fundyense blooms in the Northport-Huntington Bay complex, NY, USA. A bloom in 2007 was short and small (3 weeks, 103 cells L-1 maximal density) compared to 2008 when the A. fundyense bloom, which persisted for six weeks, achieved cell densities >106 cells L-1 and water column saxitoxin concentrations >2.4 x 104 pmol STX eq. L-1. During the 2008 bloom, both deployed mussels (used as indicator species) and wild soft shell clams became highly toxic (1,400 and 600μg STX eq./100g shellfish tissue, respectively) resulting in the closure of shellfish beds. The densities of benthic A. fundyense cysts at the onset of this bloom were four orders of magnitude lower than levels needed to account for observed cell densities, indicating in situ growth of vegetative cells was responsible for elevated bloom densities. Experimental enrichment of bloom water with nitrogenous compounds, particularly ammonium, significantly increased A. fundyense densities and particulate saxitoxin concentrations relative to unamended control treatments. The δ15N signatures (12 to 23‰) of particulate organic matter (POM) during blooms were similar to those of sewage (10 to 30‰) and both toxin and A. fundyense densities were significantly correlated with POM δ15N (p < 0.001). These findings suggest A. fundyense growth was supported by a source of wastewater such as the sewage treatment plant which discharges into Northport Harbor. Warmer than average atmospheric temperatures in the late winter and spring of 2008 and a cooler May contributed to an extended period of water column temperatures optimal for A. fundyense growth (12 – 20ºC), and thus may have also contributed toward the larger and longer bloom in 2008. Together this evidence suggests sewage-derived N loading and above average spring temperatures can promote intense and toxic A. fundyense blooms in estuaries.This work was supported by a grant from EPA’s Long Island Sound Study, New York Sea Grant, and the New York State Department of Environmental Conservation (to CJG) and from the NOAA Sea Grant Program (Grant No. NA06OAR4170021 (R/B-177)) to DMA