Genetic analysis of immunological traits in tilapia

The immunological response to handling stress of four tilapia species is evaluated.Polymorphism is examined in genes known to influence immune response in fish

SNPmplexViewer--toward a cost-effective traceability system

<p>Abstract</p> <p>Background</p> <p>Beef traceability has become mandatory in many regions of the world and is typically achieved through the use of unique numerical codes on ear tags and animal passports. DNA-based traceability uses the animal's own DNA code to identify it and the products derived from it. Using <it>SNaPshot</it>, a primer-extension-based method, a multiplex of 25 SNPs in a single reaction has been practiced for reducing the expense of genotyping a panel of SNPs useful for identity control.</p> <p>Findings</p> <p>To further decrease <it>SNaPshot</it>'s cost, we introduced the Perl script <it>SNPmplexViewer</it>, which facilitates the analysis of trace files for reactions performed without the use of fluorescent size standards. <it>SNPmplexViewer </it>automatically aligns reference and target trace electropherograms, run with and without fluorescent size standards, respectively. <it>SNPmplexViewer </it>produces a modified target trace file containing a normalised trace in which the reference size standards are embedded. <it>SNPmplexViewer </it>also outputs aligned images of the two electropherograms together with a difference profile.</p> <p>Conclusions</p> <p>Modified trace files generated by <it>SNPmplexViewer </it>enable genotyping of <it>SnaPshot </it>reactions performed without fluorescent size standards, using common fragment-sizing software packages. <it>SNPmplexViewer</it>'s normalised output may also improve the genotyping software's performance. Thus, <it>SNPmplexViewer </it>is a general free tool enabling the reduction of <it>SNaPshot</it>'s cost as well as the fast viewing and comparing of trace electropherograms for fragment analysis. <it>SNPmplexViewer </it>is available at <url>http://cowry.agri.huji.ac.il/cgi-bin/SNPmplexViewer.cgi</url>.</p

Scanning Mechanical Microscopy of Laser Ablated Volumes Related to Inductively Coupled Plasma-Mass Spectrometry

Scanning mechanical microscopy based on the point by point sampling of the target surface was used to characterize volumes of minerals ablated by laser pulses (Nd: YAG, = 1064 nm, 140 μs pulse-width). Differentiated volumes resulting from vaporization and exfoliation mechanisms were selectively measured. Ablated volumes of natural pyrite (cubic FeS2), marcasite (orthorhombic FeS2) and arsenopyrite AsFeS, were transported into an inductively coupled plasma torch for subsequent mass analysis. The log of the S34 Fe57, and As75 mass intensities was linearly correlated with the log of the dimensions of the vaporized crater induced by the laser shots while large particles had no effect on the measured intensities. A memory effect for As was observed when a nylon tube was used to carry the ablated materials into the plasma torch. The memory effect was decreased by using a copper tube resulting probably from a difference in the electrical properties of the tubing systems leading to a lower adsorption of As within the copper tube than for the case of the nylon tube

DNA BARCODING OF FISH SPECIES FROM THE MEDITERRANEAN COAST OF ISRAEL

Accurately-classified genomic data in the Barcode of Life Data System (BOLD) database is vital to the protection and conservation of marine biodiversity in the Mediterranean Sea. The taxonomic classifications of 468 fish of 50 Mediterranean species were analyzed using the BOLD Identifier tool for variation in the cytochrome oxidase subunit I (COI) mitochondrial gene. Within species, nucleotide maximum composite likelihood was low with a mean of 0.0044±0.0008. Three presumptive species had significantly higher values e.g., Arnoglossus spp. (0.07), Torquigener flavimaculosus (0.013) and Boops boops (0.028). However, samples of Arnoglossus species were sub-classified into two groups that were finally identified as two different species e.g., Arnoglossus laterna and Arnoglossus thori. For the different species, BLAST searches against the BOLD database using our DNA barcoding data as the query sequences designated the most similar targets into groups. For each analyzed species, the similarity of the first and second threshold groups ranged from 95 to 99% and from 83 to 98%, respectively. Sequence based classification for the first threshold group was concordant with morphology-based identification. However, for 34 analyzed species (68%) overlaps of species between the two threshold groups hampered classification. Tree-based phylogeny analysis detected more than one cluster in the first threshold group for 22 out of 50 species, representing genetic subgroups and geographic origins. There was a tendency for higher conservation and lower number of clusters in the Lessepsian (Red Sea) migrant versus indigenous species

Recruiting Diverse Smokers: Enrollment Yields and Cost

To help tobacco control research better include vulnerable populations, we sought to identify effective ways to recruit diverse smokers. In 2014–2015, we recruited 2149 adult cigarette smokers in California and North Carolina, United States, to participate in a randomized trial of pictorial cigarette pack warnings. The most effective means of recruiting smokers were the classified advertising website Craigslist (28% of participants), word of mouth (23%), Facebook (16%), and flyers or postcards (14%). Low-income and African American smokers were more likely to respond to interpersonal contact (including staff in-person recruitment and word of mouth) than were high-income and non-African American smokers (all p < 0.05). Hispanic and gay, lesbian, and bisexual smokers were more likely to be recruited by Craigslist than non-Hispanic and straight smokers (both p < 0.05). Of the recruitment methods requiring cost, the cheapest was Craigslist ($3–7 per smoker). The most expensive methods were newspaper ads in California ($375 per smoker) and staff in-person recruiting in North Carolina ($180 per smoker). Successfully recruiting diverse smokers requires using multiple methods including interpersonal, online, and other media. Craigslist and word of mouth are especially useful and low-cost ways to recruit diverse smokers

Effect of Pictorial Cigarette Pack Warnings on Changes in Smoking Behavior: A Randomized Clinical Trial

Pictorial warnings on cigarette packs draw attention and increase quit intentions, but their effect on smoking behavior remains uncertain

Experimental design for three interrelated marine ice sheet and ocean model intercomparison projects: MISMIP v. 3 (MISMIP +), ISOMIP v. 2 (ISOMIP +) and MISOMIP v. 1 (MISOMIP1)

Coupled ice sheet–ocean models capable of simulating moving grounding lines are just becoming available. Such models have a broad range of potential applications in studying the dynamics of marine ice sheets and tidewater glaciers, from process studies to future projections of ice mass loss and sea level rise. The Marine Ice Sheet–Ocean Model Intercomparison Project (MISOMIP) is a community effort aimed at designing and coordinating a series of model intercomparison projects (MIPs) for model evaluation in idealized setups, model verification based on observations, and future projections for key regions of the West Antarctic Ice Sheet (WAIS). Here we describe computational experiments constituting three interrelated MIPs for marine ice sheet models and regional ocean circulation models incorporating ice shelf cavities. These consist of ice sheet experiments under the Marine Ice Sheet MIP third phase (MISMIP+), ocean experiments under the Ice Shelf-Ocean MIP second phase (ISOMIP+) and coupled ice sheet–ocean experiments under the MISOMIP first phase (MISOMIP1). All three MIPs use a shared domain with idealized bedrock topography and forcing, allowing the coupled simulations (MISOMIP1) to be compared directly to the individual component simulations (MISMIP+ and ISOMIP+). The experiments, which have qualitative similarities to Pine Island Glacier Ice Shelf and the adjacent region of the Amundsen Sea, are designed to explore the effects of changes in ocean conditions, specifically the temperature at depth, on basal melting and ice dynamics. In future work, differences between model results will form the basis for the evaluation of the participating models

Set of Points on Elliptic Curve in Projective Coordinates

In this article, we formalize a set of points on an elliptic curve over GF(p). Elliptic curve cryptography [10], whose security is based on a difficulty of discrete logarithm problem of elliptic curves, is important for information security.Futa Yuichi - Shinshu University, Nagano, JapanOkazaki Hiroyuki - Shinshu University, Nagano, JapanShidama Yasunari - Shinshu University, Nagano, JapanGrzegorz Bancerek. Cardinal numbers. Formalized Mathematics, 1(2):377-382, 1990.Grzegorz Bancerek. The fundamental properties of natural numbers. Formalized Mathematics, 1(1):41-46, 1990.Grzegorz Bancerek and Krzysztof Hryniewiecki. Segments of natural numbers and finite sequences. Formalized Mathematics, 1(1):107-114, 1990.Józef Białas. Group and field definitions. Formalized Mathematics, 1(3):433-439, 1990.Czesław Byliński. Functions and their basic properties. Formalized Mathematics, 1(1):55-65, 1990.Czesław Byliński. Functions from a set to a set. Formalized Mathematics, 1(1):153-164, 1990.Czesław Byliński. Some basic properties of sets. Formalized Mathematics, 1(1):47-53, 1990.Agata Darmochwał. Finite sets. Formalized Mathematics, 1(1):165-167, 1990.Krzysztof Hryniewiecki. Basic properties of real numbers. Formalized Mathematics, 1(1):35-40, 1990.G. Seroussi I. Blake and N. Smart. Elliptic Curves in Cryptography. Number 265 in London Mathematical Society Lecture Note Series. Cambridge University Press, 1999.Eugeniusz Kusak, Wojciech Leończuk, and Michał Muzalewski. Abelian groups, fields and vector spaces. Formalized Mathematics, 1(2):335-342, 1990.Rafał Kwiatek. Factorial and Newton coefficients. Formalized Mathematics, 1(5):887-890, 1990.Konrad Raczkowski and Paweł Sadowski. Equivalence relations and classes of abstraction. Formalized Mathematics, 1(3):441-444, 1990.Christoph Schwarzweller. The ring of integers, euclidean rings and modulo integers. Formalized Mathematics, 8(1):29-34, 1999.Christoph Schwarzweller. The binomial theorem for algebraic structures. Formalized Mathematics, 9(3):559-564, 2001.Andrzej Trybulec. Domains and their Cartesian products. Formalized Mathematics, 1(1):115-122, 1990.Andrzej Trybulec. Tuples, projections and Cartesian products. Formalized Mathematics, 1(1):97-105, 1990.Michał J. Trybulec. Integers. Formalized Mathematics, 1(3):501-505, 1990.Wojciech A. Trybulec. Groups. Formalized Mathematics, 1(5):821-827, 1990.Wojciech A. Trybulec. Vectors in real linear space. Formalized Mathematics, 1(2):291-296, 1990.Zinaida Trybulec. Properties of subsets. Formalized Mathematics, 1(1):67-71, 1990.Edmund Woronowicz. Relations and their basic properties. Formalized Mathematics, 1(1):73-83, 1990.Edmund Woronowicz and Anna Zalewska. Properties of binary relations. Formalized Mathematics, 1(1):85-89, 1990

Multisystem synthesis of radar sounding observations of the Amundsen Sea sector from the 2004‐2005 field season

The Amundsen Sea Embayment of the West Antarctic Ice Sheet contains Thwaites and Pine Island Glaciers, two of the most rapidly changing glaciers in Antarctica. To date, Pine Island and Thwaites Glaciers have only been observed by independent airborne radar sounding surveys, but a combined cross-basin analysis that investigates the basal conditions across the Pine Island-Thwaites Glaciers boundary has not been performed. Here, we combine two radar surveys and correct for their differences in system parameters to produce unified englacial attenuation and basal relative reflectivity maps spanning both Pine Island and Thwaites Glaciers. Relative reflectivities range from -24.8 to +37.4 dB with the highest values beneath fast-flowing ice at the ice sheet margin. By comparing our reflectivity results with previously derived radar specularity and trailing bed echoes at Thwaites Glacier, we find a highly diverse subglacial landscape and hydrologic condition that evolve along flow. Together, these findings highlight the potential for joint airborne radar analysis with ground-based seismic and geomorphological observations to understand variations in the bed properties and cross-catchment interactions of ice streams and outlet glaciers