Rapid Mapping of Zebrafish Mutations With SNPs and Oligonucleotide Microarrays

Large-scale genetic screens in zebrafish have identified thousands of mutations in hundreds of essential genes. The genetic mapping of these mutations is necessary to link DNA sequences to the gene functions defined by mutant phenotypes.Here, we report two advances that will accelerate the mapping of zebrafish mutations: (1) The construction of a first generation single nucleotide polymorphism (SNP) map of the zebrafish genome comprising 2035 SNPs and 178 small insertions/deletions, and (2) the development of a method for mapping mutations in which hundreds of SNPs can be scored in parallel with an oligonucleotide microarray.We have demonstrated the utility of the microarray technique in crosses with haploid and diploid embryos by mapping two known mutations to their previously identified locations.We have also used this approach to localize four previously unmapped mutations.We expect that mapping with SNPs and oligonucleotide microarrays will accelerate the molecular analysis of zebrafish mutations

Application of ultrafast gold luminescence to measuring the instrument response function for multispectral multiphoton fluorescence lifetime imaging

When performing multiphoton fluorescence lifetime imaging in multiple spectral emission channels, an instrument response function must be acquired in each channel if accurate measurements of complex fluorescence decays are to be performed. Although this can be achieved using the reference reconvolution technique, it is difficult to identify suitable fluorophores with a mono-exponential fluorescence decay across a broad emission spectrum. We present a solution to this problem by measuring the IRF using the ultrafast luminescence from gold nanorods. We show that ultrafast gold nanorod luminescence allows the IRF to be directly obtained in multiple spectral channels simultaneously across a wide spectral range. We validate this approach by presenting an analysis of multispectral autofluorescence FLIM data obtained from human skin ex vivo

Association between a high number of isolated lymph nodes in T1 to T4 N0M0 colorectal cancer and the microsatellite instability phenotype

Hypothèse : Les carcinomes colorectaux de stade I ou II microsatellites instables (MSI) sont caractérisés par plus de ganglions lymphatiques isolés sur la pièce de résection par rapport à leurs homologues microsatellites stables (MSS). Conception : Étude prospective. Patients : Le statut MSI a été déterminé de façon prospective chez 135 patients opérables, par l’utilisation d’une PCR pentaplex. Puis, les défauts de réparation des mésappariements de l’ADN ont été étudiés par immunohistochimie. Résultats : Parmi les 82 cancers colorectaux de stade I ou II, 11 étaient MSI et 71 MSS, avec une moyenne (écart-type) de 23,6 (3,1) et 13,7 (1,0) ganglions négatifs, respectivement (p = .001). Le nombre moyen de ganglions pour tous les cancers colorectaux de stade I ou II analysés dans notre hôpital était de 15. La prévalence des MSI dans les tumeurs avec plus de 15 ganglions prélevés était de 25 % (9 sur 36) et 82 % (9 sur 11) des tumeurs MSI appartenaient à ce groupe. Conclusions : Un nombre élevé de ganglions isolés en cas de cancer colorectal de stade I ou II est associé au phénotype MSI. Le bon pronostic qui est habituellement associé à des tumeurs ayant un nombre élevé de ganglions N0 pourrait refléter la prévalence élevée des MSI chez ces tumeurs. Le nombre de ganglions examinés comme un critère de qualité doit être utilisé avec prudence. Limiter le phénotypage MSI aux tumeurs colorectales de stade I ou II ayant plus que le nombre moyen de ganglions identifie presque toutes les tumeurs MSI.Hypothèse : Les carcinomes colorectaux de stade I ou II microsatellites instables (MSI) sont caractérisés par plus de ganglions lymphatiques isolés sur la pièce de résection par rapport à leurs homologues microsatellites stables (MSS). Conception : Étude prospective. Patients : Le statut MSI a été déterminé de façon prospective chez 135 patients opérables, par l’utilisation d’une PCR pentaplex. Puis, les défauts de réparation des mésappariements de l’ADN ont été étudiés par immunohistochimie. Résultats : Parmi les 82 cancers colorectaux de stade I ou II, 11 étaient MSI et 71 MSS, avec une moyenne (écart-type) de 23,6 (3,1) et 13,7 (1,0) ganglions négatifs, respectivement (p = .001). Le nombre moyen de ganglions pour tous les cancers colorectaux de stade I ou II analysés dans notre hôpital était de 15. La prévalence des MSI dans les tumeurs avec plus de 15 ganglions prélevés était de 25 % (9 sur 36) et 82 % (9 sur 11) des tumeurs MSI appartenaient à ce groupe. Conclusions : Un nombre élevé de ganglions isolés en cas de cancer colorectal de stade I ou II est associé au phénotype MSI. Le bon pronostic qui est habituellement associé à des tumeurs ayant un nombre élevé de ganglions N0 pourrait refléter la prévalence élevée des MSI chez ces tumeurs. Le nombre de ganglions examinés comme un critère de qualité doit être utilisé avec prudence. Limiter le phénotypage MSI aux tumeurs colorectales de stade I ou II ayant plus que le nombre moyen de ganglions identifie presque toutes les tumeurs MSI

Looking ahead: forecasting and planning for the longer-range future, April 1, 2, and 3, 2005

This repository item contains a single issue of the Pardee Conference Series, a publication series that began publishing in 2006 by the Boston University Frederick S. Pardee Center for the Study of the Longer-Range Future. This was the Center's spring Conference that took place during April 1, 2, and 3, 2005.The conference allowed for many highly esteemed scholars and professionals from a broad range of fields to come together to discuss strategies designed for the 21st century and beyond. The speakers and discussants covered a broad range of subjects including: long-term policy analysis, forecasting for business and investment, the National Intelligence Council Global Trends 2020 report, Europe’s transition from the Marshal plan to the EU, forecasting global transitions, foreign policy planning, and forecasting for defense

Bose-Einstein Correlations of Three Charged Pions in Hadronic Z^0 Decays

Bose-Einstein Correlations (BEC) of three identical charged pions were studied in 4 x 10^6 hadronic Z^0 decays recorded with the OPAL detector at LEP. The genuine three-pion correlations, corrected for the Coulomb effect, were separated from the known two-pion correlations by a new subtraction procedure. A significant genuine three-pion BEC enhancement near threshold was observed having an emitter source radius of r_3 = 0.580 +/- 0.004 (stat.) +/- 0.029 (syst.) fm and a strength of \lambda_3 = 0.504 +/- 0.010 (stat.) +/- 0.041 (syst.). The Coulomb correction was found to increase the \lambda_3 value by \~9% and to reduce r_3 by ~6%. The measured \lambda_3 corresponds to a value of 0.707 +/- 0.014 (stat.) +/- 0.078 (syst.) when one takes into account the three-pion sample purity. A relation between the two-pion and the three-pion source parameters is discussed.Comment: 19 pages, LaTeX, 5 eps figures included, accepted by Eur. Phys. J.

E-commerce transactions in a virtual environment: Virtual transactions

E-commerce is a fundamental method of doing business, such that for a firm to say it is trading at all in the modern market-place it must have some element of on-line presence. Coupled with this is the explosion of the "population" of Massively Multiplayer On-line Role Playing Games and other shared virtual environments. Many suggest this will lead to a further dimension of commerce: virtual commerce. We discuss here the issues, current roadblocks and present state of an e-commerce transaction carried out completely within a virtual environment; a virtual transaction. Although technically such transactions are in a sense trivial, they raise many other issues in complex ways thus making V-transactions a highly interesting cross-disciplinary issue. We also discuss the social, ethical and regulatory implications for the virtual communities in these environments of such v-transactions, how their implementation affects the nature and management of a virtual environment, and how they represent a fundamental merging of the real and virtual worlds for the purpose of commerce. We highlight the minimal set of features a v-transaction capable virtual environment requires and suggest a model of how in the medium term they could be carried out via a methodology we call click-through, and that the developers of such environments will need to take on the multi-modal behavior of their users, as well as elements of the economic and political sciences in order to fully realize the commercial potential of the v-transaction. © 2012 Springer Science+Business Media, LLC

The Fourteenth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the extended Baryon Oscillation Spectroscopic Survey and from the second phase of the Apache Point Observatory Galactic Evolution Experiment

The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since July 2014. This paper describes the second data release from this phase, and the fourteenth from SDSS overall (making this, Data Release Fourteen or DR14). This release makes public data taken by SDSS-IV in its first two years of operation (July 2014-2016). Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey (eBOSS); the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data driven machine learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS website (www.sdss.org) has been updated for this release, and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020, and will be followed by SDSS-V.Comment: SDSS-IV collaboration alphabetical author data release paper. DR14 happened on 31st July 2017. 19 pages, 5 figures. Accepted by ApJS on 28th Nov 2017 (this is the "post-print" and "post-proofs" version; minor corrections only from v1, and most of errors found in proofs corrected

A Multiparent Advanced Generation Inter-Cross to Fine-Map Quantitative Traits in Arabidopsis thaliana

Identifying natural allelic variation that underlies quantitative trait variation remains a fundamental problem in genetics. Most studies have employed either simple synthetic populations with restricted allelic variation or performed association mapping on a sample of naturally occurring haplotypes. Both of these approaches have some limitations, therefore alternative resources for the genetic dissection of complex traits continue to be sought. Here we describe one such alternative, the Multiparent Advanced Generation Inter-Cross (MAGIC). This approach is expected to improve the precision with which QTL can be mapped, improving the outlook for QTL cloning. Here, we present the first panel of MAGIC lines developed: a set of 527 recombinant inbred lines (RILs) descended from a heterogeneous stock of 19 intermated accessions of the plant Arabidopsis thaliana. These lines and the 19 founders were genotyped with 1,260 single nucleotide polymorphisms and phenotyped for development-related traits. Analytical methods were developed to fine-map quantitative trait loci (QTL) in the MAGIC lines by reconstructing the genome of each line as a mosaic of the founders. We show by simulation that QTL explaining 10% of the phenotypic variance will be detected in most situations with an average mapping error of about 300 kb, and that if the number of lines were doubled the mapping error would be under 200 kb. We also show how the power to detect a QTL and the mapping accuracy vary, depending on QTL location. We demonstrate the utility of this new mapping population by mapping several known QTL with high precision and by finding novel QTL for germination data and bolting time. Our results provide strong support for similar ongoing efforts to produce MAGIC lines in other organisms

Subject Benchmark Statement Forensic Science

This document is a QAA Subject Benchmark Statement for Forensic Science that defines what can be expected of a graduate in the subject, in terms of what they might know, do and understand at the end of their studies. Subject Benchmark Statements also describe the nature and characteristics of awards in a particular subject or area. Subject Benchmark Statements are published in QAA's capacity as a membership organisation on behalf of the higher education sector. A summary of the Statement is also available on the QAA website

Microbial regulation of the soil carbon cycle: evidence from gene-enzyme relationships.

A lack of empirical evidence for the microbial regulation of ecosystem processes, including carbon (C) degradation, hinders our ability to develop a framework to directly incorporate the genetic composition of microbial communities in the enzyme-driven Earth system models. Herein we evaluated the linkage between microbial functional genes and extracellular enzyme activity in soil samples collected across three geographical regions of Australia. We found a strong relationship between different functional genes and their corresponding enzyme activities. This relationship was maintained after considering microbial community structure, total C and soil pH using structural equation modelling. Results showed that the variations in the activity of enzymes involved in C degradation were predicted by the functional gene abundance of the soil microbial community (R2>0.90 in all cases). Our findings provide a strong framework for improved predictions on soil C dynamics that could be achieved by adopting a gene-centric approach incorporating the abundance of functional genes into process models