136 Works

Silencing the ASI gustatory neuron pair increases expression of the stress-resistance gene sod-3 in a daf-16 and daf-3 independent manner

Peter Chisnell & Cynthia Kenyon
Ablation of the gustatory neuron pair ASI has been shown to extend lifespan, and this lifespan extension requires the function of the transcription factor daf-16/FOXO (Alcedo and Kenyon 2004). Given this relationship, we tested whether silencing the neuron pair ASI with the tetanus toxin light chain (Tetx), as opposed to ablating it, could increase the expression of a well- known DAF-16 target, the stress-resistance gene sod-3 (Furuyama et al. 2000; Honda and Honda 1999). Tetanus...

Future opportunities for using forest and sawmill residues in Australia

Peter Lock & Linden Whittle
The Australian forest industry generates millions of tonnes of wood residues every year as a by-product of harvesting and sawmilling operations. The efficient use of harvest and sawmill residues can reduce disposal costs and create additional revenue streams, contributing to the international competitiveness and sustainability of the Australian forest and wood processing industry. This report presents estimates of the potential production and use of harvest and sawmill residues in Australia in 2050. The modelling framework...

A snapshot of Australian Fisheries and Aquaculture

Australian Bureau Of Agricultural Resource Economics And Sciences (ABARES)

NADIR Technical manual

Cristina Knapic & Riccardo Smareglia
Manuale tecnico descrittivo del software di gestione ed archiviazione dati astronomici chiamato New Archiving Distributed InfrastructuRe (NADIR).

A first record of the vanishing silhouette goby Silhouettea evanida (Gobiidae) in Indonesian waters

Muhammad Iqbal, Doni Setiawan, Riza Kadarisman, Arum Setiawan & Indra Yustian
In April 2017, some individuals of the vanishing silhouette goby Silhouettea evanida were identified and photographed in the estuary of the Sembilang River, South Sumatra province, Indonesia. There is no previous report on the occurrence of Silhouettea evanidain Indonesia, and this observation constitutes a first record for the country.

Simplified detection of a point mutation in C. elegans using tetra-primer ARMS-PCR

Matthew T Sullenberger & Eleanor M Maine
Single nucleotide polymorphisms (SNPs) can be difficult to detect using traditional PCR and gel electrophoresis, especially when no enzyme restriction sites overlap the SNP. Although alleles can be identified through amplification with flanking primers and sequencing, this adds time and cost, and sequencing is typically outsourced. Tetra-primer Amplification-Refractory Mutation System (ARMS)-PCR allows SNPs to be distinguished through a 3' primer mismatch at the SNP site for one allele, and an additional mismatch 1 - 3...

Microorganisms facilitate uptake of dissolved organic nitrogen by seagrass leaves

Flavia Tarquinio, Jeremy Bourgoure, Annette Koenders, Bonnie Laverock, Christin Säwström & Glenn Hyndes
The database compiles data (used in Tarquinio et al. 2018, ISME Journal, accepted for publication) obtained from nitrogen stable isotope analysis (IRMS) and Nanoscale secondary ion mass spectrometry (NanoSIMS) of seagrass (Posidonia sinuosa) leaves and associated microorganisms. Row data (IRMS) are presented for bulk tissue 15N enrichment of P. sinuosa leaves at different times of incubation (plotted as bar chart in the manuscript), as well as the enrichment detected through the drawing of regions of...

Performance of direct N-body code on ARM64 SoC

David Goz, Luca Tornatore, Sara Bertocco & Giuliano Taffoni
The ExaNeSt H2020 project will produce a prototype based on ARM64 CPUs and FPGA-based accelerators implementing a co-design approach where scientific applications requirements are driving the hardware design. We present strategies adopted in order to port our direct N-body code on an ARM SoC cluster, called INCAS, deployed at INAF-OATs. Each computational node is based on 64-bit ARMv8 Cortex-A72/Cortex-A53 core design, powered by the Mali-T864 GPU. We present the strategies to optimize the code and...

A C. elegans model for the rare human channelopathy, Timothy syndrome type 1.

Ross C. Lagoy, Heesun Kim, Craig C. Mello & Dirk R. Albrecht
Timothy syndrome (TS) type 1 is a rare genetic human disease caused by a gain-of-function (GOF) missense mutation G406R in the L-type voltage-gated calcium channel (VGCC) α1 subunit gene CACNA1C, which results in severe cardiac arrhythmia and autism (Splawski et al. 2004). The C. elegans ortholog is EGL-19 (Fig. 1a), which is expressed in muscle and neurons (Lee et al. 1997). GOF mutations in egl-19 cause myotonic phenotypes, while reduction-of-function (ROF) mutants are flaccid, variably...

Italian Report to the 42nd Cospar Scientific Assembly

Maria Teresa Capria, Livia Giacomini, Eleonora Ferroni, Pietro Ubertini & Davide Coero Borga
The Italian Report to the 42nd COSPAR General Assembly to be held in Pasadena, edited by the National Institute of Astrophysics (INAF),the formal Italian national body that by the law supports the COSPAR activities, with the collaboration of ASI, the Italian Space Agency, and the other stakeholders playing a major role in the Italian scientific space programmes (INFN, CNR, INGV, etc.). This Report summarizes the last two years of space science activity in Italy.

Chemotaxis based enrichment for transgenic animals containing the rol-6 marker

John L. Carter, Rafael Morales & Steven M. Johnson
Utilizing the chemotaxis of C. elegans, we can separate wild-type C. elegans from “rollers.” If a mixed population of transgenic worms harboring the rol-6 marker, and their non-transgenic siblings are plated a distance from food, “rollers” will be unable to efficiently migrate towards the food due to impaired locomotion, while non-transgenic C. elegans will have normal locomotion and be able to quickly migrate to the food source. This will efficiently separate the two types of...

INCAS: INtensive Clustered ARM SoC - Cluster Deployment

Sara Bertocco, David Goz, Luca Tornatore & Giuliano Taffoni
The report describes the work done to deploy an Heterogeneous Computing Cluster using CPUs and GPUs integrated on a System on Chip architecture, in the environment of the ExaNeSt H2020 project. After deployment, this cluster will provide a testbed to validate and optimize several HPC codes developed to be run on heterogeneous hardware. The work done includes: a technology watching phase to choose the SoC best fitting our requirements; installation of the Operative System Ubuntu...

SapTrap assembly of repair templates for Cas9-triggered homologous recombination with a self-excising cassette

Daniel J. Dickinson, Mark M. Slabodnick, Alicia H. Chen & Bob Goldstein
The advent of CRISPR/Cas9 technology in C. elegans has enabled an unprecedented level of control over this organism’s genome, which is facilitating research in a wide variety of fields. Several different experimental approaches exist for CRISPR in this organism (Dickinson and Goldstein 2016). One particularly powerful approach uses a drug selection with a Self-Excising Cassette (SEC) to isolate the desired genetically-modified animals following Cas9-triggered homologous recombination (Dickinson et al. 2015). The most labor-intensive step in...

Australian Fisheries and Aquaculture Statistics 2017

Australian Bureau Of Agricultural Resource Economics And Sciences (ABARES)

Performance of direct N-body code on ARM64 SoC

David Goz, Luca Tornatore, Sara Bertocco & Giuliano Taffoni
The ExaNeSt H2020 project will produce a prototype based on ARM64 CPUs and FPGA-based accelerators implementing a co-design approach where scientific applications requirements are driving the hardware design. We present strategies adopted in order to port our direct N-body code on an ARM SoC cluster, called INCAS, deployed at INAF-OATs. Each computational node is based on 64-bit ARMv8 Cortex-A72/Cortex-A53 core design, powered by the Mali-T864 GPU. We present the strategies to optimize the code and...

Snapshot of Australia's agricultural workforce

Bill Binks, Nyree Stenekes, Heleen Kruger & Robert Kancans
his snapshot describes Australia’s agricultural workforce, providing key information and statistics in one place. We cover where workers live, what sub-industries and occupations they work in, and the mobility and educational attainment of the workforce. The snapshot also describes the involvement of Indigenous people, People from Culturally and Linguistically Diverse backgrounds, women and young people in the agricultural workforce.

L'Alternanza Scuola Lavoro in INAF a.s. 2016/2017

Livia Giacomini & Marco Ziggiotti
In Italia, tutti gli studenti frequentanti un Istituto di Istruzione Superiore devono per legge effettuare nel corso del triennio finale dei progetti di Alternanza Scuola Lavoro (ASL). L’obbligatorietà dell’ASL riguarda nel 2017/2018 circa 1 milione e mezzo di studenti. Questo documento costituisce la prima analisi globale delle attività didattiche di ASL svolte da INAF nell’anno 2016/2017, per un totale di 35.800 ore per studente erogate nelle 15 sedi coinvolte sul territorio italiano..

Direct N-body code designed for a cluster based on heterogeneous computational nodes

David Goz, Luca Tornatore, Sara Bertocco & Giuliano Taffoni
The ExaNeSt H2020 project is developing an exascale ready prototype based on hybrid hardware (CPUs+accelerators). Astrophysical codes are used to test and validate the exascale platform. At the same time, astrophysical applications must be re-engineered in order to exploit heterogeneous hardware. We present and test the parallel scheme of a state-of-the-art direct N -body code (called ExaHiGPUs) conceived to be run on hybrid architecture.

Drosophila balancer reengineering using polycistronic gRNA for CRISPR/Cas9 gene editing

Leif Benner & Brian Oliver
A number of reagents have been generated for CRISPR/Cas9 genome editing in Drosophila (Gratz et al. 2014; Ren et al. 2013; Kondo and Ueda 2013; Port et al. 2014; Port and Bullock 2016). The ability to efficiently express multiple gRNAs from a single vector provides the advantage of creating multiple CRISPR/Cas9 alleles at a time. An elegant design has previously shown that gRNAs separated by tRNAs allow for genomic editing at multiple loci in Drosophila...

2018 Update on Protein-Protein Interaction Data in WormBase

Jaehyoung Cho, Christian Grove, Kimberly Van Auken, Juancarlos Chan, Sibyl Gao & Paul W. Sternberg
Protein interaction is an important data type to understand the biological function of proteins involved in the interaction, and helps researchers to deduce the biological nature of unknown proteins from the well-characterized functions of their interaction partners. High-throughput studies, coupled with the aggregation of individual experiments, provides a global 'snapshot' of the protein interactions occurring at all levels of biological processes or circumstances. This snapshot of the interaction network, the interactome, is important to understand...

Kompleksowe urządzanie obszarów wiejskich jako szansa dla rozwoju wsi

Franciszek Woch, Jacek Pijanowski & Tadeusz Kuryłowicz

Two new functions in the WormBase Enrichment Suite

David Angeles-Albores, Raymond Y.N. Lee, Juancarlos Chan & Paul W. Sternberg
​Genome-wide experiments routinely generate large amounts of data that can be hard to interpret biologically. A common approach to interpreting these results is to employ enrichment analyses of controlled languages, known as ontologies, that describe various biological parameters such as gene molecular or biological function. In C. elegans, three distinct ontologies, the Gene Ontology (GO), Anatomy Ontology (AO), and the Worm Phenotype Ontology (WPO) are used to annotate gene function, expression and phenotype, respectively (Ashburner...

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  • 2018
    136

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  • DataPaper
    136

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