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Practical Microsoft Visual Studio 2015
Learn the details of the most highly recommended practices of software development using the latest version of Visual Studio 2015. Recommended practices are grouped by development phase and explained in far more detail than the typical tips and tricks compilations. This book also contains detailed coverage of recognized patterns and practices used to create software in a timely manner with expected quality in the context of using specific Visual Studio 2015 features. Creating software is part defined process and part empirical process. While there is no single \"best\" process to employ in all development scenarios, MVP author Peter Ritchie helps readers navigate the complexity of development options and decide which techniques and Visual Studio 2015 features to use based on the needs of their particular project. Readers will learn practices such as those related to working in teams, design and architecture, refactoring, source code control workflows, unit testing, performance testing, coding practices, use of common patterns, code analysis, IDE extensions, and more. What You Will Learn Use patterns and practices within Visual Studio Implement practices of software creation Work in teams Develop workflows for software projects Who This Book Is For Beginning and intermediate software developers and architects. -- Provided by publisher.
Book
High-Density Linkage Map and QTLs for Growth in Snapper (Chrysophrys auratus)
Characterizing the genetic variation underlying phenotypic traits is a central objective in biological research. This research has been hampered in the past by the limited genomic resources available for most non-model species. However, recent advances in sequencing technologies and related genotyping methods are rapidly changing this. Here we report the use of genome-wide SNP data from the ecologically and commercially important marine fish species Chrysophrys auratus (snapper) to 1) construct the first linkage map for this species, 2) scan for growth QTL, and 3) search for putative candidate genes in the surrounding QTL regions. The newly constructed linkage map contained ∼11K SNP markers and is one of the densest maps to date in the fish family Sparidae. Comparisons with genome scaffolds of the recently assembled snapper genome indicated that marker placement was mostly consistent between the scaffolds and linkage map (R = 0.7), but that at fine scales (< 5 cM) some precision limitations occurred. Of the 24 linkage groups, which likely reflect the 24 chromosomes of this species, three were found to contain QTL with genome-wide significance for growth-related traits. A scan of 13 candidate growth genes located the growth hormone, myogenin, and parvalbumin genes within 5.3, 9.6, and 25.0 cM of these QTL, respectively. The linkage map and QTL found in this study will advance the investigation of genome structure and aquaculture breeding efforts in this and related species.
Journal Article
DNA degradation in fish: Practical solutions and guidelines to improve DNA preservation for genomic research
The more demanding requirements of DNA preservation for genomic research can be difficult to meet when field conditions limit the methodological approaches that can be used or cause samples to be stored in suboptimal conditions. Such limitations may increase rates of DNA degradation, potentially rendering samples unusable for applications such as genome‐wide sequencing. Nonetheless, little is known about the impact of suboptimal sampling conditions. We evaluated the performance of two widely used preservation solutions (1. DESS: 20% DMSO, 0.25 M EDTA, NaCl saturated solution, and 2. Ethanol >99.5%) under a range of storage conditions over a three‐month period (sampling at 1 day, 1 week, 2 weeks, 1 month, and 3 months) to provide practical guidelines for DNA preservation. DNA degradation was quantified as the reduction in average DNA fragment size over time (DNA fragmentation) because the size distribution of DNA segments plays a key role in generating genomic datasets. Tissues were collected from a marine teleost species, the Australasian snapper, Chrysophrys auratus. We found that the storage solution has a strong effect on DNA preservation. In DESS, DNA was only moderately degraded after three months of storage while DNA stored in ethanol showed high levels of DNA degradation already within 24 hr, making samples unsuitable for next‐generation sequencing. Here, we conclude that DESS was the most promising solution when storing samples for genomic applications. We recognize that the best preservation protocol is highly dependent on the organism, tissue type, and study design. We highly recommend performing similar experiments before beginning a study. This study highlights the importance of testing sample preservation protocols and provides both practical and economical advice to improve DNA preservation when sampling for genome‐wide applications. The initial stages of DNA preservation can be crucial for obtaining high‐quality data for genomic research. However, environmental conditions in the field and during transport are typically suboptimal for preserving DNA, potentially spoiling costly samples. Here, we evaluate two cost‐effective preservation solutions and provide a comprehensive background on what causes DNA to degrade and practical guidelines on how to ensure the best approach for preserving DNA in field‐collected samples.
Journal Article
A Retrospective Approach to Testing the DNA Barcoding Method
Notes now, a decade ago, DNA barcoding was proposed as a standardised method for identifying existing species and speeding the discovery of new species. Points out, despite its numerous successes across a range of taxa, its frequent failures have brought into question its accuracy as a short-cut taxonomic method. Uses a retrospective approach in applying the method to the classification of New Zealand skinks as it stood in 1977 (primarily based upon morphological characters). Compares the method to the current taxonomy reached using both morphological and molecular approaches. Source: National Library of New Zealand Te Puna Matauranga o Aotearoa, licensed by the Department of Internal Affairs for re-use under the Creative Commons Attribution 3.0 New Zealand Licence.
Journal Article
Unlocking the potential of ancient fish DNA in the genomic era
Fish are the most diverse group of vertebrates, fulfil important ecological functions and are of significant economic interest for aquaculture and wild fisheries. Advances in DNA extraction methods, sequencing technologies and bioinformatic applications have advanced genomic research for nonmodel organisms, allowing the field of fish ancient DNA (aDNA) to move into the genomics era. This move is enabling researchers to investigate a multitude of new questions in evolutionary ecology that could not, until now, be addressed. In many cases, these new fields of research have relevance to evolutionary applications, such as the sustainable management of fisheries resources and the conservation of aquatic animals. Here, we focus on the application of fish aDNA to (a) highlight new research questions, (b) outline methodological advances and current challenges, (c) discuss how our understanding of fish ecology and evolution can benefit from aDNA applications and (d) provide a future perspective on how the field will help answer key questions in conservation and management. We conclude that the power of fish aDNA will be unlocked through the application of continually improving genomic resources and methods to well‐chosen taxonomic groups represented by well‐dated archaeological samples that can provide temporally and/or spatially extensive data sets.
Journal Article
Genome assembly and isoform analysis of a highly heterozygous New Zealand fisheries species, the tarakihi (Nemadactylus macropterus)
Although being some of the most valuable and heavily exploited wild organisms, few fisheries species have been studied at the whole-genome level. This is especially the case in New Zealand, where genomics resources are urgently needed to assist fisheries management. Here, we generated 55 Gb of short Illumina reads (92× coverage) and 73 Gb of long Nanopore reads (122×) to produce the first genome assembly of the marine teleost tarakihi [Nemadactylus macropterus (Forster, 1801)], a highly valuable fisheries species in New Zealand. An additional 300 Mb of Iso-Seq reads were obtained to assist in gene annotation. The final genome assembly was 568 Mb long with an N50 of 3.37 Mb. The genome completeness was high, with 97.8% of complete Actinopterygii Benchmarking Universal Single-Copy Orthologs. Heterozygosity values estimated through k-mer counting (1.00%) and bi-allelic SNPs (0.64%) were high compared with the same values reported for other fishes. Iso-Seq analysis recovered 91,313 unique transcripts from 15,515 genes (mean ratio of 5.89 transcripts per gene), and the most common alternative splicing event was intron retention. This highly contiguous genome assembly and the isoform-resolved transcriptome will provide a useful resource to assist the study of population genomics and comparative eco-evolutionary studies in teleosts and related organisms.
Journal Article
Biomarkers of nanomaterials hazard from multi-layer data
There is an urgent need to apply effective, data-driven approaches to reliably predict engineered nanomaterial (ENM) toxicity. Here we introduce a predictive computational framework based on the molecular and phenotypic effects of a large panel of ENMs across multiple in vitro and in vivo models. Our methodology allows for the grouping of ENMs based on multi-omics approaches combined with robust toxicity tests. Importantly, we identify mRNA-based toxicity markers and extensively replicate them in multiple independent datasets. We find that models based on combinations of omics-derived features and material intrinsic properties display significantly improved predictive accuracy as compared to physicochemical properties alone.
Nanomaterials have a range of potential applications, however, toxicity remains a concern, limiting application and requiring extensive testing. Here, the authors report on a predictive framework made using a range of tests linking materials properties with toxicity, allowing the prediction of toxicity from physiochemical and biological properties.
Journal Article
Domestication and Temperature Modulate Gene Expression Signatures and Growth in the Australasian Snapper Chrysophrys auratus
Identifying genes and pathways involved in domestication is critical to understand how species change in response to human-induced selection pressures, such as increased temperatures. Given the profound influence of temperature on fish metabolism and organismal performance, a comparison of how temperature affects wild and domestic strains of snapper is an important question to address. We experimentally manipulated temperature conditions for F1-hatchery and wild Australasian snapper (Chrysophrys auratus) for 18 days to mimic seasonal extremes and measured differences in growth, white muscle RNA transcription and hematological parameters. Over 2.2 Gb paired-end reads were assembled de novo for a total set of 33,017 transcripts (N50 = 2,804). We found pronounced growth and gene expression differences between wild and domesticated individuals related to global developmental and immune pathways. Temperature-modulated growth responses were linked to major pathways affecting metabolism, cell regulation and signaling. This study is the first step toward gaining an understanding of the changes occurring in the early stages of domestication, and the mechanisms underlying thermal adaptation and associated growth in poikilothermic vertebrates. Our study further provides the first transcriptome resources for studying biological questions in this non-model fish species.
Journal Article
Adaptive Potential of Syzygium maire, a Critically Threatened Habitat Specialist Tree Species in Aotearoa New Zealand
The restoration of swampland is vital for the recovery of both biodiversity and cultural values in Aotearoa New Zealand. Syzygium maire, an endemic wetland tree species, is a focus of many wetland restoration efforts. Formerly widespread, extant populations are small, fragmented, and under pressure from myrtle rust. Restoration initiatives may be unknowingly compounding these threats to the species by failing to represent the complete genetic diversity of populations. What genetic diversity remains in remnants and how it is distributed is not known. We therefore aimed to assess the national scale population structure, genetic diversity, and adaptive potential of S. maire to inform species conservation. We identified over 760,000 high‐quality single nucleotide variants in 269 reproductive age trees from across the species' range, using low coverage whole genome resequencing. At a national scale, we found five distinct regional‐scale genetic clusters, which in turn exhibit local structure and admixture. In the North Island: Northland, Bay of Plenty in the central east, Taranaki in the central west, and Greater Wellington/Manawatū in the south. A single cluster was identified in the South Island, Marlborough. Within‐cluster substructure was particularly evident for Greater Wellington/Manawatū. Genetic diversity and fixation indices (FST) were relatively uniform across all clusters, and there was some evidence of north to south increase in kinship and shorter time since radiation. These patterns are likely to reflect glaciation cycles that resulted in complex contractions into local microrefugia and subsequent re‐radiations of the species over time. Genotype by environment analysis detected genetic variants potentially contributing to environmental adaptation, notably precipitation seasonality. Restoration and conservation goals would best be served by capturing diversity within regional clusters. Information on the geographic and environmentally structured distribution of this tree's genetic diversity supports conservation and restoration strategies through ensuring the complete extant diversity is captured, identifying regions at most risk of genetic degradation, and facilitating planning regarding the movement of adaptive diversity in a changing environment.
Journal Article