scholarly journals Chromosome-length haplotigs for yak and cattle from trio binning assembly of an F1 hybrid

2019 ◽  
Author(s):  
Edward S. Rice ◽  
Sergey Koren ◽  
Arang Rhie ◽  
Michael P. Heaton ◽  
Theodore S. Kalbfleisch ◽  
...  
Keyword(s):  
Bos Taurus ◽  
Chromosome Length ◽  
Single Individual ◽  
F1 Hybrid ◽  
Short Reads ◽  
Long Reads ◽  
Interspecies Hybrids ◽  
Paternal Haplotype ◽  
The Individual ◽  
First Time

AbstractBackgroundAssemblies of diploid genomes are generally unphased, pseudo-haploid representations that do not correctly reconstruct the two parental haplotypes present in the individual sequenced. Instead, the assembly alternates between parental haplotypes and may contain duplications in regions where the parental haplotypes are sufficiently different. Trio binning is an approach to genome assembly that uses short reads from both parents to classify long reads from the offspring according to maternal or paternal haplotype origin, and is thus helped rather than impeded by heterozygosity. Using this approach, it is possible to derive two assemblies from an individual, accurately representing both parental contributions in their entirety with higher continuity and accuracy than is possible with other methods.ResultsWe used trio binning to assemble reference genomes for two species from a single individual using an interspecies cross of yak (Bos grunniens) and cattle (Bos taurus). The high heterozygosity inherent to interspecies hybrids allowed us to confidently assign >99% of long reads from the F1 offspring to parental bins using unique k-mers from parental short reads. Both the maternal (yak) and paternal (cattle) assemblies contain over one third of the acrocentric chromosomes, including the two largest chromosomes, in single haplotigs.ConclusionsThese haplotigs are the first vertebrate chromosome arms to be assembled gap-free and fully phased, and the first time assemblies for two species have been created from a single individual. Both assemblies are the most continuous currently available for non-model vertebrates.

scholarly journals Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle

GigaScience ◽  
2020 ◽  
Vol 9 (4) ◽  
Author(s):  
Edward S Rice ◽  
Sergey Koren ◽  
Arang Rhie ◽  
Michael P Heaton ◽  
Theodore S Kalbfleisch ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Bos Taurus ◽  
Single Copy ◽  
Gap Filling ◽  
F1 Hybrid ◽  
Cell Numbers ◽  
Bos Grunniens ◽  
Hybrid Offspring ◽  
The Individual ◽  
Reference Genomes

Abstract Background The development of trio binning as an approach for assembling diploid genomes has enabled the creation of fully haplotype-resolved reference genomes. Unlike other methods of assembly for diploid genomes, this approach is enhanced, rather than hindered, by the heterozygosity of the individual sequenced. To maximize heterozygosity and simultaneously assemble reference genomes for 2 species, we applied trio binning to an interspecies F1 hybrid of yak (Bos grunniens) and cattle (Bos taurus), 2 species that diverged nearly 5 million years ago. The genomes of both of these species are composed of acrocentric autosomes. Results We produced the most continuous haplotype-resolved assemblies for a diploid animal yet reported. Both the maternal (yak) and paternal (cattle) assemblies have the largest 2 chromosomes in single haplotigs, and more than one-third of the autosomes similarly lack gaps. The maximum length haplotig produced was 153 Mb without any scaffolding or gap-filling steps and represents the longest haplotig reported for any species. The assemblies are also more complete and accurate than those reported for most other vertebrates, with 97% of mammalian universal single-copy orthologs present. Conclusions The high heterozygosity inherent to interspecies crosses maximizes the effectiveness of the trio binning method. The interspecies trio binning approach we describe is likely to provide the highest-quality assemblies for any pair of species that can interbreed to produce hybrid offspring that develop to sufficient cell numbers for DNA extraction.

Victorian Pain

2017 ◽  
Author(s):  
Rachel Ablow
Keyword(s):  
Nineteenth Century ◽  
Victorian Literature ◽  
Social Life ◽  
Charles Darwin ◽  
Harriet Martineau ◽  
The Status ◽  
History Of ◽  
The Individual ◽  
Natural Philosophers ◽  
First Time

The nineteenth century introduced developments in science and medicine that made the eradication of pain conceivable for the first time. This new understanding of pain brought with it a complex set of moral and philosophical dilemmas. If pain serves no obvious purpose, how do we reconcile its existence with a well-ordered universe? Examining how writers of the day engaged with such questions, this book offers a compelling new literary and philosophical history of modern pain. The book provides close readings of novelists Charlotte Brontë and Thomas Hardy and political and natural philosophers John Stuart Mill, Harriet Martineau, and Charles Darwin, as well as a variety of medical, scientific, and popular writers of the Victorian age. The book explores how discussions of pain served as investigations into the status of persons and the nature and parameters of social life. No longer conceivable as divine trial or punishment, pain in the nineteenth century came to seem instead like a historical accident suggesting little or nothing about the individual who suffers. A landmark study of Victorian literature and the history of pain, the book shows how these writers came to see pain as a social as well as a personal problem. Rather than simply self-evident to the sufferer and unknowable to anyone else, pain was also understood to be produced between persons—and even, perhaps, by the fictions they read.

ADHD with Comorbid Bipolar Disorders: A Systematic Review of Neurobiological, Clinical and Pharmacological Aspects Across the Lifespan

2019 ◽  
Vol 26 (38) ◽  
pp. 6942-6969 ◽  
Author(s):  
Federico Mucci ◽  
Maria Teresa Avella ◽  
Donatella Marazziti
Keyword(s):  
Clinical Features ◽  
Adult Adhd ◽  
Neurodevelopmental Disorder ◽  
Bipolar Disorders ◽  
Mood Stabilizers ◽  
Disruptive Behaviour ◽  
Single Individual ◽  
Pharmacological Management ◽  
Long Time ◽  
The Individual

Background: Attention deficit hyperactivity (ADHD) disorder is a neurodevelopmental disorder characterized by inattention, hyperactivity, disruptive behaviour, and impulsivity. Despite considered typical of children for a long time, the persistence of ADHD symptoms in adulthood gained increasing interest during the last decades. Indeed, its diagnosis, albeit controversial, is rarely carried out even because ADHD is often comorbid with several other psychiatric diosrders, in particular with bipolar disorders (BDs), a condition that complicates the clinical picture, assessment and treatment. Aims: The aim of this paper was to systematically review the scientific literature on the neurobiological, clinical features and current pharmacological management of ADHD comorbid with BDs across the entire lifespan, with a major focus on the adulthood. Discussion: The pharmacology of ADHD-BD in adults is still empirical and influenced by the individual experience of the clinicians. Stimulants are endowed of a prompt efficacy and safety, whilst non-stimulants are useful when a substance abuse history is detected, although they require some weeks in order to be fully effective. In any case, an in-depth diagnostic and clinical evaluation of the single individual is mandatory. Conclusions: The comorbidity of ADHD with BD is still a controversial matter, as it is the notion of adult ADHD as a distinct nosological category. Indeed, some findings highlighted the presence of common neurobiological mechanisms and overlapping clinical features, although disagreement does exist. In any case, while expecting to disentangle this crucial question, a correct management of this comorbidity is essential, which requires the co-administration of mood stabilizers. Further controlled clinical studies in large samples of adult ADHD-BD patients appear extremely urgent in order to better define possible therapeutic guidelines, as well as alternative approaches for this potentially invalidating condition.

A University Education

2017 ◽  
Author(s):  
David Willetts
Keyword(s):  
Higher Education ◽  
Modern Society ◽  
University Education ◽  
Modern World ◽  
Controversial Issues ◽  
The Us ◽  
The Individual ◽  
The University ◽  
First Time ◽  
The Relationship

Universities have a crucial role in the modern world. In England, entrance to universities is by nation-wide competition which means English universities have an exceptional influence on schools--a striking theme of the book. This important book first investigates the university as an institution and then tracks the individual on their journey to and through university. In A University Education, David Willetts presents a compelling case for the ongoing importance of the university, both as one of the great institutions of modern society and as a transformational experience for the individual. The book also makes illuminating comparisons with higher education in other countries, especially the US and Germany. Drawing on his experience as UK Minister for Universities and Science from 2010 to 2014, the author offers a powerful account of the value of higher education and the case for more expansion. He covers controversial issues in which he was involved from access for disadvantaged students to the introduction of L9,000 fees. The final section addresses some of the big questions for the future, such as the the relationship between universities and business, especially in promoting innovation.. He argues that the two great contemporary trends of globalisation and technological innovation will both change the university significantly. This is an authoritative account of English universities setting them for the first time in their new legal and regulatory framework.

The Republic

2019 ◽  
pp. 205-229
Author(s):  
Dominic Scott
Keyword(s):  
Political Theory ◽  
Left Behind ◽  
Ideal State ◽  
The Republic ◽  
Individual Justice ◽  
The Individual ◽  
Political Right ◽  
First Time ◽  
The Ideal

This chapter presents a reading of Plato’s Republic. The Republic is among Plato’s most complex works. From its title, the first-time reader will expect a dialogue about political theory, yet the work starts from the perspective of the individual, coming to focus on the question of how, if at all, justice contributes to an agent’s happiness. Only after this question has been fully set out does the work evolve into an investigation of politics—of the ideal state and of the institutions that sustain it, especially those having to do with education. But the interest in individual justice and happiness is never left behind. Rather, the work weaves in and out of the two perspectives, individual and political, right through to its conclusion. All this may leave one wondering about the unity of the work. The chapter shows that, despite the enormous range of topics discussed, the Republic fits together as a coherent whole.

Biosynthetic strategies for tetramic acid formation

2021 ◽  
Author(s):  
Xuhua Mo ◽  
Tobias A. M. Gulder
Keyword(s):  
Molecular Mechanism ◽  
Gene Clusters ◽  
Acid Formation ◽  
Biosynthetic Gene ◽  
Tetramic Acid ◽  
Biosynthetic Gene Clusters ◽  
The Individual ◽  
First Time ◽  
Acid Unit

Over 30 biosynthetic gene clusters for natural tetramate have been identified. This highlight reviews the biosynthetic strategies for formation of tetramic acid unit for the first time, discussing the individual molecular mechanism in detail.

scholarly journals nPhase: an accurate and contiguous phasing method for polyploids

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Omar Abou Saada ◽  
Andreas Tsouris ◽  
Chris Eberlein ◽  
Anne Friedrich ◽  
Joseph Schacherer
Keyword(s):  
Genome Sequencing ◽  
Population Genomics ◽  
Short Reads ◽  
Link Type ◽  
Long Reads

AbstractWhile genome sequencing and assembly are now routine, we do not have a full, precise picture of polyploid genomes. No existing polyploid phasing method provides accurate and contiguous haplotype predictions. We developed nPhase, a ploidy agnostic tool that leverages long reads and accurate short reads to solve alignment-based phasing for samples of unspecified ploidy (https://github.com/OmarOakheart/nPhase). nPhase is validated by tests on simulated and real polyploids. nPhase obtains on average over 95% accuracy and a contiguous 1.25 haplotigs per haplotype to cover more than 90% of each chromosome (heterozygosity rate ≥ 0.5%). nPhase allows population genomics and hybrid studies of polyploids.

scholarly journals Kinetical Study, Thermo-Mechanical Characteristics and Recyclability of Epoxidized Camelina Oil Cured with Antagonist Structure (Aliphatic/Aromatic) or Functionality (Acid/Amine) Hardeners

Polymers ◽  
2021 ◽  
Vol 13 (15) ◽  
pp. 2503
Author(s):  
Chiara Di Mauro ◽  
Aratz Genua ◽  
Alice Mija
Keyword(s):  
Disulfide Bonds ◽  
Mechanical Characteristics ◽  
Dicarboxylic Acids ◽  
Thermomechanical Properties ◽  
Chemical Recycling ◽  
Camelina Oil ◽  
Ft Ir ◽  
Tan Δ ◽  
The Individual ◽  
First Time

In an attempt to prepare sustainable epoxy thermosets, this study introduces for the first time the idea to use antagonist structures (aromatic/aliphatic) or functionalities (acid/amine) as hardeners to produce reprocessable resins based on epoxidized camelina oil (ECMO). Two kinds of mixtures were tested: one combines aromatic/aliphatic dicarboxylic acids: 2,2′-dithiodibenzoic acid (DTBA) and 3,3′-dithiodipropionic acid (DTDA); another is the combination of two aromatic structures with acid/amine functionality: DTBA and 4-aminophenyl disulfide (4-AFD). DSC and FT-IR analyses were used as methods to analyze the curing reaction of ECMO with the hardeners. It was found that the thermosets obtained with the dual crosslinked mechanism needed reduced curing temperatures and reprocessing protocols compared to the individual crosslinked thermosets. Thanks to the contribution of disulfide bonds in the network topology, the obtained thermosets showed recycling ability. The final thermomechanical properties of the virgin and mechanical reprocessed materials were analyzed by DMA and TGA. The obtained thermosets range from elastomeric to rigid materials. As an example, the ECMO/DTBA704-AFD30 virgin or reprocessed thermosets have tan δ values reaching 82–83 °C. The study also investigates the chemical recycling and the solvent resistance of these vitrimer-like materials.

scholarly journals Evaluating the accuracy of Listeria monocytogenes assemblies from quasimetagenomic samples using long and short reads

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Seth Commichaux ◽  
Kiran Javkar ◽  
Padmini Ramachandran ◽  
Niranjan Nagarajan ◽  
Denis Bertrand ◽  
...  
Keyword(s):  
Public Health ◽  
Public Health Response ◽  
High Quality ◽  
Short Read ◽  
Short Reads ◽  
The Core ◽  
Long Reads ◽  
Health Response ◽  
Long Read ◽  
Core Genes

Abstract Background Whole genome sequencing of cultured pathogens is the state of the art public health response for the bioinformatic source tracking of illness outbreaks. Quasimetagenomics can substantially reduce the amount of culturing needed before a high quality genome can be recovered. Highly accurate short read data is analyzed for single nucleotide polymorphisms and multi-locus sequence types to differentiate strains but cannot span many genomic repeats, resulting in highly fragmented assemblies. Long reads can span repeats, resulting in much more contiguous assemblies, but have lower accuracy than short reads. Results We evaluated the accuracy of Listeria monocytogenes assemblies from enrichments (quasimetagenomes) of naturally-contaminated ice cream using long read (Oxford Nanopore) and short read (Illumina) sequencing data. Accuracy of ten assembly approaches, over a range of sequencing depths, was evaluated by comparing sequence similarity of genes in assemblies to a complete reference genome. Long read assemblies reconstructed a circularized genome as well as a 71 kbp plasmid after 24 h of enrichment; however, high error rates prevented high fidelity gene assembly, even at 150X depth of coverage. Short read assemblies accurately reconstructed the core genes after 28 h of enrichment but produced highly fragmented genomes. Hybrid approaches demonstrated promising results but had biases based upon the initial assembly strategy. Short read assemblies scaffolded with long reads accurately assembled the core genes after just 24 h of enrichment, but were highly fragmented. Long read assemblies polished with short reads reconstructed a circularized genome and plasmid and assembled all the genes after 24 h enrichment but with less fidelity for the core genes than the short read assemblies. Conclusion The integration of long and short read sequencing of quasimetagenomes expedited the reconstruction of a high quality pathogen genome compared to either platform alone. A new and more complete level of information about genome structure, gene order and mobile elements can be added to the public health response by incorporating long read analyses with the standard short read WGS outbreak response.

scholarly journals Sequencing an F1 hybrid of Silurus asotus and S. meridionalis enabled the assembly of high-quality parental genomes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Weitao Chen ◽  
Ming Zou ◽  
Yuefei Li ◽  
Shuli Zhu ◽  
Xinhui Li ◽  
...  
Keyword(s):  
De Novo ◽  
Parental Species ◽  
F1 Hybrids ◽  
Pelteobagrus Fulvidraco ◽  
F1 Hybrid ◽  
Short Reads ◽  
Final Assembly ◽  
Genome Complexity ◽  
Hybrid Genome ◽  
Silurus Asotus

AbstractGenome complexity such as heterozygosity may heavily influence its de novo assembly. Sequencing somatic cells of the F1 hybrids harboring two sets of genetic materials from both of the paternal and maternal species may avoid alleles discrimination during assembly. However, the feasibility of this strategy needs further assessments. We sequenced and assembled the genome of an F1 hybrid between Silurus asotus and S. meridionalis using the SequelII platform and Hi-C scaffolding technologies. More than 300 Gb raw data were generated, and the final assembly obtained 2344 scaffolds composed of 3017 contigs. The N50 length of scaffolds and contigs was 28.55 Mb and 7.49 Mb, respectively. Based on the mapping results of short reads generated for the paternal and maternal species, each of the 29 chromosomes originating from S. asotus and S. meridionalis was recognized. We recovered nearly 94% and 96% of the total length of S. asotus and S. meridionalis. BUSCO assessments and mapping analyses suggested that both genomes had high completeness and accuracy. Further analyses demonstrated the high collinearity between S. asotus, S. meridionalis, and the related Pelteobagrus fulvidraco. Comparison of the two genomes with that assembled only using the short reads from non-hybrid parental species detected a small portion of sequences that may be incorrectly assigned to the different species. We supposed that at least part of these situations may have resulted from mitotic recombination. The strategy of sequencing the F1 hybrid genome can recover the vast majority of the parental genomes and may improve the assembly of complex genomes.

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