scholarly journals Metagenomic assembly of new (sub)arctic Cyanobacteria and their associated microbiome from non-axenic cultures

2018 ◽  
Author(s):  
Luc Cornet ◽  
Amandine R. Bertrand ◽  
Marc Hanikenne ◽  
Emmanuelle J. Javaux ◽  
Annick Wilmotte ◽  
...  
Keyword(s):  
Heterotrophic Bacteria ◽  
Point Of View ◽  
High Quality ◽  
Culture Collections ◽  
Associated Bacteria ◽  
Complete Genomes ◽  
Axenic Cultures ◽  
Metagenomic Assembly ◽  
Genome Assemblies ◽  
Public Collection

AbstractCyanobacteria form one of the most diversified phylum of Bacteria. They are important ecologically as primary producers, for Earth evolution and biotechnological applications. Yet, Cyanobacteria are notably difficult to purify and grow axenically, and most strains in culture collections contain heterotrophic bacteria that were likely associated to Cyanobacteria in the environment. Obtaining cyanobacterial DNA without contaminant sequences is thus a challenging and time-consuming task. Here, we deploy a metagenomic pipeline that enables the easy recovery of high-quality genomes from non-axenic cultures. We tested this pipeline on 17 cyanobacterial cultures from the BCCM/ULC public collection and generated novel genome sequences for 15 arctic or subarctic strains, of which 14 early-branching organisms that will be useful for cyanobacterial phylogenomics. In parallel, we managed to assemble 31 co-cultivated bacteria from the same cultures and showed that they mostly belong to Bacteroidetes and Proteobacteria, some of them being very closely related in spite of geographically distant sampling sites.ImportanceComplete genomes of cold-adapted Cyanobacteria are underrepresented in databases, due to the difficulty to grow them axenically. In this work, we report the genome sequencing of 12 (sub)arctic and 3 temperate Cyanobacteria, along with 21 Proteobacteria and 5 Bacteroidetes recovered from their microbiome. Following the use of a state-of-the-art metagenomic pipeline, 12 of our new cyanobacterial genome assemblies are of high-quality, which indicates that even non-axenic cultures can yield complete genomes suitable for phylogenomics and comparative genomics. From a methodological point of view, we investigate the fate of SSU rRNA (16S) genes during metagenomic binning and observe that multi-copy rRNA operons are lost because of higher sequencing coverage and divergent tetranucleotide frequencies. Moreover, we devised a measure of genomic identity to compare metagenomic bins of different completeness, which allowed us to show that Cyanobacteria-associated bacteria can be highly related in spite of considerable distance between collection points.

scholarly journals The contribution of the Italian residents in neurology to the COVID-19 crisis: admirable generosity but neurological training remains their priority

2021 ◽  
Author(s):  
Cristina Tassorelli ◽  
Vincenzo Silani ◽  
Alessandro Padovani ◽  
Paolo Barone ◽  
Paolo Calabresi ◽  
...  
Keyword(s):  
Clinical Training ◽  
Real Life ◽  
Healthcare Management ◽  
Point Of View ◽  
Research Activity ◽  
High Quality ◽  
Research Activities ◽  
Italian Regions ◽  
Training And Research

Abstract Background The coronavirus disease 2019 (COVID-19) pandemic has severely impacted the Italian healthcare system, underscoring a dramatic shortage of specialized doctors in many disciplines. The situation affected the activity of the residents in neurology, who were also offered the possibility of being formally hired before their training completion. Aims (1) To showcase examples of clinical and research activity of residents in neurology during the COVID-19 pandemic in Italy and (2) to illustrate the point of view of Italian residents in neurology about the possibility of being hired before the completion of their residency program. Results Real-life reports from several areas in Lombardia—one of the Italian regions more affected by COVID-19—show that residents in neurology gave an outstanding demonstration of generosity, collaboration, reliability, and adaptation to the changing environment, while continuing their clinical training and research activities. A very small minority of the residents participated in the dedicated selections for being hired before completion of their training program. The large majority of them prioritized their training over the option of earlier employment. Conclusions Italian residents in neurology generously contributed to the healthcare management of the COVID-19 pandemic in many ways, while remaining determined to pursue their training. Neurology is a rapidly evolving clinical field due to continuous diagnostic and therapeutic progress. Stakeholders need to listen to the strong message conveyed by our residents in neurology and endeavor to provide them with the most adequate training, to ensure high quality of care and excellence in research in the future.

scholarly journals Hapo-G, haplotype-aware polishing of genome assemblies with accurate reads

2021 ◽  
Vol 3 (2) ◽  
Author(s):  
Jean-Marc Aury ◽  
Benjamin Istace
Keyword(s):  
Single Molecule ◽  
Direct Consequence ◽  
High Quality ◽  
Sequencing Errors ◽  
Coding Regions ◽  
Sequencing Technologies ◽  
Long Reads ◽  
Oxford Nanopore ◽  
Long Read ◽  
Genome Assemblies

Abstract Single-molecule sequencing technologies have recently been commercialized by Pacific Biosciences and Oxford Nanopore with the promise of sequencing long DNA fragments (kilobases to megabases order) and then, using efficient algorithms, provide high quality assemblies in terms of contiguity and completeness of repetitive regions. However, the error rate of long-read technologies is higher than that of short-read technologies. This has a direct consequence on the base quality of genome assemblies, particularly in coding regions where sequencing errors can disrupt the coding frame of genes. In the case of diploid genomes, the consensus of a given gene can be a mixture between the two haplotypes and can lead to premature stop codons. Several methods have been developed to polish genome assemblies using short reads and generally, they inspect the nucleotide one by one, and provide a correction for each nucleotide of the input assembly. As a result, these algorithms are not able to properly process diploid genomes and they typically switch from one haplotype to another. Herein we proposed Hapo-G (Haplotype-Aware Polishing Of Genomes), a new algorithm capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.

scholarly journals Filling the Gaps in the Cyanobacterial Tree of Life—Metagenome Analysis of Stigonema ocellatum DSM 106950, Chlorogloea purpurea SAG 13.99 and Gomphosphaeria aponina DSM 107014

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 389
Author(s):  
Pia Marter ◽  
Sixing Huang ◽  
Henner Brinkmann ◽  
Silke Pradella ◽  
Michael Jarek ◽  
...  
Keyword(s):  
Heterotrophic Bacteria ◽  
Morphological Diversity ◽  
Cell Types ◽  
Phylogenetic Position ◽  
Metagenome Analysis ◽  
New Family ◽  
Metagenome Sequencing ◽  
Axenic Strains ◽  
Reliable Classification ◽  
Metagenomic Assembly

Cyanobacteria represent one of the most important and diverse lineages of prokaryotes with an unparalleled morphological diversity ranging from unicellular cocci and characteristic colony-formers to multicellular filamentous strains with different cell types. Sequencing of more than 1200 available reference genomes was mainly driven by their ecological relevance (Prochlorococcus, Synechococcus), toxicity (Microcystis) and the availability of axenic strains. In the current study three slowly growing non-axenic cyanobacteria with a distant phylogenetic positioning were selected for metagenome sequencing in order to (i) investigate their genomes and to (ii) uncover the diversity of associated heterotrophs. High-throughput Illumina sequencing, metagenomic assembly and binning allowed us to establish nearly complete high-quality draft genomes of all three cyanobacteria and to determine their phylogenetic position. The cyanosphere of the limnic isolates comprises up to 40 heterotrophic bacteria that likely coexisted for several decades, and it is dominated by Alphaproteobacteria and Bacteriodetes. The diagnostic marker protein RpoB ensured in combination with our novel taxonomic assessment via BLASTN-dependent text-mining a reliable classification of the metagenome assembled genomes (MAGs). The detection of one new family and more than a dozen genera of uncultivated heterotrophic bacteria illustrates that non-axenic cyanobacteria are treasure troves of hidden microbial diversity.

THE ROAD AHEAD TO BETTER MEDICAL CARE FOR CHILDREN

PEDIATRICS ◽  
1950 ◽  
Vol 6 (3) ◽  
pp. 553-556
Keyword(s):  
Child Health ◽  
Medical Care ◽  
Medical Center ◽  
Point Of View ◽  
Medical Services ◽  
High Quality ◽  
The Road ◽  
Provide Child Care ◽  
Ultimate Objective ◽  
The Many

THE road to better child health has been discussed in relation to the doctor and his training, health services and their distribution. We have dealt with the unavoidable question of costs. Particular attention has been given to some of the advantages and dangers of decentralization of pediatric education and services. Each of the various subjects has been discussed from the point of view of its bearing on the ultimate objective of better health for all children and the steps necessary to attain this goal. Now, we may stand back from the many details of the picture, view the whole objectively and note its most outstanding features. First is the fact that the improvement of child health depends primarily upon better training for all doctors who provide child care, general practitioners as well as specialists. This is the foundation without which the rest of the structure cannot stand. The second dominant fact is the need for extending to outlying and isolated areas the high quality medical care of the medical centers, without at the same time diluting the service or training at the center. The road to better medical care, therefore, begins at the medical center and extends outward through a network of integrated community hospitals and health centers, finally reaching the remote and heretofore isolated areas. Inherent in all medical schools is a unique potential for rendering medical services as well as actually training physicians. The very nature of medical education—whereby doctors in training work under the tutelage of able specialists in the clinic, hospital ward, and out-patient department—provides medical services of high quality to people in the neighboring communities.

scholarly journals Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise

2019 ◽  
Author(s):  
Valentina Peona ◽  
Mozes P.K. Blom ◽  
Luohao Xu ◽  
Reto Burri ◽  
Shawn Sullivan ◽  
...  
Keyword(s):  
Dark Matter ◽  
Genome Assembly ◽  
Sex Chromosome ◽  
De Novo ◽  
Model Organism ◽  
Technology Choice ◽  
High Quality ◽  
Sequencing Technologies ◽  
Downstream Analysis ◽  
Genome Assemblies

AbstractGenome assemblies are currently being produced at an impressive rate by consortia and individual laboratories. The low costs and increasing efficiency of sequencing technologies have opened up a whole new world of genomic biodiversity. Although these technologies generate high-quality genome assemblies, there are still genomic regions difficult to assemble, like repetitive elements and GC-rich regions (genomic “dark matter”). In this study, we compare the efficiency of currently used sequencing technologies (short/linked/long reads and proximity ligation maps) and combinations thereof in assembling genomic dark matter starting from the same sample. By adopting different de-novo assembly strategies, we were able to compare each individual draft assembly to a curated multiplatform one and identify the nature of the previously missing dark matter with a particular focus on transposable elements, multi-copy MHC genes, and GC-rich regions. Thanks to this multiplatform approach, we demonstrate the feasibility of producing a high-quality chromosome-level assembly for a non-model organism (paradise crow) for which only suboptimal samples are available. Our approach was able to reconstruct complex chromosomes like the repeat-rich W sex chromosome and several GC-rich microchromosomes. Telomere-to-telomere assemblies are not a reality yet for most organisms, but by leveraging technology choice it is possible to minimize genome assembly gaps for downstream analysis. We provide a roadmap to tailor sequencing projects around the completeness of both the coding and non-coding parts of the genomes.

scholarly journals The genomic variation landscape of globally-circulating clades of SARS-CoV-2 defines a genetic barcoding scheme

2020 ◽  
Author(s):  
Qingtian Guan ◽  
Mukhtar Sadykov ◽  
Raushan Nugmanova ◽  
Michael J. Carr ◽  
Stefan T. Arold ◽  
...  
Keyword(s):  
Viral Proteins ◽  
Genomic Variation ◽  
Genome Replication ◽  
High Quality ◽  
Dynamic Changes ◽  
Health Measures ◽  
Complete Genomes ◽  
Major Mutation ◽  
Genetic Barcoding ◽  
Over Time

ABSTRACTWe describe fifteen major mutation events from 2,058 high-quality SARS-CoV-2 genomes deposited up to March 31st, 2020. These events define five major clades (G, I, S, D and V) of globally-circulating viral populations, representing 85.7% of all sequenced cases, which we can identify using a 10 nucleotide genetic classifier or barcode. We applied this barcode to 4,000 additional genomes deposited between March 31st and April 15th and classified successfully 95.6% of the clades demonstrating the utility of this approach. An analysis of amino acid variation in SARS-CoV-2 ORFs provided evidence of substitution events in the viral proteins involved in both host-entry and genome replication. The systematic monitoring of dynamic changes in the SARS-CoV-2 genomes of circulating virus populations over time can guide therapeutic and prophylactic strategies to manage and contain the virus and, also, with available efficacious antivirals and vaccines, aid in the monitoring of circulating genetic diversity as we proceed towards elimination of the agent. The barcode will add the necessary genetic resolution to facilitate tracking and monitoring of infection clusters to distinguish imported and indigenous cases and thereby aid public health measures seeking to interrupt transmission chains without the requirement for real-time complete genomes sequencing.

scholarly journals SIGAR: Inferring features of genome architecture and DNA rearrangements by split read mapping

2020 ◽  
Author(s):  
Yi Feng ◽  
Leslie Y. Beh ◽  
Wei-Jen Chang ◽  
Laura F. Landweber
Keyword(s):  
Genome Assembly ◽  
Repetitive Sequences ◽  
Genome Architecture ◽  
Dna Rearrangements ◽  
High Quality ◽  
Microbial Eukaryotes ◽  
Ciliate Species ◽  
Split Read ◽  
High Level ◽  
Genome Assemblies

AbstractCiliates are microbial eukaryotes with distinct somatic and germline genomes. Post-zygotic development involves extensive remodeling of the germline genome to form somatic chromosomes. Ciliates therefore offer a valuable model for studying the architecture and evolution of programmed genome rearrangements. Current studies usually focus on a few model species, where rearrangement features are annotated by aligning reference germline and somatic genomes. While many high-quality somatic genomes have been assembled, a high quality germline genome assembly is difficult to obtain due to its smaller DNA content and abundance of repetitive sequences. To overcome these hurdles, we propose a new pipeline SIGAR (Splitread Inference of Genome Architecture and Rearrangements) to infer germline genome architecture and rearrangement features without a germline genome assembly, requiring only short germline DNA sequencing reads. As a proof of principle, 93% of rearrangement junctions identified by SIGAR in the ciliate Oxytricha trifallax were validated by the existing germline assembly. We then applied SIGAR to six diverse ciliate species without germline genome assemblies, including Ichthyophthirius multifilii, a fish pathogen. Despite the high level of somatic DNA contamination in each sample, SIGAR successfully inferred rearrangement junctions, short eliminated sequences and potential scrambled genes in each species. This pipeline enables pilot surveys or exploration of DNA rearrangements in species with limited DNA material access, thereby providing new insights into the evolution of chromosome rearrangements.

scholarly journals Efficient Dilution-to-Extinction isolation of novel virus-host model systems for fastidious heterotrophic bacteria

2020 ◽  
Author(s):  
Holger H. Buchholz ◽  
Michelle Michelsen ◽  
Luis M. Bolaños ◽  
Emily Browne ◽  
Michael J. Allen ◽  
...  
Keyword(s):  
Heterotrophic Bacteria ◽  
Nutrient Recycling ◽  
Model Systems ◽  
Metagenomic Data ◽  
Culture Collections ◽  
Genomic Databases ◽  
New Members ◽  
Host Interactions ◽  
Infection Dynamics ◽  
Ecological Patterns

AbstractMicrobes and their associated viruses are key drivers of biogeochemical processes in marine and soil biomes. While viruses of phototrophic cyanobacteria are well-represented in model systems, challenges of isolating marine microbial heterotrophs and their viruses have hampered experimental approaches to quantify the importance of viruses in nutrient recycling. A resurgence in cultivation efforts has improved the availability of fastidious bacteria for hypothesis testing, but this has not been matched by similar efforts to cultivate their associated bacteriophages. Here, we describe a high-throughput method for isolating important virus-host systems for fastidious heterotrophic bacteria that couples advances in culturing of hosts with sequential enrichment and isolation of associated phages. Applied to six monthly samples from the Western English Channel, we first isolated one new member of the globally dominant bacterial SAR11 clade and three new members of the methylotrophic bacterial clade OM43. We used these as bait to isolate 117 new phages including the first known siphophage infecting SAR11, and the first isolated phage for OM43. Genomic analyses of 13 novel viruses revealed representatives of three new viral genera, and infection assays showed that the viruses infecting SAR11 have ecotype-specific host-ranges. Similar to the abundant human-associated phage ΦCrAss001, infection dynamics within the majority of isolates suggested either prevalent lysogeny or chronic infection, despite a lack of associated genes; or host phenotypic bistability with lysis putatively maintained within a susceptible subpopulation. Broader representation of important virus-host systems in culture collections and genomic databases will improve both our understanding of virus-host interactions, and accuracy of computational approaches to evaluate ecological patterns from metagenomic data.

John Gower, Mentor for Royalty: Richard II

PMLA ◽  
1954 ◽  
Vol 69 (4-Part1) ◽  
pp. 953-964
Author(s):  
George R. Coffman
Keyword(s):  
Middle Class ◽  
Present Article ◽  
Point Of View ◽  
John Gower ◽  
High Quality ◽  
Richard Ii ◽  
Unresolved Problem ◽  
Edward Iii ◽  
Standard Edition

This paragraph introduces a paper which illustrates a larger project: a study of aspects of Gower's works in fourteenth-century historical relationships. The objective is an interpretation of his writings as mirroring the attitude and point of view of a conservative middle-class Englishman for the years 1381-1400 and through them an interpretation of the England of his day. Though these writings show the long heritage of an economic, political, ethical, and religious past, our interest always centers in his immediate present. Non-literary contemporary records consequently provide the first essential materials for this interpretation. Macaulay's standard edition of his works, published half a century ago, based on all manuscripts then available, constitutes the printed source for this study. The high quality of Gower's preserved manuscripts, which give his own revisions, and the fact that these revisions show important changes in his attitudes toward individuals and organizations or institutions, make a re-examination of all of them now available an essential part of this interpretation and raise again the unresolved problem of his ethical integrity. Gardiner Stillwell's able article, “John Gower and the Last Years of Edward III,” provides a suggestive introduction for the interested student. The title of the present article is John Gower, Mentor for Royalty: Richard II.

On the Maturity of Software Maintenance and Other IT Services

2011 ◽  
pp. 51-74
Author(s):  
Frank Niessink
Keyword(s):  
Service Quality ◽  
Software Development ◽  
Software Maintenance ◽  
Two Dimensions ◽  
Point Of View ◽  
Technical Quality ◽  
It Services ◽  
High Quality ◽  
Functional Quality

In this chapter, we examine the differences between software maintenance and software development from a service point of view, and the consequences thereof for the maturity of software maintenance organizations. We argue that software maintenance can be seen as providing a service, whereas software development is primarily concerned with the development of products. Differences between products and services affect the way in which customers assess their respective quality. In particular, service quality is assessed in two dimensions: the technical quality — what the result of the service is — and the functional quality — how the service is delivered. Consequently, customers will judge the quality of software maintenance differently from that of software development. This in turn means that to deliver high quality results in software maintenance, both the functional quality and the technical quality dimension are important.

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