Integrating independent microbial studies to build predictive models of anaerobic digestion inhibition by ammonia and phenol

2020 ◽  
Author(s):  
Simon Poirier ◽  
Sébastien Déjean ◽  
Cédric Midoux ◽  
Kim-Anh Lê Cao ◽  
Olivier Chapleur
Keyword(s):  
Anaerobic Digestion ◽  
High Throughput Sequencing ◽  
Economic Losses ◽  
List Type ◽  
Community Patterns ◽  
Microbial Indicators ◽  
Sequencing Technologies ◽  
External Data ◽  
Wide Range ◽  
Process Failure

AbstractAnaerobic digestion (AD) is a microbial process that can efficiently degrade organic waste into renewable energies such as methane-rich biogas. However, the underpinning microbial mechanisms are highly vulnerable to a wide range of inhibitory compounds, leading to process failure and economic losses. High-throughput sequencing technologies enable the identification of microbial indicators of digesters inhibition and can provide new insights into the key phylotypes at stake during AD process. But yet, current studies have used different inocula, substrates, geographical sites and types of reactors, resulting in indicators that are not robust or reproducible across independent studies. In addition, such studies focus on the identification of a single microbial indicator that is not reflective of the complexity of AD. Our study proposes the first analysis of its kind that seeks for a robust signature of microbial indicators of phenol and ammonia inhibitions, whilst leveraging on 4 independent in-house and external AD microbial studies. We applied a recent multivariate integrative method on two-in-house studies to identify such signature, then predicted the inhibitory status of samples from two datasets with more than 90% accuracy. Our study demonstrates how we can efficiently analyze existing studies to extract robust microbial community patterns, predict AD inhibition, and deepen our understanding of AD towards better AD microbial management.HighlightsRobust biomarkers of AD inhibition were tagged by integrating independent 16S studiesIncrease of the Clostridiales relative abundance is an early warning of AD inhibitionCloacimonetes is associated with good performance of biomethane productionMultivariate model predicts ammonia inhibition with 90% accuracy in external data

scholarly journals Expedited Assessment of Terrestrial Arthropod Diversity by Coupling Malaise Traps with DNA Barcoding

2017 ◽  
Author(s):  
JR deWaard ◽  
V Levesque-Beaudin ◽  
SL deWaard ◽  
NV Ivanova ◽  
JTA McKeown ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
National Park ◽  
High Throughput Sequencing ◽  
Species Abundance ◽  
List Type ◽  
Arthropod Diversity ◽  
Sequencing Technologies ◽  
Data Release ◽  
Speed And Accuracy ◽  
Malaise Traps

SummaryMonitoring changes in terrestrial arthropod communities over space and time requires a dramatic increase in the speed and accuracy of processing samples that cannot be achieved with morphological approaches.The combination of DNA barcoding and Malaise traps allows expedited, comprehensive inventories of species abundance whose cost will rapidly decline as high-throughput sequencing technologies advance.Aside from detailing protocols from specimen sorting to data release, this paper describes their use in a survey of arthropod diversity in a national park that examined 20,000 specimens representing 2200 species.These protocols can support arthropod monitoring programs at regional, national, and continental scales.

scholarly journals The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 1229
Author(s):  
David Salgado ◽  
Irina M. Armean ◽  
Michael Baudis ◽  
Sergi Beltran ◽  
Salvador Capella-Gutierrez ◽  
...  
Keyword(s):  
Copy Number ◽  
High Throughput Sequencing ◽  
Population Genomics ◽  
Genetic Diseases ◽  
White Paper ◽  
Copy Number Variations ◽  
Direct Result ◽  
Sequencing Technologies ◽  
Wide Range ◽  
Definition Of

Copy number variations (CNVs) are major causative contributors both in the genesis of genetic diseases and human neoplasias. While “High-Throughput” sequencing technologies are increasingly becoming the primary choice for genomic screening analysis, their ability to efficiently detect CNVs is still heterogeneous and remains to be developed. The aim of this white paper is to provide a guiding framework for the future contributions of ELIXIR’s recently established human CNV Community, with implications beyond human disease diagnostics and population genomics. This white paper is the direct result of a strategy meeting that took place in September 2018 in Hinxton (UK) and involved representatives of 11 ELIXIR Nodes. The meeting led to the definition of priority objectives and tasks, to address a wide range of CNV-related challenges ranging from detection and interpretation to sharing and training. Here, we provide suggestions on how to align these tasks within the ELIXIR Platforms strategy, and on how to frame the activities of this new ELIXIR Community in the international context.

scholarly journals Fast sequence-based microsatellite genotyping development workflow

2019 ◽  
Author(s):  
Olivier Lepais ◽  
Emilie Chancerel ◽  
Christophe Boury ◽  
Franck Salin ◽  
Aurélie Manicki ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Ad Hoc ◽  
De Novo ◽  
Microsatellite Genotyping ◽  
Sequencing Technologies ◽  
Wide Range ◽  
Genetic Diversity And Structure ◽  
Genomic Resource ◽  
Analytical Frameworks ◽  
Different Levels

AbstractApplication of high-throughput sequencing technologies to microsatellite genotyping (SSRseq) has been shown to remove many of the limitations of electrophoresis-based methods and to refine inference of population genetic diversity and structure. We present here a streamlined SSRseq development workflow that includes microsatellite development, multiplexed marker amplification and sequencing, and automated bioinformatics data analysis. We illustrate its application to five groups of species across phyla (fungi, plant, insect and fish) with different levels of genomic resource availability. We found that relying on previously developed microsatellite assay is not optimal and leads to a resulting low number of reliable locus being genotyped. In contrast, de novo ad hoc primer designs gives highly multiplexed microsatellite assays that can be sequenced to produce high quality genotypes for 20 to 40 loci. We highlight critical upfront development factors to consider for effective SSRseq setup in a wide range of situations. Sequence analysis accounting for all linked polymorphisms along the sequence, quickly generates a powerful multi-allelic haplotype-based genotypic dataset, calling to new theoretical and analytical frameworks to extract more information from multi-nucleotide polymorphism marker systems.

scholarly journals Asymmetric Inheritance of Cell Fate Determinants: Focus on RNA

2019 ◽  
Vol 5 (2) ◽  
pp. 38 ◽  
Author(s):  
Yelyzaveta Shlyakhtina ◽  
Katherine L. Moran ◽  
Maximiliano M. Portal
Keyword(s):  
Cell Fate ◽  
Mammalian Cells ◽  
High Throughput Sequencing ◽  
General Pattern ◽  
Nuclear Architecture ◽  
Biological Information ◽  
Current Evidence ◽  
Rna Molecules ◽  
Sequencing Technologies ◽  
Wide Range

During the last decade, and mainly primed by major developments in high-throughput sequencing technologies, the catalogue of RNA molecules harbouring regulatory functions has increased at a steady pace. Current evidence indicates that hundreds of mammalian RNAs have regulatory roles at several levels, including transcription, translation/post-translation, chromatin structure, and nuclear architecture, thus suggesting that RNA molecules are indeed mighty controllers in the flow of biological information. Therefore, it is logical to suggest that there must exist a series of molecular systems that safeguard the faithful inheritance of RNA content throughout cell division and that those mechanisms must be tightly controlled to ensure the successful segregation of key molecules to the progeny. Interestingly, whilst a handful of integral components of mammalian cells seem to follow a general pattern of asymmetric inheritance throughout division, the fate of RNA molecules largely remains a mystery. Herein, we will discuss current concepts of asymmetric inheritance in a wide range of systems, including prions, proteins, and finally RNA molecules, to assess overall the biological impact of RNA inheritance in cellular plasticity and evolutionary fitness.

scholarly journals Designing Efficient Spaced Seeds for SOLiD Read Mapping

2010 ◽  
Vol 2010 ◽  
pp. 1-12 ◽  
Author(s):  
Laurent Noé ◽  
Marta Gîrdea ◽  
Gregory Kucherov
Keyword(s):  
High Throughput Sequencing ◽  
Color Space ◽  
Major Advance ◽  
Read Mapping ◽  
Sequencing Technologies ◽  
Reading Errors ◽  
Spaced Seeds ◽  
Algorithmic Solution ◽  
Wide Range ◽  
Genomic Studies

The advent of high-throughput sequencing technologies constituted a major advance in genomic studies, offering new prospects in a wide range of applications.We propose a rigorous and flexible algorithmic solution to mapping SOLiD color-space reads to a reference genome. The solution relies on an advanced method of seed design that uses a faithful probabilistic model of read matches and, on the other hand, a novel seeding principle especially adapted to read mapping. Our method can handle both lossy and lossless frameworks and is able to distinguish, at the level of seed design, between SNPs and reading errors. We illustrate our approach by several seed designs and demonstrate their efficiency.

scholarly journals Taking Advantage of the Genomics Revolution for Monitoring and Conservation of Chondrichthyan Populations

Diversity ◽  
2019 ◽  
Vol 11 (4) ◽  
pp. 49 ◽  
Author(s):  
Shaili Johri ◽  
Michael Doane ◽  
Lauren Allen ◽  
Elizabeth Dinsdale
Keyword(s):  
High Throughput Sequencing ◽  
Metagenomic Data ◽  
Vertebrate Species ◽  
Design And Implementation ◽  
Sequencing Technologies ◽  
Wide Range ◽  
Population Structures ◽  
Genomic Studies ◽  
Species Groups ◽  
Data Deficient

Chondrichthyes (sharks, rays, skates and chimaeras) are among the oldest extant predators and are vital to top-down regulation of oceanic ecosystems. They are an ecologically diverse group occupying a wide range of habitats and are thus, exploited by coastal, pelagic and deep-water fishing industries. Chondrichthyes are among the most data deficient vertebrate species groups making design and implementation of regulatory and conservation measures challenging. High-throughput sequencing technologies have significantly propelled ecological investigations and understanding of marine and terrestrial species’ populations, but there remains a paucity of NGS based research on chondrichthyan populations. We present a brief review of current methods to access genomic and metagenomic data from Chondrichthyes and discuss applications of these datasets to increase our understanding of chondrichthyan taxonomy, evolution, ecology and population structures. Last, we consider opportunities and challenges offered by genomic studies for conservation and management of chondrichthyan populations.

scholarly journals In Silico Estimation of the Abundance and Phylogenetic Significance of the Composite Oct4-Sox2 Binding Motifs within a Wide Range of Species

Data ◽  
2020 ◽  
Vol 5 (4) ◽  
pp. 111
Author(s):  
Arman Kulyyassov ◽  
Ruslan Kalendar
Keyword(s):  
High Throughput ◽  
Dna Sequences ◽  
High Throughput Sequencing ◽  
Regulatory Elements ◽  
Scoring Method ◽  
Sequencing Technologies ◽  
Wide Range ◽  
Multiple Species ◽  
Eukaryotic Organisms ◽  
The Impact

High-throughput sequencing technologies have greatly accelerated the progress of genomics, transcriptomics, and metagenomics. Currently, a large amount of genomic data from various organisms is being generated, the volume of which is increasing every year. Therefore, the development of methods that allow the rapid search and analysis of DNA sequences is urgent. Here, we present a novel motif-based high-throughput sequence scoring method that generates genome information. We found and identified Utf1-like, Fgf4-like, and Hoxb1-like motifs, which are cis-regulatory elements for the pluripotency transcription factors Sox2 and Oct4 within the genomes of different eukaryotic organisms. The genome-wide analysis of these motifs was performed to understand the impact of their diversification on mammalian genome evolution. Utf1-like, Fgf4-like, and Hoxb1-like motif diversity was evaluated across genomes from multiple species.

scholarly journals Fast sequence-based microsatellite genotyping development workflow

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9085 ◽  
Author(s):  
Olivier Lepais ◽  
Emilie Chancerel ◽  
Christophe Boury ◽  
Franck Salin ◽  
Aurélie Manicki ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Ad Hoc ◽  
De Novo ◽  
Microsatellite Genotyping ◽  
Sequencing Technologies ◽  
Wide Range ◽  
Genetic Diversity And Structure ◽  
Genomic Resource ◽  
Analytical Frameworks ◽  
Different Levels

Application of high-throughput sequencing technologies to microsatellite genotyping (SSRseq) has been shown to remove many of the limitations of electrophoresis-based methods and to refine inference of population genetic diversity and structure. We present here a streamlined SSRseq development workflow that includes microsatellite development, multiplexed marker amplification and sequencing, and automated bioinformatics data analysis. We illustrate its application to five groups of species across phyla (fungi, plant, insect and fish) with different levels of genomic resource availability. We found that relying on previously developed microsatellite assay is not optimal and leads to a resulting low number of reliable locus being genotyped. In contrast, de novo ad hoc primer designs gives highly multiplexed microsatellite assays that can be sequenced to produce high quality genotypes for 20–40 loci. We highlight critical upfront development factors to consider for effective SSRseq setup in a wide range of situations. Sequence analysis accounting for all linked polymorphisms along the sequence quickly generates a powerful multi-allelic haplotype-based genotypic dataset, calling to new theoretical and analytical frameworks to extract more information from multi-nucleotide polymorphism marker systems.

Comparison of Deterministic and Linear Cosine Spatial Filtering of Transmission Electron Micrographs

1972 ◽  
Vol 30 ◽  
pp. 596-597
Author(s):  
David A. Ansley
Keyword(s):  
Spherical Aberration ◽  
Focal Length ◽  
Chromatic Aberration ◽  
Spatial Filter ◽  
Operating Conditions ◽  
Objective Lens ◽  
List Type ◽  
Spatial Filters ◽  
Transmission Electron ◽  
Wide Range

The coherence of the electron flux of a transmission electron microscope (TEM) limits the direct application of deconvolution techniques which have been used successfully on unmanned spacecraft programs. The theory assumes noncoherent illumination. Deconvolution of a TEM micrograph will, therefore, in general produce spurious detail rather than improved resolution.A primary goal of our research is to study the performance of several types of linear spatial filters as a function of specimen contrast, phase, and coherence. We have, therefore, developed a one-dimensional analysis and plotting program to simulate a wide 'range of operating conditions of the TEM, including adjustment of the:(1) Specimen amplitude, phase, and separation(2) Illumination wavelength, half-angle, and tilt(3) Objective lens focal length and aperture width(4) Spherical aberration, defocus, and chromatic aberration focus shift(5) Detector gamma, additive, and multiplicative noise constants(6) Type of spatial filter: linear cosine, linear sine, or deterministic

Triply-periodic nanostructures in surfactant, block copolymer, and biomembrane systems, and simulation of TEMs

1993 ◽  
Vol 51 ◽  
pp. 884-885
Author(s):  
David M. Anderson ◽  
Tomas Landh
Keyword(s):  
Liquid Crystalline ◽  
Diblock Copolymers ◽  
Cubic Phase ◽  
List Type ◽  
Interpenetrating Networks ◽  
Triply Periodic ◽  
Wide Range ◽  
Bicontinuous Cubic ◽  
Phase Liquid ◽  
Dividing Surface

First discovered in surfactant-water liquid crystalline systems, so-called ‘bicontinuous cubic phases’ have the property that hydropnilic and lipophilic microdomains form interpenetrating networks conforming to cubic lattices on the scale of nanometers. Later these same structures were found in star diblock copolymers, where the simultaneous continuity of elastomeric and glassy domains gives rise to unique physical properties. Today it is well-established that the symmetry and topology of such a morphology are accurately described by one of several triply-periodic minimal surfaces, and that the interface between hydrophilic and hydrophobic, or immiscible polymer, domains is described by a triply-periodic surface of constant, nonzero mean curvature. One example of such a dividing surface is shown in figure 5.The study of these structures has become of increasing importance in the past five years for two reasons:1)Bicontinuous cubic phase liquid crystals are now being polymerized to create microporous materials with monodispersed pores and readily functionalizable porewalls; figure 3 shows a TEM from a polymerized surfactant / methylmethacrylate / water cubic phase; and2)Compelling evidence has been found that these same morphologies describe biomembrane systems in a wide range of cells.

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