scholarly journals Taming the Wild West of Molecular Tools Application in Aquatic Research and Biomonitoring

2019 ◽  
Vol 3 ◽  
Author(s):  
Alexander Weigand ◽  
Agnès Bouchez ◽  
Pieter Boets ◽  
Kat Bruce ◽  
Fedor Ciampor ◽  
...  
Keyword(s):  
Working Group ◽  
High Throughput Sequencing ◽  
Group Structure ◽  
Time Budget ◽  
Good Practice ◽  
Dna Barcode ◽  
Environmental Parameters ◽  
Full Potential ◽  
Molecular Tools ◽  
Wild West

Modern high-throughput sequencing technologies are becoming a game changer in many fields of aquatic research and biomonitoring. To unfold their full potential, however, the independent development of approaches has to be streamlined. This discussion must be fuelled by stakeholders and practitioners and, scientific results collaboratively filtered to identify the most promising avenues. Furthermore, aspects such as time, budget, skills and the application context have to be considered, finally communicating good practice strategies to target audiences. Since 2016, the EU COST Action DNAqua-Net is taming the wild west of molecular tools application in aquatic research and biomonitoring. After nucleating available knowledge by the formation of a highly international and transdisciplinary network of scientists, stakeholders, practitioners and enterprises, fields of high methodological diversity were identified. Relevant aspects are currently ground truthed, thereby reducing the plethora of pipelines, parameters and protocols to a subset of good practices or standardisations. To effectively bridge the science-application interface, the very same network is exploited for the dissemination of results (Leese et al. 2018). The internal working group structure of DNAqua-Net is used to provide an overview of existing methodological fields of diversity in DNA-based aquatic biomonitoring: WG1 -DNA Barcode References: Different marker systems are targeted for the same organism group. Even in case the same molecular marker is investigated, different primer pairs are frequently applied for DNA metabarcoding. Both aspects challenge the further development of high-quality and complete DNA barcode reference libraries (Weigand et al. 2019). WG2 -Biotic Indices & Metrics: Index systems are developed from molecular data in various ways: from the estimation of species' biomass (as a proxy for abundance) from sequence reads, to the correlation of presence/absence data of molecular operational taxonomic units (MOTUs) with environmental parameters (Pawlowski et al. 2018). WG3 -Field & Lab Protocols: Using environmental DNA (eDNA) metabarcoding as an example, diverse sampling techniques based on varying water volumes, different filter systems and collection devices as well as a multitude of laboratory protocols for PCR, replication and sequencing are considered. WG4 -Data Analysis & Storage: During the process of MOTU identification, varying threshold values and conceptually different pipelines are used, potentially impacting the final list of MOTUs or species retrieved. Furthermore, routine storage concepts for big biodiversity data are only in development and some sample types (e.g. eDNA) have no sophisticated metadata descriptions. WG5 -Implementation Strategy & Legal Issues: The working group picks up collaboratively filtered good practice strategies and generates room for discussions at the science-policy interface (Hering et al. 2018). The CEN working group WG28 "DNA methods" has been initiated and the development of standardisations is fostered.

scholarly journals Increased peak detection accuracy in over-dispersed ChIP-seq data with supervised segmentation models

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Arnaud Liehrmann ◽  
Guillem Rigaill ◽  
Toby Dylan Hocking
Keyword(s):  
Histone Modifications ◽  
Count Data ◽  
High Throughput Sequencing ◽  
Genetic Regulation ◽  
Regulation Of Gene Expression ◽  
Basic Mechanism ◽  
R Package ◽  
Detection Accuracy ◽  
Full Potential ◽  
Segmentation Models

Abstract Background Histone modification constitutes a basic mechanism for the genetic regulation of gene expression. In early 2000s, a powerful technique has emerged that couples chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq). This technique provides a direct survey of the DNA regions associated to these modifications. In order to realize the full potential of this technique, increasingly sophisticated statistical algorithms have been developed or adapted to analyze the massive amount of data it generates. Many of these algorithms were built around natural assumptions such as the Poisson distribution to model the noise in the count data. In this work we start from these natural assumptions and show that it is possible to improve upon them. Results Our comparisons on seven reference datasets of histone modifications (H3K36me3 & H3K4me3) suggest that natural assumptions are not always realistic under application conditions. We show that the unconstrained multiple changepoint detection model with alternative noise assumptions and supervised learning of the penalty parameter reduces the over-dispersion exhibited by count data. These models, implemented in the R package CROCS (https://github.com/aLiehrmann/CROCS), detect the peaks more accurately than algorithms which rely on natural assumptions. Conclusion The segmentation models we propose can benefit researchers in the field of epigenetics by providing new high-quality peak prediction tracks for H3K36me3 and H3K4me3 histone modifications.

Development of an autonomous robotic system for beard shaving assistance of disabled people based on an adaptive force tracking impedance control

2021 ◽  
pp. 095440622098482
Author(s):  
Oladayo S Ajani ◽  
Samy FM Assal
Keyword(s):  
Impedance Control ◽  
Environmental Parameters ◽  
Robotic System ◽  
Robotic Systems ◽  
Full Potential ◽  
Robotic Assistance ◽  
Head Pose ◽  
Detection And Tracking ◽  
Control Scheme ◽  
Force Tracking

Recently, people with upper arm disabilities due to neurological disorders, stroke or old age are receiving robotic assistance to perform several activities such as shaving, eating, brushing and drinking. Although the full potential of robotic assistance lies in the use of fully autonomous robotic systems, these systems are limited in design due to the complexities and the associated risks. Hence, rather than the shared controlled or active robotic systems used for such tasks around the head, an adaptive compliance control scheme-based autonomous robotic system for beard shaving assistance is proposed. The system includes an autonomous online face detection and tracking as well as selected geometrical features-based beard region estimation using the Kinect RGB-D camera. Online trajectory planning for achieving the shaving task is enabled; with the capability of online re-planning trajectories in case of unintended head pose movement and occlusion. Based on the dynamics of the UR-10 6-DOF manipulator using ADAMS and MATLAB, an adaptive force tracking impedance controller whose parameters are tuned using Genetic Algorithm (GA) with force/torque constraints is developed. This controller can regulate the contact force under head pose changing and varying shaving region stiffness by adjusting the target stiffness of the controller. Simulation results demonstrate the system capability to achieve beard shaving autonomously with varying environmental parameters that can be extended for achieving other tasks around the head such as feeding, drinking and brushing.

scholarly journals Consensus for the General Use of Equine Water Treadmills for Healthy Horses

Animals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 305
Author(s):  
Kathryn Nankervis ◽  
Carolyne Tranquille ◽  
Persephone McCrae ◽  
Jessica York ◽  
Morgan Lashley ◽  
...  
Keyword(s):  
Working Group ◽  
Best Practice ◽  
Treadmill Exercise ◽  
Good Practice ◽  
Belt Speed ◽  
Research Programmes ◽  
Potential Benefits ◽  
Water Treadmill ◽  
Selection Of

Water treadmill exercise has become popular in recent years for the training and rehabilitation of equine athletes. In 2019, an equine hydrotherapy working group was formed to establish what was commonly considered to be best practice in the use of the modality. This article describes the process by which general guidelines for the application of water treadmill exercise in training and rehabilitation programmes were produced by the working group. The guidelines describe the consensus reached to date on (1) the potential benefits of water treadmill exercise, (2) general good practice in water treadmill exercise, (3) introduction of horses to the exercise, (4) factors influencing selection of belt speed, water depth and duration of exercise, and (5) monitoring movement on the water treadmill. The long-term goal is to reach a consensus on the optimal use of the modality within a training or rehabilitation programme. Collaboration between clinicians, researchers and experienced users is needed to develop research programmes and further guidelines regarding the most appropriate application of the modality for specific veterinary conditions.

scholarly journals Assessing and Maximizing Cultivated Diversity with Plate-Wash PCR and High Throughput Sequencing

2020 ◽  
Author(s):  
Emily N. Junkins ◽  
Bradley S. Stevenson
Keyword(s):  
High Throughput ◽  
Drug Targets ◽  
High Throughput Sequencing ◽  
Multidrug Resistant ◽  
Molecular Techniques ◽  
Bioactive Metabolites ◽  
Plate Count ◽  
Molecular Tools ◽  
Vast Number ◽  
Sequencing Studies

AbstractMolecular techniques continue to reveal a growing disparity between the immense diversity of microbial life and the small proportion that is in pure culture. The disparity, originally dubbed “the great plate count anomaly” by Staley and Konopka, has become even more vexing given our increased understanding of the importance of microbiomes to a host and the role of microorganisms in the vital biogeochemical functions of our biosphere. Searching for novel antimicrobial drug targets often focuses on screening a broad diversity of microorganisms. If diverse microorganisms are to be screened, they need to be cultivated. Recent innovative research has used molecular techniques to assess the efficacy of cultivation efforts, providing invaluable feedback to cultivation strategies for isolating targeted and/or novel microorganisms. Here, we aimed to determine the efficiency of cultivating representative microorganisms from a non-human, mammalian microbiome, identify those microorganisms, and determine the bioactivity of isolates. Molecular methods indicated that around 57% of the ASVs detected in the original inoculum were cultivated in our experiments, but nearly 53% of the total ASVs that were present in our cultivation experiments were not detected in the original inoculum. In light of our controls, our data suggests that when molecular tools were used to characterize our cultivation efforts, they provided a more complete, albeit more complex, understanding of which organisms were present compared to what was eventually cultivated. Lastly, about 3% of the isolates collected from our cultivation experiments showed inhibitory bioactivity against a multidrug-resistant pathogen panel, further highlighting the importance of informing and directing future cultivation efforts with molecular tools.ImportanceCultivation is the definitive tool to understand a microorganism’s physiology, metabolism, and ecological role(s). Despite continuous efforts to hone this skill, researchers are still observing yet-to-be cultivated organisms through high-throughput sequencing studies. Here, we use the very same tool that highlights biodiversity to assess cultivation efficiency. When applied to drug discovery, where screening a vast number of isolates for bioactive metabolites is common, cultivating redundant organisms is a hindrance. However, we observed that cultivating in combination with molecular tools can expand the observed diversity of an environment and its community, potentially increasing the number of microorganisms to be screened for natural products.

scholarly journals Diversity of dinoflagellate assemblages in coastal temperate and offshore tropical waters of Australia

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Tahnee Manning ◽  
Arjun Venkatesh Thilagaraj ◽  
Dmitri Mouradov ◽  
Richard Piola ◽  
Clare Grandison ◽  
...  
Keyword(s):  
Dissolved Oxygen ◽  
High Throughput ◽  
Harmful Algal Blooms ◽  
Algal Blooms ◽  
High Throughput Sequencing ◽  
Environmental Parameters ◽  
Marine Phytoplankton ◽  
Tropical Waters ◽  
Total Sequence ◽  
Phytoplankton Communities

Abstract Background Dinoflagellates are a ubiquitous and ecologically important component of marine phytoplankton communities, with particularly notable species including those associated with harmful algal blooms (HABs) and those that bioluminesce. High-throughput sequencing offers a novel approach compared to traditional microscopy for determining species assemblages and distributions of dinoflagellates, which are poorly known especially in Australian waters. Results We assessed the composition of dinoflagellate assemblages in two Australian locations: coastal temperate Port Phillip Bay and offshore tropical waters of Davies Reef (Great Barrier Reef). These locations differ in certain environmental parameters reflecting latitude as well as possible anthropogenic influences. Molecular taxonomic assessment revealed more species than traditional microscopy, and it showed statistically significant differences in dinoflagellate assemblages between locations. Bioluminescent species and known associates of HABs were present at both sites. Dinoflagellates in both areas were mainly represented by the order Gymnodiniales (66%—82% of total sequence reads). In the warm waters of Davies Reef, Gymnodiniales were equally represented by the two superclades, Gymnodiniales sensu stricto (33%) and Gyrodinium (34%). In contrast, in cooler waters of Port Phillip Bay, Gymnodiniales was mainly represented by Gyrodinium (82%). In both locations, bioluminescent dinoflagellates represented up to 0.24% of the total sequence reads, with Protoperidinium the most abundant genus. HAB-related species, mainly represented by Gyrodinium, were more abundant in Port Phillip Bay (up to 47%) than at Davies Reef (28%), potentially reflecting anthropogenic influence from highly populated and industrial areas surrounding the bay. The entire assemblage of dinoflagellates, as well as the subsets of HAB and bioluminescent species, were strongly correlated with water quality parameters (R2 = 0.56–0.92). Significant predictors differed between the subsets: HAB assemblages were explained by salinity, temperature, dissolved oxygen, and total dissolved solids; whereas, bioluminescent assemblages were explained only by salinity and dissolved oxygen, and had greater variability. Conclusion High-throughput sequencing and genotyping revealed greater diversity of dinoflagellate assemblages than previously known in both subtropical and temperate Australian waters. Significant correlations of assemblage structure with environmental variables suggest the potential for explaining the distribution and composition of both HAB species and bioluminescent species.

scholarly journals debar, a sequence-by-sequence denoiser for COI-5P DNA barcode data

2021 ◽  
Author(s):  
Cameron M. Nugent ◽  
Tyler A. Elliott ◽  
Sujeevan Ratnasingham ◽  
Paul D. N. Hebert ◽  
Sarah J. Adamowicz
Keyword(s):  
High Throughput Sequencing ◽  
Dna Barcode ◽  
R Package ◽  
Error Rates ◽  
Real World Data ◽  
Species Discovery ◽  
Consensus Sequences ◽  
In Silico Studies ◽  
Coi Sequences

AbstractDNA barcoding and metabarcoding are now widely used to advance species discovery and biodiversity assessments. High-throughput sequencing (HTS) has expanded the volume and scope of these analyses, but elevated error rates introduce noise into sequence records that can inflate estimates of biodiversity. Denoising —the separation of biological signal from instrument (technical) noise—of barcode and metabarcode data currently employs abundance-based methods which do not capitalize on the highly conserved structure of the cytochrome c oxidase subunit I (COI) region employed as the animal barcode. This manuscript introduces debar, an R package that utilizes a profile hidden Markov model to denoise indel errors in COI sequences introduced by instrument error. In silico studies demonstrated that debar recognized 95% of artificially introduced indels in COI sequences. When applied to real-world data, debar reduced indel errors in circular consensus sequences obtained with the Sequel platform by 75%, and those generated on the Ion Torrent S5 by 94%. The false correction rate was less than 0.1%, indicating that debar is receptive to the majority of true COI variation in the animal kingdom. In conclusion, the debar package improves DNA barcode and metabarcode workflows by aiding the generation of more accurate sequences aiding the characterization of species diversity.

scholarly journals Composition and predictive functional analysis of bacterial communities in the surface seawater of the Changjiang Estuary

2017 ◽  
Author(s):  
Dong-Mei Wu ◽  
Jian-Xin Wang ◽  
Xiao-Hui Liu ◽  
Ying-Ping Fan ◽  
Ran Jiang ◽  
...  
Keyword(s):  
Dissolved Oxygen ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Carbon Fixation ◽  
Oxygen Demand ◽  
Environmental Parameters ◽  
Changjiang Estuary ◽  
Surface Seawater ◽  
The Changjiang Estuary

The objective of this study was to characterize the structure and function of microbial communities in surface seawater from the Changjiang Estuary and adjacent areas, China. Sample water was collected at 12 sites and environmental parameters were measured. Community structure was analyzed using high-throughput sequencing of 16S rDNA genes. Predictive metagenomic approach was used to predict the function of bacterial communities. Result showed that sample site A0102 had the highest bacterial abundance and diversity. The heatmap indicated that different samples could be clustered into six groups. Phylogenetic analysis showed that Proteobacteria was the predominant phylum in all samples, followed by Bacteroidetes and Actinobacteria. Alphaproteobacteria and Gammaproteobacteria were the dominant classes. The analysis of predictive metagenomic showed carbon fixation pathways in prokaryotes, nitrogen metabolism, carbon fixation in photosynthetic organisms, photosynthesis and polycyclic aromatic hydrocarbon degradation were enriched in all samples. Redundancy analysis (RDA) identified that dissolved oxygen (DO) and PO43– concentration had positive correlations with the bacterial communities while chemical oxygen demand (COD), dissolved oxygen (DO) and PO43– concentration were significantly associated with microbial functional diversity. This study adds to our knowledge of functional and taxonomic composition of microbial communities.

scholarly journals IEEE ITRW Working Group Position Paper-Packaging and Integration: Unlocking the Full Potential of Wide-Bandgap Devices

2018 ◽  
Vol 5 (2) ◽  
pp. 26-33 ◽  
Author(s):  
Mark Johnson ◽  
Peter R. Wilson ◽  
Lee Empringham ◽  
Liliana De Lillo
Keyword(s):  
Working Group ◽  
Wide Bandgap ◽  
Position Paper ◽  
Full Potential ◽  
Group Position

scholarly journals Fungal Community Analysis and Biodeterioration of Waterlogged Wooden Lacquerware from the Nanhai No. 1 Shipwreck

2020 ◽  
Vol 10 (11) ◽  
pp. 3797
Author(s):  
Yin Jia ◽  
Liuyu Yin ◽  
Fengyu Zhang ◽  
Mei Wang ◽  
Mingliang Sun ◽  
...  
Keyword(s):  
Fusarium Solani ◽  
High Throughput Sequencing ◽  
Environmental Parameters ◽  
Community Analysis ◽  
Fungal Species ◽  
Potato Dextrose Agar ◽  
Fungal Communities ◽  
Cellulolytic Enzymes ◽  
Biocidal Products

To avoid the lacquerware of the Nanhai No. 1 shipwreck from being corroded by microorganisms and to improve the knowledge on microbial ecology of the wood lacquers, we conducted a series of tests on the two water samples storing the lacquerware and colonies on the surface of the lacquerware. The high-throughput sequencing detected dominant fungal communities. After that, the fungal strains were isolated and then identified by amplification of ITS- 18S rRNA. Then the activity of ligninolytic and cellulolytic enzymes was detected on potato dextrose agar (PDA) plates with 0.04% (v/v) guaiacol and carboxymethyl cellulose (CMC) agar plates. Finally, we tested the biocide susceptibility of these fungi. Penicillium chrysogenum (NK-NH3) and Fusarium solani (NK- NH1) were the dominant fungi in the sample collected in April 2016 and June 2017. What is more, both showed activity of ligninolytic and cellulolytic enzymes. Four biocidal products (Preventol® D7, P91, BIT 20N, and Euxyl® K100) inhibited the growth of the fungal species in vitro effectively. In further research, the microbial community and environmental parameters in the museum should be monitored to assess the changes in the community and to detect potential microbial outbreaks.

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