scholarly journals Protocols for assessing the distribution of pathogens in individual Hymenopteran pollinators

2021 ◽  
Author(s):  
Joachim R de Miranda ◽  
Ivan Meeus ◽  
Orlando Yañez ◽  
Niels Piot ◽  
Laura Jara ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Species Identification ◽  
Pathogen Detection ◽  
Sample Processing ◽  
Raw Data ◽  
Cost Action ◽  
The Cost ◽  
Bee Decline ◽  
Positive Controls ◽  
Key Innovations

Abstract This protocol was developed for the COST-Action “Super-B”, whose purpose was to coordinate research, outreach and policy towards sustainable pollination1-3. The protocol addresses the detection of parasites and pathogens across bee species, as one of several possible drivers of bee decline4,5. It consists of four major components:1. A sample collecting protocol, based around a dominant bee species driving pathogen distribution among other bee species2. A sample processing protocol, based on analyzing nucleic acids from individual bees3. A pathogen detection protocol, based on RT-qPCR with broad-range primers for several common pathogens4. A barcoding protocol, for accurate bee species identification The protocols have largely been adapted from existing knowledge and protocols but also include two key innovations: the use of passive reference nucleic acids and synthetic positive controls, that significantly improve the quality and robustness of the raw data, and thus the reliability of the analyses and conclusions.

scholarly journals Visual multiple cross displacement amplification for the rapid identification of S. agalactiae immediately from vaginal and rectal swabs

AMB Express ◽  
2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Xueqin Cheng ◽  
Zhiqian Dou ◽  
Jing Yang ◽  
Dexi Liu ◽  
Yulong Gu ◽  
...  
Keyword(s):  
Pathogen Detection ◽  
Clinical Specimen ◽  
Rapid Identification ◽  
Sample Collection ◽  
Special Equipment ◽  
Multiple Cross ◽  
Rectal Swabs ◽  
Cost Efficient ◽  
The Cost ◽  
Positive Results

AbstractStreptococcus agalactiae (S. agalactiae) is an important pathogen that can lead to neonatus and mother infection. The current existing techniques for the identification of S. agalactiae are limited by accuracy, speed and high-cost. Therefore, a new multiple cross displacement amplification (MCDA) assay was developed for test of the target pathogen immediately from vaginal and rectal swabs. MCDA primers screening were conducted targeting S. agalactiae pcsB gene, and one set of MCDA primers with better rapidity and efficiency was selected for establishing the S. agalactiae-MCDA assay. As a result, the MCDA method could be completed at a constant temperature of 61 °C, without the requirement of special equipment. The detection limit is 250 fg (31.5 copies) per reaction, all S. agalactiae strains displayed positive results, but not for non-S. agalactiae strains. The visual MCDA assay detected 16 positive samples from 200 clinical specimen, which were also detected positive by enrichment/qPCR. While the CHROMagar culture detected 6 positive samples. Thus, the MCDA assay is prefer to enrichment/qPCR and culture for detecting S. agalactiae from clinical specimen. Particularly, the whole test of MCDA takes about 63.1 min, including sample collection (3 min), DNA preparation (15 min), MCDA reaction (45 min) and result reporting (6 s). In addition, the cost was very economic, with only US$ 4.9. These results indicated that our S. agalaciae-MCDA assay is a rapid, sensitive and cost-efficient technique for target pathogen detection, and is more suitable than conventional assays for an urgent detection, especially for 'on-site' laboratories and resource-constrained settings.

scholarly journals Current Perspectives on High-Throughput Sequencing (HTS) for Adventitious Virus Detection: Upstream Sample Processing and Library Preparation

Viruses ◽  
2018 ◽  
Vol 10 (10) ◽  
pp. 566 ◽  
Author(s):  
Siemon Ng ◽  
Cassandra Braxton ◽  
Marc Eloit ◽  
Szi Feng ◽  
Romain Fragnoud ◽  
...  
Keyword(s):  
Sample Preparation ◽  
Nucleic Acids ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Virus Detection ◽  
Extraction Methods ◽  
Control Measures ◽  
Acid Extraction ◽  
Library Preparation ◽  
Sample Processing

A key step for broad viral detection using high-throughput sequencing (HTS) is optimizing the sample preparation strategy for extracting viral-specific nucleic acids since viral genomes are diverse: They can be single-stranded or double-stranded RNA or DNA, and can vary from a few thousand bases to over millions of bases, which might introduce biases during nucleic acid extraction. In addition, viral particles can be enveloped or non-enveloped with variable resistance to pre-treatment, which may influence their susceptibility to extraction procedures. Since the identity of the potential adventitious agents is unknown prior to their detection, efficient sample preparation should be unbiased toward all different viral types in order to maximize the probability of detecting any potential adventitious viruses using HTS. Furthermore, the quality assessment of each step for sample processing is also a critical but challenging aspect. This paper presents our current perspectives for optimizing upstream sample processing and library preparation as part of the discussion in the Advanced Virus Detection Technologies Interest group (AVDTIG). The topics include: Use of nuclease treatment to enrich for encapsidated nucleic acids, techniques for amplifying low amounts of virus nucleic acids, selection of different extraction methods, relevant controls, the use of spike recovery experiments, and quality control measures during library preparation.

Quality control plan for road bridges – overview of COST Action TU1406 WG3 final report

2019 ◽  
Author(s):  
Matej Kušar ◽  
Poul Linneberg ◽  
Joao Amado ◽  
Snežana Mašović ◽  
Nikola Tanasić ◽  
...  
Keyword(s):  
Quality Control ◽  
Failure Modes ◽  
Final Report ◽  
Control Plan ◽  
Cost Action ◽  
Working Groups ◽  
Group 3 ◽  
Arch Bridges ◽  
The Cost ◽  
Damage Processes

<p>The main objective of the COST Action TU1406 is to develop a guideline for the establishment of Quality Control plans for roadway bridges. The guideline is based on conclusions of Working groups 1 and 2 of the Action and is further developed with the contributions and findings of members of Working group 3. The paper presents the overview of the developed framework, where gradual damage processes as well as sudden events are being addressed in evaluation of Key Performance Indicators. The proposed framework relies on data from design and construction phase, as well as from results from visual inspections that are used for an assessment of safety and serviceability - the primary concerns of bridge managers. Special attention is aimed at possible Failure modes and related bridge Vulnerable zones. These are, for instance high moment regions, high shear regions and constructions joints, but can also be zones of bridge conceptual weaknesses. Since there are differences in design and materials for various bridge types, the suitability of the framework is tested separately for girder/frame bridges and arch bridges. Due to the specifics of sudden events, the application of the framework is given separately from gradual damage processes. Emphasis is given on flooding and scour as these are the most common culprits of bridge failures. The steps in the implementation of the framework are briefly shown and an illustrative example is presented.</p>

Challenges of Semantic 3D City Models

2015 ◽  
Vol 4 (2) ◽  
pp. 68-76 ◽  
Author(s):  
Roland Billen ◽  
Anne-Françoise Cutting-Decelle ◽  
Claudine Métral ◽  
Gilles Falquet ◽  
Sisi Zlatanova ◽  
...  
Keyword(s):  
Urban Development ◽  
Sustainable Urban Development ◽  
Cost Action ◽  
3D City Models ◽  
Semantic Enrichment ◽  
Technical Paper ◽  
Information Models ◽  
Urban Models ◽  
The Cost ◽  
City Models

This technical paper is a contribution to the identification of current challenges of semantic 3D city models. They are presented in four parts, namely 3D enriched city models and their connection with urban information models and smartcities, urban models integration, urban analyses and data. This work is an output of the COST Action TU0801 “Semantic Enrichment of 3D city models for sustainable urban development”.

scholarly journals Targeted Enrichment for Pathogen Detection and Characterization in Three Felid Species

2017 ◽  
Vol 55 (6) ◽  
pp. 1658-1670 ◽  
Author(s):  
Justin S. Lee ◽  
Ryan S. Mackie ◽  
Thomas Harrison ◽  
Basir Shariat ◽  
Trey Kind ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Pathogen Detection ◽  
Clinical Samples ◽  
Complex Samples ◽  
Diagnostic Assays ◽  
Subspecies Level ◽  
Low Copy Number ◽  
Limited Application ◽  
Pathogen Characterization ◽  
Next Generation Sequencing Ngs

ABSTRACT Traditional diagnostic assays often lack sensitivity and can be difficult to multiplex across many pathogens. Next-generation sequencing (NGS) can overcome some of these problems but has limited application in the detection of low-copy-number pathogens in complex samples. Targeted genome capture (TGC) utilizes oligonucleotide probes to enrich specific nucleic acids in heterogeneous extracts and can therefore increase the proportion of NGS reads for low-abundance targets. While earlier studies have demonstrated the utility of this technology for detection of novel pathogens in human clinical samples, the capacity and practicality of TGC-NGS in a veterinary diagnostic setting have not yet been evaluated. Here we report the use of TGC-NGS assays for the detection and characterization of diverse feline pathogen taxa. We detected 31 pathogens comprising nine pathogen taxa in 28 felid samples analyzed. This included 20 pathogens detected via traditional PCR and 11 additional pathogens that had not been previously detected in the same samples. Most of the pathogens detected were sequenced at sufficient breadth and depth to confidently classify them at the species or subspecies level. Target nucleic acids were enriched from a low of 58-fold to 56 million-fold relative to host nucleic acids. Despite the promising performance of these assays, a number of pathogens detected by conventional PCR or serology were not isolated by TGC-NGS, suggesting that further validation is required before this technology can be used in lieu of quality-controlled standard assays. We conclude that TGC-NGS offers great potential as a broad multiplex pathogen characterization assay in veterinary diagnostic and research settings.

Ambient seismic noise suppression in COST action G2Net

2020 ◽  
Author(s):  
Velimir Ilić ◽  
Alessandro Bertolini ◽  
Fabio Bonsignorio ◽  
Dario Jozinović ◽  
Tomasz Bulik ◽  
...  
Keyword(s):  
Machine Learning ◽  
Gravitational Waves ◽  
Seismic Noise ◽  
Noise Suppression ◽  
Real Life ◽  
Low Frequency ◽  
Ambient Seismic Noise ◽  
Cost Action ◽  
The Cost ◽  
Life Challenge

&lt;p&gt;The analysis of low-frequency gravitational waves (GW) data is a crucial mission of GW science and the performance of Earth-based GW detectors is largely influenced by ability of combating the low-frequency ambient seismic noise and other seismic influences. This tasks require multidisciplinary research in the fields of seismic sensing, signal processing, robotics, machine learning and mathematical modeling.&lt;br&gt;&lt;br&gt;In practice, this kind of research is conducted by large teams of researchers with different expertise, so that project management emerges as an important real life challenge in the projects for acquisition, processing and interpretation of seismic data from GW detector site. A prominent example that successfully deals with this aspect could be observed in the COST Action G2Net (CA17137 - A network for Gravitational Waves, Geophysics and Machine Learning) and its seismic research group, which counts more than 30 members.&amp;#160;&lt;/p&gt;&lt;div&gt;In this talk we will review the structure of the group, present the goals and recent activities of the group, and present new methods for combating the seismic influences at GW detector site that will be developed and applied within this collaboration.&lt;/div&gt;&lt;div&gt; &lt;p&gt;&amp;#160;&lt;/p&gt; &lt;p&gt;This publication is based upon work from CA17137 - A network for Gravitational Waves, Geophysics and Machine Learning, supported by COST (European Cooperation in Science and Technology).&lt;/p&gt; &lt;/div&gt;

Perspectives for Planning Approaches in Promoting Underground Built Heritage - COST Action Underground4value

2020 ◽  
Author(s):  
Carlos Smaniotto Costa ◽  
Tatiana Ruchinskaya ◽  
Konstantinos Lalenis
Keyword(s):  
Local Level ◽  
Collaborative Relationships ◽  
Cost Action ◽  
The Public ◽  
Built Heritage ◽  
Educational Paradigm ◽  
The One ◽  
The Cost ◽  
Planning Approaches

&lt;p&gt;The COST Action 18110 Underground4value (http://underground4value.eu) aims to advance knowledge on how to guarantee continuity of use and significance of underground historic fabric. It is collecting information, experiences and knowhow to base the development of research and training. The Action focusses on underground regeneration, revitalisation of the public realm and skills development for people concerned with underground heritage.&lt;/p&gt;&lt;p&gt;This contribution centres the attention of the Working Group on Planning Approaches. It also looks at the role of local authorities, as enablers and facilitators, in coordination, use &amp;#160;and management of underground built heritage. In this framework underground built heritage is considered as a social resource with integrated programmes of physical, economic and social measures, backed by strategic stakeholder dialogue.&lt;/p&gt;&lt;p&gt;On the one hand, this contribution discusses the structure and goals of the WG, as it pays attention to the necessary complementarities between functional approaches &amp;#8211; at the level of regions and city &amp;#8211; and social and cultural approaches involving citizens&amp;#8217; engagement and empowerment &amp;#8211; at the local level. This WG aims to provide a reflection on sustainable approaches to preserve the underground built heritage and, at the same time, to unfold the case by case approach for potential use of underground space. On the other hand, to achieve its objectives the WG on Planning Approaches is setting together potentials and constraints in the efforts to make better use of underground heritage. This contribution, therefore, sheds lights on the preliminary results of the WG. It is centred on the learned lessons, challenges and barriers - from a planning science perspective - that experts met in their efforts to tackle Underground Built Heritage. Achieving this goal makes the call for an educational paradigm shift - as the Action is not only interested in compiling the results, rather on experiences that can be analysed and learned. This requires a dynamic understanding of knowledge, abilities and skills, towards creating more effective coalitions of &amp;#8216;actors&amp;#8217; within localities, by developing structures, which encourage long term collaborative relationships. Enabled by the gained knowledge, the WG will define the best tailored ways to forward this knowledge for planners and decision-makers.&lt;/p&gt;

Nanosafety forum for young scientists: a meeting report

2015 ◽  
Vol 7 (3) ◽  
Author(s):  
Antonio Pietroiusti ◽  
Lang Tran ◽  
Luisa Campagnolo
Keyword(s):  
Meeting Report ◽  
Cost Action ◽  
Working Groups ◽  
The Cost ◽  
Young Researchers ◽  
The Eu

AbstractIn October of 2014, a meeting jointly organized by the EU Nanosafety Cluster and the COST Action TD 1204, was held on the beautiful island of Ortygia in Syracuse (Sicily). The meeting was specifically conceived to give the opportunity to young researchers in the field of nanotoxicology to present and discuss the results of their research. Presentations were divided into eight sessions over 2 days, reflecting the eight working groups of the Nanosafety Cluster. This report gives a description of the meeting activities and a summary of the data presented there.

scholarly journals Differences in codon bias and GC content contribute to the balanced expression of TLR7 and TLR9

2016 ◽  
Vol 113 (10) ◽  
pp. E1362-E1371 ◽  
Author(s):  
Zachary R. Newman ◽  
Janet M. Young ◽  
Nicholas T. Ingolia ◽  
Gregory M. Barton
Keyword(s):  
Nucleic Acids ◽  
Codon Bias ◽  
Codon Optimization ◽  
Immune Surveillance ◽  
Gc Content ◽  
Surveillance Strategy ◽  
Protein Levels ◽  
Low Levels ◽  
The Cost ◽  
Control Of Expression

The innate immune system detects diverse microbial species with a limited repertoire of immune receptors that recognize nucleic acids. The cost of this immune surveillance strategy is the potential for inappropriate recognition of self-derived nucleic acids and subsequent autoimmune disease. The relative expression of two closely related receptors, Toll-like receptor (TLR) 7 and TLR9, is balanced to allow recognition of microbial nucleic acids while limiting recognition of self-derived nucleic acids. Situations that tilt this balance toward TLR7 promote inappropriate responses, including autoimmunity; therefore, tight control of expression is critical for proper homeostasis. Here we report that differences in codon bias limit TLR7 expression relative to TLR9. Codon optimization of Tlr7 increases protein levels as well as responses to ligands, but, unexpectedly, these changes only modestly affect translation. Instead, we find that much of the benefit attributed to codon optimization is actually the result of enhanced transcription. Our findings, together with other recent examples, challenge the dogma that codon optimization primarily increases translation. We propose that suboptimal codon bias, which correlates with low guanine-cytosine (GC) content, limits transcription of certain genes. This mechanism may establish low levels of proteins whose overexpression leads to particularly deleterious effects, such as TLR7.

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