scholarly journals A user guide to environmental protistology: primers, metabarcoding, sequencing, and analyses

2019 ◽  
Author(s):  
Stefan Geisen ◽  
Daniel Vaulot ◽  
Frédéric Mahé ◽  
Enrique Lara ◽  
Colomban de Vargas ◽  
...  
Keyword(s):  
Cost Efficiency ◽  
Major Part ◽  
High Throughput Sequencing ◽  
Ecosystem Processes ◽  
Universal Primers ◽  
Ecological Research ◽  
Ecological Studies ◽  
Great Cost ◽  
Molecular Approaches ◽  
Near Future

AbstractProtists – all eukaryotes besides fungi, animals, and plants - represent a major part of the taxonomic and functional diversity of eukaryotic life on the planet and drive many ecosystem processes. However, knowledge of protist communities and their diversity lags behind that of most other groups of organisms, largely due to methodological constraints. While protist communities differ markedly between habitats and biomes, they can be studied in very similar ways. Here we provide a guide to current molecular approaches used for studying protist diversity, with a particular focus on amplicon-based high-throughput sequencing (metabarcoding). We highlight that the choice of suitable primers artificially alters community profiles observed in metabarcoding studies. While there are no true ‘universal’ primers to target all protist taxa as a whole, we identify some primer combinations with a wide taxonomic coverage and provide detailed information on their properties. Although environmental protistan ecological research will probably shift towards PCR-free metagenomics or/and transcriptomic approaches in a near future, metabarcoding will remain the method of choice for in-depth community analyses and taxon inventories in biodiversity surveys and ecological studies, due its great cost-efficiency, sensitivity, and throughput. In this paper we provide a guide for scientists from a broad range of disciplines to implement protists in their ecological analyses.

scholarly journals PSV-37 Reemergence of cyathostomins species demonstrates anthelmintic resistance following drug administration in horses

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 335-335
Author(s):  
Alexa C Johnson ◽  
Amy S Biddle
Keyword(s):  
Anthelmintic Resistance ◽  
Macrocyclic Lactones ◽  
Number Of Species ◽  
Molecular Approaches ◽  
Pyrantel Pamoate ◽  
Drug Classes ◽  
Blast Database ◽  
Resistance Patterns ◽  
Near Future ◽  
Ncbi Blast

Abstract Arbitrary administration of anthelmintics to control equine gastrointestinal worms has led to increased resistance to the three broad-spectrum drug classes; benzimidazoles, tetrahydropyrimidines, and macrocyclic lactones. With little promise of new drug classes to target cyathostomins being introduced to the market in the near future, anthelmintic drugs must be administered judiciously to prevent complete anthelmintic parasite resistance. The objective of this study is to determine the reemergence rate of cyathostomins following three commercial horse dewormers during summer. Nine horses housed at two locations were enrolled to the study and was repeated June–September through 2017–2019. Horses were removed from the study if sequencing failed due to low egg recovery for more than 50% of the timepoints. Ivermectin (macrocyclic lactones; n = 6), Moxidectin (macrocyclic lactones; n = 8) and Strongid (pyrantel pamoate; n = 8) were administered to horses and fecal samples were collected every 14d for 98d. Samples were tested using fecal egg counts with a modified McMaster technique and 18S rRNA profiling of the V5.8 and ITS1 regions. Sequences were clustered and taxonomy was assigned against a custom NCBI Blast+ database with the aligned sequences of 19 cyathostomins. Data were analyzed using presence/absence methods in R studio. Treatment and Day significantly impacted the average number of species present (P < 0.001). Moxidectin had the lowest number of species present followed by Strongid then Ivermectin (7.14, 10.17, 11.09, respectively). Equine shedder status had no effect on the average number of species present (P > 0.05). Six species, CO. labiatus, CS. catinatum, CY. auriculatus, CY. elongatus, CT. goldi and CT. longibursatus, showed resistance to the three treatments (P > 0.05). Moxidectin was the most effective at eradicating cyathostomins infestations (P < 0.05). Identifying resistance patterns at the species level will enable mechanistic molecular approaches to determine anthelmintic resistance in cyathostomins.

scholarly journals Health Information Accessed on the Internet: The Development in 5 European Countries

2012 ◽  
Vol 2012 ◽  
pp. 1-3 ◽  
Author(s):  
Per Egil Kummervold ◽  
Rolf Wynn
Keyword(s):  
Health Information ◽  
Major Part ◽  
Information Access ◽  
European Countries ◽  
Northern Europe ◽  
The Internet ◽  
Continuous Growth ◽  
Media Source ◽  
Use Of The Internet ◽  
Near Future

The aim of this study was to summarize and analyse findings from four prior studies on the use of the Internet as a source of health information in five European countries (Norway, Denmark, Germany, Greece, and Portugal). A cross-study comparison of data was performed. All the studies included fit with a trend of a sharp and continuous growth in the use of the Internet for health information access in the major part of the last decade. Importantly, the Internet has become an important mass media source of health information in northern Europe. While the use of the Internet for health information is somewhat less common in the south European countries, its use is also clearly increasing there. We discuss the advantages of cross-study comparisons of data and methodological challenges. As the use of the Internet for health information is likely to peak in some countries in the near future, new population surveys on health information access should focus more on the details of information that is accessed and which sites that are most used and trusted.

Ecological Research for Studies of Violence: A Methodological Guide

2019 ◽  
Vol 34 (23-24) ◽  
pp. 4860-4880
Author(s):  
April M. Zeoli ◽  
Jennifer K. Paruk ◽  
Jesenia M. Pizarro ◽  
Jason Goldstick
Keyword(s):  
Research Question ◽  
Population Level ◽  
Ecological Research ◽  
Ecological Studies ◽  
Individual Level ◽  
Research Guidelines ◽  
Units Of Analysis ◽  
Research Designs ◽  
Ecological Unit ◽  
Existing Data

Ecological research is important to the study of violence in communities. The phrases “ecological research” and “ecologic study” describe those research studies that use grouped or geographic units of analysis, such as zip codes, cities, or states. This type of research allows for the investigation of group-level effects and can be inexpensive and relatively quick to conduct if the researcher uses existing data. And, importantly, ecological studies are an efficient means for hypothesis generation prior to, and can be used to justify, costlier individual-level studies. Ecological research designs may be employed to study violence outcomes when the research question is at the population level, either for theoretical reasons, or when an exposure or intervention is at the population level, or when individual-level studies are not feasible; however, ecological research results must not be used to make individual-level inferences. This article will discuss reasons to conduct ecological-level research, guidelines for choosing the ecological unit of analysis, frequently used research designs, common limitations of ecological research, including the ecological fallacy, and issues to consider when using existing data.

scholarly journals A49 Emerging rodent-borne viral pathogens in Italy: Overview of seroprevalence and genomic investigations

2019 ◽  
Vol 5 (Supplement_1) ◽  
Author(s):  
N Alfano ◽  
V Tagliapietra ◽  
D Arnoldi ◽  
F Rosso ◽  
C Rossi ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Rna Viruses ◽  
Case Fatality ◽  
Lymphocytic Choriomeningitis ◽  
Immunofluorescence Assay ◽  
Sudden Increase ◽  
Viral Pathogens ◽  
Molecular Approaches ◽  
Northeastern Italy

Abstract Rodents play a key role as reservoirs of many zoonotic pathogens which represent an emerging public health threat worldwide. Among these, Dobrava-Belgrade virus (DOBV) is the most pathogenic hantavirus in Europe with a case-fatality rate of up to 12 per cent, while Lymphocytic choriomeningitis virus (LCMV) has a mortality rate below 1 per cent. Both viruses are predominantly transmitted to humans through the inhalation of infected particles in aerosolized urine, feces, or saliva that are shed in the environment by chronically infected hosts, such as the yellow-necked mouse Apodemus flavicollis. Although no human cases of DOBV or LCMV have been reported in the Province of Trento (northeastern Italy) thus far, in order to evaluate the human hazard for these viruses, the prevalence of antibodies to DOBV and LCMV has been monitored using a specific immunofluorescence assay test in a wild population of A. flavicollis since 2000. These investigations have shown that the two RNA viruses circulate silently in this species in the study area. In particular, a sudden increase (up to 12.5%) in DOBV seroprevalence was observed in this rodent species between 2010 and 2012. Several efforts have been undertaken to isolate these viruses and characterize their genomes, but it has not yet been possible to detect viral RNA from seropositive mice using traditional methods such as RT-PCR. Since RNA viruses are very diverse and often difficult to isolate, innovative molecular methods based on viral targeted enrichment and high-throughput sequencing have been applied. We intend to report on this long-term seroprevalence study and provide an overview of the molecular approaches adopted in the attempt to confirm the presence of these viruses, and identify which variants are circulating in the region, as well as their pathogenicity.

scholarly journals Current Status and Future Perspective on Enzyme Involving in Biocontrol of Plant Pathogen

2021 ◽  
Vol 8 (4) ◽  
Author(s):  
Ami Chaudhari ◽  
Jesal Patel
Keyword(s):  
Crop Yield ◽  
Plant Diseases ◽  
Current Status ◽  
Future Perspective ◽  
Lytic Enzymes ◽  
Molecular Approaches ◽  
Yield And Quality ◽  
And Control ◽  
Near Future ◽  
Rhizosphere Microorganism

To sustain the quality and abundance of fruit, feed and fiber provided by farmers all over the world, plant diseases must be regulated. Plant diseases may be prevented, mitigated, or regulated using a variety of methods. Growers also rely on chemical fertilizers and pesticides for good agronomic and horticultural practices. Such agricultural inputs have taken a vital part in spectacular increases in crop yield and quality over the last 100 years. Microbial enzymes function as biocatalysts for key biochemical reactions and also assist microbes reproduce in a particular niche. The ability of rhizosphere microorganism to increase the growth of plant and control phytopathogens has long been known. Rhizosphere microbes may aid plants in several ways in their fight against phytopathogens. Of all recognized biocontrol pathways, the excretion of lytic enzymes is known as an important way to prevent phytopathogens from living in the region of the rhizosphere. Rhizosphere microorganism produces chitinases, cellulases, proteases, and glucanases in reaction to phytopathogen assault. For assessing antagonist-pathogen interactions, ecological characteristics of antagonists in the rhizosphere, and optimizing the effectiveness of bacterial, fungal, and viral biocontrol agents, new molecular approaches have become available. Given the experience of fungicides in near future, biological management would be another method to control diseases of plant. Since agro-ecosystem is a flexible and functioning structure that involves many variables that affect disease and production of crop, other IPM methods to control diseases of crop are also important in different surrounding conditions. As result, to successfully minimize disease production and crop yield loss in various crop systems, other IPM management mechanisms other than biological control should be considered and implemented.

scholarly journals Identification of Awaous guamensis and A. grammepomus based on morphology and molecular analysis

2017 ◽  
Vol 26 (1) ◽  
pp. 83-90
Author(s):  
Hawa Jahan ◽  
Mehnus Tabassum ◽  
Gulshan Ara Latifa
Keyword(s):  
Sequence Data ◽  
Coi Gene ◽  
Universal Primers ◽  
Morphological Identification ◽  
Cytochrome Oxidase Subunit ◽  
Mitochondrial Cytochrome Oxidase Subunit ◽  
Specific Variation ◽  
Near Future ◽  
Mitochondrial Cytochrome Oxidase ◽  
Awaous Guamensis

Work on two freshwater Gobi fish species such as Awaous guamensis and A. grammepomus was carried out on morphometric and meristic study for their morphological identification. Sequence data of mitochondrial cytochrome oxidase subunit I (COI) gene was used for this purpose. Around 620 bp sequences were obtained when universal primers were used. An alignment was performed between the sequences which showed some inter-specific variation. An entropy plot was generated for all the aligned positions which showed that the entropy rarely touches a scale of one, which is a sign of better alignment in the region. This work can be utilized for species identification, phylogenetic analysis, to study molecular diversity and evolution, and most importantly for the conservation of these fauna in near future. Dhaka Univ. J. Biol. Sci. 26(1): 83-90, 2017 (January)

scholarly journals Trash or Treasure? Considerations for Future Ecological Research to Inform Oil and Gas Decommissioning

2021 ◽  
Vol 8 ◽  
Author(s):  
Marie-Lise Schläppy ◽  
Lucy M. Robinson ◽  
Victoria Camilieri-Asch ◽  
Karen Miller
Keyword(s):  
Structural Integrity ◽  
Oil And Gas ◽  
Complete Removal ◽  
Ecological Impacts ◽  
Ecological Knowledge ◽  
Ecological Research ◽  
Temporal Scales ◽  
Spatial And Temporal Scales ◽  
The Status ◽  
Near Future

Numerous oil and gas (O&G) installations worldwide will need to be decommissioned in the near future. Complete removal of subsea structures is often the default approach although some regions retain structures under rigs-to-reefs programs. Here, we reviewed the published literature to understand the status of global research on decommissioning, and specifically identify gaps in ecological knowledge. We estimated the frequency of different research categories (i.e., themes, and spatial/temporal scales), and tested the assumption that the number of papers across the categories of each research aspect was even in distribution. However, the frequency of studies focusing on biodiversity at a local (≤100 km2) scale (relative to regional and oceanic and pan-oceanic scales) were significantly higher; while other theme categories (e.g., eco-toxicology, connectivity, structural-integrity, restoration and other) were significantly lower than expected. Temporally, ≤1-year studies were more frequent than multi-year studies, but these frequencies did not significantly deviate from the assumed distribution of equal frequencies. We propose that further research be carried out to evaluate the benefits of both retention and removal of structures. Ecological research on decommissioning should extend its focus beyond biodiversity, to include eco-toxicology, structural-integrity, connectivity at larger spatial and temporal scales. This would provide a more holistic assessment of ecological impacts to inform sustainable and equitable development choices in multiple Blue Economy sectors, as we transition from offshore O&G to marine renewables.

scholarly journals Novel Universal Primers for Metabarcoding eDNA Surveys of Marine Mammals and Other Marine Vertebrates

2019 ◽  
Author(s):  
Elena Valsecchi ◽  
Jonas Bylemans ◽  
Simon J. Goodman ◽  
Roberto Lombardi ◽  
Ian Carr ◽  
...  
Keyword(s):  
Marine Mammals ◽  
High Throughput Sequencing ◽  
Environmental Dna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Taxonomic Resolution ◽  
Universal Primers ◽  
Marine Biodiversity ◽  
Primer Sets ◽  
Marine Megafauna

ABSTRACTMetabarcoding studies using environmental DNA (eDNA) and high throughput sequencing (HTS) are rapidly becoming an important tool for assessing and monitoring marine biodiversity, detecting invasive species, and supporting basic ecological research. Several barcode loci targeting teleost fish and elasmobranchs have previously been developed, but to date primer sets focusing on other marine megafauna, such as marine mammals have received less attention. Similarly, there have been few attempts to identify potentially ‘universal’ barcode loci which may be informative across multiple marine vertebrate Orders. Here we describe the design and validation of four new sets of primers targeting hypervariable regions of the vertebrate mitochondrial 12S and 16S rRNA genes, which have conserved priming sites across virtually all cetaceans, pinnipeds, elasmobranchs, boney fish, sea turtles and birds, and amplify fragments with consistently high levels of taxonomically diagnostic sequence variation. ‘In silico’ validation using the OBITOOLS software showed our new barcode loci outperformed most existing vertebrate barcode loci for taxon detection and resolution. We also evaluated sequence diversity and taxonomic resolution of the new barcode loci in 680 complete marine mammal mitochondrial genomes demonstrating that they are effective at resolving amplicons for most taxa to the species level. Finally, we evaluated the performance of the primer sets with eDNA samples from aquarium communities with known species composition. These new primers will potentially allow surveys of complete marine vertebrate communities in single HTS metabarcoding assessments, simplifying workflows, reducing costs, and increasing accessibility to a wider range of investigators.

scholarly journals The role of replication studies in ecology

2019 ◽  
Author(s):  
Hannah Fraser ◽  
Timothy H. Parker ◽  
Fiona Fidler ◽  
Ashley Barnett
Keyword(s):  
Large Scale ◽  
Limited Resources ◽  
Ecological Research ◽  
Ecological Studies ◽  
Median Response ◽  
Replication Studies

Recent large-scale projects in other disciplines have shown that results often fail to replicate when studies are repeated. The conditions contributing to this problem are also present in ecology but there have not been any equivalent replication projects. Here we examine ecologists’ understanding of and opinions about replication studies. When asked what percentage of ecological studies are replicated, the median response given by ecologists is 10%. The majority of ecologists in our sample considered replication studies to be important (97%), not prevalent enough (91%), worth funding even given limited resources (61%), and suitable for publication in all journals (62%). However, there is a disconnect between this enthusiasm and the prevalence of direct replication studies in the literature which, is much lower than our participants’ estimate of 10%. This may be explained by the obstacles our participants identified including the difficulty of conducting replication studies and of funding and publishing them. We conclude by offering suggestions for how replications could be better integrated into ecological research.

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