scholarly journals Sediment eDNA Metabarcoding for monitoring impacts from offshore oil extraction

2021 ◽  
Vol 4 ◽  
Author(s):  
Anders Lanzén ◽  
Jon Thomassen Hestetun ◽  
Andrea Bagi ◽  
Thomas Dahlgren
Keyword(s):  
Barents Sea ◽  
De Novo ◽  
Oil Extraction ◽  
Attractive Alternative ◽  
Accurate Information ◽  
Sensitivity Index ◽  
Biotic Indices ◽  
Anthropogenic Pressures ◽  
Minimum Criteria ◽  
Offshore Oil

Routine biological monitoring of the areas affected by offshore oil drilling and extraction is critical for ensuring proper environmental management. In addition to sufficient knowledge of the ecosystem affected, formalised e.g. as biotic indices of indicator species, adequate temporal and spatial resolution is also required, to provide accurate information. As already demonstrated in several types of environments, environmental DNA (eDNA) metabarcoding offers an attractive alternative to current morphology-based assessments, including for impacts of oil extraction or spills. We have recently studied the influence of different experimental strategies on the accuracy of marine sediment metabarcoding, suggesting minimum criteria for technical and spatial replication (Hestetun et al. 2020). Here, we aim to evaluate the predictive power of this strategy, through agreement with assessments based on physicochemical measurements and current bioindicators. To this end, we targeted the metazoan, and total eukaryotic benthic communities, using COI and 18S V1-V2 markers, respectively. Sampled sites ranged from high to low impacts. The studied areas were located near active production installations and reference sites on the Norwegian continental shelf, in the North Sea and Barents Sea. As a proxy for accumulated impact, we developed a simple physicochemical pressure index (PI) based on total hydrocarbons, PAH16, barium and copper, all of which agreed well with impact reported from recent routine monitoring. Alpha diversity of both molecular datasets, as well as of morphology data, correlated strongly with this PI. However, the correlation was stronger yet with the macroinvertebrate-based Norwegian Sensitivity Index (NSI) derived from COI metabarcoding data, which also agreed well with NSI values derived from morphology-based monitoring. We also identified a set of bioindicator taxa from each of the two metabarcoding datasets, used to develop two novel metabarcoding-based biotic indeces. Using cross-validation, we demonstrated that predictions based on these indeces agreed well with PI. Predictive performance was better, and similar to NSI, for the COI-based index, but also high for the 18S-based version. In conclusion, this study demonstrates how de novo biotic indices can be developed, that perform comparably to existing biotic indices. We are confident that, using a larger set of samples, performance can be improved beyond that of current monitoring practices. Thanks to the reduced costs of eDNA analysis in comparison to morphological identifiation, this would also pave the way for improved spatial and temporal resolution employed in routine environmental monitoring. In doing so, it can also provide valuable raw data for improving our understanding of benthic ecology, biodiversity and its sensitivity to anthropogenic pressures.

scholarly journals Disentangling LiDAR Contribution in Modelling Species–Habitat Structure Relationships in Terrestrial Ecosystems Worldwide. A Systematic Review and Future Directions

2021 ◽  
Vol 13 (17) ◽  
pp. 3447
Author(s):  
Pablo Acebes ◽  
Paula Lillo ◽  
Carlos Jaime-González
Keyword(s):  
Habitat Structure ◽  
Temperate Forest ◽  
Canopy Cover ◽  
Terrestrial Ecosystems ◽  
Accurate Information ◽  
Ecosystem Structure ◽  
Anthropogenic Pressures ◽  
Future Directions ◽  
Taxonomic Groups ◽  
Biodiversity Mapping

Global biodiversity is threatened by unprecedented and increasing anthropogenic pressures, including habitat loss and fragmentation. LiDAR can become a decisive technology by providing accurate information about the linkages between biodiversity and ecosystem structure. Here, we review the current use of LiDAR metrics in ecological studies regarding birds, mammals, reptiles, amphibians, invertebrates, bryophytes, lichens, and fungi (BLF). We quantify the types of research (ecosystem and LiDAR sources) and describe the LiDAR platforms and data that are currently available. We also categorize and harmonize LiDAR metrics into five LiDAR morphological traits (canopy cover, height and vertical distribution, understory and shrubland, and topographic traits) and quantify their current use and effectiveness across taxonomic groups and ecosystems. The literature review returned 173 papers that met our criteria. Europe and North America held most of the studies, and birds were the most studied group, whereas temperate forest was by far the most represented ecosystem. Globally, canopy height was the most used LiDAR trait, especially in forest ecosystems, whereas canopy cover and terrain topography traits performed better in those ecosystems where they were mapped. Understory structure and shrubland traits together with terrain topography showed high effectiveness for less studied groups such as BLF and invertebrates and in open landscapes. Our results show how LiDAR technology has greatly contributed to habitat mapping, including organisms poorly studied until recently, such as BLF. Finally, we discuss the forthcoming opportunities for biodiversity mapping with different LiDAR platforms in combination with spectral information. We advocate (i) for the integration of spaceborne LiDAR data with the already available airborne (airplane, drones) and terrestrial technology, and (ii) the coupling of it with multispectral/hyperspectral information, which will allow for the exploration and analyses of new species and ecosystems.

A Cost-Driven, High-Level Optimization of OSV Operations in the Flemish Pass

2018 ◽  
Author(s):  
Philippe Gauthier ◽  
David Molyneux
Keyword(s):  
Programming Model ◽  
Oil Extraction ◽  
Non Linear Programming ◽  
Non Linear ◽  
High Level ◽  
Non Linear System ◽  
Offshore Oil ◽  
The Impact ◽  
Pareto Frontiers ◽  
Made In

This paper presents a cost driven, high-level optimization of Offshore Supply Vessel (OSV) operations in the Flemish Pass sector. This is an area located in the offshore waters of Newfoundland where significant oil discoveries were made in recent years, but where oil extraction will pose logistical challenges due to the increased distance from shore bases. In the first part of this paper, a simple non-linear programming model is used to minimize the monthly costs to supply a hypothetical offshore oil installation located in the Flemish Pass and to assess whether hypothetical fast supply vessels make economic sense. The second part of this paper explores the application of Pareto frontiers to the non-linear system, to evaluate the impact of schedule slack on costs, but also to look at winter operations in the Flemish Pass area.

scholarly journals Drug Coated Balloon-Only Strategy in De Novo Lesions of Large Coronary Vessels

2019 ◽  
Vol 2019 ◽  
pp. 1-8 ◽  
Author(s):  
Mark Rosenberg ◽  
Matthias Waliszewski ◽  
Florian Krackhardt ◽  
Kenneth Chin ◽  
Wan Azman Wan Ahmad ◽  
...  
Keyword(s):  
Coronary Arteries ◽  
De Novo ◽  
Small Vessel Disease ◽  
Coronary Vessels ◽  
Large Vessel ◽  
Attractive Alternative ◽  
Interventional Treatment ◽  
Vessel Disease ◽  
Large Coronary Arteries ◽  
Large Vessels

Objectives. We analyzed the efficacy of drug coated balloons (DCB) as a stand-alone-therapy in de novo lesions of large coronary arteries. DCBs seem to be an attractive alternative for the stent-free interventional treatment of de novo coronary artery disease (CAD). However, data regarding a DCB-only approach in de novo CAD are currently limited to vessels of small caliber. Methods. By means of propensity score (PS) matching 234 individuals with de novo CAD were identified with similar demographic characteristics. This patient population was stratified in a 1:1 fashion according to a reference vessel diameter cut-off of 2.75 mm in small and large vessel disease. The primary endpoint was the rate of clinically driven target lesion revascularization (TLR) at 9 months. Results. Patients with small vessel disease had an average reference diameter of 2.45 ± 0.23 mm, while the large vessel group averaged 3.16 ± 0.27 mm. Regarding 9-month major adverse cardiac event (MACE), 5.7% of the patients with small and 6.1% of the patients with large vessels had MACE (p=0.903). Analysis of the individual MACE components revealed a TLR rate of 3.8% in small and 1.0% in large vessels (p=0.200). Of note, no thrombotic events in the DCB treated coronary segments occurred in either group during the 9-month follow-up. Conclusions. Our data demonstrate for the first time that DCB-only PCI of de novo lesions in large coronary arteries (>2.75 mm) is safe and as effective. Interventional treatment for CAD without permanent or temporary scaffolding, demonstrated a similar efficacy for large and small vessels.

Ability of phytoplankton trait sensitivity to highlight anthropogenic pressures in Mediterranean lagoons: A size spectra sensitivity index (ISS-phyto)

2013 ◽  
Vol 34 ◽  
pp. 113-125 ◽  
Author(s):  
Maria Rosaria Vadrucci ◽  
Elena Stanca ◽  
Cristina Mazziotti ◽  
Serena Fonda Umani ◽  
Assimakopoulou Georgia ◽  
...  
Keyword(s):  
Sensitivity Index ◽  
Anthropogenic Pressures ◽  
Size Spectra ◽  
Mediterranean Lagoons

scholarly journals DiaThor: R package for computing diatom metrics and biotic indices

2021 ◽  
Author(s):  
Maria Mercedes Nicolosi Gelis ◽  
Maria Belen Sathicq ◽  
Jonathan Jupke ◽  
Joaquin Cochero
Keyword(s):  
Water Quality ◽  
Web Application ◽  
Water Quality Assessment ◽  
R Package ◽  
Morphological Data ◽  
Sensitivity Index ◽  
Biotic Indices ◽  
Ecological Data ◽  
Diatom Index ◽  
Open Platform

1- Diatoms are widely used to detect changes in water quality due to their specific sensibility to a variety of environmental conditions. Among the different diatom-based tools to measure water quality, the biotic indices, ecological and morphological traits are the most commonly used. 2- DiaThor, contains 19 functions that provide morphological data of the samples (number and shape of chloroplasts, total biovolume), ecological data (species richness, evenness, diversity, size classes, ecological guilds, ecological preferences) and biotic indices (Descy Index, EPID Index, Indice Diatomique Artois-Picardie, Swiss Diatom Index, Pampean Diatom Index, ILM index, Specific Pollution sensitivity Index, Lobo Index, Sladecek index, SPEAR(herbicides) index and the Trophic index). A web application (in Shiny) was also developed to provide access to the package for those users not familiar with the R environment. 3- The structure of the package, how it functions and the structure of the input and output data are explained. To demonstrate the most common use of DiaThor, an example of the package performance is also provided. 4- The DiaThor package aims to contribute to the water quality assessment based on diatom assemblages, while also providing researchers with an open platform to suggest new statistics and functionalities to be integrated into future builds.

scholarly journals DEVELOPING AN EMERGENCY RESPONSE MODEL FOR OFFSHORE OIL SPILL DISASTER MANAGEMENT USING SPATIAL DECISION SUPPORT SYSTEM (SDSS)

2018 ◽  
Vol IV-3 ◽  
pp. 21-27 ◽  
Author(s):  
Abdul-Lateef Balogun ◽  
Abdul-Nasir Matori ◽  
Kelvin Wong Toh Kiak
Keyword(s):  
Decision Support ◽  
Decision Support System ◽  
Emergency Response ◽  
Oil Spill ◽  
Support System ◽  
Sensitivity Index ◽  
Spatial Decision Support System ◽  
Spatial Decision Support ◽  
Environmental Sensitivity ◽  
Offshore Oil

Environmental resources face severe risks during offshore oil spill disasters and Geographic Information System (GIS) Environmental Sensitivity Index (ESI) maps are increasingly being used as response tools to minimize the huge impacts of these spills. However, ESI maps are generally unable to independently harmonize the diverse preferences of the multiple stakeholders’ involved in the response process, causing rancour and delay in response time. This paper’s Spatial Decision Support System (SDSS) utilizes the Analytic Hierarchy Process (AHP) model to perform tradeoffs in determining the most significant resources to be secured considering the limited resources and time available to perform the response operation. The AHP approach is used to aggregate the diverse preferences of the stakeholders and reach a consensus. These preferences, represented as priority weights, are incorporated in a GIS platform to generate Environmental sensitivity risk (ESR) maps. The ESR maps provide a common operational platform and consistent situational awareness for the multiple parties involved in the emergency response operation thereby minimizing discord among the response teams and saving the most valuable resources.

scholarly journals New Technologies and Strategies for Grapevine Breeding Through Genetic Transformation

2021 ◽  
Vol 12 ◽  
Author(s):  
Gabriela Campos ◽  
Constanza Chialva ◽  
Silvana Miras ◽  
Diego Lijavetzky
Keyword(s):  
Tissue Culture ◽  
Transgenic Plants ◽  
Genetic Transformation ◽  
New Technologies ◽  
De Novo ◽  
Culture Media ◽  
Ectopic Expression ◽  
Attractive Alternative ◽  
Culture Methods ◽  
Woody Perennials

Grapevine, as other woody perennials, has been considered a recalcitrant crop to produce transgenic plants. Since the production of transgenic and/or edited plants requires the ability to regenerate plants from transformed tissues, this step is often the biggest bottleneck in the process. The objective of this work is to review the state of the art technologies and strategies for the improvement of grapevine transformation and regeneration, focusing on three aspects: (i) problems associated with grapevine transformation; (ii) genes that promote grapevine regeneration; and (iii) vehicles for gene delivery. Concerning the first aspect, it is well documented that one of the main factors explaining the low success rate in obtaining transgenic plants is the regeneration process. After transgenic integration into receptor cells, tissue culture is required to regenerate transgenic seedlings from transformed cells. This process is time consuming and often requires the addition of environmentally damaging reagents (antibiotics and herbicides) to the culture medium to select transgenic plants. On the other hand, the expression of genes such as the so-called developmental regulators (DR), which induce specific development programs, can be used to avoid traditional tissue culture methods. The ectopic expression of specific combinations of DR in somatic cells has the potential to induce de novo meristems in diverse crops, including grapevine. Successful genome editing by de novo reprogramming of plant meristems in somatic tissues has been reported. Moreover, it has been shown that the expression of certain transcription factors can increase the regeneration efficiency in wheat, citrus, and rice. Finally, recent reports showed the use of nanoparticles, such as carbon dots (CDs), as an attractive alternative to Agrobacterium- and biolistic-mediated plant genetic transformation. In this way, the use of antibiotics in culture media is avoided, overcoming the loss of viability of plant tissues and accelerating the regeneration processes. It has been shown that CDs can act as a vehicle to transport plasmids to plant cells in transient transformation in several crops without negative impacts on photosynthesis or growth. Based on these advances, it is possible to combine these new available strategies and technologies to overcome the regeneration problems of species such as grapevine and other crops considered as recalcitrant.

91 Effect of heat stress during mice germ-cell DNA methylation programming on oocyte developmental competence: A preliminary study

2021 ◽  
Vol 33 (2) ◽  
pp. 153
Author(s):  
M. T. Moura ◽  
C. A. I. Carvalho ◽  
F. R. O. Barros ◽  
F. Mossa ◽  
D. Bebbere ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Heat Stress ◽  
Germ Cell ◽  
Cell Function ◽  
De Novo ◽  
Chorionic Gonadotrophin ◽  
Developmental Competence ◽  
Attractive Alternative ◽  
Oocyte Growth ◽  
Female Mice

Heat stress (HS) is characterised by an elevation in body temperature that ultimately undermines organism physiology. Most livestock production occurs in tropical regions under potential HS conditions that diminish productive and reproductive potential. Despite extensive evidence of HS-mediated effects in cell function, stage-specific detrimental effects of HS during oogenesis remain elusive. Mouse models represent an attractive alternative for faster interrogation of stage-specific phenomena during oogenesis. Therefore, the aim of the study was to determine the effects of HS exposure during the major window of female mice germ-cell DNA methylation programming. CD1/Swiss female mice with litters (F0 progeny) at postnatal Day 10 (P10) were randomly allocated to HS (35°C/12-h light; 21°C/12-h dark) or control (CTL: 21°C/24h) for 11 days. The F0 progeny were weaned at P21 and superovulated after reaching puberty at P35. F0 females were superovulated by intraperitoneal injections with 5.0IU of equine chorionic gonadotrophin (PMSG) followed by 5.0IU of human chorionic gonadotrophin (hCG) within a 48-h interval. Pre-implantation embryos were harvested at Day E3.5 in M2 medium under a stereomicroscope. One F0 female per litter was randomly mated to control mice when it reached 6 weeks of age. Data were subjected to least-squares analysis of variance using the General Linear Models procedure of SAS (SAS Institute Inc.). The experiment was replicated twice (CTL: n=4 F0 females and HS: n=4 F0 females). Preliminary results are given as LSM±s.e.m. There was no effect of heat stress on the number of embryos collected per female (CTL: 9.75±4.87 vs. HS: 11.25±4.81) or the percentage of non-viable embryos (CTL: 25.0±0.23% vs. HS: 42.5±0.25%). However, heat stress tended (P=0.07) to reduce the percentage of embryos that reached the morula stage from 63.5±0.08% for CTL to 35.1±0.09% for HS. The percentage of blastocysts collected (CTL: 11.45±0.18% vs. HS: 22.32±0.19%) and litter size of F0 females (CTL: 7.47±1.76 vs. HS: 7.66±1.47) was not affected by treatment. In conclusion, exposure of female mice to 11-day HS during the major wave of de novo DNA methylation during oocyte growth tended to reduce subsequent pre-implantation embryonic development, although it did not affect full-term development after natural mating.

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