scholarly journals Autonomous in situ sampling and analysis of eDNA using an Environmental Sample Processor (ESP)

2021 ◽  
Vol 4 ◽  
Author(s):  
Magnus Jacobsen
Keyword(s):  
Environmental Sample ◽  
Sea Water ◽  
Detection System ◽  
Environmental Dna ◽  
Temporal Analysis ◽  
Marine Biodiversity ◽  
Biological Communities ◽  
Interesting Candidate ◽  
Good Proxy

Monitoring of marine offshore biodiversity is expensive and has traditionally relied on invasive techniques like net fishing or direct observations that can only be conducted in calm seas by experts. Analysis of environmental DNA (eDNA) is a non-invasive method and can easily be collected from sea water by water filtration followed by DNA extraction. Due to the fast degradation time in sea water it is considered a good proxy for present living biodiversity. It allows direct identification of species based on their unique DNA sequence and is cheaper compared to traditional methods, which often are carried out from dedicated fishing or research vessels. However, while eDNA collection may reduce operational cost of offshore sampling, it still relies on boat time. Thus, traditional eDNA sampling still presents substantial costs for offshore biodiversity monitoring. This may reduce the number of samples that can be collected and analysed, limiting the sampling to single ‘time shots’, which may not give an adequate picture of the present biodiversity. The 2nd generation Environmental Sample Processor (2G-ESP) is an autonomous sampler/analyser of eDNA. It can collect, extract and analyse eDNA samples in situ using quantitative PCR (qPCR) or store filters for subsequent laboratory analysis after deployment. The instrument can be deployed directly on the seabed or in pelagic configuration where it can operate for several months depending on power supply and power consumption, while it is controlled by, and sends back results to scientists on land. These unique features make the 2G-ESP an interesting candidate for offshore monitoring of marine biodiversity, as well as a potential early warning/detection system e.g. for invasive species. Moreover, the possibility to preserve filters aboard makes it possible to investigate temporal changes of full biological communities by applying metabarcoding techniques on the collected samples. Here we present the major results of three years of work testing the potential use of a second generation Environmental Sample Processor (2G-ESP) for marine monitoring. These include both practical and analytical issues that we have encountered along the way, as well as results on target species detection and temporal analysis using qPCR and metabarcoding methods.

scholarly journals Improved biodiversity detection using a large-volume environmental DNA sampler with in situ filtration and implications for marine eDNA sampling strategies

2022 ◽  
Author(s):  
Annette F. Govindarajan ◽  
Luke McCartin ◽  
Allan Adams ◽  
Elizabeth Allan ◽  
Abhimanyu Belani ◽  
...  
Keyword(s):  
Large Volume ◽  
Small Volume ◽  
Deep Ocean ◽  
Environmental Dna ◽  
Marine Biodiversity ◽  
Robotic Vehicle ◽  
Seawater Samples ◽  
Biodiversity Changes ◽  
Collection Strategies

Metabarcoding analysis of environmental DNA samples is a promising new tool for marine biodiversity and conservation. Typically, seawater samples are obtained using Niskin bottles and filtered to collect eDNA. However, standard sample volumes are small relative to the scale of the environment, conventional collection strategies are limited, and the filtration process is time consuming. To overcome these limitations, we developed a new large-volume eDNA sampler with in situ filtration, capable of taking up to 12 samples per deployment. We conducted three deployments of our sampler on the robotic vehicle Mesobot in the Flower Garden Banks National Marine Sanctuary in the northwestern Gulf of Mexico and collected samples from 20 to 400 m depth. We compared the large volume (~40-60 liters) samples collected by Mesobot with small volume (~2 liters) samples collected using the conventional CTD-mounted Niskin bottle approach. We sequenced the V9 region of 18S rRNA, which detects a broad range of invertebrate taxa, and found that while both methods detected biodiversity changes associated with depth, our large volume samples detected approximately 66% more taxa than the CTD small volume samples. We found that the fraction of the eDNA signal originating from metazoans relative to the total eDNA signal decreased with sampling depth, indicating that larger volume samples may be especially important for detecting metazoans in mesopelagic and deep ocean environments. We also noted substantial variability in biological replicates from both the large volume Mesobot and small volume CTD sample sets. Both of the sample sets also identified taxa that the other did not; although the number of unique taxa associated with the Mesobot samples was almost four times larger than those from the CTD samples. Large volume eDNA sampling with in situ filtration, particularly when coupled with robotic platforms, has great potential for marine biodiversity surveys, and we discuss practical methodological and sampling considerations for future applications.

scholarly journals Remote Sensing of Ice Conditions in the Southeastern Baltic Sea and in the Curonian Lagoon and Validation of SAR-Based Ice Thickness Products

2020 ◽  
Vol 12 (22) ◽  
pp. 3754
Author(s):  
Igor E. Kozlov ◽  
Elena V. Krek ◽  
Andrey G. Kostianoy ◽  
Inga Dailidienė
Keyword(s):  
Sea Water ◽  
Temporal Analysis ◽  
In Situ Measurements ◽  
Curonian Lagoon ◽  
Ice Thickness ◽  
Finnish Meteorological Institute ◽  
Ice Conditions ◽  
Ice Regime ◽  
Sar Data

Here we analyze ice conditions in the Southeastern Baltic (SEB) Sea and in the Curonian Lagoon (CL) using spaceborne synthetic aperture radar (SAR) data combined with in-situ measurements from coastal stations during four winter seasons between 2009–2013. As shown, the ice conditions in the SEB and in the CL are strongly varying from year to year and do not always correlate with each other. In the SEB, ice cover may form only within 5–15 km band along the coast or spread up to 100 km offshore covering almost the entire region. The mean ice season duration here is 45 days. The CL is almost fully ice-covered every year apart of its northern part subjected to sea water inflow and active shipping. The ice regime is also more stable here, however, it also possesses multiple periods of partial melting and re-freezing. In this study we also perform a validation of three SAR-based ice thickness products (Envisat ASAR 0.5-km and 1-km, and RADARSAT-2 0.5-km) produced by the Finnish Meteorological Institute versus in-situ measurements in the CL. As shown, all satellite products perform rather well for the periods of gradual ice thickness growth. When the ice thickness grows rapidly, all products underestimate the observed values by 10–20 cm (20–50%). The best results were obtained for the RADARSAT-2 ice thickness product with the highest R2 value (0.68) and the root mean square error around 8 cm. The results of the study clearly show that multi-mission SAR data are very useful for spatial and temporal analysis of the ice regime in coastal waters and semi-enclosed shallow water bodies where the number of field observations is insufficient or lacking.

High performance Nanogold™-in situ hybridzation and its use in the detection of hybridized and PCR-amplified microscopical preparations

1996 ◽  
Vol 54 ◽  
pp. 896-897
Author(s):  
G. W. Hacker ◽  
I. Zehbe ◽  
J. Hainfeld ◽  
A.-H. Graf ◽  
C. Hauser-Kronberger ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Messenger Rna ◽  
High Performance ◽  
Detection System ◽  
Direct Methods ◽  
Genetic Alterations ◽  
Chain Reaction ◽  
Protein Encoding ◽  
Polymerase Chain

In situ hybridization (ISH) with biotin-labeled probes is increasingly used in histology, histopathology and molecular biology, to detect genetic nucleic acid sequences of interest, such as viruses, genetic alterations and peptide-/protein-encoding messenger RNA (mRNA). In situ polymerase chain reaction (PCR) (PCR in situ hybridization = PISH) and the new in situ self-sustained sequence replication-based amplification (3SR) method even allow the detection of single copies of DNA or RNA in cytological and histological material. However, there is a number of considerable problems with the in situ PCR methods available today: False positives due to mis-priming of DNA breakdown products contained in several types of cells causing non-specific incorporation of label in direct methods, and re-diffusion artefacts of amplicons into previously negative cells have been observed. To avoid these problems, super-sensitive ISH procedures can be used, and it is well known that the sensitivity and outcome of these methods partially depend on the detection system used.

scholarly journals Mammographic microcalcifications and risk of breast cancer

2021 ◽  
Author(s):  
Shadi Azam ◽  
Mikael Eriksson ◽  
Arvid Sjölander ◽  
Marike Gabrielson ◽  
Roxanna Hellgren ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Postmenopausal Women ◽  
Detection System ◽  
Premenopausal Women ◽  
Computer Aided Detection ◽  
Comprehensive Information ◽  
Estimated Risk ◽  
Logistic Regressions ◽  
Microcalcification Clusters

Abstract Background Mammographic microcalcifications are considered early signs of breast cancer (BC). We examined the association between microcalcification clusters and the risk of overall and subtype-specific BC. Furthermore, we studied how mammographic density (MD) influences the association between microcalcification clusters and BC risk. Methods We used a prospective cohort (n = 53,273) of Swedish women with comprehensive information on BC risk factors and mammograms. The total number of microcalcification clusters and MD were measured using a computer-aided detection system and the STRATUS method, respectively. Cox regressions and logistic regressions were used to analyse the data. Results Overall, 676 women were diagnosed with BC. Women with ≥3 microcalcification clusters had a hazard ratio [HR] of 2.17 (95% confidence interval [CI] = 1.57–3.01) compared to women with no clusters. The estimated risk was more pronounced in premenopausal women (HR = 2.93; 95% CI = 1.67–5.16). For postmenopausal women, microcalcification clusters and MD had a similar influence on BC risk. No interaction was observed between microcalcification clusters and MD. Microcalcification clusters were significantly associated with in situ breast cancer (odds ratio: 2.03; 95% CI = 1.13–3.63). Conclusions Microcalcification clusters are an independent risk factor for BC, with a higher estimated risk in premenopausal women. In postmenopausal women, microcalcification clusters have a similar association with BC as baseline MD.

Real-time in-situ determination of free Cu(II) at picomolar levels in sea water using a fluorescence lifetime-based fiber optic biosensor

2002 ◽  
Author(s):  
Richard B. Thompson ◽  
Hui-Hui Zeng ◽  
Carol A. Fierke ◽  
Gary Fones ◽  
James W. Moffett
Keyword(s):  
Real Time ◽  
Fluorescence Lifetime ◽  
Fiber Optic ◽  
Sea Water

scholarly journals Observing and modelling phytoplankton community structure in the North Sea

2017 ◽  
Vol 14 (6) ◽  
pp. 1419-1444 ◽  
Author(s):  
David A. Ford ◽  
Johan van der Molen ◽  
Kieran Hyder ◽  
John Bacon ◽  
Rosa Barciela ◽  
...  
Keyword(s):  
Community Structure ◽  
North Sea ◽  
Phytoplankton Community ◽  
Marine Biodiversity ◽  
Phytoplankton Community Structure ◽  
Pigment Analysis ◽  
The North ◽  
The North Sea ◽  
In Situ Observations

Abstract. Phytoplankton form the base of the marine food chain, and knowledge of phytoplankton community structure is fundamental when assessing marine biodiversity. Policy makers and other users require information on marine biodiversity and other aspects of the marine environment for the North Sea, a highly productive European shelf sea. This information must come from a combination of observations and models, but currently the coastal ocean is greatly under-sampled for phytoplankton data, and outputs of phytoplankton community structure from models are therefore not yet frequently validated. This study presents a novel set of in situ observations of phytoplankton community structure for the North Sea using accessory pigment analysis. The observations allow a good understanding of the patterns of surface phytoplankton biomass and community structure in the North Sea for the observed months of August 2010 and 2011. Two physical–biogeochemical ocean models, the biogeochemical components of which are different variants of the widely used European Regional Seas Ecosystem Model (ERSEM), were then validated against these and other observations. Both models were a good match for sea surface temperature observations, and a reasonable match for remotely sensed ocean colour observations. However, the two models displayed very different phytoplankton community structures, with one better matching the in situ observations than the other. Nonetheless, both models shared some similarities with the observations in terms of spatial features and inter-annual variability. An initial comparison of the formulations and parameterizations of the two models suggests that diversity between the parameter settings of model phytoplankton functional types, along with formulations which promote a greater sensitivity to changes in light and nutrients, is key to capturing the observed phytoplankton community structure. These findings will help inform future model development, which should be coupled with detailed validation studies, in order to help facilitate the wider application of marine biogeochemical modelling to user and policy needs.

scholarly journals Determination of 137Cs in Sea Water Samples Using Gamma Spectrometry

2020 ◽  
Vol 13 ◽  
pp. 247
Author(s):  
N. Evaggeliou ◽  
Ch. Lykomitrou ◽  
A. Zafiropoulou
Keyword(s):  
Gamma Spectrometry ◽  
Comparative Evaluation ◽  
Sea Water ◽  
Germanium Detector ◽  
Advantages And Disadvantages ◽  
High Purity Germanium ◽  
Co Precipitation ◽  
Radioanalytical Procedures

In the present study a comparative evaluation of two methods for 137Cs determination (pretreatment for gamma spectrometry) is attempted. One of them is the conventional AMP (ammonium molybdophosphate, (ΝΗ4)3Ρ(Μo3O10)4) method (radiochemical treatment based on coprecipitation) and the other one is a method based on pre-concentration of cesium in situ by using the Mark III Centrifugal Pump. The pump, which is described analytically in the study, is composed of a mo­tor (pump), four cartridge housings (containing the scavengers), a flow meter and a pressure tube (containing the battery pack and the timer board). For justification, this method is compared with the AMP co-precipitation one. Following up the radioanalytical procedures, the gamma spectrometry system (relative efficiency of high purity germanium detector 90%) is also demonstrated, as conformed to mea­ suring obtained parameters. Finally, the advantages and disadvantages of these two methods are recorded and the application of each one is suggested.

scholarly journals Progress in radionuclide characterisation in marine sediments using an underwater gamma-ray spectrometer in 2π geometry

2019 ◽  
Vol 21 ◽  
pp. 29
Author(s):  
E. G. Androulakaki ◽  
C. Tsabaris ◽  
M. Kokkoris ◽  
G. Eleftheriou ◽  
D. L. Patiris ◽  
...  
Keyword(s):  
Gamma Ray ◽  
Detection System ◽  
Full Energy Peak ◽  
Gamma Ray Spectrometry ◽  
Peak Efficiency ◽  
Full Energy ◽  
Effective Manner ◽  
Energy Peak ◽  
Full Energy Peak Efficiency

The in-situ gamma-ray spectrometry is a well suited method for seabed mapping applications, since it provides rapid results in a cost effective manner. Moreover, the in-situ method is preferable to the commonly applied laboratory measurements, due to its beneficial characteristics. Therefore, the development of in-situ systems for seabed measurements continuously grows. However, an efficiency calibration of the detection system is necessary for obtaining quantitative results in the full spectral range. In the present work, an approach for calculating the full-energy peak efficiency of an underwater insitu spectrometer for measure- ments on the seabed is presented. The experimental work was performed at the coastal site of Vasilikos (Cyprus). The experimental full-energy peak efficiency of the in-situ was determined in the energy range 1400–2600 keV, by combining the in-situ and laboratory reference measurements. The experimental effi- ciency results were theoretically reproduced by means of Monte Carlo (MC) simulations, using the MCNP5 code.

scholarly journals Environmental DNA variability in lake sediment cores

2021 ◽  
Vol 4 ◽  
Author(s):  
John Pearman ◽  
Georgia Thomson-Laing ◽  
Jamie Howarth ◽  
Marcus Vandergoes ◽  
Lucy Thompson ◽  
...  
Keyword(s):  
16S Rrna ◽  
General Trend ◽  
Sediment Cores ◽  
Environmental Dna ◽  
Biological Communities ◽  
The Core ◽  
Community Dissimilarity ◽  
Sample Heterogeneity ◽  
Read Abundance ◽  
Natural Archives

Lake sediments are natural archives that accumulate information about biological communities and their surrounding catchments. Paleolimnology has traditionally focussed on identifying fossilized organisms to reconstruct past environments. In the last decade, the application of molecular methodologies has increased in paleolimnological studies, but further studies investigating factors such as sample heterogeneity and DNA degradation are required. Here we investigated bacterial community heterogeneity (16S rRNA metabarcoding) within depth slices. Sediment cores were collected from three lakes with differing sediment compositions. Samples were collected from a variety of depths (1-cm width) which represent a period of time of approximately 1,200 years. Triplicate samples were collected from each slice and bacterial 16S rRNA metabarcoding was undertaken on each sample. Rarefaction curves showed that except for the deepest (oldest) slices, the combination of three replicate samples were insufficient to characterise the entire bacterial diversity. However, shared Amplicon Sequence Variants (ASVs) accounted for the majority of the reads in each slice (max. shared proportional read abundance 96%, 86%, 65% in the three lakes). Within slice similarity was higher than between slice similarity. No general trend was observed in variability among replicates with depth amongst the lakes. In one core. there was a higher community dissimilarity in older sediment, which may be due to laminae not being horizontal. These results highlight the fact that microbial communities can be differentiated with depth however it is critical to interpret these results in the context of the stratigraphic data of the core.

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