Trap Samples Research Articles

Deactivated fused silica tubing: A solution for flexible time weighted averaging needle trap sampling

In time-weighted averaging (TWA) with needle trap extraction (NTE), the control of the sampling rate is critical for accurate analysis. By adjusting the diffusion length and cross-sectional area, the sampling rate can be modified in accordance with Fick's first law of diffusion. In this study, deactivated fused silica tubing (DFST) of varying lengths was used to fine-tune these parameters, allowing for precise control of the sampling rate in TWA-NTE devices.The fabricated devices were used to extract benzene, toluene, ethylbenzene, o-xylene (BTEX), and selected alkanes as model compounds. Experimental sampling rates were obtained using a standard gas flow generating system and compared to theoretical values, showing statistical similarity. The devices were tested in various real-world environments, including a parking lot, garages, and a box containing a burning candle, and their practical applicability was confirmed. The use of DFST effectively controlled both diffusion length and cross-sectional area, thereby enhancing sampling performance.The results of this study demonstrate that DFST serves as a versatile and adjustable attachment for needle trap devices (NTD), significantly broadening the range of NTD applications in terms of concentration and sampling time. This approach not only reduces analysis costs but also improves adherence to Fick's law by minimizing the influence of other mass transfer mechanisms. Consequently, more consistent and predictable extraction behavior was observed, particularly for higher molecular weight species, strengthening the overall applicability of the TWA-NTE method.

Denoising and Augmented Negative Sampling for Collaborative Filtering

Negative sampling plays a crucial role in implicit-feedback-based collaborative filtering, where it leverages massive unlabeled data to generate negative signals for guiding supervised learning. The current state-of-the-art approaches focus on utilizing hard negative samples that contain more information to establish a better decision boundary. To strike a balance between efficiency and effectiveness, most existing methods adopt a two-pass approach: in the first pass, a fixed number of unobserved items are sampled using a simple static distribution, while, in the second pass, a more sophisticated negative sampling strategy is employed to select the final negative items. However, selecting negative samples solely from the original items in a dataset is inherently restricted due to the limited available choices, and thus may not be able to effectively contrast positive samples. In this paper, we empirically validate this observation through meticulously designed experiments and identify three major limitations of existing solutions: ambiguous trap, information discrimination, and false negative samples. Our response to such limitations is to introduce “denoised” and “augmented” negative samples that may not exist in the original dataset. This direction renders a few substantial technical challenges. First, constructing augmented negative samples may introduce excessive noise that eventually distorts the decision boundary. Second, the scarcity of supervision signals hampers the denoising process. To this end, we introduce a novel generic denoising and augmented negative sampling (DANS) paradigm and provide a concrete instantiation. First, we disentangle the hard and easy factors of negative items. Then, we regulate the augmentation of easy factors by carefully considering the direction and magnitude. Next, we propose a reverse attention mechanism to learn a user’s negative preference, which allows us to perform a dimension-level denoising procedure on hard factors. Finally, we design an advanced negative sampling strategy to identify the final negative samples, taking into account both the score function used in existing methods and a novel metric called synthesization gain. Through extensive experiments on real-world datasets, we demonstrate that our method substantially outperforms state-of-the-art baselines. Our code is publicly available at https://github.com/Asa9aoTK/ANS-Recbole.

Synchronised monitoring of plant and insect diversity: a case study using automated Malaise traps and DNA-based methods.

The occurrence and distribution of insects and their possible associations with plant species are largely unknown in Germany and baseline data to monitor future trends are urgently needed. Using newly-designed automated Malaise trap multi-samplers, the occurrence of insect species and their potential associations with plants was monitored synchronously at two contrasting field sites in Germany: an urban botanical garden and a forest research station. Taxa were identified by metabarcoding of the insects and the plant traces present in the preservative ethanol of the Malaise trap samples. For comparison, a botanical survey was conducted in the vicinity of the traps. Across both sites, we identified a total of 1290 exact sequence variants (ESVs) assigned to Insecta, of which 205 are known to be pollinators. In the botanical garden, we detected the occurrence of 128 plant taxa, of which 41 also had one of their known insect pollinator species detected. Insect species richness was highest in May, mainly attributed to an increase in Diptera. These results present a case study of the applicability of automated sampling and DNA-based methods to monitor the timings of flowering and corresponding activity of plant-visiting insects.

Unveiling South African insect diversity: DNA barcoding’s contribution to biodiversity data

Insects are one of the most species-rich groups on Earth. They comprise much of animal diversity and play vital roles in ecosystems, including pollination, pest control, and decomposition. However, only a fraction of this diversity has been formally described. South Africa is recognised as one of the most biologically diverse countries globally, with an estimated 44 000 insect species. Many crops rely on insect pollinators, including canola, apples, oranges, and sunflowers. A shortage of wild pollinators currently threatens crop yields, yet our knowledge of insect diversity within South Africa is sparse. There are few taxonomic specialists relative to South Africa’s biodiversity, and the methods used for insect identification can be time-consuming and expensive. DNA barcoding provides an important research tool to accelerate insect biodiversity research. In this review, we queried the public DNA barcoding BOLD (Barcode of Life Data System) database for records of “Insecta” within South Africa, and 416 211 published records assigned to 28 239 unique BINs (Barcode Index Numbers) were returned. We identified five taxonomic orders with more BINs than known species in southern Africa (Hymenoptera, Diptera, Thysanoptera, Plecoptera, and Strepsiptera). Most of the barcoded records were derived from Malaise trap sampling in Gauteng, Mpumalanga and Limpopo, while the rest of South Africa remains poorly sampled. We suggest that there is a need for a comprehensive national sampling effort alongside increased investment in taxonomic expertise to generate critical baseline data on insect biodiversity before species are lost to extinction.

Living on the edge: Insights into habitat patterns of forest-dwelling mammals in the buffer zone of Melghat Tiger Reserve, India

Buffer zones surrounding protected areas act as interfaces between humans and wildlife, providing sustainable resource utilization while minimizing negative interactions. This study analyzed data from camera trap sampling to understand habitat use and the effects of anthropogenic impacts on medium and large-sized forest-dwelling mammals in the buffer zone of Melghat Tiger Reserve in Central India. The human population in this region is increasing at a rate of 15 % in a decade. There are instances of human death and injury and frequent cattle lifting by carnivores. Crop damage by wild herbivores is common. These factors impede long term conservation goals in the tiger reserve. Camera trap sampling was carried out in the buffer zone for a period of 33 to 46 days. Camera trap data were analyzed using occupancy modeling to estimate habitat use probability (Ψ) and detection probability (p). Naïve estimates of habitat use ranged from 0.11 to 0.64, while Ψ values based on occupancy modeling ranged from 0.23 to 0.71. The study showed a fairly high level of habitat use by mammals in the buffer zone of the tiger reserve. Leopards were found to be associated with abundance of large prey species and human presence. Hyena, gaur, and sambar showed an association with forest cover, while nilgai showed association with scrubland. Chausingha and langur showed an association with sloping terrain. Overall, the study showed that the buffer zone plays an important role as a wildlife habitat and provided insights for prioritizing conservation efforts and management strategies in the study area.

Effectiveness of Malaise trap and sweep net sampling in sawfly research (Hymenoptera: Symphyta)

Malaise traps and sweep nets are commonly used to study sawfly faunas, seasonality and communities. Here we analyse a large dataset obtained with these methods in Slovakia and Hungary over the last two and a half decades. The dataset included collections from twenty-one sites, each covering the entire growing season, eleven of which were obtained with the Malaise trap and ten with the sweep net. We conclude that both methods are suitable for faunistic studies of sawflies (Hymenoptera, Symphyta), although they may lead to certain biased results for some Symphyta groups. Special attention should be paid to Siricidae, Orussidae, Xiphidriidae and Cimbicidae, which were only weakly recorded with both methods. Argidae, Blennocampinae, Dolerinae and Tenthredininae were underrepresented in the Malaise trap samples and Allantinae in the sweep net samples. Both methods gave equally good results in measuring species richness in an one-year study. Ideally, they should be used together as they complement each other well. The net method has a great advantage in determining the exact population density. In contrast, the Malaise trap collections were often heavily dominated by only a few species, with males being preferentially trapped. Use of Malasie trap should be preferred for the study of seasonal flight activity.

Evolutionary history and environmental variability structure contemporary tropical vertebrate communities

AbstractAimTropical regions harbour over half of the world's mammals and birds, but how their communities have assembled over evolutionary timescales remains unclear. To compare eco‐evolutionary assembly processes between tropical mammals and birds, we tested how hypotheses concerning niche conservatism, environmental stability, environmental heterogeneity and time‐for‐speciation relate to tropical vertebrate community phylogenetic and functional structure.LocationTropical rainforests worldwide.Time periodPresent.Major taxa studiedGround‐dwelling and ground‐visiting mammals and birds.MethodsWe used in situ observations of species identified from systematic camera trap sampling as realized communities from 15 protected tropical rainforests in four tropical regions worldwide. We quantified standardized phylogenetic and functional structure for each community and estimated the multi‐trait phylogenetic signal (PS) in ecological strategies for the four regional species pools of mammals and birds. Using linear regression models, we test three non‐mutually exclusive hypotheses by comparing the relative importance of colonization time, palaeo‐environmental changes in temperature and land cover since 3.3 Mya, contemporary seasonality in temperature and productivity and environmental heterogeneity for predicting community phylogenetic and functional structure.ResultsPhylogenetic and functional structure showed non‐significant yet varying tendencies towards clustering or dispersion in all communities. Mammals had stronger multi‐trait PS in ecological strategies than birds (mean PS: mammal = 0.62, bird = 0.43). Distinct dominant processes were identified for mammal and bird communities. For mammals, colonization time and elevation range significantly predicted phylogenetic clustering and functional dispersion tendencies respectively. For birds, elevation range and contemporary temperature seasonality significantly predicted phylogenetic and functional clustering tendencies, respectively, while habitat diversity significantly predicted functional dispersion tendencies.Main conclusionsOur results reveal different eco‐evolutionary assembly processes structuring contemporary tropical mammal and bird communities over evolutionary timescales that have shaped tropical diversity. Our study identified marked differences among taxonomic groups in the relative importance of historical colonization and sensitivity to environmental change.

Distribution of the invasive ambrosia beetle Anisandrus maiche (Coleoptera, Scolytinae) in Switzerland and first record in Europe of its ambrosia fungus Ambrosiella cleistominuta

Ambrosia beetles are highly successful as invaders because they are often transported internationally with wood packaging and other wood products and because their inbreeding mating systems facilitates establishment of invading populations. In 2022, two independent insect surveys in canton Ticino (southern Switzerland) revealed the widespread occurrence of the invasive ambrosia beetle Anisandrus maiche (Kurentzov, 1941) from southern to central-upper Ticino. This species is native to east Asia and has previously been found as a non-native invasive species in the United States, Canada, western Russia, Ukraine and, in 2021, in northern Italy. Here, we present the results of several trapping studies using different trap types (bottle traps, funnel traps and Polytrap intercept traps) and attractants and a map of the distribution of the species. In total, 715 specimens of A. maiche, all female, were trapped, and the identity of selected individuals was confirmed by morphological and molecular identification based on three mitochondrial and nuclear markers (COI, 28S and CAD). Trap samples from early April to early September 2022 in intervals of two to four weeks showed that flights of A. maiche occurred mainly from June to mid-August. Isolation of fungal associates of A. maiche from beetles trapped alive revealed the presence of four fungal species, including the ambrosia fungus Ambrosiella cleistominuta, the known mutualist of A. maiche. The identity of A. cleistominuta was confirmed by comparing DNA sequences of its nuclear, internal transcribed spacer (ITS) gene with reference sequences in NCBI and BOLDSYSTEMS. This represents the first record of A. cleistominuta in Europe. Of the other fungal associates isolated from A. maiche in Ticino, Fusarium lateritium is of note as there is a possibility that A. maiche could act as a vector of this plant pathogen. We highlight several research needs that should be addressed to gain insight into the potential impact of these non-native species and to overcome problems with heteroplasmy in COI sequences in studies of invasion and population genetics of ambrosia beetles.

Combining camera trap surveys and IUCN range maps to improve knowledge of species distributions.

Reliable maps of species distributions are fundamental for biodiversity research and conservation. The International Union for Conservation of Nature (IUCN) range maps are widely recognized as authoritative representations of species' geographic limits, yet they might not always align with actual occurrence data. In recent area of habitat (AOH) maps, areas that are not habitat have been removed from IUCN ranges to reduce commission errors, but their concordance with actual species occurrence also remains untested. We tested concordance between occurrences recorded in camera trap surveys and predicted occurrences from the IUCN and AOH maps for 510 medium- to large-bodied mammalian species in 80 camera trap sampling areas. Across all areas, cameras detected only 39% of species expected to occur based on IUCN ranges and AOH maps; 85% of the IUCN only mismatches occurred within 200km of range edges. Only 4% of species occurrences were detected by cameras outside IUCN ranges. The probability of mismatches between cameras and the IUCN range was significantly higher for smaller-bodied mammals and habitat specialists in the Neotropics and Indomalaya and in areas with shorter canopy forests. Our findings suggest that range and AOH maps rarely underrepresent areas where species occur, but they may more often overrepresent ranges by including areas where a species may be absent, particularly at range edges. We suggest that combining range maps with data from ground-based biodiversity sensors, such as camera traps, provides a richer knowledge base for conservation mapping and planning.

Environmental DNA metabarcoding of pan trap water to monitor arthropod‐plant interactions

AbstractGlobally, the diversity of arthropods and the plants upon which they rely are under increasing pressure due to a combination of biotic and abiotic anthropogenic stressors. Unfortunately, conventional survey methods used to monitor ecosystems are often challenging to conduct on large scales. Pan traps are a commonly used pollinator survey method and environmental DNA (eDNA) metabarcoding of pan trap water may offer a high‐throughput alternative to aid in the detection of both arthropods and the plant resources they rely on. Here, we examined if eDNA metabarcoding can be used to identify arthropods and plant species from pan trap water, and investigated the effect of different DNA extraction methods. We then compared plant species identified by metabarcoding with observation‐based floral surveys and also assessed the contribution of airborne plant DNA (plant DNA not carried by arthropods) using marble traps to reduce putative false positives in the pan trap dataset. Arthropod eDNA was only detected in 17% of pan trap samples and there was minimal overlap between the eDNA results and morphological identifications. In contrast, for plants, we detected 64 taxa, of which 53 were unique to the eDNA dataset, and no differences were identified between the two extraction kits. We were able to significantly reduce the contribution of airborne plant DNA to the final dataset using marble traps. This study demonstrates that eDNA metabarcoding of pan trap water can detect plant resources used by arthropods and highlights the potential for eDNA metabarcoding to be applied to investigations of arthropod‐plant interactions.

Standardising bee sampling: A systematic review of pan trapping and associated floral surveys.

The use of coloured pan traps (bee bowls, Moericke traps) for sampling bees (and other pollinators) has continuously increased over the last two decades. Although a number of methodological studies and conceptual frameworks offer guidance on standardised sampling, pan trap setups vary widely in characteristics even when optimised for capturing bees. Moreover, some uncertainty persists as to how local flower abundance and diversity influence sampling. We systematically reviewed peer-reviewed studies that used pan traps for bee collection and that were listed in the Web of Science core collection. To gauge methodological variation, we identified a set of relevant methodological criteria and assessed the studies accordingly. For obtaining evidence that pan trap samples and floral environment around traps are correlated, we screened the relevant studies for such correlations. While some aspects of pan trapping (e.g., trap coloration and elevation) were similar in the majority of studies, other aspects varied considerably (e.g., trap volume/diameter and sampling duration). Few studies used floral abundance and/or diversity as an explanatory variable in their analyses of bee samples. Among these studies, we found a considerable variation in key aspects of floral survey methods, such as time and space between vegetation surveys and pan trap sampling, abundance measures (quantitative, semi-quantitative and presence-absence), and processing of raw data prior to analysis. Often studies did not find any correlation between the floral environment and bee samples. Reported correlations varied markedly across studies, even within groups of studies applying a similar method or analysing a similar group of bees. Our synthesis helps to identify key issues of further standardisation of pan trap methodology and of associated floral surveys. In addition to the few aspects that have been standardised over the past decades, we suggest methodological direction for future research using pan traps as a better standardised method for the collection of wild bees. We encourage further studies to illuminate if and how varying floral resources around traps bias bee samples from pan traps. More generally, our synthesis shows that trapping methodologies should be reviewed regularly when their use increases to ensure standardisation.

Sediment trap samples reveal regional differences in the population structure of Calanus hyperboreus from the Arctic Ocean

Abstract Calanus hyperboreus is one of the dominant copepod species in the Arctic zooplankton communities. The impact of climate change varies among regions within the Arctic, implying that C. hyperboreus populations may be differently affected at different locations, but knowledge on seasonal population dynamics in relation to biogeography is scarce. To fill this gap, we counted C. hyperboreus in samples from sediment traps that were moored from 2009 to 2014 in three regions of the Arctic Ocean (eastern Fram Strait, northern Chukchi Sea and MacKenzie Trough). The C. hyperboreus flux increased between April and May in all regions, likely associated with the ascent from overwintering depth to the surface. In the descent period, high fluxes were observed between July and September in the Fram Strait, between September and November in the northern Chukchi Sea, and between August and October in the MacKenzie Trough, suggesting that the timing of descent varied among the regions characterized by differences in light regime, phytoplankton development and water temperature. The copepodite stage composition in the eastern Fram Strait and the MacKenzie Trough varied with season, suggesting successful local reproduction while it was uniform in the northern Chukchi Sea, possibly because the population is fueled by advection.

Millennial-scale variations in Arctic sea ice are recorded in sedimentary ancient DNA of the microalga Polarella glacialis

Sea ice is a critical component of the Earth’s Climate System and a unique habitat. Sea-ice changes prior to the satellite era are poorly documented, and proxy methods are needed to constrain its past variability. Here, we demonstrate the potential of sedimentary DNA from Polarella glacialis, a sea-ice microalga, for tracing past sea-ice conditions. We quantified P. glacialis DNA (targeting the nuclear ribosomal ITS1 region) in Arctic marine and fjord surface sediments and a sediment core from northern Baffin Bay spanning 12,000 years. Sea ice and sediment trap samples confirmed that cysts of P. glacialis are common in first-year sea ice and sinking particulate matter following sea-ice melt. Its detection is more efficient with our molecular approach than standard micropaleontological methods. Given that the species inhabits coastal and marine environments in the Arctic and Antarctic, P. glacialis DNA has the potential to become a useful tool for circum-polar sea-ice reconstructions.

Two-photon microscopy of acoustofluidic trapping for highly sensitive cell analysis.

We combine two-photon-excited fluorescence microscopy and acoustofluidic trapping in a spherical microchamber to in vitro study cells and cell clusters three-dimensionally close to in vivo conditions. The two-photon microscopy provides the in-depth 3D analysis of the spherical microchamber dimensions as well as the positions of trapped samples therein with high spatial precision and high temporal resolution enabling even tracking of the fast moving particles. Furthermore, optical sectioning allows to gather information of individual cells in trapped cell clusters inside the chamber. We demonstrate real-time monitoring of osmosis in A549 lung cells and red blood cells as one possible biomedical application. The observed osmosis reduced the cell membrane diameter by approximately 4 μm in the A549 cells and by approximately 2 μm in the red blood cells. Our approach provides an important optical tool for future investigations of cell functions and cell-cell interactions avoiding wall-contact inside an acoustofluidic device.

Performance of biochemical tools as fish waste particle tracers in a dispersive marine system

As finfish aquaculture expands to more dispersive coastal environments, inputs of aquaculture-derived organic matter become more diffuse, but widespread. Significant amounts of organic material are likely to be exported beyond the near-farm area, where it may encounter sensitive habitats. Biochemical tracers of organic matter, such as stable isotopes and fatty acids may be useful tools for detecting diffuse waste deposition. We used numerical modelling of direct and resuspended farm waste deposition and empirical environmental measurements to evaluate a range of biochemical indicators (major nutrients, bulk stable isotopes, fatty acids, minor and trace elements) for their efficacy as particle tracers of fish waste around a shallow water (∼30 m) salmon farm, in a dispersive coastal farming area. We also compared their efficacy across a range of sampling approaches (in sediment trap material, sediment and Mytilus edulis as a bio-indicator). Elemental carbon, nitrogen and zinc indicators could accurately reflect predicted waste deposition close to the farm, but only terrestrial fatty acid indicators were able to reflect diffuse wastes farther afield suggesting they are more sensitive tracers of fish waste. Their performance as tracers also differed between sediment trap and sediment samples, with most performing better in sediment trap samples. Although translocated mussels showed evidence of fish waste assimilation in areas of high waste deposition, tissue concentrations of fish waste tracers correlated relatively poorly with modelled waste deposition. Our results highlight the sensitivity of terrestrial fatty acids as fish waste tracers for detecting diffuse waste deposition, and demonstrate that concentrations of a number of elements can be used for mapping acute waste deposition. Our findings can inform selection of biochemical tracers for improved monitoring and management of farm wastes in dispersive marine systems.

A workflow for the detection of antibiotic residues, measurement of water chemistry and preservation of hospital sink drain samples for metagenomic sequencing

Hospital sinks are environmental reservoirs that harbour healthcare-associated (HCA) pathogens. Selective pressures in sink environments, such as antibiotic residues, nutrient waste and hardness ions, may promote antibiotic resistance gene (ARG) exchange between bacteria. However, cheap and accurate sampling methods to characterize these factors are lacking. To validate a workflow to detect antibiotic residues and evaluate water chemistry using dipsticks. Secondarily, to validate boric acid to preserve the taxonomic and ARG ('resistome') composition of sink trap samples for metagenomic sequencing. Antibiotic residue dipsticks were validated against serial dilutions of ampicillin, doxycycline, sulfamethoxazole and ciprofloxacin, and water chemistry dipsticks against serial dilutions of chemical calibration standards. Sink trap aspirates were used for a 'real-world' pilot evaluation of dipsticks. To assess boric acid as a preservative of microbial diversity, the impact of incubation with and without boric acid at ∼22°C on metagenomic sequencing outputs was evaluated at Day 2 and Day 5 compared with baseline (Day 0). The limits of detection for each antibiotic were: 3μg/L (ampicillin), 10μg/L (doxycycline), 20μg/L (sulfamethoxazole) and 8μg/L (ciprofloxacin). The best performing water chemistry dipstick correctly characterized 34/40 (85%) standards in a concentration-dependent manner. One trap sample tested positive for the presence of tetracyclines and sulphonamides. Taxonomic and resistome composition were largely maintained after storage with boric acid at ∼22°C for up to five days. Dipsticks can be used to detect antibiotic residues and characterize water chemistry in sink trap samples. Boric acid was an effective preservative of trap sample composition, representing a low-cost alternative to cold-chain transport.

Observed size distribution changes in American lobsters over a 12-year period in southwestern Nova Scotia, Canada.

Size distribution and size frequency information of American lobsters (Homarus americanus) are often used to help estimate the age distributions, and reproductive output for the species and to guide the determination of appropriate minimum legal sizes for the fishery. This study used truncated linear regression models to estimate the effects of sampling year, sampling month, lobster sex and water depth on the lobster size. A dataset of almost 130,000 trap-caught lobsters from the two most important lobster fishing areas of Atlantic Canada collected over a 12-year period (2004-2015) was analyzed. It was shown that truncated models can help to account for biases due to the trap sampling method from vessels and from wharf samplings. There were significant annual and seasonal changes in size distribution, and data collected outside the fishing season showed a significant increase in carapace length in 2014 and 2015, potentially reflecting a northward shift of the range of lobster populations due to more favourable settlement and recruitment habitats. Size also increased in late summer, likely due to moult. Our results demonstrated that landed lobsters, especially females, were smaller than the predicted size-at-maturity in the region (96.5 mm carapace length), which could have long-term repercussions for the stock's reproductive potential.

Efficient qPCR estimation and discrimination of airborne inoculum of Leptosphaeria maculans and L. biglobosa, the causal organisms of phoma leaf spotting and stem canker of oilseed rape.

Detection of the inoculum of phytopathogens greatly assists in the management of diseases, but is difficult for pathogens with airborne fungal propagules. Here, we present experiments to determine the abundance and distribution frequencies of the ascospores of Leptosphaeria (Plenodomus) species that were collected on the tapes of volumetric Hirst-type traps near oilseed rape fields in Poznan, Poland and Harpenden, UK. Fungal detection and species discrimination were achieved using a SYBR-Green quantitative polymerase chain reaction (qPCR) with two different pairs of primers previously reported to differentiate Leptosphaeria maculans (Plenodomus lingam) or L. biglobosa (P. biglobosus). Detection was successful even at fewer than five spores per m3 of air. The primer pairs differed in the correlation coefficients obtained between DNA yields and the daily abundance of ascospores that were quantified by microscopy on duplicate halves of the spore trap tapes. Important differences in the specificity and sensitivity of the published SYBR-Green assays were also found, indicating that the Liu primers did not detect L. biglobosa subclade 'canadensis', whereas the Mahuku primers detected L. biglobosa subclade 'canadensis' and also the closely related Plenodomus dezfulensis. Comparisons confirmed that application of qPCR assays to spore trap samples can be used for the early detection, discrimination and quantification of aerially dispersed L. maculans and L. biglobosa propagules before leaf spot symptoms are visible in winter oilseed rape fields. The specificity of the primers must be taken into consideration because the final result will greatly depend on the local population of the pathogen. © 2023 Society of Chemical Industry.

A Protein Suspension-Trapping Sample Preparation for Tear Proteomics by Liquid Chromatography-Tandem Mass Spectrometry.

Tear fluid is one of the easily accessible biofluids that can be collected non-invasively. Tear proteomics has the potential to discover biomarkers for several ocular diseases and conditions. The suspension trapping column has been reported to be an efficient and user-friendly sample preparation workflow for the broad application of downstream proteomic analysis. Yet, this strategy has not been well-studied in the analysis of human tear proteome. The present protocol describes an integrated workflow from clinical human tear samples to purified peptides for non-invasive tear protein biomarker research using mass spectrometry, which provides insights into disease biomarkers and monitoring when combined with bioinformatics analysis. A protein suspension trapping sample preparation was applied and demonstrated the discovery of tear proteome with fast, reproducible, and user-friendly procedures, as a universal, optimized sample preparation for human tear fluid analysis. In particular, the suspension trapping procedure outperformed in-solution sample preparation in terms of peptide recovery, protein identification, and shorter sample preparation time.

Sources, Transport, and accumulation of Mercury in the northwestern Mediterranean margin sediments during the Industrial Era and influence of turbiditic events

Sources and pathways of the Hg accumulated in the sediments of the Gulf of Lion (GoL) and its adjacent marine areas (Northwestern Mediterranean) have been explored using sediment grab samples, sediment cores, and sediment trap samples. The main source of Hg along this margin is the Rhône River, whose suspended sediments settle mainly in the prodelta area but also along the mid-shelf, then reaching the continental rise via wave resuspension and cascading of dense shelf waters. Seaward, these riverine particles are mixed with carbonated ooze conveyed to the bottom by the biological pump. The Hg is enriched in surface sediments of the GoL with decreasing concentrations westward and seaward from the Rhône prodelta to the continental rise. Dated cores from the Rhône prodelta give access to riverine sediments deposited over the last 400 years and show that the Hg concentration time trend resembles the evolution of coal consumption in France, peaking during in the 1960s. Similar trends were observed in sediment cores collected along the GoL slope and submarine canyons along with the preservation of traces of erosion and sediment instability events. Seaward, on the continental rise, the Hg concentration distribution suggests the deposition of fine planktonic-derived material and particles episodically advected from the shelf during deep cascading pulses. Anthropogenic Hg accumulated in GoL and continental rise sediments during the Industrialized Era is ∼ 150 Mg (tons), two-thirds of which are buried in the Rhône prodelta area. Significant correlations are found between Hg and organic matter in GoL sediments, but the relationships differ between areas and are disrupted by the inputs of anthropogenic Hg and by the Hg availability in the Rhône River watershed during the pre-industrial period. The HgT availability in waters appears to be the limiting factor to the Hg enrichment of the particulate organic matter. Monomethyl mercury (MMHg), which represents on average 0.3 % of the total Hg, was positively correlated to total Hg. Their distributions suggest in situ MMHg formation and a more effective net Hg methylation for surface sediment or particles collected in traps compared with particles buried in the sedimentary column.