Unpreserved Samples Research Articles

Effectiveness of Selected Preservatives in Protecting Bamboo Against Termite Attack

Bamboo is highly susceptible to insect attacks. To promote its use as an alternative to wood, it is crucial to assess its preservation methods to increase its service life. This study investigated the effectiveness of preservatives in protecting bamboo against termite attack. Three bamboo species were extracted, air-dried, and pressure-treated with different concentrations of crude-lake salt, borax-boric acid, and tanalith. Preserved and unpreserved samples for each treatment were weighed and exposed to Macrotermes bellicosus termites in Kasagala Central Forest Reserve. After 21 days, durability classes and mass loss were determined following European standards. The results showed that termite resistance depends on the type of preservative. All the untreated and crude lake salt-treated bamboo samples were attacked and classified into the not-durable class. Samples treated with Tanalith were classified under the durable class. Borax-boric acid provided moderate resistance to bamboo samples and belonged to the moderately durable class. Crude lake salt did not provide sufficient protection against termites. The difference in species did not influence termite resistance. Untreated B. vulgaris had the highest mass loss and O. alpina the lowest. The findings from the study will contribute to improved utilisation of bamboo by proper preservation

Examining effects of sample concentration on estimates of live phytoplankton abundance

With the entry into force of the International Maritime Organization's International Ballast Water Management Convention in September 2017, ships have begun to install and operate onboard ballast water management systems (BWMS) to reduce the number of live organisms in ballast water. Scientific methods were developed to assess the effectiveness of BWMS at reducing the number of live organisms in ballast water. However, detecting low organism concentrations in treated ballast water is challenging when considering the small sample volume (6 mL) analyzed for organisms in the 10–50 μm size class. The volume analyzed can be increased by concentrating the sample prior to analysis, but it is important to assess the effects of the sample concentration method due to potential cell loss experienced during the concentration step. Therefore, laboratory experiments were conducted to assess the effects of a gravity filtration method to concentrate samples to a factor of 40:1. Experiments were conducted for both low and high organism abundances. For unpreserved samples at low organism abundances (∼10 cells mL−1), concentrated samples had on average 31% fewer live cells mL−1 than unconcentrated samples for four out of five experiments. At high organism abundances (≥ 120 cells mL−1), unpreserved concentrated samples had on average 55% fewer live cells than unconcentrated samples. Alternatively, with preserved samples at low organism abundances, concentrated samples had on average 4.5× more cells than unconcentrated samples. At high organism abundances, concentrated samples had on average 6.4× more cells than unconcentrated samples. Differences were also observed between preserved and unpreserved samples. These findings can help to improve ballast water monitoring procedures and BWMS assessments, addressing a critical challenge to maritime environmental protection.

Effects of sample preservation techniques on dogs' (Canis familiaris) ability to detect koi carp (Cyprinus rubrofuscus)

Koi carp (Cyprinus rubrofuscus) are an invasive fish that has caused significant ecological impacts to freshwater ecosystems around the world. Current detection methods such as observation, netting, electrofishing, and environmental DNA can be time-, labour-, and cost-intensive, especially when fish densities are low. Evaluation of water samples for invasive fish by scent detection dogs could offer a more efficient method of detection. However, the odour profiles of such samples are likely unstable, and without effective preservation from the time of collection to the time of analysis by dogs, samples could degrade, making the target scent less recognisable to dogs. The aim of this study was to determine whether refrigeration (4°C), freezing (-18°C), or the addition of potassium sorbate (1.7 mM) could be used to preserve scent in water samples assessed by dogs. An ABACADA reversal design was employed. The dogs performed a baseline evaluation (A) of unpreserved water samples from aquaria containing carp (target scent; n = 7), goldfish (Carassius auratus; non-target distractor scent; n = 5), or no fish (non-target scent; n = 5) before preservation treatments were applied to the samples. The treatment phases (B = refrigeration, C = frozen, and D = dark cupboard with potassium sorbate) involved applying a preservation method to carp, goldfish, or no-fish water samples 7 or 8 days prior to assessment by the dogs. There was weak evidence that refrigeration impaired the dogs’ detection performance. In contrast, once stability criteria had been met, detection performances on frozen or potassium sorbate preserved samples were similar to or returned back to baseline levels. These findings suggest that freezing and potassium sorbate were effective in retarding scent degradation over the storage period and have the potential to be used as preservatives for water samples awaiting assessment by scent detection dogs. If laboratory-based canine scent detection becomes an invasive fish detection method, the use of dogs could prove more time- and cost-efficient than current detection methods.

EFFECT OF ETHANOLIC EXTRACT OF BLACK PEPPER (Piper nigrum) ON PRESERVATION OF AFRICAN CATFISH (Clarias gariepinus)

Fish preservation is an important stage of fish production as it helps in the reduction of post-harvest losses. This leads to the study of ethanolic extract of black pepper as a preservative of African catfish. A sample size of five (5) fish of average weight 600g for each treatment were slaughtered and gutted before they were dipped in the black pepper extract for 10minutes and 20 minutes in separate bowls. The fish samples that had been preserved with the plant extract were monitored for spoilage at an interval of four (4) hours for the period of forty eight (48) hours and the organoleptic characteristics were observed and recorded. The shelf life of the experimental African catfish was extended from 20 hours as seen in the unpreserved sample to between 24 – 26 hours in the preserved sample. The study also indicated that the duration of dip did not have any effect on the preservative action of black pepper seed extract and this was because the extract was only able to extend the shelf life of the sample to 24 – 26 hours before becoming unfit for consumption at 28 hours for both the 10 and 20 minutes dipping durations. It can therefore be concluded from the findings of this research that African catfish can be preserved using natural preservatives (plants) and thereby reducing post-harvest losses.

Old core, new tricks: a comparative study of old and new mudstone cores for applications in the energy transition

Repurposing depleted oil and gas reservoirs for secondary storage may play an important role in the transition to low-carbon energy. The integrity of the cap rocks overlying the reservoirs is an important factor for gas storage and needs to be understood prior to repurposing. In some cases, old cap-rock cores collected during exploration and development of oil and gas fields may be available for characterization using modern techniques but after being stored for decades these cores are likely to have experienced many changes in moisture, which can lead to physical changes. A comparative study of samples taken from old, unpreserved mudstone core and samples from a recently acquired and preserved core taken from the same formation shows that the mineralogy, porosity and permeability results are relatively similar between the two cores. The differences in the porosity measurements between the old and new core samples are primarily due to natural variations in grain size, rather than the preservation status of the cores. Geomechanical data, however, show significant and non-systematic differences between the old samples and the new samples, suggesting that old core samples are not suitable for geomechanical characterization. In the absence of new, well-preserved core, old core samples may provide suitable porosity, permeability and mineralogical data, whereas the old, unpreserved core is unlikely to provide reliable geomechanical data. Supplementary material: Individual BIB-SEM porosity measurements for each sample are available at https://doi.org/10.6084/m9.figshare.c.6725765 Thematic collection: This article is part of the Fault and top seals 2022 collection available at: https://www.lyellcollection.org/topic/collections/fault-and-top-seals-2022

UAS™—A Urine Preservative for Oncology Applications

Liquid biopsy is a revolutionary tool that is gaining momentum in the field of cancer research. As a body fluid, urine can be used in non-invasive diagnostics for various types of cancer. We investigated the performance of UAS™ as a preservative for urinary analytes. Firstly, the need for urine preservation was investigated using urine samples from healthy volunteers. Secondly, the performance of UAS™ was assessed for cell-free DNA (cfDNA) and host cell integrity during storage at room temperature (RT) and after freeze-thaw cycling. Finally, UAS™ was used in a clinical setting on samples from breast and prostate cancer patients. In the absence of a preservative, urinary cfDNA was degraded, and bacterial overgrowth occurred at RT. In urine samples stored in UAS™, no microbial growth was seen, and cfDNA and cellular integrity were maintained for up to 14 days at RT. After freeze-thaw cycling, the preservation of host cell integrity and cfDNA showed significant improvements when using UAS™ compared to unpreserved urine samples. Additionally, UAS™ was found to be compatible with several commercially available isolation methods.

Reducing bias in microbiome research: Comparing methods from sample collection to sequencing.

Microbiota profiles are strongly influenced by many technical aspects that impact the ability of researchers to compare results. To investigate and identify potential biases introduced by technical variations, we compared several approaches throughout the entire workflow of a microbiome study, from sample collection to sequencing, using commercially available mock communities (from bacterial strains as well as from DNA) and multiple human fecal samples, including a large set of positive controls created as a random mix of several participant samples. Human fecal material was sampled, and aliquots were used to test two commercially available stabilization solutions (OMNIgene·GUT and Zymo Research) in comparison to samples frozen immediately upon collection. In addition, the methodology for DNA extraction, input of DNA, or the number of PCR cycles were analyzed. Furthermore, to investigate the potential batch effects in DNA extraction, sequencing, and barcoding, we included 139 positive controls. Samples preserved in both the stabilization buffers limited the overgrowth of Enterobacteriaceae when compared to unpreserved samples stored at room temperature (RT). These stabilized samples stored at RT were different from immediately frozen samples, where the relative abundance of Bacteroidota was higher and Actinobacteriota and Firmicutes were lower. As reported previously, the method used for cell disruption was a major contributor to variation in microbiota composition. In addition, a high number of cycles during PCR lead to an increase in contaminants detected in the negative controls. The DNA extraction had a significant impact on the microbial composition, also observed with the use of different Illumina barcodes during library preparation and sequencing, while no batch effect was observed in replicate runs. Our study reaffirms the importance of the mechanical cell disruption method and immediate frozen storage as critical aspects in fecal microbiota studies. A comparison of storage conditions revealed that the bias was limited in RT samples preserved in stabilization systems, and these may be a suitable compromise when logistics are challenging due to the size or location of a study. Moreover, to reduce the effect of contaminants in fecal microbiota profiling studies, we suggest the use of ~125 pg input DNA and 25 PCR cycles as optimal parameters during library preparation.

SHEAR AND BENDING PERFORMANCE OF HORIZONTAL LAMINATED BAMBOO LUMBER BONDED WITH UREA-FORMALDEHYDE AND PRESERVED WITH DELTAMETHRIN

Deltamethrin has potential to be used for bamboo strip preservation in laminated bamboo lumber (LBL) beam industry. However, there is a lack of information regarding the effect of deltamethrin preservation on the structural performance of the LBL beam. This study was intended to observe shear and bending performance of LBL beam made of Dendrocalamus asper, preserved by deltamethrin, and glued by urea-formaldehyde. The adhesive bonding strength test following ASTM D905 and MD Block method and static bending test based on ASTM D143 were performed toward preserved and unpreserved samples. The performance was observed by calculating adhesive bonding strength, MOE, MOR, ductility index, and investigating failure modes. The results show that the average adhesive bonding strength of the treated sample is 7.28 MPa (ASTM D905) and 7.03 MPa (MD Block), while the average adhesive bonding strength of the untreated sample is 7.67 MPa (ASTM D905) and 7.41 MPa (MD Block). The average MOE (modulus of elasticity) and MOR (modulus of rupture) of the treated specimen is 18,840 MPa and 110 MPa, respectively. The untreated specimen's average MOE and MOR are 18,199 MPa and 109 MPa, respectively. The average ductility index of untreated and treated specimens is 4.8 and 3.9, respectively. The adhesive bonding strength of treated and untreated samples are higher than the bamboo shear strength. The result indicates that deltamethrin has no significant effect on the adhesive bonding strength, MOR, and MOE of the LBL beam. The LBL beams show significant plastic deformation before final beam failure.

A comprehensive assessment of four whole blood stabilizers for flow-cytometric analysis of leukocyte populations.

Though cryopreservation of cell fractions is widely used in flow cytometry studies, whole blood cryopreservation is more challenging due to the presence of erythrocytes and effects of fixatives commonly used for preservation. Here, we evaluated and compared head-to-head the performance of four commercial whole blood cryopreservation kits; (1) Cytodelics, (2) Stable-Lyse V2 and Stable-Store V2 (SLSS-V2), (3) Proteomic stabilizer (PROT-1), and (4) Transfix. We found that PROT-1, Transfix, and Cytodelics maintained the distribution of major leukocyte subsets-granulocytes, T cells, natural killer cells, and B cells, on a comparable level to unpreserved samples, despite the attenuation of fluorescence intensities in flow cytometric assays. Moreover, these three stabilizers also maintained the activated phenotypes of neutrophils upon stimulation with N-formylmethionyl-leucyl-phenylalanine and lipopolysaccharides. The upregulation of adhesion molecules (CD11b), Fc receptors (CD16), and granule proteins (CD66b), as well as the shedding of surface L-selectin (CD62L), was conserved most efficiently in PROT-1 and Cytodelics when compared to samples only treated with erythrocyte lysing. However, none of the stabilizers provided a reliable detection of CCR7 for accurate quantification of T cell maturation stages. We also evaluated the performance of Cytodelics in longitudinal clinical samples obtained from acute COVID-19 patients, where it allowed reliable detection of lymphopenia and granulocyte expansion. These results support the feasibility of whole blood cryopreservation for immunophenotyping by flow cytometry, particularly in longitudinal studies. In conclusion, the performance of different stabilizers is variable and therefore the choice of stabilizers should depend on cell type of interest, as well as antibody clones and experimental design of each study.

Use of Cotton Balls in Diapers for Collection of Urine Samples Impacts the Analysis of Routine Chemistry Tests: An Evaluation of Cotton Balls, Diapers, and Chemistry Analyzers

To evaluate the suitability of urine samples collected with cotton balls placed into diapers for routine laboratory chemistry analyses. Twenty pools of residual unpreserved urine samples were separated into control and treated aliquots. The treated samples were absorbed into 2 different brands of cotton balls, wrapped in 3 different brands of diapers, and incubated at 37°C for 1hour. The urine-soaked cotton balls were placed into a syringe and expressed via plunger depression. Urine sodium, potassium, creatinine, urea, calcium, magnesium, inorganic phosphorus, albumin, and total protein were measured on all samples on 5 automated clinical chemistry platforms: Ortho Vitros 4600, Siemens Dimension Vista 500, Beckman Coulter AU5822, Roche Cobas 6000, and Abbott Architect c8000 at 5 separate hospital laboratories. Criteria used to exclude the presence of significant effects of urine from presoaked cotton balls in a diaper on the measurement of chemistry laboratory tests were R2 >0.95, slope of 0.9-1.1, and mean bias within ±10%. Albumin and total protein measurements demonstrated significant negative bias in urine from both brands of presoaked cotton balls with all brands of diapers on all 5 chemistry platforms compared with the control urine. We did not observe a significant effect of presoaking urine in cotton balls in a diaper on the measurement of sodium, inorganic phosphorus, and urea. The remaining tests demonstrated significant effects when measured in urine from presoaked cotton balls and/or diapers that were specific to the chemistry analyzer platform or diaper. Diaper and cotton ball-based urine collection significantly impacts the measurement of several common chemistry assays.

Novel Preservation Methods for Inorganic Arsenic Speciation in Model and Natural Water Samples by Stripping Voltammetric Method

In this study, the preservation of As(III) in model solutions and natural groundwater samples from four locations in Croatia was conducted. Model laboratory samples were spiked with As(III) and As(V), and different complexing agents. Solutions were analysed in intervals of 24, 48 h and during ten days after preparation. Model samples containing citric acid, sodium citrate, sodium oxalate and potassium sodium tartrate in combination with acetic acid, spiked with As(III)and As(V), showed good species preservation. As(III), in model samples, was preserved for 7 days with citric acid, and citric acid in combination with acetic acid, as well as with tartrate. As(III), in natural samples, was preserved for 6 to 12 days with potassium sodium tartrate, citric acid, and citric acid in combination with acetic acid and showed improvement, compared with unpreserved samples (oxidation in 3 days). The results showed that acetic acid alone was not successful in preserving As speciation. Good resolution of inorganic arsenic species was achieved using differential pulse anodic stripping voltammetry technique (DPASV). Since this technique is comparatively cheaper and more convenient to use than other available techniques it could become a method of choice for arsenic speciation in water.

Do Ballast Water Management Systems Reduce Phytoplankton Introductions to Canadian Waters?

Global coastal aquatic ecosystems are negatively impacted by the introduction of harmful aquatic species through the discharge of ships’ ballast water. To reduce discharges of harmful aquatic organisms and pathogens, such as toxic phytoplankton species, ships are now transitioning to the use of ballast water management systems (BWMS) instead of ballast water exchange (BWE). This study examines the abundance and diversity of phytoplankton in ballast water managed by BWMS (or a combination of both BWE + BWMS) in comparison to those in ballast water managed by BWE alone (collected from ships arriving to Canada’s Pacific coast in 2017–2018 and 2008, respectively). The abundance and diversity of phytoplankton species were also examined in relation to key variables such as ballast water salinity and ballast water age. Total abundance of phytoplankton was significantly lower in preserved samples managed by either a BWMS or BWE + BWMS compared to BWE alone. Abundances in preserved samples were higher than observed in fresh (unpreserved) samples at the time of collection, with all samples managed by a BWMS meeting international limits for the number of viable organisms ≥10 and <50 μm in minimum dimension (based on six 1-mL live counts). While there was no apparent influence of factors such as treatment type [e.g., ultraviolet (UV) or chlorine], presence of filtration, ballast water salinity, ballast water age, nor location of last ballast water uptake on phytoplankton abundances in preserved samples, power to detect differences may be limited by sample size. Ballast water managed by BWMS also tended to have lower abundances of harmful phytoplankton species, although the difference was not statistically significant – additional research into the community composition of live cells in fresh samples could be valuable to discriminate the risk associated with phytoplankton surviving ballast water treatment.

Evaluation of different respiratory samples and saliva for the detection of SARS-CoV-2 RNA

Objective: We aimed to analyse the positivity rate and cycle threshold values indicating viral loads for SARS CoV-2 among different respiratory specimens. Additionally, we evaluated the diagnostic efficacy of saliva samples. Patients and Methods: We included combined oropharyngeal and nasopharyngeal swab (cONS), sputum, and tracheal aspirate (TA) specimens of patients. Unpreserved saliva samples were collected prospectively from hospitalized patients within 72 hours of admission. SARS CoV-2 RNA was extracted by using Bio-Speedy viral nucleic acid buffer than RT-PCR was performed with Bio- Speedy COVID-19 qPCR detection kit. Results: Retrospective evaluation revealed SARS CoV-2 RNA in 19.66% of cONS (n: 5819), 30.77% of sputum (n: 39), 29.41% of TA samples (n: 34) from 4812 patients. In the majority (86.72%) of the samples, the first cONS sample was positive. Consecutive cONS and sputum/TA samples were investigated in 52 patients of whom 11 were positive with either of these samples. Saliva positivity was detected in 60% of cONS positive (n: 20) and 30% of cONS negative (n: 12) patients. Conclusion: Although, cONS samples show the greatest diagnostic guidance, repeated sampling from multiple sites of the respiratory tract increases the possibility of COVID-19 diagnosis. Saliva samples might be considered as an alternative specimen.

Extended Stability Evaluation of Selected Cathinones.

Understanding the stability of drugs in a forensic toxicology setting is critical for the evaluation of drug concentrations. Synthetic cathinones are new psychoactive substances structurally derived from cathinone, the psychoactive component of Catha edulis (“khat”), a shrub that is indigenous to the Middle East and East Africa. Previous research has evaluated the stability of synthetic cathinones in biological matrices, including blood preserved with the combination of NaF and K2C2O4 used in gray-top tubes. However, it does not assess their stability in blood preserved with Na2EDTA, used for some clinical samples. Further, stability in unpreserved urine samples was only studied for two weeks. This research evaluates the stabilities of four Schedule I synthetic cathinones: mephedrone, MDPV (3,4-methylenedioxypyrovalerone), naphyrone, and α-PVP (alpha-pyrrolidinopentiophenone) at 20°C (room temperature), 4°C (refrigerator), and −20°C (freezer). Stability was assessed in methanolic and acetonitrile solutions, as well as in Na2EDTA-preserved blood and unpreserved urine. Solutions (1 mg/L) of each drug in each matrix stored in aliquots (100 μL, solvents; 1.2 mL, biological samples; n = 12) at each of the three temperatures for triplicate analysis on days 3, 7, 14, and 30. On day 0 of each study, three additional aliquots of each solution were analyzed. Biological samples underwent solid-phase extraction before analysis. All samples were analyzed in full-scan by gas chromatography-mass spectrometry (GC-MS). The results of this study show that under room temperature and refrigerator storage conditions, mephedrone, naphyrone, and MDPV will degrade in methanol. This degradation starts are early as day 3. Additionally, all four drugs will degrade in Na2EDTA-preserved human whole blood samples in at least one evaluated storage environment. However, when in acetonitrile-based working solutions and unpreserved urine samples, they proved to be more stable. Methanolic working solutions and samples of Na2EDTA-preserved blood containing these cathinones should be stored in the freezer and used or tested with urgency to ensure that quantitative sample analysis is as accurate as possible in forensic casework.

Challenges Associated with Generating Reliable Nanogram‐per‐Liter Measurements of Hexavalent Chromium in Groundwater

The US Environmental Protection Agency (USEPA) and several states are considering regulatory limits for hexavalent chromium (Cr(VI)) <100 ng/L, increasing the importance of obtaining accurate and reliable data. The present study presents the results of 2 studies investigating the effectiveness of chemical preservation on ng/L concentrations of Cr(VI) in groundwater. Chemically preserved and unpreserved aliquots of a groundwater sample were spiked with a known amount of Cr(VI), and then analyzed in tandem with sets of preserved and unpreserved performance test samples over 28 d. The studies showed that although Cr(VI) appears to be relatively stable over 28 d, it may be sensitive to minor matrix changes after collection. The studies also demonstrated significant challenges to measuring Cr(VI) below 100 ng/L, because the results can be subject to positive bias or contamination that may not be readily apparent. We conclude that Cr(VI) measurements using a USEPA published method below 100 ng/L may be categorized as semiquantitative at best. Environ Toxicol Chem 2020;39:1526-1533. © 2020 SETAC.

Evaluation of Copan FecalSwab™ preserved stool specimens with the BD MAX™ Enteric Bacterial Panel and the BD MAX™ Extended Enteric Bacterial Panel

The objectives of this study were to assess the ideal volume of Copan FecalSwab™ (FS) preserved stool sample to use with the BD MAX™ Enteric Bacterial Panel and the Extended Enteric Bacterial Panel (BDM GIP) and to compare the performance of FS to the recommended Meridian Para-Pak Cary-Blair medium (PP) for the BDM GIP. Three different input volumes (10, 25, and 50 μL) of stool inoculated with American Type Culture Collection strains representing the targets detected by BDM GIP were tested. Additionally, 144 unpreserved stool samples submitted for gastrointestinal (GI) testing were transferred to PP and FS media and tested by the BDM GIP using 10 μL of PP and 50 μL of FS media. A 100% agreement was observed between PP and FS results. The performance of 50 μL of FS stool preserved sample was equivalent to 10 μL of traditional Cary-Blair PP preserved specimens for GI pathogens detection using the BDM GIP.

Optimization of Preservation Methods Allows Deeper Insights into Changes of Raw Milk Microbiota.

The temporal instability of raw milk microbiota drastically affects the reliability of microbiome studies. However, little is known about the microbial integrity in preserved samples. Raw cow milk samples were preserved with azidiol or bronopol and stored at 4 °C, or with dimethyl sulfoxide (DMSO) or a mixture of azidiol and DMSO and stored at −20 °C for up to 30 days. Aliquots of 5-, 10-, and 30-day post-storage were treated with propidium monoazide (PMA), then analyzed by sequencing the 16S rRNA gene V3-V4 and V6-V8 regions. The V6-V8 gave a higher richness and lower diversity than the V3-V4 region. After 5-day storage at 4 °C, the microbiota of unpreserved samples was characterized by a drastic decrease in diversity, and a significant shift in community structure. The treatment with azidiol and DMSO conferred the best community stabilization in preserved raw milk. Interestingly, the azidiol treatment performed as well for up to 10 days, thus appearing as a suitable alternative. However, neither azidiol nor bronopol could minimize fungal proliferation as revealed by PMA-qPCR assays. This study demonstrates the preservative ability of a mixture of azidiol and DMSO and provides deeper insights into the microbial changes occurring during the cold storage of preserved raw milk.

Long-term stability of water samples — reanalysis of 20-year-old unpreserved samples

The current study compiles data from the reanalysis of 25 water samples stored unpreserved at ambient temperature for 20 years. Small changes in pH, conductivity and chloride and no significant effects on Al and total hardness were detected. The small effects measured, even during long-term storage under unsuitable conditions, suggest that samples taken from pristine water bodies remain chemically stable over many years.

A modified Swanson method to determine permeability from mercury intrusion data in marine muds

Abstract The permeability of shallow marine sediments is an extremely important parameter to constrain, as it affects fluid and nutrient transport near the sediment-water interface, mediates mass exchange between igneous basement and oceans, and plays a role in seismicity along convergent margins. Determining the permeability of these sediments in the laboratory is difficult because existing methods typically require fully saturated, intact samples of large volume (tens of cm3), which are usually not collected with high spatial resolution in scientific ocean drilling operations. We demonstrate how mercury injection capillary pressure (MICP) data may be used to predict the permeability of marine muds using a modification of the widely used Swanson method. Our results show that MICP measurements performed on small, irregular, and, most importantly, unpreserved samples can yield important permeability information. This will improve the spatial resolution of permeability data in the shallow marine subsurface and allow analyses to be performed on the significant quantities of existing legacy core.

Optimization of routine microscopic and molecular detection of parasitic protozoa in SAF-fixed faecal samples in Sweden

Background: Nucleic acid-based methods are increasingly used for screening of gastrointestinal parasites. Microscopy is still used and Swedish routine protocol consists of formalin ethyl-acetate concentration and do not include screening for trophozoites or Cryptosporidium spp. This study aimed to compare detection with the Swedish routine microscopy method to an extended method that includes screening for trophozoites and Cryptosporidium. Furthermore, we also developed a method for DNA recovery from SAF-fixed faecal samples and compared the real-time PCR detection of Giardia intestinalis, Dientamoeba fragilis, Cryptosporidium spp., Entamoeba histolytica and Entamoeba dispar from SAF-fixed and unpreserved faecal samples. PCR results were then compared with microscopy results.Methods: SAF-fixed and unpreserved faecal samples from 1000 patients at the Clinical microbiology laboratory in Region Jönköping County, Sweden, were included. Samples were analysed with routine formalin ethyl-acetate concentration, wet mounts from both concentrated and unconcentrated samples, Ziehl–Neelsen staining on patients with certain symptoms and real-time PCR.Results: We found a significant higher detection rate of parasites with the extended microscopy method compared to the Swedish routine microscopy method when SAF-fixed samples were used. The detection rate with real-time PCR in SAF-fixed samples was equal to the detection rate in unpreserved samples. There was no significant difference in detection comparing extended microscopy and real-time PCR.Conclusion: In conclusion, this study showed that the extended microscopy method increased detection of intestinal protozoa with detection of both trophozoites and Cryptosporidium spp. We also showed that SAF-fixative can be used for detection of parasite-DNA with real-time PCR.