Sample Preservation Research Articles

An Epidemiologic Investigation for an Outbreak of Norovirus Infection in a Daycare Center in Gyeonggi-Do, Republic of Korea, 2023

Background/Objectives: Norovirus is one of the primary causes of foodborne illness in South Korea. This study aimed to identify the cause of a norovirus outbreak in a daycare center in a city in February 2023 and to prevent further spread through an epidemiologic investigation. Methods: A total of 93 individuals, including daycare staff, children, and kitchen staff, were included. A field epidemiologic investigation was conducted, consisting of case definition, collection of environmental and preserved food samples, and human specimens, along with interviews. A matched case-control study (1:3 ratio) was designed to analyze risk factors, and a statistical analysis, including odds ratios with 95% confidence intervals and chi-square tests, was performed to identify associations between food consumption and infection. Person-to-person transmission was also assessed through epidemiological data analysis. Results: Among the 93 individuals, 16 (17.2%) were identified as cases, of which nine (9.7%) were confirmed cases. The same genotype of norovirus (GII) was detected in eight human samples. No significant association was found between specific food items and infection. The epidemic curve and transmission network analysis suggested that the primary mode of transmission was person-to-person contact within the daycare center. Conclusions: This study highlights the critical role of hygiene practices in daycare settings to prevent person-to-person transmission of norovirus. Regular public health education, environmental disinfection, and early symptom recognition are essential preventive measures.

Weak genetic divergence and signals of adaptation obscured by high gene flow in an economically important aquaculture species

BackgroundThe genetic diversity of a population defines its ability to adapt to episodic and fluctuating environmental changes. For species of agricultural value, available genetic diversity also determines their breeding potential and remains fundamental to the development of practices that maintain health and productivity. In this study, we used whole-genome resequencing to investigate genetic diversity within and between naturalized and captively reared populations of Pacific oysters from the US Pacific coast. The analyses included individuals from preserved samples dating to 1998 and 2004, two contemporary naturalized populations, and one domesticated population.ResultsDespite high overall heterozygosity, there was extremely low but significant genetic divergence between populations, indicative of high gene flow and/or little variability from founding events. The captive population, which was reared for over 25 years was the most genetically distinct population and exhibited reduced nucleotide diversity, attributable to inbreeding. Individuals from populations that were separated both geographically and temporally did not show detectable genetic differences, illustrating the consequences of human intervention in the form translocation of animals between farms, hatcheries and natural settings. Fifty-nine significant FST outlier sites were identified, the majority of which were present in high proportions of the captive population individuals, and which are possibly associated with domestication.ConclusionPacific oysters in the US Pacific coast harbor high genetic heterozygosity which obscures weak population structure. Differences between these Pacific oyster populations could be leveraged for breeding and might be a source of adaptation to new environments.

P1344 Impaired health-related quality of life is associated with alterations in gut microbiota signatures in patients with Inflammatory Bowel Disease: baseline data from the Australian IBD Microbiome study

Abstract Background Inflammatory Bowel Disease (IBD) activity as well as disease monitoring and management have a substantial impact on the health-related quality of life (HRQoL) of affected patients1. This study investigated the association between HRQoL and gut microbial composition in IBD patients using the 32-item Inflammatory Bowel Disease Questionnaire (IBDQ-32). Methods Paired faecal and oral samples alongside participant demographics, disease characteristics and the IBDQ-32 survey were collected at baseline from patients with Crohn’s disease (CD) or ulcerative colitis (UC) enrolled in the Australian IBD Microbiome (AIM) study2 from June 2019 to November 2023. IBDQ-32 scores range from 32 to 224, with a higher score indicating better HRQoL. Patients were divided into two groups: impaired HRQoL (cumulative score <170) and preserved HRQoL (>170). Faecal and oral samples were self-collected in DNA stabilising buffer, aliquoted and stored at -80oC until extraction. Samples underwent 16S rRNA sequencing with annotation of DNA sequences to operational taxonomic units at the genus level. Differences in alpha diversity (Chao1) between groups were assessed using Mann-Whitney U tests. Linear discriminant analysis was performed between groups to identify significantly enriched bacterial taxa. Beta diversity (weighted UniFrac dissimilarity) in bacterial communities were shown using Principal Coordinate Analysis (PCoA), and significance of variance was tested using ADONIS in R. Results 446 participants (232 CD, 214 UC) returned baseline faecal (n = 403) and/or oral samples (n = 436) and were included in the analysis, with patient and HRQoL characteristics in Table 1. Most CD and UC patients were in clinical remission at baseline (77.4% and 65.2% respectively, Table 1). Despite this, impaired HRQoL was common in both CD (42%) and UC (41%). Patients with impaired HRQoL had lower faecal microbial alpha and beta diversity (Fig 1A,B). There were no differences in alpha or beta diversity in oral samples. Linear discriminant analysis showed 9 and 36 significantly altered genera enrichment in impaired and preserved HRQoL faecal samples respectively (Fig 1C). Conclusion Despite a high proportion of clinical and biochemical remission, impaired HRQoL was common amongst UC and CD patients within the AIM study. Lower faecal but not oral alpha diversity was associated with impaired HRQoL, indicating reduced microbial richness in the gut. A high number of bacterial taxa had differential enrichment according to HRQoL status. Identification of a distinct microbial signature associated with impaired HRQoL may help to identify patients that require both optimisation of disease control and greater psychosocial support.

Reviving diversity: cryoprotectants and culturing methods enhance recovery of mammalian gut microbes from field samples

Abstract The field of microbial ecology is increasingly recognizing the need for methods to isolate and culture gut microbes to better understand how these microorganisms impact animal physiology, especially in mammalian hosts. Currently, there is a lack of clear methods to store microbial samples for cultivability, especially when samples are collected from the field, transported to the laboratory, and preserved under long-term storage for weeks to months compared to mere days in the biomedical field. Here, the cecal contents of groundhogs (Marmota monax) were processed and stored with or without various preservation solutions at −80 °C for at least 2 months. All microbial samples were then grown in distinct nutrient media in liquid and plate conditions and were incubated under anaerobic and aerobic environments. Treatment comparisons revealed that the samples stored in preservation solutions containing 1 or more cryoprotectants provided the greatest and most consistent bacterial densities. To test the long-term storage efficacy of the preservation solutions, we inventoried taxonomic identities and abundances of these cultures using 16S rRNA amplicon sequencing. Our findings highlight that: (1) preserved samples containing cryoprotectants exhibited the highest microbial richness and diversity and resembled the original cecal samples the most when grown under anaerobic conditions; and (2) the effect of individual animal identity was detectable in the membership of cultured communities, irrespective of preservation solutions. Our study is the first to demonstrate the importance of preservation solutions containing multiple cryoprotectants for long-term storage and further microbial culturing and novel isolation. Understanding and improving storage methods that preserve microbial physiology and conserve their compositional diversity is essential for field-collected samples useful in mammalian microbiome and culturomics studies, promoting a better comprehension of the identity and function of wild host-associated microbiomes.

InDrops-2: a flexible, versatile and cost-efficient droplet microfluidic approach for high-throughput scRNA-seq of fresh and preserved clinical samples.

The expansion of single-cell analytical techniques has empowered the exploration of diverse biological questions at the individual cells. Droplet-based single-cell RNA sequencing (scRNA-seq) methods have been particularly widely used due to their high-throughput capabilities and small reaction volumes. While commercial systems have contributed to the widespread adoption of droplet-based scRNA-seq, their relatively high cost limits the ability to profile large numbers of cells and samples. Moreover, as the scale of single-cell sequencing continues to expand, accommodating diverse workflows and cost-effective multi-biospecimen profiling becomes more critical. Herein, we present inDrops-2, an open-source scRNA-seq technology designed to profile live or preserved cells with a sensitivity matching that of state-of-the-art commercial systems but at a 6-fold lower cost. We demonstrate the flexibility of inDrops-2, by implementing two prominent scRNA-seq protocols, based on exponential and linear amplification of barcoded-complementary DNA, and provide useful insights into the advantages and disadvantages inherent to each approach. We applied inDrops-2 to simultaneously profile multiple human lung carcinoma samples that had been subjected to cell preservation, long-term storage and multiplexing to obtain a multiregional cellular profile of the tumor microenvironment. The scalability, sensitivity and cost efficiency make inDrops-2 stand out among other droplet-based scRNA-seq methods, ideal for large-scale studies on rare cell molecular signatures.

Sampling mass mortality events to enable diagnoses: A protocol using freshwater mussels

Abstract Many taxa around the globe are threatened by often unexplained mass mortality events (MMEs), which can decimate populations and compromise key ecosystem functions. One example of a highly threatened taxon facing frequent MMEs is freshwater mussels (Unionida). There has been a recent increase in interest in understanding the causes of freshwater mussel MMEs, but standardised methodologies for how best to respond to them to facilitate diagnoses are unavailable. When an MME is observed, swift and appropriate sample collection is imperative owing to the transient nature of these phenomena. Here we provide structured guidance that will facilitate rapid and appropriate sampling of MMEs, using freshwater mussels as an example. We set out standardised procedures for sample collection, preparation and preservation. The procedures we outline will improve our capacity for diagnostic investigations of MMEs and other mortality events, not only in freshwater mussels but also across many other taxa. This, in turn, can inform appropriate management responses.

Effects of Different Voided Urine Sample Storage Time, Temperature, and Preservatives on Analysis with Multiplex Bead-Based Oncuria Bladder Cancer Immunoassay.

Background/Objectives: Urinalysis accuracy requires reliable sample stability that is dependent on the chosen collection and storage conditions. The multiplex Oncuria bladder cancer immunoassay currently needs urine samples stored at 4 °C until analysis, which requires more effort, equipment, and workflow than storing samples at room temperature. Thus, successful sample storage at room temperature (20 °C) may reduce laboratory handling time and expenses. This study evaluated whether different voided urine sample collection and storage parameters affected subsequent biomarker analysis with Oncuria. The Oncuria simultaneously quantifies 10 protein analytes in urine to generate a bladder cancer diagnostic signature. Methods: Samples were stored at varied temperatures (20 °C, 4 °C, -20 °C) for up to 1 month. The effects of adding two commercial urine sample stabilizers and antibiotics (trimethoprim) were also assessed. Subsequently, multiple potential biospecimen stabilizers were tested in urine samples and evaluated with Oncuria in hopes of allowing the urine sample to remain at room temperature for extended periods of time. Results: First, it was demonstrated that voided urine samples stored at room temperate without such stabilizers had different levels of the 10 analytes associated with the Oncuria test compared to voided urine samples stored at 4 °C. Next, we evaluated the effects of commercially available biospecimen stabilizers. Despite the addition of these stabilizers, the levels of the 10 analytes were altered when the samples were stored at room temperature for prolonged periods of time. Therefore, we could not identify a suitable biospecimen stabilizer that would not require sample refrigeration. Conclusions: To minimize sample degradation/alteration after collection, voided urine samples should be refrigerated until analyzed with Oncuria as the refrigeration is advantageous for the storage and the transport of these urine samples.

Witnessing a discrete microdroplet freezing event via real-time electrochemical monitoring of solution temperature.

Temperature monitoring has immediate relevance to many areas of research, from atmospheric environmental studies to biological sample and food preservation to chemical reactions. Here, we use a triple-barrel electrode to provide temperature readouts in bulk solution and microdroplets, as well as electrochemically monitor freezing events in a microdroplet. Using this method, we are able to identify distinct characteristics of a freezing aqueous droplet (supercooling, ice formation beginning and end, temperature change, and thawing) with greater temporal resolution than a standard thermocouple and without the use of microscopy. By correlating the amperometric signal change caused by alterations in the diffusion coefficient of the electrochemical system in response to temperature changes, we can calculate the instantaneous temperature at our electrode, as well as the physical behavior of ice formation and expansion. Our results suggest that these electrochemical techniques can provide real-time monitoring of the physical processes involved in aqueous temperature change and ice nucleation events. Here, we employ a novel technique using triple-barrel electrodes to provide temperature readouts in bulk solution and microdroplets, as well as electrochemically monitor freezing events in a microdroplet. Because ice nucleation spans many research fields, it is important to have a variety of tools that can be used to better understand these frozen systems. Our data shows that electrochemistry can provide real-time information on the thermal properties of aqueous environments, and these types of measurements can be extended to microdroplets. The electrochemical signal details all the significant moments in a droplet freezing event, allowing us to use electrochemistry as a stand-alone tool for monitoring freezing events with excellent temporal and spatial resolution.

An all-in-one microfluidic cryopreservation system and protocols with gradually increasing CPA concentration.

In regular biosample cryopreservation operations, dropwise pipetting and continuous swirling are ordinarily needed to prevent cell damage (e.g. sudden osmotic change, toxicity and dissolution heat) caused by the high-concentration cryoprotectant (CPA) addition process. The following CPA removal process after freezing and rewarming also requires multiple sample transfer processes and manual work. In order to optimize the cryopreservation process, especially for trace sample preservation, here we present a microfluidic approach integrating CPA addition, sample storage, CPA removal and sample resuspension processes on a 30 × 30 × 4 mm3 three-layer chip. The sample solution could be added into CPA solution with pre-generated increasing concentration to decrease possible osmotic damage. Utilizing specially designed microfluidic structure and fluid field analysis, on-chip sample enrichment and CPA removal were achieved. A novel dead-end micro valve strategy with a simplified control module was applied and evaluated to assist on-chip mixing and sample pellet resuspension. The entire biosample cryopreservation process was also performed that verified the functions of the integrated microfluidic platform. Altogether, this developed platform could be an effective approach to realize automatic, all-in-one, low-damage cryopreservation operation.

Determination of Sodium and Potassium in Groundwater (Borewell) Samples of Baglan Region of Maharashtra by Flame Photometry

Groundwater is a critical resource for drinking and agriculture in the Baglan region of Maharashtra, India. This study focuses on assessing the concentrations of sodium (Na⁺) and potassium (K⁺) in borewell water samples from six locations: Taharabad, Satana, Nampur, Bramhangaon, Deola, and Nirpur. Samples were collected once during January 2024, ensuring proper sampling techniques and preservation. The analysis was performed using flame photometry, a reliable and cost-effective method for quantifying alkali metals in water. Sodium concentrations ranged from 7.36 to 9.94 mg/L, while potassium levels varied between 5.25 and 7.27 mg/L, both within permissible limits established by the World Health Organization (WHO) and Bureau of Indian Standards (BIS). Higher concentrations in samples from Nampur and Nirpur suggest possible anthropogenic influences, such as fertilizer use, and geological variations. The study underscores the potential health implications of ion levels in drinking water and their impact on soil salinity and agricultural productivity. While sodium levels are safe for consumption, potassium concentrations near the upper threshold highlight the need for continuous monitoring. Recommendations include raising awareness about sustainable agricultural practices, implementing water quality management strategies, and conducting further research to analyze seasonal variations and additional ion parameters. These findings are crucial for ensuring the safe and sustainable use of groundwater in the region.

SnRNA-seq of long-preserved FFPE samples from colorectal liver metastasis lesions with diverse prognoses

Differences in prognostic outcomes are prevalent in patients with colorectal cancer liver metastases. Comparative analysis of tissue samples, particularly applying single-cell transcriptome sequencing technology, can provide a deeper understanding of potential impacting factors. However, long-term monitoring for prognosis determination necessitates extended preservation of tissue samples using formalin-fixed and paraffin-embedded (FFPE) treatments, which can cause substantial RNA degradation, presenting challenges to single-cell or single-nucleus sequencing. In this study, employing snRandom-seq, a single-nucleus RNA sequencing (snRNA-seq) technology specifically for FFPE samples, we tested multiple lesion samples from 18 distinctive colorectal cancer liver metastasis cases with diverse prognostic outcomes that have been preserved for at least three years (mostly over five years). The process yielded expression data from 82,285 cells. The high-quality snRNA-seq data demonstrate the feasibility of single-nucleus sequencing in long-term preserved FFPE samples, offering potential insights into the heterogeneity between different prognoses of colorectal cancer liver metastases, and the relationship between the heterogeneity within different lesions of the same patient and prognosis.

The use of 10% buffered formalin as a preservative agent when cerebrospinal fluid analysis is delayed.

To evaluate the utility of 10% buffered formalin in preserving canine cerebrospinal fluid samples when analysis was delayed. Inclusion criteria were dogs >10 kg having cerebrospinal fluid analysis performed as part of investigations at a referral hospital. Samples were submitted to an external laboratory in tubes containing Ethylenediaminetetraacetic acid (ETDA) as paired 0.5 mL samples; one with the addition of 0.05 mL of 10% buffered formalin and the other without. The samples were reviewed by a single pathologist who was blinded as to which sample contained formalin. Nucleated cell preservation was graded by the pathologist from 1 to 4 (1 being poor and 4 being excellent). Total protein was measured in both samples. Forty-five paired samples were included. There was no significant difference in detectability of nucleated cells between plain and formalin samples. Grade 3 was taken as the cut off for acceptable cell preservation. Based on all available samples and assessing the preservation of both nucleated cells and red blood cells, samples containing formalin were significantly more likely to be acceptably preserved. This preservation analysis was repeated on the 17 samples with at least one nucleated cell in both formalin and plain samples and was not statistically significant. The addition of formalin did not significantly improve the preservation of cerebrospinal fluid samples when analysis was delayed; however, concerns raised by previous authors regarding reduced cell preservation with addition of formalin were also not confirmed. Further large-scale studies are required to investigate the effect on nucleated cell preservation.

NMR metabolomics as a complementary tool to brix-acid tests for navel orange quality control of long-term cold storage.

Quality control plays a crucial role in maintaining the reputation of agricultural organizations by ensuring that their products meet the expected standards and preventing any loss during the packaging process. A significant responsibility of quality control is conducting periodic product assessments. However, subjective interpretation during physical inspections of fruits can lead to variability in reporting. To counter this, assessing total soluble solids (Brix) and percent acidity (Acid) can provide a more objective approach. Nevertheless, it is essential to note that many fruit metabolites can impact these parameters. Nuclear magnetic resonance (NMR) spectroscopy, particularly 1H-NMR, has become a popular tool for quality control in recent years due to its precision, sample preservation, and high throughput analysis. This manuscript investigates if the standard Brix/Acid tests are directly related to the levels of metabolites during cold storage. Using citrus as the model system, a metabolomics analysis was conducted to identify patterns in the cold storage metabolite profiles of the juice, albedo, and flavedo tissues. The results show that Brix (or total dissolved solids) correlates well with sucrose, glucose, and fructose levels and moderately with choline levels. Acid(percent acidity) levels displayed a negative correlation with both fructose and choline levels. Interestingly, the formate levels were susceptible to storage time and directly related to Acid measurements. This study suggests metabolomics could be a complementary technique to quality control of fruits in cold storage, especially with cost-effective desktop NMR spectrometers.

Are spinal cord and medulla samples from embalmed donors suitable for histological examination? A pilot study.

A general belief exists that tissue from anatomical donors, especially from the central nervous system (CNS), may not be suitable for histological investigation. This is based on the idea that fixation routinely used in embalming whilst optimal for enabling dissection, insufficiently preserves tissue architecture at the cellular level. However, anatomical donors represent a precious resource for microscopical investigation, provided that preservation is sufficient to enable recognition of structures at the histological level. This could considerably extend the biomedical knowledge currently gained from donations. In this study, we addressed this question and examined histologically, samples of medulla and spinal cord from donors from the Anatomical Gift Programme of RCSI in Dublin. Samples of medulla and spinal cord in the cervical, thoracic and lumbar regions were obtained with appropriate permissions from four different donors that had been previously embalmed for routine anatomical examination. The tissue obtained was processed for paraffin embedding and routine histology. Analysis revealed that several features were identifiable with good histological detail. A scoring system was applied to evaluate the level of histological preservation in the various samples by assessing the following parameters: tissue integrity, presence of leptomeninges along the entire section surface, distinction/adherence grey/white matter, identification of neurons, other cell nuclei, neuropil pattern, capillaries and other intraneural vessels. Lumbar spinal cord and to a lesser extent medulla and cervical spinal cord showed on average good quality of preservation. Conversely, thoracic spinal cord tended, in general, to be less well preserved. We can conclude that spinal cord and medulla samples from embalmed donors can be suitable for histological examination. These findings open new avenues of study of spinal cord and brain stem anatomy on cadaveric tissue from donors already existing in anatomy donation programmes. These results also pave the way for the potential development of new human models of study useful to spinal cord and brain stem researchers. Finally, this expands considerably the impact of the generosity of anatomical donors for the advancement of biomedical knowledge.

Benchmarking three DNA metabarcoding technologies for efficient detection of non-native cerambycid beetles in trapping collections

Individual sorting and identification of thousands of insects collected in mass trapping biosurveillance programmes is a labour-intensive and time-consuming process. Metabarcoding allows the simultaneous identification of multiple individuals in a single mixed sample and has the potential to expedite this process. However, detecting all the species present in a bulk sample can be challenging, especially when under-represented non-native specimens are intercepted. In this study, we quantified the effectiveness of DNA metabarcoding at detecting exotic species within six different mock communities of native and non-native species of European xylophagous cerambycid beetles. The main objective is to compare three different sequencing technologies (MinION, Illumina and IonTorrent) to evaluate which one is the most suitable in this context. Additionally, dry and wet (monopropylene glycol and water) collection methods were compared. Although not observing significant differences in the total number of species detected amongst the three sequencing technologies, the MinION detected a greater number of species in field-like samples. All three sequencing technologies achieved success in detecting and identifying closely-related species and species in low abundance. The capture method of insects in the field greatly influenced sample preservation and detection. Individuals captured in traps containing monopropylene and water had lower DNA concentration, leading to lower species detection rates compared to individuals killed using just an insecticide without any collection medium.

Volunteer Accuracy in a Benthic Macroinvertebrate Participatory Science Project

Concerns about the accuracy of volunteer-derived aquatic macroinvertebrate identifications and the resulting influence on calculated water quality metrics can limit use of volunteer-generated data in freshwater-focused participatory science programs. To address these concerns, we assessed 357 benthic macroinvertebrate quality control (QC) samples collected by volunteers using leaf packs, kick nets, and visual assessments between 2011 and 2016 for the Environmental Quality Institute (EQI) in North Carolina, USA. We reviewed each sample for quality, and compared macroinvertebrate identifications and water quality metric scores determined by volunteers to identification and metrics determined by an entomologist. About 80% of the QC samples were identified to be of high quality, indicating proper preparation, preservation, and labeling of samples. The majority of samples that received low quality ratings were improperly or poorly preserved. We recommend use of 95% (rather than 70%) ethanol for macroinvertebrate preservation, and increased communication to volunteers during QC sampling periods to enhance their success in properly preserving samples. We observed significant (p < 0.005) linear relationships between volunteer and entomologist-derived water quality metrics including a biotic index, Taxa Richness, and percent intolerant Ephemeroptera, Plecoptera and Trichoptera (EPT) taxa. However, visual assessments – those in which no sampling equipment was used to collect aquatic macroinvertebrates – reduced the goodness of fit between volunteer and entomologist-derived biotic index scores and artificially increased the goodness of fit between volunteer and entomologist derived Taxa Richness and percent EPT scores. We recommend calculating water quality metrics based only on leaf pack and kick net samples collected by volunteers.

Practical considerations for plunge freezing samples over 40 °C for Cryo-EM

Cryo-EM is now an established tool for examining samples in their native, hydrated states—a leap made possible by vitrification. Utilising this sample preparation method to directly visualise temperature-responsive samples allows for deeper insights into their structural behaviours under functional conditions. This requires samples to be plunge-frozen at elevated temperatures and presents additional challenges, including condensation within the blotting chamber and difficulties in maintaining a stable sample temperatures. Here, we address these challenges and suggest practical strategies to minimise condensation and reduce temperature fluctuations during the plunge-freezing of samples at elevated temperatures (>40 °C). By preheating equipment and reducing chamber humidity and blotting times, we can improve sample preservation and grid reproducibility. These considerations are then demonstrated on poly(N-isopropylacrylamide) microgels, which exhibit a volume phase transition due to temperature changes.

On the generation of light hydrocarbons from the closed pores of Jurassic strata, Sichuan Basin

Light hydrocarbons (C1-C9) offer a specific opportunity to study petroleum generation mechanisms. However, a significant amount of light hydrocarbons evaporate during sample collection, preservation, and preparation. This study aims to identify the origin of light hydrocarbons preserved in the closed pores of Jurassic shale strata from the Sichuan Basin where evaporative losses have been minimized. Twenty-one samples of various maturity levels and lithofacies were investigated using a new approach based on online decrepitation-gas chromatography. Light hydrocarbons were released from the closed pores of finely stratified mudstone, limestone, and siltstone. Among these, gaseous hydrocarbons in the C1-C5 range were utilized to discriminate between petroleum generated by two opposing reactions, i.e., free radical and carbenium ion cracking. Accordingly, in situ petroleum can be divided into three types. (1) Free radical cracking type: a predominance of methane and straight-chain alkanes in the gaseous hydrocarbon range; (2) Carbenium ion cracking type: a deficiency of methane and straight-chain alkanes in gaseous hydrocarbons; (3) Mixed cracking type: their gaseous hydrocarbons exhibit intermediate compositions between those of free radical and carbenium ion cracking types. Differences in the chemical composition of the gaseous hydrocarbons, which can be used to discriminate between the two generation mechanisms, were further supported by variations in the mineral composition, e.g., calcite and mixed-layer clay minerals are characteristic of free radical reaction and carbenium ion reaction, respectively. The present classification diagrams for gaseous hydrocarbons are based on the Jurassic shale strata of the Sichuan Basin. This novel approach for determining the whole range of hydrocarbons from closed pores shows promising prospects for deciphering the origin of light hydrocarbons and thus may be extended to other regions of interest.

QLTI-09. CLINICAL TRIALS IN NEURO-ONCOLOGY: DESIGN, LOGISTICS, CHALLENGES, AND PRACTICAL CONSIDERATIONS

Abstract Timely, secure and reliable transportation, precise handling and storage of biological specimens are critical for the success of clinical research. Research in neuro-oncology often involves complex assays such as next-generation sequencing where the integrityof brain tumor specimens is paramount. These challenges are pronounced in most Lower Middle-Income Countries (LMIC), due to climatic factors and infrastructure limitations, necessitating stringent measures to preserve sample quality and their genetic data integrity for downstream analysis. In this study, we conducted extensive cohort analysis on 80 tissues randomly picked samples of the 3600 samples collected across India to assess the impact of collection protocols, transportation logistics, and long-term storage on the genetic material of tissues. The quality and quantity of the isolated nucleic acids was determined by BioAnalyzer and Qubit parameters. Tissue samples were collected and stored at -80°C in RNAstable® within 4-12 hrs of collection. The DNA and RNA obtained from tissue samples stored for over one year was found to be of good quality with corresponding DNA Integrity Number (DIN) and RNA Integrity Number (RIN)between 7-9. Also, optimum quantity of DNA and RNA was obtained for whole exome and transcriptome sequencing. Upon sequencing, these samples showed good read coverage of 100X or more. These findings provide critical insights into the measures necessary for optimizing sample preservation and transportation to ensure accurate research outcomes. The results indicate that appropriate sample collection, transportation, and long-term storage of bio-specimens can be used effectively for future research. Additionally, the outcome underscores the potential for long-term studies in neuro-oncology using archived biological samples without compromising data integrity.

An outbreak of Clostridium perfringens infection on a training ship anchored in Busan, Korea.

In September 2023, an outbreak of food-borne disease occurred among students on a training ship docked in Busan. This was an epidemiological investigation with the aim of improving infection prevention activities and group meal service practices on board ships. In this study, a case was defined as an individual who experienced diarrhea more than twice a day during their training period aboard the training ship. A total of 171 exposed individuals including 6 food handlers was well-defined; therefore, a retrospective cohort study was conducted. We administered a questionnaire and conducted laboratory tests including 38 rectal swab samples. Relative risk (95% confidence interval) for each food item was calculated. Of the 165 students and school staff members, 41 met the case definition, resulting in an attack rate of 24.8%; all cases were students. The shape of the epidemic curve was unimodal, with the peak from 00:00 to 06:00 on September 7, 2023. Clostridium perfringens was detected in 9 cases, and no other pathogens were found. Significant relative risk was shown in 11 different food items. C. perfringens was the causative pathogen of this outbreak on the training ship. Due to the lack of preserved food samples, the exact source of infection could not be confirmed. Ships are not classified as collective dining facilities, leaving them in a management blind spot. Therefore, specialized guidelines, voluntary inspections by the operating entities, and continuous education for managers and staff are necessary.