Extraction Protocol Research Articles

Rice Husk as a Sustainable Amendment for Heavy Metal Immobilization in Contaminated Soils: A Pathway to Environmental Remediation

Rice husk is a waste byproduct of rice production. This material has a moderate cost and is readily available, representing 20–22% of the biomass produced by rice cultivation. This study focused on the properties of rice husk in the remediation of soils contaminated by heavy metals. The effect of particle size, pH, and the presence of organic ligands on sorption efficiency was evaluated for Cd, Cu, and Mn. The continuous flow method was used to select suitable operative conditions and maximize the retention of heavy metals. Subsequently, pot experiments were carried out by growing two broadleaf plants, Lactuca sativa and Spinacia oleracea, in aliquots of soil collected in a Piedmont (Northwest Italy) site heavily contaminated by Cu, Cr, and Ni. Rice husk was added to the contaminated soil to evaluate its effectiveness in immobilizing heavy metals. The availability of Cr, Mn, Ni, Cu, Zn, Cd, and Pb in soil was studied using Tessier’s sequential extraction protocol. The content of the elements was also analyzed in plants and the uptake of heavy metals was evaluated in relation to the addition of rice husk. The growth of both plants was more efficient in the presence of rice husk due to its ability to reduce the mobility of heavy metals in the soil. The simplicity, cost-effectiveness, and scalability of its employment make the use of rice husk suitable for practical applications in soil remediation.

Validation of a triiodothyronine (T3) ELISA for mouse fecal samples.

Acquiring sufficient blood for hormone analysis in mice can be a limiting step. Hormone analysis techniques using non-invasive sample collection have been vigorously developed for endangered species, from whom blood sampling is prohibited, or from species that are otherwise difficult to handle in a laboratory setting. Because there are interactions between glucocorticoids and thyroid hormones (T3 and T4), reducing the animal's "distress" during sample collection is imperative. Measurement of fecal T3 provides less sensitive, baseline information regarding thyroid function while permitting a non-invasive technique for more frequent sampling. We demonstrated that using a methanol extraction protocol produced the most reliable fecal T3 measurement in an enzyme-linked immunosorbent assay (ELISA). We found that during a thyroid hormone-treated state, fecal and plasma T3 measurements from mice are directly related, while during a methimazole-treated state, fecal and plasma T3 measurements from mice are inversely related. Fecal samples are a useful way to monitor thyroid hormone function in laboratory mice.

Comparison of different diagnostic protocols for the detection of Toxocara spp. in faecal samples of cats and dogs

BackgroundToxocara canis and Toxocara cati are parasitic nematodes that occur worldwide. As embryonated Toxocara spp. eggs in the environment pose a zoonotic risk, especially for children, optimal diagnostic approaches are necessary for effective disease response and management, including surveillance. However, little is known about the performance of different diagnostic protocols for detecting Toxocara spp. in the faeces of cats and dogs, hampering movement towards an optimal diagnostic process. This study aimed to compare detection methods, including a newly developed sequential sieving protocol (SF-SSV) and a high-throughput multiplex qPCR-based method to facilitate epidemiological studies.MethodsSpecies-specific Toxocara spp. egg suspensions and canine and feline faecal samples from the field were used to estimate analytical and diagnostic sensitivity of the protocols. The performance of two automated DNA extraction protocols using enzymatic and mechanical lysis were compared by multiplex qPCR, targeting both T. canis and T. cati-specific genomic sequences. All samples were examined by microscopy-based techniques, the sedimentation flotation technique (SF) and a newly developed SF-SSV for the detection, enrichment and purification of parasite eggs. The costs and processing times necessary for all protocols were estimated and compared for both single samples and sets of 100 samples.ResultsTo detect Toxocara spp. eggs, SF-SSV showed the highest analytical sensitivity and a significantly higher diagnostic sensitivity than the DNA detection methods. Mechanical lysis performed better than enzymatic lysis for automated DNA extraction. In automated DNA extraction, 96-well plates performed better than 24-well plates. DNA detection and microscopy-based parasitological methods showed substantial agreement between the results generated by each method. Microscopy-based techniques required the lowest costs and least hands-on time for a single sample. However, when costs and labour were estimated for a set of 100 samples, the DNA detection protocol using 96-well plates for extraction revealed costs similar to SF-SSV and the fastest processing times.ConclusionsSF-SSV was superior in terms of analytical and diagnostic sensitivity for the detection of Toxocara spp. eggs. For larger sets of samples, multiplex qPCR-based DNA detection represents an alternative to microscopy-based methods, based on the possibility of faster sample processing at similar costs to SF-SSV, and the ability to provide species-specific diagnoses.Graphical

NANOPORE-BASED INTRA-OPERATIVE CLASSIfiCATION OF CENTRAL NERVOUS SYSTEM TUMOURS IN THE NHS

Abstract AIMS The 2021 WHO classification of CNS tumours necessitates the use of molecular testing in order to reach a confident diagnosis of many tumour types. At present, this is achieved using array-based technology delivered by a centralised model. This approach has inherent delays that mean it is often several weeks before the treating clinical team is informed of diagnosis, delaying the start of adjuvant therapy and causing significant distress for patients. As such, there is an urgent need to rethink this pathway and improve time to diagnosis. Nanopore longread sequencing technology has the potential to enable a paradigm shift in diagnostic and therapeutic pathways, offering rapid, comprehensive molecular diagnosis that can be performed in the intra-operative setting. We aimed to test the hypothesis that intra-operative methylation-based classification can be performed using nanopore sequencing and thereby expediently inform surgical and oncological decision-making. METHOD Oxford Nanopore Technology (ONT) is a native-strand, long-read sequencing platform that can perform copy- number profiling along with parallel single-gene methylation, structural variant, mutational and methylation analyses. Capital and consumable costs are relatively low, and testing can be performed in the local setting on single samples. We have optimised DNA extraction and library preparation for rapid tissue processing. We have developed a robust bioinformatic pipeline which is able to produce intraoperative classification within minutes of sequencing and full molecular profiling after 24 hours. RESULTS We demonstrate the feasibility of using ONT to deliver intra-operative methylation-based classification of CNS tumours in ‘realtime’ within an NHS hospital setting and will discuss the challenges of implementing this testing and the opportunities to inform neuro-oncological practice. CONCLUSION By giving a summary of our novel protocol of rapid DNA extraction, library preparation and bioinformatic analysis, we will show that this approach can revolutionise the diagnosis of brain tumours and has the potential for rapid adoption by non-expert laboratories.

Prevalence and Diversity of Plant Parasitic Nematodes in Irish Peatlands

The prevalence of plant parasitic nematodes (PPN) in the Irish peatlands was investigated in five different peatland habitats—raised bog, cutover scrub/woodlands, fens and peat grasslands, which were further sub-categorised into fourteen different sub-habitats. Within the raised bog habitat were healthy bog hummock (HBH), healthy bog lawn (HBL), degraded bog hummock (DBH) and degraded bog lawn (DBL) and the fen habitats were fen peat (FP) and rich fen peat (R-FP). Cutover scrub or woodland habitat included cutover scrub rewetted (C-RW), cutover scrub non-rewetted (C-NRW), woodlands rewetted (W-RW) and woodlands non-rewetted (W-NRW). Grassland included wasted peat (WP), rough grazing (RG-I) and improved fen peat grassland (IFPG-RW and IFPG-NRW). Soil samples from peatlands were all collected between July and December 2023 when the temperature ranged from 12 to 20 °C. One half of each sample was used for molecular nematode analysis and the other half for morphological identification of nematodes. For the morphological identification, a specific nematode extraction protocol was optimised for peatland soils, and the extracted nematodes were fixed onto slides to be studied under a high-power light microscope. Subsequently, the other part of the soil was processed to isolate total DNA, from which the 18S rRNA gene was sequenced for the identification of nematode taxa. The extracted DNA was also used for randomly amplified polymorphic DNA (RAPD) fingerprinting analysis to determine banding patterns that could classify different bog habitats based on PPN random primers. Compared to that in the climax habitats (HBH, HBL, DBH, DBL, FP, R-FP), PPN prevalence was recorded as being higher in grasslands (WP, RG-I, IFPG-RW and IFPG-NRW) and scrub/woodland ecosystems (C-RW, C-NRW, W-RW, W-NRW). The results indicate that nematode populations are different across the various bog habitats. Emerging and current quarantine PPN belonging to the families Pratylenchidae, Meloidogynidae, Anguinidae and Heteroderidae were noted to be above the threshold limits mentioned under EPPO guidelines, in grassland and wooded peatland habitats. Future actions for PPN management may need to be considered, along with the likelihood that these PPN might impact future paludiculture and other crops and trees growing in nearby agricultural lands.

Quantitation of Copper Tripeptide in Cosmetics via Fabric Phase Sorptive Extraction Combined with Zwitterionic Hydrophilic Interaction Liquid Chromatography and UV/Vis Detection

The increasing demand for effective cosmetics has driven the development of innovative analytical techniques to ensure product quality. This work presents the development and validation of a zwitterionic hydrophilic interaction liquid chromatography method, coupled with ultraviolet detection, for the quantification of copper tripeptide in cosmetics. A novel protocol for sample preparation was developed using fabric phase sorptive extraction to extract the targeted analyte from the complex cosmetic cream matrix, followed by chromatographic separation on a ZIC®-pHILIC analytical column. A thorough investigation of the chromatographic behavior of the copper tripeptide on the HILIC column was performed during method development. The mobile phase consisted of 133 mM ammonium formate (pH 9, adjusted with ammonium hydroxide) and acetonitrile at a 40:60 (v/v) ratio, with a flow rate of 0.2 mL/min. A design of experiments (DOE) approach allowed precise adjustments to various factors influencing the extraction process, leading to the optimization of the fabric phase sorptive extraction protocol for copper tripeptide analysis. The method demonstrated excellent linearity over a concentration range of 0.002 to 0.005% w/w for copper tripeptide, with a correlation coefficient exceeding 0.998. The limits of detection and quantitation were 5.3 × 10−4% w/w and 2.0 × 10−3% w/w, respectively. The selectivity of the method was verified through successful separation of copper tripeptide from other cream components within 10 min, establishing its suitability for high-throughput quality control of cosmetic formulations.

Mycobacterium tuberculosis complex sample processing by mechanical lysis, an essential step for reliable whole genome sequencing

Mycobacterium tuberculosis complex (MTBC) whole genome sequencing (WGS) turnaround time and WGS success rates are highly influenced by DNA extraction protocols even from cultures. Efficient mycobacterial lysis is crucial for obtaining sufficient DNA from cultures to facilitate reliable genomic drug susceptibility prediction and accurate genotyping with WGS. We compared four DNA extraction protocols from BD BACTEC™ Mycobacterial Growth Indicator Tubes (MGIT) for WGS with a focus on the lysis step: protocol A) column-based protocol without mechanical lysis; protocol B) an adapted protocol including a bead beating step; protocol C) DNA extraction from primary received cultures using bead beating: and protocol D) DNA extraction from pre MGIT-positive (enriched) cultures. Protocol B increased DNA yield approximately 60-fold, and significantly improved the sequencing success rate. The increased yield also allowed DNA extraction from primary cultures with high success rates (protocol C). Additionally, by using pre-positive enriched MGIT cultures, we demonstrated that bead beating opens the possibility of reliable WGS up to five days before a MGIT tube would be flagged positive (protocol D). The most optimal bead beating-based DNA extraction was also evaluated for Nanopore sequencing. Shortening bead beating duration to 15 s resulted in longer read lengths (N50 from 1.4 kb to 2.6 kb) while still providing efficient lysis. Furthermore, AmpureXP bead beating-based DNA capture / purification proved to be as efficient as Qiagen column-based DNA extraction, further simplifying and shortening the DNA extraction protocol. Adding a mechanical lysis step to our routine MTBC DNA extraction protocol has allowed us to reduce the turnaround time while maintaining DNA quality sequencing success rates.

Molecular Characterization of Adhesives (Glue Lining Pastes) Used in Restoration.

The molecular characterization of samples from works of art can provide valuable insights into the composition of ancient restoration materials and their conservation state. Here, we present a novel analytical protocol for the molecular characterization of a specific adhesive used in historical painting restoration, known as "glue lining pastes." Due to the high molecular complexity of these adhesives, we propose a multistep extraction protocol to recover and fractionate from a single microsample the three main classes of biomolecules contained in glue pastes (lipids, polysaccharides, and proteins). High-performance separation coupled with high-resolution mass spectrometry (MS) techniques were applied to the isolated fractions to identify specific components. The proposed method was optimized using test specimens of various traditional glue pastes applied to canvases and successfully applied to a historical glue paste sample from the 17th-century painting "La fuga in Egitto," part of the Pagliara collection at the University Suor Orsola Benincasa (Naples, Italy). The data collected in this work provide insights into the specific recipe used for adhesive preparation, supporting artistic and historical interpretations and contributing to a broader understanding of old restoration practices. Data are available via ProteomeXchange with the identifier PXD051480.

Evaluation of protein extraction protocols for MALDI-TOF Biotyper analysis of mycobacteria

Infections caused by Mycobacterium tuberculosis and nontuberculous mycobacteria represent a significant global threat and medical concern. Therefore, accurate and reliable methods must be employed to identify mycobacteria rapidly. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a technique that compares the cellular protein profiles of unknown isolates with reference mass spectra in a database to identify microorganisms. However, the thick and waxy lipid layer, which is rich in mycolic acids and is present in mycobacterial cells, makes protein extraction challenging. To identify the optimal protocol for correctly identifying bacilli using MALDI-TOF mass spectrometry, this study compared four different cellular protein extraction methods. Four strains of M. bovis BCG were selected as representatives of slow-growing mycobacteria, while three strains of fast-growing mycobacteria were also included: M. peregrinum, M. smegmatis, and M. farcinogenes. The extraction method that proved most effective was the extraction of inactivated cells with chloroform and methanol, which partially delipidates the cells. These cells were then extracted with formic acid, as is standard practice for protein extraction. The advantage of this method is that it allows the parallel analysis of cellular lipids and proteins from a single sample. It is therefore important to optimize mycobacterial protein extraction for MALDI-TOF MS analysis in clinical microbiology laboratories.

Oxygen exposure decreases the yield of high-molecular-weight DNA from some anaerobic bacteria and bacterial communities during DNA extraction

ObjectivesThe central challenge in third-generation sequencing lies in meeting the requirements for DNA quality (integrity and purity) and quantity. Therefore, novel improvements in DNA extraction methods are needed to satisfy these requirements. We reasoned that in anaerobic microbial communities, the presence of certain strict anaerobes containing oxygen-activated DNase activity might contribute substantially to the poor integrity of extracted metagenomic DNA (or genomic DNA from some pure cultures) if exposed to air. MethodsTo test this hypothesis, we developed an enhanced genomic and metagenomic DNA isolation technique that we applied to a specifically chosen set of both strict and aerotolerant anaerobes, as well as to the hindgut microbiota of a herbivorous marine fish. ResultsConsidering the quality (or degradation) of extracted DNA obtained under anaerobic versus aerobic conditions, we found that DNA extracted aerobically from cells of some strict anaerobes showed more degradation of high molecular weight DNA than analogous preparations under anaerobic conditions. In contrast, with the selected aerotolerant anaerobes, no discernible difference was found between the molecular sizes of DNA extracted aerobically and anaerobically. Metagenomic DNA extracted from the fish hindgut microbiota showed higher yields and better quality under anaerobic conditions compared to aerobic conditions. ConclusionOur study effectively demonstrates the advantages of our improved extraction protocol in anaerobic conditions. This is evident through the improved quality of extracted DNA. Such findings may be valuable for studies, especially metagenomic studies, where the quality and quantity of DNA are crucial for downstream analysis.

Comparative analysis of features extraction protocols for LC-HRMS untargeted metabolomics in mountain cheese ‘identitation’

This study presents a comprehensive metabolomic analysis of Parmigiano Reggiano samples to differentiate between those designated as Mountain Quality Certification (QC) and conventional Protected Designation of Origin (PDO). Despite following the same production protocol, these cheese varieties differ in the cows’ feeding regimes and milk stable locations, with mountain-certified samples adhering to specific requirements regarding milk origin and feed composition. An untargeted approach with Liquid Chromatography-High Resolution Mass Spectrometry (LC-HRMS) was proposed to characterize the cheese metabolome. High-resolution LC-MS data can generate gigabyte-sized files, making data compression essential for manageable multivariate analysis and noise reduction. This study employs the Region of Interest-Multivariate Curve Resolution (ROI-MCR) protocol to achieve effective data compression and chromatographic resolution, thereby extracting the most informative features. This method was compared with a classical approach for feature extraction from chromatographic data, namely Compound Discoverer (CD) software. The features extracted by both methods were analysed through Principal Component Analysis (PCA) and ASCA (ANOVA Simultaneous Component Analysis). The comparison of ROI-MCR and CD approaches demonstrated that while both methods yielded similar overall conclusions, ROI-MCR provided a more streamlined and manageable dataset, facilitating easier interpretation of the metabolic differences. Both approaches indicated that amino acids, fatty acids, and bacterial activity-related compounds played significant roles in distinguishing between the two sample types.

Assessment of Skimmed Milk Flocculation for Bacterial Enrichment from Water Samples, and Benchmarking of DNA Extraction and 16S rRNA Databases for Metagenomics.

Water samples for bacterial microbiome studies undergo biomass concentration, DNA extraction, and taxonomic identification steps. Through benchmarking, we studied the applicability of skimmed milk flocculation (SMF) for bacterial enrichment, an adapted in-house DNA extraction protocol, and six 16S rRNA databases (16S-DBs). Surface water samples from two rivers were treated with SMF and vacuum filtration (VF) and subjected to amplicon or shotgun metagenomics. A microbial community standard underwent five DNA extraction protocols, taxonomical identification with six different 16S-DBs, and evaluation by the Measurement Integrity Quotient (MIQ) score. In SMF samples, the skimmed milk was metabolized by members of lactic acid bacteria or genera such as Polaromonas, Macrococcus, and Agitococcus, resulting in increased relative abundance (p < 0.5) up to 5.0 log fold change compared to VF, rendering SMF inapplicable for bacterial microbiome studies. The best-performing DNA extraction protocols were FastSpin Soil, the in-house method, and EurX. All 16S-DBs yielded comparable MIQ scores within each DNA extraction kit, ranging from 61-66 (ZymoBIOMICs) up to 80-82 (FastSpin). DNA extraction kits exert more bias toward the composition than 16S-DBs. This benchmarking study provided valuable information to inform future water metagenomic study designs.

Validation of the performance of a point of care molecular test for leprosy: From a simplified DNA extraction protocol to a portable qPCR.

The study aimed to optimize qPCR reactions using oligonucleotides from the first Brazilian molecular diagnostic kit for leprosy on a portable platform (Q3-Plus). In addition, we sought to develop a simplified protocol for DNA extraction that met point-of-care criteria. During optimization on the Q3-Plus, optical parameters, thresholds, and cutoffs for the 16S rRNA and RLEP targets of M. leprae were established using synthetic DNA, purified DNA from M. leprae, and pre-characterized clinical samples. For the simplified extraction protocol, different lysis solutions were evaluated using chaotropic agents, and purification was carried out by transferring the lysed material to FTA cards. The complete protocol (simplified extraction + qPCR on the portable platform) was then evaluated with pre-characterized clinical skin biopsy samples and compared with standard equipment (QuantStudio-5). LOD95% for the optimized reactions was 113.31 genome-equivalents/μL for 16S rRNA and 17.70 genome-equivalents/μL for RLEP. Among the lysis solutions, the best-performing was composed of urea (2 M), which provided good dissolution of the skin fragment and a lower Ct value, indicating higher concentrations of DNA. The complete technological solution showed a sensitivity of 52% in reactions. Our results highlight the need for additional optimization to deal with paucibacillary samples, but also demonstrate the feasibility of the portable platform for the qPCR detection of M. leprae DNA in low infrastructure settings.

Protocols for bulk off-line fluid inclusion extraction for the analysis of δ13C-CH4 and δ13C-CO2 using a cavity ring-down spectroscopy (CRDS) analyser

Fluid inclusions are a window into deep geological fluids, providing unique access to their nature and composition. The isotopic composition of CO2 and CH4 hosted in fluid inclusions is a powerful proxy to assess the origin and transformation of deep geological fluids, giving insights into carbon sources, fluxes, and degassing in a wide variety of geodynamic settings. Over the last 5 decades, techniques have been developed to extract fluid inclusions from their host minerals and measure their bulk composition. These techniques are often challenged by analytical artifacts including high blank levels of CO2 and CH4, fluid re-speciation, gas adsorption, and diffusion. Since these processes may alter the pristine composition of gases liberated from fluid inclusions, rigorous protocols are needed in order to evaluate the isotopic integrity of the extracted volatile species. In this study, we introduce new protocols for bulk off-line fluid inclusion extraction for the analysis of δ13C-CH4 and δ13C-CO2 using a Cavity Ring-Down Spectroscopy (CRDS) analyser (Picarro G2201-i). Two mechanical fluid extraction techniques are compared: ball milling in ZrO2 jars and sample crushing in a stainless steel sealed tube under a hydraulic press. Blanks and isotopically labelled tests with the ball milling technique suggest that rotation speed, grinding stock filling degree and filling type alter the CH4 and CO2 concentrations and isotopic compositions measured by the CRDS analyser. In contrast, the crushing technique does not generate measurable quantities of blank CH4 and CO2. The protocols presented in this study allow to extract, detect, and analyse δ13C of CH4 and CO2 for concentrations above 10 and 1,000 ppm respectively. Interlaboratory experiments allowed to replicate previously measured δ13C-CH4 values in natural fluid inclusions within 1‰ with both extraction techniques. This study highlights the potential of combining simple bulk off-line fluid inclusion extraction techniques with a CRDS analyser for δ13C analysis of CO2 and CH4 without gas separation being required.

A novel green cloud point extraction-based switchable hydrophilicity solvent method for antimony separation and quantification from various bottled beverages by HGAAS

Herein, switchable hydrophilicity solvent (SHS) was used as a synergistic reagent in the cloud point extraction (CPE) protocol to increase the procedure’s efficiency and sensitivity. At room temperature, the CPE-SHS method was created for the fast and accurate extraction of antimony from a variety of drinks. Hydride generation atomic absorption spectroscopy (HGAAS) was used to antimony detection in various samples following the CPE-SHS protocol. The N,N-dimethylamine (DMA), TritonX-100, and p-tert-butyl-tetrakis[(diethylamide)methoxy]tetrathiacalix[4]arene (BTDMTA) were used as a SHS, surfactant, and chelation reagent, respectively. This procedure’s criteria for validation have been identified, including linearity (0.01–700 µg/L), accuracy, precision, limit of detection (LOD = 0.007 µg/L), limit of quantification (LOQ = 0.023 µg/L), enhancement factor (EF = 160), and matrix influence. This approach was validated using certified reference material. The environmentally friendly practices of this method were assessed using recent tools like Complex Modified GAPI (ComplexMoGAPI) software, Analytical GREEnness Calculator (AGREE) software, Blue Applicability Grade Index (BAGI) software, and Sample Preparation Metric of Sustainability (SPMS) program.

Recommendations for Accurate Lipid Annotation and Semi-absolute Quantification from LC-MS/MS Datasets.

Recent developments in LC-MS instrumentation and analytical technologies together with bioinformatics tools supporting high-throughput processing of large omics datasets significantly enhanced our capabilities and efficiency of identification and quantification of lipids in diverse biological materials. However, each biological matrix is characterized by its unique lipid composition, thus requiring optimization of analytical and bioinformatics workflows for each studied lipidome. Here, we describe an integrated workflow for deep lipidome profiling, accurate annotation, and semi-absolute quantification of complex lipidomes based on reversed phase chromatography and high resolution mass spectrometry. This chapter provides details on selection of the optimal extraction protocol, acquisition of LC-MS/MS data for accurate annotation of lipid molecular species, and design of lipidome-specific mixtures of internal standards to assist quantitative analysis of complex, native lipidomes.

Chitinase and proteinase K treatments enhance the DNA yield of microsporidium Ecytonucleospora hepatopenaei spores

Microsporidium Ecytonucleospora hepatopenaei (EHP) spores were purified from the hepatopancreas of Penaeus vannamei infected with EHP by percoll density gradient centrifugation and differential centrifugation. The EHP spores contain a thick chitin wall and might not rupture using the routine DNA extraction protocol. In this study, three enzymes were used, including chitinase, proteinase K, and DNase I. Chitinase or proteinase K digestions caused weakened fluorescence of chitin showing by a blurred edge of EHP spores stained with calcofluor white under a fluorescence microscope. Different combinations of these enzymes followed by DNA extraction with phenol–chloroform from EHP spores showed significant increases in the copy number of the EHP SSU gene per spore. The combination of the chitinase and proteinase K treatments resulted 4.46 ± 1.07 copies/spore detected, which is 31.6 ± 20.7 folds of no treatment groups, accounting to (55.7 ± 13.4)% of the total copies of the gene in the spore. The additional treatment with chitinase to the conventional extraction protocol with a proteinase K digestion step for feces and hepatopancreas samples of P. vannamei resulted in a significant difference in EHP copies in the DNA of (83.8 ± 64.1)% and (55.3 ± 88.0)% increases. The study proved that chitinase and proteinase K treatment enhance the DNA extraction from microsporidian spores resulting in high yield.

High-Quality Genomic DNA Extraction Protocol for Bacillus and Clostridium Species.

High-quality DNA with sufficient yield is the goal of DNA extraction protocols. We present an optimized, cost-effective method for extracting next-generation sequencing (NGS)-quality genomic DNA from Bacillus and Clostridium species using the chloroform-isoamyl approach. The protocol involves two main procedures: cultivation of the bacteria under appropriate conditions, followed by DNA extraction through cell lysis, phase separation, DNA precipitation, and cleanup. This method has been successfully applied to several hundred strains of Bacillus and Clostridium species in our laboratory, including B. cereus, B. licheniformis, C. sporogenes, and C. tyrobutyricum, demonstrating its efficacy and reliability for producing high-quality DNA that meets NGS quality control standards. © 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Culturing Bacillus and Clostridium species Basic Protocol 2: DNA extraction © 2024 by John Wiley & Sons, Inc.

Enhancing phenolic compounds recovery from Arnica montana L. flowers through optimized green extraction protocols

Enhancing phenolic compounds recovery from Arnica montana L. flowers through optimized green extraction protocols

A low-cost homogenizing device for in-field and remote DNA and RNA extraction

Environmental monitoring of microorganisms is critical for the protection and enhancement of human and ecosystem health. Even though these molecular methods have overtaken traditional culture-based methods and become more accessible, these techniques still require expensive equipment and dedicated facilities to process samples which in the context of a global pandemic, remote sampling areas or low-income countries can be extremely challenging. Sample preparation and sample homogenisation are critical steps for molecular-based techniques, especially for the extraction of DNA and RNA. This study developed a low-cost, open-source, freely available 3D printed homogenizer for the processing of DNA and RNA extraction. The BoSL Beater 3D is a portable device that allows researcher to perform bead-beating steps commonly required for environmental sample extraction protocols in the field and without access to main’s power. The BoSL Beater 3D was tested on filtered wastewater samples and passive samplers exposed to wastewater over a 24-hour period and showed similar or better performance to the traditional laboratory bead beater for both the extraction of DNA and RNA. The cost of this 3D homogeniser is roughly $18 AUD ($296 AUD with the jigsaw, which is roughly 57 times cheaper than a traditional bead beater) and has the added usability of being portable and easily adaptable to any type of jigsaw. In combination to newly developed field extraction kits as well as portable PCR machines, this 3D homogeniser could provide the tool necessary to enable access to molecular testing in remote setting as well as developing countries, which may not have access to fully equipped laboratories, but also allow for timely reporting. In addition, the BoSL Beater 3D, in combination with field extraction kit, can allow more flexibility to researchers while sampling, shipping, and processing DNA and RNA samples, whilst maintaining quality of these samples.