Protocols for dry DNA storage and shipment at room temperature

The globalization of DNA barcoding will require core analytical facilities to develop cost‐effective, efficient protocols for the shipment and archival storage of DNA extracts and PCR products. We evaluated three dry‐state DNA stabilization systems: commercial Biomatrica^® DNAstable^® plates, home‐made trehalose and polyvinyl alcohol (PVA) plates on 96‐well panels of insect DNA stored at 56 °C and at room temperature. Controls included unprotected samples that were stored dry at room temperature and at 56 °C, and diluted samples held at 4 °C and at ?20 °C. PCR and selective sequencing were performed over a 4‐year interval to test the condition of DNA extracts. Biomatrica^® provided better protection of DNA at 56 °C and at room temperature than trehalose and PVA, especially for diluted samples. PVA was the second best protectant after Biomatrica^® at room temperature, whereas trehalose was the second best protectant at 56 °C. In spite of lower PCR success, the DNA stored at ?20 °C yielded longer sequence reads and stronger signal, indicating that temperature is a crucial factor for DNA quality which has to be considered especially for long‐term storage. Although it is premature to advocate a transition to DNA storage at room temperature, dry storage provides an additional layer of security for frozen samples, protecting them from degradation in the event of freezer failure. All three forms of DNA preservation enable shipment of dry DNA and PCR products between barcoding facilities.     

An investigation of adequate volume for the diagnosis of malignancy in pleural fluids

S. C. Thomas, L. R. R. Davidson and M. E. McKean An investigation of adequate volume for the diagnosis of malignancy in pleural fluids Objective: The cytological examination of pleural effusions is an important investigation in the diagnosis of malignancy. Maximizing the chances of identifying malignant effusions is therefore desirable. Recent Royal College of Pathologists guidelines, based on the British Society for Clinical Cytology codes of practice, have suggested that a minimum of 20 ml of pleural fluid is required for diagnostic purposes. Methods & Results: We examined 2155 pleural fluids received over a 6‐year period in order to define a minimum required volume for adequacy. By examining the plateau phase of a graph of threshold volumes for initial samples received for each patient (n = 1584) we determine that a minimum fluid volume of 25 ml is required and that more than 50 ml does not improve sensitivity. Conclusion: Between 25 and 50 ml of fluid are required for the adequate assessment of pleural effusions for malignancy.     

Effect of storage time of pleural effusions on immunocytochemical cell surface analysis of tumor cells.

To determine how long tumor cells can be stored without losing their immunocytochemical reactivity, five malignant pleural effusions in EDTA-coated tubes were analyzed after different storage times at either 4 degrees C or room temperature. Only minor differences were observed between the cells from the two storage conditions. Though there was a considerable decrease in the number of tumor cells attached to the slides from day 0 to 1, the number of tumor cells was still sufficient to allow their clear detection with the monoclonal antibody HEA-125 even on day 4 of storage in all cases. Therefore, for routine purposes, pleural fluids in EDTA-coated tubes can be stored for at least one day prior to immunocytochemical staining if the cells are gently handled during preparation. Pleural fluid is a richly nutritious medium not only for keeping cells alive but also for preserving their immunoreactivity.     

A method for preserving saliva samples at ambient temperatures

To facilitate biochemical and biopharmaceutical studies when cold storage is unavailable, we assessed the stability of saliva samples containing preservatives stored at room temperature over a 1-year period. Two preservative mixtures were evaluated: sodium benzoate and citric acid (P1), and ethyl and propyl paraben (P2). Saliva samples were spiked with acetaminophen (APAP) or antipyrine (AP) and stored in preservative-coated vials and examined for concentrations of APAP, AP, melatonin, and cortisol at regular intervals as a function of preservative type and storage duration. Samples were stored at room temperature or at -20 degrees C (positive control) and analyzed periodically for APAP and AP by high-performance liquid chromatography and for melatonin and cortisol by radioimmunoassay. The effectiveness of the preservatives was determined by calculating the value of samples stored at room temperature in terms of percent of control (-20 degrees C) values. P1 effectively maintained the stability of APAP (100%) and AP (100%) for 360 days at room temperature; concentrations in samples at room temperature on day 360 were comparable to those on day 01. P1 also effectively maintained melatonin (100%) and cortisol (95%) concentrations for 180 days at room temperature. P2 preserved AP and cortisol in saliva for 60 days, but APAP for only 14 days.     

The use of a transport medium (L15M15) for bulk tissue storage and retention of viability

Twenty-five human or mouse tissue samples, some up to 8×4×2 cm, were immersed in a special transport medium (TM), L15M15, up to 7 days before being processed or placed in tissue culture. To test the efficacy of this medium, we concurrently placed pieces of the same tissues in a sterile phosphate buffered solution (PBS). We also tested the preservative capabilities of TM and PBS at room temperature and with refrigeration. Differences between TM and PBS are demonstrated, which are more pronounced using room temperature up to 4 days time. The tissues stored in TM show fewer degenerative or autolytic changes than the same tissue stored in PBS under identical conditions. Using regrigeration further enhanced the preservative qualities of TM up to 4 days, but not PBS. There were no obvious differences between tissues stored in TM and PBS with refrigeration after 7 days. We conclude that transport medium L15M15 is a useful medium for preserving tissue viability, especially large tissue samples, up to 4 days, especially if refrigerated.     

Pericarp anatomy and hormone profiles of cypselas in dormant and non‐dormant inbred sunflower lines

The pericarp anatomy and the effects of storage after harvest, storage temperature and early cypsela imbibition on phytohormone profiles were studied in inbred sunflower lines B123 and B91. On day 0, germination of B123 cypselas was near 0%, indicating dormancy, whereas that of B91 cypselas was near 100%, indicating non‐dormancy. The germination of B123 and B91 on day 33 at room temperature (25 °C) storage was similar. Cell wall thickness and sclerification of the pericarp were higher in B123 than B91, suggesting that structural characteristics may contribute to physical dormancy in B123. Jasmonates (JAs), salicylic acid (SA) and abscisic acid (ABA) were measured in dry and imbibed pericarps. SA content of dry pericarp was higher on day 33 than day 0. SA content during imbibition on day 33 was similar for room and low (?20 °C) storage temperatures. ABA content after 12 h imbibition was similar on days 0 and 33 at low temperature, but it increased on day 33 at room temperature for B123. 12‐Oxo‐phytodienoic acid (OPDA) was maximal on day 0 for B123, but peaked at day 33 at low temperature for B91. JA was higher on days 0 and 33 at room temperature as compared with low temperature. Our findings indicate that pericarp hormone profiles are affected in the two lines with different dormancy degree depending on storage conditions and imbibition processes.     

Freeze-dried plasma proteins are stable at room temperature for at least 1 year

Thirty human EDTA plasma samples from male and female subjects ranging in age from 24 to 74 years were collected on ice, processed ice cold and stored frozen at ?80 °C, in liquid nitrogen (LN2), or freeze dried and stored at room temperature in a desiccator (FDRT) or freeze dried and stored at ?20 °C for 1 year (FD-20). In a separate experiment, EDTA plasma samples were collected onto ice, processed ice cold and maintained on ice ± protease inhibitors versus incubated at room temperature for up to 96 h. Random and independent sampling by liquid chromatography and tandem mass spectrometry (LC–ESI–MS/MS), as correlated by the MASCOT, OMSSA, X!TANDEM and SEQUEST algorithms, showed that tryptic peptides from complement component 4B (C4B) were rapidly released in plasma at room temperature. Random sampling by LC–ESI–MS/MS showed that peptides from C4B were undetectable on ice, but peptides were cleaved from the mature C4B protein including NGFKSHALQLNNR within as little as 1 h at room temperature. The frequency and intensity of precursors within ± 3 m/z of the C4B peptide NGFKSHALQLNNR was confirmed by automated targeted analysis where the precursors from MS/MS spectra that correlated to the target sequence were analyzed in SQL/R. The C4B preproprotein was processed at the N terminus to release the mature chain that was cleaved on the carboxyl side of the isoprene C2 domain within a polar C terminal sequence of the mature C4B protein, to reveal the thioester reaction site, consistent with LC–ESI–MS/MS and Western blot. Random sampling showed that proteolytic peptides from complement component C4B were rarely observed with long term storage at ? 80 °C in a freezer or in liquid nitrogen (LN2), freeze drying with storage at ? 20 °C (FD-20 °C) or freeze drying and storage at room temperature (FDRT). Plasma samples maintained at room temperature (RT) showed at least 10-fold to 100-fold greater frequency of peptide correlation to C4B and measured peptide intensity compared to samples on ice for up to 72 h or stored at ? 80 °C, LN2, FDRT or FD-20 °C for up to a year.     

Vitrification induces critical subcellular damages in ram spermatozoa

The aim of the present study was to analyse morphological variations in ovine spermatozoa subjected to different cryopreservation protocols using high resolution imaging techniques. Ejaculates were pooled and diluted in Tris-based extender. Aliquots containing 300 × 10⁶ spz/ml were prepared and evaluated a) after the semen collection and pooling, b) after conventional freezing, c) after vitrification of samples maintained at room temperature (22 °C) prior to vitrification, and d) after vitrification of samples maintained at 5 °C prior to vitrification. Sperm motility, acrosome integrity, DNA fragmentation and morphology were assessed. Subcellular sperm changes were assessed and described by light microscopy, scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The maintenance of spermatozoa at 5 °C prior to vitrification and the use of 0.4 M sucrose pointed out lower dimensions of area, length and width than fresh, frozen and sperm maintained at 22 °C prior to vitrification. It was observed that the head width and length are significantly higher (P < 0.0001) in fresh spermatozoa than in the vitrified sperm samples. It could be hypothesized that greater intracellular fluid loss during vitrification could prevent damages in the spermatozoon throughout the reduced ice crystals formation, but mainly by the reduction of extracellular ice crystals due to the physical properties modification obtained when high concentrations of sugars are added. This is the first ultramicroscopic study carried out in ovine vitrified spermatozoa, which confirms the functional sperm alterations previously detected.     

Preservation of nucleic acid integrity in guanidine thiocyanate lysates of whole blood

High-molecular-mass RNA and DNA have been shown to retain their integrity for three days at room temperature, no less than two weeks at +4°C, and more than a year at ?20°C when whole blood samples are stored as lysates containing 4 M guanidine thiocyanate. Storage time at room temperature can be prolonged at least up to 14 days if nucleic acids were precipitated by two volumes of isopropanol. This preservation technique allows storage and transportation of samples at ambient temperature and is completely compatible with the procedure of subsequent isolation of nucleic acids.     

The room temperature preservation of filtered environmental DNA samples and assimilation into a phenol–chloroform–isoamyl alcohol DNA extraction

Current research targeting filtered macrobial environmental DNA (eDNA) often relies upon cold ambient temperatures at various stages, including the transport of water samples from the field to the laboratory and the storage of water and/or filtered samples in the laboratory. This poses practical limitations for field collections in locations where refrigeration and frozen storage is difficult or where samples must be transported long distances for further processing and screening. This study demonstrates the successful preservation of eDNA at room temperature (20 °C) in two lysis buffers, CTAB and Longmire's, over a 2‐week period of time. Moreover, the preserved eDNA samples were seamlessly integrated into a phenol–chloroform–isoamyl alcohol (PCI) DNA extraction protocol. The successful application of the eDNA extraction to multiple filter membrane types suggests the methods evaluated here may be broadly applied in future eDNA research. Our results also suggest that for many kinds of studies recently reported on macrobial eDNA, detection probabilities could have been increased, and at a lower cost, by utilizing the Longmire's preservation buffer with a PCI DNA extraction.     

Reduction in Listeria monocytogenes and spoilage bacteria on smoked catfish using X-ray treatments

Aims: To determine the efficacy of X‐ray processes in inactivating L. monocytogenes levels in smoked catfish during storage at 5°C and to determine the effects of X‐ray doses on controlling the growth of spoilage bacteria on smoked catfish during storage at 5°C for up to 5 weeks. Methods and Results: Smoked catfish fillets inoculated with L. monocytogenes were treated with 0·0–2·0 kGy X‐ray and stored at 5°C for 5 weeks. The negative controls (uninoculated/untreated) and uninoculated samples treated with the lowest (0·1 kGy) and highest (2·0 kGy) doses were stored at 5°C and tested for psychrotrophs count during the 5 weeks of storage. The initial L. monocytogenes population on smoked catfish was significantly (P < 0·05) reduced to undetectable level by a treatment of 1·0 kGy or higher. The initial psychrotrophs count on smoked catfish was significantly reduced from 4·7 CFU g^?1 to below the detectable level by a treatment with 2·0 kGy. Conclusions: Smoked catfish treated with 2·0 kGy X‐ray had no detectable L. monocytogenes throughout 35 days of storage at 5°C. A treatment with 2·0 kGy X‐ray also kept the levels of psychrotrophs in the smoked catfish within the acceptable level until 35 days. Significance and Impact of the Study: The results of this investigation indicate that X‐ray at 2·0 kGy can eliminate L. monocytogenes and extend the shelf life of smoked catfish stored at refrigeration temperature.     

Rhythmic cortisol secretion in the equine: Analysis and physiological mechanisms

Abstract

Four Thoroughbred mares (no. 1–4) were maintained under constant temperature (24°C) and controlled light (L/D:12/12 with lights on at 06.00 hr) conditions. They were fed and watered ad libitum with fresh feed and water given at 09.00 hr. After a 45‐day pre‐conditioning period, blood samples were obtained by veinipuncture at 4‐hr intervals for 14 days to determine circadian and day‐to‐day variation. The horses exhibited a circadian rhythm with maximum values attained at about 12.00 hr, however, there are periods of days in which no rhythm is distinguishable. Ultradian rhythms with mean periods of 105 to 128 and 24 to 31 min are superimposed upon the circadian rhythm. The individual rhythms are quite variable from horse to horse and within the same horse. During periods of decline in plasma cortisol with metabolic half‐lives of approximately 70 min, secretion of cortisol was very low or had ceased. During periods of increasing plasma concentration, secretion was occurring at a faster rate than degradation. Rapid decreases in plasma concentration (metabolic half‐life of approximately 30 min) was accompanied by a rise in specific activity indicating cortisol with a high specific activity was entering the plasma pool from other storage pools.     

Subcellular fractionation of postmortem brain

Abstract— Procedures used to separate subcellular organelles from fresh brain were applied to brains which had been removed from guinea pigs (1) immediately after death; (2) after the dead animal was maintained at room temperature for 3 h, followed by 16–17 h at 4°C; or (3) after the dead animal was maintained for 19–20 h at room temperature. Subcellular fractionation of the brains in 0.32 M sucrose was followed by discontinuous density gradient centrifugation of the crude mitochondrial fraction. After overnight storage of brains at room temperature, there was a moderate shift in succinate dehydrogenase activity from sub-fraction C (mitochondria) to subfraction B (synaptosomes). There was little change in the distribution of galactolipid among particulate subfractions. There was little change in distributions of monoamine oxidase or acetylcholinesterase activities. Under the less extreme postmortem conditions, there were no shifts in the subcellular distributions of brain enzymes. Ultrastructural changes were much more profound and consisted of losses of identifiable mitochondria and synaptosomes and a progressive increase in very dense bodies. Our results suggest that in spite of the marked morphological changes, meaningful separation of subcellular organelles can be achieved with postmortem tissue.     

Stable Protein Gel Storage in Acetonitrile for Mass Spectrometric Analysis

Long‐term storage of protein samples for transportation is a challenge in the field of mass spectrometric analysis because the low temperature condition is not easy to be maintained. Here we introduce a simple method to preserve proteins at room temperature for at least one month. In this method, the protein sample is run shortly into a polyacrylamide gel which is then excised after Coomassie staining. The protein gel band is then dehydrated by 100% acetonitrile three times and kept in 100% acetonitrile for storage at room temperature. By the TMT 10‐plex based quantitative proteomic analyses, we have found that these proteins are stable in their levels and modifications (phosphorylation, oxidation, and ubiquitination) for 30 days. Further analysis has revealed this storage method also well preserves proteins even at 45 °C. We therefore recommend to use acetonitrile to dehydrate and store protein gel pieces as an effective alternative for sample shipping over days. Therefore, it might facilitate worldwide collaborations in the mass spectrometry‐based proteomic research.     

The positive impact of cytological specimens for EGFR mutation testing in non‐small cell lung cancer: a single South East Asian laboratory’s analysis of 670 cases

B. Pang, D. Matthias, C.W. Ong, A.N. Dhewar, S. Gupta, G.L. Lim, M.‐E. Nga, J.E. Seet, A. Qasim, T.‐M. Chin, R. Soo, R. Soong and M. Salto‐Tellez The positive impact of cytological specimens for EGFR mutation testing in non‐small cell lung cancer: a single South East Asian laboratory’s analysis of 670 cases Objectives: To compare the rejection rates of non‐small cell lung cancer (NSCLC) samples obtained by differing sampling methods for testing by Sanger sequencing for epidermal growth factor receptor (EGFR) mutations. To assess the association between unsatisfactory outcomes and the quantity of DNA extracted from cytological versus histological samples. Methods: Six hundred and seventy NSCLC samples referred to our centre from 2008 to 2010 were reviewed as a consequence of sample rejection, presence of EGFR mutations, cytological versus histological sampling methods, DNA quantity and the unsatisfactory genotyping rate. Results: Eighty samples were rejected for testing in similar proportions of histological and cytological samples (11.9% versus 10.9%) usually (n = 75) because the amount of cellular material was judged insufficient in small biopsies or cytology samples. The remaining 590 samples on which EGFR testing was attempted yielded 51 (8.6%) unsatisfactory test outcomes caused by failure of the polymerase chain reaction (PCR) (n = 47 cases), uninterpretable Sanger chromatograms (n = 3 cases) and insufficient DNA extracted for PCR (n = 1 case). The difference in rates of unsatisfactory outcomes between cytological samples (seven of 147 samples or 4.7%) versus tissue samples (44 of 443 samples or 9.9%) was clinically relevant but not statistically significant (Mann–Whitney test; P < 0.081). There was no association between the concentration of DNA extracted and the likelihood of an unsatisfactory analysis; which was similar in all types of sections (large and small) while 0% of 37 cytology slides were unsatisfactory. Conclusions: Utilizing cytology samples for EGFR testing avoids unnecessary patient re‐biopsing and yields a clinically superior satisfactory rate to the overall satisfactory rate of tissue biopsies of NSCLC. The quality rather than quantity of DNA extracted may be a more important determinant of a satisfactory result.     

Growth of enterotoxigenic Staphylococcus aureus in povi masima, a traditional Pacific island food

AIMS: To obtain preliminary data on the microbiology and hurdles to pathogen growth in the traditional Pacific Island food, povi masima, which is essentially beef brisket cured in brine. METHODS AND RESULTS: Six containers of povi masima were prepared and two were inoculated with five enterotoxigenic strains of Staphyloccocus aureus. The povi masima were divided into two lots each containing two uninoculated control and an inoculated container. Lot 1 was incubated at room temperature (20 degrees C) and lot 2 under refrigeration (4-5 degrees C) for up to 98 days. During storage, samples were removed and tested for aerobic plate count, coagulase-producing Staphylococci, Clostridium perfringens, staphylococcal enterotoxin and various chemical parameters of the food. Coagulase-producing Staphylococci and aerobic plate counts grew to high levels in both the inoculated and uninoculated lots stored at room temperature, but enterotoxin was only detected at one time point in these lots and this may represent a false positive result. The concentration of NaCl in the meat increased with time as concentrations equilibrated, and nitrite was rapidly lost in those lots stored at room temperature. Storage at 4-5 degrees C prevented proliferation of coagulase-producing Staphylococci. CONCLUSIONS: For safe curing and storage, this food should be kept under refrigeration as this prevented growth of staphylococci. Optimum storage would also be achieved with improved attempts to ensure equal distribution of NaCl prior to storage. SIGNIFICANCE AND IMPACT OF THE STUDY: Under conditions traditionally used to cure and store this food, enterotoxigenic staphylococci can grow to numbers where toxigenesis might occur, especially during the early stages of curing where the salt has not diffused from the brine into the meat.     

Preservation methods for the storage of anaerobic sludges

Different preservation methods were evaluated for the storage of anaerobic sludges: room temperature, refrigeration at 4 °C, freezing at –20 °C and freeze-drying. Specific methanogenic activity for glucose and acetate were used as indicators of the subsequent recovery of the anaerobic sludge. Storage at room temperature and refrigeration resulted in a better conservation of the methanogenic activity than freezing and freeze-drying.     

Effect of heat‐assisted pulsed electric fields and bacteriophage on enterohemorrhagic Escherichia coli O157:H7

Pulsed electric fields (PEF), heat‐assisted PEF (H‐PEF), and virulent bacteriophage (VP) are non‐thermal techniques for pathogen inactivation in liquids that were investigated individually, and in combination (PEF/VP, H‐PEF/VP) to control enterohemorrhagic Escherichia coli (EHEC) O157:H7 in Luria‐Bertani broth (LBB) and Ringer's solution (RS). Treated cells were subsequently incubated at refrigeration (4°C) and temperature‐abuse conditions (12°C) for 5 days. When EHEC cells grown in LBB were subjected to non‐thermal processing and subsequently stored at 12°C for 5 days, reductions in count of between 0.1 and 0.6 log cycles were observed and following storage at 4°C the decrease in counts varied between 0.2 and 1.1 log₁₀. For bacteria cells suspended in RS values ranged from 0.1 to ≥3.9 log cycles at both storage temperatures. The most effective treatments were H‐PEF and H‐PEF/VP, both producing a >3.4 log cycle reduction of cells suspended in non‐nutrient RS. Analysis of EHEC recovery on selective and non‐selective media indicated no occurrence of sub‐lethal damage for VP, PEF/VP, and H‐PEF/VP‐treated cells. The findings indicate that combining PEF and lytic phage may represent a suitable alternative to conventional fluid decontamination following further process optimization. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 31:110–118, 2015     

Increased production of PGI2-like activity by frozen-thawed rat aorta

The effects of storage conditions, temperature, and time on the ability of the rat thoracic aorta to produce a platelet aggregation inhibitor were investigated. Aortic fragments were incubated in Tris buffer, aliquots of which were then tested for their ability to inhibit ADP-induced human platelet aggregation. The incubation fluid of samples that had been soaked in Tris buffer at 4°C for 24 hours contained no inhibitor activity, whereas the incubation fluid of similar samples that had been kept at 4°C but not soaked in buffer contained comparable inhibitor activity as that of fresh samples. The incubation fluid of samples that had been kept at ?20°C or ?80°C contained greater inhibitor activity than that of fresh samples, and was maintained in ?20°C samples for 7 days, and ?80° samples for 28 days. The aortic inhibitor had similar properties as PGI₂.