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.     

Encapsulation of Trichoderma harzianum conidia as a method of conidia preservation at room temperature and propagation in submerged culture

The objective of the present work was to develop a method for the preservation of T. harzianum conidia at room temperature and the immobilised conidia propagation in submerged culture. This was accomplished by immobilising the strain in sodium alginate capsules (white capsules) and subsequently propagating them in a column bubble reactor (green capsules). Three capsule diameters were tested (micro, medium and large capsules), which were produced by emulsion internal gelation and dripping methods. Tested variables were the immobilised conidia propagation in submerged culture for free conidia production, the immobilised conidia viability throughout the time (two years), the resistance of the encapsulated conidia to the UV irradiation of short and long wavelength, and the antagonistic effect of the encapsulated T. harzianum against four phytopathogenic fungi. It was found that the medium capsules (1.5?±?0.3?mm) favoured the massive production of released conidia in submerged culture and that the higher the density of conidia per capsule, the greater the protection against the ultraviolet irradiation. Regarding the conidia preservation in calcium alginate, a viability loss of around 30% was observed two years after storage at environmental temperature in both white and green capsules; along the two years that the viability of conidia was analyzed, the purity of the formulation was corroborated. The results presented here show the efficacy of the green and white capsules for T. harzianum preservation at room temperature for a long period of time.     

A simplified method of tissue processing for immunostaining with good preservation of antigens and morphology

A simple and rapid method of tissue processing has been developed for immunostaining. Human and murine tissues were fixed in a PVA solution, diluted in a special buffer and embedded in paraffin or stored in a stock solution before preparing frozen sections. By indirect immunofluorescence, several antigens (collagen isotypes, laminin and fibronectin) were better demonstrated in the samples processed by the present method than with frozen or deparaffinized sections. In addition, this method allows a histological preservation quite identical to that seen in classical histology.     

A method for the medium-term storage of plant tissue samples at room temperature and successive cycles of DNA extraction

Based on the protocol originally described by Stein et al. (2001), we have developed a method that allows for medium-term conservation at room temperature of wheat (Triticum aestivum) tissue samples to use for DNA extraction. DNA quality was suitable for analysis by PCR and Southern hybridization, even after 2 months of storage at room temperature. This method allows successive DNA re-extractions from a previously extracted sample and maximization of the DNA yield that can be recovered from precious samples. This method has applications for conservation of leaf samples and management of DNA extraction. Our method can help improve data recovery in many plant molecular genetics research projects.     

The preservation of ciliated protozoa at low temperature

Reasonable recovery after exposure to ?196 °C and after storage in liquid nitrogen refrigeration for as long as 4 years has been achieved with Tetrahymena pyriformis and with syngens 1 and 4 of Paramecium aurelia, although the percentage of cells surviving has usually been low. A procedure evolved with one stock may have to be altered for other stocks, which is not surprising, since the “species” T. pyriformis includes organisms probably more distantly separated evolutionarily than are fish and man. Attempts to explain the ability of relatively few cells to survive these conditions by resistance to salt, age of the cultures, etc. have so far been inconclusive and suggest interaction among the many variables.     

Lyophilization is suitable for storage and shipment of fresh tissue samples without altering RNA and protein levels stored at room temperature

Lyophilization has been widely used for preservation, such as in food industry, pharmacy, biotechnology and tissues engineering, etc. However, there is no report on whether it could affect stability of RNA and protein levels in biological tissue samples. Herein we show that lyophilization can be used for storage of biological tissue samples without loss of bioactivities even stored at room temperature for 7-14?days. To address this issue, C57BL mouse tissues were prepared and dried by lyophilization and a baking method, respectively, followed by examination of morphological structure and total proteins by SDS-PAGE as well as gelatin zymography. Subsequently, the stability of RNAs and proteins, which were lyophilized and stored at room temperature (23°C) for 14?days was further examined by RT-PCR, SDS-PAGE and western blot. Results demonstrated that lyophilization did not alter total protein activities of various tissues, including enzyme activities, immunoreactivities and phosphorylation, and did not affect several RNAs in lyophilized tissues. Taken together, lyophilization may represent a valuable approach for preservation and long-distance shipment of biological samples, particularly for the international exchange of biological samples without altering their bioactivities.     

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.     

Processing tissue and cells for transmission electron microscopy in diagnostic pathology and research

In transmission electron microscopy (TEM), electrons are transmitted through a plastic-embedded specimen, and an image is formed. TEM enables the resolution and visualization of detail not apparent via light microscopy, even when combined with immunohistochemical analysis. Ultrastructural examination of tissues, cells and microorganisms plays a vital role in diagnostic pathology and biologic research. TEM is used to study the morphology of cells and their organelles, and in the identification and characterization of viruses, bacteria, protozoa and fungi. In this protocol, we present a TEM method for preparing specimens obtained in clinical or research settings, discussing the particular requirements for tissue and cell preparation and analysis, the need for rapid fixation and the possibility of analysis of tissue already fixed in formalin or processed into paraffin blocks. Details of fixation, embedding and how to prepare thin and semi-thin sections, which can be used for analysis complementary to that performed ultimately using TEM, are also described.     

Convenient preparation of 68Ga-based PET-radiopharmaceuticals at room temperature

A straightforward labeling using generator produced positron emitting (68)Ga, which provides high quality images, may result in kit type production of PET radiopharmaceuticals and make PET examinations possible also at centers lacking accelerators. The introduction of macrocyclic bifunctional chelators that would provide fast (68)Ga-complexation at room temperature would simplify even further tracer preparation and open wide possibilities for (68)Ga-labeling of fragile and potent macromolecules. Gallium-68 has the potential to facilitate development of clinically practical PET and to promote PET technique for individualized medicine. The macrocyclic chelator, 1,4,7-triazacyclononanetriacetic acid (NOTA), and its derivative coupled to an eight amino acid residue peptide (NODAGA-TATE, [NODAGA (0), Tyr(3)]Octreotate) were labeled with (68)Ge/(68)Ga-generator produced positron emitting (68)Ga. Formation kinetics of (68)Ga-NOTA was studied as a function of pH and formation kinetics of (68)Ga-NODAGA-TATE was studied as a function of the bioconjugate concentration. The nearly quantitative radioactivity incorporation (RAI>95%) for (68)Ga-NOTA was achieved within less than 10 min at room temperature and pH 3.5. The concentrations of NODAGA-TATE required for RAI of >90% and >95% were, respectively, 2-5 and 10 microM. In both cases the purification of the (68)Ga-labeled products was not necessary since the radiochemical purity was >95% and the preparation buffer, 4-(2-hydroxyethyl) piperazine-1-ethanesulfonic acid (HEPES) is suitable for human use. In order to confirm the identity of the products, complexes comprising (nat)Ga were synthesized and analyzed by mass spectrometry. The complex was found to be stable in the reaction mixture, phosphate buffer, and human plasma during 4.5 h incubation. Free and peptide conjugated NOTA formed stable complexes with (68)Ga at room temperature within 10 min. This might be of special interest for the labeling of fragile and potent macromolecules and allow for kit type preparation of (68)Ga-based radiopharmaceuticals.     

Crystallization of bacteriorhodopsin from bicelle formulations at room temperature

We showed previously that high-quality crystals of bacteriorhodopsin (bR) from Halobacterium salinarum can be obtained from bicelle-forming DMPC/CHAPSO mixtures at 37 degrees C. As many membrane proteins are not sufficiently stable for crystallization at this high temperature, we tested whether the bicelle method could be applied at a lower temperature. Here we show that bR can be crystallized at room temperature using two different bicelle-forming compositions: DMPC/CHAPSO and DTPC/CHAPSO. The DTPC/CHAPSO crystals grown at room temperature are essentially identical to the previous, twinned crystals: space group P21 with unit cell dimensions of a = 44.7 A, b = 108.7 A, c = 55.8 A, beta = 113.6 degrees . The room-temperature DMPC/CHAPSO crystals are untwinned, however, and belong to space group C222(1) with the following unit cell dimensions: a = 44.7 A, b = 102.5 A, c = 128.2 A. The bR protein packs into almost identical layers in the two crystal forms, but the layers stack differently. The new untwinned crystal form yielded clear density for a previously unresolved CHAPSO molecule inserted between protein subunits within the layers. The ability to grow crystals at room temperature significantly expands the applicability of bicelle crystallization.     

Luminescence of thymine aqueous solutions at the room temperature

The distinguishing features of luminescence of aqueous thymine solutions at room temperature (a broadening of luminescence spectra as compared with low-temperature spectra and differences between excitation and absorption spectra) are discussed. It is shown that these features are due to bimolecular photochemical reactions that lead to the formation of photoproducts (at the first stages, photoadducts) with a comparatively high luminescence ability.     

The storage of cow eggs at room temperature and at low temperatures.

The survival and development of cow eggs in the rabbit oviduct after storage at room temperature and after cooling and storage at 0-7-5 degrees C was examined. In PBS medium at room temperature 88% of Day-5 and 85% of Day-3 eggs showed normal development, but in TCM 199, 71% of Day-5 and only 49% of Day-3 eggs showed normal development. Duration of storage (1 1/2-2 hr or 6 1/2-7 1/2 hr) and cleavage stage before storage had no appreciable effect on development. Some retardation of development occurred in Day-3 eggs after 96 hr in the rabbit oviduct when compared to Day-5 eggs after 48 hr. Cooling of Day-5 and Day-6 eggs to 0-7-5 degrees C resulted in degeneration of a large proportion of eggs. Of the factors examined, storage medium (PBS or PBS+20%FCS), storage time (2 min, 24 hr) and storage temperature (0, 2, 5 or 7-5 degrees C) had little effect, but slower cooling rates tended to improve survival of eggs although the differences were not significant. More morulae (greater than 32 cells) than 8-to 24-celled eggs developed normally.     

Fixation and tissue preservation for antibody studies

Synopsis The methods of fixation and preparation of lymphoid tissues for the immuno-enzyme technique are reviewed. For this technique an enzyme is used first as an antigen and then as a marker to demonstrate its specific antibody. A variety of commonly employed fixatives satisfactorily conserve tissues for the light microscopic detection of antibody but, for electron microscopy, glutaraldehyde or formaldehyde or both are the fixatives of choice. The main technical problem for electron microscopy is to reduce the size of the tissue fragments sufficiently so that the enzymes and their substrates permeate through the fixed tissues. The merits and short-comings of the different preparative techniques are examined and it is shown that the most reproducible results are obtained with 40 m frozen sections. Some of the problems of non-specific staining arising from fixation procedures, as well as endogenous enzyme activity, are discussed. The evidence for and against antibody inactivation by fixation and enzyme inactivation by interaction with its specific antibody is reviewed.     

Enhancement of structural preservation and immunocytochemical staining in low temperature embedded pancreatic tissue

The recently developed low temperature embedding procedure with the resin Lowicryl K4M (Carlemalm E, Garavito M, Villiger W: Proc 7th Eur Cong Electron Microsc, 1980, p 656; Garavito M, Carlemalm E, Villiger W: Proc 7th Eur Cong Electron Microsc, 1980, p 658) was tested for its suitability for embedding of glutaraldehyde-fixed rat pancreatic tissue and for postembedding staining of thin sections with the protein A-gold (pAg) technique (Roth J, Bendayan M, Orci L: J Histochem Cytochem 26:1074, 1978) for amylase. Compared to conventional Epon embedding of glutaraldehyde fixed tissue, the low temperature embedding method with Lowicryl K4M resulted in a superior preservation of the general cellular fine structure, particularly in the Golgi apparatus. For low temperature embedded tissue, the quantitative evaluation of the immunocytochemical labeling for amylase showed a more specific staining of the rough endoplasmic reticulum, the Golgi apparatus, and the zymogen granules. This was due to a significant lowering of the background staining over all cellular organelles. The use of Lowicryl K4M at low temperature, due to the superior preservation, yields improved resolution and specificity in immunocytochemical postembedding staining.