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.     

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.     

Light-induced protein-matrix uncoupling and protein relaxation in dry samples of trehalose-coated MbCO at room temperature

In humid samples of trehalose-coated carboxy-myoglobin (MbCO), thermally driven conformational relaxation takes place after photodissociation of the carbon monoxide (CO) molecule at room temperature. In such samples, because of the extreme viscosity of the external matrix, photodissociated CO cannot diffuse out of the protein and explores the whole (proximal and distal side) heme pocket, experiencing averaged protein heme pocket structures, as a results of the presence of Brownian motions. At variance, in very dry samples, a lower portion of the photodissociated CO diffuses from the distal to the proximal heme pocket side probing in nonaveraged structures. We revisit here the flash photolysis data by Librizzi et al. (2002) and report on new, room temperature experiments in MbCO-trehalose samples, shortly illuminated prior the laser pulse. In dry samples, pre-illumination increased the diffusion of CO from the distal to the proximal heme pocket side, which resulted in less structure than in non-pre-illuminated samples. Such an effect, which is absent in humid samples, stems from a decoupling of the protein internal degrees of freedom from those of the external water-sugar matrix. We suggest that such a decoupling can be brought about by the continuous attempts performed by the protein during pre-illumination to undergo relaxation toward the photodissociated deoxy state. This, in turn, causes a collapse in the hydrogen bond network, which connects the protein surface to the water-sugar matrix, as reported by Cottone et al. (2002) and Giuffrida et al. (2003). In the conclusion section, we discuss the possible involvement of the processes invoked to rationalize the present data, in the function of macromolecules and interactions in living cells.     

Effect of temperature and storage time on cellular analysis of fresh pleural fluid samples

L. Antonangelo, F. S. Vargas, M. M. P. Acencio, A. P. Corá, L. R. Teixeira, E. H. Genofre and R. K. B. Sales
Effect of temperature and storage time on cellular analysis of fresh pleural fluid samples Objective: Despite the methodological variability in preparation techniques for pleural fluid cytology, it is fundamental that the cells should be preserved, permitting adequate morphological classification. We evaluated numerical and morphological changes in pleural fluid specimens processed after storage at room temperature or under refrigeration. Methods: Aliquots of pleural fluid from 30 patients, collected in ethylenediaminetetraacetic acid‐coated tubes and maintained at room temperature (21 °C) or refrigeration (4 °C) were evaluated after 2 and 6 hours and 1, 2, 3, 4, 7 and 14 days. Evaluation of cytomorphology and global and percentage counts of leucocytes, macrophages and mesothelial cells were included . Results: The samples had quantitative cellular variations from day 3 or 4 onwards, depending on the storage conditions. Morphological alterations occurred earlier in samples maintained at room temperature (day 2) than in those under refrigeration (day 4). Conclusions: This study confirms that storage time and temperature are potential pre‐analytical causes of error in pleural fluid cytology.     

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.     

Cytochrome oxidase subunit VI of Trypanosoma brucei is imported without a cleaved presequence and is developmentally regulated at both RNA and protein levels

Mitochondrial respiration in the African trypanosome undergoes dramatic developmental stage regulation. This requires co-ordinated control of components encoded by both the nuclear genome and the kinetoplast, the unusual mitochondrial genome of these parasites. As a model for understanding the co-ordination of these genomes, we have examined the regulation and mitochondrial import of a nuclear-encoded component of the cytochrome oxidase complex, cytochrome oxidase subunit VI (COXVI). By generating transgenic trypanosomes expressing intact or mutant forms of this protein, we demonstrate that COXVI is not imported using a conventional cleaved presequence and show that sequences at the N-terminus of the protein are necessary for correct mitochondrial sorting. Analyses of endogenous and transgenic COXVI mRNA and protein expression in parasites undergoing developmental stage differentiation demonstrates a temporal order of control involving regulation in the abundance of, first, mRNA and then protein. This represents the first dissection of the regulation and import of a nuclear-encoded protein into the cytochrome oxidase complex in these organisms, which were among the earliest eukaryotes to possess a mitochondrion.     

Isolation of high-molecular-weight DNA from small samples of blood having nucleated erythrocytes,collected, transported,and stored at room temperature

Blood samples collected in the field for isolating DNA suitable for molecular analysis need special care in their storage and handling. In this article, we describe a simple method for the isolation of good-quality high-molecular-weight DNA that does not require low temperature conditions during collection, storage, and/or transportation of blood samples. This method involves smearing small aliquots of blood onto clean slides and air drying them at room temperature. The slides with blood smears can then be transported or stored at room temperature and still serve as a very good source of high-molecular-weight DNA. Genomic DNA from these samples can be extracted by organic phase separation (phenol-chloroform extraction) after lysis. The DNA thus obtained is of high quality and yields DNA fingerprints qualitatively similar to those prepared from corresponding control DNA isolated from frozen blood samples. Needing minimal facilities at field sites, the method is very convenient for conducting RFLP analysis of wild/field populations for demographic, behavioral, and ecologic studies.     

One-step preservation of phosphoproteins and tissue morphology at room temperature for diagnostic and research specimens

Background

There is an urgent need to measure phosphorylated cell signaling proteins in cancer tissue for the individualization of molecular targeted kinase inhibitor therapy. However, phosphoproteins fluctuate rapidly following tissue procurement. Snap-freezing preserves phosphoproteins, but is unavailable in most clinics and compromises diagnostic morphology. Formalin fixation preserves tissue histomorphology, but penetrates tissue slowly, and is unsuitable for stabilizing phosphoproteins. We originated and evaluated a novel one-step biomarker and histology preservative (BHP) chemistry that stabilizes signaling protein phosphorylation and retains formalin-like tissue histomorphology with equivalent immunohistochemistry in a single paraffin block.

Results

Total protein yield extracted from BHP-fixed, routine paraffin-embedded mouse liver was 100% compared to snap-frozen tissue. The abundance of 14 phosphorylated proteins was found to be stable over extended fixation times in BHP fixed paraffin embedded human colon mucosa. Compared to matched snap-frozen tissue, 8 phosphoproteins were equally preserved in mouse liver, while AMPKβ1 Ser108 was slightly elevated after BHP fixation. More than 25 tissues from mouse, cat and human specimens were evaluated for preservation of histomorphology. Selected tissues were evaluated in a multi-site, independent pathology review. Tissue fixed with BHP showed equivalent preservation of cytoplasmic and membrane cytomorphology, with significantly better nuclear chromatin preservation by BHP compared to formalin. Immunohistochemical staining of 13 non-phosphorylated proteins, including estrogen receptor alpha, progesterone receptor, Ki-67 and Her2, was equal to or stronger in BHP compared to formalin. BHP demonstrated significantly improved immunohistochemical detection of phosphorylated proteins ERK Thr202/Tyr204, GSK3-α/β Ser21/Ser9, p38-MAPK Thr180/Tyr182, eIF4G Ser1108 and Acetyl-CoA Carboxylase Ser79.

Conclusion

In a single paraffin block BHP preserved the phosphorylation state of several signaling proteins at a level comparable to snap-freezing, while maintaining the full diagnostic immunohistochemical and histomorphologic detail of formalin fixation. This new tissue fixative has the potential to greatly facilitate personalized medicine, biobanking, and phospho-proteomic research.     

Development of normal mice after microinjection of round spermatids into oocytes stored at room temperature for one day

Early studies have shown that some mouse cumulus-oocyte complexes (COCs) stored at room temperature for 24 hr still retained full developmental potential. In this study, we stored mouse COCs and denuded oocytes (DOs) at room temperature for 24 hr and activated these oocytes with 10 mM SrCl(2) or injected the oocytes with round spermatids. We found that DOs were better than COCs when stored at room temperature for 1 day and more normal oocytes were obtained when COCs were stored in more H-CZB medium at room temperature for 1 day. The rates of normal oocytes were significantly different after preservation with three schemes (90.01%, 55.81%, and 86.70%, P < 0.05). Our results also indicated that oocytes stored at room temperature for 1 day were fertilized normally (extrusion of the second polar body and formation of male and female pronuclei [PN]) after microinjection of round spermatid nuclei, and that the existence of cumulus cells (CCs) during oocyte storage did not significantly influence the early cleavage but had a detrimental effect on later embryo development and full-term development. After fertilization, most embryos developed to two-cell stage after being cultured for 24 hr, and the development rates of four- to eight-cell embryos between two experiments were similar. However, the rates of morula/blastocyst formation were significantly different (47.44% and 26.27%, respectively, P < 0.05). The birth of four healthy pups from stored DOs indicated that the storage of DOs at room temperature for 1 day might become a practical procedure in mammalian reproduction.     

Automated sampling and RNA isolation at room temperature for measurements of circadian rhythms in Chlamydomonas reinhardtii

The development of techniques allowing the unattended collection of RNA from cell samples at room temperature makes practical accurate and facile monitoring of circadian rhythms in Chlamydomonas reinhardtii. The utility of these methods was demonstrated by collecting RNA samples for three days from cells maintained in continuous darkness. Every hour, cells were automatically collected and lysed with buffer containing SDS and proteinase K. Samples were maintained at room temperature with little or no evidence of degradation of RNA. Strong, non-damping circadian rhythms of cab mRNA abundance were measured. Free-running rhythms of about 24 h were measured from cultures maintained at 16, 20, 25 and 30 °C, thus demonstrating temperature compensation of circadian period. Simultaneous collections from cultures previously entrained to 12 h light/12 h dark cycles of opposite phase displayed circadian rhythms of cab mRNA abundance that were in phase with their previous entraining light cycles. Thus, this result suggests that the measured circadian rhythms of cab mRNA abundance was not an artifact of the collection procedure.     

Effect of cervical and vaginal insemination with liquid semen stored at room temperature on fertility of goats

The effect of vaginal and cervical deposition of liquid semen stored at room temperature on the fertility of goats was tested in a field trial in which 217 Norwegian Dairy goats aged between 6 months and 7.5 years from 14 farms were inseminated after natural oestrous. Cervical insemination with 200 x 10(6) spermatozoa resulted in 25-day non-return and kidding rates of 87.0 and 78.0%, and vaginal insemination gave 85.5 and 74.3%, respectively. There was no significant difference between the cervical and vaginal inseminations (P = 0.59 for the 25-day non-return and P = 0.40 for the kidding rates). Farm had a significant effect on the 25-day non-return rate (P = 0.03) but not on the kidding rate (P = 0.07). There were no significant differences between the fertility rates for different bucks (P = 0.36 for the 25-day non-return and P = 0.15 for the kidding rates). Fertility results after vaginal insemination were encouragingly high. Vaginal insemination is a simple, less costly and time consuming technique compared to others, also bringing into focus the animal welfare aspects of the artificial insemination procedure. As the final goal is to establish a technique that could be applied similarly on a large scale by all farmers, vaginal insemination must be considered as a method that would simplify the use of liquid buck semen in Norway.     

新鲜土壤样品储存温度和时间对不同形态氮素的影响

土壤氮素形态及含量具有重要的生态学研究意义,而土壤样品的储存对土壤氮素含量的准确测定有很大影响.为了选择合理的土壤样品储存方法,本研究以福建省建瓯市万木林保护区罗浮栲林土壤为研究对象,测定在不同温度(25、4和-20 ℃)、不同储存时间(0、7和30 d)下土壤铵态氮、硝态氮、总氮、可溶性有机氮、氨基酸氮含量和微生物生物量氮,以及冷冻后常温培养过程中的氮素含量.结果表明: 在7 d的储存时间内,除氨基酸氮以外,常温培养样品下其余的氮素含量均有所增加;与新鲜样品相比,冷藏、冷冻样品的所有氮素含量之间均无显著性差异,且氮素含量变化较常温培养下更加稳定.因低温储存样品有刺激氮矿化的效果,在30 d储存时间内,与新鲜样品相比,除可溶性有机氮外,冷藏、冷冻样品的所有氮素含量均显著升高;两种冷储存方法之间无显著差异.因此,新鲜样品带回实验室后应及时处理;如需要冷储藏,时间不要超过半个月.如果需要较长的储存时间,则需将样品放置于更低的温度(-40或-80 ℃).在对储存土壤样品进行培养试验之前,需要进行预培养处理.在预培养过程中,除硝态氮含量呈现先下降再迅速升高的趋势外,其余氮素均随着培养时间逐渐趋近于新鲜土壤样品含量,在培养一周左右恢复到与新鲜土壤样品氮含量最为接近的状态.结合已有研究,对野外取样和风干样品需要5～14 d的预培养,冷储存样品预培养时间不应少于一周.     

Oxylipin profile and antioxidant status of potato tubers during extended storage at room temperature

Potato tubers (cv. Bintje) (Solanum tuberosum L.) were stored under extreme conditions at 20 °C for 350 days without sprout inhibitors in order to assess whether aging- and/or senescence-related processes occurred. Under these extreme storage conditions, multiple sprouting followed by the formation of daughter tubers occurs. At the same time, an increase in respiration intensity, as evidenced by cytochrome c oxidase activity (E.C. 1.9.3.1), is observed, leading to a potential increase in reactive oxygen species (ROS) production. As polyunsaturated fatty acids are priority targets of oxidative attacks, the damage to lipids was assessed by oxylipin profiling in both free and esterified forms. Oxylipin profiling showed a predominance of linoleic acid-derived oxylipins and of 9-hydroxy and 9-hydroperoxy fatty acids in both free and esterified forms. No significant accumulation of individual oxylipin was observed 350 days after harvest. To further understand the absence of lipid breakdown products accumulation, the main enzymatic and non-enzymatic antioxidants were assessed. Antioxidant enzyme activities [superoxide dismutase (E.C. 1.15.1.1), catalase (E.C. 1.11.1.6.), ascorbate peroxidase (E.C. 1.11.1.11)] were enhanced during the advanced phase of aging. The main non-enzymatic antioxidant compound, ascorbate, decreased markedly in the early stages of storage, followed by a slower decline. Total radical scavenging activity was also maintained at the end of the storage period. Our results indicate that the enhanced aging process occurring during storage at room temperature does not seem to be associated with the changes classically encountered during leaf senescence or seed aging and that the observed degenerative processes do not surpass the protective potential of the tubers.     

Successful retrieval of mRNA from hair follicles stored at room temperature: implications for studying gene expression in wild mammals

We evaluated some products and protocols designed for reliable RNA extraction from minute tissue samples and safe tissue storage at room temperature without RNA degradation. Success of RNA retrieval was compared for varying amounts of tissue (3, 5, 10 hair follicles), stored at different temperatures (room temperature, ?20 °C) for variable durations (1, 3, 6, 12 weeks). We also compared two RNA isolation kits specialized for small samples. RNA was successfully retrieved from as few as 3 hairs stored at room temperature for up to 6 weeks, suggesting the potential for gene expression analyses on minimally invasive samples from natural populations.     

Chain and conformation stability of solid-state DNA: implications for room temperature storage

There is currently wide interest in room temperature storage of dehydrated DNA. However, there is insufficient knowledge about its chemical and structural stability. Here, we show that solid-state DNA degradation is greatly affected by atmospheric water and oxygen at room temperature. In these conditions DNA can even be lost by aggregation. These are major concerns since laboratory plastic ware is not airtight. Chain-breaking rates measured between 70°C and 140°C seemed to follow Arrhenius’ law. Extrapolation to 25°C gave a degradation rate of about 1–40 cuts/10⁵ nucleotides/century. However, these figures are to be taken as very tentative since they depend on the validity of the extrapolation and the positive or negative effect of contaminants, buffers or additives. Regarding the secondary structure, denaturation experiments showed that DNA secondary structure could be preserved or fully restored upon rehydration, except possibly for small fragments. Indeed, below about 500 bp, DNA fragments underwent a very slow evolution (almost suppressed in the presence of trehalose) which could end in an irreversible denaturation. Thus, this work validates using room temperature for storage of DNA if completely protected from water and oxygen.     

Full term development of normal mice after transfer of IVF embryos derived from oocytes stored at room temperature for 1 day

Early studies have shown that some mouse cumulus-oocyte complexes (COCs) stored at room temperature for 24 h still retained full developmental potential. In this study, we stored denuded mouse oocytes (DOs) at room temperature (25 degrees C) for 24 h and activated these oocytes with 10 mM SrCl2 or fertilized the oocytes by IVF. We found that nearly half of the DOs stored at room temperature for 1 day can be fertilized normally by IVF and that two foster mothers gave birth to seven pups. Embryos from stored oocytes were cultured in CZB medium with or without 1 microg/ml 17beta-estradiol (E2). The numbers of embryo that developed to morula/blastocyst stage after parthenogenetic activation and IVF were significantly increased when E2 was added to the culture (p<0.05). These results suggest that E2 might improve mouse embryo development in vitro. The birth of seven agouti pups and their healthy growth indicated that the storage of DOs at room temperature for 1 day may be a practical procedure for mammalian reproduction.     

5种马鞭草科植物种子萌发对低温层积和干燥贮藏的响应及其更新对策

研究了冬季相对低温(15、4和0℃)湿藏和室温干燥贮藏对亚热带5种马鞭草科植物马缨丹(Lantana camara)、假连翘(Duranta repens)、假马鞭(Stachytarpheta jamaicensis)、牡荆(Vitex negundo var.cannabifolia)和单叶蔓荆(Vitex trifolia var.simplicifolia)种子萌发的影响。结果表明,5种马鞭草科植物种子扩散时萌发率较低(50%)或不萌发,低温层积可以破除部分种子休眠,提高萌发率或加快萌发速度。马缨丹种子扩散时萌发率是10.7%,经过15℃湿藏后萌发率达到45.3%;假马鞭种子扩散时萌发率为10%和49.3%(25℃和25/15℃),经过低温层积和室温干燥贮藏后萌发率分别达到22.7%~34%和55%以上(除0℃贮藏以外);牡荆种子扩散时萌发率为10%,经过低温层积和室温干燥贮藏后萌发率达到20%~30%;单叶蔓荆种子扩散时不萌发,经过15和4℃湿润贮藏后萌发率达到45.3%和42%;假连翘种子经不同贮藏后萌发率不足6%。亚热带冬季相对低温是5种植物种子萌发的环境暗示,使其在最适宜幼苗存活和生长的春季萌发,增大物种适合度。