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Methods in Molecular Biology (Clifton,... 2019Arthropods comprise an amazingly diverse group of life forms that are extensively studied in almost every field of the biological sciences. Given that the vast majority... (Review)
Review
Arthropods comprise an amazingly diverse group of life forms that are extensively studied in almost every field of the biological sciences. Given that the vast majority of animals are arthropods (primarily insects, arachnids, and crustaceans), knowledge of the specific methods to collect and preserves these organisms for scientific purposes can be indispensable. The application of this research can play major roles in fundamental aspects of human society, including agriculture and medicine. With something on the order of 5-10 million or more arthropod species in existence, it is a challenge for any biologist to attempt to assess and document biodiversity, but many of us find ourselves in a position to either perform this task, or assist others in doing so. It is therefore of utmost importance that proper collection and preservation techniques are used for arthropods which are then made available to scientists for diverse fields of research. The actual practical details of collection and preservation are nearly as diverse as the organisms themselves, so we can only attempt to give basic guidelines here, discussing equipment, trapping techniques, preservation methods, and documentation methods necessary for scientists inexperienced in arthropod collecting to preserve research-quality specimens.
Topics: Animals; Arthropods; Biological Specimen Banks; Humans; Preservation, Biological; Specimen Handling
PubMed: 30539445
DOI: 10.1007/978-1-4939-8935-5_17 -
Reproduction & Fertility Apr 2022To present an overview of different approaches and recent advances for long-term preservation of germ cells and gonadal tissues at ambient temperatures. (Review)
Review
OBJECTIVE
To present an overview of different approaches and recent advances for long-term preservation of germ cells and gonadal tissues at ambient temperatures.
METHODS
Review of the existing literature.
RESULTS
Preserving viable spermatozoa, eggs, embryos, and gonadal tissues for the long term is critical in human fertility treatment and for the management of animal populations (livestock, biomedical models, and wild species). The need and number of banked germplasms are growing very fast in all disciplines, but current storage options at freezing temperatures are often constraining and not always sustainable. Recent research indicates that structures and functions of gametes or gonadal tissues can be preserved for the long term using different strategies based on dehydration and storage at supra-zero temperatures. However, more studies are needed in rehydration and reanimation of germplasms (including proper molecular and cellular evaluations).
CONCLUSIONS
While a lot of research is still warranted to optimize drying and rehydration conditions for each sample type and each species, alternative preservation methods will change the paradigm in fertility preservation and biobanking. It will transform the way we maintain and manage precious biomaterials for the long term.
LAY SUMMARY
Living sperm cells, eggs, embryos, and reproductive tissues can be preserved at freezing temperatures for human fertility treatments and used to manage breeding in livestock, laboratory animals, and wild species through assisted reproduction. These cells can be stored in cell banks and demand for them is growing fast. However, current long-term storage options at freezing temperatures are expensive. Instead of using low temperatures, recent research indicates that these cells can be dried and stored above freezing temperatures for an extended amount of time. While a lot of research is still needed to optimize how different samples are dried and rehydrated, alternative methods of preserving cells will make fertility preservation and cell banking easier. It will also transform the way we keep and manage samples for the long term.
Topics: Animals; Biological Specimen Banks; Cryopreservation; Freeze Drying; Gonads; Humans; Male; Ovum; Preservation, Biological; Semen; Spermatozoa; Temperature
PubMed: 35514540
DOI: 10.1530/RAF-22-0008 -
Fungal Biology Feb 2014Basidiomycetes are used in industrial processes, in basic or applied research, teaching, systematic and biodiversity studies. Efficient work with basidiomycete cultures... (Review)
Review
Basidiomycetes are used in industrial processes, in basic or applied research, teaching, systematic and biodiversity studies. Efficient work with basidiomycete cultures requires their reliable source, which is ensured by their safe long-term storage. Repeated subculturing, frequently used for the preservation, is time-consuming, prone to contamination, and does not prevent genetic and physiological changes during long-term maintenance. Various storage methods have been developed in order to eliminate these disadvantages. Besides lyophilization (unsuitable for the majority of basidiomycetes), cryopreservation at low temperatures seems to be a very efficient way to attain this goal. Besides survival, another requirement for successful maintenance of fungal strains is the ability to preserve their features unchanged. An ideal method has not been created so far. Therefore it is highly desirable to develop new or improve the current preservation methods, combining advantages and eliminate disadvantages of individual techniques. Many reviews on preservation of microorganisms including basidiomycetes have been published, but the progress in the field requires an update. Although herbaria specimens of fungi (and of basidiomycetes in particular) are very important for taxonomic and especially typological studies, this review is limited to live fungal cultures.
Topics: Basidiomycota; Mycology; Preservation, Biological
PubMed: 24528635
DOI: 10.1016/j.funbio.2013.12.002 -
Journal of Microbiological Methods Aug 2006The preservation of micro-organisms by different drying methodologies has been used for decades. Freeze drying in particular is the preferred method for transporting and... (Review)
Review
The preservation of micro-organisms by different drying methodologies has been used for decades. Freeze drying in particular is the preferred method for transporting and storing vast culture collections of micro-organism strain types. The literature on drying and preserving micro-organisms is extensive, but is often specific to one particular strain. This review attempts to draw some similar concepts and findings together in one paper, to compare different drying techniques, with specific reference to microorganisms. The main topics covered are cell growth phases and concentration, inducing drying tolerance in microbial cells, drying methods, rehydration of dried cells and packaging and storage conditions. Also, particular attention has been paid to the use of freeze drying and the protective matrices used to improve microbial cell viability after drying.
Topics: Bacteria; Cryoprotective Agents; Desiccation; Freeze Drying; Microbial Viability; Preservation, Biological
PubMed: 16632005
DOI: 10.1016/j.mimet.2006.02.017 -
Mycorrhiza Jul 2014Short- to long-term preservation of mycorrhizal fungi is essential for their in-depth study and, in the case of culture collections, for safeguarding their biodiversity.... (Review)
Review
Short- to long-term preservation of mycorrhizal fungi is essential for their in-depth study and, in the case of culture collections, for safeguarding their biodiversity. Many different maintenance/preservation methods have been developed in the last decades, from soil- and substrate-based maintenance to preservation methods that reduce (e.g., storage under water) or arrest (e.g., cryopreservation) growth and metabolism; all have advantages and disadvantages. In this review, the principal methods developed so far for ectomycorrhizal and arbuscular mycorrhizal fungi are reported and described given their distinct biology/ecology/evolutionary history. Factors that are the most important for their storage are presented and a protocol proposed which is applicable, although not generalizable, for the long-term preservation at ultra-low temperature of a large panel of these organisms. For ECM fungi, isolates should be grown on membranes or directly in cryovials until the late stationary growth phase. The recommended cryopreservation conditions are: a cryoprotectant of 10% glycerol, applied 1-2 h prior to cryopreservation, a slow cooling rate (1 °C min(-1)) until storage below -130 °C, and fast thawing by direct plunging in a water bath at 35-37 °C. For AMF, propagules (i.e., spores/colonized root pieces) isolated from cultures in the late or stationary phase of growth should be used and incorporated in a carrier (i.e., soil or alginate beads), preferably dried, before cryopreservation. For in vitro-cultured isolates, 0.5 M trehalose should be used as cryoprotectant, while isolates produced in vivo can be preserved in dried soil without cryoprotectant. A fast cryopreservation cooling rate should be used (direct immersion in liquid nitrogen or freezing at temperatures below -130 °C), as well as fast thawing by direct immersion in a water bath at 35 °C.
Topics: Mycorrhizae; Preservation, Biological
PubMed: 24292254
DOI: 10.1007/s00572-013-0541-8 -
Bioanalysis Apr 2017With the wide use of biomarkers to enable critical drug-development decisions, there is a growing concern from scientific community on the need for a 'standardized... (Review)
Review
With the wide use of biomarkers to enable critical drug-development decisions, there is a growing concern from scientific community on the need for a 'standardized process' for ensuring biomarker specimen stability and hence, a strong desire to share best practices on preserving the integrity of biomarker specimens in clinical trials and the design of studies to evaluate analyte stability. By leveraging representative industry experience, we have attempted to provide an overview of critical aspects of biomarker specimen stability commonly encountered during clinical development, including: planning of clinical sample collection procedures, clinical site training, selection of sample preservation buffers, shipping logistics, fit-for-purpose stability assessments in the analytical laboratory and presentation of case studies covering widely utilized biomarker specimen types.
Topics: Biomarkers; Humans; Preservation, Biological; Protein Stability; Proteins; Specimen Handling; Transportation
PubMed: 28508714
DOI: 10.4155/bio-2017-0009 -
Molecular Ecology Resources Jan 2020Environmental DNA (eDNA) is rapidly growing in popularity as a tool for community assessments and species detection. While eDNA approaches are now widely applied, there... (Review)
Review
Environmental DNA (eDNA) is rapidly growing in popularity as a tool for community assessments and species detection. While eDNA approaches are now widely applied, there is not yet agreement on best practices for sample collection and processing. Investigators looking to integrate eDNA approaches into their research programme are required to examine a growing collection of disparate studies to make an often uncertain decision about which protocols best fit their needs. To promote the application of eDNA approaches and to encourage the generation of high-quality data, here we review the most common techniques for the collection, preservation and extraction of metazoan eDNA from water samples. Specifically, we focus on experimental studies that compare various methods and outline the numerous challenges associated with eDNA. While the diverse applications of eDNA do not lend themselves to a one-size-fits-all recommendation, in most cases, capture/concentration of eDNA on cellulose nitrate filters (with pore size determined by water turbidity), followed by storage of filters in Longmire's buffer and extraction with a DNeasy Blood & Tissue Kit (or similar) has been shown to provide sufficient, high-quality DNA. However, we also emphasize the importance of testing and optimizing protocols for the system of interest.
Topics: DNA, Environmental; Fresh Water; Polymerase Chain Reaction; Preservation, Biological
PubMed: 31633859
DOI: 10.1111/1755-0998.13107 -
BioEssays : News and Reviews in... Jan 2018Exceptionally preserved fossils are the product of complex interplays of biological and geological processes including burial, autolysis and microbial decay, authigenic... (Review)
Review
Soft-Bodied Fossils Are Not Simply Rotten Carcasses - Toward a Holistic Understanding of Exceptional Fossil Preservation: Exceptional Fossil Preservation Is Complex and Involves the Interplay of Numerous Biological and Geological Processes.
Exceptionally preserved fossils are the product of complex interplays of biological and geological processes including burial, autolysis and microbial decay, authigenic mineralization, diagenesis, metamorphism, and finally weathering and exhumation. Determining which tissues are preserved and how biases affect their preservation pathways is important for interpreting fossils in phylogenetic, ecological, and evolutionary frameworks. Although laboratory decay experiments reveal important aspects of fossilization, applying the results directly to the interpretation of exceptionally preserved fossils may overlook the impact of other key processes that remove or preserve morphological information. Investigations of fossils preserving non-biomineralized tissues suggest that certain structures that are decay resistant (e.g., the notochord) are rarely preserved (even where carbonaceous components survive), and decay-prone structures (e.g., nervous systems) can fossilize, albeit rarely. As we review here, decay resistance is an imperfect indicator of fossilization potential, and a suite of biological and geological processes account for the features preserved in exceptional fossils.
Topics: Animals; Biological Evolution; Fossils; Geological Phenomena; Molecular Biology; Phylogeny; Preservation, Biological
PubMed: 29193177
DOI: 10.1002/bies.201700167 -
Clinical Anatomy (New York, N.Y.) Mar 2019The adverse effects formaldehyde fixation has on tissues both gross anatomically and histologically are well documented. Consequently, researchers are seeking... (Comparative Study)
Comparative Study
The adverse effects formaldehyde fixation has on tissues both gross anatomically and histologically are well documented. Consequently, researchers are seeking alternative embalming techniques that better preserve in vivo characteristics of tissues. Phenol-based embalming is one method that has shown promise in its ability to adequately preserve the in vivo qualities of tissues through preliminary explorations at the gross anatomical level. The literature on phenol-based embalming is currently scarce, especially with regard to its effects on tissues at the microscopic level. For the current study we aimed to document the histologic effects of a formaldehyde-free phenol-based embalming solution on neural tissue, with the hope of providing novel insight into the effects of soft-embalming on tissues at the microscopic level. Cerebral and cerebellar tissue obtained from porcine brains was fixed in phenol- and formaldehyde-based fixatives; the latter served as a control. Fixed samples were processed for histological analysis. The phenol-based embalming solution provided excellent preservation of the cerebral and cerebellar tissue morphology. Of note was the decrease in separation artifact seen in both tissue types relative to the control tissue, as well as anomalous circular artifacts in the white matter. The results of this study indicate that the phenol-based embalming solution preserves neural tissue at the histological level, perhaps superiorly in many aspects when compared to the formaldehyde-fixed samples. Further investigations of both gross anatomy and histology are recommended on the basis of these promising new findings to determine its potential utilities within research and education. Clin. Anat. 32:224-230, 2019. © 2018 Wiley Periodicals, Inc.
Topics: Animals; Cerebellum; Cerebral Cortex; Fixatives; Formaldehyde; Nerve Tissue; Phenol; Preservation, Biological; Swine
PubMed: 30281854
DOI: 10.1002/ca.23290 -
Microbiology Spectrum Dec 2021A critical step in studies of the intestinal microbiome using meta-omics approaches is the preservation of samples before analysis. Preservation is essential for...
A critical step in studies of the intestinal microbiome using meta-omics approaches is the preservation of samples before analysis. Preservation is essential for approaches that measure gene expression, such as metaproteomics, which is used to identify and quantify proteins in microbiomes. Intestinal microbiome samples are typically stored by flash-freezing and storage at -80°C, but some experimental setups do not allow for immediate freezing of samples. In this study, we evaluated methods to preserve fecal microbiome samples for metaproteomics analyses when flash-freezing is not possible. We collected fecal samples from C57BL/6 mice and stored them for 1 and 4 weeks using the following methods: flash-freezing in liquid nitrogen, immersion in RNA, immersion in 95% ethanol, immersion in a RNA-like buffer, and combinations of these methods. After storage, we extracted protein and prepared peptides for liquid chromatography with tandem mass spectrometry (LC-MS/MS) analysis to identify and quantify peptides and proteins. All samples produced highly similar metaproteomes, except for ethanol-preserved samples that were distinct from all other samples in terms of protein identifications and protein abundance profiles. Flash-freezing and RNA (or RNA-like treatments) produced metaproteomes that differed only slightly, with less than 0.7% of identified proteins differing in abundance. In contrast, ethanol preservation resulted in an average of 9.5% of the identified proteins differing in abundance between ethanol and the other treatments. Our results suggest that preservation at room temperature in RNA or an RNA-like solution performs as well as freezing for the preservation of intestinal microbiome samples before metaproteomics analyses. Metaproteomics is a powerful tool to study the intestinal microbiome. By identifying and quantifying a large number of microbial, dietary, and host proteins in microbiome samples, metaproteomics provides direct evidence of the activities and functions of microbial community members. A critical step for metaproteomics workflows is preserving samples before analysis because protein profiles are susceptible to fast changes in response to changes in environmental conditions (air exposure, temperature changes, etc.). This study evaluated the effects of different preservation treatments on the metaproteomes of intestinal microbiome samples. In contrast to prior work on preservation of fecal samples for metaproteomics analyses, we ensured that all steps of sample preservation were identical so that all differences could be attributed to the preservation method.
Topics: Animals; Bacteria; Bacterial Proteins; Chromatography, Liquid; Feces; Female; Gastrointestinal Microbiome; Male; Mice; Mice, Inbred C57BL; Peptides; Preservation, Biological; Proteomics; Tandem Mass Spectrometry
PubMed: 34908431
DOI: 10.1128/Spectrum.01877-21