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Scientific Reports Oct 2020Ancient DNA (aDNA) analyses necessitate the destructive sampling of archaeological material. Currently, the cochlea, part of the osseous inner ear located inside the...
Ancient DNA (aDNA) analyses necessitate the destructive sampling of archaeological material. Currently, the cochlea, part of the osseous inner ear located inside the petrous pyramid, is the most sought after skeletal element for molecular analyses of ancient humans as it has been shown to yield high amounts of endogenous DNA. However, destructive sampling of the petrous pyramid may not always be possible, particularly in cases where preservation of skeletal morphology is of top priority. To investigate alternatives, we present a survey of human aDNA preservation for each of ten skeletal elements in a skeletal collection from Medieval Germany. Through comparison of human DNA content and quality we confirm best performance of the petrous pyramid and identify seven additional sampling locations across four skeletal elements that yield adequate aDNA for most applications in human palaeogenetics. Our study provides a better perspective on DNA preservation across the human skeleton and takes a further step toward the more responsible use of ancient materials in human aDNA studies.
Topics: Archaeology; Bone and Bones; DNA, Ancient; Ear, Inner; Germany; History, Medieval; Humans; Petrous Bone; Preservation, Biological; Tooth
PubMed: 33106554
DOI: 10.1038/s41598-020-75163-w -
Microbiological Research Jun 2020Freeze-drying technology has been widely considered for decades as a suitable technique to preserve microorganisms. However, protective agents must be added prior to...
Freeze-drying technology has been widely considered for decades as a suitable technique to preserve microorganisms. However, protective agents must be added prior to freeze drying to improve the survival and storage stability of the bacteria. The objective of our study was to evaluate the effect of a new protectant medium containing sucrose (10 %), trehalose (10 %), skimmed milk (10 %) and antioxidants on the viability of gut bacteria under different storage conditions. Two strains were tested, Escherichia coli and Akkermansia muciniphila, as examples of facultative aerobic and anaerobic bacteria, respectively. We studied the cell viability and bacterial morphology in 5 fecal samples in the presence and absence of this protectant medium using plating technique, flow cytometry and scanning electron microscopy. The results of bacterial viability assessed by plating method showed that the protectant medium yielded higher survival rates for both strains whatever the storage conditions (85-93 %) compared to normal saline solution (0.36-37.50 %). It also showed its effectiveness on fecal samples, where bacterial viability after freeze-drying was 89.47 ± 7.63 % and 84.01 ± 7.44 %, as evidenced by flow cytometry analysis and plating method. However unprotected samples showed the lowest cell viability at 19.01 ± 12.88 % and 13.23 ± 9.56 %, as measured by flow cytometry and plating method. In addition, bacterial size and shape were conserved in the protectant medium. In contrast, storage without protectant medium severely damaged bacterial morphology. In conclusion, our study is the first to use morphological features as well as culture-dependant and culture-independent tests to evaluate the effectiveness of a new protectant medium.
Topics: Animals; Bacteria; Culture Media; Freeze Drying; Microbial Viability; Milk; Preservation, Biological; Sucrose; Trehalose
PubMed: 32200250
DOI: 10.1016/j.micres.2020.126454 -
PloS One 2020In this paper, we propose a technique that can efficiently express the preservation and breakup of liquid sheets by eliminating over-preserved liquid sheets using the...
In this paper, we propose a technique that can efficiently express the preservation and breakup of liquid sheets by eliminating over-preserved liquid sheets using the motion of water particles projected onto the screen. First, we project three-dimensional water particles onto a two-dimensional screen. When multiple particles are projected onto the same pixel, we select one of the front most particles as a screened particle by comparing their depth values. Based on the anisotropic kernel and density, the motion of the screened water particles is tracked to determine whether preservation and breakup should be performed. As a result, new water particles are added or existing ones are deleted, which makes it possible to express two characteristics of particle-based fluids: preservation and breakup of liquid sheets. The proposed technique is based on particle-based fluids, which can be used to remove the over-preserved liquid sheets and thus improve the quality of liquid sheets without surface noise.
Topics: Computer Simulation; Imaging, Three-Dimensional; Models, Molecular; Preservation, Biological; Surface Properties; Water
PubMed: 32023259
DOI: 10.1371/journal.pone.0227590 -
International Journal of Legal Medicine Jul 2024Accurate minimum post-mortem interval (minPMI) estimations often rely on a precise age determination of insect developmental stages, which is significantly influenced by...
Accurate minimum post-mortem interval (minPMI) estimations often rely on a precise age determination of insect developmental stages, which is significantly influenced by environmental temperature. An optimal preservation of the entomological samples collected at crime scenes is pivotal for a reliable aging of immature insect samples. For blow flies (Diptera: Calliphoridae), the most widely used insect indicators in forensic investigations, an appropriate preservation of tissues is particularly important in the case of puparial samples because aging methods for intra-puparial forms usually depend on morphological analyses; however, although informative soft tissues and structures could be discoloured and/or distorted if they are not properly fixed, there is a lack of studies to assess different methods for the optimal preservation of intra-puparial forms collected in forensic investigations. The present study compares three preservation methods for intra-puparial forms of the blow fly Calliphora vicina Robineau-Desvoidy, 1830: (i) direct immersion into 80% ethanol, (ii) puncturing of the puparium and hot water killing (HWK) prior to preservation in 80% ethanol, and (iii) HWK without puncturing before preservation in 80% ethanol. External and internal morphological analyses of intra-puparial forms of different ages were conducted to assess the quality of preservation. The results indicate that direct immersion in ethanol led to poor preservation, affecting both external and internal tissues. Both methods with HWK resulted in a better preservation, but puncturing resulted, in some cases, in physical damage of the specimens. HWK without puncturing emerged as the optimal preservation method, consistently yielding high preservation scores for both external and internal morphological analyses. These findings have practical implications for forensic practitioners and emphasise the need for updating some published guidelines and protocols in forensic entomology.
Topics: Animals; Forensic Entomology; Calliphoridae; Pupa; Specimen Handling; Postmortem Changes; Ethanol; Immersion; Preservation, Biological; Hot Temperature
PubMed: 38326653
DOI: 10.1007/s00414-024-03172-9 -
Folia Parasitologica Dec 2018Plastination is a preservation method for biological specimens, with important advantages over classic conservation techniques with formaldehyde or alcohol. Plastinated...
Plastination is a preservation method for biological specimens, with important advantages over classic conservation techniques with formaldehyde or alcohol. Plastinated specimens are dry, odourless, and free of carcinogenic and toxic solutions. There are only few references about the plastination of parasites. Moreover, there is no information on the effect of plastination on the morphology and morphometry of these animals. The aim of this study was to define a plastination protocol to preserve various species of parasites, namely the nematodes Parascaris equorum (Goeze, 1782); Ascaris suum Goeze, 1782 and Dirofilaria immitis (Leidy, 1856); the acanthecephalan Macracanthorhynchus hirudinaceus (Pallas, 1781); the trematodes Fasciola hepatica Linnaeus, 1758 and Dicrocoelium dendriticum (Rudolphi, 1819) and the tapeworm Taenia sp. in the best morphological and morphometric conditions. Results showed that some individuals suffered collapse (P. equorum, A. suum, and D. dendriticum). However, other parasites presented good results with almost no change after plastination (D. immitis, M. hirudinaceus and F. hepatica). In conclusion, conventional plastination allowed anatomical preservation of all helminths tested, but modifications to the protocol are needed to prevent collapse.
Topics: Acanthocephala; Animals; Cestoda; Male; Nematoda; Parasites; Plastination; Trematoda
PubMed: 30593008
DOI: 10.14411/fp.2018.019 -
Scientific Reports Apr 2022The rise of eukaryotic macroalgae in the late Mesoproterozoic to early Neoproterozoic was a critical development in Earth's history that triggered dramatic changes in...
The rise of eukaryotic macroalgae in the late Mesoproterozoic to early Neoproterozoic was a critical development in Earth's history that triggered dramatic changes in biogeochemical cycles and benthic habitats, ultimately resulting in ecosystems habitable to animals. However, evidence of the diversification and expansion of macroalgae is limited by a biased fossil record. Non-mineralizing organisms are rarely preserved, occurring only in exceptional environments that favor fossilization. Investigating the taphonomy of well-preserved macroalgae will aid in identifying these target environments, allowing ecological trends to be disentangled from taphonomic overprints. Here we describe the taphonomy of macroalgal fossils from the Tonian Dolores Creek Formation (ca. 950 Ma) of northwestern Canada (Yukon Territory) that preserves cm-scale macroalgae. Analytical microscopy, including scanning electron microscopy and tomographic x-ray microscopy, was used to investigate fossil preservation, which was the result of a combination of pyritization and aluminosilicification, similar to accessory mineralization observed in Paleozoic Burgess Shale-type fossils. These new Neoproterozoic fossils help to bridge a gap in the fossil record of early algae, offer a link between the fossil and molecular record, and provide new insights into evolution during the Tonian Period, when many eukaryotic lineages are predicted to have diversified.
Topics: Animals; Biological Evolution; Ecosystem; Eukaryota; Fossils; Pain; Preservation, Biological; Yukon Territory
PubMed: 35418588
DOI: 10.1038/s41598-022-10223-x -
International Journal of Molecular... Aug 2023Extracellular vesicles (EVs), detectable in all bodily fluids, mediate intercellular communication by transporting molecules between cells. The capacity of EVs to...
Extracellular vesicles (EVs), detectable in all bodily fluids, mediate intercellular communication by transporting molecules between cells. The capacity of EVs to transport molecules between distant organs has drawn interest for clinical applications in diagnostics and therapeutics. Although EVs hold potential for nucleic-acid-based and other molecular therapeutics, the lack of standardized technologies, including isolation, characterization, and storage, leaves many challenges for clinical applications, potentially resulting in misinterpretation of crucial findings. Previously, several groups demonstrated the problems of commonly used storage methods that distort EV integrity. This work aims to evaluate the process to optimize the storage conditions of EVs and then characterize them according to the experimental conditions and the models used previously. Our study reports a highly efficient EV storage condition, focusing on EV capacity to protect their molecular cargo from biological, chemical, and mechanical damage. Compared with commonly used EV storage conditions, our EV storage buffer leads to less size and particle number variation at both 4 °C and -80 °C, enhancing the ability to protect EVs while maintaining targeting functionality.
Topics: Preservation, Biological; Extracellular Vesicles; Cell Communication; Nucleic Acids; Plant Leaves
PubMed: 37629020
DOI: 10.3390/ijms241612841 -
ELife Mar 2017Many discoveries in the life sciences have been made using material from living stock collections. These collections provide a uniform and stable supply of living...
Many discoveries in the life sciences have been made using material from living stock collections. These collections provide a uniform and stable supply of living organisms and related materials that enhance the reproducibility of research and minimize the need for repetitive calibration. While collections differ in many ways, they all require expertise in maintaining living organisms and good logistical systems for keeping track of stocks and fulfilling requests for specimens. Here, we review some of the contributions made by living stock collections to research across all branches of the tree of life, and outline the challenges they face.
Topics: Biological Specimen Banks; Biomedical Research; Preservation, Biological; United States
PubMed: 28266913
DOI: 10.7554/eLife.24611 -
FEMS Microbiology Ecology Feb 2013Field collections of environmental samples, for example corals, for molecular microbial analyses present distinct challenges. The lack of laboratory facilities in remote... (Comparative Study)
Comparative Study
Field collections of environmental samples, for example corals, for molecular microbial analyses present distinct challenges. The lack of laboratory facilities in remote locations is common, and preservation of microbial community DNA for later study is critical. A particular challenge is keeping samples frozen in transit. Five nucleic acid preservation methods that do not require cold storage were compared for effectiveness over time and ease of use. Mixed microbial communities of known composition were created and preserved by DNAgard(™), RNAlater(®), DMSO-EDTA-salt (DESS), FTA(®) cards, and FTA Elute(®) cards. Automated ribosomal intergenic spacer analysis and clone libraries were used to detect specific changes in the faux communities over weeks and months of storage. A previously known bias in FTA(®) cards that results in lower recovery of pure cultures of Gram-positive bacteria was also detected in mixed community samples. There appears to be a uniform bias across all five preservation methods against microorganisms with high G + C DNA. Overall, the liquid-based preservatives (DNAgard(™), RNAlater(®), and DESS) outperformed the card-based methods. No single liquid method clearly outperformed the others, leaving method choice to be based on experimental design, field facilities, shipping constraints, and allowable cost.
Topics: Bacteria; Base Composition; DNA, Bacterial; Environmental Microbiology; Polymerase Chain Reaction; Preservation, Biological
PubMed: 22974342
DOI: 10.1111/1574-6941.12008 -
PloS One 2017Preservation of three-dimensional structure in the gut is necessary in order to analyze the spatial organization of the gut microbiota and gut luminal contents. In this...
Preservation of three-dimensional structure in the gut is necessary in order to analyze the spatial organization of the gut microbiota and gut luminal contents. In this study, we evaluated preparation methods for mouse gut with the goal of preserving micron-scale spatial structure while performing fluorescence imaging assays. Our evaluation of embedding methods showed that commonly used media such as Tissue-Tek Optimal Cutting Temperature (OCT) compound, paraffin, and polyester waxes resulted in redistribution of luminal contents. By contrast, a hydrophilic methacrylate resin, Technovit H8100, preserved three-dimensional organization. Our mouse intestinal preparation protocol optimized using the Technovit H8100 embedding method was compatible with microbial fluorescence in situ hybridization (FISH) and other labeling techniques, including immunostaining and staining with both wheat germ agglutinin (WGA) and 4', 6-diamidino-2-phenylindole (DAPI). Mucus could be visualized whether the sample was fixed with paraformaldehyde (PFA) or with Carnoy's fixative. The protocol optimized in this study enabled simultaneous visualization of micron-scale spatial patterns formed by microbial cells in the mouse intestines along with biogeographical landmarks such as host-derived mucus and food particles.
Topics: Animals; Cryoultramicrotomy; Formaldehyde; Gastrointestinal Microbiome; Germ-Free Life; In Situ Hybridization, Fluorescence; Methacrylates; Mice, Inbred C57BL; Mucus; Paraffin Embedding; Polymers; Preservation, Biological; Sepharose; Tissue Fixation
PubMed: 29176788
DOI: 10.1371/journal.pone.0188257