Years Of Preservation Research Articles

Magnetic Bead Spherical Nucleic Acid Microstructure for Reliable DNA Preservation and Repeated DNA Reading.

DNA is an attractive medium for long-term data storage because of its density, ease of copying, sustainability, and longevity. Recent advances have focused on the development of new encoding algorithms, automation, and sequencing technologies. Despite progress in these subareas, the most challenging hurdle in the deployment of DNA storage remains the reliability of preservation and the repeatability of reading. Herein, we report the construction of a magnetic bead spherical nucleic acid (MB-SNA) composite microstructure and its use as a cost-effective platform for reliable DNA preservation and repeated reading. MB-SNA has an inner core of silica@γ-Fe2O3@silica microbeads and an outer spherical shell of double-stranded DNA (dsDNA) with a density as high as 34 pmol/cm2. For MB-SNA, each strand of dsDNA stored a piece of data, and the high-density packing of dsDNA achieved high-capacity storage. MB-SNA was advantageous in terms of reliable preservation over free DNA. By accelerated aging tests, the data of MB-SNA is demonstrated to be readable after 0.23 million years of preservation at -18 °C and 50% relative humidity. Moreover, MB-SNA facilitated repeated reading by facile PCR-magnetic separation. After 10 cycles of PCR access, the retention rate of dsDNA for MB-SNA is demonstrated to be as high as 93%, and the accuracy of sequencing is more than 98%. In addition, MB-SNA makes cost-effective DNA storage feasible. By serial dilution, the physical limit for MB-SNA to achieve accurate reading is probed to be as low as two microstructures.

Comparison of Efficiency of Bonded retainers and Vacuum formed retainers- A Randomized Clinical trial

Background: Major goal of orthodontic treatment is long term stability of the corrected teeth after orthodontic treatment. After orthodontic treatment there is always chance of relapse. To prevent relapse several appliances are available as a retention device such as bonded fixed retainers, vacuum formed retainers, removable Hawley retainer, Begg’s retainer. Now a days vacuum formed retainer has become more acceptable due to low cost, esthetic and easy fabrication. Objective: The purpose of this study was to analyze the clinical success of bonded retainers with vacuumformed retainers, as far as keeping up the consequences of orthodontic treatment in the lower arch as long as a year after debond. Methods: This was a randomized clinical trial (RCT) carried out at the department of Orthodontics, Bangabandhu Sheikh Mujib Medical University, Dhaka. In the study a total of 40 subjects who had fulfilled the selection criteria were randomly allocated to one of two groups, receiving either a vacuum-formed retainer or a bonded retainer for the mandibular arch. Qualification criteria was patients approaching debond after treatment with preadjusted edgewise fixed orthodontic appliance whose pretreatment records and study models were accessible to confirm pretreatment labial segment crowding or spacing and who had clinically acceptable alignment after treatment. The principle purpose was to research the clinical adequacy of the 2 kinds of retainers regarding changes in incisor irregularity at one year of preservation of treatment outcome. The following measurements were documented at each time point (6 and 12 months) with a digital caliper: Little’s irregularity index, intercanine width, intermolar width, arch length, extraction space opening. Result: The two groups were very much coordinated as for age, sex, clinical qualities, and treatment plans. Four patients did not attend in the follow up period and the study finished up in 36 patients. There was a statistically significant difference between the groups for changes in Little’s irregularity index and arch length. Vacuum-formed retainer group showed greater changes than the bonded retainer group (P value 0.035 and 0.022). There were also no statistically significant changes at any time for intercanine width and intermolar width. Conclusion: Some relapse is likely after fixed orthodontic treatment regardless of retainer choice, and this is negligible in many patients after debond. Bonded retainers have a superior capacity to hold the mandibular incisor arrangement after orthodontic treatment than vacuum-formed retainers. Trial registration: not done. Bangladesh Medical Res Counc Bull 2022; 48: 105-111

Assessing tradeoffs between current and desired vegetation condition in a National Park using historical maps and high‐resolution lidar data

In the United States, National Park Service Civil War battlefield units are managed for both historical accuracy (i.e. to represent landscape conditions at the time of the conflict for historical interpretation), and for natural resource protection. However, managing for both goals can create conflicts as many battlefields were largely open or in second growth forests historically, but now harbor significant forest resources after more than 100 years of preservation. Managing for historical accuracy therefore may require maintenance of the landscape in a successional stage out of phase with the current landscape. We use historical landscape maps and current high‐resolution forest structure data derived from lidar to examine tradeoffs in returning the landscape of a major Civil War battlefield (Wilderness Battlefield) to conditions present at the time of the battle. We demonstrate that National Park battlefield units can harbor significant forest resources in contrast to the surrounding landscape, especially in areas of intense commercial, urban, and suburban development. Managing for or restoring landscapes to historical conditions could have important ecological implications.

The diversity and evolutionary relationships of ticks and tick-borne bacteria collected in China

BackgroundTicks (order Ixodida) are ectoparasites, vectors and reservoirs of many infectious agents affecting humans and domestic animals. However, the lack of information on tick genomic diversity leaves significant gaps in the understanding of the evolution of ticks and associated bacteria.ResultsWe collected > 20,000 contemporary and historical (up to 60 years of preservation) tick samples representing a wide range of tick biodiversity across diverse geographic regions in China. Metagenomic sequencing was performed on individual ticks to obtain the complete or near-complete mitochondrial (mt) genome sequences from 46 tick species, among which mitochondrial genomes of 23 species were recovered for the first time. These new mt genomes data greatly expanded the diversity of many tick groups and revealed five cryptic species. Utilizing the same metagenomic sequence data we identified divergent and abundant bacteria in Haemaphysalis, Ixodes, Dermacentor and Carios ticks, including nine species of pathogenetic bacteria and potentially new species within the genus Borrelia. We also used these data to explore the evolutionary relationship between ticks and their associated bacteria, revealing a pattern of long-term co-divergence relationship between ticks and Rickettsia and Coxiella bacteria.ConclusionsIn sum, our study provides important new information on the genetic diversity of ticks based on an analysis of mitochondrial DNA as well as on the prevalence of tick-borne pathogens in China. It also sheds new light on the long-term evolutionary and ecological relationships between ticks and their associated bacteria.Graphical

Volatile Sample Return in the Solar System

We advocate for the realization of volatile sample return from various destinations including: small bodies, the Moon, Mars, ocean worlds/satellites, and plumes. As part of recent mission studies (e.g., Comet Astrobiology Exploration SAmple Return (CAESAR) and Mars Sample Return), new concepts, technologies, and protocols have been considered for specific environments and cost. Here we provide a plan for volatile sample collection and identify the associated challenges with the environment, transit/storage, Earth re-entry, and curation. Laboratory and theoretical simulations are proposed to verify sample integrity during each mission phase. Sample collection mechanisms are evaluated for a given environment with consideration for alteration. Transport and curation are essential for sample return to maximize the science investment and ensure pristine samples for analysis upon return and after years of preservation. All aspects of a volatile sample return mission are driven by the science motivation: isotope fractionation, noble gases, organics and prebiotic species; plus planetary protection considerations for collection and for the sample. The science value of sample return missions has been clearly demonstrated by previous sample return programs and missions. Sample return of volatile material is key to understanding (exo)planet formation, evolution, and habitability. Returning planetary volatiles poses unique and potentially severe technical challenges. These include preventing changes to samples between (and including) collection and analyses, and meeting planetary protection requirements.

Evaluation of DNA and RNA quality from archival formalin-fixed paraffin-embedded tissue for next-generation sequencing - Retrospective study in Japanese single institution.

Genetic analysis on formalin-fixed paraffin-embedded (FFPE) tissue specimens has become a mainstream method, from conventional direct sequencing to comprehensive analysis using next-generation sequencing (NGS). In this study, we evaluated the quality of DNA and RNA extracted from FFPE sections, derived from surgical specimens of different tumor types. Electrophoresis was performed using a 4200 TapeStation to evaluate DNA and RNA fragmentation. DNA Ct values were higher and significantly increased over a period of 4 years compared with those from cell lines or frozen tissues. The RNA integrity number equivalent (RIN) ranged from 1 to 4.1 and DV200 ranged from 7.3 to 81%. Twelve of the 108 cases were analyzed by NGS using the AmpliSeq Cancer HotSpot Panel v2 on a Miniseq system. A sufficient number of reads and coverage were obtained in all cases. Our results revealed that NGS analysis was sufficient for FFPE-derived DNA within 4 years of preservation. Conversely, approximately 20% of the RNA derived from FFPE within 4 years from the collection could be inappropriate for gene analysis based on RIN and DV200. It was suggested that FFPE would be adequate for genetic analysis, although it is desirable to store frozen specimens for the tumor tissues to be subjected to genetic analysis.

A new low-cost method for long-term preservation of filamentous fungi

Abstract Preservation of fungi for commercial and research purposes for a long time, is a very tedious task. Cryopreservation and lyophilization have been extensively used as long-term preservation techniques. Here, we introduced a novel method for long preservation and fast revival of filamentous fungi using sterile cotton balls (CB). A 16 fungal genera and 47 species represented by 135 strains have been preserved on cotton balls moistened with Potato Dextrose Agar (PDA) and incubated at 25 ± 2 °C until giving sufficient growth, then preserved at 17–20 °C for 36 months. The revival of the fungal growth on PDA was monitored every 6 months. A 135 fungal strains have been revived by the CB method with an overall revival rate of 100% after two years of long-term preservation. While, 76 strains were revived after three years of preservation and the revival rate was 59%. The viability or the mycelial morphology was unaffected by the new method even after three years of preservation. It is an easy, cost-effective, and convenient method for preservation of filamentous fungi for long period without contamination risk. We believe that the CB method is a very convenient method for a cheap delivery of filamentous fungi between research institutes.

Fifty Years of Preservation: Historic American Engineering Record

On its 50th anniversary, the Historic American Engineering Record celebrates its chronicling of America’s industrial heritage while facing an uncertain future.

Reuse for Research: Curating Astrophysical Datasets for Future Researchers

“Our data are going to be valuable for science for the next 50 years, so please make sure you preserve them and keep them accessible for active research for at least that period.”
 These were approximately the words used by the principal investigator of the Kepler Asteroseismic Science Consortium (KASC) when he presented our task to us. The data in question consists of data products produced by KASC researchers and working groups as part of their research, as well as underlying data imported from the NASA archives.
 The overall requirements for 50 years of preservation while, at the same time, enabling reuse of the data for active research presented a number of specific challenges, closely intertwining data handling and data infrastructure with scientific issues. This paper reports our work to deliver the best possible solution, performed in close cooperation between the research team and library personnel.

Long-Term Stability of Cryopreserved Human Hepatocytes: Evaluation of Phase I and II Drug-Metabolizing Enzyme Activities and CYP3A4/5 Induction for More than a Decade

We evaluated the long-term stability of hepatocytes stored in the vapor phase of liquid nitrogen for their viability, cytochrome P450 (CYP) 1A2 activity, CYP3A4/5 activity, uridine diphosphate-glucuronosyl transferase (UGT) activity, sulfotransferase (SULT) activity, and CYP3A4/5 induction during 14 years of preservation. No substantial degradation of viability, CYP1A2 activity, UGT activity, or CYP3A4/5 induction was observed. CYP3A4/5 activity showed a slight decrease after 7 years of storage, and SULT activity gradually decreased during storage, although substantial activities remained even after 14 years. These results indicate that cryopreserved human hepatocytes can be stored stably for more than a decade with little or no change in viability, activity of drug-metabolizing enzymes, or CYP3A4/5 induction, and can be widely applicable to qualitative research in drug metabolism.

Preparation of an immunoaffinity chromatography column for chloramphenicol binding

Anti-chloramphenicol rabbit antibody was covalently bound to Sepharose CL 4B-CNBr gel at 5, 10 and 15 mg antibody per mL gel and was fed into columns to prepare three respective immunoaffinity chromatography columns for chloramphenicol (CAP) binding. Examination of CAP-binding efficiency of these columns being fed with 0.5, 1 and 10 ng CAP showed that the column with 10 mg antibody per ml gel (IAC-CAP-10 column) could bind more than 90 % of the CAP amount having been fed into the column at all three examined CAP amounts. This IAC-CAP-10 column showed a coefficient of variants (CV) between columns upon CAP binding of 5.18 % for 1 ng fed CAP and 1.98 % for 10 ng, respectively, a loading capacity of 153,37 ± 10,32 ng CAP, stable CAP-binding performance during at least 2 years of preservation at 4 °C. The coupling of this IAC-CAP-10 column with liquid chromatography - tandem mass spectrometry LC MS/MS could make CAP analysis become possible with a limit of detection LOD of 0.033 ng and a limit of quantification LOQ of 0.101 ng. The column could also bind to the other two phenicol antibiotics: florfenicol and thiamphenicol with a binding efficiency of 90.73 % for florfenicol and 84.29 % for thiamphenicol.

Revealing Invisible Beauty, Ultra Detailed: The Influence of Low Cost UV Exposure on Natural History Specimens in 2D+ Digitization.

Digitization of the natural history specimens usually occurs by taking detailed pictures from different sides or producing 3D models. Additionally this is normally limited to imaging the specimen while exposed by light of the visual spectrum. However many specimens can see in or react to other spectra as well. Fluorescence is a well known reaction to the ultraviolet (UV) spectrum by animals, plants, minerals etc. but rarely taken into account while examining natural history specimens. Our tests show that museum specimens still fluoresce when exposed to UV light of 395 nm and 365 nm, even after many years of preservation. When the UV exposure is used in the digitization of specimens using our low cost focus stacking (2D+) setup, the resulting pictures reveal more detail than the conventional 2D+ images. Differences in fluorescence using 395 nm or 365 nm UV lights were noticed, however there isn’t a preferred wavelength as some specimens react more to the first, while others have better results with the latter exposure. Given the increased detail and the low cost of the system, UV exposure should be considered while digitizing natural history museum collections.

Evaluation of the Viabilities and Stabilities of Pathogenic Mold and Yeast Species Using Three Different Preservation Methods Over a 12-Year Period Along with a Review of Published Reports

Serious mycological work requires a reliable source of cultures that are maintained under safe long-term storage. In this study, 1186 clinical fungal isolates consisting of molds (20 species in 11 genera) and yeasts (21 species in seven genera) maintained in water, under mineral oil at room temperature and cryopreserved at -80°C for periods ranging from 1 to 12years, were evaluated for their viabilities and stabilities. The strains were subcultured onto either Sabouraud dextrose agar or potato dextrose agar to determine the viabilities and purities. The stabilities of the dermatophytes were investigated using urease test medium, the Trichophyton agar test and morphological examination. The stabilities of yeasts were evaluated by microscopic morphology and by determining the antifungal susceptibilities of random samples of yeasts (n=120). Additionally, 365 strains (dermatophytes, n=115; yeasts, n=250) were further characterized by "matrix-assisted laser desorption/ionization time-of-flight mass spectrometry." After 12years of preservation, the survival rates with the three different preservation techniques, i.e., in water, under mineral oil and by freezing, were assessed as 94.7, 82.0 and 97.4%, respectively. Viability was generally unrelated to the duration of storage. More stable and consistent growth was achieved after storage in water and freezing compared with mineral oil preservation. Our results demonstrate that the procedure for maintaining fungal cultures in water is a simple and inexpensive method, next to cryopreservation, and that both can be reliably used for the long-term preservation of most fungal isolates.

Morphological and molecular discrimination of two closely related jellyfish species, Cyanea capillata and C. lamarckii (Cnidaria, Scyphozoa), from the northeast Atlantic

Detecting fluctuations in the species composition of bloom-forming jellyfish requires the ability to correctly identify each species in each developmental stage. We verified diagnostic morphological and molecular genetic characters to discriminate Cyanea lamarckii and Cyanea capillata from northern European waters. Intrusions in the subumbrellar muscle folds were present in all C. capillata > 80 mm r-diameter (between opposite rhopalia tips), but absent in C. lamarckii. Clearly visible wart-like papillae on the central exumbrella were present in all C. lamarckii > 10-80 mm r-diameter, but absent in C. capillata. Both morphological features were retained in formaldehyde-seawater (4%) preserved medusae which had shrunk by 12.8% (± 2.7%) after 1 year of preservation. Our molecular genetic analyses demonstrated that fragments of mitochondrial cytochrome c oxidase subunit I (COI) and nuclear 18S rDNA clearly distinguished C. lamarckii from C. capillata, with intra- and inter-specific pairwise genetic distances of 0.0-1.5% and 15.5-17.0% (COI) and 0.0 and 0.2% (18S rDNA), respectively. The study revealed various bell colours in both species underlining that the identification based on the bell colours can result in misidentification. Our integrated taxonomic approach can help to correctly identify jellyfish species, which is fundamentally important for understanding the causes of jellyfish fluctuations and the development of jellyfish blooms.

Sclerotization as a long-term preservation method for Rosellinia necatrix strains

This work describes a simple protocol for long-term preservation of strains of Rosellinia necatrix based on sclerotia production combined with storage at 4°C in liquid substrate, without affecting the growth and pathogenic characteristics of the fungal isolates recovered. The sclerotization process was set up in both liquid and solid media, and the sclerotia-like structures (pseudosclerotia) obtained were preserved in liquid media or water at 4°C. R. necatrix pseudosclerotia viability after 6 years of preservation at 4°C was confirmed by growth and microscopic characteristics, with no differences when compared with the fungal strains routinely preserved by periodic transfers. Additionally, pathogenicity on avocado plants by the preserved R. necatrix strains showed no difference from those preserved by periodic transfers. The albino strain used in this study should continue to be preserved by periodic subculturing.

Length adjustment of larval and early-juvenile cod (Gadus morhua) after up to 3 years of preservation in alcohol

Summary Comparison of live Baltic cod larvae lengths and early-juveniles with corresponding lengths after preservation in 95% ethyl alcohol for periods of one to 3 years resulted in an average shrinkage of 0.70 mm for the entire size range of 4–40 mm standard length cod. Although the relative shrinkage depended on fish size and varied from 2 to 20% of the fresh length, the absolute shrinkage values were not size dependent and did not change during the observed preservation period. Thus a general additive correction value of +0.7 mm can be used to calculate live lengths from measured standard lengths of alcohol-preserved material.

Is the Megamouth Shark susceptible to mega-distortion? Investigating the effects of twenty-two years of fixation and preservation on a large specimen of Megachasma pelagios (Chondrichthyes: Megachasmidae)

On 18 August 1988, the third reported Megamouth Shark (Megachasma pelagios Taylor, Compagno and Struhsaker, 1983) became stranded on a beach in Western Australia. The 5.15 m TL male shark (WAM P.29940–001) was preserved at the Western Australian Museum (WAM) and put on public display. Many deep water chondrichthyan species, including M. pelagios, possess soft and fl abby muscle tissue and a poorly calcifi ed skeleton. Such species are prone to distortion through dehydration due to the fi xation and preservation process. Such distortions may result in taxonomic and nomenclatural issues. The WAM Megamouth Shark was recently relocated, providing an opportunity to remeasure the specimen to allow a comparison with measurements taken of the specimen when it was fresh, and to assess the extent of change to these measurements after 22 years of preservation. We found that with the exception of the pelvic-fi n, that we hypothesise is the fl eshiest part of M. pelagios with the least skeletal support, the specimen has suffered little to no distortion over this time. However, there has been some degradation of teeth and denticles that is most likely due to the acidity of the formalin solution.

Sclerotization as a long-term preservation method for <i>Rosellinia necatrix</i> strains

This work describes a simple protocol for longterm preservation of strains of Rosellinia necatrix based on sclerotia production combined with storage at 4°C in liquid substrate, without affecting the growth and pathogenic characteristics of the fungal isolates recovered. The sclerotization process was set up in both liquid and solid media, and the sclerotia-like structures (pseudosclerotia) obtained were preserved in liquid media or water at 4°C. R. necatrix pseudosclerotia viability after 6 years of preservation at 4°C was confirmed by growth and microscopic characteristics, with no differences when compared with the fungal strains routinely preserved by periodic transfers. Additionally, pathogenicity on avocado plants by the preserved R. necatrix strains showed no difference from those preserved by periodic transfers. The albino strain used in this study should continue to be preserved by periodic subculturing.

Comparative study of pediculicidal effect of medical plants

Comparative study of pediculicidal effect of medical plants

Método para preservação da viabilidade e atividade antagônica de Trichoderma stromaticum , agente de biocontrole da vassoura-de-bruxa do cacaueiro

Avaliou-se a viabilidade da massa esporógena de Trichoderma stromaticum, através do crescimento micelial em meio de cultivo e a atividade antagônica (parasitária) em vassouras secas de cacaueiro, após a preservação de quatro isolados (Ts1606, Ts3107, Ts0108, Ts2705) do antagonista por quatro anos em fragmentos de vassoura secas, acondicionados em tubos de ensaio e mantidos em refrigerador com temperatura aproximada de 5 °C. Todos os isolados preservados apresentaram-se viáveis, com crescimento e esporulação normais e continuavam antagônicos a Crinipellis perniciosa. Os resultados obtidos indicam a eficiência do método, que é capaz de manter os isolados de T. stromaticum viáveis por longos períodos de tempo, preservando características morfológicas, fisiológicas e antagônicas.