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Journal articles on the topic 'Biological specimens, collection and preservation'
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1
Utpal Kumar Biswas, Nashid Tabassum Khan, Mohammad Ahad Hossain, and Abdul Kader. "Collection, preservation and forwarding of biological samples for toxicological analysis in medico legal autopsy cases." Z H Sikder Women’s Medical College Journal 1, Number 2 (July 1, 2019): 25–28. http://dx.doi.org/10.47648/zhswmcj.2020.v0102.07.
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Collection of proper autopsy specimen is an essential step in the process of toxicology case work. Improper collection of these specimens can greatly alter or negate chemical and toxicological analysis. This article is an update about the standard methods of biological specimen collection procedures for toxicological analysis which will be helpful for the forensic pathologist and forensicscientists.
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McLachlan, Rowan H., Kerri L. Dobson, Emily R. Schmeltzer, Rebecca Vega Thurber, and Andréa G. Grottoli. "A review of coral bleaching specimen collection, preservation, and laboratory processing methods." PeerJ 9 (July 8, 2021): e11763. http://dx.doi.org/10.7717/peerj.11763.
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Under current climate warming predictions, the future of coral reefs is dire. With projected coral reef decline, it is likely that coral specimens for bleaching research will increasingly become a more limited resource in the future. By adopting a holistic approach through increased collaborations, coral bleaching scientists can maximize a specimen’s investigative yield, thus reducing the need to remove more coral material from the reef. Yet to expand a specimen’s utility for additional analytic methods, information on how corals are collected is essential as many methods are variably sensitive to upstream handling and processing. In an effort to identify common practices for coral collection, sacrifice, preservation, and processing in coral bleaching research, we surveyed the literature from the last 6.5 years and created and analyzed the resulting dataset of 171 publications. Since January 2014, at least 21,890 coral specimens were collected for bleaching surveys or bleaching experiments. These specimens spanned 122 species of scleractinian corals where the most frequently sampled were Acropora millepora, Pocillopora damicornis, and Stylophora pistillata. Almost 90% of studies removed fragments from the reef, 6% collected skeletal cores, and 3% collected mucus specimens. The most common methods for sacrificing specimens were snap freezing with liquid nitrogen, chemical preservation (e.g., with ethanol or nucleic acid stabilizing buffer), or airbrushing live fragments. We also characterized 37 distinct methodological pathways from collection to processing of specimens in preparation for a variety of physiological, -omic, microscopy, and imaging analyses. Interestingly, almost half of all studies used only one of six different pathways. These similarities in collection, preservation, and processing methods illustrate that archived coral specimens could be readily shared among researchers for additional analyses. In addition, our review provides a reference for future researchers who are considering which methodological pathway to select to maximize the utility of coral bleaching specimens that they collect.
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Das, Arabinda, Arunprasad Gunasekaran, Heather R. Stephens, Penny Sekerak, Joseph Mark, Daniel G. McDonald, Milad Yazdani, et al. "QLTI-02. AUTOMATED INTRAOPERATIVE RESECTION TECHNOLOGY GENERATES INCREASED TISSUE YIELD AND IMPROVED BIOLOGICAL PRESERVATION OF BRAIN TUMOR SPECIMENS FOR NEURO-ONCOLOGY RESEARCH." Neuro-Oncology 24, Supplement_7 (November 1, 2022): vii234. http://dx.doi.org/10.1093/neuonc/noac209.904.
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Abstract Glioblastoma (GB) is an aggressive tumor showing extensive intertumoral and intratumoral heterogeneity. While preserving as much surrounding normal brain tissue as possible, neurosurgeons must aim to harvest maximal tumor tissue from a variety of tumor locations in an effort to capture heterogenic samples in high volume for molecular and pathologic diagnosis and translational research. A key challenge is the ability to consistently procure high-quality biologically active specimens. In this investigation, we implemented an automated intraoperative system to eliminate inconsistencies in the methodology of tissue collection, handling, and biological preservation immediately in the OR suite to establish a repeatable, standardized practice for obtaining high-quality tissue samples without the need for additional staff. Through this process, we were able to characterize matched specimens from GB patients or GB tumors from corresponding GB-allograft mice and compare the quality of traditional handling and collection processes of intraoperative tissue used in most neurosurgical operating rooms versus an automated resection, collection, and biological preservation system (APS) that captures, preserves, and biologically maintains tissue in a prescribed and controlled microenvironment. Matched specimens/or tissues were then processed in parallel at various time points and temperatures, evaluating viability, RNA and protein concentrations, and isolation of GB cell lines. We found that APS-derived GB slices stored in an APS modified medium remained viable and maintained high-quality RNA and protein concentration for up to 24 hours. Our results showed that primary GB cell cultures derived in this manner had improved growth over the widely used collection and preservation methods. Currently, we are continuing the investigation of collected samples in brain tumor animal models to further understand potential differences within the tumor region harvested and the cellular changes that occur over time. Our hope is this research will lead to new discoveries in the diagnosis and treatment of brain tumors.
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Rivera-Quiroz, F. Andres, and Jeremy Abraham Miller. "Old Brains in Alcohol: The Usability of Legacy Collection Material to Study the Spider Neuroarchitecture." Diversity 13, no. 11 (November 21, 2021): 601. http://dx.doi.org/10.3390/d13110601.
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Natural history collections include rare and significant taxa that might otherwise be unavailable for comparative studies. However, curators must balance the needs of current and long-term research. Methods of data extraction that minimize the impact on specimens are therefore favored. Micro-CT has the potential to expose new character systems based on internal anatomy to taxonomic and phylogenetic analysis without dissection or thin sectioning for histology. However, commonly applied micro-CT protocols involve critical point drying, which permanently changes the specimen. Here, we apply a minimally destructive method of specimen preparation for micro-CT investigation of spider neuroanatomy suitable for application to legacy specimens in natural history collections. We used two groups of female spiders of the common species Araneus diadematus—freshly captured (n = 11) vs. legacy material between 70 and 90 years old (n = 10)—to qualitatively and quantitatively assess the viability of micro-CT scanning and the impact of aging on their neuroarchitecture. We statistically compared the volumes of the supraesophageal ganglion (syncerebrum) and used 2D geometric morphometrics to analyze variations in the gross shape of the brain. We found no significant differences in the brain shape or the brain volume relative to the cephalothorax size. Nonetheless, a significant difference was observed in the spider size. We considered such differences to be explained by environmental factors rather than preservation artifacts. Comparison between legacy and freshly collected specimens indicates that museum specimens do not degrade over time in a way that might bias the study results, as long as the basic preservation conditions are consistently maintained, and where lapses in preservation have occurred, these can be identified. This, together with the relatively low-impact nature of the micro-CT protocol applied here, could facilitate the use of old, rare, and valuable material from collections in studies of internal morphology.
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Pinnell, Lee J., Cory A. Wolfe, Jake Castle, William B. Crosby, Enrique Doster, and Paul S. Morley. "Effectiveness of stabilization methods for the immediate and short-term preservation of bovine fecal and upper respiratory tract genomic DNA." PLOS ONE 19, no. 4 (April 2, 2024): e0300285. http://dx.doi.org/10.1371/journal.pone.0300285.
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Previous research on stabilization methods for microbiome investigations has largely focused on human fecal samples. There are a few studies using feces from other species, but no published studies investigating preservation of samples collected from cattle. Given that microbial taxa are differentially impacted during storage it is warranted to study impacts of preservation methods on microbial communities found in samples outside of human fecal samples. Here we tested methods of preserving bovine fecal respiratory specimens for up to 2 weeks at four temperatures (room temperature, 4°C, -20°C, and -80°C) by comparing microbial diversity and community composition to samples extracted immediately after collection. Importantly, fecal specimens preserved and analyzed were technical replicates, providing a look at the effects of preservation method in the absence of biological variation. We found that preservation with the OMNIgene®•GUT kit resulted in community structure most like that of fresh samples extracted immediately, even when stored at room temperature (~20°C). Samples that were flash-frozen without added preservation solution were the next most representative of original communities, while samples preserved with ethanol were the least representative. These results contradict previous reports that ethanol is effective in preserving fecal communities and suggest for studies investigating cattle either flash-freezing of samples without preservative or preservation with OMNIgene®•GUT will yield more representative microbial communities.
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Suaste-Dzul, Alba P., José Manuel Rodríguez-Vélez, Beatriz Rodríguez-Vélez, Hugo Cesar Arredondo-Bernal, and Adrien Gallou. "Non-destructive DNA extraction methods for entomophagous insects with emphasis on biological control." Genome 62, no. 4 (April 2019): 287–93. http://dx.doi.org/10.1139/gen-2018-0045.
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One of the major challenges in molecular analysis of arthropods, especially for natural enemies of insect pests, is the intact preservation of the specimens to be integrated into entomological collections. However, most of the DNA extraction protocols involve maceration of the tissue, avoiding the preservation of the original specimen. Two general methods were adapted into non-destructive DNA extraction protocols, DNeasy® Blood & Tissue Kit (A) and the CaCl2 lysis buffer method (B), while the potential of the method with the alkaline lysis buffer (HotSHOT; C) was evaluated for the first time on insect specimens. These protocols were assessed for the recovery of DNA from Ceraeochrysa valida, Tamarixia radiata, and Hippodamia convergens. Photographical records showed that morphological features of the specimens were preserved after the DNA extraction process. COI fragments were successfully amplified with method A (100%), B (77%), and C (88%), respectively. We conclude that these non-destructive DNA extraction methods avoid the destruction of tissue and preserve the original insects and their morphological characteristics for future reference.
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Cho, Soowon, Samantha W. Epstein, Kim Mitter, Chris A. Hamilton, David Plotkin, Charles Mitter, and Akito Y. Kawahara. "Preserving and vouchering butterflies and moths for large-scale museum-based molecular research." PeerJ 4 (June 22, 2016): e2160. http://dx.doi.org/10.7717/peerj.2160.
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Butterflies and moths (Lepidoptera) comprise significant portions of the world’s natural history collections, but a standardized tissue preservation protocol for molecular research is largely lacking. Lepidoptera have traditionally been spread on mounting boards to display wing patterns and colors, which are often important for species identification. Many molecular phylogenetic studies have used legs from pinned specimens as the primary source for DNA in order to preserve a morphological voucher, but the amount of available tissue is often limited. Preserving an entire specimen in a cryogenic freezer is ideal for DNA preservation, but without an easily accessible voucher it can make specimen identification, verification, and morphological work difficult. Here we present a procedure that creates accessible and easily visualized “wing vouchers” of individual Lepidoptera specimens, and preserves the remainder of the insect in a cryogenic freezer for molecular research. Wings are preserved in protective holders so that both dorsal and ventral patterns and colors can be easily viewed without further damage. Our wing vouchering system has been implemented at the University of Maryland (AToL Lep Collection) and the University of Florida (Florida Museum of Natural History, McGuire Center of Lepidoptera and Biodiversity), which are among two of the largest Lepidoptera molecular collections in the world.
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Mihaly, Andriy V., Vasyl I. Sabadosh, Vasyl I. Roman, and Myroslav V. Shevera. "Database and Digitization of Regional Historical Herbaria: A Case Study of Margittai Collection in the Uzhhorod National University Herbarium (UU)." Diversity 16, no. 4 (March 30, 2024): 211. http://dx.doi.org/10.3390/d16040211.
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The digitization of herbarium collections guarantees a preservation and long-term use of scientifically valuable objects, e.g., wide and convenient access to these materials online and exchange between institutions. These are also important elements in the education and popularization of botanical knowledge. No less significant is the practical aspect of these studies due to the danger of these collections’ destruction as a result of Russian aggression—some of them have already been destroyed. The analyzed Margittai collection (1500 specimens) is kept at the Uzhhorod National University Herbarium (UU) and belongs to the historical and regional ones. This material is valuable because of its scientific, historical and cultural significance. By the initiative and thanks to the efforts of Prof. S. Fodor, the studied collection (most of which are doublet specimens) was transferred in 1965 from the Hungarian Natural History Museum (BP), where the main herbarium of the researcher is preserved (40,000 specimens), to the Uzhhorod State University. Due to the fact that the collection has not been studied, in 2021, the authors began a special investigation of this collection and assessment of its current state. The structure of the database has been developed, it is being filled, and the digitization of type materials has begun.
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WAZEMA, CLAUDIA TIEMI, OTÁVIO GUILHERME MORAIS DA SILVA, FABRÍCIO SEVERO MAGALHÃES, LÍVIA PIRES DO PRADO, VICTOR HIDEKI NAGATANI, NATHALIA SAMPAIO DA SILVA, JULIANA APARECIDA CALISTO VAZ, et al. "Preserving a Legacy: Ensuring the Access and Conservation of the Harold (Harry) G. Fowler (1950–2018) Ant Collection and Data." Zootaxa 5418, no. 4 (March 1, 2024): 339–56. http://dx.doi.org/10.11646/zootaxa.5418.4.3.
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Biological collections are important repositories of biodiversity, as they include various types of data potentially useful to different areas of science and can contribute to the establishment of biodiversity conservation policies. For a long time, scientific collections were considered only as physical databases; in this context Harold G. Fowler (1950–2018) built an ant collection at the Universidade Estadual Paulista, campus Rio Claro (São Paulo state, Brazil), over the course of a 34-year career, comprising around 20,000 ant specimens. Most specimens came from the Brazilian Atlantic Forest, but many others came from distinct locations in Brazil and abroad. After his death, the collection was left without the necessary curatorial care for a period of time, which required a project to be conceived for its recovery and conservation, with the goal of incorporating it to the Zoology Museum of the University of São Paulo (MZSP). In addition to applying modern technical curation protocols, other activities such as checking, material identification and digitization of the information contained on the sample labels were carried out, forming an accurate database. This process enabled the identification of new distribution records and the discovery of possible undescribed species and unpublished natural history data. After validating this information, we counted 524 valid species and 201 morphospecies belonging to 105 genera and 10 subfamilies. In addition, we integrated technical curation activities with scientific outreach to draw the general public’s attention to the importance of biological collections, thus fostering interest in science, biodiversity and nature conservation. Our work highlights the importance of preserving the areas sampled by Fowler’s research group. The preservation of vouchers using curatorial practices reinforces the role of scientific collections as important tools for the study, understanding and preservation of biodiversity.
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LaRocco, Mark T., Jacob Franek, Elizabeth K. Leibach, Alice S. Weissfeld, Colleen S. Kraft, Robert L. Sautter, Vickie Baselski, Debra Rodahl, Edward J. Peterson, and Nancy E. Cornish. "Effectiveness of Preanalytic Practices on Contamination and Diagnostic Accuracy of Urine Cultures: a Laboratory Medicine Best Practices Systematic Review and Meta-analysis." Clinical Microbiology Reviews 29, no. 1 (November 23, 2015): 105–47. http://dx.doi.org/10.1128/cmr.00030-15.
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SUMMARYBackground.Urinary tract infection (UTI) in the United States is the most common bacterial infection, and urine cultures often make up the largest portion of workload for a hospital-based microbiology laboratory. Appropriately managing the factors affecting the preanalytic phase of urine culture contributes significantly to the generation of meaningful culture results that ultimately affect patient diagnosis and management. Urine culture contamination can be reduced with proper techniques for urine collection, preservation, storage, and transport, the major factors affecting the preanalytic phase of urine culture.Objectives.The purposes of this review were to identify and evaluate preanalytic practices associated with urine specimens and to assess their impact on the accuracy of urine culture microbiology. Specific practices included collection methods for men, women, and children; preservation of urine samples in boric acid solutions; and the effect of refrigeration on stored urine. Practice efficacy and effectiveness were measured by two parameters: reduction of urine culture contamination and increased accuracy of patient diagnosis. The CDC Laboratory Medicine Best Practices (LMBP) initiative's systematic review method for assessment of quality improvement (QI) practices was employed. Results were then translated into evidence-based practice guidelines.Search strategy.A search of three electronic bibliographic databases (PubMed, SCOPUS, and CINAHL), as well as hand searching of bibliographies from relevant information sources, for English-language articles published between 1965 and 2014 was conducted.Selection criteria.The search contained the following medical subject headings and key text words: urinary tract infections, UTI, urine/analysis, urine/microbiology, urinalysis, specimen handling, preservation, biological, preservation, boric acid, boric acid/borate, refrigeration, storage, time factors, transportation, transport time, time delay, time factor, timing, urine specimen collection, catheters, indwelling, urinary reservoirs, continent, urinary catheterization, intermittent urethral catheterization, clean voided, midstream, Foley, suprapubic, bacteriological techniques, and microbiological techniques.Main results.Both boric acid and refrigeration adequately preserved urine specimens prior to their processing for up to 24 h. Urine held at room temperature for more than 4 h showed overgrowth of both clinically significant and contaminating microorganisms. The overall strength of this body of evidence, however, was rated as low. For urine specimens collected from women, there was no difference in rates of contamination for midstream urine specimens collected with or without cleansing. The overall strength of this evidence was rated as high. The levels of diagnostic accuracy of midstream urine collection with or without cleansing were similar, although the overall strength of this evidence was rated as low. For urine specimens collected from men, there was a reduction in contamination in favor of midstream clean-catch over first-void specimen collection. The strength of this evidence was rated as high. Only one study compared midstream collection with cleansing to midstream collection without cleansing. Results showed no difference in contamination between the two methods of collection. However, imprecision was due largely to the small event size. The diagnostic accuracy of midstream urine collection from men compared to straight catheterization or suprapubic aspiration was high. However, the overall strength of this body of evidence was rated as low. For urine specimens collected from children and infants, the evidence comparing contamination rates for midstream urine collection with cleansing, midstream collection without cleansing, sterile urine bag collection, and diaper collection pointed to larger reductions in the odds of contamination in favor of midstream collection with cleansing over the other methods of collection. This body of evidence was rated as high. The accuracy of diagnosis of urinary tract infection from midstream clean-catch urine specimens, sterile urine bag specimens, or diaper specimens compared to straight catheterization or suprapubic aspiration was varied.Authors' conclusions.No recommendation for or against is made for delayed processing of urine stored at room temperature, refrigerated, or preserved in boric acid. This does not preclude the use of refrigeration or chemical preservatives in clinical practice. It does indicate, however, that more systematic studies evaluating the utility of these measures are needed. If noninvasive collection is being considered for women, midstream collection with cleansing is recommended, but no recommendation for or against is made for midstream collection without cleansing. If noninvasive collection is being considered for men, midstream collection with cleansing is recommended and collection of first-void urine is not recommended. No recommendation for or against is made for collection of midstream urine without cleansing. If noninvasive collection is being considered for children, midstream collection with cleansing is recommended and collection in sterile urine bags, from diapers, or midstream without cleansing is not recommended. Whether midstream collection with cleansing can be routinely used in place of catheterization or suprapubic aspiration is unclear. The data suggest that midstream collection with cleansing is accurate for the diagnosis of urinary tract infections in infants and children and has higher average accuracy than sterile urine bag collection (data for diaper collection were lacking); however, the overall strength of evidence was low, as multivariate modeling could not be performed, and thus no recommendation for or against can be made.
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Lykova, T., and M. Bulgakova. "Experience of creating, storing and using an entomological collection for educational purposes at the Department of Biology and Soil Science of Orenburg State University." Ekosistemy, no. 37 (June 21, 2024): 82–88. http://dx.doi.org/10.29039/2413-1733-2024-37-82-88.
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The experience of creating and storing an entomological collection at the Department of Biology and Soil Science of Orenburg State University is presented. The features of using various methods of collecting insects in the arid climate of the steppe zone are described: individual insect trapping with an entomological net, sweep netting, manual insect collection and the use of soil traps. Methods that ensure the representativeness of the created entomological collection in relation to the representation of various ecosystems of the region, systematic and ecological groups of entomofauna are discussed through specific examples. The necessity of compiling an educational entomological collection across sections such as «External structure of insects,» «Insect developmental biology,» «Biological diversity of insects,» and «Pests of agricultural and ornamental crops» is substantiated and exemplified. The experience of identifying damage and restoring collection exhibits that have lost their value and no longer serve as demonstrative material is discussed. Recommendations for the protection of collection specimens and their long-term preservation are provided
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Cruz-Rodríguez, Cristian, Julieth Stella Cárdenas, and Héctor E. Ramírez-Chaves. "Evaluating the Ethanol Levels and Storage Containers for Efficient Preservation of Historical Collections at the Museo De La Salle, Bogotá, Colombia." Collection Forum 35, no. 1 (January 1, 2021): 52–61. http://dx.doi.org/10.14351/0831-4985-35.1.52.
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Abstract The Museo de La Salle–Bogotá (MLS) houses biological specimens of which 30% (17,001 specimens) are stored in fluid (ethanol 70%). The collections have historical significance for documenting Colombian biodiversity and contain the oldest zoological specimens in the country. For these reasons, the curation and management of the specimens require special attention and endless vigilance. In this study we assessed the decrease in ethanol level in jars of the MLS fluid collections over a 3-year period from 2013 to 2016 and evaluated the relation between container and lid type and ethanol loss. We did not observe a relevant decrease in the percentage of ethanol levels during 2013–2016. However, the type of lid used influenced the amount of ethanol that evaporated; we found that the pressure and twist lids were more effective in maintaining the ethanol levels in the containers, since they have a pressurized rotation system that allows a more secure closure in contrast to the pressure cap, which does not prevent the evaporation of ethanol. Based on our evaluation, we suggest the use of pressure and twist closure caps or caps with a continuous thread closure type along with a tamper-evident seal between the jar mouth and the container cap to ensure a tight and secure seal for minimizing the risk of fluid loss and ensuring the preservation of fluid-fixed specimens of this historical collection.
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Annaratone, Laura, Giuseppe De Palma, Giuseppina Bonizzi, Anna Sapino, Gerardo Botti, Enrico Berrino, Chiara Mannelli, et al. "Basic principles of biobanking: from biological samples to precision medicine for patients." Virchows Archiv 479, no. 2 (July 13, 2021): 233–46. http://dx.doi.org/10.1007/s00428-021-03151-0.
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AbstractThe term “biobanking” is often misapplied to any collection of human biological materials (biospecimens) regardless of requirements related to ethical and legal issues or the standardization of different processes involved in tissue collection. A proper definition of biobanks is large collections of biospecimens linked to relevant personal and health information (health records, family history, lifestyle, genetic information) that are held predominantly for use in health and medical research. In addition, the International Organization for Standardization, in illustrating the requirements for biobanking (ISO 20387:2018), stresses the concept of biobanks being legal entities driving the process of acquisition and storage together with some or all of the activities related to collection, preparation, preservation, testing, analysing and distributing defined biological material as well as related information and data. In this review article, we aim to discuss the basic principles of biobanking, spanning from definitions to classification systems, standardization processes and documents, sustainability and ethical and legal requirements. We also deal with emerging specimens that are currently being generated and shaping the so-called next-generation biobanking, and we provide pragmatic examples of cancer-associated biobanking by discussing the process behind the construction of a biobank and the infrastructures supporting the implementation of biobanking in scientific research.
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Shiyan, Natalia. "Type collections of plants and fungi in Ukraine: realities and prospects." Novitates Theriologicae, no. 12 (June 16, 2021): 358–70. http://dx.doi.org/10.53452/nt1255.
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For the stability of the nomenclature of biological organisms an important condition is the presence and preservation of type specimens of the described taxa. The type specimens of plants and fungi typically are accumulated and stored in herbaria of specialized scientific institutions (e.g. botanical gardens and universities) or natural history museums. In Ukraine, there are nearly 80 herbaria of various volumes of collections but only 22 of them have type materials of taxa of different ranks, which were described from the territory of Ukraine and the world. The article includes a quantitative assessment of type materials of Ukrainian herbaria and emphasizes their role in regional and global biodiversity surveys. On the basis of own research of the Ukrainian herbarium fund, the estimation of preservation conditions of type specimens of plants and fungi and their collections in Ukraine is given, and the prospects of functioning of these collections are considered.
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Vivien, Régis, Inge Werner, and Benoit J. D. Ferrari. "Simultaneous preservation of the DNA quality, the community composition and the density of freshwater oligochaetes for the development of genetically based biological indices." PeerJ 6 (December 5, 2018): e6050. http://dx.doi.org/10.7717/peerj.6050.
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IntroductionOligochaetes are recognized as valuable bioindicators of sediment quality in streams and lakes. The development of an oligochaete index based on the identification of specimens using DNA barcodes requires a method for simultaneously preserving the DNA quality and information on the specimen density and oligochaete community composition. Absolute ethanol optimally preserves DNA but fixation of freshwater oligochaetes with this medium can cause disintegration and fragmentation of specimens. Here, we investigated the possibility to preserve oligochaete specimens in low-pH formalin and in neutral buffered formalin for up to four weeks before genetic analyses and tested if the addition of absolute ethanol to formalin-fixed oligochaetes resulted in a loss of specimens and/or species.MethodsWe performed guanidine extraction and polymerase chain reaction (PCR) amplification/sequencing of a fragment of the cytochrome c oxidase I (COI) gene on tissue fragments preserved in low-pH formalin for up to 3 weeks and in neutral buffered formalin for up to 4 weeks. In addition, we compared the density and taxonomic composition of formalin-fixed oligochaetes of several sieved sediment samples before and after the addition of absolute ethanol.ResultsThe COI fragment of all oligochaete specimens preserved in neutral buffered formalin for up to 28 days was successfully amplified by PCR and obtained sequences were complete and of high quality. The amplification success rate for low-pH formalin fixed specimens declined after 7 days of storage. The addition of absolute ethanol to formalin-fixed oligochaete communities did not alter density or diversity estimates.DiscussionOur results indicate that sediment samples can be stored in neutral buffered formalin for up to 4 weeks and the sieved material can then be transferred to absolute ethanol, without affecting DNA quality, density and community composition of oligochaetes. Based on these results, a protocol for preserving freshwater oligochaetes, describing all the steps from collection of sediments to preservation of the biological material in absolute ethanol, is proposed. This method of fixation/preservation is of relevance for establishing DNA barcode reference databases, inventories of genetic diversity and developing genetically based biological indices.
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Promnun, Pattarapon, Kanokporn Panpong, Amonpong Khlaipet, Veera Vilasri, and Jenjit Khudamrongsawat. "Herpetological Collections in the Thailand Natural History Museum as a Valuable Resource for Conservation and Education." Diversity 15, no. 11 (November 6, 2023): 1133. http://dx.doi.org/10.3390/d15111133.
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The history of collecting and cataloging Thailand’s diverse herpetofauna is long-standing, with many specimens housed at the Thailand Natural History Museum (THNHM). This work aimed to assess the diversity of herpetofauna within the THNHM collection, ascertain conservation status of species, and track the geographical coverage of these specimens within the country. The THNHM collection boasts an impressive inventory, numbering 173 amphibian species and 335 reptile species. This collection reflects the substantial biodiversity within these taxonomic groups, rivaling the total number of herpetofauna species ever recorded in Thailand. However, the evaluation of their conservation status, as determined by the IUCN Red List, CITES, and Thailand’s Wild Animal Preservation and Protection Act (WARPA), has unveiled disparities in the degree of concern for certain species, possibly attributable to differential uses of the assessment criteria. Notably, the museum houses a number of type specimens, including 27 holotypes, which remain understudied. Sampling efforts have grown considerably since the year 2000, encompassing nearly all regions of the country. This extensive and systematic collection of diverse herpetofauna at the THNHM serves as a valuable resource for both research and educational purposes, enriching our understanding of these species and their significance in the broader context of biodiversity conservation.
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Vega Thurber, Rebecca, Emily R. Schmeltzer, Andréa G. Grottoli, Robert van Woesik, Robert J. Toonen, Mark Warner, Kerri L. Dobson, et al. "Unified methods in collecting, preserving, and archiving coral bleaching and restoration specimens to increase sample utility and interdisciplinary collaboration." PeerJ 10 (November 2, 2022): e14176. http://dx.doi.org/10.7717/peerj.14176.
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Coral reefs are declining worldwide primarily because of bleaching and subsequent mortality resulting from thermal stress. Currently, extensive efforts to engage in more holistic research and restoration endeavors have considerably expanded the techniques applied to examine coral samples. Despite such advances, coral bleaching and restoration studies are often conducted within a specific disciplinary focus, where specimens are collected, preserved, and archived in ways that are not always conducive to further downstream analyses by specialists in other disciplines. This approach may prevent the full utilization of unexpended specimens, leading to siloed research, duplicative efforts, unnecessary loss of additional corals to research endeavors, and overall increased costs. A recent US National Science Foundation-sponsored workshop set out to consolidate our collective knowledge across the disciplines of Omics, Physiology, and Microscopy and Imaging regarding the methods used for coral sample collection, preservation, and archiving. Here, we highlight knowledge gaps and propose some simple steps for collecting, preserving, and archiving coral-bleaching specimens that can increase the impact of individual coral bleaching and restoration studies, as well as foster additional analyses and future discoveries through collaboration. Rapid freezing of samples in liquid nitrogen or placing at −80 °C to −20 °C is optimal for most Omics and Physiology studies with a few exceptions; however, freezing samples removes the potential for many Microscopy and Imaging-based analyses due to the alteration of tissue integrity during freezing. For Microscopy and Imaging, samples are best stored in aldehydes. The use of sterile gloves and receptacles during collection supports the downstream analysis of host-associated bacterial and viral communities which are particularly germane to disease and restoration efforts. Across all disciplines, the use of aseptic techniques during collection, preservation, and archiving maximizes the research potential of coral specimens and allows for the greatest number of possible downstream analyses.
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Song, Jiaojiao, and Junmei Zhou. "Effects of preservation duration at 4 °C on the quality of RNA in rabbit blood specimens." PeerJ 8 (April 10, 2020): e8940. http://dx.doi.org/10.7717/peerj.8940.
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A prolonged preservation duration of blood specimens at 4 °C may occur due to the distance from collection points to storage facilities in many biobanks, especially for multicenter studies. This could lead to RNA degradation, affecting downstream analyses. However, effects of preservation durations at 4 °C on RNA quality in blood specimens need to be studied. We collected rabbit blood using EDTA tubes and stored them at 4 °C for different preservation durations. Then, we examined the quality of RNA from whole blood and leukocytes isolated from rabbit blood. Our results show that the purity of whole blood RNA and leukocyte RNA does not indicate significant change after rabbit blood is stored at 4 °C for different preservation durations (from 1 h to 7 days). The integrity of leukocyte RNA indicates the same result as above, but the integrity of whole blood RNA is significantly decreased after rabbit blood is stored at 4 °C for over 3 days. Moreover, expression of SMAD7, MKI67, FOS, TGFβ1 and HIF1α of whole blood RNA and leukocyte RNA remains basically stable, but PCNA expression of whole blood RNA or leukocyte RNA is significantly decreased after rabbit blood is stored at 4 °C for over 24 h or 7 days. Therefore, these results suggest that high-quality RNA is obtained from the fresher blood specimens and if blood specimens are stored for over 3 days at 4 °C, the quality of leukocyte RNA is more stable and of better quality than that of whole blood RNA.
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Motz, Gary, Alexander Zimmerman, Kimberly Cook, and Alyssa Bancroft. "Collections Management and High-Throughput Digitization using Distributed Cyberinfrastructure Resources." Biodiversity Information Science and Standards 2 (July 5, 2018): e25643. http://dx.doi.org/10.3897/biss.2.25643.
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Collections digitization relies increasingly upon computational and data management resources that occasionally exceed the capacity of natural history collections and their managers and curators. Digitization of many tens of thousands of micropaleontological specimen slides, as evidenced by the effort presented here by the Indiana University Paleontology Collection, has been a concerted effort in adherence to the recommended practices of multifaceted aspects of collections management for both physical and digital collections resources. This presentation highlights the contributions of distributed cyberinfrastructure from the National Science Foundation-supported Extreme Science and Engineering Discovery Environment (XSEDE) for web-hosting of collections management system resources and distributed processing of millions of digital images and metadata records of specimens from our collections. The Indiana University Center for Biological Research Collections is currently hosting its instance of the Specify collections management system (CMS) on a virtual server hosted on Jetstream, the cloud service for on-demand computational resources as provisioned by XSEDE. This web-service allows the CMS to be flexibly hosted on the cloud with additional services that can be provisioned on an as-needed basis for generating and integrating digitized collections objects in both web-friendly and digital preservation contexts. On-demand computing resources can be used for the manipulation of digital images for automated file I/O, scripted renaming of files for adherence to file naming conventions, derivative generation, and backup to our local tape archive for digital disaster preparedness and long-term storage. Here, we will present our strategies for facilitating reproducible workflows for general collections digitization of the IUPC nomenclatorial types and figured specimens in addition to the gigapixel resolution photographs of our large collection of microfossils using our GIGAmacro system (e.g., this slide of conodonts). We aim to demonstrate the flexibility and nimbleness of cloud computing resources for replicating this, and other, workflows to enhance the findability, accessibility, interoperability, and reproducibility of the data and metadata contained within our collections.
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Lopez-Gonzalez, Celia, Cynthia Elizalde-Arellano, Miguel Angel Briones-Salas, Mario Lavariega Nolasco, and Juan Carlos Lopez-Vidal. "65 years of museum-based mammal research in Mexico: from taxonomy to worldwide information networks." Therya 12, no. 1 (January 30, 2021): 57–74. http://dx.doi.org/10.12933/therya-21-978.
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Biological collections have become a key tool for biodiversity research. They are repositories of germplasm and data on modified or extinct natural populations, providing valuable information for understanding anthropogenic impacts on the natural world. We appraised the scientific value of the three mammal collections maintained by the Instituto Politécnico Nacional of Mexico (IPN): Escuela Nacional de Ciencias Biológicas (ENCB), CIIDIR Durango (CRD), and CIIDIR Oaxaca (OAXMA). We evaluated their specimen inventory, geographic coverage, and scientific importance for mammalogy. We assessed their physical conditions and provided insights into their future as data sources for understanding natural changes in the 21st century. We measured the scientific importance of the collections in terms of the number of specimens and taxa held and their geographic coverage. We also quantified research projects, publications, theses, and dissertations that have used at least one specimen, associated data, or materials deposited in these collections. We assessed their physical conditions by comparison with the standards set by the American Society of Mammalogists. As of 2018, these collections held a total of 61,560 cataloged specimens (ENCB 44,275; CRD 12,163; OAXMA 5,122), the largest repository of Mexican mammals in the Americas. All the orders, 86 % of the genera, and 69% (342) of the species of terrestrial mammals known to inhabit Mexico are represented in these collections. Specimens from all the Mexican States are included, with CRD focusing mostly on the northern part of the country, ENCB on central and southeastern Mexico, and OAXMA on the southeast. Materials from these collections have been used for at least 285 peer-reviewed publications, 91 research projects, and 107 theses and dissertations. CRD keeps >9,000 tissue samples, while OAXMA keeps >300 tissue samples plus 1,139 echolocation recordings of 24 bat species. All collections meet most curatorial standards of specimen preservation and availability and are being actively used in research projects. Nonetheless, we believe a sound institutional policy is necessary for the IPN mammal collections to successfully face the 21st-century challenges, particularly for ensuring the availability of usable data for the scientific community, digitizing the holdings, and designing and implementing a long-term preservation strategy.
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Roberts, Katherine, Jessica Nakano, and Kelsey Falquero. "Establishing Legal Title for Non-Accessioned Collections: All Collections Matter." Biodiversity Information Science and Standards 2 (July 17, 2018): e28231. http://dx.doi.org/10.3897/biss.2.28231.
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The Education and Outreach (E&O) Collection at the Smithsonian National Museum of Natural History (NMNH) contains around 125,000 specimens and objects representing all seven of NMNH’s research departments: Anthropology, Botany, Entomology, Invertebrate Zoology, Mineral Sciences, Paleobiology, and Vertebrate Zoology. The primary source of the E&O Collection is the NMNH’s former Naturalist Center (NC) that began in 1976 and closed in 2011. Almost a year after the NC’s closure, the Collection was repurposed as the core of the E&O Collection for the new science learning center, Q?rius, at NMNH. The E&O Collection was designated a collecting unit that needed to meet the Smithsonian Institution’s standards of care, holding non-accessioned collections to the same principles as accessioned collections. For museums to claim full legal title, all acquired collections require proof of offer from the donor, acceptance by the museum, and physical custody of the objects. Title status is necessary to comply with the exceptions and regulations surrounding intellectual property rights and to fulfill legal and ethical obligations. E&O collection items derived from several different sources, including donations, purchases, exchanges, collecting trips, and most commonly from former NC docents who routinely deposited items into the Collection. At the start of 2013, the E&O Collection’s team along with graduate-level interns from The George Washington University began the legal title project for the E&O Collection. In order to ensure that NMNH holds full title to the E&O Collection, interns research original acquisition records and federal and international regulations on cultural and biological materials. In 2016, through the Collections Care Preservation Fund, a contractor was hired to: 1) create a comprehensive digital and paper record to re-enforce the integrity of the non-accessioned collections and their future actions for exhibition, loan, or disposal, and 2) conduct thorough research and review of collection items’ acquisition histories to record that NMNH has done its due diligence to understand what is in the E&O Collection and how it arrived there. Over the past five years, we have investigated legal title for over 9,000 collection lots and worked with over 44 interns. We have digitized over 1,097 transaction records and have linked over 20,090 catalog records to a transaction. Ultimately, the E&O legal title research process ensures collection items have full legal title, mitigates risk of losing collection data by digitizing acquisition records and legal title research, and promotes best practices for acquired but not accessioned education collections.
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Bettio, Valentina, Eleonora Mazzucco, Chiara Aleni, Silvia Cracas, Carmela Rinaldi, Annamaria Antona, Marco Varalda, et al. "UPO Biobank: The Challenge of Integrating Biobanking into the Academic Environment to Support Translational Research." Journal of Personalized Medicine 13, no. 6 (May 29, 2023): 911. http://dx.doi.org/10.3390/jpm13060911.
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Biobanks are driving motors of precision and personalized medicine by providing high-quality biological material/data through the standardization and harmonization of their collection, preservation, and distribution. UPO Biobank was established in 2020 as an institutional, disease, and population biobank within the University of Piemonte Orientale (UPO) for the promotion and support of high-quality, multidisciplinary studies. UPO Biobank collaborates with UPO researchers, sustaining academic translational research, and supports the Novara Cohort Study, a longitudinal cohort study involving the population in the Novara area that will collect data and biological specimens that will be available for epidemiological, public health, and biological studies on aging. UPO Biobank has been developed by implementing the quality standards for the field and the ethical and legal issues and normative about privacy protection, data collection, and sharing. As a member of the “Biobanking and Biomolecular Resources Research Infrastructure” (BBMRI) network, UPO Biobank aims to expand its activity worldwide and launch cooperation with new national and international partners and researchers. The objective of this manuscript is to report an institutional and operational experience through the description of the technical and procedural solutions and ethical and scientific implications associated with the establishment of this university research biobank.
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Pérez, J. H., F. G. Gaviria-Ortiz, W. I. G. Santos, E. Carneiro, O. H. H. Mielke, and M. M. Casagrande. "Long term survey of the butterfly fauna of Curitiba, Paraná, Brazil: How does a scientific collection gather local biodiversity information? (Lepidoptera: Papilionoidea)." SHILAP Revista de lepidopterología 45, no. 179 (September 30, 2017): 433–46. http://dx.doi.org/10.57065/shilap.934.
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Butterfly species lists are commonly published aiming to describe local or regional diversity, thus being primordial tools for subsiding nature preservation and management. However, tropical lands usually lack this kind of information. Inventories of megadiverse organisms, such as butterflies, usually require long term studies to detect a substantial fraction of species present in certain location. Through biological collections in scientific institutions it is possible to preserve a considerate amount of biodiversity information, which is not available in the literature, but can promote studies over time. Aiming at supplementing the knowledge on butterfly diversity in Curitiba, Paraná, Brazil, and to demonstrate how a scientific collection accumulates such information from the nearby surroundings, this study lists all species of butterflies recorded in the city since 1938. Since then, 554 species were recorded. Although there have been large sampling efforts since the 60s, 45 species were only recorded in the last decade. Species lists published in 1938, 1995, 2011 and 2015 contributed to a considerable fraction of species records and monitoring, but species richness observed in each study is usually low (less than 1/3 of all historical records). Therefore, the long term deposition of specimens gathered in a single collection evidences that Curitiba harbors a distinct higher number of species, though new records are still frequent. Taking into account that long term surveys of megadiverse insects offer a more complete analysis of their biological diversity, studies measuring diversity impacts, such as urban sprawl, must include historical data whenever available.
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Desjardins, Rebecca B. "Arsenic and pre-1970s museum specimens: Using a hand-held XRF analyzer to determine the prevalence of arsenic at Naturalis Biodiversity Center." Collection Forum 30, no. 1-2 (January 1, 2016): 7–14. http://dx.doi.org/10.14351/0831-4985-30.1.7.
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Abstract The use of arsenic in the preservation of biological specimens was common practice prior to 1970. Because the Naturalis Center for Biodiversity (Naturalis) has extensive collections from before 1950, it was suspected that it held many contaminated specimens. In 2013, Naturalis tested 220 objects for the presence of arsenic over a period of 2 days using a handheld x-ray fluorescence analyzer, which detects arsenic, lead, mercury, and some other metals on objects. This testing provides an estimate of the prevalence of contaminated specimens, as well as a way to determine whether arsenic had spread into noncollection areas. In addition to specimens, floors, desks, keyboards, gloves, elevators, and lab coats were tested for arsenic presence and quantity. The results indicate that mounted specimens do not spread large amounts of arsenic onto the surrounding areas. However, there was sufficient contamination to warrant concern such that the arsenic-handling policy was modified to include different categories of contamination. From this framework, policy and physical changes to the building were made to minimize exposure by collections staff and visitors.
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Yu, Meng, Chen Du, Qingyu Yan, Chi Zhang, Feixiang Wu, and Cheng Zhou. "On the Construction of Biobank in General Hospitals." Advanced Emergency Medicine 9, no. 3 (October 10, 2020): 65. http://dx.doi.org/10.18686/aem.v9i3.171.
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<p><strong>Objective:</strong> discussion on a series of biospecimen related issues are conducted, such as collection and preservation, quality control, as well as management and application, during the construction of human tissue biobank in a general hospital. <strong>Methods:</strong> To develop a set of standardized operational procedures and to collect tissue samples, such as whole blood, serum, plasma, fresh frozen tissues, cerebrospinal fluid, and paraffin-embedded tissues, which were classified and made aliquots according to different requirements, and stored at -80℃ temperature refrigerator or in liquid nitrogen. At the same time, a set of information management software was used to realize management of the biobank. <strong>Results:</strong> currently, there are more than 20,000 specimens of various benign and malignant cases, which cover 380 diseases, being collected in the biological database in our hospital. These specimens include paraffin-embedded tissue, fresh frozen tissue, femoral head, whole blood, plasma, serum and cerebrospinal fluid, etc. A large number of these specimensare beneficial is used in clinical research at present. <strong>Conclusion:</strong> the establishment of biological sample bank can maximize the value of non-reborn human tissue specimens, and provide normal control standards as well as benign and malignant disease standards for clinical diagnosis and treatment, which is of great significance to the research of disease pathogenesis and the development of detection technology.</p>
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Guerrero, Andrea, and Adán Pérez-García. "Shell Anomalies in the European Aquatic Stem Turtle Pleurosternon bullockii (Paracryptodira, Pleurosternidae)." Diversity 13, no. 11 (October 22, 2021): 518. http://dx.doi.org/10.3390/d13110518.
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The uppermost Jurassic to lowermost Cretaceous stem turtle Pleurosternon bullockii is the pleurosternid (Testudinata, Paracryptodira) known by the largest number of specimens worldwide, composing the largest European collection of Lower Cretaceous complete and partial shells for a turtle taxon. The availability of numerous specimens as well as their generally good preservation allowed for recent detailed characterization of the shell of this species, including states that are variable at the intraspecific level (individual variability, sexual dimorphism, and ontogenetic development). However, extreme cases of morphological variation corresponding to anomalies have not been addressed in detail, neither for P. bullockii nor for any other member of Paracryptodira. In this context, the study of several shell anomalies in P. bullockii is carried out here. Fourteen specimens showing anomalies are recognized and examined here to determine the frequency and distribution of these shell anatomical deviations. All these anomalies are described and figured. The morphogenetic cause of each of them is discussed. As a consequence, a relatively broad spectrum of anomalies is reported for P. bullockii. None of the anomalies seem to present negative consequences for vital activities of the specimens since none compromised the main functions of the shell.
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Carruthers, Lauren V., Arinaitwe Moses, Moses Adriko, Christina L. Faust, Edridah M. Tukahebwa, Lindsay J. Hall, Lisa C. Ranford-Cartwright, and Poppy H. L. Lamberton. "The impact of storage conditions on human stool 16S rRNA microbiome composition and diversity." PeerJ 7 (December 2, 2019): e8133. http://dx.doi.org/10.7717/peerj.8133.
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Background Multiple factors can influence stool sample integrity upon sample collection. Preservation of faecal samples for microbiome studies is therefore an important step, particularly in tropical regions where resources are limited and high temperatures may significantly influence microbiota profiles. Freezing is the accepted standard to preserve faecal samples however, cold chain methods are often unfeasible in fieldwork scenarios particularly in low and middle-income countries and alternatives are required. This study therefore aimed to address the impact of different preservative methods, time-to-freezing at ambient tropical temperatures, and stool heterogeneity on stool microbiome diversity and composition under real-life physical environments found in resource-limited fieldwork conditions. Methods Inner and outer stool samples collected from one specimen obtained from three children were stored using different storage preservation methods (raw, ethanol and RNAlater) in a Ugandan field setting. Mixed stool was also stored using these techniques and frozen at different time-to-freezing intervals post-collection from 0–32 h. Metataxonomic profiling was used to profile samples, targeting the V1–V2 regions of 16S rRNA with samples run on a MiSeq platform. Reads were trimmed, combined and aligned to the Greengenes database. Microbial diversity and composition data were generated and analysed using Quantitative Insights Into Microbial Ecology and R software. Results Child donor was the greatest predictor of microbiome variation between the stool samples, with all samples remaining identifiable to their child of origin despite the stool being stored under a variety of conditions. However, significant differences were observed in composition and diversity between preservation techniques, but intra-preservation technique variation was minimal for all preservation methods, and across the time-to-freezing range (0–32 h) used. Stool heterogeneity yielded no apparent microbiome differences. Conclusions Stool collected in a fieldwork setting for comparative microbiome analyses should ideally be stored as consistently as possible using the same preservation method throughout.
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Milchakova, N. A., and V. G. Ryabogina. "THE HERBARIUM OF MACROPHYTES OF THE A.O. KOVALEVSKY INSTITUTE OF BIOLOGY OF THE SOUTHERN SEAS OF RAS (SIBS), AND THE STAGES OF ITS FORMATION." Ботанический журнал 108, no. 8 (August 1, 2023): 752–66. http://dx.doi.org/10.31857/s0006813623060066.
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The paper presents the results of a retrospective analysis of the history of the formation of the macrophyte herbarium of Kovalevsky Institute of Biology of the Southern Seas of RAS (IBSS, Sevastopol, until 1963 – Sevastopol Biological Station, SBS). For the analysis, the electronic database of the herbarium, sources and archival materials published over a period of more than a hundred years, memoirs of the oldest employees of the SBS were used. Three stages of the herbarium fund formation were distinguished, its beginning dating back to 1878. The first herbarium specimens were collected and designed by S.M. Pereyaslavtseva, the first Russian female zoologist and the first head of the SBS. According to archival data, by the beginning of the World War II, the herbarium contained about 3 000 herbarium sheets; like all museum collections of the SBS, it burned down in 1942. The beginning of its restoration dates back to 1945, today it contains 30914 sheets of 715 species and 198 genera from 734 localities, it is included in the international herbarium database Index Herbariorum (its acronym is SIBS). The paper summarizes the data on collection sites in the Atlantic, Arctic, Pacific, Indian and Southern Oceans. The historical collections of famous algologists N.V. Morozova-Vodyanitskaya (collection from 1920 to 1931) and A.A. Kalugina-Gutnik (from 1960 to 1991), and of a collector of the Karadag Biological Station G.M. Stanilovsky (from 1924 to 1946) are characterized; they account for 71% of the total volume of the fund. It is shown that the key macroalgae of the Black Sea are represented by collections for more than half a century from the same locality (Phyllophora crispa (Hudson) P.S. Dixon, Ericaria crinita (Duby) Molinari et Guiry, Gongolaria barbata (Stackhouse) Kuntze, Ulva rigida C. Agardh, etc.). There are unique macroalgae specimens from the underwater uplifts of the Mediterranean Sea, 14 islands and atolls of the Seychelles archipelago, the islands of Antarctica, of the seagrasses of the Indian Ocean, whose localities are not found in the herbaria of the world. To expand access to the herbarium fund, it is necessary to export data to the global bank and the global biodiversity information system (GBIF). On the basis of the studies performed, a rationale was prepared of naming the herbarium of macrophytes of world ocean IBSS after A.A. Kalugina-Gutnik (1929–1994), taking into account her significant contribution to the preservation of scientific heritage and traditions, and the creation of the collection fund.
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TRIAPITSYN, SERGUEI V., PAUL F. RUGMAN-JONES, and THOMAS M. PERRING. "Re-collection and identity of Ooencyrtus californicus (Hymenoptera: Encyrtidae), and its new synonym, Ooencyrtus lucidus." Zootaxa 4966, no. 1 (April 30, 2021): 97–100. http://dx.doi.org/10.11646/zootaxa.4966.1.11.
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Girault (1917) very briefly described and diagnosed the encyrtid wasp species Ooencyrtus californicus Girault (Hymenoptera: Encyrtidae) with the following limited data (p. 22): “Sacramento, California, from bug eggs on Pinus sabiniana, September”. The first author examined its two syntypes, poorly mounted on a slide, of which only parts of the four antennae and a slightly damaged fore wing remain (Triapitsyn et al. 2020). They concluded that this species was better considered a nomen dubium until fresh specimens could be collected from the same host plant in or near the type locality. In July 2019, an effort was made to re-collect O. californicus from foothill (or gray) pine, Pinus sabiniana (Pinaceae), in the Oakhurst area of Madera County, California, USA, where this pine is abundant, but no specimens were captured. At the same time, a very similar insect was collected from sentinel eggs of the invasive stink bug Bagrada hilaris (Burmeister) in Riverside, California. This insect was cultured in the laboratory as part of a B. hilaris biological control program. Due to the poor preservation of the type specimens and in the absence of genetic evidence, it was impossible to positively and properly attribute specimens of this newly collected parasitoid to O. californicus. Therefore, to provide a much needed scientific name for this native egg parasitoid, it was described as Ooencyrtus lucidus Triapitsyn & Ganjisaffar in Triapitsyn et al. (2020). The two nominal species were separated based on minor differences in the proportions of the scape, pedicel, and first funicular segment of the female antenna (Triapitsyn et al. 2020). John S. Noyes, world expert on Encyrtidae and one of the reviewers of Triapitsyn et al. (2020), disagreed with the erection of O. lucidus as a new taxon based on the morphological similarities of the female antenna with that of O. californicus, so the description was published with the understanding that the two might be conspecific. But to settle this one way or another new specimens of O. californicus had to be collected to allow morphological and molecular analyses.
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Carter, Julian. "Workshop: Care & Conservation of Zoological Collections." Biodiversity Information Science and Standards 2 (July 25, 2018): e28621. http://dx.doi.org/10.3897/biss.2.28621.
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Zoological collections house a huge range of biological diversity preserved in a wide variety of ways ranging from microscope mounts to whole animals preserved in fluids. The result is that these collections consist of a wide range of differing materials which can make the long term care and conservation of such collections a considerable challenge. This workshop is designed for museum professionals with the aim of giving an introductory overview on museum conservation approaches towards the care of zoological collections. This will be achieved through identifying the key risks and looking at the application of both remedial and preventative conservation methodologies to their care. The format of the workshop will be lectures on specific topics with group discussions, along with (where feasible) activities in small groups and practical examinations of specimens. Topics covered will include: Introduction to the concepts of ‘museum conservation’ and its application within the Natural Sciences. The types of material found in zoological collections – an overview of the core collection types, the chemistry of preservation and the potential long term challenges these present. An overview of the key agents of deterioration. Environmental effects and how to recognise them. Awareness of hazardous materials and core H&S issues encountered with the care and handling of zoological collections. Assessing collections and deciding conservation priorities. Fur, feathers and bones - practical conservation approaches to cleaning, consolidation and repair. Fluid collections - practical conservation approaches to handling, identifying fluids and carrying out remedial activities. Other key collection areas – e.g. conservation of entomology and other dried invertebrate collections; microscope slide collections. Consideration of the care and conservation of specialist collections e.g. historic models such as Blaschka glass models. Discussion and feedback from attendees will be a core part of the day.
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Wepf, Roger, and Heinz Gross. "Pt/Ir/C, a new, powerful coating material for High-Resolution SEM." Proceedings, annual meeting, Electron Microscopy Society of America 48, no. 3 (August 12, 1990): 6–7. http://dx.doi.org/10.1017/s0424820100157565.
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In-lens field emission SEM allows to image specimen surfaces with subnanometer resolution by collecting type I secondary electrons, with an incident electron probe size of abut 0.5 nm in diameter. To achieve such high topographic resolution on biological specimens adequate structural preservation and high resolving thin continuous coating films are necessary.Careful freeze-drying (“maintaining hydration shells”) followed by heavy metal shadowing at -250°C under ultra high vacuum conditions (UHV) allows to extract surface features ≤2 nm with TEM. TEM-shadowing films (Pt/C, Ta/W) are stabilized with a C-backing layer. Such a C-coat would blurr fine details when investigated with the SEM.At the right composition (C-content 25-40%, metal content 75-60%) only about 1.5 nm thick Pt/Ir/C-films remain three-dimensionally stable when transferred to atmospheric conditions after freeze-drying samples with macromolecular dimensions. Pt/Ir/C is made by evaporating a Pt/Ir cylinder (diameter 1.5 mm, 70% Ir) inserted into a graphite rod (diameter 2 mm).
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Towner, Ronald H. "Collecting and Caring for Tree-Ring Samples in the Southwest." Advances in Archaeological Practice 3, no. 4 (November 2015): 397–406. http://dx.doi.org/10.7183/2326-3768.3.4.397.
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AbstractDendrochronology is the most precise and accurate dating technique available to archaeologists, with resolution to the year and sometimes season. As biological specimens from human-produced contexts, dendroarchaeological samples inherently contain three kinds of information: chronological, behavioral, and environmental. The purpose of this short article is to educate archaeologists on how to avoid degrading any of these three types of information through improper sample selection, collection, preparation, or transportation techniques. Dendroarchaeology is not without limitations. First and foremost, it is dependent on the behaviors of people who built structures, made artifacts, and burned wood for fuel. If past people did not use wood, or used undateable tree species, dendrochronology will simply not be useful. In some cases, people used dateable species, but their selection criteria did not meet one of the four basic criteria necessary for successful dating. The second most important factor in successful tree-ring dating of archaeological materials is the behavior of archaeologists. Finally, preservation plays an important role in successful dating and the nature of the derived dates, but the paucity of long-lived old trees and degradation of “legacy” wood on the ground have hampered the development of millennia-long chronologies in more mesic areas.
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Lobo, Leonardo Souza, Orlando Nelson Grillo, and Sergio Alex Kugland de Azevedo. "Morphology, Pandemic, and 3D." Arquivos de Zoologia 52, no. 2 (June 1, 2021): 33–40. http://dx.doi.org/10.11606/2176-7793/2021.52.02.
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The COVID‑19 pandemic imposes the biggest restrictions on access to morphological information housed in scientific collections, compromising the progress of scientific research. Even though it is not the first event to impose restrictions on access, it is undoubtedly the most global in range. Based on this, we discuss the barriers to access information and we show 3D technology as an important tool to create routes to mitigate the effects of future restrictions. In a global sphere, there are initiatives of inter-institutional integration and international networks focused on facilitating and disseminate the implementation of digitization tools and techniques to facilitate access to diverse biological information. Notwithstanding, when we speak in 3D technology in Latin American countries, as is well noted in Brazil, this type of progress is lacking, with only isolated initiatives from some laboratories and research centers that implement 3D digitization tools, but often as experimental uses. Moreover, recent events, such as the Museu Naciona fire and the mobility restriction imposed by the COVID‑19 pandemic, reinforce the need and urgency to discuss the virtualization of natural history collections in the national territory. In this sense, we recommend photogrammetry as a more accessible and versatile technology, which could be quickly implemented in curatorial procedures. We, also, have defined criteria to establish priorities for virtualizing the collection. The virtualization of the type specimens is an inevitable and necessary task to ensure their access and expansion of their safe preservation, as established by the ICZN, and should therefore be considered as a high priority, followed by reference specimens, which are frequently accessed. Finally, to ensure Latin America advances to levels similar to those observed in other continents, it is important to establish a collaborative network of museums and other research institutions.
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Privalov, F. I., A. V. Kilchevskij, S. I. Grib, V. N. Retsetnikov, Z. A. Kozlovskaja, S. A. Dmitrieva, A. I. Kovalevich, and I. S. Matys. "PLANTS GENETIC RESOURCES IN THE REPUBLIC OF BELARUS – THE FUNDAMENTAL PRINCIPLE OF FOOD, ENVIRONMENTAL AND BIOLOGICAL SECURITY OF THE COUNTRY." Proceedings of the National Academy of Sciences of Belarus. Agrarian Series 56, no. 3 (August 25, 2018): 304–20. http://dx.doi.org/10.29235/1817-7204-2018-56-3-304-320.
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Breeding of new domestic varieties of economically useful plants for different purposes (food, fodder, technical, medicinal, decorative, etc.) is the basis for food, environmental and social security of the republic population. Therefore, preservation, study, mobilization and rational use of genetic resources in the context of global climate change and steady increase of anthropogenic pressure on nature is a planetary problem. The welfare and life of the present and future generations of mankind depends on successful solution of this problem. The paper presents history in chronicles of genetic resources preservation in the Republic of Belarus – from conception of this trend to the present day. Particular attention is paid to the presentation of the results obtained by the implementing organizations of the State Program “Plant Gene Pool” over a 17-year period (2000-2017), including 11 academic institutions and 2 higher educational institutions of the republic. The contribution of each organization to the national genetic bank formation is reflected. Basic, active, working, field, double, target, indicative, core and training collections of the main resource crops, economically significant crops and forest-forming species were formed by their efforts. The largest and most valuable genetic collections of 7 implementing organizations are included in the State Register of Scientific Objects, which constitute the national treasure of the Republic. These collections are a source of valuable genetic material and, at the same time, they are successfully used in scientific, environmental, educational and other programs. Currently, genetic collections in general include over 78,300.00 specimens belonging to 1,680.00 species of crop plants and their wild relatives. 1,016.00 varieties of crop plants were created based on them. The paper also reflects the main approaches and perspectives of preservation and rational use of the plant gene pool. Sophisticated and time-consuming processes of genetic collections formation in modern hard economic and regional natural conditions, taking into account the results of similar studies of other states, will serve as a scientific and information basis for increasing efficiency and improving work in this direction. In practical terms, the high level of species, variety and form biological diversity of genetic collections serves as a guarantee for their efficient use in crop production and selection as sources and donors of valuable genetic material.
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Strekopytov, Stanislav. "Corrosive sublimate and its introduction as an insecticide for preserving natural history specimens in the eighteenth century." Archives of Natural History 48, no. 1 (April 2021): 22–41. http://dx.doi.org/10.3366/anh.2021.0686.
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By the mid-eighteenth century, the need to protect zoological and botanical collections from attacks of insects became pressing for the community of naturalists. Living ornamental and economically important plants and their seeds also needed to be protected from insects when transported by sail. John Ellis ( c.1710–1776), one of the pioneers of plant transportation, was instrumental in disseminating the knowledge of insecticidal properties of corrosive sublimate (mercury(II) chloride or mercuric chloride, HgCl2). Although the use of corrosive sublimate for the protection of zoological collections had been proposed by John Woodward (1665–1728) in 1696, it was probably not widely used by naturalists until Ellis had published his Directions for bringing over seeds in 1770, recommending this substance for the protection of living plants, seeds and specimens during transport. Ellis possibly learned about the insecticidal properties of corrosive sublimate from the emerging use of this compound to control bedbugs ( Cimex lectularius). The history of bedbug management in eighteenth-century London, and some early exterminators, including John Southall ( fl.1726–1738), George Bridges ( c.1695–1768) and Thomas Tiffin ( fl.1760–1783), are discussed. Only a few days after the Directions was printed, Ellis asked Thomas Davies ( c.1737–1812) to publish a method of preparing bird skins that involved corrosive sublimate and was probably involved in drafting it. Following these two publications, corrosive sublimate was frequently used for the preservation of natural history collections including bird skins and herbarium specimens.
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DUELLI, PETER, and MARTIN K. OBRIST. "In search of the real Pseudomallada prasinus (Neuroptera, Chrysopidae)." Zootaxa 4571, no. 4 (March 28, 2019): 510. http://dx.doi.org/10.11646/zootaxa.4571.4.4.
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Three sympatric morphs of Pseudomallada prasinus (Burmeister, 1839) were hybridized in search of reproductively separated species. In addition, 26 morphological and biological traits were recorded for living and preserved specimens of the three morphotypes. Cross-breeding experiments showed that the prasinoid morph “marianus” is a different species from either the “greenhead” or “sulfurhead” morphs. All three are morphologically and biologically distinct. “Greenhead” and “sulfurhead” are small to medium sized and deposit eggs singly, without obligatory diapause in the second instar. In most specimens of these two smaller “prasinus” morphs there is a red or brown suture below the antennae, which can fade with age or preservation. P. “marianus” is a large species, depositing bundled eggs, with an obligatory diapause in about half of the L2. In none of the collected or reared P. “marianus” was a red or brown suture below the eyes observed. The forewing sizes of the type specimens of Chrysopa prasina Burmeister, 1839, C. coerulea Brauer, 1851, and C. marianus Navás, 1915 differ significantly from those of C. aspersa Wesmael, 1841 and other, later synonymized type specimens such as C. sachalinensis Matsumura, 1911, C. burri Navás, 1914, C. caucasica Navás, 1914, or C. vernalis Navás, 1926. This strongly suggests that the “marianus” morph is the real P. prasinus and the “greenhead” and “sulfurhead” morphs correspond to P. aspersus or one of the later synonymized species with smaller wing size.Pseudomallada marianus (Navás, 1905) is confirmed as a synonym of P. prasinus, depositing bundled eggs, whereas smaller prasinoid morphs, depositing single eggs, are not P. prasinus—and are morphologically distinct from P. abdominalis (Brauer, 1856). Pseudomallada aspersus (Wesmael, 1841) is a valid species, but at this point it is not possible to assign it to one of the prasinoid morphs because most of the live color traits are not discernible in old type specimens. A diagnostic description of the “real” P. prasinus can separate almost all P. prasinus specimens, even in museum collections, from P. aspersus (likely to be the “greenhead” morph) and the Mediterranean “sulfurhead”.
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Smith, Andrew B. "Intrinsic versus extrinsic biases in the fossil record: contrasting the fossil record of echinoids in the Triassic and early Jurassic using sampling data, phylogenetic analysis, and molecular clocks." Paleobiology 33, no. 2 (2007): 310–23. http://dx.doi.org/10.1666/06073.1.
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Four independent lines of evidence, (1) the quality of specimen preservation, (2) taxonomic collection curves, (3) molecular divergence estimates, and (4) ghost lineage analysis of a genus-level cladogram, point to echinoids having a much poorer fossil record in the Triassic than in the Lower Jurassic. Furthermore, preservational differences between Triassic and Lower Jurassic echinoids have remained a consistent feature over 160 years of discovery. Differences exist in how effectively paleontologists have collected the fauna from available outcrops in the Triassic and Lower Jurassic. Collection curves suggest that rocks have been more efficiently searched for their fossils in Europe than elsewhere in the world, and that Lower Jurassic faunas are better sampled from available outcrop than Triassic faunas. The discovery of Triassic taxa has quickened in pace over the past 4 decades (though largely driven by a single Lagerstätte—the St. Cassian beds) while discoveries of new taxa from the Lower Jurassic have slowed. Molecular analysis of extant families and ghost lineage analysis of Triassic and Lower Jurassic genera both point to poorer sampling of Triassic faunas. This difference in the quality of the fossil record may be partially explained by differences in rock outcrop area, as marine sedimentary rocks are much less common in the Triassic than in the Lower Jurassic. However, improving biomechanical design of the echinoid test over this critical time interval was probably as important, and better explains observed preservational trends. Changes in the quality of the echinoid fossil record were thus driven as much by intrinsic biological factors as by sampling patterns.
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Garin, E. V., and D. V. Garina. "Herbaria of Russia: The role in the study of biodiversity of the country, the problems of conservation and management." Журнал общей биологии 84, no. 2 (March 1, 2023): 144–54. http://dx.doi.org/10.31857/s0044459623020033.
Full textAbstract:
In order to preserve biodiversity on Earth, it is necessary to carry out an inventory of all forms of life as soon as possible, and this task is especially relevant for little-studied territories, including Russia. The terrestrial and aquatic ecosystems of Russia represent the largest array of natural extratropical ecosystems in Eurasia. To solve the problem of inventorying flora and fauna, biological collections are of particular importance; in a number of reviews by scientists (mainly foreign ones) the attention of the scientific and civil community is drawn to the problem of preserving and increasing the use of collections. The article examines the role of herbaria in the study of biodiversity in Russia based on a quantitative analysis of collections, their representation in various regions of the country, the degree of their digitalization and integration into the global world network of biological collections. It is concluded that the herbarium fund of Russia is insufficient in terms of the number of specimens and unevenly distributed across the regions, the smallest number of plant specimens is available for a number of regions of the north-east of Russia. About half of all Russian herbaria are not registered in Index Herbariorum, although the pace of digitalization of botanical collections in Russia has somewhat accelerated in recent decades. It also highlights the problem of the preservation of herbarium collections, outlines ways to solve it and prospects for the use of herbaria in the future. The authors believe that the priority measures should be: 1) the formation of a regulatory framework for working with biocollections, which, in particular, will make it possible to recognize herbarium collections as objects of cultural and scientific heritage, and provide special funding for collections; 2) introduction into the practice of centralized accounting of Russian herbaria and their inclusion in the international database; 3) a ban on writing off herbarium collections by organizations; 4) increasing the pace of digitalization of botanical collections; 5) staffing of herbaria by professional researchers; introducing of a herbarium course in specialized universities; 6) the allocation of separate rooms for herbariums, equipped with specialized cabinets and ventilation.
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Badgley, Catherine. "Taphonomy of mammalian fossil remains from Siwalik rocks of Pakistan." Paleobiology 12, no. 2 (1986): 119–42. http://dx.doi.org/10.1017/s0094837300013610.
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Siwalik rocks of Pakistan are a virtually continuous, continental sedimentary sequence, extending in age from 18 to 1 ma b.p. This paper describes taphonomic features of late Miocene mammalian assemblages from a highly fossiliferous interval about 400 m thick, based on field documentation of sedimentary environments at 42 fossil localities and systematic fossil collection of 21 localities.Within a broadly fluvial system, I recognize four sedimentary environments of bone accumulation, distinguished by lithology, unit-thickness, unit-geometry, contacts, sedimentary structures, and relationship to adjacent units. Each environment corresponds to an association of lithofacies. Facies Association I is interpreted as the persistent, major channel bodies of a meandering fluvial system; Facies Association II as coarse-grained flood deposits, such as crevasse splays, deposited beyond the main channels; Facies Association III as channel margins, including levees and swales; and Facies Association IV as predominantly subaerial floodplains.Taphonomic features of bone assemblages from each facies association include skeletal-element composition, surface distribution of specimens, degree of articulation, hydraulic equivalence between organic and inorganic sedimentary particles, frequency of juvenile remains, size distribution of fauna, and an estimate of duration of accumulation of individual fossil localities. The distribution of these features among the four facies associations suggests that bone assemblages in Facies Associations I and II accumulated by the action of currents in river channels or floods, whereas bone assemblages in Facies Associations III and IV accumulated through concentration by biological agents and/or attrition at a repeatedly used site of predation.Inclusion in fluvial accumulations depends on initial availability of skeletal remains and hydraulic characteristics of individual skeletal elements, but not taxonomic identity per se. For biological accumulations, however, taxonomic composition reflects the preferences of the individual agents of accumulation. The probability of preservation of taxa in fluvial accumulations is probably mainly a function of body size, as reflected in the sizes of isolated skeletal elements. Thus, in this Siwalik system, bone assemblages that experienced fluvial transport are better representations of original community composition than bone assemblages created by biological agents or passive accumulation.
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Zazolina, E. V. "The Criminalization of Activities Related To the Extraction and Trafficking of Particularly Valuable Plants and Fungi that Are Listed in the Red Book of the Russian Federation and/or Protected By International Treaties to Which the Russian Federation Is a Party." Siberian Law Review 21, no. 2 (June 20, 2024): 238–50. http://dx.doi.org/10.19073/2658-7602-2024-21-2-238-250.
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The paper addresses the complexities surrounding the establishment of criminal liability for actions concerning the destruction, illegal extraction, and trafficking of particularly valuable, rare, and protected flora specimens. Official statistics data regarding the frequency of criminal acts committed in the realm of natural resource management and environmental protection are provided, offering a clear depiction of the state of legal protection and conservation efforts concerning flora specimens. To substantiate the rationale behind criminalizing acts pertaining to the destruction, illicit trafficking, and extraction of rare plant and fungi species, the author furnishes specific examples showcasing legislative violations in the realm of flora protection. An analysis of current criminal law, particularly Chapter 26 “Environmental Crimes”, is conducted to evaluate the efficacy of existing measures in safeguarding particularly valuable and rare flora specimens. Upon analyzing judicial statistics data, it has been determined that the current provisions of criminal law concerning the protection of flora specimens (Article 259 of the Criminal Code of the Russian Federation) are ineffective and largely unenforced. To enhance the effectiveness of protecting particularly valuable flora specimens, it is imperative to implement new legal mechanisms aimed at preserving and sustaining Russia's unique biological diversity. The article provides a description of the offense, for which liability is stipulated in Article 260.1 of the Criminal Code of the Russian Federation: “Intentional destruction or damage, as well as illegal extraction, collection, and trafficking of particularly valuable plants and fungi species belonging to those listed in the Red Book of the Russian Federation and/or protected by international treaties of the Russian Federation”. It is especially noted that with the enactment of Article 260.1 of the Criminal Code of the Russian Federation, the legislator has adopted a unified approach to the criminal law protection and preservation of both wildlife and plant species listed in the Red Book of the Russian Federation and/ or protected by international treaties of the Russian Federation. The elements of criminal offenses (as well as sanctions for them), the responsibility for which is established by Article 260.1 of the Criminal Code of the Russian Federation, are constructed by analogy with Article 258.1 of the Criminal Code of the Russian Federation. The conclusion is made about the expediency and necessity of criminalization in domestic legislation of acts related to the extraction and trafficking of especially valuable plants and fungi listed in the Red Book of the Russian Federation. The author makes proposals to improve criminal legislation in the field of establishing liability provided for in Article 260.1 of the Criminal Code of the Russian Federation.
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Li, Shuoguo, Gang Ji, Xiaojun Huang, Lei Sun, Jianguo Zhang, Wei Xu, and Fei Sun. "A New Solution of Non-integrated Correlative Light and Electron Microscopy Based on High-vacuum Optical Platform." Microscopy and Microanalysis 22, S3 (July 2016): 248–49. http://dx.doi.org/10.1017/s1431927616002099.
Full textAbstract:
Abstract Correlative light and electron microscopy (CLEM) offers a means of guiding the search for the unique or rare events by fluorescence microscopy (FM) and allows electron microscopy (EM) to zoom in on them for subsequent EM examination in three-dimensions (3D) and with nanometer-scale resolution. FM visualizes the localization of specific antigens by using fluorescent tags or proteins in a large field-of-view to study their cellular function, whereas EM provides the high level of resolution for complex structures. And cryo CLEM combines the advantages of maintaining structural preservation in a near-native state throughout the entire imaging process and by avoiding potentially harmful pre-treatments, such as chemical fixation, dehydration and staining with heavy metals. Besides for frozen-hydrated biological samples, CLEM combines the advantages of a close-to-life preservation of biological materials by keeping them embedded in vitreous ice throughout the entire imaging process and the frozen-hydrated condition is very suitable to maintain fluorescent signals. In recent years, many new instruments and software which intended to optimize the workflow and to obtain better experimental results of CLEM have been presented or even commoditized. While, the specimen damage during transfer from FM to EM and the resolution of CLEM were still need to be improved. Here we set up a High-vacuum Optical Platform to develop CLEM imaging technology (HOPE), which was designed to realize high-vacuum optical ( fluorescent) imaging for cryo-sample on EM cryo-holder (e.g. Gatan 626). A non-integrated high-vacuum cryo-optical stage, which adapted to the EM cryo holder, was fixed on epi-fluorescence microscope (or super-resolution microscope) to obtain fluorescent images. And then the EM cryo holder would be transferred to EM for collection of EM data. This protocol was aimed to minimize the specimen damage during transfer from FM to EM and it was versatile to expend to different types of light microscopy or electron microscopy. Our HOPE had already passed correlative imaging test, and the results showed that it was convenient and effective.
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Boudinot, Brendon E., Bernhard L. Bock, Michael Weingardt, Daniel Tröger, Jan Batelka, Di LI, Adrian Richter, et al. "Et latet et lucet: Discoveries from the Phyletisches Museum amber and copal collection in Jena, Germany." Deutsche Entomologische Zeitschrift 71, no. 1 (April 19, 2024): 111–76. http://dx.doi.org/10.3897/dez.71.112433.
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As the only direct records of the history of evolution, it is critical to determine the geological source of biota-bearing fossils. Through the application of synchrotron-radiation micro-computed tomography (SR-µ-CT), Fourier-transformed infrared-spectroscopy (FT-IR), visual evaluation of ultraviolet fluorescence (UV-VS), radiocarbon dating (14C quantification), and historical sleuthing, we were able to identify and sort 161 (83 Baltic amber, 71 Copal and 7 Kauri gum pieces) individually numbered and largely mislabeled pieces of East African Defaunation resin (~145 years old) and copal (~390 years old), as well as Baltic amber (~35 million years old) from the Phyletisches Museum collection. Based on this collection, we define two new species: ‡Amphientomum knorrei Weingardt, Bock & Boudinot, sp. nov. (Psocodea: Amphientomidae, copal) and †Baltistena nigrispinata Batelka, Tröger & Bock, sp. nov. (Coleoptera: Mordellidae, Baltic amber). For selected taxa, we provide systematic reviews of the fossil record, including: Amphientomidae, for which we provide a key to all species of Amphientomum, extant and extinct, and recognize the junior synonymy of Am. ectostriolatum Li, 2002 (an unjustified emendation) under Am. ectostriolate Li, 1999 (syn. nov.); the fossil ant genus †Yantaromyrmex and the clades Dorylinae, Plagiolepidini, Camponotus, Crematogaster, and Pheidole (Formicidae); the Nevrorthidae (Neuroptera); and Doliopygus (Coleoptera: Curculionidae: Platypodinae). We synonymize Palaeoseopsis Enderlein, 1925 with Amphientomum Pictet, 1854, syn. nov. and transfer one species from Amphientomum, forming Lithoseopsis indentatum (Turner, 1975), comb. nov. To prevent the uncritical usage of unidentifiable fossils attributed to Camponotus for macroevolutionary analysis, we transfer 29 species to the form genus †Camponotites Steinbach, 1967, which we consider to be most useful as incertae sedis in the Formicinae. We treat †Ctt. ullrichi (Bachmayer, 1960), comb. nov. as unidentifiable hence invalid stat. nov. We also transfer †Ca. mengei Mayr, 1868 and its junior synonym †Ca. igneus Mayr, 1868 to a new genus, †Eocamponotus Boudinot, gen. nov., which is incertae sedis in the Camponotini. Concluding our revision of Camponotus fossils, we transfer †Ca. palaeopterus (Zhang, 1989) to Liometopum (Dolichoderinae), resulting in †L. palaeopterumcomb. nov. and the junior synonymy of †Shanwangella Zhang, 1989, syn. nov. under Liometopum Mayr, 1861. Because the type specimens of the genera †Palaeosminthurus Pierce & Gibron, 1962, stat. rev. and †Pseudocamponotus Carpenter, 1930 are unidentifiable due to poor preservation, we consider these taxa unidentifiable hence invalid stat. nov. To avoid unsupported use of the available fossils names attributed to Crematogaster for divergence dating calibration points, we transfer three species to a new collective taxon that is incertae sedis in Myrmicinae, †Incertogaster Boudinot, gen. nov., forming †In. aurora (LaPolla & Greenwalt, 2015), †In. praecursor (Emery, 1891), comb. nov., and †In. primitiva (Radchenko & Dlussky, 2019), comb. nov. Finally, we transfer †Ph. cordata (Holl, 1829) back to Pheidole, and designate a neotype from our copal collection based on all available evidence. All new species plus the neotype of ‡Ph. cordata are depicted with 3D cybertypes from our µ-CT scan data. We introduce the convention of a double dagger symbol (‡) to indicate fossils in copal or Defaunation resin, as these may yet be extant. To further contextualize our results, we provide a discussion of amber history and classification, as well as the Kleinkuhren locality, to which multiple specimens were attributed. We conclude with conspecti on key biological problems and increasing potential of µ-CT for phylogenetic paleontology.
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Barreto Linhares, Ladaha Pequeno Menna, Bruna Vanessa Nunes Pereira, Maria Karoline Gomes Dantas, Wislayne Mirelly da Silva Bezerra, Daniela de Araújo Viana-Marques, Luiza Rayanna Amorim de Lima, and Pedro Henrique Sette-de-Souza. "Schinopsis brasiliensis Engler—Phytochemical Properties, Biological Activities, and Ethnomedicinal Use: A Scoping Review." Pharmaceuticals 15, no. 8 (August 20, 2022): 1028. http://dx.doi.org/10.3390/ph15081028.
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Brazil has the most incredible biodiversity globally and has a vast storehouse of molecules to be discovered. However, there are no pharmacological and phytochemical studies on most native plants. Parts of Schinopsis brasiliensis Engler, a tree from the Anacardiaceae family, are used by several traditional communities to treat injuries and health problems. The objective of this scoping review was to summarize the pharmacological information about S. brasiliensis, from ethnobotanical to phytochemical and biological studies. Data collection concerning the geographical distribution of S. brasiliensis specimens was achieved through the Reflora Virtual Herbarium. The study’s protocol was drafted using the Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR). The search strategy used the keyword “Schinopsis brasiliensis” in the databases: PUBMED, EMBASE, SCOPUS, Science Direct, Web of Science, SciFinder, and SciELO. Rayyan was used for the selection of eligible studies. In total, 35 studies were included in the paper. The most recurrent therapeutic indications were for general pain, flu and inflammation. The bark was the most studied part of the plant. The most used preparation method was decoction and infusion, followed by syrup. Phytochemical investigations indicate the presence of tannins, flavonoids, phenols, and polyphenols. Most of the substances were found in the plant’s leaf and bark. Important biological activities were reported, such as antimicrobial, antioxidant, and anti-inflammatory. S. brasiliensis is used mainly by communities in the semi-arid region of northeastern Brazil to treat several diseases. Pharmacological and phytochemical studies together provide scientific support for the popular knowledge of the medicinal use of S. brasiliensis. In vitro and in vivo analyses reported antimicrobial, antioxidant, anti-inflammatory, antinociceptive, cytotoxic, photoprotective, preservative, molluscicidal, larvicidal, and pupicidal effects. It is essential to highlight the need for future studies that elucidate the mechanisms of action of these phytocompounds.
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Belvedere, Matteo, Matthew R. Bennett, Daniel Marty, Marcin Budka, Sally C. Reynolds, and Rashid Bakirov. "Stat-tracks and mediotypes: powerful tools for modern ichnology based on 3D models." PeerJ 6 (January 11, 2018): e4247. http://dx.doi.org/10.7717/peerj.4247.
Full textAbstract:
Vertebrate tracks are subject to a wide distribution of morphological types. A single trackmaker may be associated with a range of tracks reflecting individual pedal anatomy and behavioural kinematics mediated through substrate properties which may vary both in space and time. Accordingly, the same trackmaker can leave substantially different morphotypes something which must be considered in creating ichnotaxa. In modern practice this is often captured by the collection of a series of 3D track models. We introduce two concepts to help integrate these 3D models into ichnological analysis procedures. The mediotype is based on the idea of using statistically-generated three-dimensional track models (median or mean) of the type specimens to create a composite track to support formal recognition of a ichno type. A representative track (mean and/or median) is created from a set of individual reference tracks or from multiple examples from one or more trackways. In contrast, stat-tracks refer to other digitally generated tracks which may explore variance. For example, they are useful in: understanding the preservation variability of a given track sample; identifying characteristics or unusual track features; or simply as a quantitative comparison tool. Both concepts assist in making ichnotaxonomical interpretations and we argue that they should become part of the standard procedure when instituting new ichnotaxa. As three-dimensional models start to become a standard in publications on vertebrate ichnology, the mediotype and stat-track concepts have the potential to help guiding a revolution in the study of vertebrate ichnology and ichnotaxonomy.
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Krambrich, Janina, Emelie Bringeland, Jenny C. Hesson, Tove Hoffman, Åke Lundkvist, Johanna F. Lindahl, and Jiaxin Ling. "Usage of FTA® Classic Cards for Safe Storage, Shipment, and Detection of Arboviruses." Microorganisms 10, no. 7 (July 18, 2022): 1445. http://dx.doi.org/10.3390/microorganisms10071445.
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Infections caused by arthropod-borne RNA viruses are overrepresented among emerging infectious diseases. Effective methods for collecting, storing, and transporting clinical or biological specimens are needed worldwide for disease surveillance. However, many tropical regions where these diseases are endemic lack analytical facilities and possibility of continuous cold chains, which presents challenges from both a biosafety and material preservation perspective. Whatman® FTA® Classic Cards may serve as an effective and safe option for transporting hazardous samples at room temperature, particularly for RNA viruses classified as biosafety level (BSL) 2 and 3 pathogens, from sampling sites to laboratories. In this study, we investigated the biosafety and perseverance of representative alpha- and flaviviruses stored on FTA® cards. To evaluate the virus inactivation capacity of FTA® cards, we used Sindbis virus (SINV), chikungunya virus (CHIKV), and Japanese encephalitis virus (JEV). We inoculated susceptible cells with dilution series of eluates from viral samples stored on the FTA® cards and observed for cytopathic effect to evaluate the ability of the cards to inactivate viruses. All tested viruses were inactivated after storage on FTA® cards. In addition, we quantified viral RNA of JEV, SINV, and tick-borne encephalitis virus (TBEV) stored on FTA® cards at 4 °C, 25 °C, and 37 °C for 30 days using two reverse transcriptase quantitative PCR assays. Viral RNA of SINV stored on FTA® cards was not reduced at either 4 °C or 25 °C over a 30-day period, but degraded rapidly at 37 °C. For JEV and TBEV, degradation was observed at all temperatures, with the most rapid degradation occurring at 37 °C. Therefore, the use of FTA® cards provides a safe and effective workflow for the collection, storage, and analysis of BSL 2- and 3-virus RNA samples, but there is a risk of false negative results if the cards are stored at higher temperatures for long periods of time. Conscious usage of the cards can be useful in disease surveillance and research, especially in tropical areas where transportation and cold chains are problematic.
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Joseph Costello, M. "Cryopreservation of biological specimens." Proceedings, annual meeting, Electron Microscopy Society of America 51 (August 1, 1993): 492–93. http://dx.doi.org/10.1017/s0424820100148290.
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Rapid cooling is the first, critical step in the preservation of biological specimens for examination using a wide variety of electron microscopic techniques. The choice of which cooling method to use depends on many factors, such as the restrictions of specimen geometry, the type of structural information desired and the microscopic techniques to be employed. This summary will highlight some recent technical innovations and novel applications of cryopreservation of biological specimens to study ultrastructure, chemical composition, and dynamic processes.For cryofixation to give realistic preservation of structural details, the specimen must be rapidly brought into intimate contact with the coolant and the contact must be maintained throughout the critical stages of the cooling process. During the last decade, four cooling methods have become prominent because they produce excellent preservation without cryoprotectants, are commercially available and are relatively simple to use: plunge cooling, jet cooling, slam cooling, and high-pressure cooling.Plunge cooling, the most commonly used method for cryofixation, is simply the immersion of a specimen into a liquid coolant usually held near its melting point.
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Simon, Martha N., Beth Y. Lin, and Joseph S. Wall. "Improved preservation of freeze-dried biological specimens." Proceedings, annual meeting, Electron Microscopy Society of America 50, no. 1 (August 1992): 736–37. http://dx.doi.org/10.1017/s0424820100124082.
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Specimens prepared by the wet-film technique (injecting unstained biological specimens into a drop of buffer on a thin carbon substrate which has never seen air, washing extensively, blotting to a thin layer of liquid, plunging the grid into nitrogen slush, and freeze-drying overnight) then visualized in the scanning transmission electron microscope (STEM) usually have reasonably wel1-preserved structures. However, there is a certain variability from day to day and sometimes even from one area to another on a given grid. This can occur for different reasons which may be inextricably related. The thin carbon film can be non-uniform at the molecular level with hot spots for strong attachment of some specimens, a part of a biological specimen may attach strongly while the rest of it thrashes about in Brownian motion ruining any perceivable structure, and the final thickness of liquid before freeze-drying may vary slightly which may affect the preservation of the structure.
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Engelmann, George. "Instructions for the Collection and Preservation of Botanical Specimens." Annals of the Missouri Botanical Garden 73, no. 3 (1986): 504. http://dx.doi.org/10.2307/2399189.
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Müller, M., and R. Hermann. "High-Resolution Scanning Electron Microscopy of Biological Specimens." Proceedings, annual meeting, Electron Microscopy Society of America 46 (1988): 186–87. http://dx.doi.org/10.1017/s0424820100103012.
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Three major factors must be concomitantly assessed in order to extract relevant structural information from the surface of biological material at high resolution (2-3nm).Procedures based on chemical fixation and dehydration in graded solvent series seem inappropriate when aiming for TEM-like resolution. Cells inevitably shrink up to 30-70% of their initial volume during gehydration; important surface components e.g. glycoproteins may be lost. These problems may be circumvented by preparation techniques based on cryofixation. Freezedrying and freeze-substitution followed by critical point drying yields improved structural preservation in TEM. An appropriate preservation of dimensional integrity may be achieved by freeze-drying at - 85° C. The sample shrinks and may partially collapse as it is warmed to room temperature for subsequent SEM study. Observations at low temperatures are therefore a necessary prerequisite for high fidelity SEM. Compromises however have been unavoidable up until now. Aldehyde prefixation is frequently needed prior to freeze drying, rendering the sample resistant to treatment with distilled water.
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Lomax, Dean, J. C. Lamsdell, and S. J. Jr Ciurca. "A collection of eurypterids from the Silurian of Lesmahagow collected pre 1900." Geological Curator 9, no. 6 (December 2011): 331–48. http://dx.doi.org/10.55468/gc75.
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A rediscovered collection of scientifically significant eurypterid fossil specimens, assigned to Slimonia acuminata and Erettopterus bilobus, is held in the Doncaster Museum and Art Gallery. The specimens are from the historically important late Silurian Lesmahagow inlier of Lanarkshire, Scotland and are described herein. The material ranges from partial to complete specimens, with a wide range in size of both genera. Most specimens have either no or minimal damage. Some interesting features include the orientation and preservation of the eurypterids.