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Journal articles on the topic 'Preserved organisms'
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1
Kenchington, Charlotte G., and Philip R. Wilby. "Of Time and Taphonomy: Preservation in the Ediacaran." Paleontological Society Papers 20 (October 2014): 101–22. http://dx.doi.org/10.1017/s1089332600002825.
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The late Neoproterozoic witnessed a revolution in the history of life: the transition from a microbial world to the one known today. The enigmatic organisms of the Ediacaran hold the key to understanding the early evolution of metazoans and their ecology, and thus the basis of Phanerozoic life. Crucial to interpreting the information they divulge is a thorough understanding of their taphonomy: what is preserved, how it is preserved, and also what is not preserved. Fortunately, this Period is also recognized for its abundance of soft-tissue preservation, which is viewed through a wide variety of taphonomic windows. Some of these, such as pyritization and carbonaceous compression, are also present throughout the Phanerozoic, but the abundance and variety of moldic preservation of body fossils in siliciclastic settings is unique to the Ediacaran. In rare cases, one organism is preserved in several preservational styles which, in conjunction with an increased understanding of the taphonomic processes involved in each style, allow confident interpretations of aspects of the biology and ecology of the organisms preserved. Several groundbreaking advances in this field have been made since the 1990s, and have paved the way for increasingly thorough analyses and elegant interpretations.
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McKinney, Frank K. "Taphonomic Effects and Preserved Overgrowth Relationships among Encrusting Marine Organisms." PALAIOS 10, no. 3 (June 1995): 279. http://dx.doi.org/10.2307/3515258.
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Garcia, Lynne S., and Robyn Y. Shimizu. "Evaluation of Intestinal Protozoan Morphology in Human Fecal Specimens Preserved in EcoFix: Comparison of Wheatley’s Trichrome Stain and EcoStain." Journal of Clinical Microbiology 36, no. 7 (1998): 1974–76. http://dx.doi.org/10.1128/jcm.36.7.1974-1976.1998.
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As a result of disposal problems related to the use of mercury compounds, many laboratories have switched from mercuric chloride-based Schaudinn’s and polyvinyl alcohol (PVA) stool preservatives to other, non-mercury-based preservatives. A comparison of organism recoveries and morphologies of the intestinal protozoa was undertaken with PVA containing the EcoFix zinc-based Schaudinn’s preservative (Meridian Diagnostics, Inc.); both Wheatley’s modification of Gomori’s trichrome stain (WT) and EcoStain (ES) were used to stain 51 human fecal specimens. Morphology, clarity of nuclear and cytoplasmic detail, overall color differences, and the ease or difficulty in detecting intestinal protozoa in fecal debris were assessed for the two permanent stained smears. Overall, organism morphology of the intestinal protozoa stained with WT and that of protozoa stained with ES were not equal in nuclear and cytoplasmic detail or range of color. However, the same organisms were identified in stained fecal smears with either WT or ES, with the exception of situations in which organism numbers were characterized as rare. Included were 67 protozoan challenges (number of organisms): Entamoeba histolytica-Entamoeba dispar (5), Entamoeba coli (9),Entamoeba hartmanni (6), Endolimax nana (12),Iodamoeba bütschlii (8), Blastocystis hominis (19), Giardia lamblia (6), Dientamoeba fragilis (2), yeast (2), and leukocytes (2). Five specimens were negative for parasites but contained fecal debris that was compared for morphologic detail and color range. The ES produces a more gray-green monotone with very little pink or red tone; contrast among the various colors is less than that seen with WT. Stain intensity for all organisms was acceptable, and there were no problems with stain deposition. The quality of the protozoan morphology with ES was often comparable to that with WT (36 of 67 [53.7%]) and, in some cases, better (24 of 67 [35.8%]). Organisms on the WT-stained smear exhibited better morphology in a few instances (4 of 67 [6%]), and in three instances, there were discrepant organism numbers.
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Key, Marcus M., Gregory A. Schumacher, Loren E. Babcock, Robert C. Frey, William P. Heimbrock, Stephen H. Felton, Dan L. Cooper, Walter B. Gibson, Debbie G. Scheid, and Sylvester A. Schumacher. "Paleoecology of commensal epizoans fouling Flexicalymene (Trilobita) from the Upper Ordovician, Cincinnati Arch region, USA." Journal of Paleontology 84, no. 6 (November 2010): 1121–34. http://dx.doi.org/10.1666/10-018.1.
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Commensal epizoozoans and episkeletozoans are rarely preserved attached to the external exoskeleton of the Late Ordovician trilobite Flexicalymene. Of nearly 15,000 Flexicalymene specimens examined, 0.1% show epizoozoans or episkeletozoans. Factors limiting Flexicalymene fouling include a shallow burrowing life style, frequent molting of the host, larval preference for other substrates, observational bias caused by overlooking small fouling organisms, and the loss of the non-calcified, outermost cuticle prior to fossilization or as the trilobite weathers from the encasing sediment. Trepostome bryozoans, articulate and inarticulate brachiopods, cornulitids, and a tube-dwelling/boring nonbiomineralized organism represent the preserved members of the Late Ordovician marine hard substrate community fouling Flexicalymene. This assemblage of organisms is less diverse than the hard substrate community fouling Late Ordovician sessile epibenthic organisms. Fouling is not restricted to only large Flexicalymene specimens as observed in previous studies but occurs in medium to large individuals interpreted as early to late holaspid specimens.Epizoozoans fouling the carcasses or molt ensembles of 16 Flexicalymene specimens provide insight into the life habits of the host and these fouling organisms. Trepostome bryozoans, articulate and inarticulate brachiopods, and cornulitids preferentially attached to elevated portions of the dorsal exoskeleton, and preferentially aligned in either the direct line or lee side of currents generated by Flexicalymene walking on the sea floor or swimming through the water column.
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Wilson, Mark A., and Timothy J. Palmer. "A Review of Evolutionary Trends in Carbonate Hardground Communities." Paleontological Society Special Publications 5 (1990): 137–52. http://dx.doi.org/10.1017/s2475262200005475.
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Ancient and modern marine carbonate hardgrounds offer unusual opportunities to study the evolution of communities from the Early Cambrian into the Holocene. Throughout this time the general physical conditions of a hardground community have been similar. The substrate is hard so sessile organisms must either attach to its surface, nestle in cavities, or bore into it for occupation. These organisms are thus preserved in situ. Since space is often the limiting physical resource, organisms must have ways of obtaining and defending it, and these competitive hierarchies are often preserved in the spatial relationships of the species. Scouring and/or burial in sediment usually marks the end of the brief habitation.
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Poinar, George. "Associations between Fossil Beetles and Other Organisms." Geosciences 9, no. 4 (April 21, 2019): 184. http://dx.doi.org/10.3390/geosciences9040184.
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The present work reveals plant and animal associates of 16 families and subfamilies of fossil beetles that have been preserved in amber from Mexico, the Dominican Republic, and Myanmar. The associates include mites, pseudoscorpions, spiders, insect parasites and predators, fungi, angiosperm parts, vertebrates, and nematodes. The presence of these fossil associates can be attributed to the rapid preservation of organisms in resin, thus maintaining natural associations almost “in situ”. Examples of present-day associations similar to those of the fossils show that specific behavioral patterns are often far more ancient than the specific lineages involved.
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Xiao, Shuhai, Zhe Chen, Ke Pang, Chuanming Zhou, and Xunlai Yuan. "The Shibantan Lagerstätte: insights into the Proterozoic–Phanerozoic transition." Journal of the Geological Society 178, no. 1 (September 10, 2020): jgs2020–135. http://dx.doi.org/10.1144/jgs2020-135.
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The Shibantan Lagerstätte (551–543 Ma) in the Yangtse Gorges area in South China is one of the best-known examples of terminal Ediacaran fossil assemblages preserved in marine carbonate rocks. Taxonomically dominated by benthic organisms, the Shibantan Lagerstätte preserves various photoautotrophs, biomineralizing tubular fossils, Ediacara-type macrofossils (including rangeomorphs, arboreomorphs, erniettomorphs, palaeopascichnids, a possible dickinsoniomorph, the mobile bilaterian Yilingia and soft-bodied tubular fossils), abundant ichnofossils and a number of problematic and dubious fossils. Shibantan fossils provide intriguing insights into ecological interactions among mobile bilaterians, sessile benthic Ediacara-type organisms and microbial mats, thus offering important data to test various hypotheses accounting for the decline of the Ediacara biota and the concurrent expansion of bilaterian bioturbation and mobility across the Proterozoic–Phanerozoic transition.
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Knoll, A. H., E. J. Javaux, D. Hewitt, and P. Cohen. "Eukaryotic organisms in Proterozoic oceans." Philosophical Transactions of the Royal Society B: Biological Sciences 361, no. 1470 (May 5, 2006): 1023–38. http://dx.doi.org/10.1098/rstb.2006.1843.
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The geological record of protists begins well before the Ediacaran and Cambrian diversification of animals, but the antiquity of that history, its reliability as a chronicle of evolution and the causal inferences that can be drawn from it remain subjects of debate. Well-preserved protists are known from a relatively small number of Proterozoic formations, but taphonomic considerations suggest that they capture at least broad aspects of early eukaryotic evolution. A modest diversity of problematic, possibly stem group protists occurs in ca 1800–1300 Myr old rocks. 1300–720 Myr fossils document the divergence of major eukaryotic clades, but only with the Ediacaran–Cambrian radiation of animals did diversity increase within most clades with fossilizable members. While taxonomic placement of many Proterozoic eukaryotes may be arguable, the presence of characters used for that placement is not. Focus on character evolution permits inferences about the innovations in cell biology and development that underpin the taxonomic and morphological diversification of eukaryotic organisms.
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Bromley, R. G., and A. A. Ekdale. "Composite ichnofabrics and tiering of burrows." Geological Magazine 123, no. 1 (January 1986): 59–65. http://dx.doi.org/10.1017/s0016756800026534.
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AbstractInfaunal communities in marine environments typically are tiered; that is, different taxa live at different depths within the sediment. Tiered suites of biogenic structures yield complex biogenic sedimentary fabrics (ichnofabrics), with the traces of deep-burrowing organisms overprinted on those of shallow-burrowing organisms. Careful analysis of crosscutting relationships of burrows in such composite ichnofabrics allows reconstruction of the tiered nature of fossil endobenthic communities. It is important to recognize that the best preserved and most prominently displayed trace fossils in most assemblages usually represent the deepest tier. Thus, they were farther removed from the sea floor and therefore less indicative of actual sea floor conditions than the more poorly preserved traces of the shallower tiers, on which the deeper traces are juxtaposed.
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Wendruff, Andrew J., Loren E. Babcock, Joanne Kluessendorf, and Donald G. Mikulic. "Paleobiology and taphonomy of exceptionally preserved organisms from the Waukesha Biota (Silurian), Wisconsin, USA." Palaeogeography, Palaeoclimatology, Palaeoecology 546 (May 2020): 109631. http://dx.doi.org/10.1016/j.palaeo.2020.109631.
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Morard, Raphaël, Franck Lejzerowicz, Kate F. Darling, Béatrice Lecroq-Bennet, Mikkel Winther Pedersen, Ludovic Orlando, Jan Pawlowski, Stefan Mulitza, Colomban de Vargas, and Michal Kucera. "Planktonic foraminifera-derived environmental DNA extracted from abyssal sediments preserves patterns of plankton macroecology." Biogeosciences 14, no. 11 (June 6, 2017): 2741–54. http://dx.doi.org/10.5194/bg-14-2741-2017.
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Abstract. Deep-sea sediments constitute a unique archive of ocean change, fueled by a permanent rain of mineral and organic remains from the surface ocean. Until now, paleo-ecological analyses of this archive have been mostly based on information from taxa leaving fossils. In theory, environmental DNA (eDNA) in the sediment has the potential to provide information on non-fossilized taxa, allowing more comprehensive interpretations of the fossil record. Yet, the process controlling the transport and deposition of eDNA onto the sediment and the extent to which it preserves the features of past oceanic biota remains unknown. Planktonic foraminifera are the ideal taxa to allow an assessment of the eDNA signal modification during deposition because their fossils are well preserved in the sediment and their morphological taxonomy is documented by DNA barcodes. Specifically, we re-analyze foraminiferal-specific metabarcodes from 31 deep-sea sediment samples, which were shown to contain a small fraction of sequences from planktonic foraminifera. We confirm that the largest portion of the metabarcode originates from benthic bottom-dwelling foraminifera, representing the in situ community, but a small portion (< 10 %) of the metabarcodes can be unambiguously assigned to planktonic taxa. These organisms live exclusively in the surface ocean and the recovered barcodes thus represent an allochthonous component deposited with the rain of organic remains from the surface ocean. We take advantage of the planktonic foraminifera portion of the metabarcodes to establish to what extent the structure of the surface ocean biota is preserved in sedimentary eDNA. We show that planktonic foraminifera DNA is preserved in a range of marine sediment types, the composition of the recovered eDNA metabarcode is replicable and that both the similarity structure and the diversity pattern are preserved. Our results suggest that sedimentary eDNA could preserve the ecological structure of the entire pelagic community, including non-fossilized taxa, thus opening new avenues for paleoceanographic and paleoecological studies.
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Briggs, Derek E. G., and Amanda J. Kear. "Decay and preservation of polychaetes: taphonomic thresholds in soft-bodied organisms." Paleobiology 19, no. 1 (1993): 107–35. http://dx.doi.org/10.1017/s0094837300012343.
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A series of experiments was carried out to investigate the nature and controls (oxygen, microbial populations, agitation) on the degradation of soft tissues. Decay was monitored in terms of morphological change, weight loss, and change in chemical composition in the polychaete Nereis virens. Polychaetes include a range of tissue types of differing chemical composition and preservation potential: muscle, cuticle, setae, and jaws. Regardless of conditions, all the muscle had broken down and fluid loss through the ruptured cuticle had reduced the carcass to two dimensions within 8 days at 20°C. In most cases some cuticle, in addition to the jaws and setae, remained after 30 days. Where oxygen was completely eliminated, the rate of decay of the more volatile issues was significantly reduced. The degree of both osmotic uptake of water by the carcass and changes in water pH differed depending on whether the system was open or closed to oxygen diffusion. Autolytic and chemical processes are not sufficient to fully degrade the carcass in the absence of bacteria. Where internal bacteria are present, the presence or absence of water column bacteria made little difference to decay rate. Initial degradation (in the first 3 days) affects mainly the lipid fraction and the collagen of the cuticle. Later decay reduces the nonsoluble protein and increases the relative proportion of refractory structural components (tanned chitin and collagen) to more than 95% by day 30. Thus, only the sclerotized tissues are likely to survive beyond 30 days in the absence of early diagenetic mineralization. The sequence of degradation predicted from the relative decay resistance of macromolecules in the sedimentary record (protein → carbohydrate → lipid) is not, therefore, a consistent indicator of the preservation potential of structural tissues which incorporate them.The experiments reveal five stages in the decay of polychaete carcasses; whole/shriveled, flaccid, unsupported gut, cuticle sac, jaws and setae. All are represented in the fossil record. This allows an estimation of how far decay proceeded before it was halted by the fossilization process. The most complete preservations occur in the Cambrian where the Burgess Shale preserves evidence of muscle tissues. Traces of the gut and cuticle are more widely preserved, as at Mazon Creek, Grès à Voltzia, Solnhofen, and Hakel. Preservation varies within Konservat-Lagerstätten. The most common whole body preservation includes only the more recalcitrant tissues, jaws (where present) and setae, with an impression of the body outline. The stage of decay can be used as a taphonomic threshold, to provide an indication of how significantly the diversity of an exceptionally preserved biota is likely to have been reduced by taphonomic loss.
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Palinska, Katarzyna A., Christian F. Thomasius, Jürgen Marquardt, and Stjepko Golubic. "Phylogenetic evaluation of cyanobacteria preserved as historic herbarium exsiccata." International Journal of Systematic and Evolutionary Microbiology 56, no. 10 (October 1, 2006): 2253–63. http://dx.doi.org/10.1099/ijs.0.64417-0.
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Dried herbarium specimens of cyanobacteria (exsiccata) deposited over 100 years ago were analysed and characterized using combined morphological and molecular approaches. Six representative coccoid and filamentous cyanobacteria from two historic collections and a 15-year-old air-dried environmental sample were studied. Morphological features observed by light and electron microscopy were correlated with the results of 16S rRNA gene sequencing. Historic identifications achieved by means of classical morphology could thus be confirmed by extracted, amplified and sequenced 16S rRNA gene fragments. The results of this study open the possibility of providing genotypic characterizations to botanical type specimens, thus reconciling the botanical and bacteriological approaches to the taxonomic treatment of these micro-organisms.
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Ausich, William I., Mark A. Wilson, and Oive Tinn. "Kalana Lagerstätte crinoids: Early Silurian (Llandovery) of central Estonia." Journal of Paleontology 94, no. 1 (May 14, 2019): 131–44. http://dx.doi.org/10.1017/jpa.2019.27.
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AbstractThe Kalana Lagerstätte of early Aeronian (Llandovery, Silurian) age in central Estonia preserves a diverse shallow marine biota dominated by non-calcified algae. This soft-tissue flora and decalcified and calcified crinoids are preserved in situ, in a lens of microlaminated, dolomitized micrite interbedded in a sequence of dolomitized packstones and wackestones. Although the Lagerstätte is dominated by non-calcified algae, crinoids (together with brachiopods and gastropods) are among the most common organisms that were originally comprised of a carbonate skeleton. Two new crinoids are described from this unit, Kalanacrinus mastikae n. gen. n. sp. (large camerate) and Tartucrinus kalanaensis n. gen. n. sp. (small disparid). Interestingly, these two crinoids display contrasting preservation, with the more common large camerate preserved primarily as a decalcified organic residue, whereas the smaller disparid is preserved primarily in calcite. Preservation was assessed using elemental mapping of C, Ca, S, and Si. Columns have the highest portion of Ca, once living soft tissue is indicated by C, S was dispersed as pyrite or associated with organics, and Si is probably associated with clay minerals in the matrix. This new fauna increases our understanding of the crinoid radiation on Baltica following Late Ordovician extinctions.UUID: http://zoobank.org/fb1f98c4-d35a-43f4-aa0d-75e4f8154a13
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Boyd, P., S. Eaton, and J. Magee. "The stability of micro-organisms preserved in LENTICULE discs, demonstrated by repeat sample distributions of the EQUAL Scheme for Indicator Organisms (water microbiology)." Journal of Applied Microbiology 100, no. 2 (February 2006): 272–78. http://dx.doi.org/10.1111/j.1365-2672.2005.02774.x.
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Stanley, George D., and Thomas E. Yancey. "A new late Paleozoic chondrophorine (Hydrozoa, Velellidae) by-the-wind sailor from Malaysia." Journal of Paleontology 60, no. 1 (January 1986): 76–83. http://dx.doi.org/10.1017/s0022336000021533.
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A new medusoid hydrozoan,Plectodiscus malayitesn. sp., belonging to the Family Velellidae is described from Carboniferous rocks of the Malay Peninsula. They are preserved as flattened internal float structures or pneumatophores and are the first examples from this part of the world. In contrast to other occurrences, the great abundance of these sailed organisms suggests that, like extant species ofVelella, these organisms were an important component of the pelagic fauna and were at least locally abundant in open seas of the late Paleozoic.
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Vyse, Ernest. "Comparison of Mitochodrial DNA in Wolves and Coyotes in the Northern Rockies using the Polymerase Chain Reaction Technique." UW National Parks Service Research Station Annual Reports 14 (January 1, 1990): 183–86. http://dx.doi.org/10.13001/uwnpsrc.1990.2937.
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Conservation of biological species, often involves the introduction of organisms from one population to a site in which a population has gone locally extinct. The genetic constitution of the introduced organisms is of immediate concern both in terms of restoring the original population as nearly as possible and to maintain genetic diversity of the introduced organisms. Molecular techniques using protein or isozyme variation and DNA Restriction Fragment Length Polymorphisms (RFLPs), have been used to estimate genetic variation. These techniques are not sensitive enough to make comparisons using limited sample sizes or to analyze samples from preserved specimens of extinct organisms. The advent of the Polymerase Chain Reaction (PCR) (Saiki et al. 1985, 1988) which amplifies small segments of DNA millions of times has extended the application of molecular biology techniques to the genetic comparisons of dried or alcohol preserved museum specimens to extant organisms (Paabo 1989 and Paabo et al. 1989). Application of this technique has allowed the comparison of extinct organisms to each other and to extant species (Thomas et al. 1990). PCR synthesizes many copies of the target sequence greatly increasing the quantity of the amplified sequence. PCR involves denaturing or strand separation of the DNA, hybridization of primers to the denatured single strands and then enzymatic extension of the primers using strands of the sample DNA as a template. This cycle is repeated many times, theoretically amplyfying the target DNA twofold with each cycle. Therefore, after n cycles there is 2 to the nth power as much of the target sequence DNA as there was in the original sample. Essentials of the PCR technique are shown in Figures 1 and 2 taken from Arnheim et al. (1990).
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Kaputkina, Lyudmila M., Vera Prokoshkina, and A. G. Svyazhin. "New Corrosion-Resistant Bactericidal Nitrogen-Containing Steels with Increased Strength." Advances in Science and Technology 76 (October 2010): 72–77. http://dx.doi.org/10.4028/www.scientific.net/ast.76.72.
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The new high-strength stainless steels alloyed by copper and nitrogen and possessing high resistance to corrosion by active micro-organisms in carbon-oxidizing, heterotrophic and sulfate-regenerating bacteria mediums are developed. The introducing of small addition of nitrogen (about 0.22 %) to the corrosion resistant steel С0.5Cr15Ni5Cu2NMoNbTi results in a decrease of adhesive micro-organisms quantity on a sample surface by 8 times, while increasing of nickel content to 9 % results in their decrease only by 2 times. It is supposed that the effect of nitrogen can be related to formation of biocide substances. High copper (Cu = 2.5-5 %) nitrogen-containing cast steels are in austenitic (non-magnetic) condition. Due to a dendritic segregation, the structure of steel corresponds to a natural composite structure, and it is preserved on heating to high temperatures. After cold deformation with up to 85 % reduction, the steels preserve austenitic structure, and its hardness attains a level close to the hardness level of the martensitic structure. The developed corrosion-resistant antimicrobial steels with the increased hardness can be used as a material for the surgical instrument.
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Reamer, Richard, B. R. Dey, and Nitin Thaker. "Cryopreservation of Bacterial Vegetative Cells Used in Antibiotic Assay." Journal of AOAC INTERNATIONAL 78, no. 4 (July 1, 1995): 997–1001. http://dx.doi.org/10.1093/jaoac/78.4.997.
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Abstract A long-term cryopreservation study of vegetative cells of Micrococcus lutea ATCC 9341a, Micrococcus lutea ATCC 15957, and Staphylococcus epidermidis ATCC 12228 cells, used in our antibiotic bioassay procedure, was conducted. The cryoprotective abilities of 1% methylcellulose solution and a 15% glycerol solution at −14°C were determined. More organisms remained viable in 1% methylcellulose than in 15% glycerol. Overall survival of Staphylococcus epidermidis ATCC 12228 after 365 days was 1.5 logs lower than the other 2 organisms. The sensitivity and the resistance of the preserved organisms to various antibiotics did not change: The methodology is simple and inexpensive, saves analytical time, and avoids risk of contamination and sudden loss of a well-characterized culture.
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Malinky, John M., Robert M. Linsley, and Ellis L. Yochelson. "Taxonomic revision of Hyolitha from the middle Paleozoic of North America." Journal of Paleontology 61, no. 6 (November 1987): 1173–86. http://dx.doi.org/10.1017/s0022336000029541.
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Collection of over a dozen specimens of Hyolithes aclis Hall from the Middle Devonian of New York indicates that this species belongs to a new genus, Hallotheca, to which the species Hyolithes halli (Hall) is also assigned. However, the generic assignments of the Silurian species Hyolithes cliftonensis Foerste and the Devonian species H. centennialis Barrett, H. ceratophilus Clarke, H. neapolis Clarke, and H. triliratus Hall are uncertain because of poor preservation of their type specimens. Use of these names should be confined to the types until better preserved topotypes become available. Finally, H. cooperi (Williams) consists of organisms of uncertain affinities, and the type of H. principalis Hall may be a fragment of Devonian sandstone rather than an organism.
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Kaasalainen, Ulla, Jochen Heinrichs, Matthew A. M. Renner, Lars Hedenäs, Alfons Schäfer-Verwimp, Gaik Ee Lee, Michael S. Ignatov, Jouko Rikkinen, and Alexander R. Schmidt. "A Caribbean epiphyte community preserved in Miocene Dominican amber." Earth and Environmental Science Transactions of the Royal Society of Edinburgh 107, no. 2-3 (June 2016): 321–31. http://dx.doi.org/10.1017/s175569101700010x.
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ABSTRACTFossil tree resins preserve a wide range of animals, plants, fungi and microorganisms in microscopic fidelity. Fossil organisms preserved in an individual piece of amber lived at the same time in Earth history and mostly even in the same habitat, but they were not necessarily parts of the same interacting community. Here, we report on an in situ preserved corticolous community from a piece of Miocene Dominican amber which is composed of a lichen, a moss and three species of leafy liverworts. The lichen is assigned to the extant genus Phyllopsora (Ramalinaceae, Lecanoromycetes) and is described as P.magna Kaasalainen, Rikkinen & A. R. Schmidt sp. nov. The moss, Aptychellites fossilis Schäf.-Verw., Hedenäs, Ignatov & Heinrichs gen. & sp. nov., closely resembles the extant genus Aptychella of the family Pylaisiadelphaceae. The three leafy liverworts comprise the extinct Lejeuneaceae species Cheilolejeunea antiqua (Grolle) Ye & Zhu, 2010 and Lejeunea miocenica Heinrichs, Schäf.-Verw., M. A. M. Renner & G. E. Lee sp. nov. and the extinct Radulaceae species Radula intecta M. A. M. Renner, Schäf.-Verw. & Heinrichs sp. nov. The presence of five associated extinct cryptogam species, four of which belong to extant genera, further substantiates the notion of a stasis in morphotype diversity, but a certain turnover of species, in the Caribbean since the early Miocene.
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Putman, Nathan F., and Ruoying He. "Tracking the long-distance dispersal of marine organisms: sensitivity to ocean model resolution." Journal of The Royal Society Interface 10, no. 81 (April 6, 2013): 20120979. http://dx.doi.org/10.1098/rsif.2012.0979.
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Ocean circulation models are widely used to simulate organism transport in the open sea, where challenges of directly tracking organisms across vast spatial and temporal scales are daunting. Many recent studies tout the use of ‘high-resolution’ models, which are forced with atmospheric data on the scale of several hours and integrated with a time step of several minutes or seconds. However, in many cases, the model's outputs that are used to simulate organism movement have been averaged to considerably coarser resolutions (e.g. monthly mean velocity fields). To examine the sensitivity of tracking results to ocean circulation model output resolution, we took the native model output of one of the most sophisticated ocean circulation models available, the Global Hybrid Coordinate Ocean Model, and averaged it to commonly implemented spatial and temporal resolutions in studies of basin-scale dispersal. Comparisons between simulated particle trajectories and in situ near-surface drifter trajectories indicated that ‘over averaging’ model output yields predictions inconsistent with observations. Further analyses focused on the dispersal of juvenile sea turtles indicate that very different inferences regarding the pelagic ecology of these animals are obtained depending on the resolution of model output. We conclude that physical processes occurring at the scale of days and tens of kilometres should be preserved in ocean circulation model output to realistically depict the movement marine organisms and the resulting ecological and evolutionary processes.
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Trevisan, Bruna, Daniel M. C. Alcantara, Denis Jacob Machado, Fernando P. L. Marques, and Daniel J. G. Lahr. "Genome skimming is a low-cost and robust strategy to assemble complete mitochondrial genomes from ethanol preserved specimens in biodiversity studies." PeerJ 7 (September 13, 2019): e7543. http://dx.doi.org/10.7717/peerj.7543.
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Global loss of biodiversity is an ongoing process that concerns both local and global authorities. Studies of biodiversity mainly involve traditional methods using morphological characters and molecular protocols. However, conventional methods are a time consuming and resource demanding task. The development of high-throughput sequencing (HTS) techniques has reshaped the way we explore biodiversity and opened a path to new questions and novel empirical approaches. With the emergence of HTS, sequencing the complete mitochondrial genome became more accessible, and the number of genome sequences published has increased exponentially during the last decades. Despite the current state of knowledge about the potential of mitogenomics in phylogenetics, this is still a relatively under-explored area for a multitude of taxonomic groups, especially for those without commercial relevance, non-models organisms and with preserved DNA. Here we take the first step to assemble and annotate the genomes from HTS data using a new protocol of genome skimming which will offer an opportunity to extend the field of mitogenomics to under-studied organisms. We extracted genomic DNA from specimens preserved in ethanol. We used Nextera XT DNA to prepare indexed paired-end libraries since it is a powerful tool for working with diverse samples, requiring a low amount of input DNA. We sequenced the samples in two different Illumina platform (MiSeq or NextSeq 550). We trimmed raw reads, filtered and had their quality tested accordingly. We performed the assembly using a baiting and iterative mapping strategy, and the annotated the putative mitochondrion through a semi-automatic procedure. We applied the contiguity index to access the completeness of each new mitogenome. Our results reveal the efficiency of the proposed method to recover the whole mitogenomes of preserved DNA from non-model organisms even if there are gene rearrangement in the specimens. Our findings suggest the potential of combining the adequate platform and library to the genome skimming as an innovative approach, which opens a new range of possibilities of its use to obtain molecular data from organisms with different levels of preservation.
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Edwards, Dianne, Paul Kenrick, and Liam Dolan. "History and contemporary significance of the Rhynie cherts—our earliest preserved terrestrial ecosystem." Philosophical Transactions of the Royal Society B: Biological Sciences 373, no. 1739 (December 18, 2017): 20160489. http://dx.doi.org/10.1098/rstb.2016.0489.
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The Rhynie cherts Unit is a 407 million-year old geological site in Scotland that preserves the most ancient known land plant ecosystem, including associated animals, fungi, algae and bacteria. The quality of preservation is astonishing, and the initial description of several plants 100 years ago had a huge impact on botany. Subsequent discoveries provided unparalleled insights into early life on land. These include the earliest records of plant life cycles and fungal symbioses, the nature of soil microorganisms and the diversity of arthropods. Today the Rhynie chert (here including the Rhynie and Windyfield cherts) takes on new relevance, especially in relation to advances in the fields of developmental genetics and Earth systems science. New methods and analytical techniques also contribute to a better understanding of the environment and its organisms. Key discoveries are reviewed, focusing on the geology of the site, the organisms and the palaeoenvironments. The plants and their symbionts are of particular relevance to understanding the early evolution of the plant life cycle and the origins of fundamental organs and tissue systems. The Rhynie chert provides remarkable insights into the structure and interactions of early terrestrial communities, and it has a significant role to play in developing our understanding of their broader impact on Earth systems. This article is part of a discussion meeting issue ‘The Rhynie cherts: our earliest terrestrial ecosystem revisited’.
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Feldman, Howard R., Christopher G. Maples, Allen W. Archer, Ronald R. West, and Erik P. Kvale. "An estuarine model for Pennsylvanian Lagerstätten." Paleontological Society Special Publications 6 (1992): 95. http://dx.doi.org/10.1017/s2475262200006559.
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Estuaries were important sites of deposition throughout most of the Pennsylvanian in the Midcontinent. Modern estuaries typically occur within flooded river valleys where marine and fresh waters mix. Characteristic estuarine circulation results in locally high rates of deposition of muddy sediment that can lead to good preservation of fossils. Several Pennsylvanian conservat-Lagerstätten are best interpreted as having formed within ancient estuaries. Three types of estuarine deposits have been identified. Type 1 estuarine systems are large-scale transgressive systems that start with fluvial sands overlying an erosional surface. This is overlain successively by middle-estuarine laminated mudstone, and finally marine mudstone and shale. Well-preserved fossils occur in laminated mudstones and siltstones. This sequence may include within in it type 3 estuarine Lagerstätten. An example is the Douglas Group (Missourian, Kansas).Type 2 estuarine Lagerstätten consist of thin estuarine deposits confined to narrow paleochannels. This includes the Garnett (Missourian, Kansas) and Hamilton (Virgilian, Kansas) deposits, both of which contain articulated vertebrates and well-preserved plants. Both channels are filled with mixed siliciclastic and carbonate sediments. Fine grained facies from which the best fossils are recovered in both contain evidence of tidal deposition, although tidal rhythmicity is best developed in the Hamilton channel. Plant assemblages in both are dominated by the conifer Walchia, probably indicating a relatively dry climate.Type 3 estuarine Lagerstätten consist of thick gray-shale wedges that overlie coals. The best-known example is the Francis Creek Shale (Desmoinesian, Illinois). A relatively wet climate is indicated by abundant fern and seed-fern foliage. Laminations in shale facies commonly show well-developed tidal rhythmicity. A typical stratigraphic succession starts with laminated shale overlying coal. This grades upwards into flaser and lenticular bedding to ripple and then large-scale cross-bedded sandstone. Upright trees rooted in the coal indicate rapid burial. Well-preserved fossils are recovered from early-diagenetic siderite concretions from the laminated shale.Preservation of fossils is best in laminated mudstones deposited in middle-estuarine environments where conditions are ideal for good preservation. In all cases so far studied the zones of best preservation are well laminated and have sparse (if any) burrows and sessile benthic fossils. Most of the well-preserved organisms are terrestrial, nektonic, or at least mobile. Brackish and fluctuating salinities restricted scavenging and burrowing organisms that may scatter skeletons. High turbidity and deposition rate may have further discouraged many organisms. Matching bedding rhythmicity with tidal cycles allows calculation of depositional rates of 1 cm or more of compacted sediment per 2-week neap-spring tidal cycle. This is consistent with the high rates of deposition known from modern tidal environments. High depositional rates assured that any organism that fell to the sea floor was buried in a few hours to a few days. Once buried anoxic conditions established around decaying carcasses may have led to early mineralization.
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Schultze, Hans-Peter, Christopher G. Maples, and Christopher R. Cunningham. "The Hamilton Konservat-Lagerstätte: Stephanian terrestrial biota in a marginal-marine setting." Earth and Environmental Science Transactions of the Royal Society of Edinburgh 84, no. 3-4 (1993): 443–51. http://dx.doi.org/10.1017/s0263593300006246.
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ABSTRACTThe Stephanian Konservat-Lagerstätte of Hamilton, Kansas, deposited in a marine-estuarine environment preserves a mixture of terrestrial, fresh-water, and marine fossil organisms. The marine component is the most diverse taxonomically, whereas one ostracod species, commonly interpreted as a fresh-water form, together with vascular plant debris dominates volumetrically. Well-preserved terrestrial and aquatic vertebrates and arthropods were embedded in rapidly deposited calcareous mud conducive to microbial early-diagenesis of vertebrate soft tissues in a tidal estuarine setting. Many vertebrate fossils show no evidence of preburial decay or disarticulation. Dark-coloured body silhouettes (‘skin preservation’) are composed of calcitic bacteria, calcite crystals and organic material, and have been interpreted to reflect preservation under saline conditions. The aquatic vertebrates had a broader tolerance of salinity than today. The fishes were perhaps migratory (anadromous or catadromous), and some used the estuarine environment for spawning. The tetrapods (dissorophid amphibians) retained their tolerance to salinity from their marine ancestors and were able to spawn in near-shore environments. The terrestrial biota was dominated by the conifer Walchia and was subjected to forest fires, as evidenced by preserved charcoal fragments.
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Church, Stephen B. "A new Lower Ordovician species of Calathium, and skeletal structure of western Utah calathids." Journal of Paleontology 65, no. 4 (July 1991): 602–10. http://dx.doi.org/10.1017/s0022336000030699.
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Conical and vase-shaped calathids are found in the Lower Ordovician Fillmore Formation of western Utah associated with intraformational conglomerates and small patch reefs. Calathium yersini n. sp. exhibits patterns of both the inner and outer walls of calathid two-wall construction. The broadly annulate walls are constructed from meroms with fused proximal merom feet forming the inner wall. The reticulate-patterned outer wall is formed by interlocking stellate ribs at the distal end of each merom. Latitudinal (horizontal) ribs interlock adjacent merom ribs side by side at the tips of ribs while meridional (vertical) ribs overlap merom shaft to merom shaft. Inner and outer walls are perforate. Pore-canal casts preserved in silicified molds suggest an exit and entrance current circulation for inner and outer wall pores. Upper ends of the calathids are not preserved, but an open cup is interpreted from infill material and encrustation of the interior cup wall by epibionts. Epibionts commonly encrust and thicken Calathium outer walls, with the cyanobacterium Girvanella as the dominant encrusting organism. Calathium yersini n. sp., among the earliest of receptaculitids, has a morphology suitable for water circulation consistent with that of filter-feeding organisms.
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von Bitter, Peter H., Mark A. Purnell, Denis K. Tetreault, and Christopher A. Stott. "Eramosa Lagerstätte—Exceptionally preserved soft-bodied biotas with shallow-marine shelly and bioturbating organisms (Silurian, Ontario, Canada)." Geology 35, no. 10 (2007): 879. http://dx.doi.org/10.1130/g23894a.1.
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SALAMON, MARIUSZ A., JIH-PAI LIN, PIOTR DUDA, PRZEMYSŁAW GORZELAK, WILLIAM I. AUSICH, and TATSUO OJI. "PALEOENVIRONMENTAL AND BIOSTRATIGRAPHIC IMPLICATIONS OF ECHINODERM OSSICLES TRAPPED WITHIN BURMESE AMBER." PALAIOS 34, no. 12 (December 23, 2019): 652–56. http://dx.doi.org/10.2110/palo.2019.084.
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ABSTRACT Marine organisms are uncommonly preserved in amber. Recently, they were reported to be associated with Burmese amber. However, most of specimens from previous reports were preserved on the amber surface or within the sediment surrounding the amber. Based on X-ray tomography and thin-section optical microscopy of Burmese amber, we report here the first genuine and unambiguous evidence of inclusion of crinoid ossicles preserved in the fossil resin. Preservation of this exclusively marine group in amber gives insights into the paleoenvironment of the crinoid-amber association and provides additional evidence to support previous observations of shallow-water stalked crinoids from the mid-Cretaceous, when many stalked crinoids started to shift offshore due to increased predation pressure during the Mesozoic Marine Revolution. Crinoid remains, represented by disarticulated stem and arm ossicles assignable to Isocrinus cf. legeri (Repelin), point to a mid-Cretaceous age for the Burmese amber and support some previous hypotheses suggesting a close proximity between the resin-producing trees and seawater.
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Sumrall, Colin D., and Christopher A. Brochu. "Viewing Paleobiology Through the Lens of Phylogeny." Paleontological Society Papers 14 (October 2008): 165–83. http://dx.doi.org/10.1017/s1089332600001674.
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Phylogenetic systematics is the dominant form of taxonomy for most biologists, vertebrate paleontologists and to a lesser degree invertebrate paleontologists. Taxonomies are based strictly on evolutionary relationships with traits of organisms such as morphology and sequence data, being used as evidence for relationships. Two types of taxa are recognized - species that may be monophyletic or paraphyletic and clades that must be monophyletic. The phylogeny is an hypothesis of relationships that can be used to illuminate many areas of paleobiology including: unsampled morphology from incompletely preserved organisms, temporal distribution of taxa, and evolutionary patterns and mechanisms. Consequently, an understanding of phylogenetic assumptions, experimental design, and language are critical for the incorporation of phylogenetic taxonomies into larger studies of paleobiology.
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Evans, Scott D., Ian V. Hughes, James G. Gehling, and Mary L. Droser. "Discovery of the oldest bilaterian from the Ediacaran of South Australia." Proceedings of the National Academy of Sciences 117, no. 14 (March 23, 2020): 7845–50. http://dx.doi.org/10.1073/pnas.2001045117.
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Analysis of modern animals and Ediacaran trace fossils predicts that the oldest bilaterians were simple and small. Such organisms would be difficult to recognize in the fossil record, but should have been part of the Ediacara Biota, the earliest preserved macroscopic, complex animal communities. Here, we describeIkaria wariootiagen. et sp. nov. from the Ediacara Member, South Australia, a small, simple organism with anterior/posterior differentiation. We find that the size and morphology ofIkariamatch predictions for the progenitor of the trace fossilHelminthoidichnites—indicative of mobility and sediment displacement. In the Ediacara Member,Helminthoidichnitesoccurs stratigraphically below classic Ediacara body fossils. Together, these suggest thatIkariarepresents one of the oldest total group bilaterians identified from South Australia, with little deviation from the characters predicted for their last common ancestor. Further, these trace fossils persist into the Phanerozoic, providing a critical link between Ediacaran and Cambrian animals.
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Strullu-Derrien, C., P. Kenrick, J. P. Rioult, and D. G. Strullu. "Evidence of parasitic Oomycetes (Peronosporomycetes) infecting the stem cortex of the Carboniferous seed fern Lyginopteris oldhamia." Proceedings of the Royal Society B: Biological Sciences 278, no. 1706 (September 15, 2010): 675–80. http://dx.doi.org/10.1098/rspb.2010.1603.
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Thin sections of petrified fossils made during the latter part of the nineteenth and early twentieth centuries to investigate the internal tissue systems of plants now provide an important new source of information on associated micro-organisms. We report a new heterokont eukaryote ( Combresomyces williamsonii sp. nov.) based on exquisitely preserved fossil oogonia, antheridia and hyphae from the Carboniferous (Pennsylvanian: Bashkirian stage) of UK. The structure of the oogonia and antheridia and features observed within the hyphae demonstrate a relationship with Oomycetes (Peronosporomycetes). The fossil micro-organism was documented in situ in petrified stem cortex and rootlets of the extinct seed fern Lyginopteris oldhamia (Pteridospermales). The main observed features point towards a pythiaceous Oomycete but links to biotrophic Albuginales or Peronosporaceae cannot be ruled out owing to the observation of a possible haustorium. Our study provides the earliest evidence for parasitism in Oomycetes.
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Roy, Stéphane, Alley E. Watada, William S. Conway, Eric F. Erbe, and William P. Wergin. "Low-temperature Scanning Electron Microscopy of Frozen Hydrated Apple Tissues and Surface Organisms." HortScience 29, no. 4 (April 1994): 305–9. http://dx.doi.org/10.21273/hortsci.29.4.305.
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Frozen hydrated buds and epicarp of `Golden Delicious' apple (Malus domestica Borkh.) were observed with a low-temperature, field emission scanning electron microscope (SEM). In addition to observing surface features of these specimens, holders were modified to observe fractured specimens. A modified hinged holder retained both halves of a fractured specimen for examination of the complementary faces of frozen hydrated tissues. Low-temperature SEM avoided artifacts, such as extraction, solubilization, and shrinkage, which are normally encountered with chemical fixation, dehydration, and drying, respectively. The technique allowed observations of well-preserved frozen hydrated structures, such as the platelets of epicuticular wax; loosely associated organisms on plant surfaces, such as spider-mite eggs; delicate structures, such as fungal hyphae; and partially hydrated tissues, such as fruit epicarp and winter bud scales.
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SU, YOU NING. "A simple and quick method of displaying liquid-preserved morphological structures for microphotography." Zootaxa 4208, no. 6 (December 21, 2016): 592. http://dx.doi.org/10.11646/zootaxa.4208.6.6.
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Stabilising microstructures and small organisms for microphotography can be frustrating. If it is desired to take photographs in water from structures just cleared in potassium hydroxide, some sort of stabilisation is necessary otherwise the structures drift. Similarly, specimens taken from glycerol or alcohol, or those placed in alcohol, drift even more as the alcohol evaporates. Bits of crushed coverslip, glass beads, micro pins and dobs of Vaseline® have all been used to help keep the structures in place. In an attempt to solve the problem of “drifting genitalia” a simple solution was inadvertently discovered. A method used for whole insects by Sam Droege and his colleagues of the United States Geological Survey (Droege 2016; USGS Bee Inventory and Monitoring Lab 2016) was adapted for use with insect genitalia.
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Ding, Rubai. "3-D analysis of spindle structure in the yeast, Schizosaccharomyces pombe (S. pombe)." Proceedings, annual meeting, Electron Microscopy Society of America 50, no. 1 (August 1992): 902–3. http://dx.doi.org/10.1017/s0424820100124914.
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Mitosis in yeast is currently the subject of many genetic and molecular biological studies, but structural work on yeast mitosis has been comparatively limited due in part to the difficulty of obtaining well preserved samples. A structural study of yeast spindles is important because yeast are unicellular, eukaryotic organisms that may provide a simple model of mitosis. S. pombe was chosen because much is known about its molecular biology, and there are several mutants that affect its mitosis. Here we describe a method for obtaining well preserved samples of S. pombe during mitosis using high pressure freezing. This method has been used together with EM of serial sections and computer facilitated reconstruction to build three dimensional (3-D) models of spindle structures.
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Narbonne, Guy M., and Robert W. Dalrymple. "Taphonomy and ecology of deep-water Ediacaran organisms from northwestern Canada." Paleontological Society Special Publications 6 (1992): 219. http://dx.doi.org/10.1017/s2475262200007796.
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Although most occurrences of Ediacaran fossils are from shallow-shelf deposits, taxonomically-similar assemblages have recently been described from a 2.5 km-thick succession of dark mudstones and turbiditic sandstones in the Windermere Supergroup of the Mackenzie Mountains, northwestern Canada. The paleogeographic position (20-40 km seaward of the shelf edge), abundant evidence of mass flow, and the complete absence of in situ shallow-water features imply that deposition took place on a slope considerably below storm wave-base. Ediacaran fossils were not observed in axial trough deposits (lower parts of the Twitya and Sheepbed formations), but megafossils occur sporadically in lower to middle slope deposits higher in the same formations. Megafossils and trace fossils are present in upper slope settings (Blueflower Formation) at the top of the Ediacaran succession. The megafossil assemblage varies stratigraphically, but in all formations is dominated by discoid forms (e.g. Cyclomedusa, Ediacaria, Nimbia); frondose forms and vendomiids are very rare.Megafossils are preserved mainly as positive features on the soles of thin turbidite beds. Most fossiliferous beds begin with the rippled layer of the turbidite (Tc), but a few begin with the graded (Ta) or parallel-laminated (Tb) layer. Consistent orientation and high relief of individuals, evidence of mutual deformation during growth of adjacent organisms, and other taphonomic features imply that virtually all of the taxa represent benthic polypoid and frond-like organisms (not jellyfish). Slump structures occur commonly in the sandstone fill of fossils, suggesting that many of the organisms were buried alive by the turbidite and later decomposed. Other individuals, even on the same bedding plane, exhibit graded to laminated fill identical to that of the overlying turbidite bed, indicating that the depressions on the sea bottom produced by these individuals were empty at the time of turbidite deposition. Escape structures are absent, suggesting that the Ediacaran organisms were not capable of burrowing up through even thin layers of sand.Ediacaran megafossils are invariably preserved on black, wrinkled surfaces similar to those elsewhere interpreted as microbial mats. Molding of delicate features (including tentacles), preservation of open molds as negative epireliefs, and sedimentological evidence of considerable cohesion of these surfaces relative to the underlying turbiditic muds (Td,e) supports this interpretation, and suggests that microbial mats were as important in the preservation of these deep-water Ediacara faunas as they were in their shallow-water equivalents. The presence of the wrinkled mats and their associated Ediacaran fossils almost exclusively in the pyritic intervals of the succession suggests that both may have lived under exaerobic conditions in this deep-water setting.
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Bomfleur, Benjamin, Thomas Mörs, Marco Ferraguti, Marcelo A. Reguero, and Stephen McLoughlin. "Fossilized spermatozoa preserved in a 50-Myr-old annelid cocoon from Antarctica." Biology Letters 11, no. 7 (July 2015): 20150431. http://dx.doi.org/10.1098/rsbl.2015.0431.
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The origin and evolution of clitellate annelids—earthworms, leeches and their relatives—is poorly understood, partly because body fossils of these delicate organisms are exceedingly rare. The distinctive egg cases (cocoons) of Clitellata, however, are relatively common in the fossil record, although their potential for phylogenetic studies has remained largely unexplored. Here, we report the remarkable discovery of fossilized spermatozoa preserved within the secreted wall layers of a 50-Myr-old clitellate cocoon from Antarctica, representing the oldest fossil animal sperm yet known. Sperm characters are highly informative for the classification of extant Annelida. The Antarctic fossil spermatozoa have several features that point to affinities with the peculiar, leech-like ‘crayfish worms' (Branchiobdellida). We anticipate that systematic surveys of cocoon fossils coupled with advances in non-destructive analytical methods may open a new window into the evolution of minute, soft-bodied life forms that are otherwise only rarely observed in the fossil record.
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Day, M. F. C., H. Hewson, M. Fagg, J. Doran, J. Turnbull, J.Ilic, S. Jeffrey, et al. "The Biological Collections in CSIRO: a National Heritage?" Historical Records of Australian Science 15, no. 1 (2004): 1. http://dx.doi.org/10.1071/hr04002.
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From the organization's earliest days, several Divisions of CSIRO have assembled substantial collections of biological species. These include a wide variety of plants and animals. Some collections consist of live organisms, some of preserved material. The origins and the functions of the collections vary; most of them now contain material of considerable value. Their history is intriguing, and their future has continued to be a question of importance.
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Tomašových, Adam, Paolo G. Albano, Tomáš Fuksi, Ivo Gallmetzer, Alexandra Haselmair, Michał Kowalewski, Rafał Nawrot, Vedrana Nerlović, Daniele Scarponi, and Martin Zuschin. "Ecological regime shift preserved in the Anthropocene stratigraphic record." Proceedings of the Royal Society B: Biological Sciences 287, no. 1929 (June 17, 2020): 20200695. http://dx.doi.org/10.1098/rspb.2020.0695.
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Palaeoecological data are unique historical archives that extend back far beyond the last several decades of ecological observations. However, the fossil record of continental shelves has been perceived as too coarse (with centennial-millennial resolution) and incomplete to detect processes occurring at yearly or decadal scales relevant to ecology and conservation. Here, we show that the youngest (Anthropocene) fossil record on the northern Adriatic continental shelf provides decadal-scale resolution that accurately documents an abrupt ecological change affecting benthic communities during the twentieth century. The magnitude and the duration of the twentieth century shift in body size of the bivalve Corbula gibba is unprecedented given that regional populations of this species were dominated by small-size classes throughout the Holocene. The shift coincided with compositional changes in benthic assemblages, driven by an increase from approximately 25% to approximately 70% in median per-assemblage abundance of C. gibba . This regime shift increase occurred preferentially at sites that experienced at least one hypoxic event per decade in the twentieth century. Larger size and higher abundance of C. gibba probably reflect ecological release as it coincides with an increase in the frequency of seasonal hypoxia that triggered mass mortality of competitors and predators. Higher frequency of hypoxic events is coupled with a decline in the depth of intense sediment mixing by burrowing benthic organisms from several decimetres to less than 20 cm, significantly improving the stratigraphic resolution of the Anthropocene fossil record and making it possible to detect sub-centennial ecological changes on continental shelves.
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Lautenschlager, Stephan. "DIGITAL RECONSTRUCTION OF SOFT-TISSUE STRUCTURES IN FOSSILS." Paleontological Society Papers 22 (September 2016): 101–17. http://dx.doi.org/10.1017/scs.2017.10.
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AbstractIn the last two decades, advances in computational imaging techniques and digital visualization have created novel avenues for the study of fossil organisms. As a result, paleontology has undergone a shift from the pure study of physically preserved bones and teeth, and other hard tissues, to using virtual computer models to study specimens in greater detail, restore incomplete specimens, and perform biomechanical analyses. The rapidly increasing application of these techniques has further paved the way for the digital reconstruction of soft-tissue structures, which are rarely preserved or otherwise available in the fossil record. In this contribution, different types of digital soft-tissue reconstructions are introduced and reviewed. Provided examples include methodological approaches for the reconstruction of musculature, endocranial components (e.g., brain, inner ear, and neurovascular structures), and other soft tissues (e.g., whole-body and life reconstructions). Digital techniques provide versatile tools for the reconstruction of soft tissues, but given the nature of fossil specimens, some limitations and uncertainties remain. Nevertheless, digital reconstructions can provide new information, in particular if interpreted in a phylogenetically grounded framework. Combined with other digital analytical techniques (e.g., finite element analysis [FEA], multibody dynamics analysis [MDA], and computational fluid dynamics [CFD]), soft-tissue reconstructions can be used to elucidate the paleobiology of extinct organisms and to test competing evolutionary hypotheses.
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Gold, David A. "The slow rise of complex life as revealed through biomarker genetics." Emerging Topics in Life Sciences 2, no. 2 (June 29, 2018): 191–99. http://dx.doi.org/10.1042/etls20170150.
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Organic molecules preserved in ancient rocks can function as ‘biomarkers’, providing a unique window into the evolution of life. While biomarkers demonstrate intriguing patterns through the Neoproterozoic, it can be difficult to constrain particular biomarkers to specific organisms. The goal of the present paper is to demonstrate the utility of biomarkers when we focus less on which organisms produce them, and more on how their underlying genetic pathways evolved. Using this approach, it becomes clear that there are discrepancies between the biomarker, fossil, and molecular records. However, these discrepancies probably represent long time periods between the diversification of eukaryotic groups through the Neoproterozoic and their eventual rise to ecological significance. This ‘long fuse’ hypothesis contrasts with the adaptive radiations often associated with the development of complex life.
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Reshetnyk, M., V. Gritsenko, and A. Martyshyn. "EVIDENCE OF THE BACTERIAL NATURE OF THE WENDOMAN ORGANISMS NEMIANA SIMPLEX." Visnyk of Taras Shevchenko National University of Kyiv. Geology, no. 1 (92) (2021): 6–10. http://dx.doi.org/10.17721/1728-2713.92.01.
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Nemiana simplex were found in Vendian deposits of Transnistria a hundred years ago. They are present in layers with determined age of 557 million. There are fourteen places with such fossils in the world. Nemiana simplex are the markers of all deposits of the Yampilian layers of the Vendian. We need to take a closer look at the Nemiana simplex analysis, as their exact nature has not been determined so far. They were considered to be raindrops, jellyfish or polyps, which is not justified. The large fluctuations in their size, and the peculiarities of their location relative to each other, indicate their biological nature. Usually, these fossils have the appearance of convex lenticular projections on the lower surfaces of sandstone layers 1-40 mm in size. They do not have any signs of the mouth opening and any other structural elements of the intestinal cavity. There are similar Nemiana prints of Beltanella and Beltanelliformis. Beltanelliformis has recently been recognized as "benthic colonies of cyanobacteria" by organic petrified films, sometimes preserved on their prints. Nemiana's prints do not contain such petrified films on the surface of the nuclei, so one cannot ascertain from biochemical analysis what they were during lifetime. Nemiana is not similar to Beltanelliformis: the distinctive features of Beltanelliformis are the absence of pronounced convex casts and concentric folds along the contour of flat prints. Although there are differences in the shape of the prints, Beltanelliformis and Nemiana are the most similar among the Vendian fossils. Given that Beltanelliformis are reflections of cyanodacetrians, we can assume that Nemiana is also a cyanobacterium. The print sizes of Nemiana simplex Palij are close to the size of modern spherical colonies of cyanobacteria Nostoc prunum. Large colonies of modern Nostoc prunum are often surrounded by smaller colonies, and in Nemiana simplex prints large prints together with smaller ones create a "cluster". Such clusters consist of entire "settlements". Nostoc colonies can appear very close to the main colony, creating "kidneys", with Nemiana simplex prints showing such "buds". Colonies of Nostoc cyanobacteria are widespread in fresh water, less often in the seas; Nemiana is found in deposits of huge deltas, that is, also in significantly desalinated seawater. It is likely that such Nostoc forms existed earlier than 550 million years ago and are still preserved in the Nemiana simplex prints on the Yampilian sandstones. Nemiana simplex prints are found on all modern continents, which indicates the conjugacy of the sea basins and the homogeneous climatic conditions on the planet during the Upper Vendee. The restoration of "settlements" of Nemiana simplex, which were systematically covered with sandy sediments, indicates their high ability to survive and the variability of reproduction.
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Miller, Kelly B., and Sara H. Lubkin. "Calicovatellus petrodytes, a new genus and species of primitive vatelline diving beetle (Coleoptera: Dytiscidae: Hydroporinae: Vatellini) from the Miocene Barstow Formation, southern California, USA." Journal of Paleontology 75, no. 4 (July 2001): 890–94. http://dx.doi.org/10.1017/s0022336000016991.
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Relatively few fossil dytiscids have been described. This is unfortunate since fossils can provide useful phylogenetic and evolutionary information including unique character combinations not present in extant taxa and minimum ages for divergences. However, even when fossils are found, important characters are often not visible since they may be poorly preserved or obscured. The fossil insects present in calcareous nodules from the Miocene Barstow Formation of the Calico Mountains in Southern California are exceptionally well preserved (Palmer, 1957). The original organisms are replaced by silica or other minerals and when the nodules are dissolved in formic acid, the three-dimensional fossil can be retrieved from the resulting residue. These nodules have yielded a wide variety of fossils, including larvae of the dytiscid species Schistomerus californense Palmer, 1957 and numerous other terrestrial and fresh-water arthropods (Palmer, 1957). The purposes of this paper are to describe a new dytiscid genus and species from an exceptionally well-preserved specimen from the Barstow Formation and to present a hypothesis of the phylogenetic placement of the new taxon.
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Liang, Yan, Olle Hints, Peng Tang, Chenyang Cai, Daniel Goldman, Jaak Nõlvak, Erik Tihelka, Ke Pang, Joseph Bernardo, and Wenhui Wang. "Fossilized reproductive modes reveal a protistan affinity of Chitinozoa." Geology 48, no. 12 (August 19, 2020): 1200–1204. http://dx.doi.org/10.1130/g47865.1.
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Abstract Reproduction is a key aspect of evolution, but the process is rarely preserved in the fossil record. Organisms fortuitously preserved undergoing reproduction provide an exceptional window illuminating the biology of extinct taxa, especially those with unknown phylogenetic position. Here we report exceptional specimens of chitinozoans (enigmatic Paleozoic organic-walled microfossils) preserved as “test-in-test” morphology, which have previously been interpreted as teratological forms. Application of advanced imaging techniques on newly recovered and reexamined Ordovician materials enabled documentation of critical morphological details of the test’s inner ultrastructure for the first time. The results show that the newly observed spongy material and dendritic structure on or inside the chitinozoan test as well as the test wall itself are all made of clustered rounded spherical particles. Morphological details suggest that those specimens represent key stages of new asexual reproductive strategies, hitherto undescribed, which produce either one or several offspring at a time. This observation challenges the prevailing hypothesis that chitinozoans are eggs of cryptic extinct marine metazoans. Instead, it is more plausible that they represent a new isolated group of protists.
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Taylor, G. M., G. R. Stewart, M. Cooke, S. Chaplin, S. Ladva, J. Kirkup, S. Palmer, and D. B. Young. "Koch's Bacillus – a look at the first isolate of Mycobacterium tuberculosis from a modern perspective." Microbiology 149, no. 11 (November 1, 2003): 3213–20. http://dx.doi.org/10.1099/mic.0.26654-0.
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Using molecular methods the authors have studied mycobacterial DNA taken from a 19th century victim of tuberculosis. This was the case from which Robert Koch first isolated and cultured the organism responsible for tuberculosis. The mycobacteria were preserved within five glass culture tubes as abundant bacterial colonies on slopes of a gelatinous culture medium of unknown composition. Originally presented by Koch to surgical laryngologist Walter Jobson Horne in London in 1901, the relic has, since 1983, been in the care of the Royal College of Surgeons of England. Light and electron microscopy established the presence of acid-fast mycobacteria but showed that morphological preservation was generally poor. Eleven different genomic loci were successfully amplified by PCR. This series of experiments confirmed that the organisms were indeed Mycobacterium tuberculosis and further showed that the original strain was in evolutionary terms similar to ‘modern’ isolates, having undergone the TB D1 deletion. Attempts to determine the genotypic group of the isolate were only partially successful, due in part to the degraded nature of the DNA and possibly also to a truncation in the katG gene, which formed part of the classification scheme. Spoligotyping resulted in amplification of DR spacers consistent with M. tuberculosis but with discrepancies between independent extracts, stressing the limitations of this typing method when applied to poorly preserved material.
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Moczydłowska, Małgorzata, Frances Westall, and Frédéric Foucher. "Microstructure and Biogeochemistry of the Organically Preserved Ediacaran MetazoanSabellidites." Journal of Paleontology 88, no. 2 (March 2014): 224–39. http://dx.doi.org/10.1666/13-003.
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Metazoans (multicellular animals) evolved during the Ediacaran Period as shown by the record of their imprints, carbonaceous compressions, trace fossils, and organic bodies and skeletal fossils. Initial evolutionary experiments produced unusual bodies that are poorly understood or conceived of as non-metazoan. It is accepted that sponges, ctenophorans, cnidarians, placozoans, and bilaterians were members of the Ediacaran fauna, many of which have uncertain affinities. The fossilSabellidites cambriensisYanishevsky, 1926, derived from the terminal Ediacaran strata, is the earliest known organically preserved animal that belonged to a newly evolving fauna, which replaced the Ediacara-type metazoans. Morphologically simple soft-bodied tubular fossils, such asS. cambriensis, and biomineralized, as contemporaneousSinotubulitessp., are not easy to recognize phylogenetically because many unrelated organisms developed encasing tubes independently. Therefore, in addition to morphologic information, evidence derived from the microstructure of the organic wall and its biochemistry may be vital to resolving fossil origins and phylogenetic relationships. Here we present morphological, microstructural and biogeochemical studies onS. cambriensisusing various microscopic and spectroscopic techniques, which provide new evidence that supports its siboglinid, annelidan affinity. The late Ediacaran age ofSabelliditesfossil constrains the minimum age of siboglinids and the timing of the divergence of including them annelids by fossil record and this could be tested using molecular clock estimates. The fine microstructure of the organic tube inSabelliditesis multi-layered and has discrete layers composed of differently orientated and perfectly shaped fibers embedded in an amorphous matrix. The highly ordered and specific pattern of fiber alignment (i.e., the texture of organic matter) is similar to that of representatives of the family Siboglinidae. The biogeochemistry of the organic matter that comprised the tube, which was inferred from its properties, composition, and microstructure, is consistent with chitin and proteins as in siboglinids.
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Yossa, Nadine, James Smiley, Mei-Chiung Jo Huang, Lanlan Yin, Rebecca Bell, Sandra Tallent, Eric Brown, and Thomas Hammack. "Comparison of TEMPO® BC with Spiral Plating Methods for the Enumeration of Bacillus cereus in Cosmetic Products Either Naturally Preserved or Preserved with Phenoxyethanol." Journal of AOAC INTERNATIONAL 102, no. 4 (July 1, 2019): 1080–90. http://dx.doi.org/10.5740/jaoacint.18-0375.
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Abstract Background: The U.S. Food and Drug Administration’s (FDA) Bacteriological Analytical Manual (BAM) uses Bacillus cereus rapid agar (BACARA) and Mannitol-yolk-polymyxin (MYP) agar for the enumeration of the members of B. cereus group. Objective: The automated TEMPO Most Probable Number system was compared with the FDA BAM method for the detection of B. cereus group members in cosmetic products. Methods: We inoculated a range of cosmetic products with pure B. cereus spore suspensions (density = 0.5 McFarland) at high (6 log CFU/mL), medium (5 log CFU/mL), and low (4 log CFU/mL) levels. Test portions were aged for 72 h. Five replicates per sample were analyzed; uninoculated test portions served as controls. We also evaluated whether TEMPO BC erroneously detected non-B. cereus or other adulterant organisms. Results: No significant differences (P > 0.05) were found among the TEMPO BC and the BAM spiral plating methods. Correlations between TEMPO BC – BACARA and TEMPO BC – MYP were 0.895 and 0.893 for powder type products, 0.834 and 0.846 for cream and oil-based products, and 0.929 and 0.923 for liquid products, respectively. Non-B. cereus strains were not detected by TEMPO BC. Conclusions: The TEMPO BC method can be used for the detection of B. cereus in cosmetic products without preservatives, or those preserved with either phenoxyethanol or other organic substances.
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Vega, Francisco J., Rodney M. Feldmann, and Victor M. Davila-Alcocer. "Cuticular structure in Costacopluma mexicana Vega and Perrilliat, from the Difunta Group (Maastrichtian) of northeastern Mexico, and its paleoenvironmental implications." Journal of Paleontology 68, no. 5 (September 1994): 1074–81. http://dx.doi.org/10.1017/s0022336000026688.
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Examination of extremely well-preserved cuticle samples from the Maastrichtian retroplumid crab, Costacopluma mexicana Vega and Perrilliat, collected in the Difunta Group in Nuevo León State, Mexico, documents the preservation of corpses in an anoxic microenvironment produced by decomposition of soft tissue of the organisms. All four cuticular layers, epicuticle, exocuticle, endocuticle, and membranous layer, as well as pore canals and tegumental glands, can be recognized. There is no evidence of resorption that accompanies molting. X-ray analysis of the cuticle indicates that the organic matrix was replaced by carbonate-hydroxyapatite, that the original calcitic material was replaced by quartz, and that the replacement proceeded from the outer and inner surfaces of the cuticle toward the interior. The specimens were interpreted to have been preserved in an organic-rich, restricted lagoon in which pH was changed by periodic influxes of fresh water.
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Wirth, Alexander, Bettina Wolf, Cheng-Kai Huang, Silke Glage, Sebastian J. Hofer, Marion Bankstahl, Christian Bär, et al. "Novel aspects of age-protection by spermidine supplementation are associated with preserved telomere length." GeroScience 43, no. 2 (January 31, 2021): 673–90. http://dx.doi.org/10.1007/s11357-020-00310-0.
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AbstractAgeing provokes a plethora of molecular, cellular and physiological deteriorations, including heart failure, neurodegeneration, metabolic maladaptation, telomere attrition and hair loss. Interestingly, on the molecular level, the capacity to induce autophagy, a cellular recycling and cleaning process, declines with age across a large spectrum of model organisms and is thought to be responsible for a subset of age-induced changes. Here, we show that a 6-month administration of the natural autophagy inducer spermidine in the drinking water to aged mice is sufficient to significantly attenuate distinct age-associated phenotypes. These include modulation of brain glucose metabolism, suppression of distinct cardiac inflammation parameters, decreased number of pathological sights in kidney and liver and decrease of age-induced hair loss. Interestingly, spermidine-mediated age protection was associated with decreased telomere attrition, arguing in favour of a novel cellular mechanism behind the anti-ageing effects of spermidine administration.
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Ivleva, A. D., and A. S. Karpov. "THE STUDY OF THE EVOLUTION OF ROAMING PRESERVED GRAFTS IN LIVING ORGANISMS (FOR EXAMPLE, BONE TISSUE) IN THE LABORATORY." Современные проблемы науки и образования (Modern Problems of Science and Education), no. 3 2018 (2018): 84. http://dx.doi.org/10.17513/spno.27576.
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