Prehistoric Pendants as Instigators of Sound and Body Movements : A Traceological Case Study from Northeast Europe, c. 8200 cal. BP

Supplementary audiovisual material: https://youtu.be/K-EE9YY6pHY https://youtu.be/gRpxQOx9ugsIn the Late Mesolithic graves of Yuzhniy Oleniy Ostrov, Northwest Russia, large amounts of Eurasian elk (Alces alces) incisors have been found. These teeth, for the most part fashioned into portable pendants, seem to have formed decorative sets for the garments or accessories of the deceased. This article examines both the technologies associated with these artefacts and their uses, as well as reflecting on the sensorial experiences generated by them. Osteological analysis of a sample of 100 specimens indicates that all types of incisors were used for making the pendants. Traceological analysis indicates that the teeth were modified by scraping, grooving, grinding, and retouching. Traces of wear consist of general wear and distinctive pits or pecks on the perimeters of the crowns. These traces indicate that the pendants were worn before their deposition in the graves, in such a way that they were in contact with both soft and solid materials. The pattern of pits or pecks has until now been unreported in the traceological literature. In experiments, a similar pattern emerged when pendants of fresh elk incisors were hung in rows and bunches and struck against one another. These strokes created a rattling sound. Thus, the elk incisors of Yuzhniy Oleniy Ostrov appear to provide insight into previously unattainable sonic experiences and activities of Mesolithic hunter-gatherers, as well as the early history of the instrument category of rattles.Peer reviewe

Let’s groove : Attachment techniques of Eurasian elk (Alces alces) tooth pendants at the Late Mesolithic cemetery Yuzhniy Oleniy Ostrov (Lake Onega, Russia)

More than 4300 Eurasian elk (Alces alces) incisors, most of them pendants, were found in 84 burials in the Late Mesolithic cemetery of Yuzhniy Oleniy Ostrov, Northwest Russia. We analysed the manufacture techniques of elk teeth (4014), in the collection of the Peter the Great Museum of Anthropology and Ethnography, St Petersburg. A striking observation is that the manufacture of these pendants is similar in all burials. Teeth were worked by carving one or several grooves around the root tip. In addition to grooved ones, a number of teeth were not worked at all. The uniformity of the chosen species, tooth and techniques indicates that strict norms prevailed in the pendant industry. Despite the overall similarity, our study shows some variation in making pendants. A groove can cut the whole circumference of the root, or several distinct grooves can mark opposite sides of the root. Sometimes the grooves are deep and made carefully, and sometimes they are weak and made hastily. A typology of various groove types was created. In many graves, one groove type dominates. We interpret that this inter-burial variation and domination of one type resulted from personal choice and taste based on practicality. Such variation could also be associated with kin identifiers, but we did not find clear support for that in our study. Our study indicates that the groove types as such had no connection with particular ornaments, garments or hanging positions.Peer reviewe

Aging Induces Profound Changes in sncRNA in Rat Sperm and These Changes Are Modified by Perinatal Exposure to Environmental Flame Retardant

Advanced paternal age at fertilization is a risk factor for multiple disorders in offspring and may be linked to age-related epigenetic changes in the father’s sperm. An understanding of aging-related epigenetic changes in sperm and environmental factors that modify such changes is needed. Here, we characterize changes in sperm small non-coding RNA (sncRNA) between young pubertal and mature rats. We also analyze the modification of these changes by exposure to environmental xenobiotic 2,2′,4,4′-tetrabromodiphenyl ether (BDE-47). sncRNA libraries prepared from epididymal spermatozoa were sequenced and analyzed using DESeq 2. The distribution of small RNA fractions changed with age, with fractions mapping to rRNA and lncRNA decreasing and fractions mapping to tRNA and miRNA increasing. In total, 249 miRNA, 908 piRNA and 227 tRNA-derived RNA were differentially expressed (twofold change, false discovery rate (FDR) p ≤ 0.05) between age groups in control animals. Differentially expressed miRNA and piRNA were enriched for protein-coding targets involved in development and metabolism, while piRNA were enriched for long terminal repeat (LTR) targets. BDE-47 accelerated age-dependent changes in sncRNA in younger animals, decelerated these changes in older animals and increased the variance in expression of all sncRNA. Our results indicate that the natural aging process has profound effects on sperm sncRNA profiles and this effect may be modified by environmental exposure

Comparative genome analysis of Pseudogymnoascus spp. reveals primarily clonal evolution with small genome fragments exchanged between lineages

Abstract Background Pseudogymnoascus spp. is a wide group of fungi lineages in the family Pseudorotiaceae including an aggressive pathogen of bats P. destructans. Although several lineages of P. spp. were shown to produce ascospores in culture, the vast majority of P. spp. demonstrates no evidence of sexual reproduction. P. spp. can tolerate a wide range of different temperatures and salinities and can survive even in permafrost layer. Adaptability of P. spp. to different environments is accompanied by extremely variable morphology and physiology. Results We sequenced genotypes of 14 strains of P. spp., 5 of which were extracted from permafrost, 1 from a cryopeg, a layer of unfrozen ground in permafrost, and 8 from temperate surface environments. All sequenced genotypes are haploid. Nucleotide diversity among these genomes is very high, with a typical evolutionary distance at synonymous sites dS ≈ 0.5, suggesting that the last common ancestor of these strains lived >50Mya. The strains extracted from permafrost do not form a separate clade. Instead, each permafrost strain has close relatives from temperate environments. We observed a strictly clonal population structure with no conflicting topologies for ~99% of genome sequences. However, there is a number of short (~100–10,000 nt) genomic segments with the total length of 67.6 Kb which possess phylogenetic patterns strikingly different from the rest of the genome. The most remarkable case is a MAT-locus, which has 2 distinct alleles interspersed along the whole-genome phylogenetic tree. Conclusions Predominantly clonal structure of genome sequences is consistent with the observations that sexual reproduction is rare in P. spp. Small number of regions with noncanonical phylogenies seem to arise due to some recombination events between derived lineages of P. spp., with MAT-locus being transferred on multiple occasions. All sequenced strains have heterothallic configuration of MAT-locus.http://deepblue.lib.umich.edu/bitstream/2027.42/111733/1/12864_2015_Article_1570.pd

Mitochondrial RNA editing in Trypanoplasma borreli: new tools, new revelations

The kinetoplastids are unicellular flagellates that derive their name from their ‘kinetoplast’, a region within each flagellate’s single mitochondrion harboring its organellar genome of high DNA content. Some protein products of this mitochondrial genome are encoded as cryptogenes; their transcripts require editing to generate an open reading frame. This happens through an RNA editing process, whereby small regulatory guide RNAs direct the proper insertion and deletion of one or more uridines at each editing site within specific transcript regions. An accurate perspective of the mitochondrial DNA expansion of kinetoplastids and the evolution of their unique uridine insertion/deletion editing across the entire group has been difficult to achieve. Here, we resolved outstanding questions about the organization of the mitochondrial genome and its editing in the kinetoplastid Trypanoplasma borreli that is evolutionarily distant from the frequently-studied trypanosomatids. We find that its mitochondrial DNA consists of circular molecules of 42 kb that harbor the rRNA and mRNAs, and 17 different contigs of approximately 70 kb carrying an average of 23 putative guide RNA loci per contig. These contigs may be linear molecules; they contain repetitive termini. Our analysis uncovered a putative gRNA population with unique length and sequence parameters that is massive relative to the editing needs of this parasite. We validated or determined the sequence identity of each of the four edited mRNA species – including one coding for ATP synthase 6 that was previously thought to be missing. We utilized our computational methods to show that the T. borreli transcriptome includes a substantial number of transcripts with editing patterns not consistent with the identified product, a result of non-canonical editing. We also discovered that this species is more likely than other kinetoplastids to utilize uridine deletion to enforce amino acid conservation of cryptogene products, although deletion is still less common than insertion. Finally, in three tested kinetoplastid mitochondrial transcriptomes, uridine deletion is more common in the raw mitochondrial read population than it appears when the fully edited translationally competent mRNAs only are considered. We conclude that the organization of mitochondrial DNA across all kinetoplastids can be described as variations on several central themes. These themes include partitioned coding and repetitive regions of a circular molecule encoding mRNA and rRNA, and guide RNA loci positioned on a malleable population of multiple molecules that differ in relative abundance in different strains. Likewise, while all kinetoplastids possess the central mechanism of uridine insertion/deletion RNA editing, its output parameters are species-specific

Bone Stress-Strain State Evaluation Using CT Based FEM

Nowadays, the use of a digital prototype in numerical modeling is one of the main approaches to calculating the elements of an inhomogeneous structure under the influence of external forces. The article considers a finite element analysis method based on computed tomography data. The calculations used a three-dimensional isoparametric finite element of a continuous medium developed by the authors with a linear approximation, based on weighted integration of the local stiffness matrix. The purpose of this study is to describe a general algorithm for constructing a numerical model that allows static calculation of objects with a porous structure according to its computed tomography data. Numerical modeling was carried out using kinematic boundary conditions. To evaluate the results obtained, computational and postprocessor grids were introduced. The qualitative assessment of the modeling data was based on the normalized error. Three-point bending of bone specimens of the pig forelimbs was considered as a model problem. The numerical simulation results were compared with the data obtained from a physical experiment. The relative error ranged from 3 to 15%, and the crack location, determined by the physical experiment, corresponded to the area where the ultimate strength values were exceeded, determined by numerical modeling. The results obtained reflect not only the effectiveness of the proposed approach, but also the agreement with experimental data. This method turned out to be relatively non-resource-intensive and time-efficient

Modelling the potential non-breeding distribution of Spoon-billed Sandpiper Calidris pygmaea

The Spoon-billed Sandpiper Calidris pygmaea is a ‘Critically Endangered’ migratory shorebird. The species faces an array of threats in its non-breeding range, making conservation intervention essential. However, conservation efforts are reliant on identifying the species’ key stopover and wintering sites. Using Maximum Entropy models, we predicted Spoon-billed Sandpiper distribution across the non-breeding range, using data from recent field surveys and satellite tracking. Model outputs suggest only a limited number of stopover sites are suitable for migrating birds, with sites in the Yellow Sea and on the Jiangsu coast in China highlighted as particularly important. All the previously known core wintering sites were identified by the model including the Ganges-Brahmaputra Delta, Nan Thar Island and the Gulf of Mottama. In addition, the model highlighted sites subsequently found to be occupied, and pinpointed potential new sites meriting investigation, notably on Borneo and Sulawesi, and in parts of India and the Philippines. A comparison between the areas identified as most likely to be occupied and protected areas showed that very few locations are covered by conservation designations. Known sites must be managed for conservation as a priority, and potential new sites should be surveyed as soon as is feasible to assess occupancy status. Site protection should take place in concert with conservation interventions including habitat management, discouraging hunting, and fostering alternative livelihoods.Additional co-authors: Christoph Zockler, Graeme M Buchana

Crowdsourcing Fungal Biodiversity : Revision of Inaturalist Observations in Northwestern Siberia

The paper presents the first analysis of crowdsourcing data of all observations of fungi (including lichens) and myxomycetes in Northwestern Siberia uploaded to iNaturalist.org to date (24.02.2022). The Introduction presents an analysis of fungal diversity crowdsourcing globally, in Russia, and in the region of interest. Materials and methods describe the protocol of uploading data to iNaturalist.org, the structure of the crowdsourcing community. initiative to revise the accumulated data. procedures of data analysis, and compilation of a dataset of revised crowdsourced data. The Results present the analysis of accumulated data by several parameters: temporal, geographical and taxonomical scope, observation and identification efforts, identifiability of various taxa, species novelty and Red Data Book categories and the protection status of registered observations. The Discussion provides data on usability of crowdsourcing data for biodiversity research and conservation of fungi, including pros and contras. The Electronic Supplements to the paper include an annotated checklist of observations of protected species with information on Red Data Book categories and the protection status, and an annotated checklist of regional records of new taxa. The paper is supplemented with a dataset of about 15 000 revised and annotated records available through Global Biodiversity Information Facility (GBIF). The tradition of crowdsourcing is rooted in mycological societies around the world, including Russia. In Northwestern Siberia, a regional mycological club was established in 2018, encouraging its members to contribute observations of fungi on iNaturalist.org. A total of about 15 000 observations of fungi and myxomycetes were uploaded so far, by about 200 observers, from three administrative regions (Yamalo-Nenetsky Autonomous Okrug, Khanty-Mansi Autonomous Okrug, and Tyumen Region). The geographical coverage of crowdsourcing observations remains low. However. the observation activity has increased in the last four years. The goal of this study consisted of a collaborative effort of professional mycologists invited to help with the identification of these observations and analysis of the accumulated data. As a result, all observations were reviewed by at least one expert. About half of all the observations have been identified reliably to the species level and received Research Grade status. Of those, 90 species (195 records) represented records of taxa new to their respective regions: 876 records of 53 species of protected species provide important data for conservation programmes. The other half of the observations consists of records still under-identified for various reasons: poor quality photographs, complex taxa (impossible to identify without microscopic or molecular study). or lack of experts in a particular taxonomic group. The Discussion section summarises the pros and cons of the use of crowdsourcing for the study and conservation of regional fungal diversity, and summarises the dispute on this subject among mycologists. Further research initiatives involving crowdsourcing data must focus on an increase in the quality of observations and strive to introduce the habit of collecting voucher specimens among the community of amateurs. The timely feedback from experts is also important to provide quality and the increase of personal involvement.Peer reviewe