Visualisation of gene expression within the context of tissues using an X-ray computed tomography-based multimodal approach

The development of an organism is orchestrated by the spatial and temporal expression of genes. Accurate visualisation of gene expression patterns in the context of the surrounding tissues offers a glimpse into the mechanisms that drive morphogenesis. We developed correlative light-sheet fluorescence microscopy and X-ray computed tomography approach to map gene expression patterns to the whole organism`s 3D anatomy. We show that this multimodal approach is applicable to gene expression visualized by protein-specific antibodies and fluorescence RNA in situ hybridisation offering a detailed understanding of individual phenotypic variations in model organisms. Furthermore, the approach offers a unique possibility to identify tissues together with their 3D cellular and molecular composition in anatomically less-defined in vitro models, such as organoids. We anticipate that the visual and quantitative insights into the 3D distribution of gene expression within tissue architecture, by multimodal approach developed here, will be equally valuable for reference atlases of model organisms development, as well as for comprehensive screens, and morphogenesis studies of in vitro models.

Unravelling the link between embryogenesis and adult stem cell potential in the ciliary marginal zone: A comparative study between mammals and teleost fish

The discovery and study of adult stem cells have revolutionized regenerative medicine by offering new opportunities for treating various medical conditions. Anamniote stem cells, which retain their full proliferative capacity and full differentiation range throughout their lifetime, harbour a greater potential compared to mammalian adult stem cells, which only exhibit limited stem cell potential. Therefore, understanding the mechanisms underlying these differences is of significant interest. In this review, we examine the similarities and differences of adult retinal stem cells in anamniotes and mammals, from their embryonic stages in the optic vesicle to their residence in the postembryonic retinal stem cell niche, the ciliary marginal zone located in the retinal periphery. In anamniotes, developing precursors of retinal stem cells are exposed to various environmental cues during their migration in the complex morphogenetic remodelling of the optic vesicle to the optic cup. In contrast, their mammalian counterparts in the retinal periphery are primarily instructed by neighbouring tissues once they are in place. We explore the distinct modes of optic cup morphogenesis in mammals and teleost fish and highlight molecular mechanisms governing morphogenesis and stem cells instruction. The review concludes with the molecular mechanisms of ciliary marginal zone formation and offers a perspective on the impact of comparative single cell transcriptomic studies to reveal the evolutionary similarities and differences.

Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel

BACKGROUND

The teleost medaka (Oryzias latipes) is a well-established vertebrate model system, with a long history of genetic research, and multiple high-quality reference genomes available for several inbred strains. Medaka has a high tolerance to inbreeding from the wild, thus allowing one to establish inbred lines from wild founder individuals.

RESULTS

We exploit this feature to create an inbred panel resource: the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel. This panel of 80 near-isogenic inbred lines contains a large amount of genetic variation inherited from the original wild population. We use Oxford Nanopore Technologies (ONT) long read data to further investigate the genomic and epigenomic landscapes of a subset of the MIKK panel. Nanopore sequencing allows us to identify a large variety of high-quality structural variants, and we present results and methods using a pan-genome graph representation of 12 individual medaka lines. This graph-based reference MIKK panel genome reveals novel differences between the MIKK panel lines and standard linear reference genomes. We find additional MIKK panel-specific genomic content that would be missing from linear reference alignment approaches. We are also able to identify and quantify the presence of repeat elements in each of the lines. Finally, we investigate line-specific CpG methylation and performed differential DNA methylation analysis across these 12 lines.

CONCLUSIONS

We present a detailed analysis of the MIKK panel genomes using long and short read sequence technologies, creating a MIKK panel-specific pan genome reference dataset allowing for investigation of novel variation types that would be elusive using standard approaches.

The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel

Background

Unraveling the relationship between genetic variation and phenotypic traits remains a fundamental challenge in biology. Mapping variants underlying complex traits while controlling for confounding environmental factors is often problematic. To address this, we establish a vertebrate genetic resource specifically to allow for robust genotype-to-phenotype investigations. The teleost medaka (Oryzias latipes) is an established genetic model system with a long history of genetic research and a high tolerance to inbreeding from the wild.

Results

Here we present the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel: the first near-isogenic panel of 80 inbred lines in a vertebrate model derived from a wild founder population. Inbred lines provide fixed genomes that are a prerequisite for the replication of studies, studies which vary both the genetics and environment in a controlled manner, and functional testing. The MIKK panel will therefore enable phenotype-to-genotype association studies of complex genetic traits while allowing for careful control of interacting factors, with numerous applications in genetic research, human health, drug development, and fundamental biology.

Conclusions

Here we present a detailed characterization of the genetic variation across the MIKK panel, which provides a rich and unique genetic resource to the community by enabling large-scale experiments for mapping complex traits.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13059-022-02623-z.

Behavioural responses of breeding arctic sandpipers to ground-surface temperature and primary productivity

Most birds incubate their eggs, which requires time and energy at the expense of other activities. Birds generally have two incubation strategies: biparental where both mates cooperate in incubating eggs, and uniparental where a single parent incubates. In harsh and unpredictable environments, incubation is challenging due to high energetic demands and variable resource availability. We studied the relationships between the incubation behaviour of sandpipers (genus Calidris) and two environmental variables: temperature and a proxy of primary productivity (i.e. NDVI). We investigated how these relationships vary between incubation strategies and across species among strategies. We also studied how the relationship between current temperature and incubation behaviour varies with previous day's temperature. We monitored the incubation behaviour of nine sandpiper species using thermologgers at 15 arctic sites between 2016 and 2019. We also used thermologgers to record the ground surface temperature at conspecific nest sites and extracted NDVI values from a remote sensing product. We found no relationship between either environmental variables and biparental incubation behaviour. Conversely, as ground-surface temperature increased, uniparental species decreased total duration of recesses (TDR) and mean duration of recesses (MDR), but increased number of recesses (NR). Moreover, small species showed stronger relationships with ground-surface temperature than large species. When all uniparental species were combined, an increase in NDVI was correlated with higher mean duration, total duration and number of recesses, but relationships varied widely across species. Finally, some uniparental species showed a lag effect with a higher nest attentiveness after a warm day while more recesses occurred after a cold day than was predicted based on current temperatures. We demonstrate the complex interplay between shorebird incubation strategies, incubation behaviour, and environmental conditions. Understanding how species respond to changes in their environment during incubation helps predict their future reproductive success.

Restoration of the biodiversity of technogenic landscapes of anthracite deposits in Siberia

The features of self-restoring of plant communities in connection with the edaphic conditions of the dumps of anthracite deposits are revealed. It is shown that the development of tree communities is confined to areas with bumpy terrain, and grassy to horizontal areas.

Parasitoids indicate major climate-induced shifts in arctic communities

Climatic impacts are especially pronounced in the Arctic, which as a region is warming twice as fast as the rest of the globe. Here, we investigate how mean climatic conditions and rates of climatic change impact parasitoid insect communities in 16 localities across the Arctic. We focus on parasitoids in a widespread habitat, Dryas heathlands, and describe parasitoid community composition in terms of larval host use (i.e., parasitoid use of herbivorous Lepidoptera vs. pollinating Diptera) and functional groups differing in their closeness of host associations (koinobionts vs. idiobionts). Of the latter, we expect idiobionts-as being less fine-tuned to host development-to be generally less tolerant to cold temperatures, since they are confined to attacking hosts pupating and overwintering in relatively exposed locations. To further test our findings, we assess whether similar climatic variables are associated with host abundances in a 22 year time series from Northeast Greenland. We find sites which have experienced a temperature rise in summer while retaining cold winters to be dominated by parasitoids of Lepidoptera, with the reverse being true for the parasitoids of Diptera. The rate of summer temperature rise is further associated with higher levels of herbivory, suggesting higher availability of lepidopteran hosts and changes in ecosystem functioning. We also detect a matching signal over time, as higher summer temperatures, coupled with cold early winter soils, are related to high herbivory by lepidopteran larvae, and to declines in the abundance of dipteran pollinators. Collectively, our results suggest that in parts of the warming Arctic, Dryas is being simultaneously exposed to increased herbivory and reduced pollination. Our findings point to potential drastic and rapid consequences of climate change on multitrophic-level community structure and on ecosystem functioning and highlight the value of collaborative, systematic sampling effort.

THE POTENTIAL OF FLOUR FROM SOLVENT-EXTRACTION HEMP OILCAKE AS AN INGREDIENT OF LOW-MOISTURE BAKERY PRODUCTS

The paper focuses on how to improve the nutritional value of traditional low moisture bakery products from wheat flour by using flour from hemp oilcakes obtained by solvent extraction of oil. It has been considered how to provide enough raw materials in the case of wide use of hemp and products of its processing in the food industry. The main tendencies in cultivating and applying industrial hemp in Ukraine and worldwide have been outlined; the chemical composition of hemp seeds (the plant’s part mainly used in food products) has been analysed and characterised; and it has been suggested how hemp by-products can be used in the bakery technology. It has been studied whether flour from hemp extraction cake can be used in the technology of low-moisture bakery products such as breadsticks. It has been found that 10, 15, and 20% of hemp flour added to wheat flour increase the water absorption capacity of the resulting flour blend by 3, 6, and 13% respectively, in comparison with the control. If hemp flour is included in the formulation of breadstick dough, the slackness of a dough ball increases by 6.1, 7.4, and 11%, and this increase is bigger, the higher the hemp flour content in the formulation is. However, it has been found that if the flour component of the recipe is partly replaced with hemp flour, this changes the growth medium of yeast cells and lactic acid bacteria and thus leads to a 23, 16, and 30% decrease in the amount of carbon dioxide formed during the 180 min fermentation period of the dough. The 6, 16, and 40% increase of titratable acidity in the samples analysed is due to the content of biogenic and oligobiogenic elements in the flour mixture, which satisfy the needs of lactic acid bacteria rather than those of baker’s yeast. The quality assessment of the finished products by their sensory and physicochemical characteristics has shown how promising it is to use hemp flour in the breadstick technology, provided that the recipe and the production parameters are modified to improve the products’ rheological properties and quality.

Improving dialogue among researchers, local and indigenous peoples and decision-makers to address issues of climate change in the North

The Circumpolar North has been changing rapidly within the last decades, and the socioeconomic systems of the Eurasian Arctic and Siberia in particular have displayed the most dramatic changes. Here, anthropogenic drivers of environmental change such as migration and industrialization are added to climate-induced changes in the natural environment such as permafrost thawing and increased frequency of extreme events. Understanding and adapting to both types of changes are important to local and indigenous peoples in the Arctic and for the wider global community due to transboundary connectivity. As local and indigenous peoples, decision-makers and scientists perceive changes and impacts differently and often fail to communicate efficiently to respond to changes adequately, we convened a meeting of the three groups in Salekhard in 2017. The outcomes of the meeting include perceptions of how the three groups each perceive the main issues affecting health and well-being and recommendations for working together better.

Formation of local immunity in infants on different types of feeding

Rational feeding from the early days of life programs the health, growth and development of the child over the following years. By the age of 6 months children on artificial feeding are reliably more likely to form excess body weight. The nature of nutrition depends on the condition of the overall and local immune protection of the child. Application of non-invasive methods for determining sIgA (in oral fluid (saliva), in coprofiltrate) allows to assess local immunity in infancy age. Breastfed infants receive sIgA with mother’s milk and have additional protection against the pathogens of respiratory and intestinal infections. The level of sIgA in the mother’s breast milk can be determined to assess the condition of children’s immunity. Children on breastfeeding experience acute respiratory diseases less often compared to children fed with adapted milk formula.

Multicenter study of serotype distribution of Streptococcus pneumoniae nasopharyngeal isolates from healthy children in the Russian Federation after introduction of PCV13 into the National Vaccination Calendar

Russia introduced PCV13 in 2014. We studied the serotype composition of S. pneumoniae isolated from the nasopharynx of healthy children younger than 6 years in St. Petersburg, Smolensk, Perm, Krasnoyarsk, Khanty-Mansiysk and Khabarovsk, between 2016 and 2018. 2.4% of children had completed a 3-dose course of PCV13, while 25.6% had received 1 or 2 doses. Pneumococcal DNA detection by PCR demonstrated S. pneumoniae in 37.2% of samples with regional variation between sites (27.3 to 56.9%). There was little difference between vaccinated, partially vaccinated and un-vaccinated children. Children who had received at least 1 dose of PCV13 had lower carriage rates of vaccine serotypes than their unvaccinated peers (49.9 vs. 61.4%; p < 0.001). Children who had received at least 1 dose of PCV13 showed increased carriage rates of non-vaccine serotypes (50 vs 38.6%; P < 0.001). Especially serogroup 15AF was more prevalent among fully immunized children than among their peers (12.5 vs 2.7%; P < 0.05).

Consequences of past climate change and recent human persecution on mitogenomic diversity in the arctic fox

Ancient DNA provides a powerful means to investigate the timing, rate and extent of population declines caused by extrinsic factors, such as past climate change and human activities. One species probably affected by both these factors is the arctic fox, which had a large distribution during the last glaciation that subsequently contracted at the start of the Holocene. More recently, the arctic fox population in Scandinavia went through a demographic bottleneck owing to human persecution. To investigate the consequences of these processes, we generated mitogenome sequences from a temporal dataset comprising Pleistocene, historical and modern arctic fox samples. We found no evidence that Pleistocene populations in mid-latitude Europe or Russia contributed to the present-day gene pool of the Scandinavian population, suggesting that postglacial climate warming led to local population extinctions. Furthermore, during the twentieth-century bottleneck in Scandinavia, at least half of the mitogenome haplotypes were lost, consistent with a 20-fold reduction in female effective population size. In conclusion, these results suggest that the arctic fox in mainland Western Europe has lost genetic diversity as a result of both past climate change and human persecution. Consequently, it might be particularly vulnerable to the future challenges posed by climate change. This article is part of a discussion meeting issue 'The past is a foreign country: how much can the fossil record actually inform conservation?'

OPTIMIZATION OF RECIPE FOR BAKERY PRODUCTSWITH LOW-MOISTURE CONTENTFOR REDUCING THE GLYCEMIC INDEX

The modern concept of recipe development and improvement has to be based on fundamental knowledge about the chemical composition of ingredients as well as mechanisms of their assimilation. Glycemic index of food products, including bakery products, becomes important in the aspect of the spread of a metabolic syndrome that is a complex of various metabolic disorders that lead to the development of atherosclerosis and cardiovascular disease. The article shows the possibility of creating a recipe for sweet baked goods with low moisture content and reduced glycemic index due to using the buckwheat flour, dry wheat gluten, oat bran and aqueous extract of stevia. We have used modern methods of setting up the experiment and processing their results. The influence of these ingredients on the glycemic index has been characterized. The efficiency of using Stevia as natural sweeteners, has shown, for developing approaches to reduce the energy value and the glycemic index of bakery products. The coefficients of the regression model were given as a result; it has helped to find out the patterns of influence of both selected components and their dosage on the glycemic index, energy value and sensory characteristics of the product. The article presents the results of multicriteria optimization, which can be used to create recipe compositions using selected ingredients using of modern software Design-Expert 11. The amount of buckwheat flour was in range 5–20%, dry wheat gluten – 5–15%, oat bran – 2–6% of the total number of dry ingredients in the formulation. A rational ratio of the main ingredients has been found to provide an optimal ratio of the factors "low glycemic index - excellent taste". The glycemic index of developed baked goods with low moisture content was 57–58.This article has shown the possibility of using an integrated approach in forming the recipe of low-moisture bakery products with a reduced glycemic index.

Weak effects of geolocators on small birds: A meta-analysis controlled for phylogeny and publication bias

Currently, the deployment of tracking devices is one of the most frequently used approaches to study movement ecology of birds. Recent miniaturization of light-level geolocators enabled studying small bird species whose migratory patterns were widely unknown. However, geolocators may reduce vital rates in tagged birds and may bias obtained movement data. There is a need for a thorough assessment of the potential tag effects on small birds, as previous meta-analyses did not evaluate unpublished data and impact of multiple life-history traits, focused mainly on large species and the number of published studies tagging small birds has increased substantially. We quantitatively reviewed 549 records extracted from 74 published and 48 unpublished studies on over 7,800 tagged and 17,800 control individuals to examine the effects of geolocator tagging on small bird species (body mass <100 g). We calculated the effect of tagging on apparent survival, condition, phenology and breeding performance and identified the most important predictors of the magnitude of effect sizes. Even though the effects were not statistically significant in phylogenetically controlled models, we found a weak negative impact of geolocators on apparent survival. The negative effect on apparent survival was stronger with increasing relative load of the device and with geolocators attached using elastic harnesses. Moreover, tagging effects were stronger in smaller species. In conclusion, we found a weak effect on apparent survival of tagged birds and managed to pinpoint key aspects and drivers of tagging effects. We provide recommendations for establishing matched control group for proper effect size assessment in future studies and outline various aspects of tagging that need further investigation. Finally, our results encourage further use of geolocators on small bird species but the ethical aspects and scientific benefits should always be considered.

ATM mutation spectrum in Russian children with ataxia-telangiectasia

Ataxia-telangiectasia (AT) is a severe autosomal recessive orphan disease characterized by a number of peculiar clinical manifestations. Genetic diagnosis of AT is complicated due to a large size of the causative gene, ATM. We used next-generation sequencing (NGS) technology for the ATM analysis in 17 children with the clinical diagnosis of AT. Biallelic mutations in the ATM gene were identified in all studied subjects; these lesions included one large gene rearrangement, which was reliably detected by NGS and validated by multiplex ligation-dependent probe amplification (MLPA). There was a pronounced founder effect, as 17 of 30 (57%) pathogenic ATM alleles in the patients of Slavic origin were represented by three recurrent mutations (c.5932G > T, c.450_453delTTCT, and c.1564_1565delGA). These data have to be taken into account while considering the genetic diagnosis and screening for ataxia-telangiectasia syndrome.

From Library Co-operation to Consortia: Comparing Experiences in the European Union with the Russian Federation

Copeter is one of the few Tempus/Tacis projects about consortium building: bringing libraries together in a consortium in order to achieve common goals. This article will attempt to answer three main questions: 1. What factors create good library co-operation? 2. What are the conditions for success? 3. Is the Copeter consortium fulfilling these requirements?

Review of Z39.50 servers and Z39.50 environment in Russia

The article covers the five‐year history of the implementation of Z39.50‐type products in Russia. All existing projects are mentioned in the order of their development. Since the authors are from RUSLANet, that project is described in greater detail. The architecture of a distributed library system, as well as its basic components, are presented, and the place and role of Z39.50 facilities in Russian libraries are highlighted. The obstacles the Russian library community faces in moving to a networked environment are covered. The need to develop uniquely Russian Z39.50 databases grew from specific document‐ processing features within the libraries. Some prospects for future development and use of Z39.50 environment in Russian libraries are also given.

Embryonic development and pattern formation

During embryogenesis, information encoded in the genome is translated into cell proliferation, morphogenesis, and early stages of differentiation. Embryonic pattern arises from the spatial and temporal regulation and coordination of these events. The vitamin A (retinol) derivative retinoic acid (RA) is essential for normal development. Mammalian embryos are protected against vitamin A deficiency by maternal retinoid homeostasis until stored retinoids fall to very low levels. Retinol binding protein, which is synthesized in the yolk sac placenta of rodent embryos and in the syncytiotrophoblast of the human placenta, is essential for access of retinol to the embryo. Synthesis and metabolism of RA may involve cytoplasmic binding proteins, but the observation that mutants lacking these proteins are normal or near-normal suggests that they are not essential. Severe congenital vitamin A deficiency results in a spectrum of malformations including defects of the eye, lungs, cardiovascular system, and urogenital system. Extreme deficiency results as well in forelimb abnormalities and cleft face, but the embryos are not viable. Similar abnormalities are observed in embryos lacking two retinoid receptors, but loss of one receptor results in either normal development or mild abnormalities. Two single-receptor null mutants, RARgamma-/- and RXRalpha-/-, show regional pattern-specific resistance to teratogenic levels of RA. Mutations leading to abnormality of the structure or regulation of RA signaling pathway genes may be an important cause of human congenital abnormality.