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.

Taking the beat of the Arctic: are lemming population cycles changing due to winter climate?

Reports of fading vole and lemming population cycles and persisting low populations in some parts of the Arctic have raised concerns about the spread of these fundamental changes to tundra food web dynamics. By compiling 24 unique time series of lemming population fluctuations across the circumpolar region, we show that virtually all populations displayed alternating periods of cyclic/non-cyclic fluctuations over the past four decades. Cyclic patterns were detected 55% of the time (n = 649 years pooled across sites) with a median periodicity of 3.7 years, and non-cyclic periods were not more frequent in recent years. Overall, there was an indication for a negative effect of warm spells occurring during the snow onset period of the preceding year on lemming abundance. However, winter duration or early winter climatic conditions did not differ on average between cyclic and non-cyclic periods. Analysis of the time series shows that there is presently no Arctic-wide collapse of lemming cycles, even though cycles have been sporadic at most sites during the last decades. Although non-stationary dynamics appears a common feature of lemming populations also in the past, continued warming in early winter may decrease the frequency of periodic irruptions with negative consequences for tundra ecosystems.

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.

The Adaption to Online Synchronous Teaching and Voice Fatigue: Acoustic and Clinical Data.

At the onset of the COVID-19 pandemic in 2020, educators around the world suddenly shifted to online teaching., In 2021, we presented research on the impact of this new professional reality on the vocal load of Saint Petersburg State University professors. The online synchronous teaching caused the significant increase in the vocal fatigue in university professors in comparison with the prepandemic studies. We continued our study during the postpandemic semester (winter-spring 2022). The goal of this study was to find out whether adaptation mechanisms during the pandemic period were developed to adjust to the different types of teaching modes. The acoustic and clinical data from the pre/post comparative study are now presented.

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.

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.

Automatic detection of pupil reactions in cataract surgery videos.

In the light of an increased use of premium intraocular lenses (IOL), such as EDOF IOLs, multifocal IOLs or toric IOLs even minor intraoperative complications such as decentrations or an IOL tilt, will hamper the visual performance of these IOLs. Thus, the post-operative analysis of cataract surgeries to detect even minor intraoperative deviations that might explain a lack of a post-operative success becomes more and more important. Up-to-now surgical videos are evaluated by just looking at a very limited number of intraoperative data sets, or as done in studies evaluating the pupil changes that occur during surgeries, in a small number intraoperative picture only. A continuous measurement of pupil changes over the whole surgery, that would achieve clinically more relevant data, has not yet been described. Therefore, the automatic retrieval of such events may be a great support for a post-operative analysis. This would be especially true if large data files could be evaluated automatically. In this work, we automatically detect pupil reactions in cataract surgery videos. We employ a Mask R-CNN architecture as a segmentation algorithm to segment the pupil and iris with pixel-based accuracy and then track their sizes across the entire video. We can detect pupil reactions with a harmonic mean (H) of Recall, Precision, and Ground Truth Coverage Rate (GTCR) of 60.9% and average prediction length (PL) of 18.93 seconds. However, we consider the best configuration for practical use the one with the H value of 59.4% and PL of 10.2 seconds, which is much shorter. We further investigate the generalization ability of this method on a slightly different dataset without retraining the model. In this evaluation, we achieve the H value of 49.3% with the PL of 18.15 seconds.

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.

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.

Next generation sequencing analysis of consecutive Russian patients with clinical suspicion of inborn errors of immunity.

Primary immune deficiencies are usually attributed to genetic defects and, therefore, frequently referred to as inborn errors of immunity (IEI). We subjected the genomic DNA of 333 patients with clinical signs of IEI to next generation sequencing (NGS) analysis of 344 immunity-related genes and, in some instances, additional genetic techniques. Genetic causes of the disease were identified in 69/333 (21%) of subjects, including 11/18 (61%) of children with syndrome-associated IEIs, 45/202 (22%) of nonsyndromic patients with Jeffrey Modell Foundation (JMF) warning signs, 9/56 (16%) of subjects with periodic fever, 3/30 (10%) of cases of autoimmune cytopenia, 1/21 (5%) of patients with unusually severe infections and 0/6 (0%) of individuals with isolated elevation of IgE level. There were unusual clinical observations: twins with severe immunodeficiency carried a de novo CHARGE syndrome-associated SEMA3E c.2108C>T (p.S703L) allele; however, they lacked clinical features of CHARGE syndrome. Additionally, there were genetically proven instances of Netherton syndrome, Х-linked agammaglobulinemia, severe combined immune deficiency (SCID), IPEX and APECED syndromes, among others. Some patients carried recurrent pathogenic alleles, such as AIRE c.769C>T (p.R257*), NBN c.657del5, DCLRE1C c.103C>G (p.H35D), NLRP12 c.1054C>T (p.R352C) and c.910C>T (p.H304Y). NGS is a powerful tool for high-throughput examination of patients with malfunction of immunity.

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.

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).

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.

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?'

Flexibility in a changing arctic food web: Can rough-legged buzzards cope with changing small rodent communities?

Indirect effects of climate change are often mediated by trophic interactions and consequences for individual species depend on how they are tied into the local food web. Here we show how the response of demographic rates of an arctic bird of prey to fluctuations in small rodent abundance changed when small rodent community composition and dynamics changed, possibly under the effect of climate warming. We observed the breeding biology of rough-legged buzzards (Buteo lagopus) at the Erkuta Tundra Monitoring Site in southern Yamal, low arctic Russia, for 19 years (1999-2017). At the same time, data on small rodent abundance were collected and information on buzzard diet was obtained from pellet dissection. The small rodent community experienced a shift from high-amplitude cycles to dampened fluctuations paralleled with a change in species composition toward less lemmings and more voles. Buzzards clearly preferred lemmings as prey. Breeding density of buzzards was positively related to small rodent abundance, but the shift in small rodent community lead to lower numbers relative to small rodent abundance. At the same time, after the change in small rodent community, the average number of fledglings was higher relative to small rodent abundance than earlier. These results suggest that the buzzard population adapted to a certain degree to the changes in the major resource, although at the same time density declined. The documented flexibility in the short-term response of demographic rates to changes in structure and dynamics of key food web components make it difficult to predict how complex food webs will be transformed in a warmer Arctic. The degree of plasticity of functional responses is indeed likely to vary between species and between regions, depending also on the local food web context.

Predator traits determine food-web architecture across ecosystems.

Predator-prey interactions in natural ecosystems generate complex food webs that have a simple universal body-size architecture where predators are systematically larger than their prey. Food-web theory shows that the highest predator-prey body-mass ratios found in natural food webs may be especially important because they create weak interactions with slow dynamics that stabilize communities against perturbations and maintain ecosystem functioning. Identifying these vital interactions in real communities typically requires arduous identification of interactions in complex food webs. Here, we overcome this obstacle by developing predator-trait models to predict average body-mass ratios based on a database comprising 290 food webs from freshwater, marine and terrestrial ecosystems across all continents. We analysed how species traits constrain body-size architecture by changing the slope of the predator-prey body-mass scaling. Across ecosystems, we found high body-mass ratios for predator groups with specific trait combinations including (1) small vertebrates and (2) large swimming or flying predators. Including the metabolic and movement types of predators increased the accuracy of predicting which species are engaged in high body-mass ratio interactions. We demonstrate that species traits explain striking patterns in the body-size architecture of natural food webs that underpin the stability and functioning of ecosystems, paving the way for community-level management of the most complex natural ecosystems.