The Functions of N6-Methyladenosine in Nuclear RNAs.

N6-methyladenosine (m6A) is one of the most common modifications in both eukaryotic and prokaryotic mRNAs. It has been experimentally confirmed that m6A methylation is involved in the regulation of stability and translation of various mRNAs. Until recently, the majority of m6A-related studies have been focused on the cytoplasmic functions of this modification. Here, we review new data on the role of m6A in several key biological processes taking place in the cell nucleus, such as transcription, chromatin organization, splicing, nuclear-cytoplasmic transport, and R-loop metabolism. Based on analysis of these data, we suggest that m6A methylation of nuclear RNAs is another level of gene expression regulation which, together with DNA methylation and histone modifications, controls chromatin structure and functioning in various biological contexts.

Ca2+ -depended signaling pathways regulate self-renewal and pluripotency of stem cells.

Ca2+ -mediated signaling is widely spread in nature and plays critical role in the individual development of various organisms ranging from microorganisms to mammals. In vertebrates, Ca2+ is involved in important developmental events: fertilization, body plan establishment, and organogenesis. The two later events are defined by embryonic stem cells (ESCs). ESCs are capable of self-renewal and are pluripotent by nature, that is, can give rise to all types of cells that make up the body. Given the paramount importance of Ca2+ signalization in the development, it is therefore not surprising this process also plays role in the biology of stem cells. In this review, we scrutinize the published experimental data on the role of Ca2+ ions in embryonic stem cells self-renewal and pluripotency. In line with this, we also discuss possible mechanisms of p53 inhibition as a major hindrance to self-renewal of ESCs. Finally, we argue about the role of G-protein-coupled receptors (GPCRs), the largest family of heteromeric transmembrane receptors, and GPCR-mediated signalization in stem cells, and propose the role for the GPCR-G-protein-PLC-Ca2+ -downstream signaling pathway in the regulation of pluripotency of both mouse and human ESCs.

ATMIN is a transcriptional regulator of both lung morphogenesis and ciliogenesis.

Initially identified in DNA damage repair, ATM-interactor (ATMIN) further functions as a transcriptional regulator of lung morphogenesis. Here we analyse three mouse mutants, Atmin(gpg6/gpg6), Atmin(H210Q/H210Q) and Dynll1(GT/GT), revealing how ATMIN and its transcriptional target dynein light chain LC8-type 1 (DYNLL1) are required for normal lung morphogenesis and ciliogenesis. Expression screening of ciliogenic genes confirmed Dynll1 to be controlled by ATMIN and further revealed moderately altered expression of known intraflagellar transport (IFT) protein-encoding loci in Atmin mutant embryos. Significantly, Dynll1(GT/GT) embryonic cilia exhibited shortening and bulging, highly similar to the characterised retrograde IFT phenotype of Dync2h1. Depletion of ATMIN or DYNLL1 in cultured cells recapitulated the in vivo ciliogenesis phenotypes and expression of DYNLL1 or the related DYNLL2 rescued the effects of loss of ATMIN, demonstrating that ATMIN primarily promotes ciliogenesis by regulating Dynll1 expression. Furthermore, DYNLL1 as well as DYNLL2 localised to cilia in puncta, consistent with IFT particles, and physically interacted with WDR34, a mammalian homologue of the Chlamydomonas cytoplasmic dynein 2 intermediate chain that also localised to the cilium. This study extends the established Atmin-Dynll1 relationship into a developmental and a ciliary context, uncovering a novel series of interactions between DYNLL1, WDR34 and ATMIN. This identifies potential novel components of cytoplasmic dynein 2 and furthermore provides fresh insights into the molecular pathogenesis of human skeletal ciliopathies.

From the principle of sustainable non-equilibrium to sustainable development.

Ervin Bauer was Hungarian and Soviet scientist, who had a short, but bright and talented life. In 1935, working at the Institute of Experimental Medicine in the USSR, he published the book «Theoretical Biology¼, in which he proposed an idea of a special "non-equilibrium" state of living systems and the existence of internal machineries in the organism that work against thermodynamic equilibrium and increase the organism's capacity for work. Currently, this idea is called "the principle of sustainable non-equilibrium" or "Bauer's principle". During the repressions of the 1930s in the USSR, Bauer was executed, the book « Theoretical Biology¼ was banned. Currently, his works are poorly known, especially outside the post-socialist region. We believe that his ideas could help in rethinking not only the biochemistry and bioenergetics of cells and tissues of living organisms, but also biogeochemical and civilizational processes on a planetary scale.

Diversity and abundance of soil macroinvertebrates along a contamination gradient in the Central Urals, Russia.

BACKGROUND: Since the late 1980s, long-term monitoring of terrestrial ecosystems in metal-contaminated areas near the Middle Ural Copper Smelter has been carried out in the Central Urals. As a part of these monitoring programmes, the data on species diversity, community composition and abundance of soil macroinvertebrates continue to be gathered. NEW INFORMATION: The dataset (available from the GBIF network at https://www.gbif.org/dataset/61e92984-382b-4158-be6b-e391c7ed5a64) includes a 2004 census for soil macroinvertebrates of spruce-fir forests along a pollution gradient in the Central Urals. The dataset describes soil macrofauna's abundance (the number of individuals per sample, i.e. the density) and community structure (list of supraspecific taxa, list of species for most abundant taxa and supraspecific taxa or species abundance). Seventeen sampling plots differed in the levels of toxic metal (Cu, Zn, Pb, Cd and Fe) soil contamination from air emissions of the Middle Ural Copper Smelter (heavily polluted, moderately polluted and unpolluted areas). The dataset consists of 340 sampling events (= samples corresponding to upper and lower layers of the 170 soil monoliths) and 64658 rows (2907 and 61751 for non-zero and zero density of taxa, respectively). Arachnida (Araneae and Opiliones), Carabidae (imagoes), Elateridae (larvae), Chilopoda, Diplopoda, Gastropoda, Staphylinidae (imagoes) and Lumbricidae were identified to species level. In contrast, Mermithida, Enchytraeidae, Lepidoptera larvae, Diptera larvae, Hemiptera, Hymenoptera and some other insects were identified to family or order levels. In total, 8430 individuals of soil macroinvertebrates were collected in two soil layers (organic and organic-mineral horizons), including 1046 Arachnida (spiders and harvestmen), 45 Carabidae, 300 Elateridae, 529 Myriapoda, 741 Gastropoda, 437 Staphylinidae, 623 Lumbricidae and 4709 other invertebrates. The presence-absence data on each taxon are provided for each sampling event. An overwhelming majority of such absences can be interpreted as "pseudo-absences" at the scale of sampling plots or study sites. The dataset contains information helpful for long-term ecotoxicological monitoring of forest ecosystems and contributes to studying soil macrofauna diversity in the Urals.

Memetic approach to cultural evolution.

Charles Darwin, the founder of the idea of natural selection, believed that this selection is not limited exclusively to biology: changes in language, consciousness, and technology are also adaptive. The transmission of culture is not a human prerogative. To date, several approaches for the understanding of the biological basis of cultural evolution were developed. Memetics stands out among other interdisciplinary theories that consider the development of culture and society through the prism of biological phenomena, because it is based on the concept of the biological replicator, meme and the mechanisms of cultural evolution are understood by analogy with biological evolution. The concepts of the biological and cultural replicators are similar; however, the nature of memes and the specific mechanisms of their replication are still poorly understood. In this review, we consider the strengths and weaknesses of the memetic approach to the study of cultural phenomena in the context of the cultural and technological evolution of mankind.

Long-term dynamics of the abundance of earthworms and enchytraeids (Annelida, Clitellata: Lumbricidae, Enchytraeidae) in forests of the Central Urals, Russia.

BACKGROUND: Since the late 1980s, long-term monitoring of terrestrial ecosystems in metal-contaminated areas has been carried out in the Central Urals. As a part of these monitoring programmes, the data on soil macroinvertebrates in undisturbed areas as reference sites continues to be gathered. These data help study the local biodiversity and long-term dynamics of soil macroinvertebrate abundance in non-polluted areas. NEW INFORMATION: The dataset (available from the GBIF network at https://www.gbif.org/dataset/bf5bc7f6-71a3-4abd-8abc-861ee3cbf84a) includes information from a long-term monitoring programme for two taxa of Annelids, Lumbricidae and Enchytraeidae, which dwell in the topsoil of spruce-fir, birch, pine and floodplain forests in the Central Urals. The dataset includes information on the earthworm community structure (list of species, species abundance, number of egg cocoons, cocoon exuvia, juveniles and adults) and enchytraeid abundance. The dataset consists of 553 sampling events (= samples, corresponding to upper and lower layers of the soil monoliths) and 12739 occurrences (earthworms, mainly identified to species and earthworm cocoons and enchytraeids, identified to family) collected during 1990-1991, 2004, 2014-2016 and 2018-2020. In total, 3305 individuals of earthworms were collected, representing ten (out of twelve) species and all eight genera recorded for the fauna of the Central Urals. In addition, 7292 earthworm egg cocoons and cocoon exuvia and 6926 individuals of enchytraeids were accumulated. The presence-absence data on each of the ten earthworm species, egg cocoons, cocoon exuvia and enchytraeids are provided for each sampling event. All data were collected in undisturbed non-polluted areas and are used as a local reference for ecotoxicological monitoring. The dataset provides valuable information for estimating the composition and abundance of earthworm communities in different habitats over a long time and contributes to the study of soil fauna biodiversity in the Urals.

Analysis of the asymmetrically expressed Ablim1 locus reveals existence of a lateral plate Nodal-independent left sided signal and an early, left-right independent role for nodal flow.

BACKGROUND: Vertebrates show clear asymmetry in left-right (L-R) patterning of their organs and associated vasculature. During mammalian development a cilia driven leftwards flow of liquid leads to the left-sided expression of Nodal, which in turn activates asymmetric expression of the transcription factor Pitx2. While Pitx2 asymmetry drives many aspects of asymmetric morphogenesis, it is clear from published data that additional asymmetrically expressed loci must exist. RESULTS: A L-R expression screen identified the cytoskeletally-associated gene, actin binding lim protein 1 (Ablim1), as asymmetrically expressed in both the node and left lateral plate mesoderm (LPM). LPM expression closely mirrors that of Nodal. Significantly, Ablim1 LPM asymmetry was detected in the absence of detectable Nodal. In the node, Ablim1 was initially expressed symmetrically across the entire structure, resolving to give a peri-nodal ring at the headfold stage in a flow and Pkd2-dependent manner. The peri-nodal ring of Ablim1 expression became asymmetric by the mid-headfold stage, showing stronger right than left-sided expression. Node asymmetry became more apparent as development proceeded; expression retreated in an anticlockwise direction, disappearing first from the left anterior node. Indeed, at early somite stages Ablim1 shows a unique asymmetric expression pattern, in the left lateral plate and to the right side of the node. CONCLUSION: Left LPM Ablim1 is expressed in the absence of detectable LPM Nodal, clearly revealing existence of a Pitx2 and Nodal-independent left-sided signal in mammals. At the node, a previously unrecognised action of early nodal flow and Pkd2 activity, within the pit of the node, influences gene expression in a symmetric manner. Subsequent Ablim1 expression in the peri-nodal ring reveals a very early indication of L-R asymmetry. Ablim1 expression analysis at the node acts as an indicator of nodal flow. Together these results make Ablim1 a candidate for controlling aspects of L-R identity and patterning.

The novel mouse mutant, chuzhoi, has disruption of Ptk7 protein and exhibits defects in neural tube, heart and lung development and abnormal planar cell polarity in the ear.

BACKGROUND: The planar cell polarity (PCP) signalling pathway is fundamental to a number of key developmental events, including initiation of neural tube closure. Disruption of the PCP pathway causes the severe neural tube defect of craniorachischisis, in which almost the entire brain and spinal cord fails to close. Identification of mouse mutants with craniorachischisis has proven a powerful way of identifying molecules that are components or regulators of the PCP pathway. In addition, identification of an allelic series of mutants, including hypomorphs and neomorphs in addition to complete nulls, can provide novel genetic tools to help elucidate the function of the PCP proteins. RESULTS: We report the identification of a new N-ethyl-N-nitrosourea (ENU)-induced mutant with craniorachischisis, which we have named chuzhoi (chz). We demonstrate that chuzhoi mutant embryos fail to undergo initiation of neural tube closure, and have characteristics consistent with defective convergent extension. These characteristics include a broadened midline and reduced rate of increase of their length-to-width ratio. In addition, we demonstrate disruption in the orientation of outer hair cells in the inner ear, and defects in heart and lung development in chuzhoi mutants. We demonstrate a genetic interaction between chuzhoi mutants and both Vangl2Lp and Celsr1Crsh mutants, strengthening the hypothesis that chuzhoi is involved in regulating the PCP pathway. We demonstrate that chuzhoi maps to Chromosome 17 and carries a splice site mutation in Ptk7. This mutation results in the insertion of three amino acids into the Ptk7 protein and causes disruption of Ptk7 protein expression in chuzhoi mutants. CONCLUSIONS: The chuzhoi mutant provides an additional genetic resource to help investigate the developmental basis of several congenital abnormalities including neural tube, heart and lung defects and their relationship to disruption of PCP. The chuzhoi mutation differentially affects the expression levels of the two Ptk7 protein isoforms and, while some Ptk7 protein can still be detected at the membrane, chuzhoi mutants demonstrate a significant reduction in membrane localization of Ptk7 protein. This mutant provides a useful tool to allow future studies aimed at understanding the molecular function of Ptk7.

Professor Lev Beloussov and the birth of morphomechanics.

The first explanations of the mechanisms of development of living organisms were proposed in antiquity. At that time two competing ideas existed, about the strict determination of embryonic structures (we call it the "Hippocrates line") and about the possible formation of structures from the unstructured condition ("Aristotle line"). We can trace the opposition between the "Hippocrates line" and "Aristotle line" from antiquity till the present time. At the end of the XIX century, experimental investigation of the mechanisms of integrity of development had started. In the XX century, the "Aristotle line" finds its expression in the Morphogenetic Field Theory of A.G. Gurwitsch, according to which cells of the organism are integrated in an organic whole. Since the 1970s, mechanical forces and tensions have been considered as integral factors of ontogenesis. One of the most productive scientific teams which worked in this area was the laboratory of Professor L.V. Beloussov from the Lomonossov Moscow State University, Russia. In the 1970s, Lev Beloussov and his colleagues discovered the presence of "passive" and "active" (i.e. metabolically-dependent) mechanical stresses in the tissues of developing organisms, their organization and stage-specific patterns. In 1980-1990 s, a lot of experimental data about the role of the patterns of mechanical stresses in morphogenesis and cell differentiation was accumulated. Based on the experimental data, Professor Beloussov and his colleagues developed a theory of the regulation of the development of living organisms on the basis of the interaction of passive and active mechanical stresses (Belousov-Mittenthal Theory), which forms the basis of a new science - morphomechanics.

Morphomechanical reactions and mechanically stressed structures in amphibian embryos, as related to gastrulation and axial organs formation.

Reactions of embryonic tissues to a distributed and concentrated stretching are described and compared with the mechanics of the normal gastrulation movements. A role of mechanically stressed dynamic cell structures in the gastrulation, demarcation of notochord borders and in providing proportionality of the axial rudiments is demonstrated. A morphomechanical scheme of amphibian gastrulation is presented.

Gastrulation in amphibian embryos, regarded as a succession of biomechanical feedback events.

Gastrulation in amphibian embryos is a composition of several differently located morphogenetic movements which are perfectly coordinated with each other both in space and time. We hypothesize that this coordination is mediated by biomechanical interactions between different parts of a gastrulating embryo based upon the tendency of each part to hyper-restore the value of its mechanical stress. The entire process of gastrulation in amphibian embryos is considered as a chain of these mutually coupled reactions, which are largely dependent upon the geometry of a given embryo part. We divide gastrulation into several partly overlapped steps, give a theoretical interpretation for each of them, formulate the experiments for testing our interpretation and describe the experimental results which confirm our point of view. Among the predicted experimental results are: inhibition of radial cell intercalation by relaxation of tensile stresses at the blastula stage; inversion of convergent intercalation movements by relaxation of circumferential stresses at the early gastrula stage; stress-promoted reorientation of axial rudiments, and others. We also show that gastrulation is going on under a more or less constant average value of tensile stresses which may play a role as rate-limiting factors. A macro-morphological biomechanical approach developed in this paper is regarded as complementary to exploring the molecular machinery of gastrulation.

Primary Cilia as a Possible Link between Left-Right Asymmetry and Neurodevelopmental Diseases.

Cilia have multiple functions in the development of the entire organism, and participate in the development and functioning of the central nervous system. In the last decade, studies have shown that they are implicated in the development of the visceral left-right asymmetry in different vertebrates. At the same time, some neuropsychiatric disorders, such as schizophrenia, autism, bipolar disorder, and dyslexia, are known to be associated with lateralization failure. In this review, we consider possible links in the mechanisms of determination of visceral asymmetry and brain lateralization, through cilia. We review the functions of seven genes associated with both cilia, and with neurodevelopmental diseases, keeping in mind their possible role in the establishment of the left-right brain asymmetry.

Current genome editing tools in gene therapy: new approaches to treat cancer.

Gene therapy suggests a promising approach to treat genetic diseases by applying genes as pharmaceuticals. Cancer is a complex disease, which strongly depends on a particular genetic make-up and hence can be treated with gene therapy. From about 2,000 clinical trials carried out so far, more than 60% were cancer targeted. Development of precise and effective gene therapy approaches is intimately connected with achievements in the molecular biology techniques. The field of gene therapy was recently revolutionized by the introduction of "programmable" nucleases, including ZFNs, TALENs, and CRISPR, which target specific genomic loci with high efficacy and precision. Furthermore, when combined with DNA transposons for the delivery purposes into cells, these programmable nucleases represent a promising alternative to the conventional viral-mediated gene delivery. In addition to "programmable" nucleases, a new class of TALE- and CRISPR-based "artificial transcription effectors" has been developed to mediate precise regulation of specific genes. In sum, these new molecular tools may be used in a wide plethora of gene therapy strategies. This review highlights the current status of novel genome editing tools and discusses their suitability and perspectives in respect to cancer gene therapy studies.

A role for intracellular calcium downstream of G-protein signaling in undifferentiated human embryonic stem cell culture.

Multiple signalling pathways maintain human embryonic stem cells (hESC) in an undifferentiated state. Here we sought to define the significance of G protein signal transduction in the preservation of this state distinct from other cellular processes. Continuous treatment with drugs targeting G(αs)-, G(α-i/o)- and G(α-q/11)-subunit signalling mediators were assessed in independent hESC lines after 7days to discern effects on normalised alkaline phosphatase positive colony frequency vs total cell content. This identified PLCß, intracellular free calcium and CAMKII kinase activity downstream of G(α-q/11) as of particular importance to the former. To confirm the significance of this finding we generated an agonist-responsive hESC line transgenic for a G(α-q/11) subunit-coupled receptor and demonstrated that an undifferentiated state could be promoted in the presence of an agonist without exogenously supplied bFGF and that this correlated with elevated intracellular calcium. Similarly, treatment of unmodified hESCs with a range of intracellular free calcium-modulating drugs in biologically defined mTESR culture system lacking exogenous bFGF promoted an hESC phenotype after 1week of continuous culture as defined by co-expression of OCT4 and NANOG. At least one of these drugs, lysophosphatidic acid significantly elevates phosphorylation of calmodulin and STAT3 in this culture system (p<0.05). These findings substantiate a role for G-protein and calcium signalling in undifferentiated hESC culture.

Mouse mutagenesis identifies novel roles for left-right patterning genes in pulmonary, craniofacial, ocular, and limb development.

Vertebrate organs show consistent left-right (L-R) asymmetry in placement and patterning. To identify genes involved in this process we performed an ENU-based genetic screen. Of 135 lines analyzed 11 showed clear single gene defects affecting L-R patterning, including 3 new alleles of known L-R genes and mutants in novel L-R loci. We identified six lines (termed "gasping") that, in addition to abnormal L-R patterning and associated cardiovascular defects, had complex phenotypes including pulmonary agenesis, exencephaly, polydactyly, ocular and craniofacial malformations. These complex abnormalities are present in certain human disease syndromes (e.g., HYLS, SRPS, VACTERL). Gasping embryos also show defects in ciliogenesis, suggesting a role for cilia in these human congenital malformation syndromes. Our results indicate that genes controlling ciliogenesis and left-right asymmetry have, in addition to their known roles in cardiac patterning, major and unexpected roles in pulmonary, craniofacial, ocular and limb development with implications for human congenital malformation syndromes.