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Gap junctional (GJ) intercellular channels are an important way of intercellular communication. Currently, two unrelated families of GJ proteins, innexins/pannexins, and connexins, are known, either or both of which are present in most multicellular animals. A striking exception is the echinoderms which have functional GJs but until recently were believed to be lacking both innexins and connexins, which suggests the presence of the third, yet the unknown family of GJ proteins. In the recent work Welzel and Schuster (Welzel and Schuster, 2022) have reported several putative innexins and one connexin from echinoderms, therefore undermining such a hypothesis. Here we provide evidence showing that all reported connexin and innexin sequences from echinoderms are cross-species contaminations, indicating that a search for a third GJ protein family is still a subject of immediate scientific research interest.

Over the past decade, molecular phylogenetics has reshaped our understanding of the fungal tree of life by unraveling a hitherto elusive diversity of the protistan relatives of Fungi. Aphelida constitutes one of these novel deep branches that precede the emergence of osmotrophic fungal lifestyle and hold particular significance as the pathogens of algae. Here, we obtain and analyze the genomes of aphelid species Amoeboaphelidium protococcarum and Amoeboaphelidium occidentale. Genomic data unmask the vast divergence between these species, hidden behind their morphological similarity, and reveal hybrid genomes with a complex evolutionary history in two strains of A. protococcarum. We confirm the proposed sister relationship between Aphelida and Fungi using phylogenomic analysis and chart the reduction of characteristic proteins involved in phagocytic activity in the evolution of Holomycota. Annotation of aphelid genomes demonstrates the retention of actin nucleation-promoting complexes associated with phagocytosis and amoeboid motility and also reveals a conspicuous expansion of receptor-like protein kinases, uncharacteristic of fungal lineages. We find that aphelids possess multiple carbohydrate-processing enzymes that are involved in fungal cell wall synthesis but do not display rich complements of algal cell-wall-processing enzymes, suggesting an independent origin of fungal plant-degrading capabilities. Aphelid genomes show that the emergence of Fungi from phagotrophic ancestors relied on a common cell wall synthetic machinery but required a different set of proteins for digestion and interaction with the environment.

ᅟ Some tumor cells can evolve into transmissible parasites. Notable examples include the Tasmanian devil facial tumor disease, the canine transmissible venereal tumor and transmissible cancers of mollusks. We present a hypothesis that such transmissible tumors existed in the past and that some modern animal taxa are descendants of these tumors. We expect potential candidates for SCANDALs (speciated by cancer development animals) to be simplified relatives of more complex metazoans and have genomic alterations typical for cancer progression (such as deletions of universal apoptosis genes). We considered several taxa of simplified animals for our hypothesis: dicyemida, orthonectida, myxosporea and trichoplax. Based on genomic analysis we conclude that Myxosporea appear to be the most suitable candidates for a tumor ancestry. They are simplified parasitic cnidarians that universally lack major genes implicated in cancer progression including all genes with Caspase and BCL2 domains as well as any p53 and apoptotic protease activating factor – 1 (Apaf-1) homologs, suggesting the disruption of main apoptotic pathways in their early evolutionary history. Further comparative genomics and single-cell transcriptomic studies may be helpful to test our hypothesis of speciation via a cancerous stage. Reviewers This article was reviewed by Eugene Koonin, Mikhail Gelfand and Gregory M Woods. Electronic supplementary material The online version of this article (10.1186/s13062-019-0233-1) contains supplementary material, which is available to authorized users.

In humans and other vertebrates pannexin protein family was discovered by homology to invertebrate gap junction proteins. Several biological functions were attributed to three vertebrate pannexins members. Six clinically significant independent variants of the PANX1 gene lead to human infertility and oocyte development defects, and the Arg217His variant was associated with pronounced symptoms of primary ovarian failure, severe intellectual disability, sensorineural hearing loss, and kyphosis. At the same time, only mild phenotypes were observed in Panx1 knockout mice. In addition, a passenger mutation was identified in a popular line of Panx1 knockout mice, questioning even those effects. Using CRISPR/Cas9, we created a new line of Panx1 knockout mice and a new line of mice with the clinically significant Panx1 substitution (Arg217His). In both cases, we observed no significant changes in mouse size, weight, or fertility. In addition, we attempted to reproduce a previous study on sleep/wake and locomotor activity functions in Panx1 knockout mice and found that previously reported effects were probably not caused by the Panx1 knockout itself. We consider that the pathological role of Arg217His substitution in Panx1, and some Panx1 functions in general calls for a re-evaluation.

Background SARS-CoV-2 is a novel coronavirus that causes COVID-19 infection, with a closest known relative found in bats. For this virus, hundreds of genomes have been sequenced. This data provides insights into SARS-CoV-2 adaptations, determinants of pathogenicity and mutation patterns. A comparison between patterns of mutations that occurred before and after SARS-CoV-2 jumped to human hosts may reveal important evolutionary consequences of zoonotic transmission. Methods We used publically available complete genomes of SARS-CoV-2 to calculate relative frequencies of single nucleotide variations. These frequencies were compared with relative substitutions frequencies between SARS-CoV-2 and related animal coronaviruses. A similar analysis was performed for human coronaviruses SARS-CoV and HKU1. Results We found a 9-fold excess of G–U transversions among SARS-CoV-2 mutations over relative substitution frequencies between SARS-CoV-2 and a close relative coronavirus from bats (RaTG13). This suggests that mutation patterns of SARS-CoV-2 have changed after transmission to humans. The excess of G–U transversions was much smaller in a similar analysis for SARS-CoV and non-existent for HKU1. Remarkably, we did not find a similar excess of complementary C–A mutations in SARS-CoV-2. We discuss possible explanations for these observations.

Pannexin 1 (Panx1) forms plasma membrane channels that release ATP, an important vascular tone regulator. However, despite the abundant expression of Panx1 in the vascular system, its effects on smooth muscle contraction are not evident in all arteries. In this study, we tested the hypothesis that the functional consequences of Panx1 deficiency can be masked by the augmented action of ATP secreted in a Panx1-independent way. Experiments were performed on small mesenteric arteries obtained from Panx1-knockout (Panx1–/–) and C57Bl/6 (Panx1+/+) male mice using wire myography of endothelium-denuded arterial preparations and reverse-transcription quantitative PCR techniques. Arterial contractile responses to phenylephrine did not differ in two experimental groups. Ecto-ATPase inhibitor ARL67156 (100 μM) potentiated the responses to phenylephrine in Panx1+/+ but not in Panx1–/–, while ARL67156 did not affect the contractile responses to the thromboxane A2 receptor agonist in any of the two groups. Contractile responses to exogenous ATP (10 μM) were smaller in Panx1+/+ than in Panx1–/– mice. By contrast, NTPDase1 mRNA content was higher in Panx1+/+ than in Panx1–/– mice. These results suggest that ATP released from smooth muscle cells through Panx1 channels can potentiate contractile responses of murine mesenteric arteries upon activation of α1-adrenoceptors. In Panx1–/– mice an increased arterial ATP sensitivity and diminished NTPDase1 activity may augment the contractile effects of Panx1-independent ATP.

Pannexins are membrane channel proteins that play a role in a number of critical biological processes (Panchin et al., 2000; Shestopalov, Panchin, 2008). Among other cellular functions, pannexin hemichannels serve as purine nucleoside conduits providing ATP efflux into the extracellular space (Dahl, 2015), where it is rapidly degraded to adenosine. Pannexin1 (Panx1) is abundantly expressed in the brain and has been shown to contribute to adenosine signaling in nervous system tissues (Prochnow et al., 2012). We hypothesized that pannexin1 may contribute to sleep-wake cycle regulation through extracellular adenosine, a well-established paracrine factor in slow wave sleep. To investigate this link, EEG and movement activity throughout the light/dark cycle were compared in Panx1-/- and Panx1+/+ mice. We found a significant increase in waking and a correspondent decrease in slow wave sleep percentages in the Panx1-/- animals. These changes were especially pronounced during the dark period. Furthermore, we found a significant increase in movement activity of Panx1-/- mice. These findings are consistent with the hypothesis that extracellular adenosine is relatively depleted in Panx1-/- animals due to the absence of the ATP-permeable hemichannels. At the same time, sleep rebound after a 6-h sleep deprivation remained unchanged in Panx1-/- mice as compared to the control animals. Behavioral tests revealed that Panx1-/- mice were significantly faster during their descent along the vertical pole but more sluggish during their run through the horizontal pole as compared to the control mice.

Inverted repeats are common DNA elements, but they rarely overlap with protein-coding sequences due to the ensuing conflict with the structure and function of the encoded protein. We discovered numerous perfect inverted repeats of considerable length (up to 284 bp) embedded within the protein-coding genes in mitochondrial genomes of four Nematomorpha species. Strikingly, both arms of the inverted repeats encode conserved regions of the amino acid sequence. We confirmed enzymatic activity of the respiratory complex I encoded by inverted repeat-containing genes. The nucleotide composition of inverted repeats suggests strong selection at the amino acid level in these regions. We conclude that the inverted repeat-containing genes are transcribed and translated into functional proteins. The survey of available mitochondrial genomes reveals that several other organisms possess similar albeit shorter embedded repeats. Mitochondrial genomes of Nematomorpha demonstrate an extraordinary evolutionary compromise where protein function and stringent secondary structure elements within the coding regions are preserved simultaneously.

Two enigmatic groups of morphologically simple parasites of invertebrates, the Dicyemida (syn. Rhombozoa) and the Orthonectida, since the 19th century have been usually considered as two classes of the phylum Mesozoa. Early molecular evidence suggested their relationship within the Spiralia (=Lophotrochozoa), however, high rates of dicyemid and orthonectid sequence evolution led to contradicting phylogeny reconstructions. Genomic data for orthonectids revealed that they are highly simplified spiralians and possess a reduced set of genes involved in metazoan development and body patterning. Acquiring genomic data for dicyemids, however, remains a challenge due to complex genome rearrangements including chromatin diminution and generation of extrachromosomal circular DNAs, which are reported to occur during the development of somatic cells. We performed genomic sequencing of one species of Dicyema, and obtained transcriptomic data for two Dicyema spp. Homeodomain (homeobox) transcription factors, G-protein-coupled receptors, and many other protein families have undergone a massive reduction in dicyemids compared to other animals. There is also apparent reduction of the bilaterian gene complements encoding components of the neuromuscular systems. We constructed and analyzed a large dataset of predicted orthologous proteins from three species of Dicyema and a set of spiralian animals including the newly sequenced genome of the orthonectid Intoshia linei. Bayesian analyses recovered the orthonectid lineage within the Annelida. In contrast, dicyemids form a separate clade with weak affinity to the Rouphozoa (Platyhelminthes plus Gastrotricha) or (Entoprocta plus Cycliophora) suggesting that the historically proposed Mesozoa is a polyphyletic taxon. Thus, dramatic simplification of body plans in dicyemids and orthonectids, as well as their intricate life cycles that combine metagenesis and heterogony, evolved independently in these two lineages.

Background Gap junctions (GJ) are one of the most common forms of intercellular communication. GJs are assembled from proteins that form channels connecting the cytoplasm of adjacent cells. They are considered to be the main or the only type of intercellular channels and the universal feature of all multicellular animals. Two unrelated protein families are currently considered to be involved in this function, namely, connexins and pannexins (pannexins/innexins). Pannexins were hypothesized to be the universal GJ proteins of multicellular animals, distinct from connexins that are characteristic of chordates only. Here we have revised this supposition by applying growing high throughput sequencing data from diverse metazoan species. Results Pannexins were found in Chordates, Ctenophores, Cnidarians, and in the most major groups of bilateral protostomes. Yet some metazoans appear to have neither connexins nor pannexins in their genomes. We detected no connexins or pannexins/innexins homologues in representatives of all five classes of echinoderms and their closest relatives hemichordates with available genomic sequences. Despite this, our intracellular recordings demonstrate direct electrical coupling between blastomeres at the 2-cell embryo of the echinoderm (starfish Asterias rubens). In these experiments, carboxyfluorescein fluorescent dye did not diffuse between electrically coupled cells. This excludes the possibility that the observed electrical coupling is mediated by incomplete cytoplasm separation during cleavage. Conclusion Functional GJs are present in representatives of the clade that lack currently recognized GJ protein families. New undiscovered protein families utilized for intercellular channels are predicted. It is possible that the new type(s) of intercellular channels are present in parallel to pannexin and connexin gap junctions in animal groups, other than Echinodermata.

The central pattern generator (CPG) is defined as a set of neurons involved in joint production of patterned motor output. The roundtable discussion on the CPG was a part of the 5th All-Russian Conference on Animal Behavior (Moscow, Nov. 21, 2012). The discussion centred on three core themes: 1) the mechanisms of the organization and reconfiguration of pattern generating neuronal ensembles, 2) extrapolations that extend the CPG concept beyond the motor systems, and 3) evolutionary and developmental aspects of CPG.

Summary Orthonectids are rare parasites of marine invertebrates [1] that are commonly treated in textbooks as a taxon of uncertain affinity [2]. Trophic forms of orthonectids reside in the tissues of their hosts as multinucleated plasmodia, generating short-lived, worm-like ciliated female and male organisms that exit into the environment for copulation [3]. These ephemeral males and females are composed of just several hundred somatic cells and are deprived of digestive, circulatory, or excretory systems. Since their discovery in the 19 th century, the orthonectids were described as organisms with no differentiated cell types and considered as part of Mesozoa, a putative link between multicellular animals and their unicellular relatives. More recently, this view was challenged as the new data suggested that orthonectids are animals that became simplified due to their parasitic way of life [3, 4]. Here, we report the genomic sequence of Intoshia linei , one of about 20 known species of orthonectids. The genomic data confirm recent morphological analysis asserting that orthonectids are members of Spiralia and possess muscular and nervous systems [5]. The 43-Mbp genome of I. linei encodes about 9,000 genes and retains those essential for the development and activity of muscular and nervous systems. The simplification of orthonectid body plan is associated with considerable reduction of metazoan developmental genes, leaving what might be viewed as the minimal gene set necessary to retain critical bilaterian features.

Many features of mitochondrial genomes of animals, such as patterns of gene arrangement, nucleotide content and substitution rate variation are extensively used in evolutionary and phylogenetic studies. Nearly 6,000 mitochondrial genomes of animals have already been sequenced, covering the majority of animal phyla. One of the groups that escaped mitogenome sequencing is phylum Kinorhyncha-an isolated taxon of microscopic worm-like ecdysozoans. The kinorhynchs are thought to be one of the early-branching lineages of Ecdysozoa, and their mitochondrial genomes may be important for resolving evolutionary relations between major animal taxa. Here we present the results of sequencing and analysis of mitochondrial genomes from two members of Kinorhyncha, Echinoderes svetlanae (Cyclorhagida) and Pycnophyes kielensis (Allomalorhagida). Their mitochondrial genomes are circular molecules approximately 15 Kbp in size. The kinorhynch mitochondrial gene sequences are highly divergent, which precludes accurate phylogenetic inference. The mitogenomes of both species encode a typical metazoan complement of 37 genes, which are all positioned on the major strand, but the gene order is distinct and unique among Ecdysozoa or animals as a whole. We predict four types of start codons for protein-coding genes in E. svetlanae and five in P. kielensis with a consensus DTD in single letter code. The mitochondrial genomes of E. svetlanae and P. kielensis encode duplicated methionine tRNA genes that display compensatory nucleotide substitutions. Two distant species of Kinorhyncha demonstrate similar patterns of gene arrangements in their mitogenomes. Both genomes have duplicated methionine tRNA genes; the duplication predates the divergence of two species. The kinorhynchs share a few features pertaining to gene order that align them with Priapulida. Gene order analysis reveals that gene arrangement specific of Priapulida may be ancestral for Scalidophora, Ecdysozoa, and even Protostomia.

We studied the distribution of 1–7 bp words in a dataset that includes 139 complete eukaryotic genomes, 33 masked eukaryotic genomes and coding regions from 35 genomes. We tested different statistical models to determine over- and under-represented words. The method described by Karlin et al. has the strongest predictive power compared to other methods. Using this method we identified over- and under-represented words consistent within a large array of taxonomic groups. Some of those words have not yet been described as exclusive. For example, CGCG is over-represented in CG-deficient organisms. We also describe exceptions for widely known exclusive words, such as CG and TA.

Gap junctions (GJs) are composed of proteins that form a channel connecting the cytoplasm of adjacent cells. Connexins were initially considered to be the only proteins capable of GJ formation. Another family of GJ proteins (innexins) were first found in invertebrates and were proposed to be renamed pannexins after their orthologs were discovered in vertebrates. The lack of both connexins and pannexins in the genomes of some metazoans suggests that other, still undiscovered GJ proteins exist. In vertebrates, connexins and pannexins co-exist. Here we discuss whether vertebrate pannexins have a nonredundant role in animal physiology. Pannexin channels appear to be suited for ATP and calcium signaling and play a role in the maintenance of calcium homeostasis by mechanisms implicating both GJ and nonjunctional function. Suggested roles in the ischemic death of neurons, schizophrenia, inflammation and tumor suppression have drawn much attention to exploring the molecular properties and cellular functions of pannexins.

Connexins had been considered to be the only class of the vertebrate proteins capable of gap junction formation; however, new candidates for this function with no homology to connexins, termed pannexins were discovered. So far three pannexins were described in rodent and human genomes: Panx1, Panx2 and Panx3. Expressions of pannexins can be detected in numerous brain structures, and now found both in neuronal and glial cells. Hypothetical roles of pannexins in the nervous system include participating in sensory processing, hippocampal plasticity, synchronization between hippocampus and cortex, and propagation of the calcium waves supported by glial cells, which help maintain and modulate neuronal metabolism. Pannexin also may participate in pathological reactions of the neural cells, including their damage after ischemia and subsequent cell death. Recent study revealed non-gap junction function of Panx1 hemichannels in erythrocytes, where they serve as the conduits for the ATP release in response to the osmotic stress. High-throughput studies produced some evidences of the pannexin involvement in the process of tumorigenesis. According to brain cancer gene expression database REMBRANDT, PANX2 expression levels can predict post diagnosis survival for patients with glial tumors. Further investigations are needed to verify or reject hypotheses listed.

Expression of the Panx1 and Panx2 members of the pannexin family of gap junction proteins was studied in the retina by in situ hybridization and qRT-PCR. Both pannexins showed robust expression across the retina with predominant accumulation in the retinal ganglion cells (RGCs). In concordance, immunohistochemical analysis showed accumulation of the Panx1 protein in RGCs, amacrine, horizontal cells and their processes. Two Panx1 isoforms were detected: a ubiquitously expressed 58kDa protein, and a 43kDa isoform that specifically accumulated in the retina and brain. Our results indicated that Panx1 and Panx2 are abundantly expressed in the retina, and may therefore contribute to the electrical and metabolic coupling, or to signaling between retinal neurons via the secondary messengers.

In the pteropod mollusk Clione limacina, locomotor rhythm is produced by the central pattern generator (CPG), due mainly to the activity of interneurons of groups 7 (active in the phase of the dorsal flexion of the wings) and 8 (active in the phase of the ventral flexion). Each of these groups excites the neurons active in the same phase of the locomotor cycle, and inhibits the neurons of the opposite phase. In this work, the nature of connections formed by group 7 interneurons was studied. Riluzole (2-amino-6-trifluoro-methoxybenzothiazole), which is known to inhibit the presynaptic release of glutamate, suppressed the action of the type 7 interneurons onto the follower neurons of the same and of the antagonistic phase of the locomotor cycle. The main pattern of rhythmic activity of CPG with alternation of two phases could be maintained after suppression of inhibitory connections from group 7 interneurons to antagonistic neurons. This suggests redundancy of the mechanisms controlling swimming rhythm generation, which ensures the reliable operation of the system.

In the pteropod mollusc Clione limacina, two groups of locomotor motoneurons, located in the pedal ganglion, innervate the dorsal and ventral muscle layers of the ipsilateral wing through the wing nerve. Separate branches of this nerve go either only to the dorsal muscle layer or only to the ventral one. In the present study, growth of novel neurites of the wing motoneurons was induced by cutting the wing nerve. In addition, all other peripheral nerves and connectives of the pedal ganglion were cut, except for the pedal commissure to the contralateral pedal ganglion. Thus, the neurites were allowed to grow only towards the contralateral pedal ganglion. We have found that the novel neurites, entering the contralateral pedal ganglion, were capable of growing everywhere inside the central nervous system (CNS) and into any peripheral nerve. However, they preferred the wing nerve. This finding suggests that the preference is caused by the guiding cues in the wing nerve or the attractive influence of the wing muscles. Because the contralateral pedal ganglion and nerves were left intact, the growth direction of the new neurites could be determined only by factors permanently existing in the CNS, rather than induced by nerve injury or muscle denervation. Within the wing nerve, the neurites could not discriminate between the nerve branches going to the dorsal and ventral muscle layers. They formed synapses on muscles of both layers, despite the fact that the muscles were innervated by their own motoneurons.

Early cleavages of the marine nematode Enoplus brevis are symmetrical and occur in synchrony. At the 2- to 16-cell stages, blastomeres are indistinguishable. The progeny of blastomeres was investigated by intracellular injections of fluorescent dyes and horse radish peroxidase. One blastomere of the 2-cell embryo gives rise to a compact group of cells occupying about half of an embryo. The border between labeled and unlabeled cells differs in each embryo dividing it to anterior-posterior, left-right or intermediate parts. At the 8-cell stage, one blastomere gives rise to only endoderm, whereas the other blastomeres produce progeny that form multiple cell types, including nerve, muscle and hypoderm cells, in various proportions. Thus the fates of the blastomeres of early E. brevis embryos, with the exception of the endoderm precursor, are not determined. The process of gastrulation in E. brevis is very similar to that in Caenorhabditis elegans and other nematodes. At the beginning of gastrulation, the 2-celled endoderm precursor lies on the surface of embryo and then sinks inwards. After labeling of cells on the ventral side (near endoderm precursor) at the beginning of gastrulation, their progeny differentiate predominantly into body muscles or pharyngeal cells of the first stage larva. Cells that are located more laterally give rise mainly to neurons. The dorsal blastomeres differentiated principally into hypoderm cells. Our study suggests that a precise cell lineage is not a necessary attribute of nematode development.

In Clione limacina, locomotory rhythm is produced in the central pattern generator by reciprocal activity of two groups of interneurons. Dorsal (D) and ventral (V) phase interneurons activate neurons of the same phase and inhibit neurons of the opposite phase. Which neurotransmitters are used by these interneurons is not clear. In this study, identified follower neurons to V and D interneurons were isolated, and their responses to the local application of potential neurotransmitters were examined. Acetylcholine exerted inhibitory action on the isolated D-phase neurons and excitatory action on V-phase neurons. Glutamate produced excitation in D-phase neurons, and inhibition in V-phase neurons. These results suggest that acetylcholine is the neurotransmitter of D-phase interneurons, while glutamate might be the neurotransmitter of V-phase interneurons.

The neural network underlying rhythmic wing movements in the molluscClione limacina is well-studied. Two different groups of motoneurons innervate two distinct groups of wing muscles. The locomotor rhythm generated in the left and right pedal ganglia is synchronized by interneurons. When the axons of the locomotor motoneurons are crushed, numerous fine neurites sprout towards the denervated muscles and reach them in 8–15 days. At this stage motoneurons project to and synapse on not only correct but equally incorrect muscle targets. After 2 weeks of regeneration the number of incorrect neurites and synaptic connections begins to decrease and following 1.5–2 months all incorrect connections are eliminated, incorrect axons are withdrawn and the behavioral deficit is compensated. In this study the regeneration of interneurons and the growth profiles of inter- and motoneurons were also studiedin vitro. Two individually isolated pedal ganglia were co-cultured in three different configurations: a) the wing nerve stump from one ganglion was fixed against the commissural stump from another ganglion; b) the wing nerve stumps were fixed against each other; c) the commissural stumps were fixed against each other. Under the above experimental conditions we found that the interneurons were able to cross only the contact between two commissural stumps, and in this case found their original targets, restored correct connections and synchronized the rhythm in two pedal ganglia. In contrast, motoneurons were able to cross all types of contacts.

According to much quoted Russian/American geneticist Theodosius Dobzhansky, “Nothing in biology makes sense except in the light of evolution” [1]. Coined in 1973, this famous phrase remains up to date. Fascinating variety of the phenotypes seen as either visible or subtle differences in species, populations, and individual organisms inhabiting our planet attracts an unwavering inquiry. The results of these inquiries are shedding some light both at intricate molecular programs continuously executed within living bodies and at checks and balances within homeostatic ecosystems. In fact, every transformative technology so far invented to improve human medicine or other areas of applied science was immediately embraced by traditional biologists and contributed to the extraction of evolutionary insights. Some years ago, that happened with PCR. Recently, we entered systems biology driven turn of an inquiry spiral. This turn is enabled by an advent of NextGen sequencing. Importantly, a few final steps on this spiral became computationally heavy. Hence, the aid of bioinformatics was summoned, and computationally derived conclusions came in droves. While the mining of completed genomes remains an obvious source is information on evolutionary processes, we also see the emergence of a novel kind of the full-genome studies, ones that aim at the tinkering with the evolutionary theory itself. By their scale and potential, these studies may be compared to the two previous technological developments that changed the history of evolutionary studies. The first of these methodological revolutions is a comparative analysis of traits that was started by Lamarck [2] and Darwin [3] and still is a source of novel evolutionary inferences. The second one was the introduction of the molecular analysis (see [4]) that approximately coincided with the establishment of the synthetic theory of evolution. Since that, the methods of the analysis of molecular traits kept progressing. By now, it is clear that molecular-based inquiry opened whole new field of questions which may be asked and answered, for example, one that relates to the evolution of the intracellular parasites, microbial communities, or populations of the cells within human body burdened with a tumor. The introduction of NextGen sequencing dramatically increased the amount of information that may be extracted from the sample of biological material and added the whole new level of integration of organismal data, thus enabling the systems biology in its true sense. Nowadays, one may be certain that widespread adoption of NextGen sequencing will uplift the evolutionary theory to new heights, however, where will it bring us even in next few years is substantially harder to predict. We should not forget that evolutionary genomics is still an emerging field in biology. For now, it does not have a road map, a master plan, or even a template—one who starts the analysis of data collected from the study of living system never knows where this analysis might end. This volume is yet another attempt to provide a bird's view at bioinformatics-driven forays into the field of evolutionary biology. However, it is an opinion of the Editors that presented eclectic collection of papers is not without its merits. In case of existing data, even a mere push to extract an evolutionary insight enables the scientist to see the pattern that would be very difficult to discern otherwise. So much better it is for the studies specifically designed to solve one or another biological enigma. In this issue, we are glad to present an eclectic collection of papers that cover a range of topics from analysis of intron evolution across kingdoms to the study of the divergence in salmonid species and to comparative genomics of cancer-specific genes. These manuscripts are a sampler of future insights yet to come from the troves of genome sequences thoroughly dissected with bioinformatics tools. Enjoy! Dmitry Sherbakov Yuri Panchin Ancha Baranova

Substitution rates strongly depend on their nucleotide context. One of the most studied examples is the excess of C > T mutations in the CG context in various groups of organisms, including vertebrates. Studies on the molecular mechanisms underlying this mutation regularity have provided insights into evolution, mutagenesis, and cancer development. Recently several other hypermutable motifs were identified in the human genome. There is an increased frequency of T > C mutations in the second position of the words ATTG and ATAG and an increased frequency of A > C mutations in the first position of the word ACAA. For a better understanding of evolution, it is of interest whether these mutation regularities are human specific or present in other vertebrates, as their presence might affect the validity of currently used substitution models and molecular clocks. A comprehensive analysis of mutagenesis in 4 bp mutation contexts requires a vast amount of mutation data. Such data may be derived from the comparisons of individual genomes or from single nucleotide polymorphism (SNP) databases. Using this approach, we performed a systematical comparison of mutation regularities within 2–4 bp contexts inMus musculusandHomo sapiensand uncovered that even closely related organisms may have notable differences in context-dependent mutation regularities.

In general, mutation frequencies are context-dependent: specific adjacent nucleotides may influence the probability to observe a specific type of mutation in a genome. Recently, several hypermutable motifs were identified in the human genome. Namely, there is an increased frequency of T>C mutations in the second position of the words ATTG and ATAG and an increased frequency of A>C mutations in the first position of the word ACAA. Previous studies have also shown that there is a remarkable difference between the mutagenesis of humans and drosophila. While C>T mutations are overrepresented in the CG context in humans (and other vertebrates), this mutation regularity is not observed inDrosophila melanogaster. Such differences in the observed regularities of mutagenesis between representatives of different taxa might reflect differences in the mechanisms involved in mutagenesis. We performed a systematical comparison of mutation regularities within 2–4 bp contexts inHomo sapiensandDrosophila melanogasterand found that the aforementioned contexts are not hypermutable in fruit flies. It seems that most mutation contexts affect mutation rates in a similar manner inH. sapiensandD. melanogaster; however, several important exceptions are noted and discussed.

A cluster of electrically interconnected neurosecretory cells (the ‘white cells’) involved in the control of reproductive behavior was identified in the right pleural ganglion of the marine mollusc, Clione limacina. Pleural ganglia also contain large neurons (PL1 and PL2) having no connections with each other and with the white cells. Most isolated white cells put into the simple unconditioned medium (50% L-15) adhered to the bottom of uncoated dishes and demonstrated neurite outgrowth for 7–10 days. If growing processes overlapped, the white cells formed electrical connections with each other, but they formed no connections with the PL1 and PL2 neurons. It is concluded that in the case which was under study cellular intrinsic properties were sufficient for the formation of ‘correct’ connections between neurones.

The effects of gamma-aminobutyric acid (GABA) on the behaviour of the marine pteropod mollusc Clione limacina were studied. In intact molluscs, injection of GABA evoked the consummatory stage of feeding behaviour, i.e. protracting the tentacles, opening the mouth, catching and swallowing prey, as well as some acceleration of locomotion. In the isolated CNS, GABA (10(-5)-10(-4) M) strongly activated the feeding rhythm generator, excited the cerebral motoneurons innervating tentacle muscles (TenMNs), and accelerated locomotor rhythm. A direct excitatory action of GABA (10(-8) M) upon TenMNs was demonstrated on isolated cells extracted from cerebral ganglia. It is concluded that GABA plays an important role in activation of various neuronal networks (organization of 'functional synergy') responsible for the consummatory stage of feeding behaviour.

Animal genomes contain approximately 20,000 genes. Additionally millions of genes for antigen receptors are generated in cells of the immune system from the sets of separate gene segments by a mechanism known as the V(D)J somatic recombination. The components of the V(D)J recombination system, Recombination-Activating Gene proteins (RAG1 and RAG2) and recombination signal sequence (RSS), are thought to have "entered" the vertebrate genome as a hypothetical "RAG transposon". Recently discovered mobile elements have terminal inverted repeats (TIRs) similar to RSS and may encode proteins with a different degree of similarity to RAG1. We describe a novel N-RAG-TP transposon identified from the sea slug Aplysia californica that encodes a protein similar to the N-terminal part of RAG1 in vertebrates. This refines the "RAG transposon" hypothesis and allows us to propose a scenario for V(D)J recombination machinery evolution from a relic transposon related to the existing mobile elements N-RAG-TP, Chapaev, and Transib.

Expressed sequence tags (ESTs) represent 500–1000-bp-long sequences corresponding to mRNAs derived from different sources (cell lines, tissues, etc.). The human EST database contains over 8,000,000 sequences, with over 4,000,000,000 total nucleotides. RNA molecules are transcribed from a genomic DNA template; therefore, all ESTs should match corresponding genomes. Nevertheless, we have found in the human EST database approximately 11,000 ESTs not matching sequences in the human genome database. The presence of "trash" ESTs (TESTs) in the EST database could result from DNA or RNA contamination of the laboratory equipment, tissues, or cell lines. TESTs could also represent sequences from unidentified human genes or from species inhabiting the human body. Here, we attempt to identify the sources of human EST database contaminations. In particular, we discuss systematic contamination of the mammalian EST databases with sequences of plants.

Summary Molecular analyses of Aplysia, a well-established model organism for cellular and systems neural science, have been seriously handicapped by a lack of adequate genomic information. By sequencing cDNA libraries from the central nervous system (CNS), we have identified over 175,000 expressed sequence tags (ESTs), of which 19,814 are unique neuronal gene products and represent 50%–70% of the total Aplysia neuronal transcriptome. We have characterized the transcriptome at three levels: (1) the central nervous system, (2) the elementary components of a simple behavior: the gill-withdrawal reflex—by analyzing sensory, motor, and serotonergic modulatory neurons, and (3) processes of individual neurons. In addition to increasing the amount of available gene sequences of Aplysia by two orders of magnitude, this collection represents the largest database available for any member of the Lophotrochozoa and therefore provides additional insights into evolutionary strategies used by this highly successful diversified lineage, one of the three proposed superclades of bilateral animals.

SUMMARYGap junctions provide one of the most common forms of intercellular communication. They are composed of membrane proteins that form a channel that is permeable to ions and small molecules, connecting the cytoplasm of adjacent cells. Gap junctions serve similar functions in all multicellular animals(Metazoa). Two unrelated protein families are involved in this function;connexins, which are found only in chordates, and pannexins, which are ubiquitous and present in both chordate and invertebrate genomes. The involvement of mammalian pannexins to gap junction formation was recently confirmed. Now it is necessary to consider the role of pannexins as an alternative to connexins in vertebrate intercellular communication.

In the pteropod mollusc, locomotor rhythm is produced by the central pattern generator (CPG), mainly by the reciprocal activity of interneurons, groups 7 and 8, which are active in the phases of the dorsal and ventral flexion of the wings, respectively. Both groups produce excitation in the CPG neurons controlling the same phase of the locomotor cycle, and inhibition in the neurons of the opposite phase. As previously suggested, the connections of the group 7 interneurons to the follower CPG neurons are glutamatergic. However, the properties of the glutamatergic receptors in the postsynaptic cells are unknown. In this work, the identified CPG motoneurons of the antagonistic groups 1 and 2 were isolated from the CNS, and their responses to the local application of glutamate agonists were examined. Glutamate elicited opposite effects in the neurons of these two groups, reproducing excitatory and inhibitory influence of the group 7 interneurons. Interestingly, micromolar concentrations of glutamate agonists kainate, domoate and AMPA elicited excitation in both types of the motoneurons. To test for the possible of the NMDA receptors, NMDA was applied, as well as an equimolar mixture of NMDA and glycine. The isolated motoneurons showed excitatory response to these applications only at high (millimolar) concentrations. These results suggest that the motoneurons of group 1 possess excitatory glutamate receptors and that motoneurons of group 2 may posses a composite population of receptors, which are responsible for the inhibitory action of glutamate and excitatory action of its AMPA/kainate agonists.

Pannexin1 is ubiquitously expressed in vertebrate tissues, but the role it plays in vascular tone regulation remains unclear. We found that Pannexin1 expression level is much higher in the endothelium relative to smooth muscle of saphenous artery. The ability of endothelium-intact arteries for dilation was significantly impaired whereas contractile responses were considerably increased in mice with genetic ablation of Pannexin1. No such increased contractile responses were detected in the endothelium-denuded arteries. Combined, our findings suggest a new function of Pannexin1 as an important player in normal endothelium-dependent regulation of arterial tone, where it facilitates vessel dilation and attenuates constriction. Reviewed by Dr. Armen Mulkidjanian and Dr. Alexander Lobkovsky.

Neural network for rhythmic wing movements in the swimming mollusc Clione limacina is a well-studied system. After nerve transection the efferent wing neurons cannot reach muscles and consequently display intensive central sprouting. In the present work it was shown that two types of efferent neurons with different neurotransmitters: acethylcholinergic locomotor motoneurons and serotonergic modulatory efferent neurons – when deprived of their normal targets, release their neurotransmitter intended for peripheral muscles, in the unusual compartment—neuropile. Such ‘unauthorized’ release of neurotransmitter may cause nervous system dysfunctions in the damaged brain of other animals.

The swimming mollusk Clione is normally oriented vertically. As water is warmed, this orientation is lost or reversed. CPB3 interneurons, which transmit signals from the statocyst receptors (SRCs) to the tail motoneurons and play a key role in space orientation, were strongly depolarized upon warming. Normally, intracellular stimulation of the rostro-dorsal SRC (DSRC) excited CPB3b. Upon warming the excitation gradually decreased and in some cases was even replaced by inhibition. The reversal potential for the synaptic potentials (PSP) produced in CPB3b by DSRC stimulation is depolarized relative to the normal membrane potential at lower temperature. Warming causes depolarization of the membrane potential such that the PSP reversal potential is approached and even passed, with attenuant effects on PSP amplitude and polarity. This effect provides a mechanism for the temperature sensitive changes in the orientation of Clione.

Background The substitution rates within different nucleotide contexts are subject to varying levels of bias. The most well known example of such bias is the excess of C to T (C > T) mutations in CpG (CG) dinucleotides. The molecular mechanisms underlying this bias are important factors in human genome evolution and cancer development. The discovery of other nucleotide contexts that have profound effects on substitution rates can improve our understanding of how mutations are acquired, and why mutation hotspots exist. Results We compared rates of inherited mutations in 1-4 bp nucleotide contexts using reconstructed ancestral states of human single nucleotide polymorphisms (SNPs) from intergenic regions. Chimp and orangutan genomic sequences were used as outgroups. We uncovered 3.5 and 3.3-fold excesses of T > C mutations in the second position of ATTG and ATAG words, respectively, and a 3.4-fold excess of A > C mutations in the first position of the ACAA word. Conclusions Although all the observed biases are less pronounced than the 5.1-fold excess of C > T mutations in CG dinucleotides, the three 4 bp mutation contexts mentioned above (and their complementary contexts) are well distinguished from all other mutation contexts. This provides a challenge to discover the underlying mechanisms responsible for the observed excesses of mutations.

Background Cutting edge research of human microbiome diversity has led to the development of the microbiome-gut-brain axis concept, based on the idea that gut microbes may have an impact on the behavior of their human hosts. Many examples of behavior-altering parasites are known to affect members of the animal kingdom. Some prominent examples include Ophiocordyceps unilateralis (fungi), Toxoplasma gondii (protista), Wolbachia (bacteria), Glyptapanteles sp. (arthropoda), Spinochordodes tellinii (nematomorpha) and Dicrocoelium dendriticum (flat worm). These organisms belong to a very diverse set of taxonomic groups suggesting that the phenomena of parasitic host control might be more common in nature than currently established and possibly overlooked in humans. Presentation of the hypothesis Some microorganisms would gain an evolutionary advantage by encouraging human hosts to perform certain rituals that favor microbial transmission. We hypothesize that certain aspects of religious behavior observed in the human society could be influenced by microbial host control and that the transmission of some religious rituals could be regarded as the simultaneous transmission of both ideas (memes) and parasitic organisms. Testing the hypothesis We predict that next-generation microbiome sequencing of samples obtained from gut or brain tissues of control subjects and subjects with a history of voluntary active participation in certain religious rituals that promote microbial transmission will lead to the discovery of microbes, whose presence has a consistent and positive association with religious behavior. Our hypothesis also predicts a decline of participation in religious rituals in societies with improved sanitation. Implications of the hypothesis If proven true, our hypothesis may provide insights on the origin and pervasiveness of certain religious practices and provide an alternative explanation for recently published positive associations between parasite-stress and religiosity. The discovery of novel microorganisms that affect host behavior may improve our understanding of neurobiology and neurochemistry, while the diversity of such organisms may be of interest to evolutionary biologists and religious scholars. Reviewers This article was reviewed by Prof. Dan Graur, Dr. Rob Knight and Dr. Eugene Koonin