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Mikhailov KV, Konstantinova AV, Nikitin MA, Troshin PV, Rusin LY, Lyubetsky VA, Panchin YV, Mylnikov AP, Moroz LL, Kumar S, Aleoshin VV. The origin of Metazoa: a transition from temporal to spatial cell differentiation. Bioessays 2009; 31:758-68. [PMID: 19472368 DOI: 10.1002/bies.200800214] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
For over a century, Haeckel's Gastraea theory remained a dominant theory to explain the origin of multicellular animals. According to this theory, the animal ancestor was a blastula-like colony of uniform cells that gradually evolved cell differentiation. Today, however, genes that typically control metazoan development, cell differentiation, cell-to-cell adhesion, and cell-to-matrix adhesion are found in various unicellular relatives of the Metazoa, which suggests the origin of the genetic programs of cell differentiation and adhesion in the root of the Opisthokonta. Multicellular stages occurring in the complex life cycles of opisthokont protists (mesomycetozoeans and choanoflagellates) never resemble a blastula. Here, we discuss a more realistic scenario of transition to multicellularity through integration of pre-existing transient cell types into the body of an early metazoon, which possessed a complex life cycle with a differentiated sedentary filter-feeding trophic stage and a non-feeding blastula-like larva, the synzoospore. Choanoflagellates are considered as forms with secondarily simplified life cycles.
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Review |
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Janouškovec J, Paskerova GG, Miroliubova TS, Mikhailov KV, Birley T, Aleoshin VV, Simdyanov TG. Apicomplexan-like parasites are polyphyletic and widely but selectively dependent on cryptic plastid organelles. eLife 2019; 8:49662. [PMID: 31418692 PMCID: PMC6733595 DOI: 10.7554/elife.49662] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 08/14/2019] [Indexed: 12/22/2022] Open
Abstract
The phylum Apicomplexa comprises human pathogens such as Plasmodium but is also an under-explored hotspot of evolutionary diversity central to understanding the origins of parasitism and non-photosynthetic plastids. We generated single-cell transcriptomes for all major apicomplexan groups lacking large-scale sequence data. Phylogenetic analysis reveals that apicomplexan-like parasites are polyphyletic and their similar morphologies emerged convergently at least three times. Gregarines and eugregarines are monophyletic, against most expectations, and rhytidocystids and Eleutheroschizon are sister lineages to medically important taxa. Although previously unrecognized, plastids in deep-branching apicomplexans are common, and they contain some of the most divergent and AT-rich genomes ever found. In eugregarines, however, plastids are either abnormally reduced or absent, thus increasing known plastid losses in eukaryotes from two to four. Environmental sequences of ten novel plastid lineages and structural innovations in plastid proteins confirm that plastids in apicomplexans and their relatives are widespread and share a common, photosynthetic origin. Microscopic parasites known collectively as apicomplexans are responsible for several infectious diseases in humans including malaria and toxoplasmosis. The cells of the malaria parasite and many other apicomplexans contain compartments known as cryptic chloroplasts that produce molecules the parasites need to survive. Cryptic chloroplasts are similar to the chloroplasts found in plant cells, but unlike plants the compartments in apicomplexans are unable to harvest energy from sunlight. Since the cells of humans and other animals do not contain chloroplasts, cryptic chloroplasts are a potential target for new drugs to treat diseases caused by apicomplexans. However, it remains unclear how widespread cryptic chloroplasts are in these parasites, largely because few apicomplexans have been successfully grown in the laboratory. To address this question, Janouškovec et al. used an approach called single-cell transcriptomics to study ten different apicomplexans. This provided new data about the genetic make-up of each parasite that the team analysed to find out how they are related to one another. The analysis revealed that, unexpectedly, apicomplexan parasites do not share a close common ancestor and are therefore not a natural grouping from an evolutionary perspective. Instead, their similar physical appearances and lifestyles evolved independently on at least three separate occasions. Further analysis demonstrated that cryptic chloroplasts are common in apicomplexan parasites, including in lineages where they were not previously known to exist. However, at least three lineages of apicomplexans have independently lost their cryptic chloroplasts. The findings of Janouškovec et al. shed new light on the importance of chloroplasts in the evolution of life and may help develop new treatments for diseases caused by apicomplexan parasites. Several drugs targeting the cryptic chloroplasts in malaria parasites are currently in clinical trials, and this work suggests that these drugs may also have the potential to be used against other apicomplexan parasites in the future.
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Karpov SA, Mikhailov KV, Mirzaeva GS, Mirabdullaev IM, Mamkaeva KA, Titova NN, Aleoshin VV. Obligately phagotrophic aphelids turned out to branch with the earliest-diverging fungi. Protist 2012; 164:195-205. [PMID: 23058793 DOI: 10.1016/j.protis.2012.08.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 08/08/2012] [Accepted: 08/09/2012] [Indexed: 01/01/2023]
Abstract
Reconstructing the early evolution of fungi and metazoans, two of the kingdoms of multicellular eukaryotes thriving on earth, is a challenging task for biologists. Among extant organisms having characters intermediate between fungi and hypothetical protistan ancestors, from which both fungi and metazoans are believed to have evolved, aphelids are unfairly neglected. The phylogenetic position of these microalgal endoparasites remained uncertain, since no nucleotide sequence data have been reported to date. Aphelids resemble some primitive zoosporic fungi in life cycle, but, unlike fungi, they live by phagotrophy. Here we present a phylogeny, in which a cultured aphelid species, Amoeboaphelidium protococcarum, forms a monophyletic group with Rozella and microsporidia as a sister group to Fungi. We also report a non-canonical nuclear genetic code in A. protococcarum.
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Tikhonenkov DV, Janouškovec J, Mylnikov AP, Mikhailov KV, Simdyanov TG, Aleoshin VV, Keeling PJ. Description of Colponema vietnamica sp.n. and Acavomonas peruviana n. gen. n. sp., two new alveolate phyla (Colponemidia nom. nov. and Acavomonidia nom. nov.) and their contributions to reconstructing the ancestral state of alveolates and eukaryotes. PLoS One 2014; 9:e95467. [PMID: 24740116 PMCID: PMC3989336 DOI: 10.1371/journal.pone.0095467] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2014] [Accepted: 03/27/2014] [Indexed: 11/21/2022] Open
Abstract
The evolutionary and ecological importance of predatory flagellates are too often overlooked. This is not only a gap in our understanding of microbial diversity, but also impacts how we interpret their better-studied relatives. A prime example of these problems is found in the alveolates. All well-studied species belong to three large clades (apicomplexans, dinoflagellates, and ciliates), but the predatory colponemid flagellates are also alveolates that are rare in nature and seldom cultured, but potentially important to our understanding of alveolate evolution. Recently we reported the first cultivation and molecular analysis of several colponemid-like organisms representing two novel clades in molecular trees. Here we provide ultrastructural analysis and formal species descriptions for both new species, Colponema vietnamica n. sp. and Acavomonas peruviana n. gen. n. sp. Morphological and feeding characteristics concur with molecular data that both species are distinct members of alveolates, with Acavomonas lacking the longitudinal phagocytotic groove, a defining feature of Colponema. Based on ultrastructure and molecular phylogenies, which both provide concrete rationale for a taxonomic reclassification of Alveolata, we establish the new phyla Colponemidia nom. nov. for the genus Colponema and its close relatives, and Acavomonidia nom. nov. for the genus Acavomonas and its close relatives. The morphological data presented here suggests that colponemids are central to our understanding of early alveolate evolution, and suggest they also retain features of the common ancestor of all eukaryotes.
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Zverkov OA, Mikhailov KV, Isaev SV, Rusin LY, Popova OV, Logacheva MD, Penin AA, Moroz LL, Panchin YV, Lyubetsky VA, Aleoshin VV. Dicyemida and Orthonectida: Two Stories of Body Plan Simplification. Front Genet 2019; 10:443. [PMID: 31178892 PMCID: PMC6543705 DOI: 10.3389/fgene.2019.00443] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 04/29/2019] [Indexed: 01/22/2023] Open
Abstract
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.
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Romanova EV, Aleoshin VV, Kamaltynov RM, Mikhailov KV, Logacheva MD, Sirotinina EA, Gornov AY, Anikin AS, Sherbakov DY. Evolution of mitochondrial genomes in Baikalian amphipods. BMC Genomics 2016; 17:1016. [PMID: 28105939 PMCID: PMC5249044 DOI: 10.1186/s12864-016-3357-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Amphipods (Crustacea) of Lake Baikal are a very numerous and diverse group of invertebrates generally believed to have originated by adaptive radiation. The evolutionary history and phylogenetic relationships in Baikalian amphipods still remain poorly understood. Sequencing of mitochondrial genomes is a relatively feasible way for obtaining a set of gene sequences suitable for robust phylogenetic inferences. The architecture of mitochondrial genomes also may provide additional information on the mechanisms of evolution of amphipods in Lake Baikal. RESULTS Three complete and four nearly complete mitochondrial genomes of Baikalian amphipods were obtained by high-throughput sequencing using the Illumina platform. A phylogenetic inference based on the nucleotide sequences of all mitochondrial protein coding genes revealed the Baikalian species to be a monophyletic group relative to the nearest non-Baikalian species with a completely sequenced mitochondrial genome - Gammarus duebeni. The phylogeny of Baikalian amphipods also suggests that the shallow-water species Eulimnogammarus has likely evolved from a deep-water ancestor, however many other species have to be added to the analysis to test this hypothesis. The gene order in all mitochondrial genomes of studied Baikalian amphipods differs from the pancrustacean ground pattern. Mitochondrial genomes of four species possess 23 tRNA genes, and in three genomes the extra tRNA gene copies have likely undergone remolding. Widely varying lengths of putative control regions and other intergenic spacers are typical for the mitochondrial genomes of Baikalian amphipods. CONCLUSIONS The mitochondrial genomes of Baikalian amphipods display varying organization suggesting an intense rearrangement process during their evolution. Comparison of complete mitochondrial genomes is a potent approach for studying the amphipod evolution in Lake Baikal.
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Tikhonenkov DV, Mikhailov KV, Hehenberger E, Karpov SA, Prokina KI, Esaulov AS, Belyakova OI, Mazei YA, Mylnikov AP, Aleoshin VV, Keeling PJ. New Lineage of Microbial Predators Adds Complexity to Reconstructing the Evolutionary Origin of Animals. Curr Biol 2020; 30:4500-4509.e5. [PMID: 32976804 DOI: 10.1016/j.cub.2020.08.061] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/20/2020] [Accepted: 08/17/2020] [Indexed: 02/05/2023]
Abstract
The origin of animals is one of the most intensely studied evolutionary events, and our understanding of this transition was greatly advanced by analyses of unicellular relatives of animals, which have shown many "animal-specific" genes actually arose in protistan ancestors long before the emergence of animals [1-3]. These genes have complex distributions, and the protists have diverse lifestyles, so understanding their evolutionary significance requires both a robust phylogeny of animal relatives and a detailed understanding of their biology [4, 5]. But discoveries of new animal-related lineages are rare and historically biased to bacteriovores and parasites. Here, we characterize the morphology and transcriptome content of a new animal-related lineage, predatory flagellate Tunicaraptor unikontum. Tunicaraptor is an extremely small (3-5 μm) and morphologically simple cell superficially resembling some fungal zoospores, but it survives by preying on other eukaryotes, possibly using a dedicated but transient "mouth," which is unique for unicellular opisthokonts. The Tunicaraptor transcriptome encodes a full complement of flagellar genes and the flagella-associated calcium channel, which is only common to predatory animal relatives and missing in microbial parasites and grazers. Tunicaraptor also encodes several major classes of animal cell adhesion molecules, as well as transcription factors and homologs of proteins involved in neurodevelopment that have not been found in other animal-related lineages. Phylogenomics, including Tunicaraptor, challenges the existing framework used to reconstruct the evolution of animal-specific genes and emphasizes that the diversity of animal-related lineages may be better understood only once the smaller, more inconspicuous animal-related lineages are better studied. VIDEO ABSTRACT.
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Mikhailov KV, Simdyanov TG, Aleoshin VV. Genomic Survey of a Hyperparasitic Microsporidian Amphiamblys sp. (Metchnikovellidae). Genome Biol Evol 2017; 9:454-467. [PMID: 27694476 PMCID: PMC5381614 DOI: 10.1093/gbe/evw235] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2016] [Indexed: 12/18/2022] Open
Abstract
Metchnikovellidae are a group of unusual microsporidians that lack some of the defining ultrastructural features characteristic of derived Microsporidia and are thought to be one of their earliest-branching lineages. The basal position of metchnikovellids was never confirmed by molecular phylogeny in published research, and thus far no genomic data for this group were available. In this work, we obtain a partial genome of metchnikovellid Amphiamblys sp. using multiple displacement amplification, next-generation sequencing, and metagenomic binning approaches. The partial genome, which we estimate to be close to 90% complete, displays genome compaction on par with gene-dense microsporidian genomes, but contains an unusual repertoire of unique repeat elements. Phylogenetic analyses of multigene datasets place Amphiamblys sp. as the first branch of the microsporidian lineage following the divergence of a mitochondriate microsporidian Mitosporidium. We find evidence for a mitochondrial remnant presumably functionally equivalent to a mitosome in Amphiamblys sp. and the common enzymatic complement for microsporidian anaerobic metabolism. Comparative genomic analyses identify the conservation of components for clathrin vesicle formation as one of the key features distinguishing the metchnikovellid from its highly derived relatives. The presented data confirm the notion of Metchnikovellidae as a less derived microsporidian group, and provide an additional stepping stone for reconstruction of an evolutionary transition from the early diverging parasitic fungi to derived Microsporidia.
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Simdyanov TG, Guillou L, Diakin AY, Mikhailov KV, Schrével J, Aleoshin VV. A new view on the morphology and phylogeny of eugregarines suggested by the evidence from the gregarine Ancora sagittata (Leuckart, 1860) Labbé, 1899 (Apicomplexa: Eugregarinida). PeerJ 2017; 5:e3354. [PMID: 28584702 PMCID: PMC5452951 DOI: 10.7717/peerj.3354] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 04/26/2017] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Gregarines are a group of early branching Apicomplexa parasitizing invertebrate animals. Despite their wide distribution and relevance to the understanding the phylogenesis of apicomplexans, gregarines remain understudied: light microscopy data are insufficient for classification, and electron microscopy and molecular data are fragmentary and overlap only partially. METHODS Scanning and transmission electron microscopy, PCR, DNA cloning and sequencing (Sanger and NGS), molecular phylogenetic analyses using ribosomal RNA genes (18S (SSU), 5.8S, and 28S (LSU) ribosomal DNAs (rDNAs)). RESULTS AND DISCUSSION We present the results of an ultrastructural and molecular phylogenetic study on the marine gregarine Ancora sagittata from the polychaete Capitella capitata followed by evolutionary and taxonomic synthesis of the morphological and molecular phylogenetic evidence on eugregarines. The ultrastructure of Ancora sagittata generally corresponds to that of other eugregarines, but reveals some differences in epicytic folds (crests) and attachment apparatus to gregarines in the family Lecudinidae, where Ancora sagittata has been classified. Molecular phylogenetic trees based on SSU (18S) rDNA reveal several robust clades (superfamilies) of eugregarines, including Ancoroidea superfam. nov., which comprises two families (Ancoridae fam. nov. and Polyplicariidae) and branches separately from the Lecudinidae; thus, all representatives of Ancoroidea are here officially removed from the Lecudinidae. Analysis of sequence data also points to possible cryptic species within Ancora sagittata and the inclusion of numerous environmental sequences from anoxic habitats within the Ancoroidea. LSU (28S) rDNA phylogenies, unlike the analysis of SSU rDNA alone, recover a well-supported monophyly of the gregarines involved (eugregarines), although this conclusion is currently limited by sparse taxon sampling and the presence of fast-evolving sequences in some species. Comparative morphological analyses of gregarine teguments and attachment organelles lead us to revise their terminology. The terms "longitudinal folds" and "mucron" are restricted to archigregarines, whereas the terms "epicystic crests" and "epimerite" are proposed to describe the candidate synapomorphies of eugregarines, which, consequently, are considered as a monophyletic group. Abolishing the suborders Aseptata and Septata, incorporating neogregarines into the Eugregarinida, and treating the major molecular phylogenetic lineages of eugregarines as superfamilies appear as the best way of reconciling recent morphological and molecular evidence. Accordingly, the diagnosis of the order Eugregarinida Léger, 1900 is updated.
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Konorov EA, Nikitin MA, Mikhailov KV, Lysenkov SN, Belenky M, Chang PL, Nuzhdin SV, Scobeyeva VA. Genomic exaptation enables Lasius niger adaptation to urban environments. BMC Evol Biol 2017; 17:39. [PMID: 28251870 PMCID: PMC5333191 DOI: 10.1186/s12862-016-0867-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background The world is rapidly urbanizing, and only a subset of species are able to succeed in stressful city environments. Efficient genome-enabled stress response appears to be a likely prerequisite for urban adaptation. Despite the important role ants play in the ecosytem, only the genomes of ~13 have been sequenced so far. Here, we present the draft genome assembly of the black garden ant Lasius niger – the most successful urban inhabitant of all ants – and we compare it with the genomes of other ant species, including the closely related Camponotus floridanus. Results Sequences from 272 M Illumina reads were assembled into 41,406 contigs with total length of 245 MB, and N50 of 16,382 bp, similar to other ant genome assemblies enabling comparative genomic analysis. Remarkably, the predicted proteome of L. niger is significantly enriched relative to other ant genomes in terms of abundance of domains involved in nucleic acid binding, DNA repair, and nucleotidyl transferase activity, reflecting transposable element proliferation and a likely genomic response. With respect to environmental stress, we note a proliferation of various detoxification genes, including glutatione-S-transferases and those in the cytochrome P450 families. Notably, the CYP9 family is highly expanded with 19 complete and 21 nearly complete members - over twice as many compared to other ants. This family exhibits the signatures of strong directional selection, with eleven positively selected positions in ligand-binding pockets of enzymes. Gene family contraction was detected for several components of the olfactory system, accompanied by instances of both directional selection and relaxation. Conclusions Our results suggest that the success of L. niger in urbanized areas may be the result of fortuitous coincidence of several factors, including the expansion of the CYP9 cytochrome family due to coevolution with parasitic fungi, the diversification of DNA repair systems as an answer to proliferation of retroelements, and the reduction of olfactory system and behavioral preadaptations from non-territorial subdominant life strategies found in natural environments. Diversification of cytochromes and DNA repair systems along with reduced odorant communication are the basis of L. niger pollutant resistance and polyphagy, while non-territorial and mobilization strategies allows more efficient exploitation of large but patchy food sources. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0867-x) contains supplementary material, which is available to authorized users.
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Stepanyan S, Hicks K, Carman DS, Pasyuk E, Schumacher RA, Smith ES, Tedeschi DJ, Todor L, Adams G, Ambrozewicz P, Anciant E, Anghinolfi M, Asavapibhop B, Audit G, Avakian H, Bagdasaryan H, Ball JP, Barrow SP, Battaglieri M, Beard K, Bektasoglu M, Bellis M, Berman BL, Bianchi N, Biselli AS, Boiarinov S, Bouchigny S, Bradford R, Branford D, Briscoe WJ, Brooks WK, Burkert VD, Butuceanu C, Calarco JR, Carnahan B, Chen S, Ciciani L, Cole PL, Coleman A, Cords D, Corvisiero P, Crabb D, Crannell H, Cummings JP, De Sanctis E, Degtyarenko PV, Denizli H, Dennis L, De Vita R, Dharmawardane KV, Dhuga KS, Djalali C, Dodge GE, Doughty D, Dragovitsch P, Dugger M, Dytman S, Dzyubak OP, Egiyan H, Egiyan KS, Elouadrhiri L, Empl A, Eugenio P, Fatemi R, Feuerbach RJ, Ficenec J, Forest TA, Funsten H, Garçon M, Gavalian G, Gilfoyle GP, Giovanetti KL, Gordon CIO, Gothe R, Griffioen K, Guidal M, Guillo M, Guo L, Gyurjyan V, Hadjidakis C, Hakobyan RS, Hardie J, Heddle D, Heimberg P, Hersman FW, Hicks RS, Holtrop M, Hu J, Hyde-Wright CE, Ito MM, Jenkins D, Joo K, Juengst HG, Kellie JD, Khandaker M, Kim KY, Kim K, Kim W, Klein A, Klein FJ, et alStepanyan S, Hicks K, Carman DS, Pasyuk E, Schumacher RA, Smith ES, Tedeschi DJ, Todor L, Adams G, Ambrozewicz P, Anciant E, Anghinolfi M, Asavapibhop B, Audit G, Avakian H, Bagdasaryan H, Ball JP, Barrow SP, Battaglieri M, Beard K, Bektasoglu M, Bellis M, Berman BL, Bianchi N, Biselli AS, Boiarinov S, Bouchigny S, Bradford R, Branford D, Briscoe WJ, Brooks WK, Burkert VD, Butuceanu C, Calarco JR, Carnahan B, Chen S, Ciciani L, Cole PL, Coleman A, Cords D, Corvisiero P, Crabb D, Crannell H, Cummings JP, De Sanctis E, Degtyarenko PV, Denizli H, Dennis L, De Vita R, Dharmawardane KV, Dhuga KS, Djalali C, Dodge GE, Doughty D, Dragovitsch P, Dugger M, Dytman S, Dzyubak OP, Egiyan H, Egiyan KS, Elouadrhiri L, Empl A, Eugenio P, Fatemi R, Feuerbach RJ, Ficenec J, Forest TA, Funsten H, Garçon M, Gavalian G, Gilfoyle GP, Giovanetti KL, Gordon CIO, Gothe R, Griffioen K, Guidal M, Guillo M, Guo L, Gyurjyan V, Hadjidakis C, Hakobyan RS, Hardie J, Heddle D, Heimberg P, Hersman FW, Hicks RS, Holtrop M, Hu J, Hyde-Wright CE, Ito MM, Jenkins D, Joo K, Juengst HG, Kellie JD, Khandaker M, Kim KY, Kim K, Kim W, Klein A, Klein FJ, Klimenko AV, Klusman M, Kossov M, Kramer LH, Kuang Y, Kubarovsky V, Kuhn SE, Kuhn J, Lachniet J, Lawrence D, Li J, Lima A, Livingston K, Lukashin K, Manak JJ, McAleer S, McNabb JWC, Mecking BA, Mehrabyan S, Melone JJ, Mestayer MD, Meyer CA, Mikhailov K, Minehart R, Mirazita M, Miskimen R, Mokeev V, Morand L, Morrow S, Muccifora V, Mueller J, Murphy LY, Mutchler GS, Napolitano J, Nasseripour R, Niccolai S, Niculescu G, Niculescu I, Niczyporuk BB, Niyazov RA, Nozar M, O'Brien J, O'Rielly GV, Opper AK, Osipenko M, Park K, Peterson G, Philips SA, Pivnyuk N, Pocanic D, Pogorelko O, Polli E, Pozdniakov S, Preedom BM, Price JW, Prok Y, Protopopescu D, Qin LM, Raue BA, Riccardi G, Ricco G, Ripani M, Ritchie BG, Ronchetti F, Rossi P, Rowntree D, Rubin P, Sabatié F, Salgado C, Santoro J, Sapunenko V, Serov VS, Sharabian YG, Shaw J, Simionatto S, Skabelin AV, Smith LC, Sober DI, Strakovsky II, Stavinsky A, Stoler P, Suleiman R, Taiuti M, Taylor S, Thoma U, Thompson R, Tur C, Ungaro M, Vineyard MF, Vlassov AV, Wang K, Weinstein LB, Weller H, Weygand DP, Whisnant CS, Wolin E, Wood MH, Yegneswaran A, Yun J. Observation of an exotic S = +1 baryon in exclusive photoproduction from the deuteron. PHYSICAL REVIEW LETTERS 2003; 91:252001. [PMID: 14754107 DOI: 10.1103/physrevlett.91.252001] [Show More Authors] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2003] [Indexed: 05/24/2023]
Abstract
In an exclusive measurement of the reaction gammad-->K(+)K(-)pn, a narrow peak that can be attributed to an exotic baryon with strangeness S=+1 is seen in the K(+)n invariant mass spectrum. The peak is at 1.542+/-0.005 GeV/c(2) with a measured width of 0.021 GeV/c(2) FWHM, which is largely determined by experimental mass resolution. The statistical significance of the peak is (5.2+/-0.6)sigma. The mass and width of the observed peak are consistent with recent reports of a narrow S=+1 baryon by other experimental groups.
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Girod FX, Niyazov RA, Avakian H, Ball J, Bedlinskiy I, Burkert VD, De Masi R, Elouadrhiri L, Garçon M, Guidal M, Jo HS, Joo K, Kubarovsky V, Kuleshov SV, MacCormick M, Niccolai S, Pogorelko O, Sabatié F, Stepanyan S, Stoler P, Ungaro M, Zhao B, Amaryan MJ, Ambrozewicz P, Anghinolfi M, Asryan G, Bagdasaryan H, Baillie N, Ball JP, Baltzell NA, Batourine V, Battaglieri M, Bellis M, Benmouna N, Berman BL, Biselli AS, Blaszczyk L, Bouchigny S, Boiarinov S, Bradford R, Branford D, Briscoe WJ, Brooks WK, Bültmann S, Butuceanu C, Calarco JR, Careccia SL, Carman DS, Casey L, Chen S, Cheng L, Cole PL, Collins P, Coltharp P, Crabb D, Crede V, Dashyan N, De Sanctis E, De Vita R, Degtyarenko PV, Deur A, Dharmawardane KV, Dickson R, Djalali C, Dodge GE, Donnelly J, Doughty D, Dugger M, Dzyubak OP, Egiyan H, Egiyan KS, El Fassi L, Eugenio P, Fedotov G, Feldman G, Funsten H, Gavalian G, Gilfoyle GP, Giovanetti KL, Goetz JT, Gonenc A, Gothe RW, Griffioen KA, Guler N, Guo L, Gyurjyan V, Hafidi K, Hakobyan H, Hanretty C, Hersman FW, Hicks K, Hleiqawi I, Holtrop M, Hyde CE, Ilieva Y, Ireland DG, Ishkhanov BS, Isupov EL, Ito MM, Jenkins D, et alGirod FX, Niyazov RA, Avakian H, Ball J, Bedlinskiy I, Burkert VD, De Masi R, Elouadrhiri L, Garçon M, Guidal M, Jo HS, Joo K, Kubarovsky V, Kuleshov SV, MacCormick M, Niccolai S, Pogorelko O, Sabatié F, Stepanyan S, Stoler P, Ungaro M, Zhao B, Amaryan MJ, Ambrozewicz P, Anghinolfi M, Asryan G, Bagdasaryan H, Baillie N, Ball JP, Baltzell NA, Batourine V, Battaglieri M, Bellis M, Benmouna N, Berman BL, Biselli AS, Blaszczyk L, Bouchigny S, Boiarinov S, Bradford R, Branford D, Briscoe WJ, Brooks WK, Bültmann S, Butuceanu C, Calarco JR, Careccia SL, Carman DS, Casey L, Chen S, Cheng L, Cole PL, Collins P, Coltharp P, Crabb D, Crede V, Dashyan N, De Sanctis E, De Vita R, Degtyarenko PV, Deur A, Dharmawardane KV, Dickson R, Djalali C, Dodge GE, Donnelly J, Doughty D, Dugger M, Dzyubak OP, Egiyan H, Egiyan KS, El Fassi L, Eugenio P, Fedotov G, Feldman G, Funsten H, Gavalian G, Gilfoyle GP, Giovanetti KL, Goetz JT, Gonenc A, Gothe RW, Griffioen KA, Guler N, Guo L, Gyurjyan V, Hafidi K, Hakobyan H, Hanretty C, Hersman FW, Hicks K, Hleiqawi I, Holtrop M, Hyde CE, Ilieva Y, Ireland DG, Ishkhanov BS, Isupov EL, Ito MM, Jenkins D, Johnstone JR, Juengst HG, Kalantarians N, Kellie JD, Khandaker M, Kim W, Klein A, Klein FJ, Klimenko AV, Kossov M, Krahn Z, Kramer LH, Kuhn J, Kuhn SE, Lachniet J, Laget JM, Langheinrich J, Lawrence D, Lee T, Livingston K, Lu HY, Markov N, Mattione P, Mazouz M, McKinnon B, Mecking BA, Mestayer MD, Meyer CA, Mibe T, Michel B, Mikhailov K, Mirazita M, Miskimen R, Mokeev V, Moriya K, Morrow SA, Moteabbed M, Munevar E, Mutchler GS, Nadel-Turonski P, Nasseripour R, Niculescu G, Niculescu I, Niczyporuk BB, Niroula MR, Nozar M, Osipenko M, Ostrovidov AI, Park K, Pasyuk E, Paterson C, Anefalos Pereira S, Pierce J, Pivnyuk N, Pocanic D, Pozdniakov S, Price JW, Procureur S, Prok Y, Protopopescu D, Raue BA, Ricco G, Ripani M, Ritchie BG, Rosner G, Rossi P, Salamanca J, Salgado C, Santoro JP, Sapunenko V, Schumacher RA, Serov VS, Sharabian YG, Sharov D, Shvedunov NV, Smith ES, Smith LC, Sober DI, Sokhan D, Stavinsky A, Stepanyan SS, Stokes BE, Strakovsky II, Strauch S, Taiuti M, Tedeschi DJ, Tkabladze A, Tkachenko S, Tur C, Vineyard MF, Vlassov AV, Voutier E, Watts DP, Weinstein LB, Weygand DP, Williams M, Wolin E, Wood MH, Yegneswaran A, Zana L, Zhang J, Zhao ZW. Measurement of deeply virtual compton scattering beam-spin asymmetries. PHYSICAL REVIEW LETTERS 2008; 100:162002. [PMID: 18518188 DOI: 10.1103/physrevlett.100.162002] [Show More Authors] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Indexed: 05/26/2023]
Abstract
The beam-spin asymmetries in the hard exclusive electroproduction of photons on the proton (e p-->epgamma) were measured over a wide kinematic range and with high statistical accuracy. These asymmetries result from the interference of the Bethe-Heitler process and of deeply virtual Compton scattering. Over the whole kinematic range (x(B) from 0.11 to 0.58, Q2 from 1 to 4.8 GeV2, -t from 0.09 to 1.8 GeV2), the azimuthal dependence of the asymmetries is compatible with expectations from leading-twist dominance, A approximately a sinphi/(1+c cosphi). This extensive set of data can thus be used to constrain significantly the generalized parton distributions of the nucleon in the valence quark sector.
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Tikhonenkov DV, Mikhailov KV, Gawryluk RMR, Belyaev AO, Mathur V, Karpov SA, Zagumyonnyi DG, Borodina AS, Prokina KI, Mylnikov AP, Aleoshin VV, Keeling PJ. Microbial predators form a new supergroup of eukaryotes. Nature 2022; 612:714-719. [PMID: 36477531 DOI: 10.1038/s41586-022-05511-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 11/02/2022] [Indexed: 12/12/2022]
Abstract
Molecular phylogenetics of microbial eukaryotes has reshaped the tree of life by establishing broad taxonomic divisions, termed supergroups, that supersede the traditional kingdoms of animals, fungi and plants, and encompass a much greater breadth of eukaryotic diversity1. The vast majority of newly discovered species fall into a small number of known supergroups. Recently, however, a handful of species with no clear relationship to other supergroups have been described2-4, raising questions about the nature and degree of undiscovered diversity, and exposing the limitations of strictly molecular-based exploration. Here we report ten previously undescribed strains of microbial predators isolated through culture that collectively form a diverse new supergroup of eukaryotes, termed Provora. The Provora supergroup is genetically, morphologically and behaviourally distinct from other eukaryotes, and comprises two divergent clades of predators-Nebulidia and Nibbleridia-that are superficially similar to each other, but differ fundamentally in ultrastructure, behaviour and gene content. These predators are globally distributed in marine and freshwater environments, but are numerically rare and have consequently been overlooked by molecular-diversity surveys. In the age of high-throughput analyses, investigation of eukaryotic diversity through culture remains indispensable for the discovery of rare but ecologically and evolutionarily important eukaryotes.
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Kubarovsky V, Guo L, Weygand DP, Stoler P, Battaglieri M, DeVita R, Adams G, Li J, Nozar M, Salgado C, Ambrozewicz P, Anciant E, Anghinolfi M, Asavapibhop B, Audit G, Auger T, Avakian H, Bagdasaryan H, Ball JP, Barrow S, Beard K, Bektasoglu M, Bellis M, Benmouna N, Berman BL, Bianchi N, Biselli AS, Boiarinov S, Bouchigny S, Bradford R, Branford D, Briscoe WJ, Brooks WK, Burkert VD, Butuceanu C, Calarco JR, Carman DS, Carnahan B, Cetina C, Chen S, Ciciani L, Cole PL, Connelly J, Cords D, Corvisiero P, Crabb D, Crannell H, Cummings JP, De Sanctis E, Degtyarenko PV, Denizli H, Dennis L, Dharmawardane KV, Djalali C, Dodge GE, Doughty D, Dragovitsch P, Dugger M, Dytman S, Dzyubak OP, Egiyan H, Egiyan KS, Elouadrhiri L, Empl A, Eugenio P, Farhi L, Fatemi R, Feuerbach RJ, Ficenec J, Forest TA, Frolov V, Funsten H, Gaff SJ, Garçon M, Gavalian G, Gilfoyle GP, Giovanetti KL, Girard P, Gothe R, Gordon CIO, Griffioen K, Guidal M, Guillo M, Gyurjyan V, Hadjidakis C, Hakobyan RS, Hancock D, Hardie J, Heddle D, Heimberg P, Hersman FW, Hicks K, Holtrop M, Hu J, Ilieva Y, Ito MM, Jenkins D, Joo K, Juengst HG, Kelley JH, et alKubarovsky V, Guo L, Weygand DP, Stoler P, Battaglieri M, DeVita R, Adams G, Li J, Nozar M, Salgado C, Ambrozewicz P, Anciant E, Anghinolfi M, Asavapibhop B, Audit G, Auger T, Avakian H, Bagdasaryan H, Ball JP, Barrow S, Beard K, Bektasoglu M, Bellis M, Benmouna N, Berman BL, Bianchi N, Biselli AS, Boiarinov S, Bouchigny S, Bradford R, Branford D, Briscoe WJ, Brooks WK, Burkert VD, Butuceanu C, Calarco JR, Carman DS, Carnahan B, Cetina C, Chen S, Ciciani L, Cole PL, Connelly J, Cords D, Corvisiero P, Crabb D, Crannell H, Cummings JP, De Sanctis E, Degtyarenko PV, Denizli H, Dennis L, Dharmawardane KV, Djalali C, Dodge GE, Doughty D, Dragovitsch P, Dugger M, Dytman S, Dzyubak OP, Egiyan H, Egiyan KS, Elouadrhiri L, Empl A, Eugenio P, Farhi L, Fatemi R, Feuerbach RJ, Ficenec J, Forest TA, Frolov V, Funsten H, Gaff SJ, Garçon M, Gavalian G, Gilfoyle GP, Giovanetti KL, Girard P, Gothe R, Gordon CIO, Griffioen K, Guidal M, Guillo M, Gyurjyan V, Hadjidakis C, Hakobyan RS, Hancock D, Hardie J, Heddle D, Heimberg P, Hersman FW, Hicks K, Holtrop M, Hu J, Ilieva Y, Ito MM, Jenkins D, Joo K, Juengst HG, Kelley JH, Khandaker M, Kim KY, Kim K, Kim W, Klein FJ, Klimenko AV, Klusman M, Kossov M, Kramer LH, Kuhn SE, Kuhn J, Lachniet J, Laget JM, Langheinrich J, Lawrence D, Longhi A, Lukashin K, Major RW, Manak JJ, Marchand C, McAleer S, McNabb JWC, Mecking BA, Mehrabyan S, Melone JJ, Mestayer MD, Meyer CA, Mikhailov K, Minehart R, Mirazita M, Miskimen R, Mokeev V, Morand L, Morrow SA, Mozer MU, Muccifora V, Mueller J, Mutchler GS, Napolitano J, Nasseripour R, Nelson SO, Niccolai S, Niculescu G, Niculescu I, Niczyporuk BB, Niyazov RA, O'Brien JT, O'Rielly GV, Opper AK, Osipenko M, Park K, Pasyuk E, Peterson G, Philips SA, Pivnyuk N, Pocanic D, Pogorelko O, Polli E, Pozdniakov S, Preedom BM, Price JW, Prok Y, Protopopescu D, Qin LM, Raue BA, Riccardi G, Ripani M, Ritchie BG, Ronchetti F, Rossi P, Rowntree D, Rubin PD, Sabatié F, Sabourov K, Santoro JP, Sapunenko V, Sargsyan M, Schumacher RA, Serov VS, Shafi A, Sharabian YG, Shaw J, Simionatto S, Skabelin AV, Smith ES, Smith T, Smith LC, Sober DI, Spraker M, Stavinsky A, Stepanyan S, Strakovsky II, Strauch S, Taiuti M, Taylor S, Tedeschi DJ, Thoma U, Thompson R, Todor L, Tur C, Ungaro M, Vineyard MF, Vlassov AV, Wang K, Weinstein LB, Weisberg A, Whisnant CS, Wolin E, Wood MH, Yegneswaran A, Yun J. Observation of an exotic baryon with S=+1 in photoproduction from the proton. PHYSICAL REVIEW LETTERS 2004; 92:032001. [PMID: 14753864 DOI: 10.1103/physrevlett.92.032001] [Show More Authors] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2003] [Indexed: 05/24/2023]
Abstract
The reaction gamma p-->pi(+)K(-)K(+)n was studied at Jefferson Laboratory using a tagged photon beam with an energy range of 3-5.47 GeV. A narrow baryon state with strangeness S=+1 and mass M=1555+/-10 MeV/c(2) was observed in the nK(+) invariant mass spectrum. The peak's width is consistent with the CLAS resolution (FWHM=26 MeV/c(2)), and its statistical significance is (7.8+/-1.0)sigma. A baryon with positive strangeness has exotic structure and cannot be described in the framework of the naive constituent quark model. The mass of the observed state is consistent with the mass predicted by the chiral soliton model for the Theta(+) baryon. In addition, the pK(+) invariant mass distribution was analyzed in the reaction gamma p-->K(-)K(+)p with high statistics in search of doubly charged exotic baryon states. No resonance structures were found in this spectrum.
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Mikhailov KV, Karpov SA, Letcher PM, Lee PA, Logacheva MD, Penin AA, Nesterenko MA, Pozdnyakov IR, Potapenko EV, Sherbakov DY, Panchin YV, Aleoshin VV. Genomic analysis reveals cryptic diversity in aphelids and sheds light on the emergence of Fungi. Curr Biol 2022; 32:4607-4619.e7. [PMID: 36126656 DOI: 10.1016/j.cub.2022.08.071] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/26/2022] [Accepted: 08/24/2022] [Indexed: 11/28/2022]
Abstract
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.
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Aleoshin VV, Mylnikov AP, Mirzaeva GS, Mikhailov KV, Karpov SA. Heterokont Predator Develorapax marinus gen. et sp. nov. - A Model of the Ochrophyte Ancestor. Front Microbiol 2016; 7:1194. [PMID: 27536283 PMCID: PMC4971089 DOI: 10.3389/fmicb.2016.01194] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 07/19/2016] [Indexed: 12/15/2022] Open
Abstract
Heterotrophic lineages of Heterokonta (or stramenopiles), in contrast to a single monophyletic group of autotrophs, Ochrophyta, form several clades that independently branch off the heterokont stem lineage. The nearest neighbors of Ochrophyta in the phylogenetic tree appear to be almost exclusively bacterivorous, whereas the hypothesis of plastid acquisition by the ancestors of the ochrophyte lineage suggests an ability to engulf eukaryotic alga. In line with this hypothesis, the heterotrophic predator at the base of the ochrophyte lineage may be regarded as a model for the ochrophyte ancestor. Here, we present a new genus and species of marine free-living heterotrophic heterokont Develorapax marinus, which falls into an isolated heterokont cluster, along with the marine flagellate Developayella elegans, and is able to engulf eukaryotic cells. Together with environmental sequences D. marinus and D. elegans form a class-level clade Developea nom. nov. represented by species adapted to different environmental conditions and with a wide geographical distribution. The position of Developea among Heterokonta in large-scale phylogenetic tree is discussed. We propose that members of the Developea clade represent a model for transition from bacterivory to a predatory feeding mode by selection for larger prey. Presumably, such transition in the grazing strategy is possible in the presence of bacterial biofilms or aggregates expected in eutrophic environment, and has likely occurred in the ochrophyte ancestor.
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Aleshin VV, Konstantinova AV, Mikhailov KV, Nikitin MA, Petrov NB. Do we need many genes for phylogenetic inference? BIOCHEMISTRY (MOSCOW) 2008; 72:1313-23. [PMID: 18205615 DOI: 10.1134/s000629790712005x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Fifty-six nuclear protein coding genes from Taxonomically Broad EST Database and other databases were selected for phylogenomic-based examination of alternative phylogenetic hypotheses concerning intergroup relationship between multicellular animals (Metazoa) and other representatives of Opisthokonta. The results of this work support sister group relationship between Metazoa and Choanoflagellata. Both of these groups form the taxon Holozoa along with the monophyletic Ichthyosporea or Mesomycetozoea (a group that includes Amoebidium parasiticum, Sphaeroforma arctica, and Capsaspora owczarzaki). These phylogenetic hypotheses receive high statistical support both when utilizing whole alignment and when only 5000 randomly selected alignment positions are used. The presented results suggest subdivision of Fungi into Eumycota and lower fungi, Chytridiomycota. The latter form a monophyletic group that comprises Chytridiales+Spizellomycetales+Blastocladiales (Batrachochytrium, Spizellomyces, Allomyces, Blastocladiella), contrary to the earlier reports based on the analysis of 18S rRNA and a limited set of protein coding genes. The phylogenetic distribution of genes coding for a ubiquitin-fused ribosomal protein S30 implies at least three independent cases of gene fusion: in the ancestors of Holozoa, in heterotrophic Heterokonta (Oomycetes and Blastocystis) and in the ancestors of Cryptophyta and Glaucophyta. Ubiquitin-like sequences fused with ribosomal protein S30 outside of Holozoa are not FUBI orthologs. Two independent events of FUBI replacement by the ubiquitin sequence were detected in the lineage of C. owczarzaki and in the monophyletic group of nematode worms Tylenchomorpha+Cephalobidae. Bursaphelenchus xylophilus (Aphelenchoidoidea) retains a state typical of the rest of the Metazoa. The data emphasize the fact that the reliability of phylogenetic reconstructions depends on the number of analyzed genes to a lesser extent than on our ability to recognize reconstruction artifacts.
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Egiyan KS, Dashyan NB, Sargsian MM, Strikman MI, Weinstein LB, Adams G, Ambrozewicz P, Anghinolfi M, Asavapibhop B, Asryan G, Avakian H, Baghdasaryan H, Baillie N, Ball JP, Baltzell NA, Batourine V, Battaglieri M, Bedlinskiy I, Bektasoglu M, Bellis M, Benmouna N, Biselli AS, Bonner BE, Bouchigny S, Boiarinov S, Bradford R, Branford D, Brooks WK, Bültmann S, Burkert VD, Bultuceanu C, Calarco JR, Careccia SL, Carman DS, Carnahan B, Chen S, Cole PL, Coltharp P, Corvisiero P, Crabb D, Crannell H, Cummings JP, De Sanctis E, DeVita R, Degtyarenko PV, Denizli H, Dennis L, Dharmawardane KV, Djalali C, Dodge GE, Donnelly J, Doughty D, Dragovitsch P, Dugger M, Dytman S, Dzyubak OP, Egiyan H, Elouadrhiri L, Empl A, Eugenio P, Fatemi R, Fedotov G, Feuerbach RJ, Forest TA, Funsten H, Gavalian G, Gevorgyan NG, Gilfoyle GP, Giovanetti KL, Girod FX, Goetz JT, Golovatch E, Gothe RW, Griffioen KA, Guidal M, Guillo M, Guler N, Guo L, Gyurjyan V, Hadjidakis C, Hardie J, Hersman FW, Hicks K, Hleiqawi I, Holtrop M, Hu J, Huertas M, Hyde-Wright CE, Ilieva Y, Ireland DG, Ishkhanov BS, Ito MM, Jenkins D, Jo HS, Joo K, Juengst HG, Kellie JD, Khandaker M, Kim KY, Kim K, et alEgiyan KS, Dashyan NB, Sargsian MM, Strikman MI, Weinstein LB, Adams G, Ambrozewicz P, Anghinolfi M, Asavapibhop B, Asryan G, Avakian H, Baghdasaryan H, Baillie N, Ball JP, Baltzell NA, Batourine V, Battaglieri M, Bedlinskiy I, Bektasoglu M, Bellis M, Benmouna N, Biselli AS, Bonner BE, Bouchigny S, Boiarinov S, Bradford R, Branford D, Brooks WK, Bültmann S, Burkert VD, Bultuceanu C, Calarco JR, Careccia SL, Carman DS, Carnahan B, Chen S, Cole PL, Coltharp P, Corvisiero P, Crabb D, Crannell H, Cummings JP, De Sanctis E, DeVita R, Degtyarenko PV, Denizli H, Dennis L, Dharmawardane KV, Djalali C, Dodge GE, Donnelly J, Doughty D, Dragovitsch P, Dugger M, Dytman S, Dzyubak OP, Egiyan H, Elouadrhiri L, Empl A, Eugenio P, Fatemi R, Fedotov G, Feuerbach RJ, Forest TA, Funsten H, Gavalian G, Gevorgyan NG, Gilfoyle GP, Giovanetti KL, Girod FX, Goetz JT, Golovatch E, Gothe RW, Griffioen KA, Guidal M, Guillo M, Guler N, Guo L, Gyurjyan V, Hadjidakis C, Hardie J, Hersman FW, Hicks K, Hleiqawi I, Holtrop M, Hu J, Huertas M, Hyde-Wright CE, Ilieva Y, Ireland DG, Ishkhanov BS, Ito MM, Jenkins D, Jo HS, Joo K, Juengst HG, Kellie JD, Khandaker M, Kim KY, Kim K, Kim W, Klein A, Klein FJ, Klimenko A, Klusman M, Kramer LH, Kubarovsky V, Kuhn J, Kuhn SE, Kuleshov S, Lachniet J, Laget JM, Langheinrich J, Lawrence D, Lee T, Livingston K, Maximon LC, McAleer S, McKinnon B, McNabb JWC, Mecking BA, Mestayer MD, Meyer CA, Mibe T, Mikhailov K, Minehart R, Mirazita M, Miskimen R, Mokeev V, Morrow SA, Mueller J, Mutchler GS, Nadel-Turonski P, Napolitano J, Nasseripour R, Niccolai S, Niculescu G, Niculescu I, Niczyporuk BB, Niyazov RA, O'Relly GV, Osipenko M, Ostrovidov AI, Park K, Pasyuk E, Peterson C, Pierce J, Pivnyuk N, Pocanic D, Pogorelko O, Polli E, Pozdniakov S, Preedom BM, Price JW, Prok Y, Protopopescu D, Qin LM, Raue BA, Riccardi G, Ricco G, Ripani M, Ritchie BG, Ronchetti F, Rosner G, Rossi P, Rowntree D, Rubin PD, Sabatié F, Salgado C, Santoro JP, Sapunenko V, Schumacher RA, Serov VS, Sharabian YG, Shaw J, Smith ES, Smith LC, Sober DI, Stavinsky A, Stepanyan S, Stokes BE, Stoler P, Strauch S, Suleiman R, Taiuti M, Taylor S, Tedeschi DJ, Thompson R, Tkabladze A, Tkachenko S, Todor L, Tur C, Ungaro M, Vineyard MF, Vlassov AV, Weygand DP, Williams M, Wolin E, Wood MH, Yegneswaran A, Yun J, Zana L, Zhang J. Measurement of two- and three-nucleon short-range correlation probabilities in nuclei. PHYSICAL REVIEW LETTERS 2006; 96:082501. [PMID: 16606174 DOI: 10.1103/physrevlett.96.082501] [Show More Authors] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2005] [Indexed: 05/08/2023]
Abstract
The ratios of inclusive electron scattering cross sections of 4He, 12C, and 56Fe to 3He have been measured at 1 < xB <. At Q2 > 1.4 GeV2, the ratios exhibit two separate plateaus, at 1.5 < xB < 2 and at xB > 2.25. This pattern is predicted by models that include 2- and 3-nucleon short-range correlations (SRC). Relative to A = 3, the per-nucleon probabilities of 3-nucleon SRC are 2.3, 3.1, and 4.4 times larger for A = 4, 12, and 56. This is the first measurement of 3-nucleon SRC probabilities in nuclei.
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Marić I, Yang L, Li X, Santiago GM, Pappas CG, Qiu X, Dijksman JA, Mikhailov K, van Rijn P, Otto S. Tailorable and Biocompatible Supramolecular-Based Hydrogels Featuring two Dynamic Covalent Chemistries. Angew Chem Int Ed Engl 2023; 62:e202216475. [PMID: 36744522 DOI: 10.1002/anie.202216475] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/17/2023] [Accepted: 02/01/2023] [Indexed: 02/07/2023]
Abstract
Dynamic covalent chemistry (DCC) has proven to be a valuable tool in creating fascinating molecules, structures, and emergent properties in fully synthetic systems. Here we report a system that uses two dynamic covalent bonds in tandem, namely disulfides and hydrazones, for the formation of hydrogels containing biologically relevant ligands. The reversibility of disulfide bonds allows fiber formation upon oxidation of dithiol-peptide building block, while the reaction between NH-NH2 functionalized C-terminus and aldehyde cross-linkers results in a gel. The same bond-forming reaction was exploited for the "decoration" of the supramolecular assemblies by cell-adhesion-promoting sequences (RGD and LDV). Fast triggered gelation, cytocompatibility and ability to "on-demand" chemically customize fibrillar scaffold offer potential for applying these systems as a bioactive platform for cell culture and tissue engineering.
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Lachniet J, Afanasev A, Arenhövel H, Brooks WK, Gilfoyle GP, Higinbotham D, Jeschonnek S, Quinn B, Vineyard MF, Adams G, Adhikari KP, Amaryan MJ, Anghinolfi M, Asavapibhop B, Asryan G, Avakian H, Bagdasaryan H, Baillie N, Ball JP, Baltzell NA, Barrow S, Batourine V, Battaglieri M, Beard K, Bedlinskiy I, Bektasoglu M, Bellis M, Benmouna N, Berman BL, Biselli AS, Bonner BE, Bookwalter C, Bouchigny S, Boiarinov S, Bradford R, Branford D, Briscoe WJ, Bültmann S, Burkert VD, Calarco JR, Careccia SL, Carman DS, Casey L, Cheng L, Cole PL, Coleman A, Collins P, Cords D, Corvisiero P, Crabb D, Crede V, Cummings JP, Dale D, Daniel A, Dashyan N, De Masi R, De Vita R, De Sanctis E, Degtyarenko PV, Denizli H, Dennis L, Deur A, Dhamija S, Dharmawardane KV, Dhuga KS, Dickson R, Djalali C, Dodge GE, Doughty D, Dragovitsch P, Dugger M, Dytman S, Dzyubak OP, Egiyan H, Egiyan KS, El Fassi L, Elouadrhiri L, Empl A, Eugenio P, Fatemi R, Fedotov G, Fersch R, Feuerbach RJ, Forest TA, Fradi A, Gabrielyan MY, Garçon M, Gavalian G, Gevorgyan N, Giovanetti KL, Girod FX, Goetz JT, Gohn W, Golovatch E, Gothe RW, Graham L, Griffioen KA, Guidal M, Guillo M, Guler N, et alLachniet J, Afanasev A, Arenhövel H, Brooks WK, Gilfoyle GP, Higinbotham D, Jeschonnek S, Quinn B, Vineyard MF, Adams G, Adhikari KP, Amaryan MJ, Anghinolfi M, Asavapibhop B, Asryan G, Avakian H, Bagdasaryan H, Baillie N, Ball JP, Baltzell NA, Barrow S, Batourine V, Battaglieri M, Beard K, Bedlinskiy I, Bektasoglu M, Bellis M, Benmouna N, Berman BL, Biselli AS, Bonner BE, Bookwalter C, Bouchigny S, Boiarinov S, Bradford R, Branford D, Briscoe WJ, Bültmann S, Burkert VD, Calarco JR, Careccia SL, Carman DS, Casey L, Cheng L, Cole PL, Coleman A, Collins P, Cords D, Corvisiero P, Crabb D, Crede V, Cummings JP, Dale D, Daniel A, Dashyan N, De Masi R, De Vita R, De Sanctis E, Degtyarenko PV, Denizli H, Dennis L, Deur A, Dhamija S, Dharmawardane KV, Dhuga KS, Dickson R, Djalali C, Dodge GE, Doughty D, Dragovitsch P, Dugger M, Dytman S, Dzyubak OP, Egiyan H, Egiyan KS, El Fassi L, Elouadrhiri L, Empl A, Eugenio P, Fatemi R, Fedotov G, Fersch R, Feuerbach RJ, Forest TA, Fradi A, Gabrielyan MY, Garçon M, Gavalian G, Gevorgyan N, Giovanetti KL, Girod FX, Goetz JT, Gohn W, Golovatch E, Gothe RW, Graham L, Griffioen KA, Guidal M, Guillo M, Guler N, Guo L, Gyurjyan V, Hadjidakis C, Hafidi K, Hakobyan H, Hanretty C, Hardie J, Hassall N, Heddle D, Hersman FW, Hicks K, Hleiqawi I, Holtrop M, Hu J, Huertas M, Hyde-Wright CE, Ilieva Y, Ireland DG, Ishkhanov BS, Isupov EL, Ito MM, Jenkins D, Jo HS, Johnstone JR, Joo K, Juengst HG, Kageya T, Kalantarians N, Keller D, Kellie JD, Khandaker M, Khetarpal P, Kim KY, Kim K, Kim W, Klein A, Klein FJ, Klusman M, Konczykowski P, Kossov M, Kramer LH, Kubarovsky V, Kuhn J, Kuhn SE, Kuleshov SV, Kuznetsov V, Laget JM, Langheinrich J, Lawrence D, Lima ACS, Livingston K, Lowry M, Lu HY, Lukashin K, Maccormick M, Malace S, Manak JJ, Markov N, Mattione P, McAleer S, McCracken ME, McKinnon B, McNabb JWC, Mecking BA, Mestayer MD, Meyer CA, Mibe T, Mikhailov K, Mineeva T, Minehart R, Mirazita M, Miskimen R, Mokeev V, Moreno B, Moriya K, Morrow SA, Moteabbed M, Mueller J, Munevar E, Mutchler GS, Nadel-Turonski P, Nasseripour R, Niccolai S, Niculescu G, Niculescu I, Niczyporuk BB, Niroula MR, Niyazov RA, Nozar M, O'Rielly GV, Osipenko M, Ostrovidov AI, Park K, Park S, Pasyuk E, Paterson C, Pereira SA, Philips SA, Pierce J, Pivnyuk N, Pocanic D, Pogorelko O, Polli E, Popa I, Pozdniakov S, Preedom BM, Price JW, Prok Y, Protopopescu D, Qin LM, Raue BA, Riccardi G, Ricco G, Ripani M, Ritchie BG, Rosner G, Rossi P, Rowntree D, Rubin PD, Sabatié F, Saini MS, Salamanca J, Salgado C, Sandorfi A, Santoro JP, Sapunenko V, Schott D, Schumacher RA, Serov VS, Sharabian YG, Sharov D, Shaw J, Shvedunov NV, Skabelin AV, Smith ES, Smith LC, Sober DI, Sokhan D, Starostin A, Stavinsky A, Stepanyan S, Stepanyan SS, Stokes BE, Stoler P, Stopani KA, Strakovsky II, Strauch S, Suleiman R, Taiuti M, Taylor S, Tedeschi DJ, Thompson R, Tkabladze A, Tkachenko S, Ungaro M, Vlassov AV, Watts DP, Wei X, Weinstein LB, Weygand DP, Williams M, Wolin E, Wood MH, Yegneswaran A, Yun J, Yurov M, Zana L, Zhang J, Zhao B, Zhao ZW. Precise measurement of the neutron magnetic form factor G(M)n in the few-GeV2 region. PHYSICAL REVIEW LETTERS 2009; 102:192001. [PMID: 19518944 DOI: 10.1103/physrevlett.102.192001] [Show More Authors] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2008] [Indexed: 05/27/2023]
Abstract
The neutron elastic magnetic form factor was extracted from quasielastic electron scattering on deuterium over the range Q;{2}=1.0-4.8 GeV2 with the CLAS detector at Jefferson Lab. High precision was achieved with a ratio technique and a simultaneous in situ calibration of the neutron detection efficiency. Neutrons were detected with electromagnetic calorimeters and time-of-flight scintillators at two beam energies. The dipole parametrization gives a good description of the data.
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Finoshin AD, Adameyko KI, Mikhailov KV, Kravchuk OI, Georgiev AA, Gornostaev NG, Kosevich IA, Mikhailov VS, Gazizova GR, Shagimardanova EI, Gusev OA, Lyupina YV. Iron metabolic pathways in the processes of sponge plasticity. PLoS One 2020; 15:e0228722. [PMID: 32084159 PMCID: PMC7034838 DOI: 10.1371/journal.pone.0228722] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 01/21/2020] [Indexed: 12/11/2022] Open
Abstract
The ability to regulate oxygen consumption evolved in ancestral animals and is intrinsically linked to iron metabolism. The iron pathways have been intensively studied in mammals, whereas data on distant invertebrates are limited. Sea sponges represent the oldest animal phylum and have unique structural plasticity and capacity to reaggregate after complete dissociation. We studied iron metabolic factors and their expression during reaggregation in the White Sea cold-water sponges Halichondria panicea and Halisarca dujardini. De novo transcriptomes were assembled using RNA-Seq data, and evolutionary trends were analyzed with bioinformatic tools. Differential expression during reaggregation was studied for H. dujardini. Enzymes of the heme biosynthesis pathway and transport globins, neuroglobin (NGB) and androglobin (ADGB), were identified in sponges. The globins mutate at higher evolutionary rates than the heme synthesis enzymes. Highly conserved iron-regulatory protein 1 (IRP1) presumably interacts with the iron-responsive elements (IREs) found in mRNAs of ferritin (FTH1) and a putative transferrin receptor NAALAD2. The reaggregation process is accompanied by increased expression of IRP1, the antiapoptotic factor BCL2, the inflammation factor NFκB (p65), FTH1 and NGB, as well as by an increase in mitochondrial density. Our data indicate a complex mechanism of iron regulation in sponge structural plasticity and help to better understand general mechanisms of morphogenetic processes in multicellular species.
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Chen S, Avakian H, Burkert VD, Eugenio P, Adams G, Amarian M, Ambrozewicz P, Anghinolfi M, Asryan G, Bagdasaryan H, Baillie N, Ball JP, Baltzell NA, Barrow S, Batourine V, Battaglieri M, Beard K, Bedlinskiy I, Bektasoglu M, Bellis M, Benmouna N, Berman BL, Biselli AS, Bonner BE, Bouchigny S, Boiarinov S, Bosted P, Bradford R, Branford D, Briscoe WJ, Brooks WK, Bültmann S, Butuceanu C, Calarco JR, Careccia SL, Carman DS, Carnahan B, Cazes A, Cole PL, Collins P, Coltharp P, Cords D, Corvisiero P, Crabb D, Crannell H, Crede V, Cummings JP, DeMasi R, DeVita R, De Sanctis E, Degtyarenko PV, Denizli H, Dennis L, Deur A, Dharmawardane KV, Dhuga KS, Djalali C, Dodge GE, Donnelly J, Doughty D, Dugger M, Dytman S, Dzyubak OP, Egiyan H, Egiyan KS, El Fassi L, Elouadrhiri L, Fatemi R, Fedotov G, Feldman G, Feuerbach RJ, Forest TA, Funsten H, Garçon M, Gavalian G, Gilfoyle GP, Giovanetti KL, Girod FX, Goetz JT, Golovatch E, Gonenc A, Gothe RW, Griffioen KA, Guidal M, Guillo M, Guler N, Guo L, Gyurjyan V, Hadjidakis C, Hafidi K, Hakobyan H, Hakobyan RS, Hardie J, Heddle D, Hersman FW, Hicks K, Hleiqawi I, Holtrop M, Huertas M, Hyde-Wright CE, et alChen S, Avakian H, Burkert VD, Eugenio P, Adams G, Amarian M, Ambrozewicz P, Anghinolfi M, Asryan G, Bagdasaryan H, Baillie N, Ball JP, Baltzell NA, Barrow S, Batourine V, Battaglieri M, Beard K, Bedlinskiy I, Bektasoglu M, Bellis M, Benmouna N, Berman BL, Biselli AS, Bonner BE, Bouchigny S, Boiarinov S, Bosted P, Bradford R, Branford D, Briscoe WJ, Brooks WK, Bültmann S, Butuceanu C, Calarco JR, Careccia SL, Carman DS, Carnahan B, Cazes A, Cole PL, Collins P, Coltharp P, Cords D, Corvisiero P, Crabb D, Crannell H, Crede V, Cummings JP, DeMasi R, DeVita R, De Sanctis E, Degtyarenko PV, Denizli H, Dennis L, Deur A, Dharmawardane KV, Dhuga KS, Djalali C, Dodge GE, Donnelly J, Doughty D, Dugger M, Dytman S, Dzyubak OP, Egiyan H, Egiyan KS, El Fassi L, Elouadrhiri L, Fatemi R, Fedotov G, Feldman G, Feuerbach RJ, Forest TA, Funsten H, Garçon M, Gavalian G, Gilfoyle GP, Giovanetti KL, Girod FX, Goetz JT, Golovatch E, Gonenc A, Gothe RW, Griffioen KA, Guidal M, Guillo M, Guler N, Guo L, Gyurjyan V, Hadjidakis C, Hafidi K, Hakobyan H, Hakobyan RS, Hardie J, Heddle D, Hersman FW, Hicks K, Hleiqawi I, Holtrop M, Huertas M, Hyde-Wright CE, Ilieva Y, Ireland DG, Ishkhanov BS, Isupov EL, Ito MM, Jenkins D, Jo HS, Joo K, Juengst HG, Keith C, Kellie JD, Khandaker M, Kim KY, Kim K, Kim W, Klein A, Klein FJ, Klusman M, Kossov M, Kramer LH, Kubarovsky V, Kuhn J, Kuhn SE, Kuleshov SV, Lachniet J, Laget JM, Langheinrich J, Lawrence D, Li J, Lima ACS, Livingston K, Lu H, Lukashin K, MacCormick M, Markov N, McAleer S, McKinnon B, McNabb JWC, Mecking BA, Mestayer MD, Meyer CA, Mibe T, Mikhailov K, Minehart R, Mirazita M, Miskimen R, Mokeev V, Morand L, Morrow SA, Moteabbed M, Mueller J, Mutchler GS, Nadel-Turonski P, Napolitano J, Nasseripour R, Natasha N, Niccolai S, Niculescu G, Niculescu I, Niczyporuk BB, Niroula MR, Niyazov RA, Nozar M, O'Rielly GV, Osipenko M, Ostrovidov AI, Park K, Pasyuk E, Paterson C, Philips SA, Pierce J, Pivnyuk N, Pocanic D, Pogorelko O, Polli E, Popa I, Pozdniakov S, Preedom BM, Price JW, Prok Y, Protopopescu D, Qin LM, Raue BA, Riccardi G, Ricco G, Ripani M, Ritchie BG, Ronchetti F, Rosner G, Rossi P, Rowntree D, Rubin PD, Sabatié F, Salgado C, Santoro JP, Sapunenko V, Schumacher RA, Serov VS, Sharabian YG, Shaw J, Shvedunov NV, Skabelin AV, Smith ES, Smith LC, Sober DI, Stavinsky A, Stepanyan SS, Stepanyan S, Stokes BE, Stoler P, Strakovsky II, Strauch S, Suleiman R, Taiuti M, Tedeschi DJ, Thoma U, Tkabladze A, Tkachenko S, Todor L, Tur C, Ungaro M, Vanderhaeghen M, Vineyard MF, Vlassov AV, Watts DP, Weinstein LB, Weygand DP, Williams M, Wolin E, Wood MH, Yegneswaran A, Yun J, Zana L, Zhang J, Zhao B, Zhao Z. Measurement of deeply virtual compton scattering with a polarized-proton target. PHYSICAL REVIEW LETTERS 2006; 97:072002. [PMID: 17026221 DOI: 10.1103/physrevlett.97.072002] [Show More Authors] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2006] [Indexed: 05/12/2023]
Abstract
The longitudinal target-spin asymmetry AUL for the exclusive electroproduction of high-energy photons was measured for the first time in ep-->e;'pgamma. The data have been accumulated at JLab with the CLAS spectrometer using 5.7 GeV electrons and a longitudinally polarized NH3 target. A significant azimuthal angular dependence was observed, resulting from the interference of the deeply virtual Compton scattering and Bethe-Heitler processes. The amplitude of the sinvarphi moment is 0.252+/-0.042stat+/-0.020sys. Theoretical calculations are in good agreement with the magnitude and the kinematic dependence of the target-spin asymmetry, which is sensitive to the generalized parton distributions H and H.
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Mikhailov KV, Janouškovec J, Tikhonenkov DV, Mirzaeva GS, Diakin AY, Simdyanov TG, Mylnikov AP, Keeling PJ, Aleoshin VV. A Complex Distribution of Elongation Family GTPases EF1A and EFL in Basal Alveolate Lineages. Genome Biol Evol 2014; 6:2361-7. [PMID: 25179686 PMCID: PMC4217694 DOI: 10.1093/gbe/evu186] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Translation elongation factor-1 alpha (EF1A) and the related GTPase EF-like (EFL) are two proteins with a complex mutually exclusive distribution across the tree of eukaryotes. Recent surveys revealed that the distribution of the two GTPases in even closely related taxa is frequently at odds with their phylogenetic relationships. Here, we investigate the distribution of EF1A and EFL in the alveolate supergroup. Alveolates comprise three major lineages: ciliates and apicomplexans encode EF1A, whereas dinoflagellates encode EFL. We searched transcriptome databases for seven early-diverging alveolate taxa that do not belong to any of these groups: colpodellids, chromerids, and colponemids. Current data suggest all seven are expected to encode EF1A, but we find three genera encode EFL: Colpodella, Voromonas, and the photosynthetic Chromera. Comparing this distribution with the phylogeny of alveolates suggests that EF1A and EFL evolution in alveolates cannot be explained by a simple horizontal gene transfer event or lineage sorting.
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Romanova EV, Mikhailov KV, Logacheva MD, Kamaltynov RM, Aleoshin VV, Sherbakov DY. The complete mitochondrial genome of a deep-water Baikalian amphipoda Brachyuropus grewingkii (Dybowsky, 1874). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4158-4159. [PMID: 25600751 DOI: 10.3109/19401736.2014.1003891] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this study, we present a complete mitochondrial genome of a deep-water amphipoda Brachyuropus grewingkii (Dybowsky, 1874) from Lake Baikal. A circular mitochondrial DNA has 17,118 bp in length and contains 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, a putative control region, and five intergenic spacers. An extended control region and altered positions of some tRNA genes distinguish mitochondrial genome of B. grewingkii from the mitochondrial genomes described for other Baikalian amphipoda species.
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Romanova EV, Mikhailov KV, Logacheva MD, Kamaltynov RM, Aleoshin VV, Sherbakov DY. The complete mitochondrial genome of Baikalian amphipoda Eulimnogammarus vittatus Dybowsky, 1874. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1795-7. [PMID: 25264843 DOI: 10.3109/19401736.2014.963817] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
A complete mitochondrial genome sequence of amphipoda Eulimnogammarus vittatus Dybowsky, 1874 from Lake Baikal was obtained using next-generation sequencing approach. Mitochondrial DNA with the length of 15,534 bp contains 13 protein-coding genes, 2 ribosomal RNA, 23 transfer RNA and non-coding sequences: a putative control region and 7 intergenic spacers. A brief comparative analysis of mitochondrial genomes of E. vittatus and its sister species Eulimnogammarus verrucosus was performed.
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