Gene Recruitments and Dismissals in the Argonaut Genome Provide Insights into Pelagic Lifestyle Adaptation and Shell-like Eggcase Reacquisition.

The paper nautilus or greater argonaut, Argonauta argo, is a species of octopods which is characterized by its pelagic lifestyle and by the presence of a protective spiral-shaped shell-like eggcase in females. To reveal the genomic background of how the species adapted to the pelagic lifestyle and acquired its shell-like eggcase, we sequenced the draft genome of the species. The genome size was 1.1 Gb, which is the smallest among the cephalopods known to date, with the top 215 scaffolds (average length 5,064,479 bp) covering 81% (1.09 Gb) of the total assembly. A total of 26,433 protein-coding genes were predicted from 16,802 assembled scaffolds. From these, we identified nearly intact HOX, Parahox, Wnt clusters, and some gene clusters that could probably be related to the pelagic lifestyle, such as reflectin, tyrosinase, and opsin. The gene models also revealed several homologous genes related to calcified shell formation in Conchiferan mollusks, such as Pif-like, SOD, and TRX. Interestingly, comparative genomics analysis revealed that the homologous genes for such genes were also found in the genome of the shell-less octopus, as well as Nautilus, which has a true outer shell. Therefore, the draft genome sequence of Arg. argo presented here has helped us to gain further insights into the genetic background of the dynamic recruitment and dismissal of genes to form an important, converging extended phenotypic structure such as the shell and the shell-like eggcase. Additionally, it allows us to explore the evolution of from benthic to pelagic lifestyles in cephalopods and octopods.

Exogenous mitochondrial transfer and endogenous mitochondrial fission facilitate AML resistance to OxPhos inhibition.

Acute myeloid leukemia (AML) cells are highly dependent on oxidative phosphorylation (OxPhos) for survival, and they continually adapt to fluctuations in nutrient and oxygen availability in the bone marrow (BM) microenvironment. We investigated how the BM microenvironment affects the response to OxPhos inhibition in AML by using a novel complex I OxPhos inhibitor, IACS-010759. Cellular adhesion, growth, and apoptosis assays, along with measurements of expression of mitochondrial DNA and generation of mitochondrial reactive oxygen species indicated that direct interactions with BM stromal cells triggered compensatory activation of mitochondrial respiration and resistance to OxPhos inhibition in AML cells. Mechanistically, inhibition of OxPhos induced transfer of mitochondria derived from mesenchymal stem cells (MSCs) to AML cells via tunneling nanotubes under direct-contact coculture conditions. Inhibition of OxPhos also induced mitochondrial fission and increased functional mitochondria and mitophagy in AML cells. Mitochondrial fission is known to enhance cell migration, so we used electron microscopy to observe mitochondrial transport to the leading edge of protrusions of AML cells migrating toward MSCs. We further demonstrated that cytarabine, a commonly used antileukemia agent, increased mitochondrial transfer of MSCs to AML cells triggered by OxPhos inhibition. Our findings indicate an important role of exogenous mitochondrial trafficking from BM stromal cells to AML cells as well as endogenous mitochondrial fission and mitophagy in the compensatory adaptation of leukemia cells to energetic stress in the BM microenvironment.

Genomic and Transcriptomic Analyses of Bioluminescence Genes in the Enope Squid Watasenia scintillans.

Watasenia scintillans, a sparkling enope squid, has bioluminescence organs to illuminate its body with its own luciferase activity. To clarify the molecular mechanism underlying its scintillation, we analysed high-throughput sequencing data acquired previously and obtained draft genome sequences accomplished with comparative genomic data among the cephalopods. The genome mapped by transcriptome data showed that (1) RNA editing contributed to transcriptome variation of lineage specific genes, such as W. scintillans luciferase, and (2) two types of luciferase enzymes were characterized with reasonable 3D models docked to a luciferin molecule. We report two different types of luciferase in one organism and possibly related to variety of colour types in the W. scintillans fluorescent organs.

Aging of spermatogonial stem cells by Jnk-mediated glycolysis activation.

Because spermatogonial stem cells (SSCs) are immortal by serial transplantation, SSC aging in intact testes is considered to be caused by a deteriorated microenvironment. Here, we report a cell-intrinsic mode of SSC aging by glycolysis activation. Using cultured SSCs, we found that aged SSCs proliferated more actively than young SSCs and showed enhanced glycolytic activity. Moreover, they remained euploid and exhibited stable androgenetic imprinting patterns with robust SSC activity despite having shortened telomeres. Aged SSCs showed increased Wnt7b expression, which was associated with decreased Polycomb complex 2 activity. Our results suggest that aberrant Wnt7b expression activated c-jun N-terminal kinase (JNK), which down-regulated mitochondria numbers by suppressing Ppargc1a Down-regulation of Ppargc1a probably decreased reactive oxygen species and enhanced glycolysis. Analyses of the Klotho-deficient aging mouse model and 2-y-old aged rats confirmed JNK hyperactivation and increased glycolysis. Therefore, not only microenvironment but also intrinsic activation of JNK-mediated glycolysis contributes to SSC aging.

Maser: one-stop platform for NGS big data from analysis to visualization.

Database URL: http://cell-innovation.nig.ac.jp/maser/.

Phylogenetic relationships of Russian far eastern flatfish (Pleuronectiformes, Pleuronectidae) based on two mitochondrial gene sequences, Co-1 and Cyt-b, with inferences in order phylogeny using complete mitogenome data.

The systematics and phylogeny of flatfish is investigated on the complete sequence of nucleotides at subunit 1 cytochrome c oxidase (Co-1) and cytochrome b (Cyt-b) genes. In total 17 species from our collection and some species from GenBank were analyzed. Four types of trees were built: Bayesian (BA), maximum likelihood (ML), maximum parsimony (MP), and neighbor joining (NJ). These trees showed similar topology. Two separate clusters on the trees support subfamily Hippoglossoidinae and Hippoglossinae subdivision and monophyletic status of these taxa. The subfamily Pleuronectinae also can be considered monophyletic, if the tribe Microstomini is excluded from it and genus Lepidopsetta is moved into the tribe Pleuronectini. Mitogenomes represented by 25 complete sequences from NCBI GenBank were analyzed. After alignment two sets of nucleotide sequences were formed and investigated independently. One set included 13 structural genes (14,886 bp), the second set comprised by the mtDNA without ND6 gene (10,457 bp). Both data sets give congruent phylogenetic signal that agreed with conventional views on the taxonomy of the order Pleuronectiformes; however, the first set gives better topology. In BA gene tree there are two well supported nodes which include the representatives of suborders Pleuronectoidei and Psettoidei. Within Pleuronectoidei two superfamilies, Pleuronectoidea and Soleidea are highly supported in BA but in all four kinds of gene trees (BA, ML, MP and NJ) the only superfamily Pleuronectoidea is well supported. At the top of hierarchy, all flatfishes belonging to the order Pleuronectiformes forming also a monophyletic clade in our data, with support level of 100% but in BA tree only. The monophyly of the family Pleuronectidae is well supported both by single gene data and by complete mtDNA sequences.

Copper-catalyzed extended Pummerer reactions of ketene dithioacetal monoxides with alkynyl sulfides and ynamides with an accompanying oxygen rearrangement.

The first examples of metal-catalyzed extended Pummerer reactions through the activation of sulfoxides are described. The copper-catalyzed reactions of ketene dithioacetal monoxides with alkynyl sulfides and ynamides provided a wide variety of γ,γ-disulfanyl-ß,γ-unsaturated carbonyl compounds with an accompanying oxygen rearrangement. The products can be easily converted into 1,4-dicarbonyl compounds and substituted heteroaromatics. DFT calculations and mechanistic experiments revealed a new interesting stepwise addition/oxygen rearrangement mechanism.

Phylogeny and biogeography of highly diverged freshwater fish species (Leuciscinae, Cyprinidae, Teleostei) inferred from mitochondrial genome analysis.

The distribution of freshwater taxa is a good biogeographic model to study pattern and process of vicariance and dispersal. The subfamily Leuciscinae (Cyprinidae, Teleostei) consists of many species distributed widely in Eurasia and North America. Leuciscinae have been divided into two phyletic groups, leuciscin and phoxinin. The phylogenetic relationships between major clades within the subfamily are poorly understood, largely because of the overwhelming diversity of the group. The origin of the Far Eastern phoxinin is an interesting question regarding the evolutionary history of Leuciscinae. Here we present phylogenetic analysis of 31 species of Leuciscinae and outgroups based on complete mitochondrial genome sequences to clarify the phylogenetic relationships and to infer the evolutionary history of the subfamily. Phylogenetic analysis suggests that the Far Eastern phoxinin species comprised the monophyletic clades Tribolodon, Pseudaspius, Oreoleuciscus and Far Eastern Phoxinus. The Far Eastern phoxinin clade was independent of other Leuciscinae lineages and was closer to North American phoxinins than European leuciscins. All of our analysis also suggested that leuciscins and phoxinins each constituted monophyletic groups. Divergence time estimation suggested that Leuciscinae species diverged from outgroups such as Tincinae to be 83.3 million years ago (Mya) in the Late Cretaceous and leuciscin and phoxinin shared a common ancestor 70.7 Mya. Radiation of Leuciscinae lineages occurred during the Late Cretaceous to Paleocene. This period also witnessed the radiation of tetrapods. Reconstruction of ancestral areas indicates Leuciscinae species originated within Europe. Leuciscin species evolved in Europe and the ancestor of phoxinin was distributed in North America. The Far Eastern phoxinins would have dispersed from North America to Far East across the Beringia land bridge. The present study suggests important roles for the continental rearrangements during the Late Cretaceous to form the present-day distribution of organisms. Furthermore, the Late Cretaceous biotic turnover influenced for the modern terrestrial biodiversity.

Needle-free jet injection of small doses of Japanese encephalitis DNA and inactivated vaccine mixture induces neutralizing antibodies in miniature pigs and protects against fetal death and mummification in pregnant sows.

Japanese encephalitis (JE) virus causes abortion and stillbirth in swine, and encephalitis in humans and horses. We have previously reported that immunogenicity of a DNA vaccine against JE was synergistically enhanced in mice by co-immunization with a commercial inactivated JE vaccine (JEVAX) under a needle-free injection system. Here, we found that this immunization strategy was also effective in miniature pigs. Because of the synergism, miniature pigs immunized twice with a mixture of 10 µg of DNA and a 1/100 dose of JEVAX developed a high neutralizing antibody titer (1:190 at 90% plaque reduction assay). Even using 1 µg of DNA, 3 of 4 pigs developed neutralizing antibodies. Following challenge, all miniature pigs with detectable neutralizing antibodies were protected against viremia. Pregnant sows inoculated with 10 or 1 µg of DNA mixed with JEVAX (1/100 dose) developed antibody titers of 1:40-1:320. Following challenge, fetal death and mummification were protected against in DNA/JEVAX-immunized sows.

Dengue tetravalent DNA vaccine increases its immunogenicity in mice when mixed with a dengue type 2 subunit vaccine or an inactivated Japanese encephalitis vaccine.

We previously developed a dengue tetravalent DNA vaccine that can induce neutralizing antibodies against four dengue viruses in mice. Here, we demonstrated that immunogenicity of our tetravalent vaccine is synergistically increased in mice by co-immunization with dengue type 2 virus (DENV2) subviral extracellular particles (D2EPs) or inactivated Japanese encephalitis vaccine (JEVAX). A single immunization with a mixture of 100 microg of the tetravalent vaccine and 150 ng of D2EPs or a 1/10 dose of JEVAX induced moderate levels of neutralizing antibodies in a 90% plaque reduction assay. Immunized mice were protected from "artificial" viremia created by intravenous injection with DENV2.

Dengue tetravalent DNA vaccine inducing neutralizing antibody and anamnestic responses to four serotypes in mice.

We developed a dengue tetravalent DNA vaccine consisting of plasmids expressing premembrane and envelope genes of each of four serotypes of dengue viruses. BALB/c mice immunized twice with the tetravalent vaccine at a dose of 100 microg (25 microg for each serotype) using a needle-free jet injector developed neutralizing antibodies against all serotypes. There was no interference among the four components included in this combination vaccine. Tetravalent vaccine-immunized mice showed anamnestic neutralizing antibody responses following challenge with each dengue serotype: responses to challenges from serotypes different to those used for neutralization tests were also induced.

Needle-free jet injection of a mixture of Japanese encephalitis DNA and protein vaccines: a strategy to effectively enhance immunogenicity of the DNA vaccine in a murine model.

Combined immunization with gene-based and protein-based vaccines can increase vaccine effectiveness. We previously demonstrated, using a murine model for Japanese encephalitis (JE), that simultaneous immunization with a DNA vaccine (pcJEME) by the intramuscular route and a protein vaccine consisting of subviral extracellular particles (EPs) by the subcutaneous route provided a synergistic increase in immunogenicities of these vaccines. Here, we investigated a novel immunization protocol consisting of a single inoculation with a mixture of DNA and protein vaccines using a needle-free jet injector. Immunization of ddY mice with 1 microg of pcJEME mixed with 1 microg of EPs or a 1/100 dose of commercial inactivated JE vaccine (JEVAX) induced neutralizing antibody titers of 1:40 to 1:80 (90% plaque reduction) 6 weeks after immunization, whereas immunization with DNA or protein alone only induced low titers (< or =1:10). Co-immunization with pcDNA3, a CpGcontaining vector of the vaccine plasmid, increased immunogenicity of JEVAX to some extent. IgG1/IgG2a isotype profiles supported increased production of EPs in pcJEME-inoculated mice by needle-free injection and an adjuvant effect of the vector on immunogenicity of JEVAX.

Simultaneous immunization with DNA and protein vaccines against Japanese encephalitis or dengue synergistically increases their own abilities to induce neutralizing antibody in mice.

Gene-based and protein-based vaccines are two distinct types of vaccines. In this report, we examined if combined use of DNA and protein vaccines would increase their own abilities to induce neutralizing antibody in murine models for Japanese encephalitis (JE) or dengue type 2 (DEN2). DNA vaccines for JE (pcJEME) or DEN2 (pcD2ME) were inoculated intramuscularly, and protein vaccines consisting of subviral extracellular particles (EPs) containing JE (JEEP) or DEN2 (D2EP) virus antigens were inoculated subcutaneously with Freund's adjuvant. Two immunizations of ICR mice with pcJEME and/or JEEP in the prime-boost protocol indicated that levels of neutralizing antibody induced by the pcJEME prime-JEEP boost vaccination were two to eight-fold higher than those induced by pcJEME alone, but were equivalent to those induced by JEEP alone and slightly higher than those induced by the JEEP prime-pcJEME boost regimen. On the other hand, simultaneous immunization of ICR mice with pcJEME and JEEP provided synergistically higher neutralizing antibody titers than those provided by immunization with either immunogen. Immunization with graded doses of pcJEME and JEEP confirmed the synergism. The synergistic increase in neutralizing antibody titer by simultaneous immunization with DNA and protein vaccines was also shown by immunization with pcD2ME and D2EP in ICR and ddY mice. Both IgG1 and IgG2a antibodies were induced by combined immunization with pcJEME and JEEP.