Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes

The International Crocodilian Genomes Working Group (ICGWG) will sequence and assemble the American alligator (Alligator mississippiensis), saltwater crocodile (Crocodylus porosus) and Indian gharial (Gavialis gangeticus) genomes. The status of these projects and our planned analyses are described.     

Chromobacterium pathogenicity island 1 type III secretion system is a major virulence determinant for Chromobacterium violaceum‐induced cell death in hepatocytes

Chromobacterium violaceum is a Gram‐negative bacterium that causes fatal septicaemia in humans and animals. C. violaceum ATCC 12472 possesses genes associated with two distinct type III secretion systems (T3SSs). One of these systems is encoded by Chromobacterium pathogenicity islands 1 and 1a (Cpi‐1/‐1a), another is encoded by Chromobacterium pathogenicity island 2 (Cpi‐2). Here we show that C. violaceum causes fulminant hepatitis in a mouse infection model, and Cpi‐1/‐1a‐encoded T3SS is required for its virulence. In addition, using C. violaceum strains with defined mutations in the genes that encode the Cpi‐1/‐1a or Cpi‐2 locus in combination with cultured mammalian cell lines, we found that C. violaceum is able to induce cytotoxicity in a Cpi‐1/‐1a‐dependent manner. Characterization of Chromobacterium‐induced cytotoxicity revealed that cell lysis by C. violaceum infection involves the formation of pore structures on the host cell membrane, as demonstrated by protection by cytotoxicity in the presence of osmoprotectants. Finally, we demonstrated that CipB, a Cpi‐1/‐1a effector, is implicated in translocator‐mediated pore formation and the ability of CipB to form a pore is essential for Chromobacterium‐induced cytotoxicity. These results strongly suggest that Cpi‐1/‐1a‐encoded T3SS is a virulence determinant that causes fatal infection by the induction of cell death in hepatocytes.     

Outcomes of written living wills in Japan--a survey of the deceased ones' families

A study was recently done to investigate the outcomes of written living wills in Japan, which, unlike the United States, does not legally recognize advance directives. This study collected demographic information and predictors of living will use among families and guardians who used the living will form provided by the Japan Society for Dying with Dignity. According to the results of the study, affliction with cancer and death in a hospital was the best predictor of written living will use. Research on physicians' treatment limitation and withdrawal behaviors in the clinical setting is needed to better understand the actual impact of living wills. Such research can provide better understanding of where boundaries of self-determination are drawn and how to respect autonomy in Japan.     

Sequence divergence and expression of a transformer gene in the branchiopod crustacean,Daphnia magna

Environmental decline triggers a switch in reproductive strategy of Daphnia magna from asexual to sexual reproduction; however, the molecular basis of such environmental sex determination remains largely unknown. In insects most closely related to branchiopod crustaceans, orthologs of the Drosophila transformer gene such as dipteran transformer (tra), honeybee feminizer (fem) and complementary sex determiner (csd) function as sex determining factors. Therefore, we cloned a D. magna transformer gene (dmagtra) and analyzed its expression. The predicted amino acid sequence has 380 amino acids including an arginine–serine-rich region, which is characteristic of insect orthologs of Tra. Residues 180 to 205 are highly conserved with known Tra orthologs. The domain organization of DmagTra is distinct from known Tra orthologs; moreover, dmagtra does not display any detectable sexual dimorphic differences in expression or splicing patterns. We infer from these results that dmagtra may not be responsible for sex determination in D. magna.     

Elucidating the multiple genetic lineages and population genetic structure of the brooding coral <Emphasis Type="Italic">Seriatopora</Emphasis> (Scleractinia: Pocilloporidae) in the Ryukyu Archipelago

The elucidation of species diversity and connectivity is essential for conserving coral reef communities and for understanding the characteristics of coral populations. To assess the species diversity, intraspecific genetic diversity, and genetic differentiation among populations of the brooding coral Seriatopora spp., we conducted phylogenetic and population genetic analyses using a mitochondrial DNA control region and microsatellites at ten sites in the Ryukyu Archipelago, Japan. At least three genetic lineages of Seriatopora (Seriatopora-A, -B, and -C) were detected in our specimens. We collected colonies morphologically similar to Seriatopora hystrix, but these may have included multiple, genetically distinct species. Although sexual reproduction maintains the populations of all the genetic lineages, Seriatopora-A and Seriatopora-C had lower genetic diversity than Seriatopora-B. We detected significant genetic differentiation in Seriatopora-B among the three populations as follows: pairwise F _ST = 0.064–0.116 (all P = 0.001), pairwise G′′_ST = 0.107–0.209 (all P = 0.001). Additionally, only one migrant from an unsampled population was genetically identified within Seriatopora-B. Because the peak of the settlement of Seriatopora larvae is within 1 d and almost all larvae are settled within 5 d of spawning, our observations may be related to low dispersal ability. Populations of Seriatopora in the Ryukyu Archipelago will probably not recover unless there is substantial new recruitment from distant populations.     

Revision of the Capsaspora genome using read mating information adjusts the view on premetazoan genome

The genome sequences of unicellular holozoans, the closest relatives to animals, are shedding light on the evolution of animal multicellularity, shaping the genetic contents of the putative premetazoans. However, the assembly quality of the genomes remains poor compared to the major model organisms such as human and fly. Improving the assembly is critical for precise comparative genomics studies and further molecular biological studies requiring accurate sequence information such as enhancer analysis and genome editing. In this report, we present a new strategy to improve the assembly by fully exploiting the information of Illumina mate-pair reads. By visualizing the distance and orientation of the mapped read pairs, we could highlight the regions where possible assembly errors exist in the genome sequence of Capsaspora, a lineage of unicellular holozoans. Manual modification of these errors repaired 590 assembly problems in total and reassembled 84 supercontigs into 55. Our telomere prediction analysis using the read pairs containing the pan-eukaryotic telomere-like sequence identified at least 13 chromosomes. The resulting new assembly posed us a re-annotation of 112 genes, including 15 putative receptor protein tyrosine kinases. Our strategy thus provides a useful approach for improving assemblies of draft genomes, and the new Capsaspora genome offers us an opportunity to adjust the view on the genome of the unicellular animal ancestor.     

Argifin; efficient solid phase total synthesis and evalution of analogues of acyclic peptide

An effective solid phase synthesis of Argifin, providing subsequent access to effective synthesis of analogues, was developed in 13% overall yield, as well as elucidating structure–activity relationships. The novel acyclic peptide 18b, prepared from a synthetic intermediate of Argifin, was found to be 70 times more potent as an inhibitor of Serratia marcescens chitinases B than Argifin itself     

Phosphatidylserine induces apoptosis in adherent cells

Phosphatidylserine (PS) is exposed on the outer leaflet of the plasma membrane in apoptotic cell death. However, the roles of PS in apoptotic signaling are still unclear. In this study, we found that exogenous PS, but not other phospholipids, induced cell death in adherent cells, but not in suspension culture. The cell death exhibited typical features of apoptosis such as cell shrinkage, nuclear fragmentation and abnormal chromatin condensation. When PS was added to CHO-K1 cells in monolayer culture, they began to show changes in cell shape and actin cytoskeleton and protein kinase C (PKC) activity, followed by cell detachment, caspase activation, cleavage of focal adhesion kinase (FAK) and finally loss of viability. These results suggested that PS causes apoptosis through actin disorganization, cell detachment and cleavage of FAK.