Although many de novo genome assembly projects have recently been conducted using high-throughput sequencers, assembling highly heterozygous diploid genomes is a substantial challenge due to the increased complexity of the de Bruijn graph structure predominantly used. To address the increasing demand for sequencing of nonmodel and/or wildtype samples, in most cases inbred lines or fosmid-based hierarchical sequencing methods are used to overcome such problems. However, these methods are costly and time consuming, forfeiting the advantages of massive parallel sequencing. Here, we describe a novel de novo assembler, Platanus, that can effectively manage high-throughput data from heterozygous samples. Platanus assembles DNA fragments (reads) into contigs by constructing de Bruijn graphs with automatically optimized k-mer sizes followed by the scaffolding of contigs based on paired-end information. The complicated graph structures that result from the heterozygosity are simplified during not only the contig assembly step but also the scaffolding step. We evaluated the assembly results on eukaryotic samples with various levels of heterozygosity. Compared with other assemblers, Platanus yields assembly results that have a larger scaffold NG50 length without any accompanying loss of accuracy in both simulated and real data. In addition, Platanus recorded the largest scaffold NG50 values for two of the three low-heterozygosity species used in the de novo assembly contest, Assemblathon 2. Platanus therefore provides a novel and efficient approach for the assembly of gigabase-sized highly heterozygous genomes and is an attractive alternative to the existing assemblers designed for genomes of lower heterozygosity.

A cell growth inhibitory effect of drupanin and baccharin, ingredients of propolis, was found in human cancer cell lines. These compounds induced apoptosis in the cells characterized by morphological and nucleosomal DNA fragmentation analysis. Their effects were less potent compared with that of artepillin C, which is a known anticancer compound from propolis. Importantly, HL60 cells were more sensitive to drupanin than were Con A-stimulated peripheral blood lymphocytes, whereas the potency of artepillin C was the opposite of that of drupanin.Key words propolis; drupanin; cell growth inhibition; apoptosis; human tumor cell Propolis is a sticky mixed substance that is collected from plant materials by honeybees.1) It has been considered that propolis is a protective wall against the enemies of bees. Propolis has been uesd as a folk medicine in Europe and Japan, and it is believed that propolis exerts a therapeutic or preventive effect in inflammation, heart disease, and even diabetes mellitus and cancer. Chemical analysis using GCmass spectrometry demonstrated that approximately 150 polyphenolic compounds including flavonoids and cinnamic acid derivatives are present in propolis.2) There have been several reports indicating various biological activities of propolis and its constituents, such as anticancer, 3,4) antioxidant, 5) antiinflammatory 6) and antibiotic 7) activities. Evaluation of the biological activities of ingredients in propolis and elucidation of the mechanisms of their functions provide substantial clues for the development of new drug candidates. In the course of phytochemical studies on biologically active compounds from propolis, we examined the anticancer activity of the ethanol extract fraction from propolis and found that two cinnamic acid derivatives showed growth inhibitory activity against human tumor cell lines. It has been reported that artepillin C (3,5-diprenyl-4-hydroxycinnamic acid) from propolis exhibits antitumor activity by induction of apoptosis in human tumor cell lines in vitro. 8,9) In the present study, we demonstrated cell growth inhibition by drupanin and (E)-3-prenyl-4-(2,3-dihydrocinnamoyloxy) cinnamic acid, named baccharin by us, in human tumor cell lines and compared them with artepillin C.Brazilian propolis was extracted with 90% ethanol (EtOH) at room temperature to yield the extract. The EtOH extract was chromatographed over silica gel and the column (70 mm i.d.ϫ330 mm) was eluted stepwise with 2-70% CHCl 3 -methanol (MeOH). The 11 CHCl 3 -MeOH-eluted fractions were evaporated and then solubilized with 100% EtOH. The fractions were examined for cell growth inhibition and the fractions showing growth inhibitory effect against human tumor cell lines were further analyzed with HPLC (column: Shiseido AG120; gradient system-A solvent: 20% CH 3 CN/2% AcOH and B solvent: 100% CH 3 CN/2% AcOH; 20-100%; 0-60 min; flow rate: 1 ml/min; detection: UV 280 nm). After purification of the active compounds, their structures were determined by nuclear magnetic resonance ( 1 H-NMR) ana...

Objective. To examine whether chemokine antagonists inhibit the initiation and progression of lupus nephritis in MRL/lpr mice.Methods. NH 2 -terminal-truncated monocyte chemoattractant protein 1 (MCP-1)/CCL2 or thymus and activation-regulated chemokine (TARC)/CCL17 analogs were inserted into the pCXN2 expression vector and transfected into a nonmetastatic fibroblastoid cell line, MRL/N-1, established from an MRL/gld mouse.Results. MCP-1 antagonist-or TARC antagonisttransfected MRL/N-1 cells were injected subcutaneously into MRL/lpr mice ages 7 weeks (before the onset of lupus nephritis) and 12 weeks (at the early stage of the disease). After 8 weeks, mice bearing the MCP-1 antagonist showed markedly diminished infiltration of macrophages and T cells, glomerular hypercellularity, glomerulosclerosis, crescent formation, and vasculitis compared with control mice. This seemed to be due to decreased production of interferon-␥ and interleukin-2 in the kidney. In contrast, there was no significant difference in renal damage between mice bearing TARC antagonist and control mice. Conclusion.We established a new system using MRL/N-1 cells that allows long-term observation of the effects of chemokine antagonists on lupus nephritis in MRL/lpr mice. We also showed that the MCP-1 antagonist ameliorated the initiation and progression of lupus nephritis and of renal vasculitis, which might provide a new approach to the treatment of the disease.

Humans and dogs are the two major hosts of Strongyloides stercoralis, an intestinal parasitic nematode. To better understand the phylogenetic relationships among S. stercoralis isolates infecting humans and dogs and to assess the zoonotic potential of this parasite, we analyzed mitochondrial Cox1, nuclear 18S rDNA, 28S rDNA, and a major sperm protein domain-containing protein genes. Overall, our analyses indicated the presence of two distinct lineages of S. stercoralis (referred to as type A and type B). While type A parasites were isolated both from humans and dogs in different countries, type B parasites were found exclusively in dogs, indicating that the type B has not adapted to infect humans. These epidemiological data, together with the close phylogenetic relationship of S. stercoralis with S. procyonis, a Strongyloides parasite of raccoons, possibly indicates that S. stercoralis originally evolved as a canid parasite, and later spread into humans. The inability to infect humans might be an ancestral character of this species and the type B might be surmised to be an origin population from which human-infecting strains are derived.

These results demonstrate that gene transfer into the liver via rapid tail vein injection can easily be achieved in the rat, which is more than 10 times larger than the mouse, and has significant value for gene function analysis in rats.