First molecular data of the Borneo Banteng Bos Javanicus lowi from Sabah, Borneo

Phylogenetic relationships among three subspecies of banteng, Burma banteng Bos javanicus birmanicus in mainland Southeast Asia, Javan banteng Bos javanicus javanicus in Java, and Bornean banteng Bos javanicus lowi in Borneo, and the presence/absence of interbreeding between wild Bornean banteng and domestic cattle in Sabah, Malaysia, were investigated by partial sequences of cytochrome b and D-loop of mitochondrial DNA. The results show that genetic distance of the Bornean banteng are relatively close to the gaur Bos gaurus/gayal Bos frontalis (the cytochrome b, 0.004–0.025; the D-loop, 0.012–0.021) followed by Burma banteng (the cytochrome b, 0.027–0.035; the D-loop, 0.040–0.045), and kouprey Bos sauveli (the cytochrome b, 0.031–0.035; the D-loop, 0.037–0.042). There are much greater distances between Bornean banteng and domestic cattle, Bos taurus and Bos indicus (the cytochrome b, 0.059–0.076; the D-loop, 0.081–0.090). These results suggest that the Bornean banteng diverged genetically from other banteng subspecies and that the wild Bornean banteng from this study are pure strain and have high conservation value

Bacterial Diversity Associated With the Rhizosphere and Endosphere of Two Halophytes: Glaux maritima and Salicornia europaea

Root-associated microbial communities are very important in the adaptation of halophytes to coastal environments. However, little has been reported on microbial community structures related to halophytes, or on comparisons of their compositions among halophytic plant species. Here, we studied the diversity and community structure of both rhizosphere and root endosphere bacteria in two halophytic plants: Glaux maritima and Salicornia europaea. We sampled the rhizosphere, the root endosphere, and bulk control soil samples, and performed bacterial 16S rRNA sequencing using the Illumina MiSeq platform to characterize the bacterial community diversities in the rhizosphere and root endosphere of both halophytes. Among the G. maritima samples, the richness and diversity of bacteria in the rhizosphere were higher than those in the root endosphere but were lower than those of the bulk soil. In contrast for S. europaea, the bulk soil, the rhizosphere, and the root endosphere all had similar bacterial richness and diversity. The number of unique operational taxonomic units within the root endosphere, the rhizosphere, and the bulk soil were 181, 366, and 924 in G. maritima and 126, 416, and 596 in S. europaea, respectively, implying habitat-specific patterns for each halophyte. In total, 35 phyla and 566 genera were identified. The dominant phyla across all samples were Proteobacteria and Bacteroidetes. Actinobacteria was extremely abundant in the root endosphere from G. maritima. Beneficial bacterial genera were enriched in the root endosphere and rhizosphere in both halophytes. Rhizobium, Actinoplanes, and Marinomonas were highly abundant in G. maritima, whereas Sulfurimonas and Coleofasciculus were highly abundant in S. europaea. A principal coordinate analysis demonstrated significant differences in the microbiota composition associated with the plant species and type of sample. These results strongly indicate that there are clear differences in bacterial community structure and diversity between G. maritima and S. europaea. This is the first report to characterize the root microbiome of G. maritima, and to compare the diversity and community structure of rhizosphere and root endosphere bacteria between G. maritima and S. europaea

First molecular data on Bornean banteng Bos javanicus lowi (Cetartiodactyla, Bovidae) from Sabah, Malaysian Borneo

Phylogenetic relationships among three subspecies of banteng, Burma banteng Bos javanicus birmanicus in mainland Southeast Asia, Javan banteng Bos javanicus javanicus in Java, and Bornean banteng Bos javanicus lowi in Borneo, and the presence/absence of interbreeding between wild Bornean banteng and domestic cattle in Sabah, Malaysia, were investigated by partial sequences of cytochrome b and D-loop of mitochondrial DNA. The results show that genetic distance of the Bornean banteng are relatively close to the gaur Bos gaurus/gayal Bos frontalis (the cytochrome b, 0.004–0.025; the D-loop, 0.012–0.021) followed by Burma banteng (the cytochrome b, 0.027–0.035; the D-loop, 0.040–0.045), and kouprey Bos sauveli (the cytochrome b, 0.031–0.035; the D-loop, 0.037–0.042). There are much greater distances between Bornean banteng and domestic cattle, Bos taurus and Bos indicus (the cytochrome b, 0.059–0.076; the D-loop, 0.081–0.090). These results suggest that the Bornean banteng diverged genetically from other banteng subspecies and that the wild Bornean banteng from this study are pure strain and have high conservation value

Correction: Enterohemorrhagic Escherichia coli O157 subclade 8b strains in Chiba Prefecture, Japan, produced larger amounts of Shiga toxin 2 than strains in subclade 8a and other clades.

[This corrects the article DOI: 10.1371/journal.pone.0191834.]

Fpr1, a primary target of rapamycin, functions as a transcription factor for ribosomal protein genes cooperatively with Hmo1 in Saccharomyces cerevisiae.

Fpr1 (FK506-sensitive proline rotamase 1), a protein of the FKBP12 (FK506-binding protein 12 kDa) family in Saccharomyces cerevisiae, is a primary target for the immunosuppressive agents FK506 and rapamycin. Fpr1 inhibits calcineurin and TORC1 (target of rapamycin complex 1) when bound to FK506 and rapamycin, respectively. Although Fpr1 is recognised to play a crucial role in the efficacy of these drugs, its physiological functions remain unclear. In a hmo1Δ (high mobility group family 1-deleted) yeast strain, deletion of FPR1 induced severe growth defects, which could be alleviated by increasing the copy number of RPL25 (ribosome protein of the large subunit 25), suggesting that RPL25 expression was affected in hmo1Δfpr1Δ cells. In the current study, extensive chromatin immunoprecipitation (ChIP) and ChIP-sequencing analyses revealed that Fpr1 associates specifically with the upstream activating sequences of nearly all RPG (ribosomal protein gene) promoters, presumably in a manner dependent on Rap1 (repressor/activator site binding protein 1). Intriguingly, Fpr1 promotes the binding of Fhl1/Ifh1 (forkhead-like 1/interacts with forkhead 1), two key regulators of RPG transcription, to certain RPG promoters independently of and/or cooperatively with Hmo1. Furthermore, mutation analyses of Fpr1 indicated that for transcriptional function on RPG promoters, Fpr1 requires its N-terminal domain and the binding surface for rapamycin, but not peptidyl-prolyl isomerase activity. Notably, Fpr1 orthologues from other species also inhibit TORC1 when bound to rapamycin, but do not regulate transcription in yeast, which suggests that these two functions of Fpr1 are independent of each other

Enterohemorrhagic <i>Escherichia coli</i> O157 subclade 8b strains in Chiba Prefecture, Japan, produced larger amounts of Shiga toxin 2 than strains in subclade 8a and other clades

<div><p>Enterohemorrhagic <i>Escherichia coli</i> O157 (O157) strains can be classified into clades (one of several phylogenetic groups) by single nucleotide polymorphisms (SNPs): these are clade 1, clade 2, clade 3, descendant and ancestral clades 4/5, clade 6, clade 7, clade 8, clade 9, and clade 12. Some recent studies showed that some O157 strains in clade 8 produced a larger amount of Shiga toxin (Stx) 2 than other strains. In this study, 1121 epidemiologically unlinked strains of O157 isolated in Chiba Prefecture, Japan were classified into clades during 1996–2014. Clade 8 strains were further classified into subclade 8a (67 strains) and subclade 8b (48 strains) using SNP analysis. In the absence of mitomycin C (MMC), subclade 8a strains in this study produced significantly greater amounts of Stx2 than subclade 8b strains. However, in the presence of MMC, the levels of Stx2 production in subclade 8b strains were significantly greater than subclade 8a strains. On the other hand, a recent study reported that the Stx2 production level in O157 strains was determined mainly by the subtypes of Stx2a phage (ϕStx2_α, β, γ, δ, ε, and ζ). Using O157 strains in this study, the Stx2a phages were classified into these subtypes. In this study, all strains of subclades 8a and 8b carried ϕStx2a_γ and ϕStx2a_δ, respectively. Some strains in clade 6 also carried ϕStx2a_δ. In the presence of MMC, subclade 8b strains produced significantly greater amounts of Stx2 than clade 6 strains carrying ϕStx2_δ. In this study, we propose that Stx2 production in subclade 8b strains in the presence of MMC might be enhanced due to genetic factors other than ϕStx2_δ.</p></div

The levels of Stx2 production in subclade 8a and 8b strains.

<p>The Stx2 titers of the subclade 8a and 8b strains in this study in the presence and absence of MCC are shown using the box-and-whisker plot. The bottoms of the lower bars show the minimum of Stx2 titers. The blue boxes show the Stx2 titers from the 25th percentile to the median. The orange boxes show the Stx2 titers from the median to the 75th percentile. The tops of the upper bars show the maximum of Stx2 titers. MMC + and MMC—indicate O157 strains that were treated and non-treated with MMC, respectively.</p

Transcriptomic characterization of gall tissue of Japanese elm tree (<i>Ulmus davidiana</i> var. japonica) induced by the aphid <i>Tetraneura nigriabdominalis</i>

<p>Insect galls are abnormal plant tissues induced by parasitic insect(s) for use as their habitat. In previous work, we suggested that gall tissues induced by the aphid <i>Tetraneura nigriabdominalis</i> on Japanese elm trees are less responsive than leaf tissues to jasmonic acid (JA), which is involved in the production of volatile organic compounds as a typical defensive reaction of plants against attack by insect pests. A comprehensive analysis of gene expression by RNA sequencing indicated that the number of JA responsive genes was markedly lower in gall tissues than in leaf tissues. This suggests that gall tissues are mostly defective in JA signaling, although JA signaling is not entirely compromised in gall tissue. Gene ontology analysis sheds light on some stress-related unigenes with higher expression levels in gall tissues, suggesting that host plants sense aphids as a biotic stress but are defective in the JA-mediated defense response in gall tissues.</p> <p>The aphid-induced gall tissues on Japanese elm trees are less responsive than leaf tissues to jasmonic acid, which may provide the aphid with beneficial environments.</p

MLPT reconstructed from SNP data of clade 8 strains analyzed using the SNP set in this study.

<p>The dashed line marks branches with Stx2a phage subtypes. Red bars (A, C, E and G) indicate branches with multiple strains with both <i>stx2a</i> and <i>stx2c</i> genes. Red arrows indicate strains with both <i>stx2a</i> and <i>stx2c</i> genes. Black bars (B, D, F, H and I) indicate branches with multiple strains with only <i>stx2a</i>. Black arrows indicate strains with <i>stx</i>2a. The green arrow indicates a strain with a Stx2a phage that could not be typed.</p