Genome sequence of Lactobacillus suebicus KCTC 3549

Lactobacillus suebicus is important in the generation of particular flavors and in other ripening processes associated with apple mash. Here, we present the draft genome sequence of the type strain Lactobacillus suebicus KCTC 3549 (2,656,936 bp, with a G+C content of 39.0%), which consists of 143 large contigs (>100 bp).     

Genome sequence of Leuconostoc inhae KCTC 3774, isolated from Kimchi

Leuconostoc inhae strain KCTC 3774 is a Gram-positive, non-spore-forming, heterofermentative, spherical or lenticular lactic acid bacterium. Here we announce the draft genome sequence of Leuconostoc inhae KCTC 3774, isolated from traditional Korean kimchi, and describe major findings from its annotation.     

Draft genome sequence of Lactobacillus zeae KCTC 3804

We announce the draft genome sequence of the type strain Lactobacillus zeae KCTC 3804 (3,110,326 bp, with a G+C content of 47.8%), which is one of the most prevalent lactic acid bacteria present during the processing of raw cow's milk. The genome consists of 113 large contigs (>100 bp). All of the contigs were assembled by Newbler Assembler 2.3 (454 Life Science).     

Induced in vitro differentiation of neural-like cells from human exfoliated deciduous teeth-derived stem cells

Stem cells from human exfoliated deciduous teeth (SHED) are highly proliferative, clonogenic and multipotent stem cells with a neural crest cell origin. Additionally, they can be collected with minimal invasiveness in comparison with other sources of mesenchymal stem cells (MSCs). Therefore, SHED could be a desirable option for potential therapeutic applications. In this study, SHEDs were established from enzyme-disaggregated deciduous dental pulp obtained from 6 to 9 year-old children. The cells had typical fibroblastoid morphology and expressed antigens characteristic of MSCs, STRO1, CD146, CD45, CD90, CD106 and CD166, but not the hematopoietic and endothelial markers, CD34 and CD31, as assessed by FACS analysis. Differentiation assessment revealed a strong osteogenic and adipogenic potential of SHEDs. In order to further evaluate the in vitro differentiation potential of SHED into neural cells, a simple short time growth factor-mediated induction was used. Immunofluorescence staining and flow cytometric analysis revealed that SHED rapidly expressed nestin and b-III tubulin, and later expressed intermediate neural markers. In addition, the intensity and percentages of nestin and b-III tubulin and mature neural markers (PSA-NCAM, NeuN, Tau, TH, or GFAP) increased significantly following treatment. Moreover, RT-PCR and Western blot analyses showed that the neural markers were strongly up-regulated after induction. In conclusion, these results provide evidence that SHED can differentiate into neural cells by the expression of a comprehensive set of genes and proteins that define neural-like cells in vitro. SHED cells might be considered as new candidates for the autologous transplantation of a wide variety of neurological diseases and neurotraumatic injuries.     

Differentiation of human embryonic stem cells to hepatocyte-like cells on a new developed xeno-free extracellular matrix

Human embryonic stem cells (hESCs) provide a new source for hepatocyte production in translational medicine and cell replacement therapy. The reported hESC-derived hepatocyte-like cells (HLCs) were commonly generated on Matrigel, a mouse cell line-derived extracellular matrix (ECM). Here, we performed the hepatic lineage differentiation of hESCs following a stepwise application of growth factors on a newly developed serum- and xeno-free, simple and cost-benefit ECM, designated “RoGel,” which generated from a modified conditioned medium of human fibroblasts. In comparison with Matrigel, the differentiated HLCs on both ECMs expressed similar levels of hepatocyte-specific genes, secreted α-fetoprotein, and metabolized ammonia, showed glycogen storage activity as well as low-density lipoprotein and indocyanine green uptake. The transplantation of hESC–HLCs into the carbon tetrachloride-injured liver demonstrated incorporation of the cells into the host mouse liver and the expression of albumin. The results suggest that the xeno-free and cost-benefit matrix may be applicable in bioartificial livers and also may facilitating a clinical application of human pluripotent stem cell-derived hepatocytes in the future.     

A reliable and efficient protocol for inducing genetically transformed roots in medicinal plant Nepeta pogonosperma

Nepeta pogonosperma is an important medicinal plant with anti-inflammatory effects. An efficient and reliable transformation system for this plant was developed through optimization of several factors which affected the rate of Agrobacterium rhizogenes mediated transformation. Five bacterial strains, A4, ATCC15834, LBA9402, MSU440 and A13, two explant types, leaves and stems, and several co-cultivation media were examined. The maximum rate of hairy root induction was obtained from stem explants using MSU440 and ATCC15834 bacterial strains. A drastic increase in the frequency of transformation (91 %) was observed when MS medium lacking NH₄NO₃, KH₂PO₄, KNO₃ and CaCl₂. Hairy root lines were confirmed by polymerase chain reaction (PCR) using primers of the rolB gene. According to Southern blot analysis, one T-DNA copy was inserted into each of the hairy root lines. In the present study, transgenic hairy roots have been obtained trough genetic transformation by A. rhizogenes harbouring two plasmids, the Ri plasmid and pBI121 binary vector harbouring gus reporter gene. Expression of the gus gene in transgenic hairy root was confirmed by histochemical GUS assay.     

Functional Evolution of Ribonuclease Inhibitor: Insights from Birds and Reptiles

Ribonuclease inhibitor (RI) is a conserved protein of the mammalian cytosol. RI binds with high affinity to diverse secretory ribonucleases (RNases) and inhibits their enzymatic activity. Although secretory RNases are found in all vertebrates, the existence of a non-mammalian RI has been uncertain. Here, we report on the identification and characterization of RI homologs from chicken and anole lizard. These proteins bind to RNases from multiple species but exhibit much greater affinity for their cognate RNases than for mammalian RNases. To reveal the basis for this differential affinity, we determined the crystal structure of mouse, bovine, and chicken RI·RNase complexes to a resolution of 2.20, 2.21, and 1.92 Å, respectively. A combination of structural, computational, and bioinformatic analyses enabled the identification of two residues that appear to contribute to the differential affinity for RNases. We also found marked differences in oxidative instability between mammalian and non-mammalian RIs, indicating evolution toward greater oxygen sensitivity in RIs from mammalian species. Taken together, our results illuminate the structural and functional evolution of RI, along with its dynamic role in vertebrate biology.     

Brain stem cells as the cell of origin in glioma

Glioma incidence rates in the United States are near 20000 new cases per year, with a median survival time of 14.6 mo for high-grade gliomas due to limited therapeutic options. The origins of these tumors and their many subtypes remain a matter of investigation. Evidence from mouse models of glioma and human clinical data have provided clues about the cell types and initiating oncogenic mutations that drive gliomagenesis, a topic we review here. There has been mixed evidence as to whether or not the cells of origin are neural stem cells, progenitor cells or differentiated progeny. Many of the existing murine models target cell populations defined by lineage-specific promoters or employ lineagetracing methods to track the potential cells of origin. Our ability to target specific cell populations will likely increase concurrently with the knowledge gleaned from an understanding of neurogenesis in the adult brain. The cell of origin is one variable in tumorigenesis, as oncogenes or tumor suppressor genes may differentially transform the neuroglial cell types. Knowledge of key driver mutations and susceptible cell types will allow us to understand cancer biology from a developmental standpoint and enable early interventional strategies and biomarker discovery.     

Ichnology and sedimentology of a tide‐influenced delta in the Ordovician from the northeastern Alborz range of Iran (Kopet Dagh region)

The Middle–Late Ordovician Ghelli Formation in the Kopet Dagh region northeastern Alborz range of Iran is composed of siliciclastic rocks deposited in a variety of turbidite to marginal marine environments (deep marine clastic fan and related environments and prodelta, distal delta front, proximal delta front and distributary channels). The ichnology of the middle member of the Ghelli Formation is here reported. Combined sedimentological and ichnological analysis allows recognition of a tide‐influenced deltaic succession in the middle member of the Ghelli Formation consisting of three main facies associations: lower distributary channels, delta front and prodelta facies. Twenty‐two ichnogenera have been identified in this marginal marine succession: Arenicolites, Arthrophycus, Bergaueria, Chondrites, Conichnus, Cruziana, Cylindrichnus, Didymaulichnus, Diplichnites, Diplocraterion, Helminthopsis, Gyrochorte, Lockeia, Macaronichnus, Monomorphichnus, Palaeophycus, Planolites, Rosselia, Rusophcus, Skolithos, Teichichnus and ?Scolicia. Their distribution is clearly linked with lithofacies and depositional palaeoenvironments. The ichnological analysis reveals that the trace fossil suites developed in these environments indicate low diversity and low to moderate abundance of burrows, poor development of tiering and sporadic distribution. Low ichnodiversity and low bioturbation intensities with higher bioturbation clusters consist of facies‐crossing ichnogenera, and the impoverishment of suspension‐feeding trophic types indicates ‘stressed’, non‐archetypal expression of the Cruziana ichnofacies. The periodic higher intensities of bioturbation due to variations in hydrodynamic regimes of tidal currents reflect the archetypal of the Cruziana ichnofacies (and rare Skolithos ichnofacies).