Genome-wide promoter methylation analysis in neuroblastoma identifies prognostic methylation biomarkers

ChIP-seq is a powerful method for obtaining genome-wide maps of protein-DNA interactions and epigenetic modifications. CHANCE (CHip-seq ANalytics and Confidence Estimation) is a standalone package for ChIP-seq quality control and protocol optimization. Our user-friendly graphical software quickly estimates the strength and quality of immunoprecipitations, identifies biases, compares the user's data with ENCODE's large collection of published datasets, performs multi-sample normalization, checks against quantitative PCR-validated control regions, and produces informative graphical reports. CHANCE is available at https://github.com/songlab/chance.     

Leptographium sinoprocerum sp. nov., an undescribed species associated with Pinus tabuliformis-Dendroctonus valens in northern China

During a study of ophiostomatoid fungi associated with the invasive pest Dendroctonus valens in the Pinus tabuliformis ecosystem in northern China, a multigenic (ITS2-LSU, beta-tubulin and EF1-alpha) phylogenetic analysis and examination of morphological features revealed in addition to Leptographium procerum the occurrence of an undescribed species. The new species, Leptographium sinoprocerum, belongs to the L. procerum-L. profanum clade. Both L. procerum and L. sinoprocerum are similar to each other and occur sympatrically in the ecosystem studied. Nevertheless L. sinoprocerum can be distinguished from L. procerum by shorter conidiophore stipes arising from both submerged and aerial hyphae, slightly more oblong conidia, a granular ornamentation on the submerged hyphae and dark olivaceous colonies on MEA.     

Taxonomy and pathogenicity of <Emphasis Type="Italic">Leptographium</Emphasis> species associated with <Emphasis Type="Italic">Ips subelongatus</Emphasis> infestations of <Emphasis Type="Italic">Larix</Emphasis> spp. in northern China,including two new species

The larch bark beetle (Ips subelongatus), which occurs in larch plantations over a vast area of eastern Asia, infects both dying and fallen trees. When its population reaches a high density, the beetle may also infect healthy trees, resulting in tree decline and, eventually, death. Leptographium spp., in both their sexual and asexual states, are mainly associated with conifer-infesting bark beetles; some species are important tree pathogens. The aims of this study were to identify the Leptographium spp. associated with I. subelongatus infestations of Larix spp. in northern China and to examine their pathogenicity towards the tree. Morphological studies and phylogenetic approaches based on multilocus DNA sequence data (ITS2- partial r28S, partial β-tubulin, and EF-1α gene regions) showed that three Leptographium species occur in association with I. subelongatus in the areas investigated: Leptographium taigense, which is recorded in China for the first time, and two new species, namely L. innermongolicum sp. nov. and L. zhangii sp. nov. Leptographium innermongolicum is closely related to L. taigense, whereas L. zhangii belongs to the Grosmannia piceaperda species complex. The pathogenicity of these Leptographium species towards mature Larix spp. was tested by stem inoculation in forests. All inoculations only resulted in small lesions on the inner bark; therefore, the three Leptographium species were not considered to be pathogenic.     

A Bacillus thuringiensis insecticidal crystal protein with a high activity against members of the family Noctuidae.

The full characterization of a novel insecticidal crystal protein, named Cry9Ca1 according to the revised nomenclature for Cry proteins, from Bacillus thuringiensis serovar tolworthi is reported. The crystal protein has 1,157 amino acids and a molecular mass of 129.8 kDa. It has the typical features of the Lepidoptera-active crystal proteins such as five conserved sequence blocks. Also, it is truncated upon trypsin digestion to a toxic fragment of 68.7 kDa by removal of 43 amino acids at the N terminus and the complete C-terminal half after conserved sequence block 5. The 68.7-kDa fragment is further degraded to a nontoxic 55-kDa fragment. The crystal protein has a fairly broad spectrum of activity against lepidopteran insects, including members of the families Pyralidae, Plutellidae, Sphingidae, and Noctuidae. A 50% lethal concentration of less than 100 ng/cm2 of diet agar was found for diamondback moth, European corn borer, cotton bollworm, and beet armyworm. It is the first insecticidal crystal protein with activity against cutworms. No activity was observed against some beetles, such as Colorado potato beetle. The protein recognizes a receptor different from that recognized by Cry1Ab5 in Ostrinia nubilalis and Plutella xylostella. In Spodoptera exigua and P. xylostella, it binds to a receptor which is also recognized by Cry1Cax but with a lower affinity. In these insects, Cry1Cax probably binds with a higher affinity to an additional receptor which is not recognized by Cry9Ca1. Elimination of a trypsin cleavage site which is responsible for the degradation to a nontoxic fragment did result in protease resistance but not in increased toxicity against O. nubilalis.     

Production and identification of natural monocyte chemotactic protein from virally infected murine fibroblasts. Relationship with the product of the mouse competence (JE) gene

Primary cultures of mouse embryonic fibroblasts and confluent monolayers of mouse fibroblastoid cells (L929) were found to secrete a chemotactic factor specific for monocytes. It biological activity was deduced from both the migration distance under agarose and the number of migrated monocytes in the micropore filter method. The monocyte chemotactic protein (MCP) was inducible in these cells by double-stranded RNA and by infection with virus. In embryonic fibroblasts MCP was also produced in response to the cytokines interleukin-1 (IL-1) and tumor necrosis factor (TNF). Under all conditions for induction of MCP tested no production of chemotactic activity for granulocytes could be detected. MCP activity from virally infected L929 cells was concentrated and purified by sequential adsorption to controlled pore glass, heparin-Sepharose chromatography, ion-exchange FPLC and reversed-phase HPLC. Pure MCP was found to occur mainly as a 7-8-kDa protein. Although the mature protein possessed a blocked NH2-terminus, it was identified by enzymatic cleavage and sequence analysis of an internal fragment. The sequence obtained corresponded to a part of the cDNA-derived protein sequence of the murine 'competence' (JE) gene, inducible in fibroblasts by cytokines and virus. In all probability the 7-8-kDa MCP form represents the natural product of the mouse gene JE. Murine MCP can thus be classified in the novel family of small inducible inflammatory proteins.     

Purification and N-terminal sequencing of style glycoproteins associated with self-incompatibility in Petunia hybrida

We report isolation and N-terminal amino acid sequencing of three style glycoproteins, which segregate with three S (self-incompatibility) alleles of Petunia hybrida. The S-glycoproteins were expressed mainly in the upper part of the pistil and showed an increasing concentration during flower development. The glycoproteins were purified by a combination of ConA-Sepharose and cation exchange fast protein liquid chromatography. The amount of S-glycoproteins recovered from style extracts varied from 0.5 to 1.6 g per style, which was 40–60% of the amount recovered by a simplified analytical method. N-terminal amino acid sequences of S₁-, S₂- and S₃-glycoprotein showed homology within the fifteen amino terminal residues. These amino acid sequences were compared with the previously published sequences of S-glycoproteins from Nicotiana alata and Lycopersicon peruvianum.     

Further biological and molecular characterization of actinophage VWB

The development cycle of the temperate actinophage VWB was investigated. Adsorption of most phage particles occurred within 30 min and the adsorption constant was 0.6 x 10(-8) ml min-1. The latent and rise periods were 140 and 100 min, respectively, and the burst size was estimated to be 130-250 p.f.u. Although phage VWB could infect only Streptomyces venezuelae ETH 14630 (ATCC 40755), of six different S. venezuelae strains tested, phage DNA could be introduced by transfection into most non-infectible strains. Upon transfection, phage DNA was propagated in these non-infectible strains and phage particles were released. In addition, the transfected strains could be lysogenized. By comparison of restriction fragments of VWB DNA, either free or integrated in the chromosomal DNA of the S. venezuelae ETH 14630 lysogen, the attachment site was localized. PAGE of the phage proteins revealed at least 17 different proteins with three major bands estimated as 16.5, 27.2 and 43 kDa in size. The N-terminal amino acid sequence of these supposed major head and tail proteins was determined. The corresponding DNA sequences on the phage genome were localized using oligonucleotides synthesized on the basis of the N-terminal amino acid sequences. The genes coding for the major structural proteins were shown to be clustered, as has been observed for other bacteriophages.     

Transformation of Bacillus thuringiensis by electroporation

Abstract A simple and reliable method of transforming Bacillus thuringiensis is described. This protocol, based on high-voltage electro-transformation (electroporation) in the presence of polyethylene glycol, allows introduction of plasmid DNA in most of the Bacillus thuringiensis strains tested. Efficiencies vary between 10² and 10⁵ transformants per μg DNA, depending on the strain or the replicon used.     

Phellinus caribaeo-quercicolus sp. nov., parasitic on Quercus cubana: taxonomy and preliminary phylogenetic relationships

Phellinus caribaeo-quercicolus sp. nov. is described from several collections made in western Cuba, so far exclusively on Quercus cubana. The species is characterized by a perennial, resupinate basidiomes, cushion-shaped to nodulose and multi-layered when old, apically hooked to hamate hymenial setae, and ellipsoid to broadly ellipsoid, thin- to thick-walled, hyaline to faintly yellowish basidiospores, 4.5-5.5 x 3.5-4.5 microm. The species is compared to other Phellinus species with hooked setae, especially Phellinus undulatus, also recorded in Cuba. The preliminary phylogenetic relationships of Ph. caribaeo-quercicolus within the poroid Hymenochaetales complex of genera is presented and discussed here.