Systematic Nomenclature for GGDEF and EAL Domain-Containing Cyclic Di-GMP Turnover Proteins of Escherichia coli

In recent years, Escherichia coli has served as one of a few model bacterial species for studying cyclic di-GMP (c-di-GMP) signaling. The widely used E. coli K-12 laboratory strains possess 29 genes encoding proteins with GGDEF and/or EAL domains, which include 12 diguanylate cyclases (DGC), 13 c-di-GMP-specific phosphodiesterases (PDE), and 4 “degenerate” enzymatically inactive proteins. In addition, six new GGDEF and EAL (GGDEF/EAL) domain-encoding genes, which encode two DGCs and four PDEs, have recently been found in genomic analyses of commensal and pathogenic E. coli strains. As a group of researchers who have been studying the molecular mechanisms and the genomic basis of c-di-GMP signaling in E. coli, we now propose a general and systematic dgc and pde nomenclature for the enzymatically active GGDEF/EAL domain-encoding genes of this model species. This nomenclature is intuitive and easy to memorize, and it can also be applied to additional genes and proteins that might be discovered in various strains of E. coli in future studies.     

Meta-analysis Reveals Genome-Wide Significance at 15q13 for Nonsyndromic Clefting of Both the Lip and the Palate,and Functional Analyses Implicate GREM1 As a Plausible Causative Gene

Nonsyndromic orofacial clefts are common birth defects with multifactorial etiology. The most common type is cleft lip, which occurs with or without cleft palate (nsCLP and nsCLO, respectively). Although genetic components play an important role in nsCLP, the genetic factors that predispose to palate involvement are largely unknown. In this study, we carried out a meta-analysis on genetic and clinical data from three large cohorts and identified strong association between a region on chromosome 15q13 and nsCLP (P = 8.13×10⁻¹⁴ for rs1258763; relative risk (RR): 1.46, 95% confidence interval (CI): 1.32–1.61)) but not nsCLO (P = 0.27; RR: 1.09 (0.94–1.27)). The 5 kb region of strongest association maps downstream of Gremlin-1 (GREM1), which encodes a secreted antagonist of the BMP4 pathway. We show during mouse embryogenesis, Grem1 is expressed in the developing lip and soft palate but not in the hard palate. This is consistent with genotype-phenotype correlations between rs1258763 and a specific nsCLP subphenotype, since a more than two-fold increase in risk was observed in patients displaying clefts of both the lip and soft palate but who had an intact hard palate (RR: 3.76, CI: 1.47–9.61, P_diff<0.05). While we did not find lip or palate defects in Grem1-deficient mice, wild type embryonic palatal shelves developed divergent shapes when cultured in the presence of ectopic Grem1 protein (P = 0.0014). The present study identified a non-coding region at 15q13 as the second, genome-wide significant locus specific for nsCLP, after 13q31. Moreover, our data suggest that the closely located GREM1 gene contributes to a rare clinical nsCLP entity. This entity specifically involves abnormalities of the lip and soft palate, which develop at different time-points and in separate anatomical regions.     

The Inflammasome and the Epidermal Growth Factor Receptor (EGFR) Are Involved in the Staphylococcus aureus-Mediated Induction of IL-1alpha and IL-1beta in Human Keratinocytes

Staphylococcus (S.) aureus is an important pathogen causing various infections including those of the skin. Keratinocytes are able to sense invading S. aureus and to initiate a fast defense reaction by the rapid release of innate defense mediators such as antimicrobial peptides and cytokines. There is increasing evidence that the cytokines IL-1alpha and IL-1beta, which both signal through the IL-1 receptor, play an important role in cutaneous defense against S. aureus. The aim of this study was to gain more insight into the underlying mechanisms leading to the S. aureus-induced IL-1alpha and IL-1beta expression in keratinocytes. Infection of human primary keratinocytes with S. aureus led to the induction of gene expression and protein secretion of IL-1alpha and IL-1beta. Full S. aureus-induced IL-1 protein release required the inflammasome components caspase-1 and ASC (apoptosis-associated speck-like protein containing a CARD) whereas gene induction of IL-1alpha and IL-beta by S. aureus was not dependent on caspase-1 and ASC. Since patients receiving anti-cancer therapy by inhibition of the epidermal growth factor receptor (EGFR) often suffer from skin infections caused by S. aureus we additionally evaluated whether the EGFR pathway may be involved in the IL-1alpha and IL-1beta induction by S. aureus. Inactivation of the EGFR with a blocking antibody decreased the S. aureus-mediated IL-1alpha and IL-1beta induction in primary keratinocytes. Moreover, the use of siRNA experiments revealed that ADAM17 (A Disintegrin and A Metalloprotease 17), a metalloproteinase known to mediate the shedding and release of EGFR ligands, was required for full induction of IL-1alpha and IL-1beta in keratinocytes infected with S. aureus. A failure of keratinocytes to adequately upregulate IL-1alpha and IL-1beta may promote S. aureus skin infections.     

Effect of interleukin-2 on the ex vivo growth of human myeloma cells

Summary Short-term cultures containing bone marrow mononuclear cells from multiple myeloma patients secrete monoclonal immunoglobulin and ₂-microglobulin into the supernatant, which can be measured quantitatively in an enzyme-linked immunosorbant assay. In this system, the addition of interleukin-2 was shown to induce tumor cell regression in the cultures from 10 out of 14 multiple myeloma patients in a dose-dependent manner. Marker analyses of culture cell populations indicate that OKT3 antibody or interleukin-2 did not directly act on the malignant clone but augmented autologous T lymphocytes, which were responsible for the regression of tumor cells in the cultures.     

5-Hydroxylation of benzimidazole by micromycetes I. Strains selection

Summary The ability of 610 strains of micromycetes to introduce a hydroxy-group into benzimidazole substrate has been investigated. Among them, 232 micromycetes have been selected and cultivated in a liquid synthetic medium. Convenient hydroxylation of benzimidazole was obtained with 78 fungi. Finally, 8 strains of micromycetes have been chosen for further investigation and optimization of this bioconversion.     

Site-specific deletion at the replication origin of the antibiotic resistance factor R1

Summary The recombinant plasmid pRK101 carrying the complete replication origin of the antibiotic resistance factor R1 suffers frequently a deletion of 218 base pairs, removing parts or all of the origin sequence. This deletion seems to occur always when the Pst-E fragment carrying the replication origin is inserted into the cloning vector pBR322 in an orientation where the direction of R1 replication is the same as that of the vector plasmid and frequently when it is inserted in the opposite direction. DNA sequence analysis around the junction site generated by the deletion in three independently isolated deletion mutants reveals that the deletion occurs at a specific site, namely the end of a 22 bp sequence which is repeated almost identically at the other end of a segment of 197 bp. During the deletion one repeat unit is removed whereas the other is retained. The DNA sequence included by the two repeats contains high symmetric structures, i.e. inverted repeats, direct repeats and palindromes which may represent regulatory sites of the origin.     

Étude cytotaxinomique de quelquesDipsacaceae d'Iran

Chromosome numbers for 28 Iranian populations ofDipsacaceae, corresponding to 14 taxa, are presented. New are those forScabiosa aff.olivieri var.pinnatisecta, S. persica, Pterocephalus canus, P. kurdicus, Dipsacus strigosus, Cephalaria dichaetophora, C. hirsuta, C. microcephala, C. subindivisa andC. aff.sublanata. Except forC. syriaca (x = 5) andC. dichaetophora (x = 7 : new basic chromosome number forCephalaria), all species examined are characterized by the basic chromosome number (x = 9). Instances of aneusomaty, B-chromosomes, aneuploidy, dysploidy, and polyploidy have also been found.

     

A simplified key for identifying homofermentative Lactobacillus and Carnobacterium spp. from meat

Species of Lactobacillus and Carnobacterium from meat and meat products could be separated by a few biochemical characteristics; presence of meso -diaminopimelic acid in the cell wall, the isomers of lactic acid produced, production of citrulline from arginine and fermentation of some carbohydrates. This identification key was checked by DNA–DNA hybridizations studies.     

Common antigenic determinants of pneumococcal penicillin-binding protein (PBP) 1a and Streptococcus pyogenes PBP 2

Abstract Antisera raised against penicillin-binding protein (PBP) 1a of Streptococcus pneumoniae reacted with PBP 2 in certain strains of Streptococcus pyogenes . Cross-reactivity could be demonstrated on immunoblots as well as by immunoprecipitation of native solubilised proteins, indicating a similar structural arrangement also in the native form of the two PBPs.