Cancer-type regulation of MIG-6 expression by inhibitors of methylation and histone deacetylation

Epigenetic silencing is one of the mechanisms leading to inactivation of a tumor suppressor gene, either by DNA methylation or histone modification in a promoter regulatory region. Mitogen inducible gene 6 (MIG-6), mainly known as a negative feedback inhibitor of the epidermal growth factor receptor (EGFR) family, is a tumor suppressor gene that is associated with many human cancers. To determine if MIG-6 is inactivated by epigenetic alteration, we identified a group of human lung cancer and melanoma cell lines in which its expression is either low or undetectable and studied the effects of methylation and of histone deacetylation on its expression. The DNA methyltransferase (DNMT) inhibitor 5-aza-2'-deoxycytidine (5-aza-dC) induced MIG-6 expression in melanoma cell lines but little in lung cancer lines. By contrast, the histone deacetylase (HDAC) inhibitor trichostatin A (TSA) induced MIG-6 expression in lung cancer lines but had little effect in melanoma lines. However, the MIG-6 promoter itself did not appear to be directly affected by either methylation or histone deacetylation, indicating an indirect regulatory mechanism. Luciferase reporter assays revealed that a short segment of exon 1 in the MIG-6 gene is responsible for TSA response in the lung cancer cells; thus, the MIG-6 gene can be epigenetically silenced through an indirect mechanism without having a physical alteration in its promoter. Furthermore, our data also suggest that MIG-6 gene expression is differentially regulated in lung cancer and melanoma.     

Complete genome sequence of Paenibacillus sp. strain JDR-2

Paenibacillus sp. strain JDR-2, an aggressively xylanolytic bacterium isolated from sweetgum (Liquidambar styraciflua) wood, is able to efficiently depolymerize, assimilate and metabolize 4-O-methylglucuronoxylan, the predominant structural component of hardwood hemicelluloses. A basis for this capability was first supported by the identification of genes and characterization of encoded enzymes and has been further defined by the sequencing and annotation of the complete genome, which we describe. In addition to genes implicated in the utilization of β-1,4-xylan, genes have also been identified for the utilization of other hemicellulosic polysaccharides. The genome of Paenibacillus sp. JDR-2 contains 7,184,930 bp in a single replicon with 6,288 protein-coding and 122 RNA genes. Uniquely prominent are 874 genes encoding proteins involved in carbohydrate transport and metabolism. The prevalence and organization of these genes support a metabolic potential for bioprocessing of hemicellulose fractions derived from lignocellulosic resources.     

Detection and characterization of Shigella species isolated from food and human stool samples in Nabeul, Tunisia, by molecular methods and culture techniques

Aims: This study was designed to isolate Shigella spp. strains from food and stool samples by a combination of PCR and culture methods and characterize their serotypes, antibiotic resistance profiles, virulence genes and pulsed‐field gel electrophoresis (PFGE) patterns to investigate possible clonal relationships amongst strains circulating. Methods and Results: Six Shigella spp. strains were isolated from 280 food samples against 16 Shigella isolates from 236 stool samples of symptomatic patients and asymptomatic food handlers during the period from January 2007 to December 2009 in Public Health Regional Laboratory of Nabeul. The detection of ipaH, ipaBCD, ial, ShET‐1 and ShET‐2 was performed by a PCR technique with specific primers. Conclusions: The use of PCR technique improved the rate of detecting Shigella in stool samples from 6·7 to 14% and in food samples from 2·1 to 8·6%. Percentage of Shigella isolates and ipaH‐specific PCR demonstrated a marked pattern of seasonality, increasing in summer and fall seasons for human and food isolates. Amongst the environmental strains, 50% of isolates were invasive. However, for the 16 clinical strains isolated, nine were found to be positive for both ial and ipaBCD gene and 11 were found to produce ShET‐1 and/or ShET‐2. XbaI PFGE analysis revealed the presence of a predominant clone amongst Shigella sonnei strains recovered from different sources circulating in Nabeul, Tunisia, throughout the years 2007–2009. Significance and Impact of the Study: This study demonstrated the existence of Shigella in food samples and dispersion of different virulence genes amongst these isolates, which appear to constitute an environmental source of epidemic spread. The clonal relationships amongst strains isolated from food elements and human stools indicate the incrimination of different kinds of foods as vehicle of transmission of Shigella, which are usually escaped from detection by traditional culture methods.     

Data uncertainty and the selectivity of extinction risk in freshwater invertebrates

Aim

To investigate the impact of different treatments of the IUCN Data Deficient (DD) category on taxonomic and geographical patterns of extinction risk in crayfish, freshwater crabs and dragonflies.

Location

Global.

Methods

We used contingency tables to evaluate taxonomic and geographical selectivity of data deficiency and extinction risk for three invertebrate taxonomic groups (crayfish, dragonflies and damselflies, and freshwater crabs) based on their IUCN Red List status. We investigated differences in patterns of data deficiency and extinction risk among taxonomic families, geographical realms and taxonomic families within geographical realms for each of the three groups. At each level, we evaluated the impact of uncertainty conferred by the conservation status of DD species on extinction risk patterns exhibited by that group. We evaluated three scenarios: excluding DD species, treating all DD species as non‐threatened and treating all DD species as threatened.

Results

At the global scale, DD species were taxonomically non‐randomly distributed in freshwater crabs and dragonflies, and geographically non‐randomly distributed in all three taxonomic groups. Although the presence of under‐ or over‐threatened families and biogeographical realms was generally unchanging across scenarios, the strength of taxonomic and geographical selectivity of extinction risk varied. There was little consistent evidence for taxonomic selectivity of extinction risk at sub‐global scales in freshwater crabs and dragonflies, either among biogeographical realms or among scenarios.

Main conclusions

Global patterns of taxonomic selectivity and geographical selectivity were generally consistent with one another and robust to different treatments of DD species. However, sub‐global scale conservation prioritization from these types of data sets will require increased investment to make accurate decisions. Given the current levels of data uncertainty, the relative importance of biological characteristics and threatening processes in driving extinctions in freshwater invertebrates cannot be easily determined. We recommend that DD species should be given high research priority to determine their true status.     

Temporal similarity between Candida albicans genotypes in a Tunisian neonatal intensive care unit suggests several nosocomial cross-contamination episodes

The nosocomial transmission of Candida albicans in neonatal intensive care units (NICUs) is an increasing concern and understanding the route of this transmission is critical for adequate infection control measures. The aim of our study was to assess the likeliness of nosocomial acquisition of C. albicans in the NICU of Farhat Hached hospital in Sousse (Tunisia). We genotyped 82 isolates from 40 neonates and 7 isolates from 5 health care workers (HCWs) with onychomycosis, by using CDC3 microsatellite length polymorphism (MLP) and the high-resolution melting (HRM) analysis. Combined MLP and HRM CD3 analysis led to the delineation of 12 genotypes. Five temporal clustering caused by five genotypes occurred during the study period. Three of these genotypes were isolated in both neonates and HCWs. The first clustering included 28 isolates obtained between January 2003 and May 2004 from 16 neonates and 2 HCWs. The second clustering included three isolates collected in 2004 from three neonates and two HCWs. The third clustering included 11 isolates obtained from 6 neonates and 1 HCW in 2006. The two remaining clustering could not be associated with any HCW's contamination. These results argue for the nosocomial transmission of C. albicans in our NICU. The combined MLP and HRM analysis is a rapid first approach for tracking cross-contamination.     

Haplo-insufficiency for different genes differentially reduces pathogenicity and virulence in a fungal phytopathogen

The main determinant of pathogenicity in Ustilago maydis is the b-mating locus, where establishment of heterozygosity is sufficient to cause galls/tumors on maize plants. However, matings between haploids where one partner contains a mutation, in e.g., the smu1 gene, encoding a Ste20-like PAK kinase, often show reduced mating and pathogenicity compared to wild type. Here we show that similarly, diploids lacking one copy of smu1, are reduced in production of aerial hyphae, but do not show significantly-reduced virulence. Haplo-insufficiency was also observed for additional genes. UmPde1 is a cyclic phosphodiesterase involved in cAMP turnover as part of the cAMP-dependent PKA pathway. Hsl7 plays a role in cell length and in the filamentous response to low ammonium in haploid cells. Diploids deleted for one copy of either the pde1 or hsl7 genes had reduced or increased production of aerial hyphae, respectively, and both were severely impaired in virulence compared to wild type diploids. rho1 and pdc1 are two genes essential for cell viability in haploids. These genes also displayed haplo-insufficiency for pathogenesis. rho1/Δrho1 diploid cells were defective in pheromone production and detection, aerial hyphae induction, and were avirulent. In contrast, pdc1/Δpdc1 diploid cells only failed to produce tumors when applied to maize whorls. We predict the haplo-insufficiency of most of these signaling components is due to stoichiometric imbalance of the respective gene products with their interacting partners, thereby impairing virulence-induction mechanism(s). Further investigation of the bases for such haplo-insufficiency as well as of additional genes displaying this phenotype will provide important insights into fundamental aspects of development in this organism as well as inter-nuclear communication and genetic control.     

Analysis of phospholipase A2, l-amino acid oxidase, and proteinase enzymatic activities of the Lachesis muta rhombeata venom

The study of venom components is an important step toward understanding the mechanism of action of such venoms and is indispensable for the development of new therapies. This work aimed to investigate the venom of Lachesis muta rhombeata and evaluate enzymes related to its toxicity. Phospholipase A2 (PLA₂), l ‐amino acid oxidase (LAAO), and proteinase activities were measured, and the molecular weights were estimated. We found the venom to contain one PLA₂ (17 kDa), one LAAO (132 kDa), and three serine proteinases (40, 31, and 20 kDa). Although only serine proteinases were observed in the zymogram, metalloproteinases were found to contribute more to the total proteolytic activity than did serine proteinases. The work confirmed the presence of highly active enzymes; and, moreover, we proposed a novel method for confirming the presence of LAAOs by zymography. We also suggested a simple step to increase the sensitivity of proteinase assays. © 2012 Wiley Periodicals, Inc. J Biochem Mol Toxicol 26:308–314, 2012; View this article online at wileyonlinelibrary.com. DOI 10:1002/jbt.21422     

<Emphasis Type="Italic">Bacillus subtilis</Emphasis> bacteriocin Bac 14B with a broad inhibitory spectrum: Purification,amino acid sequence analysis,and physicochemical characterization

Bacillus subtilis strain 14B was used to produce a novel antimicrobial peptide (bacteriocin) called Bac 14B. Pure bacteriocin was obtained after heat and acidic treatments (80°C and pH 4), precipitation by ammonium sulfate, and chromatography on Sephadex G-50 and Mono Q Sepharose columns. Based on MALDI-TOF mass spectrometry analysis, purified Bac 14B is a monomer protein with a molecular mass of 20110.13 Da. N-terminal sequencing allowed for the straightforward identification of its first 12 residues, which were of a pure bacteriocin. It also revealed that this bacteriocin contained a unique sequence, namely M-L-K-A-N-L-Q-N-P-L-N-A, suggesting the identification of a novel compound. Bac 14B was stable for 1 h at temperatures up to 80°C and pH of 4 ∼ 8. It also proved sensitive to various proteases, which demonstrated its protein nature. Bac 14B displayed a bacteriolytical mode of action and a broad range of inhibitory spectra toward Gram-positive and -negative pathogens. Interestingly, based on conventional agronomic seed vigor parameters, the application of Bac 14B (500 activity units/mL) to various crops revealed that this bacteriocin was a potent exogenous enhancer of growth that stimulated the seedling vigor of tomatoes and muskmelons. Compared to those of the control, the germination percentage, shoot weight, shoot height, and root length were all significantly enhanced in Bac 14B-treated plant seeds. Bac 14B also exhibited effective disinfectant properties against a wide range of seedborne diseases and significant effects on the control of damping off diseases, particularly at the pregermination stage. It also proved to be effective against root rot diseases caused by Alternaria solani and other bacterial seedborne pathogens such as wilt diseases. The findings indicate that Bac 14B is the first B. subtilis-produced bacteriocin ever reported to exhibit such promising biological properties.