The complete genome sequence of Chromobacterium violaceum reveals remarkable and exploitable bacterial adaptability

Chromobacterium violaceum is one of millions of species of free-living microorganisms that populate the soil and water in the extant areas of tropical biodiversity around the world. Its complete genome sequence reveals (i) extensive alternative pathways for energy generation, (ii) ≈500 ORFs for transport-related proteins, (iii) complex and extensive systems for stress adaptation and motility, and (iv) wide-spread utilization of quorum sensing for control of inducible systems, all of which underpin the versatility and adaptability of the organism. The genome also contains extensive but incomplete arrays of ORFs coding for proteins associated with mammalian pathogenicity, possibly involved in the occasional but often fatal cases of human C. violaceum infection. There is, in addition, a series of previously unknown but important enzymes and secondary metabolites including paraquat-inducible proteins, drug and heavy-metal-resistance proteins, multiple chitinases, and proteins for the detoxification of xenobiotics that may have biotechnological applications

Gene expression pattern contributing to prognostic factors in childhood acute lymphoblastic leukemia

The present study evaluated the expression profile of 19 genes previously reported in microarray studies and associated with resistance or sensitivity to vincristine (RPLP2, CD44, TCFL5, KCNN1, TRIM24), prednisolone (F8A, CDK2AP1, BLVRB, CD69), daunorubicin (MAP3K12, SHOC2, PCDH9, EGR1, KCNN4) and L-asparaginase (GPR56, MAN1A1, CLEC11A, IGFBP7, GATA3). We studied 140 bone marrow samples at diagnosis from children with acute lymphoblastic leukemia (ALL) treated according to the Brazilian Childhood Leukemia Treatment Group (GBTLI) ALL-99 protocol. the expression profiles of the genes listed above were analyzed by real-time quantitative polymerase chain reaction (PCR) and then related to the clinical and biological prognostic factors. the results showed significant associations (p <= 0.05) between the expression levels of genes GPR56, BLVRB, IGFBP7 and white blood cell (WBC) count at diagnosis; GATA3, MAN1A1, CD44, MAP3K12, CLEC11A, SHOC2 and CD10 B-lineage ALL; TCFL5 and bone marrow status at day 14; MAP3K12 and TRIM24 and bone marrow status at day 28; and CD69, TCFL5 and TRIM24 genes and ETV6/RUNX1 positive ALL. the up-regulation of SHOC2 was also associated with better 5-year event-free survival (EFS) in univariate and multivariate analysis (p = 0.02 and p = 0.03, respectively). These findings highlight genes that could be associated with clinical and biological prognostic factors in childhood ALL, suggesting that these genes may characterize and play a role in the treatment outcome of some ALL subsets.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)FAEPA (Brazil)Univ São Paulo, Fac Med Ribeirao Preto, Dept Pediat, BR-14049900 Ribeirao Preto, SP, BrazilUniv São Paulo, Fac Med Ribeirao Preto, Dept Genet, BR-14049900 Ribeirao Preto, SP, BrazilBoldrini Inst, Campinas, SP, BrazilUniversidade Federal de São Paulo, Inst Pediat Oncol, São Paulo, SP, BrazilUniv Estadual Campinas, Campinas, SP, BrazilUniversidade Federal de São Paulo, Inst Pediat Oncol, São Paulo, SP, BrazilFAPESP: 2001/13206-9FAPESP: 2002/03182-8FAPESP: 2005/50731-5Web of Scienc

Molecular Epidemiology of Agents of Human Chromoblastomycosis in Brazil with the Description of Two Novel Species

The human mutilating disease chromoblastomycosis is caused by melanized members of the order Chaetothyriales. To assess population diversity among 123 clinical strains of agents of the disease in Brazil we applied sequencing of the rDNA internal transcribed spacer region, and partial cell division cycle and β-tubulin genes. Strains studied were limited to three clusters divided over the single family Herpotrichiellaceae known to comprise agents of the disease. A Fonsecaea cluster contained the most important agents, among which F. pedrosoi was prevalent with 80% of the total set of strains, followed by 13% for F. monophora, 3% for F. nubica, and a single isolate of F. pugnacius. Additional agents, among which two novel species, were located among members of the genus Rhinocladiella and Cyphellophora, with frequencies of 3% and 1%, respectively

Multilocus tree of <i>Rhinocladiella</i> based on ITS and partial <i>BT2</i> sequences.

<p>Constructed with maximum likelihood implemented in MEGA 7. Bootstrap values of >80% from 100 resampled data sets are shown with branches. <i>Cladophialophora yegresii</i> and <i>C</i>. <i>carrionii</i> comprised the outgroup. Novel species causing chromoblastomycosis are indicated with red branches. Type strain in bold.</p

Phylogeny of a representative selection of species in Chaetothyriales, based on confidently aligned LSU sequences.

<p>Constructed with Maximum likelihood implemented in MEGA 7. Bootstrap values > 80% from 100 resampled datasets are shown with branches. Coloured boxes represent species complexes taken from de Hoog et al. [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0005102#pntd.0005102.ref021" target="_blank">21</a>], Feng et al. [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0005102#pntd.0005102.ref022" target="_blank">22</a>], and Vicente et al. [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0005102#pntd.0005102.ref023" target="_blank">23</a>]. Clades with species causing chromoblastomycosis analysed in this study are indicated with arrows. Type strain in bold.</p

<i>Rhinocladiella tropicalis</i>, microscopic morphology.

<p>(A) Colonies on SGA; (B, C) twisted hyphae and conidia; (D-G) conidiophores with conidia produced in sympodial order; (H-O) conidial apparatus with conidia. Scale bars 10 μm.</p

Cardinal temperatures of strains described.

<p>(A) <i>Cyphellophora ludoviensis</i> with optimal growth temperature at 30°C and maximum at 37°C. (B) <i>Rhinocladiella tropicalis</i> with optimal development at 27°C and maximum at 37°C.</p

<i>Cyphellophora ludoviensis</i> microscopic morphology.

<p>(A) colonies on SGA; (B-E) hyphae with chlamydospores and lateral extensions; (F) anastomosis; (G-H) spirally twisted hyphae; (I) poorly differentiated phialide producing conidia; (J-P) chlamydospores and conidia. Scale bars 10 μm.</p