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

Cockayne syndrome-derived neurons display reduced synapse density and altered neural network synchrony

Cockayne syndrome (CS) is a rare genetic disorder in which 80% of cases are caused by mutations in the Excision Repair Cross-Complementation group 6 gene (ERCC6). The encoded ERCC6 protein is more commonly referred to as Cockayne Syndrome B protein (CSB). Classical symptoms of CS patients include failure to thrive and a severe neuropathology characterized by microcephaly, hypomyelination, calcification and neuronal loss. Modeling the neurological aspect of this disease has proven difficult since murine models fail to mirror classical neurological symptoms. Therefore, a robust human in vitro cellular model would advance our fundamental understanding of the disease and reveal potential therapeutic targets. Herein, we successfully derived functional CS neural networks from human CS induced pluripotent stem cells (iPSCs) providing a new tool to facilitate studying this devastating disease. We identified dysregulation of the Growth Hormone/Insulin-like Growth Factor-1 (GH/IGF-1) pathway as well as pathways related to synapse formation, maintenance and neuronal differentiation in CSB neurons using unbiased RNA-seq gene expression analyses. Moreover, when compared to unaffected controls, CSB-deficient neural networks displayed altered electrophysiological activity, including decreased synchrony, and reduced synapse density. Collectively, our work reveals that CSB is required for normal neuronal function and we have established an alternative to previously available models to further study neural-specific aspects of CS

Profiling the resting venom gland of the scorpion <it>Tityus stigmurus</it> through a transcriptomic survey

<p>Abstract</p> <p>Background</p> <p>The scorpion <it>Tityus stigmurus</it> is widely distributed in Northeastern Brazil and known to cause severe human envenoming, inducing pain, hyposthesia, edema, erythema, paresthesia, headaches and vomiting. The present study uses a transcriptomic approach to characterize the gene expression profile from the non-stimulated venom gland of <it>Tityus stigmurus</it> scorpion.</p> <p>Results</p> <p>A cDNA library was constructed and 540 clones were sequenced and grouped into 153 clusters, with one or more ESTs (expressed sequence tags). Forty-one percent of ESTs belong to recognized toxin-coding sequences, with transcripts encoding antimicrobial toxins (AMP-like) being the most abundant, followed by alfa KTx- like, beta KTx-like, beta NaTx-like and alfa NaTx-like. Our analysis indicated that 34% of the transcripts encode “other possible venom molecules”, which correspond to anionic peptides, hypothetical secreted peptides, metalloproteinases, cystein-rich peptides and lectins. Fifteen percent of ESTs are similar to cellular transcripts. Sequences without good matches corresponded to 11%.</p> <p>Conclusions</p> <p>This investigation provides the first global view of gene expression of the venom gland from <it>Tityus stigmurus</it> under resting conditions. This approach enables characterization of a large number of venom gland component molecules, which belong either to known or non yet described types of venom peptides and proteins from the Buthidae family.</p

Cockayne syndrome-derived neurons display reduced synapse density and altered neural network synchrony

Cockayne syndrome (CS) is a rare genetic disorder in which 80% of cases are caused by mutations in the Excision Repair Cross-Complementation group 6 gene (ERCC6). The encoded ERCC6 protein is more commonly referred to as Cockayne Syndrome B protein (CSB). Classical symptoms of CS patients include failure to thrive and a severe neuropathology characterized by microcephaly, hypomyelination, calcification and neuronal loss. Modeling the neurological aspect of this disease has proven difficult since murine models fail to mirror classical neurological symptoms. Therefore, a robust human in vitro cellular model would advance our fundamental understanding of the disease and reveal potential therapeutic targets. Herein, we successfully derived functional CS neural networks from human CS induced pluripotent stem cells (iPSCs) providing a new tool to facilitate studying this devastating disease. We identified dysregulation of the Growth Hormone/Insulin-like Growth Factor-1 (GH/IGF-1) pathway as well as pathways related to synapse formation, maintenance and neuronal differentiation in CSB neurons using unbiased RNA-seq gene expression analyses. Moreover, when compared to unaffected controls, CSB-deficient neural networks displayed altered electrophysiological activity, including decreased synchrony, and reduced synapse density. Collectively, our work reveals that CSB is required for normal neuronal function and we have established an alternative to previously available models to further study neural-specific aspects of CS

Nicotinamide and Azospirillum brasilense improves the quality of Coffea arabica seedlings

ABSTRACT The use of biostimulants in coffee seedlings can promote gains in their growth and quality. Thus, this study aimed to evaluate the growth and quality characteristics of Coffea arabica seedlings under the effect of the nicotinamide and Azospirillum brasilense application. The experimental design was randomized blocks with treatments arranged in a 5 × 2 factorial scheme, with four replicates. The treatments resulted from the use of five doses of nicotinamide (0, 30, 60, 90, and 120 mg L-1 of water) combined with the absence and presence of Azospirillum brasilense applied to Coffea arabica seedlings from Catuaí Vermelho 144 cultivar. Plant height, stem diameter, number of leaves, leaf area, shoot dry mass, root dry mass, plant height:stem diameter ratio, shoot:root dry mass ratio, plant height:shoot dry mass ratio, and Dickson quality index were evaluated. The combined or isolated use of A. brasilense and nicotinamide, up to a dose of 33.5 mg L-1, increased the biometric characteristics and dry mass accumulation. However, using nicotinamide doses between 30 and 61.8 g L-1 increased the quality of Coffea arabica seedlings. The synergistic effect of the use of A. brasilense and nicotinamide was verified for the growth and quality of Coffea arabica seedlings.</div

Association of kynurenine aminotransferase II gene C401T polymorphism with immune response in patients with meningitis

<p>Abstract</p> <p><b>Background</b></p> <p>The kynurenine (KYN) pathway has been shown to be altered in several diseases which compromise the central nervous system (CNS) including infectious diseases such as bacterial meningitis (BM). The aim of this study was to assess single nucleotide polymorphisms (SNPs) in four genes of KYN pathway in patients with meningitis and their correlation with markers of immune response in BM.</p> <p>Methods</p> <p>One hundred and one individuals were enrolled in this study to investigate SNPs in the following genes: indoleamine-2,3-dioxygenase (<it>IDO1 </it>gene), kynureninase (<it>KYNU </it>gene), kynurenine aminotransferase I (<it>CCBL1 </it>gene), and kynurenine aminotransferase II (<it>AADAT </it>gene). SNP analyses were performed by primer-introduced restriction analysis-PCR (PIRA-PCR) followed by RFLP. Cytokines were measured using multiplex bead assay while immunoglobulins (IG) by immunodiffusion plates and NF-kappaB and c-Jun by dot blot assay.</p> <p>Results</p> <p>The variant allele of SNP <it>AADAT</it>+401C/T showed prevalent frequency in patients with BM. A significant decrease (<it>p </it>< 0.05) in TNF-α, IL-1β, IL-6, MIP-1αCCL3 and MIP-1β/CCL4 levels was observed in BM patients homozygous (TT) to the SNP <it>AADAT</it>+401C/T. Furthermore, a significant (<it>p </it>< 0.05) decrease in cell count was observed in cerebrospinal fluid (CSF) from patients with TT genotype. In addition, an increase in the IgG level in adults (<it>p </it>< 0.05) was observed. The variant allele for <it>KYNU</it>+715G/A was found with low frequency in the groups, and the SNPs in <it>IDO1</it>+434T/G, <it>KYNU</it>+693G/A, <it>CCBL1</it>+164T/C, and <it>AADAT</it>+650C/T had no frequency in this population.</p> <p><b>Conclusions</b></p> <p>This study is the first report of an association of SNP <it>AADAT</it>+401C/T with the host immune response to BM, suggesting that this SNP may affect the host ability in recruitment of leukocytes to the infection site. This finding may contribute to identifying potential targets for pharmacological intervention as adjuvant therapy for BM.</p

A model for the RecA protein of Mycoplasma synoviae

In this work, we predict a structural model for the RecA protein from M. synoviae (MsRecA) by theoretical homology modeling and evaluate the occurrence of polymorphisms in this protein within several isolates of this species. The structural model suggested for MsRecA conserves the main domains present in MtRecA and EcRecA. The L1 and L2 regions showed six and three amino acid substitutions, respectively, which apparently do not affect the conformation and function of MsRecA. The C-terminal domain is shorter than that found in EcRecA and MtRecA, which may increase its capacity to bind dsDNA and displace SSB, compensating the absence of recombination initiation enzymes. The MS59 isolate RecA sequence showed one polymorphism which does not affect its functions since these belong to the same physical-chemical group