Choice of Reference Sequence and Assembler for Alignment of Listeria monocytogenes Short-Read Sequence Data Greatly Influences Rates of Error in SNP Analyses

The wide availability of whole-genome sequencing (WGS) and an abundance of open-source software have made detection of single-nucleotide polymorphisms (SNPs) in bacterial genomes an increasingly accessible and effective tool for comparative analyses. Thus, ensuring that real nucleotide differences between genomes (i.e., true SNPs) are detected at high rates and that the influences of errors (such as false positive SNPs, ambiguously called sites, and gaps) are mitigated is of utmost importance. The choices researchers make regarding the generation and analysis of WGS data can greatly influence the accuracy of short-read sequence alignments and, therefore, the efficacy of such experiments. We studied the effects of some of these choices, including: i) depth of sequencing coverage, ii) choice of reference-guided short-read sequence assembler, iii) choice of reference genome, and iv) whether to perform read-quality filtering and trimming, on our ability to detect true SNPs and on the frequencies of errors. We performed benchmarking experiments, during which we assembled simulated and real Listeria monocytogenes strain 08-5578 short-read sequence datasets of varying quality with four commonly used assemblers (BWA, MOSAIK, Novoalign, and SMALT), using reference genomes of varying genetic distances, and with or without read pre-processing (i.e., quality filtering and trimming). We found that assemblies of at least 50-fold coverage provided the most accurate results. In addition, MOSAIK yielded the fewest errors when reads were aligned to a nearly identical reference genome, while using SMALT to align reads against a reference sequence that is ∼0.82% distant from 08-5578 at the nucleotide level resulted in the detection of the greatest numbers of true SNPs and the fewest errors. Finally, we show that whether read pre-processing improves SNP detection depends upon the choice of reference sequence and assembler. In total, this study demonstrates that researchers should test a variety of conditions to achieve optimal results.     

How the Context Matters. Literal and Figurative Meaning in the Embodied Language Paradigm

The involvement of the sensorimotor system in language understanding has been widely demonstrated. However, the role of context in these studies has only recently started to be addressed. Though words are bearers of a semantic potential, meaning is the product of a pragmatic process. It needs to be situated in a context to be disambiguated. The aim of this study was to test the hypothesis that embodied simulation occurring during linguistic processing is contextually modulated to the extent that the same sentence, depending on the context of utterance, leads to the activation of different effector-specific brain motor areas. In order to test this hypothesis, we asked subjects to give a motor response with the hand or the foot to the presentation of ambiguous idioms containing action-related words when these are preceded by context sentences. The results directly support our hypothesis only in relation to the comprehension of hand-related action sentences.     

Sympathetic glial cells and macrophages develop different responses to Trypanosoma cruzi infection or lipopolysaccharide stimulation

Nitric oxide (NO) participates in neuronal lesions in the digestive form of Chagasdisease and the proximity of parasitised glial cells and neurons in damaged myentericganglia is a frequent finding. Glial cells have crucial roles in manyneuropathological situations and are potential sources of NO. Here, we investigateperipheral glial cell response to Trypanosoma cruzi infection toclarify the role of these cells in the neuronal lesion pathogenesis of Chagasdisease. We used primary glial cell cultures from superior cervical ganglion toinvestigate cell activation and NO production after T. cruziinfection or lipopolysaccharide (LPS) exposure in comparison to peritonealmacrophages. T. cruzi infection was greater in glial cells, despitesimilar levels of NO production in both cell types. Glial cells responded similarlyto T. cruzi and LPS, but were less responsive to LPS thanmacrophages were. Our observations contribute to the understanding of Chagas diseasepathogenesis, as based on the high susceptibility of autonomic glial cells toT. cruzi infection with subsequent NO production. Moreover, our findingswill facilitate future research into the immune responses and activation mechanismsof peripheral glial cells, which are important for understanding the paradoxicalresponses of this cell type in neuronal lesions and neuroprotection.     

Acute dacryocystitis: another clinical manifestation of sporotrichosis

Sporotrichosis associated with exposure to domestic cats is hyperendemic in Rio deJaneiro, Brazil. A review of the clinical records at our institute revealed fourpatients with clinical signs of dacryocystitis and a positive conjunctival culturefor Sporothrix who were diagnosed with Sporothrixdacryocystitis. Three patients were children (< 13 years of age) and one patientwas an adult. Two patients reported contact with a cat that had sporotrichosis.Dacryocystitis was associated with nodular, ulcerated lesions on the face of onepatient and with granulomatous conjunctivitis in two patients; however, thiscondition manifested as an isolated disease in another patient. All of the patientswere cured of the fungal infections, but three patients had chronic dacryocystitisand one patient developed a cutaneous fistula. Sporotrichosis is usually a benigndisease, but may cause severe complications when the eye and the adnexa are affected.Physicians, especially ophthalmologists in endemic areas, should be aware of theophthalmological manifestations and complications of sporotrichosis.     

RNA-dependent dynamic histone acetylation regulates MCL1 alternative splicing

Histone deacetylases (HDACs) and lysine acetyltransferases (KATs) catalyze dynamic histone acetylation at regulatory and coding regions of transcribed genes. Highly phosphorylated HDAC2 is recruited within corepressor complexes to regulatory regions, while the nonphosphorylated form is associated with the gene body. In this study, we characterized the nonphosphorylated HDAC2 complexes recruited to the transcribed gene body and explored the function of HDAC-complex-mediated dynamic histone acetylation. HDAC1 and 2 were coimmunoprecipitated with several splicing factors, including serine/arginine-rich splicing factor 1 (SRSF1) which has roles in alternative splicing. The co-chromatin immunoprecipitation of HDAC1/2 and SRSF1 to the gene body was RNA-dependent. Inhibition of HDAC activity and knockdown of HDAC1, HDAC2 or SRSF1 showed that these proteins were involved in alternative splicing of MCL1. HDAC1/2 and KAT2B were associated with nascent pre-mRNA in general and with MCL1 pre-mRNA specifically. Inhibition of HDAC activity increased the occupancy of KAT2B and acetylation of H3 and H4 of the H3K4 methylated alternative MCL1 exon 2 nucleosome. Thus, nonphosphorylated HDAC1/2 is recruited to pre-mRNA by splicing factors to act at the RNA level with KAT2B and other KATs to catalyze dynamic histone acetylation of the MCL1 alternative exon and alter the splicing of MCL1 pre-mRNA.     

A Hematogenous Route for Medulloblastoma Leptomeningeal Metastases

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Synthesis and structure-activity relationships of 1,2,4-triazoles as a novel class of potent tubulin polymerization inhibitors

A novel triazole-containing chemical series was shown to inhibit tubulin polymerization and cause cell cycle arrest in A431 cancer cells with EC(50) values in the single digit nanomolar range. Binding experiments demonstrated that representative active compounds of this class compete with colchicine for its binding site on tubulin. The syntheses and structure-activity relationship studies for the triazole derivatives are described herein.     

Comparative proteomic analysis of Xanthomonas citri ssp. citri periplasmic proteins reveals changes in cellular envelope metabolism during in vitro pathogenicity induction

Citrus canker is a plant disease caused by Gram‐negative bacteria from the genus Xanthomonas. The most virulent species is Xanthomonas citri ssp. citri (XAC), which attacks a wide range of citrus hosts. Differential proteomic analysis of the periplasm‐enriched fraction was performed for XAC cells grown in pathogenicity‐inducing (XAM‐M) and pathogenicity‐non‐inducing (nutrient broth) media using two‐dimensional electrophoresis combined with liquid chromatography‐tandem mass spectrometry. Amongst the 40 proteins identified, transglycosylase was detected in a highly abundant spot in XAC cells grown under inducing condition. Additional up‐regulated proteins related to cellular envelope metabolism included glucose‐1‐phosphate thymidylyltransferase, dTDP‐4‐dehydrorhamnose‐3,5‐epimerase and peptidyl‐prolyl cis–trans‐isomerase. Phosphoglucomutase and superoxide dismutase proteins, known to be involved in pathogenicity in other Xanthomonas species or organisms, were also detected. Western blot and quantitative real‐time polymerase chain reaction analyses for transglycosylase and superoxide dismutase confirmed that these proteins were up‐regulated under inducing condition, consistent with the proteomic results. Multiple spots for the 60‐kDa chaperonin and glyceraldehyde‐3‐phosphate dehydrogenase were identified, suggesting the presence of post‐translational modifications. We propose that substantial alterations in cellular envelope metabolism occur during the XAC infectious process, which are related to several aspects, from defence against reactive oxygen species to exopolysaccharide synthesis. Our results provide new candidates for virulence‐related proteins, whose abundance correlates with the induction of pathogenicity and virulence genes, such as hrpD6, hrpG, hrpB7, hpa1 and hrpX. The results present new potential targets against XAC to be investigated in further functional studies.