A Genome-Wide Approach to Discovery of Small RNAs Involved in Regulation of Virulence in Vibrio cholerae

Small RNAs (sRNAs) are becoming increasingly recognized as important regulators in bacteria. To investigate the contribution of sRNA mediated regulation to virulence in Vibrio cholerae, we performed high throughput sequencing of cDNA generated from sRNA transcripts isolated from a strain ectopically expressing ToxT, the major transcriptional regulator within the virulence gene regulon. We compared this data set with ToxT binding sites determined by pulldown and deep sequencing to identify sRNA promoters directly controlled by ToxT. Analysis of the resulting transcripts with ToxT binding sites in cis revealed two sRNAs within the Vibrio Pathogenicity Island. When deletions of these sRNAs were made and the resulting strains were competed against the parental strain in the infant mouse model of V. cholerae colonization, one, TarB, displayed a variable colonization phenotype dependent on its physiological state at the time of inoculation. We identified a target of TarB as the mRNA for the secreted colonization factor, TcpF. We verified negative regulation of TcpF expression by TarB and, using point mutations that disrupted interaction between TarB and tpcF mRNA, showed that loss of this negative regulation was primarily responsible for the colonization phenotype observed in the TarB deletion mutant

Landscape genomic approach to detect selection signatures in locally adapted Brazilian swine genetic groups

Samples of 191 animals from 18 different Brazilian locally adapted swine genetic groups were genotyped using Illumina Porcine SNP60 BeadChip in order to identify selection signatures related to the monthly variation of Brazilian environmental variables. Using BayeScan software, 71 SNP markers were identified as FST outliers and 60 genotypes (58 markers) were found by Samβada software in 371 logistic models correlated with 112 environmental variables. Five markers were identified in both methods, with a Kappa value of 0.073 (95% CI: 0.011–0.134). The frequency of these markers indicated a clear north–south country division that reflects Brazilian environmental differences in temperature, solar radiation, and precipitation. Global spatial territory correlation for environmental variables corroborates this finding (average Moran's I = 0.89, range from 0.55 to 0.97). The distribution of alleles over the territory was not strongly correlated with the breed/genetic groups. These results are congruent with previous mtDNA studies and should be used to direct germplasm collection for the National gene bank

Advances in structure elucidation of small molecules using mass spectrometry

The structural elucidation of small molecules using mass spectrometry plays an important role in modern life sciences and bioanalytical approaches. This review covers different soft and hard ionization techniques and figures of merit for modern mass spectrometers, such as mass resolving power, mass accuracy, isotopic abundance accuracy, accurate mass multiple-stage MS(n) capability, as well as hybrid mass spectrometric and orthogonal chromatographic approaches. The latter part discusses mass spectral data handling strategies, which includes background and noise subtraction, adduct formation and detection, charge state determination, accurate mass measurements, elemental composition determinations, and complex data-dependent setups with ion maps and ion trees. The importance of mass spectral library search algorithms for tandem mass spectra and multiple-stage MS(n) mass spectra as well as mass spectral tree libraries that combine multiple-stage mass spectra are outlined. The successive chapter discusses mass spectral fragmentation pathways, biotransformation reactions and drug metabolism studies, the mass spectral simulation and generation of in silico mass spectra, expert systems for mass spectral interpretation, and the use of computational chemistry to explain gas-phase phenomena. A single chapter discusses data handling for hyphenated approaches including mass spectral deconvolution for clean mass spectra, cheminformatics approaches and structure retention relationships, and retention index predictions for gas and liquid chromatography. The last section reviews the current state of electronic data sharing of mass spectra and discusses the importance of software development for the advancement of structure elucidation of small molecules

Cápsulas de polvo de arándano (Vaccinium corymbosum L.) como propuesta nutracéutica para mejorar la estabilidad gastrointestinal in vitro de compuestos fenólicos

El arándano (Vaccinium corymbosum L.) posee un alto contenido de compuestos fenólicos los cuales han sido estudiados principalmente por su actividad antioxidante, antiobesogénica, antiinflamatoria, entre otras. Objetivo. Evaluar el efecto de la digestión gastrointestinal in vitro sobre la bioaccesibilidad de compuestos fenólicos y actividad antioxidante de una formulación nutracéutica de arándano (cápsula), comparado con arándano fresco y polvo. Materiales y métodos. Se obtuvieron extractos metanólicos de muestras de arándano fresco y liofilizado y se determinó su contenido de fenoles, flavonoides y antocianinas totales, así como también actividad antioxidante. Se llevó a cabo un ensayo de simulación de digestión gastrointestinal para evaluar la bioaccesibilidad de los compuestos fenólicos presentes en las muestras. Resultados. Los resultados mostraron que la digestión gástrica de arándano en polvo y en cápsula promovió una mayor bioaccesibilidad de fenoles (42% y 40%), flavonoides (52% y 33%) y antocianinas (45% y 40%) comparado con digestos de arándano fresco. Posterior a la digestión intestinal, la bioaccesibilidad de fenoles (63%) y flavonoides (67%) fue mayor en la cápsula de arándano comparada con su contraparte arándano en polvo. Las condiciones de digestión intestinal afectaron negativamente la bioaccesibilidad de las antocianinas independientemente del tipo de muestra evaluada. Conclusión. Las condiciones de digestión gástrica promueven una mayor estabilidad de los compuestos fenólicos en arándano en polvo y en cápsula lo que pudiera ser relevante para el mantenimiento de un ambiente antioxidante a este nivel. Las condiciones de digestión intestinal afectaron de manera particular a los compuestos fenólicos de arándano fresco y polvo, pero no a la cápsula, lo que puede sugerir que el encapsulamiento protegió de las condiciones alcalinas a los fenoles presentes. Se sugieren estudios posteriores sobre absorción in vitro de los componentes remanentes en intestino y sus posibles efectos sobre biomarcadores de estrés oxidativo en modelos in viv

Synergetic behavior of TiO2-supported Pd(z)Pt(1-z) catalysts in the green synthesis of methyl formate

Methyl formate (MF) is a valuable platform molecule, the industrial production of which is far from being green. In this contribution, TiO2-supported Pd(z)Pt(1−z) catalysts were found to be effective in the green synthesis of methyl formate (MF)—at T=323 K and ambient pressure—through methanol (MeOH) oxidation. Two series of catalysts with similar bulk Pd/(Pd+Pt) molar ratios, z, were prepared; one by a water-in-oil microemulsion (MicE) method and the other by an incipient wetness impregnation (IWI). The MicE method led to more efficient catalysts owing to a weak influence of z on particle size distributions and nanoparticles composition. Pd(z)Pt(1−z)-MicE catalysts exhibited strong synergistic effects for MF production but weak synergistic effects for MeOH conversion. The catalytic performance of Pd(z)Pt(1−z)-MicE was superior to that of Pd(z)Pt(1−z)-IWI catalysts despite the latter displaying synergetic effects during the reaction. The catalytic behavior of TiO2-supported Pd(z)Pt(1−z) catalysts was explained from correlations between XRD, TEM, and X-ray photoelectron spectroscopy characterizations