Normalizing untargeted periconceptional urinary metabolomics data : a comparison of approaches

Metabolomics studies of the early-life exposome often use maternal urine specimens to investigate critical developmental windows, including the periconceptional period and early pregnancy. During these windows changes in kidney function can impact urine concentration. This makes accounting for differential urinary dilution across samples challenging. Because there is no consensus on the ideal normalization approach for urinary metabolomics data, this study’s objective was to determine the optimal post-analytical normalization approach for untargeted metabolomics analysis from a periconceptional cohort of 45 women. Urine samples consisted of 90 paired pre- and post-implantation samples. After untargeted mass spectrometry-based metabolomics analysis, we systematically compared the performance of three common approaches to adjust for urinary dilution—creatinine adjustment, specific gravity adjustment, and probabilistic quotient normalization (PQN)—using unsupervised principal components analysis, relative standard deviation (RSD) of pooled quality control samples, and orthogonal partial least-squares discriminant analysis (OPLS-DA). Results showed that creatinine adjustment is not a reliable approach to normalize urinary periconceptional metabolomics data. Either specific gravity or PQN are more reliable methods to adjust for urinary concentration, with tighter quality control sample clustering, lower RSD, and better OPLS-DA performance compared to creatinine adjustment. These findings have implications for metabolomics analyses on urine samples taken around the time of conception and in contexts where kidney function may be altered

Análise do teor e da qualidade dos lipídeos presentes em sementes de oleaginosas por rmn de baixo campo

To choose among the variety of oleaginous plants for biodiesel production, the oil content of several matrices was determined through different low-field ¹H nuclear magnetic resonance (NMR) experiments with varied pulse sequences, namely single-pulse, spin-echo, CPMG, and CWFP. The experiments that involved the first three sequences showed high correlation with each other and with the solvent extraction method. The quality of the vegetable oils was also evaluated on the basis of the existing correlation between the T2 values of the oils and their properties, such as viscosity, iodine index, and cetane index. These analyses were performed using HCA and PCA chemometric tools. The results were sufficiently significant to allow separation of the oleaginous matrices according to their quality. Thus, the low-field ¹H NMR technique was confirmed as an important tool to aid in the selection of oleaginous matrices for biodiesel production

Genome of the Avirulent Human-Infective Trypanosome—Trypanosoma rangeli

Background: Trypanosoma rangeli is a hemoflagellate protozoan parasite infecting humans and other wild and domestic mammals across Central and South America. It does not cause human disease, but it can be mistaken for the etiologic agent of Chagas disease, Trypanosoma cruzi. We have sequenced the T. rangeli genome to provide new tools for elucidating the distinct and intriguing biology of this species and the key pathways related to interaction with its arthropod and mammalian hosts.  Methodology/Principal Findings: The T. rangeli haploid genome is ,24 Mb in length, and is the smallest and least repetitive trypanosomatid genome sequenced thus far. This parasite genome has shorter subtelomeric sequences compared to those of T. cruzi and T. brucei; displays intraspecific karyotype variability and lacks minichromosomes. Of the predicted 7,613 protein coding sequences, functional annotations could be determined for 2,415, while 5,043 are hypothetical proteins, some with evidence of protein expression. 7,101 genes (93%) are shared with other trypanosomatids that infect humans. An ortholog of the dcl2 gene involved in the T. brucei RNAi pathway was found in T. rangeli, but the RNAi machinery is non-functional since the other genes in this pathway are pseudogenized. T. rangeli is highly susceptible to oxidative stress, a phenotype that may be explained by a smaller number of anti-oxidant defense enzymes and heatshock proteins.  Conclusions/Significance: Phylogenetic comparison of nuclear and mitochondrial genes indicates that T. rangeli and T. cruzi are equidistant from T. brucei. In addition to revealing new aspects of trypanosome co-evolution within the vertebrate and invertebrate hosts, comparative genomic analysis with pathogenic trypanosomatids provides valuable new information that can be further explored with the aim of developing better diagnostic tools and/or therapeutic targets

Microbiological quality in the flour and starch cassava processing in traditional and model unit

O objetivo deste trabalho foi avaliar a qualidade microbiológica de farinha e fécula durante as diferentes etapas do processamento de mandioca, em unidades tradicionais e em uma unidade modelo. Foram determinados índices de coliformes totais e termotolerantes, Bacillus cereus, Salmonela spp., bactérias e fungos nas farinhas e féculas. Não foram observadas presenças de B. cereus e Salmonella spp. na farinha e fécula de mandioca produzidas nas unidades estudadas. A incidência microbiana diminui com o avanço da etapa do processamento para obtenção de farinha e foi menor na unidade modelo. Após o processo de torra, a carga microbiana estava de acordo com os valores preconizados pela legislação brasileira, concluindo-se que essa etapa pode ser considerada como crítica na obtenção de farinha. Na obtenção de fécula, a carga microbiana nas unidades tradicionais são maiores que na modelo, e o aumento do número de extrações promove o aumento da incidência de microrganismos, sendo recomendadas apenas quatro extrações. ______________________________________________________________________________________ ABSTRACT: The objective of this research was to evaluate microbiological contamination in the flour and starch during cassava processing in traditional and model units. The total and fecal coliforms indexes, Bacillus cereus, Salmonella, bacteria, yeast and fungi were determined. Bacillus cereus and Salmonella were not detected in any sample. The incidence of microorganisms decreased along the processing to obtain cassava flour, and is lower in model unit. After the roasting process, the microbial load was below the values established by the Brazilian legislation, and can be regarded as a critical step in obtaining cassava flour. Concerning starch production, the microbial load in the traditional units was higher than in the model units, and the increase of the extraction steps has promoted the growth of microorganisms. It’s recommended the used of only 4 extractions

The Helicobacter pylori Genome Project : insights into H. pylori population structure from analysis of a worldwide collection of complete genomes

Helicobacter pylori, a dominant member of the gastric microbiota, shares co-evolutionary history with humans. This has led to the development of genetically distinct H. pylori subpopulations associated with the geographic origin of the host and with differential gastric disease risk. Here, we provide insights into H. pylori population structure as a part of the Helicobacter pylori Genome Project (HpGP), a multi-disciplinary initiative aimed at elucidating H. pylori pathogenesis and identifying new therapeutic targets. We collected 1011 well-characterized clinical strains from 50 countries and generated high-quality genome sequences. We analysed core genome diversity and population structure of the HpGP dataset and 255 worldwide reference genomes to outline the ancestral contribution to Eurasian, African, and American populations. We found evidence of substantial contribution of population hpNorthAsia and subpopulation hspUral in Northern European H. pylori. The genomes of H. pylori isolated from northern and southern Indigenous Americans differed in that bacteria isolated in northern Indigenous communities were more similar to North Asian H. pylori while the southern had higher relatedness to hpEastAsia. Notably, we also found a highly clonal yet geographically dispersed North American subpopulation, which is negative for the cag pathogenicity island, and present in 7% of sequenced US genomes. We expect the HpGP dataset and the corresponding strains to become a major asset for H. pylori genomics