Project description:Polyhydroxyalkanoates (PHAs) form a highly promising class of bioplastics for the transition from fossil fuel-based plastics to bio-renewable and biodegradable plastics. Mixed microbial consortia (MMC) are known to be able to produce PHAs from organic waste streams. Knowledge of key-microbes and their characteristics in PHA-producing consortia is necessary for further process optimization and direction towards synthesis of specific types of PHAs. In this study, a PHA-producing mixed microbial consortium (MMC) from an industrial pilot plant was characterized and further enriched on acetate in a laboratory-scale selector with a working volume of 5 L, and 16S-rDNA microbiological population analysis of both the industrial pilot plant and the 5 L selector revealed that the most dominant species within the population is Thauera aminoaromatica MZ1T, a Gram-negative beta-proteobacterium belonging to the order of the Rhodocyclales. The relative abundance of this Thauera species increased from 24 to 40% after two months of enrichment in the selector-system, indicating a competitive advantage, possibly due to the storage of a reserve material such as PHA. First experiments with T. aminoaromatica MZ1T showed multiple intracellular granules when grown in pure culture on a growth medium with a C:N ratio of 10:1 and acetate as a carbon source. Nuclear magnetic resonance (NMR) analyses upon extraction of PHA from the pure culture confirmed polyhydroxybutyrate production by T. aminoaromatica MZ1T.
Project description:Differences in the clinical pathology of mammalian prion diseases reflect distinct heritable conformations of aggregated PrP proteins, called prion strains. Here, using the yeast [PSI(+) ] prion, we examine the de novo establishment of prion strains (called variants in yeast). The [PSI(+) ] prion protein, Sup35, is efficiently induced to take on numerous prion variant conformations following transient overexpression of Sup35 in the presence of another prion, e.g. [PIN(+) ]. One hypothesis is that the first [PSI(+) ] prion seed to arise in a cell causes propagation of only that seed's variant, but that different variants could be initiated in different cells. However, we now show that even within a single cell, Sup35 retains the potential to fold into more than one variant type. When individual cells segregating different [PSI(+) ] variants were followed in pedigrees, establishment of a single variant phenotype generally occurred in daughters, granddaughters or great-granddaughters - but in 5% of the pedigrees cells continued to segregate multiple variants indefinitely. The data are consistent with the idea that many newly formed prions go through a maturation phase before they reach a single specific variant conformation. These findings may be relevant to mammalian PrP prion strain establishment and adaptation.
Project description:The biodiversity and evolution of fungal communities were monitored over a period of 3 vintages in a new winery. Samples were collected before grape receipt and 3 months after fermentation from 3 different wine related environments (WRE): floor, walls and equipment and analyzed using Illumina Mi-Seq. Genera of mold and filamentous fungi (294), non-enological (10) and wine-associated yeasts (25) were detected on all WREs before the arrival of the first harvest. Among them, genera like Alternaria and Aureobasidium persisted during two vintages. Therefore, these genera are not specific to winery environment and appear to be adapted to natural or anthropic environments due to their ubiquitous character. Some genera like Candida were also detected before the first harvest but only on one WREs, whereas, on the other WREs they were found after the harvest. The ubiquitous character and phenotypic traits of these fungal genera can explain their dynamics. After the first harvest and during 3 vintages the initial consortium was enriched by oenological genera like Starmerella introduced either by harvest or by potential transfers between the different WREs. However, these establishing genera, including Saccharomyces, do not appear to persist due to their low adaptation to the stressful conditions of winery environment.
Project description:Bioremediation is crucial for recuperating polluted water and soil. By expanding the surface area of substrates, biosurfactants play a vital role in bioremediation. Biosurfactant-producing microbes release certain biosurfactant compounds, which are promoted for oil spill remediation. In the present investigation, a biosurfactant-producing bacterium Bacillus tequilensis was isolated from Chilika Lake, Odisha, India (latitude and longitude: 19.8450 N 85.4788 E). Whole-Genome Sequencing (WGS) of Bacillus tequilensis was carried out using Illumina NextSeq 500. The size of the whole genome of Bacillus tequilensis was 4.47 MB consisting of 4,478,749 base pairs forming a circular chromosome with 528 scaffolds, 4492 protein-encoding genes (ORFs), 81 tRNA genes, and 114 ribosomal RNA transcription units. The total raw reads were 4209415, and the processed reads were 4058238 with 4492 genes. The whole genome obtained from the present investigation was used for genome annotation, variant calling, variant annotation, and comparative genome analysis with other existing Bacillus species. In this study, a pathway was constructed which describes the biosurfactant metabolism of Bacillus tequilensis. The study identified that genes such as SrfAD, SrfAC, SrfAA and SrfAB are involved in biosurfactant synthesis. The sequence of the genes SrfAD, SrfAC, SrfAA, SrfAB was deposited in GenBank database with accession MUG02427.1, MUG02428.1, MUG02429.1, MUG03515.1 respectively. The whole genome sequence was submitted to GenBank with an accession RMVO00000000 and the raw fastq reads were submitted to SRA, NCBI repository with an accession: SRX5023292.
Project description:Pooled data analysis in the field of maternal and child nutrition rarely incorporates data from low- and middle-income countries and existing studies lack a description of the methods used to harmonize the data and to assess heterogeneity. We describe the creation of the Brazilian Maternal and Child Nutrition Consortium dataset, from multiple pooled longitudinal studies, having gestational weight gain (GWG) as an example. Investigators of the eligible studies published from 1990 to 2018 were invited to participate. We conducted consistency analysis, identified outliers, and assessed heterogeneity for GWG. Outliers identification considered the longitudinal nature of the data. Heterogeneity was performed adjusting multilevel models. We identified 68 studies and invited 59 for this initiative. Data from 29 studies were received, 21 were retained for analysis, resulting in a final sample of 17,344 women with 72,616 weight measurements. Fewer than 1% of all weight measurements were flagged as outliers. Women with pre-pregnancy obesity had lower values for GWG throughout pregnancy. GWG, birth length and weight were similar across the studies and remarkably similar to a Brazilian nationwide study. Pooled data analyses can increase the potential of addressing important questions regarding maternal and child health, especially in countries where research investment is limited.
Project description:Streptomyces bingchenggensis is a soil-dwelling bacterium producing the commercially important anthelmintic macrolide milbemycins. Besides milbemycins, the insecticidal polyether antibiotic nanchangmycin and some other antibiotics have also been isolated from this strain. Here we report the complete genome sequence of S. bingchenggensis. The availability of the genome sequence of S. bingchenggensis should enable us to understand the biosynthesis of these structurally intricate antibiotics better and facilitate rational improvement of this strain to increase their titers.
Project description:Ginsenosides are the primary bioactive components of ginseng, which is a popular medicinal plant that exhibits diverse pharmacological activities. Protopanaxadiol, protopanaxatriol and oleanolic acid are three basic aglycons of ginsenosides. Producing aglycons of ginsenosides in Saccharomyces cerevisiae was realized in this work and provides an alternative route compared to traditional extraction methods. Synthetic pathways of these three aglycons were constructed in S. cerevisiae by introducing β-amyrin synthase, oleanolic acid synthase, dammarenediol-II synthase, protopanaxadiol synthase, protopanaxatriol synthase and NADPH-cytochrome P450 reductase from different plants. In addition, a truncated 3-hydroxy-3-methylglutaryl-CoA reductase, squalene synthase and 2,3-oxidosqualene synthase genes were overexpressed to increase the precursor supply for improving aglycon production. Strain GY-1 was obtained, which produced 17.2 mg/L protopanaxadiol, 15.9 mg/L protopanaxatriol and 21.4 mg/L oleanolic acid. The yeast strains engineered in this work can serve as the basis for creating an alternative way for producing ginsenosides in place of extractions from plant sources.
Project description:Phototrophic consortia represent valuable model systems for the study of signal transduction and coevolution between different bacteria. The phototrophic consortium "Chlorochromatium aggregatum" consists of a colorless central rod-shaped bacterium surrounded by about 20 green-pigmented epibionts. Although the epibiont was identified as a member of the green sulfur bacteria, and recently isolated and characterized in pure culture, the central colorless bacterium has been identified as a member of the beta-Proteobacteria but so far could not be characterized further. In the present study, "C. aggregatum" was enriched chemotactically, and the 16S rRNA gene sequence of the central bacterium was elucidated. Based on the sequence information, fluorescence in situ hybridization probes targeting four different regions of the 16S rRNA were designed and shown to hybridize exclusively to cells of the central bacterium. Phylogenetic analyses of the 1,437-bp-long sequence revealed that the central bacterium of "C. aggregatum" represents a so far isolated phylogenetic lineage related to Rhodoferax spp., Polaromonas vacuolata, and Variovorax paradoxus within the family Comamonadaceae. The majority of relatives of this lineage are not yet cultured and were found in low-temperature aquatic environments or aquatic environments containing xenobiotica or hydrocarbons. In CsCl-bisbenzimidazole equilibrium density gradients, genomic DNA of the central bacterium of "Chlorochromatium aggregatum" formed a distinct band which could be detected by quantitative PCR using specific primers. Using this method, the G+C content of the central bacterium was determined to be 55.6 mol%.