Illumina paired-end reads are used to analyse microbial communities by targeting amplicons of the 16S rRNA gene. Publicly available tools are needed to assemble overlapping paired-end reads while ...correcting mismatches and uncalled bases; many errors could be corrected to obtain higher sequence yields using quality information.
PANDAseq assembles paired-end reads rapidly and with the correction of most errors. Uncertain error corrections come from reads with many low-quality bases identified by upstream processing. Benchmarks were done using real error masks on simulated data, a pure source template, and a pooled template of genomic DNA from known organisms. PANDAseq assembled reads more rapidly and with reduced error incorporation compared to alternative methods.
PANDAseq rapidly assembles sequences and scales to billions of paired-end reads. Assembly of control libraries showed a 4-50% increase in the number of assembled sequences over naïve assembly with negligible loss of "good" sequence.
Background and Aims
Governo all'uso toscano (GUT) is a traditional winemaking practice where withered grapes are added to a freshly fermented wine. This results in a second alcoholic fermentation and ...a distinctive wine, in which there is renewed interest. Grape withering is problematic for winemakers, however, both in terms of cost and risks. It is therefore important to determine the minimum amount of withered grapes needed to typify the wine in order to minimise risks and costs.
Methods and Results
During the trials, Sangiovese grapes were withered for 2 months in a dedicated room, a ‘fruttaio’, with a resulting mass loss of about 40%. Afterwards, withered grapes (5–20% berry mass/wine mass) were added to a Control wine to reproduce the GUT procedure. The GUT technique significantly changed the chemical profile of the wines. Ethanol, colour intensity and hue increased, while acidity decreased. Malolactic fermentation occurred simultaneously with the second alcoholic fermentation in all GUT wines, but not in the Control wines. The GUT practice significantly changed the volatile profile, including the concentration of several primary grape compounds, such as aromatic alcohols, C6 compounds and terpenoids, and of several fermentation compounds.
Conclusion
Under the experimental conditions, the optimal amount of withered grapes added to the base wine was 5%.
Significance of the Study
The study described the oenological effects of GUT and the optimisation of the amount of withered grapes required to make a wine with this characteristic winemaking practice clearly recognisable.
An original computer program was set up to predict and control olive paste malaxation in the range of temperature between 22 and 37 °C under exposure to air. The program consisted of four sections to ...solve the our previous literature time-temperature kinetics. It was able to predict both the apparent oil extraction yield and the relative variation of 3,4 DHPEA-EDA and sum of verbascoside diastereoisomers contents in steady and unsteady-conditions; it was also able to determine optimal malaxation time-temperature conditions to maximize the oil extraction yield and minimize the oxidative degradation of phenolic compounds. Simulation examples were carried out to test prediction potentiality. The malaxation treatments at low temperatures appeared preferable, since they seemed to be unaffected by time-temperature profiles under unsteady-state conditions. However, it seemed more difficult to identify optimal time-temperature conditions at a low temperature than at a high temperature in some operating states.
•An original computer program was written to optimize olive paste malaxation under exposure to air.•Simulation examples were carried out to predict oil yield and damage to phenols.•Malaxation at low temperature and intermediate time appeared preferable.•Some operating states appeared critical to identify optimal conditions.
Ammonia-oxidizing archaea (AOA) outnumber ammonia-oxidizing bacteria (AOB) in many terrestrial and aquatic environments. Although nitrification is the primary function of aquarium biofilters, very ...few studies have investigated the microorganisms responsible for this process in aquaria. This study used quantitative real-time PCR (qPCR) to quantify the ammonia monooxygenase (amoA) and 16S rRNA genes of Bacteria and Thaumarchaeota in freshwater aquarium biofilters, in addition to assessing the diversity of AOA amoA genes by denaturing gradient gel electrophoresis (DGGE) and clone libraries. AOA were numerically dominant in 23 of 27 freshwater biofilters, and in 12 of these biofilters AOA contributed all detectable amoA genes. Eight saltwater aquaria and two commercial aquarium nitrifier supplements were included for comparison. Both thaumarchaeal and bacterial amoA genes were detected in all saltwater samples, with AOA genes outnumbering AOB genes in five of eight biofilters. Bacterial amoA genes were abundant in both supplements, but thaumarchaeal amoA and 16S rRNA genes could not be detected. For freshwater aquaria, the proportion of amoA genes from AOA relative to AOB was inversely correlated with ammonium concentration. DGGE of AOA amoA genes revealed variable diversity across samples, with nonmetric multidimensional scaling (NMDS) indicating separation of freshwater and saltwater fingerprints. Composite clone libraries of AOA amoA genes revealed distinct freshwater and saltwater clusters, as well as mixed clusters containing both freshwater and saltwater amoA gene sequences. These results reveal insight into commonplace residential biofilters and suggest that aquarium biofilters may represent valuable biofilm microcosms for future studies of AOA ecology.
An original kinetic study of both oil coalescence phenomena and potential extra virgin olive oil extraction yield (i.e. apparent Extractability Index) was carried out at different malaxation ...time-temperature conditions using Abencor lab equipment to process olives (Frantoio cv) of a known degree of ripeness.
The apparent Extractability Index was modelled at every malaxation temperature by pseudo first-order kinetics, where the yield rate constant was temperature dependent following the Arrhenius equation (k0 = 7.50 107 min−1; Ea = 54512 J/mol). Oil droplet coalescence, which was expressed as a relative variation in the percentage of oil droplets with a diameter of >30 μm, proved to be an time-dependent phenomenon only; the pseudo zero-order kinetics modelling was statistically significant, where the coalescence rate constant was equal to 0.033 min−1. The above kinetics were applied in order to propose a synoptic chart to predict the potential effect of malaxation in isothermal conditions on EVOO extraction yield.
•An original experimental approach was used to study olive paste malaxation.•A time-temperature kinetic study was applied to predict malaxation phenomena.•An apparent Extractability Index and oil droplet coalescence phenomena were considered.•A synoptic chart was proposed to predict the potential effect of malaxation on yield.•Phenomena that condition oil extraction yield changed as a function of temperature.
Olive oil extraction conditions are usually a compromise between quality and yield. Enhancing yield decreases quality, and vice versa. We aim to understand if a change in temperature between ...malaxation and centrifugation can result in a better compromise. Thus, malaxation is carried out at 20°C and oil is extracted at 20°C, 27°C, and 35°C. The results show that a moderate increase in temperature between malaxation and centrifugation (i.e. from 20°C to 27°C) increases both yield and quality of the oil. Conversely, an excessive temperature increase (i.e. from 20°C to 35°C) leads to the production of rancid-related compounds.
Abstract
Soil pH is an important determinant of microbial community composition and diversity, yet few studies have characterized the specific effects of pH on individual bacterial taxa within ...bacterial communities, both abundant and rare. We collected composite soil samples over 2 years from an experimentally maintained pH gradient ranging from 4.5 to 7.5 from the Craibstone Experimental Farm (Craibstone, Scotland). Extracted nucleic acids were characterized by bacterial and group-specific denaturing gradient gel electrophoresis and next-generation sequencing of bacterial 16S rRNA genes. Both methods demonstrated comparable and reproducible shifts within higher taxonomic bacterial groups (e.g. Acidobacteria,Alphaproteobacteria,Verrucomicrobia, and Gammaproteobacteria) across the pH gradient. In addition, we used non-negative matrix factorization (NMF) for the first time on 16S rRNA gene data to identify positively interacting (i.e. co-occurring) operational taxonomic unit (OTU) clusters (i.e. ‘components’), with abundances that correlated strongly with pH, and sample year to a lesser extent. All OTUs identified by NMF were visualized within principle coordinate analyses of unifrac distances and subjected to taxonomic network analysis (SSUnique), which plotted OTU abundance and similarity against established taxonomies. Most pH-dependent OTUs identified here would not have been identified by previous methodologies for microbial community profiling and were unrelated to known lineages.
It is extremely common to need to select a subset of reads from a BAM file based on their specific properties. Typically, a user unpacks the BAM file to a text stream using SAMtools, parses and ...filters the lines using AWK, then repacks them using SAMtools. This process is tedious and error-prone. In particular, when working with many columns of data, mix-ups are common and the bit field containing the flags is unintuitive. There are several libraries for reading BAM files, such as Bio-SamTools for Perl and pysam for Python. Both allow access to the BAM's read information and can filter reads, but require substantial boilerplate code; this is high overhead for mostly ad hoc filtering.
We have created a query language that gathers reads using a collection of predicates and common logical connectives. Queries run faster than equivalents and can be compiled to native code for embedding in larger programs.
BAMQL provides a user-friendly, powerful and performant way to extract subsets of BAM files for ad hoc analyses or integration into applications. The query language provides a collection of predicates beyond those in SAMtools, and more flexible connectives.
Prostate tumours are highly variable in their response to therapies, but clinically available prognostic factors can explain only a fraction of this heterogeneity. Here we analysed 200 whole-genome ...sequences and 277 additional whole-exome sequences from localized, non-indolent prostate tumours with similar clinical risk profiles, and carried out RNA and methylation analyses in a subset. These tumours had a paucity of clinically actionable single nucleotide variants, unlike those seen in metastatic disease. Rather, a significant proportion of tumours harboured recurrent non-coding aberrations, large-scale genomic rearrangements, and alterations in which an inversion repressed transcription within its boundaries. Local hypermutation events were frequent, and correlated with specific genomic profiles. Numerous molecular aberrations were prognostic for disease recurrence, including several DNA methylation events, and a signature comprised of these aberrations outperformed well-described prognostic biomarkers. We suggest that intensified treatment of genomically aggressive localized prostate cancer may improve cure rates.
The emission of carbon dioxide (CO₂) from olive paste during malaxation was investigated in a lab experiment using a hermetically sealed malaxation chamber. A rapid increase in the concentration of ...CO₂ during malaxation was observed, with an average increase of 32 ml/(l min) for the initial 5 min. Then, the emission progressively decreased to a mean rate of 1.1 ml/(l min). This was probably the result of an initial acceleration in respiration followed by the gradual onset of fermentation processes as ambient oxygen was depleted. After malaxation, small amounts of cellular fermentation products (e.g. ethanol and lactic acid) were detected in the wastewater. In order to examine this phenomenon of the inhibition of oxidation due to evolved CO₂, malaxation experiments were conducted in both a sealed and an open-air mixing apparatus. The differences in chlorophyll concentration of the resulting oils were then measured. Large amounts of chlorophyll, about twice as much, were found in the oil produced under sealed conditions. This increase in the concentration of chlorophyll resulted from the limited oxidation of the sample by atmospheric oxygen due to the protection of the evolved CO₂.
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