Top PDF Analysis of Grape Berry Epiphytic Microbiomes via QIIME

Analysis of Grape Berry Epiphytic Microbiomes via QIIME

Analysis of Grape Berry Epiphytic Microbiomes via QIIME

microbiome, by examining the epiphytic microbiome of developing and sour rot infected grapes in New York and Tasmania. Sour rot is characterized by a distinct vinegar smell that is caused by the combination of Drosophila spp., fermentative yeasts, the acetic acid producing bacteria Acetobacter and Gluconobacter. Total DNA was extracted from rinsate berry samples, and the bacterial 16S ribosomal RNA (rRNA) and fungal internal transcribed spacer (ITS) regions were amplified for Illumina sequencing. The tool Quantitative Insights into Microbial Ecology (Qiime) was used to quality filter the sequences and identify the operational taxonomic units (OTUs) present in each sample. The taxonomies of these OTUs were assigned using the Greengenes and Unite databases. Statistical analysis was done in Statistical Analysis of
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Amplicon Sequence Variant-Based Oral Microbiome Analysis Using QIIME 2

Amplicon Sequence Variant-Based Oral Microbiome Analysis Using QIIME 2

investigated the optimal parameters for sequence denoising, using DADA2, and found the trimming of the first 20 nucleotides from 5′-end of both paired reads avoided excessive sequence loss during chimera removal. Truncating reads at positions 240–245 allowed the removal of low-quality sequences while maintaining sufficient length to merge matching paired ends. Taxonomic assignment, using the naïve Bayes classifier trained with the V3-V4 region of reference 16S rRNA sequences in the extended human oral microbiome database (eHOMD), resulted in bacterial compositions similar to those of OTU-based analyses. Contrary to OTU-based clustering, ASV-based analysis showed taxonomic abundance at the genus or species level to not differ significantly in tongue microbiomes, regardless of brushing. QIIME 2 can, therefore, be a standard pipeline for ASV-based analysis of oral microbiomes.
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Transmission of viruses via our microbiomes

Transmission of viruses via our microbiomes

Analysis of shared sequence similarities present in each virome was performed by creating custom BLAST databases for each virome, comparing each database with all other viromes using BLASTN analysis (E-value <10 − 10 ), and these compiled data used to calculate Sorensen distances using Ion Assist (http://www.thepri- delaboratory.org/). Sorensen distances are measured on a scale of 0 to 1, where 0 represents no sharing and 1 would represent identical viromes. These distances were determined for all pairs of housemates and compared with distances between subjects from different house- holds. Statistical significance was determined by the Mann–Whitney U test using MaxStat Pro (http:// www.maxstat.de/). Bray Curtis distances (equivalent to 1 minus Sorensen values) also were determined and used as input for principal coordinates analysis using QIIME [23]. We determined persistence of viruses by construct- ing global assemblies from all contigs within a subject over time, and using the contribution of each time point to the assemblies to decipher the time points that con- tributed to the construction of each virus, as has previ- ously been described [12]. We utilized this technique to decipher those contigs that were unique to a subject within a household and those shared between house- mates. We also created global assemblies from both sub- jects within a household to determine the presence/ absence of viruses at each subject and time point and identify viruses that may have been transmitted between housemates. We defined any virus that was present in one subject, absent in their housemate, and later appeared in at least two time points in the housemate as a putative transmission. Statistical significance was determined by comparisons between groups by the Mann–Whitney U test using MaxStat Pro (http://www.maxstat.de/).
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Analysis of the bacterial epiphytic microbiota of oak leaf lettuce with 16S ribosomal RNA gene analysis

Analysis of the bacterial epiphytic microbiota of oak leaf lettuce with 16S ribosomal RNA gene analysis

Forward and reverse reads were joined using fastq-join from the ea-utils software package (Aronesty, 2011). The sequences were then quality-filtered to exclude sequences with ambiguous bases (N) and sequences containing base calls with less than 99% confidence (Phred score of < 20). The QIIME bioinformatics software suite (version 1.5.0) was used to subsample the resultant sequences (82,311, 99,654 and 95,216 sequences, respectively), to cluster those sequences into 97% identity operational taxonomic units (OTU) with UCLUST (Aronesty, 2011), to taxonomically classify each OTU with RDP classifier (Edgar 2010) at 97% sequence homology placement into the GreenGenes 12_10 database (DeSantis et al., 2006). All QIIME scripts were run using default parameters unless otherwise stated. The sequences were deposited in the NCBI sequence read archive (SRA) under the numbers SRR1523744 (sample 1), SRR1265099 (sample 2) and SRR1265426 (sample 3).
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Grape seed-derived procyanidins alleviate gout pain via NLRP3 inflammasome suppression

Grape seed-derived procyanidins alleviate gout pain via NLRP3 inflammasome suppression

Procyanidins inhibited the phosphorylation of NR1, p38, and ERK and the activation of c-fos in the spinal cord Studies have shown that activated macrophages can re- lease proinflammatory cytokines, such as IL-1β and TNF-α, which lead to the phosphorylation of MAPKs and NMDA, in turn resulting in central sensitization and hyperalgesia [27]. We investigated the effects of pro- cyanidins on MSU-induced central sensitization in vivo. Western blot analysis revealed that phosphorylated NR1 was upregulated in the spinal cords of mice treated with MSU crystals in the ankles (Fig. 5a). However, procyani- dins suppressed this increase in NR1 phosphorylation.
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A STUDY ON EPIPHYTIC LICHENS FROM PRUNUS PERSICA

A STUDY ON EPIPHYTIC LICHENS FROM PRUNUS PERSICA

TLC analysis of the acetone extracts of the lichens gave a picture about the presence of several compounds in lichens with reference to standards (Fig. 2 and Table 6). It was observed that majority of the lichens have atranorin and salazinic acids. R. conduplicans was identical with the presence of sekikaic acid. Usnea sp. reported the presence of stictic and norstictic acid along its characteristic usnic acid. It was interesting to note that no distinctive chromatogram developed for R. sinensis and H. curatellae. L. cinesia had only atranorin while L. caesiorubella also reported protocetraric acid. Divaricatic acid complex along with atranorin was found in C. texana.
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Production of Tea from Turkey Berry

Production of Tea from Turkey Berry

Tea is consumed for different reasons and by different people around the world. Most people are increasingly becoming aware of the benefits of con- suming herbal beverages, hence the need for production of tea from health and medicinal plants. This work was aimed to produce tea from Turkey berry and access the acceptance of Turkey berry tea in when compared with other tea product on the market. Sensory evaluation was done on a five-point he- donic scale. The samples were: Sample A (100% Lipton), Sample B (100% Turkey berry tea), Sample C (Lipton with milk and sugar) and Sample D (Turkey berry tea with milk and sugar). The appearance, colour, taste and aroma of the Turkey berry tea were liked by the respondents. However, a few of them did not like the colour and aroma of the Turkey berry tea only (with- out milk).
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Microbiomes, Community Ecology, and the Comparative Method

Microbiomes, Community Ecology, and the Comparative Method

In my laboratory. We are investigating how phylogenetic comparative methods perform using 16S data and assessing model fit across neutral models, models that incorporate selection, and models that contain no phylogenetic signal. We are coding the microbiome in terms of composition and diversity, under the null hypothesis that the microbiome contains phylogenetic signal. We are gathering data on the functional capabilities of microbiomes and will code them for phylogenetic comparative method analysis to compare to the models that fit the taxonomic (16S) data. Importantly, our analyses benefit greatly from the wealth of ornithological research on bird life histories, physiology, ecology, and behaviors. Avian microbiome science can also leverage the extensive avian genomics literature to both construct and test hypotheses about the relationships between birds and microbes. One exciting example of this is the Open- Wings Project (http://www.openwings.org/)—an ongoing collaboration among 12 ma- jor ornithological collections that will gather genomic data (ultraconserved elements [UCEs]) from each of the 10,560 named bird species.
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The sensory characteristics of berry flavoured kefir

The sensory characteristics of berry flavoured kefir

The titratable acidity and pH values of the samples were determined as described by KURT et al. (1993). The amount of alcohol was determined according to the reactive index as stated by Official Methods of Analysis (2003), whereas CO 2 was evaluated by the titrimetric method (ANONYMOUS 1988). Flavoured kefir samples were served for judging in small cups at 4 ± 1°C from the refrigerator. The sensory char- acteristics of the flavoured kefir drink were judged by 10 panelists after preliminary training sessions to instruct the panel, according to a modified method described by MUIR et al. (1999), using the sensory rating scale of 1 to 5 (unacceptable/excellent). The judges were selected in the dependence on their availability and willingness to participate in the study. The experimental vocabulary was similar to that developed for profiling natural fermented milks (IRIGOYEN et al. 2005), and was modified for the berry-flavoured kefir samples. The list of attributes comprised three terms for odour (fruity, acid/sour, and creamy/milky), five flavour characteristics (in- tensity, fruity, sweet, acid/sour, and creamy/milky; flavour perceived in the mouth ranging from weak to strong, not added berry-like to added berry flavour like, not sweet to sweet, not sour/acid to sour/acid, and not creamy/milky to creamy milky), and four attributes encompassing texture and mouth-feel (viscosity, gummy/sticky, serum separation, and effervescence), and overall acceptability.
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The Reverend Christopher D. Berry

The Reverend Christopher D. Berry

 Developed and implemented the Western Men Against Violence Program for the Prevention and Wellness Services Lifestyle Advisor Program for Western Washington University..  Nineteen y[r]

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Berry phase quantum thermometer

Berry phase quantum thermometer

This model is a type of Unruh–DeWitt detector [6–10] that has been previously studied in other contexts [4, 11, 12] and whose effectiveness and suitability has been deeply analyzed in [13–15]. It generally describes a multi-level quantum emitter (typically an atom) interacting with an infinite number of harmonic oscillators that may correspond to a scalar field. This model describes any harmonic detector coupled to the field (e.g. the electronic or vibrational spectrum of a many-level atom is very well approximated by harmonic oscillators) and is strongly related to the standard two-level approaches typically used to model atoms coupled to a scalar or EM field. In fact, there is a well-known mapping between this model and the standard Jaynes–Cummings model via the Holstein–Primakoff transformations [16]; the equivalence of the two models for the relevant regimes can be seen in [17, 18].
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WILLIAM L. BERRY. Education:

WILLIAM L. BERRY. Education:

Bill Berry is Professor of Management at the McColl School of Business at Queens University of Charlotte. He received his B.S. degree in Geophysics from Virginia Tech, served in the U.S. Army and worked as a development engineer for the Kendall Corporation. In pursuit of an academic career, he earned his doctorate from the Harvard Business School. While there he participated in the International Teachers Program in Leysin, Switzerland.

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Stuart C Berry, Ed.D.

Stuart C Berry, Ed.D.

and  knowledge  conversion:  Controversy  and  advancement  in   organizational  knowledge  creation  theory.  Design-­‐based  research  and  [r]

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Sewage Reflects the Microbiomes of Human Populations

Sewage Reflects the Microbiomes of Human Populations

Previous comparisons of individual gut microbiomes demon- strate high community composition variability among individuals and that no single core set of bacterial species dominates all hu- man guts (7, 26). By sampling sewage, we find that U.S. popula- tions have a much less variable fecal bacterial community compo- sition than that of individuals. This community composition convergence among populations suggests that a finite level of composition variability is present, at least among U.S. popula- tions, and this variability can be overcome with large sample sizes to make meaningful inferences about the gut microbiome. From the sewage sampling, we also identified a set of “core” bacteria that are both common to and abundant in U.S. populations. Although no single species dominates the fecal microbial communities among individuals, our results demonstrate consistent differential abundance in human populations for some bacterial taxa over others. Previous attempts to classify core species, using a ⬎ 50% occurrence among adult individuals as the definition of core, identified Faecalibacterium prausnitzii, Roseburia intestinalis, Bac- teroides vulgatus, Bacteroides uniformis, Eubacterium rectale, and Ruminococcus bromii among other undescribed species as primary members (4, 26). Except for Roseburia intestinalis, each of these species matched one of our core oligotypes. We also defined an- other 21 oligotypes as core members, most of which resolved to various Bacteroides spp. or Lachnospiraceae genera (see Table S2 in the supplemental material). The high representation of Bacte- roides in the sewage samples is consistent with reports that adults from the United States have higher abundances of the genus Bac-
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Concentration of Colourful Wild Berry Fruit Juices by Membrane Osmotic Distillation via Cascade Model Systems

Concentration of Colourful Wild Berry Fruit Juices by Membrane Osmotic Distillation via Cascade Model Systems

Four types of colourful wild berry juices were concentrated by the MOD procedure, which had not been investigated so far by membrane technology. The results of the MOD process are shown in Figure 6, where the volume of the juices and the concentrations are presented as a function of time. 50-60 °Brix concentration was achieved. It can be seen that each juice has its characteristics, thus the processes can differ in time and mass transport rate. The results are depicted in Figure 6 (left, the concentration of blackthorn and white beam, while in the right diagram, concentration of cornelian cherry and elderberry juices can be seen).
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DIVERSITY OF EPIPHYTIC AND ENDOPHYTIC MICROORGANISMS IN SOME DOMINANT WEEDS

DIVERSITY OF EPIPHYTIC AND ENDOPHYTIC MICROORGANISMS IN SOME DOMINANT WEEDS

Diversity in epi and endophytic microorganisms from the local weeds is thoroughly studied in this paper. For this purpose, 46 fungal and 19 bacterial strains were isolated from the surfaces and the inner tissues of four dominant agricultural weeds. Leaf wash and homogenized leaf mixture solution were used for the isolations from healthy leaves of four weeds viz. Chenopodium album, Euphorbia helioscopia, Parthenium hysterophorus and Convolvulus arvensis. Our study indicated that complex interactions existed between the host and their epi and endophytic microflora. Each weed has specific bacterial community with the reference of epi and endo phyllosphere. The number and species of bacterial strains varied not only with their host weed plants but also in epi and endo phyllospere. Sørensen’s QS of all tested weeds for the endophytic and epiphytic bacterial assemblages was 0.00 that indicated no species overlap / similarity between the communities. Five fungal genera were common as epi and endophytes in all weeds samples: Aspergillus (56% of all isolates), Drechslera (10%), Alternaria (10%) Penicillium (6%) and Cladosporium (4%). Frequency of all five common genera differed significantly among weeds. It was also noted that endophytic fungal communities were not noticeably less speciose than epiphyte communities. Sørensen’s QS of E. helipscopia (0.23), C. album (0.37) and C. arvensis (0.46) for the endophytic and epiphytic fungal assemblages was intermediate in the range (0.12–0.79) of previous studies. In case of P. hysterophorus, the value for Sørensen’s QS was 0.00 indicating no species similarity. The other identified genera were rare, such as Absidia, Cuvularia, Phoma and Trichoderma.
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Performance Analysis of a Solar Grape Dryer with Thermal Energy Storage by PCM

Performance Analysis of a Solar Grape Dryer with Thermal Energy Storage by PCM

growing interest in agricultural products dryer from the point of view of the commercial value for farmers and reduction in the wastage. This research includes the design and manufacturing of solar grape dryer. The use of solar energy in recent years had reached a remarkable edge. The continuous research for an alternative power source due to the perceived scarcity of fuel fossils is its driving force. It had become even more popular as the cost of fossil fuel continues to rise. Of all the renewable sources of energy available, solar energy is the most abundant one and is available in both direct as well as indirect forms. There has been a remarkable achievement in solar drying of grapes due to sustained research and development associated with the adoption of advanced technologies. Grape is one of the world’s largest fruit crops. The world production of grapes is currently 73,516 million tones out of which India accounts for 1.2 million tones.
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Grape Bud MiteTests

Grape Bud MiteTests

This table indicates that the number of colonies per vine and the amount of leaf damage was at first smaller in the HETP plus DDT plots, but at the end of 35 days the number of colonies [r]

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Study of epiphytic bryophytes in the ifrane national park in Morocco

Study of epiphytic bryophytes in the ifrane national park in Morocco

mosses and only one hepatic; no hornwort were found on the main forest species of the study area. The recorded species are divided into 10 families and 21 genera with the predominance of the family of brachytheciaceae in terms of species richness with 7 taxa. The species with the most important cover are: Antitrichia californica, Brachythecium velutinum, Fabronia pusilla, Homalothecium lutescens, Homalothecium sericeum, Hypnum cupressiforme, Orthotrichum cupulatum, Orthotrichum rupestre, Pterigynandrum filiforme, Pterogonium gracile and Tortula laevipila. All these species, except Antitrichia californica, are found on Quercus rotundifolia, whose epiphytic bryophyte number reaches 29 taxa. The number of bryophyte species recorded on Quercus faginea is 28, while that of the Atlas cedar does not exceed 24 taxa. The prospection carried out at INP for more than two years and having covered all the seasons made it possible to note the strong anthropozoogenic pressure that would lead to the deterioration of the forest species if it continues. The shrub layer is even overgrazed in some places. The edges of forests are entirely therophytised. This phenomenon inevitably affects the bryological flora. The number of species listed on tree trunks remains lower than the potentialities that these ecosystems can offer if they are well conserved. An awakening by the managers of the need for protecting this rich nature was crowned by the creation in 2004 of the Ifrane National Park and by UNESCO’s declaration of Middle Atlas cedar massif as a biosphere reserve, in February 2016, in the concern of its protection.
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Expression analysis of K+ transporter genes associated with salinity tolerance in grape

Expression analysis of K+ transporter genes associated with salinity tolerance in grape

The most studied members of the KT/KUP/HAK family belong to the two largest groups, which were named I and II (2). In growing grapevine fruits ( Vitis vinifera ), the expression of VvKUP1 and VvKUP2 potassium transporter genes is dependent on their developmental stage. It is likely that these transporters are required for the potassium-driven cell expansion in young grape berries (5). VvK1.1 is mainly expressed in the root cortex like its Arabidopsis AKT1 counterpart, which has been shown to be involved in K +

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