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Open accessJournal ArticleDOI: 10.1038/S41598-021-84691-Y

Gene expression for secondary metabolite biosynthesis in hop (Humulus lupulus L.) leaf lupulin glands exposed to heat and low-water stress

04 Mar 2021-Scientific Reports (Springer Science and Business Media LLC)-Vol. 11, Iss: 1, pp 5138-5138
Abstract: Hops are valued for their secondary metabolites, including bitter acids, flavonoids, oils, and polyphenols, that impart flavor in beer. Previous studies have shown that hop yield and bitter acid content decline with increased temperatures and low-water stress. We looked at physiological traits and differential gene expression in leaf, stem, and root tissue from hop (Humulus lupulus) cv. USDA Cascade in plants exposed to high temperature stress, low-water stress, and a compound treatment of both high temperature and low-water stress for six weeks. The stress conditions imposed in these experiments caused substantial changes to the transcriptome, with significant reductions in the expression of numerous genes involved in secondary metabolite biosynthesis. Of the genes involved in bitter acid production, the critical gene valerophenone synthase (VPS) experienced significant reductions in expression levels across stress treatments, suggesting stress-induced lability in this gene and/or its regulatory elements may be at least partially responsible for previously reported declines in bitter acid content. We also identified a number of transcripts with homology to genes shown to affect abiotic stress tolerance in other plants that may be useful as markers for breeding improved abiotic stress tolerance in hop. Lastly, we provide the first transcriptome from hop root tissue.

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Topics: Abiotic stress (56%), Humulus lupulus (55%), Hop (networking) (52%)
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5 results found


Open accessJournal ArticleDOI: 10.1007/S00425-021-03648-7
25 May 2021-Planta
Abstract: The drought conditions and the application of ABA reduce the photosynthetic activity, and the processes related to the transpiration of Dracocephalum moldavica L. At the same time, the plant increases the production of phenolic compounds and essential oil as a response to stress conditions. In the semi-arid regions, drought stress is the most important environmental limitations for crop production. Abscisic acid (ABA) plays a crucial role in the reactions of plants towards environmental stress such as drought. Field experiments for two consecutive years in 2016 and 2017 were conducted to evaluate the effect of three watering regimes (well-watered, moderate and severe drought) and five exogenous ABA concentrations (0, 5, 10, 20 and 40 μM) on growth, photosynthesis, total phenolic and essential oil content of Dracocephalum moldavica L. Without ABA application, the highest photosynthetic rate (6.1 μmol CO2 m−2 s−1) was obtained under well-watered condition and, moderate and severe drought stress decreased photosynthesis rate by 26.39% and 34.43%, respectively. Some growth parameters such as stem height, leaf area, leaf dry weight and biological yield were also reduced by drought stress. ABA application showed a decreasing trend in photosynthesis rate and mentioned plant growth parameters under all moisture regimes. The highest seed yield (1243.56 kg ha−1) was obtained under well-watered condition without ABA application. Increasing ABA concentration decreased seed yield in all moisture regimes. The highest total phenolic content (8.9 mg g−1 FW) and essential oil yield (20.58 kg ha−1) were obtained from 20 and 5 μM ABA concentration, respectively, under moderate drought stress.

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Topics: Dracocephalum moldavica (59%), Abscisic acid (53%), Transpiration (50%)

7 Citations


Open accessJournal ArticleDOI: 10.3390/FOODS10092006
Mathieu Schwartz1, Francis Canon1, Gilles Feron1, Fabrice Neiers1  +1 moreInstitutions (2)
26 Aug 2021-Foods
Abstract: Flavor perception during food intake is one of the main drivers of food acceptability and consumption. Recent studies have pointed to the oral microbiota as an important factor modulating flavor perception. This review introduces general characteristics of the oral microbiota, factors potentially influencing its composition, as well as known relationships between oral microbiota and chemosensory perception. We also review diverse evidenced mechanisms enabling the modulation of chemosensory perception by the microbiota. They include modulation of the chemosensory receptors activation by microbial metabolites but also modification of receptors expression. Specific enzymatic reactions catalyzed by oral microorganisms generate fragrant molecules from aroma precursors in the mouth. Interestingly, these reactions also occur during the processing of fermented beverages, such as wine and beer. In this context, two groups of aroma precursors are presented and discussed, namely, glycoside conjugates and cysteine conjugates, which can generate aroma compounds both in fermented beverages and in the mouth. The two entailed families of enzymes, i.e., glycosidases and carbon–sulfur lyases, appear to be promising targets to understand the complexity of flavor perception in the mouth as well as potential biotechnological tools for flavor enhancement or production of specific flavor compounds.

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Topics: Flavor (53%)

3 Citations


Open accessJournal ArticleDOI: 10.1021/ACSEARTHSPACECHEM.0C00299
19 Aug 2021-
Abstract: Author(s): Dewhirst, RA; Handakumbura, P; Clendinen, CS; Arm, E; Tate, K; Wang, W; Washton, NM; Young, RP; Mortimer, JC; McDowell, NG; Jardine, KJ | Abstract: High temperatures alter the thermal sensitivities of numerous physiological and biochemical processes that impact tree growth and productivity. Foliar and root applications of methanol have been implicated in plant acclimation to high temperature via the C1 pathway. Here, we characterized temperature acclimation at 35 °C of leaf gas exchange, chlorophyll fluorescence, and extractable metabolites of potted Populus trichocarpa saplings and examined potential influences of mM concentrations of methanol added during soil watering over a two-month period. Relative to plants grown under the low growth temperature (LGT), high growth temperature (HGT) plants showed a suppression of leaf water use and carbon cycling including transpiration (E), net photosynthesis (Pn), an estimate of photorespiration (Rp), and dark respiration (Rd), attributed to reductions in stomatal conductance and direct negative effects on gas exchange and photosynthetic machinery. In contrast, HGT plants showed an upregulation of nonphotochemical quenching (NPQt), the optimum temperature for ETR, and leaf isoprene emissions at 40 °C. A large number of metabolites (867) were induced under HGT, many implicated in flavonoid biosynthesis highlighting a potentially protective role for these compounds. Methanol application did not significantly alter leaf gas exchange but slightly reduced the suppression of Rd and Rp by the high growth temperature while slightly impairing ETR, Fv′/Fm′, and qp. However, we were unable to determine if soil methanol was sufficiently taken up by the plant to have a direct effect on foliar processes. A small number of extracted leaf tissue metabolites (55 out of 10 015) showed significantly altered abundances under LGT and methanol treatments relative to water controls, and this increased in compound number (222) at the HGT. The results demonstrate the large physiological and biochemical impacts of high growth temperature on poplar seedlings and highlight the enhancement of the optimum temperature of ETR as a rapid thermal acclimation mechanism. Although no large effect on leaf physiology was observed, the results are consistent with methanol both impairing photochemistry of the light reactions via formaldehyde toxicity and stimulating photosynthesis and dark respiration through formate oxidation to CO2.

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Topics: Stomatal conductance (55%), Chlorophyll fluorescence (54%), Photorespiration (52%) ... read more

1 Citations


Open accessJournal ArticleDOI: 10.1080/03610470.2021.1973328
Abstract: The transcriptome from lupulin glands and associated bracts from cone tissue of hop (Humulus lupulus) c.v. ‘Cascade’, during three stages of development: early, mid, and late or near-harvest, was s...

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Topics: Humulus lupulus (61%), Hop (networking) (54%)

Open accessJournal ArticleDOI: 10.3390/IJMS22179373
Kai Hong1, Limin Wang1, Agbaka Johnpaul1, Chenyan Lv1  +1 moreInstitutions (1)
Abstract: Humulus lupulus L. is an essential source of aroma compounds, hop bitter acids, and xanthohumol derivatives mainly exploited as flavourings in beer brewing and with demonstrated potential for the treatment of certain diseases. To acquire a comprehensive understanding of the biosynthesis of these compounds, the primary enzymes involved in the three major pathways of hops’ phytochemical composition are herein critically summarized. Hops’ phytochemical components impart bitterness, aroma, and antioxidant activity to beers. The biosynthesis pathways have been extensively studied and enzymes play essential roles in the processes. Here, we introduced the enzymes involved in the biosynthesis of hop bitter acids, monoterpenes and xanthohumol derivatives, including the branched-chain aminotransferase (BCAT), branched-chain keto-acid dehydrogenase (BCKDH), carboxyl CoA ligase (CCL), valerophenone synthase (VPS), prenyltransferase (PT), 1-deoxyxylulose-5-phosphate synthase (DXS), 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HDR), Geranyl diphosphate synthase (GPPS), monoterpene synthase enzymes (MTS), cinnamate 4-hydroxylase (C4H), chalcone synthase (CHS_H1), chalcone isomerase (CHI)-like proteins (CHIL), and O-methyltransferase (OMT1). Furthermore, research advancements of each enzyme in terms of reaction conditions, substrate recognition, enzyme structures, and use in engineered microbes are described in depth. Hence, an extensive review of the key enzymes involved in the phytochemical compounds of hops will provide fundamentals for their applications in beer production.

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Topics: Chalcone synthase (58%), Xanthohumol (58%), Chalcone isomerase (52%) ... read more
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100 results found


Open accessJournal ArticleDOI: 10.1093/BIOINFORMATICS/BTP352
Heng Li1, Bob Handsaker2, Alec Wysoker2, T. J. Fennell2  +5 moreInstitutions (4)
01 Aug 2009-Bioinformatics
Abstract: Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: [email protected]

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Topics: Variant Call Format (62%), Stockholm format (61%), FASTQ format (56%) ... read more

35,747 Citations


Open accessJournal ArticleDOI: 10.1186/S13059-014-0550-8
05 Dec 2014-Genome Biology
Abstract: In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html .

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Topics: MRNA Sequencing (54%), Integrator complex (51%), Count data (50%) ... read more

29,675 Citations


Open accessBook
13 Aug 2009-
Abstract: This book describes ggplot2, a new data visualization package for R that uses the insights from Leland Wilkisons Grammar of Graphics to create a powerful and flexible system for creating data graphics. With ggplot2, its easy to: produce handsome, publication-quality plots, with automatic legends created from the plot specification superpose multiple layers (points, lines, maps, tiles, box plots to name a few) from different data sources, with automatically adjusted common scales add customisable smoothers that use the powerful modelling capabilities of R, such as loess, linear models, generalised additive models and robust regression save any ggplot2 plot (or part thereof) for later modification or reuse create custom themes that capture in-house or journal style requirements, and that can easily be applied to multiple plots approach your graph from a visual perspective, thinking about how each component of the data is represented on the final plot. This book will be useful to everyone who has struggled with displaying their data in an informative and attractive way. You will need some basic knowledge of R (i.e. you should be able to get your data into R), but ggplot2 is a mini-language specifically tailored for producing graphics, and youll learn everything you need in the book. After reading this book youll be able to produce graphics customized precisely for your problems,and youll find it easy to get graphics out of your head and on to the screen or page.

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Topics: Data visualization (58%), Graphics (56%)

23,839 Citations


Open accessJournal ArticleDOI: 10.1093/BIOINFORMATICS/BTS635
01 Jan 2013-Bioinformatics
Abstract: Motivation Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases. Results To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, we experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy. Availability and implementation STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license and can be downloaded from http://code.google.com/p/rna-star/.

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Topics: MRNA Sequencing (57%)

20,172 Citations


Open accessJournal ArticleDOI: 10.1111/J.1558-5646.1989.TB04220.X
William R. Rice1Institutions (1)
01 Jan 1989-Evolution
Abstract: Technique non parametrique pour la signification statistique de tables de tests utilisees dans les etudes sur l'evolution notamment

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14,379 Citations