Proof of Concept for Cell Culture-Based Coffee.

The global coffee production is facing serious challenges including land use, climate change, and sustainability while demand is rising. Cellular agriculture is a promising alternative to produce plant-based commodities such as coffee, which are conventionally produced by farming. In this study, the complex process of drying and roasting was adapted for bioreactor-grown coffee cells to generate a coffee-like aroma and flavor. The brews resulting from different roasting regimes were characterized with chemical and sensory evaluation-based approaches and compared to conventional coffee. Roasting clearly influenced the aroma profile. In contrast to conventional coffee, the dominant odor and flavor attributes were burned sugar-like and smoky but less roasted. The intensities of bitterness and sourness were similar to those of conventional coffee. The present results demonstrate a proof of concept for a cellular agriculture approach as an alternative coffee production platform and guide future optimization work.

Raspberry Ketone Accumulation in Nicotiana benthamiana and Saccharomyces cerevisiae by Expression of Fused Pathway Genes.

Raspberry ketone has generated interest in recent years both as a flavor agent and as a health promoting supplement. Raspberry ketone can be synthesized chemically, but the value of a natural nonsynthetic product is among the most valuable flavor compounds on the market. Coumaroyl-coenzyme A (CoA) is the direct precursor for raspberry ketone but also an essential precursor for flavonoid and lignin biosynthesis in plants and therefore highly regulated. The synthetic fusion of 4-coumaric acid ligase (4CL) and benzalacetone synthase (BAS) enables the channeling of coumaroyl-CoA from the ligase to the synthase, proving to be a powerful tool in the production of raspberry ketone in both N. benthamiana and S. cerevisiae. To the best of our knowledge, the key pathway genes for raspberry ketone formation are transiently expressed in N. benthamiana for the first time in this study, producing over 30 µg/g of the compound. Our raspberry ketone producing yeast strains yielded up to 60 mg/L, which is the highest ever reported in yeast.

Anti-Angiogenic Effect of Cantharellus cibarius Extracts, its Correlation with Lipoxygenase Inhibition, and Role of the Bioactives Therein.

Angiogenesis is a complex physiological process that cannot be treated with single agent therapy. Several edible fungi have been known to encompass bioactive compounds, and are promising sources of multi-component drugs. One such widely consumed edible fungi is Cantharellus cibarius, which has been explored for its biological activities. The present study focused on assessing the anti-angiogenic activity of petroleum ether and ethanol extracts of C. cibarius using chick chorioallantoic membrane (CAM) assay. Both the extracts showed a dose-dependent response which was compared with the anti-angiogenic activity of the positive controls silibinin, and lenalidomide. The extracts were also studied for their lipoxygenase (LOX) inhibitory potential and compared to ascorbic acid as the positive control. The IC50 values of the petroleum ether extract, ethanol extract, and ascorbic acid for LOX inhibition assay were 135.4, 113.1, and 41.5 µg/mL, respectively. Although both the extracts showed similar responses in CAM assay, ethanol extract proved to be more potent in LOX inhibition assay. Finally, the extracts were investigated for their chemical composition using GC-MS. A correlation between LOX inhibition and anti-angiogenic potential was established at the molecular level. A meticulous literature search was carried out to correlate the biochemical composition of the extracts to their anti-angiogenic activity.

Contrasting Dihydronaphthoquinone Patterns in Closely Related Drosera (Sundew) Species Enable Taxonomic Distinction and Identification.

Dihydronaphthoquinones are described as constituents of sundews (Drosera), Venus flytraps (Dionaea), and dewy pines (Drosophyllum) for the first time. As in the corresponding naphthoquinones, these reduced derivatives may occur in two regio-isomeric series distinguished by the relative position of a methyl group (at position 2 or 7 in the naphthalene skeleton), depending on the taxon. Species producing plumbagin (2-methyljuglone, 1) do commonly contain the corresponding dihydroplumbagin (5), while species containing ramentaceone (7-methyljuglone, 2) also contain dihydroramentaceone (7-methyl-ß-dihydrojuglone, 6). So far, only few species containing plumbagin (1) and dihydroplumbagin (5) additionally form dihydroramentaceone (6) but not ramentaceone (2). Thus, subtle but constant differences in the chemism of closely related and morphologically similar species reliably define and distinguish taxa within D. sect. Arachnopus, which is taken to exemplify their chemotaxonomic utility. The joint presence of quinones and hydroquinones allows observations and predictions on the chemical structures and the reactions of these intriguing natural products.

Anti-angiogenic and anti-inflammatory activity of the summer truffle (Tuber aestivum Vittad.) extracts and a correlation with the chemical constituents identified therein.

Fungi are a huge source of unexplored bioactive compounds. Owing to their biological activities, several fungi have shown commercial application in the health industry. Tuber aestivum Vittad. is one such edible fungi with an immense scope for practical biological applications. In the present study, the anti-angiogenic activity of petroleum ether and ethanol extracts of T. aestivum was investigated using the chick chorioallantoic membrane assay and compared to the positive controls silibinin and lenalidomide. Both the extracts showed a dose-dependent anti-angiogenic response. The extracts were also assessed for their anti-inflammatory potential by lipoxygenase-inhibition assay. The IC50 values for LOX inhibition assay, computed by the Boltzmann plot, were 368.5, 147.3 and 40.2 µg/mL, for the petroleum ether extract, ethanol extract, and the positive control ascorbic acid, respectively. The ethanol extract of T. aestivum showed superior anti-angiogenic and anti-inflammatory activity than the petroleum ether extract. Compositional investigation of the extracts by GC-MS revealed the presence of various bioactive compounds. The compounds were correlated to their anti-angiogenic and anti-inflammatory activity based on a meticulous literature search.

Liquid Chromatography-Mass Spectrometry (LC-MS)-Based Analysis of Molecular Lipids in Algae Samples.

In this paper, an analytical method for the analysis of molecular lipids in algae samples is reported. The sample preparation is based on a modified Folch extraction, and the analysis is carried out with ultrahigh performance liquid chromatography combined with mass spectrometry (UPLC-MS). For further characterization of lipids, MS/MS analyses are carried out utilizing either a separate instrument (e.g., LTQ-Orbitrap mass spectrometer) or simultaneous fragmentation with the same instrument. Throughput of the method is over 100 samples/d. The repeatability is good, and the relative standard deviation of spiked samples is <15%.

UPLC-ELSD Analysis of Algal Lipid Classes and Derivatization of Bound and Free Fatty Acids and Sterols for GC-MS Methods.

Constituents of microalgae and sample preparation for UPLC-ELSD and GC-MS analyses are described. Bound fatty acids from acylglycerols, alkylacylglycerols, galactosyldiacylglycerols, glycerophospholipids, and sterol esters are derivatized by using transesterification with sodium methoxide to form fatty acid methyl esters. Compounds containing free hydroxyl groups, either present originally or formed during previous step, like free fatty acids, sterols, α-tocopherol, phytol, and nonesterified alkoxyglycerols, are trimethylsilylated. The compounds in algal lipid extract are subsequently derivatized by these two steps.

Metabolite profiling and mechanisms of bioactivity of snake autolysate - A traditional Uzbek medicine.

ETHNOPHARMACOLOGICAL RELEVANCE: Aqueous autolysate from the snake Eryx miliaris (SNA) has been used in traditional medicine of Uzbekistan as anti-inflammatory, hepatoprotective and immunomodulatory agent. However, little is known about the chemical composition and its mechanisms of activity. AIM OF THE STUDY: This is our first attempt to analyse the composition of snake autolysate using gas chromatography with mass spectrometry (GC-MS) and to investigate the mechanisms of anti-inflammatory and hyaluronidase activity of fingerprinted E. miliaris autolysate to support their use in the traditional Uzbek medicine. MATERIALS AND METHODS: Aqueous autolysate was evaporated and derivatised for GC-MS analysis of metabolites. For quantification, lipids were extracted from autolysate by solvent extraction and derivatised by esterification and silylation. Biological activity was evaluated with lipid peroxidation, cyclooxygenase (COX) inhibition and antihyaluronidase activity tests. RESULTS: GC-MS analysis of SNA enabled the identification of 27 compounds. Short chain fatty acids (SCFA, 21%), amino acid/derivatives 39% (incl. 2-piperidinone 19%), phenyl (7%), and OH-Phenyl (10%) derivatives covered 77%. Other derivatives (9%) included succinic acid and 3-indole acetic acid). Long chain fatty acids (C16-C18) accounted for 3%. The lipid concentration of SNA was 1.2 mg/mL (0.12%). Three concentration levels (1.0-20.0 µg/mL) did not inhibit COX-1 and COX-2 in vitro and malondialdehyde level was not decreased by SNA in lipid peroxidation model. However, SNA was a potent inhibitor of the hyaluronidase enzyme activity in a dose dependent manner with IC50 = 0.086 mL/mL. CONCLUSION: The results from GC-MS analyses of SNA lead us to the identification of a wide range of major chemical structures of the metabolites and their derivatives with several categories. Pharmacological studies support the traditional use of SNA and show one of its possible mechanisms of activity via inhibition of hyaluronidase.

Methyljasmonate Elicitation Increases Terpenoid Indole Alkaloid Accumulation in Rhazya stricta Hairy Root Cultures.

Methyl jasmonate is capable of initiating or improving the biosynthesis of secondary metabolites in plants and therefore has opened up a concept for the biosynthesis of valuable constituents. In this study, the effect of different doses of methyl jasmonate (MeJA) elicitation on the accumulation of terpenoid indole alkaloids (TIAs) in the hairy root cultures of the medicinal plant, Rhazya stricta throughout a time course (one-seven days) was investigated. Gas chromatography-mass spectrometry (GC-MS) analyses were carried out for targeted ten major non-polar alkaloids. Furthermore, overall alterations in metabolite contents in elicited and control cultures were investigated applying proton nuclear magnetic resonance (1H NMR) spectroscopy. Methyl jasmonate caused dosage- and time course-dependent significant rise in the accumulation of TIAs as determined by GC-MS. The contents of seven alkaloids including eburenine, quebrachamine, fluorocarpamine, pleiocarpamine, tubotaiwine, tetrahydroalstonine, and ajmalicine increased compared to non-elicited cultures. However, MeJA-elicitation did not induce the accumulation of vincanine, yohimbine (isomer II), and vallesiachotamine. Furthermore, principal component analysis (PCA) of 1H NMR metabolic profiles revealed a discrimination between elicited hairy roots and control cultures with significant increase in total vindoline-type alkaloid content and elevated levels of organic and amino acids. In addition, elicited and control samples had different sugar and fatty acid profiles, suggesting that MeJA also influences the primary metabolism of R. stricta hairy roots. It is evident that methyl jasmonate is applicable for elevating alkaloid accumulation in "hairy root" organ cultures of R. strica.

A Small In Vitro Fermentation Model for Screening the Gut Microbiota Effects of Different Fiber Preparations.

The development of prebiotic fibers requires fast high-throughput screening of their effects on the gut microbiota. We demonstrated the applicability of a mictotiter plate in the in vitro fermentation models for the screening of potentially-prebiotic dietary fibers. The effects of seven rye bran-, oat- and linseed-derived fiber preparations on the human fecal microbiota composition and short-chain fatty acid production were studied. The model was also used to study whether fibers can alleviate the harmful effects of amoxicillin-clavulanate on the microbiota. The antibiotic induced a shift in the bacterial community in the absence of fibers by decreasing the relative amounts of Bifidobacteriaceae, Bacteroidaceae, Prevotellaceae, Lachnospiraceae and Ruminococcaceae, and increasing proteobacterial Sutterilaceae levels from 1% to 11% of the total microbiota. The fermentation of rye bran, enzymatically treated rye bran, its insoluble fraction, soluble oat fiber and a mixture of rye fiber:soluble oat fiber:linseed resulted in a significant increase in butyrate production and a bifidogenic effect in the absence of the antibiotic. These fibers were also able to counteract the negative effects of the antibiotic and prevent the decrease in the relative amount of bifidobacteria. Insoluble and soluble rye bran fractions and soluble oat fiber were the best for controlling the level of proteobacteria at the level below 2%.

Interlaboratory Coverage Test on Plant Food Bioactive Compounds and their Metabolites by Mass Spectrometry-Based Untargeted Metabolomics.

Bioactive compounds present in plant-based foods, and their metabolites derived from gut microbiota and endogenous metabolism, represent thousands of chemical structures of potential interest for human nutrition and health. State-of-the-art analytical methodologies, including untargeted metabolomics based on high-resolution mass spectrometry, are required for the profiling of these compounds in complex matrices, including plant food materials and biofluids. The aim of this project was to compare the analytical coverage of untargeted metabolomics methods independently developed and employed in various European platforms. In total, 56 chemical standards representing the most common classes of bioactive compounds spread over a wide chemical space were selected and analyzed by the participating platforms (n = 13) using their preferred untargeted method. The results were used to define analytical criteria for a successful analysis of plant food bioactives. Furthermore, they will serve as a basis for an optimized consensus method.

In Vitro Gut Metabolism of [U-13 C]-Quinic Acid, The Other Hydrolysis Product of Chlorogenic Acid.

SCOPE: Quinic acid in its free form is broadly abundant in plants, and can accumulate in copious amounts in coffee, tea, and certain fruits. However, it has been mostly studied as chlorogenic acid, an ester of caffeic and quinic acids. When chlorogenic acid reaches the colon, it is hydrolyzed by microbial esterases releasing caffeic and quinic acids. While biotransformation of chlorogenic and caffeic acids have been elucidated by in vitro and in vivo studies, the gut metabolism of quinic acid has been so far overlooked. METHODS AND RESULTS: [U-13 C]-Quinic acid is submitted to a colonic model using human fecal microbiota for assessing its metabolic fate. The metabolite profiles formed along microbial biotransformation are monitored by a combined metabolomics approach, using both 2D GC- and ultra-HPLC-MS. Six metabolic intermediates are identified by incorporation of isotopic label. CONCLUSION: Two parallel degradation pathways could be proposed: (1) an oxidative route, leading to aromatization and accumulation of protocatechuic acid, and a (2) reductive route, including dehydroxylation to cyclohexane carboxylic acid. Elucidating the biotransformation of food bioactives by the gut microbiota is of relevance for understanding nutrition, interindividual variability and potential effects on human metabolism.

Prepartal high-energy feeding with grass silage-based diets does not disturb the hepatic adaptation of dairy cows during the periparturient period.

The liver of dairy cow naturally undergoes metabolic adaptation during the periparturient period in response to the increasing demand for nutrients. The hepatic adaptation is affected by prepartal energy intake level and is potentially associated with inflammatory responses. To study the changes in the liver function during the periparturient period, 16 cows (body condition score = 3.7 ± 0.3, mean ± standard deviation; parity = second through fourth) were allocated to a grass silage-based controlled-energy diet (104 MJ/d) or a high-energy diet (135 MJ/d) during the last 6 wk before the predicted parturition. Liver samples were collected by biopsy at 8 d before the predicted parturition (-8 d) and at 1 and 9 d after the actual parturition (1 and 9 d). The lipidomic profile of liver samples collected at -8 and 9 d was analyzed using ultra performance liquid chromatography-mass spectrometry-based lipidomics. Liver samples from all the time points were subjected to microarray analysis and the subsequent pathway analysis with Ingenuity Pathway Analysis software (Ingenuity Systems, Mountain View, CA). Prepartal energy intake level affected hepatic gene expression and lipidomic profiles prepartum, whereas little or no effect was observed postpartum. At -8 d, hepatic lipogenesis was promoted by prepartal high-energy feeding through the activation of X receptor/retinoid X receptor pathway and through increased transcription of thyroid hormone-responsive (THRSP). Hepatic inflammatory and acute phase responses at -8 d were suppressed (z-score = -2.236) by prepartal high-energy feeding through the increase in the mRNA abundance of suppressor of cytokine signaling 3 (SOCS3) and the decrease in the mRNA abundance of interleukin 1 (IL1), nuclear factor kappa B 1 (NFKB1), apolipoprotein A1 (APOA1), serum amyloid A3 (SAA3), haptoglobin (HP), lipopolysaccharide-binding protein (LBP), and inter-α-trypsin inhibitor heavy chain 3 (ITIH3). Moreover, prepartal high-energy feeding elevated hepatic concentrations of C18- (7%), C20- (17%), C21- (26%), C23-sphingomyelins (26%), and total saturated sphingomyelin (21%). In addition, cows in both groups displayed increased lipogenesis at the gene expression level after parturition and alterations in the concentration of various sphingolipids between the first and last samplings. In conclusion, prepartal high-energy feeding promoted lipogenesis and suppressed inflammatory and acute phase responses in the liver before parturition, whereas only minor effects were observed after parturition.

Euglena gracilis growth and cell composition under different temperature, light and trophic conditions.

BACKGROUND: Euglena gracilis, a photosynthetic protist, produces protein, unsaturated fatty acids, wax esters, and a unique ß-1,3-glucan called paramylon, along with other valuable compounds. The cell composition of E. gracilis was investigated in this study to understand how light and organic carbon (photo-, mixo- and heterotrophic conditions) affected growth and cell composition (especially lipids). Comparisons were primarily carried out in cultures grown at 23 °C, but the effect of growth at higher temperatures (27 or 30 °C) was also considered. CELL GROWTH: Specific growth rates were slightly lower when E. gracilis was grown on glucose in either heterotrophic or mixotrophic conditions than when grown photoautotrophically, although the duration of exponential growth was longer. Temperature determined the rate of exponential growth in all cultures, but not the linear growth rate during light-limited growth in phototrophic conditions. Temperature had less effect on cell composition. CELL COMPOSITION: Although E. gracilis was not expected to store large amounts of paramylon when grown phototrophically, we observed that phototrophic cells could contain up to 50% paramylon. These cells contained up to 33% protein and less than 20% lipophilic compounds, as expected. The biomass contained about 8% fatty acids (measured as fatty acid methyl esters), most of which were unsaturated. The fatty acid content of cells grown in mixotrophic conditions was similar to that observed in phototrophic cells, but was lower in cells grown heterotrophically. Heterotrophic cells contained less unsaturated fatty acids than phototrophic or mixotrophic cells. α-Linolenic acid was present at 5 to 18 mg g-1 dry biomass in cells grown in the presence of light, but at < 0.5 mg g-1 biomass in cells grown in the dark. Eicosapentaenoic and docosahexaenoic acids were detected at 1 to 5 mg g-1 biomass. Light was also important for the production of vitamin E and phytol.

Plant cells as food - A concept taking shape.

Plant cell cultures from cloudberry, lingonberry and stoneberry were studied in terms of their nutritional properties as food. Carbohydrate, lipid and protein composition, in vitro protein digestibility and sensory properties were investigated. Dietary fibre content varied between 21.2 and 36.7%, starch content between 0.3 and 1.3% and free sugar content between 17.6 and 33.6%. Glucose and fructose were the most abundant sugars. High protein contents between 13.7 and 18.9% were recorded and all samples had a balanced amino acid profile. In vitro protein digestion assay showed hydrolysis by digestive enzymes in fresh cells but only limited hydrolysis in freeze-dried samples. The lipid analysis indicated that the berry cells were rich sources of essential, polyunsaturated fatty acids. In sensory evaluation, all fresh berry cells showed fresh odour and flavour. Fresh cell cultures displayed a rather sandy, coarse mouthfeel, whereas freeze-dried cells melted quickly in the mouth. All in all the potential of plant cells as food was confirmed.

Chemical Profiling and Bioactivity of Body Wall Lipids from Strongylocentrotus droebachiensis.

The lipids from gonads and polyhydroxynaphthoquinone pigments from body walls of sea urchins are intensively studied. However, little is known about the body wall (BW) lipids. Ethanol extract (55 °C) contained about equal amounts of saturated (SaFA) and monounsaturated fatty acids (MUFA) representing 60% of total fatty acids, with myristic, palmitic and eicosenoic acids as major SaFAs and MUFAs, respectively. Non-methylene-interrupted dienes (13%) were composed of eicosadienoic and docosadienoic acids. Long-chain polyunsaturated fatty acids (LC-PUFA) included two main components, n6 arachidonic and n3 eicosapentaenoic acids, even with equal concentrations (15 µg/mg) and a balanced n6/n3 PUFA ratio (0.86). The UPLC-ELSD analysis showed that a great majority of the lipids (80%) in the ethanolic extract were phosphatidylcholine (60 µg/mg) and phosphatidylethanolamine (40 µg/mg), while the proportion of neutral lipids remained lower than 20%. In addition, alkoxyglycerol derivatives-chimyl, selachyl, and batyl alcohols-were quantified. We have assumed that the mechanism of action of body wall lipids in the present study is via the inhibition of MAPK p38, COX-1, and COX-2. Our findings open the prospective to utilize this lipid fraction as a source for the development of drugs with anti-inflammatory activity.

Inheritance of brewing-relevant phenotypes in constructed Saccharomyces cerevisiae × Saccharomyces eubayanus hybrids.

BACKGROUND: Interspecific hybridization has proven to be a potentially valuable technique for generating de novo lager yeast strains that possess diverse and improved traits compared to their parent strains. To further enhance the value of hybridization for strain development, it would be desirable to combine phenotypic traits from more than two parent strains, as well as remove unwanted traits from hybrids. One such trait, that has limited the industrial use of de novo lager yeast hybrids, is their inherent tendency to produce phenolic off-flavours; an undesirable trait inherited from the Saccharomyces eubayanus parent. Trait removal and the addition of traits from a third strain could be achieved through sporulation and meiotic recombination or further mating. However, interspecies hybrids tend to be sterile, which impedes this opportunity. RESULTS: Here we generated a set of five hybrids from three different parent strains, two of which contained DNA from all three parent strains. These hybrids were constructed with fertile allotetraploid intermediates, which were capable of efficient sporulation. We used these eight brewing strains to examine two brewing-relevant phenotypes: stress tolerance and phenolic off-flavour formation. Lipidomics and multivariate analysis revealed links between several lipid species and the ability to ferment in low temperatures and high ethanol concentrations. Unsaturated fatty acids, such as oleic acid, and ergosterol were shown to positively influence growth at high ethanol concentrations. The ability to produce phenolic off-flavours was also successfully removed from one of the hybrids, Hybrid T2, through meiotic segregation. The potential application of these strains in industrial fermentations was demonstrated in wort fermentations, which revealed that the meiotic segregant Hybrid T2 not only didn't produce any phenolic off-flavours, but also reached the highest ethanol concentration and consumed the most maltotriose. CONCLUSIONS: Our study demonstrates the possibility of constructing complex yeast hybrids that possess traits that are relevant to industrial lager beer fermentation and that are derived from several parent strains. Yeast lipid composition was also shown to have a central role in determining ethanol and cold tolerance in brewing strains.

Variability in the production of tannins and other polyphenols in cell cultures of 12 Nordic plant species.

MAIN CONCLUSION: The polyphenol profiles of 18 cell cultures from 12 plant species were screened. The detected polyphenol fingerprints were diverse and differed from polyphenol profiles typically found in corresponding plant species. Cell cultures originating from 12 different plant species growing or grown in the Nordic countries were screened for their ability to synthesize polyphenols to assess their suitability for future studies and applications. The focus was on plant families Rosaceae and Ericaceae. On average, the Rosaceae cultures were the most efficient to produce hydrolysable tannins and the Ericaceae cultures were the most efficient to produce proanthocyanidins. This is in line with the general trend of polyphenols found in Rosaceae and Ericaceae leaves and fruits, even though several individual cell cultures differed from natural plants in their polyphenolic composition. Overall, several of the studied cell cultures exhibited capability in producing a large variety of polyphenols, including tannins with a high molecular weight, thus also showing promise for further studies concerning, for example, the accumulation of specific polyphenols or biosynthesis of polyphenols in the cell cultures.

Metabolite profiling of the carnivorous pitcher plants Darlingtonia and Sarracenia.

Sarraceniaceae is a New World carnivorous plant family comprising three genera: Darlingtonia, Heliamphora, and Sarracenia. The plants occur in nutrient-poor environments and have developed insectivorous capability in order to supplement their nutrient uptake. Sarracenia flava contains the alkaloid coniine, otherwise only found in Conium maculatum, in which its biosynthesis has been studied, and several Aloe species. Its ecological role and biosynthetic origin in S. flava is speculative. The aim of the current research was to investigate the occurrence of coniine in Sarracenia and Darlingtonia and to identify common constituents of both genera, unique compounds for individual variants and floral scent chemicals. In this comprehensive metabolic profiling study, we looked for compound patterns that are associated with the taxonomy of Sarracenia species. In total, 57 different Sarracenia and D. californica accessions were used for metabolite content screening by gas chromatography-mass spectrometry. The resulting high-dimensional data were studied using a data mining approach. The two genera are characterized by a large number of metabolites and huge chemical diversity between different species. By applying feature selection for clustering and by integrating new biochemical data with existing phylogenetic data, we were able to demonstrate that the chemical composition of the species can be explained by their known classification. Although transcriptome analysis did not reveal a candidate gene for coniine biosynthesis, the use of a sensitive selected ion monitoring method enabled the detection of coniine in eight Sarracenia species, showing that it is more widespread in this genus than previously believed.

Whole-genome metabolic model of Trichoderma reesei built by comparative reconstruction.

BACKGROUND: Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis. RESULTS: A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model. CONCLUSIONS: The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes.