Multiscale metabolic modeling of C4 plants: connecting nonlinear genome-scale models to leaf-scale metabolism in developing maize leaves

C4 plants, such as maize, concentrate carbon dioxide in a specialized compartment surrounding the veins of their leaves to improve the efficiency of carbon dioxide assimilation. Nonlinear relationships between carbon dioxide and oxygen levels and reaction rates are key to their physiology but cannot be handled with standard techniques of constraint-based metabolic modeling. We demonstrate that incorporating these relationships as constraints on reaction rates and solving the resulting nonlinear optimization problem yields realistic predictions of the response of C4 systems to environmental and biochemical perturbations. Using a new genome-scale reconstruction of maize metabolism, we build an 18000-reaction, nonlinearly constrained model describing mesophyll and bundle sheath cells in 15 segments of the developing maize leaf, interacting via metabolite exchange, and use RNA-seq and enzyme activity measurements to predict spatial variation in metabolic state by a novel method that optimizes correlation between fluxes and expression data. Though such correlations are known to be weak in general, here the predicted fluxes achieve high correlation with the data, successfully capture the experimentally observed base-to-tip transition between carbon-importing tissue and carbon-exporting tissue, and include a nonzero growth rate, in contrast to prior results from similar methods in other systems. We suggest that developmental gradients may be particularly suited to the inference of metabolic fluxes from expression data.Comment: 57 pages, 14 figures; submitted to PLoS Computational Biology; source code available at http://github.com/ebogart/fluxtools and http://github.com/ebogart/multiscale_c4_sourc

Expression of multidisciplinary flavour science : proceedings of the 12th Weurman Symposium

The 12th Weurman Flavour Research Symposium contributed 177 lectures and posters to the wealth of flavor knowledge; these were presented in eight sessions: biology, retention and release, psychophysics, quality, thermal generation, bioflavors, impact molecules, and analytics. Emerging topics were discussed in three workshops dealing with flavor and health, in vivo flavor research, and flavor metabolomics. It has been an excellent forum for passionate exchange of recent results obtained in traditional and emerging fields of flavor research. The symposium allowed coverage of the broad diversity of flavor-related topics: comprising odor and taste; applying targeted and holistic approaches; using sensorial, chemical, biological, physical, and chemometric techniques; as well as considering nutrition and health aspects

Expression of multidisciplinary flavour science : proceedings of the 12th Weurman Symposium

The 12th Weurman Flavour Research Symposium contributed 177 lectures and posters to the wealth of flavor knowledge; these were presented in eight sessions: biology, retention and release, psychophysics, quality, thermal generation, bioflavors, impact molecules, and analytics. Emerging topics were discussed in three workshops dealing with flavor and health, in vivo flavor research, and flavor metabolomics. It has been an excellent forum for passionate exchange of recent results obtained in traditional and emerging fields of flavor research. The symposium allowed coverage of the broad diversity of flavor-related topics: comprising odor and taste; applying targeted and holistic approaches; using sensorial, chemical, biological, physical, and chemometric techniques; as well as considering nutrition and health aspects

Nutra-Cosmeceuticals from Algae for Health and Wellness

Microalgae and seaweeds are a renewable source of potent bioactive ingredients with confirmed positive impacts on health and wellness. The interest in—and awareness of—the need to improve quality of life and well-being has led to a greater consumption of nutraceuticals, as well as the use of cosmeceuticals for “well-aging”. In this context, algae and microalgae are currently gaining immense popularity within the functional food, nutraceutical, and cosmeceutical industries. Recent advances in the characterization and evaluation of the biological properties of the whole material, fractions, or isolated compounds of algae and microalgae enable their use as ingredients for the development of novel nutraceutical and cosmeceutical products

Mass spectrometry-based applications and analytical method development for metabolomics

Metabolites are small molecules present in a biological system that have multiple important biological functions. Changes in metabolite levels reflect genetic and environmental alterations and play a role in multiple diseases. Metabolomics is a discipline that aims to analyze all the small molecules in a biological system simultaneously. Since metabolites represent a diverse group of compounds with varying chemical and physical properties with a wide concentration range, metabolomic analysis is technically challenging. Due to its high sensitivity and selectivity, mass spectrometry coupled with chromatographic separation is the most commonly used analytical tool. Currently, there is no comprehensive universal analytical tool to detect all metabolites simultaneously and multiple methods are required. The aim of this study was to develop and apply mass spectrometry-based analytical methods for metabolomics studies. Neonatal rodents can fully regenerate their hearts after an injury. However, this regenerative capacity is lost within 7 days after birth. The molecular mechanism behind this phenomenon is unknown and understanding the biology behind this loss of regeneration capacity is necessary for the development of regeneration-inducing therapies. To investigate this mechanism, changes in mouse heart metabolite, protein, and transcript levels during the early postnatal period were studied. Non-targeted metabolomics methods utilizing liquid chromatography-mass spectrometry (LC-MS) and two-dimensional gas chromatography-mass spectrometry (GCxGC-MS) were applied to detect the metabolic changes of neonatal mouse hearts. Two complementary techniques increased metabolite coverage. A total of 151 identified metabolites showed differences in the neonatal period, reflecting changes in multiple metabolic pathways. The most significant changes observed in all levels (metabolite, protein, and transcript) were branched chain amino acid (BCAA) catabolism, fatty acid metabolism, and the mevalonate and ketogenesis pathways, thus revealing possible associations with regeneration capacity or regulation of the cardiomyocyte cell cycle. Insulin resistance (IR), metabolic syndrome, and type 2 diabetes have been shown to induce metabolic changes; the origin of the changes is unknown. In this study, human serum metabolite profiles from non-diabetic individuals were associated with IR. Gut microbiota were identified as a possible origin of the metabolic changes. Serum metabolites were detected with GCxGC-MS and lipids with LC-MS method. In total, 19 serum metabolite clusters were significantly associated with the IR phenotype, including 26 polar metabolites from five separate clusters and 367 lipids from 14 clusters. IR and changed metabolites were further associated with gut microbiota metagenomics and gut microbiota functional modules, showing that gut microbiota impacts the human serum metabolites associated with IR. Individuals with the IR phenotype had increased BCAA levels, which was influenced by bacterial species with increased BCAA biosynthesis potential and the absence of species with active bacterial inward BCAA transport. Sample throughput is often limited when chromatographic separation is used in metabolomics applications; a short analysis time is of great importance in large metabolic studies. The feasibility of direct infusion electrospray microchip MS (chip-MS) for global non-targeted metabolomics to detect metabolic differences between two cell types was studied and was compared to the more traditional LC-MS method. We observed that chip-MS was a rapid and simple method that allowed high sample throughput from small sample volumes. The chip-MS method was capable of separating cells based on their metabolic profiles and could detect changes of several metabolites. However, the selectivity of chip-MS was limited compared to LC-MS and chip-MS suffers more from ion suppression. Many biologically important low-abundance metabolites are not detectable with non-targeted metabolomics methods and separate more sensitive targeted methods are required. An in-house developed capillary photoionization (CPI) source was shown to have high ion transmission efficacy and high sensitivity towards non-polar compounds such as steroids. In this study, the CPI prototype was developed to increase its sensitivity. The feasibility of the ion source for the quantitative analysis of biological samples was studied by analyzing 18 endogenous steroids in urine with gas chromatography capillary photoionization tandem mass spectrometry (GC-CPI-MS/MS). The GC-CPI-MS/MS method showed good chromatographic resolution, acceptable linearity and repeatability, and low limits of detection (2-100 pg mL-1). In total, 15 steroids were quantified either as a free steroid or glucuronide conjugate from the human urine samples. Additionally, the applicability of the CPI interface for LC applications was explored for the first time using low flow rates. The feasibility of the LC-CPI-MS/MS for the quantitative analysis of four steroids was studied in terms of linearity, repeatability, and limits of detection. The method showed good quantitative performance and high sensitivity at a low femtomole level.Metaboliitit ovat molekyylipainoltaan pieniä aineenvaihduntatuotteita, joilla on merkittäviä biologisia tehtäviä elimistössä. Aineenvaihduntatuotteiden muutoksien on osoitettu liittyvän moniin sairauksiin, jonka takia niiden analysoiminen on tärkeää sairauksien diagnosoimiseksi, ennustamiseksi, sairausmekanismin selvittämiseksi, sekä lääkehoidon kehittämiseksi. Metabolomiikka pyrkii analysoimaan aineenvaihduntatuotteet samanaikaisesti biologisista näytteistä ja vertailemaan aineenvaihduntatuotteiden tasoja eri fysiologisten tilojen välillä ja sitä voidaankin hyödyntää useissa lääketieteellisen tutkimuksen eri vaiheissa. Aineenvaihduntatuotteiden pitoisuudet ja kemialliset ominaisuudet kuitenkin vaihtelevat merkittävästi, mikä tekee aineenvaihduntatuotteiden samanaikaisen analysoinnin haastavaksi. Tällä hetkellä ei ole olemassa yhtä kaikkien aineenvaihduntatuotteiden samanaikaiseen analyysiin soveltuvaa menetelmää. Parhaiten metaboliittien analyysiin soveltuu massaspektrometria, usein yhdistettynä kromatografisiin erotustekniikoihin, sen ylivoimaisen herkkyyden ja spesifisyyden vuoksi. Tässä työssä pyrittiin soveltamaan massaspektrometrisiä kohdentamattomia profilointimenetelmiä uuden biologisen tiedon tuottamiseksi muuttuneista aineenvaihduntatuotteista. Työssä pyrittiin myös kehittämään uusia herkempiä ja nopeampia massaspektrometrisiä menetelmiä metabolomiikkaan. Ensimmäisessä osatutkimuksessa kohdentamatonta metabolomiikkaa sovellettiin lääkehoidon kohdemolekyylin etsintään solujen uusiutumisen aktivoimiseksi massiivisia soluvaurioita aiheuttavien sairauksien hoidossa. Aineenvaihduntareiteissä tapahtuvia muutoksia tutkittiin hiirien sydämistä, jotka menettävät sydänsolujen uusiutumiskyvyn pian syntymän jälkeen. Metabolomiikalla havaittiin muutoksia useilla aineenvaihduntareiteillä syntymän jälkeisellä ajanjaksolla, jolloin sydänsolujen uusiutumiskapasiteetti heikkenee. Tuloksia yhdistettiin muiden biomolekyylien analyysituloksiin ja saatiin kattavaa tietoa syntymän jälkeisistä molekyylimuutoksista. Erityisesti ketogeneesi-aineenvaihduntareitin havaittiin vaikuttavan solujen jakautumiseen ja lisääntymiseen. Insuliiniresistenssin, metabolisen oireyhtymän ja tyypin 2 diabeteksen on osoitettu aiheuttavan metabolisia muutoksia ihmisissä, mutta muutosten syy on ollut tuntematon. Työn toisessa osatutkimuksessa tutkittiin suoliston mikrobiston yhteyttä insuliiniresistenssiin ja metabolisiin muutoksiin seerumissa. Tutkimuksessa havaittiin seerumin metaboliittien muutoksilla olevan yhteys insuliiniresistenssiin, sekä yksilöiden suolistomikrobeihin ja niiden toimintoihin. Insuliiniresistentillä ryhmällä havaittiin kohonneet haaroittuneiden aminohappojen pitoisuudet seerumissa, sekä enemmän bakteerilajeja, jotka syntetisoivat haaroittuneita aminohappoja. Tutkimus antoi viitteitä, että suolistomikrobeilla on yhteys insuliiniresistenssin ja tyypin 2 diabeteksen puhkeamiseen. Kolmannessa osatutkimuksessa tutkittiin suorasyöttömikrosirun soveltuvuutta kohdentamattomaan metaboliseen profilointiin vertailemalla menetelmää yleisesti käytettyyn nestekromatografia-massaspektrometria menetelmään solujen metaboliittien erojen havaitsemiseksi. Mikrosiru-menetelmän etuna on nopea alle minuutin analyysiaika, joka mahdollistaa ison näytemäärän analysoinnin lyhyessä ajassa pienestä näytemäärästä. Erot solujen metabolisten profiileiden välillä pystyttiin havaitsemaan molemmilla menetelmillä. Mikrosiru-menetelmän selektiivisyys oli kuitenkin heikompi ja ionien supressio massaspektrometrissa oli merkittävämpää. Neljännessä ja viidennessä osatutkimuksessa tutkittiin kapillaarifotoionisaatio ionisaatiotekniikan soveltuvuutta metabolomiikkaan. Kohdentamattomien profilointimenetelmien herkkyys ei riitä matalien pitoisuuksien analysointiin, jonka vuoksi myös kohdennettuja herkempiä menetelmiä tarvitaan tiettyjen yhdisteryhmien määrittämiseksi. Kapillaarifotoionisaation soveltuvuutta tutkittiin kehittämällä menetelmä steroidien määrittämiseksi virtsasta kaasukromatografia-massaspektrometrilla. Menetelmällä saavutettiin hyvä herkkyys ja menetelmän todettiin soveltuvan steroidien kvantitatiiviseen analytiikkaan biologisesta matriisista. Kapillaarifotoionisaation soveltuvuutta steroidien analysoimiseksi myös nestekromatografia-massaspektrometrialla tutkittiin ensimmäistä kertaa. Tutkimuksessa havaittiin kapillaarifotoionisaation soveltuvan myös nestekromatografiaan pienillä virtausnopeuksilla. Kohdentamattomalla metabolomiikalla saavutettiin merkittävää tietoa muuttuneista aineenvaihduntatuotteista ja havaittavien metaboliittien määrää laajennettiin käyttämällä kahta rinnakkaista menetelmää. Työssä kapillaarifotoionisaation ja mikrosirutekniikan osoitettiin soveltuvan käytettäväksi metabolomiikassa

Novel Analysis on Aroma Compounds of Wine, Vinegar and Derived Products

Aroma compounds are some of the main compounds responsible for the acceptance of oenological products such as wine, vinegar and derived products. These kinds of compounds are produced during the winemaking process and they can be affected by natural, geographical and human factors: raw material, alcoholic and acetic fermentation, ageing, distillation, technological processes, etc. Therefore, it is very important to study and to characterize the aromatic fraction of these oenological beverages in order to improve the quality of the final product. Therefore, this book is focused on some recent studies related to the study of the volatile composition of wine, vinegar and derived products, in many different fields of science: oenology, chemistry, food science and technology, biochemistry, microbiology, biotechnology, engineering, sensory analysis, etc., and it shows the great importance of both sensory and analytical study of oenological products aroma and how they are influenced by the different stages and conditions under which they are elaborated. In this book, you will find 12 valuable scientific contributions: 2 literature reviews and 10 original research works, which deal with the latest advances in both sensory and analytical tools in order to evaluate the effects of different techniques or winemaking stages on the oenological products’ aromas

Health-Promoting Components of Fruits and Vegetables in Human Health

Diet and lifestyle choices can substantially predispose an individual to, or protect against, many age- and obesity-related chronic diseases. According to the NIH Office of Dietary Supplements, dietary bioactives arecompounds in foodsnot needed for basic human nutrition but responsible for changes in health status.1 These compounds are safe at normal food consumption levels (e.g., anthocyanins in berries) and their biological activities may come from a single compound (e.g., lutein in spinach) or a class of compounds (e.g., avenanthramides in oats) even if the exact identity and composition are unknown. Bioactive compounds of plants; can vary significantly in their ratios and relative concentrations depending onfactors such as cultivation, soil, altitude, and weather conditions. Substantial scientific evidence is available for some health promoting phytochemicals, such as dose-response relations, for performance and/or reduction in the risk of chronic disease. However, several limitations relating to absorption, distribution, metabolism and excretion of many dietary bioactives still exist and must be better understood This Special Issue compiles recent discoveries that advance our understanding of how dietary bioactive, particularly from fruits and vegetables, influence long-term health maintenance and disease prevention

Food Waste Valorization

Food waste is becoming an important and growing concern at both local and global levels. According to the Food and Agriculture Organization of the United Nations (FAO), one-third of all food production is wasted globally, and in particular, 1.3 billion tons of food produced for human consumption is wasted per year, representing an economic loss of EUR 800 billion. The main foods wasted are represented by vegetables, fruits, meat, and fish. Considering the high availability and the composition of food waste, there is an increasing interest in their bio-valorization. Moreover, according to the global Sustainable Development Goals (SDGs 12 and 13), an appropriate waste management represents an essential prerequisite for the sustainable development.This reprint collects interesting manuscripts regarding innovative research focused on food waste valorization through fermentation processes for obtaining value-added products such as enzymes, feed additives, biofuels, animal feeds as well as other useful chemicals or products, food-grade pigments, and single-cell protein (SCP), enhancing food security and environmentally sustainable development