An archaeal RNA binding protein, FAU-1, is a novel ribonuclease related to rRNA stability in Pyrococcus and Thermococcus

Ribosome biogenesis and turnover are processes necessary for cell viability and proliferation, and many kinds of proteins are known to regulate these processes. However, many questions still remain, especially in the Archaea. Generally, several ribonucleases are required to process precursor rRNAs to their mature forms, and to degrade rRNAs for quality control. Here, we found that FAU-1, which is known to be an RNA binding protein, possesses an RNase activity against precursor 5S rRNA derived from P. furiosus and T. kodakarensis in the order Thermococcales in vitro. An in vitro analysis revealed that UA sequences in the upstream of 5S rRNA were preferentially degraded by addition of FAU-1. Moreover, a fau-1 gene deletion mutant of T. kodakarensis showed a delay of exponential phase, reduction of maximum cell number and significant changes in the nucleotide sequence lengths of its 5S, 16S, and 23S rRNAs in early exponential phase. Our results suggest that FAU-1 is a potential RNase involved in rRNA stability through maturation and/or degradation processes.

Effect of masticatory stimulation on the quantity and quality of saliva and the salivary metabolomic profile

Background

This study characterized the changes in quality and quantity of saliva, and changes in the salivary metabolomic profile, to understand the effects of masticatory stimulation.

Methods

Stimulated and unstimulated saliva samples were collected from 55 subjects and salivary hydrophilic metabolites were comprehensively quantified using capillary electrophoresis-time-of-flight mass spectrometry.

Results

In total, 137 metabolites were identified and quantified. The concentrations of 44 metabolites in stimulated saliva were significantly higher than those in unstimulated saliva. Pathway analysis identified the upregulation of the urea cycle and synthesis and degradation pathways of glycine, serine, cysteine and threonine in stimulated saliva. A principal component analysis revealed that the effect of masticatory stimulation on salivary metabolomic profiles was less dependent on sample population sex, age, and smoking. The concentrations of only 1 metabolite in unstimulated saliva, and of 3 metabolites stimulated saliva, showed significant correlation with salivary secretion volume, indicating that the salivary metabolomic profile and salivary secretion volume were independent factors.

Conclusions

Masticatory stimulation affected not only salivary secretion volume, but also metabolite concentration patterns. A low correlation between the secretion volume and these patterns supports the conclusion that the salivary metabolomic profile may be a new indicator to characterize masticatory stimulation.

Dynamic Organization of Chromatin Domains Revealed by Super-Resolution Live-Cell Imaging

The eukaryotic genome is organized within cells as chromatin. For proper information output, higher-order chromatin structures can be regulated dynamically. How such structures form and behave in various cellular processes remains unclear. Here, by combining super-resolution imaging (photoactivated localization microscopy [PALM]) and single-nucleosome tracking, we developed a nuclear imaging system to visualize the higher-order structures along with their dynamics in live mammalian cells. We demonstrated that nucleosomes form compact domains with a peak diameter of ∼160 nm and move coherently in live cells. The heterochromatin-rich regions showed more domains and less movement. With cell differentiation, the domains became more apparent, with reduced dynamics. Furthermore, various perturbation experiments indicated that they are organized by a combination of factors, including cohesin and nucleosome-nucleosome interactions. Notably, we observed the domains during mitosis, suggesting that they act as building blocks of chromosomes and may serve as information units throughout the cell cycle.

Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus

Tardigrada, a phylum of meiofaunal organisms, have been at the center of discussions of the evolution of Metazoa, the biology of survival in extreme environments, and the role of horizontal gene transfer in animal evolution. Tardigrada are placed as sisters to Arthropoda and Onychophora (velvet worms) in the superphylum Panarthropoda by morphological analyses, but many molecular phylogenies fail to recover this relationship. This tension between molecular and morphological understanding may be very revealing of the mode and patterns of evolution of major groups. Limnoterrestrial tardigrades display extreme cryptobiotic abilities, including anhydrobiosis and cryobiosis, as do bdelloid rotifers, nematodes, and other animals of the water film. These extremophile behaviors challenge understanding of normal, aqueous physiology: how does a multicellular organism avoid lethal cellular collapse in the absence of liquid water? Meiofaunal species have been reported to have elevated levels of horizontal gene transfer (HGT) events, but how important this is in evolution, and particularly in the evolution of extremophile physiology, is unclear. To address these questions, we resequenced and reassembled the genome of H. dujardini, a limnoterrestrial tardigrade that can undergo anhydrobiosis only after extensive pre-exposure to drying conditions, and compared it to the genome of R. varieornatus, a related species with tolerance to rapid desiccation. The 2 species had contrasting gene expression responses to anhydrobiosis, with major transcriptional change in H. dujardini but limited regulation in R. varieornatus. We identified few horizontally transferred genes, but some of these were shown to be involved in entry into anhydrobiosis. Whole-genome molecular phylogenies supported a Tardigrada+Nematoda relationship over Tardigrada+Arthropoda, but rare genomic changes tended to support Tardigrada+Arthropoda.

Synthetic Biomarker Design by Using Analyte-Responsive Acetaminophen

The use of synthetic biomarkers is an emerging technique to improve disease diagnosis. Here, we report a novel design strategy that uses analyte-responsive acetaminophen (APAP) to expand the catalogue of analytes available for synthetic biomarker development. As proof-of-concept, we designed hydrogen peroxide (H₂ O₂ )-responsive APAP (HR-APAP) and succeeded in H₂ O₂ detection with cellular and animal experiments. In fact, for blood samples following HR-APAP injection, we demonstrated that the plasma concentration ratio [APAP+APAP conjugates]/[HR-APAP] accurately reflects in vivo differences in H₂ O₂ levels. We anticipate that our practical methodology will be broadly useful for the preparation of various synthetic biomarkers.

Draft Genome Sequence of Roseovarius sp. A-2, an Iodide-Oxidizing Bacterium Isolated from Natural Gas Brine Water, Chiba, Japan

Roseovarius sp. A-2 is a heterotrophic iodide (I^-)-oxidizing bacterium isolated from iodide-rich natural gas brine water in Chiba, Japan. This strain oxidizes iodide to molecular iodine (I₂) by means of an extracellular multicopper oxidase. Here we report the draft genome sequence of strain A-2. The draft genome contained 46 tRNA genes, 1 copy of a 16S-23S-5S rRNA operon, and 4,514 protein coding DNA sequences, of which 1,207 (27%) were hypothetical proteins. The genome contained a gene encoding IoxA, a multicopper oxidase previously found to catalyze the oxidation of iodide in Iodidimonas sp. Q-1. This draft genome provides detailed insights into the metabolism and potential application of Roseovarius sp. A-2.

Eggshell membrane powder ameliorates intestinal inflammation by facilitating the restitution of epithelial injury and alleviating microbial dysbiosis

Gut microbiota is an essential factor in the shaping of intestinal immune system development and driving inflammation in inflammatory bowel disease (IBD). We report the effects and microbe-host interactions underlying an intervention using fine powder of eggshell membrane (ESM) against IBD. ESM attenuated lipopolysaccharide-induced inflammatory cytokine production and promoted the Caco-2 cell proliferation by up-regulating growth factors in vitro. In a murine model of dextran sodium sulphate-induced colitis, ESM significantly suppressed the disease activity index and colon shortening. These effects were associated with significant ameliorations of gene expressions of inflammatory mediators, intestinal epithelial cell proliferation, restitution-related factors and antimicrobial peptides. Multifaceted integrated omics analyses revealed improved levels of energy metabolism-related genes, proteins and metabolites. Concomitantly, cecal metagenomic information established an essential role of ESM in improving dysbiosis characterized by increasing the diversity of bacteria and decreasing absolute numbers of pathogenic bacteria such as Enterobacteriaceae and E. coli, as well as in the regulation of the expansion of Th17 cells by suppressing the overgrowth of segmented filamentous bacteria. Such modulations have functional effects on the host; i.e., repairing the epithelium, regulating energy requirements and eventually alleviating mucosal inflammation. These findings are first insights into ESM’s modulation of microbiota and IBD suppression, providing new perspectives on the prevention/treatment of IBD.

Developmental changes in the balance of glycolytic ATP production and oxidative phosphorylation in ventricular cells: A simulation study

The developmental program of the heart requires accurate regulation to ensure continuous circulation and simultaneous cardiac morphogenesis, because any functional abnormalities may progress to congenital heart malformation. Notably, energy metabolism in fetal ventricular cells is regulated in a manner that differs from adult ventricular cells: fetal cardiomyocytes generally have immature mitochondria and fetal ventricular cells show greater dependence on glycolytic ATP production. However, although various characteristics of energy metabolism in fetal ventricular cells have been reported, to our knowledge, a quantitative description of the contributions of these factors to fetal ventricular cell functions has not yet been established. Here, we constructed a mathematical model to integrate various characteristics of fetal ventricular cells and predicted the contribution of each characteristic to the maintenance of intracellular ATP concentration and sarcomere contraction under anoxic conditions. Our simulation results demonstrated that higher glycogen content, higher hexokinase activity, and lower creatine concentration helped prolong the time for which ventricular cell contraction was maintained under anoxic conditions. The integrated model also enabled us to quantitatively assess the contributions of factors related to energy metabolism in ventricular cells. Because fetal cardiomyocytes exhibit similar energy metabolic profiles to stem cell-derived cardiomyocytes and those in the failing heart, an improved understanding of these fetal ventricular cells will contribute to a better comprehension of the processes in stem cell-derived cardiomyocytes or under pathological conditions.

Differential Binding of Three Major Human ADAR Isoforms to Coding and Long Non-Coding Transcripts

RNA editing by deamination of adenosine to inosine is an evolutionarily conserved process involved in many cellular pathways, from alternative splicing to miRNA targeting. In humans, it is carried out by no less than three major adenosine deaminases acting on RNA (ADARs): ADAR1-p150, ADAR1-p110, and ADAR2. However, the first two derive from alternative splicing, so that it is currently impossible to delete ADAR1-p110 without also knocking out ADAR1-p150 expression. Furthermore, the expression levels of ADARs varies wildly among cell types, and no study has systematically explored the effect of each of these isoforms on the cell transcriptome. In this study, RNA immunoprecipitation (RIP)-sequencing on overexpressed ADAR isoforms tagged with green fluorescent protein (GFP) shows that each ADAR is associated with a specific set of differentially expressed genes, and that they each bind to distinct set of RNA targets. Our results show a good overlap with known edited transcripts, establishing RIP-seq as a valid method for the investigation of RNA editing biology.

Rearing and observation of immature stages of the hoverfly Microdon katsurai (Diptera, Syrphidae)

Background

The hoverfly Microdon (Chymophila) katsurai Maruyama et Hironaga 2004 was speculated to be a myrmecophilous species associated with the ant Polyrhachislamellidens based on observations of adults near the ant nest. However, there have been no reports regarding the observation of immature stages of this species in association with P.lamellidens.

New information

For the first time, we found three M.katsurai larvae inside a P.lamellidens nest and conducted rearing experiments on the larval M.katsurai. P.lamellidens workers did not show any inspection or attack behavior against the M.katsurai larvae under rearing conditions, suggesting that M.katsurai larvae can survive inside a P.lamellidens nest. Although no predatory behavior by the M.katsurai larvae was observed, all the M.katsurai larvae pupated and emerged in a rearing environment. The dorsal surface of the larval M.katsurai has a distinct pale green color with a uniform reticular structure. The puparium of M.katsurai shows several morphological features that are characteristic of the subgenus Chymophila. We conclude that M.katsurai is likely a myrmecophilous species that utilizes P.lamellidens as a specific host and that classification of M.katsurai based on puparium morphology is concordant with that based on adult morphology.

Morphology and phylogeny of a new wall-less freshwater volvocalean flagellate, Hapalochloris nozakii gen. et sp. nov. (Volvocales, Chlorophyceae)

New strains of a wall-less unicellular volvocalean flagellate were isolated from a freshwater environment in Japan. Observations of the alga, described here as Hapalochloris nozakii Nakada, gen. et sp. nov., were made using light, fluorescence, and electron microscopy. Each vegetative cell had two flagella, four contractile vacuoles, and a spirally furrowed cup-shaped chloroplast with an axial pyrenoid, and mitochondria located in the furrows. Based on the morphology, H. nozakii was distinguished from other known wall-less volvocalean flagellates. Under electron microscopy, fibrous material, instead of a cell wall and dense cortical microtubules, was observed outside and inside the cell membrane, respectively. Based on the phylogenetic analyses of 18S rRNA gene sequences, H. nozakii was found to be closely related to Asterococcus, Oogamochlamys, Rhysamphichloris, and "Dunaliella" lateralis and was separated from other known wall-less flagellate volvocaleans, indicating independent secondary loss of the cell wall in H. nozakii. In the combined 18S rRNA and chloroplast gene tree, H. nozakii was sister to Lobochlamys.

A serum metabolomics-based profile in low bone mineral density postmenopausal women

Osteoporosis is characterized as a metabolic disorder of bone tissue, and various metabolic markers are now available to support its diagnosis and evaluate treatment effects. Substances produced as end products of metabolomic activities are the correlated factors to the biological or metabolic status, and thus, metabolites are considered highly sensitive markers of particular pathological states, including osteoporosis. Here we undertook comprehensive serum metabolomics analysis in postmenopausal women with or without low bone mineral density (low BMD vs controls) for the first time using capillary electrophoresis/mass spectrometry. Among the metabolites tested, 57 were detected in sera. Levels of hydroxyproline, Gly-Gly and cystine, differed significantly between groups, with Gly-Gly and cystine significantly lower in the low BMD group and hydroxyproline, a reported marker of osteoporosis, significantly higher. Levels of TRACP5b, a bone resorption marker, were significantly higher in the low BMD group, supporting the study's validity. Taken together, our findings represent novel metabolomic profiling in low BMD in postmenopausal women.

Metabolomic Profiling as a Possible Reverse Engineering Tool for Estimating Processing Conditions of Dry-Cured Hams

Dry-cured hams are popular among consumers. To increase the attractiveness of the product, objective analytical methods and algorithms to evaluate the relationship between observable properties and consumer acceptability are required. In this study, metabolomics, which is used for quantitative profiling of hundreds of small molecules, was applied to 12 kinds of dry-cured hams from Japan and Europe. In total, 203 charged metabolites, including amino acids, organic acids, nucleotides, and peptides, were successfully identified and quantified. Metabolite profiles were compared for the samples with different countries of origin and processing methods (e.g., smoking or use of a starter culture). Principal component analysis of the metabolite profiles with sensory properties revealed significant correlations for redness, homogeneity, and fat whiteness. This approach could be used to design new ham products by objective evaluation of various features.

Systematic characterization of artificial small RNA-mediated inhibition of Escherichia coli growth

A new screening system for artificial small RNAs (sRNAs) that inhibit the growth of Escherichia coli was constructed. In this system, we used a plasmid library to express RNAs of ∼120 nucleotides, each with a random 30-nucleotide sequence that can recognize its target mRNA(s). After approximately 60,000 independent colonies were screened, several plasmids that inhibited bacterial growth were isolated. To understand the inhibitory mechanism, we focused on one sRNA, S-20, that exerted a strong inhibitory effect. A time-course analysis of the proteome of S-20-expressing E. coli and a bioinformatic analysis were used to identify potential S-20 target mRNAs, and suggested that S-20 binds the translation initiation sites of several mRNAs encoding enzymes such as peroxiredoxin (osmC), glycyl-tRNA synthetase α subunit (glyQ), uncharacterized protein ygiM, and tryptophan synthase β chain (trpB). An in vitro translation analysis of chimeric luciferase-encoding mRNAs, each containing a potential S-20 target sequence, indicated that the translation of these mRNAs was inhibited in the presence of S-20. A gel shift analysis combined with the analysis of a series of S-20 mutants suggested that S-20 targets multiple mRNAs that are responsible for inhibiting E. coli growth. These data also suggest that S-20 acts like an endogenous sRNA and that E. coli can utilize artificial sRNAs.

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Daoust RD, Lessard JL, Marquis MM, Paquet JP, Siemens K, Sangaran D, Hunt BJ, Durward A, Nyman A, Murdoch IA, Tibby SM, Ampatzidou F, Moisidou D, Dalampini E, Nastou M, Vasilarou E, Kalaizi V, Chatzikostenoglou H, Drossos G, Spadaro S, Fogagnolo A, Fiore T, Schiavi A, Fontana V, Taccone F, Volta C, Chochliourou E, Volakli E, Violaki A, Samkinidou E, Evlavis G, Panagiotidou V, Sdougka M, Mothukuri R, Battle C, Guy K, Mills G, Evans P, Wijesuriya J, Keogh S, Docherty A, O’Donnell R, Brunskill S, Trivella M, Doree C, Holst L, Parker M, Gregersen M, Almeida J, Walsh T, Stanworth S, Moravcova S, Mansell J, Rogers A, Smith RA, Hamilton-Davies C, Omar A, Allam M, Bilala O, Kindawi A, Ewila H, Ampatzidou F, Moisidou D, Nastou M, Dalampini E, Malamas A, Vasilarou E, Drossos G, Ferreira G, Caldas J, Fukushima J, Osawa EA, Arita E, Camara L, Zeferino S, Jardim J, Gaioto F, Dallan L, Jatene FB, Kalil Filho R, Galas F, Hajjar LA, Mitaka C, Ohnuma T, Murayama T, Kunimoto F, Nagashima M, Takei T, Tomita M, Omar A, Mahmoud K, Hanoura S, Sudarsanan S, Sivadasan P, Othamn H, Shouman Y, Singh R, Al Khulaifi A, Mandel I, Mikheev S, Suhodolo I, Kiselev V, Svirko Y, Podoksenov Y, Jenkins SA, Griffin R, Tovar Doncel MS, Lima A, Aldecoa C, Ince C, Taha A, Shafie A, Mostafa M, Syed N, Hon H, Righetti F, Colombaroli E, Castellano G, Righetti F, Colombaroli E, Hravnak M, Chen LC, Dubrawski AD, Clermont GC, Pinsky MR, Gonzalez S, Macias D, Acosta J, Jimenez P, Loza A, Lesmes A, Lucena F, Leon C, Tovar Doncel MS, Ince C, Aldecoa C, Lima A, Bastide M, Richecoeur J, Frenoy E, Lemaire C, Sauneuf B, Tamion F, Nseir S, Du Cheyron D, Dupont H, Maizel J, Shaban M, Kolko R, Salahuddin N, Sharshir M, AbuRageila M, AlHussain A, Mercado P, Maizel J, Kontar L, Titeca D, Brazier F, Riviere A, Joris M, Soupison T, De Cagny B, Slama M, Wagner J, Körner A, Kubik M, Kluge S, Reuter D, Saugel B, Colombaroli E, Righetti F, Castellano G, Tran T, De Bels D, Cudia A, Strachinaru M, Ghottignies P, Devriendt J, Pierrakos C, Martínez González Ó, Blancas R, Luján J, Ballesteros D, Martínez Díaz C, Núñez A, Martín Parra C, López Matamala B, Alonso Fernández M, Chana M, Huber W, Eckmann M, Elkmann F, Gruber A, Klein I, Schmid RM, Lahmer T, Moller PW, Sondergaard S, Jakob SM, Takala J, Berger D, Bastoni D, Aya H, Toscani L, Pigozzi L, Rhodes A, Cecconi M, Ostrowska C, Aya H, Abbas A, Mellinghoff J, Ryan C, Dawson D, Rhodes A, Cecconi M, Cronhjort M, Wall O, Nyberg E, Zeng R, Svensen C, Mårtensson J, Joelsson-Alm E, Aguilar Arzapalo M, Barradas L, Lopez V, Cetina M, Parenti N, Palazzi C, Amidei LA, Borrelli FB, Campanale SC, Tagliazucchi FT, Sedoni GS, Lucchesi DL, Carella EC, Luciani AL, Mackovic M, Maric N, Bakula M, Aya H, Rhodes A, Grounds RM, Fletcher N, Cecconi M, Avard B, Zhang P, Mezidi M, Charbit J, Ould-Chikh M, Deras P, Maury C, Martinez O, Capdevila X, Hou P, Linde-Zwirble WZ, Douglas ID, Shapiro NS, Ben Souissi A, Mezghani I, Ben Aicha Y, Kamoun S, Laribi B, Jeribi B, Riahi A, Mebazaa MS, Pereira C, Marinho R, Antunes R, Marinho A, Crivits M, Raes M, Decruyenaere J, Hoste E, Bagin V, Rudnov V, Savitsky A, Astafyeva M, Korobko I, Vein V, Kampmeier T, Arnemann P, Hessler M, Wald A, Bockbreder K, Morelli A, Van Aken H, Rehberg S, Ertmer C, Arnemann P, Hessler M, Kampmeier T, Rehberg S, Van Aken H, Ince C, Ertmer C, Reddy S, Bailey M, Beasley R, Bellomo R, Mackle D, Psirides A, Young P, Reddy S, Bailey M, Beasley R, Bellomo R, Mackle D, Young P, Venkatesh H, Ramachandran S, Basu A, Nair H, Egan S, Bates J, Oliveira S, Rangel Neto NR, Reis FQ, Lee CP, Lin XL, Choong C, Eu KM, Sim WY, Tee KS, Pau J, Abisheganaden J, Maas K, De Geus H, Lafuente E, Marinho R, Moura J, Antunes R, Marinho A, Doris TE, Monkhouse D, Shipley T, Kardasz S, Gonzalez I, Stads S, Groeneveld AJ, Elsayed I, Ward N, Tridente A, Raithatha A, Steuber A, Pelletier C, Schroeder S, Michael E, Slowinski T, Kindgen-Milles D, Ghabina S, Turani F, Belli A, Busatti S, Barettin G, Candidi F, Gargano F, Barchetta R, Falco M, Demirkiran O, Kosuk M, Bozbay S, Weber V, Hartmann J, Harm S, Linsberger I, Eichhorn T, Valicek G, Miestinger G, Hoermann C, Faenza S, Ricci D, Mancini E, Gemelli C, Cuoghi A, Magnani S, Atti M, Laddomada T, Doronzio A, Balicco B, Gruda MC, O’Sullivan P, Dan VP, Guliashvili T, Scheirer A, Golobish TD, Capponi VJ, Chan PP, Kogelmann K, Drüner M, Jarczak D, Turani F, Belli AB, Martni SM, Cotticelli VC, Mounajergi F, Barchetta R, Morimoto S, Ishikura H, Hussain I, Salahuddin N, Nadeem A, Ghorab K, Maghrabi K, Kloesel SK, Goldfuss C, Stieglitz A, Stieglitz AS, Krstevska L, Albuszies G, Aguilar Arzapalo M, Barradas L, Lopez V, Escalante A, Jimmy G, Cetina M, Izawa J, Iwami T, Uchino S, Takinami M, Kitamura T, Kawamura T, Powell-Tuck JG, Crichton S, Raimundo M, Camporota L, Wyncoll D, Ostermann M, Hana A, De Geus HR, De Geus HR, Hana A, Aydogdu M, Boyaci N, Yuksel S, Gursel G, Cayci Sivri AB, Meza-Márquez J, Nava-López J, Carrillo-Esper R, Dardashti A, Grubb A, Maizel J, Wetzstein M, Titeca D, Kontar L, Brazier F, De Cagny B, Riviere A, Soupison T, Joris M, Slama M, Peters E, Njimi H, Pickkers P, Vincent JL, Waraich M, Doyle J, Samuels T, Forni L, Desai N, Baumber R, Gunning P, Sell A, Lin S, Torrence H, O’Dwyer M, Kirwan C, Prowle J, Kim T, O’Connor ME, Hewson RW, Kirwan CJ, Pearse RM, Prowle J, Hanoura S, Omar A, Othamn H, Sudarsanan S, Allam M, Maksoud M, Singh R, Al Khulaifi A, O’Connor ME, Hewson RW, Kirwan CJ, Pearse RM, Prowle J, Uzundere O, Memis D, Ýnal M, Gultekin A, Turan N, Aydin MA, Basar H, Sencan I, Kapuagasi A, Ozturk M, Uzundurukan Z, Gokmen D, Ozcan A, Kaymak C, Artemenko VA, Budnyuk A, Pugh R, Bhandari S, Mauri T, Turrini C, Langer T, Taccone P, Volta CA, Marenghi C, Gattinoni L, Pesenti A, Sweeney L, O’Sullivan A, Kelly P, Mukeria E, MacLoughlin R, Pfeffer M, Thomas JT, Bregman GB, Karp GK, Kishinevsky EK, Stavi DS, Adi NA, Poropat T, Knafelj R, Llopart E, Batlle M, De Haro C, Mesquida J, Artigas A, Pavlovic D, Lewerentz L, Spassov A, Schneider R, De Smet S, De Raedt S, Derom E, Depuydt P, Oeyen S, Benoit D, Decruyenaere J, Gobatto A, Besen B, Tierno P, Melro L, Mendes P, Cadamuro F, Park M, Malbouisson LM, Civantos BC, Lopez JL, Robles A, Figueira J, Yus S, Garcia A, Oglinda A, Ciobanu G, Oglinda C, Schirca L, Sertinean T, Lupu V, Kelly P, O’Sullivan A, Sweeney L, MacLoughlin R, O’Sullivan A, Kelly P, Sweeney L, Mukeria E, Wolny M, MacLoughlin R, Pagano A, Numis F, Visone G, Saldamarco L, Russo T, Porta G, Paladino F, Bell C, Liu J, Debacker J, Lee C, Tamberg E, Campbell V, Mehta S, Silva-Pinto A, Sarmento A, Santos L, Kara Ý, Yýldýrým F, Zerman A, Güllü Z, Boyacý N, Basarýk Aydogan B, Gaygýsýz Ü, Gönderen K, Arýk G, Turkoglu M, Aydogdu M, Aygencel G, Ülger Z, Gursel G, Boyacý N, Isýkdogan Z, Özdedeoglu Ö, Güllü Z, Badoglu M, Gaygýsýz U, Aydogdu M, Gursel G, Kongpolprom N, Sittipunt C, Eden A, Kokhanovsky Y, Bursztein – De Myttenaere S, Pizov R, Neilans L, MacIntyre N, Radosevich M, Wanta B, Weber V, Meyer T, Smischney N, Brown D, Diedrich D, Fuller A, McLindon P, Sim K, Shoaeir M, Noeam K, Mahrous A, Matsa R, Ali A, Dridi C, Koubaji S, Kamoun S, Haddad F, Ben Souissi A, Laribi B, Riahi A, Mebazaa MS, Pérez-Calatayud A, Carrillo-Esper R, Zepeda-Mendoza A, Diaz-Carrillo M, Arch-Tirado E, Carbognin S, Pelacani L, Zannoni F, Agnoli A, Gagliardi G, Cho R, Adams A, Lunos S, Ambur S, Shapiro R, Prekker M, Thijssen M, Janssen L, Foudraine N, Voscopoulos CJ, Freeman J, Voscopoulos CJ, Freeman J, George E, Voscopoulos CJ, Eversole D, Freeman J, George E, Muttini S, Bigi R, Villani G, Patroniti N, Williams G, Voscopoulos CJ, Freeman J, George E, Waldmann A, Böhm S, Windisch W, Strassmann S, Karagiannidis C, Waldmann A, Böhm S, Windisch W, Strassmann S, Karagiannidis C, Karagiannidis CK, Waldmann AW, Böhm SB, Strassmann S, Windisch WW, Persson P, Lundin S, Stenqvist O, Porta G, Numis F, Serra CS, Pagano AP, Masarone MM, Rinaldi LR, Amelia AA, Fascione MF, Adinolfi LA, Ruggiero ER, Asota F, O’Rourke K, Ranjan S, Morgan P, DeBacker JW, Tamberg E, O’Neill L, Munshi L, Burry L, Fan E, Mehta S, Poo S, Mahendran K, Fowles J, Gerrard C, Vuylsteke A, Loveridge R, Chaddock C, Patel S, Kakar V, Willars C, Hurst T, Park C, Best T, Vercueil A, Auzinger G, Borgman A, Proudfoot AG, Grins E, Emiley KE, Schuitema J, Fitch SJ, Marco G, Sturgill J, Dickinson MG, Strueber M, Khaghani A, Wilton P, Jovinge SM, Sampson C, Harris-Fox S, Cove ME, Vu LH, Sen A, Federspiel WJ, Kellum JA, Mazo Torre C, Riera J, Ramirez S, Borgatta B, Lagunes L, Rello J, Kuzovlev AK, Moroz V, Goloubev A, Polovnikov S, Nenchuk S, Karavana V, Glynos C, Asimakos A, Pappas K, Vrettou C, Magkou M, Ischaki E, Stathopoulos G, Zakynthinos S, Spadaro S, Kozhevnikova I, Dalla Corte F, Grasso S, Casolari P, Caramori G, Volta C, Andrianjafiarinoa T, Randriamandrato T, Rajaonera T, El-Dash S, Costa ELV, Tucci MR, Leleu F, Kontar L, De Cagny B, Brazier F, Titeca D, Bacari-Risal G, Maizel J, Amato M, Slama M, Mercado P, Maizel J, Kontar L, 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B, Salgueiro A, Marinho A, Marinho R, Santos M, Lafuente E, Castro H, Cabral S, Moura J, Martins P, Oliveira B, Salgueiro A, Duarte S, Castro S, Melo M, Casteloes P, Marinho A, Gray S, Maipang K, Bhurayanontachai R, Grädel LG, Schütz P, Langlois P, Manzanares W, Tincu R, Cobilinschi C, Tomescu D, Ghiorghiu Z, Macovei R, Manzanares W, Langlois P, Lemieux M, Elke G, Bloos F, Reinhart K, Heyland D, Langlois P, Lemieux M, Aramendi I, Heyland D, Manzanares W, Su Y, Marinho R, Babo N, Marinho A, Hoshino M, Haraguchi Y, Kajiwara S, Mitsuhashi T, Tsubata T, Aida M, Rattanapraphat T, Bhurayanontachai R, Kongkamol C, Khwannimit B, Marinho R, Santos M, Castro H, Lafuente E, Salgueiro A, Cabral S, Martins P, Moura J, Oliveira B, Melo M, Xavier B, Valente J, Magalhaes C, Casteloes P, Marinho A, Moisidou D, Ampatzidou F, Koutsogiannidis C, Moschopoulou M, Drossos G, Taskin G, Çakir M, Güler AK, Taskin A, Öcal N, Özer S, Yamanel L, Wong JM, Fitton C, Anwar S, Stacey S, Aggou M, Fyntanidou B, 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N, Avard B, Burns R, Patarchi A, Spina T, Tanaka H, Otani N, Ode S, Ishimatsu S, Cho J, Moon JB, Park CW, Ohk TG, Shin MC, Won MH, Dakova S, Ramsheva Z, Ramshev K, Cho J, Moon JB, Park CW, Ohk TG, Shin MC, Cho J, Moon JB, Park CW, Ohk TG, Shin MC, Marudi A, Baroni S, Gaspari A, Bertellini E, Orhun G, Senturk E, Ozcan PE, Sencer S, Ulusoy C, Tuzun E, Esen F, Tincu R, Cobilinschi C, Tomescu D, Ghiorghiu Z, Macovei R, Van Assen M, Admiraal MM, Van Putten MJ, Tjepkema-Cloostermans M, Van Rootselaar AF, Horn J, Fallenius M, Skrifvars MB, Reinikainen M, Bendel S, Raj R, Abu-Habsa M, Hymers C, Borowska A, Sivadhas H, Sahiba S, Perkins S, Rubio J, Rubio JA, Sierra R, English S, Chasse M, Turgeon A, Lauzier F, Griesdale D, Garland A, Fergusson D, Zarychanski R, Tinmouth A, Van Walraven C, Montroy K, Ziegler J, Dupont Chouinard R, Carignan R, Dhaliwal A, Lum C, Sinclair J, Pagliarello G, McIntyre L, English S, Chasse M, Turgeon A, Lauzier F, Griesdale D, Garland A, Fergusson D, Zarychanski R, Tinmouth A, Van Walraven C, Montroy K, Ziegler J, Dupont Chouinard R, Carignan R, Dhaliwal A, Lum C, Sinclair J, Pagliarello G, McIntyre L, Groza T, Moreau N, Castanares-Zapatero D, Hantson P, Carbonara M, Ortolano F, Zoerle T, Magnoni S, Pifferi S, Conte V, Stocchetti N, Carteron L, Suys T, Patet C, Quintard H, Oddo M, Rubio JA, Rubio J, Sierra R, Spatenkova V, Pokorna E, Suchomel P, Ebert N, Jancik J, Rhodes H, Bylinski T, Hawthorne C, Shaw M, Piper I, Kinsella J, Kink AK, Rätsep IR, Boutin A, Moore L, Chasse M, Zarychanski R, Lauzier F, English S, McIntyre L, Lacroix J, Griesdale D, Lessard-Bonaventure P, Turgeon AF, Boutin A, Moore L, Green R, Lessard-Bonaventure P, Erdogan M, Butler M, Lauzier F, Chasse M, English S, McIntyre L, Zarychanski R, Lacroix J, Griesdale D, Desjardins P, Fergusson DA, Turgeon AF, Goncalves B, Vidal B, Valdez C, Rodrigues AC, Miguez L, Moralez G, Hong T, Kutz A, Hausfater P, Amin D, Struja T, Haubitz S, Huber A, Mueller B, Schuetz P, Brown T, Collinson J, Pritchett C, Slade T, Le Guen M, Hellings S, Ramsaran R, Alsheikhly A, Abe T, Kanapeckaite L, Abu-Habsa M, Bahl R, Russell MQ, Real KJ, Abu-Habsa M, Lyon RM, Oveland NP, Penketh J, Mcdonald M, Kelly F, Alfafi M, Alsolamy S, Almutairi W, Alotaibi B, Van den Berg AE, Schriel Y, Dawson L, Meynaar IA, Talaie H, Silva D, Fernandes S, Gouveia J, Santos Silva J, Foley J, Kaskovagheorgescu A, Evoy D, Cronin J, Ryan J, Huck M, Hoffmann C, Renner J, Laitselart P, Donat N, Cirodde A, Schaal JV, Masson Y, Nau A, Leclerc T, Howarth O, Davenport K, Jeanrenaud P, Raftery S, MacTavish P, Devine H, McPeake J, Daniel M, Kinsella J, Quasim T, Alrabiee S, Alrashid A, Alsolamy S, Gundogan O, Bor C, Akýn Korhan E, Demirag K, Uyar M, Frame F, Ashton C, Bergstrom Niska L, Dilokpattanamongkol P, Suansanae T, Suthisisang C, Morakul S, Karnjanarachata C, Tangsujaritvijit V, Mahmood S, Al Thani H, Almenyar A, Vakalos A, Avramidis V, Sharvill R, Penketh J, Morton SE, Chiew YS, Pretty C, Chase JG, Shaw GM, Knafelj R, Kordis P, Patel S, Grover V, Kuchyn I, Bielka K, Aidoni Z, Grosomanidis V, Kotzampassi K, Stavrou G, Fyntanidou B, Patsatzakis S, Skourtis C, Lee SD, Williams K, Weltes ID, Berhane S, Arrowsmith C, Peters C, Robert S, Caldas J, Panerai RB, Robinson TG, Camara L, Ferreira G, Borg-Seng-Shu E, De Lima Oliveira M, Mian NC, Santos L, Nogueira R, Zeferino SP, Jacobsen Teixeira M, Galas F, Hajjar LA, Killeen P, McPhail M, Bernal W, Maggs J, Wendon J, Hughes T, Taniguchi LU, Siqueira EM, Vieira Jr JM, Azevedo LC, Ahmad AN, Abu-Habsa M, Bahl R, Helme E, Hadfield S, Loveridge R, Shak J, Senver C, Howard-Griffin R, Wacharasint P, Fuengfoo P, Sukcharoen N, Rangsin R, Sbiti-Rohr D, Schuetz P, Na H, Song S, Lee S, Jeong E, Lee K, Cooper M, Milinis K, Williams G, McCarron E, Simants S, Patanwala I, Welters ID, Zoumpelouli E, Volakli EA, Chrysohoidou V, Georgiou S, Charisopoulou K, Kotzapanagiotou E, Panagiotidou V, Manavidou K, Stathi Z, Sdougka M, Salahuddin N, AlGhamdi B, Marashly Q, Zaza K, Sharshir M, Khurshid M, Ali Z, Malgapo M, Jamil M, Shafquat A, Shoukri M, Hijazi M, Abe T, Uchino S, Takinami M, Rangel Neto NR, Oliveira S, Reis FQ, Rocha FA, Moralez G, Ebecken K, Rabello LS, Lima MF, Hatum R, De Marco FV, Alves A, Pinto JE, Godoy M, Brasil PE, Bozza FA, Salluh JI, Soares M, Krinsley J, Kang G, Perry J, Hines H, Wilkinson KM, Tordoff C, Sloan B, Bellamy MC, Moreira E, Verga F, Barbato M, Burghi G, Soares M, Silva UV, Azevedo LC, Torelly AP, Kahn JM, Angus DC, Knibel MF, Brasil PE, Bozza FA, Salluh JI, Velasco MB, Dalcomune DM, Marshall R, Gilpin T, Tridente A, Raithatha A, Mota D, Loureiro B, Dias J, Afonso O, Coelho F, Martins A, Faria F, Al-Dorzi H, Al Orainni H, AlEid F, Tlaygeh H, Itani A, Hejazi A, Arabi Y, Gaudry S, Messika J, Ricard JD, Guillo S, Pasquet B, Dubief E, Dreyfuss D, Tubach F, Battle C, James K, Temblett P, Davies L, Battle C, Lynch C, Pereira S, Cavaco S, Fernandes J, Moreira I, Almeida E, Seabra Pereira F, Malheiro M, Cardoso F, Aragão I, Cardoso T, Fister M, Knafelj R, Muraray Govind P, Brahmananda Reddy N, Pratheema R, Arul ED, Devachandran J, Velasco MB, Dalcomune DM, Knafelj R, Fister M, Chin-Yee N, D’Egidio G, Thavorn K, Heyland D, Kyeremanteng K, Murchison AG, Swalwell K, Mandeville J, Stott D, Guerreiro I, Devine H, MacTavish P, McPeake J, Quasim T, Kinsella J, Daniel M, Goossens C, Marques MB, Derde S, Vander Perre S, Dufour T, Thiessen SE, Güiza F, Janssens T, Hermans G, Vanhorebeek I, De Bock K, Van den Berghe G, Langouche L, Devine H, MacTavish P, Quasim T, Kinsella J, Daniel M, McPeake J, Miles B, Madden S, Devine H, Weiler M, Marques P, Rodrigues C, Boeira M, Brenner K, Leães C, Machado A, Townsend R, Andrade J, MacTavish P, McPeake J, Devine H, Kinsella J, Daniel M, Kishore R, Fenlon C, Quasim T, Fiks T, Ruijter A, Te Raa M, Spronk P, Chiew YS, Docherty P, Dickson J, Moltchanova E, Scarrot C, Pretty C, Shaw GM, Chase JG, Hall T, Ngu WC, Jack JM, Morgan P, Avard B, Pavli A, Gee X, Bor C, Akin Korhan E, Demirag K, Uyar M, Shirazy M, Fayed A, Gupta S, Kaushal A, Dewan S, Varma A, Ghosh E, Yang L, Eshelman L, Lord B, Carlson E, Helme E, Broderick R, Hadfield S, Loveridge R, Ramos J, Forte D, Yang F, Hou P, Dudziak J, Feeney J, Wilkinson K, Bauchmuller K, Shuker K, Faulds M, Raithatha A, Bryden D, England L, Bolton N, Tridente A, Bauchmuller K, Shuker K, Tridente A, Faulds M, Matheson A, Gaynor J, Bryden D, ᅟ SSYHRC, Ramos J, Peroni B, Daglius-Dias R, Miranda L, Cohen C, Carvalho C, Velasco I, Forte D, Kelly JM, Neill A, Rubenfeld G, Masson N, Min A, Boezeman E, Hofhuis J, Hovingh A, De Vries R, Spronk P, Cabral-Campello G, Aragão I, Cardoso T, Van Mol M, Nijkamp M, Kompanje E, Ostrowski P, Omar A, Kiss K, Köves B, Csernus V, Molnár Z, Hoydonckx Y, Vanwing S, Stessel B, Van Assche A, Jamaer L, Dubois J, Medo V, Galvez R, Miranda JP, Stone C, Wigmore T, Arunan Y, Wheeler A, Bauchmuller K, Bryden D, Wong Y, Poi C, Gu C, Molmy P, Van Grunderbeeck N, Nigeon O, Lemyze M, Thevenin D, Mallat J, Ramos J, Correa M, Carvalho RT, Forte D, Fernandez A, McBride C, Koonthalloor E, Walsh C, Webber A, Ashe M, Smith K, Jeanrenaud P, Marudi A, Baroni S, Ragusa F, Bertellini E, Volakli EA, Chochliourou E, Dimitriadou M, Violaki A, Mantzafleri P, Samkinidou E, Vrani O, Arbouti A, Varsami T, Sdougka M, Bollen JA, Van Smaalen TC, De Jongh WC, Ten Hoopen MM, Ysebaert D, Van Heurn LW, Van Mook WN, Sim K, Fuller A, Roze des Ordons A, Couillard P, Doig C, Van Keer RV, Deschepper RD, Francke AF, Huyghens LH, Bilsen JB, Nyamaizi B, Dalrymple C, Molokhia A, Dobru A, Marrinan E, Ankuli A, Molokhia A, McPeake J, Struthers R, Crawford R, Devine H, Mactavish P, Quasim T, Morelli P, Degiovanangelo M, Lemos F, MArtinez V, Verga F, Cabrera J, Burghi G, Rutten A, Van Ieperen S, De Geer S, Van Vugt M, Der Kinderen E, Giannini A, Miccinesi G, Marchesi T, Prandi E. Erratum to: 36th International Symposium on Intensive Care and Emergency Medicine: Brussels, Belgium. 15-18 March 2016

[This corrects the article DOI: 10.1186/s13054-016-1208-6.].

Metabolic Profiling of Total Physical Activity and Sedentary Behavior in Community-Dwelling Men

Objective

Physical activity is known to be preventive against various non-communicable diseases. We investigated the relationship between daily physical activity level and plasma metabolites using a targeted metabolomics approach in a population-based study.

Methods

A total of 1,193 participants (male, aged 35 to 74 years) with fasting blood samples were selected from the baseline survey of a cohort study. Information on daily total physical activity, classified into four levels by quartile of metabolic equivalent scores, and sedentary behavior, defined as hours of sitting per day, was collected through a self-administered questionnaire. Plasma metabolite concentrations were quantified by capillary electrophoresis mass spectrometry method. We performed linear regression analysis models with multivariable adjustment and corrected p-values for multiple testing in the original population (n = 808). The robustness of the results was confirmed by replication analysis in a separate population (n = 385) created by random allocation.

Results

Higher levels of total physical activity were associated with various metabolite concentrations, including lower concentrations of amino acids and their derivatives, and higher concentrations of pipecolate (FDR p <0.05 in original population). The findings persisted after adjustment for age, body mass index, smoking, alcohol intake, and energy intake. Isoleucine, leucine, valine, 4-methyl-2-oxoisopentanoate, 2-oxoisopentanoate, alanine, and proline concentrations were lower with a shorter sitting time.

Conclusions

Physical activity is related to various plasma metabolites, including known biomarkers for future insulin resistance or type 2 diabetes. These metabolites might potentially play a key role in the protective effects of higher physical activity and/or less sedentary behavior on non-communicable diseases.

Identification of salivary metabolomic biomarkers for oral cancer screening

The objective of this study was to explore salivary metabolite biomarkers by profiling both saliva and tumor tissue samples for oral cancer screening. Paired tumor and control tissues were obtained from oral cancer patients and whole unstimulated saliva samples were collected from patients and healthy controls. The comprehensive metabolomic analysis for profiling hydrophilic metabolites was conducted using capillary electrophoresis time-of-flight mass spectrometry. In total, 85 and 45 metabolites showed significant differences between tumor and matched control samples, and between salivary samples from oral cancer and controls, respectively (P < 0.05 correlated by false discovery rate); 17 metabolites showed consistent differences in both saliva and tissue-based comparisons. Of these, a combination of only two biomarkers yielded a high area under receiver operating characteristic curves (0.827; 95% confidence interval, 0.726-0.928, P < 0.0001) for discriminating oral cancers from controls. Various validation tests confirmed its high generalization ability. The demonstrated approach, integrating both saliva and tumor tissue metabolomics, helps eliminate pseudo-molecules that are coincidentally different between oral cancers and controls. These combined salivary metabolites could be the basis of a clinically feasible method of non-invasive oral cancer screening.

Serum metabolome profiles characterized by patients with hepatocellular carcinoma associated with hepatitis B and C

AIM: To clarify the characteristics of metabolite profiles in virus-related hepatocellular carcinoma (HCC) patients using serum metabolome analysis.

METHODS: The serum levels of low-molecular-weight metabolites in 68 patients with HCC were quantified using capillary electrophoresis chromatography and mass spectrometry. Thirty and 38 of the patients suffered from hepatitis B virus-related HCC (HCC-B) and hepatitis C virus-related HCC (HCC-C), respectively.

RESULTS: The main metabolites characteristic of HCC were those associated with glutathione metabolism, notably 13 γ-glutamyl peptides, which are by-products of glutathione induction. Two major profiles, i.e., concentration patterns, of metabolites were identified in HCC patients, and these were classified into two groups: an HCC-B group and an HCC-C group including some of the HCC-B cases. The receiver operating characteristic curve for the multiple logistic regression model discriminating HCC-B from HCC-C incorporating the concentrations of glutamic acid, methionine and γ-glutamyl-glycine-glycine showed a highly significant area under the curve value of 0.94 (95%CI: 0.89-1.0, P < 0.0001).

CONCLUSION: The serum levels of γ-glutamyl peptides, as well as their concentration patterns, contribute to the development of potential biomarkers for virus-related HCC. The difference in metabolite profiles between HCC-B and HCC-C may reflect the respective metabolic reactions that underlie the different pathogeneses of these two types of HCC.

Mice carrying a human GLUD2 gene recapitulate aspects of human transcriptome and metabolome development

Whereas all mammals have one glutamate dehydrogenase gene (GLUD1), humans and apes carry an additional gene (GLUD2), which encodes an enzyme with distinct biochemical properties. We inserted a bacterial artificial chromosome containing the human GLUD2 gene into mice and analyzed the resulting changes in the transcriptome and metabolome during postnatal brain development. Effects were most pronounced early postnatally, and predominantly genes involved in neuronal development were affected. Remarkably, the effects in the transgenic mice partially parallel the transcriptome and metabolome differences seen between humans and macaques analyzed. Notably, the introduction of GLUD2 did not affect glutamate levels in mice, consistent with observations in the primates. Instead, the metabolic effects of GLUD2 center on the tricarboxylic acid cycle, suggesting that GLUD2 affects carbon flux during early brain development, possibly supporting lipid biosynthesis.

Smad2/3 Proteins Are Required for Immobilization-induced Skeletal Muscle Atrophy

Skeletal muscle atrophy promotes muscle weakness, limiting activities of daily living. However, mechanisms underlying atrophy remain unclear. Here, we show that skeletal muscle immobilization elevates Smad2/3 protein but not mRNA levels in muscle, promoting atrophy. Furthermore, we demonstrate that myostatin, which negatively regulates muscle hypertrophy, is dispensable for denervation-induced muscle atrophy and Smad2/3 protein accumulation. Moreover, muscle-specific Smad2/3-deficient mice exhibited significant resistance to denervation-induced muscle atrophy. In addition, expression of the atrogenes Atrogin-1 and MuRF1, which underlie muscle atrophy, did not increase in muscles of Smad2/3-deficient mice following denervation. We also demonstrate that serum starvation promotes Smad2/3 protein accumulation in C2C12 myogenic cells, an in vitro muscle atrophy model, an effect inhibited by IGF1 treatment. In vivo, we observed IGF1 receptor deactivation in immobilized muscle, even in the presence of normal levels of circulating IGF1. Denervation-induced muscle atrophy was accompanied by reduced glucose intake and elevated levels of branched-chain amino acids, effects that were Smad2/3-dependent. Thus, muscle immobilization attenuates IGF1 signals at the receptor rather than the ligand level, leading to Smad2/3 protein accumulation, muscle atrophy, and accompanying metabolic changes.

Taxonomic revision of Chlamydomonas subg. Amphichloris (Volvocales, Chlorophyceae), with resurrection of the genus Dangeardinia and descriptions of Ixipapillifera gen. nov. and Rhysamphichloris gen. nov

Chlamydomonas (Cd.) is one of the largest but most polyphyletic genera of freshwater unicellular green algae. It consists of 400-600 morphological species and requires taxonomic revision. Toward reclassification, each morphologically defined classical subgenus (or subgroup) should be examined using culture strains. Chlamydomonas subg. Amphichloris is characterized by a central nucleus between two axial pyrenoids, however, the phylogenetic structure of this subgenus has yet to be examined using molecular data. Here, we examined 12 strains including six newly isolated strains, morphologically identified as Chlamydomonas subg. Amphichloris, using 18S rRNA gene phylogeny, light microscopy, and mitochondria fluorescent microscopy. Molecular phylogenetic analyses revealed three independent lineages of the subgenus, separated from the type species of Chlamydomonas, Cd. reinhardtii. These three lineages were further distinguished from each other by light and fluorescent microscopy-in particular by the morphology of the papillae, chloroplast surface, stigmata, and mitochondria-and are here assigned to three genera: Dangeardinia emend., Ixipapillifera gen. nov., and Rhysamphichloris gen. nov. Based on the molecular and morphological data, two to three species were recognized in each genus, including one new species, I. pauromitos. In addition, Cd. deasonii, which was previously assigned to subgroup "Pleiochloris," was included in the genus Ixipapillifera as I. deasonii comb. nov.

De novo assembly and comparative transcriptome analysis of Euglena gracilis in response to anaerobic conditions

Background

The phytoflagellated protozoan, Euglena gracilis, has been proposed as an attractive feedstock for the accumulation of valuable compounds such as β-1,3-glucan, also known as paramylon, and wax esters. The production of wax esters proceeds under anaerobic conditions, designated as wax ester fermentation. In spite of the importance and usefulness of Euglena, the genome and transcriptome data are currently unavailable, though another research group has recently published E.gracilis transcriptome study during our submission. We herein performed an RNA-Seq analysis to provide a comprehensive sequence resource and some insights into the regulation of genes including wax ester metabolism by comparative transcriptome analysis of E.gracilis under aerobic and anaerobic conditions.

Results

The E.gracilis transcriptome analysis was performed using the Illumina platform and yielded 90.3 million reads after the filtering steps. A total of 49,826 components were assembled and identified as a reference sequence of E.gracilis, of which 26,479 sequences were considered to be potentially expressed (having FPKM value of greater than 1). Approximately half of all components were estimated to be regulated in a trans-splicing manner, with the addition of protruding spliced leader sequences. Nearly 40 % of 26,479 sequences were annotated by similarity to Swiss-Prot database using the BLASTX program. A total of 2080 transcripts were identified as differentially expressed genes (DEGs) in response to anaerobic treatment for 24 h. A comprehensive pathway enrichment analysis using the KEGG pathway revealed that the majority of DEGs were involved in photosynthesis, nucleotide metabolism, oxidative phosphorylation, fatty acid metabolism. We successfully identified a candidate gene set of paramylon and wax esters, including novel β-1,3-glucan and wax ester synthases. A comparative expression analysis of aerobic- and anaerobic-treated E.gracilis cells indicated that gene expression changes in these components were not extensive or dynamic during the anaerobic treatment.

Conclusion

The RNA-Seq analysis provided comprehensive transcriptome information on E.gracilis for the first time, and this information will advance our understanding of this unique organism. The comprehensive analysis indicated that paramylon and wax ester metabolic pathways are regulated at post-transcriptional rather than the transcriptional level in response to anaerobic conditions.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2540-6) contains supplementary material, which is available to authorized users.