Methods to study splicing from high-throughput RNA Sequencing data

The development of novel high-throughput sequencing (HTS) methods for RNA (RNA-Seq) has provided a very powerful mean to study splicing under multiple conditions at unprecedented depth. However, the complexity of the information to be analyzed has turned this into a challenging task. In the last few years, a plethora of tools have been developed, allowing researchers to process RNA-Seq data to study the expression of isoforms and splicing events, and their relative changes under different conditions. We provide an overview of the methods available to study splicing from short RNA-Seq data. We group the methods according to the different questions they address: 1) Assignment of the sequencing reads to their likely gene of origin. This is addressed by methods that map reads to the genome and/or to the available gene annotations. 2) Recovering the sequence of splicing events and isoforms. This is addressed by transcript reconstruction and de novo assembly methods. 3) Quantification of events and isoforms. Either after reconstructing transcripts or using an annotation, many methods estimate the expression level or the relative usage of isoforms and/or events. 4) Providing an isoform or event view of differential splicing or expression. These include methods that compare relative event/isoform abundance or isoform expression across two or more conditions. 5) Visualizing splicing regulation. Various tools facilitate the visualization of the RNA-Seq data in the context of alternative splicing. In this review, we do not describe the specific mathematical models behind each method. Our aim is rather to provide an overview that could serve as an entry point for users who need to decide on a suitable tool for a specific analysis. We also attempt to propose a classification of the tools according to the operations they do, to facilitate the comparison and choice of methods.Comment: 31 pages, 1 figure, 9 tables. Small corrections adde

The Bacterium Endosymbiont of Crithidia deanei Undergoes Coordinated Division with the Host Cell Nucleus

In trypanosomatids, cell division involves morphological changes and requires coordinated replication and segregation of the nucleus, kinetoplast and flagellum. In endosymbiont-containing trypanosomatids, like Crithidia deanei, this process is more complex, as each daughter cell contains only a single symbiotic bacterium, indicating that the prokaryote must replicate synchronically with the host protozoan. In this study, we used light and electron microscopy combined with three-dimensional reconstruction approaches to observe the endosymbiont shape and division during C. deanei cell cycle. We found that the bacterium replicates before the basal body and kinetoplast segregations and that the nucleus is the last organelle to divide, before cytokinesis. In addition, the endosymbiont is usually found close to the host cell nucleus, presenting different shapes during the protozoan cell cycle. Considering that the endosymbiosis in trypanosomatids is a mutualistic relationship, which resembles organelle acquisition during evolution, these findings establish an excellent model for the understanding of mechanisms related with the establishment of organelles in eukaryotic cells

Composition, Diversity, and Origin of the Bacterial Community in Grass Carp Intestine

Gut microbiota has become an integral component of the host, and received increasing attention. However, for many domestic animals, information on the microbiota is insufficient and more effort should be exerted to manage the gastrointestinal bacterial community. Understanding the factors that influence the composition of microbial community in the host alimentary canal is essential to manage or improve the microbial community composition. In the present study, 16S rRNA gene sequence-based comparisons of the bacterial communities in the grass carp (Ctenopharyngodon idellus) intestinal contents and fish culture-associated environments are performed. The results show that the fish intestinal microbiota harbors many cellulose-decomposing bacteria, including sequences related to Anoxybacillus, Leuconostoc, Clostridium, Actinomyces, and Citrobacter. The most abundant bacterial operational taxonomic units (OTUs) in the grass carp intestinal content are those related to feed digestion. In addition, the potential pathogens and probiotics are important members of the intestinal microbiota. Further analyses show that grass carp intestine holds a core microbiota composed of Proteobacteria, Firmicutes, and Actinobacteria. The comparison analyses reveal that the bacterial community in the intestinal contents is most similar to those from the culture water and sediment. However, feed also plays significant influence on the composition of gut microbiota

Expression of two barley proteinase inhibitors in tomato promotes endogenous defensive response and enhances resistance to Tuta absoluta

[EN] Background: For as long as 350 million years, plants and insects have coexisted and developed a set of relationships which affect both organisms at different levels. Plants have evolved various morphological and biochemical adaptations to cope with herbivores attacks. However, Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae) has become the major pest threatening tomato crops worldwide and without the appropriated management it can cause production losses between 80 to 100%. Results: The aim of this study was to investigate the in vivo effect of a serine proteinase inhibitor (BTI-CMe) and a cysteine proteinase inhibitor (Hv-CPI2) from barley on this insect and to examine the effect their expression has on tomato defensive response. We found that larvae fed on the double transgenic plants showed a notable reduction in weight. Moreover, only 56% of the larvae reached the adult stage. The emerged adults showed wings deformities and reduced fertility. We also investigated the effect of proteinase inhibitors ingestion on the insect digestive enzymes. Our results showed a decrease in larval trypsin activity. Transgenes expression had no harmful effect on Nesidiocoris tenuis (Reuter) (Heteroptera: Miridae), a predator of Tuta absoluta, despite transgenic tomato plants attracted the mirid. We also found that barley cystatin expression promoted plant defense by inducing the expression of the tomato endogenous wound inducible Proteinase inhibitor 2 (Pin2) gene, increasing the production of glandular trichomes and altering the emission of volatile organic compounds. Conclusion: Our results demonstrate the usefulness of the co-expression of different proteinase inhibitors for the enhancement of plant resistance to Tuta absoluta.This work was partly supported by grants BIO2013-40747-R and AGL2014-55616-C3 from the Spanish Ministry of Economy and Competitiveness (MINECO)Hamza, R.; Pérez-Hedo, M.; Urbaneja, A.; Rambla Nebot, JL.; Granell Richart, A.; Gaddour, K.; Beltran Porter, JP.... (2018). Expression of two barley proteinase inhibitors in tomato promotes endogenous defensive response and enhances resistance to Tuta absoluta. BMC Plant Biology. 18. https://doi.org/10.1186/s12870-018-1240-6S18Oerke EC. Crop losses to pests. J Agric Sci. 2005;144(01):31.Jouanin L, Bonadé-Bottino M, Girard C, Morrot G, Giband M. Transgenic plants for insect resistance. Plant Sci. 1998;131(1):1–11.Markwick NP, Docherty LC, Phung MM, Lester MT, Murray C, Yao JL, Mitra DS, Cohen D, Beuning LL, Kutty-Amma S, et al. Transgenic tobacco and apple plants expressing biotin-binding proteins are resistant to two cosmopolitan insect pests, potato tuber moth and lightbrown apple moth, respectively. Transgenic Res. 2003;12(6):671–81.Koiwa H, Bressan RA, Hasegawa PM. Regulation of protease inhibitors and plant defense. Trends Plant Sci. 1997;2(10):379–84.Ryan CA. Protease inhibitors in plants: genes for improving defenses against insects and pathogens. Annu Rev Phytopathol. 1990;28(1):425–49.Abdeen A, Virgos A, Olivella E, Villanueva J, Aviles X, Gabarra R, Prat S. Multiple insect resistance in transgenic tomato plants over-expressing two families of plant proteinase inhibitors. Plant Mol Biol. 2005;57(2):189–202.Quilis J, López-García B, Meynard D, Guiderdoni E, San Segundo B. Inducible expression of a fusion gene encoding two proteinase inhibitors leads to insect and pathogen resistance in transgenic rice. Plant Biotechnol J. 2014;12(3):367–77.Smigocki AC, Ivic-Haymes S, Li H, Savic J. Pest protection conferred by a Beta vulgaris serine proteinase inhibitor gene. PLoS One. 2013;8(2):e57303.Mazumdar-Leighton S, Broadway RM. Transcriptional induction of diverse midgut trypsins in larval Agrotis ipsilon and Helicoverpa zea feeding on the soybean trypsin inhibitor. Insect Biochem Mol Biol. 2001;31(6–7):645–57.Oppert B, Morgan TD, Hartzer K, Kramer KJ. Compensatory proteolytic responses to dietary proteinase inhibitors in the red flour beetle, Tribolium castaneum (Coleoptera: Tenebrionidae). Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology. 2005;140(1):53–8.Broadway RM. Dietary regulation of serine proteinases that are resistant to serine proteinase inhibitors. J Insect Physiol. 1997;43(9):855–74.Zhu-Salzman K, Koiwa H, Salzman R, Shade R, Ahn JE. Cowpea bruchid Callosobruchus maculatus uses a three-component strategy to overcome a plant defensive cysteine protease inhibitor. Insect Mol Biol. 2003;12(2):135–45.Oppert B, Morgan TD, Hartzer K, Lenarcic B, Galesa K, Brzin J, Turk V, Yoza K, Ohtsubo K, Kramer KJ. Effects of proteinase inhibitors on digestive proteinases and growth of the red flour beetle, Tribolium castaneum (Herbst) (Coleoptera: Tenebrionidae). Comparative biochemistry and physiology Toxicology & pharmacology : CBP. 2003;134(4):481–90.Duan X, Li X, Xue Q, Abo-El-Saad M, Xu D, Wu R. Transgenic rice plants harboring an introduced potato proteinase inhibitor II gene are insect resistant. Nat Biotechnol. 1996;14(4):494–8.Pompermayer P, Lopes AR, Terra WR, Parra JRP, Falco MC, Silva-Filho MC. Effects of soybean proteinase inhibitor on development, survival and reproductive potential of the sugarcane borer, Diatraea saccharalis. Entomologia Experimentalis et Applicata. 2001;99(1):79–85.Alfonso-Rubí J, Ortego F, Castañera P, Carbonero P, Díaz I. Transgenic expression of trypsin inhibitor CMe from barley in indica and japonica rice, confers resistance to the rice weevil Sitophilus oryzae. Transgenic Res. 2003;12(1):23–31.Altpeter F, Diaz I, Mc Auslane H, Gaddour K, Carbonero P, Vasil IK. Increased insect resistance in transgenic wheat stably expressing trypsin inhibitor CMe. Mol Breed. 1999;5(1):53–63.Martinez M, Cambra I, Carrillo L, Diaz-Mendoza M, Diaz I. Characterization of the entire cystatin gene family in barley and their target cathepsin L-like cysteine-proteases, partners in the hordein mobilization during seed germination. Plant Physiol. 2009;151(3):1531–45.FAOSTAT: Food and Organization of the United Nations, statistics division. 2017.Mueller LA, Lankhorst RK, Tanksley SD, Giovannoni JJ, White R, Vrebalov J, Fei Z, van Eck J, Buels R, Mills AA, et al. A snapshot of the emerging tomato genome sequence. The Plant Genome. 2009;2(1):78–92.Ellul P, Garcia-Sogo B, Pineda B, Rios G, Roig L, Moreno V. The ploidy level of transgenic plants in agrobacterium-mediated transformation of tomato cotyledons (Lycopersicon esculentum L. mill.) is genotype and procedure dependent. Theor Appl Genet. 2003;106(2):231–8.Pino LE, Lombardi-Crestana S, Azevedo MS, Scotton DC, Borgo L, Quecini V, Figueira A, Peres LE. The Rg1 allele as a valuable tool for genetic transformation of the tomato'Micro-Tom'model system. Plant Methods. 2010;6(1):23.Sharma MK, Solanke AU, Jani D, Singh Y, Sharma AK. A simple and efficient agrobacterium-mediated procedure for transformation of tomato. J Biosci. 2009;34(3):423–33.van Eck J, Kirk DD, Walmsley AM. Tomato (Lycopersicum esculentum). Agrobacterium Protocols. 2006:459–74.Dan Y, Yan H, Munyikwa T, Dong J, Zhang Y, Armstrong CL. MicroTom—a high-throughput model transformation system for functional genomics. Plant Cell Rep. 2006;25(5):432–41.Pearce G, Strydom D, Johnson S, Ryan CA. A polypeptide from tomato leaves induces wound-inducible proteinase inhibitor proteins. Science. 1991;253(5022):895–9.Farmer EE, Ryan CA. Interplant communication: airborne methyl jasmonate induces synthesis of proteinase inhibitors in plant leaves. Proc Natl Acad Sci. 1990;87(19):7713–6.Bosch M, Wright LP, Gershenzon J, Wasternack C, Hause B, Schaller A, Stintzi A. Jasmonic acid and its precursor 12-oxophytodienoic acid control different aspects of constitutive and induced herbivore defenses in tomato. Plant Physiol. 2014;166(1):396–410.Christensen SA, Nemchenko A, Borrego E, Murray I, Sobhy IS, Bosak L, DeBlasio S, Erb M, Robert CA, Vaughn KA. The maize lipoxygenase, ZmLOX10, mediates green leaf volatile, jasmonate and herbivore-induced plant volatile production for defense against insect attack. Plant J. 2013;74(1):59–73.Boughton AJ, Hoover K, Felton GW. Methyl jasmonate application induces increased densities of glandular trichomes on tomato, Lycopersicon esculentum. J Chem Ecol. 2005;31(9):2211–6.Li L, Zhao Y, McCaig BC, Wingerd BA, Wang J, Whalon ME, Pichersky E, Howe GA. The tomato homolog of CORONATINE-INSENSITIVE1 is required for the maternal control of seed maturation, jasmonate-signaled defense responses, and glandular trichome development. Plant Cell. 2004;16(1):126–43.Peiffer M, Tooker JF, Luthe DS, Felton GW. Plants on early alert: glandular trichomes as sensors for insect herbivores. New Phytol. 2009;184(3):644–56.Bryant J, Green TR, Gurusaddaiah T, Ryan CA. Proteinase inhibitor II from potatoes: isolation and characterization of its protomer components. Biochemistry. 1976;15(16):3418–24.Johnson R, Narvaez J, An G, Ryan C. Expression of proteinase inhibitors I and II in transgenic tobacco plants: effects on natural defense against Manduca sexta larvae. Proc Natl Acad Sci. 1989;86(24):9871–5.Klopfenstein NB, Allen KK, Avila FJ, Heuchelin SA, Martinez J, Carman RC, Hall RB, Hart ER, McNabb HS. Proteinase inhibitor II gene in transgenic poplar: chemical and biological assays. Biomass Bioenergy. 1997;12(4):299–311.Dicke M, Takabayashi J, Posthumus MA, Schütte C, Krips OE. Plant—Phytoseiid interactions mediated by herbivore-induced plant volatiles: variation in production of cues and in responses of predatory mites. Exp Appl Acarol. 1998;22(6):311–33.Turlings T, Loughrin JH, Mccall PJ, Röse U, Lewis WJ, Tumlinson JH. How caterpillar-damaged plants protect themselves by attracting parasitic wasps. Proc Natl Acad Sci. 1995;92(10):4169–74.Levin DA. The role of trichomes in plant defense. Q Rev Biol. 1973;48(1, Part 1):3–15.Traw BM, Dawson TE. Differential induction of trichomes by three herbivores of black mustard. Oecologia. 2002;131(4):526–32.Handley R, Ekbom B, Ågren J. Variation in trichome density and resistance against a specialist insect herbivore in natural populations of Arabidopsis thaliana. Ecological Entomology. 2005;30(3):284–92.Valverde P, Fornoni J, NÚÑez-Farfán J. Defensive role of leaf trichomes in resistance to herbivorous insects in Datura stramonium. J Evol Biol. 2001;14(3):424–32.Elle E, Hare J. Environmentally induced variation in floral traits affects the mating system in Datura wrightii. Funct Ecol. 2002;16(1):79–88.Agrawal AA. Benefits and costs of induced plant defense for Lepidium virginicum (Brassicaceae). Ecology. 2000;81(7):1804–13.Dalin P, Björkman C. Adult beetle grazing induces willow trichome defence against subsequent larval feeding. Oecologia. 2003;134(1):112–8.Campos MR, Biondi A, Adiga A, Guedes RN, Desneux N. From the western Palaearctic region to beyond: Tuta absoluta 10 years after invading Europe. J Pest Sci. 2017:1–10.Desneux N, Wajnberg E, Wyckhuys KA, Burgio G, Arpaia S, Narváez-Vasquez CA, González-Cabrera J, Ruescas DC, Tabone E, Frandon J. Biological invasion of European tomato crops by Tuta absoluta: ecology, geographic expansion and prospects for biological control. J Pest Sci. 2010;83(3):197–215.Urbaneja A, Montón H, Mollá O. Suitability of the tomato borer Tuta absoluta as prey for Macrolophus pygmaeus and Nesidiocoris tenuis. J Appl Entomol. 2009;133(4):292–6.Pérez-Hedo M, Urbaneja A. Prospects for predatory mirid bugs as biocontrol agents of aphids in sweet peppers. J Pest Sci. 2015;88(1):65–73.Hewitt E. The composition of the nutrient solution. Sand and water culture methods used in the study of plant Nutrition. 1966:187–246.Karimi M, Inzé D, Depicker A. GATEWAY™ vectors for agrobacterium-mediated plant transformation. Trends Plant Sci. 2002;7(5):193–5.Martín-Trillo M, Grandío EG, Serra F, Marcel F, Rodríguez-Buey ML, Schmitz G, Theres K, Bendahmane A, Dopazo H, Cubas P. Role of tomato BRANCHED1-like genes in the control of shoot branching. Plant J. 2011;67(4):701–14.Vargas C. Observations on the bionomics and natural enemies of the tomato moth, Gnorimoschema absoluta (Meyrick)(Lep. Gelechiidae). Idesia. 1970;1:75–110.Mollá O, Biondi A, Alonso-Valiente M, Urbaneja A. A comparative life history study of two mirid bugs preying on Tuta absoluta and Ephestia kuehniella eggs on tomato crops: implications for biological control. BioControl. 2014;59(2):175–83.Abbot C. Solar variation and the weather. Science (New York, NY). 1925;62(1605):307.Bradford MM. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem. 1976;72(1–2):248–54.Bouagga S, Urbaneja A, Rambla JL, Granell A, Pérez-Hedo M. Orius laevigatus strengthens its role as a biological control agent by inducing plant defenses. J Pest Sci. 2017:1–10.Hilder VA, Gatehouse AM, Sheerman SE, Barker RF, Boulter D. A novel mechanism of insect resistance engineered into tobacco. Nature. 1987;330(6144):160–3.Saikia K, Kalita J, Saikia PK. Biology and life cycle generations of common crow–Euploea core core Cramer (Lepidoptera: Danainae) on Hemidesmus indica host plant. Int J NeBIO. 2010;1(3):28–37.Srinivasan A, Giri AP, Gupta VS. Structural and functional diversities in lepidopteran serine proteases. Cellular & molecular biology letters. 2006;11(1):132.Tamhane VA, Chougule NP, Giri AP, Dixit AR, Sainani MN, Gupta VS. In vivo and in vitro effect of Capsicum annum proteinase inhibitors on Helicoverpa armigera gut proteinases. Biochimica et Biophysica Acta (BBA)-General Subjects. 2005;1722(2):156–67.Telang M, Srinivasan A, Patankar A, Harsulkar A, Joshi V, Damle A, Deshpande V, Sainani M, Ranjekar P, Gupta G. Bitter gourd proteinase inhibitors: potential growth inhibitors of Helicoverpa armigera and Spodoptera litura. Phytochemistry. 2003;63(6):643–52.Damle MS, Giri AP, Sainani MN, Gupta VS. Higher accumulation of proteinase inhibitors in flowers than leaves and fruits as a possible basis for differential feeding preference of Helicoverpa armigera on tomato (Lycopersicon esculentum mill, cv. Dhanashree). Phytochemistry. 2005;66(22):2659–67.De Leo F, Bonadé-Bottino MA, Ceci LR, Gallerani R, Jouanin L. Opposite effects on spodoptera littoralis larvae of high expression level of a trypsin proteinase inhibitor in transgenic plants. Plant Physiol. 1998;118(3):997–1004.Rahbé Y, Ferrasson E, Rabesona H, Quillien L. Toxicity to the pea aphid Acyrthosiphon pisum of anti-chymotrypsin isoforms and fragments of Bowman–Birk protease inhibitors from pea seeds. Insect Biochem Mol Biol. 2003;33(3):299–306.Luo M, Ding L-W, Ge Z-J, Wang Z-Y, Hu B-L, Yang X-B, Sun Q-Y, Xu Z-F. The characterization of SaPIN2b, a plant trichome-localized proteinase inhibitor from Solanum americanum. Int J Mol Sci. 2012;13(11):15162–76.Dalin P, Ågren J, Björkman C, Huttunen P, Kärkkäinen K. Leaf trichome formation and plant resistance to herbivory. In: Dordrecht SA, editor. Induced plant resistance to herbivory. Netherlands: Springer; 2008. p. 89–105.Gonzáles WL, Negritto MA, Suárez LH, Gianoli E. Induction of glandular and non-glandular trichomes by damage in leaves of Madia sativa under contrasting water regimes. Acta Oecol. 2008;33(1):128–32.Luo M, Wang Z, Li H, Xia K-F, Cai Y, Xu Z-F. Overexpression of a weed (Solanum americanum) proteinase inhibitor in transgenic tobacco results in increased glandular trichome density and enhanced resistance to Helicoverpa armigera and Spodoptera litura. Int J Mol Sci. 2009;10(4):1896–910.Björkman C, Dalin P, Ahrné K. Leaf trichome responses to herbivory in willows: induction, relaxation and costs. New Phytol. 2008;179(1):176–84.Duffey S. Plant glandular trichomes: their partial role in defence against insects. Insects and the plant surface. London: Edward Arnold; 1986. p. 151–72.James DG. Further field evaluation of synthetic herbivore-induced plan volatiles as attractants for beneficial insects. J Chem Ecol. 2005;31(3):481–95.Naselli M, Zappalà L, Gugliuzzo A, Garzia GT, Biondi A, Rapisarda C, Cincotta F, Condurso C, Verzera A, Siscaro G. Olfactory response of the zoophytophagous mirid Nesidiocoris tenuis to tomato and alternative host plants. Arthropod Plant Interact. 2017;11(2):121–31.Tholl D. Biosynthesis and biological functions of terpenoids in plants. Advances in Biochemical Engineering and Biotechnology. 2015;148:63-106.Lange BM, Rujan T, Martin W, Croteau R. Isoprenoid biosynthesis: the evolution of two ancient and distinct pathways across genomes. Proc Natl Acad Sci. 2000;97(24):13172–7.Dudareva N, Klempien A, Muhlemann JK, Kaplan I. Biosynthesis, function and metabolic engineering of plant volatile organic compounds. New Phytol. 2013;198(1):16–32.Razal RA, Ellis S, Singh S, Lewis NG, Towers GHN. Nitrogen recycling in phenylpropanoid metabolism. Phytochemistry. 1996;41(1):31–5.Effmert U, Große J, Röse US, Ehrig F, Kägi R, Piechulla B. Volatile composition, emission pattern, and localization of floral scent emission in Mirabilis jalapa (Nyctaginaceae). Am J Bot. 2005;92(1):2–12.Guterman I, Masci T, Chen X, Negre F, Pichersky E, Dudareva N, Weiss D, Vainstein A. Generation of phenylpropanoid pathway-derived volatiles in transgenic plants: rose alcohol acetyltransferase produces phenylethyl acetate and benzyl acetate in petunia flowers. Plant Mol Biol. 2006;60(4):555–63.Vogel JT, Tan B-C, McCarty DR, Klee HJ. The carotenoid cleavage dioxygenase 1 enzyme has broad substrate specificity, cleaving multiple carotenoids at two different bond positions. J Biol Chem. 2008;283(17):11364–73.Colquhoun TA, Kim JY, Wedde AE, Levin LA, Schmitt KC, Schuurink RC, Clark DG. PhMYB4 fine-tunes the floral volatile signature of petunia×hybrida through PhC4H. J Exp Bot. 2011;62(3):1133–43.Kolosova N, Gorenstein N, Kish CM, Dudareva N. Regulation of circadian methyl benzoate emission in diurnally and nocturnally emitting plants. Plant Cell. 2001;13(10):2333–47.Maeda H, Shasany AK, Schnepp J, Orlova I, Taguchi G, Cooper BR, Rhodes D, Pichersky E, Dudareva N. RNAi suppression of arogenate dehydratase1 reveals that phenylalanine is synthesized predominantly via the arogenate pathway in petunia petals. Plant Cell. 2010;22(3):832–49.Lerdau M, Gray D. Ecology and evolution of light-dependent and light-independent phytogenic volatile organic carbon. New Phytol. 2003;157(2):199–211.Martin DM, Gershenzon J, Bohlmann J. Induction of volatile terpene biosynthesis and diurnal emission by methyl jasmonate in foliage of Norway spruce. Plant Physiol. 2003;132(3):1586–99.van Doorn WG, Woltering EJ. Physiology and molecular biology of petal senescence. J Exp Bot. 2008;59(3):453–80

The potential for immunoglobulins and host defense peptides (HDPs) to reduce the use of antibiotics in animal production

Abstract Innate defense mechanisms are aimed at quickly containing and removing infectious microorganisms and involve local stromal and immune cell activation, neutrophil recruitment and activation and the induction of host defense peptides (defensins and cathelicidins), acute phase proteins and complement activation. As an alternative to antibiotics, innate immune mechanisms are highly relevant as they offer rapid general ways to, at least partially, protect against infections and enable the build-up of a sufficient adaptive immune response. This review describes two classes of promising alternatives to antibiotics based on components of the innate host defense. First we describe immunoglobulins applied to mimic the way in which they work in the newborn as locally acting broadly active defense molecules enforcing innate immunity barriers. Secondly, the potential of host defense peptides with different modes of action, used directly, induced in situ or used as vaccine adjuvants is described

Extensive Gene-Specific Translational Reprogramming in a Model of B Cell Differentiation and Abl-Dependent Transformation

To what extent might the regulation of translation contribute to differentiation programs, or to the molecular pathogenesis of cancer? Pre-B cells transformed with the viral oncogene v-Abl are suspended in an immortalized, cycling state that mimics leukemias with a BCR-ABL1 translocation, such as Chronic Myelogenous Leukemia (CML) and Acute Lymphoblastic Leukemia (ALL). Inhibition of the oncogenic Abl kinase with imatinib reverses transformation, allowing progression to the next stage of B cell development. We employed a genome-wide polysome profiling assay called Gradient Encoding to investigate the extent and potential contribution of translational regulation to transformation and differentiation in v-Abl-transformed pre-B cells. Over half of the significantly translationally regulated genes did not change significantly at the level of mRNA abundance, revealing biology that might have been missed by measuring changes in transcript abundance alone. We found extensive, gene-specific changes in translation affecting genes with known roles in B cell signaling and differentiation, cancerous transformation, and cytoskeletal reorganization potentially affecting adhesion. These results highlight a major role for gene-specific translational regulation in remodeling the gene expression program in differentiation and malignant transformation

Response of cell wall composition and RNA-seq transcriptome to methyl-jasmonate in Brachypodium distachyon callus

Main conclusion: Methyl-jasmonate induces large increases in p-coumarate linked to arabinoxylan in Brachypodium and in abundance of GT61 and BAHD family transcripts consistent with a role in synthesis of this linkage. Jasmonic acid (JA) signalling is required for many stress responses in plants, inducing large changes in the transcriptome, including up-regulation of transcripts associated with lignification. However, less is known about the response to JA of grass cell walls and the monocot-specific features of arabinoxylan (AX) synthesis and acylation by ferulic acid (FA) and para-coumaric acid (pCA). Here, we show that methyl-jasmonate (MeJA) induces moderate increases in FA monomer, > 50% increases in FA dimers, and five–sixfold increases in pCA ester-linked to cell walls in Brachypodium callus. Direct measurement of arabinose acylated by pCA (Araf-pCA) indicated that most or all the increase in cell-wall pCA was due to pCA ester-linked to AX. Analysis of the RNA-seq transcriptome of the callus response showed that these cell-wall changes were accompanied by up-regulation of members of the GT61 and BAHD gene families implicated in AX decoration and acylation; two BAHD paralogues were among the most up-regulated cell-wall genes (seven and fivefold) after 24 h exposure to MeJA. Similar responses to JA of orthologous BAHD and GT61 transcripts are present in the RiceXPro public expression data set for rice seedlings, showing that they are not specific to Brachypodium or to callus. The large response of AX-pCA to MeJA may, therefore, indicate an important role for this linkage in response of primary cell walls of grasses to JA signalling

Cationic Host Defence Peptides:Potential as Antiviral Therapeutics

There is a pressing need to develop new antiviral treatments; of the 60 drugs currently available, half are aimed at HIV-1 and the remainder target only a further six viruses. This demand has led to the emergence of possible peptide therapies, with 15 currently in clinical trials. Advancements in understanding the antiviral potential of naturally occurring host defence peptides highlights the potential of a whole new class of molecules to be considered as antiviral therapeutics. Cationic host defence peptides, such as defensins and cathelicidins, are important components of innate immunity with antimicrobial and immunomodulatory capabilities. In recent years they have also been shown to be natural, broad-spectrum antivirals against both enveloped and non-enveloped viruses, including HIV-1, influenza virus, respiratory syncytial virus and herpes simplex virus. Here we review the antiviral properties of several families of these host peptides and their potential to inform the design of novel therapeutics