Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

<p>Abstract</p> <p>Background</p> <p>Alfalfa, [<it>Medicago sativa </it>(L.) sativa], a widely-grown perennial forage has potential for development as a cellulosic ethanol feedstock. However, the genomics of alfalfa, a non-model species, is still in its infancy. The recent advent of RNA-Seq, a massively parallel sequencing method for transcriptome analysis, provides an opportunity to expand the identification of alfalfa genes and polymorphisms, and conduct in-depth transcript profiling.</p> <p>Results</p> <p>Cell walls in stems of alfalfa genotype 708 have higher cellulose and lower lignin concentrations compared to cell walls in stems of genotype 773. Using the Illumina GA-II platform, a total of 198,861,304 expression sequence tags (ESTs, 76 bp in length) were generated from cDNA libraries derived from elongating stem (ES) and post-elongation stem (PES) internodes of 708 and 773. In addition, 341,984 ESTs were generated from ES and PES internodes of genotype 773 using the GS FLX Titanium platform. The first alfalfa (<it>Medicago sativa</it>) gene index (MSGI 1.0) was assembled using the Sanger ESTs available from GenBank, the GS FLX Titanium EST sequences, and the <it>de novo </it>assembled Illumina sequences. MSGI 1.0 contains 124,025 unique sequences including 22,729 tentative consensus sequences (TCs), 22,315 singletons and 78,981 pseudo-singletons. We identified a total of 1,294 simple sequence repeats (SSR) among the sequences in MSGI 1.0. In addition, a total of 10,826 single nucleotide polymorphisms (SNPs) were predicted between the two genotypes. Out of 55 SNPs randomly selected for experimental validation, 47 (85%) were polymorphic between the two genotypes. We also identified numerous allelic variations within each genotype. Digital gene expression analysis identified numerous candidate genes that may play a role in stem development as well as candidate genes that may contribute to the differences in cell wall composition in stems of the two genotypes.</p> <p>Conclusions</p> <p>Our results demonstrate that RNA-Seq can be successfully used for gene identification, polymorphism detection and transcript profiling in alfalfa, a non-model, allogamous, autotetraploid species. The alfalfa gene index assembled in this study, and the SNPs, SSRs and candidate genes identified can be used to improve alfalfa as a forage crop and cellulosic feedstock.</p

Identyfikacja atrybutów struktury programowania neurolingwistycznego (NLP) z naciskiem na komunikację oraz technikami jego wdrażania w pracy menadżerskiej

Effective communication is one of the basic pillars of activities for which cooperation of people is inevitable. At the same time, it is also a significant issue discussed in the context of managerial work, entrepreneurship, business, services, and many other areas of economic environment. Neuro-Linguistic Programming (NLP) is a significant attribute of improving the quality and effectiveness of communication. The NLP concept explains seemingly autonomous behaviour as constructed behaviour created by the series of consecutive stages which we often perceive as one action. By accepting the fact, that what we experience comes from programmed sequences of thinking and behaviour, NLP provides us with the knowledge and tools for discovering the structure of these programmes. Based on the identification of the attributes of neurolinguistics programming structure with the focus on communication and techniques of their implementation in managerial work, the aim of the paper is to verify the methods, which enable to specify the factors of assessing NLP in managerial work. The research was carried out on the sample of 124 managers, out of which 58 were women and 66 men. Based on the research results, two original NLP methods were verified: NLPC - Neuro linguistic programming communication and NLPT - Neuro linguistic programming techniques. By the means of a factor analysis, the factors of Representational systems and Rapport were extracted within the first methodology. Within the second methodology, the factors of Leading and Pacing were extracted. In the paper, the researchers present the basic psychometric parameters of both methodologies - eigenvalues, the percentage of explained variance, Cronbach’s alphas, intercorrelations of factors. Both methodologies contribute to the operationalization of the NLP issue. These methodologies can be used in managerial practice mainly in the area of education and training of managers.Skuteczna komunikacja jest jednym z podstawowych filarów działań, dla których współpraca ludzi jest nieunikniona. Jednocześnie jest to również istotna kwestia poruszana w kontekście pracy menedżerskiej, przedsiębiorczości, biznesu, usług i wielu innych obszarów środowiska gospodarczego. Programowanie neurolingwistyczne (NLP) jest istotnym atrybutem poprawy jakości i skuteczności komunikacji. Koncepcja NLP tłumaczy pozornie autonomiczne zachowanie jako skonstruowane zachowanie stworzone przez serię kolejnych etapów, które często postrzegamy jako jedno działanie. Akceptując fakt, że to, czego doświadczamy, pochodzi z zaprogramowanych sekwencji myślenia i zachowania, NLP dostarcza nam wiedzy i narzędzi do odkrywania struktury tych programów. W oparciu o identyfikację cech struktury programowania neurolingwistyki z naciskiem na komunikację i techniki ich wdrażania w pracy menedżerskiej, celem pracy jest weryfikacja metod, które pozwalają określić czynniki oceny NLP w pracy menedżerskiej. Badania przeprowadzono na próbie 124 menedżerów, z których 58 stanowiły kobiety a 66 mężczyźni. Na podstawie wyników badań zweryfikowano dwie oryginalne metody NLP: NLPC - Neurolingwistyczna komunikacja programistyczna i NLPT - Neurolingwistyczne techniki programowania. Za pomocą analizy czynnikowej, zostały wyodrębnione czynniki systemów reprezentacyjnych i dobrych stosunków w ramach pierwszej metodologii. W ramach drugiej metodologii wyodrębniono czynniki Wiodący i Stymulujący. W pracy przedstawiono podstawowe parametry psychometryczne obu metodologii - wartości własne, procent wyjaśnionej wariancji, alfa Cronbacha, interkorelacje czynników. Obie metodologie przyczyniają się do operacjonalizacji problemu NLP. Metodologie te mogą być stosowane w praktyce zarządczej, głównie w obszarze edukacji i szkolenia menedżerów

A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development.

Multiple plant developmental processes, such as lateral root development, depend on auxin distribution patterns that are in part generated by the PIN-formed family of auxin-efflux transporters. Here we propose that AUXIN RESPONSE FACTOR7 (ARF7) and the ARF7-regulated FOUR LIPS/MYB124 (FLP) transcription factors jointly form a coherent feed-forward motif that mediates the auxin-responsive PIN3 transcription in planta to steer the early steps of lateral root formation. This regulatory mechanism might endow the PIN3 circuitry with a temporal 'memory' of auxin stimuli, potentially maintaining and enhancing the robustness of the auxin flux directionality during lateral root development. The cooperative action between canonical auxin signalling and other transcription factors might constitute a general mechanism by which transcriptional auxin-sensitivity can be regulated at a tissue-specific level