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

Novel 2-(ω-phosphonooxy-2-oxaalkyl)acrylate monomers for self-etching self-priming one part adhesive

Novel hydrolysis stable 2-(ω-phosphonooxy-2-oxaalkyl)acrylate monomers 3 with phosphoric acid moieties were synthesized by a three step synthesis via Baylis–Hillman reaction of ethyl acrylate and formaldehyde, and subsequent etherification of the obtained product with diols and phosphorylation using POCl3. The polymerization enthalpy of 2-(ω-phosphonooxy-2-oxaalkyl)acrylates 3 as measured by DSC ranges from −29 to −53 kJ·mol−1. The shear bond strength of adhesive compositions 4, comprising of polymerizable acids 3, ranges from 5.8 to 19.3 MPa on enamel and from 8.7 to 16.9 MPa on dentin

N-alkyl-N-(phosphonoethyl) substituted (meth)acrylamides – new adhesive monomers for self-etching self-priming one part dental adhesive

Novel N-alkyl-N-(phosphonoethyl) substituted mono-, bis- and tris(meth)acrylamides 3 were synthesized by two different three-step reactions and characterized by IR, 1H NMR and 13C NMR spectroscopy as well as refractive index and viscosity. The phosphonoethyl substituted (meth)acrylamide monomers show improved hydrolytic stability compared to carboxylic esters. The highest stability was found for the phosphonoethyl substituted acrylamide monomers. Acrylamides have a larger polymerization enthalpy ranging from −50 to −70 kJ·mol−1 per double bond compared to methacrylamides which show −8.57 to −25.1 kJ·mol−1 per double bond. Depending on their structure (meth)acrylamides 3 exhibit an adhesion to enamel and dentin up to 19.5 MPa. The monomer 3c shows the highest adhesion values to both substrates, namely 15.3 ± 3.4 MPa to enamel and 18.5 ± 2.3 MPa to dentin

Influence of Nanoparticles on the Coupling Between Optical Dipoles in Epoxy-Silica Nanocomposites During Network Formation

High-performance refractometry and infrared spectroscopy are combined in order to elucidate the gelation process and the glass transition during the network formation of epoxies and epoxy-based nanocomposites. Whereas infrared spectroscopy yields the chemical conversion due to the opening of oxirane rings during the covalent network formation, high-performance refractometry is extremely sensitive to the accompanying changes of the arrangement of the molecular network. In accordance with the Lorentz-Lorenz relationship, the evolution of the refractive index seems to reflect that of the mass density during polymerization of the epoxy-based systems within the limits of a few percent. The slight deviations from the Lorentz-Lorenz relationship, which occur during the gelation of the epoxy-based systems, are attributed to long-ranged dipole-dipole interactions, which respond at optical frequencies. This point of view is supported by the fact that chemically inert silica nanoparticles embedded in the pure epoxy matrix as disturbances for these dipole-dipole interactions are able to diminish or even to suppress totally this excess contribution of the refractive index

Silyl Glyoxylates as a New Class of High Performance Photoinitiators: Blue LED Induced Polymerization of Methacrylates in Thin and Thick Films

Silyl glyoxylates are proposed here as a new class of high performance type I photoinitiators for free radical polymerization under air or in laminate (e.g., (meth)­acrylates) upon exposure to different near-UV (at 395 nm; at 405 nm) and blue (at 477 nm) LEDs. The new proposed photoinitiators can also be used in the presence of additives that can enhance their initiating ability: an iodonium salt and an amine or a phosphine. The silyl glyoxylate-based photoinitiating systems exhibit excellent polymerization performances upon blue LED light (at 477 nm) with exceptional bleaching properties compared to camphorquinone (CQ)-based systems. This can be highly worthwhile for the preparation of colorless polymers upon visible light. Real-time Fourier transform infrared spectroscopy (RT-FTIR) experiments are used to monitor the polymerization profiles. The involved chemical mechanisms are investigated by fluorescence, laser flash photolysis, electron spin resonance (ESR), and steady state photolysis experiments. Molecular orbital calculations are also carried out. The overall excited state processes and the chemical mechanisms involved in the initiation step are detailed

BCG Vaccination in Humans Elicits Trained Immunity via the Hematopoietic Progenitor Compartment.

Induction of trained immunity by Bacille-Calmette-Guérin (BCG) vaccination mediates beneficial heterologous effects, but the mechanisms underlying its persistence and magnitude remain elusive. In this study, we show that BCG vaccination in healthy human volunteers induces a persistent transcriptional program connected to myeloid cell development and function within the hematopoietic stem and progenitor cell (HSPC) compartment in the bone marrow. We identify hepatic nuclear factor (HNF) family members 1a and b as crucial regulators of this transcriptional shift. These findings are corroborated by higher granulocyte numbers in BCG-vaccinated infants, HNF1 SNP variants that correlate with trained immunity, and elevated serum concentrations of the HNF1 target alpha-1 antitrypsin. Additionally, transcriptomic HSPC remodeling was epigenetically conveyed to peripheral CD14+ monocytes, displaying an activated transcriptional signature three months after BCG vaccination. Taken together, transcriptomic, epigenomic, and functional reprogramming of HSPCs and peripheral monocytes is a hallmark of BCG-induced trained immunity in humans

The rasterstereographic–dynamic analysis of posture in adolescents using a modified Matthiass test

The Matthiass posture test is a clinical test to detect posture changes in children and adolescents. Aim of this study was to objectify this test using a dynamic rasterstereographic measuring device. We examined 31 healthy athletes during a modified Matthiass test with a dynamic rasterstereographic measuring system. Hereby the trunk inclination, kyphosis and lordosis angle were measured. The trunk inclination decreased by about 50% of the basic value just by raising the arms. Additional weight loads of only 5% body weight (bw) resulted in significant changes of the posture (lordosis and kyphosis angle) during this test. With this rasterstereographic measuring device it seems to be possible to determine spinal posture changes under dynamic conditions. The results suggest that additional weights of 5% bw during the Matthias-test are enough to create significant deviations in posture parameters, even in healthy subjects