Allele mining in diverse accessions of tropical grasses to improve forage quality and reduce environmental impact

Background and AimsThe C₄Urochloa species (syn. Brachiaria) and Megathyrsus maximus (syn. Panicum maximum) are used as pasture for cattle across vast areas in tropical agriculture systems in Africa and South America. A key target for variety improvement is forage quality: enhanced digestibility could decrease the amount of land required per unit production, and enhanced lipid content could decrease methane emissions from cattle. For these traits, loss-of-function (LOF) alleles in known gene targets are predicted to improve them, making a reverse genetics approach of allele mining feasible. We therefore set out to look for such alleles in diverse accessions of Urochloa species and Megathyrsus maximus from the genebank collection held at the CIAT.MethodsWe studied allelic diversity of 20 target genes (11 for digestibility, nine for lipid content) in 104 accessions selected to represent genetic diversity and ploidy levels of U. brizantha, U. decumbens, U. humidicola, U. ruziziensis and M. maximum. We used RNA sequencing and then bait capture DNA sequencing to improve gene models in a U. ruziziensis reference genome to assign polymorphisms with high confidence.Key ResultsWe found 953 non-synonymous polymorphisms across all genes and accessions; within these, we identified seven putative LOF alleles with high confidence, including those in the non-redundant SDP1 and BAHD01 genes present in diploid and tetraploid accessions. These LOF alleles could respectively confer increased lipid content and digestibility if incorporated into a breeding programme.ConclusionsWe demonstrated a novel, effective approach to allele discovery in diverse accessions using a draft reference genome from a single species. We used this to find gene variants in a collection of tropical grasses that could help reduce the environmental impact of cattle production.     

Dynamic compression counteracts IL-1β induced inducible nitric oxide synthase and cyclo-oxygenase-2 expression in chondrocyte/agarose constructs

Background  

Nitric oxide and prostaglandin E₂ (PGE₂play pivotal roles in both the pathogenesis of osteoarthritis and catabolic processes in articular cartilage. These mediators are influenced by both IL-1β and mechanical loading, and involve alterations in the inducible nitric oxide synthase (iNOS) and cyclo-oxygenase (COX)-2 enzymes. To identify the specific interactions that are activated by both types of stimuli, we examined the effects of dynamic compression on levels of expression of iNOS and COX-2 and involvement of the p38 mitogen-activated protein kinase (MAPK) pathway.     

SUGAR-DEPENDENT6 encodes a mitochondrial flavin adenine dinucleotide-dependent glycerol-3-p dehydrogenase, which is required for glycerol catabolism and post germinative seedling growth in Arabidopsis

The aim of this study was to clone and characterize the SUGAR-DEPENDENT6 (SDP6) gene, which is essential for postgerminative growth in Arabidopsis (Arabidopsis thaliana). Mutant alleles of sdp6 were able to break down triacylglycerol following seed germination but failed to accumulate soluble sugars, suggesting that they had a defect in gluconeogenesis. Map-based cloning of SDP6 revealed that it encodes a mitochondrial flavin adenine dinucleotide (FAD)-dependent glycerol-3-P (G3P) dehydrogenase:ubiquinone oxidoreductase called FAD-GPDH. This gene has previously been proposed to play a role both in the break down of glycerol (derived from triacylglycerol) and in NAD(+)/NADH homeostasis. Germinated seeds of sdp6 were severely impaired in the metabolism of [U-(14)C]glycerol to CO(2) and accumulated high levels of G3P. These data suggest that SDP6 is essential for glycerol catabolism. The activity of the glycolytic enzyme phosphoglucose isomerase is competitively inhibited by G3P in vitro. We show that phosphoglucose isomerase is likely to be inhibited in vivo because there is a 6-fold reduction in the transfer of (14)C-label into the opposing hexosyl moiety of sucrose when [U-(14)C]glucose or [U-(14)C]fructose is fed to sdp6 seedlings. A block in gluconeogenesis, at the level of hexose phosphate isomerization, would account for the arrested seedling growth phenotype of sdp6 and explain its rescue by sucrose and glucose but not by fructose. Measurements of NAD(+) and NADH levels in sdp6 seedlings also suggest that NAD(+)/NADH homeostasis is altered, and this observation is consistent with the hypothesis that SDP6 participates in a mitochondrial G3P shuttle by cooperating with the cytosolic NAD-dependent GPDH protein GPDHC1.     

Enhancing the in vitro and in vivo detection of aneuploidy by fluorescence in situ hybridization with the use of bromodeoxyuridine as a proliferation marker

alpha,beta-Unsaturated aldehydes are ubiquitous environmental pollutants, important industrial chemicals, have mani-fold biological functions in plants and insects and are natural products in food. They are endogenously formed in animals and humans during lipid peroxidation and arachidonic acid oxidation and are genotoxic, mutagenic and carcinogenic. Crotonaldehyde and 2-hexenal in food may contribute to general carcinogenicity in humans. The high bacterial toxicity of these compounds leads to problems in genotoxicity testing in bacterial systems. Recently, we have shown that using ethanol as solvent instead of dimethylsulfoxide (DMSO) results in an increase in the induction factors and the SOS-inducing potency of alpha,beta-unsaturated ketones in the SOS chromotest. Here, we demonstrate that utilization of ethanol as solvent also improves the testing of alpha,beta-unsaturated aldehydes. Five aldehydes out of nine tested were clearly positive in the SOS chromotest according to the criteria of Quillardet, i.e. acrolein, crotonaldehyde, 2,4-hexadienal, 2-methylacrolein and 2-ethylacrolein, three further, 2-hexenal, 2-heptenal and 2-propylacrolein showed a dose dependent increase of the induction factors which was however lower than 1.5 times that of the background. Only 2-butylacrolein did not lead to an increase in the induction factors. With DMSO as solvent only the three aldehydes acrolein, crotonaldehyde and 2,4-hexadienal showed an increase in the induction factor, which was however lower than 1.5 that of the background. Utilization of ethanol allows to establish structure genotoxicity relationships for alpha,beta-unsaturated aldehydes in the SOS chromotest. Genotoxicity decreases with increasing degree of substitution. The decreasing genotoxicities can be explained (a) by increasing bacterial toxicity due to increasing lipophilicities of the higher substituted aldehydes and (b) by decreasing reactivity due to steric hindrance by the alkyl substituents.     

Is trehalose-6-phosphate a regulator of sugar metabolism in plants?

It has recently emerged that many higher plants can synthesize trace amounts of trehalose. In arabidopsis disruption of the first step of trehalose synthesis, catalysed by trehalose-6-phosphate synthase (TPS), has lethal consequences, demonstrating an important physiological role. It is not yet clear what the precise function of trehalose synthesis is, but there is mounting evidence that trehalose-6-phosphate is implicated in the regulation of sugar metabolism. Further work is necessary to confirm this hypothesis and determine the underlying mechanism.     

Presentation of IFN-gamma to nitric oxide-producing cells: a novel function for mast cells

We report that mast cells can bind and present IFN-gamma in a functionally active form to macrophages. Flow-cytometric analysis revealed that biotinylated IFN-gamma bound equally well to purified peritoneal mast cells from both IFN-gammaR knockout and wild-type mice, indicating a non-IFN-gammaR binding site. Purified peritoneal mast cells, loaded with IFN-gamma for 30 min and washed, were able to induce NO synthesis by peritoneal macrophages. This response required cell contact and expression of IFN-gammaR on the responding macrophages, but not the mast cells. Human HMC-1 mast cells were also able to present IFN-gamma to mouse macrophages. Enzyme treatment of mouse mast cells revealed that binding of IFN-gamma was predominantly to chondroitin sulfate B (dermatan sulfate). Binding of IFN-gamma to dermatan sulfate was confirmed by inhibition ELISA. This study demonstrates for the first time that mast cells can present IFN-gamma to other cells via glycosaminoglycans. Mast cells may act as a reservoir of surface-stored functionally active cytokines.     

Non-disjunction events induced by albendazole in human cells

Albendazole (ABZ), a benzimidazole carbamate used for the treatment of several human helminthiases has high affinity for tubulin, which results in an inhibition of microtubule polymerization, blocking several vital processes in the parasites, such as motility and nutrient uptake. The ability of ABZ to act as mitotic spindle poison leads to a potential risk for aneuploidy induction in exposed human beings. ABZ, as well as albendazole sulphoxide (ABZSO), its main metabolite, induce micronuclei in human cells in a dose-dependent manner. Despite recognition that ABZ and ABZSO increase micronucleus frequency, their potential as inducers of non-disjunction in human cells, an event considered more frequent than chromosome loss, and one of the main mechanisms involved in aneuploidy induction, has not been evaluated. In the present work, we investigated the ability of ABZ and ABZSO to induce non-disjunction in cultured human lymphocytes. Non-disjunction was scored by chromosome-specific FISH using a classical or alpha satellite probe for chromosomes 1 and 7, respectively. Significant increase in non-disjunction events that involved either chromosome were observed in cells treated with ABZ or ABZSO. Both ABZ and ABZSO induced non-disjunction at lower concentrations than those at which MN were observed.     

Differential cell cycle-specificity for chromosomal damage induced by merbarone and etoposide in V79 cells

Merbarone, a topoisomerase II (topo II) inhibitor which, in contrast to etoposide, does not stabilize topo II-DNA cleavable complexes, was previously shown to be a potent clastogen in vitro and in vivo. To investigate the possible mechanisms, we compared the cell cycle-specificity of the clastogenic effects of merbarone and etoposide in V79 cells. Using flow cytometry and BrdU labeling techniques, etoposide was shown to cause a rapid and persistent G2 delay while merbarone was shown to cause a prolonged S-phase followed by a G2 delay. To identify the stages which are susceptible to DNA damage, we performed the micronucleus (MN) assay with synchronized cells or utilized a combination of BrdU pulse labeling and the cytokinesis-blocked MN assay with non-synchronized cells. Treatment of M phase cells with either agent did not result in increased MN formation. Etoposide but not merbarone caused a significant increase in MN when cells were treated during G2 phase. When treated during S-phase, both chemicals induced highly significant increases in MN. However, the relative proportion of MN induced by merbarone was substantially higher than that induced by etoposide. Both chemicals also caused significant increases in MN in cells that were treated during G1 phase. To confirm the observations in the MN assay, first division metaphases were evaluated in the chromosome aberration assay. The chromosomes of cells treated with merbarone and etoposide showed increased frequencies of both chromatid- and chromosome-type of aberrations. Our findings indicate that while etoposide causes DNA damage more evenly throughout the G1, S and G2 phases of the cell cycle, an outcome which may be closely associated with topo II-mediated DNA strand cleavage, merbarone induces DNA breakage primarily during S-phase, an effect which is likely due to the stalling of replication forks by inhibition of topo II activity.     

Introns and reading frames: correlation between splicing sites and their codon positions

Computer analyses of the entire GenBank database were conducted to examine correlation between splicing sites and codon positions in reading frames. Intron insertion patterns (i.e., splicing site locations with respect to codon positions) have been analyzed for all of the 74 codons of all the eukaryote taxonomic groups: primates, rodents mammals, vertebrates, invertebrates, and plants. We found that reading frames are interrupted by an intron at a codon boundary (as opposed to the middle of a codon) significantly more often than expected. This observation is consistent with the exon shuffling hypothesis, because exons that end at codon boundaries can be concatenated without causing a frame shift and thus are evolutionarily advantageous. On the other hand, when introns interrupt at the middles of codons, they exist in between the first and second bases much more frequently than between the second and third bases, despite the fact that boundaries between the first and second bases of codons are generally far more important than those between the second and third bases. The reason for this is not clear and yet to be explained. We also show that the length of an exon is a multiple of 3 more frequently than expected. Furthermore, the total length of two consecutive exons is also more frequently a multiple of 3. All the observations above are consistent with results recently published by Long, Rosenberg, and Gilbert (1995).      

Metabolome and metaboproteome remodeling in nuclear reprogramming

Nuclear reprogramming resets differentiated tissue to generate induced pluripotent stem (iPS) cells. While genomic attributes underlying reacquisition of the embryonic-like state have been delineated, less is known regarding the metabolic dynamics underscoring induction of pluripotency. Metabolomic profiling of fibroblasts vs. iPS cells demonstrated nuclear reprogramming-associated induction of glycolysis, realized through augmented utilization of glucose and accumulation of lactate. Real-time assessment unmasked downregulated mitochondrial reserve capacity and ATP turnover correlating with pluripotent induction. Reduction in oxygen consumption and acceleration of extracellular acidification rates represent high-throughput markers of the transition from oxidative to glycolytic metabolism, characterizing stemness acquisition. The bioenergetic transition was supported by proteome remodeling, whereby 441 proteins were altered between fibroblasts and derived iPS cells. Systems analysis revealed overrepresented canonical pathways and interactome-associated biological processes predicting differential metabolic behavior in response to reprogramming stimuli, including upregulation of glycolysis, purine, arginine, proline, ribonucleoside and ribonucleotide metabolism, and biopolymer and macromolecular catabolism, with concomitant downregulation of oxidative phosphorylation, phosphate metabolism regulation, and precursor biosynthesis processes, prioritizing the impact of energy metabolism within the hierarchy of nuclear reprogramming. Thus, metabolome and metaboproteome remodeling is integral for induction of pluripotency, expanding on the genetic and epigenetic requirements for cell fate manipulation.