A genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genes

Background

Cassava, Manihot esculenta Crantz, is one of the most important crops world-wide representing the staple security for more than one billion of people. The development of dense genetic and physical maps, as the basis for implementing genetic and molecular approaches to accelerate the rate of genetic gains in breeding program represents a significant challenge. A reference genome sequence for cassava has been made recently available and community efforts are underway for improving its quality. Cassava is threatened by several pathogens, but the mechanisms of defense are far from being understood. Besides, there has been a lack of information about the number of genes related to immunity as well as their distribution and genomic organization in the cassava genome.

Results

A high dense genetic map of cassava containing 2,141 SNPs has been constructed. Eighteen linkage groups were resolved with an overall size of 2,571 cM and an average distance of 1.26 cM between markers. More than half of mapped SNPs (57.4%) are located in coding sequences. Physical mapping of scaffolds of cassava whole genome sequence draft using the mapped markers as anchors resulted in the orientation of 687 scaffolds covering 45.6% of the genome. One hundred eighty nine new scaffolds are anchored to the genetic cassava map leading to an extension of the present cassava physical map with 30.7 Mb. Comparative analysis using anchor markers showed strong co-linearity to previously reported cassava genetic and physical maps. In silico based searching for conserved domains allowed the annotation of a repertory of 1,061 cassava genes coding for immunity-related proteins (IRPs). Based on physical map of the corresponding sequencing scaffolds, unambiguous genetic localization was possible for 569 IRPs.

Conclusions

This is the first study reported so far of an integrated high density genetic map using SNPs with integrated genetic and physical localization of newly annotated immunity related genes in cassava. These data build a solid basis for future studies to map and associate markers with single loci or quantitative trait loci for agronomical important traits. The enrichment of the physical map with novel scaffolds is in line with the efforts of the cassava genome sequencing consortium.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1397-4) contains supplementary material, which is available to authorized users.     

Bite force and body mass of the fossil rodent Telicomys giganteus (Caviomorpha,Dinomyidae)

An exceptionally well-preserved skull of the Pliocene rodent Telicomys giganteus allowed the first estimation of body mass and analysis of the bite mechanics of this species of South American giant rodent. In this study, we reconstructed the main anatomical features of the skull of this Pliocene rodent and related them to the bite force at the incisors. The average of an estimation body mass gives 100 kg. We also estimated the bite force using three different techniques. Two methods suggest that bite forces at the incisors have a range of 500–1000 N. However, the incisors seem to be stronger than expected for this bite force, implying that the bite forces may have been greater than 2000 N. We consider the hypothesis of defense against predators or other agonistic behavior to explain our results.     

Drug-polymer microparticles produced by supercritical assisted atomization

The supercritical assisted atomization (SAA) was proposed as a new technique to produce composite microparticles for drug controlled release. Ampicillin trihydrate and chitosan were selected as model drug and carrier, respectively, and 1% v/v acetic acid aqueous solution was used as solvent. The effect of the polymer/drug ratio on particle morphology and drug release rate was evaluated. SEM analysis indicated that non-coalescing spherical microparticles formed by chitosan/ampicillin were produced by SAA. All coprecipitates produced have a sharp particle distribution, with diameters ranging between about 0.1 and 6 microm. SAA composite microparticles were characterized by X-ray, DSC, EDX and UV-vis analysis. A solid solution of the chitosan and ampicillin was produced and a stabilizing effect of the polymer on the drug has resulted that protects ampicillin from thermal degradation. A prolonged release from SAA coprecipitates with respect to raw drug and physical mixtures of chitosan and ampicillin was obtained; moreover, the polymer/drug ratio has revealed to be a controlling parameter for drug release. Drug release mechanisms characteristic of swelling-controlled systems were observed, with ampicillin release depending on both relaxation and diffusive mechanisms. An empirical binomial equation was used to describe experimental data, showing a fair good agreement with ampicillin release data if both the relaxational and the diffusional parameters are function of the polymer/drug ratio.     

C-Npys (S-3-nitro-2-pyridinesulfenyl) and peptide derivatives can inhibit a serine-thiol proteinase activity from Paracoccidioides brasiliensis

The inhibitory capacity of C-Npys (S-[3-nitro-2-pyridinesulfenyl]) derivatives over thiol-containing serine proteases has never been tested. In the present work we used an extracellular serine-thiol proteinase activity from the fungal pathogen Paracoccidioides brasiliensis (PbST) to describe a potent inhibitory capacity of Bzl-C(Npys)KRLTL-NH(2) and Bzl-MKRLTLC(Npys)-NH(2). The assays were performed with PbST enriched upon affinity chromatography in a p-aminobenzamidine (pABA)-Sepharose column. Although PbST can cleave the fluorescence resonance energy transfer peptide Abz-MKRLTL-EDDnp between L-T, the C(Npys) derivatives were not substrates nor were they toxic in a cell detachment assay, allowing therapeutic use. The best inhibitor was Bzl-C(Npys)KRLTL-NH(2) (K(i)=16nM), suggesting that the peptide sequence promoted a favorable interaction, especially when C(Npys) was placed at a further position from the L-T bond, at the N-terminus. Inhibition was completely reverted with dithioerythritol, indicating that it was due to the reactivity of the C(Npys) moiety with a free SH- group.     

Cost and benefits of attractive floral traits in the annual species Madia sativa (Asteraceae)

The maintenance of flower size variation within populations might be explained by conflicting selection pressures on floral traits that may involve biological agents, such as mutualists and antagonists, and allocation costs associated with floral display. The annual species Madia sativa (Asteraceae) exhibits ample variation in the number of ray florets in natural populations. This field study aimed at evaluating the costs and benefits associated with floral traits in M. sativa. In particular, we addressed two main questions: (1) Is the number of ray florets positively associated with pollinator visitation rate? (2) Is there a fitness cost of ray floret maintenance when pollinators are absent? We detected one benefit of conspicuous ray capitula: a strong preference by insect pollinators. We also confirmed the occurrence of costs: when pollinators were excluded conspicuous ray capitula had a reduced reproductive assurance via autogamous selfing, and there were trade-offs between the number of ray florets and seed mass and seed germination. Results suggest that the maintenance of within-population variation in the number of ray florets in M. sativa is explained, at least in part, by the balance between costs and benefits associated with this floral trait.     

Characterization of intramolecular interactions of HIV-1 accessory protein Nef by differential scanning calorimetry

The interactions between the N-terminal arm and the structural core of Nef, an HIV-1 accessory protein, have been studied by high sensitivity differential scanning calorimetry. Critical interactions have been identified by measuring the structural energetics of both truncation and point mutants of the protein. These studies demonstrate that the N-terminal arm of Nef strongly interacts with the core and that it contributes close to 4.3 kcal/mol to the stability of the entire protein. The interactions are not evenly distributed through the N-terminal arm. Two strongly interacting regions have been identified: the region between residues 1 and 40 that contributes 1.6 kcal/mol to the stability of Nef; and, the region between residues 50 and 61 that contributes 2.7 kcal/mol. Other regions (e.g. residues 41 to 49) appear to contribute little to the interaction. The identification of these, until now, elusive interactions provides a physical foundation for allosteric effects between N-terminal arm and protein core elicited by different binding partners.     

Chelation of ThIV, EuIII and NdIII by dianionic N,N'-bis(pyridoxylideneiminato)ethylene, (Pyr2en)2-. On the search of feasible modelings for heavy metals damage inhibition in living beings

The neutral Schiff base N,N'-bis(pyridoxylideneiminato)ethylene {H(2)pyr(2)en} reacts with Th(NO(3))4.4H2O, NdCl3.6H2O and EuCl3.6H2O to give [Th(pyr(2)en)2(H2O)] (1), [Nd(pyr(2)en)(Hpyr(2)en)].12H2O (2) and [Eu(pyr(2)en)(Hpyr(2)en)] (3). In the three not yet reported bimolecular chelate systems the endo hydroxyl groups of the rings undergo deprotonation confirming the remarkable ability of the pyridoxal-containing ligand H(2)pyr(2)en to yield stable heavy metal chelates with unusual coordination polyhedra. Complexes 2 and 3 show a coordination number 8 for Nd and Eu, achieving a distorted quadratic antiprism. In complex 1 the additional water molecule increases the coordination number of Th to 9 producing a capped square antiprism. The synthesis and structural elucidation of the title complexes starting from a probably non-toxic metabolite like H(2)pyr(2)en should represent a useful contribution to the research on models of prevention and therapy of damage caused by radioactive and heavy elements.     

Effects of Irradiation on the Postnatal Development of the Brain in a Genetic Mouse Model of Globoid Cell Leukodystrophy

Irradiation is one way to condition Twitcher mice--a natural model of globoid cell leukodystrophy (GLD)--prior to receive bone marrow transplantation (BMT). BMT showed to delay but not to completely prevent GLD disease in treated mutants. The reasons why BMT is not completely preventive in Twitchers are unclear but we speculate that irradiation might contribute to worsen the neurological impairments generated by the disease by altering postnatal neurogenesis. To test this hypothesis, we examined proliferation, migration and differentiation of neural precursors in neurogenic areas of the Twitcher brain after exposure of 5 day-old mutant pups to 620 rad, a non-lethal dose that leads to 80-90% of bone-marrow engraftment in classic BMT. Twitchers showed to be sensitive to irradiation, leading to a severe retardation of body growth of irradiated mutants. Irradiated Twitchers had reduced proliferation of neural precursors and increased astrogliosis and microgliosis, with reduced numbers of migratory neuroblasts and significantly less brain myelination. These effects were accompanied by caspase-3 activation and appeared largely irreversible in the lifespan of the Twitcher. Our work confirms that exposure of the neonatal brain to irradiation conditions such as those performed prior to BMT, can lead to long-lasting alterations of postnatal neurogenesis and myelination, which might contribute to worsen the progression of disease in these myelin mutants and to reduce the success of BMT.     

Ensifer mexicanus sp. nov. a new species nodulating Acacia angustissima (Mill.) Kuntze in Mexico

A new lineage of Ensifer nodulating the American legume Acacia angustissima in the tropical forest of Chiapas and Morelos, Mexico is described. Bacteria were identified as Ensifer with ssb or nolR specific primers. Phylogenetic analysis with partial sequences of the five chromosomal genes gyrA, nolR, recA, rpoB and rrs revealed that this new lineage is related to African Ensifer terangae. The results of total DNA-DNA hybridization and selected phenotypic tests among the A. angustissima strains and E. terangae indicated that they belong to different species. The phylogeny with the symbiotic nifH gene also separates this group as a different clade but with close affinities to bacteria belonging to the genus Ensifer isolated from American hosts. ITTG R7(T) (=CFN ER1001, HAMBI 2910, CIP 109033, ATCC BAA-1312, DSM18446) is the type strain of a new species for which the name Ensifer mexicanus sp. nov. is proposed.     

Role of Reactive Oxygen Species in the Initiation of Plant Retrograde Signaling

The interaction between the nucleus and the different organelles is important in the physiology of the plant. Reactive oxygen species (ROS) are a by-product of the oxidation of organic molecules to obtain energy by the need to carry out the electron transfer between the different enzymatic complexes. However, they also have a role in the generation of what is known as retrograde signaling. This signal comes from the different organelles in which the oxidation of molecules or the electron transference is taking place such as mitochondria and chloroplasts. Furthermore, ROS can also induce the release of signals from the apoplast. It seems that these signals plays a role communicating to the nucleus the current status of the different parts of the plant cell to induce a changes in gene expression. In this review, the molecular mechanism of ROS retrograde signaling is described.