Genetic variation and association mapping of silica concentration in rice hulls using a germplasm collection

An association analysis on the genetic variability for silica concentration in rice hulls was performed using a "Mini-Core" set of 174 accessions representative of the germplasm diversity found in the USDA world collection of rice. Hull silica concentration was determined in replicated trials conducted in two southern states in the USA and was analyzed for its association with 164 genome-wide DNA markers. Among the accessions, the average silica concentration ranged from 120 to 251?mg?g(-1). Ample variation was seen within each of the five sub-populations of rice, as well as the 14 geographic regions that the accessions originated from. There was also an effect due to location and accession?×?location (G?×?E) interaction demonstrating the importance of assessing silica concentration across multiple environments. Twelve markers on ten chromosomes were significantly associated with hull silica concentration. Six markers (RM5644, RM5371, RM1335, RM283, RM263, and RM178) corroborated quantitative trait locus for silica concentration identified in other mapping studies. Our results provide germplasm and genetic markers that will assist breeding efforts to develop cultivars that have either high or low hull silica concentration. High silica hulls are good raw material for silica based industrial compounds, while low silica hulls are more biodegradable.     

Ecophysiology of photosynthesis in bryophytes: major roles for oxygen photoreduction and non‐photochemical quenching?

CO₂ fixation in mosses saturates at moderate irradiances. Relative electron transport rate (RETR) inferred from chlorophyll fluorescence saturates at similar irradiance in shade species (e.g. Plagiomnium undulatum, Trichocolea tomentella), but many species of unshaded habitats (e.g. Andreaea rothii, Schistidium apocarpum, Sphagnum spp. and Frullania dilatata) show non‐saturating RETR at high irradiance, with high non‐photochemical quenching (NPQ). In P. undulatum and S. apocarpum, experiments in different gas mixtures showed O₂ and CO₂ as interchangeable electron sinks. Nitrogen + saturating CO₂ gave high RETR and depressed NPQ. In S. apocarpum, glycolaldehyde (inhibiting photosynthesis and photorespiration) depressed RETR in air more at low than at high irradiance; in CO₂‐free air RETR was maintained at all irradiances. Non‐saturating electron flow was not suppressed in ambient CO₂ with 1% O₂. The results indicate high capacity for oxygen photoreduction when CO₂ assimilation is limited. Non‐saturating light‐dependent H₂O₂ production, insensitive to glycolaldehyde, suggests that electron transport is supported by oxygen photoreduction, perhaps via the Mehler‐peroxidase reaction. Consistent with this, mosses were highly tolerant to paraquat, which generates superoxide at photosystem I (PSI). Protection against excess excitation energy in mosses involves high capacity for photosynthetic electron transport to oxygen and high NPQ, activated at high irradiance, alongside high reactive oxygen species (ROS) tolerance.     

Angiotensin II utilizes Janus kinase 2 in hypertension, but not in the physiological control of blood pressure, during low-salt intake

Janus kinase (JAK) 2 is activated by ANG II in vitro and in vivo, and chronic blockade of JAK2 by the JAK2 inhibitor AG-490 has been shown recently to attenuate ANG II hypertension in mice. In this study, AG-490 was infused intravenously in chronically instrumented rats to determine if the blunted hypertension was linked to attenuation of the renal actions of ANG II. In male Sprague-Dawley rats, after a control period, ANG II at 10 ng·kg(-1)·min(-1) was infused intravenously with or without AG-490 at 10 ng·kg(-1)·min(-1) iv for 11 days. ANG II infusion (18 h/day) increased mean arterial pressure from 91 ± 3 to 168 ± 7 mmHg by day 11. That response was attenuated significantly in the ANG II + AG-490 group, with mean arterial pressure increasing only from 92 ± 5 to 127 ± 3 mmHg. ANG II infusion markedly decreased urinary sodium excretion, caused a rapid and sustained decrease in glomerular filtration rate to ～60% of control, and increased renal JAK2 phosphorylation; all these responses were blocked by AG-490. However, chronic AG-490 treatment had no effect on the ability of a separate group of normal rats to maintain normal blood pressure when they were switched rapidly to a low-sodium diet, whereas blood pressure fell dramatically in losartan-treated rats on a low-sodium diet. These data suggest that activation of the JAK/STAT pathway is critical for the development of ANG II-induced hypertension by mediating its effects on renal sodium excretory capability, but the physiological control of blood pressure by ANG II with a low-salt diet does not require JAK2 activation.     

A novel approach for multi-domain and multi-gene family identification provides insights into evolutionary dynamics of disease resistance genes in core eudicot plants

Background

Recent advances in DNA sequencing techniques resulted in more than forty sequenced plant genomes representing a diverse set of taxa of agricultural, energy, medicinal and ecological importance. However, gene family curation is often only inferred from DNA sequence homology and lacks insights into evolutionary processes contributing to gene family dynamics. In a comparative genomics framework, we integrated multiple lines of evidence provided by gene synteny, sequence homology and protein-based Hidden Markov Modelling to extract homologous super-clusters composed of multi-domain resistance (R)-proteins of the NB-LRR type (for NUCLEOTIDE BINDING/LEUCINE-RICH REPEATS), that are involved in plant innate immunity.

Results

To assess the diversity of R-proteins within and between species, we screened twelve eudicot plant genomes including six major crops and found a total of 2,363 NB-LRR genes. Our curated R-proteins set shows a 50% average for tandem duplicates and a 22% fraction of gene copies retained from ancient polyploidy events (ohnologs). We provide evidence for strong positive selection and show significant differences in molecular evolution rates (Ka/Ks-ratio) among tandem- (mean = 1.59), ohnolog (mean = 1.36) and singleton (mean = 1.22) R-gene duplicates. To foster the process of gene-edited plant breeding, we report species-specific presence/absence of all 140 NB-LRR genes present in the model plant Arabidopsis and describe four distinct clusters of NB-LRR “gatekeeper” loci sharing syntenic orthologs across all analyzed genomes.

Conclusion

By curating a near-complete set of multi-domain R-protein clusters in an eudicot-wide scale, our analysis offers significant insight into evolutionary dynamics underlying diversification of the plant innate immune system. Furthermore, our methods provide a blueprint for future efforts to identify and more rapidly clone functional NB-LRR genes from any plant species.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-966) contains supplementary material, which is available to authorized users.     

A computational study of dsDNA pairs and vibrational resonance in separating water

This article investigates the relationship between molecular sequence and dependent interacting behavior of molecular segment pairs and secondly, sequence dependent, vibrational resonance in surrounding normal saline, protein-free water. The development of a molecular model to explore these systems phenomena, the results of several nanoscale molecular dynamics simulations, and analysis of behavior of interacting ΦX174 double-stranded DNA segment pair models in various configurations are presented. Fourier analysis revealed intriguing vibration frequencies within the solvent plane between the segments, while subsequent frequency domain transformation of the time domain waveforms revealed statistically significant resonating harmonic signals in the THz range.

Electronic supplementary material

The online version of this article (doi:10.1007/s11693-014-9157-3) contains supplementary material, which is available to authorized users.     

Reduced leg blood flow during dynamic exercise in older endurance-trained men

It is currentlyunclear whether aging alters the perfusion of active muscles duringlarge-muscle dynamic exercise in humans. To study this issue, directmeasurements of leg blood flow (femoral vein thermodilution) andsystemic arterial pressure during submaximal cycle ergometry (70, 140, and 210 W) were compared between six younger (Y; 22-30 yr) and sixolder (O; 55-68 yr) chronically endurance-trainedmen. Whole body O₂uptake, ventilation, and arterial and femoral venous samples forblood-gas, catecholamine, and lactate determinations were alsoobtained. Training duration (min/day), estimated leg muscle mass(dual-energy X-ray absorptiometry; Y, 21.5 ± 1.2 vs. O, 19.9 ± 0.9 kg), and blood hemoglobin concentration (Y, 14.9 ± 0.4 vs. O, 14.7 ± 0.2 g/dl) did not significantly differ (P > 0.05) between groups. Leg bloodflow, leg vascular conductance, and femoral venousO₂ saturation were ~20-30%lower in the older men at each work rate (allP < 0.05), despite similarlevels of whole body O₂ uptake. At210 W, leg norepinephrine spillover rates and femoral venous lactateconcentrations were more than twofold higher in the older men.Pulmonary ventilation was also higher in the older men at 140 (+24%)and 210 (+39%) W. These results indicate that leg blood flow andvascular conductance during cycle ergometer exercise are significantlylower in older endurance-trained men in comparison to their youngercounterparts. The mechanisms responsible for this phenomenon and theextent to which they operate in other groups of older subjects deservefurther attention.

     

Augmented expression of polysaccharide intercellular adhesin in a defined Staphylococcus epidermidis mutant with the small-colony-variant phenotype

While coagulase-negative staphylococci (CoNS), with their ability to form a thick, multilayered biofilm on foreign bodies, have been identified as the major cause of implant-associated infections, no data are available about biofilm formation by staphylococcal small-colony variants (SCVs). In the past years, a number of device-associated infections due to staphylococcal SCVs were described, among them, several pacemaker infections due to SCVs of CoNS auxotrophic to hemin. To test the characteristics of SCVs of CoNS, in particular, to study the ability of SCVs to form a biofilm on foreign bodies, we generated a stable mutant in electron transport by interrupting one of the hemin biosynthetic genes, hemB, in Staphylococcus epidermidis. In fact, this mutant displayed a stable SCV phenotype with tiny colonies showing strong adhesion to the agar surface. When the incubation time was extended to 48 h or a higher inoculum concentration was used, the mutant produced biofilm amounts on polystyrene similar to those produced by the parent strain. When grown under planktonic conditions, the mutant formed markedly larger cell clusters than the parental strain which were completely disintegrated by the specific beta-1,6-hexosaminidase dispersin B but were resistant to trypsin treatment. In a dot blot assay, the mutant expressed larger amounts of polysaccharide intercellular adhesin (PIA) than the parent strain. In conclusion, interrupting a hemin biosynthetic gene in S. epidermidis resulted in an SCV phenotype. Markedly larger cell clusters and the ability of the hemB mutant to form a biofilm are related to the augmented expression of PIA.     

Reactivity and fate of benzene and formaldehyde in culture medium with and without fetal calf serum; relevance to in vitro mutagenicity testing

Gas chromatographic-mass spectrometric analyses were performed to determine the reactivity and fate of benzene (BEN) and formaldehyde (FA) in culture medium. BEN (solubility in water: 500 ppm) does not react with culture medium, either with or without fetal calf serum, but its volatility, even in closed vials, is so great that 90% of a 250-ppm solution is lost to the head space after 1 h at 24°C. FA, as a 37% aqueous solution, is a complex mixture that changes composition after 15-min incubation at 38°C. FA is extremely reactive in culture medium containing fetal calf serum, and is much less reactive with medium components in the absence of serum. There is a dramatic increase in the number of daughter products in FA-treated medium over time, such that those seen immediately after FA is added to medium have been replaced after 60-min incubation (38°C in closed vials) by many other interaction products. Methods ensuring maximum solubilization and minimal volatilization of BEN during exposure are essential for obtaining reproducible data on the mutagenic potential of BEN. The volatilization of FA from stock formalin solutions, and, more importantly, the interaction product(s) formed by this highly reactive compound with medium components, especially those in serum, are probably the critical aspects of an effective testing protocol for FA.