High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species

Background: High-throughput SNP genotyping has become an essential requirement for molecular breeding and population genomics studies in plant species. Large scale SNP developments have been reported for several mainstream crops. A growing interest now exists to expand the speed and resolution of genetic analysis to outbred species with highly heterozygous genomes. When nucleotide diversity is high, a refined diagnosis of the target SNP sequence context is needed to convert queried SNPs into high-quality genotypes using the Golden Gate Genotyping Technology (GGGT). This issue becomes exacerbated when attempting to transfer SNPs across species, a scarcely explored topic in plants, and likely to become significant for population genomics and inter specific breeding applications in less domesticated and less funded plant genera. Results: We have successfully developed the first set of 768 SNPs assayed by the GGGT for the highly heterozygous genome of Eucalyptus from a mixed Sanger/454 database with 1,164,695 ESTs and the preliminary 4.5X draft genome sequence for E. grandis. A systematic assessment of in silico SNP filtering requirements showed that stringent constraints on the SNP surrounding sequences have a significant impact on SNP genotyping performance and polymorphism. SNP assay success was high for the 288 SNPs selected with more rigorous in silico constraints; 93% of them provided high quality genotype calls and 71% of them were polymorphic in a diverse panel of 96 individuals of five different species. SNP reliability was high across nine Eucalyptus species belonging to three sections within subgenus Symphomyrtus and still satisfactory across species of two additional subgenera, although polymorphism declined as phylogenetic distance increased. Conclusions: This study indicates that the GGGT performs well both within and across species of Eucalyptus notwithstanding its nucleotide diversity >= 2%. The development of a much larger array of informative SNPs across multiple Eucalyptus species is feasible, although strongly dependent on having a representative and sufficiently deep collection of sequences from many individuals of each target species. A higher density SNP platform will be instrumental to undertake genome-wide phylogenetic and population genomics studies and to implement molecular breeding by Genomic Selection in Eucalyptus.

Chronostratigraphy and radiocarbon age inversion in the Holocene regressive barrier of Parana, southern Brazil

Twenty-two (14)C datings were performed at the central sector of the Parana coast to define Holocene regressive barrier evolution. The barrier Pleistocene substratum was ascribed an age between 40400 and 30000 yr BP, but it can also represent the penultimate sea level highstand during marine isotope stage 5e. The Holocene barrier samples provided ages between 8542-8279 and 2987-2751 cal yr BP, and showed at least six age inversions that were related to age differences between in situ or low-distance transported shells or trunk fragments, and high-distance transported vegetal debris, wood fragments and organic matter samples. The regressive Holocene barrier age was 4402-4135 cal yr BP near the base, and 2987-2751 cal yr BP near the top. Most of the vegetal remains were transported by ebb tidal currents from the estuaries to the inner shelf below wave base level during the mid-Holocene highstand; they were transported onshore by storm waves and littoral currents during the sea level lowering after the sea level maximum, and were deposited mainly as middle shoreface swaley cross-stratification facies. (C) 2008 Published by Elsevier B.V.

Modulation of respiratory responses to chemoreflex activation by L-glutamate and ATP in the rostral ventrolateral medulla of awake rats

Moraes DJA, Bonagamba LGH, Zoccal DB, Machado BH. Modulation of respiratory responses to chemoreflex activation by L-glutamate and ATP in the rostral ventrolateral medulla of awake rats. Am J Physiol Regul Integr Comp Physiol 300: R1476-R1486, 2011. First published March 16, 2011; doi:10.1152/ajpregu.00825.2010.-Presympathetic neurons in the different anteroposterior aspects of rostral ventrolateral medulla (RVLM) are colocalized with expiratory [Botzinger complex (BotC)] and inspiratory [pre-Botzinger complex (pre-BotC)] neurons of ventral respiratory column (VRC), suggesting that this region integrates the cardiovascular and respiratory chemoreflex responses. In the present study, we evaluated in different anteroposterior aspects of RVLM of awake rats the role of ionotropic glutamate and purinergic receptors on cardiorespiratory responses to chemoreflex activation. The bilateral ionotropic glutamate receptors antagonism with kynurenic acid (KYN) (8 nmol/50 nl) in the rostral aspect of RVLM (RVLM/BotC) enhanced the tachypneic (120 +/- 9 vs. 180 +/- 9 cpm; P < 0.01) and attenuated the pressor response (55 +/- 2 vs. 15 +/- 1 mmHg; P < 0.001) to chemoreflex activation (n = 7). On the other hand, bilateral microinjection of KYN into the caudal aspect of RVLM (RVLM/pre-BotC) caused a respiratory arrest in four awake rats used in the present study. Bilateral P2X receptors antagonism with PPADS (0.25 nmol/50 nl) in the RVLM/BotC reduced chemoreflex tachypneic response (127 +/- 6 vs. 70 +/- 5 cpm; P < 0.001; n = 6), but did not change the chemoreflex pressor response. In addition, PPADS into the RVLM/BtC attenuated the enhancement of the tachypneic response to chemoreflex activation elicited by previous microinjections of KYN into the same subregion (188 +/- 2 vs. 157 +/- 3 cpm; P < 0.05; n = 5). Our findings indicate that: 1) L-glutamate, but not ATP, in the RVLM/BtC is required for pressor response to peripheral chemoreflex and 2) both transmitters in the RVLM/BtC are required for the processing of the ventilatory response to peripheral chemoreflex activation in awake rats.

Stereological and allometric studies on neurons and axo-dendritic synapses in the superior cervical ganglia of rats, capybaras and horses

The superior cervical ganglion (SCG) in mammals varies in structure according to developmental age, body size, gender, lateral asymmetry, the size and nuclear content of neurons and the complexity and synaptic coverage of their dendritic trees. In small and medium-sized mammals, neuron number and size increase from birth to adulthood and, in phylogenetic studies, vary with body size. However, recent studies on larger animals suggest that body weight does not, in general, accurately predict neuron number. We have applied design-based stereological tools at the light-microscopic level to assess the volumetric composition of ganglia and to estimate the numbers and sizes of neurons in SCGs from rats, capybaras and horses. Using transmission electron microscopy, we have obtained design-based estimates of the surface coverage of dendrites by postsynaptic apposition zones and model-based estimates of the numbers and sizes of synaptophysin-labelled axo-dendritic synaptic disks. Linear regression analysis of log-transformed data has been undertaken in order to establish the nature of the relationships between numbers and SCG volume (V(scg)). For SCGs (five per species), the allometric relationship for neuron number (N) is N=35,067xV (scg) (0.781) and that for synapses is N=20,095,000xV (scg) (1.328) , the former being a good predictor and the latter a poor predictor of synapse number. Our findings thus reveal the nature of SCG growth in terms of its main ingredients (neurons, neuropil, blood vessels) and show that larger mammals have SCG neurons exhibiting more complex arborizations and greater numbers of axo-dendritic synapses.

Shared and differential traits in the accessory olfactory bulb of caviomorph rodents with particular reference to the semiaquatic capybara

The vomeronasal system is crucial for social and sexual communication in mammals. Two populations of vomeronasal sensory neurons, each expressing G alpha i2 or G alpha o proteins, send projections to glomeruli of the rostral or caudal accessory olfactory bulb, rAOB and cAOB, respectively. In rodents, the G alpha i2- and G alpha o-expressing vomeronasal pathways have shown differential responses to small/volatile vs. large/non-volatile semiochemicals, respectively. Moreover, early gene expression suggests predominant activation of rAOB and cAOB neurons in sexual vs. aggressive contexts, respectively. We recently described the AOB of Octodon degus, a semiarid-inhabiting diurnal caviomorph. Their AOB has a cell indentation between subdomains and the rAOB is twice the size of the cAOB. Moreover, their AOB receives innervation from the lateral aspect, contrasting with the medial innervation of all other mammals examined to date. Aiming to relate AOB anatomy with lifestyle, we performed a morphometric study on the AOB of the capybara, a semiaquatic caviomorph whose lifestyle differs remarkably from that of O. degus. Capybaras mate in water and scent-mark their surroundings with oily deposits, mostly for male-male communication. We found that, similar to O. degus, the AOB of capybaras shows a lateral innervation of the vomeronasal nerve, a cell indentation between subdomains and heterogeneous subdomains, but in contrast to O. degus the caudal portion is larger than the rostral one. We also observed that four other caviomorph species present a lateral AOB innervation and a cell indentation between AOB subdomains, suggesting that those traits could represent apomorphies of the group. We propose that although some AOB traits may be phylogenetically conserved in caviomorphs, ecological specializations may play an important role in shaping the AOB.

Osteocyte Density in the Peri-Implant Bone of Immediately Loaded and Submerged Dental Implants

Background: The role of osteocytes in bone structure and function remains partially unresolved. Their participation in mechanotransduction, i.e., the conversion of a physical stimulus into a cellular response, has been hypothesized. The present study was an evaluation of the osteocyte density in the peri-implant bone of immediately loaded and submerged dental implants. Methods: Fourteen male patients were included in the study; all of them were partially edentulous and needed a posterior mandibular restoration. Implants were inserted in these areas; half of the sample was loaded immediately (included in a fixed provisional prosthesis on the same day as implant surgery), whereas the other half was left to heal submerged. Fourteen implants (seven immediately loaded and seven unloaded) were retrieved with a trephine after a healing period of 8 weeks. The specimens were treated to obtain thin ground sections, and histomorphometry was used to evaluate the osteocyte index in the peri-implant bone. Results: A higher and statistically significant number of osteocytes was found in the peri-implant bone around immediately loaded implants (P=0.0081). A correlation between the percentage of bone-implant contact and osteocyte density was found for immediately loaded implants (P=0.0480) but not for submerged implants (P=0.2667). Conclusion: The higher number of osteocytes in the peri-implant bone around immediately loaded implants could be related to the functional adaptation required by the loading stimulus, which also explains the hypothesized involvement of the osteocytes in the maintenance of the bone matrix. J Periodontol 2009;80:499-504.

Observation in the MINOS far detector of the shadowing of cosmic rays by the sun and moon

The shadowing of cosmic ray primaries by the moon and sun was observed by the MINOS far detector at a depth of 2070 mwe using 83.54 million cosmic ray muons accumulated over 1857.91 live-days. The shadow of the moon was detected at the 5.6 sigma level and the shadow of the sun at the 3.8 sigma level using a log-likelihood search in celestial coordinates. The moon shadow was used to quantify the absolute astrophysical pointing of the detector to be 0.17 +/- 0.12 degrees. Hints of interplanetary magnetic field effects were observed in both the sun and moon shadow. Published by Elsevier B.V.

Drag reduction by polyethylene glycol in the tail arterial bed of normotensive and hypertensive rats

This study was designed to evaluate the effect of drag reducer polymers (DRP) on arteries from normotensive (Wistar) and spontaneously hypertensive rats (SHR). Polyethylene glycol (PEG 4000 at 5000 ppm) was perfused in the tail arterial bed with (E+) and without endothelium (E-) from male, adult Wistar (N = 14) and SHR (N = 13) animals under basal conditions (constant flow at 2.5 mL/min). In these preparations, flow-pressure curves (1.5 to 10 mL/min) were constructed before and 1 h after PEG 4000 perfusion. Afterwards, the tail arterial bed was fixed and the internal diameters of the arteries were then measured by microscopy and drag reduction was assessed based on the values of wall shear stress (WSS) by computational simulation. In Wistar and SHR groups, perfusion of PEG 4000 significantly reduced pulsatile pressure (Wistar/E+: 17.5 ± 2.8; SHR/E+: 16.3 ± 2.7%), WSS (Wistar/E+: 36; SHR/E+: 40%) and the flow-pressure response. The E- reduced the effects of PEG 4000 on arteries from both groups, suggesting that endothelial damage decreased the effect of PEG 4000 as a DRP. Moreover, the effects of PEG 4000 were more pronounced in the tail arterial bed from SHR compared to Wistar rats. In conclusion, these data demonstrated for the first time that PEG 4000 was more effective in reducing the pressure-flow response as well as WSS in the tail arterial bed of hypertensive than of normotensive rats and these effects were amplified by, but not dependent on, endothelial integrity. Thus, these results show an additional mechanism of action of this polymer besides its mechanical effect through the release and/or bioavailability of endothelial factors.

Intestinal Anti-Inflammatory Activity of Baccharis dracunculifolia in the Trinitrobenzenesulphonic Acid Model of Rat Colitis

Baccharis dracunculifolia DC (Asteraceae) is a Brazilian medicinal plant popularly used for its antiulcer and anti-inflammatory properties. This plant is the main botanical source of Brazilian green propolis, a natural product incorporated into food and beverages to improve health. The present study aimed to investigate the chemical profile and intestinal anti-inflammatory activity of B. dracunculifolia extract on experimental ulcerative colitis induced by trinitrobenzenosulfonic acid (TNBS). Colonic damage was evaluated macroscopically and biochemically through its evaluation of glutathione content and its myeloperoxidase (MPO) and alkaline phosphatase activities. Additional in vitro experiments were performed in order to test the antioxidant activity by inhibition of induced lipid peroxidation in the rat brain membrane. Phytochemical analysis was performed by HPLC using authentic standards. The administration of plant extract (5 and 50 mgkg(-1)) significantly attenuated the colonic damage induced by TNBS as evidenced both macroscopically and biochemically. This beneficial effect can be associated with an improvement in the colonic oxidative status, since plant extract prevented glutathione depletion, inhibited lipid peroxidation and reduced MPO activity. Caffeic acid, p-coumaric acid, aromadendrin-4-O-methyl ether, 3-prenyl-p-coumaric acid, 3,5-diprenyl-p-coumaric acid and baccharin were detected in the plant extract.

The role of disulfide bridges in the 3-D structures of the antimicrobial peptides gomesin and protegrin-1: a molecular dynamics study

Some antimicrobial peptides have a broad spectrum of action against many different kinds of microorganisms. Gomesin and protegrin-1 are examples of such antimicrobial peptides, and they were studied by molecular dynamics in this research. Both have a beta-hairpin conformation stabilized by two disulfide bridges and are active against Gram-positive and Gram-negative bacteria, as well as fungi. In this study, the role of the disulfide bridge in the maintenance of the tertiary peptide structure of protegrin-1 and gomesin is analyzed by the structural characteristics of these peptides and two of their respective variants, gomy4 and proty4, in which the four cysteines are replaced by four tyrosine residues. The absence of disulfide bridges in gomy4 and proty4 is compensated by overall reinforcement of the original hydrogen bonds and extra attractive interactions between the aromatic rings of the tyrosine residues. The net effects on the variants with respect to the corresponding natural peptides are: i) maintenance of the original beta-hairpin conformation, with great structural similarities between the mutant and the corresponding natural peptide; ii) combination of positive F and. Ramachandran angles within the hairpin head region with a qualitative change to a combination of positive (F) and negative (.) angles, and iii) significant increase in structural flexibility. Experimental facts about the antimicrobial activity of the gomesin and protegrin-1 variants have also been established here, in the hope that the detailed data provided in the present study may be useful for understanding the mechanism of action of these peptides.

Fossil groups in the Millennium Simulation Evolution of the brightest galaxies

Aims. We create a catalogue of simulated fossil groups and study their properties, in particular the merging histories of their first-ranked galaxies. We compare the simulated fossil group properties with those of both simulated non-fossil and observed fossil groups. Methods. Using simulations and a mock galaxy catalogue, we searched for massive (>5 x 10(13) h(-1) M-circle dot) fossil groups in the Millennium Simulation Galaxy Catalogue. In addition, we attempted to identify observed fossil groups in the Sloan Digital Sky Survey Data Release 6 using identical selection criteria. Results. Our predictions on the basis of the simulation data are: (a) fossil groups comprise about 5.5% of the total population of groups/clusters with masses larger than 5 x 10(13) h(-1) M-circle dot. This fraction is consistent with the fraction of fossil groups identified in the SDSS, after all observational biases have been taken into account; (b) about 88% of the dominant central objects in fossil groups are elliptical galaxies that have a median R-band absolute magnitude of similar to-23.5-5 log h, which is typical of the observed fossil groups known in the literature; (c) first-ranked galaxies of systems with M > 5 x 10(13) h(-1) M-circle dot, regardless of whether they are either fossil or non-fossil, are mainly formed by gas-poor mergers; (d) although fossil groups, in general, assembled most of their virial masses at higher redshifts in comparison with non-fossil groups, first-ranked galaxies in fossil groups merged later, i.e. at lower redshifts, compared with their non-fossil-group counterparts. Conclusions. We therefore expect to observe a number of luminous galaxies in the centres of fossil groups that show signs of a recent major merger.

Positive Selection Results in Frequent Reversible Amino Acid Replacements in the G Protein Gene of Human Respiratory Syncytial Virus

Human respiratory syncytial virus (HRSV) is the major cause of lower respiratory tract infections in children under 5 years of age and the elderly, causing annual disease outbreaks during the fall and winter. Multiple lineages of the HRSVA and HRSVB serotypes co-circulate within a single outbreak and display a strongly temporal pattern of genetic variation, with a replacement of dominant genotypes occurring during consecutive years. In the present study we utilized phylogenetic methods to detect and map sites subject to adaptive evolution in the G protein of HRSVA and HRSVB. A total of 29 and 23 amino acid sites were found to be putatively positively selected in HRSVA and HRSVB, respectively. Several of these sites defined genotypes and lineages within genotypes in both groups, and correlated well with epitopes previously described in group A. Remarkably, 18 of these positively selected tended to revert in time to a previous codon state, producing a ""flipflop'' phylogenetic pattern. Such frequent evolutionary reversals in HRSV are indicative of a combination of frequent positive selection, reflecting the changing immune status of the human population, and a limited repertoire of functionally viable amino acids at specific amino acid sites.

Frustration and anomalous behavior in the Bell-Lavis model of liquid water

We have reconsidered the Bell-Lavis model of liquid water and investigated its relation to its isotropic version, the antiferromagnetic Blume-Emery-Griffiths model on the triangular lattice. Our study was carried out by means of an exact solution on the sequential Husimi cactus. We show that the ground states of both models share the same topology and that fluid phases (gas and low- and high-density liquids) can be mapped onto magnetic phases (paramagnetic, antiferromagnetic, and dense paramagnetic, respectively). Both models present liquid-liquid coexistence and several thermodynamic anomalies. This result suggests that anisotropy introduced through orientational variables play no specific role in producing the density anomaly, in agreement with a similar conclusion discussed previously following results for continuous soft core,models. We propose that the presence of liquid anomalies may be related to energetic frustration, a feature common to both models.

Autocatalysis in the open circuit interaction of alcohol molecules with oxidized Pt surfaces

We studied the open circuit interaction of methanol and ethanol with oxidized platinum electrodes using in situ infrared spectroscopy. For methanol, it was found that formic acid is the main species formed in the initial region of the transient and that the steep decrease of the open circuit potential coincides with an explosive increase in the CO(2) production, which is followed by an increase in the coverage of adsorbed CO. For ethanol, acetaldehyde was the main product detected and only traces of dissolved CO(2) and adsorbed CO were found after the steep potential decay. In both cases, the transients were interpreted in terms of (a) the emergence of sub-surface oxygen in the beginning of the transient, where the oxide content is high, and (b) the autocatalytic production of free platinum sites for lower oxide content during the steep decay of the open circuit potential.

Changes in soil organic carbon storage under different agricultural management systems in the Southwest Amazon Region of Brazil

The Cerrado and Amazon regions of Brazil are probably the largest agricultural frontier of the world, and Could be a sink or source for C depending on the net effect of land use change and subsequent management on soil organic C pools. We evaluated the effects of agricultural management systems on soil organic C (SOC) stocks in the Brazilian states of Rondonia and Mato Grosso, and derived regional specific factors for soil C stock change associated with different management systems. We used 50 observations (data points) in this study, including 42 dealing with annual cropping practices and 8 dealing with perennial cropping, and analyzed the data in linear mixed-effect models. No tillage (NT) systems in Cerrado areas increased SOC Storage by 1.08 +/- 0.06 relative to SOC stocks under native conditions, while SOC storage increased by a modest factor of 1.01 +/- 0.17 in Cerradao and Amazon Forest conditions. Full tillage (FT) had negative effect on SOC storage relative to NT, decreasing SOC stocks by a factor of 0.94 +/- 0.04. but did not significantly reduce SOC stocks relative to native levels when adopted in the Cerrado region. Perennial cropping had a minimal impact on SOC stocks, estimated at a factor Value of 0.98 +/- 0.14, suggesting these systems maintain about 98% of the SOC stock found under native vegetation. The results Suggest that NT adoption may be increasing SOC with land use change from native vegetation to cropland management in the Cerrado region of Brazil. (C) 2009 Elsevier B.V. All rights reserved.