A preliminary linkage map of the tick, Ixodes scapularis

A linkage map of the Ixodes scapularis genome was constructed based upon segregation amongst 127 loci. These included 84 random amplified polymorphic DNA (RAPD) markers, 32 Sequence-Tagged RAPD (STAR) markers, 5 cDNAs, and 5 microsatellites in 232 F1 intercross progeny from a single, field-collected P1 female. A preliminary linkage map of 616 cM was generated across 14 linkage groups with one marker every 10.8 cM. Assuming a genome size of ∼109 bp, the relationship of physical to genetic distance is ∼300 kb/cM in the I. scapularis genome.

Determining spatial and temporal scales for management: lessons from whaling

Selection of the appropriate management unit is critical to the conservation of animal populations. Defining such units depends upon knowledge of population structure and upon the timescale being considered. Here, we examine the trajectory of eleven subpopulations of five species of baleen whales to investigate temporal and spatial scales in management. These subpopulations were all extirpated by commercial whaling, and no recovery or repopulation has occurred since. In these cases, time elapsed since commercial extinction ranges from four decades to almost four centuries. We propose that these subpopulations did not recover either because cultural memory of the habitat has been lost, because widespread whaling among adjacent stocks eliminated these as sources for repopulation, and/or because segregation following exploitation produced the abandonment of certain areas. Spatial scales associated with the extirpated subpopulations are frequently smaller than those typically employed in management. Overall, the evidence indicates that: (1) the time frame for management should be at most decadal in scope (i.e., <100 yr) and based on both genetic and nongenetic evidence of population substructure, and (2) at least some stocks should be defined on a smaller spatial scale than they currently are.

Genetic Mapping of Quantitative Trait Loci Associated with Bioenergy Traits, and The Assessment of Genetic Variability in Sweet Sorghum (Sorghum bicolor (L.). Moench)

Sweet sorghum, a botanical variety of sorghum is a potential source of bioenergy because high sugar levels accumulate in its stalks. The objectives of this study were to explore the global diversity of sweet sorghum germplasm, and map the genomic regions that are associated with bioenergy traits. In assessing diversity, 142 sweet sorghum accessions were evaluated with three marker types (SSR, SRAP, and morphological markers) to determine the degree of relatedness among the accessions. The traits measured (anthesis date [AD], plant height [PH], biomass yield [BY], and moisture content [MC]) were all significantly different (P<0.05) among accessions. Morphological marker clustered the accessions into five groups based on PH, MC and AD. The three traits accounted for 92.5% of the variation. There were four and five groups based on SRAP and SSR data respectively classifying accessions mainly on their origin or breeding history. The observed difference between SSR and SRAP based clusters could be attributed to the difference in marker type. SSRs amplify any region of the genome whereas SRAP amplify the open reading frames and promoter regions. Comparing the three marker-type clusters, the markers complimented each other in grouping accessions and would be valuable in assisting breeders to select appropriate lines for crossing. In evaluating QTLs that are associated with bioenergy traits, 165 recombinant inbred lines (RILs) were planted at four environments in Nebraska. A genetic linkage map constructed spanned a length of 1541.3 cM, and generated 18 linkage groups that aligned to the 10 sorghum chromosomes. Fourteen QTLs (6 for brix, 3 for BY, 2 each for AD and MC, and 1 for PH) were mapped. QTLs for the traits that were significantly correlated, colocalized in two clusters on linkage group Sbi01b. Both parents contributed beneficial alleles for most of traits measured, supporting the transgressive segregation in this population. Additional work is needed on exploiting the usefulness of chromosome 1 in breeding sorghum for bioenergy.

Estudo da formação de domínios em membranas modelos induzidos por peptídeos antimicrobianos e sua ação interfacial

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Photopatternable di-ureasil-zirconium oxocluster organic-inorganic hybrids as cost effective integrated optical substrates

Organic-inorganic hybrids containing methacrylic acid (McOH, CH(2)= C(CH(3))COOH)) modified zirconium tetrapropoxide, Zr(OPr(n))(4), classed as di-ureasil-zirconium oxo-cluster hybrids, have been prepared and structurally characterized by X-ray diffraction (XRD), small-angle X-ray scattering (SAXS), Fourier transform infrared (FT-IR) and Raman (FT-Raman) spectroscopies, Si and C nuclear magnetic resonance (NMR), and atomic force microscopy (AFM). XRD and SAXS results have pointed out the presence of Si- and Zr-based nanobuilding blocks (NBBs) dispersed into the organic phase. Inter-NBBs correlation distances have been estimated for the pure di-ureasil and a model compound obtained. by hydrolysis/condensation of Zr(OPr(n))(4):McOH (molar ratio 1: 1): d(Si) approximate to 26 +/- 1 angstrom and d(Zr) approximate to 16 +/- 1 angstrom, respectively. In the case of the di-ureasil-zirconium oxo-cluster hybrids, these distances depend on the Zr relative molar percentage (rel. mol. Zr %) (d(Si) ranges from 18 to 25 angstrom and d(Zr) from 14 to 23 angstrom, as the rel. mol. Zr % increases from 5 to 75), suggesting that the Si- and Zr-based clusters are interconstrained. Complementary data from FT-IR, FT-Raman, (29)Si and (13)C NMR, and AFM support to a structural model where McOH-modified Zr-based NBBs (Zr-OMc) are present over the whole range of composition. At low Zr-OMc contents (rel. mol. Zr % <30) the clusters are well-dispersed within the di-ureasil host, whereas segregation occurs at the 0.1 mu m scale at high Zr-OMc concentration (rel. mol. Zr % = 50). No Zr-O-Si heterocondensation has been discerned. Monomode waveguides, diffractions gratings, and Fabry-Perot cavities have been written through the exposure of the hybrid monoliths to UV light. FT-Raman has shown that the chemical process that takes place under illumination is the polymerization of the methacrylate groups of the Zr-OMc NBBs. The guidance region in patterned channels is a Gaussian section located below the exposed surface with typical dimensions of 320 mu m wide and 88 mu m deep. The effective refractive index is 1.5162 (maximum index contrast on the order of 1 x 10(-4)) and the reflection coeficient of the Fabry-Perot cavity (formed by a grating patterned into a 0.278 cm channel) is 0.042 with a free spectral range value of 35.6 GHz.

Geochemical signatures of metasedimentary rocks of high-pressure granulite facies and their relation with partial melting: Carvalhos Klippe, Southern Brasilia Belt, Brazil

High-grade metasedimentary rocks can preserve geochemical signatures of their sedimentary protolith if significant melt extraction did not occur. Retrograde reaction textures provide the main evidence for trapped melt in the rock fabrics. Carvalhos Klippe rocks in Southern Brasilia Orogen, Brazil, present a typical high-pressure granulite assemblage with evidence of mica breakdown partial melting (Ky + Grt + Kfs +/- Bt +/- Rt). The metamorphic peak temperatures obtained by Zr-in-Rt and ternary feldspar geothermometers are between 850 degrees C and 900 degrees C. The GASP bane peak pressure obtained using grossular rich garnet core is 16 kbar. Retrograde reaction textures in which the garnet crystals are partially to totally replaced by Bt + Qtz +/- Fsp intergrowths are very common in the Carvalhos Klippe rocks. These reactions are interpreted as a result of interactions between residual phases and trapped melt during the retrograde path. In the present study the geochemical signatures of three groups of Carvalhos Klippe metasedimentary rocks are analysed. Despite the high metamorphic grade these three groups show well-defined geochemical features and their REE patterns are similar to average compositions of post-Archean sedimentary rocks (PAAS, NASC). The high-pressure granulite facies Grt-Bt-Pl gneisses with immature arenite (wacke, arkose or lithic-arenite) geochemical signatures present in the Carvalhos Klippe are compared to similar rocks in amphibolite facies from the same tectonic framework (Andrelandia Nappe System). The similar geochemical signatures between Grt-Bt-Pl gneisses metamorphosed in high-pressure granulite facies and Grt-Bt-Pl-Qtz schists from the Andrelandia and Liberdade Nappes, with minimal to absent melting conditions, are suggestive of low rates of melt extraction in these high-grade rocks. The rocks with pelitic compositions most likely had higher melt extraction and even under such circumstances nevertheless tend to show REE patterns similar to average compositions of post-Archean sedimentary rocks (PAAS, NASC). (C) 2012 Elsevier Ltd. All rights reserved.

Synthesis and characterization of silver/alanine nanocomposites for radiation detection in medical applications: the influence of particle size on the detection properties

Silver/alanine nanocomposites with varying mass percentage of silver have been produced. The size of the silver nanoparticles seems to drive the formation of the nanocomposite, yielding a homogeneous dispersion of the silver nanoparticles in the alanine matrix or flocs of silver nanoparticles segregated from the alanine crystals. The alanine crystalline orientation is modified according to the particle size of the silver nanoparticles. Concerning a mass percentage of silver below 0.1%, the nanocomposites are homogeneous, and there is no particle aggregation. As the mass percentage of silver is increased, the system becomes unstable, and there is particle flocculation with subsequent segregation of the alanine crystals. The nanocomposites have been analyzed by transmission electron microscopy (TEM), UV-Vis absorption spectroscopy, X-ray diffraction (XRD), and Fourier transform infrared (FTIR) spectroscopy and they have been tested as radiation detectors by means of electron spin resonance (ESR) spectroscopy in order to detect the paramagnetic centers created by the radiation. In fact, the sensitivity of the radiation detectors is optimized in the case of systems containing small particles (30 nm) that are well dispersed in the alanine matrix. As the agglomeration increases, particle growth (up to 1.5 mu m) and segregation diminish the sensitivity. In conclusion, nanostructured materials can be used for optimization of alanine sensitivity, by taking into account the influence of the particles size of the silver nanoparticles on the detection properties of the alanine radiation detectors, thus contributing to the construction of small-sized detectors.

RefZ Facilitates the Switch from Medial to Polar Division during Spore Formation in Bacillus subtilis

During sporulation, Bacillus subtilis redeploys the division protein FtsZ from midcell to the cell poles, ultimately generating an asymmetric septum. Here, we describe a sporulation-induced protein, RefZ, that facilitates the switch from a medial to a polar FtsZ ring placement. The artificial expression of RefZ during vegetative growth converts FtsZ rings into FtsZ spirals, arcs, and foci, leading to filamentation and lysis. Mutations in FtsZ specifically suppress RefZ-dependent division inhibition, suggesting that RefZ may target FtsZ. During sporulation, cells lacking RefZ are delayed in polar FtsZ ring formation, spending more time in the medial and transition stages of FtsZ ring assembly. A RefZ-green fluorescent protein (GFP) fusion localizes in weak polar foci at the onset of sporulation and as a brighter midcell focus at the time of polar division. RefZ has a TetR DNA binding motif, and point mutations in the putative recognition helix disrupt focus formation and abrogate cell division inhibition. Finally, chromatin immunoprecipitation assays identified sites of RefZ enrichment in the origin region and near the terminus. Collectively, these data support a model in which RefZ helps promote the switch from medial to polar division and is guided by the organization of the chromosome. Models in which RefZ acts as an activator of FtsZ ring assembly near the cell poles or as an inhibitor of the transient medial ring at midcell are discussed.

Segregated anatomical input to sub-regions of the rodent superior colliculus associated with approach and defense

The superior colliculus (SC) is responsible for sensorimotor transformations required to direct gaze toward or a way from unexpected, biologically salient events. Significant changes in the external world are signaled to SC through primary multisensory afferents, spatially organized according to a retinotopic topography. For animals, where anunexpected event could indicate the presence of either predator or prey, early decisions to approach or avoid are particularly important. Rodents' ecology dictates predators are most often detected initially as movements in upper visual field (mapped in medial SC), while appetitive stimuli are normally found in lower visual field (mapped in lateral SC). Our purpose was to exploit this functional segregation to reveal neural sites that can bias or modulate initial approach or avoidance responses. Small injections of Fluoro-Gold were made into medial or lateral sub-regions of intermediate and deep layers of SC (SCm/SCl). A remarkable segregation of input to these two functionally defined areas was found. (i) There were structures that projected only to SCm (e.g., specific cortical areas, lateral geniculate and suprageniculate thalamic nuclei, ventromedial and premammillary hypothalamic nuclei, and several brain-stem areas) or SCl (e.g., primary somatosensory cortex representing upper body parts and vibrissae and parvicellular reticular nucleus in the brainstem). (ii) Other structures projected to both SCm and SCl but from topographically segregated populations of neurons (e.g., zona incerta and substantia nigra pars reticulata). (iii) There were a few brainstem areas in which retrogradely labeled neurons were spatially overlapping (e.g., pedunculopontine nucleus and locus coeruleus). These results indicate significantly more structures across the rat neuraxis are in a position to modulate defense responses evoked from SCm, and that neural mechanisms modulating SC-mediated defense or appetitive behavior are almost entirely segregated.

DivIVA-Mediated Polar Localization of ComN, a Posttranscriptional Regulator of Bacillus subtilis

ComN (YrzD) is a small, 98-amino-acid protein recently shown to be involved in the posttranscriptional control of the late competence comE operon in Bacillus subtilis. We show here that ComN localizes to the division site and cell poles in a DivIVA-dependent fashion. Yeast two-hybrid and glutathione S-transferase pulldown experiments showed that ComN interacts directly with DivIVA. ComN is not essential for the polar assembly of the core competence DNA uptake machinery. Nevertheless, polar localization of ComN should play some role in competence acquisition because delocalization of ComN leads to a small reduction in competence efficiency. We found that ComN promotes the accumulation of its target comE mRNA to septal and polar sites. Thus, we speculate that localized translation of ComE proteins may be required for efficient competence development. Our results underscore the versatility of DivIVA as a promoter of the differentiation of bacterial poles and demonstrate that the repertoire of polarly localized molecules in B. subtilis is broad, including a regulator of gene expression and its target mRNA. Moreover, our findings suggest that mRNA localization may play a role in the subcellular organization of bacteria.

A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers

Background: The development of sugarcane as a sustainable crop has unlimited applications. The crop is one of the most economically viable for renewable energy production, and CO2 balance. Linkage maps are valuable tools for understanding genetic and genomic organization, particularly in sugarcane due to its complex polyploid genome of multispecific origins. The overall objective of our study was to construct a novel sugarcane linkage map, compiling AFLP and EST-SSR markers, and to generate data on the distribution of markers anchored to sequences of scIvana_1, a complete sugarcane transposable element, and member of the Copia superfamily. Results: The mapping population parents ('IAC66-6' and 'TUC71-7') contributed equally to polymorphisms, independent of marker type, and generated markers that were distributed into nearly the same number of co-segregation groups (or CGs). Bi-parentally inherited alleles provided the integration of 19 CGs. The marker number per CG ranged from two to 39. The total map length was 4,843.19 cM, with a marker density of 8.87 cM. Markers were assembled into 92 CGs that ranged in length from 1.14 to 404.72 cM, with an estimated average length of 52.64 cM. The greatest distance between two adjacent markers was 48.25 cM. The scIvana_1-based markers (56) were positioned on 21 CGs, but were not regularly distributed. Interestingly, the distance between adjacent scIvana_1-based markers was less than 5 cM, and was observed on five CGs, suggesting a clustered organization. Conclusions: Results indicated the use of a NBS-profiling technique was efficient to develop retrotransposon-based markers in sugarcane. The simultaneous maximum-likelihood estimates of linkage and linkage phase based strategies confirmed the suitability of its approach to estimate linkage, and construct the linkage map. Interestingly, using our genetic data it was possible to calculate the number of retrotransposonscIvana_1 (similar to 60) copies in the sugarcane genome, confirming previously reported molecular results. In addition, this research possibly will have indirect implications in crop economics e. g., productivity enhancement via QTL studies, as the mapping population parents differ in response to an important fungal disease.

Predictive models for mutations in mismatch repair genes: implication for genetic counseling in developing countries

Background: Lynch syndrome (LS) is the most common form of inherited predisposition to colorectal cancer (CRC), accounting for 2-5% of all CRC. LS is an autosomal dominant disease characterized by mutations in the mismatch repair genes mutL homolog 1 (MLH1), mutS homolog 2 (MSH2), postmeiotic segregation increased 1 (PMS1), post-meiotic segregation increased 2 (PMS2) and mutS homolog 6 (MSH6). Mutation risk prediction models can be incorporated into clinical practice, facilitating the decision-making process and identifying individuals for molecular investigation. This is extremely important in countries with limited economic resources. This study aims to evaluate sensitivity and specificity of five predictive models for germline mutations in repair genes in a sample of individuals with suspected Lynch syndrome. Methods: Blood samples from 88 patients were analyzed through sequencing MLH1, MSH2 and MSH6 genes. The probability of detecting a mutation was calculated using the PREMM, Barnetson, MMRpro, Wijnen and Myriad models. To evaluate the sensitivity and specificity of the models, receiver operating characteristic curves were constructed. Results: Of the 88 patients included in this analysis, 31 mutations were identified: 16 were found in the MSH2 gene, 15 in the MLH1 gene and no pathogenic mutations were identified in the MSH6 gene. It was observed that the AUC for the PREMM (0.846), Barnetson (0.850), MMRpro (0.821) and Wijnen (0.807) models did not present significant statistical difference. The Myriad model presented lower AUC (0.704) than the four other models evaluated. Considering thresholds of >= 5%, the models sensitivity varied between 1 (Myriad) and 0.87 (Wijnen) and specificity ranged from 0 (Myriad) to 0.38 (Barnetson). Conclusions: The Barnetson, PREMM, MMRpro and Wijnen models present similar AUC. The AUC of the Myriad model is statistically inferior to the four other models.

Ab initio studies of pristine and oxidized Cu3Au(100) and (111) surfaces

We review the previous literature and our recent work on first-principles studies of Cu3Au(100) and (111) surfaces, with focus on the segregation of atomic species to the surface at pristine conditions and in the presence of oxygen. In particular, the combined use of experimental and theoretical tools to achieve chemical identification at an atomic level of the surface species is emphasized and discussed.

Diversification in the use of resources by Idarnes species: bypassing functional constraints in the fig-fig wasp interaction

Mutualisms such as the figfig wasp mutualism are generally exploited by parasites. We demonstrate that amongst nonpollinating fig wasps (NPFWs) parasitic on Ficus citrifolia, a species of Idarnes galls flowers and another species feeds on galls induced by other wasps killing their larvae. The galling wasp inserts its ovipositor through the fig wall into the fig cavity. The ovipositor then follows a sinuous path and is introduced through the stigma and style of the flower. The egg is deposited between the integument and nucellus, in the exact location where the pollinating mutualistic wasp would have laid its egg. Gall induction is a complex process. In contrast, the path followed by the ovipositor of the other species is straightforward: attacking a larva within a developed gall poses different constraints. Shifts in feeding regime have occurred repeatedly in NPFWs. Monitoring traits associated with such repeated evolutionary shifts may help understand underlying functional constraints. (c) 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106, 114122.

Haploinsufficiency of a Spliceosomal GTPase Encoded by EFTUD2 Causes Mandibulofacial Dysostosis with Microcephaly

Mandibulofacial dysostosis with microcephaly (MFDM) is a rare sporadic syndrome comprising craniofacial malformations, microcephaly, developmental delay, and a recognizable dysmorphic appearance. Major sequelae, including choanal atresia, sensorineural hearing loss, and cleft palate, each occur in a significant proportion of affected individuals. We present detailed clinical findings in 12 unrelated individuals with MFDM; these 12 individuals compose the largest reported cohort to date. To define the etiology of MFDM, we employed whole-exome sequencing of four unrelated affected individuals and identified heterozygous mutations or deletions of EFTUD2 in all four. Validation studies of eight additional individuals with MFDM demonstrated causative EFTUD2 mutations in all affected individuals tested. A range of EPTUD2-mutation types, including null alleles and frameshifts, is seen in MFDM, consistent with haploinsufficiency; segregation is de novo in all cases assessed to date. U5-116kD, the protein encoded by EFTUD2, is a highly conserved spliceosomal GTPase with a central regulatory role in catalytic splicing and post-splicing-complex disassembly. MFDM is the fast multiple-malformation syndrome attributed to a defect of the major spliceosome. Our findings significantly extend the range of reported spliceosomal phenotypes in humans and pave the way for further investigation in related conditions such as Treacher Collins syndrome.