A Feasibility Study of Fricke Dosimetry as an Absorbed Dose to Water Standard for 192Ir HDR Sources

High dose rate brachytherapy (HDR) using ¹⁹²Ir sources is well accepted as an important treatment option and thus requires an accurate dosimetry standard. However, a dosimetry standard for the direct measurement of the absolute dose to water for this particular source type is currently not available. An improved standard for the absorbed dose to water based on Fricke dosimetry of HDR ¹⁹²Ir brachytherapy sources is presented in this study. The main goal of this paper is to demonstrate the potential usefulness of the Fricke dosimetry technique for the standardization of the quantity absorbed dose to water for ¹⁹²Ir sources. A molded, double-walled, spherical vessel for water containing the Fricke solution was constructed based on the Fricke system. The authors measured the absorbed dose to water and compared it with the doses calculated using the AAPM TG-43 report. The overall combined uncertainty associated with the measurements using Fricke dosimetry was 1.4% for k = 1, which is better than the uncertainties reported in previous studies. These results are promising; hence, the use of Fricke dosimetry to measure the absorbed dose to water as a standard for HDR ¹⁹²Ir may be possible in the future.     

Production of Destruxins from Metarhizium spp. Fungi in Artificial Medium and in Endophytically Colonized Cowpea Plants

Destruxins (DTXs) are cyclic depsipeptides produced by many Metarhizium isolates that have long been assumed to contribute to virulence of these entomopathogenic fungi. We evaluated the virulence of 20 Metarhizium isolates against insect larvae and measured the concentration of DTXs A, B, and E produced by these same isolates in submerged (shaken) cultures. Eight of the isolates (ARSEF 324, 724, 760, 1448, 1882, 1883, 3479, and 3918) did not produce DTXs A, B, or E during the five days of submerged culture. DTXs were first detected in culture medium at 2–3 days in submerged culture. Galleria mellonella and Tenebrio molitor showed considerable variation in their susceptibility to the Metarhizium isolates. The concentration of DTXs produced in vitro did not correlate with percent or speed of insect kill. We established endophytic associations of M. robertsii and M. acridum isolates in Vigna unguiculata (cowpeas) and Cucumis sativus (cucumber) plants. DTXs were detected in cowpeas colonized by M. robertsii ARSEF 2575 12 days after fungal inoculation, but DTXs were not detected in cucumber. This is the first instance of DTXs detected in plants endophytically colonized by M. robertsii. This finding has implications for new approaches to fungus-based biological control of pest arthropods.     

A Testing Platform for Durability Studies of Polymers and Fiber-reinforced Polymer Composites under Concurrent Hygrothermo-mechanical Stimuli

The durability of polymers and fiber-reinforced polymer composites under service condition is a critical aspect to be addressed for their robust designs and condition-based maintenance. These materials are adopted in a wide range of engineering applications, from aircraft and ship structures, to bridges, wind turbine blades, biomaterials and biomedical implants. Polymers are viscoelastic materials, and their response may be highly nonlinear and thus make it challenging to predict and monitor their in-service performance. The laboratory-scale testing platform presented herein assists the investigation of the influence of concurrent mechanical loadings and environmental conditions on these materials. The platform was designed to be low-cost and user-friendly. Its chemically resistant materials make the platform adaptable to studies of chemical degradation due to in-service exposure to fluids. An example of experiment was conducted at RT on closed-cell polyurethane foam samples loaded with a weight corresponding to ~50% of their ultimate static and dry load. Results show that the testing apparatus is appropriate for these studies. Results also highlight the larger vulnerability of the polymer under concurrent loading, based on the higher mid-point displacements and lower residual failure loads. Recommendations are made for additional improvements to the testing apparatus.     

Characterization of rumen bacterial strains isolated from enrichments of rumen content in the presence of propolis

Propolis presents many biological properties, including antibacterial activities, and has been proposed as an additive in ruminant nutrition. Twenty bacterial strains, previously isolated from enrichments of Brazilian cow rumen contents in the presence of different propolis extracts (LLOS), were characterized using phenotyping and 16S rRNA identification. Seven strains were assigned to Streptococcus sp., most likely S. bovis, and were all degrading starch. One amylolytic lactate-utilizing strain of Selenomonas ruminantium was also found. Two strains of Clostridium bifermentans were identified and showed proteolytic activity. Two strains were assigned to Mitsuokella jalaludinii and were saccharolytic. One strain belonged to a Bacillus species and seven strains were affiliated with Escherichia coli. All of the 20 strains were able to use many sugars, but none of them were able to degrade the polysaccharides carboxymethylcellulose and xylans. The effect of three propolis extracts (LLOS B1, C1 and C3) was tested on the in vitro growth of four representative isolates of S. bovis, E. coli, M. jalaludinii and C. bifermentans. The growth of S. bovis, E. coli and M. jalaludinii was not affected by the three propolis extracts at 1 mg ml^?1. C. bifermentans growth was completely inhibited at this LLOS concentration, but this bacterium was partially resistant at lower concentrations. LLOS C3, with the lower concentration of phenolic compounds, was a little less inhibitory than B1 and C1 on this strain.     

Beta-diversity in seasonally dry tropical forests (SDTF) in the Caatinga Biogeographic Domain, Brazil, and its implications for conservation

Tropical biomes are species rich, but some biomes such as seasonally dry tropical forests (SDTFs) are still inadequately studied compared to their co-occurring rain forest and savanna. SDTFs occur in areas of high environmental heterogeneity, resulting in high beta (β)-diversity or species turnover, but this has so far only been accessed using a single β-diversity measure, and at a spatial scale that is of limited applicability for reserve planning. The Caatinga Biogeographic Domain in Brazil contains the largest known extent of SDTF which are poorly studied and inadequately reserved. We therefore studied the variation in species richness and species turnover among SDTF between localities and between known floristic communities. From six localities within the Caatinga Biogeographic Domain we recorded all tree species with a circumference at breast height equaling or exceeding 10 cm within 106 400 m² survey plots. From the species presence/absence data we calculated three measures of β-diversity between pairs of study localities and between different floristic communities representing: (i) species similarity, (ii) differences between species richness, and (iii) species gain and loss. Our results confirm the high β-diversity of SDTFs and species turnover between localities and also between floristic communities. The three indices were also complementary to each other and can be used to maximize accuracy in β-diversity studies. The implications of our study for conservation and reserve planning of SDTFs are discussed.     

Pattern‐oriented modelling of population genetic structure

Although several statistical approaches can be used to describe patterns of genetic variation and infer stochastic differentiation, selective responses, or interruptions of gene flow due to physical or environmental barriers, it is worthwhile to note that similar processes, controlled by several parameters in theoretical models, frequently give rise to similar patterns. Here, we develop a Pattern‐Oriented Modelling (POM) approach that allows us to determine how a complex set of parameters potentially driving empirical genetic differentiation among populations generate alternative scenarios that can be fitted to observed data. We generated 10 000 random combinations of parameters related to population size, gene flow and response to gradients (both driven by dispersal and selection) in a spatially explicit model, and analysed simulated patterns with F_ST statistics and mean correlograms using Moran's I spatial autocorrelation coefficients. These statistics were compared with observed patterns for a tree species endemic to the Brazilian Cerrado. For a best match with observed F_ST (equal to 0.182), the important parameters driving simulated scenario are mainly related to population structure, including low population size with closed populations (low N_m), strong distance decay of gene flow, in addition to a strong effect of the initial variance of allele frequencies. These scenarios present a low autocorrelation of allele frequencies. Best matching of correlograms, on the other hand, appears in simulations with a large population size, high N_m and low population differentiation and F_ST (as well as more gene flow). Thus, targeting the two statistics (correlograms and F_ST) shows that best matches with empirical data with two distinct sets of parameters in the simulations, because observed patterns involve both a relatively high F_ST and significant autocorrelation. This conflict can be resolved by assuming that initial variance in allele frequencies can be interpreted as reflecting deep‐time historical variation and evolutionary dynamics of allele frequencies, creating a relatively high level of population differentiation, whereas current patterns in gene flow creates spatial autocorrelation. This make sense in terms of the previous knowledge on population differentiation in D. alata, especially if patterns are explained by a combination of isolation‐by‐distance and allelic surfing due to range expansion after the last glacial maximum. This reveals the potential for more complex applications of POM in population genetics. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 1152–1161.     

Brassicaceae INDEHISCENT genes specify valve margin cell fate and repress replum formation

Members of the Brassicaceae family, including Arabidopsis thaliana and oilseed rape (Brassica napus), produce dry fruits that open upon maturity along a specialised tissue called the valve margin. Proper development of the valve margin in Arabidopsis is dependent on the INDEHISCENT (IND) gene, the role of which in genetic and hormonal regulation has been thoroughly characterised. Here we perform phylogenetic comparison of IND genes in Arabidopsis and Brassica to identify conserved regulatory sequences that are responsible for specific expression at the valve margin. In addition we have taken a comparative development approach to demonstrate that the BraA.IND.a and BolC.IND.a genes from B. rapa and B. oleracea share identical function with Arabidopsis IND since ethyl methanesulphonate (EMS) mutant alleles and silenced transgenic lines have valve margin defects. Furthermore we show that the degree of these defects can be fine‐tuned for crop improvement. Wild‐type Arabidopsis produces an outer replum composed of about six cell files at the medial region of the fruits, whereas Brassica fruits lack this tissue. A strong loss‐of‐function braA.ind.a mutant gained outer replum tissue in addition to its defect in valve margin development. An enlargement of replum size was also observed in the Arabidopsis ind mutant suggesting a general role of Brassicaceae IND genes in preventing valve margin cells from adopting replum identity.     

<Emphasis Type="Italic">Escherichia coli</Emphasis> phylogenetic group determination and its application in the identification of the major animal source of fecal contamination

Background  

Escherichia coli strains are commonly found in the gut microflora of warm-blooded animals. These strains can be assigned to one of the four main phylogenetic groups, A, B1, B2 and D, which can be divided into seven subgroups (A₀, A₁, B1, B2₂, B2₃, D₁ and D₂), according to the combination of the three genetic markers chuA, yjaA and DNA fragment TspE4.C2. Distinct studies have demonstrated that these phylo-groups differ in the presence of virulence factors, ecological niches and life-history. Therefore, the aim of this work was to analyze the distribution of these E. coli phylo-groups in 94 human strains, 13 chicken strains, 50 cow strains, 16 goat strains, 39 pig strains and 29 sheep strains and to verify the potential of this analysis to investigate the source of fecal contamination.     

Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels

Background

Although the overwhelming majority of genes found in angiosperms are members of gene families, and both gene- and genome-duplication are pervasive forces in plant genomes, some genes are sufficiently distinct from all other genes in a genome that they can be operationally defined as 'single copy'. Using the gene clustering algorithm MCL-tribe, we have identified a set of 959 single copy genes that are shared single copy genes in the genomes of Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera and Oryza sativa. To characterize these genes, we have performed a number of analyses examining GO annotations, coding sequence length, number of exons, number of domains, presence in distant lineages, such as Selaginella and Physcomitrella, and phylogenetic analysis to estimate copy number in other seed plants and to demonstrate their phylogenetic utility. We then provide examples of how these genes may be used in phylogenetic analyses to reconstruct organismal history, both by using extant coverage in EST databases for seed plants and de novo amplification via RT-PCR in the family Brassicaceae.

Results

There are 959 single copy nuclear genes shared in Arabidopsis, Populus, Vitis and Oryza ["APVO SSC genes"]. The majority of these genes are also present in the Selaginella and Physcomitrella genomes. Public EST sets for 197 species suggest that most of these genes are present across a diverse collection of seed plants, and appear to exist as single or very low copy genes, though exceptions are seen in recently polyploid taxa and in lineages where there is significant evidence for a shared large-scale duplication event. Genes encoding proteins localized in organelles are more commonly single copy than expected by chance, but the evolutionary forces responsible for this bias are unknown. Regardless of the evolutionary mechanisms responsible for the large number of shared single copy genes in diverse flowering plant lineages, these genes are valuable for phylogenetic and comparative analyses. Eighteen of the APVO SSC single copy genes were amplified in the Brassicaceae using RT-PCR and directly sequenced. Alignments of these sequences provide improved resolution of Brassicaceae phylogeny compared to recent studies using plastid and ITS sequences. An analysis of sequences from 13 APVO SSC genes from 69 species of seed plants, derived mainly from public EST databases, yielded a phylogeny that was largely congruent with prior hypotheses based on multiple plastid sequences. Whereas single gene phylogenies that rely on EST sequences have limited bootstrap support as the result of limited sequence information, concatenated alignments result in phylogenetic trees with strong bootstrap support for already established relationships. Overall, these single copy nuclear genes are promising markers for phylogenetics, and contain a greater proportion of phylogenetically-informative sites than commonly used protein-coding sequences from the plastid or mitochondrial genomes.

Conclusions

Putatively orthologous, shared single copy nuclear genes provide a vast source of new evidence for plant phylogenetics, genome mapping, and other applications, as well as a substantial class of genes for which functional characterization is needed. Preliminary evidence indicates that many of the shared single copy nuclear genes identified in this study may be well suited as markers for addressing phylogenetic hypotheses at a variety of taxonomic levels.