Influence of NaOH treatment of rubber aggregates on the durability properties of rubberized mortars

The work presented in this paper aims to study the durability of mortars, in which part of the sand has been replaced with rubber aggregates from used tires and have undergone a surface treatment with a sodium hydroxide solution (NaOH). The substitution rates studied are 10%, 17.5%, and 25%. The results are compared with ordinary mortar and mortars with untreated rubber aggregates while samples with the same substitution rates were used. To do this, the following properties have been studied: compressive strength, flexural tensile strength, water absorption by capillarity, water absorption by total immersion, water-accessible porosity, water permeability, and resistance to the chemical degradation by sulfuric acid H2SO4. The results obtained show that the treatment of rubber aggregates by the solution method (NaOH) presented a considerable improvement in mechanical performance (increase in compressive strength and flexural tensile strength) and better durability compared to reference mortar and mortar with untreated rubber granulate.

Lineage-Specific Variation in IR Boundary Shift Events, Inversions, and Substitution Rates among Caprifoliaceae s.l. (Dipsacales) Plastomes

Caprifoliaceae s.l. plastid genomes (plastomes) show that one inversion and two inverted repeat boundary shifts occurred in the common ancestor of this family, after which the plastomes are generally conserved. This study reports plastome sequences of five additional species, Fedia cornucopiae, Valeriana fauriei, and Valerianella locusta from the subfamily Valerianoideae, as well as Dipsacus japonicus and Scabiosa comosa from the subfamily Dipsacoideae. Combined with the published plastomes, these plastomes provide new insights into the structural evolution of plastomes within the family. Moreover, the three plastomes from the subfamily Valerianoideae exhibited accelerated nucleotide substitution rates, particularly at synonymous sites, across the family. The patterns of accD sequence divergence in the family are dynamic with structural changes, including interruption of the conserved domain and increases in nonsynonymous substitution rates. In particular, the Valeriana accD gene harbors a large insertion of amino acid repeat (AAR) motifs, and intraspecific polymorphism with a variable number of AARs in the Valeriana accD gene was detected. We found a correlation between intron losses and increased ratios of nonsynonymous to synonymous substitution rates in the clpP gene with intensified positive selection. In addition, two Dipsacoideae plastomes revealed the loss of the plastid-encoded rps15, and a potential functional gene transfer to the nucleus was confirmed.

Genetic barriers to gene flow separate divergent substitution rates across a butterfly hybrid zone

Substitution rate defines the fundamental timescale of molecular evolution which often varies in a species-specific manner. However, it is unknown under what conditions lineage-specific rates can be preserved between natural populations with frequent hybridization. Here, we show in a hybrid zone between two butterflies, Papilio syfanius and Papilio maackii, that genome-wide barriers to gene flow can effectively separate different rates of molecular evolution in linked regions. The increased substitution rate in the lowland lineage can be largely explained by temperature-induced changes to the spontaneous mutation rate. A novel method based on entropy is developed to test for the existence of barrier loci using a minimal number of samples from the hybrid zone, a robust framework when system complexity far exceeds sample information. Overall, our results suggest that during the process of speciation, the separation of substitution rates can occur locally in the genome in parallel to the separation of gene pools.

Comparative Mitogenomic Analysis and the Evolution of Rhizoctonia solani Anastomosis Groups

Mitochondria are the major energy source for cell functions. However, for the plant fungal pathogens, mitogenome variations and their roles during the host infection processes remain largely unknown. Rhizoctonia solani, an important soil-borne pathogen, forms different anastomosis groups (AGs) and adapts to a broad range of hosts in nature. Here, we reported three complete mitogenomes of AG1-IA RSIA1, AG1-IB RSIB1, and AG1-IC, and performed a comparative analysis with nine published Rhizoctonia mitogenomes (AG1-IA XN, AG1-IB 7/3/14, AG3, AG4, and five Rhizoctonia sp. mitogenomes). These mitogenomes encoded 15 typical proteins (cox1-3, cob, atp6, atp8-9, nad1-6, nad4L, and rps3) and several LAGLIDADG/GIY-YIG endonucleases with sizes ranging from 109,017 bp (Rhizoctonia sp. SM) to 235,849 bp (AG3). We found that their large sizes were mainly contributed by repeat sequences and genes encoding endonucleases. We identified the complete sequence of the rps3 gene in 10 Rhizoctonia mitogenomes, which contained 14 positively selected sites. Moreover, we inferred a robust maximum-likelihood phylogeny of 32 Basidiomycota mitogenomes, representing that seven R. solani and other five Rhizoctonia sp. lineages formed two parallel branches in Agaricomycotina. The comparative analysis showed that mitogenomes of Basidiomycota pathogens had high GC content and mitogenomes of R. solani had high repeat content. Compared to other strains, the AG1-IC strain had low substitution rates, which may affect its mitochondrial phylogenetic placement in the R. solani clade. Additionally, with the published RNA-seq data, we investigated gene expression patterns from different AGs during host infection stages. The expressed genes from AG1-IA (host: rice) and AG3 (host: potato) mainly formed four groups by k-mean partitioning analysis. However, conserved genes represented varied expression patterns, and only the patterns of rps3-nad2 and nad1-m3g18/mag28 (an LAGLIDADG endonuclease) were conserved in AG1-IA and AG3 as shown by the correlation coefficient analysis, suggesting regulation of gene repertoires adapting to infect varied hosts. The results of variations in mitogenome characteristics and the gene substitution rates and expression patterns may provide insights into the evolution of R. solani mitogenomes.

Extensive genomic rearrangements mediated by repetitive sequences in plastomes of Medicago and its relatives

Background Although plastomes are highly conserved with respect to gene content and order in most photosynthetic angiosperms, extensive genomic rearrangements have been reported in Fabaceae, particularly within the inverted repeat lacking clade (IRLC) of Papilionoideae. Two hypotheses, i.e., the absence of the IR and the increased repeat content, have been proposed to affect the stability of plastomes. However, this is still unclear for the IRLC species. Here, we aimed to investigate the relationships between repeat content and the degree of genomic rearrangements in plastomes of Medicago and its relatives Trigonella and Melilotus, which are nested firmly within the IRLC. Results We detected abundant repetitive elements and extensive genomic rearrangements in the 75 newly assembled plastomes of 20 species, including gene loss, intron loss and gain, pseudogenization, tRNA duplication, inversion, and a second independent IR gain (IR ~ 15 kb in Melilotus dentata) in addition to the previous first reported cases in Medicago minima. We also conducted comparative genomic analysis to evaluate plastome evolution. Our results indicated that the overall repeat content is positively correlated with the degree of genomic rearrangements. Some of the genomic rearrangements were found to be directly linked with repetitive sequences. Tandem repeated sequences have been detected in the three genes with accelerated substitution rates (i.e., accD, clpP, and ycf1) and their length variation could be explained by the insertions of tandem repeats. The repeat contents of the three localized hypermutation regions around these three genes with accelerated substitution rates are also significantly higher than that of the remaining plastome sequences. Conclusions Our results suggest that IR reemergence in the IRLC species does not ensure their plastome stability. Instead, repeat-mediated illegitimate recombination is the major mechanism leading to genome instability, a pattern in agreement with recent findings in other angiosperm lineages. The plastome data generated herein provide valuable genomic resources for further investigating the plastome evolution in legumes.

ProteinEvolverABC: coestimation of recombination and substitution rates in protein sequences by approximate Bayesian computation

Motivation The evolutionary processes of mutation and recombination, upon which selection operates, are fundamental to understand the observed molecular diversity. Unlike nucleotide sequences, the estimation of the recombination rate in protein sequences has been little explored, neither implemented in evolutionary frameworks, despite protein sequencing methods are largely used. Results In order to accommodate this need, here I present a computational framework, called ProteinEvolverABC, to jointly estimate recombination and substitution rates from alignments of protein sequences. The framework implements the approximate Bayesian computation approach, with and without regression adjustments and includes a variety of substitution models of protein evolution, demographics and longitudinal sampling. It also implements several nuisance parameters such as heterogeneous amino acid frequencies and rate of change among sites and, proportion of invariable sites. The framework produces accurate coestimation of recombination and substitution rates under diverse evolutionary scenarios. As illustrative examples of usage, I applied it to several viral protein families, including coronaviruses, showing heterogeneous substitution and recombination rates. Availability and implementation ProteinEvolverABC is freely available from https://github.com/miguelarenas/proteinevolverabc, includes a graphical user interface for helping the specification of the input settings, extensive documentation and ready-to-use examples. Conveniently, the simulations can run in parallel on multicore machines. Supplementary information Supplementary data are available at Bioinformatics online.

Study of the Properties of Full Component Recycled Dry-Mixed Masonry Mortar and Concrete Prepared from Construction Solid Waste

Solutions are needed to solve the problem of a large amount of construction solid waste and a shortage of natural aggregate (coarse and fine aggregates). In this paper, simple-crushed coarse aggregate (SCRCA) and simple-crushed fine aggregate (SCRFA) were obtained by simple-crushing of construction solid waste. On this basis, SCRCA and SCRFA were treated with particle-shaping to obtain particle-shaping coarse aggregate (PSRCA) and particle-shaping fine aggregate (PSRFA), and the recycled powder (RP) produced in the process of particle-shaping was collected. Under the condition of a 1:4 cement-sand ratio, RP was used to replace cement with four substitution rates of 0, 10%, 20%, and 30%, and dry-mixed masonry mortar was prepared with 100% SCRFA, PSRFA, and river sand (RS). The basic and mechanical properties and microstructure of hydration products of dry-mixed mortar were analyzed, and the maximum substitution rate of RP was determined. Under the condition that the amount of cementitious material is 400 kg/m3 and the RP is at the maximum replacement rate, three different aggregate combinations to prepare concrete are the 100% use of SCRCA and SCRFA, PSRCA and PSRFA, and RS and natural aggregate (NCA); the workability, mechanical properties, and aggregate interface transition zone of the prepared concrete were analyzed. The results show that when the replacement rate of RP is less than 20%, it has little effect on the properties of products. The performance of PSRCA and PSRFA after treatment is better than that of SCRCA and SCRFA. Under different RP substitution rates, the performance of dry-mixed mortar prepared with PSRFA is very close to that prepared with RS. The performance of recycled concrete prepared with PSRCA and PSRFA is also very close to that of products prepared with NCA and RS. The failure morphology of PSRCA and RSRFA concrete is also similar to that of NCA and RS concrete.

Investigating the reliability of molecular estimates of evolutionary time when substitution rates and speciation rates vary

Background An accurate timescale of evolutionary history is essential to testing hypotheses about the influence of historical events and processes, and the timescale for evolution is increasingly derived from analysis of DNA sequences. But variation in the rate of molecular evolution complicates the inference of time from DNA. Evidence is growing for numerous factors, such as life history and habitat, that are linked both to the molecular processes of mutation and fixation and to rates of macroevolutionary diversification. However, the most widely used models of molecular rate variation, such as the uncorrelated and autocorrelated lognormal clocks, rely on idealised models of rate variation and molecular dating methods are rarely tested against complex models of rate change. One relationship that is not accounted for in molecular dating is the potential for interaction between molecular substitution rates and speciation, a relationship that has been supported by empirical studies in a growing number of taxa. If these relationships are as widespread as evidence indicates, they may have a significant influence on molecular dates. Results We simulate phylogenies and molecular sequences under three different realistic rate variation models - one in which speciation rates and substitution rates both vary but are unlinked, one in which they covary continuously and one punctuated model in which molecular change is concentrated in speciation events, using empirical case studies to parameterise realistic simulations. We test two commonly used "relaxed clock" molecular dating methods against these realistic simulations to explore the degree of error in molecular dates under each model. We find average divergence time inference errors ranging from 12% of node age for the unlinked model when reconstructed under an uncorrelated rate prior, to up to 93% when punctuated simulations are reconstructed under an autocorrelated prior. Conclusions We demonstrate the potential for substantial errors in molecular dates when both speciation rates and substitution rates vary between lineages. This study highlights the need for tests of molecular dating methods against realistic models of rate variation generated from empirical parameters and known relationships.