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Here we show how major rivers can efficiently connect to the deep-sea, by analysing the longest runout sediment flows (of any type) yet measured in action on Earth. These seafloor turbidity currents originated from the Congo River-mouth, with one flow travelling >1,130 km whilst accelerating from 5.2 to 8.0 m/s. In one year, these turbidity currents eroded 1,338-2,675 [>535-1,070] Mt of sediment from one submarine canyon, equivalent to 19–37 [>7–15] % of annual suspended sediment flux from present-day rivers. It was known earthquakes trigger canyon-flushing flows. We show river-floods also generate canyon-flushing flows, primed by rapid sediment-accumulation at the river-mouth, and sometimes triggered by spring tides weeks to months post-flood. It is demonstrated that strongly erosional turbidity currents self-accelerate, thereby travelling much further, validating a long-proposed theory. These observations explain highly-efficient organic carbon transfer, and have important implications for hazards to seabed cables, or deep-sea impacts of terrestrial climate change.

The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics., Trends in Genetics, 39 (7), ISSN:0168-9525

Next-generation sequencing of pooled samples (Pool-seq) is an important tool in population genomics and molecular ecology. In Pool-seq, the relative number of reads with an allele reflects the allele frequencies in the sample. However, unequal individual contributions to the pool and sequencing errors can lead to inaccurate allele frequency estimates. When designing Pool-seq studies, researchers need to decide the pool size (number of individuals) and average depth of coverage (sequencing effort). An efficient sampling design should maximize the accuracy of allele frequency estimates while minimizing the sequencing effort. We introduce an R package,poolHelper, enabling users to simulate Pool-seq data under different combinations of average depth of coverage, pool sizes and number of pools, accounting for unequal individual contribution and sequencing errors, modelled by parameters that users can modify.poolHelpercan be used to assess how different combinations of those parameters influence the error of sample allele frequencies and expected heterozygosity. The mean absolute error is computed by comparing the sample allele frequencies obtained based on individual genotypes with the frequency estimates obtained with Pool-seq. Using simulations under a single population model, we illustrate that increasing the depth of coverage does not necessarily lead to more accurate estimates, reinforcing that finding the best Pool-seq study design is not straightforward. Moreover, we show that simulations can be used to identify different combinations of parameters with similarly low mean absolute errors. ThepoolHelperpackage provides tools for performing simulations with different combinations of parameters before sampling and generating data, allowing users to define sampling schemes that minimize the sequencing effort.

Next-generation sequencing of pooled samples (Pool-seq) is a popular method to assess genome-wide diversity patterns in natural and experimental populations. However, Pool-seq is associated with specific sources of noise, such as unequal individual contributions. Consequently, using Pool-seq for the reconstruction of evolutionary history has remained underexplored. Here we describe a method to simulate Pool-seq data, implemented in an Approximate Bayesian Computation (ABC) framework to infer demographic history under models with two and four populations. By jointly modeling Pool-seq data, demographic history and the effects of selection due to barrier loci, we obtain estimates of demographic history parameters accounting for technical errors associated with Pool-seq. Rather than simulating genome-wide data, we perform ABC on subsets of loci, using relative summary statistics and parameter estimates. Our simulation study results indicate Pool-seq data allows distinction between general scenarios of ecotype formation (single versus parallel origin), and to infer relevant demographic parameters (e.g., effective sizes, split times). We exemplify the application of our method to Pool-seq data from the rocky-shore gastropod \textit{Littorina saxatilis}, sampled on a narrow geographical scale at two Swedish locations where two ecotypes (wave and crab) are found. Our model choice and parameter estimates show that ecotypes formed before colonization of the two locations (i.e., single origin) and are maintained despite gene flow. These results indicate that demographic modeling and inference can be successful based on pool-sequencing using ABC, contributing to the development of suitable null models that allow for a better understanding of the genetic basis of divergent adaptation.

Chemicals derived from equilibrium-limited reactions represent a huge challenge mainly from the process sustainability point of view. Usually, high temperatures are required to reach reasonable kin...

Shrinkage of hardened cement paste is a direct result of its desorption isotherm. The relationship between the desorption isotherm and the relative humidity in a hydrating cement paste is mainly controlled by the pore size distribution (nanopores to micropores). There are several hydration models to describe the microstructure of cement paste, but the desorption isotherm and self-desiccation are not direct outputs from those models as they are usually given as constitutive inputs. In this study an attempt was made to fill this gap by predicting the sorption isotherm, the drying shrinkage and the self-desiccation of cement paste directly from the evolution of its microstructure. A simple hydration model was developed to predict the microstructure of Portland cement pastes, as well as the nanostructure of calcium silicate hydrate (C-S-H), considering its densification during cement hydration. Predictions from the model were compared with some recent experimental findings from studies in the literature where the influence of the water-to-cement ratio was evaluated. The main contribution of this work is the integration of nanoscale and microscale material models towards determining the macroscopic properties of cement paste.

A process for catalytic production of dihydroxyacetone through glycerol oxidation and dihydroxyacetone purification by chromatographic processes is herein presented. Glycerol oxidation over commerc...

With the global biodiesel production growing as never seen before, encouraged by government policies, fiscal incentives, and emissions laws to control air pollution, there has been the collateral effect of generating massive amounts of crude glycerol, a by-product from the biodiesel industry. The positive effect of minimizing CO2 emissions using biofuels is jeopardized by the fact that the waste generated by this industry represents an enormous environmental disadvantage. The strategy of viewing “waste as a resource” led the scientific community to propose numerous processes that use glycerol as raw material. Solketal, the product of the reaction of glycerol and acetone, stands out as a promising fuel additive capable of enhancing fuel octane number and oxidation stability, diminishing particle emissions and gum formation, and enhancing properties at low temperatures. The production of this chemical can rely on several of the Green Chemistry principles, besides fitting the Circular Economy Model, once it can be reinserted in the biofuel production chain. This paper reviews the recent advances in solketal production, focusing on continuous production processes and on Process Intensification strategies. The performance of different catalysts under various operational conditions is summarized and the proposed industrial solketal production processes are compared.

The European sardine (Sardina pilchardus, Walbaum 1792) is indisputably a commercially important species. Previous studies using uneven sampling or a limited number of makers have presented sometimes conflicting evidence for the genetic structure of S. pilchardus populations. Here we show that whole genome data from 108 individuals from 16 sampling areas across 5,000 Km of the species’ distribution range (from the Eastern Mediterranean to the archipelago of Azores) supports at least three genetic clusters. One includes individuals from Azores and Madeira, with evidence of substructure separating these two archipelagos in the Atlantic. Another cluster broadly corresponds to the center of the distribution including the sampling sites around Iberia, separated by the Almeria-Oran front from the third cluster that includes all of the Mediterranean samples, except those from the Alboran Sea. Individuals from the Canary Islands appear as belonging to the same ancestral group as those from the Mediterranean. This suggests at least two important geographical barriers to gene flow, even though these do not seem complete, with many individuals from around Iberia and the Mediterranean showing some patterns compatible with admixture with other genetic clusters. Genomic regions corresponding to the top outliers of genetic differentiation are located in areas of low recombination indicative that genetic architecture also has a role in shaping population structure. These regions include genes related to otolith formation, a calcium carbonate structure in the inner ear previously used to distinguish S. pilchardus populations. Our results provide a baseline for further characterization of physical and genetic barriers that divide European sardine populations, and information for transnational stock management of this highly exploited species towards sustainable fisheries.

Understanding the genetic targets of natural selection is one of the most challenging goals of population genetics. Some of the earliest candidate genes were identified from associations between allozyme allele frequencies and environmental variation. One such example is the clinal polymorphism in the arginine kinase (Ak) gene in the marine snail Littorina fabalis. While other enzyme loci do not show differences in allozyme frequencies among populations, the Ak alleles are near differential fixation across repeated wave exposure gradients in Europe. Here, we use this case to illustrate how a new sequencing toolbox can be employed to characterize the genomic architecture associated with historical candidate genes. We found that the Ak alleles differ by nine nonsynonymous substitutions, which perfectly explain the different migration patterns of the allozymes during electrophoresis. Moreover, by exploring the genomic context of the Ak gene, we found that the three main Ak alleles are located on different arrangements of a putative chromosomal inversion that reaches near fixation at the opposing ends of two transects covering a wave exposure gradient. This shows Ak is part of a large (3/4 of the chromosome) genomic block of differentiation, in which Ak is unlikely to be the only target of divergent selection. Nevertheless, the nonsynonymous substitutions among Ak alleles and the complete association of one allele with one inversion arrangement suggest that the Ak gene is a strong candidate to contribute to the adaptive significance of the inversion.

Local adaptation leads to differences between populations within a species. In many systems, similar environmental contrasts occur repeatedly, sometimes driving parallel phenotypic evolution. Understanding the genomic basis of local adaptation and parallel evolution is a major goal of evolutionary genomics. It is now known that by preventing the break-up of favourable combinations of alleles across multiple loci, genetic architectures that reduce recombination, like chromosomal inversions, can make an important contribution to local adaptation. However, little is known about whether inversions also contribute disproportionately to parallel evolution. Our aim here is to highlight this knowledge gap, to showcase existing studies, and to illustrate the differences between genomic architectures with and without inversions using simple models. We predict that by generating stronger effective selection, inversions can sometimes speed up the parallel adaptive process or enable parallel adaptation where it would be impossible otherwise, but this is highly dependent on the spatial setting. We highlight that further empirical work is needed, in particular to cover a broader taxonomic range and to understand the relative importance of inversions compared to genomic regions without inversions. This article is part of the theme issue ‘Genomic architecture of supergenes: causes and evolutionary consequences’.

The Simulated Moving Bed (SMB) is a separation device whose use has been increasing, especially in separations that demand high purities like the chiral separation. Process Design is a topic often discussed in the literature and is usually limited to a sensitivity analysis. An optimal design of a SMB unit offers challenges due to its complexity on dynamics and numerical levels. Thus, there is a lack of a consistent methodology to optimize the SMB design. This work is focused on the SMB design which will be made using the Particles Swarm Optimization (PSO) method. For the first time, PSO will be used to choose the configuration, i.e., length of each section, of the True Moving Bed (the theoretical model of the SMB) unit for the case of the separation of the bi-naphthol enantiomers. The operating conditions, in terms of flowrates, will also be optimized. Globally, with the design strategy that was implemented, the system’s productivity is at least 30% higher than previous results reported in the literature for the TMB without optimization of the device configuration. The SMB that was designed from this configuration enables to increase the separation productivity at least 20% in comparison with previous results.

Simulated Moving bed adsorption processes are characterized by their complex dynamic behavior. Due to this issue, as deeper are explored their design possibilities, more complexity is expected. One example of this is the Varicol configuration. In this operating mode, it is possible to use more than one configuration in two consecutive switches through an asynchronous switch, reducing the unit costs in comparison with standard configurations. This work presents a new strategy for the design and concomitant optimization of SMB devices considering a Varicol operating mode. The optimization will include both the operating conditions and the configuration of the device. The optimization results enable the design of a Varicol configuration for the separation of the bi-naphthol enantiomers which can also be generelazied for other systems. The results have shown that including the configuration in the optimization process allows to increase the productivity of the separation process by 15% while reducing the total unit size.

The aromatics complex is a petrochemical facility where the main products are benzene and p-xylene. The xylene isomer is produced through an energy-intensive cycle loop in which the p-xylene separa...

Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics., Trends in Ecology & Evolution, 37 (3), ISSN:0169-5347, ISSN:1872-8383

Here we document for the first time how major rivers connect directly to the deep-sea, by analysing the longest runout sediment flows (of any type) yet measured in action. These seafloor turbidity currents originated from the Congo River-mouth, with one flow travelling >1,130 km whilst accelerating from 5.2 to 8.0 m/s. In one year, these turbidity currents eroded 1-2 km3 of sediment from just one submarine canyon, equivalent to 14-28% of the annual global-flux from rivers. It was known earthquakes trigger canyon-flushing flows. We show major river-floods also generate canyon-flushing flows, primed by rapid sediment-accumulation at the river-mouth, but triggered by spring tides weeks to months after the flood. This is also the first field-confirmation that turbidity currents which erode can self-accelerate, thereby travelling much further. These observations explain highly-efficient organic carbon transfer, and have important implications for hazards to seabed cables, or how terrestrial climate change impacts the deep-sea.

International audience; Understanding population divergence that eventually leads to speciation is essential for evolutionary biology. High species diversity in the sea was regarded as a paradox when strict allopatry was considered necessary for most speciation events because geographical barriers seemed largely absent in the sea, and many marine species have high dispersal capacities. Combining genome-­wide data with demographic modelling to infer the demographic history of divergence has introduced new ways to address this classical issue. These models assume an ancestral population that splits into two subpopulations diverging according to different scenarios that allow tests for periods of gene flow. Models can also test for heterogeneities in population sizes and migration rates along the genome to account, respectively, for background selection and selection against introgressed ancestry. To investigate how barriers to gene flow arise in the sea, we compiled studies modelling the demographic history of divergence in marine organisms and extracted preferred demographic scenarios together with estimates of demographic parameters. These studies show that geographical barriers to gene flow do exist in the sea but that divergence can also occur without strict isolation. Heterogeneity of gene flow was detected in most population pairs suggesting the predominance of semipermeable barriers during divergence. We found a weak positive relationship between the fraction of the genome experiencing reduced gene flow and levels of genome-­wide differentiation. Furthermore, we found that the upper bound of the ‘grey zone of speciation’ for our dataset extended beyond that found before, implying that gene flow between diverging taxa is possible at higher levels of divergence than previously thought. Finally, we list recommendations for further strengthening the use of demographic modelling in speciation research. These include a more balanced representation of taxa, more consistent and comprehensive modelling, clear reporting of results and simulation studies to rule out nonbiological explanations for general results.

Identifying patterns of genetic structure, diversity, and connectivity in marine species is helpful for conservation purposes. We conducted a range-wide, comparative study of genetic structure and diversity in anadromous and landlocked populations of two Eurasian shad species (Alosa alosa and Alosa fallax). Samples of A. alosa from 13 (N = 660) locations, and A. fallax from 30 (N = 747), were studied with 21 and 18 microsatellite loci, respectively. The average pairwise FST among all anadromous A. alosa sampled in different drainages was 0.083 compared to 0.306 in A. fallax. Genetic clustering analysis identified five to six clusters for A. alosa and up to 16 for A. fallax. In most cases, the clusters identified were comprised of populations that spawn in geographically neighboring drainages. A positive correlation between genetic and geographic distance was found in anadromous A. fallax, but not in A. alosa. Within each species, landlocked populations were more genetically differentiated than anadromous ones. Our results show migration and gene flow are higher in A. alosa than A. fallax, which should be taken into account when determining the geographic scale at which to enact conservation measures to protect each species. Most A. alosa and A. fallax populations were genetically differentiated, indicating that the loss of any could result in a reduction of the adaptive potential for that species.

Background Knowledge on clinical profiles of late-onset phenotypes of Fabry disease (FD) is essential to better define their natural history. Our study aims to demonstrate a founder effect of FD due to the GLA gene mutation c.337T>C (p.F113L) in the Portuguese region of Guimaraes; and to characterize the clinical profile of this late-onset phenotype in a large cohort of genetically related adult patients, living in the same region. Methods and Results FD screening was performed in 150 adult patients with hypertrophic cardiomyopathy (HCM) and found 25 Fabry patients (16.6%). The p.F113L mutation was found in 21 of them, leading to a genealogy study and haplotype analysis of the p.F113L patients. Genealogy research revealed a 12-generation family tree with a common ancestor to p.F113L patients, suggesting a founder effect that was supported by haplotype findings. Pedigree analysis was performed and 120 consecutive p.F113L patients underwent a predefined diagnostic evaluation of FD multiorgan involvement. This late-onset phenotype was characterized by common and/or potentially severe cardiac manifestations (left ventricular hypertrophy 40.8%, atrial fibrillation 5%, non-sustained ventricular tachycardia 12.5%, atrioventricular block 18.3%, bifascicular block 13.4%). Extracardiac manifestations included albuminuria>30 mg/24 h 36.1%, chronic kidney disease≥G3 7.6%, brain white matter lesions 54.4%, stroke 3.3%, sensorineural deafness 44.5%, cornea verticillata 13.9%. Plasma lyso-GB3 was undetectable in females, regardless of clinical manifestations. Conclusion A founder effect of FD due to p.F113L mutation was documented by genealogy and genetics in a Portuguese region. In this late-onset phenotype, although cardiac manifestations carry the highest prognostic impact, extracardiac involvement is common.

Genetic incompatibilities contribute to reproductive isolation between many diverging populations, but it is still unclear to what extent they play a role if divergence happens with gene flow. In contact zones between the "Crab" and "Wave" ecotypes of the snail Littorina saxatilis, divergent selection forms strong barriers to gene flow, while the role of post‐zygotic barriers due to selection against hybrids remains unclear. High embryo abortion rates in this species could indicate the presence of such barriers. Post‐zygotic barriers might include genetic incompatibilities (e.g. Dobzhansky–Muller incompatibilities) but also maladaptation, both expected to be most pronounced in contact zones. In addition, embryo abortion might reflect physiological stress on females and embryos independent of any genetic stress. We examined all embryos of >500 females sampled outside and inside contact zones of three populations in Sweden. Females' clutch size ranged from 0 to 1,011 embryos (mean 130 ± 123), and abortion rates varied between 0% and 100% (mean 12%). We described female genotypes by using a hybrid index based on hundreds of SNPs differentiated between ecotypes with which we characterized female genotypes. We also calculated female SNP heterozygosity and inversion karyotype. Clutch size did not vary with female hybrid index, and abortion rates were only weakly related to hybrid index in two sites but not at all in a third site. No additional variation in abortion rate was explained by female SNP heterozygosity, but increased female inversion heterozygosity added slightly to increased abortion. Our results show only weak and probably biologically insignificant post‐zygotic barriers contributing to ecotype divergence, and the high and variable abortion rates were marginally, if at all, explained by hybrid index of females., High abortion rates (12% in average) among females of the snail Littorina saxatilis might suggest postzygotic barriers to gene flow between ecotypes living in adjacent microhabitats. However, sampling several microhabitat transects did not more than marginally support increased rates of abortion in hybrid zones.

In this work, the main results of a thermodynamic and kinetic study of glycerol ketalization to produce solketal in the presence of a solvent are presented. A catalyst and a solvent screening was c...

Coefficient of thermal expansion (CTE) of concrete changes at early ages mainly due to microstructural modifications that occur during cement hydration. This paper proposes an innovative way to assess the CTE of concrete since very early ages, with the original inclusion of an internal heating/cooling system, that allows to speed up the thermal balance cycles, and increase the number of CTE measurements during the early ages. The method comprises a specimen of 154 mm diameter and 300 mm height, submitted to successive heating and cooling steps with thermal variations of 5 °C, right after casting. A spiral heating/cooling tube, embedded in concrete, is used to circulate the controlled temperature water bath inside the specimen. This paper demonstrates the feasibility of the strategy for accelerating thermal equilibrium of the specimen, both experimentally and through numerical simulation. The short duration of the thermal cycle in this proposal strongly increases the ability of the method in capturing the early kinetics of CTE evolution, allowing to measure the CTE as soon as 4.1 h after mixing. With durations of each full temperature cycle of 1.5 h, it was possible to obtain as many as 12 CTE measurements within the first 24 h of testing, which is an important improvement in regard to similarly sized specimens in the literature. Furthermore, when the information obtained from the proposed test method is combined with the continuous feed about E-modulus of concrete that can be obtained through application of the EMM-ARM technique, very definite conclusions can be attained about the expectable stress levels that can be attained in concrete elements at early ages, due to the early variation of CTE. Three concrete mixtures are used to verify applicability of the proposed method for measuring early age CTE of concrete. The calculated values for these concrete mixtures are in agreement with the data found in the literature.

The structural design of reinforced concrete (RC) structures requires the use of adequate methodologies for control of crack widths, in order to ensure proper service life behavior. When RC elements are subjected to the combined effect of restrained deformations and external loads, which is a relatively common situation in civil engineering structures, current design codes and recommendations generally fail to provide specific/clear instructions for measures to be taken for reinforcement design in view of crack width control. This paper intends to show the influence of different approaches for quantification of the necessary reinforcement on the service life behavior of these structures, through conduction of a parametric study. Such study is performed in order to understand how the variation of the longitudinal reinforcement affects the structural behavior of a solid one-way RC slab subjected to restrained shrinkage and external applied vertical loads (in quasi-permanent load combination). The structural behavior of the slab is simulated for 5 distinct quantities of longitudinal reinforcement, with a 3D thermo-higro-mechanical model, where the non-uniform distribution of stresses due to heat of hydration and drying shrinkage are considered. The attained results allowed conclusions to be withdrawn in regard to the expected behavior when reinforcement is underdesigned (by neglecting restraint) or overdesigned (by considering the cracking force of concrete when evaluating axial restraint). Intermediate solutions, matching some simplified approaches in the literature where found to be the most reasonable.