Correlated patterns of genetic diversity and differentiation across an avian family

Comparative studies of closely related taxa can provide insights into the evolutionary forces that shape genome evolution and the prevalence of convergent molecular evolution. We investigated patterns of genetic diversity and differentiation in stonechats (genus Saxicola), a widely distributed avian species complex with phenotypic variation in plumage, morphology, and migratory behavior, to ask whether similar genomic regions have become differentiated in independent, but closely related, taxa. We used whole-genome pooled sequencing of 262 individuals from 5 taxa and found that levels of genetic diversity and divergence are strongly correlated among different stonechat taxa. We then asked if these patterns remain correlated at deeper evolutionary scales and found that homologous genomic regions have become differentiated in stonechats and the closely related Ficedula flycatchers. Such correlation across a range of evolutionary divergence and among phylogenetically independent comparisons suggests that similar processes may be driving the differentiation of these independently evolving lineages, which in turn may be the result of intrinsic properties of particular genomic regions (e.g., areas of low recombination). Consequently, studies employing genome scans to search for areas important for reproductive isolation or adaptation should account for corresponding regions of differentiation, as these regions may not necessarily represent speciation islands or evidence of local adaptation

Structured adsorbents for isolation of functional food ingredients

Separation and purification of functional ingredients from raw or waste streams are often done via processes that include a chromatographic step using a packed bed of resin particles that have affinity for the ingredients to be separated. A column packed with these particles presents numerous bottlenecks when dealing with untreated or large streams: a trade-off between mass transfer and hydraulic permeability, a high pressure drop and susceptibility to plugging and fouling. The large equipment (column diameters) and volume of resin needed for a moderate pressure drop and a high capacity, poses problems of elevated costs and complex operation. Other technologies such as radial flow chromatography and polymeric resins membranes may represent an improvement in other applications (e.g. pharma or fine chemicals), but at this point their capacity and costs do not seem to be feasible for the separation of small molecules from larger food streams. The aim of the research discussed in this thesis was to find the principles that determine the suitability of different structured adsorbents, such as monoliths, for the selective adsorption and recovery of high-added value food ingredients of relatively low molecular weight, such as oligosaccharides and bioactive peptides. To ensure a cost-effective process and high capacity for small molecules, we demonstrated the feasibility of using activated carbon, and compared its adsorptive and hydraulic performance in two different structures: porous particles and channeled monoliths (”honeycomb” structures). Furthermore, we assessed the feasibility and window of operation of monoliths in terms of adsorbent and column volume required, compared to packed beds. To demonstrate the isolation of bioactive peptides from crude mixtures with activated carbon, we used activated carbon to recover a lacto-tripeptide IPP from a commercial hydrolyzate (1.5% w/w) in chapter 2. The purity of the initial crude mixture was doubled in the isolate, to up to 35% with a recovery of IPP of about 80% in the first cycles of adsorption. This was repeated over many consecutive adsorption-desorption cycles until the activated carbon packed bed column was exhausted. This exhaustion was found to be caused not only by the occupation of irreversible sites but also by pore blockage. Finally, guidelines were given for the competitive exhaustion of the adsorbent for process optimization in order to obtain higher purity and yield. In chapter 3 we showed the benefits of using channeled monoliths for processing untreated streams. We compared the use of channeled monoliths with a packed bed, both made of the same type of activated carbon, for the adsorption of the lactotripeptide IPP from a crude hydrolyzate. The results showed similar productivity and dynamic adsorptive capacities at comparable linear velocities and residence times, but the packed bed showed a strong pressure drop increase during continuous loading of the column and the same consecutive adsorption-desorption cycles as studied in chapter 2. This indicates the occurrence of pore blockage and plugging of the column. These fouling mechanisms were confirmed with two semi-empirical model analogies: one analogous to membrane fouling and another using an analogy with a set of parallel channels. The strong pressure drop increase was even more noticeable at high velocities (and short residence times). These trends were not observed in the channeled monoliths: no significant pressure drop increase was found here, and high velocities were eminently feasible. In chapter 4 the adsorption of lactose onto a bed of activated carbon particles and activated carbon channeled monoliths was described with a detailed chromatographic model, taking into account the different mass transfer resistances. First, the single component adsorption isotherm parameters were obtained using frontal analysis on both adsorbents. Second, the kinetics of adsorption of lactose on both activated carbon adsorbents were estimated using the shallow bed method, assuming an infinite bath. The uptake curves were fitted to the homogeneous surface diffusion model and the linear driving force approximation. The estimation of the intraparticle diffusion coefficient and the film mass transfer coefficient showed a similar intraparticle mass transfer performance during the uptake adsorptive process. Fitting of the breakthrough data to the general rate model describing the full column operation showed differences in performance during the overall column operation. These differences could be related to higher axial dispersion in the squared channeled monoliths. The difference between the experimentally-derived axial dispersion and he expected assuming tubular coated tubes, suggested that the squared shape was responsible for the inhomogeneity of the flow. In chapter 5, we presented guidelines for the configuration of industrial scale chromatographic separation of small molecules. A window was identified that defines the feasible configurations to use for the highest productivity for a given set of process requirements. The performance of different axial packed beds, channeled monoliths and a continuous monolith assuming silica as base material were compared by means of HETP (height equivalent of theoretical plates) and pressure drop relations. The relations as a function of velocity were used to calculate the resultant velocity and packing length for different conditions (efficiency, pressure drop, affinity constant and throughput). The specific productivity of channeled monoliths was shown to be up to 2.5 orders of magnitude higher than that of a packed bed. Therefore, at large scales (in which the pressure drops need to be limited, and the flow rate is high), channeled monoliths are preferred since they may reduce the equipment size up to 100 times and the required adsorbent volume up to 1000 times. Finally, in chapter 6 we discussed the suitability of activated carbon regarding its re-usability and purification potential in the separation of small food ingredients. The suitability of channeled monoliths for certain applications was also highlighted. Finally, other suitable adsorbents were suggested, and some future prospects in the selection of adsorbents were given.</p

High voltage atmospheric cold plasma decontamination of Salmonella enteritidis on chicken eggs

Salmonella enteritidis (SE) accounts for more than 70% of Salmonella spp. infections in humans with a primary source being chicken eggs, that can result from post-lay SE cross-contamination of the shell from contaminated equipment or the environment. The objective of this study was to apply a HVACP treatment that can achieve a minimum 5-log reduction in SE on the surface of artificially inoculated shell eggs with an initial bacterial load of 108 CFU/egg, after a previous disinfection. Optimized HVACP treatment conditions were an indirect treatment with air at 60% humidity at 100 kV for one minute treatment and six hours post-treatment or alternatively, five minutes of treatment and four hours post-treatment. Egg quality parameters of Haugh unit (HU), pH, color, and vitelline membrane and shell strength were tested under the optimized conditions and showed no significant difference (p > 0.05) between treated and untreated eggs. Industrial relevance: Missing information for a possible scale up of a cold plasma system for egg surface decontamination has been addressed by an optimization of HVACP treatment focused on treatment and posttreatment time, essential parameters to have into account in the food industry. These results demonstrate that HVACP is an effective decontamination method for SE on chicken shell eggs and provides a baseline for a future scale up of the process, showing that different combinations of treatment variables can achieve the desired decontamination without affecting to key quality parameters of the egg such as Haugh Unit or vitelline membrane strength.This work was supported by Ontario Ministry of Agriculture, Food and Rural Affairs (OMAFRA), and the Barrett Family Foundation Chair in Sustainable Food Engineering

Potential use of Sargassum muticum as source of plant biostimulants after three different drying methods

Seaweed derived biostimulants are gaining attention as an important tool in sustainable agriculture. This offers a unique opportunity to alleviate the environmental impact of Sargassum muticum (Ochrophyta, Phaeophyceae) as an invasive species by finding new applications for its biomass. In this sense, incorporating green extraction technologies is fundamental to ensure environmental-friendly goals. This research was initiated in an attempt to contribute to an integral valorization system of S. muticum biomass, exploring the biostimulant potential of the solubles obtained from pressed solids, through an autohydrolysis treatment. In addition, we compared the effect of three different liquid phase drying techniques (spray-drying, freeze-drying and convective air-drying). Low stress drying techniques as spray-drying showed better conservation of bioactive compounds and biostimulant potential. A bioassay with Nastrium officinale showed no phytotoxic effects despite high electric conductivity in most of the extracts and concentrations. Dried extracts showed mainly an amorphous structure but occasional crystal formation when spray-dried at low temperatures (T out  = 50 ºC) and after convective air drying (T = 40 ºC). Significant increases in root development were achieved at a concentration of 5 mg L −1 of spray-dried extracts and 50 mg L −1 in case of freeze-dried extracts. Munoo-Liisa vitality index showed best results with 50 mg L −1 of freeze-dried extracts. This study provides important information about the influence of different drying techniques on the physicochemical properties and biostimulant potential of S. muticum aqueous extracts and contributes to the integral valorization of its biomass.Agencia Estatal de Investigación | Ref. RYC2018-024454-IXunta de Galicia | Ref. ED431F 2020/01Xunta de Galicia | Ref. ED481D-2022/018Universidade de Vigo/CISU

Valorization of brewer’s spent grain by furfural recovery/removal from subcritical water hydrolysates by pervaporation

This work is focused on the development of a sustainable process for the valorisation of the main by-product generated in the brewing industry, the brewer’s spent grain (BSG). A two-step process combining subcritical water treatment and pervaporation (PV) was proposed to hydrolyse the hemicelluloses fraction of this lignocellulosic biomass and further removal/recovery of some of the degradation products of sugars by using two different organophilic membranes, polydimethylsiloxane (PDMS) and polyoctilmethylsiloxane (POMS) membranes. Specifically, furfural is the dehydration product of pentoses and it is one of the top biomass-based chemicals being an important platform chemical. For synthetic binary mixtures, lower total permeation flux but higher enrichment factors for furfural were determined for POMS. When dealing with subW hydrolysates, POMS membranes yielded the highest furfural recovery, 94.1 %, with permeate concentrations as high as 40 g⋅L1 . Furthermore, it was assessed that PV is a suitable detoxification method that yielded a retentate nearly free of furfural allowing its use as growth media in the opposite to the subW hydrolysate with inhibitory furfural concentrations for microbial bioprocesses.publishe

Population-specific association of Clock gene polymorphism with annual cycle timing in stonechats

Timing is essential for survival and reproduction of organisms across the tree of life. The core circadian clock gene Clk has been implicated in annual timing and shows highly conserved sequence homology across vertebrates except for one variable region of poly Glutamine repeats. Clk genotype varies in some species with latitude, seasonal timing and migration. However, findings are inconsistent, difficult to disentangle from environmental responses, and biased towards high latitudes. Here we combine field data with a common-garden set up to study associations of Clk with latitude, migration and annual-cycle timing within the stonechat species complex with trans-equatorial distribution range. Including 950 individuals from nine populations with diverse migratory strategies. Gene diversity was lowest in resident African and Canary Island populations and increased with latitude, independently of migration distance. Repeat length and annual-cycle timing was linked in a population-specific way. Specifically, equatorial African stonechats showed delayed timing with longer repeat length for all annual-cycle stages. Our data suggest that at low latitudes with constant photoperiod, Clk genotype might orchestrate a range of consistent, individual chronotypes. In contrast, the influence of Clk on annual-cycle timing at higher latitudes might be mediated by its interactions with genes involved in (circadian) photoperiodic pathways

The evolutionary history and genomics of European blackcap migration

Seasonal migration is a taxonomically widespread behaviour that integrates across many traits. The European blackcap exhibits enormous variation in migration and is renowned for research on its evolution and genetic basis. We assembled a reference genome for blackcaps and obtained whole genome resequencing data from individuals across its breeding range. Analyses of population structure and demography suggested divergence began ~30,000 ya, with evidence for one admixture event between migrant and resident continent birds ~5000 ya. The propensity to migrate, orientation and distance of migration all map to a small number of genomic regions that do not overlap with results from other species, suggesting that there are multiple ways to generate variation in migration. Strongly associated single nucleotide polymorphisms (SNPs) were located in regulatory regions of candidate genes that may serve as major regulators of the migratory syndrome. Evidence for selection on shared variation was documented, providing a mechanism by which rapid changes may evolve

Analysis of the iron coatings formed during marcasite and arsenopyrite oxidation at neutral-alkaline conditions

In order to study the nature of the precipitates formed on arsenopyrite and marcasite after reacting with neutral to alkaline solutions, a combination of techniques including Scanning Electron Microscope-Energy Dispersive Spectroscopy (SEM-EDS), X-ray Photoelectron Spectroscopy (XPS) and synchrotron-based techniques such as micro-X-Ray diffraction (µXRD) and Micro-X-ray Absorption Near Edge Structure (µXANES) have been used. The results showed that the oxidation of marcasite and arsenopyrite under neutral to alkaline conditions leads to the formation of an Fe rich coating which seems to prevent the oxidation of these sulphides. SEM observations confirmed the presence newly-formed phases after the sulphides reaction under the studied conditions. XPS analysis showed that iron, sulphur and arsenic in the case of the arsenopyrite are in oxidized states in the sulphide surfaces. The microscale analysis of the S and Fe speciation performed by µXANES suggested that due to the sulphide oxidation an increase in the oxidation state of those elements took place together with an increase of the sulphate content in the surface layer (grain boundary). Micro-X-ray diffraction results indicated that goethite (a-FeOOH) is the only crystalline newly-formed phase when the reaction occurs at pH 12 whereas at lower pH the products formed on the sulphide surfaces seem to be poorly crystalline and they do not contribute to the diffraction effects in the XRD diagrams