Spectra of Sol-manifolds: arithmetic and quantum monodromy

Spectra of Sol-manifolds: arithmetic and quantum monodrom

Genomic signatures of parasite-driven natural selection in north European Atlantic salmon (Salmo salar)

Abstract Understanding the genomic basis of host-parasite adaptation is important for predicting the long-term viability of species and developing successful management practices. However, in wild populations, identifying specific signatures of parasite-driven selection often presents a challenge, as it is difficult to unravel the molecular signatures of selection driven by different, but correlated, environmental factors. Furthermore, separating parasite-mediated selection from similar signatures due to genetic drift and population history can also be difficult. Populations of Atlantic salmon (Salmo salar L.) from northern Europe have pronounced differences in their reactions to the parasitic flatworm Gyrodactylus salaris Malmberg 1957 and are therefore a good model to search for specific genomic regions underlying inter-population differences in pathogen response. We used a dense Atlantic salmon SNP array, along with extensive sampling of 43 salmon populations representing the two G. salaris response extremes (extreme susceptibility vs resistant), to screen the salmon genome for signatures of directional selection while attempting to separate the parasite effect from other factors. After combining the results from two independent genome scan analyses, 57 candidate genes potentially under positive selection were identified, out of which 50 were functionally annotated. This candidate gene set was shown to be functionally enriched for lymph node development, focal adhesion genes and anti-viral response, which suggests that the regulation of both innate and acquired immunity might be an important mechanism for salmon response to G. salaris. Overall, our results offer insights into the apparently complex genetic basis of pathogen susceptibility in salmon and highlight methodological challenges for separating the effects of various environmental factors.Peer reviewe

Footprints of directional selection in wild atlantic salmon populations: Evidence for parasite-driven evolution?

Mechanisms of host-parasite co-adaptation have long been of interest in evolutionary biology; however, determining the genetic basis of parasite resistance has been challenging. Current advances in genome technologies provide new opportunities for obtaining a genome-scale view of the action of parasite-driven natural selection in wild populations and thus facilitate the search for specific genomic regions underlying inter-population differences in pathogen response. European populations of Atlantic salmon (Salmo salar L.) exhibit natural variance in susceptibility levels to the ectoparasite Gyrodactylus salaris Malmberg 1957, ranging from resistance to extreme susceptibility, and are therefore a good model for studying the evolution of virulence and resistance. However, distinguishing the molecular signatures of genetic drift and environment-associated selection in small populations such as land-locked Atlantic salmon populations presents a challenge, specifically in the search for pathogen-driven selection. We used a novel genome-scan analysis approach that enabled us to i) identify signals of selection in salmon populations affected by varying levels of genetic drift and ii) separate potentially selected loci into the categories of pathogen (G. salaris)-driven selection and selection acting upon other environmental characteristics. A total of 4631 single nucleotide polymorphisms (SNPs) were screened in Atlantic salmon from 12 different northern European populations. We identified three genomic regions potentially affected by parasite-driven selection, as well as three regions presumably affected by salinity-driven directional selection. Functional annotation of candidate SNPs is consistent with the role of the detected genomic regions in immune defence and, implicitly, in osmoregulation. These results provide new insights into the genetic basis of pathogen susceptibility in Atlantic salmon and will enable future searches for the specific genes involved

Comparison of anadromous and landlocked Atlantic salmon genomes reveals signatures of parallel and relaxed selection across the Northern Hemisphere

Most Atlantic salmon (Salmo salarL.) populations follow an anadromous life cycle, spending early life in freshwater, migrating to the sea for feeding, and returning to rivers to spawn. At the end of the last ice age similar to 10,000 years ago, several populations of Atlantic salmon became landlocked. Comparing their genomes to their anadromous counterparts can help identify genetic variation related to either freshwater residency or anadromy. The objective of this study was to identify consistently divergent loci between anadromous and landlocked Atlantic salmon strains throughout their geographical distribution, with the long-term aim of identifying traits relevant for salmon aquaculture, including fresh and seawater growth, omega-3 metabolism, smoltification, and disease resistance. We used a Pool-seq approach (n = 10-40 individuals per population) to sequence the genomes of twelve anadromous and six landlocked Atlantic salmon populations covering a large part of the Northern Hemisphere and conducted a genomewide association study to identify genomic regions having been under different selection pressure in landlocked and anadromous strains. A total of 28 genomic regions were identified and includedcadm1on Chr 13 andppargc1aon Chr 18. Seven of the regions additionally displayed consistently reduced heterozygosity in fish obtained from landlocked populations, including the genes gpr132, cdca4, and sertad2 on Chr 15. We also found 16 regions, includingigf1on Chr 17, which consistently display reduced heterozygosity in the anadromous populations compared to the freshwater populations, indicating relaxed selection on traits associated with anadromy in landlocked salmon. In conclusion, we have identified 37 regions which may harbor genetic variation relevant for improving fish welfare and quality in the salmon farming industry and for understanding life-history traits in fish.Peer reviewe

A microsatellite baseline for genetic stock identification of European Atlantic salmon (Salmo salar L.)

Atlantic salmon (Salmo salar L.) populations from different river origins mix in the North Atlantic during the marine life stage. To facilitate marine stock identification, we developed a genetic baseline covering the European component of the species’ range excluding the Baltic Sea, from the Russian River Megra in the north-east, the Icelandic Ellidaar in the west, and the Spanish Ulla in the south, spanning 3737 km North to South and 2717 km East to West. The baseline encompasses data for 14 microsatellites for 26 822 individual fish from 13 countries, 282 rivers, and 467 sampling sites. A hierarchy of regional genetic assignment units was defined using a combination of distance-based and Bayesian clustering. At the top level, three assignment units were identified comprising northern, southern, and Icelandic regions. A second assignment level was also defined, comprising eighteen and twenty-nine regional units for accurate individual assignment and mixed stock estimates respectively. The baseline provides the most comprehensive geographical coverage for an Atlantic salmon genetic data-set, and a unique resource for the conservation and management of the species in Europe. It is freely available to researchers to facilitate identification of the natal origin of European salmon

Optical Fibers Functionally Enhanced by Photoactive Molecules

The experimental platform to study optical fibers (OFs) functionally enhanced by layers of photoactive molecules was developed. The used multimode step-index OFs were preliminary mechanically or chemically modified. Photonic crystal fibers (PCFs) were used as supplied. The photoactive layers were deposited using Langmuir-Blodgett and self-assembling monolayer (SAM) techniques. Two types of compounds were used for the fiber functionalization, porphyrin derivatives and Citrine (modified yellow fluorescent protein). This work is the first demonstration of SAM deposition of porphyrin derivatives on conventional OFs and inside the channels of PCFs, as well as Citrine SAM deposition on OFs. The developed experimental optical setup together with installed modified OFs rendered possible: i) to deliver the excitation light to the photoactive molecules, and ii) to collect the fluorescence and deliver it to the measuring system. Moreover, the same experimental system was used to optimize SAM process. It can also be used for real-time monitoring of SAM deposition of any type of photoactive molecules. The light guided by conventional multimode step-index fibers can only interact with molecules on its surface if the cladding layer is essentially thinned or removed completely. This can be done either by tapering or chemical etching of an OF. The optimum geometries for the tapered regions were determined by two methods based on fluorescence intensity measurements of the molecular films. The optimum tip diameter of a tapered OF was found to be 35-48 µm for the fibers with 105 µm core and 125 µm cladding diameters. For the etched OFs the reasonable tip diameter was 70 µm for the same fiber, and sufficient tip length was 2.5 mm. The modified OFs were tested in sensor applications for detecting pH, Ca2+, and volatile organic compounds (diethylamine was used in this study). A reasonable reproducibility of pH measurements was demonstrated for OF sensor with free-base porphyrin probe in the pH range of 0.6-3.8 and for Citrine probe in the pH range of 6.5-9. The sensitivity of Ca2+ ion sensor with Citrine SAM was on the level of a few tens of µM and diethylamine was detected at a few mM concentration using Zn-porphyrin OF sensor. The strongest fluorescence response of functionalized OFs in typical sensor application configuration was obtained for hollow core PCFs. The photoactive SAMs were deposited inside the light guiding channels, thus providing the most efficient excitation and fluorescence collection among the studied fibers. These OFs can be used in applications that require high sensitivity and the smallest amount of analyte. Alternatively, chemically etched conventional OFs are relatively easy to produce and functionalize. They provide reasonably high efficiency of SAM excitation and fluorescence collection and can be successfully used in less demanding optical sensor applications

Optical Fibers Functionally Enhanced by Photoactive Molecules

The experimental platform to study optical fibers (OFs) functionally enhanced by layers of photoactive molecules was developed. The used multimode step-index OFs were preliminary mechanically or chemically modified. Photonic crystal fibers (PCFs) were used as supplied. The photoactive layers were deposited using Langmuir-Blodgett and self-assembling monolayer (SAM) techniques. Two types of compounds were used for the fiber functionalization, porphyrin derivatives and Citrine (modified yellow fluorescent protein). This work is the first demonstration of SAM deposition of porphyrin derivatives on conventional OFs and inside the channels of PCFs, as well as Citrine SAM deposition on OFs. The developed experimental optical setup together with installed modified OFs rendered possible: i) to deliver the excitation light to the photoactive molecules, and ii) to collect the fluorescence and deliver it to the measuring system. Moreover, the same experimental system was used to optimize SAM process. It can also be used for real-time monitoring of SAM deposition of any type of photoactive molecules. The light guided by conventional multimode step-index fibers can only interact with molecules on its surface if the cladding layer is essentially thinned or removed completely. This can be done either by tapering or chemical etching of an OF. The optimum geometries for the tapered regions were determined by two methods based on fluorescence intensity measurements of the molecular films. The optimum tip diameter of a tapered OF was found to be 35-48 µm for the fibers with 105 µm core and 125 µm cladding diameters. For the etched OFs the reasonable tip diameter was 70 µm for the same fiber, and sufficient tip length was 2.5 mm. The modified OFs were tested in sensor applications for detecting pH, Ca2+, and volatile organic compounds (diethylamine was used in this study). A reasonable reproducibility of pH measurements was demonstrated for OF sensor with free-base porphyrin probe in the pH range of 0.6-3.8 and for Citrine probe in the pH range of 6.5-9. The sensitivity of Ca2+ ion sensor with Citrine SAM was on the level of a few tens of µM and diethylamine was detected at a few mM concentration using Zn-porphyrin OF sensor. The strongest fluorescence response of functionalized OFs in typical sensor application configuration was obtained for hollow core PCFs. The photoactive SAMs were deposited inside the light guiding channels, thus providing the most efficient excitation and fluorescence collection among the studied fibers. These OFs can be used in applications that require high sensitivity and the smallest amount of analyte. Alternatively, chemically etched conventional OFs are relatively easy to produce and functionalize. They provide reasonably high efficiency of SAM excitation and fluorescence collection and can be successfully used in less demanding optical sensor applications

Chaos and integrability in SL(2,R)-geometry

The integrability of the geodesic flow on the three-folds $\mathcal M^3$ admitting $SL(2,\mathbb R)$-geometry in Thurston's sense is investigated. The main examples are the quotients $\mathcal M^3_\Gamma=\Gamma\backslash PSL(2,\mathbb R)$, where $\Gamma \subset PSL(2,\mathbb R)$ is a cofinite Fuchsian group. We show that the corresponding phase space $T^*M_\Gamma^3$ contains two open regions with integrable and chaotic behaviour with zero and positive topological entropy respectively. As a concrete example we consider the case of modular 3-fold with the modular group $\Gamma=PSL({2,\mathbb Z})$, when $\mathcal M^3_\Gamma$ is known to be homeomorphic to the complement of a trefoil knot $\mathcal K$ in 3-sphere. Ghys proved a remarkable fact that the lifts of the periodic geodesics to the modular surface to $\mathcal M^3_\Gamma$ produce the same isotopy class of knots, which appeared in the chaotic version of the celebrated Lorenz system and were extensively studied by Birman and Williams. We show that in the integrable limit of the geodesic system on $\mathcal M^3_\Gamma$ they are replaced by the simple class of cable knots of trefoil