Structure and Evolution of Lizard Immunity Genes

One of the most important gene families to play a role in adaptive immunity is the major histocompatibility complex (MHC). MHC class II loci are considered to be the most variable loci in the vertebrate genome, and studies have shown that this variability can be maintained through complex co-evolutionary dynamics between host and parasite. Despite the rich body of research into the MHC, there is comparatively little understanding of its genomic architecture in reptiles. Similarly, loci associated with innate immunity have received little attention in reptiles compared to other vertebrates. In the first chapter, we investigated the structure and organization of the MHC in the Anolis carolinensis genome by sequencing and annotating five bacterial artificial chromosomes (BAC) from the green anole genome library. We were able to identify three mhc2a, four mhc2b, and up to 15 mhc1 loci in A. carolinensis. Furthermore, we were able to link 17 scaffolds and provide sequence data to fill two significant gaps in the genome assembly. In the second chapter, we investigated the relative importance of drift and selection in shaping mhc2 variability in the reptile Podarcis erhardii. We sequenced the mhc2 gene from lizard populations from 14 islands in the Aegean that have experienced bottlenecks of differing duration and intensity. Despite signals of balancing selection, patterns of mhc2 variation were similar to microsatellites, providing evidence that the dominant evolutionary force in this system is drift. In the third chapter, we investigated how parasite infection rates impact innate immune variability in A. sabanus, a lizard indigenous to Saba Island where natural fluctuations in Plasmodium infection rates have been documented. We developed primers and sequenced part of the peptide binding region of three Toll-like receptors (TLRs) - tlr4, tlr6, and tlr13 and several beta-defensin (BD) loci. Although we were unable to characterize BD variability, we found three different haplotypes in tlr4, and five in tlr6. However, nucleotide variability was low (π \u3c 0.005) and was not associated with infection status. We nevertheless present primers for multiple TLR genes and two BDs that could be of use in future studies of reptile innate immunity

Gyrification brain abnormalities as predictors of outcome in anorexia nervosa.

Gyrification brain abnormalities are considered a marker of early deviations from normal developmental trajectories and a putative predictor of poor outcome in psychiatric disorders. The aim of this study was to explore cortical folding morphology in patients with anorexia nervosa (AN). A MRI brain study was conducted on 38 patients with AN, 20 fully recovered patients, and 38 healthy women. Local gyrification was measured with procedures implemented in FreeSurfer. Vertex-wise comparisons were carried out to compare: (1) AN patients and healthy women; (2) patients with a full remission at a 3-year longitudinal follow-up assessment and patients who did not recover. AN patients exhibited significantly lower gyrification when compared with healthy controls. Patients with a poor 3-year outcome had significantly lower baseline gyrification when compared to both healthy women and patients with full recovery at follow-up, even after controlling for the effects of duration of illness and gray matter volume. No significant correlation has been found between gyrification, body mass index, amount of weight loss, onset age, and duration of illness. Brain gyrification significantly predicted outcome at follow-up even after controlling for the effects of duration of illness and other clinical prognostic factors. Although the role of starvation in determining our findings cannot be excluded, our study showed that brain gyrification might be a predictor of outcome in AN. Further studies are needed to understand if brain gyrification abnormalities are indices of early neurodevelopmental alterations, the consequence of starvation, or the interaction between both factors

On subspace designs

Guruswami and Xing introduced subspace designs in 2013 to give the first construction of positive rate rank metric codes list-decodable beyond half the distance. In this paper we provide bounds involving the parameters of a subspace design, showing they are tight via explicit constructions. We point out a connection with sum-rank metric codes, dealing with optimal codes and minimal codes with respect to this metric. Applications to two-intersection sets with respect to hyperplanes, two-weight codes, cutting blocking sets and lossless dimension expanders are also provided

On the minimum size of linear sets

Recently, a lower bound was established on the size of linear sets in projective spaces, that intersect a hyperplane in a canonical subgeometry. There are several constructions showing that this bound is tight. In this paper, we generalize this bound to linear sets meeting some subspace $\pi$ in a canonical subgeometry. We obtain a tight lower bound on the size of any $\mathbb F_q$-linear set spanning $\text{PG}(d,q^n)$ in case that $n \leq q$ and $n$ is prime. We also give constructions of linear sets attaining equality in the former bound, both in the case that $\pi$ is a hyperplane, and in the case that $\pi$ is a lower dimensional subspace.Comment: 24 pages; the updated version contains a consequences of the recent paper by Csajb\'ok, Marino and Pepe (arXiv:2306.07488), providing a tight lower bound in some case

Cytoprotective and Antigenotoxic Properties of Organic vs. Conventional Tomato Puree: Evidence in Zebrafish Model

In this in vivo study, we investigated cytoprotective and antigenotoxic effects of commercial tomato puree obtained from conventional vs. organic farming systems (pesticides vs. pesticide-free agriculture, respectively). This is relevant as pesticides are widely used in agriculture to prevent pests, weeds, and the spread of plant pathogens. By exposing zebrafish to tomato puree alone and in combination with H2O2 (a well-known genotoxic agent), we analyzed the percentage of fish survival, cell viability, intracellular concentration of reactive oxygen species (ROS), DNA fragmentation index (DFI%), and genomic template stability (GTS%). Fish exposed to organic puree showed higher fish survival and cellular viability, lower DFI% and ROS, and improved GTS%. Our results suggest a higher cytoprotective and antigenotoxic effect of organic pesticide-free tomatoes, probably because the activity of natural phytochemicals is not affected by the presence of toxic residues, which are otherwise produced by pesticides used in conventional farming systems. Our study points out the importance of considering alternative strategies in agriculture to minimize the genotoxic impact of chemical pesticides

Understanding hydrologic controls of sloping soil response to precipitation through machine learning analysis applied to synthetic data

Soil and underground conditions prior to the initiation of rainfall events control the hydrological processes that occur in slopes, affecting the water exchange through their boundaries. The present study aims at identifying suitable variables to be monitored to predict the response of sloping soil to precipitation. The case of a pyroclastic coarse-grained soil mantle overlaying a karstic bedrock in the southern Apennines (Italy) is described. Field monitoring of stream level recordings, meteorological variables, and soil water content and suction has been carried out for a few years. To enrich the field dataset, a synthetic series of 1000 years has been generated with a physically based model coupled to a stochastic rainfall model. Machine learning techniques have been used to unwrap the non-linear cause–effect relationships linking the variables. The k-means clustering technique has been used for the identification of seasonally recurrent slope conditions in terms of soil moisture and groundwater level, and the random forest technique has been used to assess how the conditions at the onset of rainfall controlled the attitude of the soil mantle to retain much of the infiltrating rainwater. The results show that the response in terms of the fraction of rainwater remaining stored in the soil mantle at the end of rainfall events is controlled by soil moisture and groundwater level prior to the rainfall initiation, giving evidence of the activation of effective drainage processes.</p

Benzyl alcohol selective oxidation via in-situ generated oxidants

Benzyl alcohol oxidation has been carried out through the in situ generation of oxidative species originated from the interaction of an atmosphere of hydrogen and oxygen gases diluted in carbon dioxide, a solution of benzyl alcohol and a catalyst composed of supported gold and palladium nanoparticles. For the selection of the reaction conditions they were taken into account both those used for the direct synthesis of hydrogen peroxide and those used for the benzyl alcohol oxidation. The idea behind this choice was that a compromise is required which could satisfy both the reaction requirements. It has been demonstrated that the reaction proceeds through a radical mechanism, as the addition of quenchers for specific radicals formation suppressed conversion. Optimum conversion and selectivity towards benzaldehyde have been observed when carrying out the reaction with benzyl alcohol using methanol as solvent, as this promotes high hydrogen peroxide synthesis rates and also allows the breaking down of the hydrogen peroxide into oxidative radical species. Testing the benzyl alcohol in situ oxidation in flow conditions has revealed that the benzyl alcohol conversion is inversely proportional to the residence time of the substrate with the fixed catalyst bed, moreover the in situ oxidation reaction has appeared to be limited by the hydrogen mass transfer which by generation of peroxide species increases the substrate conversion up to a maximum value. However, at the same time, the presence of hydrogen in the system may originate side reactions that are in competition with the selective oxidation of benzyl alcohol to benzaldehyde