TNFRSF13B Genetic variability an anthropological - evolutionary approach to Biomedical Research

In the recent years TNFRSF13B coding variants have been implicated by clinical genetics studies in Common Variable Immunodeficiency (CVID), the most common clinically relevant primary immunodeficiency in individuals of European ancestry, but their functional effects in relation to the development of the disease have not been entirely established. To examine the potential contribution of such variants to CVID, the more comprehensive perspective of an evolutionary approach was applied in this study, underling the belief that evolutionary genetics methods can play a role in dissecting the origin, causes and diffusion of human diseases, representing a powerful tool also in human health research. For this purpose, TNFRSF13B coding region was sequenced in 451 healthy individuals belonging to 26 worldwide populations, in addition to 96 control, 77 CVID and 38 Selective IgA Deficiency (IgAD) individuals from Italy, leading to the first achievement of a global picture of TNFRSF13B nucleotide diversity and haplotype structure and making suggestion of its evolutionary history possible. A slow rate of evolution, within our species and when compared to the chimpanzee, low levels of genetic diversity geographical structure and the absence of recent population specific selective pressures were observed for the examined genomic region, suggesting that geographical distribution of its variability is more plausibly related to its involvement also in innate immunity rather than in adaptive immunity only. This, together with the extremely subtle disease/healthy samples differences observed, suggests that CVID might be more likely related to still unknown environmental and genetic factors, rather than to the nature of TNFRSF13B variants only.

Effects of ambient temperature on cardiovascular regulation during sleep in hypocretin-deficient narcoleptic mice

Hypocretin 1 and 2 (HCRT, also called Orexin A and B) are neuropeptides released by neurons in the lateral hypothalamus. HCRT neurons widely project to the entire neuroaxis. HCRT neurons have been reported to participate in various hypothalamic physiological processes including cardiovascular functions, wake-sleep cycle, and they may also influence metabolic rate and the regulation of body temperature. HCRT neurons are lost in narcolepsy, a rare neurological disorder, characterized by excessive daytime sleepiness, cataplexy, sleep fragmentation and occurrence of sleep-onset rapid-eye-movement episodes. We investigated whether HCRT neurons mediate the sleep-dependent cardiovascular adaptations to changes in ambient temperature (Ta). HCRT-ataxin3 transgenic mice with genetic ablation of HCRT neurons (n = 11) and wild-type controls (n = 12) were instrumented with electrodes for sleep scoring and a telemetric blood pressure (BP) transducer (DSI, Inc.). Simultaneous sleep and BP recordings were performed on mice undisturbed and freely-behaving at 20 °C, 25 °C, and 30 °C for 48 hours at each Ta. Analysis of variance of BP indicated a significance of the main effects of wake-sleep state and Ta, their interaction effect, and the wake-sleep state x mouse strain interaction effect. BP increased with decreasing Ta. This effect of Ta on BP was significantly lower in rapid-eye-movement sleep (REMS) than either in non-rapid-eye-movement sleep (NREMS) or wakefulness regardless of the mouse strain. BP was higher in wakefulness than either in NREMS or REMS. This effect of sleep on BP was significantly reduced in mice lacking HCRT neurons at each Ta, particularly during REMS. These data suggest that HCRT neurons play a critical role in mediating the effects of sleep but not those of Ta on BP in mice. HCRT neurons may thus be part of the central neural pathways which mediate the phenomenon of blood pressure dipping on passing from wakefulness to sleep.

Comparing genetic and linguistic diversity in African populations with a focus on the Khoisan of southern Africa

The interaction between disciplines in the study of human population history is of primary importance, profiting from the biological and cultural characteristics of humankind. In fact, data from genetics, linguistics, archaeology and cultural anthropology can be combined to allow for a broader research perspective. This multidisciplinary approach is here applied to the study of the prehistory of sub-Saharan African populations: in this continent, where Homo sapiens originally started his evolution and diversification, the understanding of the patterns of human variation has a crucial relevance. For this dissertation, molecular data is interpreted and complemented with a major contribution from linguistics: linguistic data are compared to the genetic data and the research questions are contextualized within a linguistic perspective. In the four articles proposed, we analyze Y chromosome SNPs and STRs profiles and full mtDNA genomes on a representative number of samples to investigate key questions of African human variability. Some of these questions address i) the amount of genetic variation on a continental scale and the effects of the widespread migration of Bantu speakers, ii) the extent of ancient population structure, which has been lost in present day populations, iii) the colonization of the southern edge of the continent together with the degree of population contact/replacement, and iv) the prehistory of the diverse Khoisan ethnolinguistic groups, who were traditionally understudied despite representing one of the most ancient divergences of modern human phylogeny. Our results uncover a deep level of genetic structure within the continent and a multilayered pattern of contact between populations. These case studies represent a valuable contribution to the debate on our prehistory and open up further research threads.

Analysis of cumulative effects of multiple stressors on saltmarshes and consideration of management options

Natural systems face pressures exerted by natural physical-chemical forcings and a myriad of co-occurring human stressors that may interact to cause larger than expected effects, thereby presenting a challenge to ecosystem management. This thesis aimed to develop new information that can contribute to reduce the existing knowledge gaps hampering the holistic management of multiple stressors. I undertook a review of the state-of-the-art methods to detect, quantify and predict stressor interactions, identifying techniques that could be applied in this thesis research. Then, I conducted a systematic review of saltmarsh multiple stressor studies in conjunction with a multiple stressor mapping exercise for the study system in order to infer potential important synergistic stressor interactions. This analysis identified key stressors that are affecting the study system, but also pointed to data gaps in terms of driver and pressure data and raised issues for potentially overlooked stressors. Using field mesocosms, I explored how a local stressor (nutrient availability) affects the responses of saltmarsh vegetation to a global stressor (increased inundation) in different soil types. Results indicate that saltmarsh vegetation would be more drastically affected by increased inundation in low than in medium organic matter soils, and especially in estuaries already under high nutrient availability. In another field experiment, I examined the challenges of managing co-occurring and potentially interacting local stressors on saltmarsh vegetation: recreational trampling and smothering by deposition of excess macroalgal wrack due to high nutrient loads. Trampling and wrack prevention had interacting effects, causing non-linear responses of the vegetation to simulated management of these stressors, such that vegetation recovered only in those treatments simulating the combined prevention of both stressors. During this research I detected, using molecular genetic methods, a widespread presence of S. anglica (and to a lesser extent S. townsendii), two previously unrecorded non-native Spartinas in the study areas.

Acquired and inherited cardiomyopathies: evaluation of cardiotoxic effects in preclinical models

Cardiomyopathies are a heterogeneous group of myocardial disorders defined by structural and functional alterations of the heart. These cardiac diseases can have both non-genetic and genetic origin. Nevertheless, a different etiology can trigger the same phenotype, as in the case of anthracycline-induced cardiotoxicity and desmin-related cardiomyopathy (DRM). Therefore, the aim of this study was to investigate the cellular mechanisms driving the development of these cardiotoxic conditions in in vitro models. Doxorubicin (DOX) is a commonly used antineoplastic drug for the treatment of a wide range of tumors. Besides, its clinical use is restricted because of dose-dependent cardiotoxicity. Our findings provided evidence that phospholipase C Beta 2 (PLCβ2) may have a critical role in DOX-induced cardiotoxicity in undifferentiated and differentiated H9c2 cell line. Interestingly, the results obtained revealed that cardiomyocytes are less sensitive to DOX, following the evaluation of cellular mechanisms such as: oxidative stress, apoptosis and cell proliferation. Nonetheless, the treatment induced a significant upregulation of PLCβ2 associated to morphological changes in both models, demonstrating the implication in a hypertrophic response. On the other hand, a hereditary DRM was associated to a missense mutation of aB crystallin (CRYAB), a chaperone protein involved in the regulation of the intermediate filament network. Since research has only been conducted on transgenic (TG) mice and neonatal rat cardiomyocytes, this study aimed at investigating cellular mechanisms triggered by CRYABR120G mutation in a hiPSC-derived DRM model. Our model confirmed the impairment of the cytoskeletal organization resulting in the formation of desmin and CRYAB aggregates and myofibril misalignment. Moreover, the missense mutation confirmed a hypertrophic cardiomyopathy phenotype, a feature of DRM patients, on cardiac engineered tissues. Lastly, these data obtained suggest that further research on PLCβ2 and CRYAB are needed to comprehend the molecular mechanisms behind the development of these 2 cardiac diseases.

Advanced studies on two animal models, murine and fish. RadKI21A626T mouse model: new insights into molecular mechanisms of enteric neuro-epithelial pathology. European sea bass: study of the effects of essential oils in different diets on the gastric system.

My PhD research period was focused on the anatomical, physiological and functional study of the gastrointestinal system on two different animal models. In two different contexts, the purpose of these two lines of research was contribute to understand how a specific genetic mutation or the adoption of a particular dietary supplement can affect gastrointestinal function. Functional gastrointestinal disorders are chronic conditions characterized by symptoms for which no organic cause can be found. Although symptoms are generally mild, a small subset of cases shows severe manifestations. This subset of patients may also have recurrent intestinal sub-occlusive episodes, but in absence of mechanical causes. This condition is referred to as chronic intestinal pseudo-obstruction, a rare, intractable chronic disease. Some mutations have been associated with CIPO. A novel causative RAD21 missense mutation was identified in a large consanguineous family, segregating a recessive form of CIPO. The present thesis was aimed to elucidate the mechanisms leading to neuropathy underlying CIPO via a recently developed conditional KI mouse carrying the RAD21 mutation. The experimental studies are based on the characterization and functional analysis of the conditional KI Rad21A626T mouse model. On the other hand aquaculture is increasing the global supply of foods. The species selected and feeds used affects the nutrients available from aquaculture, with a need to improve feed efficiency, both for economic and environmental reasons, but this will require novel innovative approaches. Nutritional strategies focused on the use of botanicals have attracted interest in animal production. Previous research indicates the positive results of using essential oils (EOs) as natural feed additives for several farmed animals. Therefore, the present study was designed to compare the effects of feed EO supplementation in two different forms (natural and composed of active ingredients obtained by synthesis) on the gastric mucosa in European sea bass.

Growth performance, gut health, and metabolism of broilers under thermoneutral and heat stress conditions: multidisciplinary studies on the effects of nutritional strategies and genotype

This PhD project aimed to (i) investigate the effects of three nutritional strategies (supplementation of a synbiotic, a muramidase, or arginine) on growth performance, gut health, and metabolism of broilers fed without antibiotics under thermoneutral and heat stress conditions and to (ii) explore the impacts of heat stress on hypothalamic regulation of feed intake in three broiler lines from diverse stages of genetic selection and in the red jungle fowl, the ancestor of domestic chickens. Synbiotic improved feed efficiency and footpad health, increased Firmicutes and reduced Bacteroidetes in the ceca of birds kept in thermoneutral conditions, while did not mitigate the impacts of heat stress on growth performance. Under optimal thermal conditions, muramidase increased final body weight and reduced cumulative feed intake and feed conversion ratio in a dose-dependent way. The highest dose reduced the risk of footpad lesions, cecal alpha diversity, the Firmicutes to Bacteroidetes ratio, and butyrate producers, increased Bacteroidaceae and Lactobacillaceae, plasmatic levels of bioenergetic metabolites, and reduced the levels of pro-oxidant metabolites. The same dose, however, failed to reduce the effects of heat stress on growth performance. Arginine supplementation improved growth rate, final body weight, and feed efficiency, increased plasmatic levels of arginine and creatine and hepatic levels of creatine and essential amino acids, reduced alpha diversity, Firmicutes, and Proteobacteria (especially Escherichia coli), and increased Bacteroidetes and Lactobacillus salivarius in the ceca of thermoneutral birds. No arginine-mediated attenuation of heat stress was found. Heat stress altered protein metabolism and caused the accumulation of antioxidant and protective molecules in oxidative stress-sensitive tissues. Arginine supplementation, however, may have partially counterbalanced the effects of heat stress on energy homeostasis. Stable gene expression of (an)orexigenic neuropeptides was found in the four chicken populations studied, but responses to hypoxia and heat stress appeared to be related to feed intake regulation.

Evaluation of clinical implications correlate to genetic polymorphisms and pharmacokinetic of transdermal fentanyl

ABSTRACT Background:Strong opioids are the treatment of choice for moderate to severe cancer-related pain. Fentanyl is a synthetic opioid with high affinity for the μ-opioid receptor and is 75–100 times more potent than morphine. Fentanyl is metabolised rapidly, particularly in the liver and only 10% is excreted as intact substance. The use of CYP3A4 inhibitors and inducers, impaired liver function, and heating of the patch potentially influence fentanyl pharmacokinetics in a clinically relevant way. The influence of BMI and gender on fentanyl pharmacokinetics is questionable. Pharmacogenetic, may influence fentanyl pharmacokinetic and other factors have been studied but did not show significant and clinically relevant effects on fentanyl pharmacokinetic. Method: This is a biological interventional prospective, single-center study in 49 patients with solid or haematological neoplasm treated with transdermal fentanyl undergoing 5-step pharmacokinetic and pharmacogenetic withdrawals from administration of the fentanyl patch. Objective:to evaluate the pharmacokinetic and pharmacogenetic of transdermal fentanyl in relation to the patient's clinical response on pain Results: Sex was the only parameter with evidence of different distribution between responders and non-responders , showing a major chance for male to be responders than females. We found some correlation with pharmacokinetic parameters and sex, regarding adverse events and NRS correlation with BPI. NAT2 and UGT2B7 polymorphisms are associated with AUC and Cmax kinetics parameters, NAT2 and CYP4F2 showed some evidence of association with the fentanyl dosage and CYP2B6 polymorphism seemed to be correlate with side effects. Conclusion: Small sample size of study population make difficult do find some significant correlation between pharmacogenetic, pharmacokinetic and clinical response. Larger studies are needed to increase knowledge about response to opioid treatment in cancer patients to better individualized pain treatment.

Investigation of plant genetic-microbiome interactions in different plant species

The rhizosphere, i.e. the soil surrounding the plant roots, and endosphere, i.e. the microbial communities within the plant organs harbors microbes known to influence root and plant physiological processes. An important question is to what extent plant species, genotypes and environmental conditions affect bacterial and fungal communities. The objectives of the first research study were to unravel and compare the rhizospheric microbiota of grape in two independent vineyards using 16S and ITS amplicon sequencing, evaluate location and varietal effects, and test the correlation between bioavailable copper levels and other soil parameters with microbiota composition and diversity. Our results showed that the microbial alpha diversity based on Shannon index differed significantly between vineyards while it did not differ between two grape cultivars. In the second study, we were focusing on different wheat species and genotypes such as Bread Wheat, Wild Emmer Wheat, Domesticated Emmer Wheat, Durum Wheat Landraces, Durum Wheat cultivars, T. monococcum and triticale in two fields located in Bologna and Foggia. The objectives of this research experiment were to elucidate and compare the rhizospheric and endophytic microbiota of 30 diverse wheat genotypes in two different fields using 16S amplicon sequencing. Our results showed that the microbial alpha diversity based on Shannon index differed significantly between fields of Bologna and Foggia, in which Bologna had a higher diversity in respect to Foggia for both rhizospheric and endophytic communities. Using Shannon index there was significant differences, for instance, between Durum Emmer Wheat and Wild Emmer Wheat in Bologna, and between Bread Wheat and Durum Wheat Landraces in Foggia. Our results contribute to understand the role of wheat species and genotype and the filed management on the root-microbe-soil interactions in the perspective of understanding their impact on crop systems sustainability.