Associations between BMI and the FTO Gene Are Age Dependent: Results from the GINI and LISA Birth Cohort Studies up to Age 6 Years

Objective: The association between polymorphisms in intron 1 of the fat mass and obesity associated gene (FTO) and obesity-related traits is one of the most robust associations reported for complex traits and is established both in adults and children. However, little is known about the longitudinal dynamics of these polymorphisms on body mass index (BMI), overweight, and obesity. Methods: This study is based on the 2,732 full-term neonates of the German GINI-plus and LISA-plus birth cohorts, for whom genotyping data on the FTO variants rs1558902 (T>A) or rs9935401 (G>A) were available. Children were followed from birth up to age 6 years. Up to 9 anthropometric measurements of BMI were obtained. Fractional-Polynomial-Generalized-Estimation-Equation modeling was used to assess developmental trends and their potential dependence on genotype status. Results: We observed no evidence for BMI differences between genotypes of both variants for the first 3 years of life. However, from age 3 years onwards, we noted a higher BMI for the homozygous minor alleles carriers in comparison to the other two genotype groups. However, evidence for statistical significance was reached from the age of 4 years onwards. Conclusions: This is one of the first studies investigating in detail the development of BMI depending on FTO genotype between birth and the age of 6 years in a birth cohort not selected for the phenotype studied. We observed that the association between BMI and FTO genotype evolves gradually and becomes descriptively detectable from the age of 3 years onwards

Determining Plasmodium falciparum Malaria Transmission Networks Through Sequenom And Capillary Electrophoresis Genotyping

Declining malaria transmission leads to infection hotspots which need to be targeted to eliminate and eradicate malaria. The degree of parasite mixing in and around transmission foci is likely to impact the effectiveness of targeted interventions and should be considered when developing control programmes. Few studies currently provide empiric evidence on parasite mixing over time and space, making it hard to predict the likely outcomes of targeted interventions. Here, spatio-temporal malaria transmission networks were inferred using genetic data. P. falciparum SNP data were analysed at micro-epidemiological scales in two sites in Kenya and one site in The Gambia, and in a subsequent study at macro-epidemiological scales in Western Kenya. Principal component analysis and linear regression were used to analyse population structure and genetic relatedness in time and space, respectively. Study sites were analysed for parasite genotype clusters, barriers to, and directionality in parasite movement. Parasite genetic relatedness was predicted by relatedness in time and space at micro-geographical scales, but no evidence of population structure was seen over larger areas. No barriers to parasite movement were detected at micro or macro-epidemiological scales, although directional movement was observed in two regions of Western Kenya. PfAMA1 and surf4.2 capillary sequence data from parasites collected between 1995 – 2014 in Kilifi county were used to validate SNP data results. Sequence data showed high parasite mixing, with no clustering of distinct haplotypes in time or space. Time and distance interacted antagonistically such that distance no longer predicted genetic variation for parasites collected more than 1 year apart. These findings show parasite populations that are well mixed in time and space, thus targeting hotspots is likely to benefit surrounding communities. However, this high parasite movement is likely to lead to re-introduction of infection from surrounding regions following “one-off” interventions, although repeated targeted interventions may be effective

Genome-Wide Linkage Analysis of Malaria Infection Intensity and Mild Disease

Although balancing selection with the sickle-cell trait and other red blood cell disorders has emphasized the interaction between malaria and human genetics, no systematic approach has so far been undertaken towards a comprehensive search for human genome variants influencing malaria. By screening 2,551 families in rural Ghana, West Africa, 108 nuclear families were identified who were exposed to hyperendemic malaria transmission and were homozygous wild-type for the established malaria resistance factors of hemoglobin (Hb)S, HbC, alpha(+) thalassemia, and glucose-6-phosphate-dehydrogenase deficiency. Of these families, 392 siblings aged 0.5–11 y were characterized for malaria susceptibility by closely monitoring parasite counts, malaria fever episodes, and anemia over 8 mo. An autosome-wide linkage analysis based on 10,000 single-nucleotide polymorphisms was conducted in 68 selected families including 241 siblings forming 330 sib pairs. Several regions were identified which showed evidence for linkage to the parasitological and clinical phenotypes studied, among them a prominent signal on Chromosome 10p15 obtained with malaria fever episodes (asymptotic z score = 4.37, empirical p-value = 4.0 × 10(−5), locus-specific heritability of 37.7%; 95% confidence interval, 15.7%–59.7%). The identification of genetic variants underlying the linkage signals may reveal as yet unrecognized pathways influencing human resistance to malaria

Piima laapumisomaduste modelleerimine ja geneetiline determineeritus

Milk coagulation properties (milk coagulation time and curd firmness) are of great importance for the cheese industry because of their influence on cheese outcome and quality. This thesis focuses on possibilities for the genetic improvement of these economically important traits in Estonian Holstein cattle and also evaluates transformation possibilities of milk coagulation measurements into one scale, between different analytical techniques. This study is the first large-scale study of genetic parameters of milk coagulation traits based on the optical method for measuring these traits. Estimates of heritability, repeatability and genetic correlations among milk coagulation, production, milk fat and protein percentage, somatic cell score, urea content and pH were found. Effect of β-κ-casein genotype on the milk traits referred to above and their additive genetic variation were also examined. Genetic parameters were estimated based on 17,577 first lactation milk samples from 4,191 Estonian Holstein cows, while β-κ-casein genotype effects were evaluated based on 23,970 milk samples for the first to third lactation from 2,859 genotyped Estonian Holstein cows. To study the transformability of measurements of milk coagulation traits, these traits were measured for 165 milk samples in two laboratories in Italy, using two different mechanical methods, and in Estonian laboratory using the optical method. The analyses of subsamples from the same cow were performed on the same day in all three laboratories. The study revealed that precision of transformation was high for milk coagulation time, while transformability of curd firmness remained moderate between mechanical methods, and modest between optical and mechanical methods. The association between milk coagulation traits, measured by the optical method, and cheese outcome and quality remains unclear. Genetic study showed that heritable additive genetic variation described about one-third of the phenotypic variation in milk coagulation traits of Estonian Holstein cows. Further, the β-κ-casein genotype described half of the additive genetic variation of curd firmness. Genetic associations of milk coagulation traits with milk production, pH and composition traits were predominantly low and favourable. It could be concluded that genetic determination of milk coagulation traits enables the improvement of these milk properties by using breeding methods, such as direct selection, on these traits as well as selection on the basis of genetic markers considering the high frequency found for β-κ-casein genotypes with an unfavourable effect on milk coagulation properties. However, a lack of high capacity equipment and analytical techniques for measuring milk coagulation traits makes routine recording of these traits on a whole dairy cow population unfeasible. Nevertheless, genetic evaluation can be applied to a limited number of breeding animals (e. g. bulls or bull dams).Piima laapumisomadustest (laapumisaeg ja kalgendi tugevus) sõltub juustu väljatulek ja kvaliteet, mistõttu on need piima kvaliteedinäitajad vajalikud eelkõige juustutööstusele. Doktoritöö keskendub nende piima kvaliteedinäitajate parandamisvõimaluste väljaselgitamisele aretuse teel eesti holsteini tõugu lehmadel, hinnates ka laapumisnäitajate teisendamisvõimalusi erinevate määramismeetodite vahel. Käesolev uurimistöö on esimene suuremahuline optilisel määramismeetodil baseeruv piima laapumisomaduste geneetiliste parameetrite uuring. Uuringu käigus anti hinnangud piima laapumisomaduste, piima toodangu, rasva- ja valgusisalduse, somaatiliste rakkude arvu skoori, karbamiidisisalduse ja pH geneetilistele parameetritele (päritavus, korduvus, omavahelised geneetilised korrelatsioonid). Ühtlasi uuriti ka β-κ-kaseiini genotüübi mõju mainitud piimanäitajatele ning nende aditiivgeneetilisele varieeruvusele. Geneetilised parameetrid leiti 4191 eesti holsteini tõugu lehma esimese laktatsiooni piimaproovi alusel (kokku 17577 proovi) ning β-κ-kaseiini genotüübi mõju hindamine baseerus 2859 genotüpiseeritud eesti holsteini tõugu lehma esimese kolme laktatsiooni piimaproovidel (kokku proove 23970). Laapumisomaduste teisendamisvõimaluste hindamiseks kasutati 165 lehma piimaproovi laapumisomaduste määramist paralleelselt kahes Itaalia laboris mehaaniliste meetoditega ning Eesti laboris optilise meetodiga. Uurimistöö tulemused näitasid, et laapumisaja teisendustäpsus oli kõrge, samas kui kalgendi tugevusel jäi see mehaaniliste meetodite vahel mõõdukaks ning optilise ja mehaaniliste meetodite vahel tagasihoidlikuks. Optilisel meetodil määratud laapumisomaduste seosed juustu väljatuleku ning kvaliteediga vajavad täiendavat uurimist. Geneetilised hinnangud näitasid, et eesti holsteini tõugu lehmade piima laapumisomaduste varieeruvusest ligikaudu kolmandiku moodustas päritav aditiivgeneetiline variatsioon, millest kalgendi tugevusel kirjeldas omakorda poole β-κ-kaseiini genotüüp. Valdavalt olid laapumisnäitajate ja teiste oluliste piimanäitajate vahel nõrgad soodsa suunaga geneetilised seosed. Toodud geneetiliste hinnangute tulemusena saab aretuse seisukohast väita, et piima laapumisomaduste geneetiline determineeritus võimaldab kõne all olevate omaduste parandamist nii otsese selektsiooni teel kui ka geneetiliste markerite alusel. Selektsiooniks soodne oli ka populatsiooni geneetiline struktuur, kuna laapumisomadustele negatiivset mõju avaldavad β-κ-kaseiini genotüübid olid suure esinemissagedusega. Praktilisest seisukohast on kogu populatsiooni laapumisomaduste mõõtmine ja rutiinne registreerimine tõhusa määramismeetodi puudumise tõttu hetkel küll raskendatud, kuid piiratud arvu aretusloomade (vaid valik pulle ja/või pulliemasid) geneetiline hindamine siiski võimalik.Publication of this dissertation is supported by the Estonian University of Life Sciences and by Bio-Competence Centre of Healthy Dairy Products LLC

Low-level visual processing and its relation to neurological disease

Retinal neurons extract changes in image intensity across space, time, and wavelength. Retinal signal is transmitted to the early visual cortex, where the processing of low-level visual information occurs. The fundamental nature of these early visual pathways means that they are often compromised by neurological disease. This thesis had two aims. First, it aimed to investigate changes in visual processing in response to Parkinson’s disease (PD) by using electrophysiological recordings from animal models. Second, it aimed to use functional magnetic resonance imaging (fMRI) to investigate how low-level visual processes are represented in healthy human visual cortex, focusing on two pathways often compromised in disease; the magnocellular pathway and chromatic S-cone pathway. First, we identified a pathological mechanism of excitotoxicity in the visual system of Drosophila PD models. Next, we found that we could apply machine learning classifiers to multivariate visual response profiles recorded from the eye and brain of Drosophila and rodent PD models to accurately classify these animals into their correct class. Using fMRI and psychophysics, found that measurements of temporal contrast sensitivity differ as a function of visual space, with peripherally tuned voxels in early visual areas showing increased contrast sensitivity at a high temporal frequency. Finally, we used 7T fMRI to investigate systematic differences in achromatic and S-cone population receptive field (pRF) size estimates in the visual cortex of healthy humans. Unfortunately, we could not replicate the fundamental effect of pRF size increasing with eccentricity, indicating complications with our data and stimulus

Mapping the functional landscape of frequent phenylalanine hydroxylase (PAH) genotypes promotes personalised medicine in phenylketonuria

Background: In phenylketonuria, genetic heterogeneity, frequent compound heterozygosity, and the lack of functional data for phenylalanine hydroxylase genotypes hamper reliable phenotype prediction and individualised treatment. Methods: A literature search revealed 690 different phenylalanine hydroxylase genotypes in 3066 phenylketonuria patients from Europe and the Middle East. We determined phenylalanine hydroxylase function of 30 frequent homozygous and compound heterozygous genotypes covering 55% of the study population, generated activity landscapes, and assessed the phenylalanine hydroxylase working range in the metabolic (phenylalanine) and therapeutic (tetrahydrobiopterin) space. Results: Shared patterns in genotype-specific functional landscapes were linked to biochemical and pharmacological phenotypes, where (1) residual activity below 3.5% was associated with classical phenylketonuria unresponsive to pharmacological treatment; (2) lack of defined peak activity induced loss of response to tetrahydrobiopterin; (3) a higher cofactor need was linked to inconsistent clinical phenotypes and low rates of tetrahydrobiopterin response; and (4) residual activity above 5%, a defined peak of activity, and a normal cofactor need were associated with pharmacologically treatable mild phenotypes. In addition, we provide a web application for retrieving country-specific information on genotypes and genotype-specific phenylalanine hydroxylase function that warrants continuous extension, updates, and research on demand. Conclusions: The combination of genotype-specific functional analyses with biochemical, clinical, and therapeutic data of individual patients may serve as a powerful tool to enable phenotype prediction and to establish personalised medicine strategies for dietary regimens and pharmacological treatment in phenylketonuria

Blood group probabilities by next of kin

For rare blood groups the recruitment of donor relatives, for example siblings, is expected to be effective, since the probability of a similar rare blood group is likely. However, the likelihood differs between blood groups and is not commonly available. This paper provides a unified mathematical formulation to calculate such likelihoods. From a mathematical and probabilistic point of view, it is shown that these likelihoods can be obtained from the computation of a stationary genotype distribution. This, in turn, can be brought down to a system of quadratic stochastic operators. A generic mathematical approach is presented which directly leads to a stationary genotype distribution for arbitrary blood groups. The approach enables an exact computation for the effectiveness of recruiting next of kin for blood donorship. Next to an illustration of computations for ‘standard’ ABO and Rhesus-D blood groups, it is particularly illustrated for the extended Rhesus blood group system. Also other applications requiring next of kin blood group associations can be solved directly by using the unified mathematical formulation

The role of TASK-3 potassium channels in theta oscillations and behaviour

The two pore-domain potassium channel TASK-3 provides a potassium leak conductance in the mammalian brain and is activated by volatile anaesthetics. Previous studies have shown that TASK-3 knockout (KO) mice have a number of physiological and behavioural abnormalities. In particular, TASK-3 KO mice lack the type-2 theta oscillation (4-8 Hz) usually present in the electroencephalogram (EEG) under halothane anaesthesia, while the higher frequency type-1 theta oscillation (8-12 Hz) recorded during exploratory behaviour is unaffected. That TASK-3 KO mice also have moderate memory impairments, led us to ask whether there might be a link between type-2 theta deficits and impaired mnemonic behaviour. Our results indicate that TASK-3 KO mice also have impaired type-2 theta oscillations during freezing behaviour in a predator exposure test, suggesting possible sensorimotor integration problems. TASK-3 KO mice were found to have a mild impairment in working memory in the T-maze, but object recognition and emotional memory were intact, excluding a role for the TASK-3-dependent theta oscillation in these processes. Further studies then sought to understand the mechanistic role of TASK-3 in the theta oscillation using recombinant Adeno-associated viruses (rAAVs). We first investigated a possible functional role for the type-2 theta oscillation in mediating anaesthesia, and then confirmed that the halothane-associated theta oscillation was dependent upon cholinergic input from the medial septum to the hippocampus. TASK-3 was then re-expressed via rAAV in the medial septum in KO mice, resulting in partial rescue of the type-2 theta oscillation. Our results show that (1) the type-2 theta oscillation plays a redundant role in halothane anaesthesia, (2) type-2 theta deficits in TASK-3 KO mice have minimal effect on memory processing, and (3) that TASK-3 channels in the medial septum play a facilitatory role in type-2 theta oscillations