Development and Application of Genomic Control Methods for Genome-Wide Association Studies Using Non-Additive Models

Genome-wide association studies (GWAS) comprise a powerful tool for mapping genes of complex traits. However, an inflation of the test statistic can occur because of population substructure or cryptic relatedness, which could cause spurious associations. If information on a large number of genetic markers is available, adjusting the analysis results by using the method of genomic control (GC) is possible. GC was originally proposed to correct the Cochran-Armitage additive trend test. For non-additive models, correction has been shown to depend on allele frequencies. Therefore, usage of GC is limited to situations where allele frequencies of null markers and candidate markers are matched. In this work, we extended the capabilities of the GC method for non-additive models, which allows us to use null markers with arbitrary allele frequencies for GC. Analytical expressions for the inflation of a test statistic describing its dependency on allele frequency and several population parameters were obtained for recessive, dominant, and over-dominant models of inheritance. We proposed a method to estimate these required population parameters. Furthermore, we suggested a GC method based on approximation of the correction coefficient by a polynomial of allele frequency and described procedures to correct the genotypic (two degrees of freedom) test for cases when the model of inheritance is unknown. Statistical properties of the described methods were investigated using simulated and real data. We demonstrated that all considered methods were effective in controlling type 1 error in the presence of genetic substructure. The proposed GC methods can be applied to statistical tests for GWAS with various models of inheritance. All methods developed and tested in this work were implemented using R language as a part of the GenABEL package.     

Changes in microbiota of rainbow trout caused by sediments contamination

The abundance, composition and hydrocarbon-degrading bacteria, as possible biomarkers of contamination with oil hydrocarbons, of autochthonous and alochtonous microbiota of the digestive tract of rainbow trout have been estimated. The samples of the bottom sediments for microbiological tests have been collected and a response of natural bacterial communities in the digestive tract of rainbow trout and nutritional changes has been investigated. Experimental fish have been fed with a mixture of three substances with the aim to assess the influence of hydrocarbon-degrading bacteria contained in the sediments on the microbiota of rainbow trout’s digestive tracts. The abundance values of rainbow trout intestinal heterotrophic bacteria were found to change depending on alochtonous microbiota of different bottom sediments given to the experimental fish with food in vitro. According to the results of our research, it is likely that the changes in the abundance values of the microbiota of the digestive tract of fish and in the proportions of functional groups of the bacteria allow us to determine changes in the functional activity of bacteria depending on food composition. Any relative increase or decrease of abundance or activity of alochtonous microbiota allows the prediction of toxic effects of the contaminants on animals and the environment.     

Antimalarial activity of compounds comprising a primary benzene sulfonamide fragment

Despite the urgent need for effective antimalarial drugs with novel modes of action no new chemical class of antimalarial drug has been approved for use since 1996. To address this, we have used a rational approach to investigate compounds comprising the primary benzene sulfonamide fragment as a potential new antimalarial chemotype. We report the in vitro activity against Plasmodium falciparum drug sensitive (3D7) and resistant (Dd2) parasites for a panel of fourteen primary benzene sulfonamide compounds. Our findings provide a platform to support the further evaluation of primary benzene sulfonamides as a new antimalarial chemotype, including the identification of the target of these compounds in the parasite.     

Binding of antibiotic amphotericin B to lipid membranes: monomolecular layer technique and linear dichroism-FTIR studies

Amphotericin B (AmB) is one of the main antibiotics applied in treatment of deep-seated mycotic infections. Tensiometric technique has been applied to monitor binding of AmB, from the water subphase, to the lipid monomolecular layers, formed with dipalmitoylphosphatidylcholine at the air-water interface. Time dependencies of surface pressure in the monolayers demonstrate strong enhancement of AmB binding to monolayers brought about by sterols present in the membranes. The monolayers have been deposited to a solid support and examined by means of FTIR spectroscopy. FTIR measurements show that majority of the AmB molecules which bind to the membranes are localized in the polar headgroup region. The results of the linear dichroism-FTIR measurements are consistent with the microscopic picture according to which the molecules of the membrane-bound AmB are distributed among two orientational fractions: one horizontal and one vertical with respect to the plane of the membrane (59% versus 41% respectively, in the case of the membrane formed with the pure lipid without sterols). The presence of cholesterol in the membranes (50 mol% with respect to lipid) slightly affects such a distribution (53% horizontal versus 47% vertical) but the presence of ergosterol has a pronounced effect in the increase in population of the fraction of horizontally bound AmB (85% horizontal vs. 15% vertical). The results of the measurements indicate that mode of action of the AmB consists in disruption of the polar headgroup region of biomembranes, brought about by the AmB molecules bound horizontally with respect to the plane of the membrane.     

Water-in-oil microemulsions as the reaction medium for the solvent-sensitive yellow laccases

To determine the applicability of water-in-oil microemulsions for enzymatic conversions catalysed by yellow laccase from Pleurotus ostreatus (YLPO) D1 the following were studied: (i) the catalytic activity of the YLPO D1 in the oxidation of typical phenolic substrates: catechol (CAT), 2,6-dimethoxyphenol (DMOP) and 2,2^′-azino-bis-(3-ethylbenzothiazoline-6-sulphonic acid) diammonium salt (ABTS), at the appropriate pH optimum values in aqueous buffer solutions and in 62?mM bis-2-(ethylhexyl) sulfosuccinate sodium salt (AOT) in isooctane water-in-oil microemulsions; (ii) the effect of acetonitrile (ACN) on the kinetic parameters of DMOP oxidation catalysed by this laccase; (iii) the optimum conditions for the laccase catalytic activity in AOT in isooctane w/o microemulsions (w, laccase, AOT concentration); (iiv) the possibility of using the optimum water-in-oil microemulsions for the oxidation of aromatic alcohols (veratryl alcohol (VA) and benzyl alcohol (BA)) and the oxidative degradation of selected pollutants (3-chlorophenol, anthracene (ANT) and fluorene (FLU)).     

Overwinter survival depends on immune defence and body length in male Aquarius najas water striders

Winter survival of organisms has a crucial effect on their fitness in a seasonal environment. We tested whether overwinter survival of male water striders, Aquarius najas (De Geer) (Heteroptera: Gerridae), is associated with the time of season they leave the water for winter diapause. This was performed by comparing parameters of males leaving the water at the beginning of autumn and 1 month later. The results show significantly higher overwinter survival in males of the early diapausing group. They were found to be larger than late diapausing individuals. Overall, overwinter survival was found to be associated with body length. The strength of immune defence measured as encapsulation response against nylon monofilament appeared to be stronger in the early than in the late dia‐pausing group. Body length had an effect on the encapsulation rates of water striders, with larger males having a stronger encapsulation response. The amount of lipids was larger in males of the early diapausing group, and the relationship between body length and absolute lipid reserves was positive in both groups. However, a correlation between body reserves and body length was not found when lipid content was expressed as a proportion of total body weight. The results suggest that body length is the main variable linking overwinter survival and resistance against pathogens and parasitoids. This study shows that differences in resistance can explain differential winter survival of larger and smaller A. najas water striders.     

Body size of newborns in relation to mother's ethnicity and education: a pilot study from Vilnius City (Lithuania), 2005-2010

The purpose of this study was to analyse body size indices of newborns in Vilnius city (Lithuania) during 2005-2010 in relation with mother's education and ethnicity, and in parallel with the changes of socio-economic situation during the recent years. The present results were based on data (N = 18,084) from the Vilnius University Clinic of Obstetrics and Gynaecology. Comparison of the present Lithuanian data with other newborn studies was made. The analysis of socio-economic and demographic indicators of Lithuania, and the comparison of Gross Domestic Product of various countries was performed. The comparison of body size of newborns' data from the different countries showed that Lithuanian newborns were among the biggest babies. Some statistically significant differences in body size of newborns from different ethnic groups were established. Body length of Lithuanian newborns (M = 52.6 cm, SD = 2.5) was higher than length of Russian, Ukrainian and Romanian newborns. Body weight of Lithuanian newborns (M = 3511 g, SD = 485) was bigger than birth weight of Russian, Polish, Ukrainian and Romanian newborns. The analysis of newborns size by mother's education showed that body weight of neonates from mothers with the university education and from each other education group was bigger in comparison with the babies from respectively lower education group. The comparison of newborns weight by mother's ethnicity in relation to education level revealed nearly no discrepancies between size of newborns from mothers with the same education level at different ethnic group. The analysis of birth parameters by year has not established a statistically significant difference between the mean values for the body weight and body length of the whole investigated contingent of the full-term, single-birth newborns from Vilnius city during the 2005-2010. However, the tendency has been revealed that newborns from mothers with lower education were the most susceptible to negative economic changes after the 2008.     

CNN3 Regulates Trophoblast Invasion and Is Upregulated by Hypoxia in BeWo Cells

CNN3 is an ubiquitously expressed F-actin binding protein, shown to regulate trophoblast fusion and hence seems to play a role in the placentation process. In this study we demonstrate that CNN3 levels are upregulated under low oxygen conditions in the trophoblast cell line BeWo. Since hypoxia is discussed to be a pro-migratory stimulus for placental cells, we examined if CNN3 is involved in trophoblast invasion. Indeed, when performing a matrigel invasion assay we were able to show that CNN3 promotes BeWo cell invasion. Moreover, CNN3 activates the MAPKs ERK1/2 and p38 in trophoblast cells and interestingly, both kinases are involved in BeWo invasion. However, when we repeated the experiments under hypoxic conditions, CNN3 did neither promote cell invasion nor MAPK activation. These results indicate that CNN3 promotes invasive processes by the stimulation of ERK1/2 and/or p38 under normoxic conditions in BeWo cells, but seems to have different functions at low oxygen levels. We further speculated that CNN3 expression might be altered in human placentas derived from pregnancies complicated by IUGR and preeclampsia, since these placental disorders have been described to go along with impaired trophoblast invasion. Our studies show that, at least in our set of placenta samples, CNN3 expression is neither deregulated in IUGR nor in preeclampsia. In summary, we identified CNN3 as a new pro-invasive protein in trophoblast cells that is induced under low oxygen conditions.