Converting estimated breeding values from the observed to probability scale for health traits.

Dairy cattle health traits are paramount from a welfare and economic viewpoint; therefore, modern breeding programs prioritize the genetic improvement of these traits. Estimated breeding values for health traits are published as the probability of animals staying healthy. They are obtained using threshold models, which assume that the observed binary phenotype (i.e., healthy or sick) is dictated by an underlying normally distributed liability exceeding or not a threshold. This methodology requires significant computing time and faces convergence challenges as it implies a nonlinear system of equations. Linear models have more straightforward computations and provide a robust approximation to threshold models; thus, they could be used to overcome the mentioned challenges. However, linear models yield estimated breeding values on the observed scale, requiring an approximation to the liability scale analogous to that from threshold models to later obtain the estimated breeding values on the probability scale. In addition, the robustness of the approximation of linear to threshold models depends on the amount of information and the incidence of the trait, with extreme incidence (i.e., ≤ 5%) deviating from optimal approximation. Our objective was to test a transformation from the observed to the liability and then to the probability scale in the genetic evaluation of health traits with moderate and very low (extreme) incidence. Data comprised displaced abomasum (5.1M), ketosis (3.6M), lameness (5M), and mastitis (6.3M) records from a Holstein population with a pedigree of 6M animals, of which 1.7M were genotyped. Univariate threshold and linear models were performed to predict breeding values. The agreement between estimated breeding values on the probability scale derived from threshold and linear models was assessed using Spearman rank correlations and comparison of estimated breeding values distributions. Correlations were at least 0.95, and estimated breeding value distributions almost entirely overlapped for all the traits but displaced abomasum, the trait with the lowest incidence (2%). Computing time was ∼3x longer for threshold than for linear models. In this Holstein population, the approximation was suboptimal for a trait with extreme incidence (2%). However, when the incidence was ≥6%, the approximation was robust, and its use is recommended along with linear models for analyzing categorical traits in large populations to ease the computational burden.

Molecular evolution of DNMT1 in vertebrates: Duplications in marsupials followed by positive selection.

DNA methylation is mediated by a conserved family of DNA methyltransferases (Dnmts). The human genome encodes three active Dnmts (Dnmt1, Dnmt3a and Dnmt3b), the tRNA methyltransferase Dnmt2, and the regulatory protein Dnmt3L. Despite their high degree of conservation among different species, genes encoding Dnmts have been duplicated and/or lost in multiple lineages throughout evolution, indicating that the DNA methylation machinery has some potential to undergo evolutionary change. However, little is known about the extent to which this machinery, or the methylome, varies among vertebrates. Here, we study the molecular evolution of Dnmt1, the enzyme responsible for maintenance of DNA methylation patterns after replication, in 79 vertebrate species. Our analyses show that all studied species exhibit a single copy of the DNMT1 gene, with the exception of tilapia and marsupials (tammar wallaby, koala, Tasmanian devil and opossum), each of which displays two apparently functional DNMT1 copies. Our phylogenetic analyses indicate that DNMT1 duplicated before the radiation of major marsupial groups (i.e., at least ~75 million years ago), thus giving rise to two DNMT1 copies in marsupials (copy 1 and copy 2). In the opossum lineage, copy 2 was lost, and copy 1 recently duplicated again, generating three DNMT1 copies: two putatively functional genes (copy 1a and 1b) and one pseudogene (copy 1ψ). Both marsupial copies (DNMT1 copies 1 and 2) are under purifying selection, and copy 2 exhibits elevated rates of evolution and signatures of positive selection, suggesting a scenario of neofunctionalization. This gene duplication might have resulted in modifications in marsupial methylomes and their dynamics.

Phylogenetic Distribution of CMP-Neu5Ac Hydroxylase (CMAH), the Enzyme Synthetizing the Proinflammatory Human Xenoantigen Neu5Gc.

The enzyme CMP-N-acetylneuraminic acid hydroxylase (CMAH) is responsible for the synthesis of N-glycolylneuraminic acid (Neu5Gc), a sialic acid present on the cell surface proteins of most deuterostomes. The CMAH gene is thought to be present in most deuterostomes, but it has been inactivated in a number of lineages, including humans. The inability of humans to synthesize Neu5Gc has had several evolutionary and biomedical implications. Remarkably, Neu5Gc is a xenoantigen for humans, and consumption of Neu5Gc-containing foods, such as red meats, may promote inflammation, arthritis, and cancer. Likewise, xenotransplantation of organs producing Neu5Gc can result in inflammation and organ rejection. Therefore, knowing what animal species contain a functional CMAH gene, and are thus capable of endogenous Neu5Gc synthesis, has potentially far-reaching implications. In addition to humans, other lineages are known, or suspected, to have lost CMAH; however, to date reports of absent and pseudogenic CMAH genes are restricted to a handful of species. Here, we analyze all available genomic data for nondeuterostomes, and 322 deuterostome genomes, to ascertain the phylogenetic distribution of CMAH. Among nondeuterostomes, we found CMAH homologs in two green algae and a few prokaryotes. Within deuterostomes, putatively functional CMAH homologs are present in 184 of the studied genomes, and a total of 31 independent gene losses/pseudogenization events were inferred. Our work produces a list of animals inferred to be free from endogenous Neu5Gc based on the absence of CMAH homologs and are thus potential candidates for human consumption, xenotransplantation research, and model organisms for investigation of human diseases.

Reduced folate, increased vitamin B(12) and homocysteine concentrations in women delivering preterm.

BACKGROUND AND AIM: Maternal nutrition is an important determinant of the duration of pregnancy and fetal growth, and thereby influences pregnancy outcome. Folic acid and vitamin B(12) are involved in one-carbon metabolism and are reported to underlie intrauterine programming of adult diseases. METHODS: In the present study, the levels of folate, vitamin B(12) and homocysteine were measured in mothers delivering preterm (PT; gestation <37 weeks; n = 67), those delivering preterm due to preeclampsia (PT-PE; n = 49) and women delivering at term (control group; n = 76). RESULTS: Increased vitamin B(12) and homocysteine levels (p < 0.05 for both) were seen in the PT-PE and PT groups as compared to the controls. In addition, reduced folate levels (p < 0.05) were observed in the PT group. A negative association of maternal plasma homocysteine with birth weight was seen in the idiopathic preterm group. CONCLUSIONS: Altered maternal micronutrients and resultant increased homocysteine concentrations exist in women delivering preterm. These alterations may also be partly associated with other factors such as undiagnosed inflammatory conditions or inadequate placentation in some women. Since these micronutrients play an important role in epigenetic regulation of vital genes involved in the fetal programming of adult diseases, further studies need to be undertaken to understand their role in preterm deliveries.

Dynamic proteome in enigmatic preeclampsia: an account of molecular mechanisms and biomarker discovery.

The coevolution of genomics and proteomics has led to advancements in the field of diagnosis and molecular mechanisms of disease. Proteomics is now stepping into the field of obstetrics, where early diagnosis of pregnancy complication such as preeclampsia (PE) is imperative. PE is a multifactorial disease characterized by hypertension with proteinuria, which is a leading cause of maternal and neonatal morbidity and mortality occurring in 5-7% of pregnancies worldwide. This review discusses the probable molecular mechanisms that lead to PE and summarizes the proteomics research carried out in understanding the pathogenicity of PE, and for identifying the candidate biomarker for diagnosis of the disease.

Effect of maternal micronutrients (folic acid, vitamin B12) and omega 3 fatty acids on liver fatty acid desaturases and transport proteins in Wistar rats.

A disturbed fatty acid metabolism increases the risk of adult non-communicable diseases. This study examines the effect of maternal micronutrients on the fatty acid composition, desaturase activity, mRNA levels of fatty acid desaturases and transport proteins in the liver. Pregnant female rats were divided into 6 groups at 2 levels of folic acid both in the presence and absence of vitamin B(12). The vitamin B(12) deficient groups were supplemented with omega 3 fatty acid. An imbalance of maternal micronutrients reduces liver docosahexaenoic acid, increases Δ5 desaturase activity but decreases mRNA levels, decreases Δ6 desaturase activity but not mRNA levels as compared to control. mRNA level of Δ5 desaturase reverts back to the levels of the control group as a result of omega 3 fatty acid supplementation. Our data for the first time indicates that maternal micronutrients differentially alter the activity and expression of fatty acid desaturases in the liver.

Maternal micronutrients (folic acid and vitamin B(12)) and omega 3 fatty acids: implications for neurodevelopmental risk in the rat offspring.

Altered maternal micronutrients (folic acid, vitamin B(12)) are suggested to be at the heart of intra-uterine programming of adult diseases. We have recently described interactions of folic acid, vitamin B(12) and docosahexaenoic acid in one carbon metabolism that is considered to play a key role in regulation oxidative stress and chromatin methylation. However its impact on fetal oxidative stress and brain fatty acid levels has been relatively unexplored. The present study examined the effect of imbalance in maternal micronutrients (folic acid and vitamin B(12)) and maternal omega 3 fatty acid supplementation on oxidative stress parameters and brain fatty acids and in the offspring at birth. Pregnant female rats were divided into six groups at two levels of folic acid both in the presence and absence of vitamin B(12). Both the vitamin B(12) deficient groups were supplemented with omega 3 fatty acid. Oxidative stress marker (malondialdehyde) and polyunsaturated fatty acid profiles in plasma and brain were analyzed in dam and offspring at d20. Our results for the first time indicate that imbalance in maternal micronutrients (excess maternal folic acid supplementation on a B(12) deficient diet) increases (p<0.01) oxidative stress in both mother and pups. This increased maternal oxidative stress resulted in lower (p<0.01) fetal brain DHA levels. Omega 3 fatty acid supplementation was able to restore (p<0.05) the levels of brain DHA in both the vitamin B(12) deficient groups. Our data has implications for implications for neurodevelopmental disorders since micronutrients and DHA are important modulators for neural functioning.

Effects of altered maternal folic acid, vitamin B12 and docosahexaenoic acid on placental global DNA methylation patterns in Wistar rats.

Potential adverse effects of excess maternal folic acid supplementation on a vegetarian population deficient in vitamin B(12) are poorly understood. We have previously shown in a rat model that maternal folic acid supplementation at marginal protein levels reduces brain omega-3 fatty acid levels in the adult offspring. We have also reported that reduced docosahexaenoic acid (DHA) levels may result in diversion of methyl groups towards DNA in the one carbon metabolic pathway ultimately resulting in DNA methylation. This study was designed to examine the effect of normal and excess folic acid in the absence and presence of vitamin B(12) deficiency on global methylation patterns in the placenta. Further, the effect of maternal omega 3 fatty acid supplementation on the above vitamin B(12) deficient diets was also examined. Our results suggest maternal folic acid supplementation in the absence of vitamin B(12) lowers plasma and placental DHA levels (p<0.05) and reduces global DNA methylation levels (p<0.05). When this group was supplemented with omega 3 fatty acids there was an increase in placental DHA levels and subsequently DNA methylation levels revert back to the levels of the control group. Our results suggest for the first time that DHA plays an important role in one carbon metabolism thereby influencing global DNA methylation in the placenta.

Association of omega-3 fatty acids and homocysteine concentrations in pre-eclampsia.

BACKGROUND & AIMS: The present study examines the associations of folic acid, vitamin B12 and omega-3 fatty acids and increased homocysteine which are implicated in the pathology of pre-eclampsia. METHODS: 49 Pre-eclamptic and 57 normotensive women were recruited at Bharati hospital, Pune, India. Plasma folate, vitamin B12, homocysteine and erythrocyte omega-3 and omega-6 fatty acids were analyzed. RESULTS: Homocysteine concentrations were higher in pre-eclamptic than in normotensive women (14.28±7.31 vs. 11.03±4.38 µmol/l, p<0.01) despite similar levels of folic acid and vitamin B12. In the pre-eclamptic group, plasma folate levels were positively associated with erythrocyte omega-6 fatty acids (p<0.05) while erythrocyte docosahexaenoic acid levels were negatively associated with plasma homocysteine levels (p<0.01). CONCLUSIONS: Our study provides evidence for the associations of altered omega-3 fatty acids especially docosahexaenoic acid and the resultant increased homocysteine concentrations in pre-eclampsia. Future studies need to examine if docosahexaenoic acid supplementation during pregnancy reduces homocysteine levels and ameliorates the risk of developing pre-eclampsia.

Global DNA methylation patterns in placenta and its association with maternal hypertension in pre-eclampsia.

Maternal nutrition is an important determinant of one-carbon metabolism that lies at the heart of intrauterine epigenetic programming. Exchange of nutrients and other vital molecules between the mother and fetus takes place across the placenta and hence may play direct role in fetal programming. Pre-eclampsia (PE) originates in the placenta and altered maternal nutrition may influence epigenetic patterns in the placenta, thereby affecting birth outcome. In the present study, we investigated the global DNA methylation levels in placentas of pre-eclampsia women (i.e., women delivering at term and those delivering preterm) and studied their associations with maternal blood pressure and birth outcome. Increased homocysteine and global DNA methylation levels were seen in the pre-eclampsia group (term and preterm PE) when compared with the normotensive group (p < 0.05). A positive association between global DNA methylation and systolic (p < 0.01) and diastolic (p < 0.05) blood pressure was seen in the term pre-eclampsia group, whereas there was no association with birth outcome. The study for the first time provides evidence for altered global DNA methylation patterns in pre-eclampsia placentas and its association with blood pressure. It is possible that increased homocysteine levels may be related to increased methylation in pre-eclampsia.

Reduced placental docosahexaenoic acid levels associated with increased levels of sFlt-1 in preeclampsia.

Our earlier studies, in preeclamptic women have shown altered levels of long chain polyunsaturated fatty acids (LCPUFA), essential constituents of the cell membrane lipids responsible for membrane stability as one of the key factors contributing to the pathophysiology of preeclampsia. We have also reported elevated levels of sFlt-1 in preeclampsia. The present study examines the levels of LCPUFA and their association with sFlt-1 levels in 69 pre-eclamptic women and 40 normotensive women. DHA and omega 3 fatty acid levels were lower (p<0.001) while arachidonic acid and omega 6 fatty acid levels were higher (p<0.05) in preeclamptic women as compared to normotensive women. Maternal plasma sFlt-1 levels were higher (p<0.05) in preeclamptic women and were negatively associated with DHA (p=0.008) and omega 3 fatty acids concentrations (p=0.031). Our results suggest that altered placental LCPUFA may result in altered membrane lipid fatty acid composition leading to increased release of sFlt-1 in circulation.

Circulating angiogenic factors and their association with birth outcomes in preeclampsia.

This study was designed to test the hypothesis that altered angiogenic factors together with increased oxidative stress and reduced docosahexaenoic acid (DHA) levels may be associated with altered birth outcome parameters. To test this hypothesis, levels of plasma vascular endothelial growth factor (VEGF), placental growth factor (PlGF), soluble fms-like tyrosine kinase-1 (sFlt-1), the oxidative stress marker malondialdehyde (MDA) and fatty acids were estimated in women with preeclampsia and their cord samples and compared with those in normotensive women. The association of these parameters with birth outcome was also examined. Our results show that in preeclamptic women, maternal plasma VEGF and PlGF levels were lower, whereas sFlt-1 levels were higher (P<0.05 for all) than in normotensive women. In contrast, cord plasma VEGF levels were higher (P<0.05) in preeclamptic women, whereas there was no difference in sFlt-1 levels. Plasma DHA levels in both the mother and cord were lower (P<0.05) in the preeclamptic group compared with normotensive women. Maternal plasma sFlt-1 levels were positively (n=23, r=0.415, P=0.039) associated with MDA concentrations in preeclamptic women. Maternal plasma sFlt-1 levels showed a strong negative association with baby weight (n=37, r=-0.547, P=0.001), head circumference (n=37, r=-0.472, P=0.005) and baby chest circumference (n=37, r=-0.375, P=0.032) in the preeclamptic group. Cord plasma sFlt-1 concentrations were negatively associated with cord plasma DHA concentrations (n=28, r=-0.552, P=0.004). This study suggests that dysregulation of angiogenic factors may be associated with maternal oxidative stress. Increased oxidative stress may reduce cord DHA levels and increase sFlt-1 levels, leading to poor birth outcomes in preeclampsia.

Long-chain polyunsaturated fatty acid composition of breast milk in pre-eclamptic mothers.

BACKGROUND: Maternal fatty acid nutrition during pregnancy and lactation determines the transfer of long-chain polyunsaturated fatty acids via the placenta and through human milk. Neural maturation of breast-fed infants is known to be linked to breast-milk long-chain polyunsaturated fatty acid concentrations. In spite of this, the fatty acid composition of breast milk in pre-eclamptic mothers is poorly understood. OBJECTIVES: To compare the fatty acid composition of breast milk of pre-eclamptic (n = 45) with normotensive (n = 85) mothers and examine the association of breast-milk fatty acids with plasma fatty acids. METHODS: Milk and plasma fatty acid methyl esters were prepared and analyzed by the modified method of Manku and colleagues using gas chromatography. RESULTS: Docosahexaenoic acid (DHA) concentrations were significantly increased (p < 0.01) in breast milk in spite of lower maternal plasma DHA concentrations (p < 0.05) in pre-eclamptic women. However, there was no difference in arachidonic acid levels between groups in spite of reduced maternal plasma arachidonic acid levels. CONCLUSIONS: The data suggest that in pre-eclampsia, the relation between plasma and milk DHA is altered. The resulting higher milk DHA concentrations are beneficial for infants.

Maternal caloric restriction spares fetal brain polyunsaturated fatty acids in Wistar rats.

There is increasing interest in the role of developmental programming; however, the impact on fetal oxidative stress and brain fatty acid levels has been relatively unexplored. Recent reports have shown that caloric restriction regimens in adult animals reduce the occurrence of chronic diseases by reducing the oxidative stress and altering the long chain polyunsaturated fatty acids (LCPUFA). The present study examined whether caloric restriction during pregnancy alters oxidative stress and essential fatty acid metabolism in mother and offspring at birth. Pregnant female rats were fed either a standard chow (C, n=7) or were calorie restricted (CR, n=7) by feeding 60% of the intake of the control. Oxidative stress marker (malondialdehyde) and polyunsaturated fatty acid profiles in brain and liver were analyzed in both dams and offspring. Total weight gain during pregnancy was lower (p<0.01) in the CR group as compared to the control group but did not affect the litter size and weight. Brain malondialdehyde levels were lower (p<0.05) in dams from the CR group. There was no change in brain and liver LCPUFA levels in both male and female offspring in the CR group. Most of the polyunsaturated fatty acids were reduced (p<0.05) in plasma and brain in the CR dams. Caloric restriction during pregnancy did not alter LCPUFA metabolism in the offspring suggesting that during maternal caloric restriction mothers own stores are mobilized to provide docosahexaenoic acid and arachidonic acid for fetal brain development.