α-Linolenic acid supplementation and conversion to n-3 long-chain polyunsaturated fatty acids in humans

Blood levels of polyunsaturated fatty acids (PUFA) are considered biomarkers of status. Alpha-linolenic acid, ALA, the plant omega-3, is the dietary precursor for the long-chain omega-3 PUFA eicosapentaenoic acid (EPA), docosapentaenoic acid (DPA), and docosahexaenoic acid (DHA). Studies in normal healthy adults consuming western diets, which are rich in linoleic acid (LA), show that supplemental ALA raises EPA and DPA status in the blood and in breast milk. However, ALA or EPA dietary supplements have little effect on blood or breast milk DHA levels, whereas consumption of preformed DHA is effective in raising blood DHA levels. Addition of ALA to the diets of formula-fed infants does raise DHA, but no level of ALA tested raises DHA to levels achievable with preformed DHA at intakes similar to typical human milk DHA supply. The DHA status of infants and adults consuming preformed DHA in their diets is, on average, greater than that of people who do not consume DHA. With no other changes in diet, improvement of blood DHA status can be achieved with dietary supplements of preformed DHA, but not with supplementation of ALA, EPA, or other precursors.     

Gene–gene and gene–environment interactions in ulcerative colitis

Genome-wide association studies (GWAS) have identified at least 133 ulcerative colitis (UC) associated loci. The role of genetic factors in clinical practice is not clearly defined. The relevance of genetic variants to disease pathogenesis is still uncertain because of not characterized gene–gene and gene–environment interactions. We examined the predictive value of combining the 133 UC risk loci with genetic interactions in an ongoing inflammatory bowel disease (IBD) GWAS. The Wellcome Trust Case–Control Consortium (WTCCC) IBD GWAS was used as a replication cohort. We applied logic regression (LR), a novel adaptive regression methodology, to search for high-order interactions. Exploratory genotype correlations with UC sub-phenotypes [extent of disease, need of surgery, age of onset, extra-intestinal manifestations and primary sclerosing cholangitis (PSC)] were conducted. The combination of 133 UC loci yielded good UC risk predictability [area under the curve (AUC) of 0.86]. A higher cumulative allele score predicted higher UC risk. Through LR, several lines of evidence for genetic interactions were identified and successfully replicated in the WTCCC cohort. The genetic interactions combined with the gene-smoking interaction significantly improved predictability in the model (AUC, from 0.86 to 0.89, P = 3.26E?05). Explained UC variance increased from 37 to 42 % after adding the interaction terms. A within case analysis found suggested genetic association with PSC. Our study demonstrates that the LR methodology allows the identification and replication of high-order genetic interactions in UC GWAS datasets. UC risk can be predicted by a 133 loci and improved by adding gene–gene and gene–environment interactions.     

A novel method for identifying nonlinear gene–environment interactions in case–control association studies

The genetic influences on complex disease traits generally depend on the joint effects of multiple genetic variants, environmental factors, as well as their interplays. Gene × environment (G × E) interactions play vital roles in determining an individual’s disease risk, but the underlying genetic machinery is poorly understood. Traditional analysis assuming linear relationship between genetic and environmental factors, along with their interactions, is commonly pursued under the regression-based framework to examine G × E interactions. This assumption, however, could be violated due to nonlinear responses of genetic variants to environmental stimuli. As an extension to our previous work on continuous traits, we proposed a flexible varying-coefficient model for the detection of nonlinear G × E interaction with binary disease traits. Varying coefficients were approximated by a non-parametric regression function through which one can assess the nonlinear response of genetic factors to environmental changes. A group of statistical tests were proposed to elucidate various mechanisms of G × E interaction. The utility of the proposed method was illustrated via simulation and real data analysis with application to type 2 diabetes.     

Gene–environment and gene–gene interactions of specific MTHFR,MTR and CBS gene variants in relation to homocysteine in black South Africans

The methylenetetrahydrofolate reductase (MTHFR), cystathione-β-synthase (CBS) and methionine synthase (MTR) genes interact with each other and the environment. These interactions could influence homocysteine (Hcy) and diseases contingent thereon. We determined single nucleotide polymorphisms (SNPs) within these genes, their relationships and interactions with total Hcy concentrations within black South Africans to address the increased prevalence of diseases associated with Hcy. The MTHFR 677 TT and MTR 2756 AA genotypes were associated with higher Hcy concentrations (16.6 and 10.1 μmol/L; p < 0.05) compared to subjects harboring the MTHFR 677 CT/CC and the MTR 2756 AG genotypes (10.5, 9.7 and 9.5 μmol/L, respectively). The investigated CBS genotypes did not influence Hcy. We demonstrated interactions between the area of residence and the CBS T833C/844ins68 genotypes (p = 0.005) so that when harboring the wildtype allele, rural subjects had significantly higher Hcy than their urban counterparts, but when hosting the variant allele the environment made no difference to Hcy. Between the CBS T833C/844ins68 or G9276A and MTHFR C677T genotypes, there were two-way interactions (p = 0.003 and = 0.004, respectively), with regard to Hcy. Subjects harboring the MTHFR 677 TT genotype in combination with the CBS 833 TT/homozygous 844 non-insert or the MTHFR 677 TT genotype in combination with the CBS 9276 GA/GG displayed higher Hcy concentrations.     

α-Linolenic acid-enriched butter attenuated high fat diet-induced insulin resistance and inflammation by promoting bioconversion of n-3 PUFA and subsequent oxylipin formation

α-Linolenic acid (ALA) is an essential fatty acid and the precursor for long-chain n-3 PUFA. However, biosynthesis of n-3 PUFA is limited in a Western diet likely due to an overabundance of n-6 PUFA. We hypothesized that dietary reduction of n-6/n-3 PUFA ratio is sufficient to promote the biosynthesis of long-chain n-3 PUFA, leading to an attenuation of high fat (HF) diet-induced obesity and inflammation. C57BL/6 J mice were fed a HF diet from ALA-enriched butter (n3Bu, n-6/n-3=1) in comparison with isocaloric HF diets from either conventional butter lacking both ALA and LA (Bu, n-6/n-3=6), or margarine containing a similar amount of ALA and abundant LA (Ma, n-6/n-3=6). Targeted lipidomic analyses revealed that n3Bu feeding promoted the bioconversion of long-chain n-3 PUFA and their oxygenated metabolites (oxylipins) derived from ALA and EPA. The n3Bu supplementation attenuated hepatic TG accumulation and adipose tissue inflammation, resulting in improved insulin sensitivity. Decreased inflammation by n3Bu feeding was attributed to the suppression of NF-κB activation and M1 macrophage polarization. Collectively, our work suggests that dietary reduction of the n-6/n-3 PUFA ratio, as well as total n-3 PUFA consumed, is a crucial determinant that facilitates n-3 PUFA biosynthesis and subsequent lipidomic modifications, thereby conferring metabolic benefits against obesity-induced inflammation and insulin resistance.     

Increasing long-chain n-3PUFA consumption improves small peripheral artery function in patients at intermediate–high cardiovascular risk

Dietary long-chain n-3 polyunsaturated fatty acids (LCn-3PUFA) improve endothelial function in medium–large-sized arteries, but effects on small peripheral arteries, responsible for most arterial resistance, are little known. We investigated the effects of increasing LCn-3PUFA intake with the usual diet on small artery reactive hyperemia index (saRHI). Within a clinical trial evaluating the effects of 1 year of intensive lifestyle intervention versus standard care on cardiovascular markers in subjects at risk, we selected 108 participants regardless of treatment allocation (n=47 standard care; n=61 intensive intervention) with complete baseline and follow-up information on dietary, clinical, saRHI and biochemical data, including biomarkers of inflammation and endothelial activation. At the end of follow-up, saRHI increased across tertiles of change in dietary LCn-3PUFA. Subjects in the top tertile (increased LCn-3PUFA intake) increased serum ApoA1 and decreased hs-CRP, serum TNF-α, sICAM-1, sVCAM-1 and oxLDL from baseline. After pooling data, in unadjusted models, changes in saRHI significantly correlated to changes in LCn-3PUFA intake and ApoA1 (directly) and changes in systolic blood pressure, waist circumference, TNF-α, sVCAM-1 and sE-selectin (inversely). In a multivariate model, changes in dietary LCn-3PUFA were significantly associated with changes in saRHI [B=0.08 (95% confidence interval=0.083–0.291) for an increase by 100 mg/day]. Systolic blood pressure was inversely associated with saRHI changes [B=−0.203 (−0.441 to −0.029) for a 9-mmHg increase]. We conclude that increased dietary consumption of LCn-3PUFA might be a cost-effective strategy to improve peripheral vasoactivity.     

A unified GMDR method for detecting gene–gene interactions in family and unrelated samples with application to nicotine dependence

Gene–gene and gene–environment interactions govern a substantial portion of the variation in complex traits and diseases. In convention, a set of either unrelated or family samples are used in detection of such interactions; even when both kinds of data are available, the unrelated and the family samples are analyzed separately, potentially leading to loss in statistical power. In this report, to detect gene–gene interactions we propose a generalized multifactor dimensionality reduction method that unifies analyses of nuclear families and unrelated subjects within the same statistical framework. We used principal components as genetic background controls against population stratification, and when sibling data are included, within-family control were used to correct for potential spurious association at the tested loci. Through comprehensive simulations, we demonstrate that the proposed method can remarkably increase power by pooling unrelated and offspring’s samples together as compared with individual analysis strategies and the Fisher’s combining p value method while it retains a controlled type I error rate in the presence of population structure. In application to a real dataset, we detected one significant tetragenic interaction among CHRNA4, CHRNB2, BDNF, and NTRK2 associated with nicotine dependence in the Study of Addiction: Genetics and Environment sample, suggesting the biological role of these genes in nicotine dependence development.     

Dye–tissue interactions: mechanisms,quantification and bonding parameters for dyes used in biological staining

Staining of tissues by dyes is accomplished through various types of bonds, some of which have been poorly defined in traditional biological literature. Here, basic principles of bonding are reviewed to establish uniform terminology and definitions consistent with the field of chemistry. The concept of charge – its presence or absence, magnitude, extent of delocalization and potential for being displaced by outside forces – underlies all bonding phenomena. These same attributes influence solubility and resistance to extraction during dehydration of tissue sections. Covalent bonds involve shared electrons; they are very strong and essentially irreversible under conditions encountered during staining. Polar covalent bonds within dye molecules generate partial atomic charges that create the potential for hydrogen bonding. This is measured by the hydrogen bonding parameter (h), the number of groups bearing charges within the ranges ?0.15 to ?0.50 eV or +0.15 to +0.30 eV. The potential for ionic bonding is indicated by net charge (Z), while the strength of such bonds is a function of charge site geometry on both bonding partners. Charge delocalization owing to conjugation, electron influencing groups, and resonance creates soft charge sites in which the ionic charge is spread over a large volume. Poorly delocalized charges or point charges are hard (small in volume). Firm bonds result from hard-hard or soft-soft pairs. Hard-soft combinations are weak, readily displaced in competitive interactions, and disrupted by solvents. Coordinate bonds with certain metals are involved with mordant staining and metal chelation dyes. Three different van der Waals attractions comprise the remainder of bonding types, all involving dipoles: Keesom (dipole-dipole) forces, Debye (dipole-induced dipole) forces and London (induced dipole-induced dipole) forces. Potentials for engaging in any of these is quantified by measures of polarity (dipole moment, d), polarizability (crudely with π atoms describing the size of the conjugated system, or more directly with α), hydrophobicity (with the octanol-water partition coefficient, log P or the more convenient Hydrophobic Index, HI), and the number of halogen atoms (X). By using molecular modeling software, quantitative measures of bonding potential (bonding parameters) have been determined for over 400 dyes.     

Leaf phenological shifts and plant–microbe–soil interactions can determine forest productivity and nutrient cycling under climate change in an ecosystem model

Climate change is expected to affect tree leaf phenology by extending the length of the growing season (LGS), which will affect the productivity and nutrient cycling of forests. Interactions between plants and microbes will mediate the ecosystem processes further through microbe-mediated plant–soil feedback (PSF). To investigate the possible consequences of interactions between the extension of the growing season (GS) and PSF under various conditions, we developed a simple theoretical model (LGS-PSF model). The LGS-PSF model predicts that microbe-mediated PSF will intensify the negative effects of increasing temperature on the size of soil carbon stock when compared with simulations without the PSF effect. The combined effects of increasing temperature and PSF on the size of soil carbon stock occurs through enhanced activity of individual microbes and increased microbial population size. More importantly, the model also demonstrated that a longer GS mitigates this negative effect on carbon accumulation in soil, not through increased net primary production, but through intensified competition for nutrients between plants and microbes, thus suppressing microbial population growth. Our model suggested that the interactive effects of the LGS and PSF on carbon and nitrogen dynamics in forests should be incorporated into larger scale quantitative models for better forecasting of future forest functions under climate change.     

The novel relationship between Sirt3 and autophagy in myocardial ischemia–reperfusion

Class III histone deacetylases (HDACs) belong to the proteasome family, comprising seven family members identified in mammalian cells, identified Sirt1–Sirt7. As an important member of HDACs, Sirt3 is hotly debated for its multiple functions. It was reported that Sirt3 got involved in the alleviation of multiple diseases, including myocardial infarction, neuron ischemia, hypertrophy, and diabetic myopathy. Through regulating many cellular mechanisms, such as apoptosis, autophagy, and clearance of reactive oxygen species (ROS), Sirt3 played an important role in the alleviation of myocardial ischemia–reperfusion injury. Nowadays Sirt3-induced autophagy was indicated to be involved in the process of the development of myocardial ischemia–reperfusion injury. Sirt3 could both activate and inhibit autophagy process by activating different downstream signal pathways, such as Sirt3–AMP-activated protein kinase pathway, Sirt3–Foxo3a pathway, and Sirt3–superoxide dismutase–mitochondrial ROS pathway. Whereas the Sirt3-induced autophagy in different phases of myocardial ischemia–reperfusion has not been systematically illustrated. In this review, we summarized the regulated mechanisms found in these years and listed the updated research about the relationship between Sirt3 and autophagy which are both positive and negative during myocardial ischemia–reperfusion phase. We anticipated that we may controlled the activation of autophagy by regulating the concentration of Sirt3 in myocyte. By maintaining a proper expression of autophagy in different phases of myocardial ischemia–reperfusion, we could reduce the morbidity of patients with myocardial infarction apparently in the future.     

Omega-3 PUFA profoundly affect neural,physiological, and behavioural competences – implications for systemic changes in trophic interactions

In recent decades, much conceptual thinking in trophic ecology has been guided by theories of nutrient limitation and the flow of elements, such as carbon and nitrogen, within and among ecosystems. More recently, ecologists have also turned their attention to examining the value of specific dietary nutrients, in particular polyunsaturated fatty acids (PUFA), among which the omega-3 PUFA, especially eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) play a central role as essential components of neuronal cell membranes in many organisms. This review focuses on a new neuro-ecological approach stemming from the biochemical (mechanistic) and physiological (functional) role of DHA in neuronal cell membranes, in particular in conjunction with G-protein coupled receptors (GPCRs). We link the co-evolution of these neurological functions to metabolic dependency on dietary omega-3 PUFA. We outline ways in which deficiencies in dietary DHA supply may affect, cognition, vision, and behaviour, and ultimately, the biological fitness of consumers. We then review emerging evidence that changes in access to dietary omega-3 PUFA may ultimately have profound impacts on trophic interactions leading to potential changes in community structure and ecosystem functioning that, in turn, may affect the supply of DHA within and across ecosystems, including the supply for human consumption.     

Iron–sulfur cluster scaffold (ISCU) gene is duplicated in salmonid fish and tissue and temperature dependent expressed in rainbow trout

The iron–sulfur cluster protein ISCU is a scaffold protein tasked with the building and mediation of iron–sulfur [Fe–S]-clusters. These are crucial for [Fe–S]-enzymes, which are involved in essential biological cell processes like metabolism or ion transport. Analysis of ISCU in rainbow trout (Oncorhynchus mykiss) and maraena whitefish (Coregonus maraena) revealed the existence of two gene variants in each of the two salmonids. This study presents the characterization of the duplicated ISCU cDNA sequences in both species as well as the comparative functional analysis of the genes in healthy and affected fish of two rainbow trout strains differing in trait robustness under regional aquaculture conditions. Coding sequences of trout ISCUA and ISCUB genes are spanning over five exons. Open reading frames (ORF) of trout (ISCUA: 495 bp, ISCUB: 498 bp) and whitefish (ISCUA and ISCUB: 495 bp) genes encode for evolutionary highly conserved proteins and share 72% sequence similarity with human ISCU.     

Renal excretion ofγ-carboxyglutamic acid and metabolic rate in 3–18 years old humans

Summary The modified amino acid y-carboxyglutamic acid (Gla) occurs in several proteins such as prothrombin, blood coagulation factors VII, IX and X, proteins C, S and Z as well as matrix Gla protein and osteocalcin. The amount of Gla excreted in urine is a common indicator of the whole-body degradation of these proteins. We have determined the renal excretion rates of Gla in 3, 6,10,14 and 18 years old male and female human subjects (n = 14 per age group and sex) and calculated the respective resting metabolic rates (RMR) on the basis of the body weights using published formulas. We found high correlations between the excretion rates of Gla (µmol/d/kg body weight) and the RMR (kJ/d/kg body weight) in the females (n = 70) of r = 0.70 (y = 0.003x + 0.29) and in the males (n = 70) of r = 0.70 (y = 0.0038x + 0.27) and in all subjects (n = 140) of r = 0.69 (y = 0.0035x + 0.27); p < 0.01. We postulate that in children and adolescents a causal relationship exists between the whole-body degradation rate of Gla containing proteins and the metabolic rate.