The influence of season and levels of dietary lipid on growth performance and lipid composition in rainbow trout <Emphasis Type="Italic">Parasalmo mykiss</Emphasis> (Walbaum, 1792)

We studied the growth performance and lipid composition of liver, muscles and visceral fat in rainbow trout Parasalmo mykiss (Walbaum, 1792) and the diets used in its cultivation during the spring-summer season. The differences in dietary lipid composition determined modifications in the biochemical composition of tissues of rainbow trout and had an effect on the weight and growth rate of the fish. Trophic and seasonal factors also had their influence on the studied parameters. The degree of influence depended on the functional characteristics of tissues and organs of rainbow trout.     

A computer investigation of intramolecular bond ordering: unsaturated chains of natural lipids

Computer simulations (by the Monte Carlo method) of unperturbed linear hydrocarbon chains of 18-22 carbon atoms with methylene-interrupted cis-double bonds (18:0, 20:0, 22:0, 18:1delta11cis, 18:2delta9, 12cis, 18:3delta9, 12, 15cis, 20:3delta5, 8, 11cis, 20:4delta5, 8, 11, 14cis, 20:5delta5, 8, 11, 14, 17cis, 22:6delta4, 7, 10, 13, 16, 19cis), typical components of natural lipids, at a temperature of 298 K have been carried out. The conformations generated with continuous variation of all single C-C bond rotation angles within the (0, 360 degrees) range have been considered. The energy of nonbonded interactions and torsion and electrostatic terms have been taken into account. The intramolecular bond order parameters S(CC) and S(CH) about the axes along inertia tensor eigenvectors and bond orientation distributions rho(theta) with respect to the maximum molecule span axis (theta is the angle between the bond and the axis) have been calculated. The relation of the bond orientation distributions rho(theta) to the order parameters S are analyzed in terms of angles thetamax (a "geometric" factor, rho(thetamax) = max) and widths deltatheta of the distributions (factor of "fluctuations"). The results indicate that fluctuation factors depend on both the segment chemical structure and location in the chain; fluctuations increase from the centre of the chain towards the terminals, all things being equal. The two deltatheta values of C-H bonds flanking the cis-double bond are smaller than that obtained for adjacent CH2 groups by a factor of 1.5-2. Defining these properties is a necessary step to gaining a more complete understanding of polyunsaturated lipid hydrocarbon chains significance. The mean molecule magnitudes of ?S(CH)? decrease when unsaturation increases. The cis-double bond parameters S(CC) are found to be higher than those of adjacent single C-C bonds: the parameter S(CC) odd-even effect in the polyunsaturated molecules of such structure changes the "sign" between double bonds. The order parameter profiles -S(CH) of cis-18:1 and cis-18:2 obtained from the simulations (at the portion which corresponds to the double bonds location) are in qualitative agreement with experimental data on bilayers in the liquid-crystal phase. This has made possible the quantitative prognosis of the ordering properties of experimentally uninvestigated unsaturated lipids.     

The Genome-wide Patterns of Variation Expose Significant Substructure in a Founder Population

Although high-density SNP genotyping platforms generate a momentum for detailed genome-wide association (GWA) studies, an offshoot is a new insight into population genetics. Here, we present an example in one of the best-known founder populations by scrutinizing ten distinct Finnish early- and late-settlement subpopulations. By determining genetic distances, homozygosity, and patterns of linkage disequilibrium, we demonstrate that population substructure, and even individual ancestry, is detectable at a very high resolution and supports the concept of multiple historical bottlenecks resulting from consecutive founder effects. Given that genetic studies are currently aiming at identifying smaller and smaller genetic effects, recognizing and controlling for population substructure even at this fine level becomes imperative to avoid confounding and spurious associations. This study provides an example of the power of GWA data sets to demonstrate stratification caused by population history even within a seemingly homogeneous population, like the Finns. Further, the results provide interesting lessons concerning the impact of population history on the genome landscape of humans, as well as approaches to identify rare variants enriched in these subpopulations.     

Biomarker Profiling by Nuclear Magnetic Resonance Spectroscopy for the Prediction of All-Cause Mortality: An Observational Study of 17,345 Persons

Background

Early identification of ambulatory persons at high short-term risk of death could benefit targeted prevention. To identify biomarkers for all-cause mortality and enhance risk prediction, we conducted high-throughput profiling of blood specimens in two large population-based cohorts.

Methods and Findings

106 candidate biomarkers were quantified by nuclear magnetic resonance spectroscopy of non-fasting plasma samples from a random subset of the Estonian Biobank (n = 9,842; age range 18–103 y; 508 deaths during a median of 5.4 y of follow-up). Biomarkers for all-cause mortality were examined using stepwise proportional hazards models. Significant biomarkers were validated and incremental predictive utility assessed in a population-based cohort from Finland (n = 7,503; 176 deaths during 5 y of follow-up). Four circulating biomarkers predicted the risk of all-cause mortality among participants from the Estonian Biobank after adjusting for conventional risk factors: alpha-1-acid glycoprotein (hazard ratio [HR] 1.67 per 1–standard deviation increment, 95% CI 1.53–1.82, p = 5×10⁻³¹), albumin (HR 0.70, 95% CI 0.65–0.76, p = 2×10⁻¹⁸), very-low-density lipoprotein particle size (HR 0.69, 95% CI 0.62–0.77, p = 3×10⁻¹²), and citrate (HR 1.33, 95% CI 1.21–1.45, p = 5×10⁻¹⁰). All four biomarkers were predictive of cardiovascular mortality, as well as death from cancer and other nonvascular diseases. One in five participants in the Estonian Biobank cohort with a biomarker summary score within the highest percentile died during the first year of follow-up, indicating prominent systemic reflections of frailty. The biomarker associations all replicated in the Finnish validation cohort. Including the four biomarkers in a risk prediction score improved risk assessment for 5-y mortality (increase in C-statistics 0.031, p = 0.01; continuous reclassification improvement 26.3%, p = 0.001).

Conclusions

Biomarker associations with cardiovascular, nonvascular, and cancer mortality suggest novel systemic connectivities across seemingly disparate morbidities. The biomarker profiling improved prediction of the short-term risk of death from all causes above established risk factors. Further investigations are needed to clarify the biological mechanisms and the utility of these biomarkers for guiding screening and prevention. Please see later in the article for the Editors'' Summary     

Adipose tissue gene expression analysis reveals changes in inflammatory, mitochondrial respiratory and lipid metabolic pathways in obese insulin-resistant subjects

Background

To elucidate gene expression associated with copy number changes, we performed a genome-wide copy number and expression microarray analysis of 25 pairs of gastric tissues.

Methods

We applied laser capture microdissection (LCM) to obtain samples for microarray experiments and profiled DNA copy number and gene expression using 244K CGH Microarray and Human Exon 1.0 ST Microarray.

Results

Obviously, gain at 8q was detected at the highest frequency (70%) and 20q at the second (63%). We also identified molecular genetic divergences for different TNM-stages or histological subtypes of gastric cancers. Interestingly, the C20orf11 amplification and gain at 20q13.33 almost separated moderately differentiated (MD) gastric cancers from poorly differentiated (PD) type. A set of 163 genes showing the correlations between gene copy number and expression was selected and the identified genes were able to discriminate matched adjacent noncancerous samples from gastric cancer samples in an unsupervised two-way hierarchical clustering. Quantitative RT-PCR analysis for 4 genes (C20orf11, XPO5, PUF60, and PLOD3) of the 163 genes validated the microarray results. Notably, some candidate genes (MCM4 and YWHAZ) and its adjacent genes such as PRKDC, UBE2V2, ANKRD46, ZNF706, and GRHL2, were concordantly deregulated by genomic aberrations.

Conclusions

Taken together, our results reveal diverse chromosomal region alterations for different TNM-stages or histological subtypes of gastric cancers, which is helpful in researching clinicopathological classification, and highlight several interesting genes as potential biomarkers for gastric cancer.     

Further evidence for the role of ENPP1 in obesity: association with morbid obesity in Finns

The aim of this study was to investigate a series of single-nucleotide polymorphisms (SNPs) in the genes MC2R, MC3R, MC4R, MC5R, POMC, and ENPP1 for association with obesity. Twenty-five SNPs (2-7 SNPs/gene) were genotyped in 246 Finns with extreme obesity (BMI > or = 40 kg/m2) and in 481 lean subjects (BMI 20-25 kg/m2). Of the obese subjects, 23% had concomitant type 2 diabetes. SNPs and SNP haplotypes were tested for association with obesity and type 2 diabetes. Allele frequencies differed between obese and lean subjects for two SNPs in the ENPP1 gene, rs1800949 (P = 0.006) and rs943003 (P = 0.0009). These SNPs are part of a haplotype (rs1800949 C-rs943003 A), which was observed more frequently in lean subjects compared to obese subjects (P = 0.0007). Weaker associations were detected between the SNPs rs1541276 in the MC5R, rs1926065 in the MC3R genes and obesity (P = 0.04 and P = 0.03, respectively), and between SNPs rs2236700 in the MC5R, rs2118404 in the POMC, rs943003 in the ENPP1 genes and type 2 diabetes (P = 0.03, P = 0.02 and P = 0.02, respectively); these associations did not, however, remain significant after correction for multiple testing. In conclusion, a previously unexplored ENPP1 haplotype composed of SNPs rs1800949 and rs943003 showed suggestive evidence for association with adult-onset morbid obesity in Finns. In this study, we did not find association between the frequently studied ENPP1 K121Q variant, nor SNPs in the MCR or POMC genes and obesity or type 2 diabetes.     

Lipid status of fingerlings of the Atlantic salmon <Emphasis Type="Italic">Salmo salar</Emphasis> from different microbiotopes of the Varzuga River

Mechanisms of formation of phenotypic groups of fingerlings of the Atlantic salmon are investigated, related to diversity of embryos and subsequent start possibilities of dispersion of larvae to microbiotopes differing in their life conditions. The fingerlings of salmon, which after hatching and dissolution of the yolk sac moved from the mainstream of the Varzuga River to mouths of its tributaries, had an increased level of triacylglycerols and a higher growth rate than the juveniles remaining in the coastal zone of the river. The revealed differences between the compared groups of fingerlings by the spectrum of stock and structural lipids are mainly connected with distinctions of feeding of juveniles of the same age. The found stable differences by lipid spectra in fingerlings of salmon from the investigated biotopes of the Varzuga in July, August, and October are considered as biochemical prerequisites of the origin of different phenotypic groups of juveniles. Subdivision of fingerlings into phenotypic groups may further on influence the oncoming of the smoltification time of juveniles at the age 2+, 3+, and 4+. Accordingly, this is reflected in formation of the complex age structure (by the number of years spent in the river and in the sea) of the Varzuga population of Atlantic salmon.     

A Genome-Wide Association Study of a Biomarker of Nicotine Metabolism

Individuals with fast nicotine metabolism typically smoke more and thus have a greater risk for smoking-induced diseases. Further, the efficacy of smoking cessation pharmacotherapy is dependent on the rate of nicotine metabolism. Our objective was to use nicotine metabolite ratio (NMR), an established biomarker of nicotine metabolism rate, in a genome-wide association study (GWAS) to identify novel genetic variants influencing nicotine metabolism. A heritability estimate of 0.81 (95% CI 0.70–0.88) was obtained for NMR using monozygotic and dizygotic twins of the FinnTwin cohort. We performed a GWAS in cotinine-verified current smokers of three Finnish cohorts (FinnTwin, Young Finns Study, FINRISK2007), followed by a meta-analysis of 1518 subjects, and annotated the genome-wide significant SNPs with methylation quantitative loci (meQTL) analyses. We detected association on 19q13 with 719 SNPs exceeding genome-wide significance within a 4.2 Mb region. The strongest evidence for association emerged for CYP2A6 (min p = 5.77E-86, in intron 4), the main metabolic enzyme for nicotine. Other interesting genes with genome-wide significant signals included CYP2B6, CYP2A7, EGLN2, and NUMBL. Conditional analyses revealed three independent signals on 19q13, all located within or in the immediate vicinity of CYP2A6. A genetic risk score constructed using the independent signals showed association with smoking quantity (p = 0.0019) in two independent Finnish samples. Our meQTL results showed that methylation values of 16 CpG sites within the region are affected by genotypes of the genome-wide significant SNPs, and according to causal inference test, for some of the SNPs the effect on NMR is mediated through methylation. To our knowledge, this is the first GWAS on NMR. Our results enclose three independent novel signals on 19q13.2. The detected CYP2A6 variants explain a strikingly large fraction of variance (up to 31%) in NMR in these study samples. Further, we provide evidence for plausible epigenetic mechanisms influencing NMR.     

Lipid composition in muscle and liver of sympatric coregonid fishes from Lake Baikal (<Emphasis Type="Italic">Coregonus</Emphasis> spp.) under common garden experiment

The content of total lipids, total phospholipids, and fatty acids of total lipids in muscles and liver of juvenile Lake Baikal sympatric coregonid fishes have been analyzed for the first time under a common garden experiment. Baikal omul, Coregonus migratorius Georgi, is an active migrant of the pelagic zones of the lake. Baikal (lacustrine) whitefish, C. baicalensis Dybowski, is a colonizer of the bottom habitats, which are relevant to the pelagic zones of the littoral and underwater slope. Structural lipids (phospholipids and cholesterol) dominated in total lipids of the tissues of all fish under study. Spare lipids significantly prevailed in omul muscles when compared to whitefish. The highest variability of fatty acid composition was reported in muscles of coregonid fishes. Statistically significant differences were revealed in the content of the ω3 polyunsaturated fatty acids in muscles of lacustrine whitefish and omul. Associations of lipid compositions revealed in tissues of the whitefishes under the study with their respective ecotypes have been discussed.     

Forty-Three Loci Associated with Plasma Lipoprotein Size,Concentration, and Cholesterol Content in Genome-Wide Analysis

While conventional LDL-C, HDL-C, and triglyceride measurements reflect aggregate properties of plasma lipoprotein fractions, NMR-based measurements more accurately reflect lipoprotein particle concentrations according to class (LDL, HDL, and VLDL) and particle size (small, medium, and large). The concentrations of these lipoprotein sub-fractions may be related to risk of cardiovascular disease and related metabolic disorders. We performed a genome-wide association study of 17 lipoprotein measures determined by NMR together with LDL-C, HDL-C, triglycerides, ApoA1, and ApoB in 17,296 women from the Women''s Genome Health Study (WGHS). Among 36 loci with genome-wide significance (P<5×10⁻⁸) in primary and secondary analysis, ten (PCCB/STAG1 (3q22.3), GMPR/MYLIP (6p22.3), BTNL2 (6p21.32), KLF14 (7q32.2), 8p23.1, JMJD1C (10q21.3), SBF2 (11p15.4), 12q23.2, CCDC92/DNAH10/ZNF664 (12q24.31.B), and WIPI1 (17q24.2)) have not been reported in prior genome-wide association studies for plasma lipid concentration. Associations with mean lipoprotein particle size but not cholesterol content were found for LDL at four loci (7q11.23, LPL (8p21.3), 12q24.31.B, and LIPG (18q21.1)) and for HDL at one locus (GCKR (2p23.3)). In addition, genetic determinants of total IDL and total VLDL concentration were found at many loci, most strongly at LIPC (15q22.1) and APOC-APOE complex (19q13.32), respectively. Associations at seven more loci previously known for effects on conventional plasma lipid measures reveal additional genetic influences on lipoprotein profiles and bring the total number of loci to 43. Thus, genome-wide associations identified novel loci involved with lipoprotein metabolism—including loci that affect the NMR-based measures of concentration or size of LDL, HDL, and VLDL particles—all characteristics of lipoprotein profiles that may impact disease risk but are not available by conventional assay.