Genome-wide association studies and systems biology: together at last

Following the widespread use of genome-wide association studies to elucidate the genetic architectures of complex phenotypes, there has been a push to augment existing observational studies with additional layers of molecular information. The resulting high-dimensional data have led the emergence of research in integrative systems biology. Here, we examine recent progress in characterizing biological networks as well as the corresponding conceptual and analytical challenges. Using examples from metabolomics, we contend that integrative systems biology should prompt a re-examination of conventional phenotypic measures where heterogeneous or correlated phenotypes can be fine-mapped. Although still in its infancy, it is apparent that the large-scale characterization of molecular systems will transform our understanding of phenotype, biology and pathogenesis.     

Aging-associated increase in indoleamine 2,3-dioxygenase (IDO) activity appears to be unrelated to the transcription of the IDO1 or IDO2 genes in peripheral blood mononuclear cells

Background

Old age is associated with increased levels of circulating pro-inflammatory cytokines, a phenomenon termed inflamm-aging. Elevated levels of pro-inflammatory cytokines have been associated with several age-associated diseases and with a shortened lifespan. Indoleamine 2,3-dioxygenase (IDO) has immunomodulatory properties and its activity is elevated in inflammation, autoimmune disorders and malignancies. We have previously shown that IDO activity is increased in nonagenarians compared to young individuals and that high IDO activity is associated with mortality at old age.

Findings

In this study our aim was to assess whether this difference in IDO activity in the plasma was due to the differential expression of either the IDO1 or IDO2 gene in peripheral blood mononuclear cells. Our results show that IDO1 and IDO2 are not differently expressed in nonagenarians compared to controls and that the expression of IDO genes is not associated with the level of IDO activity in the plasma.

Conclusion

The level of IDO activity in the plasma is not regulated through the expression of IDO1 or IDO2 in the peripheral blood mononuclear cells.     

Influence of electron acceptor availability and microbial community structure on sedimentary methane oxidation in a boreal estuary

Methane is produced microbially in vast quantities in sediments throughout the world’s oceans. However, anaerobic oxidation of methane (AOM) provides a near-quantitative sink for the produced methane and is primarily responsible for preventing methane emissions from the oceans to the atmosphere. AOM is a complex microbial process that involves several different microbial groups and metabolic pathways. The role of different electron acceptors in AOM has been studied for decades, yet large uncertainties remain, especially in terms of understanding the processes in natural settings. This study reports whole-core incubation methane oxidation rates along an estuarine gradient ranging from near fresh water to brackish conditions, and investigates the potential role of different electron acceptors in AOM. Microbial community structure involved in different methane processes is also studied in the same estuarine system using high throughput sequencing tools. Methane oxidation in the sediments was active in three distinct depth layers throughout the studied transect, with total oxidation rates increasing seawards. We find extensive evidence of non-sulphate AOM throughout the transect. The highest absolute AOM rates were observed below the sulphate-methane transition zone (SMTZ), strongly implicating the role of alternative electron acceptors (most likely iron and manganese oxides). However, oxidation rates were ultimately limited by methane availability. ANME-2a/b were the most abundant microbial phyla associated with AOM throughout the study sites, followed by ANME-2d in much lower abundances. Similarly to oxidation rates, highest abundances of microbial groups commonly associated with AOM were found well below the SMTZ, further reinforcing the importance of non-sulphate AOM in this system.

     

Genetic Variation in SULF2 Is Associated with Postprandial Clearance of Triglyceride-Rich Remnant Particles and Triglyceride Levels in Healthy Subjects

Context

Nonfasting (postprandial) triglyceride concentrations have emerged as a clinically significant cardiovascular disease risk factor that results from accumulation of remnant triglyceride-rich lipoproteins (TRLs) in the circulation. The remnant TRLs are cleared from the circulation by hepatic uptake, but the specific mechanisms involved are unclear. The syndecan-1 heparan sulfate proteoglycan (HSPG) pathway is important for the hepatic clearance of remnant TRLs in mice, but its relevance in humans is unclear.

Objective

We sought to determine whether polymorphisms of the genes responsible for HSPG assembly and disassembly contribute to atherogenic dyslipoproteinemias in humans.

Patients And Design

We performed an oral fat load in 68 healthy subjects. Lipoproteins (chylomicrons and very low density lipoproteins 1 and 2) were isolated from blood, and the area under curve and incremental area under curve for postprandial variables were calculated. Single nucleotide polymorphisms in genes encoding syndecan-1 and enzymes involved in the synthesis or degradation of HSPG were genotyped in the study subjects.

Results

Our results indicate that the genetic variation rs2281279 in SULF2 associates with postprandial clearance of remnant TRLs and triglyceride levels in healthy subjects. Furthermore, the SNP rs2281279 in SULF2 associates with hepatic SULF2 mRNA levels.

Conclusions

In humans, mild but clinically relevant postprandial hyperlipidemia due to reduced hepatic clearance of remnant TRLs may result from genetic polymorphisms that affect hepatic HSPG.     

Suppressing Multi-Channel Ultra-Low-Field MRI Measurement Noise Using Data Consistency and Image Sparsity

Ultra-low-field (ULF) MRI (B ₀ = 10–100 µT) typically suffers from a low signal-to-noise ratio (SNR). While SNR can be improved by pre-polarization and signal detection using highly sensitive superconducting quantum interference device (SQUID) sensors, we propose to use the inter-dependency of the k-space data from highly parallel detection with up to tens of sensors readily available in the ULF MRI in order to suppress the noise. Furthermore, the prior information that an image can be sparsely represented can be integrated with this data consistency constraint to further improve the SNR. Simulations and experimental data using 47 SQUID sensors demonstrate the effectiveness of this data consistency constraint and sparsity prior in ULF-MRI reconstruction.     

The CD34 surface antigen is restricted to glucagon-expressing cells in the early developing bovine pancreas

Controversy remains regarding the origin of the pancreatic endocrine cells. It is generally accepted that the majority of insulin-secreting cells derive from the endodermal epithelium of the gastrointestinal tract. The aim of this study was to determine the contribution made by a particular cluster of differentiation (CD)-positive cells to the development of the bovine endocrine pancreas. In bovine embryos and foetuses with crown to rump lengths (CRL) ranging from 1 to 47 cm, cells staining positively for CD34 and/or CD133 were always more numerous in the left lobe and body of pancreas than in the right lobe. In the early stages of pancreatic development (CRL <5 cm), CD34 and/or CD133-reactive cells were concentrated within the epithelial cell cords that form the primitive pancreas. In later developmental stages (CRL >5 cm), individual or groups of CD34 and/or CD133-reactive cells were present in newly formed acini, which bulged out from the duct system that had arisen from the cords. Some of the positively stained cells accumulated in focal areas associated with hyperplastic intra-acinar cells. These “acino-insula-like complexes” appeared to enlarge with age and develop into intralobular Islets of Langerhans. Most of the described CD34 and/or CD133-reactive cells displayed co-localisation with glucagon. A negligible number of these cells showed co-localisation with insulin. Glucagon-stained cells were distinct from insulin-stained cells and were more abundant in embryonic and early foetal pancreata. Our data demonstrate that CD34 and/or CD133-reactive cells contribute to the pancreatic alpha cell population during early foetal development in cattle.     

Sex difference in the regulation of plasma high density lipoprotein cholesterol by genetic and environmental factors

Association between high density lipoprotein (HDL) cholesterol concentration and restriction fragment length polymorphisms at the cholesteryl ester transfer protein (CETP) gene locus was studied in a random population-based cohort of 526 Caucasian subjects (259 men, mean age 50.9 years, and 267 women, mean age 51.8 years). HDL cholesterol concentration was adjusted for age, body mass index, alcohol consumption, smoking and plasma triglyceride and low density lipoprotein cholesterol levels. In females, the HDL cholesterol levels were associated withTagIB polymorphism (1.46 mmol/1 in the B1B1 genotype, 1.56 mmol/l in B 1B2 and 1.72 mmol/1 in B2B2,P = 0.0001 for the trend). In contrast, this was not observed in men (1.24, 1.20, 1.27 mmol/l, NS). The association was seen even in women who were current smokers (1.41, 1.56, 1.75 mmol/l,n = 72,P = 0.007), but not in male smokers (1.26, 1.19, 1.14 mmol/l,n = 102, NS). In male non-smokers the association was weak (1.22, 1.20, 1.32 mmol/l,n = 157,P = 0.05). In postmenopausal women not receiving hormone replacement therapy (n = 108), the association continued to be present, although weaker (1.50, 1.58, 1.70 mmol/l,P = 0.06). CETP activity (n = 101) tended to be lower in subjects with the 132132 genotype. In conclusion, a clear-cut sex difference was observed in the genotype effect on plasma HDL cholesterol levels. The slight attenuation of the gene dosage effect after menopause suggests that the gender difference may be, at least in part, due to sex hormones. A genetic subgroup (men with the 132132 genotype) particularly susceptible to the HDL cholesterol decreasing effect of smoking could be demonstrated.Part of this work was presented at the 67th Scientific Sessions of the American Heart Association, Dallas, Texas, USA, 14–17 November, 1994