Genetical genomic determinants of alcohol consumption in rats and humans

Background

We have used a genetical genomic approach, in conjunction with phenotypic analysis of alcohol consumption, to identify candidate genes that predispose to varying levels of alcohol intake by HXB/BXH recombinant inbred rat strains. In addition, in two populations of humans, we assessed genetic polymorphisms associated with alcohol consumption using a custom genotyping array for 1,350 single nucleotide polymorphisms (SNPs). Our goal was to ascertain whether our approach, which relies on statistical and informatics techniques, and non-human animal models of alcohol drinking behavior, could inform interpretation of genetic association studies with human populations.

Results

In the HXB/BXH recombinant inbred (RI) rats, correlation analysis of brain gene expression levels with alcohol consumption in a two-bottle choice paradigm, and filtering based on behavioral and gene expression quantitative trait locus (QTL) analyses, generated a list of candidate genes. A literature-based, functional analysis of the interactions of the products of these candidate genes defined pathways linked to presynaptic GABA release, activation of dopamine neurons, and postsynaptic GABA receptor trafficking, in brain regions including the hypothalamus, ventral tegmentum and amygdala. The analysis also implicated energy metabolism and caloric intake control as potential influences on alcohol consumption by the recombinant inbred rats. In the human populations, polymorphisms in genes associated with GABA synthesis and GABA receptors, as well as genes related to dopaminergic transmission, were associated with alcohol consumption.

Conclusion

Our results emphasize the importance of the signaling pathways identified using the non-human animal models, rather than single gene products, in identifying factors responsible for complex traits such as alcohol consumption. The results suggest cross-species similarities in pathways that influence predisposition to consume alcohol by rats and humans. The importance of a well-defined phenotype is also illustrated. Our results also suggest that different genetic factors predispose alcohol dependence versus the phenotype of alcohol consumption.     

Infectious salmon anaemia virus (ISAV) isolated from the ISA disease outbreaks in Chile diverged from ISAV isolates from Norway around 1996 and was disseminated around 2005, based on surface glycoprotein gene sequences

Background

All viruses in the family Bunyaviridae possess a tripartite genome, consisting of a small, a medium, and a large RNA segment. Bunyaviruses therefore possess considerable evolutionary potential, attributable to both intramolecular changes and to genome segment reassortment. Hantaviruses (family Bunyaviridae, genus Hantavirus) are known to cause human hemorrhagic fever with renal syndrome or hantavirus pulmonary syndrome. The primary reservoir host of Sin Nombre virus is the deer mouse (Peromyscus maniculatus), which is widely distributed in North America. We investigated the prevalence of intramolecular changes and of genomic reassortment among Sin Nombre viruses detected in deer mice in three western states.

Methods

Portions of the Sin Nombre virus small (S) and medium (M) RNA segments were amplified by RT-PCR from kidney, lung, liver and spleen of seropositive peromyscine rodents, principally deer mice, collected in Colorado, New Mexico and Montana from 1995 to 2007. Both a 142 nucleotide (nt) amplicon of the M segment, encoding a portion of the G2 transmembrane glycoprotein, and a 751 nt amplicon of the S segment, encoding part of the nucleocapsid protein, were cloned and sequenced from 19 deer mice and from one brush mouse (P. boylii), S RNA but not M RNA from one deer mouse, and M RNA but not S RNA from another deer mouse.

Results

Two of 20 viruses were found to be reassortants. Within virus sequences from different rodents, the average rate of synonymous substitutions among all pair-wise comparisons (π_s) was 0.378 in the M segment and 0.312 in the S segment sequences. The replacement substitution rate (π_a) was 7.0 × 10^-4 in the M segment and 17.3 × 10^-4 in the S segment sequences. The low π_a relative to π_s suggests strong purifying selection and this was confirmed by a Fu and Li analysis. The absolute rate of molecular evolution of the M segment was 6.76 × 10^-3 substitutions/site/year. The absolute age of the M segment tree was estimated to be 37 years. In the S segment the rate of molecular evolution was 1.93 × 10^-3 substitutions/site/year and the absolute age of the tree was 106 years. Assuming that mice were infected with a single Sin Nombre virus genotype, phylogenetic analyses revealed that 10% (2/20) of viruses were reassortants, similar to the 14% (6/43) found in a previous report.

Conclusion

Age estimates from both segments suggest that Sin Nombre virus has evolved within the past 37–106 years. The rates of evolutionary changes reported here suggest that Sin Nombre virus M and S segment reassortment occurs frequently in nature.     

Human Triallelic Sites: Evidence for a New Mutational Mechanism?

Most SNPs in the human genome are biallelic; however, there are some sites that are triallelic. We show here that there are approximately twice as many triallelic sites as we would expect by chance. This excess does not appear to be caused by natural selection or mutational hotspots. Instead we propose that a new mutation can induce another mutation either within the same individual or subsequently during recombination. We provide evidence for this model by showing that the rarer two alleles at triallelic sites tend to cluster on phylogenetic trees of human haplotypes. However, we find no association between the density of triallelic sites and the rate of recombination, which leads us to suggest that triallelic sites might be generated by the simultaneous production of two new mutations within the same individual on the same genetic background. Under this model we estimate that simultaneous mutation contributes ∼3% of all distinct SNPs. We also show that there is a twofold excess of adjacent SNPs. Approximately half of these seem to be generated simultaneously since they have identical minor allele frequencies. We estimate that the mutation of adjacent nucleotides accounts for a little less than 1% of all SNPs.ALTHOUGH the density of biallelic SNPs in the human genome is reasonably low, there are some sites that have three (triallelic sites) or even four nucleotides segregating in the human population. We show here that there are approximately twice as many triallelic sites as we would expect by chance. There are at least three mutational mechanisms that could potentially generate such an excess of triallelic sites. First, some sites may be hypermutable, and if the mutation rate of at least two pathways (e.g., C → T and C → A) is elevated at such sites, then there will be an excess of triallelic sites. The mutation rate of a site is known to depend upon the adjacent nucleotides, the best known example being the CpG dinucleotide (Coulondre et al. 1978; Bird 1980) at which the frequency of both transition and transversion mutations is elevated. However, other adjacent nucleotides also influence the mutation rate (Blake et al. 1992; Zhao et al. 2003; Hwang and Green 2004). Furthermore, we have recently shown that there is variation in the mutation rate that does not depend upon the identity of the adjacent nucleotides or any specific context (Hodgkinson et al. 2009).Second, it is possible that two of the alleles at a triallelic site are generated simultaneously within a single individual. Point mutations are generally assumed to involve the production of a single new allele per mutation event at a rate that is governed by the effects mentioned above. However, it is not difficult to imagine mechanisms that might induce mutations on both strands of the DNA duplex; for example, the presence of a base mismatch may itself be unstable, so we might go from a G-C base pair to a G-A, which then may mutate to C-A; if DNA replication reads through this mismatch, the G allele will have mutated to both C and T. Alternatively, the mutation may occur across both strands of the duplex at the same time, possibly as a result of a chemical or radiation event. Third, in a similar manner, we might imagine a single SNP inducing subsequent mutations if base mismatches are formed during recombination in heteroduplex DNA.Here we attempt to identify the cause of the excess of triallelic sites by analyzing sequence data around triallelic sites.     

A comparison of univariate and multivariate gene selection techniques for classification of cancer datasets

Background  

Gene selection is an important step when building predictors of disease state based on gene expression data. Gene selection generally improves performance and identifies a relevant subset of genes. Many univariate and multivariate gene selection approaches have been proposed. Frequently the claim is made that genes are co-regulated (due to pathway dependencies) and that multivariate approaches are therefore per definition more desirable than univariate selection approaches. Based on the published performances of all these approaches a fair comparison of the available results can not be made. This mainly stems from two factors. First, the results are often biased, since the validation set is in one way or another involved in training the predictor, resulting in optimistically biased performance estimates. Second, the published results are often based on a small number of relatively simple datasets. Consequently no generally applicable conclusions can be drawn.     

Microarray analysis of peroxisome proliferator-activated receptor-gamma induced changes in gene expression in macrophages

We used a combination of expression microarray and Northern blot analyses to identify target genes for peroxisome proliferator-activated receptor (PPAR) gamma in RAW264.7 macrophages. PPARgamma natural ligand 15-deoxy-Delta(12,14) prostaglandin and synthetic ligands ciglitazone and rosiglitazone increased the expression of scavenger receptor CD36 and ATP-binding cassette transporter A1, as well as adipophilin (a lipid droplet coating protein involved in intracellular lipid storage and transport), calpain (a protease implicated in ABCA1 protein degradation), and ADAM8 (a disintegrin and metalloprotease protein involved in cell adhesion). These findings are relevant to understanding the effect of PPARgamma activation on gene expression and cognate pathways in macrophages.     

Water relations and growth of shrubs before and after fire in a semi-arid woodland

Summary Plant water relations and shoot growth rate of shrubs resprouting after fire or unburnt were measured in a semi-arid poplar box (Eucalyptus populnea) shrub woodland of eastern Australia. In vegetation unburnt for about 60 years, the dawn xylem water potential (_x) of the dominant shrub species was about-1.0 MPa when the soil was wet and-8.0 MPa when the soil was very dry. At any one time, the dominant shrub species,Eremophila mitchellii, E. sturtii, Geijera parviflora andCassia nemophila, were similar in _x butAcacia aneura andDodonaea viscosa were consistently higher in _x than this group when the soil was moist and lower when the soil was dry. The dominant tree species,Eucalyptus populnea andE. intertexta, appeared to have access to additional water beneath the hardpan which is located 60–80 cm below the surface. When shrubs were under extreme water stress (_x of-8 MPa), the trees had a _x of-3 to-3.6 MPa. Following a fire, both _x and leaf stomatal conductance (g _s) of resprouting shrubs were higher for about 5 years than comparable-aged unburnt vegetation, with relative differences in _x increasing with drought stress. Elongation rate of resprouts was positively linked to prefire shrub height in 3 of 4 species. However, shrubs resprouting after high intensity fires had substantially higher rates of shoot elongation than after low intensity fires which were in turn higher than for foliar expansion of unburnt shrubs. It is concluded that the growth rate of resprouting shrubs is primarily determined by physiological/ morphological factors associated with plant size but is also assisted by greater availability of water and possibly nutrients for a period after fire.     

Deposition of manganese in a drinking water distribution system.

The deposition of manganese in a water distribution system with manganese-related "dirty water" problems was studied over a 1-year period. Four monitoring laboratories with Robbins biofilm sampling devices fitted to the water mains were used to correlate the relationship among manganese deposition, the level of manganese in the water, and the chlorination conditions. Manganese deposition occurred by both chemical and microbial processes. Chemical deposition occurred when Mn(II) not removed during water treatment penetrated the filters and entered the distribution system, where it was oxidized by chlorine and chlorine dioxide used for disinfection. Microbial deposition occurred in areas with insufficient chlorination to control the growth of manganese-depositing biofilm. At 0.05 mg of Mn(II) per liter, the chemical deposition rate was much greater than microbial deposition. Significant deposition occurred at 0.03 mg of manganese per liter, and dirty water complaints were not eliminated until manganese levels were continuously less than 0.02 mg/liter and chlorination levels were greater than 0.2 mg/liter. A guideline level of 0.01 mg of manganese per liter is recommended.     

Segmental identity and cerebellar granule cell induction in rhombomere 1

Background  

Cerebellar granule cell precursors are specifically generated within the hindbrain segment, rhombomere 1, which is bounded rostrally by the midbrain/hindbrain isthmus and caudally by the boundary of the Hoxa2 expression domain. While graded signals from the isthmus have a demonstrable patterning role within this region, the significance of segmental identity for neuronal specification within rhombomere 1 is unexplored. We examined the response of granule cell precursors to the overexpression of Hoxa2, which normally determines patterns of development specific to the hindbrain. How much does the development of the cerebellum, a midbrain/hindbrain structure, reflect its neuromeric origin as a hindbrain segment?     

Effects of beta-adrenergic receptor stimulation and blockade on substrate metabolism during submaximal exercise

We used beta-adrenergic receptor stimulation and blockade as a tool to study substrate metabolism during exercise. Eight moderately trained subjects cycled for 60 min at 45% of VO(2 peak) 1) during a control trial (CON); 2) while epinephrine was intravenously infused at 0.015 microg. kg(-1) x min(-1) (beta-STIM); 3) after ingesting 80 mg of propranolol (beta-BLOCK); and 4) combining beta-BLOCK with intravenous infusion of Intralipid-heparin to restore plasma fatty acid (FFA) levels (beta-BLOCK+LIPID). beta-BLOCK suppressed lipolysis (i.e., glycerol rate of appearance) and fat oxidation while elevating carbohydrate oxidation above CON (135 +/- 11 vs. 113 +/- 10 micromol x kg(-1) x min(-1); P < 0.05) primarily by increasing rate of disappearance (R(d)) of glucose (36 +/- 2 vs. 22 +/- 2 micromol x kg(-1) x min(-1); P < 0.05). Plasma FFA restoration (beta-BLOCK+LIPID) attenuated the increase in R(d) glucose by more than one-half (28 +/- 3 micromol x kg(-1) x min(-1); P < 0.05), suggesting that part of the compensatory increase in muscle glucose uptake is due to reduced energy from fatty acids. On the other hand, beta-STIM markedly increased glycogen oxidation and reduced glucose clearance and fat oxidation despite elevating plasma FFA. Therefore, reduced plasma FFA availability with beta-BLOCK increased R(d) glucose, whereas beta-STIM increased glycogen oxidation, which reduced fat oxidation and glucose clearance. In summary, compared with control exercise at 45% VO(2 peak) (CON), both beta-BLOCK and beta-STIM reduced fat and increased carbohydrate oxidation, albeit through different mechanisms.