High-throughput tissue extraction protocol for NMR- and MS-based metabolomics

In metabolomics, tissues typically are extracted by grinding in liquid nitrogen followed by the stepwise addition of solvents. This is time-consuming and difficult to automate, and the multiple steps can introduce variability. Here we optimize tissue extraction methods compatible with high-throughput, reproducible nuclear magnetic resonance (NMR) spectroscopy- and mass spectrometry (MS)-based metabolomics. Previously, we concluded that methanol/chloroform/water extraction is preferable for metabolomics, and we further optimized this here using fish liver and an automated Precellys 24 bead-based homogenizer, allowing rapid extraction of multiple samples without carryover. We compared three solvent addition strategies: stepwise, two-step, and all solvents simultaneously. Then we evaluated strategies for improved partitioning of metabolites between solvent phases, including the addition of extra water and different partition times. Polar extracts were analyzed by NMR and principal components analysis, and the two-step approach was preferable based on lipid partitioning, reproducibility, yield, and throughput. Longer partitioning or extra water increased yield and decreased lipids in the polar phase but caused metabolic decay in these extracts. Overall, we conclude that the two-step method with extra water provides good quality data but that the two-step method with 10 min partitioning provides a more accurate snapshot of the metabolome. Finally, when validating the two-step strategy using NMR and MS metabolomics, we showed that technical variability was considerably smaller than biological variability.     

Enhanced post-ischemic liver injury in iNOS-deficient mice: a cautionary note.

The objective of this study was to assess the role of inducible nitric oxide synthase (iNOS) in ischemia- and reperfusion (I/R)-induced liver injury. We found that partial hepatic ischemia involving 70% of the liver resulted in a time-dependent increase in serum alanine aminotransferase (ALT) levels at 1-6 h following reperfusion. Liver injury at 1, 3, and 6 h post-ischemia was not due to the infiltration of neutrophils as assessed by tissue myeloperoxidase (MPO) activity and histopathology. iNOS-deficient mice subjected to the same duration of ischemia and reperfusion showed dramatic and significant increases in liver injury at 3 but not 6 h following reperfusion compared to their wild type controls. Paradoxically, iNOS mRNA expression was not detected in the livers of wild type mice at any point during the reperfusion period and pharmacological inhibition of iNOS using L-N(6)(iminoethyl)-lysine (L-NIL) did not exacerbate post-ischemic liver injury at any time post-reperfusion. These data suggest that iNOS deficiency produces unanticipated genetic alterations that renders these mice more sensitive to liver I/R-induced injury.     

Identification and function of disulfide bridges in the extracellular domains of the angiotensin II type 2 receptor.

The angiotensin II (AngII) receptor family is comprised of two subtypes, type 1 (AT(1)) and type 2 (AT(2)). Although sharing low homology (only 34%), mutagenesis has identified some key residues that are conserved between both subtypes, including four extracellular cysteines. Previous AT(1) mutagenesis demonstrated that the cysteines form two disulfide bonds, one linking the first and second extracellular loops and another connecting the amino terminus to the third extracellular loop. The importance of these AT(1) disulfides in ligand binding is supported by the effect of dithiothreitol (DTT). DTT breaks disulfide bonds, thereby strongly inhibiting ligand binding in AT(1) receptors. Despite retaining the same cysteines, AT(2) receptor ligand binding is paradoxically enhanced by DTT. Thus, we constructed a series of AT(2) cysteine mutations, either individually or paired, to establish the role of the cysteines and the source of DTT's effects. The AT(2) cysteine mutants surprisingly confirmed that the cysteines form disulfide bonds in the same manner as in the AT(1) subtype. However, breaking the AT(2) disulfide bridges yielded two responses. As in AT(1) receptors, mutations disrupting the disulfide bond between the first and second extracellular loops reduced AT(2) binding by 4-fold. In contrast, mutations breaking the disulfide bridge between the amino terminus and the third extracellular loop increased AT(2) binding, mimicking DTT's effect on this subtype. Further analysis of AT(1)/AT(2) chimeric exchange mutants of these domains suggested that the AT(2) amino terminus and third extracellular loop may possess latent binding epitopes that are only uncovered after DTT exposure.     

Inverse dispersal patterns in a group of ant parasitoids (Hymenoptera: Eucharitidae: Oraseminae) and their ant hosts

When postulating evolutionary hypotheses for diverse groups of taxa using molecular data, there is a tradeoff between sampling large numbers of taxa with a few Sanger-sequenced genes or sampling fewer taxa with hundreds to thousands of next-generation-sequenced genes. High taxon sampling enables the testing of evolutionary hypotheses that are sensitive to sampling bias (i.e. dating, biogeography and diversification analyses), whereas high character sampling improves resolution of critical nodes. In a group of ant parasitoids (Hymenoptera: Eucharitidae: Oraseminae), we analyse both of these types of datasets independently (203 taxa with five Sanger loci, 92 taxa with 348 anchored hybrid enrichment loci) and in combination (229 taxa, 353 loci) to explore divergence dating, biogeography, host relationships and differential rates of diversification. Oraseminae specialize as parasitoids of the immature stages of ants in the subfamily Myrmicinae (Hymenoptera: Formicidae), with ants in the genus Pheidole being their most common and presumed ancestral host. A general assumption is that the distribution of the parasite must be limited by any range contraction or expansion of its host. Recent studies support a single New World to Old World dispersal pattern for Pheidole at c. 11–27 Ma. Using multiple phylogenetic inference methods (parsimony, maximum likelihood, dated Bayesian and coalescent analyses), we provide a robust phylogeny showing that Oraseminae dispersed in the opposite direction, from Old World to New World, c. 24–33 Ma, which implies that they existed in the Old World before their presumed ancestral hosts. Their dispersal into the New World appears to have promoted an increased diversification rate. Both the host and parasitoid show single unidirectional dispersals in accordance with the presence of the Beringian Land Bridge during the Oligocene, a time when the changing northern climate probably limited the dispersal ability of such tropically adapted groups.     

Removal of blood group determinants from bovine erythrocyte membranes. 2. Degradation of ghosts by butanol and pyridine.

Ghosts produced from erythrocytes collected from six different cattle were degraded with butanol and pyridine. Of a total of 38 different antigenic determinants available for investigation among the six cows, F, V, J and L were the only specificities detected in the subfractions resulting from either method of degradation. After butanol degradation V, J and L antigens were found in the soluble protein fraction, while F was found in the insoluble protein. Pyridine digestion resulted in all four determinants being detected in the sialoprotein layer, while J was found in the lipoprotein as well. All antigens were relatively weak, being detected in inhibition strengths of 10.0 to 1.25 mg/ml.     

Sparse Distributed Representation of Odors in a Large-scale Olfactory Bulb Circuit

In the olfactory bulb, lateral inhibition mediated by granule cells has been suggested to modulate the timing of mitral cell firing, thereby shaping the representation of input odorants. Current experimental techniques, however, do not enable a clear study of how the mitral-granule cell network sculpts odor inputs to represent odor information spatially and temporally. To address this critical step in the neural basis of odor recognition, we built a biophysical network model of mitral and granule cells, corresponding to 1/100th of the real system in the rat, and used direct experimental imaging data of glomeruli activated by various odors. The model allows the systematic investigation and generation of testable hypotheses of the functional mechanisms underlying odor representation in the olfactory bulb circuit. Specifically, we demonstrate that lateral inhibition emerges within the olfactory bulb network through recurrent dendrodendritic synapses when constrained by a range of balanced excitatory and inhibitory conductances. We find that the spatio-temporal dynamics of lateral inhibition plays a critical role in building the glomerular-related cell clusters observed in experiments, through the modulation of synaptic weights during odor training. Lateral inhibition also mediates the development of sparse and synchronized spiking patterns of mitral cells related to odor inputs within the network, with the frequency of these synchronized spiking patterns also modulated by the sniff cycle.     

Linkage of bovine erythrocyte antigen loci B, C, L, S, Z, R' and T' and the serum protein loci post-transferrin 2 (PTF 2), vitamin D binding protein (GC) and albumin (ALB) to DNA microsatellite markers

Seven bovine erythrocyte antigen loci and three serum protein loci were tentatively assigned to chromosomes or synteny groups by linkage analysis to previously assigned microsatellite DNA markers. The erythrocyte antigen locus EAB was mapped to synteny group U27; EAC to chromosome 18, synteny group U9; EAL to chromosome 3, synteny group U6; EAS to chromosome 21, synteny group U4; EAZ to chromosome 10, synteny group U5; EAR' to chromosome 16, synteny group U1; and EAT' to chromosome 19, synteny group U21. The vitamin D binding protein (GC) and albumin (ALB) loci were assigned to chromosome 6, synteny group U15 and post-transferrin 2 (PTF 2) to chromosome 19, synteny group U21.