Predicted genetic burden and frequency of phenotype-associated variants in the horse.

Disease-causing variants have been identified for less than 20% of suspected equine genetic diseases. Whole genome sequencing (WGS) allows rapid identification of rare disease causal variants. However, interpreting the clinical variant consequence is confounded by the number of predicted deleterious variants that healthy individuals carry (predicted genetic burden). Estimation of the predicted genetic burden and baseline frequencies of known deleterious or phenotype associated variants within and across the major horse breeds have not been performed. We used WGS of 605 horses across 48 breeds to identify 32,818,945 variants, demonstrate a high predicted genetic burden (median 730 variants/horse, interquartile range: 613-829), show breed differences in predicted genetic burden across 12 target breeds, and estimate the high frequencies of some previously reported disease variants. This large-scale variant catalog for a major and highly athletic domestic animal species will enhance its ability to serve as a model for human phenotypes and improves our ability to discover the bases for important equine phenotypes.

Genetic Variation and the Distribution of Variant Types in the Horse.

Genetic variation is a key contributor to health and disease. Understanding the link between an individual's genotype and the corresponding phenotype is a major goal of medical genetics. Whole genome sequencing (WGS) within and across populations enables highly efficient variant discovery and elucidation of the molecular nature of virtually all genetic variation. Here, we report the largest catalog of genetic variation for the horse, a species of importance as a model for human athletic and performance related traits, using WGS of 534 horses. We show the extent of agreement between two commonly used variant callers. In data from ten target breeds that represent major breed clusters in the domestic horse, we demonstrate the distribution of variants, their allele frequencies across breeds, and identify variants that are unique to a single breed. We investigate variants with no homozygotes that may be potential embryonic lethal variants, as well as variants present in all individuals that likely represent regions of the genome with errors, poor annotation or where the reference genome carries a variant. Finally, we show regions of the genome that have higher or lower levels of genetic variation compared to the genome average. This catalog can be used for variant prioritization for important equine diseases and traits, and to provide key information about regions of the genome where the assembly and/or annotation need to be improved.

Closed-loop superluminal passive cavity.

We demonstrate the operation of a closed-loop fast-light cavity that allows rapid (~10 ms) measurements of the cavity mode frequency and its uncertainty. We vary the scale factor by temperature tuning the atomic density of an intracavity vapor cell. The cavity remains locked even as the system passes through the critical anomalous dispersion where a pole is observed in the scale factor. Positive and negative scale-factor enhancements as large as |S| ≈70 were obtained. To our knowledge, these are the first experiments that demonstrate a scale-factor enhancement in a closed-loop fast-light device by changing the optical path length, laying the groundwork for the improvement of cavity-based metrology instruments such as optical gyroscopes.

Glutamine and asparagine synthesis in the nematodes Heligmosomoides polygyrus and Panagrellus redivivus.

Low levels of glutamine synthetase were demonstrated in Panagrellus redivivus and Heligmosomoides polygyrus. Asparagine synthetase was detected in P. redivivus but activity was too low to be detected in H. polygyrus.

Role of carnitine palmitoyltransferase I in the regulation of hepatic ketogenesis during the onset and reversal of chronic diabetes.

1. The kinetic properties of overt carnitine palmitoyltransferase (CPT I, EC 2.3.1.21) were studied in rat liver mitochondria isolated from untreated, diabetic and insulin-treated diabetic animals. A comparison was made of the time courses required for the changes in these properties of CPT I to occur and for the development of ketosis during the induction of chronic diabetes and its reversal by insulin treatment. 2. The development of hyperketonaemia over the first 5 days of insulin withdrawal from streptozotocin-treated rats was accompanied by parallel increases in the activity of CPT I and in the I0.5 (concentration required to produce 50% inhibition) of the enzyme for malonyl-CoA. 3. The rapid reversal of the ketotic state by treatment of chronically diabetic rats with 6 units of regular insulin was not accompanied by any change in the properties of CPT I over the first 4 h. Higher doses of insulin (15 units), delivered throughout a 4 h period, resulted in an increase in the affinity of CPT I for malonyl-CoA, but the sensitivity of the enzyme to the inhibitor was still significantly lower than in mitochondria from normal animals. 4. Conversely, when insulin treatment was continued over a 24 h period, full restoration of the sensitivity of the enzyme to malonyl-CoA was achieved. However, the activity of the enzyme was only decreased marginally. 5. These results are discussed in terms of the possibility that the major regulatory sites of the rate of hepatic oxidation may vary in different phases of the induction and reversal of chronic diabetes.

Studies on the activation in vitro of carnitine palmitoyltransferase I in liver mitochondria from normal, diabetic and glucagon-treated rats.

The activation of overt carnitine palmitoyltransferase activity that occurs when rat liver mitochondria are incubated at near-physiological temperatures and ionic strengths was studied for mitochondria obtained from animals in different physiological states. In all instances, it was found to be due exclusively to an increase in the catalytic capacity of the enzyme and not to an increase in affinity of the enzyme for palmitoyl-CoA. The enzyme in mitochondria from fed animals always showed a larger degree of activation than that in mitochondria from starved animals. This was the case even for mitochondria (e.g. from fed diabetic animals) in which the kinetic characteristics of carnitine palmitoyltransferase were more similar to those for the enzyme in mitochondria from starved rats. Glucagon treatment of rats before isolation of the mitochondria did not affect the characteristics either of the kinetic parameters of overt carnitine palmitoyltransferase or of its activation in vitro.

Amino acid catabolism in the nematodes Heligmosomoides polygyrus and Panagrellus redivivus. 1. Removal of the amino group.

The major transaminase in Heligmosomoides polygyrus, Panagrellus redivivus and rat liver was the 2-oxoglutarate-glutamate system, with relatively few amino acids acting as donors for the pyruvate-alanine and oxaloacetate-aspartate systems. The relative effectiveness of the different amino acid donors in the three transaminase systems was similar in all three tissues. Both H. polygyrus and P. redivivus can oxidatively deaminate a range of L-amino acids, although D-amino acid oxidase activity was low. Serine and threonine dehydratase activity and histidase activity were present in H. polygyrus and P. redivivus and both nematodes were also able to deaminate glutamine, asparagine and arginine. When NAD(H) was the cofactor the glutamate dehydrogenases of H. polygyrus and P. redivivus showed similar regulatory properties to the mammalian enzyme. However, with NADP(H) the results were anomalous. The capacity of both nematodes to transaminate and oxidatively deaminate amino acids was broadly similar and comparable to mammalian tissue. Glutamate dehydrogenase is probably the major route for deamination in these nematodes. A complete sequence of urea cycle enzymes could not be demonstrated in either P. redivivus or H. polygyrus.

Amino acid catabolism in the nematodes Heligmosomoides polygyrus and Panagrellus redivivus. 2. Metabolism of the carbon skeleton.

All of the enzymes of proline catabolism were present in Heligmosomoides polygyrus and Panagrellus redivivus and the activities were, in general, similar to those found in rat liver. Both nematodes were also shown to be able to catabolize the branched-chain amino acids leucine, isoleucine and valine, by pathways similar to those found in mammalian liver. There were no significant differences in amino acid catabolism between the animal-parasitic and free-living species of nematode.

Restoration of the properties of carnitine palmitoyltransferase I in liver mitochondria during re-feeding of starved rats.

The recovery of the parameters of the kinetic properties of carnitine palmitoyltransferase (CPT) I in liver mitochondria of starved rats was studied after re-feeding animals for various periods of time. There were no significant changes either in the activity of the enzyme at high palmitoyl-CoA concentrations or in the affinity of the enzyme for palmitoyl-CoA, or in the sensitivity of CPT I to malonyl-CoA inhibition after 3 h or 6 h re-feeding. After 24 h re-feeding, both the affinity of the enzyme for palmitoyl-CoA and the activity of the enzyme were still not significantly different from those for the enzyme in mitochondria from 24 h-starved animals. By contrast, the sensitivity of CPT I to malonyl-CoA inhibition was largely, but not fully, restored to that observed in mitochondria from fed rats.

Binding of [14C]malonyl-CoA to rat liver mitochondria after blocking of the active site of carnitine palmitoyltransferase I. Displacement of low-affinity binding by palmitoyl-CoA.

The active site of the overt activity of carnitine palmitoyltransferase (CPT I) in rat liver mitochondria was blocked by the self-catalysed formation of the S-carboxypalmitoyl-CoA ester of (-)-carnitine, followed by washing of the mitochondria. CPT I activity in treated mitochondria was inhibited by 90-95%. Binding of [14C]malonyl-CoA to these mitochondria was not inhibited as compared with that of control mitochondria. When CPT I activity was inhibited, palmitoyl-CoA could markedly displace [14C]malonyl-CoA binding from the low-affinity site for the inhibitor [Zammit, Corstorphine & Gray (1984) Biochem. J. 222, 335-342], but not from the high-affinity site for malonyl-CoA binding. The saturation characteristics of the malonyl-CoA-binding component lost in the presence of palmitoyl-CoA were sigmoidal, and thus suggestive of co-operative binding at this site. It is suggested that the site hitherto considered to be a low-affinity malonyl-CoA-binding site may be effectively a second, allosteric, acyl-CoA-binding site on CPT I under conditions that prevail in vivo, whereas the high-affinity site for malonyl-CoA may be exclusive to the inhibitor. The possibility that the competitive-type interactions of malonyl-CoA and acyl-CoA on CPT I activity could arise from the effects of separate malonyl-CoA and acyl-CoA allosteric sites is considered. The possible significance of the large difference in the capacity of the two sites and their different saturation kinetics is also discussed.

Use of selected freshwater bivalves for monitoring organochlorine pesticide residues in major Mississippi stream systems, 1972-73.

Seven species of freshwater Pelecypoda, Amblema costata, Corbicula manilensis, Elliptio crassidens, lampsilis anadontoides, Lampsilis claibornensis, Megalonaias gigantea, and Plectomerus dombeyanus, were collected and monitored for pesticide content during 1972 and 1973. Thirteen collection sites, representing five major river basins in the state of Mississippi, were sampled and compared. During the 24-month study, 26 water samples and 58 claim samples from the five river basins were analyzed. Individual samples weighed from 8 g to 20 g and consisted of 1-30 clams, depending on size. Residues of toxaphene and methyl parathion were found only in 1973 water samples. The study shows that freshwater clams are effective monitors of pesticide content. The tendency of clams to concentrate pesticides and their corresponding ability to eliminate them varies with species. Significant reductions in DDT and a corresponding buildup of p,p'-TDE were noted in 1973, following the limitations on the use of DDT and large-scale flooding throughout the state.

Fate of labeled n-alkanes in the blue crab and stripped mullet.

Results of these studies demonstrate that the blue crab was readily able to take up and discharge labeled n-alkanes, but it was not able to metabolize them. In contrast, it appears that n-alkanes taken up via the digestive tract in mullet are readily metabolized, probably via microorganisms in the gut. More limited metabolism was observed in mullet when n-alkanes were taken up via the gills.