Genome sequence, comparative analysis, and population genetics of the domestic horse

We report a high-quality draft sequence of the genome of the horse (Equus caballus). The genome is relatively repetitive but has little segmental duplication. Chromosomes appear to have undergone few historical rearrangements: 53% of equine chromosomes show conserved synteny to a single human chromosome. Equine chromosome 11 is shown to have an evolutionary new centromere devoid of centromeric satellite DNA, suggesting that centromeric function may arise before satellite repeat accumulation. Linkage disequilibrium, showing the influences of early domestication of large herds of female horses, is intermediate in length between dog and human, and there is long-range haplotype sharing among breeds.

Comparison of acoustic and kinematic approaches to measuring utterance-level speech variability

PURPOSE

The spatiotemporal index (STI) is one measure of variability. As currently implemented, kinematic data are used, requiring equipment that cannot be used with some patient groups or in scanners. An experiment is reported that addressed whether STI can be extended to an audio measure of sound pressure of the speech envelope over time that did not need specialized equipment.

METHOD

STI indices of variability were obtained from lip track (L-STI) and amplitude envelope (E-STI) signals. These measures were made concurrent while either fluent speakers or speakers who stutter repeated "Buy Bobby a puppy" 20 times.

RESULTS

L-STI and E-STI correlated significantly. STI decreased with age for both L-STI and E-STI. E-STI scores and L-STI scores discriminated successfully between fluent speakers and speakers who stutter.

CONCLUSION

The amplitude-envelope-over-time signal can be used to obtain an STI score. This STI score can be used in situations where lip movement STI scores are precluded.

Joint report of the Third International Workshop on Lymphocyte Alloantigens of the Horse, Kennett Square, Pennsylvania, 25-27 April 1984

The Third International Workshop on Lymphocyte Alloantigens of the Horse was held on 25-27 April 1984 in Kennett Square, Pennsylvania. Twelve laboratories from five countries participated. The principal purpose of this Workshop was to determine the phenotypic and gene frequencies of the 10 equine lymphocyte antigens (ELA) and a non-ELA lymphocyte antigen, ELY-2.1, in several breeds of horse. A total of 86 alloantisera characterized in previous workshops were tested against lymphocytes from 1179 horses. In addition, several experimental antisera were also tested against the same panel of lymphocytes. As a result of analysis of these data, the Workshop recognized two new equine lymphocyte alloantigens: W11 of the ELA system, and ELY-1.1, an antigen not linked to the ELA system.

Analysis of alloantisera against bovine lymphocytes. Joint report of the 1st International Bovine Lymphocyte Antigen (BoLA) workshop

The results and agreements of the 1 international BoLA workshop, held in Edinburgh, Scotland in August 1978, are reported. Most of these concern the results from a comparison test of 249 alloantisera to bovine lymphocytes, the antisera being contributed by 9 laboratories. These sera were compared directly in Edinburgh on a panel of lymphocytes from 130 cattle of 21 breeds. In the microlymphocytotoxicity test used 75% of the sera reacted. Sixty eight of these sera were grouped into clusters according to their reaction patterns against the lymphocyte panel. Eleven of these clusters were clearly defined and were given workshop BoLA designations. In addition 22 sera were assigned to subgroups of the agreed clusters. There was no evidence that the method of production of the sera had any effect on their specificity. Although genetic data was not available, the phenotypes of the test panel of lymphocytes are consistent with the clusters detecting antigens controlled by multiple alleles at a single autosomal locus. It was agreed to name the genetic region where this putative locus is located BoLA (bovine lymphocyte antigen).

Genetic differentiation associated with gait within American standardbred horses

American Standardbred horses are divided into two groups based upon gait: the trot and the pace. The tendency to trot (diagonally opposite legs moving forward together) or pace (the two legs on the same side of the body moving forward together) appears to be genetically determined, although no formal genetic analysis has been undertaken. There is nearly complete assortative mating for gait; however, about 20% of the offspring sired by trotters are registered as pacers, while fewer than 1% of those sired by pacers are registered as trotters. Electrophoretically detectable genic variation at 13 protein loci has been analysed for 371 trotters and 856 pacers, and 10 blood group loci have been examined for 600 trotters and 1227 pacers. Trotters and pacers shared common alleles at 20 of the 23 loci; however, there were significant differences in allele frequencies at 21 of the 23 loci. Highly significant fixation indices (FSTS) were observed for 17 of the loci. The extent of genetic difference between Standardbred trotters and pacers was as great as or greater than that seen between some distinct horse breeds.

Linkage disequilibrium between the ELA and the A blood group systems in Standardbred horses

The linkage group formed by the ELA and A blood group system in horses was studied in American Standardbred horses. The distance between the ELA locus and the A blood group locus was measured as 1.61 centimorgans, observing only the haplotypes contributed by the sires. Strong linkage disequilibrium was found in pacing Standardbred horses for ELA-W1 with Aa, ELA-W5 with Ab and ELA-W10 with Ab. Linkage disequilibrium was apparent at both the population and family level. Among trotting Standardbred horses, linkage disequilibrium was found for ELA-W1 with Aa and for ELA-W10 with Ab. It was not possible to investigate linkage relationships in Thoroughbred horses because of the high frequency of Aa and low frequency of other A system markers.

Joint report of the Second International Workshop on Lymphocyte Alloantigens of the Horse, held 3-8 October 1982

The Second International Workshop on Lymphocyte Alloantigens of the Horse was held 3-8 October 1982. At this workshop, the 6 specificities identified at the first workshop were confirmed and an additional 5 new specificities were identified and given workshop nomenclature. Four of the new specificities, products of the ELA locus, were named ELA-W7, W8, W9, and W10. An additional specificity, designated ELY-2.1, is the product of a locus independent of the ELA locus. Cell isolation methods were compared at this workshop. Technical variation in methods clearly affected reactivity of many reagents. However, when highly selected reagents were used, antigen assignment did not differ regardless of the cell isolation method. Based on the comparison of methods, isolation procedures in which thrombin was used were more effective than those relying on carbonyl iron or slow centrifugation.

Joint Report of the Fifth International Workshop on Lymphocyte Alloantigens of the Horse, Baton Rouge, Louisiana, 31 October-1 November 1987

Six laboratories participated in the Fifth International Workshop on Lymphocyte Alloantigens of the Horse, testing 132 alloantisera against lymphocytes of 880 horses chosen to represent different families and breeds. Most of the alloantisera were produced by lymphocyte immunization between horses matched at the ELA-A locus. All horses were also tested with antisera contributed to the workshop by participating laboratories which identified ELA specificities A1-A10 and W12-W21. Previously identified workshop specificities ELA-W14, W15 and W19 were accepted as products of the ELA-A locus based on family and population studies by the workshop. Their designations were changed to ELA-A14, ELA-A15 and ELA-A19, respectively. Two new specificities were identified, namely ELA-W22 (W22) and ELA-W23 (W23). Population and family studies indicated that W22 and W23 as well as W13 are products of an ELA locus other than ELA-A. The presence of these specificities was correlated with the presence of certain ELA-A locus specificities, e.g. W13 with A3, W22 with A2 and W23 with A5. However, the association was not complete and W13, W22 and W23 also segregated with other ELA-A specificities in some families. Evidence for recombination was found between the ELA-A locus and the locus or loci encoding these specificities resulting in seven recombinant haplotypes found among the data presented in this workshop. Further studies are required for definitive assignment of the specificities to a class I or class II locus.

Comparison of ELY-2.1 with blood group and ELY-1 markers in the horse

The distribution of ELY-2 was compared to the distribution of blood group factors Aa, Ab, Ac, Ae, Ca, Da, Db, Dc, Dd, De, Df, Dh, Dk, Ka, Pa, Pb, X, Qa, Qc, Ua, and W in 2465 American Standardbred horses and to ELY-1 in 193 American Standardbred horses. The distribution patterns were different in each case. The segregation of ELY-2.1 and factors at the A, C, D, K, P, Q, U and T (W) blood group loci and at the ELA locus indicated that ELY-2.1 is not a product of any of those loci. No segregation data were available for the ELY-1 locus. Family studies indicated that the gene for ELY-2.1 is not sex-linked.

Evidence of a second polymorphic ELA class I (ELA-B) locus and gene order for three loci of the equine major histocompatibility complex

Two antisera, B-442 and R-2046, were produced by immunizing offspring with purified peripheral blood lymphocytes from a parent matched for the ELA-A specificity carried on the unshared haplotype. Absorption analysis demonstrated that these antisera contained at least two families of cytotoxic antibodies, one directed against antigens present on T and B cells, and a second directed preferentially against antigens present on surface Ig positive cells. Immunoprecipitation studies using these antisera demonstrated that both antisera contain antibodies specific for glycoproteins with molecular weights characteristic of class I and class II MHC antigens. In lymphocyte typing tests of unfractionated lymphocytes, only the class I activity was readily detectable since the class II activity killed less than 25% of the cells. Family studies demonstrated that these antisera recognize products of genes linked to the ELA system. Based on two recombinants in an extended family it became apparent that the specificities detected by B-442 and R-2046 are not products of the ELA-A locus, but rather they are products of at least one other locus, defined in this paper as ELA-B. In this family a third recombinant was found between the A blood group system and the ELA-A locus. Based on these three recombinants, the most probable linear relationship of the following genes is: A blood group system/ELA-A/ELA-B.

Population studies on the ELA system in American standardbred and thoroughbred mares

336 Standardbred mares and 334 Thoroughbred mares in the vicinity of Lexington, Kentucky, were lymphocyte typed for 11 allelic antigenic specificities of the equine lymphocyte antigen (ELA) system. The Standardbred mares were divided into a population of pacers and a population of trotters. Substantial differences in ELA gene frequencies were found between the 3 groups. When the distribution of antigens within populations were compared to Hardy-Weinberg equilibrium expectations, relatively good agreement was found.

ELA and fertility in American Standardbred horses

We have analysed the effects of ELA alleles and sire-dam ELA incompatibility on two measures of fertility, gestation length and foaling rate, in American Standardbred horses. Using multivariate statistical methods, we corrected for the effects of confounding factors such as dam and sire age, parity, inbreeding, and sire-dam kinship. These analyses revealed substantial differences between Standardbred trotters and pacers in the effects of several confounding factors. There appear to be no ELA effects on gestation length in either trotters or pacers. However our results suggest that there may be ELA effects on foaling rate associated with specific dam alleles, with sire-dam incompatibility, and possibly with specific sire alleles, and that these effects differ between trotters and pacers.

A chromosome inversion near the KIT gene and the Tobiano spotting pattern in horses

Tobiano is a white spotting pattern in horses caused by a dominant gene, Tobiano(TO). Here, we report TO associated with a large paracentric chromosome inversion on horse chromosome 3. DNA sequences flanking the inversion were identified and a PCR test was developed to detect the inversion. The inversion was only found in horses with the tobiano pattern, including horses with diverse genetic backgrounds, which indicated a common genetic origin thousands of years ago. The inversion does not interrupt any annotated genes, but begins approximately 100 kb downstream of the KIT gene. This inversion may disrupt regulatory sequences for the KIT gene and cause the white spotting pattern.

Evaluation of Compass as a comparative mapping tool for ESTs using horse radiation hybrid maps

Loci for 9322 equine expressed sequence tags (ESTs) were predicted using the Comparative Mapping by Annotation and Sequence Similarity (Compass) strategy in order to evaluate the programme's ability to make accurate locus predictions in species with comparative gene maps. Using human genome sequence information from Build 35 (May 2004) and published marker information from the radiation hybrid (RH) maps for equine chromosomes (ECA) 17 and X, 162 ESTs were predicted to locations on ECA17 and 328 ESTs to locations on ECAX by selection of the 'top blast hit'. The locations of 30 ESTs were assessed experimentally by RH mapping analysis to evaluate the accuracy of the Compass predictions. The data revealed that 53% (16 of 30) of the ESTs predicted on ECA17 and ECAX mapped to those chromosomes. Analysis of the results suggested the need to identify expressed orthologous sequences in order to generate more accurate predictions for ESTs. Locus predictions were reassessed with three modifications to the Compass strategy's orthologue selection parameters. Selection of the 'top gene hit' improved accuracy to 72% (21 of 29), while selection of the 'top expressed gene hit' improved accuracy to 86% (24 of 28). Using the default Compass parameters with the UniGene database improved prediction accuracy to 96% (22 of 23); however, this level of accuracy came with a substantial decrease in the total number of predictions. When used with optimized prediction parameters, the Compass strategy can be a practical in silico map location prediction tool for large EST sample sets from unsequenced animal genomes.

Integrated constructed wetland systems: design, operation, and performance of low-cost decentralized wastewater treatment systems

Several different types of constructed wetland systems are being used as decentralized treatment systems including surface-flow, subsurface-flow, vertical-flow, and hybrid systems. Archetypical wetland systems have design strengths and weaknesses, and therefore it should be possible to design combined (integrated) systems to optimize a number of important treatment processes. This study provides comparative efficacy data for two integrated wetland treatment systems (IWTS) designed to enhance treatment of medium strength wastewater generated from a pilot-scale intensive fish farm. Results from the twenty eight months study included consistently high removal of COD (84% +) and ammonia nitrogen (93%) in both systems. Initially, phosphorus removal was also high (>90%) in both systems, but removal efficacy declined significantly over time. Nitrate removal was significantly better in the system that provided sequential aerobic and anoxic environments. Short hydraulic retention times coupled with sustained removal of COD and ammonia indicate that the ReCip components could be a least-cost wastewater treatment technology in the decentralized market sector.