A novel use of high density SNP assays to optimize choice of different crossbred dairy cattle genotypes in smallholder systems in East Africa

We present use of SNP technologies to obtain for the first time, rapid, large-scale, in situ estimates of performance of crossbred cows in smallholder herds. Compared to historical approaches, our approach allowed optimum crossbreed choices to be determined more rapidly and without question about the relevance of the environment. High-density SNP assays were used to estimate breed composition for a monitored population comprising 1292 cows from 610 smallholder farms in Kenya. The achieved milk yields are much lower than generally assumed and lactation curves are very flat out to 400 days. In poor production environments, lower grade crosses (containing <60% exotic dairy alleles) had the same yield as high grade crosses. Allowing for the larger size and maintenance requirements of high grade exotics, lower grade exotics will be the most economically productive animals in these environments

M180 Amelogenin Processed by MMP20 is Sufficient for Decussating Murine Enamel

Amelogenin (AMELX) and matrix metalloproteinase-20 (MMP20) are essential for proper enamel development. Amelx and Mmp20 mutations cause amelogenesis imperfecta. MMP20, a protease secreted by ameloblasts, is responsible for processing enamel proteins, including AMELX, during the secretory stage of enamel formation. Of at least 16 different amelogenin splice products, the most abundant isoform found in murine ameloblasts and developing enamel is the M180 protein. To understand the role of MMP20 processing of M180 AMELX, we generated AmelxKO/Mmp20KO (DKO) mice with an amelogenin (M180Tg) transgene. We analyzed the enamel phenotype by SEM to determine enamel structure and thickness, µCT, and by nanoindentation to quantify enamel mechanical properties. M180Tg/DKO mouse enamel had 37% of the hardness of M180Tg/AmelxKO teeth and demonstrated a complete lack of normal prismatic architecture. Although molar enamel of M180Tg/AmelxKO mice was thinner than WT, it had similar mechanical properties and decussating enamel prisms, which were abolished by the loss of MMP20 in the M180Tg/DKO mice. Retention of the C-terminus or complete lack of this domain is unable to rescue amelogenin null enamel. We conclude that among amelogenins, M180 alone is sufficient for normal enamel mechanical properties and prism patterns, but that additional amelogenin splice products are required to restore enamel thickness

Use of high density SNP genotypes to determine the breed composition of cross bred dairy cattle in smallholder farms: Assessment of reproductive and health performance

Reproductive performance and disease data were recorded for 2 years on 1,824 dairy cows in smallholder farms using participatory approaches and onfarm recording. Most animals experienced one service to conception. Calving intervals were long, ranging between 261 and 761 days, with an average of 451±101days. Herd level of production (HeL) had significant effect on calving interval. However, there was no difference between crossbreds with different levels of exotic breed percentage or in different HeL classes in disease incidence. Most animals had less than 2 treatment events, despite the high disease burden in the study areas. Mortality rates were low, ranging from 2.13% to 2.65%. Even though the crossbred animals had higher performance compared to indigenous animals, the gains obtained were below what would be possible with better management. These results suggest that crosses with low exotic proportions would be the most optimal for the production systems studied

Preliminary Terrestrial Palynological Re-investigation of the Type Coon Creek Lagerstatte, Tennessee, USA

The type locality for the Campanian Coon Creek Formation, located in McNairy County, Tennessee, is a well-known lagerstatte, with exceptionally preserved marine invertebrate and vertebrate remains in shallow shelf sediments. At the time of deposit ion, the type locality was located in an embayment proximal t o t he eastern margin of the Appalachia province that experienced alternately cool- and warm-water conditions, likely due to currents from both the Western Interior Seaway and Tethys. While marine in their entirety, the sediments contain significant quantities of terrestrial palynomorphs, especially near the top of the section and thus provide a snapshot of adjacent upper Cretaceous terrestrial ecosystems which are not otherwise preserved in this region. A recently completed biostratigraphic study of rangefinder widely-spaced samples through the section suggested that the increase in terrestrial input up-section may be the result of increased fluvial input, as total marine microfossil abundances remain largely unchanged. The biostratigraphic study suggested that more detailed examination of the terrestrial palynomorphs preserved in the section was warranted. In July 2022, the team of co-authors collected 27 fresh samples from the type locality. In this study we present the preliminary results of new biostratigraphic and paleoecological investigations of terrestrial palynomorphs recovered from the site.https://scholarworks.moreheadstate.edu/celebration_posters_2024/1047/thumbnail.jp

The Amelogenin C-Terminus Is Required for Enamel Development

The abundant amelogenin proteins are responsible for generating proper enamel thickness and structure, and most amelogenins include a conserved hydrophilic C-terminus. To evaluate the importance of the C-terminus, we generated transgenic mice that express an amelogenin lacking the C-terminal 13 amino acids (CTRNC). MicroCT analysis of TgCTRNC29 teeth (low transgene number) indicated that molar enamel density was similar to that of wild-type mice, but TgCTRNC18 molar enamel (high transgene number) was deficient, indicating that extra transgene copies were associated with a more severe phenotype. When amelogenin-null (KO) and TgCTRNC transgenic mice were mated, density and volume of molar enamel from TgCTRNCKO offspring were not different from those of KO mice, indicating that neither TgCTRNC18 nor TgCTRNC29 rescued enamel’s physical characteristics. Because transgenic full-length amelogenin partially rescues both density and volume of KO molar enamel, it was concluded that the amelogenin C-terminus is essential for proper enamel density, volume, and organization

3D MHD Flux Emergence Experiments: Idealized models and coronal interactions

This paper reviews some of the many 3D numerical experiments of the emergence of magnetic fields from the solar interior and the subsequent interaction with the pre-existing coronal magnetic field. The models described here are idealized, in the sense that the internal energy equation only involves the adiabatic, Ohmic and viscous shock heating terms. However, provided the main aim is to investigate the dynamical evolution, this is adequate. Many interesting observational phenomena are explained by these models in a self-consistent manner.Comment: Review article, accepted for publication in Solar Physic

Optimal design of low density marker panels for genotype imputation

Cost-effective genotyping of livestock species can be done through a process which involves genotyping part of the population using a high density (HD) panel and the remainder with a lower density panel and then use imputation to infer the missing genotypes that are not included on the low density panel. Therefore, it is desirable to have a method of selecting markers for an assay that maximises imputation accuracy. Here we present a marker selection method that relies on the pairwise (co)variances between single nucleotide polymorphisms (SNPs) and the minor allele frequency (MAF) of SNPs. The performance of the developed method was tested in a 5 fold cross-validation process using genotypes of crossbred dairy cattle in East Africa, a population in which it is unclear whether existing low density SNP assays designed for purebred populations will maintain high imputation accuracies. Various densities of SNPs were selected using the (co)variance method and alternative SNP selection methods and then imputed up to the HD panel. The (co)variance method provided the highest imputation accuracies at all marker densities, with accuracies being up to 19% higher than the random selection of SNPs. The presented method is straightforward in its application and can ensure high accuracies in genotype imputation of crossbred dairy population in East Africa

Rapid-Onset Obesity with Hypothalamic Dysfunction, Hypoventilation, and Autonomic Dysregulation (ROHHAD): Exome sequencing of trios, monozygotic twins and tumours

BACKGROUND: Rapid-onset Obesity with Hypothalamic Dysfunction, Hypoventilation, and Autonomic Dysregulation (ROHHAD) is thought to be a genetic disease caused by de novo mutations, though causative mutations have yet to be identified. We searched for de novo coding mutations among a carefully-diagnosed and clinically homogeneous cohort of 35 ROHHAD patients. METHODS: We sequenced the exomes of seven ROHHAD trios, plus tumours from four of these patients and the unaffected monozygotic (MZ) twin of one (discovery cohort), to identify constitutional and somatic de novo sequence variants. We further analyzed this exome data to search for candidate genes under autosomal dominant and recessive models, and to identify structural variations. Candidate genes were tested by exome or Sanger sequencing in a replication cohort of 28 ROHHAD singletons. RESULTS: The analysis of the trio-based exomes found 13 de novo variants. However, no two patients had de novo variants in the same gene, and additional patient exomes and mutation analysis in the replication cohort did not provide strong genetic evidence to implicate any of these sequence variants in ROHHAD. Somatic comparisons revealed no coding differences between any blood and tumour samples, or between the two discordant MZ twins. Neither autosomal dominant nor recessive analysis yielded candidate genes for ROHHAD, and we did not identify any potentially causative structural variations. CONCLUSIONS: Clinical exome sequencing is highly unlikely to be a useful diagnostic test in patients with true ROHHAD. As ROHHAD has a high risk for fatality if not properly managed, it remains imperative to expand the search for non-exomic genetic risk factors, as well as to investigate other possible mechanisms of disease. In so doing, we will be able to confirm objectively the ROHHAD diagnosis and to contribute to our understanding of obesity, respiratory control, hypothalamic function, and autonomic regulation. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13023-015-0314-x) contains supplementary material, which is available to authorized users

Genetic diversity of the indigenous cattle of Kenya, Uganda, Ethiopia and Tanzania using high-density SNP data

Genetic diversity of the indigenous cattle of Kenya, Uganda, Ethiopia and Tanzania using high-density SNP data. The indigenous cattle make a significant contribution to the livelihood of many communities in Ethiopia, Tanzania and other countries in eastern Africa. Here, we identify the genetic structure and the admixture levels of several East African indigenous cattle breeds in Ethiopia and Tanzania. Two ‘groups’ were studied: Indigenous cattle consisting of a number of breeds; and Mpwapwa cattle – a composite breed. A total of 386 individual animals from the two groups were genotyped using the Illumina high-density Bovine SNP chip (778k Panel). Principal component analysis was used to study the genetic structure and admixture levels of the indigenous cattle, and Mpwapwa were estimated using the ADMIXTURE program. All East African indigenous breeds other than the Ankole appear genetically closely related to each other and consist of a mixture of African taurine and indicine signals. Ethiopian indigenous breeds, Fogera, Danakil Harar and Ethiopian Boran show high purity, whereas Ethiopian Central Highland Breed and the Begait samples show significant amounts of European Bos taurus admixture. Tanzanian indigenous cattle, Singida White and Iringa Red, have a high degree of purity while the TALIRI Boran shows some European Bos taurus genetic background. The synthetic Mpwapwa breed had estimated breed proportions of Bos indicus, African Bos taurus and European Bos taurus of 0.82, 0.05 and 0.13 respectively. These results are useful for genetic conservation and genetic improvement programs

A Helicity-Based Method to Infer the CME Magnetic Field Magnitude in Sun and Geospace: Generalization and Extension to Sun-Like and M-Dwarf Stars and Implications for Exoplanet Habitability

Patsourakos et al. (Astrophys. J. 817, 14, 2016) and Patsourakos and Georgoulis (Astron. Astrophys. 595, A121, 2016) introduced a method to infer the axial magnetic field in flux-rope coronal mass ejections (CMEs) in the solar corona and farther away in the interplanetary medium. The method, based on the conservation principle of magnetic helicity, uses the relative magnetic helicity of the solar source region as input estimates, along with the radius and length of the corresponding CME flux rope. The method was initially applied to cylindrical force-free flux ropes, with encouraging results. We hereby extend our framework along two distinct lines. First, we generalize our formalism to several possible flux-rope configurations (linear and nonlinear force-free, non-force-free, spheromak, and torus) to investigate the dependence of the resulting CME axial magnetic field on input parameters and the employed flux-rope configuration. Second, we generalize our framework to both Sun-like and active M-dwarf stars hosting superflares. In a qualitative sense, we find that Earth may not experience severe atmosphere-eroding magnetospheric compression even for eruptive solar superflares with energies ~ 10^4 times higher than those of the largest Geostationary Operational Environmental Satellite (GOES) X-class flares currently observed. In addition, the two recently discovered exoplanets with the highest Earth-similarity index, Kepler 438b and Proxima b, seem to lie in the prohibitive zone of atmospheric erosion due to interplanetary CMEs (ICMEs), except when they possess planetary magnetic fields that are much higher than that of Earth.Comment: http://adsabs.harvard.edu/abs/2017SoPh..292...89