Genetic parameters and genomic prediction of resistance to koi herpesvirus disease using a low-density SNP panel on two Amur mirror carp populations

Koi herpesvirus disease (KHVD), caused by Cyprinid herpesvirus-3 (CyHV-3), is one of the most serious threats to carp farming. In the present study, we investigated the efficiency of a low-density (LD) SNP panel for estimating genetic parameters and breeding values to KHVD resistance in the Amur mirror carp (AMC). Two populations (Pop 1 and Pop 2) of AMC generated from unrelated parents were created using a partial factorial design. One-year old fish (Pop 1 = 1500 individuals.; Pop 2 = 1200 individuals) were challenged with CyHV-3 and phe-notyped to KHVD resistance. 218 SNPs originating from a medium genotyping platform previously applied to Pop 1 (15615 SNPs; denoted as MD panel) with the highest association to KHVD resistance were used as a LD panel to genotype individuals of Pop 2. Genetic parameters and estimated pedigree-based BLUP (EBV) and genomic-based GBLUP (GEBV_MD and GEBV_LD) breeding values were calculated and obtained for Pop 1 using either pedigree, MD or LD panel and for Pop 2 using either pedigree or the LD panel. The heritability estimates of KHVD resistance were very high for both populations ranging from 0.42 to 0.96. Selection for KHVD resistance in Pop 2 using the LD panel would have led to a relative increase of similar to 7% in prediction accuracy compared to the pedigree-based selection. Pearson correlation coefficients between pedigree-based and genomic-based estimated breeding values (EBV vs. GEBV_MD; EBV vs. GEBV_LD; GEBV_MD vs. GEBV_LD) showed a strong association for both populations (0.79 - 0.91). In addition, the concordance rate of individuals selected by pedigree-based (EBV) and genomic-based breeding values (GEBV_MD and GEBV_LD) within selection pressures of 5%, 10% and 20% were not statistically different in most cases. In conclusion, the low-density SNP panel could be useful for a selection program focused on the genetic improvement of KHVD resistance

Physics of Polymorphic Transitions in CeRuSn

We report a detailed study of the polymorphic transitions in ternary stannide CeRuSn on high quality single crystals through a combination of X-ray diffraction experiments conducted at 300, 275 and 120 K, and measurements of the thermal expansion, magnetization, and resistivity, along main crystallographic axes. In addition, the transition was followed as a function of pressure up to 0.8 GPa. The present X-ray diffraction data show that the room temperature polymorph consists of the lattice doubled along the c axis with respect to the CeCoAl-type structure consistent with previous reports. Upon cooling, the compound undergoes two successive transitions, first to a quintuple (290 K) and than to a triple CeCoAl superstructure at 225 K. The transitions are accompanied by a tremendous volume change due to a strong shrinking of the lattice along the c axis, which is clearly observed in thermal expansion. We advance arguments that the volume collapse originates from an increasing number of crystallographically inequivalent Ce sites and the change of ratio between the short and long Ce-Ru bonds. The observed properties of the polymorphic transition in CeRuSn are reminiscent of the transition in elementary Cerium, suggesting that similar physics, i.e., a Kondo influenced transition and strong lattice vibrations might be the driving forces

Results of Phase II Clinical Trial MPD-RC 101: Allogeneic Hematopoietic Stem Cell Transplantation Conditioned with Fludarabine/Melphalan in Patients with Myelofibrosis

n/

Estimates of recent and historical effective population size in turbot, seabream, seabass and carp selective breeding programmes

BACKGROUND: The high fecundity of fish species allows intense selection to be practised and therefore leads to fast genetic gains. Based on this, numerous selective breeding programmes have been started in Europe in the last decades, but in general, little is known about how the base populations of breeders have been built. Such knowledge is important because base populations can be created from very few individuals, which can lead to small effective population sizes and associated reductions in genetic variability. In this study, we used genomic information that was recently made available for turbot (Scophthalmus maximus), gilthead seabream (Sparus aurata), European seabass (Dicentrarchus labrax) and common carp (Cyprinus carpio) to obtain accurate estimates of the effective size for commercial populations. METHODS: Restriction-site associated DNA sequencing data were used to estimate current and historical effective population sizes. We used a novel method that considers the linkage disequilibrium spectrum for the whole range of genetic distances between all pairs of single nucleotide polymorphisms (SNPs), and thus accounts for potential fluctuations in population size over time. RESULTS: Our results show that the current effective population size for these populations is small (equal to or less than 50 fish), potentially putting the sustainability of the breeding programmes at risk. We have also detected important drops in effective population size about five to nine generations ago, most likely as a result of domestication and the start of selective breeding programmes for these species in Europe. CONCLUSIONS: Our findings highlight the need to broaden the genetic composition of the base populations from which selection programmes start, and suggest that measures designed to increase effective population size within all farmed populations analysed here should be implemented in order to manage genetic variability and ensure the sustainability of the breeding programmes. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12711-021-00680-9

Pegylated interferon alfa-2a for polycythemia vera or essential thrombocythemia resistant or intolerant to hydroxyurea

Prior studies have reported high response rates with recombinant interferon-a (rIFN-a) therapy in patients with essential thrombocythemia (ET) and polycythemia vera (PV). To further define the role of rIFN-a,we investigated the outcomes of pegylated-rIFN-a2a (PEG) therapy in ET and PV patients previously treated with hydroxyurea (HU). The Myeloproliferative Disorders Research Consortium (MPD-RC)-111 study was an investigator-initiated, international, multicenter, phase 2 trial evaluating the ability of PEG therapy to induce complete (CR) and partial (PR) hematologic responses in patients with high-risk ET or PVwho were either refractory or intolerant to HU. The study included 65 patients with ET and 50 patients with PV. The overall response rates (ORRs; CR/PR) at 12 monthswere 69.2%(43.1% and 26.2%) in ET patients and 60% (22% and 38%) in PV patients. CR rates were higher in CALR-mutated ET patients (56.5% vs 28.0%; P 5 .01), compared with those in subjects lacking a CALR mutation. The median absolute reduction in JAK2V617F variant allele fraction was 26% (range, 284%to 47%) in patients achieving a CR vs 14%(range, 218% to 56%) in patients with PR or nonresponse (NR). Therapy was associated with a significant rate of adverse events (AEs); most were manageable, and PEG discontinuation related to AEs occurred in only 13.9% of subjects. We conclude that PEG is an effective therapy for patients with ET or PV who were previously refractory and/or intolerant of HU

Reconstructing Druze population history

The Druze are an aggregate of communities in the Levant and Near East living almost exclusively in the mountains of Syria, Lebanon and Israel whose ~1000 year old religion formally opposes mixed marriages and conversions. Despite increasing interest in genetics of the population structure of the Druze, their population history remains unknown. We investigated the genetic relationships between Israeli Druze and both modern and ancient populations. We evaluated our findings in light of three hypotheses purporting to explain Druze history that posit Arabian, Persian or mixed Near Eastern-Levantine roots. The biogeographical analysis localised proto-Druze to the mountainous regions of southeastern Turkey, northern Iraq and southeast Syria and their descendants clustered along a trajectory between these two regions. The mixed Near Eastern-Middle Eastern localisation of the Druze, shown using both modern and ancient DNA data, is distinct from that of neighbouring Syrians, Palestinians and most of the Lebanese, who exhibit a high affinity to the Levant. Druze biogeographic affinity, migration patterns, time of emergence and genetic similarity to Near Eastern populations are highly suggestive of Armenian-Turkish ancestries for the proto-Druze