Artemisinin resistance phenotypes and K13 inheritance in a Plasmodium falciparum cross and Aotus model

Concerns about malaria parasite resistance to treatment with artemisinin drugs (ARTs) have grown with findings of prolonged parasite clearance t1/2s (>5 h) and their association with mutations in Plasmodium falciparum Kelch-propeller protein K13. Here, we describe a P. falciparum laboratory cross of K13 C580Y mutant with C580 wild-type parasites to investigate ART response phenotypes in vitro and in vivo. After genotyping >400 isolated progeny, we evaluated 20 recombinants in vitro: IC50 measurements of dihydroartemisinin were at similar low nanomolar levels for C580Y- and C580-type progeny (mean ratio, 1.00; 95% CI, 0.62–1.61), whereas, in a ring-stage survival assay, the C580Y-type progeny had 19.6-fold (95% CI, 9.76–39.2) higher average counts. In splenectomized Aotus monkeys treated with three daily doses of i.v. artesunate, t1/2 calculations by three different methods yielded mean differences of 0.01 h (95% CI, −3.66 to 3.67), 0.80 h (95% CI, −0.92 to 2.53), and 2.07 h (95% CI, 0.77–3.36) between C580Y and C580 infections. Incidences of recrudescence were 57% in C580Y (4 of 7) versus 70% in C580 (7 of 10) infections (−13% difference; 95% CI, −58% to 35%). Allelic substitution of C580 in a C580Y-containing progeny clone (76H10) yielded a transformant (76H10C580Rev) that, in an infected monkey, recrudesced regularly 13 times over 500 d. Frequent recrudescences of ART-treated P. falciparum infections occur with or without K13 mutations and emphasize the need for improved partner drugs to effectively eliminate the parasites that persist through the ART component of combination therapy.

Meta-analysis of sequence-based association studies across three cattle breeds reveals 25 QTL for fat and protein percentages in milk at nucleotide resolution

BackgroundGenotyping and whole-genome sequencing data have been collected in many cattle breeds. The compilation of large reference panels facilitates imputing sequence variant genotypes for animals that have been genotyped using dense genotyping arrays. Association studies with imputed sequence variant genotypes allow characterization of quantitative trait loci (QTL) at nucleotide resolution particularly when individuals from several breeds are included in the mapping populations.ResultsWe imputed genotypes for more than 28 million sequence variants in 17,229 animals of the Braunvieh (BV), Fleckvieh (FV) and Holstein (HOL) cattle breeds in order to generate large mapping populations that are required to identify sequence variants underlying milk production traits. Within-breed association tests between imputed sequence variant genotypes and fat and protein percentages in milk uncovered between six and thirteen QTL (P<1e-8) per breed. Eight of the detected QTL were significant in more than one breed. We combined the association studies across three breeds using meta-analysis and identified 25 QTL including six that were not significant in the within-breed association studies. Closer inspection of the QTL revealed that two well-known causal missense mutations in the ABCG2 (p.Y581S, rs43702337, P=4.3e-34) and GHR (p.F279Y, rs385640152, P=1.6e-74) genes were the top variants at two QTL on chromosomes 6 and 20. Another true causal missense mutation in the DGAT1 gene (p.A232K, rs109326954, P=8.4e-1436) was the second top variant at a QTL on chromosome 14 but its allelic substitution effects were not consistent across three breeds analyzed. It turned out that the conflicting allelic substitution effects resulted from flaws in the imputed genotypes due to the use of a multi-breed reference population for genotype imputation.ConclusionsMany QTL for milk production traits segregate across breeds. Metaanalysis of association studies across breeds has greater power to detect such QTL than within-breed association studies. True causal mutations can be readily detected among the most significantly associated variants at QTL when the accuracy of imputation is high. However, true causal mutations may show conflicting allelic substitution effects across breeds when the imputed sequence variant genotypes contain flaws. Validating the effect of known causal variants is highly recommended in order to assess the ability to detect true causal mutations in association studies with imputed sequence variant genotypes.

A gene for genetic background inZea mays: fine-mappingenhancer of teosinte branched1.2(etb1.2) to a YABBY class transcription factor

ABSTRACTThe effects of an allelic substitution at a gene often depend critically on genetic background, the genotype at other genes in the genome. During the domestication of maize from its wild ancestor (teosinte), an allelic substitution atteosinte branched(tb1) caused changes in both plant and ear architecture. The effects oftb1on phenotype were shown to depend on multiple background loci including one called enhancer oftb1.2 (etb1.2).We mappedetb1.2to a YABBY class transcription factor (ZmYAB2.1) and showed that the maize alleles ofZmYAB2.1are either expressed at a lower level than teosinte alleles or disrupted by insertions in the sequences.tb1andetb1.2interact epistatically to control the length of internodes within the maize ear which affects how densely the kernels are packed on the ear. The interaction effect is also observed at the level of gene expression withtb1acting as a repressor ofZmYAB2.1expression. Curiously,ZmYAB2.1was previously identified as a candidate gene for another domestication trait in maize, non-shattering ears. Consistent with this proposed role,ZmYAB2.1is expressed in a narrow band of cells in immature ears that appears to represent a vestigial abscission (shattering) zone. Expression in this band of cells may also underlie the effect on internode elongation. The identification ofZmYAB2.1as a background factor interacting withtb1is a first step toward a gene-level understanding of howtb1and the background within which it works evolved in concert during maize domestication.

Genomic scan for identifying candidate genes for paratuberculosis resistance in sheep

Breeding objectives relating to health, functional traits and welfare need to receive priority in the research programs and selection schemes, but very few reports are available on natural resistant genotypes in livestock, where some important diseases cause severe economic losses and pose serious zoonotic threats. In this study, diagnosis of paratuberculosis was performed on 759 adult sheep, from a single flock, with the serum antibody enzyme-linked immunosorbent assay; 100 sheep were selected among the extreme divergent animals for the S/P ratio obtained from the test, and were genotyped on the Illumina Ovine SNP50K BeadChip. A genome-wide scan was then performed on the individual marker genotypes, in the attempt to identify genomic regions associated with disease resistance in sheep. For each marker, the allelic substitution effect was calculated by regressing the S/P value on the number of copies of the reference allele. The position on the OARv3.1 Genome Assembly was searched for 32 markers, which showed a statistically significant allelic substitution effect (Raw P < 0.0006 and FDR P < 0.09). All markers were located within, or close to, annotated genes. Five of these genes, SEMA3, CD109, PCP4, PRDM2 and ITFG2 are referred in literature to play a role in either disease resistance or cell-mediated immune response.

Association between FSHR polymorphism with productive and reproductive traits in Antioquia Holstein cattle

Because FSH and its receptor play a fundamental role in reproduction, the objective of this research was determining the effect of the A-320T polymorphism in productive and reproductive traits in Antioquia Holstein cows. The PCR-RFLP was used to amplify a segment of 970 bp of the bovine follicle stimulating hormone receptor gene (FSHR) which was digested with the restriction enzyme TaqI. The effect of the FSHR genotypes on productive and reproductive traits was determinate by a Mixed Linear Model and Tukey Test was used to establish significant differences between means for the three genotypes. The effect of allelic substitution was studied through a linear regression model where the genotypes AA, AT and TT were transformed into a quantitative scale of 0, 1 and 2, respectively according to the number of possessed T alleles. In Antioquia Holstein cattle the most common genotype was the AT (0.485) followed by TT (0.417) and AA (0.096) genotypes. Allele frequencies were 0.339 for A and 0.660 for T, respectively. The FSHR genotypes did not exert a significant effect on the principal productive parameters, except for fat percentage (P<0.01) where the TT individuals presented the highest percent. Results showed that T allele seems to improve the solids in milk while A allele improves dairy yield. The reproductive parameters were not affected by this SNP but AT animals showed a higher number of services per conception. Further studies are required to determine whether this SNP may be used as a molecular marker.

Genetic variation within and between strains of outbred Swiss mice

The aim of this survey was to measure levels of genetic variation within and between 5 different strains of outbred Swiss mice. Ten to 15 animals from each strain (NIH, Q(S), ARC, IMVS and STUD) were typed, using allozyme electrophoresis, at 10 gene loci: Mod-1, Idh-1, Gpi-1, Es-1, Es-3, Hbb, Pep-3, Gr-1, Got-2 and Pgm-1. Polymorphic variation in at least one of the 5 strains was detected at all 10 loci. The proportion of polymorphic loci ranged from 0·3 (NIH) to 0·8 (IMVS) with a mean of 0·52. Average expected heterozygosities ranged from 0·08 (NIH) to 0·37 (IMVS) with a mean of 0·21. The inbred strain SWR was, as expected, homozygous at all 10 loci. The amount of allelic substitution between pairs of strains was quantified using Nei's genetic distance, and a dendrogram based on these genetic distances showed a close overall similarity in its branching pattern to the known genealogy of the strains. This survey showed that a considerable degree of genetic variation persists in the 5 strains examined, a level of variation similar to that previously detected by Rice and O'Brien (1980) in 3 other outbred Swiss strains.

Genetic variation and population differentiation in species of Simocephalus (Cladocera, Daphniidae)

Microgeographic analysis of enzyme genetic variation in populations in the littoral zone cladoceran Simocephalus in southwestern Ontario has disclosed very low levels of intrapopulation variability. The mean percentage of polymorphic loci per population was 10.5%, and individual heterozygosity averaged less than 5% over all populations. Population structure typifies that of randomly mating, outbred sexual species. Most populations were polyclonal, with a few common widespread clones and several rarer ones, often found in only one pond. There were no significant temporal patterns in genotypic frequencies, but spatial differentiation of populations suggested that both selection and founder effects have played roles in the evolutionary divergence of these cyclic parthenogens. Despite extremely low intrapopulation and moderate intraspecific variation, there was extensive differentiation between species. As a consequence of virtually complete allelic substitution at several loci and great similarity or identity of alleles at others, diagnostic loci were detected in three of the four species. Of the four distinct clusters of populations, differentiated at the species level, three represented species previously recognized in North America (S. cf. vetulus, S. cf. serrulatus, S. cf. exspinosus), and the fourth group was identified as S. cf. congener, related to a taxon occurring in Europe, but not reported from North America. The great amount of divergence between populations of S. cf. exspinosus suggests that a complex of at least two sibling species exists within this taxon.

The W and L allelic forms of phenylalanine hydroxylase in the rat differ by a threonine to isoleucine substitution

High performance liquid chromatography maps of tryptic and chymotryptic peptides from the W and L forms of rat phenylalanine hydroxylase differed by one peptide. Sequencing of the variant tryptic peptides showed a substitution of threonine in the W form by isoleucine in the L form and this same difference was confirmed in the chymotryptic peptides. This allelic substitution would result from a nucleotide change of ACA to ATA at amino acid position 371 of the full phenylalanine hydroxylase sequence. Altered sodium dodecyl sulphate binding is postulated to explain the change in mobility of the proteins observed on sodium dodecyl sulphate/polyacrylamide gels.

RE-INTERPRETATION OF GENETIC VARIATION IN SIMOCEPHALUS (CLADOCERA, DAPHNIIDAE)

ABSTRACT Populations of several co-existing species of Simocephalus were examined electrophoretically at 11 enzyme loci. The prevailing pattern was one of extensive allelic substitution between species and low levels of polymorphism (0-10%) within species. Genetic identity values between species were very low (10-50%). These results concur with those for other cyclic parthenogens, but are in sharp contrast to previous interpretation of data derived from populations of Simocephalus from the same sites.