Search

Transposable elements (TEs) make up around 10%-15% of the Drosophila melanogaster genome, but its sibling species Drosophila simulans carries only one third as many such repeat sequences. We do not, however, have an overall view of copy numbers of the various classes of TEs (long terminal repeat [LTR] retrotransposons, non-LTR retrotransposons, and transposons) in genomes of natural populations of both species. We analyzed 34 elements in individuals from various natural populations of these species. We show that D. melanogaster has higher average chromosomal insertion site numbers per genome than D. simulans for all TEs except five. The LTR retrotransposons gypsy, ZAM, and 1731 and the transposon bari-1 present similar low copy numbers in both species. The transposon hobo has a large number of insertion sites, with significantly more sites in D. simulans. High variation between populations in number of insertion sites of some elements of D. simulans suggests that these elements can invade the genome of the entire species starting from a local population. We propose that TEs in the D. simulans genome are being awakened and amplified as they had been a long time ago in D. melanogaster. [ABSTRACT FROM PUBLISHER]

Copy numbers of sequences homologous to the Drosophila melanogaster retrotransposable element 412, their distribution between the chromosome arms and the chromocenter, and whether they contain full-size copies were analyzed for 55 species of the Drosophila genus. Element 412 insertion sites were detected on the chromosome arms of D. melanogaster, Drosophila simulans, and a few species of the obscura group, but the chromocenter was labeled in almost all species. The presence of element 412 sequences in the majority of species shows that this element has a long evolutionary history in Drosophilidae, although it may have recently invaded the chromosomes in some species, such as D. simulans. Differences in copy number between species may be due to population size or specific endogenous or environmental factors and may follow the worldwide invasion of the species. Putative full-length copies were detected in the chromocenters of some species with no copies on the chromosome arms, suggesting that the chromocenter may be a shelter for such copies and not only for deleted ones. [ABSTRACT FROM PUBLISHER]

Background: Dominance and other non-additive genetic effects arise from the interaction between alleles, and historically these phenomena play a major role in quantitative genetics. However, most genome-wide association studies (GWAS) assume alleles act additively., Results: We systematically investigate both dominance-here representing any non-additive within-locus interaction-and additivity across 574 physiological and gene expression traits in three mammalian stocks: F2 intercross pigs, rat heterogeneous stock, and mice heterogeneous stock. Dominance accounts for about one quarter of heritable variance across all physiological traits in all species. Hematological and immunological traits exhibit the highest dominance variance, possibly reflecting balancing selection in response to pathogens. Although most quantitative trait loci (QTLs) are detectable as additive QTLs, we identify 154, 64, and 62 novel dominance QTLs in pigs, rats, and mice respectively that are undetectable as additive QTLs. Similarly, even though most cis-acting expression QTLs are additive, gene expression exhibits a large fraction of dominance variance, and trans-acting eQTLs are enriched for dominance. Genes causal for dominance physiological QTLs are less likely to be physically linked to their QTLs but instead act via trans-acting dominance eQTLs. In addition, thousands of eQTLs are associated with alternatively spliced isoforms with complex additive and dominant architectures in heterogeneous stock rats, suggesting a possible mechanism for dominance., Conclusions: Although heritability is predominantly additive, many mammalian genetic effects are dominant and likely arise through distinct mechanisms. It is therefore advantageous to consider both additive and dominance effects in GWAS to improve power and uncover causality., (© 2023. BioMed Central Ltd., part of Springer Nature.)

In this study we investigate the effects of parent of origin on complex traits in the laboratory rat, with a focus on coping style behavior in stressful situations. We develop theory, based on earlier work, to partition heritability into a component due to a combination of parent of origin, maternal, paternal and shared environment, and another component that estimates classical additive genetic variance. We use this theory to investigate the effects on heritability of the parental origin of alleles in 798 outbred heterogeneous stock rats across 199 complex traits. Parent-of-origin-like heritability was on average 2.7fold larger than classical additive heritability. Among the phenotypes with the most enhanced parent-of-origin heritability were 10 coping style behaviors, with average 3.2 fold heritability enrichment. To confirm these findings on coping behavior, and to eliminate the possibility that the parent of origin effects are due to confounding with shared environment, we performed a reciprocal F1 cross between the behaviorally divergent RHA and RLA rat strains. We observed parent-of-origin effects on F1 rat anxiety/coping-related behavior in the Elevated Zero Maze test. Our study is the first to assess genetic parent-of-origin effects in rats, and confirm earlier findings in mice that such effects influence coping and impulsive behavior, and suggest these effects might be significant in other mammals, including humans., (Copyright © 2018 Mont et al.)

Background: Above-knee amputation (AKA) is a morbid procedure and is performed for a number of conditions. Although AKA is usually performed for dysvascular disease, trauma, and malignancy, AKA is also considered in patients who have failed multiple salvage attempts at treating periprosthetic joint infection (PJI) of TKA. Although aggressive measures are being taken to treat PJI, the huge volume of TKAs might result in a large number of AKAs being performed for PJI in the United States. However, the national trends in the incidence of AKAs from different etiologies and the relative contribution of different etiologies to AKA are yet to be studied., Questions/purposes: (1) What are the temporal trends in the incidence of AKAs (from all causes) in the US population from 1998 to 2013? (2) What are the temporal trends in the incidence of AKAs by etiology (dysvascular disease, trauma, malignancy, and PJI)? (3) What are the temporal trends in the relative contribution of different etiologies to AKA?, Methods: Using the Nationwide Inpatient Sample (NIS) from 1998 to 2013, AKAs were identified using International Classification of Diseases, 9 Revision (ICD-9) procedure code 84.17. The NIS database is the largest all-payer database in the United States containing information on approximately 20% of all the hospital admissions in the country. As a result of its sampling design, it allows for estimation of procedural volumes at the national level. All AKAs were grouped into one of the following five etiologies in a sequential manner using ICD-9 diagnosis codes: malignancy, PJI, trauma, dysvascular disease (peripheral vascular disease, diabetic, or a combination), and others. All of the numbers were converted to national estimates using sampling weights provided by the NIS, and the national incidence of AKAs resulting from various etiologies was calculated using the US population as the denominator. Poisson and linear regression analyses were used to analyze the annual trends., Results: From 1998 to 2013, the incidence of AKAs decreased by 47% from 174 to 92 AKAs per 1 million adults (incidence rate ratio [IRR]; change in the number of AKAs per 1 million adults per year; 0.96; 95% confidence interval [CI], 0.96-0.96; p < 0.001). The incidence of AKAs resulting from PJI increased by 263% (IRR, 1.07; 95% CI, 1.06-1.07; p < 0.001). An increase was also observed for AKAs from malignancy (IRR, 1.01; 95% CI, 1.00-1.02; p = 0.007), although to a smaller extent. AKAs from dysvascular causes (IRR, 0.96; 95% CI, 0.95-0.96; p < 0.001) and other etiologies (IRR, 0.97; 95% CI, 0.96-0.97; p < 0.001) decreased. There was no change in the incidence of AKAs related to trauma (IRR, 1.00; 95% CI, 0.99-1.00; p = 0.088). The proportion of AKAs resulting from PJI increased by 589% from 1998 to 2013 (coefficient = 0.18; 95% CI, 0.15-0.22; p < 0.001). The proportion of AKAs resulting from dysvascular causes decreased (coefficient = 0.18; 95% CI, 0.15-0.22; p < 0.001), whereas that resulting from malignancy (coefficient = 0.04; 95% CI, 0.03-0.05; p < 0.001) and trauma (coefficient = 0.13; 95% CI, 0.09-0.18; p < 0.001) increased., Conclusions: The incidence of AKAs has decreased in the United States. AKAs related to dysvascular disease and other etiologies such as trauma and malignancy have either substantially decreased or remained fairly constant, whereas that resulting from PJI more than tripled. Given the increased resource utilization associated with limb loss, the results of this study suggest that national efforts to reduce disability should prioritize PJI. Further studies are required to evaluate the risk factors for AKA from PJI and to formulate better strategies to manage PJI., Level of Evidence: Level III, therapeutic study.

Previously, we demonstrated that skeletal mass, structure and biomechanical properties vary considerably among 11 different inbred rat strains. Subsequently, we performed quantitative trait loci (QTL) analysis in four inbred rat strains (F344, LEW, COP and DA) for different bone phenotypes and identified several candidate genes influencing various bone traits. The standard approach to narrowing QTL intervals down to a few candidate genes typically employs the generation of congenic lines, which is time consuming and often not successful. A potential alternative approach is to use a highly genetically informative animal model resource capable of delivering very high resolution gene mapping such as Heterogeneous stock (HS) rat. HS rat was derived from eight inbred progenitors: ACI/N, BN/SsN, BUF/N, F344/N, M520/N, MR/N, WKY/N and WN/N. The genetic recombination pattern generated across 50 generations in these rats has been shown to deliver ultra-high even gene-level resolution for complex genetic studies. The purpose of this study is to investigate the usefulness of the HS rat model for fine mapping and identification of genes underlying bone fragility phenotypes. We compared bone geometry, density and strength phenotypes at multiple skeletal sites in HS rats with those obtained from five of the eight progenitor inbred strains. In addition, we estimated the heritability for different bone phenotypes in these rats and employed principal component analysis to explore relationships among bone phenotypes in the HS rats. Our study demonstrates that significant variability exists for different skeletal phenotypes in HS rats compared with their inbred progenitors. In addition, we estimated high heritability for several bone phenotypes and biologically interpretable factors explaining significant overall variability, suggesting that the HS rat model could be a unique genetic resource for rapid and efficient discovery of the genetic determinants of bone fragility., (Copyright © 2010 Elsevier Inc. All rights reserved.)

There are three reports on acute haemorrhagic oedema of the skin of infants, an illness which English-speaking authors do not individualize but only regard as a clinical variety of Henoch-Schönlein purpura. Yet the features of the disease, as described in children under two years of age, are very characteristic. --Clinical feature is the sudden appearance of oedemas on face and limbs and of cocarde-like purpura with an occasional temperature. --Histological feature is the presence of leukocytoclastic vasculitis. --Immunologically the disease is characterized by the deposit of immune complexes. --Ultrastructural examination confirms the presence of leukocytoclastic vasculitis accompanied by deposit of immune complexes and of platelets. These three reports enable the authors to study the nosological aspects of the illness among the varieties of allergic vasculitis.