Whole Population Research Articles

Population dynamics of potentially harmful haplotypes: a pedigree analysis

BackgroundThe identification of low-frequency haplotypes, never observed in homozygous state in a population, is considered informative on the presence of potentially harmful alleles (candidate alleles), putatively involved in inbreeding depression. Although identification of candidate alleles is challenging, studies analyzing the dynamics of potentially harmful alleles are lacking. A pedigree of the highly endangered Gochu Asturcelta pig breed, including 471 individuals belonging to 51 different families with at least 5 offspring each, was genotyped using the Axiom PigHDv1 Array (658,692 SNPs). Analyses were carried out on four different cohorts defined according to pedigree depth and at the whole population (WP) level.ResultsThe 4,470 Linkage Blocks (LB) identified in the Base Population (10 individuals), gathered a total of 16,981 alleles in the WP. Up to 5,466 (32%) haplotypes were statistically considered candidate alleles, 3,995 of them (73%) having one copy only. The number of alleles and candidate alleles varied across cohorts according to sample size. Up to 4,610 of the alleles identified in the WP (27% of the total) were present in one cohort only. Parentage analysis identified a total of 67,742 parent-offspring incompatibilities. The number of mismatches varied according to family size. Parent-offspring inconsistencies were identified in 98.2% of the candidate alleles and 100% of the LB in which they were located. Segregation analyses informed that most potential candidate alleles appeared de novo in the pedigree. Only 17 candidate alleles were identified in the boar, sow, and paternal and maternal grandparents and were considered segregants.ConclusionsOur results suggest that neither mutation nor recombination are the major forces causing the apparition of candidate alleles. Their occurrence is more likely caused by Allele-Drop-In events due to SNP calling errors. New alleles appear when wrongly called SNPs are used to construct haplotypes. The presence of candidate alleles in either parents or grandparents of the carrier individuals does not ensure that they are true alleles. Minimum Allele Frequency thresholds may remove informative alleles. Only fully segregant candidate alleles should be considered potentially harmful alleles. A set of 16 candidate genes, potentially involved in inbreeding depression, is described.

Differential contractility regulates cancer stem cell migration

Cancer stem cells (CSCs) are known to have a high capacity for tumor initiation and the formation of metastases. We have previously shown that in collagen constructs mimetic of aligned extracellular matrix architectures observed in carcinomas, breast CSCs demonstrate enhanced directional and total motility compared with more differentiated carcinoma populations. Here, we show that CSCs maintain increased motility in diverse environments including on 2D elastic polyacrylamide gels of various stiffness, 3D randomly oriented collagen matrices, and ectopic cerebral slices representative of a common metastatic site. A consistent twofold increase of CSC motility across platforms suggests a general shift in cell migration mechanics between well-differentiated carcinoma cells and their stem-like counterparts. To further elucidate the source of differences in migration, we demonstrate that CSCs are less contractile than the whole population (WP) and develop fewer and smaller focal adhesions and show that enhanced CSC migration can be tuned via contractile forces. The WP can be shifted to a CSC-like migratory phenotype using partial myosin II inhibition. Inversely, CSCs can be shifted to a less migratory WP-like phenotype using microtubule-destabilizing drugs that increase contractility or by directly enhancing contractile forces. This work begins to reveal the mechanistic differences driving CSC migration and raises important implications regarding the potentially disparate effects of microtubule-targeting agents on the motility of different cell populations.

Genetic analysis of the Hungarian population of endangered Hucul horses

The population genetic evaluation of the Hungarian Hucul horse population was performed based on pedigree records. Herd book data of registered Hucul horses available up to 2016 were analysed using ENDOG (Gutierrez and Goyache 2005) and POPREP (Groeneveld et al. 2009) on the whole population (WP) as well as on the reference stock (RS) (breeding stock registered in 2016). Inbreeding coefficients were 5.57% (WP) and 7.18% (RS). Average relatedness was 10.39% in WP and higher in RS (12.67%). Effective population size was 52.32. Generation interval was 13.01 years for WP and 10.99 years for RS. The values for equivalent complete generations were 6.07 and 8.75, for the maximum number of generations 14.11 and 19.16, and for the number of full generations traced 3.77 and 5.50 for WP and RS, respectively. The effective number of founders (f<sub>e</sub>) was 23 both for WP and RS. The effective number of ancestors (f<sub>a</sub>) was 20 in WP and lower in RS (16). The f<sub>a</sub>/f<sub>e</sub> ratio was 0.869 in WP and 0.696 in RS. Founder genome equivalent (f<sub>g</sub>) was 9.618 in WP and 5.790 in RS. The f<sub>g</sub>/f<sub>e</sub> ratio was 0.481 in WP and 0.361 in RS. The study revealed that both the inbreeding coefficient and the average relatedness were high. The above mentioned ratios indicated loss of genetic diversity in the Hungarian Hucul population.

Aerobic and Anaerobic Test Performance Among Elite Male Football Players in Different Team Positions

Abstract The purpose was to determine the magnitude of aerobic and anaerobic performance factors among elite male football players in different team positions. Thirty-nine players from the highest Swedish division classified as defenders (n=18), midfield players (n=12) or attackers (n=9) participated. Their mean (± sd) age, height and body mass (bm) were 24.4 (±4.7) years, 1.80 (±5.9)m and 79 (±7.6)kg, respectively. Running economy (RE) and anaerobic threshold (AT) was determined at 10, 12, 14, and 16km/h followed by tests of maximal oxygen uptake (VO2max). Maximal strength (1RM) and average power output (AP) was performed in squat lifting. Squat jump (SJ), counter-movement jump with free arm swing (CMJa), 45m maximal sprint and the Wingate test was performed. Average VO2max for the whole population (WP) was 57.0mL O2•kg−1min−1. The average AT occurred at about 84% of VO2max. 1RM per kg bm0.67 was 11.9±1.3kg. Average squat power in the whole population at 40% 1RM was 70±9.5W per kg bm0.67. SJ and CMJa were 38.6±3.8cm and 48.9±4.4cm, respectively. The average sprint time (45m) was 5.78± 0.16s. The AP in the Wingate test was 10.6±0.9W•kg−1. The average maximal oxygen uptake among players in the highest Swedish division was lower compared to international elite players but the Swedish players were better off concerning the anaerobic threshold and in the anaerobic tests. No significant differences were revealed between defenders, midfielders or attackers concerning the tested parameters presented above.

Genetic Variability in Bracco Italiano Dog Breed Assessed by Pedigree Data

The Bracco Italiano is one of the oldest pointing dog breed, used for hunting ever since the Renaissance time. The complete electronic record of the breed was downloaded from the ENCI database [whole population (WP) = 24,613 animals registered since 1970 to 2011] with the aim to estimate genetic variability in Bracco Italiano dog breed using pedigree records. Up to 97% of the individuals had registered parents and 86% registered grandfathers. Average generation interval was 4.68±0.545 for stallions and 4.08±0.321 year for dams. Reference population (RP) was defined as the population of interest that include living reproductive animals approaching the last three generations and include 9006 dogs of which 34% were inbreds. The number of ancestors was 564 in WP and 188 in RP, while the effective number of ancestors was 46 and 34 respectively. To explain 50% of the genetic variability, a total of 18 and 9 ancestors enough, respectively in the WP and RP. The average inbreeding coefficient in the RP resulted 6.7% while the average increase in inbreeding was estimated to be 1.29% (Ne=38.86). Nevertheless a regular monitoring of genetic variability of the population is important and must be adopted, in order to avoid the danger of an excessive increase of inbreeding in the future, which would result in significant inbreeding depression and in significant loss of genetic variation.

Abstract B48: Aurora kinase A plays a central role in the differentiation, survival, and self-renewal of human neuroblastoma SK-N-BE(2)-derived cancer stem cells

Abstract Aurora kinase A is upregulated in numerous types of cancers. Since this protein is involved in mitotic spindle formation and cell cycle progression, its dysregulation leads to aberrant chromosomal segregation and consequent aneuploidy. It has been clarified that Aurora A is a key player in neuroblastoma because of its ability to protect the oncogene product N-myc from degradation, and the over-expression of the two of them represents a negative prognostic factor. Neuroblastoma usually develops in children and, up to the present time, the available pharmacological therapies have proven inadequate to treat the MYCN amplified sub-type of cancer, which is the most aggressive and malignant form of the tumor. Therefore, there is an urgency to develop new strategies that will improve its treatment. A novel approach to contrast cancer development and relapse is to target the subpopulation of the tumor initiating cells (or cancer stem cells), due to their multi-drug resistance and self-renewal abilities. In this study, we have employed the SK-N-BE(2) cell line as an in vitro human neuroblastoma model, and compared the effects of Aurora A inhibition on the whole population (WP) and on the derived neurospheres (NS) obtained by their continuous growth in selective medium. We tested the effects of both a specific Aurora A inhibitor, ENMD-2076, and a pan-Aurora isoforms blocker, VX-680, for their influence over cellular physiology, morphology and signaling. The specificity of the results was confirmed by the use of a validated Aurora A siRNA. In SK-N-BE(2) WP and NS, our findings confirmed the ability of Aurora A to protect N-myc from degradation. Moreover, the isolation and characterization by FACS, confocal microscopy and immunoblotting of an aldehyde dehydrogenase-positive side population, confirmed the presence of a fraction of cells with self-renewal capabilities and stem-like properties. The analysis of the signaling network of Aurora A showed functional relationships with the transcription factor STAT3, which is associated with neuronal survival and differentiation, after IL-6 challenge. Furthermore, either Aurora A pharmacological block or silencing induced the phosphorylation of the microtubule associated protein 2 (map2) specifically in the NS, an event that maintains the microtubule in a dynamic state, which is a prerequisite for neurite outgrowth. Our results suggest that Aurora A represents an amenable target for the treatment of neuroblastoma, and gives new insights into its role in regulating neuronal plasticity and differentiation. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the Second AACR International Conference on Frontiers in Basic Cancer Research; 2011 Sep 14-18; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2011;71(18 Suppl):Abstract nr B48.

The Side Population Cells in the Rabbit Limbus Sensitively Increased in Response to the Central Cornea Wounding

Side population (SP) cells are known to reside in the limbus as putative corneal epithelial stem cells. This study was performed to demonstrate the presence and the characteristics of SP cells in the rabbit limbal epithelium and explore their sensitivity in response to the central cornea wounding. To sort out the SP cells, freshly isolated rabbit limbal and central corneal epithelial cells were subjected to Hoechst 33342 dye efflux assay. For characterization of the sorted SP cells, RT-PCR analysis, semi-dry three-dimensional (3-D) cell culture, and transplantation in nude mice were performed. To explore wound sensitivity of the limbal SP cells, the rabbit central cornea was wounded by direct contact of a 6-mm paper disk soaked with 1 N NaOH, and changes in the population size of the SP cells and the colony-forming efficiency (CFE) was monitored on days 1, 2, and 5 after wounding. The SP cells were present in the rabbit limbal epithelium with an incidence of 0.73% +/- 0.14% (n = 8) and were smaller in cell size than the major population (MP) cells, quiescent in the cell cycle, and in the undifferentiated state. The SP cells were able to regenerate the cornea-like structure with basal enrichment of p63-positive cells by in vitro 3-D culture and in vivo transplantation, all of which were best achieved by the whole population (WP) of cells comprising SP and MP cells. After central cornea wounding, this rare population of the limbal SP cells increased in size fivefold on day 1 and then decreased on day 2. The transient increase in the SP cells was subsequently followed by the propagation of an increase in CFE in the limbal MP cells on day 2 and then in the corneal MP cells on day 5. In the hematopoietic colony-forming assay, the limbal SP cells gave approximately eightfold higher CFU than the limbal MP cells. The SP cells identified in the rabbit limbus are an undifferentiated and noncycling rare epithelial cell population, which sensitively respond to the central cornea wounding by their transient increase in the population size.

Étude de la transmission père-fils des variations saisonnières du diamètre testiculaire et du pourcentage de spermatozoïdes anormaux chez le bélier Ile-de-France. 1. Fils nés en février

An experiment was conducted on the Ile-de-France (IF) breed to determine if the more or less important sensitivity of the ram to photoperiodism came under genetic control. Five base breed unrelated rams (greater than or equal to 4 yr old), were chosen for this study: 2 good (I and II), 2 bad (III and IV), and an intermediate sire (V). Ram I, which died a few years before the experiment began, was selected on both the low amplitude of its sperm production during a 6-month period of artificial lighting and the very high fertilizing capacity of its sperm in spring. Rams II to V were controlled for 12 (percentage of morphologically abnormal spermatozoa, AM) or 14 (maximum antero-posterior scrotal diameter of both testes, DT) consecutive months. Following this period of control, seasonal variation in rams was assessed as follows: low (ram II), high (rams III and IV) and intermediate (ram V) seasonal variation rams. Breeding (artificial insemination) of these 5 rams to IF ewes resulted in 18 male offspring born in February and distributed as follows: rams I to III: 4 male offspring/ram (families 1 to 3, F1 to F3), rams IV and V: 3 male offspring/ram (families 4 and 5, F4 and F5). The 18 animals were controlled once a week (DT and AM) from 8, 5 to 46 months of age (7 periods, P1 to P7). Regarding DT, mean DT was higher in F1 and F2 than those of the whole population (WP) (represented by a discontinuous line of ordinate 5.0 in Graph 3), but F2 was closer to this population than F1. On the other hand, they were lower in the rams of F3 and F4. Differences between F3 or F4 and WP were lower in autumn than in spring. All families showed significant differences during the experimental periods except at P7 for pairs 3-5 and 4-5. Distances between F1, F2, F3 were always different (P less than 0.01 or P less than 0.001), whatever the size of the population (n = 3 or 4). Weekly F5 values varied in an opposite way to those of F3 and F4: increase in spring and decrease in autumn. Regarding AM, families did not differ as much as in DT (graph 4). Weekly variations in AM were also stronger. However, mean AM was almost always lower in F1 males and somewhat higher in F3 males to that of WP.(ABSTRACT TRUNCATED AT 400 WORDS)