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Artificial neural networks modeling gene-environment
interaction
Background:
Gene-environment interactions play an important role in the etiological pathway of complexdiseases. An appropriate statistical method for handling a wide variety of complex situationsinvolving interactions between variables is still lacking, especially when continuous variables areinvolved. The aim of this paper is to explore the ability of neural networks to model differentstructures of gene-environment interactions. A simulation study is set up to compare neuralnetworks with standard logistic regression models. Eight different structures of gene-environmentinteractions are investigated. These structures are characterized by penetrance functions that arebased on sigmoid functions or on combinations of linear and non-linear effects of a continuousenvironmental factor and a genetic factor with main effect or with a masking effect only.
Results:
In our simulation study, neural networks are more successful in modeling gene-environmentinteractions than logistic regression models. This outperfomance is especially pronounced whenmodeling sigmoid penetrance functions, when distinguishing between linear and nonlinearcomponents, and when modeling masking effects of the genetic factor.
Conclusion:
Our study shows that neural networks are a promising approach for analyzing gene-environmentinteractions. Especially, if no prior knowledge of the correct nature of the relationship betweenco-variables and response variable is present, neural networks provide a valuable alternative toregression methods that are limited to the analysis of linearly separable data.
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Mcm2 phosphorylation and the response to replicative stress
Background:
The replicative helicase in eukaryotic cells is comprised of minichromosome maintenance(Mcm) proteins 2 through 7 (Mcm2-7) and is a key target for regulation of cell proliferation.In addition, it is regulated in response to replicative stress. One of the protein kinases thattargets Mcm2-7 is the Dbf4-dependent kinase Cdc7 (DDK). In a previous study, we showedthat alanine mutations of the DDK phosphorylation sites at S164 and S170 in Saccharomycescerevisiae Mcm2 result in sensitivity to caffeine and methyl methanesulfonate (MMS)leading us to suggest that DDK phosphorylation of Mcm2 is required in response toreplicative stress.
Results:
We show here that a strain with the mcm2 allele lacking DDK phosphorylation sites(mcm2AA) is also sensitive to the ribonucleotide reductase inhibitor, hydroxyurea (HU) and tothe base analogue 5-fluorouracil (5-FU) but not the radiomimetic drug, phleomycin. Wescreened the budding yeast non-essential deletion collection for synthetic lethal interactionswith mcm2AA and isolated deletions that include genes involved in the control of genomeintegrity and oxidative stress. In addition, the spontaneous mutation rate, as measured bymutations in CAN1, was increased in the mcm2AA strain compared to wild type, whereas witha phosphomimetic allele (mcm2EE) the mutation rate was decreased. These results led to theidea that the mcm2AA strain is unable to respond properly to DNA damage. We examined thisby screening the deletion collection for suppressors of the caffeine sensitivity of mcm2AA.Deletions that decrease spontaneous DNA damage, increase homologous recombination orslow replication forks were isolated. Many of the suppressors of caffeine sensitivitysuppressed other phenotypes of mcm2AA including sensitivity to genotoxic drugs, theincreased frequency of cells with RPA foci and the increased mutation rate.
Conclusions:
Together these observations point to a role for DDK-mediated phosphorylation of Mcm2 inthe response to replicative stress, including some forms of DNA damage. We suggest thatphosphorylation of Mcm2 modulates Mcm2-7 activity resulting in the stabilization ofreplication forks in response to replicative stress.
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Ascertaining gene flow patterns in livestock populations of developing countries: a case study in Burkina Faso goat
Background:
Introgression of Sahel livestock genes southwards in West Africa may be favoured by humanactivity and the increase of the duration of the dry seasons since the 1970's. The aim of thisstudy is to assess the gene flow patterns in Burkina Faso goat and to ascertain the most likelyfactors influencing geographic patterns of genetic variation in the Burkina Faso goatpopulation.
Results:
A total of 520 goat were sampled in 23 different locations of Burkina Faso and genotyped fora set of 19 microsatellites. Data deposited in the Dryad repository:http://dx.doi.org/10.5061/dryad.41h46j37. Although overall differentiation is poor (FST =0.067 +/- 0.003), the goat population of Burkina Faso is far from being homogeneous. Barrieranalysis pointed out the existence of: a) genetic discontinuities in the Central and SoutheastBurkina Faso; and b) genetic differences within the goat sampled in the Sahel or the Sudanareas of Burkina Faso. Principal component analysis and admixture proportion scores werecomputed for each population sampled and used to construct interpolation maps.Furthermore, Population Graph analysis revealed that the Sahel and the Sudan environmentalareas of Burkina Faso were connected through a significant number of extended edges, whichwould be consistent with the hypothesis of long-distance dispersal. Genetic variation ofBurkina Faso goat followed a geographic-related pattern. This pattern of variation is likely tobe related to the presence of vectors of African animal trypanosomosis. Partial Mantel testidentified the present Northern limit of trypanosome vectors as the most significant landscapeboundary influencing the genetic variability of Burkina Faso goat (p = 0.008). Thecontribution of Sahel goat genes to the goat populations in the Northern and Eastern parts ofthe Sudan-Sahel area of Burkina Faso was substantial. The presence of perennial streamsexplains the existence of trypanosome vectors. The South half of the Nakambe river(Southern Ouagadougou) and the Mouhoun river loop determined, respectively, the Easternand Northern limits for the expansion of Sahelian goat genes. Furthermore, results frompartial Mantel test suggest that the introgression of Sahelian goat genes into Djallonke goatusing human-influenced genetic corridors has a limited influence when compared to thebiological boundary defined by the northern limits for the distribution of the tsetse fly.However, the genetic differences found between the goat sampled in Bobo Dioulasso and theother populations located in the Sudan area of Burkina Faso may be explained by the broadgoat trade favoured by the main road of the country.
Conclusions:
The current analysis clearly suggests that genetic variation in Burkina Faso goat: a) follows aNorth to South clinal; and b) is affected by the distribution of the tsetse fly that imposes alimit to the Sahelian goat expansion due to their trypanosusceptibility. Here we show howextensive surveys on livestock populations can be useful to indirectly assess theconsequences of climate change and human action in developing countries.
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Gene diversity, agroecological structure and introgression patterns among village chicken populations across North, West and Central Africa
Background:
Chickens represent an important animal genetic resource for improving farmers' income inAfrica. The present study provides a comparative analysis of the genetic diversity of villagechickens across a subset of African countries. Four hundred seventy-two chickens weresampled in 23 administrative provinces across Cameroon, Benin, Ghana, Cote d'Ivoire, andMorocco. Geographical coordinates were recorded to analyze the relationships betweengeographic distribution and genetic diversity. Molecular characterization was performed witha set of 22 microsatellite markers. Five commercial lines, broilers and layers, were alsogenotyped to investigate potential gene flow. A genetic diversity analysis was conducted bothwithin and between populations.
Results:
High heterozygosity levels, ranging from 0.51 to 0.67, were reported for all local populations,corresponding to the values usually found in scavenging populations worldwide. Allelicrichness varied from 2.04 for a commercial line to 4.84 for one population from Coted'Ivoire. Evidence of gene flow between commercial and local populations was observed inMorocco and in Cameroon, which could be related to long-term improvement programs withthe distribution of crossbred chicks. The impact of such introgressions seemed rather limited,probably because of poor adaptation of exotic birds to village conditions, and because of theconsumers' preference for local chickens. No such gene flow was observed in Benin, Ghana,and Cote d'Ivoire, where improvement programs are also less developed. The clusteringapproach revealed an interesting similarity between local populations found in regionssharing high levels of precipitation, from Cameroon to Cote d'Ivoire. Restricting the study toBenin, Ghana, and Cote d'Ivoire, did not result in a typical breed structure but a south-west tonorth-east gradient was observed. Three genetically differentiated areas (P < 0.01) wereidentified, matching with Major Farming Systems (namely Tree Crop, Cereal-Root Crop, andRoot Crop) described by the FAO.
Conclusions:
Local chickens form a highly variable gene pool constituting a valuable resource for humanpopulations. Climatic conditions, farming systems, and cultural practices may influence thegenetic diversity of village chickens in Africa. A higher density of markers would be neededto identify more precisely the relative importance of these factors.
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Genetic characterization of Plectorhinchus
mediterraneus yields important clues about genome
organization and evolution of multigene families
Background:
Molecular and cytogenetic markers are of great use for to fish characterization, identification,phylogenetics and evolution. Multigene families have proven to be good markers for a betterunderstanding of the variability, organization and evolution of fish species. Three differenttandemly-repeated gene families (45S rDNA, 5S rDNA and U2 snDNA) have been studied inPlectorhinchus mediterraneus (Teleostei: Haemulidae), at both molecular and cytogeneticlevel, to elucidate the taxonomy and evolution of these multigene families, as well as forcomparative purposes with other species of the family.
Results:
Four different types of 5S rDNA were obtained; two of them showed a high homology withthat of Raja asterias, and the putative implication of a horizontal transfer event and itsconsequences for the organization and evolution of the 5S rDNA have been discussed. Theother two types do not resemble any other species, but in one of them a putative tRNAderivedSINE was observed for the first time, which could have implications in the evolutionof the 5S rDNA. The ITS-1 sequence was more related to a species of another different genusthan to that of the same genus, therefore a revision of the Hamulidae family systematic hasbeen proposed. In the analysis of the U2 snDNA, we were able to corroborate that U2 snDNAand U5 snDNA were linked in the same tandem array, and this has interest for tracingevolutionary lines. The karyotype of the species was composed of 2n = 48 acrocentricchromosomes, and each of the three multigene families were located in different chromosomepairs, thus providing three different chromosomal markers.
Conclusions:
Novel data can be extracted from the results: a putative event of horizontal transfer, apossible tRNA-derived SINE linked to one of the four 5S rDNA types characterized, and alinkage between U2 and U5 snDNA. In addition, a revision of the taxonomy of theHaemulidae family has been suggested, and three cytogenetic markers have been obtained.Some of these results have not been described before in any other fish species. New cluesabout the genome organization and evolution of the multigene families are offered in thisstudy.
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Genome-wide linkage analyses identify Hfhl1 and Hfhl3 with frequency-specific effects on the hearing spectrum of NIH Swiss mice
Background:
The mammalian cochlea receives and analyzes sound at specific places along the cochlea coil, commonly referred to as the tonotopic map. Although much is known about the cell-level molecular defects responsible for severe hearing loss, the genetics responsible for less severe and frequency-specific hearing loss remains unclear. We recently identified quantitative trait loci (QTLs) Hfhl1 and Hfhl2 that affect high-frequency hearing loss in NIH Swiss mice. Here we used 2f1-f2 distortion product otoacoustic emissions (DPOAE) measurements to refine the hearing loss phenotype. We crossed the high frequency hearing loss (HFHL) line of NIH Swiss mice to three different inbred strains and performed linkage analysis on the DPOAE data obtained from the second-generation populations.
Results:
We identified a QTL of moderate effect on chromosome 7 that affected 2f1-f2 emissions intensities (Hfhl1), confirming the results of our previous study that used auditory brainstem response (ABR) thresholds to identify QTLs affecting HFHL. We also identified a novel significant QTL on chromosome 9 (Hfhl3) with moderate effects on 2f1-f2 emissions intensities. By partitioning the DPOAE data into frequency subsets, we determined that Hfhl1 and Hfhl3 affect hearing primarily at frequencies above 24 kHz and 35 kHz, respectively. Furthermore, we uncovered additional QTLs with small effects on isolated portions of the DPOAE spectrum.
Conclusions:
This study identifies QTLs with effects that are isolated to limited portions of the frequency map. Our results support the hypothesis that frequency-specific hearing loss results from variation in gene activity along the cochlear partition and suggest a strategy for creating a map of cochlear genes that influence differences in hearing sensitivity and/or vulnerability in restricted portions of the cochlea.
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The distribution of a germline methylation marker suggests a regional mechanism of LINE-1 silencing by the piRNA-PIWI system
Background:
A defense system against transposon activity in the human germline based on PIWI proteins and piRNA has recently been discovered. It represses the activity of LINE-1 elements via DNA methylation by a largely unknown mechanism. Based on the dispersed distribution of clusters of piRNA genes in a strand-specific manner on all human chromosomes, we hypothesized that this system might work preferentially on local and proximal sequences. We tested this hypothesis with a methylation-associated SNP (mSNP) marker which is based on the density of C-T transitions in CpG dinucleotides as a surrogate marker for germline methylation.
Results:
We found significantly higher density of mSNPs flanking piRNA clusters in the human genome for flank sizes of 1-16 Mb. A dose-response relationship between number of piRNA genes and mSNP density was found for up to 16 Mb of flanking sequences. The chromosomal density of hypermethylated LINE-1 elements had a significant positive correlation with the chromosomal density of piRNA genes (r = 0.41, P = 0.05). Genome windows of 1-16 Mb containing piRNA clusters had significantly more hypermethylated LINE-1 elements than windows not containing piRNA clusters. Finally, the minimum distance to the next piRNA cluster was significantly shorter for hypermethylated LINE-1 compared to normally methylated elements (14.4 Mb vs 16.1 Mb).
Conclusions:
Our observations support our hypothesis that the piRNA-PIWI system preferentially methylates sequences in close proximity to the piRNA clusters and perhaps physically adjacent sequences on other chromosomes. Furthermore they suggest that this proximity effect extends up to 16 Mb. This could be due to an unknown localization signal, transcription of piRNA genes near the nuclear membrane or the presence of an unknown RNA molecule that spreads across the chromosome and targets the methylation directed by the piRNA-PIWI complex. Our data suggest a region specific molecular mechanism which can be sought experimentally.
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Ancient DNA reveals kinship burial patterns of a pre-Columbian Andean community
Background:
A detailed genetic study of the pre-Columbian population inhabiting the Tompullo 2 archaeological site (department Arequipa, Peru) was undertaken to resolve the kin relationships between individuals buried in six different chullpas. Kin relationships were an important factor shaping the social organization in the pre-Columbian Andean communities, centering on the ayllu, a group of relatives that shared a common land and responsibilities. The aim of this study was to evaluate whether this Andean model of a social organization had an influence on mortuary practices, in particular to determine whether chullpas served as family graves.
Results:
The remains of forty-one individuals were analyzed with both uniparental (mtDNA, Y-chromosome) and biparental (autosomal microsatellites) markers. Reproducible HVRI sequences, autosomal and Y chromosomal STR profiles were obtained for 24, 16 and 11 individuals, respectively. Mitochondrial DNA diversity was comparable to that of ancient and contemporary Andean populations. The Tompullo 2 population exhibited the closest relationship with the modern population from the same region. A kinship analysis revealed complex pattern of relations within and between the graves. However mean relatedness coefficients regarding the pairs of individuals buried in the same grave were significantly higher than those regarding pairs buried in different graves. The Y chromosome profiles of 11 males suggest that only members of one male line were buried in the same grave.
Conclusions:
Genetic investigation of the population that inhabited Tompullo 2 site shows continuity between pre-Columbian and modern Native Amerindian populations inhabiting the Arequipa region. This suggests that no major demographic processes have influenced the mitochondrial DNA diversity of these populations during the past five hundred years. The kinship analysis involving uni- and biparental markers suggests that the community that inhabited the Tompullo 2 site was organized into extended family groups that were buried in different graves. This finding is in congruence with known models of social organization of Andean communities.
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Statistical properties of interval mapping methods on quantitative trait loci location: impact on QTL/eQTL analyses
Background:
Quantitative trait loci (QTL) detection on a huge amount of phenotypes, like eQTL detection on transcriptomic data, can be dramatically impaired by the statistical properties of interval mapping methods. One of these major outcomes is the high number of QTL detected at marker locations. The present study aims at identifying and specifying the sources of this bias, in particular in the case of analysis of data issued from outbred populations. Analytical developments were carried out in a backcross situation in order to specify the bias and to propose an algorithm to control it. The outbred population context was studied through simulated data sets in a wide range of situations.The likelihood ratio test was firstly analyzed under the "one QTL" hypothesis in a backcross population. Designs of sib families were then simulated and analyzed using the QTL Map software. On the basis of the theoretical results in backcross, parameters such as the population size, the density of the genetic map, the QTL effect and the true location of the QTL, were taken into account under the "no QTL" and the "one QTL" hypotheses. A combination of two non parametric tests - the Kolmogorov-Smirnov test and the Mann-Whitney-Wilcoxon test - was used in order to identify the parameters that affected the bias and to specify how much they influenced the estimation of QTL location.
Results:
A theoretical expression of the bias of the estimated QTL location was obtained for a backcross type population. We demonstrated a common source of bias under the "no QTL" and the "one QTL" hypotheses and qualified the possible influence of several parameters. Simulation studies confirmed that the bias exists in outbred populations under both the hypotheses of "no QTL" and "one QTL" on a linkage group. The QTL location was systematically closer to marker locations than expected, particularly in the case of low QTL effect, small population size or low density of markers, i.e. designs with low power. Practical recommendations for experimental designs for QTL detection in outbred populations are given on the basis of this bias quantification. Furthermore, an original algorithm is proposed to adjust the location of a QTL, obtained with interval mapping, which co located with a marker.
Conclusions:
Therefore, one should be attentive when one QTL is mapped at the location of one marker, especially under low power conditions.
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Comparative karyotype analysis and chromosome
evolution in the genus Aplastodiscus (Cophomantini,
Hylinae, Hylidae)
Background:
The frogs of the Tribe Cophomantini present, in general, 2n = 24 karyotype, but data onAplastodiscus showed variation in diploid number from 2n = 24 to 2n = 18. Five species werekaryotyped, one of them for the first time, using conventional and molecular cytogenetictechniques, with the aim to perform a comprehensive comparative analysis towards theunderstanding of chromosome evolution in light of the phylogeny.
Results:
Aplastodiscus perviridis showed 2n = 24, A. arildae and A. eugenioi, 2n = 22, A. leucopygius,2n = 18, and A. callipygius, 2n = 20. In the metaphase I cells of two species only bivalentsoccurred, whereas in A. arildae, A. callipygius, and A. leucopygius one tetravalent was alsoobserved besides the bivalents. BrdU incorporation produced replication bands especially inthe largest chromosomes, and a relatively good banding correspondence was noticed amongsome of them. Silver impregnation and FISH with an rDNA probe identified a single NORpair: the 11 in A. perviridis and A. arildae; the 6 in A. eugenioi; and the 9 in A. callipygiusand A. leucopygius. C-banding showed a predominantly centromeric distribution of theheterochromatin, and in one of the species distinct molecular composition was revealed byCMA3. The telomeric probe hybridised all chromosome ends and additionally disclosed thepresence of telomere-like sequences in centromeric regions of three species.
Conclusions:
Based on the hypothesis of 2n = 24 ancestral karyotype for Aplastodiscus, and considering thekaryotype differences and similarities, two evolutionary pathways through fusion events weresuggested. One of them corresponded to the reduction of 2n = 24 to 22, and the other, thereduction of 2n = 24 to 20, and subsequently to 18. Regarding the NOR, two conditions wererecognised: plesiomorphy, represented by the homeologous small-sized NOR-bearing pairs,and derivation, represented by the NOR in a medium-sized pair. In spite of the apparentuniformity of C-banding patterns, heterogeneity in the molecular composition of somerepetitive regions was revealed by CMA3 staining and by interstitial telomeric labelling. Themeiotic tetravalent might be due to minute reciprocal translocations or to non-chiasmaticectopic pairing between terminal repetitive sequences. The comparative cytogenetic analysisallowed to outline the chromosome evolution and contributed to enlighten the relationshipswithin the genus Aplastodiscus.
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