Historical human remains identification through maternal and paternal genetic signatures in a founder population with extensive genealogical record.

OBJECTIVES: We describe a method to identify human remains excavated from unmarked graves in historical Québec cemeteries by combining parental-lineage genetic markers with the whole-population genealogy of Québec contained in the BALSAC database. MATERIALS AND METHODS: The remains of six men were exhumed from four historical cemeteries in the province of Québec, Canada. DNA was extracted from the remains and genotyped to reveal their mitochondrial and Y-chromosome haplotypes, which were compared to a collection of haplotypes of genealogically-anchored modern volunteers. Maternal and paternal genealogies were searched in the BALSAC genealogical record for parental couples matching the mitochondrial and the Y-chromosome haplotypic signatures, to identify candidate sons from whom the remains could have originated. RESULTS: Analysis of the matching genealogies identified the parents of one man inhumed in the cemetery of the investigated parish during its operating time. The candidate individual died in 1833 at the age of 58, a plausible age at death in light of osteological analysis of the remains. DISCUSSION: This study demonstrates the promising potential of coupling genetic information from living individuals to genealogical data in BALSAC to identify historical human remains. If genetic coverage is increased, the genealogical information in BALSAC could enable the identification of 87% of the men (n = 178,435) married in Québec before 1850, with high discriminatory power in most cases since >75% of the parental couples have unique biparental signatures in most regions. Genotyping and identifying Québec's historical human remains are a key to reconstructing the genomes of the founders of Québec and reinhuming archeological remains with a marked grave.

Modeling gene-environment interactions in longitudinal family studies: a comparison of methods and their application to the association between the IGF pathway and childhood obesity.

BACKGROUND: The interactive effect of the IGF pathway genes with the environment may contribute to childhood obesity. Such gene-environment interactions can take on complex forms. Detecting those relationships using longitudinal family studies requires simultaneously accounting for correlations within individuals and families. METHODS: We studied three methods for detecting interaction effects in longitudinal family studies. The twin model and the nonparametric partition-based score test utilized individual outcome averages, whereas the linear mixed model used all available longitudinal data points. Simulation experiments were performed to evaluate the methods' power to detect different gene-environment interaction relationships. These methods were applied to the Quebec Newborn Twin Study data to test for interaction effects between the IGF pathway genes (IGF-1, IGFALS) and environmental factors (physical activity, daycare attendance and sleep duration) on body mass index outcomes. RESULTS: For the simulated data, the twin model with the mean time summary statistic yielded good performance overall. Modelling an interaction as linear when the true model had a different relationship influenced power; for certain non-linear interactions, none of the three methods were effective. Our analysis of the IGF pathway genes showed suggestive association for the joint effect of IGF-1 variant at position 102,791,894 of chromosome 12 and physical activity. However, this association was not statistically significant after multiple testing correction. CONCLUSIONS: The analytical approaches considered in this study were not robust to different gene-environment interactions. Methodological innovations are needed to improve the current methods' performances for detecting non-linear interactions. More studies are needed in order to better understand the IGF pathway's role in childhood obesity development.

Photophysics of a Ruthenium Complex with a π-Extended Dipyridophenazine Ligand for DNA Quadruplex Labeling.

The light-switch mechanism of the complex [Ru(bpy)2(Br-dpqp)](PF6)2 (1, bpy = 2,2'-bipyridine, Br-dpqp = 12-bromo-14-ethoxydipyrido[3,2- a:2',3'- c]quinolino[3,2- h]phenazine), i.e., a light-up probe for the selective labeling of G-quadruplexes, is investigated by time-resolved transient absorption and emission spectroscopy. We show that, in contrast to the prototypical light-switch complex [Ru(bpy)2(dppz)](PF6)2 (2, dppz = dipyrido[3,2- a:2',3'- c]phenazine), a 3ππ* state localized on the π-extended ligand is the state determining the excited-state properties in both protic and aprotic environments. In aprotic environments, emission originates from a bright 3MLCTphen state, which is thermally accessible from the 3ππ* state at ambient temperature. In the presence of water, i.e., in environments resembling in cellulo situations, the thermally accessible 3MLCT state is altered and becomes close in energy to the 3ππ* state, which induces a rapid excited-state deactivation of the 3ππ* state and a comparably weak emission.

Selective Luminescent Labeling of DNA and RNA Quadruplexes by π-Extended Ruthenium Light-Up Probes.

A series of RuII complexes exhibiting π-extended, acridine-based ancillary chelating heterocycles display high affinity and selectivity for DNA and RNA quadruplexes. The most promising candidates (3, 4) possess remarkable light-up luminophore properties (up to 330-fold luminescence enhancement upon interaction with quadruplexes), enabling them to discriminate quadruplexes from genomic DNA owing to a photochemical mechanism involving DNA protection against non-radiative decay (DAND), thus deviating from the other complexes of this series of ligands that exhibit an excited-state intramolecular proton transfer (ESIPT) that quenches their luminescence. The in vitro and preliminary in cellulo results shown here confirm the interest of this new family of fluorophores as invaluable molecular tools to detect G-quadruplexes in cells.

Resonance Raman Study of New Pyrrole-Anchoring Dyes for NiO-Sensitized Solar Cells.

Three dyes for p-type dye-sensitised solar cells containing a novel doubly anchored pyrrole donor group were synthesised and their solar cell performances were evaluated. Dye 1 was comprised of a phenyl-thiophene linker and a maleonitrile acceptor, which has been established as an effective motif in other push-pull dyes. Two boron dipyrromethane analogues, dyes 2 and 3, were made with different linker groups to compare their effect on the behaviour of these dyes adsorbed onto nickel oxide (dye|NiO) under illumination. The photoexcited states of dye|NiO were probed using resonance Raman spectroscopy and compared to dyes anchored using the conventional 4-aminobenzoic acid moiety (P1 and 4). All three components, the anchor, the linker and the acceptor group were found to alter both the electronic structure following excitation and the overall solar cell performance. The bodipy acceptor gave a better performance than the maleonitrile acceptor when the pyrrole anchor was used, which is the opposite of the triphenylamine push-pull dyes. The linker group was found to have a large influence on the short-circuit current and efficiency of the p-type cells constructed.

Design and characterisation of bodipy sensitizers for dye-sensitized NiO solar cells.

A series of photosensitizers for NiO-based dye-sensitized solar cells is presented. Three model compounds containing a triphenylamine donor appended to a boron dipyrromethene (bodipy) chromophore have been successfully prepared and characterised using emission spectroscopy, electrochemistry and spectroelectrochemistry, to ultimately direct the design of dyes with more complex structures. Carboxylic acid anchoring groups and thiophene spacers were appended to the model compounds to provide five dyes which were adsorbed onto NiO and integrated into dye-sensitized solar cells. Solar cells incorporating the simple Bodipy-CO2H dye were surprisingly promising relative to the more complex dye 4. Cell performances were improved with dyes which had increased electronic communication between the donor and acceptor, achieved by incorporating a less hindered bodipy moiety. Further increases in performances were obtained from dyes which contained a thiophene spacer. Thus, the best performance was obtained for 7 which generated a very promising photocurrent density of 5.87 mA cm(-2) and an IPCE of 53%. Spectroelectrochemistry combined with time-resolved transient absorption spectroscopy were used to determine the identity and lifetime of excited state species. Short-lived (ps) transients were recorded for 4, 5 and 7 which are consistent with previous studies. Despite a longer lived (25 ns) charge-separated state for 6/NiO, there was no increase in the photocurrent generated by the corresponding solar cell.

Correction: Design and characterisation of bodipy sensitizers for dye-sensitized NiO solar cells.

Correction for 'Design and characterisation of bodipy sensitizers for dye-sensitized NiO solar cells' by Gareth H. Summers et al., Phys. Chem. Chem. Phys., 2016, DOI: 10.1039/c5cp05177k.

GENLIB: an R package for the analysis of genealogical data.

BACKGROUND: Founder populations have an important role in the study of genetic diseases. Access to detailed genealogical records is often one of their advantages. These genealogical data provide unique information for researchers in evolutionary and population genetics, demography and genetic epidemiology. However, analyzing large genealogical datasets requires specialized methods and software. The GENLIB software was developed to study the large genealogies of the French Canadian population of Quebec, Canada. These genealogies are accessible through the BALSAC database, which contains over 3 million records covering the whole province of Quebec over four centuries. Using this resource, extended pedigrees of up to 17 generations can be constructed from a sample of present-day individuals. RESULTS: We have extended and implemented GENLIB as a package in the R environment for statistical computing and graphics, thus allowing optimal flexibility for users. The GENLIB package includes basic functions to manage genealogical data allowing, for example, extraction of a part of a genealogy or selection of specific individuals. There are also many functions providing information to describe the size and complexity of genealogies as well as functions to compute standard measures such as kinship, inbreeding and genetic contribution. GENLIB also includes functions for gene-dropping simulations. The goal of this paper is to present the full functionalities of GENLIB. We used a sample of 140 individuals from the province of Quebec (Canada) to demonstrate GENLIB's functions. Ascending genealogies for these individuals were reconstructed using BALSAC, yielding a large pedigree of 41,523 individuals. Using GENLIB's functions, we provide a detailed description of these genealogical data in terms of completeness, genetic contribution of founders, relatedness, inbreeding and the overall complexity of the genealogical tree. We also present gene-dropping simulations based on the whole genealogy to investigate identical-by-descent sharing of alleles and chromosomal segments of different lengths and estimate probabilities of identical-by-descent sharing. CONCLUSIONS: The R package GENLIB provides a user friendly and flexible environment to analyze extensive genealogical data, allowing an efficient and easy integration of different types of data, analytical methods and additional developments and making this tool ideal for genealogical analysis.

Unexpected drastic decrease in the excited-state electronic communication between porphyrin chromophores covalently linked by a palladium(II) bridge.

A dyad built up of a zinc(II) porphyrin and the corresponding free base, [Zn-Fb], fused to N-heterocyclic carbene (NHCs) ligands, respectively acting as singlet energy donor and acceptor, and a bridging trans-PdI2 unit, along with the corresponding [Zn-Zn] and [Fb-Fb] dimers were prepared and investigated by absorption and emission spectroscopy and density functional computations. Despite favorable structural and spectroscopic parameters, unexpectedly slow singlet energy transfer rates are measured in comparison with the predicted values by the Förster theory and those observed for other structurally related dyads. This observation is rationalized by the lack of large molecular orbital (MO) overlaps between the frontier MOs of the donor and acceptor, thus preventing a double electron exchange through the trans-PdI2 bridge, and by an electronic shielding induced by the presence of this same linker preventing the two chromophores to fully interact via their transition dipoles.

Female-to-male breeding ratio in modern humans-an analysis based on historical recombinations.

Was the past genetic contribution of women and men to the current human population equal? Was polygyny (excess of breeding women) present among hominid lineages? We addressed these questions by measuring the ratio of population recombination rates between the X chromosome and the autosomes, rho(X)/rho(A). The X chromosome recombines only in female meiosis, whereas autosomes undergo crossovers in both sexes; thus, rho(X)/rho(A) reflects the female-to-male breeding ratio, beta. We estimated beta from rho(X)/rho(A) inferred from genomic diversity data and calibrated with recombination rates derived from pedigree data. For the HapMap populations, we obtained beta of 1.4 in the Yoruba from West Africa, 1.3 in Europeans, and 1.1 in East Asian samples. These values are consistent with a high prevalence of monogamy and limited polygyny in human populations. More mutations occur during male meiosis as compared to female meiosis at the rate ratio referred to as alpha. We show that at alpha not equal 1, the divergence rates and genetic diversities of the X chromosome relative to the autosomes are complex functions of both alpha and beta, making their independent estimation difficult. Because our estimator of beta does not require any knowledge of the mutation rates, our approach should allow us to dissociate the effects of alpha and beta on the genetic diversity and divergence rate ratios of the sex chromosomes to the autosomes.

Porphyrins fused to N-heterocyclic carbenes (NHCs): modulation of the electronic and catalytic properties of NHCs by the central metal of the porphyrin.

We report herein a detailed study of the use of porphyrins fused to imidazolium salts as precursors of N-heterocyclic carbene ligands 1 M. Rhodium(I) complexes 6 M-9 M were prepared by using 1 M ligands with different metal cations in the inner core of the porphyrin (M=Ni(II) , Zn(II) , Mn(III) , Al(III) , 2H). The electronic properties of the corresponding N-heterocyclic carbene ligands were investigated by monitoring the spectroscopic changes occurring in the cod and CO ancillary ligands of [(1 M)Rh(cod)Cl] and [(1 M)Rh(CO)2 Cl] complexes (cod=1,5-cyclooctadiene). Porphyrin-NHC ligands 1 M with a trivalent metal cation such as Mn(III) and Al(III) are overall poorer electron donors than porphyrin-NHC ligands with no metal cation or incorporating a divalent metal cation such as Ni(II) and Zn(II) . Imidazolium salts 3 M (M=Ni, Zn, Mn, 2H) have also been used as NHC precursors to catalyze the ring-opening polymerization of L-lactide. The results clearly show that the inner metal of the porphyrin has an important effect on the reactivity of the outer carbene.

An X-linked haplotype of Neandertal origin is present among all non-African populations.

Recent work on the Neandertal genome has raised the possibility of admixture between Neandertals and the expanding population of Homo sapiens who left Africa between 80 and 50 Kya (thousand years ago) to colonize the rest of the world. Here, we provide evidence of a notable presence (9% overall) of a Neandertal-derived X chromosome segment among all contemporary human populations outside Africa. Our analysis of 6,092 X-chromosomes from all inhabited continents supports earlier contentions that a mosaic of lineages of different time depths and different geographic provenance could have contributed to the genetic constitution of modern humans. It indicates a very early admixture between expanding African migrants and Neandertals prior to or very early on the route of the out-of-Africa expansion that led to the successful colonization of the planet.

Determining the impact of unknown individuals in criminality using network analysis of DNA matches.

Criminal offenders missing from police files limit the capacity to reconstruct criminal networks for criminological research and operational purposes. Recent studies show that forensic DNA databanks offer potential to address this problem, through large-scale analysis of DNA matches, many of which involve unidentified offenders. Applying social network analysis (SNA) to 18 years of DNA match data from Québec, Canada, we found that 1400 unknowns do not occupy more marginal positions in the network than 13,000 known offenders, and explain up to 18% of SNA values (e.g., betweenness centrality) for the latter while supporting 46% of their clustering values. Our results contrast with previous studies, showing moreover that unknown individuals who are positioned centrally in a network may have a larger impact than previously expected on investigation policing with implications for forensic intelligence.

Haplotype allelic classes for detecting ongoing positive selection.

BACKGROUND: Natural selection eliminates detrimental and favors advantageous phenotypes. This process leaves characteristic signatures in underlying genomic segments that can be recognized through deviations in allelic or haplotypic frequency spectra. To provide an identifiable signature of recent positive selection that can be detected by comparison with the background distribution, we introduced a new way of looking at genomic polymorphisms: haplotype allelic classes. RESULTS: The model combines segregating sites and haplotypic information in order to reveal useful data characteristics. We developed a summary statistic, Svd, to compare the distribution of the haplotypes carrying the selected allele with the distribution of the remaining ones. Coalescence simulations are used to study the distributions under standard population models assuming neutrality, demographic scenarios and selection models. To test, in practice, haplotype allelic class performance and the derived statistic in capturing deviation from neutrality due to positive selection, we analyzed haplotypic variation in detail in the locus of lactase persistence in the three HapMap Phase II populations. CONCLUSIONS: We showed that the Svd statistic is less sensitive than other tests to confounding factors such as demography or recombination. Our approach succeeds in identifying candidate loci, such as the lactase-persistence locus, as targets of strong positive selection and provides a new tool complementary to other tests to study natural selection in genomic data.

Assessment of Chlamydia trachomatis infection by Cobas Amplicor PCR and in-house LightCycler assays using PreservCyt and 2-SP media in voluntary legal abortions.

Chlamydial infection of the upper genital tract after abortion is well recognized, but routine screening for infection before termination is rare, and few centres are aware of the prevalence of post-abortion complications in their patient population. Knowledge of the patient population is the best guide for developing screening strategies. The aim of this study was to determine the prevalence of chlamydial infection in patients presenting for legal termination of pregnancy, and to assess the presence of Chlamydia trachomatis by PCR on specimens collected in either PreservCyt (ThinPrep) or 2-sucrose phosphate (2-SP) transport medium. Two hundred and eleven single, sexually active women, aged 15-26 years, attending the Gynaecology and Obstetric Hospital, Amiens, France, for surgical termination of pregnancy were enrolled in this study from June 2002 to June 2003. C. trachomatis detection using a Cobas Amplicor PCR test (Roche Diagnostics) targeting a 207 bp segment of the common cryptic plasmid and a quantitative LightCycler real-time PCR (LC-PCR) (Roche Diagnostics) targeting a 123 bp fragment within the highly conserved constant domain 3 of the single-chromosome-copy ompA gene were performed on endocervical swabs in 2-SP, and on specimens collected using a cytobrush and placed in PreservCyt medium. The in-house LC-PCR was used as a chromosomal diagnosis method and to determine the load of C. trachomatis. This method was able to detect the mutant Swedish variant with a deletion of 377 bp in the target area in the cryptic plasmid, which is the region targeted by the Cobas Amplicor PCR test. C. trachomatis was detected in 19/211 patients (9 %) by both PCR methods. Among the 19 infected women, C. trachomatis was detected by the Cobas Amplicor PCR in 16 specimens in PreservCyt (7.6 %) and in 12 endocervical swabs in 2-SP (5.7 %). Specimens from only nine women were PCR-positive in both PreservCyt and 2-SP media by this method. Cobas Amplicor PCR revealed that 10.9 and 2.3 % of the PreservCyt and 2-SP samples, respectively, contained inhibitors. The same 19 infected women were LC-PCR positive in both PreservCyt and 2-SP samples. No additional infected women were found by this last method; thus, it was concluded that none of the samples contained the new variant of C. trachomatis. The load in each sample varied from 10(2) to 10(7) copies ml(-1).

STRmix™ put to the test: 300 000 non-contributor profiles compared to four-contributor DNA mixtures and the impact of replicates.

Probabilistic genotyping approaches are increasingly used for the interpretation of DNA mixtures. To explore the specificity of one of these systems (STRmix™), we conducted an extensive study using 24 complex mixtures: all were known or apparent 4-person mixtures with at least one contributor representing less than 20% of total DNA, and all mixtures had at least one contributor with suboptimal DNA quantity. Those mixtures were either generated in-house or from casework. All the mixtures were compared to 300,000 virtual non-contributors, resulting in a dataset of 7.2 million comparisons. The great majority of the non-contributor comparisons led to a LR lower than 1 for a specificity of 99.1%. The effect of using replicate amplifications to calculate the LR of non-contributors was also assessed as triplicates were used and led to an increased specificity of 99.8%. The very large extent of the analyzed data shows that STRmix™ has an excellent ability to discriminate non-contributors from complex DNA mixtures.

Investigating Gene-Gene and Gene-Environment Interactions in the Association Between Overnutrition and Obesity-Related Phenotypes.

Introduction: Animal studies suggested that NFKB1, IKBKB, and SOCS3 genes could be involved in the association between overnutrition and obesity. This study aims to investigate interactions involving these genes and macronutrient intakes affecting obesity-related phenotypes. Methods: We used a traditional statistical method, logistic regression, and compared it to alternative statistical method, multifactor dimensionality reduction (MDR) and penalized logistic regression (PLR), to better detect genes/environment interactions in the Toronto Nutrigenomics and Health Study (n = 1639) using dichotomized body mass index (BMI) and waist circumference as obesity-related phenotypes. Exposure variables included genotype on 54 single nucleotide polymorphisms (NFKB1: 18, IKBKB: 9, SOCS3: 27), macronutrient (carbohydrates, protein, fat) and alcohol intakes and ethno-cultural background. Results: After correction for multiple testing, no interaction was found using logistic regression. MDR identified interactions between SOCS3 rs6501199 and rs4969172, and IKBKB rs3747811 affecting BMI in the Caucasian population; SOCS3 rs6501199 and NFKB1 rs1609798 affecting WC in the Caucasian population; and SOCS3 rs4436839 and IKBKB rs3747811 affecting WC in the South Asian population. PLR found a main effect of SOCS3 rs12944581 on BMI among the South Asian population. Conclusion: While MDR and PLR had discordant results, some models support results from previous studies. These results emphasize the need to use alternative statistical methods to investigate high-order interactions and suggest that variants in the nutrient-responsive hypothalamic IKKB/NF-kB signaling pathway may be involved in obesity pathogenesis.

The lack of a systematic validation of reference genes: a serious pitfall undervalued in reverse transcription-polymerase chain reaction (RT-PCR) analysis in plants.

Reverse transcription-polymerase chain reaction (RT-PCR) approaches have been used in a large proportion of transcriptome analyses published to date. The accuracy of the results obtained by this method strongly depends on accurate transcript normalization using stably expressed genes, known as references. Statistical algorithms have been developed recently to help validate reference genes, and most studies of gene expression in mammals, yeast and bacteria now include such validation. Surprisingly, this important approach is under-utilized in plant studies, where putative housekeeping genes tend to be used as references without any appropriate validation. Using quantitative RT-PCR, the expression stability of several genes commonly used as references was tested in various tissues of Arabidopsis thaliana and hybrid aspen (Populus tremula x Populus tremuloides). It was found that the expression of most of these genes was unstable, indicating that their use as references is inappropriate. The major impact of the use of such inappropriate references on the results obtained by RT-PCR is demonstrated in this study. Using aspen as a model, evidence is presented indicating that no gene can act as a universal reference, implying the need for a systematic validation of reference genes. For the first time, the extent to which the lack of a systematic validation of reference genes is a stumbling block to the reliability of results obtained by RT-PCR in plants is clearly shown.

An artificial photosynthetic system for photoaccumulation of two electrons on a fused dipyridophenazine (dppz)-pyridoquinolinone ligand.

Increasing the efficiency of molecular artificial photosynthetic systems is mandatory for the construction of functional devices for solar fuel production. Decoupling the light-induced charge separation steps from the catalytic process is a promising strategy, which can be achieved thanks to the introduction of suitable electron relay units performing charge accumulation. We report here on a novel ruthenium tris-diimine complex able to temporarily store two electrons on a fused dipyridophenazine-pyridoquinolinone π-extended ligand upon visible-light irradiation in the presence of a sacrificial electron donor. Full characterization of this compound and of its singly and doubly reduced derivatives thanks to resonance Raman, EPR and (TD)DFT studies allowed us to localize the two electron-storage sites and to relate charge photoaccumulation with proton-coupled electron transfer processes.

Patterns of variation in DNA segments upstream of transcription start sites.

It is likely that evolutionary differences among species are driven by sequence changes in regulatory regions. Likewise, polymorphisms in the promoter regions may be responsible for interindividual differences at the level of populations. We present an unbiased survey of genetic variation in 2-kb segments upstream of the transcription start sites of 28 protein-coding genes, characterized in five population groups of different geographic origin. On average, we found 9.1 polymorphisms and 8.8 haplotypes per segment with corresponding nucleotide and haplotype diversities of 0.082% and 58%, respectively. We characterized these segments through different summary statistics, Hardy-Weinberg equilibria fixation index (Fst) estimates, and neutrality tests, as well as by analyzing the distributions of haplotype allelic classes, introduced here to assess the departure from neutrality and examined by coalescent simulations under a simple population model, assuming recombinations or different demography. Our results suggest that genetic diversity in some of these regions could have been shaped by purifying selection and driven by adaptive changes in the other, thus explaining the relatively large variance in the corresponding genetic diversity indices loci. However, some of these effects could be also due to linkage with surrounding sequences, and the neutralists' explanations cannot be ruled out given uncertainty in the underlying demographic histories and the possibility of random effects due to the small size of the studied segments.