The Personal Genome Project Canada: findings from whole genome sequences of the inaugural 56 participants.

BACKGROUND: The Personal Genome Project Canada is a comprehensive public data resource that integrates whole genome sequencing data and health information. We describe genomic variation identified in the initial recruitment cohort of 56 volunteers. METHODS: Volunteers were screened for eligibility and provided informed consent for open data sharing. Using blood DNA, we performed whole genome sequencing and identified all possible classes of DNA variants. A genetic counsellor explained the implication of the results to each participant. RESULTS: Whole genome sequencing of the first 56 participants identified 207 662 805 sequence variants and 27 494 copy number variations. We analyzed a prioritized disease-associated data set (n = 1606 variants) according to standardized guidelines, and interpreted 19 variants in 14 participants (25%) as having obvious health implications. Six of these variants (e.g., in BRCA1 or mosaic loss of an X chromosome) were pathogenic or likely pathogenic. Seven were risk factors for cancer, cardiovascular or neurobehavioural conditions. Four other variants - associated with cancer, cardiac or neurodegenerative phenotypes - remained of uncertain significance because of discrepancies among databases. We also identified a large structural chromosome aberration and a likely pathogenic mitochondrial variant. There were 172 recessive disease alleles (e.g., 5 individuals carried mutations for cystic fibrosis). Pharmacogenomics analyses revealed another 3.9 potentially relevant genotypes per individual. INTERPRETATION: Our analyses identified a spectrum of genetic variants with potential health impact in 25% of participants. When also considering recessive alleles and variants with potential pharmacologic relevance, all 56 participants had medically relevant findings. Although access is mostly limited to research, whole genome sequencing can provide specific and novel information with the potential of major impact for health care.

'Lnc'-ing Wnt in female reproductive cancers: therapeutic potential of long non-coding RNAs in Wnt signalling.

Recent discoveries in the non-coding genome have challenged the original central dogma of molecular biology, as non-coding RNAs and related processes have been found to be important in regulating gene expression. MicroRNAs and long non-coding RNAs (lncRNAs) are among those that have gained attention recently in human diseases, including cancer, with the involvement of many more non-coding RNAs (ncRNAs) waiting to be discovered. ncRNAs are a group of ribonucleic acids transcribed from regions of the human genome, which do not become translated into proteins, despite having essential roles in cellular physiology. Deregulation of ncRNA expression and function has been observed in cancer pathogenesis. Recently, the roles of a group of ncRNA known as lncRNA have gained attention in cancer, with increasing reports of their oncogenic involvement. Female reproductive cancers remain a leading cause of death in the female population, accounting for almost a third of all female cancer deaths in 2016. The Wnt signalling pathway is one of the most important oncogenic signalling pathways which is hyperactivated in cancers, including female reproductive cancers. The extension of ncRNA research into their mechanistic roles in human cancers has also led to novel reported roles of ncRNAs in the Wnt pathway and Wnt-mediated oncogenesis. This review aims to provide a critical summary of the respective roles and cellular functions of Wnt-associated lncRNAs in female reproductive cancers and explores the potential of circulating cell-free lncRNAs as diagnostic markers and lncRNAs as therapeutic targets. LINKED ARTICLES: This article is part of a themed section on WNT Signalling: Mechanisms and Therapeutic Opportunities. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v174.24/issuetoc.

Charge carrier transport and lifetimes in n-type and p-type phosphorene as 2D device active materials: an ab initio study.

In this work, we provide a detailed analysis of phosphorene's performance as an n-type and p-type active material. This study is based on first principles calculations of the phosphorene electronic structure, and the resulting electron and hole scattering rates and lifetimes. Emphasis is put on extreme regimes commonly found in semiconductor devices, i.e. high electric fields and heavy doping, where impact ionization and Auger recombination can occur. We found that electron-initiated impact ionization is weaker than the hole-initiated process, when compared to carrier-phonon interaction rates, suggesting resilience to impact ionization initiated breakdown. Moreover, calculated minority electron lifetimes are limited by radiative recombination only, not by Auger processes, suggesting that phosphorene could achieve good quantum efficiencies in optoelectronic devices. The provided scattering rates and lifetimes are critical input data for the modeling and understanding of phosphorene-based device physics.

Properties of atoms under pressure: bonded interactions of the atoms in three perovskites.

The crystal structures for the three perovskites, CaSnO(3), YAlO(3), and LaAlO(3), were geometry optimized at the density functional theory level for a wide range of simulated isotropic pressures up to 80 GPa. The connections between the geometry optimized bond lengths, R(M-O), the values of the electron density, ρ(r(c)), the local kinetic, G(r(c)), potential, V(r(c)), energy densities, H(r(c)), and the Laplacian, ∇(2)(r(c)), at the bond critical points, r(c), for the M-O nonequivalent bonded interactions were examined. With increasing pressure, ρ(r(c)) increases along four distinct trends when plotted in terms of the Al-O, Ca-O, Sn-O, Y-O, and La-O bond lengths, but when the bond lengths were plotted in terms of ρ(r(c))/r where r is the periodic table row number of the M atoms, the data scatter along a single trend modeled by the power law regression expression R(M-O) = 1.41(ρ(r(c))/r)(-0.21), an expression that is comparable with that obtained for the bonded interactions for a large number of silicate and oxides crystals, R(M-O) = 1.46(ρ(r(c))/r)(-0.19) and that obtained for a relatively large number of hydroxyacid molecules R(M-O) = 1.39(s/r)(-0.22) where s is the Pauling bond strength of a bonded interaction. The similarity of the expressions determined for the perovskites, silicate and oxides crystals, and hydroxyacid molecules suggest that the bonded interactions in molecules and crystal are not only similar and comparable. The close correspondence of the expressions for the perovskites, the silicate and oxide crystals, and the molecules indicates that Pauling bond strength and ρ(r(c)) are comparable measures of the bonded interactions, the larger the accumulation of the electron density between the bonded atoms the larger the value of s, the shorter the bond lengths. It also indicates that the bonded interactions that govern the bond length variations behave as if largely short ranged. Like ρ(r(c))/r, the values of G(r(c))/r, V(r(c))/r, ∇(2)(r(c))/r likewise correlate in terms of R(M-O) in a single trend. With increasing pressure, the value of V(r(c)) decreases at a faster rate than G(r(c)) increases consistent with the observation that ρ(r(c)) increases with increasing pressure thereby stabilizing the structures at high pressures. As evinced by the well-developed power law trends between R(M-O) and the bond critical point properties, the bulk of the bonded interactions for the perovskites are concluded to change progressively from closed-shell to intermediate polar covalent interactions with increasing pressure. A well-developed trend between the ratios ∣V(r(c))∣ /G(r(c)) and H(r(c))/ρ(r(c)) is consistent with this conclusion. The employment of a positive value for the Laplacian alone in distinguishing between closed shell and polar covalent bonded interactions is unsatisfactory when 2G(r(c)) > ∣V(r(c))∣ > G(r(c)).

Footprint-based estimates of arch structure are confounded by body composition in adults.

Previous research employing indirect measures of arch structure, such as those derived from footprints, have indicated that obesity results in a "flatter" foot type. In the absence of radiographic measures, however, definitive conclusions regarding the osseous alignment of the foot cannot be made. We determined the effect of body mass index (BMI) on radiographic and footprint-based measures of arch structure. The research was a cross-sectional study in which radiographic and footprint-based measures of foot structure were made in 30 subjects (10 males, 20 female) in addition to standard anthropometric measures of height, weight, and BMI. Multiple (univariate) regression analysis demonstrated that both BMI (ß = 0.39, t(26) = 2.12, p = 0.04) and radiographic arch alignment (ß = 0.51, t(26) = 3.32, p < 0.01) were significant predictors of footprint-based measures of arch height after controlling for all variables in the model (R(2) = 0.59, F(3,26) = 12.3, p < 0.01). In contrast, radiographic arch alignment was not significantly associated with BMI (ß = -0.03, t(26) = -0.13, p = 0.89) when Arch Index and age were held constant (R(2) = 0.52, F(3,26) = 9.3, p < 0.01). Adult obesity does not influence osseous alignment of the medial longitudinal arch, but selectively distorts footprint-based measures of arch structure. Footprint-based measures of arch structure should be interpreted with caution when comparing groups of varying body composition.

Anaplasma phagocytophilum-induced gene expression in both human neutrophils and HL-60 cells.

Anaplasma phagocytophilum (Ap), the etiologic agent of the tick-borne disease human granulocytic anaplasmosis, is an obligate intracellular pathogen unique in its ability to target and replicate within neutrophils. We define and compare the spectra of host gene expression in response to Ap infection of human neutrophils and of HL-60 cells using long (70-mer)-oligonucleotide array technology. In addition to apoptosis-related genes, genes involved in signaling pathways, transcriptional regulation, immune response, host defense, cell adhesion, and cytoskeleton were modulated in neutrophils infected with Ap. Ap infection affected the same pathways in HL-60 cells but transcriptional changes occurred more slowly and in a reduced spectrum of genes. Gene expression changes detected by microarray were confirmed for randomly selected genes by QRT-PCR and Western blot studies. These studies demonstrate for the first time that the ERK pathway is activated in Ap-infected neutrophils and also define multiple pathways that are activated during intracellular Ap infection, which together serve to prolong the cell survival that is needed to allow bacterial replication and survival in neutrophils, which otherwise would rapidly apoptose.

Anaplasma phagocytophilum causes global induction of antiapoptosis in human neutrophils.

Anaplasma phagocytophilum (Ap), the agent of the tick-borne disease human granulocytic anaplasmosis, is an obligate intracellular pathogen unique in its ability to target and replicate within neutrophils. It profoundly inhibits neutrophil apoptosis, prolonging neutrophil survival from hours to days. To determine the basis of antiapoptosis, we compared gene expression in Ap-infected vs mock-infected human neutrophils. Antiapoptosis genes were consistently and significantly up-regulated (2- to 15-fold) within 1-3 h. These genes synergistically inhibit apoptosis through several interconnected pathways, including p38MAPK (MAP2K3), ERK (IER3), PI3K (PRKCD), and NF-kappaB (BCL2A1, NFKB1, NFKBIA, GADD45B). Both extrinsic death receptor (TNFAIP3, CFLAR, SOD2) and intrinsic mitochondrial (BCL2A1, PIM2, BIRC3) pathways were affected as confirmed by reductions in both caspase 3 and caspase 8 activities. Several important antiapoptotic genes noted to be up-regulated in Ap-infected neutrophils were not up-regulated during Ap infection of HL-60 cells (which is not antiapoptotic). In conclusion, just as apoptosis may be triggered through multiple molecular pathways, effective antiapoptosis of neutrophils is achieved rapidly and redundantly by this intracellular pathogen dependent on cell survival.

Trigger factor retards protein export in Escherichia coli.

Trigger factor (TF) is a ribosome-associated protein that interacts with a wide variety of nascent polypeptides in Escherichia coli. Previous studies have indicated that TF cooperates with DnaK to facilitate protein folding, but the basis of this cooperation is unclear. In this study we monitored protein export in E. coli that lack or overproduce TF to obtain further insights into its function. Whereas inactivation of genes encoding most molecular chaperones (including dnaK) impairs protein export, inactivation of the TF gene accelerated protein export and suppressed the need for targeting factors to maintain the translocation competence of presecretory proteins. Furthermore, overproduction of TF (but not DnaK) markedly retarded protein export. Manipulation of TF levels produced similar effects on the export of a cytosolic enzyme fused to a signal peptide. The data strongly suggest that TF has a unique ability to sequester nascent polypeptides for a relatively prolonged period. Based on our results, we propose that TF and DnaK promote protein folding by distinct (but complementary) mechanisms.

Population Dynamics of Rhizobium leguminosarum Tn5 Mutants with Altered Cell Surface Properties Introduced into Sterile and Nonsterile Soils.

The influence of cell surface properties on attachment to soil particles and on population dynamics of introduced bacteria was studied in sterilized and nonsterilized loamy sand and silt loam. Rhizobium leguminosarum RBL5523 and three Tn5 mutants (RBL5762, RBL5810, and RBL5811) with altered cell surface properties were used. Cellulose fibrils were not produced by RBL5762. Both RBL5810 and RBL5811 produced 80 to 90% less soluble exopolysaccharides and RBL5811 had, in addition, an altered lipopolysaccharide composition. In sterilized soil the total number of cells as well as the number of particle-associated cells of RBL5523 and RBL5810 were, in general, higher as compared with cell numbers of RBL5762 and RBL5811. Differences between strains in percentage of particle-associated cells in sterilized soil were only found at high inoculum densities, when populations increased little. In the nonsterilized silt loam, final population sizes, as well as numbers of particle-associated cells, of the parental strain (RBL5523) were higher than those of strains with altered cell surface properties after 56 and 112 days of incubation. But in general, differences in survival among the strains were not very marked. The importance of association with soil particles or aggregates for the survival of introduced cells was affirmed by the pronounced increase of the percentage of particle-associated cells during incubation in nonsterilized as well as sterilized soil. However, no clear relation among altered cell surface properties, particle association, and survival was found.

Role of Microniches in Protecting Introduced Rhizobium leguminosarum biovar trifolii against Competition and Predation in Soil.

The importance of microniches for the survival of introduced Rhizobium leguminosarum biovar trifolii cells was studied in sterilized and recolonized sterilized loamy sand and silt loam. The recolonized soils contained several species of soil microorganisms but were free of protozoa. Part of these soil samples was inoculated with the flagellate Bodo saltans, precultured on rhizobial cells. The introduced organisms were enumerated in different soil fractions by washing the soil, using a standardized washing procedure. With this method, free organisms and organisms associated with soil particles or aggregates >50 mum were separated. The total number of rhizobia was influenced slightly (silt loam) or not at all (loamy sand) by the recolonization with microorganisms or by the addition of flagellates alone. However, when both flagellates and microorganisms were present, numbers of rhizobia decreased drastically. This decrease was more than the sum of both effects separately. Nevertheless, populations of rhizobia were still higher than in natural soil. In the presence of flagellates, higher percentages of rhizobia and other microorganisms were associated with soil particles or aggregates >50 mum than in the absence of flagellates. In recolonized soils, however, the percentages of particle-associated rhizobia were lower than in soils not recolonized previous to inoculation. Thus, the presence of other microorganisms hindered rhizobial colonization of sites where they are normally associated with soil particles or aggregates.