Identification of Medically Actionable Secondary Findings in the 1000 Genomes

The American College of Medical Genetics and Genomics (ACMG) recommends that clinical sequencing laboratories return secondary findings in 56 genes associated with medically actionable conditions. Our goal was to apply a systematic, stringent approach consistent with clinical standards to estimate the prevalence of pathogenic variants associated with such conditions using a diverse sequencing reference sample. Candidate variants in the 56 ACMG genes were selected from Phase 1 of the 1000 Genomes dataset, which contains sequencing information on 1,092 unrelated individuals from across the world. These variants were filtered using the Human Gene Mutation Database (HGMD) Professional version and defined parameters, appraised through literature review, and examined by a clinical laboratory specialist and expert physician. Over 70,000 genetic variants were extracted from the 56 genes, and filtering identified 237 variants annotated as disease causing by HGMD Professional. Literature review and expert evaluation determined that 7 of these variants were pathogenic or likely pathogenic. Furthermore, 5 additional truncating variants not listed as disease causing in HGMD Professional were identified as likely pathogenic. These 12 secondary findings are associated with diseases that could inform medical follow-up, including cancer predisposition syndromes, cardiac conditions, and familial hypercholesterolemia. The majority of the identified medically actionable findings were in individuals from the European (5/379) and Americas (4/181) ancestry groups, with fewer findings in Asian (2/286) and African (1/246) ancestry groups. Our results suggest that medically relevant secondary findings can be identified in approximately 1% (12/1092) of individuals in a diverse reference sample. As clinical sequencing laboratories continue to implement the ACMG recommendations, our results highlight that at least a small number of potentially important secondary findings can be selected for return. Our results also confirm that understudied populations will not reap proportionate benefits of genomic medicine, highlighting the need for continued research efforts on genetic diseases in these populations.     

New records for prehistoric introduction of Neotropical mammals to the West Indies: evidence from Carriacou,Lesser Antilles

Aim This paper investigates the prehistoric introduction of five mammalian taxa to Carriacou (Lesser Antilles) and refines the known anthropogenic ranges for these fauna in the pre‐Columbian West Indies. The importance of such records for understanding the region’s historical biogeography and ecology is considered. Location Carriacou Island, Grenada (12°28′ N, 61°26′ W). Methods Zooarchaeological assemblages from Carriacou’s earliest documented prehistoric sites, Grand Bay and Sabazan, were analysed, and exotic taxa were identified and quantified. The timing of introductions was established based on multiple radiocarbon assays, including three new accelerator mass spectrometry (AMS) direct dates obtained on the bone of exotic taxa. Source species and location(s) are considered and compared with known prehistoric records for the Caribbean to synthesize anthropogenic distributions for the pre‐Columbian period. The contexts of the zooarchaeological remains are evaluated to better understand the nature and purpose of introductions. Results Zooarchaeological investigation on Carriacou reveals the occurrence of multiple mammal introductions from South American between c. ad 700 and ad 1400. This paper presents the first records for guinea pig (Cavia sp.), armadillo (Dasypus sp.), peccary (Tayassu/Pecari sp.), opossum (Didelphis sp.) and agouti (Dasyprocta sp.) from the island. Human‐mediated transport of these taxa is indicated by their absence from the record prior to human settlement of Carriacou. Several translocated species are either rare or entirely unknown for the region, and overall West Indian distributions are temporally and spatially discontinuous. Archaeological contexts indicate that mammalian introductions arose from human subsistence needs, but other social factors may have shaped the dispersal of these fauna. Main conclusions The taxonomic combination and richness of Carriacou’s introduced fauna are unusual within the region. Importantly, the new records significantly improve the known pre‐Columbian geographic range for peccary, guinea pig and armadillo. Integrated with regional records, these data augment our understanding of the Caribbean’s historical biogeography, and have the potential to improve our understanding of human mobility and anthropogenic environmental impacts in the West Indies prior to the arrival of Europeans.     

Morphological gradients in the starling basilar papilla

The starling cochlea was studied with TEM at four locations along the basilar papilla to investigate gradients in morphological features over the papilla's length and width. Hair cell shape changes continuously from neural to abneural and from basal to apical. Unlike the situation in mammals, there are no distinct populations of hair cells; the previously described types (tall hair cells and short hair cells) are merely extremes in a continuum. Contacts between THC are a normal feature. Except at the base of the papilla, SHC have very large cuticular plates, suggesting a micromechanical function for these cells. In contrast to the THC, the SHC normally completely lack afferent innervation; this indicates that their function is restricted to within the basilar papilla itself. © 1992 Wiley-Liss, Inc.     

A Candidate Subspecies Discrimination System Involving a Vomeronasal Receptor Gene with Different Alleles Fixed in M. m. domesticus and M. m. musculus

Assortative mating, a potentially efficient prezygotic reproductive barrier, may prevent loss of genetic potential by avoiding the production of unfit hybrids (i.e., because of hybrid infertility or hybrid breakdown) that occur at regions of secondary contact between incipient species. In the case of the mouse hybrid zone, where two subspecies of Mus musculus (M. m. domesticus and M. m. musculus) meet and exchange genes to a limited extent, assortative mating requires a means of subspecies recognition. We based the work reported here on the hypothesis that, if there is a pheromone sufficiently diverged between M. m. domesticus and M. m. musculus to mediate subspecies recognition, then that process must also require a specific receptor(s), also sufficiently diverged between the subspecies, to receive the signal and elicit an assortative mating response. We studied the mouse V1R genes, which encode a large family of receptors in the vomeronasal organ (VNO), by screening Perlegen SNP data and identified one, Vmn1r67, with 24 fixed SNP differences most of which (15/24) are nonsynonymous nucleotide substitutions between M. m. domesticus and M. m. musculus. We observed substantial linkage disequilibrium (LD) between Vmn1r67 and Abpa27, a mouse salivary androgen-binding protein gene that encodes a proteinaceous pheromone (ABP) capable of mediating assortative mating, perhaps in conjunction with its bound small lipophilic ligand. The LD we observed is likely a case of association rather than residual physical linkage from a very recent selective sweep, because an intervening gene, Vmn1r71, shows significant intra(sub)specific polymorphism but no inter(sub)specific divergence in its nucleotide sequence. We discuss alternative explanations of these observations, for example that Abpa27 and Vmn1r67 are coevolving as signal and receptor to reinforce subspecies hybridization barriers or that the unusually divergent Vmn1r67 allele was not a product of fast positive selection, but was derived from an introgressed allele, possibly from Mus spretus.     

New calcium indicators and buffers with high selectivity against magnesium and protons: design, synthesis, and properties of prototype structures

A new family of high-affinity buffers and optical indicators for Ca2+ is rationally designed and synthesized. The parent compound is 1,2-bis(o-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid (BAPTA), a relative of the well-known chelator EGTA [ethylene glycol bis(beta-aminoethyl ether)-N,N,N',N'-tetraacetic acid] in which methylene links between oxygen and nitrogen are replaced by benzene rings. BAPTA and its derivatives share the high (greater than 10(5)) selectivity for Ca2+ over Mg2+ of EGTA but are very much less affected by pH changes and are faster at taking up and releasing Ca2+. The affinity of the parent compound for Ca2+ (dissociation constant 1.1 x 10(-7) M in 0.1 M KCl) may be strengthened or weakened by electron-releasing or -withdrawing substituents on the aromatic rings. The Ca2+ and Mg2+ affinities may further be altered by replacing the ether oxygens by heterocyclic nitrogen atoms. The compounds described are fluorescent Ca2+ indicators absorbing in the ultraviolet region; the very large spectral shifts observed on binding Ca2+ fit the prediction that complexation should hinder the conjugation of the nitrogen lone-pair electrons with the aromatic rings. Derivatives with quinoline nuclei are notable for their high sensitivity of fluorescent quantum yield to the binding of Ca2+ but not of Mg2+. Preliminary biological tests have so far revealed little or no binding to membranes or toxic effects following intracellular microinjection.     

Impact of vaginal microbiome communities on HIV antiretroviral-based pre-exposure prophylaxis (PrEP) drug metabolism

Despite the efficacy of antiretroviral-based pre-exposure prophylactics (PrEP) in men who have sex with men, studies in women have produced widely varying outcomes. Recent evidence demonstrates that vaginal microbial communities are associated with increased HIV acquisition risk and may impact PrEP efficacy. Here, we investigate the mechanisms underlying how vaginal bacteria alter PrEP drug levels and impact HIV infection rates ex vivo. Using cervicovaginal lavages (CVLs) from women with or without bacterial vaginosis (BV), we identified microbial metabolism of PrEP drugs in BV samples through LC-MS/MS analysis of soluble drug levels and metabolite formation in dual T-cell cultures. CVL samples were assessed for microbiome analysis using sequencing of bacterial 16S rRNA genes. We also observed non-Lactobacillus bacteria that are associated with BV may potentially impact PrEP efficacy through increased HIV infection rates in co-cultures containing Lactobacillus or BV bacteria, PrEP drugs, CEM-GFP cells, and HIV-1_LAI virus. Finally, we used these data to develop a novel predictive mathematical simulation modeling system to predict these drug interactions for future trials. These studies demonstrate how dysbiotic vaginal microbiota may impact PrEP drugs and provides evidence linking vaginal bacteria to PrEP efficacy in women.     

Water Binding in Legume Seeds

The physical status of water in seeds has a pivotal role in determining the physiological reactions that can take place in the dry state. Using water sorption isotherms from cotyledon and axis tissue of five leguminous seeds, the strength of water binding and the numbers of binding sites have been estimated using van't Hoff analyses and the D'Arcy/Watt equation. These parameters of water sorption are calculated for each of the three regions of water binding and for a range of temperatures. Water sorption characteristics are reflective of the chemical composition of the biological materials as well as the temperature at which hydration takes place. Changes in the sorption characteristics with temperature and hydration level may suggest hydration-induced structural changes in cellular components.     

Sequential activation and lethal hit measured by [Ca2+]i in individual cytolytic T cells and targets.

Changes in cytosolic free calcium ([Ca2+]i) have been continuously imaged during the interaction of the H-2Kb specific cytotoxic T cell lymphocyte (CTL) BM 3.3, with either the H-2Kb EL4.BU or the H-2Kk RDM4 cell lines. Activation of the CTLs by EL4.BU raises [Ca2+]i to several hundred nanomolar in the CTL. Frequently [Ca2+]i is preferentially elevated in the region of the CTL furthest from the site of target contact. These responses require external Ca2+ suggesting that they are generated by the plasma membrane and not internal stores. Inappropriate targets such as RDM4 evoke no changes in [Ca2+]i. Activation of the BM 3.3 CTL is followed by increases of [Ca2+]i to several micromolar or higher in the EL4.BU targets. This massive increase can be mimicked by direct application of cytolytic granules isolated from rat natural killer cells. The increase in plasma membrane permeability is ion-specific since external Mn2+ can also readily enter target cells that have been 'hit', as evidenced by the rapid selective quenching of fura-2 in those targets. The flood of Ca2+ into the target cell is followed by a leakage of the trapped fura-2. Since both processes continue after the CTL has disengaged, they provide a useful assay for the lethal hit. Furthermore, this technique can be used to follow complete cycles of CTL activation and lethal hit delivery, which under some circumstances can be as rapid as 6 min per cycle.     

Agonist-stimulated oscillations and cycling of intracellular free calcium in individual cultured muscle cells

Receptor regulation of [Ca2+]i was monitored in individual BC3H-1 muscle cells with intracellularly trapped fura-2 using digital imaging analysis techniques. Activation of alpha 1-adrenergic or H1-histaminergic receptors resulted in multiple bursts, or oscillations, of elevated [Ca2+]i with an average interval frequency of approximately 1.8 min-1. The duration of oscillatory behavior was generally more prolonged in response to phenylephrine than in response to histamine. Additionally, a larger fraction of the cells responded with [Ca2+]i oscillations to phenylephrine (approximately 90%) than to histamine (approximately 60%), although the majority of cells produced oscillations in response to both agonists. In most cells, the receptor-mediated [Ca2+]i oscillations continued for several minutes in the absence of extracellular Ca2+, although the amplitude of the individual peaks gradually decreased. The activation of [Ca2+]i oscillations by H1-receptors was more dependent upon extracellular Ca2+ than those elicited by alpha 1-receptors, reflecting the greater dependency of the histaminergic response on Ca2+ influx. Readdition of Ca2+ to the incubation buffer resulted in the resumption of the [Ca2+]i oscillations. These results indicate that considerable cycling of Ca2+ between the cytoplasm and the endoplasmic reticulum must occur. Receptor-mediated [Ca2+]i oscillations were much more prevalent in subconfluent cells than in confluent cells, possibly due to increased coupling of the cells at higher densities. The cells were capable of responding independently of one another, since sister cells displayed unique temporal responses immediately following cell division. Thus, the linkage of receptor occupancy to [Ca2+]i elevation is a functionally unique property for each individual cell and can be influenced by epigenetic factors.