Oxygen isotope compositions of conodonts – analytical challenges of in situ SIMS studies

Reliable deep-time environmental and climate reconstructions are needed to understand the drivers of Earthâs system evolution over geological time. Palaeozoic temperature estimates, including reconstructions of the climate change through the Ordovician, are based mainly on oxygen isotope (18O/16O; δ18OVSMOW) thermometry derived from carbonate rocks with fossils such as calcitic brachiopods and phosphatic conodonts that are often the best preserved repositories of environmental conditions. Palaeoenvironmental reconstructions are reliable only if the geochemical data is obtained using well-calibrated analytical tools. Most previous research devoted to oxygen isotope composition of conodonts has been conducted using the bulk method (gas source isotope ratio mass spectrometry (GS-IRMS)) that typically requires pooling several dozens of conodont elements for a single isotope ratio measurement. As such, studies of conodont-poor intervals and assessments of taxon-specific δ18O variability require extensive sample preparation and are challenging using the bulk method. Such challenges can be addressed by in situ secondary ion mass spectrometry (SIMS) analyses using only picogram sampling masses. However, several studies have reported inconsistencies between SIMS and GS-IRMS δ18O data for the same research material. We aim to solve this controversy by establishing a robust analytical protocol for conodont isotope analysis by SIMS. Here we present conodont data on Pterospathodus and Amorphognathus specimens extracted from Ordovician strata in Nurme and Mehikoorma-421 boreholes (Estonia). Oxygen isotope composition of conodonts was analysed by both SIMS and GS-IRMS, where we paid particular attention to four inorganic apatite reference materials in order to understand the offset between these two techniques that have been reported in the literature. While the results of GS-IRMS measurements conducted using high-temperature reduction of Ag3PO4 represent exclusively δ18O of phosphate-bound oxygen, SIMS analyses do not discriminate between different oxygen components (e.g., (PO4)3â, (SiO4)4â, (CO3)2â, and (OH)â) in apatite, inherently providing information on pooled isotope compositions. We conducted quantitative chemical analyses of selected conodont elements by electron probe microanalysis to assess to what extent matrix effects cause the offsets between the two isotope techniques. We also used scanning electron microscopy and white light optical profilometry to evaluate sample topography and porosity, which have a major impact on SIMS data quality. We collected oxygen isotope data using a CAMECA 1280-HR large geometry instrument at the Potsdam SIMS user facility over several months to determine reproducibility of the results and to optimise a routine measurement protocol. Our tests included a variety of instrumental settings, e.g., different raster parameters for both pre-sputtering and data collection, which yielded slightly differing results due to different instrumental mass fractionation. SIMS is a comparative method, and as such relies on reference materials that have been previously characterised by bulk methods, ideally provided by multiple laboratories. We noted that the inconsistent offsets between SIMS and GS-IRMS data obtained for a given conodont specimen (with SIMS δ18O values in most cases being higher) are linked to reference material measurements that are necessary for conodont data calibration and are often biased towards lighter δ18O values. Our tests show that such bias is even more significant when calibration is based on a single reference material characterised by a single GS-IRMS laboratory, which has been a common practice in past conodont studies

Copy number variations and cognitive phenotypes in unselected populations

IMPORTANCE: The association of copy number variations (CNVs), differing numbers of copies of genetic sequence at locations in the genome, with phenotypes such as intellectual disability has been almost exclusively evaluated using clinically ascertained cohorts. The contribution of these genetic variants to cognitive phenotypes in the general population remains unclear. OBJECTIVE: To investigate the clinical features conferred by CNVs associated with known syndromes in adult carriers without clinical preselection and to assess the genome-wide consequences of rare CNVs (frequency ≤0.05%; size ≥250 kilobase pairs [kb]) on carriers' educational attainment and intellectual disability prevalence in the general population. DESIGN, SETTING, AND PARTICIPANTS: The population biobank of Estonia contains 52,000 participants enrolled from 2002 through 2010. General practitioners examined participants and filled out a questionnaire of health- and lifestyle-related questions, as well as reported diagnoses. Copy number variant analysis was conducted on a random sample of 7877 individuals and genotype-phenotype associations with education and disease traits were evaluated. Our results were replicated on a high-functioning group of 993 Estonians and 3 geographically distinct populations in the United Kingdom, the United States, and Italy. MAIN OUTCOMES AND MEASURES: Phenotypes of genomic disorders in the general population, prevalence of autosomal CNVs, and association of these variants with educational attainment (from less than primary school through scientific degree) and prevalence of intellectual disability. RESULTS: Of the 7877 in the Estonian cohort, we identified 56 carriers of CNVs associated with known syndromes. Their phenotypes, including cognitive and psychiatric problems, epilepsy, neuropathies, obesity, and congenital malformations are similar to those described for carriers of identical rearrangements ascertained in clinical cohorts. A genome-wide evaluation of rare autosomal CNVs (frequency, ≤0.05%; ≥250 kb) identified 831 carriers (10.5%) of the screened general population. Eleven of 216 (5.1%) carriers of a deletion of at least 250 kb (odds ratio [OR], 3.16; 95% CI, 1.51-5.98; P = 1.5e-03) and 6 of 102 (5.9%) carriers of a duplication of at least 1 Mb (OR, 3.67; 95% CI, 1.29-8.54; P = .008) had an intellectual disability compared with 114 of 6819 (1.7%) in the Estonian cohort. The mean education attainment was 3.81 (P = 1.06e-04) among 248 (≥250 kb) deletion carriers and 3.69 (P = 5.024e-05) among 115 duplication carriers (≥1 Mb). Of the deletion carriers, 33.5% did not graduate from high school (OR, 1.48; 95% CI, 1.12-1.95; P = .005) and 39.1% of duplication carriers did not graduate high school (OR, 1.89; 95% CI, 1.27-2.8; P = 1.6e-03). Evidence for an association between rare CNVs and lower educational attainment was supported by analyses of cohorts of adults from Italy and the United States and adolescents from the United Kingdom. CONCLUSIONS AND RELEVANCE: Known pathogenic CNVs in unselected, but assumed to be healthy, adult populations may be associated with unrecognized clinical sequelae. Additionally, individually rare but collectively common intermediate-size CNVs may be negatively associated with educational attainment. Replication of these findings in additional population groups is warranted given the potential implications of this observation for genomics research, clinical care, and public health

Genetic risk for autism spectrum disorders and neuropsychiatric variation in the general population

Almost all genetic risk factors for autism spectrum disorders (ASDs) can be found in the general population, but the effects of that risk are unclear in people not ascertained for neuropsychiatric symptoms. Using several large ASD consortia and population based resources, we find genetic links between ASDs and typical variation in social behavior and adaptive functioning. This finding is evidenced through both inherited and de novo variation, indicating that multiple types of genetic risk for ASDs influence a continuum of behavioral and developmental traits, the severe tail of which can result in an ASD or other neuropsychiatric disorder diagnosis. A continuum model should inform the design and interpretation of studies of neuropsychiatric disease biology

First documentation of the Polygnathoides siluricus conodont Zone (Ludfordian) in South America (Argentina) and the stratigraphic significance of the younger species of Kockelella (Conodonta)

The coquinoid beds from the middle part of the Los Espejos Formation at the Poblete creek section (Talacasto Creek) yielded abundant conodonts. The genus Kockelella (Walliser) represents the most relevant biostratigraphical genus in this conodont fauna. The co-occurrence of Kockelella maenniki Serpagli and Corradini, Kockelella variabilis ichnusae Serpagli and Corradini, K. variabilis Walliser, Kockelella ortus sardoa (Serpagli & Corradini), and Kockelella ortus absidata (Barrick & Klapper) allow us to record for the first time the Polygnathoides siluricus Zone in South America, which suggests the Ludfordian Stage (late Ludlow). We also propose an accurate correlation of the Los Espejos Formation with the lower Ludfordian deposits from the Carnic Alps, Sardinia, Morocco, Czech Republic, Gotland, and North America.Fil: Gomez, Maria Jose. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Juan. Centro de Investigaciones de la Geosfera y Biosfera. Universidad Nacional de San Juan. Facultad de Ciencias Exactas Físicas y Naturales. Centro de Investigaciones de la Geosfera y Biosfera; ArgentinaFil: Mestre, Ana Paula. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Juan. Centro de Investigaciones de la Geosfera y Biosfera. Universidad Nacional de San Juan. Facultad de Ciencias Exactas Físicas y Naturales. Centro de Investigaciones de la Geosfera y Biosfera; ArgentinaFil: Garcias Paez, Yanina Vanesa. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Juan. Centro de Investigaciones de la Geosfera y Biosfera. Universidad Nacional de San Juan. Facultad de Ciencias Exactas Físicas y Naturales. Centro de Investigaciones de la Geosfera y Biosfera; ArgentinaFil: Corradini, Carlo. Università degli Studi di Cagliari; Itali

Ectopic Pregnancy as a Model to Identify Endometrial Genes and Signaling Pathways Important in Decidualization and Regulated by Local Trophoblast

The endometrium in early pregnancy undergoes decidualization and functional changes induced by local trophoblast, which are not fully understood. We hypothesized that endometrium from tubal ectopic pregnancy (EP) could be interrogated to identify novel genes and pathways involved in these processes. Gestation-matched endometrium was collected from women with EP (n = 11) and intrauterine pregnancies (IUP) (n = 13). RNA was extracted from the tissue. In addition, tissues were prepared for histological analysis for degree of decidualization. We compared a) the samples from EP that were decidualized (n = 6) with non-decidualized samples (n = 5), and b) the decidualized EP (n = 6) with decidualization-matched IUP (n = 6) samples using an Affymetrix gene array platform, with Ingenuity Pathway Analysis, combined with quantitative RT-PCR. Expression of PRL and IGFBP1 was used to confirm the degree of decidualization in each group. There were no differences in PRL or IGFBP1 expression in the decidualization-matched samples but a marked reduction (P<0.001) in the non-decidualized samples. Decidualization was associated with increased expression of 428 genes including SCARA5 (181-fold), DKK1 (71-fold) and PROK1 (32-fold), and decreased expression of 230 genes including MMP-7 (35-fold) and SFRP4 (21-fold). The top canonical pathways associated with these differentially expressed genes were Natural Killer Cell and Wnt/b-Catenin signaling. Local trophoblast was associated with much less alteration of endometrial gene expression with an increase in 56 genes, including CSH1 (8-fold), and a reduction in 29 genes including CRISP3 (8-fold). The top associated canonical pathway was Antigen Presentation. The study of endometrium from tubal EP may promote novel insights into genes involved in decidualization and those influenced by factors from neighboring trophoblast. This has afforded unique information not highlighted by previous studies and adds to our understanding of the endometrium in early pregnancy

A genome-wide association study of anorexia nervosa.

Anorexia nervosa (AN) is a complex and heritable eating disorder characterized by dangerously low body weight. Neither candidate gene studies nor an initial genome-wide association study (GWAS) have yielded significant and replicated results. We performed a GWAS in 2907 cases with AN from 14 countries (15 sites) and 14 860 ancestrally matched controls as part of the Genetic Consortium for AN (GCAN) and the Wellcome Trust Case Control Consortium 3 (WTCCC3). Individual association analyses were conducted in each stratum and meta-analyzed across all 15 discovery data sets. Seventy-six (72 independent) single nucleotide polymorphisms were taken forward for in silico (two data sets) or de novo (13 data sets) replication genotyping in 2677 independent AN cases and 8629 European ancestry controls along with 458 AN cases and 421 controls from Japan. The final global meta-analysis across discovery and replication data sets comprised 5551 AN cases and 21 080 controls. AN subtype analyses (1606 AN restricting; 1445 AN binge-purge) were performed. No findings reached genome-wide significance. Two intronic variants were suggestively associated: rs9839776 (P=3.01 × 10(-7)) in SOX2OT and rs17030795 (P=5.84 × 10(-6)) in PPP3CA. Two additional signals were specific to Europeans: rs1523921 (P=5.76 × 10(-)(6)) between CUL3 and FAM124B and rs1886797 (P=8.05 × 10(-)(6)) near SPATA13. Comparing discovery with replication results, 76% of the effects were in the same direction, an observation highly unlikely to be due to chance (P=4 × 10(-6)), strongly suggesting that true findings exist but our sample, the largest yet reported, was underpowered for their detection. The accrual of large genotyped AN case-control samples should be an immediate priority for the field