Tracemaking Activities of Crabs and Their Environmental Significance: The Ichnogenus \u3ci\u3ePsilonichnus\u3c/i\u3e

Modem crabs are common inhabitants of shallow subtidal, intertidal, and supratidal environments, and many crabs are capable of producing traces that can be preserved in the rock record. The first crabs, Early Jurassic in age, probably were not fossorial. By Cretaceous time, however, diverse endobenthic lineages were established. Many representatives of these lineages undoubtedly produced domiciles that are preserved in shallow marine to quasimarine sediments and that should be useful in characterizing the depositional environment of the sediments. Nonetheless, most such dwelling structures have been studied little and remain essentially unnamed. The ichnogenus Psilonichnus Fiirsich is amenable to the taxonomic concept of several forms of crab burrows; presently recognized ichnospecies include P. tubiformis Fiirsich and P. upsilon (n. ichnosp.). Future work may reveal the need for further ichnospecific differentiation. The occurrence of Psilonichnus upsilon and related burrow forms should prove to be a useful criterion for the identification of marine-margin facies in the rock record. Certain crabs also produce domiciles referable to Thalassinoides, Gyrolithes, and Skolithos, and possibly Macanopsis and Spongeliomorpha. Except for Skolithos, such structures traditionally have been attributed to shrimp, lobsters, or stomatopods. Ethologic and taxonomic re-evaluation of these burrow forms is needed

Ichnology and sedimentology reveal depositional characteristics of bay-margin parasequences in the Miocene Amazonian foreland basin

Proposed depositional models for Miocene Amazon foreland basin strata (Pebas Formation, Peru) are controversial. Recent depositional models include lacustrine and tidally influenced, brackish-water embayment. This paper presents data that support tidally influenced, brackish-water deposition for at least part of Pebas time (10-14 Ma). Two parasequences are presented (Santa Julia and Tamshiyacu). Both crop out along the Amazon River in Upper Amazonia near Iquitos, Peru. At these locations, abundant evidence of brackish-water, tidally influenced deposition is documented, including marginal marine bioturbation, sedimentary couplets, semidiurnal couplets (preserved in burrows), and pinstripe lamination. The deposits are locally highly bioturbated. At both locations ichnogenera normally associated with marine to brackish-water depositional environments are common. Three normally marginal-marine ichnofabrics are reported: (1) a Chondrites-reburrowed, Planolites ichnofabric resident only in massive-appearing muds; (2) a Scolicia (Laminites), Thalassinoides, Ophiomorpha ichnofabric that is manifested as intensely bioturbated silty sands; and (3) a Thalassinoides-generated ichnofabric that is interpreted to have descended into consolidated substrates and is thus representative of the Glossifungites Ichnofacies. Several trace fossils contain laminated infills organized into distinct sedimentary couplets that are best interpreted as resulting from semidiurnal processes. Six conclusions are arrived at: (1) sedimentological and ichnological data consistently indicate that sediment accumulation dominantly occurred in sporadically dysaerobic, marine to brackish water, under a tidal influence; (2) sediment accumulation occurred in bay-margin environments that prograded into a shallow, quiescent bay; (3) a stratified water column is indicated by the ichnofauna; (4) low accommodation space, repetitive and rapid adjustments of relative sea level, shallow wave base, and a stratified water column combined to generate an atypical parasequence architecture; (5) previously published isotopic data are consistent with sediment accumulation in brackish to marine water; and (6) marine incursion into Amazonia occurred during the Middle Miocene

Rapid Rule-out of Acute Myocardial Infarction With a Single High-Sensitivity Cardiac Troponin T Measurement Below the Limit of Detection: A Collaborative Meta-analysis.

Background: High-sensitivity assays for cardiac troponin T (hs-cTnT) are sometimes used to rapidly rule out acute myocardial infarction (AMI). Purpose: To estimate the ability of a single hs-cTnT concentration below the limit of detection (<0.005 µg/L) and a nonischemic electrocardiogram (ECG) to rule out AMI in adults presenting to the emergency department (ED) with chest pain. Data Sources: EMBASE and MEDLINE without language restrictions (1 January 2008 to 14 December 2016). Study Selection: Cohort studies involving adults presenting to the ED with possible acute coronary syndrome in whom an ECG and hs-cTnT measurements were obtained and AMI outcomes adjudicated during initial hospitalization. Data Extraction: Investigators of studies provided data on the number of low-risk patients (no new ischemia on ECG and hs-cTnT measurements <0.005 µg/L) and the number who had AMI during hospitalization (primary outcome) or a major adverse cardiac event (MACE) or death within 30 days (secondary outcomes), by risk classification (low or not low risk). Two independent epidemiologists rated risk of bias of studies. Data Synthesis: Of 9241 patients in 11 cohort studies, 2825 (30.6%) were classified as low risk. Fourteen (0.5%) low-risk patients had AMI. Sensitivity of the risk classification for AMI ranged from 87.5% to 100% in individual studies. Pooled estimated sensitivity was 98.7% (95% CI, 96.6% to 99.5%). Sensitivity for 30-day MACEs ranged from 87.9% to 100%; pooled sensitivity was 98.0% (CI, 94.7% to 99.3%). No low-risk patients died. Limitation: Few studies, variation in timing and methods of reference standard troponin tests, and heterogeneity of risk and prevalence of AMI across studies. Conclusion: A single hs-cTnT concentration below the limit of detection in combination with a nonischemic ECG may successfully rule out AMI in patients presenting to EDs with possible emergency acute coronary syndrome. Primary Funding Source: Emergency Care Foundation

Worldwide Distribution of the MYH9 Kidney Disease Susceptibility Alleles and Haplotypes: Evidence of Historical Selection in Africa

MYH9 was recently identified as renal susceptibility gene (OR 3–8, p<10−8) for major forms of kidney disease disproportionately affecting individuals of African descent. The risk haplotype (E-1) occurs at much higher frequencies in African Americans (≥60%) than in European Americans (<4%), revealing a genetic basis for a major health disparity. The population distributions of MYH9 risk alleles and the E-1 risk haplotype and the demographic and selective forces acting on the MYH9 region are not well explored. We reconstructed MYH9 haplotypes from 4 tagging single nucleotide polymorphisms (SNPs) spanning introns 12–23 using available data from HapMap Phase II, and by genotyping 938 DNAs from the Human Genome Diversity Panel (HGDP). The E-1 risk haplotype followed a cline, being most frequent within sub-Saharan African populations (range 50–80%), less frequent in populations from the Middle East (9–27%) and Europe (0–9%), and rare or absent in Asia, the Americas, and Oceania. The fixation indexes (FST) for pairwise comparisons between the risk haplotypes for continental populations were calculated for MYH9 haplotypes; FST ranged from 0.27–0.40 for Africa compared to other continental populations, possibly due to selection. Uniquely in Africa, the Yoruba population showed high frequency extended haplotype length around the core risk allele (C) compared to the alternative allele (T) at the same locus (rs4821481, iHs = 2.67), as well as high population differentiation (FST(CEU vs. YRI) = 0.51) in HapMap Phase II data, also observable only in the Yoruba population from HGDP (FST = 0.49), pointing to an instance of recent selection in the genomic region. The population-specific divergence in MYH9 risk allele frequencies among the world's populations may prove important in risk assessment and public health policies to mitigate the burden of kidney disease in vulnerable populations

Patterns of Cis Regulatory Variation in Diverse Human Populations

The genetic basis of gene expression variation has long been studied with the aim to understand the landscape of regulatory variants, but also more recently to assist in the interpretation and elucidation of disease signals. To date, many studies have looked in specific tissues and population-based samples, but there has been limited assessment of the degree of inter-population variability in regulatory variation. We analyzed genome-wide gene expression in lymphoblastoid cell lines from a total of 726 individuals from 8 global populations from the HapMap3 project and correlated gene expression levels with HapMap3 SNPs located in cis to the genes. We describe the influence of ancestry on gene expression levels within and between these diverse human populations and uncover a non-negligible impact on global patterns of gene expression. We further dissect the specific functional pathways differentiated between populations. We also identify 5,691 expression quantitative trait loci (eQTLs) after controlling for both non-genetic factors and population admixture and observe that half of the cis-eQTLs are replicated in one or more of the populations. We highlight patterns of eQTL-sharing between populations, which are partially determined by population genetic relatedness, and discover significant sharing of eQTL effects between Asians, European-admixed, and African subpopulations. Specifically, we observe that both the effect size and the direction of effect for eQTLs are highly conserved across populations. We observe an increasing proximity of eQTLs toward the transcription start site as sharing of eQTLs among populations increases, highlighting that variants close to TSS have stronger effects and therefore are more likely to be detected across a wider panel of populations. Together these results offer a unique picture and resource of the degree of differentiation among human populations in functional regulatory variation and provide an estimate for the transferability of complex trait variants across populations

Ribosome-associated vesicles: A dynamic subcompartment of the endoplasmic reticulum in secretory cells

The endoplasmic reticulum (ER) is a highly dynamic network of membranes. Here, we combine live-cell microscopy with in situ cryo–electron tomography to directly visualize ER dynamics in several secretory cell types including pancreatic β-cells and neurons under near-native conditions. Using these imaging approaches, we identify a novel, mobile form of ER, ribosome-associated vesicles (RAVs), found primarily in the cell periphery, which is conserved across different cell types and species. We show that RAVs exist as distinct, highly dynamic structures separate from the intact ER reticular architecture that interact with mitochondria via direct intermembrane contacts. These findings describe a new ER subcompartment within cells