Catalogue and Systematics of Pliensbachian, Toarcian and Aalenian Radiolarian Genera and Species

This volume comprises a catalogue of 90 genera, 274 species and 13 subspecies of Pliensbachian, Toarcian and Aalenian Radiolaria. Two genera, 37 species and 3 subspecies are new formal descriptions, 24 species are described in open nomenclature. Each taxon is presented with a complete and up-to-date synonymy, original description and original remarks (translated into English where necessary), subsequent emendations, remarks by the authors of this catalogue, and etymology. Descriptions of species/subspecies further contain the original measurements, type locality, and data on geographic distribution. Plates illustrate the holotype and one or several specimens from our material, from different paleogeographic realms where possible. The material was collected from 30 measured sections in the Circum-Pacific belt (Baja California Peninsula, Oregon, British Columbia, Japan) and the Tethyan realm (Oman, Turkey, Slovenia, Austria). Abbreviated locality information and a list of all treated taxa are given in the last two chapters.A useful book for paleontologists interested in taxonomy of Jurassic radiolarians.Katalog obsega 90 rodov, 274 vrst in 13 podvrst radiolarijev iz treh stopenj v spodnji in srednji juri: pliensbachija, toarcija in aalenija. Dva rodova, 37 vrst in 3 podvrste so formalno opisani novi taksoni, 24 vrst je opisanih v odprti nomenklaturi. Vsak takson je predstavljen z vso dosedanjo sinonimiko, originalnim opisom in originalnimi opombami (v prevodu, če originalni jezik ni angleščina), poznejšimi revizijami, pripombami avtorjev tega kataloga in etimologijo. Opisi vrst in podvrst vsebujejo še originalne meritve, ime tipične lokalitete in podatke o geografski razširjenosti. Vsaka vrsta ali podvrsta je predstavljena s samostojno tablo, na kateri so slike holotipa in več primerkov iz naših vzorcev. Kjer je mogoče, so ilustrirani primerki z različnih paleogeografskih območij. Vzorci so bili pobrani na 30 profilih, posnetih v cirkumpacifiškem pasu (Kalifornijski polotok, Oregon, Britanska Kolumbija, Japonska) in v območju Tetide (Oman, Turčija, Slovenija, Avstrija). Dodatek na koncu knjige vsebuje kratek opis vzorčevanih profilov in seznam vseh obravnavanih taksonov

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism

The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.

X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression profiles of X-linked genes. Tissues whose tissue-specific genes are very highly expressed (e.g., secretory tissues, tissues abundant in structural proteins) are also tissues in which gene expression is relatively rare on the X chromosome. These trends cannot be fully accounted for in terms of alternative models of biased expression. In conclusion, the notion that it is hard for genes on the Therian X to be highly expressed, owing to transcriptional traffic jams, provides a simple yet robustly supported rationale of many peculiar features of X's gene content, gene expression, and evolution

Unexpected Magnetic Behavior of Natural Hematite‐Bearing Rocks at Low Temperatures

Abstract Hematite is a commonly occurring magnetic mineral in nature that has numerous scientific and technological applications. A characteristic property of hematite is a low‐temperature spin‐flop transition called the Morin transition. Above the transition temperature, hematite is a canted antiferromagnet that can carry a remanent magnetization. Below this transition, spin canting disappears and hematite becomes a true antiferromagnet although a small defect moment is usually preserved. We observe Morin transition behavior in natural samples that has not been reported before for hematite. During repeated thermal cycling of a remanent magnetization acquired at room temperature, the remanence intensity at the end of the cycle oscillates between a high remanence state at the end of odd‐numbered cycles and a low remanence state (LRS) at the end of even‐numbered cycles. Alternation of the high and LRSs during repeated thermal cycling points to hysteretic behavior of the spin‐flop process, likely due to sublattice magnetization alignment switches along different easy magnetization axes in samples with preferred crystallographic orientations of hematite particles. We report these observations to seek to expand explanations of the magnetism of hematite

Stratigraphy of Triassic-Jurassic boundary sequences from the Kawhia coast and Awakino gorge, Murihiku Terrane, New Zealand

We have examined the stable carbon isotope stratigraphy, bio- and litho-stratigraphy of the Upper Triassic (Otapirian) - Lower Jurassic (Aratauran) boundary strata from the Awakino gorge and Kawhia coast sections, Murihiku Terrane, North Island, New Zealand. Successive occurrences of species of the bivalve genus Otapiria, O. dissimilis, O. marshalli and O. aff. marshalli, and also of age diagnostic ammonites indicate that the Hettangian strata in both sections are very thin compared with the Rhaetian sequences. Lamination structures are well developed at the Tr-Jr (Rhaetian-Hettangian) boundary transition interval. The delta C-13 values of organic matter from siltstone and carbonate nodules in the sedimentary rocks range from -28.5 to -25.5 parts per thousand and there is no correlation between delta C-13(org) and C/N ratios. The excursion patterns of delta C-13(org) from both sections are similar, showing a negative spike at the uppermost Rhaetian and a positive spike immediately below the Tr-Jr boundary. A long-lived positive shift is also recognized in the Awakino gorge section, which coincides in pattern with those reported in Tr-Jr boundary successions from the Queen Charlotte Islands, British Columbia, Canada. These results suggest that although magnitude and absolute values are slightly different, the integrated pattern of stable carbon isotope signatures over the Tr-Jr boundary could be a valuable tool for correlation, at least between sedimentary rocks from similar depositional settings in the Panthalassa

Lead isotopic record of Barremian–Aptian marine sediments: Implications for large igneous provinces and the Aptian climatic crisis

We present initial isotopic ratios of lead for Early Cretaceous (Barremian–Aptian) sections from Shatsky Rise (Pacific) and Gorgo a Cerbara (Italy). Our Pb isotopic data track an interval representing Oceanic Anoxic Event (OAE)-1a, which is characterized by quasi-global deposition of organic carbon-rich black shale. Pb isotopic compositions of sediments from Shatsky Rise decrease at the end of Barremian time, from radiogenic continental values to unradiogenic values, and subsequently remained less radiogenic until the end of early Aptian time. We explain the isotopic shift by a significant increase in supply rate of unradiogenic Pb, most likely due to massive volcanism. In contrast, the Pb isotopic compositions from the Italian section, which was situated at the western end of Tethys, are mostly identical to those of upper continental crust, showing no significant change in supply rate of unradiogenic Pb. The discrepancy between two sites is attributed to quiescent deep-submarine eruptions of Pacific large igneous provinces (LIPs) such as the Ontong Java Plateau (OJP), which severely limited dispersion of Pb-carrying particles out of the Pacific Ocean. Published Os isotopic data from the Italian section indicate two episodes of massive eruptions of OJP or contemporaneous Manihiki and Hikurangi plateaus starting from earliest Aptian time, slightly later than that indicated by the sedimentary Pb isotopic record from Shatsky Rise. Differences in isotopic variations between Pb and Os likely reflect differences in their chemical behaviors in the oceans, i.e., Pb isotopic compositions would have varied in response to local or regional changes in sediment provenances, whereas large-scale changes in Os inputs are required to explain variations in seawater Os isotopic compositions. Our Pb isotopic data, together with the published Os isotopic record, provide new evidence for the eruptive history of OJP together with contemporaneous Pacific plateaus and its environmental consequences, starting from end-Barremian time and extending through early Aptian time

Lead isotopic ratios of Barremian-Aptian marine sediments

We present initial isotopic ratios of lead for Early Cretaceous (Barremian-Aptian) sections from Shatsky Rise (Pacific) and Gorgo a Cerbara (Italy). Our Pb isotopic data track an interval representing Oceanic Anoxic Event (OAE)-1a, which is characterized by quasi-global deposition of organic carbon-rich black shale. Pb isotopic compositions of sediments from Shatsky Rise decrease at the end of Barremian time, from radiogenic continental values to unradiogenic values, and subsequently remained less radiogenic until the end of early Aptian time. We explain the isotopic shift by a significant increase in supply rate of unradiogenic Pb, most likely due to massive volcanism. In contrast, the Pb isotopic compositions from the Italian section, which was situated at the western end of Tethys, are mostly identical to those of upper continental crust, showing no significant change in supply rate of unradiogenic Pb. The discrepancy between two sites is attributed to quiescent deep-submarine eruptions of Pacific large igneous provinces (LIPs) such as the Ontong Java Plateau (OJP), which severely limited dispersion of Pb-carrying particles out of the Pacific Ocean. Published Os isotopic data from the Italian section indicate two episodes of massive eruptions of OJP or contemporaneous Manihiki and Hikurangi plateaus starting from earliest Aptian time, slightly later than that indicated by the sedimentary Pb isotopic record from Shatsky Rise. Differences in isotopic variations between Pb and Os likely reflect differences in their chemical behaviors in the oceans, i.e., Pb isotopic compositions would have varied in response to local or regional changes in sediment provenances, whereas large-scale changes in Os inputs are required to explain variations in seawater Os isotopic compositions. Our Pb isotopic data, together with the published Os isotopic record, provide new evidence for the eruptive history of OJP together with contemporaneous Pacific plateaus and its environmental consequences, starting from end-Barremian time and extending through early Aptian time