Ammonite stratigraphy of a Toarcian (Lower Jurassic) section on Nagy-Pisznice Hill (Gerecse Mts, Hungary)

Abstract In the Jurassic rocks exposed in a small abandoned quarry on the northwestern edge of Nagy-Pisznice Hill in the Gerecse Mts, fairly well preserved parts of a crocodile skeleton was found in 1996. The bed which yielded the skeletal remains is the uppermost layer of the Kisgerecse Marl Formation exposed here and was determined as belonging to the Upper Toarcian Grammoceras thouarsense Zone. The beds of the sequence above and below were carefully sampled in the late 1990s, and the encountered ammonites were evaluated biostratigraphically. As a result, the Lower Toarcian Harpoceras serpentinum Zone, the Middle Toarcian Hildoceras bifrons and Merlaites gradatus Zones, and the Upper Toarcian Grammoceras thouarsense and Geczyceras speciosum Zones were identified. Within most of these zones the subzones and even the faunal horizons were successfully recognized. The lowermost beds above the underlying Pliensbachian red limestone did not yield any fossils; thus the lowermost Toarcian Dactylioceras tenuicostatum Zone could not be documented. The highest Toarcian ammonite zones also remained unidentified, because the beds of the Tölgyhát Limestone above were not sampled all the way up. This paper presents the lithostratigraphic and biostratigraphic details of the sequence, and the paleontological descriptions of the most important ammonites

Tmetoceratidae (Ammonitina) fauna from the Gerecse Mts (Hungary)

Abstract Taxonomic and stratigraphic problems of the family Tmetoceratidae and the genera Dumortieria, Catulloceras, Cotteswoldia, Pleydellia and Tmetoceras included in it are briefly discussed. Fifteen species of Tmetoceratidae are described and illustrated from the Upper Toarcian-Aalenian ammonite assemblages of the Gerecse Mts (NE Transdanubian Range, Hungary). The fauna described here is closely allied to the Mediterranean Province of the Mediterranean-Caucasian Realm

Effective Stimuli for Constructing Reliable Neuron Models

The rich dynamical nature of neurons poses major conceptual and technical challenges for unraveling their nonlinear membrane properties. Traditionally, various current waveforms have been injected at the soma to probe neuron dynamics, but the rationale for selecting specific stimuli has never been rigorously justified. The present experimental and theoretical study proposes a novel framework, inspired by learning theory, for objectively selecting the stimuli that best unravel the neuron's dynamics. The efficacy of stimuli is assessed in terms of their ability to constrain the parameter space of biophysically detailed conductance-based models that faithfully replicate the neuron's dynamics as attested by their ability to generalize well to the neuron's response to novel experimental stimuli. We used this framework to evaluate a variety of stimuli in different types of cortical neurons, ages and animals. Despite their simplicity, a set of stimuli consisting of step and ramp current pulses outperforms synaptic-like noisy stimuli in revealing the dynamics of these neurons. The general framework that we propose paves a new way for defining, evaluating and standardizing effective electrical probing of neurons and will thus lay the foundation for a much deeper understanding of the electrical nature of these highly sophisticated and non-linear devices and of the neuronal networks that they compose

Collaborative Action of Brca1 and CtIP in Elimination of Covalent Modifications from Double-Strand Breaks to Facilitate Subsequent Break Repair

Topoisomerase inhibitors such as camptothecin and etoposide are used as anti-cancer drugs and induce double-strand breaks (DSBs) in genomic DNA in cycling cells. These DSBs are often covalently bound with polypeptides at the 3′ and 5′ ends. Such modifications must be eliminated before DSB repair can take place, but it remains elusive which nucleases are involved in this process. Previous studies show that CtIP plays a critical role in the generation of 3′ single-strand overhang at “clean” DSBs, thus initiating homologous recombination (HR)–dependent DSB repair. To analyze the function of CtIP in detail, we conditionally disrupted the CtIP gene in the chicken DT40 cell line. We found that CtIP is essential for cellular proliferation as well as for the formation of 3′ single-strand overhang, similar to what is observed in DT40 cells deficient in the Mre11/Rad50/Nbs1 complex. We also generated DT40 cell line harboring CtIP with an alanine substitution at residue Ser332, which is required for interaction with BRCA1. Although the resulting CtIPS332A/−/− cells exhibited accumulation of RPA and Rad51 upon DNA damage, and were proficient in HR, they showed a marked hypersensitivity to camptothecin and etoposide in comparison with CtIP+/−/− cells. Finally, CtIPS332A/−/−BRCA1−/− and CtIP+/−/−BRCA1−/− showed similar sensitivities to these reagents. Taken together, our data indicate that, in addition to its function in HR, CtIP plays a role in cellular tolerance to topoisomerase inhibitors. We propose that the BRCA1-CtIP complex plays a role in the nuclease-mediated elimination of oligonucleotides covalently bound to polypeptides from DSBs, thereby facilitating subsequent DSB repair

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe