The DeepMIP contribution to PMIP4: methodologies for selection, compilation and analysis of latest Paleocene and early Eocene climate proxy data, incorporating version 0.1 of the DeepMIP database

This is the final version of the article. Available from European Geosciences Union via the DOI in this record.Data availability. The data referenced in this manuscript are provided as Supplement Data Files 1 to 8. In the final version, these files will form DeepMIP database version 0.1 and will be accessible online via a citable DOI reference.The early Eocene (56 to 48 million years ago) is inferred to have been the most recent time that Earth's atmospheric CO2 concentrations exceeded 1000 ppm. Global mean temperatures were also substantially warmer than those of the present day. As such, the study of early Eocene climate provides insight into how a super-warm Earth system behaves and offers an opportunity to evaluate climate models under conditions of high greenhouse gas forcing. The Deep Time Model Intercomparison Project (DeepMIP) is a systematic model–model and model–data intercomparison of three early Paleogene time slices: latest Paleocene, Paleocene–Eocene thermal maximum (PETM) and early Eocene climatic optimum (EECO). A previous article outlined the model experimental design for climate model simulations. In this article, we outline the methodologies to be used for the compilation and analysis of climate proxy data, primarily proxies for temperature and CO2. This paper establishes the protocols for a concerted and coordinated effort to compile the climate proxy records across a wide geographic range. The resulting climate “atlas” will be used to constrain and evaluate climate models for the three selected time intervals and provide insights into the mechanisms that control these warm climate states. We provide version 0.1 of this database, in anticipation that this will be expanded in subsequent publications.Natural Environment Research Council (NERC)GNS Science Global Change through Time ProgrammeNational Science Foundation (NSF)KU Leuve

The uronic acid content of coccolith-associated polysaccharides provides insight into coccolithogenesis and past climate

Unicellular phytoplanktonic algae (coccolithophores) are among the most prolific producers of calcium carbonate on the planet, with a production of ∼1026 coccoliths per year. During their lith formation, coccolithophores mainly employ coccolith-associated polysaccharides (CAPs) for the regulation of crystal nucleation and growth. These macromolecules interact with the intracellular calcifying compartment (coccolith vesicle) through the charged carboxyl groups of their uronic acid residues. Here we report the isolation of CAPs from modern day coccolithophores and their prehistoric predecessors and we demonstrate that their uronic acid content (UAC) offers a species-specific signature. We also show that there is a correlation between the UAC of CAPs and the internal saturation state of the coccolith vesicle that, for most geologically abundant species, is inextricably linked to carbon availability. These findings suggest that the UAC of CAPs reports on the adaptation of coccolithogenesis to environmental changes and can be used for the estimation of past CO2 concentrations

Retrotransposon-Induced Heterochromatin Spreading in the Mouse Revealed by Insertional Polymorphisms

The “arms race” relationship between transposable elements (TEs) and their host has promoted a series of epigenetic silencing mechanisms directed against TEs. Retrotransposons, a class of TEs, are often located in repressed regions and are thought to induce heterochromatin formation and spreading. However, direct evidence for TE–induced local heterochromatin in mammals is surprisingly scarce. To examine this phenomenon, we chose two mouse embryonic stem (ES) cell lines that possess insertionally polymorphic retrotransposons (IAP, ETn/MusD, and LINE elements) at specific loci in one cell line but not the other. Employing ChIP-seq data for these cell lines, we show that IAP elements robustly induce H3K9me3 and H4K20me3 marks in flanking genomic DNA. In contrast, such heterochromatin is not induced by LINE copies and only by a minority of polymorphic ETn/MusD copies. DNA methylation is independent of the presence of IAP copies, since it is present in flanking regions of both full and empty sites. Finally, such spreading into genes appears to be rare, since the transcriptional start sites of very few genes are less than one Kb from an IAP. However, the B3galtl gene is subject to transcriptional silencing via IAP-induced heterochromatin. Hence, although rare, IAP-induced local heterochromatin spreading into nearby genes may influence expression and, in turn, host fitness

Heterosynaptic plasticity in the neocortex

Ongoing learning continuously shapes the distribution of neurons’ synaptic weights in a system with plastic synapses. Plasticity may change the weights of synapses that were active during the induction—homosynaptic changes, but also may change synapses not active during the induction—heterosynaptic changes. Here we will argue, that heterosynaptic and homosynaptic plasticity are complementary processes, and that heterosynaptic plasticity might accompany homosynaptic plasticity induced by typical pairing protocols. Synapses are not uniform in their susceptibility for plastic changes, but have predispositions to undergo potentiation or depression, or not to change. Predisposition is one of the factors determining the direction and magnitude of homo- and heterosynaptic changes. Heterosynaptic changes which take place according to predispositions for plasticity may provide a useful mechanism(s) for homeostasis of neurons’ synaptic weights and extending the lifetime of memory traces during ongoing learning in neuronal networks

Noise Contributions in an Inducible Genetic Switch: A Whole-Cell Simulation Study

Stochastic expression of genes produces heterogeneity in clonal populations of bacteria under identical conditions. We analyze and compare the behavior of the inducible lac genetic switch using well-stirred and spatially resolved simulations for Escherichia coli cells modeled under fast and slow-growth conditions. Our new kinetic model describing the switching of the lac operon from one phenotype to the other incorporates parameters obtained from recently published in vivo single-molecule fluorescence experiments along with in vitro rate constants. For the well-stirred system, investigation of the intrinsic noise in the circuit as a function of the inducer concentration and in the presence/absence of the feedback mechanism reveals that the noise peaks near the switching threshold. Applying maximum likelihood estimation, we show that the analytic two-state model of gene expression can be used to extract stochastic rates from the simulation data. The simulations also provide mRNA–protein probability landscapes, which demonstrate that switching is the result of crossing both mRNA and protein thresholds. Using cryoelectron tomography of an E. coli cell and data from proteomics studies, we construct spatial in vivo models of cells and quantify the noise contributions and effects on repressor rebinding due to cell structure and crowding in the cytoplasm. Compared to systems without spatial heterogeneity, the model for the fast-growth cells predicts a slight decrease in the overall noise and an increase in the repressors rebinding rate due to anomalous subdiffusion. The tomograms for E. coli grown under slow-growth conditions identify the positions of the ribosomes and the condensed nucleoid. The smaller slow-growth cells have increased mRNA localization and a larger internal inducer concentration, leading to a significant decrease in the lifetime of the repressor–operator complex and an increase in the frequency of transcriptional bursts

The DeepMIP contribution to PMIP4: methodologies for selection, compilation and analysis of latest Paleocene and early Eocene climate proxy data, incorporating version 0.1 of the DeepMIP database

The early Eocene (56 to 48 million years ago) is inferred to have been the most recent time that Earth's atmospheric CO₂ concentrations exceeded 1000 ppm. Global mean temperatures were also substantially warmer than those of the present day. As such, the study of early Eocene climate provides insight into how a super-warm Earth system behaves and offers an opportunity to evaluate climate models under conditions of high greenhouse gas forcing. The Deep Time Model Intercomparison Project (DeepMIP) is a systematic model–model and model–data intercomparison of three early Paleogene time slices: latest Paleocene, Paleocene–Eocene thermal maximum (PETM) and early Eocene climatic optimum (EECO). A previous article outlined the model experimental design for climate model simulations. In this article, we outline the methodologies to be used for the compilation and analysis of climate proxy data, primarily proxies for temperature and CO₂. This paper establishes the protocols for a concerted and coordinated effort to compile the climate proxy records across a wide geographic range. The resulting climate “atlas” will be used to constrain and evaluate climate models for the three selected time intervals and provide insights into the mechanisms that control these warm climate states. We provide version 0.1 of this database, in anticipation that this will be expanded in subsequent publications