Bighorn Basin Coring Project (BBCP): a continental perspective on early Paleogene hyperthermals

During the summer of 2011, the Bighorn Basin Coring Project (BBCP) recovered over 900m of overlapping core from 3 different sites in late Paleocene to early Eocene fluvial deposits of northwestern Wyoming. BBCP cores are being used to develop high-resolution proxy records of the Paleocene–Eocene Thermal Maximum (PETM) and Eocene Thermal Maximum 2 (ETM2) hyperthermal events. These events are short-term, large magnitude global warming events associated with extreme perturbations to the earth’s carbon cycle. Although the PETM and ETM2 occurred ~55–52 million years ago, they are analogous in many ways to modern anthropogenic changes to the carbon cycle. By applying various sedimentological, geochemical, and palynological methods to the cores, we hope to better understand what caused these events, study the biogeochemical and ecological feedbacks that operated during them, and reveal precisely how they impacted continental environments. Core recovery was > 98% in all holes and most drilling was carried out without fluid additives, showing that continuous coring of continental smectitic deposits like these can be achieved with minimal risk of contamination to molecular biomarkers. Cores were processed in the Bremen Core Repository where the science team convened for 17 days to carry out data collection and sampling protocols similar to IODP projects. Initial results show that the weathered horizon extends to as much as ~30m below the surface and variations in magnetic susceptibility within the cores record an interplay between grain size and pedogenesis. Previous investigations of outcrops near the BBCP drill sites allow detailed evaluation of the effects of weathering on common proxy methods. Studies of lithofacies, organic geochemistry, stable isotope geochemistry, calibrated XRF core scanning, paleomagnetics, and palynology are underway and will represent the highest resolution and most integrated proxy records of the PETM from a continental setting yet known. An extensive outreach program is in place to capitalize on the educational value associated with the Bighorn Basin’s unusually complete record of Phanerozoic earth history

Cis-regulatory evolution spotlights species differences in the adaptive potential of gene expression plasticity

Plasticity allows organisms to respond to environmental change. Here the authors compare the distribution of cis-regulatory variants in the transcriptomes of Arabidopsis lyrata and A. halleriafter exposure to stress, to trace the role of polygenic selection in the evolution of gene expression plasticity

Dhx34 and Nbas function in the NMD pathway and are required for embryonic development in zebrafish

The nonsense-mediated mRNA decay (NMD) pathway is a highly conserved surveillance mechanism that is present in all eukaryotes. It prevents the synthesis of truncated proteins by selectively degrading mRNAs harbouring premature termination codons (PTCs). The core NMD effectors were originally identified in genetic screens in Saccharomyces cerevisae and in the nematode Caenorhabditis elegans, and subsequently by homology searches in other metazoans. A genome-wide RNAi screen in C. elegans resulted in the identification of two novel NMD genes that are essential for proper embryonic development. Their human orthologues, DHX34 and NAG/NBAS, are required for NMD in human cells. Here, we find that the zebrafish genome encodes orthologues of DHX34 and NAG/NBAS. We show that the morpholino-induced depletion of zebrafish Dhx34 and Nbas proteins results in severe developmental defects and reduced embryonic viability. We also found that Dhx34 and Nbas are required for degradation of PTC-containing mRNAs in zebrafish embryos. The phenotypes observed in both Dhx34 and Nbas morphants are similar to defects in Upf1, Smg-5- or Smg-6- depleted embryos, suggesting that these factors affect the same pathway and confirming that zebrafish embryogenesis requires an active NMD pathway

Cryptic Variation between Species and the Basis of Hybrid Performance

Studies on natural variation in gene expression and its phenotypic effects provide fresh insights into the origins of vigour and sterility in species hybrids

Rapid Evolution of Sex Pheromone-Producing Enzyme Expression in Drosophila

Rapid evolution of gene expression patterns responsible for pheromone production in 24 species of Drosophila was mapped to simple mutations within the regulatory domain of the desatF gene

The Honey Bee Epigenomes: Differential Methylation of Brain DNA in Queens and Workers

Using genome-wide methylation profiles in honey bee queen and worker brains to understand how contrasting organismal outputs are generated from the same genotype

Adaptive Evolution of the Lactose Utilization Network in Experimentally Evolved Populations of Escherichia coli

Adaptation to novel environments is often associated with changes in gene regulation. Nevertheless, few studies have been able both to identify the genetic basis of changes in regulation and to demonstrate why these changes are beneficial. To this end, we have focused on understanding both how and why the lactose utilization network has evolved in replicate populations of Escherichia coli. We found that lac operon regulation became strikingly variable, including changes in the mode of environmental response (bimodal, graded, and constitutive), sensitivity to inducer concentration, and maximum expression level. In addition, some classes of regulatory change were enriched in specific selective environments. Sequencing of evolved clones, combined with reconstruction of individual mutations in the ancestral background, identified mutations within the lac operon that recapitulate many of the evolved regulatory changes. These mutations conferred fitness benefits in environments containing lactose, indicating that the regulatory changes are adaptive. The same mutations conferred different fitness effects when present in an evolved clone, indicating that interactions between the lac operon and other evolved mutations also contribute to fitness. Similarly, changes in lac regulation not explained by lac operon mutations also point to important interactions with other evolved mutations. Together these results underline how dynamic regulatory interactions can be, in this case evolving through mutations both within and external to the canonical lactose utilization network