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Amber is a molecular dynamics (MD) software package first conceived by Peter Kollman, his lab and collaborators to simulate biomolecular systems. The pmemd module is available as a serial version for central processing units (CPUs), NVIDIA and Advanced Micro Devices (AMD) graphics processing unit (GPU) versions as well as Message Passing Interface (MPI) parallel versions. Advanced capabilities include thermodynamic integration, replica exchange MD and accelerated MD methods. A brief update to the software and recently added capabilities is described in this Application Note. 

The extremely large slip that occurred on the shallow portion of the Japan Trench subduction zone during the 2011 Mw 9.1 Tohoku-oki earthquake directly contributed to the devastating tsunami that inundated the Pacific coast of Japan. International Ocean Discovery Program (IODP) Expedition 405 (Tracking Tsunamigenic Slip Across the Japan Trench) aimed to investigate the conditions and processes that facilitated the extremely shallow slip on the subduction interface during the 2011 Tohoku-oki earthquake to improve understanding of the factors that allow slip to the trench on subduction zones. Expedition 405 implemented a combined logging, coring, and observatory operational plan at two sites: Site C0026, ~8 km seaward of the Japan Trench, to characterize the input sediments to the subduction zone and Site C0019, ~6 km landward of the trench, where the plate boundary fault zone is present at ~825 meters below seafloor (mbsf). At Site C0026, the input section was logged to ~430 mbsf with a logging-while-drilling (LWD) assembly that characterized the succession of sediments and rocks from the seafloor to the basaltic rocks of the oceanic crust. Cores recovered from four holes as deep as 290 mbsf contain a sequence of hemipelagic and pelagic sediments that will be input into the shallow subduction system and therefore control both the localization of the plate boundary fault zone and the slip behavior of the plate boundary. Site C0019 was previously drilled in 2012 during Integrated Ocean Drilling Program Expedition 343 (Japan Trench Fast Drilling Project [JFAST]), and revisiting this site allowed temporal variations in the frontal prism and plate boundary fault zone to be evaluated. The LWD data to ~980 mbsf characterized the frontal prism, plate boundary fault zone, and lower plate to the basaltic volcanic rocks. Cores were recovered from multiple holes that contain a variety of muds from the frontal prism and the plate boundary fault zone, as well as lower plate materials. Comparison with the sediments from Site C0026 provides a basis to interpret the tectonic and sedimentological processes operating in the dynamic environment of the frontal prism. Cores from the plate boundary fault zone provide a unique window into the structural complexity of an active plate boundary fault that is known to host large seismic slip. Two borehole observatories were installed at Site C0019 that contain temperature sensors deployed to take measurements over a period of years and reveal the hydrogeologic structure of the shallow subduction system. These hugely successful drilling operations, combined with postexpedition work to measure the mechanical, frictional, paleomagnetic, and hydrogeologic properties of the core samples and to constrain the history of past seismic slip at Site C0019, will provide an unprecedented opportunity to advance our understanding of shallow subduction systems. Outreach during the expedition leveraged and elevated the success of the operations by sharing the outcomes with a variety of domestic and international audiences, including scientists, students, educators, stakeholders, and the general public. Thanks to the efforts of a large group of onboard outreach officers and their onshore support, activities included ship-to-shore broadcast events; interviews with science party members and crew; the publication of videos, blogs, magazine articles, and social media posts; and development of formalized classroom lesson plans and materials. 

Knowledge of locations and activities ofcis-regulatory elements (CREs) is needed to decipher basic mechanisms of gene regulation and to understand the impact of genetic variants on complex traits. Previous studies identified candidate CREs (cCREs) using epigenetic features in one species, making comparisons difficult between species. In contrast, we conducted an interspecies study defining epigenetic states and identifying cCREs in blood cell types to generate regulatory maps that are comparable between species, using integrative modeling of eight epigenetic features jointly in human and mouse in our Validated Systematic Integration (VISION) Project. The resulting catalogs of cCREs are useful resources for further studies of gene regulation in blood cells, indicated by high overlap with known functional elements and strong enrichment for human genetic variants associated with blood cell phenotypes. The contribution of each epigenetic state in cCREs to gene regulation, inferred from a multivariate regression, was used to estimate epigenetic state regulatory potential (esRP) scores for each cCRE in each cell type, which were used to categorize dynamic changes in cCREs. Groups of cCREs displaying similar patterns of regulatory activity in human and mouse cell types, obtained by joint clustering on esRP scores, harbor distinctive transcription factor binding motifs that are similar between species. An interspecies comparison of cCREs revealed both conserved and species-specific patterns of epigenetic evolution. Finally, we show that comparisons of the epigenetic landscape between species can reveal elements with similar roles in regulation, even in the absence of genomic sequence alignment. 

The intrinsic DNA sequence preferences and cell type–specific cooperative partners of transcription factors (TFs) are typically highly conserved. Hence, despite the rapid evolutionary turnover of individual TF binding sites, predictive sequence models of cell type–specific genomic occupancy of a TF in one species should generalize to closely matched cell types in a related species. To assess the viability of cross-species TF binding prediction, we train neural networks to discriminate ChIP-seq peak locations from genomic background and evaluate their performance within and across species. Cross-species predictive performance is consistently worse than within-species performance, which we show is caused in part by species-specific repeats. To account for this domain shift, we use an augmented network architecture to automatically discourage learning of training species–specific sequence features. This domain adaptation approach corrects for prediction errors on species-specific repeats and improves overall cross-species model performance. Our results show that cross-species TF binding prediction is feasible when models account for domain shifts driven by species-specific repeats. 

Antarctic humpback whales forage in summer, coincident with the seasonal abundance of their primary prey, the Antarctic krill. During the feeding season, humpback whales accumulate energy stores sufficient to fuel their fasting period lasting over six months. Previous animal movement modelling work (using area-restricted search as a proxy) suggests a hyperphagic period late in the feeding season, similar in timing to some terrestrial fasting mammals. However, no direct measures of seasonal foraging behaviour existed to corroborate this hypothesis. We attached high-resolution, motion-sensing biologging tags to 69 humpback whales along the Western Antarctic Peninsula throughout the feeding season from January to June to determine how foraging effort changes throughout the season. Our results did not support existing hypotheses: we found a significant reduction in foraging presence and feeding rates from the beginning to the end of the feeding season. During the early summer period, feeding occurred during all hours at high rates. As the season progressed, foraging occurred mostly at night and at lower rates. We provide novel information on seasonal changes in foraging of humpback whales and suggest that these animals, contrary to nearly all other animals that seasonally fast, exhibit high feeding rates soon after exiting the fasting period