Room for improvement in the initial martini 3 parameterization of peptide interactions

Funding Information: We thank T. Cordeiro for bringing to our attention the coiled coil system that motivated part of this study. J.K.S. acknowledges an internship sponsored by Fundação Luso-Americana para o Desenvolvimento through its Study in Portugal Network. M.N.M. thanks Fundação para a Ciência e a Tecnologia, Portugal for fellowship CEECIND/04124/2017 , and for funding project MOSTMICRO-ITQB with references UIDB/04612/2020 and UIDP/04612/2020 . Publisher Copyright: © 2023 The AuthorsThe Martini 3 coarse-grain force field has greatly improved upon its predecessor, having already been successfully employed in several applications. Here, we gauge the accuracy of Martini 2 and 3 protein interactions in two types of systems: coiled coil peptide dimers in water and transmembrane peptides. Coiled coil dimers form incorrectly under Martini 2 and not at all under Martini 3. With transmembrane peptides, Martini 3 represents better the membrane thickness–peptide tilt relationship, but shorter peptides do not remain transmembranar. We discuss related observations, and describe mitigation strategies involving either scaling interactions or restraining the system.publishersversionpublishe

A bacterial effector counteracts host autophagy by promoting degradation of an autophagy component

Beyond its role in cellular homeostasis, autophagy plays anti- and promicrobial roles in host-microbe interactions, both in animals and plants. One prominent role of antimicrobial autophagy is to degrade intracellular pathogens or microbial molecules, in a process termed xenophagy. Consequently, microbes evolved mechanisms to hijack or modulate autophagy to escape elimination. Although well-described in animals, the extent to which xenophagy contributes to plant-bacteria interactions remains unknown. Here, we provide evidence that Xanthomonas campestris pv. vesicatoria (Xcv) suppresses host autophagy by utilizing type-III effector XopL. XopL interacts with and degrades the autophagy component SH3P2 via its E3 ligase activity to promote infection. Intriguingly, XopL is targeted for degradation by defense-related selective autophagy mediated by NBR1/Joka2, revealing a complex antagonistic interplay between XopL and the host autophagy machinery. Our results implicate plant antimicrobial autophagy in the depletion of a bacterial virulence factor and unravel an unprecedented pathogen strategy to counteract defense-related autophagy in plant-bacteria interactions

Utah Heavy Oil Program

The Utah Heavy Oil Program (UHOP) was established in June 2006 to provide multidisciplinary research support to federal and state constituents for addressing the wide-ranging issues surrounding the creation of an industry for unconventional oil production in the United States. Additionally, UHOP was to serve as an on-going source of unbiased information to the nation surrounding technical, economic, legal and environmental aspects of developing heavy oil, oil sands, and oil shale resources. UHOP fulGilled its role by completing three tasks. First, in response to the Energy Policy Act of 2005 Section 369(p), UHOP published an update report to the 1987 technical and economic assessment of domestic heavy oil resources that was prepared by the Interstate Oil and Gas Compact Commission. The UHOP report, entitled 'A Technical, Economic, and Legal Assessment of North American Heavy Oil, Oil Sands, and Oil Shale Resources' was published in electronic and hard copy form in October 2007. Second, UHOP developed of a comprehensive, publicly accessible online repository of unconventional oil resources in North America based on the DSpace software platform. An interactive map was also developed as a source of geospatial information and as a means to interact with the repository from a geospatial setting. All documents uploaded to the repository are fully searchable by author, title, and keywords. Third, UHOP sponsored Give research projects related to unconventional fuels development. Two projects looked at issues associated with oil shale production, including oil shale pyrolysis kinetics, resource heterogeneity, and reservoir simulation. One project evaluated in situ production from Utah oil sands. Another project focused on water availability and produced water treatments. The last project considered commercial oil shale leasing from a policy, environmental, and economic perspective

Metabolism-dependent bioaccumulation of uranium by Rhodosporidium toruloides isolated from the flooding water of a former uranium mine

Remediation of former uranium mining sites represents one of the biggest challenges worldwide that have to be solved in this century. During the last years, the search of alternative strategies involving environmentally sustainable treatments has started. Bioremediation, the use of microorganisms to clean up polluted sites in the environment, is considered one the best alternative. By means of culture-dependent methods, we isolated an indigenous yeast strain, KS5 (Rhodosporidium toruloides), directly from the flooding water of a former uranium mining site and investigated its interactions with uranium. Our results highlight distinct adaptive mechanisms towards high uranium concentrations on the one hand, and complex interaction mechanisms on the other. The cells of the strain KS5 exhibit high a uranium tolerance, being able to grow at 6 mM, and also a high ability to accumulate this radionuclide (350 mg uranium/g dry biomass, 48 h). The removal of uranium by KS5 displays a temperature- and cell viability-dependent process, indicating that metabolic activity could be involved. By STEM (scanning transmission electron microscopy) investigations, we observed that uranium was removed by two mechanisms, active bioaccumulation and inactive biosorption. This study highlights the potential of KS5 as a representative of indigenous species within the flooding water of a former uranium mine, which may play a key role in bioremediation of uranium contaminated sites.This work was supported by the Bundesministerium für Bildung und Forschung grand nº 02NUK030F (TransAqua). Further support took place by the ERDF-co-financed Grants CGL2012-36505 and 315 CGL2014-59616R, Ministerio de Ciencia e Innovación, Spain

An Analysis of the Impact of Small Dams on River Fragmentation and Regulation in the Contiguous United States

Small dams account for 96% of the more than 50,000 anthropogenic structures on rivers in the United States (US). While dams are critical pieces of infrastructure to human systems, they have contributed to the decline of river connectivity by regulating streamflow dynamics and fragmenting river networks, which threatens the health of freshwater ecosystems. Prior studies of river regulation and fragmentation demonstrated how large dams have impacted river networks. However, small dams account for most structures and 48% of reservoir storage in the US. This study is the first to evaluate the impact of small dams on the river network of the contiguous US (CONUS). We map 51,923 structures onto the US river network to evaluate the current and historical development of fragmentation and regulation. Our results illustrate similar patterns of widespread regulation and fragmentation particularly along major river networks as previous global studies focusing on large dams. The addition of 49,990 small dams in our analysis reveals the full extent of regulation and fragmentation in CONUS. Analysis of small dams highlights the extent to which regulation has expanded into headwater systems over time and their compounding impact on total river regulation. Today, nearly every watershed in the US has high levels of anthropogenic fragmentation and spatial trends have been reversed with the highest fragment densities now occurring in humid regions which can support more structures. In these locations with the largest change in fragment density, small dams account for over 70% of the change

A market assessment of heavy oil, oil sands, and oil shale resources

presentationA presentation given at the Unconventional Fuels from Oil Shale and Oil Sands Project Review Meeting on March 10-11, 2011

Oxy-gas process heaters for efficient CO2 capture

presentationImplementation of oil shale/sands technologies in U.S. will require mitigation of greenhouse gas (GHG) emissions

Subtask 3.2: Flameless oxy-gas process heaters for efficient CO2 capture

presentationThis is a presentation given at the Unconventional Fuels from Oil Shale and Oil Sands Project Review Meeting in March 10-11, 2011

Update on North American oil shale, oil sands, and heavy oil resource development

presentationLarge unconventional fuel resources exist in the U.S. & Canada -Processing technologies for oil sands are well-developed in Canada, but those processes cannot be directly applied to U.S. resources; oil shale processing technologies have yet to be commercialized -RH&D leases are a roadmap for future unconventional fuels development -Research focusing on improving energy and water efficiency of production processes and on environmental impacts/mitigation is essential if oil sands/shale development is to proceed at a reasonable pace -Can the information gleaned from various research efforts be shared (UHOP repository is an example)? Sharing is a means of cost-sharing and maximizes efficiency