Engineering topics

Si, Dong

Publications and source records attributed to Si, Dong.

6 records

DOE OSTI2022

Structure of Geobacter OmcZ filaments suggests extracellular cytochrome polymers evolved independently multiple times

While early genetic and low-resolution structural observations suggested that extracellular conductive filaments on metal-reducing organisms such as Geobacter were composed of type IV pili, it has now been established that bacterial c -type cytochromes can polymerize to form extracellular filaments capable of long-range electron transport. Atomic structures exist for two such cytochrome filaments, formed from the hexaheme cytochrome OmcS and the tetraheme cytochrome OmcE. Due to the highly conserved heme packing within the central OmcS and OmcE cores, and shared pattern of heme coordination between subunits, it has been suggested that these polymers have a common origin. We have now used cryo-electron microscopy (cryo-EM) to determine the structure of a third extracellular filament, formed from the Geobacter sulfurreducens octaheme cytochrome, OmcZ. In contrast to the linear heme chains in OmcS and OmcE from the same organism, the packing of hemes, heme:heme angles, and between-subunit heme coordination is quite different in OmcZ. A branched heme arrangement within OmcZ leads to a highly surface exposed heme in every subunit, which may account for the formation of conductive biofilm networks, and explain the higher measured conductivity of OmcZ filaments. This new structural evidence suggests that conductive cytochrome polymers arose independently on more than one occasion from different ancestral multiheme proteins.

Cytochromes/metabolism↗

DOE OSTI2022

Cryo-EM structure of an extracellular Geobacter OmcE cytochrome filament reveals tetrahaem packing

Electrically conductive appendages from the anaerobic bacterium Geobacter sulfurreducens were first observed two decades ago, with genetic and biochemical data suggesting that conductive fibres were type IV pili. Recently, an extracellular conductive filament of G. sulfurreducens was found to contain polymerized c-type cytochrome OmcS subunits, not pilin subunits. Here we report that G. sulfurreducens also produces a second, thinner appendage comprised of cytochrome OmcE subunits and solve its structure using cryo-electron microscopy at ~4.3 A resolution. Although OmcE and OmcS subunits have no overall sequence or structural similarities, upon polymerization both form filaments that share a conserved haem packing arrangement in which haems are coordinated by histidines in adjacent subunits. Unlike OmcS filaments, OmcE filaments are highly glycosylated. In extracellular fractions from G. sulfurreducens, we detected type IV pili comprising PilA-N and -C chains, along with abundant B-DNA. OmcE is the second cytochrome filament to be characterized using structural and biophysical methods. Here, we propose that there is a broad class of conductive bacterial appendages with conserved haem packing (rather than sequence homology) that enable long-distance electron transport to chemicals or other microbial cells.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Atmospheric teleconnection associated with the Atlantic multidecadal variability in summer: assessment of the CESM1 model

Observational analysis shows that the Atlantic multidecadal variability (AMV) is associated with climate variability in the Northern Hemisphere through a zonal atmospheric teleconnection extending from the North Atlantic Ocean and propagating eastward around the Northern Hemisphere. Here, we studied the fidelity of model simulations in reproducing the observed summer AMV and the associated impacts on the mid-latitude climate by analysing simulations using the National Centre for Atmospheric Research Community Earth System Model Version 1 (CESM1), including CESM1 North Atlantic idealized and pacemaker simulations, CESM1 large ensemble twentieth century uninitialized simulations and large ensemble initialized CESM1 decadal predictions. To further compare the fidelity of CESM1, we also analysed large ensemble simulations from three other models. Our results suggest that the uninitialized large ensemble simulations from all models can produce an AMV time evolution and its regional climate impacts similar to the observations to certain degree. By initializing the observed oceanic condition in decadal prediction simulations, the simulated AMV and its regional impacts are closer to the observed ones than those in uninitialized ensemble simulations. In addition, the pacemaker simulations that nudged the time-evolving observed North Atlantic sea surface temperature anomalies produce spatiotemporal characteristics of the AMV and AMV climate impacts closer to the observed ones than the uninitialized simulations. We conclude that although coupled models can produce AMV and its regional impacts similar to observed, proper initialization and bias correction of the sea surface temperature spatial and temporal structure can improve this capability.

Initialization↗

DOE OSTI2021

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

This paper describes outcomes of the 2019 Cryo-EM Model Challenge. The goals were to (1) assess the quality of models that can be produced from cryogenic electron microscopy (cryo-EM) maps using current modeling software, (2) evaluate reproducibility of modeling results from different software developers and users and (3) compare performance of current metrics used for model evaluation, particularly Fit-to-Map metrics, with focus on near-atomic resolution. Our findings demonstrate the relatively high accuracy and reproducibility of cryo-EM models derived by 13 participating teams from four benchmark maps, including three forming a resolution series (1.8 to 3.1 Å). The results permit specific recommendations to be made about validating near-atomic cryo-EM structures both in the context of individual experiments and structure data archives such as the Protein Data Bank. We recommend the adoption of multiple scoring parameters to provide full and objective annotation and assessment of the model, reflective of the observed cryo-EM map density.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Variations in northeast Asian summer precipitation driven by the Atlantic multidecadal oscillation

By analysing a 113–year (1900–2012) observational dataset, it is shown in this work that the interdecadal fluctuation of the summer precipitation over Northeast Asia differs from that in central East Asia during the 20th century, and has experienced three interdecadal shifts in the 1920s, mid-1960s and late 1990s. That fluctuation coincides well with the multidecadal fluctuation of the sea surface temperature in the North Atlantic, known as the Atlantic Multidecadal Oscillation (AMO). The AMO affects Northeast Asia via a circumglobal teleconnection pattern extending from the North Atlantic to North America. Corresponding with the positive phase of this teleconnection pattern, a tripolar pattern emerges in the Asian–North Pacific sector, with anomalous low pressure over Northeast Asia and high pressure over Lake Baikal and the mid-latitude western North Pacific. These results suggest that the positive phase of the AMO favours the occurrence of cold vortex over Northeast Asia and anomalous highs over Lake Baikal and the mid-latitude western North Pacific in summer, which enhances the East Asian summer monsoon and southward intrusion of high-latitude cold air, and eventually increases the summer precipitation in Northeast Asia. Furthermore, initialized decadal prediction simulations using the CCSM4 model reproduce well the observed variations of the AMO and its associated atmospheric teleconnection but with slightly shifted geographic locations. The simulated anomalous Northeast Asia cold vortex and strong East Asian summer monsoon, lead to above-normal summer precipitation over Northeast Asia. The modelling results confirm that the multidecadal variability in the North Atlantic can cause the observed interdecadal variations of Northeast Asia summer precipitation. Our results suggest that to understand and predict interdecadal climate change over Northeast Asia, it is important to consider the key role of the AMO.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS2016

An Assessment of Multimodel Simulations for the Variability of Western North Pacific Tropical Cyclones and Its Association with ENSO

An assessment of simulations of the interannual variability of tropical cyclones (TCs) over the western North Pacific (WNP) and its association with El Niño-Southern Oscillation (ENSO), as well as a subsequent diagnosis for possible causes of model biases generated from simulated large-scale climate conditions, are documented in the paper. The model experiments are carried out by the Hurricane Work Group under the U.S. Climate Variability and Predictability Research Program (CLIVAR) using five global climate models (GCMs) with a total of 16 ensemble members forced by the observed sea surface temperature and spanning the 28-yr period from 1982 to 2009. The results show GISS and GFDL model ensemble means best simulate the interannual variability of TCs, and the multimodel ensemble mean (MME) follows. Also, the MME has the closest climate mean annual number of WNP TCs and the smallest root-mean-square error to the observation. Most GCMs can simulate the interannual variability of WNP TCs well, with stronger TC activities during two types of El Niño-namely, eastern Pacific (EP) and central Pacific (CP) El Niño-and weaker activity during La Niña. However, none of the models capture the differences in TC activity between EP and CP El Niño as are shown in observations. The inability of models to distinguish the differences in TC activities between the two types of El Niño events may be due to the bias of the models in response to the shift of tropical heating associated with CP El Niño.

climate models↗