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Meaningful exports

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C++, modules, templates↗

Two Outer Membrane Proteins Contribute to Caulobacter crescentus Cellular Fitness by Preventing Intracellular S-Layer Protein Accumulation

Surface layers, or S-layers, are two-dimensional protein arrays that form the outermost layer of many bacteria and archaea. They serve several functions, including physical protection of the cell from environmental threats. The high abundance of S-layer proteins necessitates a highly efficient export mechanism to transport the S-layer protein from the cytoplasm to the cell exterior. Caulobacter crescentus is unique in that it has two homologous, seemingly redundant outer membrane proteins, RsaF a and RsaF b , which together with other components form a type I protein translocation pathway for S-layer export. These proteins have homology to Escherichia coli TolC, the outer membrane channel of multidrug efflux pumps. Here we provide evidence that, unlike TolC, RsaF a and RsaF b are not involved in either the maintenance of membrane stability or the active export of antimicrobial compounds. Rather, RsaF a and RsaF b are required to prevent intracellular accumulation and aggregation of the S-layer protein RsaA; deletion of RsaF a and RsaF b led to a general growth defect and lowered cellular fitness. Using Western blotting, transmission electron microscopy, and transcriptome sequencing (RNA-seq), we show that loss of both RsaF a and RsaF b led to accumulation of insoluble RsaA in the cytoplasm, which in turn caused upregulation of a number of genes involved in protein misfolding and degradation pathways. These findings provide new insight into the requirement for RsaF a and RsaF b in cellular fitness and tolerance to antimicrobial agents and further our understanding of the S-layer export mechanism on both the transcriptional and translational levels in C. crescentus . IMPORTANCE Decreased growth rate and reduced cell fitness are common side effects of protein production in overexpression systems. Inclusion bodies typically form inside the cell, largely due to a lack of sufficient export machinery to transport the overexpressed proteins to the extracellular environment. This phenomenon can conceivably also occur in natural systems. As one example of a system evolved to prevent intracellular protein accumulation, our study demonstrates that Caulobacter crescentus has two homologous outer membrane transporter proteins that are involved in S-layer export. This is an interesting case study that demonstrates how bacteria can evolve redundancy to ensure adequate protein export functionality and maintain high cellular fitness. Moreover, we provide evidence that these two outer membrane proteins, although being the closest C. crescentus homologs to TolC in E. coli , do not process TolC functionality in C. crescentus .

59 BASIC BIOLOGICAL SCIENCES↗

A substantial role of soil erosion in the land carbon sink and its future changes

Realistic representation of land carbon sink in climate models is vital for predicting carbon climate feedbacks in a changing world. Although soil erosion that removes land organic carbon has increased substantially since the onset of agriculture, it is rarely included in the current generation of climate models. Using an Earth system model with soil erosion represented, we estimated that on average soil erosion displaces 5% of newly fixed land organic carbon downslope annually in the continental US. In the lower Mississippi river basin and the Cascades, the fraction can be as large as 40%. About 12% of the eroded organic carbon is eventually exported to inland waters, which is equal to 14% of the simulated net carbon gain by terrestrial ecosystems. By comparing the eroded organic carbon export to rivers with the particulate organic carbon export to oceans, we demonstrated that a large fraction of the carbon export to rivers could have been mineralized in inland waters. Importantly, with a direct comparison of eroded and exported soil organic carbon and land net carbon uptake, we found that Earth system models that ignore soil erosion likely offset the erosional carbon loss by increasing heterotrophic respiration implicitly. But as soil erosion and heterotrophic respiration respond differently to a warming climate, this unrealistic compensation would lead to biased predictions of future land carbon sink.

Tan, Zeli↗

Rapid Model Import Tool (RMIT)

Our project is about developing a tool to implement conversion of 3D Computer Aided Design (CAD) models produced with software such as Delmia, 3DS Max, or Maya, into a size and format compatible with the Unity 3D environment. RMIT will be used to aid KSC engineering personnel in the design, development, testing, operations, and training on spacecraft, launch vehicles, facilities, and ground support equipment. For our project, we are using Blender, a free/open-source 3D graphics software, with the goal of developing, testing, and deploying a 3D CAD model converter tool. I worked on using Blender to import 3D CAD models exported from CATIA software into Collada file format. The Collada file format has file extension DAE. Importing the Collada DAE file as is into Blender, generates dots and dashes. In 3DS Max, there is an existing OpenCollada plugin and with that plugin, 3DS Max can import the DAE file successfully. But, Blender does not seem to have an OpenCollada plugin, so I worked on writing a new OpenCollada plugin for Blender. Since 3DS Max was able to display the image, I looked into comparing differences between the original DAE file and the DAE file exported from 3DS Max using the OpenCollada plugin. As Collada documents describing digital assets are XML files with file extension DAE, Collada files contains XML tags, making them easily modifiable. After some research, it appears that Blender does not like primitive 2D tags like tristrips and trifans. Changing those tags to polygons slightly improved the image, but the pieces were exploded. I found after further research comparing differences between the original file and the file exported from 3DS Max that the values inside the translate tags in the original file are scaled down by a factor of 25.4 in the exported file from 3DS Max, representing the millimeters to inches conversion (1 inch = 25.4 millimeters). After scaling down values inside all of the translate tags by 25.4, the exploded pieces stuck back in, but the image needed further improvement. I have been able to create a new plugin in Blender that takes the original DAE file, replaces the primitive 2D tags tristrips and trifans with polygons, scales down the values inside the translate tags by a factor of 25.4, and saves the changes into a temporary DAE file. After the temporary DAE file is imported into Blender, the temp file is then deleted, keeping the original DAE file intact. Starting with a DAE file that is exported using the NASA Enterprise Visualization Application (NEVA), a Collada exporter, from CATIA gives better results. NEVA is a Design Visualization product that is used for exporting 3D models from CATIA. With NEVA, the up axis is defined in the top-level node if navigation gravity is enabled. With that file, just replacing the primitive tags tristrips and trifans with polygons in yields a much improved image in Blender. As we identify more differences between the original DAE file and the DAE file exported from 3DS Max, this plugin can be improved further. Our goal is to have a model that is formatted and sized for import into Unity, and we are trying out different 3D programs to see which will work best.

Ayyangar, Arjun↗

Increasing freshwater and dissolved organic carbon flows to Northwest Alaska’s Elson lagoon

Manifestations of climate change in the Arctic are numerous and include hydrological cycle intensification and permafrost thaw, both expected as a result of atmospheric and surface warming. Across the terrestrial Arctic dissolved organic carbon (DOC) entrained in arctic rivers may be providing a carbon subsidy to coastal food webs. Yet, data from field sampling is too often of limited duration to confidently ascertain impacts of climate change on freshwater and DOC flows to coastal waters. This study applies numerical modeling to investigate trends in freshwater and DOC exports from land to Elson Lagoon in Northwest Alaska over the period 1981-2020. While the modeling approach has limitations, the results point to significant increases in freshwater and DOC exports to the lagoon over the past four decades. The model simulation reveals significant increases in surface, subsurface (suprapermafrost), and total freshwater exports. Significant increases are also noted in surface and subsurface DOC production and export, influenced by warming soils and associated active-layer thickening. The largest changes in subsurface components are noted in September, which has experienced a ~50% increase in DOC export emanating from suprapermafrost flow. Direct coastal suprapermafrost freshwater and DOC exports in late summer more than doubled between the first and last five years of the simulation period, with a large anomaly in September 2019 representing a more than fourfold increase over September direct coastal export during the early 1980s. These trends highlight the need for dedicated measurement programs that will enable improved understanding of climate change impacts on coastal zone processes in this data sparse region of Northwest Alaska.

54 ENVIRONMENTAL SCIENCES↗

Sources of Propane Consumed in California

Project Scope: The objective of this study is to specify the sources of propane consumed in California. It answers the questions, where does the propane used in California come from and how was it produced? The results of this study provide comprehensive, transparent, and verifiable estimates, based on the 2018 market. The information provided in this report is suitable for use to assess the life cycle carbon intensity of propane used as a transportation fuel in California. As the 2009 Low Carbon Fuel Standard (LCFS) aims to reduce California’s greenhouse gas (GHG) emissions and other smog-forming and toxic air pollutants, the appropriate designation of carbon intensity for propane as a transportation fuel is important for evaluating propane’s potential to contribute to GHG goals and understandings in the context of various actions. This study focuses on estimating the shares of total propane consumed in the state of California produced from petroleum refineries, natural gas plants, and bituminous sands sources inside California and elsewhere. Results: An estimated 590 million gallons of propane were consumed in California in 2018, of which, 59.5% originated from refinery production and 40.5% originated from natural gas plants. The majority of this was sourced from refinery production in California, 334 million gallons. Most of the propane imported to California for consumption was sourced from natural gas plants, 113 million gallons, with over half of the imported volume sourced from Canada. The volume sourced from bituminous sand upgrader and fractionator operations was negligible. Details from this analysis are presented in the table below which provides an overview of the propane flows estimated in this study by region and production method. The shares and volumes presented here represent a snapshot for 2018. A significant increase in propane demand, such as could be caused by increased use of propane as a transportation fuel in the state, would affect California’s propane production, imports, and exports. The method and data sources used for the estimates provided in this report also provide the framework which could be used for future updates. Key Method Considerations: The values presented here are based on a two-step approach where the first step was to determine the flows of propane into and out of California from different regions and the second step was to estimate the propane production methods in each region. A volume balance approach is used as the primary method for tracking the volume of propane in and out of California as propane production and import volumes are available by Petroleum Administration of Defense District (PADD) from EIA and neither inter-PADD propane transfers nor state-specific non-prime supplier consumption are available from a public data source. The volume balance performed for this study covered PADD 5 (the West Coast), which includes Arizona, California, Nevada, Oregon, and Washington. The volume balance used all available public datasets to determine propane production, imports, exports, and consumption. Volumes unaccounted for by these datasets were estimated using the resulting volume balance by assuming market equilibrium. Consumption within each state in PADD 5 was estimated based on known import, export, and production volumes and this amount was used to develop the volume balance. EIA only tracks consumption at the state level by prime supplier sales. The volume balance approach provides the basis to correct for additional propane consumed in-states where propane is transferred to California. To determine the California propane sources and trade in 2018. volume of propane consumed in California, the volume balance approach is again used where it was estimated all imported volumes not specifically flagged for re-export were consumed, and the remaining consumption was produced in-state. The California Energy Commission (CEC) provided the total volume of propane imported and exported from California in 2018; this volume data set along with commodity tracking from the Canada Energy Regulator (CER) and the International Trade Commission (ITC) which tracks port of entry and final destination was used to determine where propane originated from and where it was ultimately consumed. For example, the CER tracks propane leaving Canada and entering each state within the U.S. Imported propane from Canada to California – marked for California – is assumed to be consumed in California. When no further data were available, import volumes were assumed to be consumed in California without pass-through (i.e., no propane imported to California was directly sold and exported). In most cases, the production method for each propane source region was applied to the volume of propane transferred to California. In other words, the shares of propane sourced from natural gas and refineries for each production region was assigned to California imports based on their contribution to the total volume flows into California to determine the production method for propane consumed in-state. For volumes imported into California from PADD 4, Washington State, Canada, and the rest of the world (Argentina, Chile, Norway, Peru, South Korea, and Trinidad and Tobago), the volumes sourced from petroleum refineries and natural gas plants reflect the either production ratio for the region or, in cases where the sources specific to the amounts exported to California could be determined, the sources specific to the volumes transferred to California.

03 NATURAL GAS↗