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At least 721 records · Page 40
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

A New Method of Comparing Forcing Agents in Climate Models

We describe a new method of comparing different climate forcing agents (e.g., CO2, CH4, and solar irradiance) that avoids many of the ambiguities introduced by temperature-related climate feedbacks. This is achieved by introducing an explicit feedback loop external to the climate model that adjusts one forcing agent to balance another while keeping global mean surface temperature constant. Compared to current approaches, this method has two main advantages: (i) the need to define radiative forcing is bypassed and (ii) by maintaining roughly constant global mean temperature, the effects of state dependence on internal feedback strengths are minimized. We demonstrate this approach for several different forcing agents and derive the relationships between these forcing agents in two climate models; comparisons between forcing agents are highly linear in concordance with predicted functional forms. Transitivity of the relationships between the forcing agents appears to hold within a wide range of forcing. The relationships between the forcing agents obtained from this method are consistent across both models but differ from relationships that would be obtained from calculations of radiative forcing, highlighting the importance of controlling for surface temperature feedback effects when separating radiative forcing and climate response.

CH4↗
DOE OSTI2015

Comparing Trends in the Southern Annular Mode and Surface Westerly Jet

This paper examines trends in the southern annular mode (SAM) and the strength, position, and width of the Southern Hemisphere surface westerly wind jet in observations, reanalyses, and models from phase 5 of the Coupled Model Intercomparison Project (CMIP5). First the period over 1951–2011 is considered, and it is shown that there are differences in the SAM and jet trends between the CMIP5 models, the Hadley Centre gridded SLP (HadSLP2r) dataset, and the Twentieth Century Reanalysis. The relationships between these trends demonstrate that the SAM index cannot be used to directly infer changes in any one kinematic property of the jet. The spatial structure of the observed trends in SLP and zonal winds is shown to be largest, but also most uncertain, in the southeastern Pacific. To constrain this uncertainty six reanalyses are included and compared with station-based observations of SLP. The CMIP5 mean SLP trends generally agree well with the direct observations, despite some climatological biases, while some reanalyses exhibit spuriously large SLP trends. Similarly, over the more reliable satellite era the spatial pattern of CMIP5 SLP trends is in excellent agreement with HadSLP2r, whereas several reanalyses are not. Then surface winds are compared with a satellite-based product, and it is shown that the CMIP5 mean trend is similar to observations in the core region of the westerlies, but that several reanalyses overestimate recent trends. The authors caution that studies examining the impact of wind changes on the Southern Ocean could be biased by these spuriously large trends in reanalysis products.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Stronger Tropical Cyclone–Induced Ocean Cooling in Near-Coastal Regions Compared to the Open Ocean

Abstract Tropical cyclones (TC) often induce strong mixing in the upper ocean that generates a trail of cooler sea surface temperature (Twake) in their wakes. The Twake can affect TC intensity, so its prediction is important, especially in coastal regions where TCs can make landfall. Coastal Twakes are often more complex than those in the open ocean due to the influences of coastline geometry, highly variable water depth, continental runoff, and shelf processes. Using observational data since 2002, here we show a significantly stronger global mean Twake in coastal regions compared to offshore regions. Temperature stratification is the main driver of stronger coastal Twakes in the North Atlantic and east Pacific. In the northwest Pacific and north Indian Ocean, the differences between coastal and offshore Twakes are smaller due to compensation between TC forcings and ocean stratification. The north Indian Ocean is unique in the Northern Hemisphere because salinity stratification plays a major role on the spatial distribution of Twake. In the South Pacific Ocean, TC intensity and translation speed are crucial for explaining coastal–offshore Twake differences, while ocean stratification and mixed layer depth are more important for the coastal–offshore Twake differences in the south Indian Ocean. These findings suggest that coastal–offshore differences in ocean stratification need to be properly represented in models in order to capture changes in TC-induced ocean cooling as storms approach landfall. Significance Statement Landfalling tropical cyclones (TCs) often cause considerable damage in coastal regions with dense human populations. Understanding TC–ocean interaction and how it differs between coastal and offshore regions can help predict TC intensity prior to landfall. Sea surface cooling after TC passage is an important proxy for TC–ocean interaction. A global evaluation of coastal TC-induced cooling has not been conducted. Using data covering two decades, we show significantly stronger TC-induced surface cooling in coastal regions compared to offshore regions at the global scale and in all basins except the northwest Pacific and north Indian Ocean. The difference is driven mainly by upper-ocean conditions in the North Atlantic, east Pacific, and south Indian Ocean, and by TC characteristics in the South Pacific.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

A Comparative Study of Single-pulse and Double-pulse Laser-Induced Breakdown Spectroscopy with Uranium-containing Samples

Laser-induced breakdown spectroscopy (LIBS) holds potential advantages in special nuclear material (SNM) sensing and nuclear forensics which require rapid analysis, minimal sample preparation and stand-off distance capability. SNM, such as U, however, result in crowded emission spectra with LIBS, and characteristic emission lines are challenging to discern. It is well-known that double-pulse LIBS (DPLIBS) improves the signal intensity for analytes over conventional single-pulse LIBS (SPLIBS). This study investigates U signal in a glass matrix using DPLIBS and compares to signal features obtained using SPLIBS. DPLIBS involves sequential firing of 1.06 µm Nd:YAG pre-pulse and 10.6 µm TEA CO2 heating pulse in near collinear geometry. Optimization of experimental parameters including inter-pulse delay and energy follows identification of characteristic lines and signals for bulk analyte Ca and minor constituent analyte U for both DPLIBS and SPLIBS. Spatial and temporal coupling of the two pulses in the proposed DPLIBS technique yields improvements in analytical merits with negligible further damage to the sample compared to SPLIBS. Subsequently, the study discusses optimum plasma emission conditions of U lines and relative figures of merit in both SPLIBS and DPLIBS. Investigation into plasma characteristics also addresses plausible mechanisms related to observed U analyte signal variation between SPLIBS and DPLIBS.

Skrodzki, P. J.↗
DOE OSTI2023

Comparing Regional Energy Consumption for Direct Drone and Truck Deliveries

Drone delivery, once thought of as fictitious, is becoming a reality with the efforts of both forward-looking enterprises and supportive government policies. This emerging mode of e-commerce delivery raises many concerns. One important concern is the energy efficiency of direct delivery drones compared with conventional delivery trucks at a regional systems level. Here, in this study, we develop and apply methods to quantify the regional energy impacts of drone delivery, then we assess these impacts and compare them with the impacts of truck delivery. To study this problem, we develop an optimization model that determines an optimal set of fulfillment centers (FCs) with variable service capacities that allow drones to make direct e-commerce deliveries. We adopt two drone delivery energy estimation models from the literature and use them as inputs to demonstrate the potential range of energy needs. We also develop another optimization model to account for the energy consumption of diesel trucks (DTs) and battery electric vehicles (BEVs). We test the models using validated simulation data for the Chicago metropolitan area in the U.S. to quantify the energy implications of these three delivery modes. For drone delivery, we further extend our analyses by considering the impact of wind speed and flight patterns. Our results show that direct delivery drones require 15.8% more energy than BEVs on an average windy day, and they need 15% more energy than DTs on a very windy day. We provide essential parameter values for reproducibility and list relevant open problems.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2012

Genetic diversity within the genus Francisella as revealed by comparative analyses of the genomes of two North American isolates from environmental sources

Background: Francisella tularensis is an intracellular pathogen that causes tularemia in humans and the public health importance of this bacterium has been well documented in recent history. Francisella philomiragia, a distant relative of F. tularensis, is thought to constitute an environmental lineage along with Francisella novicida. Nevertheless, both F. philomiragia and F. novicida have been associated with human disease, primarily in immune-compromised individuals. To understand the genetic relationships and evolutionary contexts among different lineages within the genus Francisella, the genome of Francisella spp. strain TX07-7308 was sequenced and compared to the genomes of F. philomiragia strains ATCC 25017 and 25015, F. novicida strain U112, and F. tularensis strain Schu S4. Results: The size of strain ATCC 25017 chromosome was 2,045,775 bp and contained 1,983 protein-coding genes. The size of strain TX07-7308 chromosome was 2,035,931 bp and contained 1,980 protein-coding genes. Pairwise BLAST comparisons indicated that strains TX07-7308 and ATCC 25017 contained 1,700 protein coding genes in common. NUCmer analyses revealed that the chromosomes of strains TX07-7308 and ATCC 25017 were mostly collinear except for a few gaps, translocations, and/or inversions. Using the genome sequence data and comparative analyses with other members of the genus Francisella (e.g., F. novicida strain U112 and F. tularensis strain Schu S4), several strain-specific genes were identified. Strains TX07-7308 and ATCC 25017 contained an operon with six open reading frames encoding proteins related to enzymes involved in thiamine biosynthesis that was absent in F. novicida strain U112 and F. tularensis strain Schu S4. Strain ATCC 25017 contained an operon putatively involved in lactose metabolism that was absent in strain TX07-7308, F. novicida strain U112, and F. tularensis strain Schu S4. In contrast, strain TX07-7308 contained an operon putatively involved in glucuronate metabolism that was absent in the genomes of strain ATCC 25017, F. novicida strain U112, and F. tularensis strain Schu S4. The polymorphic nature of polysaccharide biosynthesis/modification gene clusters among different Francisella strains was also evident from genome analyses. Conclusions: From genome comparisons, it appeared that genes encoding novel functions have contributed to the metabolic enrichment of the environmental lineages within the genus Francisella. The inability to acquire new genes coupled with the loss of ancestral traits and the consequent reductive evolution may be a cause for, as well as an effect of, niche selection of F. tularensis. Sequencing and comparison of the genomes of more isolates are required to obtain further insights into the ecology and evolution of different species within the genus Francisella.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Evolution and comparative genomics of the most common Trichoderma species

Background: The growing importance of the ubiquitous fungal genus Trichoderma (Hypocreales, Ascomycota) requires understanding of its biology and evolution. Many Trichoderma species are used as biofertilizers and biofungicides and T. reesei is the model organism for industrial production of cellulolytic enzymes. In addition, some highly opportunistic species devastate mushroom farms and can become pathogens of humans. A comparative analysis of the first three whole genomes revealed mycoparasitism as the innate feature of Trichoderma. However, the evolution of these traits is not yet understood. Results: We selected 12 most commonly occurring Trichoderma species and studied the evolution of their genome sequences. Trichoderma evolved in the time of the Cretaceous-Palaeogene extinction event 66 (±15) mya, but the formation of extant sections (Longibrachiatum, Trichoderma) or clades (Harzianum/Virens) happened in Oligocene. The evolution of the Harzianum clade and section Trichoderma was accompanied by significant gene gain, but the ancestor of section Longibrachiatum experienced rapid gene loss. The highest number of genes gained encoded ankyrins, HET domain proteins and transcription factors. We also identified the Trichoderma core genome, completely curated its annotation, investigated several gene families in detail and compared the results to those of other fungi. Eighty percent of those genes for which a function could be predicted were also found in other fungi, but only 67% of those without a predictable function. Conclusions: Our study presents a time scaled pattern of genome evolution in 12 Trichoderma species from three phylogenetically distant clades/sections and a comprehensive analysis of their genes. The data offer insights in the evolution of a mycoparasite towards a generalist.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Using Comparative Genomics for Inquiry-Based Learning to Dissect Virulence of Escherichia coli O157:H7 and Yersinia pestis

Genomics and bioinformatics are topics of increasing interest in undergraduate biological science curricula. Many existing exercises focus on gene annotation and analysis of a single genome. In this paper, we present two educational modules designed to enable students to learn and apply fundamental concepts in comparative genomics using examples related to bacterial pathogenesis. Students first examine alignments of genomes of Escherichia coli O157:H7 strains isolated from three food-poisoning outbreaks using the multiple-genome alignment tool Mauve. Students investigate conservation of virulence factors using the Mauve viewer and by browsing annotations available at the A Systematic Annotation Package for Community Analysis of Genomes database. In the second module, students use an alignment of five Yersinia pestis genomes to analyze single-nucleotide polymorphisms of three genes to classify strains into biovar groups. Students are then given sequences of bacterial DNA amplified from the teeth of corpses from the first and second pandemics of the bubonic plague and asked to classify these new samples. Learning-assessment results reveal student improvement in self-efficacy and content knowledge, as well as students' ability to use BLAST to identify genomic islands and conduct analyses of virulence factors from E. coli O157:H7 or Y. pestis. Each of these educational modules offers educators new ready-to-implement resources for integrating comparative genomic topics into their curricula.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

The Sentinel Lymph Node Biopsy Using Indocyanine Green Fluorescence Plus Radioisotope Method Compared With the Radioisotope-Only Method for Breast Cancer Patients After Neoadjuvant Chemotherapy: A Prospective, Randomized, Open-Label, Single-Center Phase 2 Trial

Background: This study aimed to compare the sentinel lymph node (SLN) identification rates for breast cancer patients after neoadjuvant chemotherapy (NAC) between the dual method (DM) of indocyanine green fluorescence (ICG-F) plus a radioisotope (RI) and RI alone. Methods: This randomized study enrolled 130 patients who received NAC for breast cancer and 122 patients who received SLN biopsy (SLNB) using either DM (n = 58) or RI only (n = 64). The study compared the identification rate, number of SLNs, and detection time of SLNB. Results: Among the 122 patients, 113 (92.6%) were clinically node-positive before NAC. The SLN identification rate was 98.3% in the DM group and 93.8% in the RI group (p = 0.14). The DM group and the RI group were similar in the average number of SLNs (2.2 ± 1.13 vs. 1.9 ± 1.33; p = 0.26) and the time to detection of the first SLN (8.7 ± 4.98 vs. 8.3 ± 4.31 min; p = 0.30). In the DM group, transcutaneous lymphatic drainage was visualized by fluorescence imaging for 65.5% (38 of 58) of the patients. The SLN identification rate was 94.7% using ICG-F and 93% using RI (p = 0.79). During and after the operation, no complications, including allergic reactions or skin necrosis, occurred. Conclusions: This study is the first randomized trial to use ICG-F for SLNB in breast cancer patients after NAC. The DM including ICG-F could be a feasible and safe method for SLNB in initially node-positive breast cancer patients with NAC.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2023

Endurance Exercise Performance Is Reduced after 6-h Dives at 1.35 ATA When Breathing 100% Oxygen Compared with Air

ABSTRACT Introduction Long-duration dives on consecutive days reduces muscular performance, potentially affecting military personnel. However, a paucity of data exists on how breathing gases affect endurance performance. This study examined the influence of long-duration diving with different breathing gases on aerobic endurance and handgrip performance. Methods Twenty-three military divers completed a single 6-h dive (single dive [SD]) and five 6-h dives over consecutive days (dive week [DW]) with 30-min cycling intervals using air (AIR,n= 13) or 100% oxygen (OXY,n= 10). Before and after SD and DW, subjects completed a maximum handgrip strength test, a handgrip endurance test at 40% maximal strength, and a time to exhaustion run. Results Handgrip endurance decreased after DW in OXY (SD, 1.9 ± 0.0 vs 1.4 ± 0.3 min) compared with AIR (1.8 ± 0.0 vs 1.8 ± 0.2 min) (P< 0.001). Run time decreased after SD (Pre, 20.7 ± 10.4 min; Post, 16.6 ± 7.6 min;P= 0.039) and DW (Pre, 21.6 ± 9.0 min; Post, 11.2 ± 4.0 min;P< 0.001) in OXY and after overall diving in AIR (Pre, 26.5 ± 10.2 min; Post, 22.3 ± 7.5 min;P= 0.025). V̇O 2 decreased after diving only in AIR (Pre, 42.6 ± 3.4 mL·kg −1 ⋅min −1 ; Post, 40.4 ± 3.7 mL·kg −1 ⋅min −1 ;P= 0.010). There were no other significant effects. Conclusions Breathing 100% oxygen during long-duration dives on consecutive days may exacerbate decreases in aerobic endurance and impairs handgrip endurance compared with air. Additional research is needed to elucidate mechanisms of action and possible mitigation strategies.

Sport Sciences↗
DOE OSTI2025

Comparing optical four-flux model results with experimental data obtained by integrating sphere measurements

Four-flux theory is a way to model scattering through multiple layers of a system based on diffuse and collimated properties. When compared with measurement results obtained using an integrating sphere or a goniophotometer, an approximation is often made as the physical instrument cannot separate the collimated component from the diffuse light scattered in the forward direction. This paper tries to clarify the meaning of the word diffuse for the different cases and outlines simple corrections to improve the accuracy when comparing four-flux models and measured data based on sample haze and the geometry of the integrating sphere.

Bilokur, Maryna (ORCID:0000000191839650)↗
DOE OSTI2021

Comparative genomic and phenotypic characterization of invasive non-typhoidal Salmonella isolates from Siaya, Kenya

Non-typhoidal Salmonella (NTS) is a major global health concern that often causes bloodstream infections in areas of the world affected by malnutrition and comorbidities such as HIV and malaria. Developing a strategy to control the emergence and spread of highly invasive and antimicrobial resistant NTS isolates requires a comprehensive analysis of epidemiological factors and molecular pathogenesis. Here, we characterize 11 NTS isolates that caused bloodstream infections in pediatric patients in Siaya, Kenya from 2003–2010. Nine isolates were identified as S . Typhimurium sequence type 313 while the other two were S . Enteritidis. Comprehensive genotypic and phenotypic analyses were performed to compare these isolates to those previously identified in sub-Saharan Africa. We identified a S . Typhimurium isolate referred to as UGA14 that displayed novel plasmid, pseudogene and resistance features as compared to other isolates reported from Africa. Notably, UGA14 is able to ferment both lactose and sucrose due to the acquisition of insertion elements on the pKST313 plasmid. These findings show for the first time the co-evolution of plasmid-mediated lactose and sucrose metabolism along with cephalosporin resistance in NTS further elucidating the evolutionary mechanisms of invasive NTS phenotypes. These results further support the use of combined genomic and phenotypic approaches to detect and characterize atypical NTS isolates in order to advance biosurveillance efforts that inform countermeasures aimed at controlling invasive and antimicrobial resistant NTS.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Comparative Omics-Driven Genome Annotation Refinement: Application across Yersiniae

Genome sequencing continues to be a rapidly evolving technology, yet most downstream aspects of genome annotation pipelines remain relatively stable or are even being abandoned. To date, the perceived value of manual curation for genome annotations is not offset by the real cost and time associated with the process. In order to balance the large number of sequences generated, the annotation process is now performed almost exclusively in an automated fashion for most genome sequencing projects. One possible way to reduce errors inherent to automated computational annotations is to apply data from 'omics' measurements (i.e. transcriptional and proteomic) to the un-annotated genome with a proteogenomic-based approach. This approach does require additional experimental and bioinformatics methods to include omics technologies; however, the approach is readily automatable and can benefit from rapid developments occurring in those research domains as well. The annotation process can be improved by experimental validation of transcription and translation and aid in the discovery of annotation errors. Here the concept of annotation refinement has been extended to include a comparative assessment of genomes across closely related species, as is becoming common in sequencing efforts. Transcriptomic and proteomic data derived from three highly similar pathogenic Yersiniae (Y. pestis CO92, Y. pestis pestoides F, and Y. pseudotuberculosis PB1/+) was used to demonstrate a comprehensive comparative omic-based annotation methodology. Peptide and oligo measurements experimentally validated the expression of nearly 40% of each strain's predicted proteome and revealed the identification of 28 novel and 68 previously incorrect protein-coding sequences (e.g., observed frameshifts, extended start sites, and translated pseudogenes) within the three current Yersinia genome annotations. Gene loss is presumed to play a major role in Y. pestis acquiring its niche as a virulent pathogen, thus the discovery of many translated pseudogenes underscores a need for functional analyses to investigate hypotheses related to divergence. Refinements included the discovery of a seemingly essential ribosomal protein, several virulence-associated factors, and a transcriptional regulator, among other proteins, most of which are annotated as hypothetical, that were missed during annotation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Comparing residue clusters from thermophilic and mesophilic enzymes reveals adaptive mechanisms

Understanding how proteins adapt to function at high temperatures is important for deciphering the energetics that dictate protein stability and folding. While multiple principles important for thermostability have been identified, we lack a unified understanding of how internal protein structural and chemical environment determine qualitative or quantitative impact of evolutionary mutations. In this work we compare equivalent clusters of spatially neighboring residues between paired thermophilic and mesophilic homologues to evaluate adaptations under the selective pressure of high temperature. We find the residue clusters in thermophilic enzymes generally display improved atomic packing compared to mesophilic enzymes, in agreement with previous research. Unlike residue clusters from mesophilic enzymes, however, thermophilic residue clusters do not have significant cavities. In addition, anchor residues found in many clusters are highly conserved with respect to atomic packing between both thermophilic and mesophilic enzymes. As a result, the improvements in atomic packing observed in thermophilic homologues are not derived from these anchor residues but from neighboring positions, which may serve to expand optimized protein core regions.

09 BIOMASS FUELS↗
DOE OSTI2020

Laboratory strains of Bacillus anthracis lose their ability to rapidly grow and sporulate compared to wildlife outbreak strains

Bacillus anthracis is the causative agent of anthrax in animals and humans. The organism lies in a dormant state in the soil until introduced into an animal via, ingestion, cutaneous inoculation or inhalation. Once in the host, spores germinate into rapidly growing vegetative cells elaborating toxins. When animals die of anthrax, vegetative bacteria sporulate upon nutrient limitation in the carcass or soil while in the presence of air. After release into the soil environment, spores form a localized infectious zone (LIZ) at and around the carcass. Laboratory strains of B. anthracis produce fewer proteins associated with growth and sporulation compared to wild strains isolated from recent zoonotic disease events. We verified wild strains grow more rapidly than lab strains demonstrating a greater responsiveness to nutrient availability. Sporulation was significantly more rapid in these wild strains compared to lab strains, indicating wild strains are able to sporulate faster due to nutrient limitation while laboratory strains have a decrease in the speed at which they utilize nutrients and an increase in time to sporulation. These findings have implications for disease control at the LIZ as well as on the infectious cycle of this dangerous zoonotic pathogen.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Comparative genetics of Enterococcus faecalis intestinal tissue isolates before and after surgery in a rat model of colon anastomosis

We have recently demonstrated that collagenolytic Enterococcus faecalis plays a key and causative role in the pathogenesis of anastomotic leak, an uncommon but potentially lethal complication characterized by disruption of the intestinal wound following segmental removal of the colon (resection) and its reconnection (anastomosis). Here we hypothesized that comparative genetic analysis of E. faecalis isolates present at the anastomotic wound site before and after surgery would shed insight into the mechanisms by which collagenolytic strains are selected for and predominate at sites of anastomotic disruption. Whole genome optical mapping of four pairs of isolates from rat colonic tissue obtained following surgical resection (herein named "pre-op" isolates) and then 6 days later from the anastomotic site (herein named "post-op" isolates) demonstrated that the isolates with higher collagenolytic activity formed a distinct cluster. In order to perform analysis at a deeper level, a single pair of E. faecalis isolates (16A pre-op and 16A post-op) was selected for whole genome sequencing and assembled using a hybrid assembly algorithm. Comparative genomics demonstrated absence of multiple gene clusters, notably a pathogenicity island in the post-op isolate. No differences were found in the fsr-gelE-sprE genes (EF1817-1822) responsible for regulation and production of collagenolytic activity. Analysis of unique genes among the 16A pre-op and post-op isolates revealed the predominance of transporter systems-related genes in the pre-op isolate and phage-related and hydrolytic enzyme-encoding genes in the post-op isolate. Despite genetic differences observed between pre-op and post-op isolates, the precise genetic determinants responsible for their differential expression of collagenolytic activity remains unknown.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Tracking cropland transitions: A comparative analysis of U.S. land cover change data

There are a growing number of land cover data available for the conterminous United States, supporting various applications ranging from biofuel regulatory decisions to habitat conservation assessments. These datasets vary in their source information, frequency of data collection and reporting, land class definitions, categorical detail, and spatial scale and time intervals of representation. These differences limit direct comparison, contribute to disagreements among studies, confuse stakeholders, and hamper our ability to confidently report key land cover trends in the U.S. Here we assess changes in cropland derived from the Land Change Monitoring, Assessment, and Projection (LCMAP) dataset from the U.S. Geological Survey and compare them with analyses of three established land cover datasets across the coterminous U.S. from 2008-2017: (1) the National Resources Inventory (NRI), (2) a dataset Lark et al. 2020 derived from the Cropland Data Layer (CDL), and (3) a dataset from Potapov et al. 2022. LCMAP reports more stable cropland and less stable noncropland in all comparisons, likely due to its more expansive definition of cropland which includes managed grasslands (pasture and hay). Despite these differences, net cropland expansion from all four datasets was comparable (5.18-6.33 million acres), although the geographic extent and type of conversion differed. LCMAP projected the largest cropland expansion in the southern Great Plains, whereas other datasets projected the largest expansion in the northwestern and central Midwest. Most of the pixel-level disagreements (86%) between LCMAP and Lark et al. 2020 were due to definitional differences among datasets, whereas the remainder (14%) were from a variety of causes. Cropland expansion in the LCMAP likely reflects conversions of more natural areas, whereas cropland expansion in other data sources also captures conversion of managed pasture to cropland. The particular research question considered (e.g., habitat versus soil carbon) should influence which data source is more appropriate.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Mono-mix strategy enables comparative proteomics of a cross-kingdom microbial symbiosis

Cross-kingdom microbial symbioses, such as those between algae and bacteria, are key players in biogeochemical cycles. The molecular changes during initiation and establishment of symbiosis are of great interest, but quantitatively monitoring such changes can be challenging, particularly when the microorganisms differ greatly in size or are intimately associated. Here, we analyze output from label-free, data-dependent acquisition (DDA) LC-MS/MS proteomics experiments investigating the well-studied interaction between the alga Chlamydomonas reinhardtii and the heterotrophic bacterium Mesorhizobium japonicum. We found that detection of bacterial proteins decreased in coculture by 50% proteome-wide due to the abundance of algal proteins. As a result, standard differential expression analysis led to numerous false-positive reports of significantly downregulated proteins, where it was not possible to distinguish meaningful biological responses to symbiosis from artifacts of the reduced protein detection in coculture relative to monoculture. We show that data normalization alone does not eliminate the impact of altered detection on differential expression analysis of the cross-kingdom symbiosis. We assessed two additional strategies to overcome this methodological artifact inherent to DDA proteomics. In the first, we combined algal and bacterial monocultures at a relative abundance that mimicked the coculture, creating a “mono-mix” control to which the coculture could be compared. This approach enabled comparable detection of bacterial proteins in the coculture and the monoculture control. In the second strategy, we enhanced detection of lowly abundant bacterial proteins by using sample fractionation upstream of LC-MS/MS analysis. When these simple approaches were combined, they allowed for meaningful comparisons of nearly 10,000 algal proteins and over 4,000 bacterial proteins in response to symbiosis by DDA. They successfully recovered expected changes in the bacterial proteome in response to algal coculture, including upregulation of sugar-binding proteins and transporters. They also revealed novel proteomic responses to coculture that guide hypotheses about algal-bacterial interactions.

Dupuis, Sunnyjoy [University of California, Berkel↗