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Otolith 87 Sr / 86 Sr identifies natal origin, movement and life history of Burbot Lota lota in the Kootenai River following 45 years of impoundment
Abstract Hydropower has long been an effective form of renewable energy, but the development of the resource has negatively impacted fishes throughout the world. Formulating recovery plans to mitigate these effects requires a firm understanding of species‐specific provenance, life history and life stage habitat requirements. However, the importance of this information is often only recognised after a substantial population decline, when obtaining it becomes demographically challenging. We provide a case study for this scenario and present a post hoc approach to gain insight into these critical data gaps for Burbot Lota lota in the upper Kootenai River in Montana and British Columbia. The population once supported a robust tribal and recreational harvest but declined following impoundment and these fisheries have remained closed or curtailed for nearly 20 years. The reasons for the decline are unknown and actions to assist recovery have been constrained by limited information regarding natal origin, life history and habitat use. We addressed this issue using strontium isotope ratios ( 87 Sr/ 86 Sr) in otoliths collected over four decades in Lake Koocanusa, the reservoir on the Kootenai River above Libby Dam. Due to the geologic heterogeneity of the basin and resulting variation in water 87 Sr/ 86 Sr, the assignment probability for Burbot to their region of natal origin approached unity. Otolith 87 Sr/ 86 Sr also indicated the population was comprised of mainstem‐ and tributary‐origin forms and their relative abundance changed over time. Mainstem Burbot was most abundant during the 1970s and 2000s, whereas tributary forms dominated between these periods. We suggest ecosystem changes following impoundment contributed to this shift in life history forms and the overall decline of the population. Our findings underscore the need for additional investigations of these impacts to guide restoration efforts.
Identifying the microstructural features associated with void nucleation during elevated–temperature deformation of copper
The microstructural-scale mechanisms that produce cracks in metals during deformation at elevated temperatures are relevant to applications that involve thermal exposure. Prior studies of cavitation during high-temperature deformation, for example, creep, suffered from an inability to directly observe the microstructural evolution that occurs during deformation and leads to void nucleation. Here the current study takes advantage of modern high-speed electron backscatter diffraction (EBSD) detectors to observe cavitation in oxygen-free, high-conductivity copper in situ during deformation at 300°C. Most voids formed at the triple junction between a twin boundary and a high-angle grain boundary (HAGB). This finding does not contradict previous studies that suggested that twins are resistant to cracking—it reveals that cracks in HAGBs originate at twin/HAGB triple junctions and that cracks preferentially grow along HAGBs rather than the accompanying twins. Atomistic simulations explored the origins of this observation and suggest that twin/HAGB triple junctions are microstructural weak points.
Identifying dominant environmental predictors of freshwater wetland methane fluxes across diurnal to seasonal time scales
While wetlands are the largest natural source of methane (CH 4 ) to the atmosphere, they represent a large source of uncertainty in the global CH 4 budget due to the complex biogeochemical controls on CH 4 dynamics. Here we present, to our knowledge, the first multi-site synthesis of how predictors of CH 4 fluxes (FCH4) in freshwater wetlands vary across wetland types at diel, multiday (synoptic), and seasonal time scales. In this work we used several statistical approaches (correlation analysis, generalized additive modeling, mutual information, and random forests) in a wavelet-based multi-resolution framework to assess the importance of environmental predictors, nonlinearities and lags on FCH4 across 23 eddy covariance sites. Seasonally, soil and air temperature were dominant predictors of FCH4 at sites with smaller seasonal variation in water table depth (WTD). In contrast, WTD was the dominant predictor for wetlands with smaller variations in temperature (e.g., seasonal tropical/subtropical wetlands). Changes in seasonal FCH4 lagged fluctuations in WTD by ~17 ± 11 days, and lagged air and soil temperature by median values of 8 ± 16 and 5 ± 15 days, respectively. Temperature and WTD were also dominant predictors at the multiday scale. Atmospheric pressure (PA) was another important multiday scale predictor for peat-dominated sites, with drops in PA coinciding with synchronous releases of CH 4 . At the diel scale, synchronous relationships with latent heat flux and vapor pressure deficit suggest that physical processes controlling evaporation and boundary layer mixing exert similar controls on CH 4 volatilization, and suggest the influence of pressurized ventilation in aerenchymatous vegetation. In addition, 1- to 4-h lagged relationships with ecosystem photosynthesis indicate recent carbon substrates, such as root exudates, may also control FCH4. By addressing issues of scale, asynchrony, and nonlinearity, this work improves understanding of the predictors and timing of wetland FCH4 that can inform future studies and models, and help constrain wetland CH 4 emissions.
Identifying Bounds of Inorganic Content in Solventless Processing of Hybrid Solid Electrolytes
Solid-state lithium batteries require safe, robust electrolytes to enable higher energy densities and improved safety over conventional cells. Hybrid polymer–ceramic electrolytes are a promising solution, combining the processability of polymers with the high ionic conductivity and mechanical strength of inorganic fillers. In this work, we demonstrate a solventless, UV-curing method to produce hybrid solid electrolytes using a poly(ethylene glycol) dimethyl ether (PEGDME)-based photocurable matrix incorporating Li 1.5 Al 0.5 Ge 1.5 (PO 4 ) 3 (LAGP) or Li 7 La 3 Zr 2 O 12 (LLZO) ceramic electrolyte. Inorganic filler loadings up to ∼55 wt.% could be successfully incorporated via this process which was the highest inorganic content at which the slurry remains processable and cured into a uniform film. The resulting UV-cured composite electrolytes remain flexible and exhibit room-temperature ionic conductivities on the order of 10 −4 S·cm −1 , along with notably improved lithium-ion transference numbers compared to conventional polymer electrolytes. Similar performance and processing limits were observed for both LAGP and LLZO, indicating that ceramic filler chemistry does not significantly affect the UV-curing process or the electrolyte's ion transport properties in this regime. Eliminating solvents from fabrication not only simplifies processing and mitigates environmental concerns but also enables higher solid contents that enhance mechanical strength and help suppress lithium dendrite formation. In conclusion, this scalable approach thus paves the way for manufacturing robust composite solid electrolytes for next-generation solid-state batteries (SSBs).
Ice-nucleating agents in sea spray aerosol identified and quantified with a holistic multimodal freezing model
Sea spray aerosol (SSA) is a widely recognized important source of ice-nucleating particles (INPs) in the atmosphere. However, composition-specific identification, nucleation processes, and ice nucleation rates of SSA-INPs have not been well constrained. Microspectroscopic characterization of ambient and laboratory-generated SSA confirms that water-borne exudates from planktonic microorganisms composed of a mixture of proteinaceous and polysaccharidic compounds act as ice-nucleating agents (INAs). These data and data from previously published mesocosm and wave channel studies are subsequently used to further develop the stochastic freezing model (SFM) producing ice nucleation rate coefficients for SSA-INPs. The SFM simultaneously predicts immersion freezing and deposition and homogeneous ice nucleation by SSA particles under tropospheric conditions. Predicted INP concentrations agree with ambient and laboratory measurements. In addition, this holistic freezing model is independent of the source and exact composition of the SSA particles, making it well suited for implementation in cloud and climate models.
Beyond low lignin: Identifying the primary barrier to plant biomass conversion by fermentative bacteria
Renewable alternatives for nonelectrifiable fossil-derived chemicals are needed and plant matter, the most abundant biomass on Earth, provide an ideal feedstock. However, the heterogeneous polymeric composition of lignocellulose makes conversion difficult. Lignin presents a formidable barrier to fermentation of nonpretreated biomass. Extensive chemical and enzymatic treatments can liberate fermentable carbohydrates from plant biomass, but microbial routes offer many advantages, including concomitant conversion to industrial chemicals. Here, testing of lignin content of nonpretreated biomass using the cellulolytic thermophilic bacterium,Anaerocellum bescii, revealed that the primary microbial degradation barrier relates to methoxy substitutions in lignin. This contrasts with optimal lignin composition for chemical pretreatment that favors high S/G ratio and low H lignin. Genetically modified poplar trees with diverse lignin compositions confirm these findings. In addition, poplar trees with low methoxy content achieve industrially relevant levels of microbial solubilization without any pretreatments and with no impact on tree fitness in greenhouse.
Identifying a next-generation antimalarial trioxolane in a landscape of artemisinin partial resistance
For over two decades, artemisinin-based combination therapy (ACT) has been the standard of care for the treatment of uncomplicated falciparum malaria. However, artemisinin partial resistance (ART-R) is now prevalent in Southeast Asia and has emerged in eastern Africa, threatening ACT efficacy. Artefenomel, a synthetic 1,2,4-trioxolane, exhibits an extended pharmacokinetic exposure profile that predicts for efficacy against ART-R parasites. Unfortunately, the development of artefenomel was halted recently after almost a decade in the clinic. Here, we describe studies of an artefenomel-adjacent chemotype that combines potent in vitro activity against clinical ART-R parasites, an extended pharmacokinetic profile with single-exposure efficacy in a murine malaria model, and enhanced stability in human microsomes and hepatocytes. Overall, our studies reveal a heretofore underexplored trioxolane chemotype with the potential to address ART-R in a next-generation trioxolane development candidate.
Dual gene expression analysis identifies factors associated with Staphylococcus aureus virulence in diabetic mice
Staphylococcus aureus is a major human pathogen of the skin. The global burden of diabetes is high, with S. aureus a major complication of diabetic wound infections. We investigated how the diabetic environment influences S. aureus skin infection and observed an increased susceptibility to infection in mouse models of both type I and type II diabetes. A dual gene expression approach was taken to investigate transcriptional alterations in both the host and bacterium after infection. While analysis of the host response revealed only minor changes between infected control and diabetic mice, we observed that S. aureus isolated from diabetic mice had significant increases in genes associated with translation, posttranslational modification and chaperones, and reductions in genes associated with amino acid transport and metabolism. One family of genes upregulated in S. aureus isolated from diabetic lesions encoded the Clp proteases associated with the misfolded protein response. The Clp proteases were found to be partially glucose regulated as well as influencing the hemolytic activity of S. aureus . Strains lacking the Clp proteases, ClpX, ClpC and ClpP were significantly attenuated in our animal model of skin infection, with significant reductions observed in dermonecrosis and bacterial burden. In particular, mutations in clpP and clpX were significantly attenuated and remained attenuation in both normal and diabetic mice. As a result, our data suggests that the diabetic environment also causes changes to occur in invading pathogens and one of these virulence determinants is the Clp protease system.
RNA Sequencing Identifies New RNase III Cleavage Sites in Escherichia coli and Reveals Increased Regulation of mRNA
ABSTRACT Ribonucleases facilitate rapid turnover of RNA, providing cells with another mechanism to adjust transcript and protein levels in response to environmental conditions. While many examples have been documented, a comprehensive list of RNase targets is not available. To address this knowledge gap, we compared levels of RNA sequencing coverage of Escherichia coli and a corresponding RNase III mutant to expand the list of known RNase III targets. RNase III is a widespread endoribonuclease that binds and cleaves double-stranded RNA in many critical transcripts. RNase III cleavage at novel sites found in aceEF , proP , tnaC , dctA , pheM , sdhC , yhhQ , glpT , aceK , and gluQ accelerated RNA decay, consistent with previously described targets wherein RNase III cleavage initiates rapid degradation of secondary messages by other RNases. In contrast, cleavage at three novel sites in the ahpF , pflB , and yajQ transcripts led to stabilized secondary transcripts. Two other novel sites in hisL and pheM overlapped with transcriptional attenuators that likely serve to ensure turnover of these highly structured RNAs. Many of the new RNase III target sites are located on transcripts encoding metabolic enzymes. For instance, two novel RNase III sites are located within transcripts encoding enzymes near a key metabolic node connecting glycolysis and the tricarboxylic acid (TCA) cycle. Pyruvate dehydrogenase activity was increased in an rnc deletion mutant compared to the wild-type (WT) strain in early stationary phase, confirming the novel link between RNA turnover and regulation of pathway activity. Identification of these novel sites suggests that mRNA turnover may be an underappreciated mode of regulating metabolism. IMPORTANCE The concerted action and overlapping functions of endoribonucleases, exoribonucleases, and RNA processing enzymes complicate the study of global RNA turnover and recycling of specific transcripts. More information about RNase specificity and activity is needed to make predictions of transcript half-life and to design synthetic transcripts with optimal stability. RNase III does not have a conserved target sequence but instead recognizes RNA secondary structure. Prior to this study, only a few RNase III target sites in E. coli were known, so we used RNA sequencing to provide a more comprehensive list of cleavage sites and to examine the impact of RNase III on transcript degradation. With this added information on how RNase III participates in transcript regulation and recycling, a more complete picture of RNA turnover can be developed for E. coli . Similar approaches could be used to augment our understanding of RNA turnover in other bacteria.
A Histoplasma capsulatum Lipid Metabolic Map Identifies Antifungal Targets
It is estimated that 150 people die per hour due to the insufficient therapeutic treatments to combat fungal infections. A major hurdle to developing antifungal therapies is the scarce knowledge on the fungal metabolic pathways and mechanisms of virulence.
Genomic Features Predict Bacterial Life History Strategies in Soil, as Identified by Metagenomic Stable Isotope Probing
Soil microbes are major players in the global carbon cycle, yet we still have little understanding of how the carbon cycle operates in soil communities. A major limitation is that carbon metabolism lacks discrete functional genes that define carbon transformations.
Using DNA affinity purification sequencing (DAP-seq) to identify in vitro binding sites of potential Novosphingobium aromaticivorans DSM12444 transcription factors
Genome-wide binding sites of 44 putative transcription factors (TFs) from Novosphingobium aromaticivorans DSM12444 were analyzed using DNA affinity purification sequencing. We report that 32 of these TFs have at least one area of enrichment. These data will help better understand aromatic metabolism and other features of N. aromaticivorans biology.
MVP: a modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes
While numerous computational frameworks and workflows are available for recovering prokaryote and eukaryote genomes from metagenome data, only a limited number of pipelines are designed specifically for viromics analysis. With many viromics tools developed in the last few years alone, it can be challenging for scientists with limited bioinformatics experience to easily recover, evaluate quality, annotate genes, dereplicate, assign taxonomy, and calculate relative abundance and coverage of viral genomes using state-of-the-art methods and standards. Here, we describe Modular Viromics Pipeline (MVP) v.1.0, a user-friendly pipeline written in Python and providing a simple framework to perform standard viromics analyses. MVP combines multiple tools to enable viral genome identification, characterization of genome quality, filtering, clustering, taxonomic and functional annotation, genome binning, and comprehensive summaries of results that can be used for downstream ecological analyses. Overall, MVP provides a standardized and reproducible pipeline for both extensive and robust characterization of viruses from large-scale sequencing data including metagenomes, metatranscriptomes, viromes, and isolate genomes. As a typical use case, we show how the entire MVP pipeline can be applied to a set of 20 metagenomes from wetland sediments using only 10 modules executed via command lines, leading to the identification of 11,656 viral contigs and 8,145 viral operational taxonomic units (vOTUs) displaying a clear beta-diversity pattern. Further, acting as a dynamic wrapper, MVP is designed to continuously incorporate updates and integrate new tools, ensuring its ongoing relevance in the rapidly evolving field of viromics. MVP is available at https://gitlab.com/ccoclet/mvp and as versioned packages in PyPi and Conda.
A High-Throughput Method for Identifying Novel Genes That Influence Metabolic Pathways Reveals New Iron and Heme Regulation in Pseudomonas aeruginosa
The ability to simultaneously and more directly correlate genes with metabolite levels on a global level would provide novel information for many biological platforms yet has thus far been challenging. Here, we describe a method to help address this problem, which we dub “Met-Seq” ( met abolite-coupled Tn seq uencing).
DOE Screening Methodology for Estimating the Prospective CO2 Storage Resource of Shales and Identifying Data Gaps
Presented by NETL at the Joint 52nd Northeastern Annual Section / 51st North-Central Annual Section Meeting - 2017; Pittsburgh, PA; March 19-21, 2017
Identifying Rare Earth Elements and Thorium and Uranium in Iron Oxide–Apatite Deposit of Gazestan Bafgh, Southeast of Iran
The Gazestan magnetite-apatite deposit is one of Kiruna-type deposits located 78 km from Bafgh in the province of Yazd, in the Bafgh Posht-e-Badam district, southeast of Iran. In the mining region of Bafgh, volcanic rocks and Precambrian volcano-sedimentary are the main host of iron-apatite deposits. Iron deposits are essentially located in Bafgh region inside the green acidic metamorphic rocks. Volcanic rocks are basically rhyolite and rhyodacitic and the sedimentary units are mostly made of dolomite. Rock units of the region belong to the Rizzo series. The Bafgh apatite compounds are fluoride-type and seen in the monazite mineral. The similarity of the rare earth elements pattern in all samples indicates the magma source. The most amount of rare earth elements in the Gazestan deposit include 7766.25 ppm and the most amount of Th is equal to 65.1 ppm and U is equal to 8.33 ppm. The most amount of P2O5 s equal to 26.5 wt% and Fe is equal to 61.3 wt%. Also, it can be concluded that due to their high correlation with rare earth elements, the deposit is of Uranium Thorium-bearing type.
The possibility of identifying the spatial location of single dislocations by topo-tomography on laboratory setups
The spatial arrangement of single linear defects in a Si single crystal (input surface (111)) has been investigated by X-ray topo-tomography using laboratory X-ray sources. The experimental technique and the procedure of reconstructing a 3D image of dislocation half-loops near the Si crystal surface are described. The sizes of observed linear defects with a spatial resolution of about 10 μm are estimated.