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    MicrobioRaman: an open-access web repository for microbiological Raman spectroscopy data
    (Springer Science and Business Media LLC, 2024-05) Lee, Kang Soo et al.; Hatzenpichler, Roland
    Here we present the establishment of an open-access web-based repository for microbiological Raman spectroscopy data. The data collection, called ‘MicrobioRaman’ (https://www.ebi.ac.uk/biostudies/MicrobioRaman/studies), was inspired by the great success and usefulness of research databases such as GenBank and UniProt. This centralized repository, residing within the BioStudies database1 — which is maintained by a public institution, the European Bioinformatics Institute — minimizes the risk of data loss or eventual abandonment, offering a long-term common reference for analysis with advantages in accessibility and transparency over commercial data analysis tools. We feel that MicrobioRaman will provide a foundation for this growing field by serving as an open-access repository for sharing microbiological Raman data and through the codification of a set of reporting standards.
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    Entropically driven aggregation of bacteria by host polymers promotes antibiotic tolerance in Pseudomonas aeruginosa
    (Proceedings of the National Academy of Sciences, 2018-10) Secor, Patrick R.; Michaels, Lia A.; Ratjen, Anina; Jennings, Laura K.; Singh, Pradeep K.
    Bacteria causing chronic infections are generally observed living in cell aggregates suspended in polymer-rich host secretions, and bacterial phenotypes induced by aggregated growth may be key factors in chronic infection pathogenesis. Bacterial aggregation is commonly thought of as a consequence of biofilm formation; however the mechanisms producing aggregation in vivo remain unclear. Here we show that polymers that are abundant at chronic infection sites cause bacteria to aggregate by the depletion aggregation mechanism, which does not require biofilm formation functions. Depletion aggregation is mediated by entropic forces between uncharged or like-charged polymers and particles (e.g., bacteria). Our experiments also indicate that depletion aggregation of bacteria induces marked antibiotic tolerance that was dependent on the SOS response, a stress response activated by genotoxic stress. These findings raise the possibility that targeting conditions that promote depletion aggregation or mechanisms of depletion-mediated tolerance could lead to new therapeutic approaches to combat chronic bacterial infections.
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    Proteomic and Transcriptomic Analyses Reveal Genes Upregulated by cis-Dichloroethene in Polaromonas sp. Strain JS666
    (American Society for Microbiology, 2009-06) Jennings, Laura; Chartrand, Michelle; Lacrampe-Couloume, Georges; Sherwood Lollar, Barbara; Spain, Jim C.; Gossett, James M.
    Polaromonas sp. strain JS666 is the only bacterial isolate capable of using cis-dichloroethene (cDCE) as a sole carbon and energy source. Studies of cDCE degradation in this novel organism are of interest because of potential bioremediation and biocatalysis applications. The primary cellular responses of JS666 to growth on cDCE were explored using proteomics and transcriptomics to identify the genes upregulated by cDCE. Two-dimensional gel electrophoresis revealed upregulation of genes annotated as encoding glutathione S-transferase, cyclohexanone monooxygenase, and haloacid dehalogenase. DNA microarray experiments confirmed the proteomics findings that the genes indicated above were among the most highly upregulated by cDCE. The upregulation of genes with antioxidant functions and the inhibition of cDCE degradation by elevated oxygen levels suggest that cDCE induces an oxidative stress response. Furthermore, the upregulation of a predicted ABC transporter and two sodium/solute symporters suggests that transport is important in cDCE degradation. The omics data were integrated with data from compound-specific isotope analysis (CSIA) and biochemical experiments to develop a hypothesis for cDCE degradation pathways in JS666. The CSIA results indicate that the measured isotope enrichment factors for aerobic cDCE degradation ranged from −17.4 to −22.4‰. Evidence suggests that cDCE degradation via monooxygenase-catalyzed epoxidation (C═C cleavage) may be only a minor degradation pathway under the conditions of these experiments and that the major degradation pathway involves carbon-chloride cleavage as the initial step, a novel mechanism. The results provide a significant step toward elucidation of cDCE degradation pathways and enhanced understanding of cDCE degradation in JS666.
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    Coupon position does not affect Pseudomonas aeruginosa and Staphylococcus aureus biofilm densities in the CDC biofilm reactor
    (Elsevier BV, 2024-08) Buckner, Elizabeth; Buckingham-Meyer, Kelli; Miller, Lindsey A.; Parker, Albert E.; Jones, Christopher J.; Goeres, Darla M.
    The CDC Biofilm Reactor method is the standard biofilm growth protocol for the validation of US Environmental Protection Agency biofilm label claims. However, no studies have determined the effect of coupon orientation within the reactor on biofilm growth. If positional effects have a statistically significant impact on biofilm density, they should be accounted for in the experimental design. Here, we isolate and quantify biofilms from each possible coupon surface in the reactor to quantitatively determine the positional effects in the CDC Biofilm Reactor. The results showed no statistically significant differences in viable cell density across different orientations and vertical positions in the reactor. Pseudomonas aeruginosa log densities were statistically equivalent among all coupon heights and orientations. While the Staphylococcus aureus cell growth showed no statistically significant differences, the densities were not statistically equivalent among all coupon heights and orientations due to the variability in the data. Structural differences were observed between biofilms on the high-shear baffle side of the reactor compared to the lower shear glass side of the reactor. Further studies are required to determine whether biofilm susceptibility to antimicrobials differs based on structural differences attributed to orientation.
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    Biodegradability of unheated and laboratory heated dissolved organic matter
    (Royal Society of Chemistry, 2024-01) Islam Promi, Saraf; Gardner, Courtney M.; Hohner, Amanda K.
    Following wildfires, partially combusted biomass remains on the forest floor and erosion from the landscape can release dissolved pyrogenic organic matter (dPyOM) to surface waters. Therefore, post-fire alterations to dissolved organic matter (DOM) in aquatic systems may play a vital role in DOM stability and biogeochemical cycles. Dissolved PyOM biodegradation remains poorly understood and is expected to vary with combustion temperature and fuel source. In this study laboratory heating and leaching of forest floor materials (soil and litter) were used to compare the biodegradability of unheated, low (250 °C), and moderate (450 °C) temperature leachates. Inoculation experiments were performed with river microbes. Dissolved organic carbon (DOC) and nitrogen (DON), inorganic nitrogen, and DOM optical properties were monitored for 38 days. Inoculation experiments showed significantly greater DOC biodegradation of low and moderate temperature samples (64% and 71%, respectively) compared to unheated samples (32%). The greater DOC biodegradation may be explained by lower molecular weight DOM composition of heated leachates which was supported by higher initial E2/E3 ratios (absorbance at 250 nm/365 nm). Further, the observed decrease in the E2/E3 ratio after incubation suggests biodegradation of smaller compounds. This trend was greater for heated samples than unheated DOM. Specific ultraviolet absorbance increased after incubation, suggesting biodegradation of aliphatic compounds. Inoculated moderate temperature samples showed the greatest DON degradation (74%), followed by low temperature (58%) and unheated (51%) samples. Overall, results suggest that low and moderate temperature dPyOM was more biodegradable than unheated DOM, which may have implications for aquatic biogeochemical cycling, ecosystem function, and water quality in fire-impacted watersheds.
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    Digital droplet RT-LAMP increases speed of SARS-CoV-2 viral RNA detection
    (Wiley, 2024-06) Yuan, Yuan; Ellis, Perry; Tao, Ye; Bikos, Dimitri A.; Loveday, Emma K.; Thomas, Mallory M.; Wilking, James N.; Chang, Connie B.; Ye, Fangfu; Weitz, David A.
    Nucleic acid amplification testing (NAAT) remains one of the most reliable methods for pathogen identification. However, conventional bulk NAATs may not be sufficiently fast or sensitive enough for the detection of clinically-relevant pathogens in point-of-care testing. Here, we have developed a digital droplet RT-LAMP (ddRT-LAMP) assay that rapidly and quantitatively detects the SARS-CoV-2 viral E gene in microfluidic drops. Droplet partitioning using ddRT-LAMP significantly accelerates detection times across a wide range of template concentrations compared to bulk RT-LAMP assays. We discover that a reduction in droplet diameter decreases assay times up to a certain size, upon which surface adsorption of the RT-LAMP polymerase reduces reaction efficiency. Optimization of drop size and polymerase concentration enables rapid, sensitive, and quantitative detection of the SARS-CoV-2 E gene in only 8 min. These results highlight the potential of ddRT-LAMP assays as an excellent platform for quantitative point-of-care testing.
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    Diversity and evolution of nitric oxide reduction in bacteria and archaea
    (Proceedings of the National Academy of Sciences, 2024-06) Murali, Ranjani; Pace, Laura A.; Sanford, Robert A.; Ward, L. M.; Lynes, Mackenzie M.; Hatzenpichler, Roland; Lingappa, Usha F.; Fischer, Woodward W.; Gennis, Robert B.; Hemp, James
    With the advent of culture-independent techniques for studying environmental microbes, our knowledge of their diversity has exploded, uncovering unique organisms, pathways, and proteins carrying out important processes in the biosphere. Novel biochemical reactions are often proposed based on sequence data, but experimental validation is difficult and rare. In this work, we used environmental sequence data to find enzymes that produce the greenhouse gas N2O from NO and validated our hypothesis with experiments. These new enzymes likely contribute to global N2O fluxes and expand the breadth of nitrogen cycling. We also demonstrated that these enzymes evolved multiple times from oxygen reductases, indicating that the evolutionary histories of aerobic respiration and denitrification—and more broadly the oxygen and nitrogen cycles—are tightly connected.
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    Beyond the Surface: Non-Invasive Low-Field NMR Analysis of Microbially-Induced Calcium Carbonate Precipitation in Shale Fractures
    (Springer Science and Business Media LLC, 2024-07) Willet, Matthew R.; Bedey, Kayla; Crandall, Dustin; Seymour, Joseph D.; Rutqvist, Jonny; Cunningham, Alfred B.; Phillips, Adrienne J.; Kirkland, Catherine M.
    Microbially-induced calcium carbonate precipitation (MICP) is a biological process in which microbially-produced urease enzymes convert urea and calcium into solid calcium carbonate (CaCO3) deposits. MICP has been demonstrated to reduce permeability in shale fractures under elevated pressures, raising the possibility of applying this technology to enhance shale reservoir storage safety. For this and other applications to become a reality, non-invasive tools are needed to determine how effectively MICP seals shale fractures at subsurface temperatures. In this study, two different MICP strategies were tested on 2.54 cm diameter and 5.08 cm long shale cores with a single fracture at 60 ℃. Flow-through, pulsed-flow MICP-treatment was repeatedly applied to Marcellus shale fractures with and without sand (“proppant”) until reaching approximately four orders of magnitude reduction in apparent permeability, while a single application of polymer-based “immersion” MICP-treatment was applied to an Eagle Ford shale fracture with proppant. Low-field nuclear magnetic resonance (LF-NMR) and X-Ray computed microtomography (micro-CT) techniques were used to assess the degree of biomineralization. With the flow-through approach, these tools revealed that while CaCO3 precipitation occurred throughout the fracture, there was preferential precipitation around proppant. Without proppant, the same approach led to premature sealing at the inlet side of the core. In contrast, immersion MICP-treatment sealed off the fracture edges and showed less mineral precipitation overall. This study highlights the use of LF-NMR relaxometry in characterizing fracture sealing and can help guide NMR logging tools in subsurface remediation efforts.
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    Aging alters the subchondral bone response 7 days after noninvasive traumatic joint injury in C57BL/6JN mice
    (Wiley, 2024) Dauenhauer, Lexia A.; Hislop, Brady D.; Brahmachary, Priyanka; Devine, Connor; Gibbs, Dustin; June, Ronald K.; Heveran, Chelsea M.
    Posttraumatic osteoarthritis (PTOA) commonly develops following anterior cruciate ligament (ACL) injuries, affecting around 50% of individuals within 10–20 years. Recent studies have highlighted early changes in subchondral bone structure after ACL injury in adolescent or young adult mice, which could contribute to the development of PTOA. However, ACL injuries do not only occur early in life. Middle-aged and older patients also experience ACL injuries and PTOA, but whether the aged subchondral bone also responds rapidly to injury is unknown. This study utilized a noninvasive, single overload mouse injury model to assess subchondral bone microarchitecture, turnover, and material properties in both young adults (5 months) and early old age (22 months) female C57BL/6JN mice at 7 days after injury. Mice underwent either joint injury (i.e., produces ACL tears) or sham injury procedures on both the loaded and contralateral limbs, allowing evaluation of the impacts of injury versus loading. The subchondral bone response to ACL injury is distinct for young adult and aged mice. While 5-month mice show subchondral bone loss and increased bone resorption postinjury, 22-month mice did not show loss of bone structure and had lower bone resorption. Subchondral bone plate modulus increased with age, but not with injury. Both ages of mice showed several bone measures were altered in the contralateral limb, demonstrating the systemic skeletal response to joint injury. These data motivate further investigation to discern how osteochondral tissues differently respond to injury in aging, such that diagnostics and treatments can be refined for these demographics.
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    Preventing heat-related deaths: The urgent need for a global early warning system for heat
    (Public Library of Science, 2024-07) Brimicombe, Chloe; Runkle, Jennifer D.; Tuholske, Cascade; Domeisen, Daniela I. V.; Gao, Chuansi; Toftum, Jørn; Otto, Ilona M.
    Heatwaves are the deadliest weather hazard and people and societies across the world continue to suffer from heat-related impacts. Future climate projections show a troubling increase in cross-sectoral impacts including health and economic risk presented by heatwaves. Many weather hazards such as floods and droughts already have a type of Early Warning System (EWS) or Global Alert System, but a global heat early warning system currently does not exist. An accurate heat EWS can save lives and can promote heat adaptation across society. Here, we (1) explore the history of Early Warning Systems as framed using the Disaster Risk Reduction paradigms and (2) identify potential barriers to an integrated Global Heat Early Warning system. Finally, we discuss what we have learned from history and the identified current barriers and outline a vision of a Global Heat Early Warning system around four key themes, incorporating systems for low-, middle-, and high-income countries and requiring cross-sectoral, cross-government, and interdisciplinary collaboration.
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