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Pozo-Morales M, Cobham AE, Centola C, McKinney MC, Liu P, Perazzolo C, Lefort A, Libert F, Bai H, Rohner N, Singh SP. Starvation-resistant cavefish reveal conserved mechanisms of starvation-induced hepatic lipotoxicity. Life Sci Alliance 2024; 7:e202302458. [PMID: 38467419 PMCID: PMC10927358 DOI: 10.26508/lsa.202302458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 02/14/2024] [Accepted: 02/19/2024] [Indexed: 03/13/2024] Open
Abstract
Starvation causes the accumulation of lipid droplets in the liver, a somewhat counterintuitive phenomenon that is nevertheless conserved from flies to humans. Much like fatty liver resulting from overfeeding, hepatic lipid accumulation (steatosis) during undernourishment can lead to lipotoxicity and atrophy of the liver. Here, we found that although surface populations of Astyanax mexicanus undergo this evolutionarily conserved response to starvation, the starvation-resistant cavefish larvae of the same species do not display an accumulation of lipid droplets upon starvation. Moreover, cavefish are resistant to liver atrophy during starvation, providing a unique system to explore strategies for liver protection. Using comparative transcriptomics between zebrafish, surface fish, and cavefish, we identified the fatty acid transporter slc27a2a/fatp2 to be correlated with the development of fatty liver. Pharmacological inhibition of slc27a2a in zebrafish rescues steatosis and atrophy of the liver upon starvation. Furthermore, down-regulation of FATP2 in Drosophila larvae inhibits the development of starvation-induced steatosis, suggesting the evolutionarily conserved importance of the gene in regulating fatty liver upon nutrition deprivation. Overall, our study identifies a conserved, druggable target to protect the liver from atrophy during starvation.
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Affiliation(s)
- Macarena Pozo-Morales
- https://ror.org/01r9htc13 IRIBHM, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Ansa E Cobham
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Cielo Centola
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | | | - Peiduo Liu
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA
| | - Camille Perazzolo
- https://ror.org/01r9htc13 IRIBHM, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Anne Lefort
- https://ror.org/01r9htc13 IRIBHM, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Frédérick Libert
- https://ror.org/01r9htc13 IRIBHM, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Hua Bai
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA
| | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, MO, USA
- Department of Cell Biology & Physiology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Sumeet Pal Singh
- https://ror.org/01r9htc13 IRIBHM, Université Libre de Bruxelles (ULB), Brussels, Belgium
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McLean IR, Erkelens IM, Cooper EA. How small changes to one eye's retinal image can transform the perceived shape of a very familiar object. Proc Natl Acad Sci U S A 2024; 121:e2400086121. [PMID: 38621132 DOI: 10.1073/pnas.2400086121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 03/07/2024] [Indexed: 04/17/2024] Open
Abstract
Vision can provide useful cues about the geometric properties of an object, like its size, distance, pose, and shape. But how the brain merges these properties into a complete sensory representation of a three-dimensional object is poorly understood. To address this gap, we investigated a visual illusion in which humans misperceive the shape of an object due to a small change in one eye's retinal image. We first show that this illusion affects percepts of a highly familiar object under completely natural viewing conditions. Specifically, people perceived their own rectangular mobile phone to have a trapezoidal shape. We then investigate the perceptual underpinnings of this illusion by asking people to report both the perceived shape and pose of controlled stimuli. Our results suggest that the shape illusion results from distorted cues to object pose. In addition to yielding insights into object perception, this work informs our understanding of how the brain combines information from multiple visual cues in natural settings. The shape illusion can occur when people wear everyday prescription spectacles; thus, these findings also provide insight into the cue combination challenges that some spectacle wearers experience on a regular basis.
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Affiliation(s)
- Iona R McLean
- Herbert Wertheim School of Optometry and Vision Science, University of California, Berkeley, CA 94720
| | | | - Emily A Cooper
- Herbert Wertheim School of Optometry and Vision Science, University of California, Berkeley, CA 94720
- Helen Wills Neuroscience Institute, University of California, Berkeley, CA 94720
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3
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Takeshita RSC. A life for a (shorter) life: The reproduction-longevity trade-off. Proc Natl Acad Sci U S A 2024; 121:e2405089121. [PMID: 38598350 DOI: 10.1073/pnas.2405089121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024] Open
Affiliation(s)
- Rafaela S C Takeshita
- Department of Anthropology and School of Biomedical Sciences, Kent State University, Kent, OH 44242
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4
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Wagner RJ, Lamont SC, White ZT, Vernerey FJ. Catch bond kinetics are instrumental to cohesion of fire ant rafts under load. Proc Natl Acad Sci U S A 2024; 121:e2314772121. [PMID: 38621122 DOI: 10.1073/pnas.2314772121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 02/18/2024] [Indexed: 04/17/2024] Open
Abstract
Dynamic networks composed of constituents that break and reform bonds reversibly are ubiquitous in nature owing to their modular architectures that enable functions like energy dissipation, self-healing, and even activity. While bond breaking depends only on the current configuration of attachment in these networks, reattachment depends also on the proximity of constituents. Therefore, dynamic networks composed of macroscale constituents (not benefited by the secondary interactions cohering analogous networks composed of molecular-scale constituents) must rely on primary bonds for cohesion and self-repair. Toward understanding how such macroscale networks might adaptively achieve this, we explore the uniaxial tensile response of 2D rafts composed of interlinked fire ants (S. invicta). Through experiments and discrete numerical modeling, we find that ant rafts adaptively stabilize their bonded ant-to-ant interactions in response to tensile strains, indicating catch bond dynamics. Consequently, low-strain rates that should theoretically induce creep mechanics of these rafts instead induce elastic-like response. Our results suggest that this force-stabilization delays dissolution of the rafts and improves toughness. Nevertheless, above 35[Formula: see text] strain low cohesion and stress localization cause nucleation and growth of voids whose coalescence patterns result from force-stabilization. These voids mitigate structural repair until initial raft densities are restored and ants can reconnect across defects. However mechanical recovery of ant rafts during cyclic loading suggests that-even upon reinstatement of initial densities-ants exhibit slower repair kinetics if they were recently loaded at faster strain rates. These results exemplify fire ants' status as active agents capable of memory-driven, stimuli-response for potential inspiration of adaptive structural materials.
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Affiliation(s)
- Robert J Wagner
- Sibley School of Mechanical & Aerospace Engineering, Cornell University, Ithaca, NY
| | - Samuel C Lamont
- Paul M. Rady School of Mechanical Engineering, University of Colorado, Boulder, CO
| | - Zachary T White
- Paul M. Rady School of Mechanical Engineering, University of Colorado, Boulder, CO
| | - Franck J Vernerey
- Paul M. Rady School of Mechanical Engineering, University of Colorado, Boulder, CO
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5
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Blom K, Song K, Vouga E, Godec A, Makarov DE. Milestoning estimators of dissipation in systems observed at a coarse resolution. Proc Natl Acad Sci U S A 2024; 121:e2318333121. [PMID: 38625949 DOI: 10.1073/pnas.2318333121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 03/14/2024] [Indexed: 04/18/2024] Open
Abstract
Many nonequilibrium, active processes are observed at a coarse-grained level, where different microscopic configurations are projected onto the same observable state. Such "lumped" observables display memory, and in many cases, the irreversible character of the underlying microscopic dynamics becomes blurred, e.g., when the projection hides dissipative cycles. As a result, the observations appear less irreversible, and it is very challenging to infer the degree of broken time-reversal symmetry. Here we show, contrary to intuition, that by ignoring parts of the already coarse-grained state space we may-via a process called milestoning-improve entropy-production estimates. We present diverse examples where milestoning systematically renders observations "closer to underlying microscopic dynamics" and thereby improves thermodynamic inference from lumped data assuming a given range of memory, and we hypothesize that this effect is quite general. Moreover, whereas the correct general physical definition of time reversal in the presence of memory remains unknown, we here show by means of physically relevant examples that at least for semi-Markov processes of first and second order, waiting-time contributions arising from adopting a naive Markovian definition of time reversal generally must be discarded.
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Affiliation(s)
- Kristian Blom
- Mathematical biophysics Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
| | - Kevin Song
- Department of Computer Science, University of Texas at Austin, Austin, TX 78712
| | - Etienne Vouga
- Department of Computer Science, University of Texas at Austin, Austin, TX 78712
| | - Aljaž Godec
- Mathematical biophysics Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
| | - Dmitrii E Makarov
- Department of Chemistry and Oden Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, TX 78712
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Celia-Sanchez BN, Mangum B, Gómez Londoño LF, Wang C, Shuman B, Brewer MT, Momany M. Pan-azole- and multi-fungicide-resistant Aspergillus fumigatus is widespread in the United States. Appl Environ Microbiol 2024; 90:e0178223. [PMID: 38557086 DOI: 10.1128/aem.01782-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/20/2024] [Indexed: 04/04/2024] Open
Abstract
Aspergillus fumigatus is an important global fungal pathogen of humans. Azole drugs are among the most effective treatments for A. fumigatus infection. Azoles are also widely used in agriculture as fungicides against fungal pathogens of crops. Azole-resistant A. fumigatus has been increasing in Europe and Asia for two decades where clinical resistance is thought to be driven by agricultural use of azole fungicides. The most prevalent mechanisms of azole resistance in A. fumigatus are tandem repeats (TR) in the cyp51A promoter coupled with mutations in the coding region which result in resistance to multiple azole drugs (pan-azole resistance). Azole-resistant A. fumigatus has been isolated from patients in the United States (U.S.), but little is known about its environmental distribution. To better understand the distribution of azole-resistant A. fumigatus in the U.S., we collected isolates from agricultural sites in eight states and tested 202 isolates for sensitivity to azoles. We found azole-resistant A. fumigatus in agricultural environments in seven states showing that it is widespread in the U.S. We sequenced environmental isolates representing the range of U.S. sample sites and compared them with publicly available environmental worldwide isolates in phylogenetic, principal component, and ADMIXTURE analyses. We found worldwide isolates fell into three clades, and TR-based pan-azole resistance was largely in a single clade that was strongly associated with resistance to multiple agricultural fungicides. We also found high levels of gene flow indicating recombination between clades highlighting the potential for azole-resistance to continue spreading in the U.S.IMPORTANCEAspergillus fumigatus is a fungal pathogen of humans that causes over 250,000 invasive infections each year. It is found in soils, plant debris, and compost. Azoles are the first line of defense antifungal drugs against A. fumigatus. Azoles are also used as agricultural fungicides to combat other fungi that attack plants. Azole-resistant A. fumigatus has been a problem in Europe and Asia for 20 years and has recently been reported in patients in the United States (U.S.). Until this study, we did not know much about azole-resistant A. fumigatus in agricultural settings in the U.S. In this study, we isolated azole-resistant A. fumigatus from multiple states and compared it to isolates from around the world. We show that A. fumigatus which is resistant to azoles and to other strictly agricultural fungicides is widespread in the U.S.
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Affiliation(s)
- B N Celia-Sanchez
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA
| | - B Mangum
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA
- Department of Plant Pathology, University of Georgia, Athens, Georgia, USA
| | - L F Gómez Londoño
- Department of Plant Pathology, University of Georgia, Athens, Georgia, USA
| | - C Wang
- Department of Plant Pathology, University of Georgia, Athens, Georgia, USA
| | - B Shuman
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA
| | - M T Brewer
- Department of Plant Pathology, University of Georgia, Athens, Georgia, USA
| | - M Momany
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA
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7
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Kalvapalle PB, Sridhar S, Silberg JJ, Stadler LB. Long-duration environmental biosensing by recording analyte detection in DNA using recombinase memory. Appl Environ Microbiol 2024; 90:e0236323. [PMID: 38551351 DOI: 10.1128/aem.02363-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 02/20/2024] [Indexed: 04/18/2024] Open
Abstract
Microbial biosensors that convert environmental information into real-time visual outputs are limited in their sensing abilities in complex environments, such as soil and wastewater, due to optical inaccessibility. Biosensors that could record transient exposure to analytes within a large time window for later retrieval represent a promising approach to solve the accessibility problem. Here, we test the performance of recombinase-memory biosensors that sense a sugar (arabinose) and a microbial communication molecule (3-oxo-C12-L-homoserine lactone) over 8 days (~70 generations) following analyte exposure. These biosensors sense the analyte and trigger the expression of a recombinase enzyme which flips a segment of DNA, creating a genetic memory, and initiates fluorescent protein expression. The initial designs failed over time due to unintended DNA flipping in the absence of the analyte and loss of the flipped state after exposure to the analyte. Biosensor performance was improved by decreasing recombinase expression, removing the fluorescent protein output, and using quantitative PCR to read out stored information. Application of memory biosensors in wastewater isolates achieved memory of analyte exposure in an uncharacterized Pseudomonas isolate. By returning these engineered isolates to their native environments, recombinase-memory systems are expected to enable longer duration and in situ investigation of microbial signaling, cross-feeding, community shifts, and gene transfer beyond the reach of traditional environmental biosensors.IMPORTANCEMicrobes mediate ecological processes over timescales that can far exceed the half-lives of transient metabolites and signals that drive their collective behaviors. We investigated strategies for engineering microbes to stably record their transient exposure to a chemical over many generations through DNA rearrangements. We identify genetic architectures that improve memory biosensor performance and characterize these in wastewater isolates. Memory biosensors are expected to be useful for monitoring cell-cell signals in biofilms, detecting transient exposure to chemical pollutants, and observing microbial cross-feeding through short-lived metabolites within cryptic methane, nitrogen, and sulfur cycling processes. They will also enable in situ studies of microbial responses to ephemeral environmental changes, or other ecological processes that are currently challenging to monitor non-destructively using real-time biosensors and analytical instruments.
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Affiliation(s)
| | - Swetha Sridhar
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, Texas, USA
| | - Jonathan J Silberg
- Department of BioSciences, Rice University, Houston, Texas, USA
- Department of Bioengineering, Rice University, Houston, Texas, USA
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas, USA
| | - Lauren B Stadler
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas, USA
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8
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Elbon CE, Stewart FJ, Glass JB. Novel Alphaproteobacteria transcribe genes for nitric oxide transformation at high levels in a marine oxygen-deficient zone. Appl Environ Microbiol 2024; 90:e0209923. [PMID: 38445905 DOI: 10.1128/aem.02099-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/09/2024] [Indexed: 03/07/2024] Open
Abstract
Marine oxygen-deficient zones (ODZs) are portions of the ocean where intense nitrogen loss occurs primarily via denitrification and anammox. Despite many decades of study, the identity of the microbes that catalyze nitrogen loss in ODZs is still being elucidated. Intriguingly, high transcription of genes in the same family as the nitric oxide dismutase (nod) gene from Methylomirabilota has been reported in the anoxic core of ODZs. Here, we show that the most abundantly transcribed nod genes in the Eastern Tropical North Pacific ODZ belong to a new order (UBA11136) of Alphaproteobacteria, rather than Methylomirabilota as previously assumed. Gammaproteobacteria and Planctomycetia also transcribe nod, but at lower relative abundance than UBA11136 in the upper ODZ. The nod-transcribing Alphaproteobacteria likely use formaldehyde and formate as a source of electrons for aerobic respiration, with additional electrons possibly from sulfide oxidation. They also transcribe multiheme cytochrome (here named ptd) genes for a putative porin-cytochrome protein complex of unknown function, potentially involved in extracellular electron transfer. Molecular oxygen for aerobic respiration may originate from nitric oxide dismutation via cryptic oxygen cycling. Our results implicate Alphaproteobacteria order UBA11136 as a significant player in marine nitrogen loss and highlight their potential in one-carbon, nitrogen, and sulfur metabolism in ODZs.IMPORTANCEIn marine oxygen-deficient zones (ODZs), microbes transform bioavailable nitrogen to gaseous nitrogen, with nitric oxide as a key intermediate. The Eastern Tropical North Pacific contains the world's largest ODZ, but the identity of the microbes transforming nitric oxide remains unknown. Here, we show that highly transcribed nitric oxide dismutase (nod) genes belong to Alphaproteobacteria of the novel order UBA11136, which lacks cultivated isolates. These Alphaproteobacteria show evidence for aerobic respiration, using oxygen potentially sourced from nitric oxide dismutase, and possess a novel porin-cytochrome protein complex with unknown function. Gammaproteobacteria and Planctomycetia transcribe nod at lower levels. Our results pinpoint the microbes mediating a key step in marine nitrogen loss and reveal an unexpected predicted metabolism for marine Alphaproteobacteria.
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Affiliation(s)
- Claire E Elbon
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Frank J Stewart
- Department of Microbiology & Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Jennifer B Glass
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
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9
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Sun Y, Staley ZR, Woodbury B, Riethoven JJ, Li X. Composting reduces the risks of resistome in beef cattle manure at the transcriptional level. Appl Environ Microbiol 2024; 90:e0175223. [PMID: 38445903 DOI: 10.1128/aem.01752-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 02/16/2024] [Indexed: 03/07/2024] Open
Abstract
Transcriptomic evidence is needed to determine whether composting is more effective than conventional stockpiling in mitigating the risk of resistome in livestock manure. The objective of this study is to compare composting and stockpiling for their effectiveness in reducing the risk of antibiotic resistance in beef cattle manure. Samples collected from the center and the surface of full-size manure stockpiling and composting piles were subject to metagenomic and metatranscriptomic analyses. While the distinctions in resistome between stockpiled and composted manure were not evident at the DNA level, the advantages of composting over stockpiling were evident at the transcriptomic level in terms of the abundance of antibiotic resistance genes (ARGs), the number of ARG subtypes, and the prevalence of high-risk ARGs (i.e., mobile ARGs associated with zoonotic pathogens). DNA and transcript contigs show that the pathogen hosts of high-risk ARGs included Escherichia coli O157:H7 and O25b:H4, Klebsiella pneumoniae, and Salmonella enterica. Although the average daily temperatures for the entire composting pile exceeded 55°C throughout the field study, more ARG and ARG transcripts were removed at the center of the composting pile than at the surface. This work demonstrates the advantage of composting over stockpiling in reducing ARG risk in active populations in beef cattle manure.IMPORTANCEProper treatment of manure before land application is essential to mitigate the spread of antibiotic resistance in the environment. Stockpiling and composting are two commonly used methods for manure treatment. However, the effectiveness of composting in reducing antibiotic resistance in manure has been debated. This work compared the ability of these two methods to reduce the risk of antibiotic resistance in beef cattle manure. Our results demonstrate that composting reduced more high-risk resistance genes at the transcriptomic level in cattle manure than conventional stockpiling. This finding not only underscores the effectiveness of composting in reducing antibiotic resistance in manure but also highlights the importance of employing RNA analyses alongside DNA analyses.
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Affiliation(s)
- Yuepeng Sun
- School of Ecology and Environment, Inner Mongolia University, Hohhot, China
- Department of Civil and Environmental Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Zachery R Staley
- Department of Civil and Environmental Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Bryan Woodbury
- USDA-ARS U.S. Meat Animal Research Center, Clay Center, Clay Center, Nebraska, USA
| | - Jean-Jack Riethoven
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Xu Li
- Department of Civil and Environmental Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
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Koblížek M, Ferrera I, Kolářová E, Duhamel S, Popendorf KJ, Gasol JM, Van Mooy BAS. Growth and mortality of aerobic anoxygenic phototrophs in the North Pacific Subtropical Gyre. Appl Environ Microbiol 2024; 90:e0003224. [PMID: 38551354 DOI: 10.1128/aem.00032-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 03/08/2024] [Indexed: 04/18/2024] Open
Abstract
Aerobic anoxygenic phototrophic (AAP) bacteria harvest light energy using bacteriochlorophyll-containing reaction centers to supplement their mostly heterotrophic metabolism. While their abundance and growth have been intensively studied in coastal environments, much less is known about their activity in oligotrophic open ocean regions. Therefore, we combined in situ sampling in the North Pacific Subtropical Gyre, north of O'ahu island, Hawaii, with two manipulation experiments. Infra-red epifluorescence microscopy documented that AAP bacteria represented approximately 2% of total bacteria in the euphotic zone with the maximum abundance in the upper 50 m. They conducted active photosynthetic electron transport with maximum rates up to 50 electrons per reaction center per second. The in situ decline of bacteriochlorophyll concentration over the daylight period, an estimate of loss rates due to predation, indicated that the AAP bacteria in the upper 50 m of the water column turned over at rates of 0.75-0.90 d-1. This corresponded well with the specific growth rate determined in dilution experiments where AAP bacteria grew at a rate 1.05 ± 0.09 d-1. An amendment of inorganic nitrogen to obtain N:P = 32 resulted in a more than 10 times increase in AAP abundance over 6 days. The presented data document that AAP bacteria are an active part of the bacterioplankton community in the oligotrophic North Pacific Subtropical Gyre and that their growth was mostly controlled by nitrogen availability and grazing pressure.IMPORTANCEMarine bacteria represent a complex assembly of species with different physiology, metabolism, and substrate preferences. We focus on a specific functional group of marine bacteria called aerobic anoxygenic phototrophs. These photoheterotrophic organisms require organic carbon substrates for growth, but they can also supplement their metabolic needs with light energy captured by bacteriochlorophyll. These bacteria have been intensively studied in coastal regions, but rather less is known about their distribution, growth, and mortality in the oligotrophic open ocean. Therefore, we conducted a suite of measurements in the North Pacific Subtropical Gyre to determine the distribution of these organisms in the water column and their growth and mortality rates. A nutrient amendment experiment showed that aerobic anoxygenic phototrophs were limited by inorganic nitrogen. Despite this, they grew more rapidly than average heterotrophic bacteria, but their growth was balanced by intense grazing pressure.
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Affiliation(s)
- Michal Koblížek
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology, Czech Academy of Science, Třeboň, Czechia
| | - Isabel Ferrera
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía (IEO-CSIC), Fuengirola, Málaga, Spain
| | - Eva Kolářová
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology, Czech Academy of Science, Třeboň, Czechia
| | - Solange Duhamel
- Department of Cellular and Molecular Biology, University of Arizona, Tucson, Arizona, USA
| | - Kimberly J Popendorf
- Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Coral Gables, Florida, USA
| | - Josep M Gasol
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
| | - Benjamin A S Van Mooy
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
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11
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Micciulla JL, Shor LM, Gage DJ. Enhanced transport of bacteria along root systems by protists can impact plant health. Appl Environ Microbiol 2024; 90:e0201123. [PMID: 38534145 DOI: 10.1128/aem.02011-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 01/25/2024] [Indexed: 03/28/2024] Open
Abstract
Soil protists have been shown to contribute to the structure and function of the rhizosphere in a variety of ways. Protists are key contributors to nutrient cycling through the microbial loop, where biomass is digested by protists and otherwise stored nutrients are returned to the environment. Protists have also been shown to feed on plant pathogenic bacteria and alter root microbiomes in ways that may benefit plants. Recently, a mechanism involving bacterial transport, facilitated by protists, has been hypothesized to contribute to the spatial distribution of bacteria in the rhizosphere. Here, we observe the differential abilities of three soil protists: a ciliate (Colpoda sp.), a flagellate (Cercomonas sp.), and a naked amoeba (Acanthamoeba castellanii) to transport nitrogen-fixing Sinorhizobium meliloti to infectible root tips. Co-inoculation of protists plus S. meliloti resulted in the movement of bacteria, as measured by the presence of nitrogen-fixing nodules, up to 15 cm farther down the root systems when compared to plants inoculated with S. meliloti alone. Co-inoculation of the ciliate, Colpoda sp., with S. meliloti, resulted in shoot weights that were similar to plants that grew in nitrogen-replete potting mix. Colpoda sp.-feeding style and motility likely contributed to their success at transporting bacteria through the rhizosphere. We observed that the addition of protists alone without the co-inoculum of S. meliloti resulted in plants with larger shoot weights than control plants. Follow-up experiments showed that protists plus their associated microbiomes were aiding in plant health, likely through means of nutrient cycling.IMPORTANCEProtists represent a significant portion of the rhizosphere microbiome and have been shown to contribute to plant health, yet they are understudied compared to their bacterial and fungal counterparts. This study elucidates their role in the rhizosphere community and suggests a mechanism by which protists can be used to move bacteria along plant roots. We found that the co-inoculation of protists with nitrogen-fixing beneficial bacteria, Sinorhizobium meliloti, resulted in nodules farther down the roots when compared to plants inoculated with S. meliloti alone, and shoot weights similar to plants that received nitrogen fertilizer. These data illustrate the ability of protists to transport viable bacteria to uninhabited regions of the root system.
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Affiliation(s)
- Jamie L Micciulla
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, Colorado, USA
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Leslie M Shor
- Center for Environmental Sciences & Engineering, University of Connecticut, Storrs, Connecticut, USA
| | - Daniel J Gage
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, Connecticut, USA
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12
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Anderson DG. Modern archaeological research and the importance of information management. Proc Natl Acad Sci U S A 2024; 121:e2403792121. [PMID: 38593085 DOI: 10.1073/pnas.2403792121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024] Open
Affiliation(s)
- David G Anderson
- Department of Anthropology, University of Tennessee, Knoxville, TN 37996-1525
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13
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Chodkowski JL, Shade A. Bioactive exometabolites drive maintenance competition in simple bacterial communities. mSystems 2024; 9:e0006424. [PMID: 38470039 DOI: 10.1128/msystems.00064-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 02/19/2024] [Indexed: 03/13/2024] Open
Abstract
During prolonged resource limitation, bacterial cells can persist in metabolically active states of non-growth. These maintenance periods, such as those experienced in stationary phase, can include upregulation of secondary metabolism and release of exometabolites into the local environment. As resource limitation is common in many environmental microbial habitats, we hypothesized that neighboring bacterial populations employ exometabolites to compete or cooperate during maintenance and that these exometabolite-facilitated interactions can drive community outcomes. Here, we evaluated the consequences of exometabolite interactions over the stationary phase among three environmental strains: Burkholderia thailandensis E264, Chromobacterium subtsugae ATCC 31532, and Pseudomonas syringae pv. tomato DC3000. We assembled them into synthetic communities that only permitted chemical interactions. We compared the responses (transcripts) and outputs (exometabolites) of each member with and without neighbors. We found that transcriptional dynamics were changed with different neighbors and that some of these changes were coordinated between members. The dominant competitor B. thailandensis consistently upregulated biosynthetic gene clusters to produce bioactive exometabolites for both exploitative and interference competition. These results demonstrate that competition strategies during maintenance can contribute to community-level outcomes. It also suggests that the traditional concept of defining competitiveness by growth outcomes may be narrow and that maintenance competition could be an additional or alternative measure. IMPORTANCE Free-living microbial populations often persist and engage in environments that offer few or inconsistently available resources. Thus, it is important to investigate microbial interactions in this common and ecologically relevant condition of non-growth. This work investigates the consequences of resource limitation for community metabolic output and for population interactions in simple synthetic bacterial communities. Despite non-growth, we observed active, exometabolite-mediated competition among the bacterial populations. Many of these interactions and produced exometabolites were dependent on the community composition but we also observed that one dominant competitor consistently produced interfering exometabolites regardless. These results are important for predicting and understanding microbial interactions in resource-limited environments.
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Affiliation(s)
- John L Chodkowski
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Ashley Shade
- Universite Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, Villeurbanne, France
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14
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Qian Y, Roy TK, Jasper AW, Sojdak CA, Kozlowski MC, Klippenstein SJ, Lester MI. Isomer-resolved unimolecular dynamics of the hydroperoxyalkyl intermediate (•QOOH) in cyclohexane oxidation. Proc Natl Acad Sci U S A 2024; 121:e2401148121. [PMID: 38602914 DOI: 10.1073/pnas.2401148121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/08/2024] [Indexed: 04/13/2024] Open
Abstract
The oxidation of cycloalkanes is important in the combustion of transportation fuels and in atmospheric secondary organic aerosol formation. A transient carbon-centered radical intermediate (•QOOH) in the oxidation of cyclohexane is identified through its infrared fingerprint and time- and energy-resolved unimolecular dissociation dynamics to hydroxyl (OH) radical and bicyclic ether products. Although the cyclohexyl ring structure leads to three nearly degenerate •QOOH isomers (β-, γ-, and δ-QOOH), their transition state (TS) barriers to OH products are predicted to differ considerably. Selective characterization of the β-QOOH isomer is achieved at excitation energies associated with the lowest TS barrier, resulting in rapid unimolecular decay to OH products that are detected. A benchmarking approach is employed for the calculation of high-accuracy stationary point energies, in particular TS barriers, for cyclohexane oxidation (C6H11O2), building on higher-level reference calculations for the smaller ethane oxidation (C2H5O2) system. The isomer-specific characterization of β-QOOH is validated by comparison of experimental OH product appearance rates with computed statistical microcanonical rates, including significant heavy-atom tunneling, at energies in the vicinity of the TS barrier. Master-equation modeling is utilized to extend the results to thermal unimolecular decay rate constants at temperatures and pressures relevant to cyclohexane combustion.
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Affiliation(s)
- Yujie Qian
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323
| | - Tarun Kumar Roy
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323
| | - Ahren W Jasper
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL 60439
| | - Christopher A Sojdak
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323
| | - Marisa C Kozlowski
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323
| | - Stephen J Klippenstein
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL 60439
| | - Marsha I Lester
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323
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15
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Xing H, de Campos LJ, Pereira AJ, Fiora MM, Aguiar-Alves F, Tagliazucchi M, Conda-Sheridan M. Engineering a nanoantibiotic system displaying dual mechanism of action. Proc Natl Acad Sci U S A 2024; 121:e2321498121. [PMID: 38593077 DOI: 10.1073/pnas.2321498121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 03/04/2024] [Indexed: 04/11/2024] Open
Abstract
In recent decades, peptide amphiphiles (PAs) have established themselves as promising self-assembling bioinspired materials in a wide range of medical fields. Herein, we report a dual-therapeutic system constituted by an antimicrobial PA and a cylindrical protease inhibitor (LJC) to achieve broad antimicrobial spectrum and to enhance therapeutic efficacy. We studied two strategies: PA-LJC nanostructures (Encapsulation) and PA nanostructures + free LJC (Combination). Computational modeling using a molecular theory for amphiphile self-assembly captures and explains the morphology of PA-LJC nanostructures and the location of encapsulated LJC in agreement with transmission electron microscopy and two-dimensional (2D) NMR observations. The morphology and release profile of PA-LJC assemblies are strongly correlated to the PA:LJC ratio: high LJC loading induces an initial burst release. We then evaluated the antimicrobial activity of our nanosystems toward gram-positive and gram-negative bacteria. We found that the Combination broadens the spectrum of LJC, reduces the therapeutic concentrations of both agents, and is not impacted by the inoculum effect. Further, the Encapsulation provides additional benefits including bypassing water solubility limitations of LJC and modulating the release of this molecule. The different properties of PA-LJC nanostructures results in different killing profiles, and reduced cytotoxicity and hemolytic activity. Meanwhile, details in membrane alterations caused by each strategy were revealed by various microscopy and fluorescent techniques. Last, in vivo studies in larvae treated by the Encapsulation strategy showed better antimicrobial efficacy than polymyxin B. Collectively, this study established a multifunctional platform using a versatile PA to act as an antibiotic, membrane-penetrating assistant, and slow-release delivery vehicle.
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Affiliation(s)
- Huihua Xing
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198
| | - Luana Janaína de Campos
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198
| | - Aramis Jose Pereira
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198
| | - Maria Mercedes Fiora
- Instituto Nacional de Tecnología Industrial, Micro y Nanotecnologías, San Martín, Buenos Aires B1650WAB, Argentina
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica Analítica y Química Física, Pabellón 2, Ciudad Universitaria, Ciudad Autónoma de Buenos Aires C1428, Argentina
- Universidad de Buenos Aires-Consejo Nacional de Investigaciones Cientificas y Tecnicas, Facultad de Ciencias Exactas y Naturales, Instituto de Quimica de los Materiales, Ambiente y Energia, Pabellon 2, Ciudad Universitaria, Ciudad Autonoma de Buenos Aires C1428
| | - Fabio Aguiar-Alves
- Department of Pharmaceutical Sciences, Lloyd L. Gregory School of Pharmacy, Palm Beach Atlantic University, FL 33401
| | - Mario Tagliazucchi
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica Analítica y Química Física, Pabellón 2, Ciudad Universitaria, Ciudad Autónoma de Buenos Aires C1428, Argentina
- Universidad de Buenos Aires-Consejo Nacional de Investigaciones Cientificas y Tecnicas, Facultad de Ciencias Exactas y Naturales, Instituto de Quimica de los Materiales, Ambiente y Energia, Pabellon 2, Ciudad Universitaria, Ciudad Autonoma de Buenos Aires C1428
| | - Martin Conda-Sheridan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198
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16
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Hogan MP, Holding ML, Nystrom GS, Colston TJ, Bartlett DA, Mason AJ, Ellsworth SA, Rautsaw RM, Lawrence KC, Strickland JL, He B, Fraser P, Margres MJ, Gilbert DM, Gibbs HL, Parkinson CL, Rokyta DR. The genetic regulatory architecture and epigenomic basis for age-related changes in rattlesnake venom. Proc Natl Acad Sci U S A 2024; 121:e2313440121. [PMID: 38578985 DOI: 10.1073/pnas.2313440121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 03/13/2024] [Indexed: 04/07/2024] Open
Abstract
Developmental phenotypic changes can evolve under selection imposed by age- and size-related ecological differences. Many of these changes occur through programmed alterations to gene expression patterns, but the molecular mechanisms and gene-regulatory networks underlying these adaptive changes remain poorly understood. Many venomous snakes, including the eastern diamondback rattlesnake (Crotalus adamanteus), undergo correlated changes in diet and venom expression as snakes grow larger with age, providing models for identifying mechanisms of timed expression changes that underlie adaptive life history traits. By combining a highly contiguous, chromosome-level genome assembly with measures of expression, chromatin accessibility, and histone modifications, we identified cis-regulatory elements and trans-regulatory factors controlling venom ontogeny in the venom glands of C. adamanteus. Ontogenetic expression changes were significantly correlated with epigenomic changes within genes, immediately adjacent to genes (e.g., promoters), and more distant from genes (e.g., enhancers). We identified 37 candidate transcription factors (TFs), with the vast majority being up-regulated in adults. The ontogenetic change is largely driven by an increase in the expression of TFs associated with growth signaling, transcriptional activation, and circadian rhythm/biological timing systems in adults with corresponding epigenomic changes near the differentially expressed venom genes. However, both expression activation and repression contributed to the composition of both adult and juvenile venoms, demonstrating the complexity and potential evolvability of gene regulation for this trait. Overall, given that age-based trait variation is common across the tree of life, we provide a framework for understanding gene-regulatory-network-driven life-history evolution more broadly.
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Affiliation(s)
- Michael P Hogan
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Matthew L Holding
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | - Gunnar S Nystrom
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Timothy J Colston
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
- Department of Biology, University of Puerto Rico at Mayagüez, Mayagüez, PR 00681
| | - Daniel A Bartlett
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Andrew J Mason
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43210
| | - Schyler A Ellsworth
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620
- School of Biological Sciences, Washington State University, Pullman, WA 99164
| | - Kylie C Lawrence
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Jason L Strickland
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
- Department of Biology, University of South Alabama, Mobile, AL 36688
| | - Bing He
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Peter Fraser
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Mark J Margres
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620
| | - David M Gilbert
- Laboratory of Chromosome Replication and Epigenome Regulation, San Diego Biomedical Research Institute, San Diego, CA 92121
| | - H Lisle Gibbs
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43210
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
- Department of Forestry and Environmental Conservation, Clemson University, Clemson, SC 29634
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
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17
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Andersen SK, Hillyard SA. The time course of feature-selective attention inside and outside the focus of spatial attention. Proc Natl Acad Sci U S A 2024; 121:e2309975121. [PMID: 38588433 DOI: 10.1073/pnas.2309975121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 03/11/2024] [Indexed: 04/10/2024] Open
Abstract
Research on attentional selection of stimulus features has yielded seemingly contradictory results. On the one hand, many experiments in humans and animals have observed a "global" facilitation of attended features across the entire visual field, even when spatial attention is focused on a single location. On the other hand, several event-related potential studies in humans reported that attended features are enhanced at the attended location only. The present experiment demonstrates that these conflicting results can be explained by differences in the timing of attentional allocation inside and outside the spatial focus of attention. Participants attended to fields of either red or blue randomly moving dots on either the left or right side of fixation with the task of detecting brief coherent motion targets. Recordings of steady-state visual evoked potentials elicited by the flickering stimuli allowed concurrent measurement of the time course of feature-selective attention in visual cortex on both the attended and the unattended sides. The onset of feature-selective attentional modulation on the attended side occurred around 150 ms earlier than on the unattended side. This finding that feature-selective attention is not spatially global from the outset but extends to unattended locations after a temporal delay resolves previous contradictions between studies finding global versus hierarchical selection of features and provides insight into the fundamental relationship between feature-based and location-based (spatial) attention mechanisms.
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Affiliation(s)
- Søren K Andersen
- Department of Psychology, University of Southern Denmark, Odense M DK-5230, Denmark
- School of Psychology, University of Aberdeen, Aberdeen AB24 3FX, United Kingdom
| | - Steven A Hillyard
- Department of Neurosciences, University of California at San Diego, La Jolla, CA 92093
- Leibniz Institute for Neurobiology, Magdeburg 39118, Germany
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18
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Noble PA, Pozhitkov A, Singh K, Woods E, Liu C, Levin M, Javan G, Wan J, Abouhashem AS, Mathew-Steiner SS, Sen CK. Unraveling the Enigma of Organismal Death: Insights, Implications, and Frontiers. Physiology (Bethesda) 2024. [PMID: 38624244 DOI: 10.1152/physiol.00004.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/11/2024] [Indexed: 04/17/2024] Open
Abstract
Significant knowledge gaps exist regarding the responses of cells, tissues, and organs to organismal death. Examining the survival mechanisms influenced by metabolism and environment, this research has the potential to transform regenerative medicine, redefine legal death, and provide insights into life's physiological limits, paralleling inquiries in embryogenesis.
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Affiliation(s)
- Peter A Noble
- University of Washington, Seattle, WA, United States
| | - Alexander Pozhitkov
- Division of Research Informatics, City Of Hope National Medical Center, Duarte, CA, United States
| | - Kanhaiya Singh
- McGowan Insitute for Regenrative Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Erik Woods
- Ossium health, Indianpolis, IN, United States
| | - ChunYu Liu
- Department of Psychiatry, SUNY Upstate Medical University, New York, United States
| | | | - Gulnaz Javan
- Department of Physical and Forensic Sciences, Alabama State University, Montgomery, AL, United States
| | - Jun Wan
- McGown Institute for regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Ahmed Safwat Abouhashem
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, IN, United States
| | - Shomita S Mathew-Steiner
- McGown Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Chandan K Sen
- McGown Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, United States
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19
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Qu F, Khemsom K, Perdoncini Carvalho C, Han J. Quasispecies are constantly selected through virus-encoded intracellular reproductive population bottlenecking. J Virol 2024; 98:e0002024. [PMID: 38445885 DOI: 10.1128/jvi.00020-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024] Open
Affiliation(s)
- Feng Qu
- Department of Plant Pathology, The Ohio State University Wooster Campus, Wooster, Ohio, USA
| | - Khwannarin Khemsom
- Department of Plant Pathology, The Ohio State University Wooster Campus, Wooster, Ohio, USA
| | | | - Junping Han
- Department of Plant Pathology, The Ohio State University Wooster Campus, Wooster, Ohio, USA
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20
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Creel RC, Miesner F, Wilkenskjeld S, Austermann J, Overduin PP. Glacial isostatic adjustment reduces past and future Arctic subsea permafrost. Nat Commun 2024; 15:3232. [PMID: 38622113 DOI: 10.1038/s41467-024-45906-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 02/06/2024] [Indexed: 04/17/2024] Open
Abstract
Sea-level rise submerges terrestrial permafrost in the Arctic, turning it into subsea permafrost. Subsea permafrost underlies ~ 1.8 million km2 of Arctic continental shelf, with thicknesses in places exceeding 700 m. Sea-level variations over glacial-interglacial cycles control subsea permafrost distribution and thickness, yet no permafrost model has accounted for glacial isostatic adjustment (GIA), which deviates local sea level from the global mean due to changes in ice and ocean loading. Here we incorporate GIA into a pan-Arctic model of subsea permafrost over the last 400,000 years. Including GIA significantly reduces present-day subsea permafrost thickness, chiefly because of hydro-isostatic effects as well as deformation related to Northern Hemisphere ice sheets. Additionally, we extend the simulation 1000 years into the future for emissions scenarios outlined in the Intergovernmental Panel on Climate Change's sixth assessment report. We find that subsea permafrost is preserved under a low emissions scenario but mostly disappears under a high emissions scenario.
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Affiliation(s)
- Roger C Creel
- Lamont-Doherty Earth Observatory, Columbia University, New York, NY, USA
- Department of Physical Oceanography, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Frederieke Miesner
- Alfred Wegener Institute Helmholtz-Centre for Polar and Marine Research, Potsdam, Germany.
| | | | | | - Pier Paul Overduin
- Alfred Wegener Institute Helmholtz-Centre for Polar and Marine Research, Potsdam, Germany
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21
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Bridges K, Pizzurro GA, Khunte M, Chen M, Salvador Rocha E, Alexander AF, Bass V, Kellman LN, Baskaran J, Miller-Jensen K. Single-Cell Analysis Reveals a Subset of High IL-12p40-Secreting Dendritic Cells within Mouse Bone Marrow-Derived Macrophages Differentiated with M-CSF. J Immunol 2024; 212:1357-1365. [PMID: 38416039 DOI: 10.4049/jimmunol.2300431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 02/01/2024] [Indexed: 02/29/2024]
Abstract
Macrophages and dendritic cells (DCs), although ontogenetically distinct, have overlapping functions and exhibit substantial cell-to-cell heterogeneity that can complicate their identification and obscure innate immune function. In this study, we report that M-CSF-differentiated murine bone marrow-derived macrophages (BMDMs) exhibit extreme heterogeneity in the production of IL-12, a key proinflammatory cytokine linking innate and adaptive immunity. A microwell secretion assay revealed that a small fraction of BMDMs stimulated with LPS secrete most IL-12p40, and we confirmed that this is due to extremely high expression of Il12b, the gene encoding IL-12p40, in a subset of cells. Using an Il12b-YFP reporter mouse, we isolated cells with high LPS-induced Il12b expression and found that this subset was enriched for genes associated with the DC lineage. Single-cell RNA sequencing data confirmed a DC-like subset that differentiates within BMDM cultures that is transcriptionally distinct but could not be isolated by surface marker expression. Although not readily apparent in the resting state, upon LPS stimulation, this subset exhibited a typical DC-associated activation program that is distinct from LPS-induced stochastic BMDM cell-to-cell heterogeneity. Overall, our findings underscore the difficulty in distinguishing macrophages and DCs even in widely used in vitro murine BMDM cultures and could affect the interpretation of some studies that use BMDMs to explore acute inflammatory responses.
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Affiliation(s)
- Kate Bridges
- Department of Biomedical Engineering, Yale University, New Haven, CT
| | | | - Mihir Khunte
- Department of Biomedical Engineering, Yale University, New Haven, CT
| | - Meibin Chen
- Department of Biomedical Engineering, Yale University, New Haven, CT
| | | | | | - Victor Bass
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT
| | - Laura N Kellman
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT
| | - Janani Baskaran
- Department of Biomedical Engineering, Yale University, New Haven, CT
| | - Kathryn Miller-Jensen
- Department of Biomedical Engineering, Yale University, New Haven, CT
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT
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22
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Hoang Y, Azaldegui CA, Dow RE, Ghalmi M, Biteen JS, Vecchiarelli AG. An experimental framework to assess biomolecular condensates in bacteria. Nat Commun 2024; 15:3222. [PMID: 38622124 DOI: 10.1038/s41467-024-47330-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 03/28/2024] [Indexed: 04/17/2024] Open
Abstract
High-resolution imaging of biomolecular condensates in living cells is essential for correlating their properties to those observed through in vitro assays. However, such experiments are limited in bacteria due to resolution limitations. Here we present an experimental framework that probes the formation, reversibility, and dynamics of condensate-forming proteins in Escherichia coli as a means to determine the nature of biomolecular condensates in bacteria. We demonstrate that condensates form after passing a threshold concentration, maintain a soluble fraction, dissolve upon shifts in temperature and concentration, and exhibit dynamics consistent with internal rearrangement and exchange between condensed and soluble fractions. We also discover that an established marker for insoluble protein aggregates, IbpA, has different colocalization patterns with bacterial condensates and aggregates, demonstrating its potential applicability as a reporter to differentiate the two in vivo. Overall, this framework provides a generalizable, accessible, and rigorous set of experiments to probe the nature of biomolecular condensates on the sub-micron scale in bacterial cells.
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Affiliation(s)
- Y Hoang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | | | - Rachel E Dow
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Maria Ghalmi
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Julie S Biteen
- Doctoral Program in Chemical Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
| | - Anthony G Vecchiarelli
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
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23
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Wagner C, Kistler KE, Perchetti GA, Baker N, Frisbie LA, Torres LM, Aragona F, Yun C, Figgins M, Greninger AL, Cox A, Oltean HN, Roychoudhury P, Bedford T. Positive selection underlies repeated knockout of ORF8 in SARS-CoV-2 evolution. Nat Commun 2024; 15:3207. [PMID: 38615031 PMCID: PMC11016114 DOI: 10.1038/s41467-024-47599-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 04/04/2024] [Indexed: 04/15/2024] Open
Abstract
Knockout of the ORF8 protein has repeatedly spread through the global viral population during SARS-CoV-2 evolution. Here we use both regional and global pathogen sequencing to explore the selection pressures underlying its loss. In Washington State, we identified transmission clusters with ORF8 knockout throughout SARS-CoV-2 evolution, not just on novel, high fitness viral backbones. Indeed, ORF8 is truncated more frequently and knockouts circulate for longer than for any other gene. Using a global phylogeny, we find evidence of positive selection to explain this phenomenon: nonsense mutations resulting in shortened protein products occur more frequently and are associated with faster clade growth rates than synonymous mutations in ORF8. Loss of ORF8 is also associated with reduced clinical severity, highlighting the diverse clinical impacts of SARS-CoV-2 evolution.
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Affiliation(s)
- Cassia Wagner
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
| | - Kathryn E Kistler
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Garrett A Perchetti
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Noah Baker
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | | | | | - Frank Aragona
- Washington State Department of Health, Shoreline, WA, USA
| | - Cory Yun
- Washington State Department of Health, Shoreline, WA, USA
| | - Marlin Figgins
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Applied Mathematics, University of Washington, Seattle, WA, USA
| | - Alexander L Greninger
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Alex Cox
- Washington State Department of Health, Shoreline, WA, USA
| | - Hanna N Oltean
- Washington State Department of Health, Shoreline, WA, USA
| | - Pavitra Roychoudhury
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
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24
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Reed KB, Brooks SM, Wells J, Blake KJ, Zhao M, Placido K, d'Oelsnitz S, Trivedi A, Gadhiyar S, Alper HS. A modular and synthetic biosynthesis platform for de novo production of diverse halogenated tryptophan-derived molecules. Nat Commun 2024; 15:3188. [PMID: 38609402 PMCID: PMC11015028 DOI: 10.1038/s41467-024-47387-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 03/31/2024] [Indexed: 04/14/2024] Open
Abstract
Halogen-containing molecules are ubiquitous in modern society and present unique chemical possibilities. As a whole, de novo fermentation and synthetic pathway construction for these molecules remain relatively underexplored and could unlock molecules with exciting new applications in industries ranging from textiles to agrochemicals to pharmaceuticals. Here, we report a mix-and-match co-culture platform to de novo generate a large array of halogenated tryptophan derivatives in Escherichia coli from glucose. First, we engineer E. coli to produce between 300 and 700 mg/L of six different halogenated tryptophan precursors. Second, we harness the native promiscuity of multiple downstream enzymes to access unexplored regions of metabolism. Finally, through modular co-culture fermentations, we demonstrate a plug-and-play bioproduction platform, culminating in the generation of 26 distinct halogenated molecules produced de novo including precursors to prodrugs 4-chloro- and 4-bromo-kynurenine and new-to-nature halogenated beta carbolines.
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Affiliation(s)
- Kevin B Reed
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, USA
| | - Sierra M Brooks
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, USA
| | - Jordan Wells
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, USA
| | - Kristin J Blake
- Mass Spectrometry Facility, Department of Chemistry, The University of Texas at Austin, 105 E 24th Street, Austin, TX, USA
| | - Minye Zhao
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, USA
| | - Kira Placido
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, USA
| | - Simon d'Oelsnitz
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX, USA
| | - Adit Trivedi
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, USA
| | - Shruti Gadhiyar
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, USA
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, USA.
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX, USA.
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25
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Eldridge DJ, Ding J, Dorrough J, Delgado-Baquerizo M, Sala O, Gross N, Le Bagousse-Pinguet Y, Mallen-Cooper M, Saiz H, Asensio S, Ochoa V, Gozalo B, Guirado E, García-Gómez M, Valencia E, Martínez-Valderrama J, Plaza C, Abedi M, Ahmadian N, Ahumada RJ, Alcántara JM, Amghar F, Azevedo L, Ben Salem F, Berdugo M, Blaum N, Boldgiv B, Bowker M, Bran D, Bu C, Canessa R, Castillo-Monroy AP, Castro I, Castro-Quezada P, Cesarz S, Chibani R, Conceição AA, Darrouzet-Nardi A, Davila YC, Deák B, Díaz-Martínez P, Donoso DA, Dougill AD, Durán J, Eisenhauer N, Ejtehadi H, Espinosa CI, Fajardo A, Farzam M, Foronda A, Franzese J, Fraser LH, Gaitán J, Geissler K, Gonzalez SL, Gusman-Montalvan E, Hernández RM, Hölzel N, Hughes FM, Jadan O, Jentsch A, Ju M, Kaseke KF, Köbel M, Lehmann A, Liancourt P, Linstädter A, Louw MA, Ma Q, Mabaso M, Maggs-Kölling G, Makhalanyane TP, Issa OM, Marais E, McClaran M, Mendoza B, Mokoka V, Mora JP, Moreno G, Munson S, Nunes A, Oliva G, Oñatibia GR, Osborne B, Peter G, Pierre M, Pueyo Y, Emiliano Quiroga R, Reed S, Rey A, Rey P, Gómez VMR, Rolo V, Rillig MC, le Roux PC, Ruppert JC, Salah A, Sebei PJ, Sharkhuu A, Stavi I, Stephens C, Teixido AL, Thomas AD, Tielbörger K, Robles ST, Travers S, Valkó O, van den Brink L, Velbert F, von Heßberg A, Wamiti W, Wang D, Wang L, Wardle GM, Yahdjian L, Zaady E, Zhang Y, Zhou X, Maestre FT. Hotspots of biogeochemical activity linked to aridity and plant traits across global drylands. Nat Plants 2024:10.1038/s41477-024-01670-7. [PMID: 38609675 DOI: 10.1038/s41477-024-01670-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 03/14/2024] [Indexed: 04/14/2024]
Abstract
Perennial plants create productive and biodiverse hotspots, known as fertile islands, beneath their canopies. These hotspots largely determine the structure and functioning of drylands worldwide. Despite their ubiquity, the factors controlling fertile islands under conditions of contrasting grazing by livestock, the most prevalent land use in drylands, remain virtually unknown. Here we evaluated the relative importance of grazing pressure and herbivore type, climate and plant functional traits on 24 soil physical and chemical attributes that represent proxies of key ecosystem services related to decomposition, soil fertility, and soil and water conservation. To do this, we conducted a standardized global survey of 288 plots at 88 sites in 25 countries worldwide. We show that aridity and plant traits are the major factors associated with the magnitude of plant effects on fertile islands in grazed drylands worldwide. Grazing pressure had little influence on the capacity of plants to support fertile islands. Taller and wider shrubs and grasses supported stronger island effects. Stable and functional soils tended to be linked to species-rich sites with taller plants. Together, our findings dispel the notion that grazing pressure or herbivore type are linked to the formation or intensification of fertile islands in drylands. Rather, our study suggests that changes in aridity, and processes that alter island identity and therefore plant traits, will have marked effects on how perennial plants support and maintain the functioning of drylands in a more arid and grazed world.
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Affiliation(s)
- David J Eldridge
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Jingyi Ding
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing, China.
| | - Josh Dorrough
- Department of Planning and Environment, Merimbula, New South Wales, Australia
- Fenner School of Environment & Society, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Seville, Spain
| | - Osvaldo Sala
- Schools of Life Sciences, School of Sustainability, and Global Drylands Center, Arizona State University, Tempe, AZ, USA
| | - Nicolas Gross
- Université Clermont Auvergne, INRAE, VetAgro Sup, Unité Mixte de Recherche Ecosystème Prairial, Clermont-Ferrand, France
| | | | - Max Mallen-Cooper
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden
| | - Hugo Saiz
- Departamento de Ciencias Agrarias y Medio Natural, Escuela Politécnica Superior, Instituto Universitario de Investigación en Ciencias Ambientales de Aragón (IUCA), Universidad de Zaragoza, Huesca, Spain
| | - Sergio Asensio
- Instituto Multidisciplinar para el Estudio del Medio 'Ramón Margalef', Universidad de Alicante, Alicante, Spain
| | - Victoria Ochoa
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Beatriz Gozalo
- Instituto Multidisciplinar para el Estudio del Medio 'Ramón Margalef', Universidad de Alicante, Alicante, Spain
| | - Emilio Guirado
- Instituto Multidisciplinar para el Estudio del Medio 'Ramón Margalef', Universidad de Alicante, Alicante, Spain
| | - Miguel García-Gómez
- Departamento de Ingeniería y Morfología del Terreno, Escuela Técnica Superior de Ingenieros de Caminos, Canales y Puertos, Universidad Politécnica de Madrid, Madrid, Spain
| | - Enrique Valencia
- Departmento de Biodiversidad, Ecología y Evolución, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Jaime Martínez-Valderrama
- Instituto Multidisciplinar para el Estudio del Medio 'Ramón Margalef', Universidad de Alicante, Alicante, Spain
- Estación Experimental de Zonas Áridas (EEZA), CSIC, Campus UAL, Almería, Spain
| | - César Plaza
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Mehdi Abedi
- Department of Range Management, Faculty of Natural Resources and Marine Sciences, Tarbiat Modares University, Noor, Iran
| | - Negar Ahmadian
- Department of Range Management, Faculty of Natural Resources and Marine Sciences, Tarbiat Modares University, Noor, Iran
| | - Rodrigo J Ahumada
- Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Agropecuaria Catamarca, Valle Viejo, Argentina
| | - Julio M Alcántara
- Instituto Interuniversitario de Investigación del Sistema Tierra de Andalucía, Universidad de Jaén, Jaén, Spain
| | - Fateh Amghar
- Laboratoire Biodiversité, Biotechnologie, Environnement et Développement Durable (Biodev), Université M'hamed Bougara de Boumerdès, Boumerdès, Algeria
| | - Luísa Azevedo
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Farah Ben Salem
- Laboratory of Eremology and Combating Desertification (LR16IRA01), IRA, Institut des Régions Arides Medenine, Medenine, Tunisia
| | - Miguel Berdugo
- Departmento de Biodiversidad, Ecología y Evolución, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain
- Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Niels Blaum
- Plant Ecology and Nature Conservation, University of Potsdam, Potsdam, Germany
| | - Bazartseren Boldgiv
- Laboratory of Ecological and Evolutionary Synthesis, Department of Biology, School of Arts and Sciences, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Matthew Bowker
- School of Forestry, Northern Arizona University, Flagstaff, AZ, USA
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Donaldo Bran
- Instituto Nacional de Tecnología Agropecuaria (INTA), Estación Experimental Agropecuaria Bariloche, Bariloche, Argentina
| | - Chongfeng Bu
- Institute of Soil and Water Conservation, Northwest A & F University, Yangling, China
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, China
| | - Rafaella Canessa
- State Museum of Natural History Stuttgart, Stuttgart, Germany
- Martin Luther University of Halle-Wittenberg, Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Andrea P Castillo-Monroy
- Grupo de Investigación en Ecología Evolutiva en los Trópicos-EETROP- Universidad de las Américas, Quito, Ecuador
| | - Ignacio Castro
- Instituto de Estudios Científicos y Tecnológicos (IDECYT), Universidad Simón Rodríguez, Caracas, Venezuela
| | - Patricio Castro-Quezada
- Grupo de Ecología Forestal y Agroecosistemas, Facultad de Ciencias Agropecuarias, Carrera de Agronomía, Universidad de Cuenca, Cuenca, Ecuador
| | - Simone Cesarz
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Roukaya Chibani
- Laboratory of Eremology and Combating Desertification (LR16IRA01), IRA, Institut des Régions Arides Medenine, Medenine, Tunisia
| | - Abel Augusto Conceição
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | | | - Yvonne C Davila
- Faculty of Science, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Balázs Deák
- HUN-REN 'Lendület' Seed Ecology Research Group, Institute of Ecology and Botany, Centre for Ecological Research, Vácrátót, Hungary
| | - Paloma Díaz-Martínez
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - David A Donoso
- Grupo de Investigación en Ecología Evolutiva en los Trópicos-EETROP- Universidad de las Américas, Quito, Ecuador
| | | | - Jorge Durán
- Misión Biológica de Galicia, Consejo Superior de Investigaciones Científicas, Pontevedra, Spain
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Hamid Ejtehadi
- Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Carlos Ivan Espinosa
- Departamento de Ciencias Biológicas, Universidad Técnica Particular de Loja, Loja, Ecuador
| | - Alex Fajardo
- Instituto de Investigación Interdisciplinaria (I3), Vicerrectoría Académica, Universidad de Talca, Talca, Chile
| | - Mohammad Farzam
- Department of Range and Watershed Management, Faculty of Natural Resources and Environment, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Ana Foronda
- Veterinary Faculty, University of Zaragoza, Zaragoza, Spain
| | - Jorgelina Franzese
- Investigaciones de Ecología en Ambientes Antropizados, Laboratorio Ecotono, INIBIOMA (Universidad Nacional del Comahue, CONICET), Bariloche, Argentina
| | - Lauchlan H Fraser
- Department of Natural Resource Science, Thompson Rivers University, Kamloops, British Columbia, Canada
| | - Juan Gaitán
- Universidad Nacional de Luján-CONICET, Luján, Argentina
| | - Katja Geissler
- Plant Ecology and Nature Conservation, University of Potsdam, Potsdam, Germany
| | - Sofía Laura Gonzalez
- Instituto de Investigaciones en Biodiversidad y Medioambiente (CONICET), Universidad Nacional del Comahue, Neuquén, Argentina
| | | | - Rosa Mary Hernández
- Instituto de Estudios Científicos y Tecnológicos (IDECYT), Universidad Simón Rodríguez, Caracas, Venezuela
| | - Norbert Hölzel
- Institute of Landscape Ecology, University of Münster, Münster, Germany
| | - Frederic Mendes Hughes
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | - Oswaldo Jadan
- Grupo de Ecología Forestal y Agroecosistemas, Facultad de Ciencias Agropecuarias, Carrera de Agronomía, Universidad de Cuenca, Cuenca, Ecuador
| | - Anke Jentsch
- Disturbance Ecology and Vegetation Dynamics, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Mengchen Ju
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, China
| | - Kudzai F Kaseke
- Earth Research Institute, University of California, Santa Barbara, CA, USA
| | - Melanie Köbel
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Anika Lehmann
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | | | - Anja Linstädter
- Biodiversity Research/Systematic Botany, University of Potsdam, Potsdam, Germany
| | - Michelle A Louw
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Quanhui Ma
- Key Laboratory of Vegetation Ecology of the Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Institute of Grassland Science, Northeast Normal University, Changchun, China
| | - Mancha Mabaso
- Department of Microbiology, Faculty of Science, Stellenbosch University, Stellenbosch, South Africa
| | | | - Thulani P Makhalanyane
- Department of Microbiology, Faculty of Science, Stellenbosch University, Stellenbosch, South Africa
| | - Oumarou Malam Issa
- Institute of Ecology and Environmental Sciences of Paris, SU/IRD/CNRS/INRAE/UPEC, Bondy, France
| | - Eugene Marais
- Gobabeb - Namib Research Institute, Walvis Bay, Namibia
| | - Mitchel McClaran
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, USA
| | - Betty Mendoza
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Móstoles, Spain
| | - Vincent Mokoka
- Risk and Vulnerability Science Centre, University of Limpopo, Mankweng, South Africa
| | - Juan P Mora
- Instituto de Investigación Interdisciplinaria (I3), Vicerrectoría Académica, Universidad de Talca, Talca, Chile
| | - Gerardo Moreno
- INDEHESA, Forestry School, Universidad de Extremadura, Plasencia, Spain
| | - Seth Munson
- US Geological Survey, Southwest Biological Science Center, Flagstaff, AZ, USA
| | - Alice Nunes
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Gabriel Oliva
- Instituto Nacional de Tecnología Agropecuaria (INTA), Estación Experimental Agropecuaria Bariloche, Bariloche, Argentina
| | - Gastón R Oñatibia
- Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA-CONICET), Cátedra de Ecología, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Brooke Osborne
- Department of Environment and Society, Utah State University, Moab, UT, USA
| | - Guadalupe Peter
- Universidad Nacional de Río Negro, Sede Atlántica, Centro de Estudios Ambientales desde la NorPatagonia (CEANPa), CONICET, Viedma, Argentina
| | - Margerie Pierre
- Normandie Universite, Unirouen, Inrae, Ecodiv, Rouen, France
| | - Yolanda Pueyo
- Instituto Pirenaico de Ecología (IPE, CSIC), Zaragoza, Spain
| | - R Emiliano Quiroga
- Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Agropecuaria Catamarca, Valle Viejo, Argentina
| | - Sasha Reed
- US Geological Survey, Southwest Biological Science Center, Moab, UT, USA
| | - Ana Rey
- Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Pedro Rey
- Instituto Interuniversitario de Investigación del Sistema Tierra de Andalucía, Universidad de Jaén, Jaén, Spain
| | | | - Víctor Rolo
- INDEHESA, Forestry School, Universidad de Extremadura, Plasencia, Spain
| | | | - Peter C le Roux
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | | | | | - Phokgedi Julius Sebei
- Mara Research Station, Limpopo Department of Agriculture and Rural Development, Makhado, South Africa
| | - Anarmaa Sharkhuu
- Laboratory of Ecological and Evolutionary Synthesis, Department of Biology, School of Arts and Sciences, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Ilan Stavi
- The Dead Sea and Arava Science Center, Yotvata, Israel
- Eilat Campus, Ben-Gurion University of the Negev, Eilat, Israel
| | - Colton Stephens
- Department of Natural Resource Science, Thompson Rivers University, Kamloops, British Columbia, Canada
| | - Alberto L Teixido
- Departmento de Biodiversidad, Ecología y Evolución, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Andrew David Thomas
- Department of Geography and Earth Science, Aberystwyth University, Aberystwyth, UK
| | | | - Silvia Torres Robles
- Universidad Nacional de Río Negro, Sede Atlántica, Centro de Estudios Ambientales desde la NorPatagonia (CEANPa), CONICET, Viedma, Argentina
| | - Samantha Travers
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Orsolya Valkó
- HUN-REN 'Lendület' Seed Ecology Research Group, Institute of Ecology and Botany, Centre for Ecological Research, Vácrátót, Hungary
| | | | - Frederike Velbert
- Institute of Landscape Ecology, University of Münster, Münster, Germany
| | - Andreas von Heßberg
- Disturbance Ecology and Vegetation Dynamics, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Wanyoike Wamiti
- Zoology Department, National Museums of Kenya, Nairobi, Kenya
| | - Deli Wang
- Key Laboratory of Vegetation Ecology of the Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Institute of Grassland Science, Northeast Normal University, Changchun, China
| | - Lixin Wang
- Department of Earth and Environmental Sciences, Indiana University Indianapolis (IUI), Indianapolis, IN, USA
| | - Glenda M Wardle
- Desert Ecology Research Group, School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Laura Yahdjian
- Cátedra de Ecología, Facultad de Agronomía, Universidad de Buenos Aires. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA-CONICET), Buenos Aires, Argentina
| | - Eli Zaady
- Department of Natural Resources, Agricultural Research Organization, Institute of Plant Sciences, Gilat Research Center, Tel Aviv, Israel
- Kaye College of Education, Be'er Sheva, Israel
| | - Yuanming Zhang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Xiaobing Zhou
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Fernando T Maestre
- Environmental Sciences and Engineering, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
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26
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Philippe R, Janet R, Khalvati K, Rao RPN, Lee D, Dreher JC. Neurocomputational mechanisms involved in adaptation to fluctuating intentions of others. Nat Commun 2024; 15:3189. [PMID: 38609372 PMCID: PMC11014977 DOI: 10.1038/s41467-024-47491-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/12/2024] [Indexed: 04/14/2024] Open
Abstract
Humans frequently interact with agents whose intentions can fluctuate between competition and cooperation over time. It is unclear how the brain adapts to fluctuating intentions of others when the nature of the interactions (to cooperate or compete) is not explicitly and truthfully signaled. Here, we use model-based fMRI and a task in which participants thought they were playing with another player. In fact, they played with an algorithm that alternated without signaling between cooperative and competitive strategies. We show that a neurocomputational mechanism with arbitration between competitive and cooperative experts outperforms other learning models in predicting choice behavior. At the brain level, the fMRI results show that the ventral striatum and ventromedial prefrontal cortex track the difference of reliability between these experts. When attributing competitive intentions, we find increased coupling between these regions and a network that distinguishes prediction errors related to competition and cooperation. These findings provide a neurocomputational account of how the brain arbitrates dynamically between cooperative and competitive intentions when making adaptive social decisions.
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Affiliation(s)
- Rémi Philippe
- CNRS-Institut des Sciences Cognitives Marc Jeannerod, UMR5229, Neuroeconomics, reward, and decision making laboratory, Lyon, France
- Université Claude Bernard Lyon 1, Lyon, France
| | - Rémi Janet
- CNRS-Institut des Sciences Cognitives Marc Jeannerod, UMR5229, Neuroeconomics, reward, and decision making laboratory, Lyon, France
- Université Claude Bernard Lyon 1, Lyon, France
| | - Koosha Khalvati
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Rajesh P N Rao
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
- Center for Neurotechnology, University of Washington, Seattle, WA, USA
| | - Daeyeol Lee
- Zanvyl Krieger Mind/Brain Institute, Johns Hopkins University, Baltimore, MD, USA
- Kavli Discovery Neuroscience Institute, Johns Hopkins University, Baltimore, MD, USA
- Department of Psychological and Brain Sciences, Johns Hopkins University, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA
| | - Jean-Claude Dreher
- CNRS-Institut des Sciences Cognitives Marc Jeannerod, UMR5229, Neuroeconomics, reward, and decision making laboratory, Lyon, France.
- Université Claude Bernard Lyon 1, Lyon, France.
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27
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Pérez-Ortega J, Akrouh A, Yuste R. Stimulus encoding by specific inactivation of cortical neurons. Nat Commun 2024; 15:3192. [PMID: 38609354 PMCID: PMC11015011 DOI: 10.1038/s41467-024-47515-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
Neuronal ensembles are groups of neurons with correlated activity associated with sensory, motor, and behavioral functions. To explore how ensembles encode information, we investigated responses of visual cortical neurons in awake mice using volumetric two-photon calcium imaging during visual stimulation. We identified neuronal ensembles employing an unsupervised model-free algorithm and, besides neurons activated by the visual stimulus (termed "onsemble"), we also find neurons that are specifically inactivated (termed "offsemble"). Offsemble neurons showed faster calcium decay during stimuli, suggesting selective inhibition. In response to visual stimuli, each ensemble (onsemble+offsemble) exhibited small trial-to-trial variability, high orientation selectivity, and superior predictive accuracy for visual stimulus orientation, surpassing the sum of individual neuron activity. Thus, the combined selective activation and inactivation of cortical neurons enhances visual encoding as an emergent and distributed neural code.
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Affiliation(s)
- Jesús Pérez-Ortega
- Neurotechnology Center, Dept. Biological Sciences, Columbia University, New York, NY, 10027, USA.
| | - Alejandro Akrouh
- Neurotechnology Center, Dept. Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Rafael Yuste
- Neurotechnology Center, Dept. Biological Sciences, Columbia University, New York, NY, 10027, USA
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28
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Betts MG, Yang Z, Hadley AS, Hightower J, Hua F, Lindenmayer D, Seo E, Healey SP. Quantifying forest degradation requires a long-term, landscape-scale approach. Nat Ecol Evol 2024:10.1038/s41559-024-02409-5. [PMID: 38609537 DOI: 10.1038/s41559-024-02409-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2024]
Affiliation(s)
- Matthew G Betts
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA.
| | - Zhiqiang Yang
- United States Department of Agriculture Forest Service, Rocky Mountain Research Station, Riverdale, UT, USA
| | | | - Jessica Hightower
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | - Fangyuan Hua
- Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - David Lindenmayer
- The Fenner School of Environment and Society, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Eugene Seo
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | - Sean P Healey
- United States Department of Agriculture Forest Service, Rocky Mountain Research Station, Riverdale, UT, USA
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29
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Erhardt R, Di Vittorio CA, Hepler SA, Lowman LEL, Wei W. Homogenized gridded dataset for drought and hydrometeorological modeling for the continental United States. Sci Data 2024; 11:375. [PMID: 38609423 PMCID: PMC11015021 DOI: 10.1038/s41597-024-03202-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
We present a novel data set for drought in the continental US (CONUS) built to enable computationally efficient spatio-temporal statistical and probabilistic models of drought. We converted drought data obtained from the widely-used US Drought Monitor (USDM) from its native geo-referenced polygon format to a 0.5 degree regular grid. We merged known environmental drivers of drought, including those obtained from the North American Land Data Assimilation System (NLDAS-2), US Geological Survey (USGS) streamflow data, and National Oceanic and Atmospheric Administration (NOAA) teleconnections data. The resulting data set permits statistical and probabilistic modeling of drought with explicit spatial and/or temporal dependence. Such models could be used to forecast drought at short-range, seasonal to sub-seasonal, and inter-annual timescales with uncertainty, extending the reach and value of the current US Drought Outlook from the National Weather Service Climate Prediction Center. This novel data product provides the first common gridded dataset that includes critical variables used to inform hydrological and meteorological drought.
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Affiliation(s)
- Robert Erhardt
- Wake Forest University, Department of Statistical Sciences, Winston-Salem, NC, USA.
| | | | - Staci A Hepler
- Wake Forest University, Department of Statistical Sciences, Winston-Salem, NC, USA
| | - Lauren E L Lowman
- Wake Forest University, Department of Engineering, Winston-Salem, NC, USA
| | - Wendy Wei
- Wake Forest University, Department of Statistical Sciences, Winston-Salem, NC, USA
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30
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Zhang J, Shen S, Puggioni D, Wang M, Sha H, Xu X, Lyu Y, Peng H, Xing W, Walters LN, Liu L, Wang Y, Hou D, Xi C, Pi L, Ishizuka H, Kotani Y, Kimata M, Nojiri H, Nakamura T, Liang T, Yi D, Nan T, Zang J, Sheng Z, He Q, Zhou S, Nagaosa N, Nan CW, Tokura Y, Yu R, Rondinelli JM, Yu P. A correlated ferromagnetic polar metal by design. Nat Mater 2024:10.1038/s41563-024-01856-6. [PMID: 38605196 DOI: 10.1038/s41563-024-01856-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 03/11/2024] [Indexed: 04/13/2024]
Abstract
Polar metals have recently garnered increasing interest because of their promising functionalities. Here we report the experimental realization of an intrinsic coexisting ferromagnetism, polar distortion and metallicity in quasi-two-dimensional Ca3Co3O8. This material crystallizes with alternating stacking of oxygen tetrahedral CoO4 monolayers and octahedral CoO6 bilayers. The ferromagnetic metallic state is confined within the quasi-two-dimensional CoO6 layers, and the broken inversion symmetry arises simultaneously from the Co displacements. The breaking of both spatial-inversion and time-reversal symmetries, along with their strong coupling, gives rise to an intrinsic magnetochiral anisotropy with exotic magnetic field-free non-reciprocal electrical resistivity. An extraordinarily robust topological Hall effect persists over a broad temperature-magnetic field phase space, arising from dipole-induced Rashba spin-orbit coupling. Our work not only provides a rich platform to explore the coupling between polarity and magnetism in a metallic system, with extensive potential applications, but also defines a novel design strategy to access exotic correlated electronic states.
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Affiliation(s)
- Jianbing Zhang
- State Key Laboratory of Low Dimensional Quantum Physics and Department of Physics, Tsinghua University, Beijing, China
| | - Shengchun Shen
- State Key Laboratory of Low Dimensional Quantum Physics and Department of Physics, Tsinghua University, Beijing, China
| | - Danilo Puggioni
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, USA
| | - Meng Wang
- State Key Laboratory of Low Dimensional Quantum Physics and Department of Physics, Tsinghua University, Beijing, China
| | - Haozhi Sha
- State Key Laboratory of New Ceramics and Fine Processing, School of Materials Science and Engineering, Tsinghua University, Beijing, China
- MOE Key Laboratory of Advanced Materials, Tsinghua University, Beijing, China
| | - Xueli Xu
- High Magnetic Field Laboratory, HFIPS, Anhui, Chinese Academy of Sciences, Hefei, China
| | - Yingjie Lyu
- State Key Laboratory of Low Dimensional Quantum Physics and Department of Physics, Tsinghua University, Beijing, China
| | - Huining Peng
- State Key Laboratory of Low Dimensional Quantum Physics and Department of Physics, Tsinghua University, Beijing, China
| | - Wandong Xing
- State Key Laboratory of New Ceramics and Fine Processing, School of Materials Science and Engineering, Tsinghua University, Beijing, China
- MOE Key Laboratory of Advanced Materials, Tsinghua University, Beijing, China
| | - Lauren N Walters
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, USA
| | - Linhan Liu
- State Key Laboratory of New Ceramics and Fine Processing, School of Materials Science and Engineering, Tsinghua University, Beijing, China
- MOE Key Laboratory of Advanced Materials, Tsinghua University, Beijing, China
| | - Yujia Wang
- State Key Laboratory of Low Dimensional Quantum Physics and Department of Physics, Tsinghua University, Beijing, China
| | - De Hou
- High Magnetic Field Laboratory, HFIPS, Anhui, Chinese Academy of Sciences, Hefei, China
| | - Chuanying Xi
- High Magnetic Field Laboratory, HFIPS, Anhui, Chinese Academy of Sciences, Hefei, China
| | - Li Pi
- High Magnetic Field Laboratory, HFIPS, Anhui, Chinese Academy of Sciences, Hefei, China
| | - Hiroaki Ishizuka
- Department of Physics, Tokyo Institute of Technology, Tokyo, Japan
| | - Yoshinori Kotani
- Center for Synchrotron Radiation Research, Japan Synchrotron Radiation Research Institute, Hyogo, Japan
| | - Motoi Kimata
- Institute of Materials Research, Tohoku University, Sendai, Japan
| | - Hiroyuki Nojiri
- Institute of Materials Research, Tohoku University, Sendai, Japan
| | - Tetsuya Nakamura
- International Center for Synchrotron Radiation Innovation Smart, Tohoku University, Sendai, Japan
| | - Tian Liang
- State Key Laboratory of Low Dimensional Quantum Physics and Department of Physics, Tsinghua University, Beijing, China
- RIKEN Center for Emergent Matter Science (CEMS), Wako, Japan
- Frontier Science Center for Quantum Information, Beijing, China
| | - Di Yi
- State Key Laboratory of New Ceramics and Fine Processing, School of Materials Science and Engineering, Tsinghua University, Beijing, China
| | - Tianxiang Nan
- School of Integrated Circuits, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, China
| | - Jiadong Zang
- Department of Physics and Astronomy, University of New Hampshire, Durham, NH, USA
| | - Zhigao Sheng
- High Magnetic Field Laboratory, HFIPS, Anhui, Chinese Academy of Sciences, Hefei, China
| | - Qing He
- Department of Physics, Durham University, Durham, UK
| | - Shuyun Zhou
- State Key Laboratory of Low Dimensional Quantum Physics and Department of Physics, Tsinghua University, Beijing, China
- Frontier Science Center for Quantum Information, Beijing, China
| | - Naoto Nagaosa
- RIKEN Center for Emergent Matter Science (CEMS), Wako, Japan
- Department of Applied Physics, University of Tokyo, Tokyo, Japan
| | - Ce-Wen Nan
- State Key Laboratory of New Ceramics and Fine Processing, School of Materials Science and Engineering, Tsinghua University, Beijing, China
| | - Yoshinori Tokura
- RIKEN Center for Emergent Matter Science (CEMS), Wako, Japan
- Department of Applied Physics, University of Tokyo, Tokyo, Japan
| | - Rong Yu
- State Key Laboratory of New Ceramics and Fine Processing, School of Materials Science and Engineering, Tsinghua University, Beijing, China.
- MOE Key Laboratory of Advanced Materials, Tsinghua University, Beijing, China.
| | - James M Rondinelli
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, USA.
| | - Pu Yu
- State Key Laboratory of Low Dimensional Quantum Physics and Department of Physics, Tsinghua University, Beijing, China.
- RIKEN Center for Emergent Matter Science (CEMS), Wako, Japan.
- Frontier Science Center for Quantum Information, Beijing, China.
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31
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Shain DH, Klein EA. Genome assembly of Pseudomonas sp. strain SED1 T, a psychrotolerant bacterium isolated from Deception Glacier (Washington, USA). Microbiol Resour Announc 2024; 13:e0012524. [PMID: 38526093 PMCID: PMC11008169 DOI: 10.1128/mra.00125-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 03/12/2024] [Indexed: 03/26/2024] Open
Abstract
Strain SED1T was isolated from glacial samples collected on Mount Deception, Washington, USA. Genome sequencing and assembly identified a DNA G + C content of 60.4 mol% with 6,125 predicted proteins. Analysis by the Type Strain Genome Server is consistent with the isolate representing a previously undescribed species in the genus Pseudomonas.
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Affiliation(s)
- Daniel H. Shain
- Biology Department, Rutgers, The State University of New Jersey, Camden, New Jersey, USA
- Center for Computational and Integrative Biology, Rutgers, The State University of New Jersey, Camden, New Jersey, USA
| | - Eric A. Klein
- Biology Department, Rutgers, The State University of New Jersey, Camden, New Jersey, USA
- Center for Computational and Integrative Biology, Rutgers, The State University of New Jersey, Camden, New Jersey, USA
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32
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Deepak SJ, Kannan P, Savariraj WR, S A, Ayyasamy E, Tuticorin Maragatham Alagesan SK, Ravindran NB, Sundaram S, Mohanadasse NQ, Shippy TD, Cull CA, Levent G, Amachawadi RG. Isolation and genomic characterization of S taphylococcus aureus bacteriophages from Chennai, India. Microbiol Resour Announc 2024; 13:e0120923. [PMID: 38456698 PMCID: PMC11008210 DOI: 10.1128/mra.01209-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 02/22/2024] [Indexed: 03/09/2024] Open
Abstract
We isolated and characterized two lytic bacteriophages against Staphylococcus aureus named TANUVAS_MVC-VPHSA1 and TANUVAS_MVC-VPHSA2, with the aim of investigating their genomic and structural features. The bacteriophages belong to the Caudoviricetes, and their genomes have sizes of 50,505 and 50,516 base pairs with a GC content of 41.4%.
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Affiliation(s)
| | - Porteen Kannan
- Department of Veterinary Public Health and Epidemiology, Madras Veterinary College, TANUVAS, Chennai, India
| | - Wilfred Ruban Savariraj
- Department of Livestock Products and Technology, Veterinary College, KVAFSU, Bengaluru, India
| | - Anbazhagan S
- ICMR-National Animal Resource Facility for Biomedical Research (NARFBR), Hyderabad, Telangana, India
| | - Elango Ayyasamy
- Veterinary College and Research Institute, TANUVAS, Salem, India
| | | | - Narendra Babu Ravindran
- Department of Livestock Products and Technology, Madras Veterinary College, TANUVAS, Chennai, India
| | - Sureshkannan Sundaram
- Department of Veterinary Public Health and Epidemiology, Madras Veterinary College, TANUVAS, Chennai, India
| | | | - Teresa D. Shippy
- Bioinformatics Center, Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | | | - Gizem Levent
- Texas Tech University School of Veterinary Medicine, Amarillo, Texas, USA
| | - Raghavendra G. Amachawadi
- Department of Clinical Sciences, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
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33
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Peruzzi JA, Steinkühler J, Vu TQ, Gunnels TF, Hu VT, Lu P, Baker D, Kamat NP. Hydrophobic mismatch drives self-organization of designer proteins into synthetic membranes. Nat Commun 2024; 15:3162. [PMID: 38605024 PMCID: PMC11009411 DOI: 10.1038/s41467-024-47163-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/22/2024] [Indexed: 04/13/2024] Open
Abstract
The organization of membrane proteins between and within membrane-bound compartments is critical to cellular function. Yet we lack approaches to regulate this organization in a range of membrane-based materials, such as engineered cells, exosomes, and liposomes. Uncovering and leveraging biophysical drivers of membrane protein organization to design membrane systems could greatly enhance the functionality of these materials. Towards this goal, we use de novo protein design, molecular dynamic simulations, and cell-free systems to explore how membrane-protein hydrophobic mismatch could be used to tune protein cotranslational integration and organization in synthetic lipid membranes. We find that membranes must deform to accommodate membrane-protein hydrophobic mismatch, which reduces the expression and co-translational insertion of membrane proteins into synthetic membranes. We use this principle to sort proteins both between and within membranes, thereby achieving one-pot assembly of vesicles with distinct functions and controlled split-protein assembly, respectively. Our results shed light on protein organization in biological membranes and provide a framework to design self-organizing membrane-based materials with applications such as artificial cells, biosensors, and therapeutic nanoparticles.
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Affiliation(s)
- Justin A Peruzzi
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Jan Steinkühler
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Timothy Q Vu
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Taylor F Gunnels
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Vivian T Hu
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Peilong Lu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Neha P Kamat
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA.
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA.
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA.
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34
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Nousias O, Zheng J, Li T, Meinhardt LW, Bailey B, Gutierrez O, Baruah IK, Cohen SP, Zhang D, Yin Y. Three de novo assembled wild cacao genomes from the Upper Amazon. Sci Data 2024; 11:369. [PMID: 38605066 PMCID: PMC11009333 DOI: 10.1038/s41597-024-03215-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 04/03/2024] [Indexed: 04/13/2024] Open
Abstract
Theobroma cacao, the chocolate tree, is indigenous to the Amazon basin, the greatest biodiversity hotspot on earth. Recent advancement in plant genomics highlights the importance of de novo sequencing of multiple reference genomes to capture the genome diversity present in different cacao populations. In this study, three high-quality chromosome-level genomes of wild cacao were constructed, de novo assembled with HiFi long reads sequencing, and scaffolded using a reference-free strategy. These genomes represent the three most important genetic clusters of cacao trees from the Upper Amazon region. The three wild cacao genomes were compared with two reference genomes of domesticated cacao. The five cacao genetic clusters were inferred to have diverged in the early and middle Pleistocene period, approximately 1.83-0.69 million years ago. The results shown here serve as an example of understanding how the Amazonian biodiversity was developed. The three wild cacao genomes provide valuable resources for studying genetic diversity and advancing genetic improvement of this species.
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Affiliation(s)
- Orestis Nousias
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jinfang Zheng
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Tang Li
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Lyndel W Meinhardt
- U.S. Department of Agriculture, Sustainable Perennial Crops Laboratory, Beltsville, MD, USA
| | - Bryan Bailey
- U.S. Department of Agriculture, Sustainable Perennial Crops Laboratory, Beltsville, MD, USA
| | - Osman Gutierrez
- U.S. Department of Agriculture, Subtropical Horticulture Research Station, Miami, FL, USA
| | - Indrani K Baruah
- U.S. Department of Agriculture, Sustainable Perennial Crops Laboratory, Beltsville, MD, USA
| | - Stephen P Cohen
- U.S. Department of Agriculture, Sustainable Perennial Crops Laboratory, Beltsville, MD, USA
| | - Dapeng Zhang
- U.S. Department of Agriculture, Sustainable Perennial Crops Laboratory, Beltsville, MD, USA.
| | - Yanbin Yin
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA.
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35
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Fromm A, Hevroni G, Vincent F, Schatz D, Martinez-Gutierrez CA, Aylward FO, Vardi A. Single-cell RNA-seq of the rare virosphere reveals the native hosts of giant viruses in the marine environment. Nat Microbiol 2024:10.1038/s41564-024-01669-y. [PMID: 38605173 DOI: 10.1038/s41564-024-01669-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 03/07/2024] [Indexed: 04/13/2024]
Abstract
Giant viruses (phylum Nucleocytoviricota) are globally distributed in aquatic ecosystems. They play fundamental roles as evolutionary drivers of eukaryotic plankton and regulators of global biogeochemical cycles. However, we lack knowledge about their native hosts, hindering our understanding of their life cycle and ecological importance. In the present study, we applied a single-cell RNA sequencing (scRNA-seq) approach to samples collected during an induced algal bloom, which enabled pairing active giant viruses with their native protist hosts. We detected hundreds of single cells from multiple host lineages infected by diverse giant viruses. These host cells included members of the algal groups Chrysophycae and Prymnesiophycae, as well as heterotrophic flagellates in the class Katablepharidaceae. Katablepharids were infected with a rare Imitervirales-07 giant virus lineage expressing a large repertoire of cell-fate regulation genes. Analysis of the temporal dynamics of these host-virus interactions revealed an important role for the Imitervirales-07 in controlling the population size of the host Katablepharid population. Our results demonstrate that scRNA-seq can be used to identify previously undescribed host-virus interactions and study their ecological importance and impact.
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Affiliation(s)
- Amir Fromm
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Gur Hevroni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
- Google Geo, Tel Aviv, Israel
| | - Flora Vincent
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
- Developmental Biology Unit, European Molecular Biological Laboratory, Heidelberg, Germany
| | - Daniella Schatz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | | | - Frank O Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.
- Center for Emerging, Zoonotic, and Arthropod-Borne Pathogens, Virginia Tech, Blacksburg, VA, USA.
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel.
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36
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Keyport Kik S, Christopher D, Glauninger H, Hickernell CW, Bard JAM, Lin KM, Squires AH, Ford M, Sosnick TR, Drummond DA. An adaptive biomolecular condensation response is conserved across environmentally divergent species. Nat Commun 2024; 15:3127. [PMID: 38605014 PMCID: PMC11009240 DOI: 10.1038/s41467-024-47355-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 03/27/2024] [Indexed: 04/13/2024] Open
Abstract
Cells must sense and respond to sudden maladaptive environmental changes-stresses-to survive and thrive. Across eukaryotes, stresses such as heat shock trigger conserved responses: growth arrest, a specific transcriptional response, and biomolecular condensation of protein and mRNA into structures known as stress granules under severe stress. The composition, formation mechanism, adaptive significance, and even evolutionary conservation of these condensed structures remain enigmatic. Here we provide a remarkable view into stress-triggered condensation, its evolutionary conservation and tuning, and its integration into other well-studied aspects of the stress response. Using three morphologically near-identical budding yeast species adapted to different thermal environments and diverged by up to 100 million years, we show that proteome-scale biomolecular condensation is tuned to species-specific thermal niches, closely tracking corresponding growth and transcriptional responses. In each species, poly(A)-binding protein-a core marker of stress granules-condenses in isolation at species-specific temperatures, with conserved molecular features and conformational changes modulating condensation. From the ecological to the molecular scale, our results reveal previously unappreciated levels of evolutionary selection in the eukaryotic stress response, while establishing a rich, tractable system for further inquiry.
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Affiliation(s)
- Samantha Keyport Kik
- Committee on Genetics, Genomics, and Systems Biology, The University of Chicago, Chicago, IL, USA
| | - Dana Christopher
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Hendrik Glauninger
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL, USA
- Interdisciplinary Scientist Training Program, The University of Chicago, Chicago, IL, USA
| | - Caitlin Wong Hickernell
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Jared A M Bard
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Kyle M Lin
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL, USA
- Interdisciplinary Scientist Training Program, The University of Chicago, Chicago, IL, USA
| | - Allison H Squires
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | | | - Tobin R Sosnick
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | - D Allan Drummond
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, USA.
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37
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van Woesik R, Kratochwill C. A global database on coral recovery following marine heatwaves. Sci Data 2024; 11:367. [PMID: 38605060 PMCID: PMC11009248 DOI: 10.1038/s41597-024-03221-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/03/2024] [Indexed: 04/13/2024] Open
Abstract
Coral reefs support the world's most diverse marine ecosystem and provide invaluable goods and services for millions of people worldwide. They are however experiencing frequent and intensive marine heatwaves that are causing coral bleaching and mortality. Coarse-grained climate models predict that few coral reefs will survive the 3 °C sea-surface temperature rise in the coming century. Yet, field studies show localized pockets of coral survival and recovery even under high-temperature conditions. Quantifying recovery from marine heatwaves is central to making accurate predictions of coral-reef trajectories into the near future. Here we introduce the world's most comprehensive database on coral recovery following marine heatwaves and other disturbances, called Heatwaves and Coral-Recovery Database (HeatCRD) encompassing 29,205 data records spanning 44 years from 12,266 sites, 83 countries, and 160 data sources. These data provide essential information to coral-reef scientists and managers to best guide coral-reef conservation efforts at both local and regional scales.
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Affiliation(s)
- Robert van Woesik
- Institute for Global Ecology, Florida Institute of Technology, Melbourne, Florida, 32901, United States of America.
| | - Chelsey Kratochwill
- Institute for Global Ecology, Florida Institute of Technology, Melbourne, Florida, 32901, United States of America
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Hayashi S, Caron BA, Heinsfeld AS, Vinci-Booher S, McPherson B, Bullock DN, Bertò G, Niso G, Hanekamp S, Levitas D, Ray K, MacKenzie A, Avesani P, Kitchell L, Leong JK, Nascimento-Silva F, Koudoro S, Willis H, Jolly JK, Pisner D, Zuidema TR, Kurzawski JW, Mikellidou K, Bussalb A, Chaumon M, George N, Rorden C, Victory C, Bhatia D, Aydogan DB, Yeh FCF, Delogu F, Guaje J, Veraart J, Fischer J, Faskowitz J, Fabrega R, Hunt D, McKee S, Brown ST, Heyman S, Iacovella V, Mejia AF, Marinazzo D, Craddock RC, Olivetti E, Hanson JL, Garyfallidis E, Stanzione D, Carson J, Henschel R, Hancock DY, Stewart CA, Schnyer D, Eke DO, Poldrack RA, Bollman S, Stewart A, Bridge H, Sani I, Freiwald WA, Puce A, Port NL, Pestilli F. brainlife.io: a decentralized and open-source cloud platform to support neuroscience research. Nat Methods 2024:10.1038/s41592-024-02237-2. [PMID: 38605111 DOI: 10.1038/s41592-024-02237-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 03/05/2024] [Indexed: 04/13/2024]
Abstract
Neuroscience is advancing standardization and tool development to support rigor and transparency. Consequently, data pipeline complexity has increased, hindering FAIR (findable, accessible, interoperable and reusable) access. brainlife.io was developed to democratize neuroimaging research. The platform provides data standardization, management, visualization and processing and automatically tracks the provenance history of thousands of data objects. Here, brainlife.io is described and evaluated for validity, reliability, reproducibility, replicability and scientific utility using four data modalities and 3,200 participants.
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Affiliation(s)
| | - Bradley A Caron
- Indiana University, Bloomington, IN, USA
- The University of Texas, Austin, TX, USA
| | | | - Sophia Vinci-Booher
- Indiana University, Bloomington, IN, USA
- Vanderbilt University, Nashville, TN, USA
| | - Brent McPherson
- Indiana University, Bloomington, IN, USA
- McGill University, Montréal, Quebec, Canada
| | | | | | - Guiomar Niso
- Indiana University, Bloomington, IN, USA
- Cajal Institute, CSIC, Madrid, Spain
| | | | - Daniel Levitas
- Indiana University, Bloomington, IN, USA
- The University of Texas, Austin, TX, USA
| | | | | | | | - Lindsey Kitchell
- Indiana University, Bloomington, IN, USA
- Applied Physics Laboratory, Johns Hopkins University, Laurel, MD, USA
| | - Josiah K Leong
- Indiana University, Bloomington, IN, USA
- University of Arkansas, Fayetteville, AR, USA
| | | | | | | | | | | | | | | | - Kyriaki Mikellidou
- University of Limassol, Nicosia, Cyprus
- University of Cyprus, Nicosia, Cyprus
| | - Aurore Bussalb
- Institut du Cerveau, CNRS, Sorbonne Université, Paris, France
| | | | - Nathalie George
- Institut du Cerveau, CNRS, Sorbonne Université, Paris, France
| | | | | | | | - Dogu Baran Aydogan
- University of Eastern Finland, Kuopio, Finland
- Aalto University School of Science, Espoo, Finland
| | | | - Franco Delogu
- Lawrence Technological University, Southfield, MI, USA
| | | | | | | | | | | | - David Hunt
- Indiana University, Bloomington, IN, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Ashley Stewart
- University of Queensland, St Lucia, Queensland, Australia
| | | | - Ilaria Sani
- The Rockefeller University, New York, NY, USA
- University of Geneva, Geneva, Switzerland
| | | | - Aina Puce
- Indiana University, Bloomington, IN, USA
| | | | - Franco Pestilli
- Indiana University, Bloomington, IN, USA.
- The University of Texas, Austin, TX, USA.
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Mosharraf FB, Marpa C, Rojas K, Bernard J, Rowell A, Bono LM. The genome sequences of lytic Pseudomonas aeruginosa bacteriophages BL1, BL2, and BL3 isolated from the environment. Microbiol Resour Announc 2024; 13:e0117123. [PMID: 38426733 PMCID: PMC11008170 DOI: 10.1128/mra.01171-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/13/2024] [Indexed: 03/02/2024] Open
Abstract
We isolated three environmental phages that infect Pseudomonas aeruginosa PAO1, an opportunistic pathogen, from Playa Lakes in Lubbock, TX. We report the genome sequences of isolated lytic bacteriophages BL1, BL2, and BL3. Sequence similarity analysis revealed that the viruses belonged to an unclassified species in the genus Pbunavirus within Caudoviricetes.
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Affiliation(s)
| | - Christopher Marpa
- Department of Biological Sciences, Texas Tech University, Lubbock, USA
| | - Karagen Rojas
- Department of Biological Sciences, Texas Tech University, Lubbock, USA
| | - Jeffrey Bernard
- Department of Biological Sciences, Texas Tech University, Lubbock, USA
| | - Austen Rowell
- Department of Biological Sciences, Texas Tech University, Lubbock, USA
| | - Lisa M. Bono
- Department of Biological Sciences, Texas Tech University, Lubbock, USA
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Mulay SA, Hahn CR, Klingeman DM, Elshahed MS, Youssef NH, Podar M. Metagenomic sequencing of a Patescibacteria-containing enrichment from Zodletone spring in Oklahoma, USA. Microbiol Resour Announc 2024; 13:e0011424. [PMID: 38497626 PMCID: PMC11008151 DOI: 10.1128/mra.00114-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 03/06/2024] [Indexed: 03/19/2024] Open
Abstract
An enrichment of sulfidic sediments from Zodletone spring was sequenced as a metagenome. Draft genomes representing Cloacimonadota, Deltabacterota, Firmicutes, and Patescibacteria were binned and annotated and will aid functional genomics and cultivation efforts.
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Affiliation(s)
- Sayali A. Mulay
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, Tennessee, USA
| | - C. Ryan Hahn
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Dawn M. Klingeman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Mostafa S. Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Noha H. Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Mircea Podar
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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41
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Stancheva R, Sethuraman A, Khadivar H, Archambeau J, Caughran E, Chang A, Hunter B, Ihenyen C, Onwukwe M, Palacios D, La Prairie C, Read N, Tsang J, Vega B, Velasquez C, Zhang X, Becket E, Read B. Characterizing the microbial metagenome of calcareous stromatolite formations in the San Felipe Creek in the Anza Borrego Desert. Microbiol Resour Announc 2024; 13:e0088123. [PMID: 38436258 PMCID: PMC11008161 DOI: 10.1128/mra.00881-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 02/15/2024] [Indexed: 03/05/2024] Open
Abstract
We describe the metagenome composition, community functional annotation, and prokaryote diversity in calcareous stromatolites from a dry stream bed of the San Felipe Creek in the Anza Borrego Desert. Analyses show a community capable of nitrogen fixation, assimilatory nitrate reduction, biofilm formation, quorum sensing, and potential thick-walled akinete formation for desiccation resistance.
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Affiliation(s)
- Rosalina Stancheva
- Department of Biological Sciences, California State University San Marcos, San Marcos, California, USA
- Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, USA
| | - Arun Sethuraman
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Hossein Khadivar
- Department of Biological Sciences, California State University San Marcos, San Marcos, California, USA
| | - Jenna Archambeau
- Department of Biological Sciences, California State University San Marcos, San Marcos, California, USA
- Department of Chemistry, American University, Washington, DC, USA
| | - Ella Caughran
- Department of Biological Sciences, California State University San Marcos, San Marcos, California, USA
- Department of Biological Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Ashley Chang
- Department of Biological Sciences, California State University San Marcos, San Marcos, California, USA
- Department of Mathematics, Amherst College, Amherst, Massachusetts, USA
| | - Brad Hunter
- Department of Biological Sciences, California State University San Marcos, San Marcos, California, USA
| | - Christian Ihenyen
- Department of Biological Sciences, California State University San Marcos, San Marcos, California, USA
- Department of Biology, Howard University, Washington DC, USA
| | - Marvin Onwukwe
- Department of Biological Sciences, California State University San Marcos, San Marcos, California, USA
- Department of Biological Sciences, University of Maryland, Baltimore County, Maryland, USA
| | - Dariana Palacios
- Department of Biological Sciences, California State University San Marcos, San Marcos, California, USA
- Department of Biosciences, Farmingdale State College, Farmingdale, New York, USA
| | - Chloe La Prairie
- Department of Biological Sciences, California State University San Marcos, San Marcos, California, USA
- Department of Biology, Millikin University, Decatur, Illinois, USA
| | - Nicole Read
- Department of Biological Sciences, California State University San Marcos, San Marcos, California, USA
| | - Julianna Tsang
- Department of Biological Sciences, California State University San Marcos, San Marcos, California, USA
- Department of Biological Sciences, Willamette University, Salem, Oregon, USA
| | - Brianna Vega
- Department of Biological Sciences, California State University San Marcos, San Marcos, California, USA
| | - Cristina Velasquez
- Department of Biological Sciences, California State University San Marcos, San Marcos, California, USA
| | - Xiaoyu Zhang
- Department of Biological Sciences, California State University San Marcos, San Marcos, California, USA
| | - Elinne Becket
- Department of Biological Sciences, California State University San Marcos, San Marcos, California, USA
| | - Betsy Read
- Department of Biological Sciences, California State University San Marcos, San Marcos, California, USA
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Saenkham-Huntsinger P, Ritter M, Donati GL, Mitchell AM, Subashchandrabose S. The inner membrane protein YhiM links copper and CpxAR envelope stress responses in uropathogenic E. coli. mBio 2024; 15:e0352223. [PMID: 38470052 PMCID: PMC11005409 DOI: 10.1128/mbio.03522-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 02/13/2024] [Indexed: 03/13/2024] Open
Abstract
Urinary tract infection (UTI) is a ubiquitous infectious condition, and uropathogenic Escherichia coli (UPEC) is the predominant causative agent of UTI. Copper (Cu) is implicated in innate immunity, including against UPEC. Cu is a trace element utilized as a co-factor, but excess Cu is toxic due to mismetalation of non-cognate proteins. E. coli precisely regulates Cu homeostasis via efflux systems. However, Cu import mechanisms into the bacterial cell are not clear. We hypothesized that Cu import defective mutants would exhibit increased resistance to Cu. This hypothesis was tested in a forward genetic screen with transposon (Tn5) insertion mutants in UPEC strain CFT073, and we identified 32 unique Cu-resistant mutants. Transposon and defined mutants lacking yhiM, which encodes a hypothetical inner membrane protein, were more resistant to Cu than parental strain. Loss of YhiM led to decreased cellular Cu content and increased expression of copA, encoding a Cu efflux pump. The CpxAR envelope stress response system was activated in the ΔyhiM mutant as indicated by increased expression of cpxP. Transcription of yhiM was regulated by CueR and CpxR, and the CpxAR system was essential for increased Cu resistance in the ΔyhiM mutant. Importantly, activation of CpxAR system in the ΔyhiM mutant was independent of NlpE, a known activator of this system. YhiM was required for optimal fitness of UPEC in a mouse model of UTI. Our findings demonstrate that YhiM is a critical mediator of Cu homeostasis and links bacterial adaptation to Cu stress with the CpxAR-dependent envelope stress response in UPEC.IMPORTANCEUPEC is a common bacterial infection. Bacterial pathogens are exposed to host-derived Cu during infection, including UTI. Here, we describe detection of genes involved in Cu homeostasis in UPEC. A UPEC mutant lacking YhiM, a membrane protein, exhibited dramatic increase in resistance to Cu. Our study demonstrates YhiM as a nexus between Cu stress and the CpxAR-dependent envelope stress response system. Importantly, our findings establish NlpE-independent activation of CpxAR system during Cu stress in UPEC. Collectively, YhiM emerges as a critical mediator of Cu homeostasis in UPEC and highlights the interlinked nature of bacterial adaptation to survival during Cu and envelope stress.
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Affiliation(s)
- Panatda Saenkham-Huntsinger
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Matthew Ritter
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - George L. Donati
- Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina, USA
| | - Angela M. Mitchell
- Department of Biology, College of Science, Texas A&M University, College Station, Texas, USA
| | - Sargurunathan Subashchandrabose
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
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43
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Gallardo B, Bacher S, Barbosa AM, Gallien L, González-Moreno P, Martínez-Bolea V, Sorte C, Vimercati G, Vilà M. Risks posed by invasive species to the provision of ecosystem services in Europe. Nat Commun 2024; 15:2631. [PMID: 38600085 PMCID: PMC11006939 DOI: 10.1038/s41467-024-46818-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 03/12/2024] [Indexed: 04/12/2024] Open
Abstract
Invasive species significantly impact biodiversity and ecosystem services, yet understanding these effects at large spatial scales remains a challenge. Our study addresses this gap by assessing the current and potential future risks posed by 94 invasive species to seven key ecosystem services in Europe. We demonstrate widespread potential impacts, particularly on outdoor recreation, habitat maintenance, crop provisioning, and soil and nitrogen retention. Exposure to invasive species was higher in areas with lower provision of ecosystem services, particularly for regulating and cultural services. Exposure was also high in areas where ecosystem contributions to crop provision and nitrogen retention were at their highest. Notably, regions vital for ecosystem services currently have low invasion suitability, but face an average 77% increase in potential invasion area. Here we show that, while high-value ecosystem service areas at the highest risk represent a small fraction of Europe (0-13%), they are disproportionally important for service conservation. Our study underscores the importance of monitoring and protecting these hotspots to align management strategies with international biodiversity targets, considering both invasion vulnerability and ecosystem service sustainability.
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Affiliation(s)
- Belinda Gallardo
- Instituto Pirenaico de Ecología (IPE), CSIC, Avda. Montañana 1005, 50192, Zaragoza, Spain.
- Biosecurity Initiative at St. Catherine's (BioRISC), Cambridge, UK.
| | - Sven Bacher
- Department of Biology, Unit Ecology & Evolution, University of Fribourg, Chemin du Musée 15, 1700, Fribourg, Switzerland
| | - Ana Marcia Barbosa
- Centro de Investigação em Ciências Geo-Espaciais (CICGE), Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Laure Gallien
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Pablo González-Moreno
- Department of Forest Engineering, University of Cordoba, Campus de Rabanales, Crta. IV, km. 396, 14071, Córdoba, Spain
| | - Víctor Martínez-Bolea
- Instituto Pirenaico de Ecología (IPE), CSIC, Avda. Montañana 1005, 50192, Zaragoza, Spain
| | - Cascade Sorte
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Giovanni Vimercati
- Department of Biology, Unit Ecology & Evolution, University of Fribourg, Chemin du Musée 15, 1700, Fribourg, Switzerland
| | - Montserrat Vilà
- Estación Biológica de Doñana (EBD), CSIC, Avda. Américo Vespucio 26, 41092, Sevilla, Spain
- Department of Plant Biology and Ecology, University of Sevilla, 41012, Sevilla, Spain
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44
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Pokharel J, Cresce A, Pant B, Yang MY, Gurung A, He W, Baniya A, Lamsal BS, Yang Z, Gent S, Xian X, Cao Y, Goddard WA, Xu K, Zhou Y. Manipulating the diffusion energy barrier at the lithium metal electrolyte interface for dendrite-free long-life batteries. Nat Commun 2024; 15:3085. [PMID: 38600128 PMCID: PMC11006908 DOI: 10.1038/s41467-024-47521-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 04/03/2024] [Indexed: 04/12/2024] Open
Abstract
Constructing an artificial solid electrolyte interphase (SEI) on lithium metal electrodes is a promising approach to address the rampant growth of dangerous lithium morphologies (dendritic and dead Li0) and low Coulombic efficiency that plague development of lithium metal batteries, but how Li+ transport behavior in the SEI is coupled with mechanical properties remains unknown. We demonstrate here a facile and scalable solution-processed approach to form a Li3N-rich SEI with a phase-pure crystalline structure that minimizes the diffusion energy barrier of Li+ across the SEI. Compared with a polycrystalline Li3N SEI obtained from conventional practice, the phase-pure/single crystalline Li3N-rich SEI constitutes an interphase of high mechanical strength and low Li+ diffusion barrier. We elucidate the correlation among Li+ transference number, diffusion behavior, concentration gradient, and the stability of the lithium metal electrode by integrating phase field simulations with experiments. We demonstrate improved reversibility and charge/discharge cycling behaviors for both symmetric cells and full lithium-metal batteries constructed with this Li3N-rich SEI. These studies may cast new insight into the design and engineering of an ideal artificial SEI for stable and high-performance lithium metal batteries.
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Affiliation(s)
- Jyotshna Pokharel
- Department of Mechanical Engineering, The University of Texas at Dallas, Richardson, TX, USA
- Department of Electrical Engineering and Computer Science, South Dakota State University, Brookings, SD, USA
| | - Arthur Cresce
- Battery Science Branch, Energy Science Division, U.S. CCDC Army Research Laboratory, Adelphi, MD, USA
| | - Bharat Pant
- Department of Materials Science and Engineering, University of Texas at Arlington, Arlington, TX, USA
| | - Moon Young Yang
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, CA, USA
| | - Ashim Gurung
- Department of Electrical Engineering and Computer Science, South Dakota State University, Brookings, SD, USA
| | - Wei He
- Department of Electrical Engineering and Computer Science, South Dakota State University, Brookings, SD, USA
| | - Abiral Baniya
- Department of Electrical Engineering and Computer Science, South Dakota State University, Brookings, SD, USA
| | - Buddhi Sagar Lamsal
- Department of Electrical Engineering and Computer Science, South Dakota State University, Brookings, SD, USA
| | - Zhongjiu Yang
- Department of Mechanical Engineering, The University of Texas at Dallas, Richardson, TX, USA
| | - Stephen Gent
- Department of Mechanical Engineering, South Dakota State University, Brookings, SD, USA
| | - Xiaojun Xian
- Department of Electrical Engineering and Computer Science, South Dakota State University, Brookings, SD, USA
| | - Ye Cao
- Department of Materials Science and Engineering, University of Texas at Arlington, Arlington, TX, USA.
| | - William A Goddard
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, CA, USA.
| | - Kang Xu
- Battery Science Branch, Energy Science Division, U.S. CCDC Army Research Laboratory, Adelphi, MD, USA.
- SolidEnergy Systems LLC, 35 Cabot Rd., Woburn, MA, USA.
| | - Yue Zhou
- Department of Mechanical Engineering, The University of Texas at Dallas, Richardson, TX, USA.
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45
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Xu Y, Liu N, Lin Y, Mao X, Zhong H, Chang Z, Shneider MN, Ju Y. Enhancements of electric field and afterglow of non-equilibrium plasma by Pb(Zr xTi 1-x)O 3 ferroelectric electrode. Nat Commun 2024; 15:3092. [PMID: 38600079 PMCID: PMC11006859 DOI: 10.1038/s41467-024-47230-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/26/2024] [Indexed: 04/12/2024] Open
Abstract
Manipulating surface charge, electric field, and plasma afterglow in a non-equilibrium plasma is critical to control plasma-surface interaction for plasma catalysis and manufacturing. Here, we show enhancements of surface charge, electric field during breakdown, and afterglow by ferroelectric barrier discharge. The results show that the ferroelectrics manifest spontaneous electric polarization to increase the surface charge by two orders of magnitude compared to discharge with an alumina barrier. Time-resolved in-situ electric field measurements reveal that the fast polarization of ferroelectrics enhances the electric field during the breakdown in streamer discharge and doubles the electric field compared to the dielectric barrier discharge. Moreover, due to the existence of surface charge, the ferroelectric electrode extends the afterglow time and makes discharge sustained longer when alternating the external electric field polarity. The present results show that ferroelectric barrier discharge offers a promising technique to tune plasma properties for efficient plasma catalysis and electrified manufacturing.
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Affiliation(s)
- Yijie Xu
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ, 08540, USA
| | - Ning Liu
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ, 08540, USA.
| | - Ying Lin
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ, 08540, USA
| | - Xingqian Mao
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ, 08540, USA
| | - Hongtao Zhong
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ, 08540, USA
- Department of Mechanical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Ziqiao Chang
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ, 08540, USA
| | - Mikhail N Shneider
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ, 08540, USA
| | - Yiguang Ju
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ, 08540, USA
- Princeton Plasma Physics Laboratory, Princeton, NJ, 08540, USA
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46
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Tomlin CM, Rajaraman S, Sebesta JT, Scheen AC, Bendiksby M, Low YW, Salojärvi J, Michael TP, Albert VA, Lindqvist C. Allopolyploid origin and diversification of the Hawaiian endemic mints. Nat Commun 2024; 15:3109. [PMID: 38600100 PMCID: PMC11006916 DOI: 10.1038/s41467-024-47247-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 03/26/2024] [Indexed: 04/12/2024] Open
Abstract
Island systems provide important contexts for studying processes underlying lineage migration, species diversification, and organismal extinction. The Hawaiian endemic mints (Lamiaceae family) are the second largest plant radiation on the isolated Hawaiian Islands. We generated a chromosome-scale reference genome for one Hawaiian species, Stenogyne calaminthoides, and resequenced 45 relatives, representing 34 species, to uncover the continental origins of this group and their subsequent diversification. We further resequenced 109 individuals of two Stenogyne species, and their purported hybrids, found high on the Mauna Kea volcano on the island of Hawai'i. The three distinct Hawaiian genera, Haplostachys, Phyllostegia, and Stenogyne, are nested inside a fourth genus, Stachys. We uncovered four independent polyploidy events within Stachys, including one allopolyploidy event underlying the Hawaiian mints and their direct western North American ancestors. While the Hawaiian taxa may have principally diversified by parapatry and drift in small and fragmented populations, localized admixture may have played an important role early in lineage diversification. Our genomic analyses provide a view into how organisms may have radiated on isolated island chains, settings that provided one of the principal natural laboratories for Darwin's thinking about the evolutionary process.
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Affiliation(s)
- Crystal M Tomlin
- Department of Biological Sciences, University at Buffalo, New York, USA
| | - Sitaram Rajaraman
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | | | | | - Mika Bendiksby
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Yee Wen Low
- Singapore Botanic Gardens, National Parks Board, Singapore, Singapore
| | - Jarkko Salojärvi
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Todd P Michael
- The Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, USA
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, New York, USA.
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47
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Francis VI, Liddle C, Camacho E, Kulkarni M, Junior SRS, Harvey JA, Ballou ER, Thomson DD, Brown GD, Hardwick JM, Casadevall A, Witton J, Coelho C. Cryptococcus neoformans rapidly invades the murine brain by sequential breaching of airway and endothelial tissues barriers, followed by engulfment by microglia. mBio 2024; 15:e0307823. [PMID: 38511961 PMCID: PMC11005363 DOI: 10.1128/mbio.03078-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/29/2024] [Indexed: 03/22/2024] Open
Abstract
Cryptococcus neoformans causes lethal meningitis and accounts for approximately 10%-15% of AIDS-associated deaths worldwide. There are major gaps in our understanding of how this fungus invades the mammalian brain. To investigate the dynamics of C. neoformans tissue invasion, we mapped fungal localization and host cell interactions in infected brain, lung, and upper airways using mouse models of systemic and airway infection. To enable this, we developed an in situ imaging pipeline capable of measuring large volumes of tissue while preserving anatomical and cellular information by combining thick tissue sections, tissue clarification, and confocal imaging. We confirm high fungal burden in mouse upper airway after nasal inoculation. Yeast in turbinates were frequently titan cells, with faster kinetics than reported in mouse lungs. Importantly, we observed one instance of fungal cells enmeshed in lamina propria of the upper airways, suggesting penetration of airway mucosa as a possible route of tissue invasion and dissemination to the bloodstream. We extend previous literature positing bloodstream dissemination of C. neoformans, by finding viable fungi in the bloodstream of mice a few days after intranasal infection. As early as 24 h post systemic infection, the majority of C. neoformans cells traversed the blood-brain barrier, and were engulfed or in close proximity to microglia. Our work presents a new method for investigating microbial invasion, establishes that C. neoformans can breach multiple tissue barriers within the first days of infection, and demonstrates microglia as the first cells responding to C. neoformans invasion of the brain.IMPORTANCECryptococcal meningitis causes 10%-15% of AIDS-associated deaths globally. Still, brain-specific immunity to cryptococci is a conundrum. By employing innovative imaging, this study reveals what occurs during the first days of infection in brain and in airways. We found that titan cells predominate in upper airways and that cryptococci breach the upper airway mucosa, which implies that, at least in mice, the upper airways are a site for fungal dissemination. This would signify that mucosal immunity of the upper airway needs to be better understood. Importantly, we also show that microglia, the brain-resident macrophages, are the first responders to infection, and microglia clusters are formed surrounding cryptococci. This study opens the field to detailed molecular investigations on airway immune response, how fungus traverses the blood-brain barrier, how microglia respond to infection, and ultimately how microglia monitor the blood-brain barrier to preserve brain function.
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Affiliation(s)
- Vanessa I. Francis
- MRC Centre for Medical Mycology at University of Exeter, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Corin Liddle
- Bioimaging Facility, University of Exeter, Exeter, United Kingdom
| | - Emma Camacho
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Madhura Kulkarni
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | | | - Jamie A. Harvey
- MRC Centre for Medical Mycology at University of Exeter, University of Exeter, Exeter, United Kingdom
| | - Elizabeth R. Ballou
- MRC Centre for Medical Mycology at University of Exeter, University of Exeter, Exeter, United Kingdom
| | - Darren D. Thomson
- MRC Centre for Medical Mycology at University of Exeter, University of Exeter, Exeter, United Kingdom
| | - Gordon D. Brown
- MRC Centre for Medical Mycology at University of Exeter, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - J. Marie Hardwick
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Arturo Casadevall
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Jonathan Witton
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Carolina Coelho
- MRC Centre for Medical Mycology at University of Exeter, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
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Royer C, Patin NV, Jesser KJ, Peña-Gonzalez A, Hatt JK, Trueba G, Levy K, Konstantinidis KT. Comparison of metagenomic and traditional methods for diagnosis of E. coli enteric infections. mBio 2024; 15:e0342223. [PMID: 38488359 PMCID: PMC11005377 DOI: 10.1128/mbio.03422-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 02/23/2024] [Indexed: 04/11/2024] Open
Abstract
Diarrheagenic Escherichia coli, collectively known as DEC, is a leading cause of diarrhea, particularly in children in low- and middle-income countries. Diagnosing infections caused by different DEC pathotypes traditionally relies on the cultivation and identification of virulence genes, a resource-intensive and error-prone process. Here, we compared culture-based DEC identification with shotgun metagenomic sequencing of whole stool using 35 randomly drawn samples from a cohort of diarrhea-afflicted patients. Metagenomic sequencing detected the cultured isolates in 97% of samples, revealing, overall, reliable detection by this approach. Genome binning yielded high-quality E. coli metagenome-assembled genomes (MAGs) for 13 samples, and we observed that the MAG did not carry the diagnostic DEC virulence genes of the corresponding isolate in 60% of these samples. Specifically, two distinct scenarios were observed: diffusely adherent E. coli (DAEC) isolates without corresponding DAEC MAGs appeared to be relatively rare members of the microbiome, which was further corroborated by quantitative PCR (qPCR), and thus unlikely to represent the etiological agent in 3 of the 13 samples (~23%). In contrast, ETEC virulence genes were located on plasmids and largely escaped binning in associated MAGs despite being prevalent in the sample (5/13 samples or ~38%), revealing limitations of the metagenomic approach. These results provide important insights for diagnosing DEC infections and demonstrate how metagenomic methods can complement isolation efforts and PCR for pathogen identification and population abundance. IMPORTANCE Diagnosing enteric infections based on traditional methods involving isolation and PCR can be erroneous due to isolation and other biases, e.g., the most abundant pathogen may not be recovered on isolation media. By employing shotgun metagenomics together with traditional methods on the same stool samples, we show that mixed infections caused by multiple pathogens are much more frequent than traditional methods indicate in the case of acute diarrhea. Further, in at least 8.5% of the total samples examined, the metagenomic approach reliably identified a different pathogen than the traditional approach. Therefore, our results provide a methodology to complement existing methods for enteric infection diagnostics with cutting-edge, culture-independent metagenomic techniques, and highlight the strengths and limitations of each approach.
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Affiliation(s)
- C. Royer
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - N. V. Patin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - K. J. Jesser
- Department of Environmental and Occupational Health, University of Washington, Seattle, Washington, USA
| | - A. Peña-Gonzalez
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotà, Colombia
| | - J. K. Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - G. Trueba
- Institute of Microbiology, Universidad San Francisco de Quito, Quito, Ecuador
| | - K. Levy
- Department of Environmental and Occupational Health, University of Washington, Seattle, Washington, USA
| | - K. T. Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
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49
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de Anda J, Kuchma SL, Webster SS, Boromand A, Lewis KA, Lee CK, Contreras M, Medeiros Pereira VF, Schmidt W, Hogan DA, O’Hern CS, O’Toole GA, Wong GCL. How P. aeruginosa cells with diverse stator composition collectively swarm. mBio 2024; 15:e0332223. [PMID: 38426789 PMCID: PMC11005332 DOI: 10.1128/mbio.03322-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 12/20/2023] [Indexed: 03/02/2024] Open
Abstract
Swarming is a macroscopic phenomenon in which surface bacteria organize into a motile population. The flagellar motor that drives swarming in Pseudomonas aeruginosa is powered by stators MotAB and MotCD. Deletion of the MotCD stator eliminates swarming, whereas deletion of the MotAB stator enhances swarming. Interestingly, we measured a strongly asymmetric stator availability in the wild-type (WT) strain, with MotAB stators produced at an approximately 40-fold higher level than MotCD stators. However, utilization of MotCD stators in free swimming cells requires higher liquid viscosities, while MotAB stators are readily utilized at low viscosities. Importantly, we find that cells with MotCD stators are ~10× more likely to have an active motor compared to cells uses the MotAB stators. The spectrum of motility intermittency can either cooperatively shut down or promote flagellum motility in WT populations. In P. aeruginosa, transition from a static solid-like biofilm to a dynamic liquid-like swarm is not achieved at a single critical value of flagellum torque or stator fraction but is collectively controlled by diverse combinations of flagellum activities and motor intermittencies via dynamic stator utilization. Experimental and computational results indicate that the initiation or arrest of flagellum-driven swarming motility does not occur from individual fitness or motility performance but rather related to concepts from the "jamming transition" in active granular matter.IMPORTANCEIt is now known that there exist multifactorial influences on swarming motility for P. aeruginosa, but it is not clear precisely why stator selection in the flagellum motor is so important. We show differential production and utilization of the stators. Moreover, we find the unanticipated result that the two motor configurations have significantly different motor intermittencies: the fraction of flagellum-active cells in a population on average with MotCD is active ~10× more often than with MotAB. What emerges from this complex landscape of stator utilization and resultant motor output is an intrinsically heterogeneous population of motile cells. We show how consequences of stator recruitment led to swarming motility and how the stators potentially relate to surface sensing circuitry.
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Affiliation(s)
- Jaime de Anda
- Department of Bioengineering, University of California Los Angeles, Los Angeles, California, USA
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, USA
- Department of Microbiology, Immunology & Molecular Genetics, University of California Los Angeles, Los Angeles, California, USA
- California NanoSystems Institute, University of California Los Angeles, Los Angeles, California, USA
| | - Sherry L. Kuchma
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Shanice S. Webster
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Arman Boromand
- Department of Mechanical Engineering & Materials Science, Yale University, New Haven, Connecticut, USA
| | - Kimberley A. Lewis
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Calvin K. Lee
- Department of Bioengineering, University of California Los Angeles, Los Angeles, California, USA
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, USA
- Department of Microbiology, Immunology & Molecular Genetics, University of California Los Angeles, Los Angeles, California, USA
- California NanoSystems Institute, University of California Los Angeles, Los Angeles, California, USA
| | - Maria Contreras
- Department of Bioengineering, University of California Los Angeles, Los Angeles, California, USA
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, USA
- Department of Microbiology, Immunology & Molecular Genetics, University of California Los Angeles, Los Angeles, California, USA
- California NanoSystems Institute, University of California Los Angeles, Los Angeles, California, USA
| | | | - William Schmidt
- Department of Bioengineering, University of California Los Angeles, Los Angeles, California, USA
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, USA
- Department of Microbiology, Immunology & Molecular Genetics, University of California Los Angeles, Los Angeles, California, USA
- California NanoSystems Institute, University of California Los Angeles, Los Angeles, California, USA
| | - Deborah A. Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Corey S. O’Hern
- Department of Mechanical Engineering & Materials Science, Yale University, New Haven, Connecticut, USA
| | - George A. O’Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Gerard C. L. Wong
- Department of Bioengineering, University of California Los Angeles, Los Angeles, California, USA
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, USA
- Department of Microbiology, Immunology & Molecular Genetics, University of California Los Angeles, Los Angeles, California, USA
- California NanoSystems Institute, University of California Los Angeles, Los Angeles, California, USA
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50
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Stewart TA, Lemberg JB, Hillan EJ, Magallanes I, Daeschler EB, Shubin NH. The axial skeleton of Tiktaalik roseae. Proc Natl Acad Sci U S A 2024; 121:e2316106121. [PMID: 38564638 PMCID: PMC11009633 DOI: 10.1073/pnas.2316106121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/30/2023] [Indexed: 04/04/2024] Open
Abstract
The axial columns of the earliest limbed vertebrates show distinct patterns of regionalization as compared to early tetrapodomorphs. Included among their novel features are sacral ribs, which provide linkage between the vertebral column and pelvis, contributing to body support and propulsion by the hindlimb. Data on the axial skeletons of the closest relatives of limbed vertebrates are sparce, with key features of specimens potentially covered by matrix. Therefore, it is unclear in what sequence and under what functional context specializations in the axial skeletons of tetrapods arose. Here, we describe the axial skeleton of the elpistostegalian Tiktaalik roseae and show that transformations to the axial column for head mobility, body support, and pelvic fin buttressing evolved in finned vertebrates prior to the origin of limbs. No atlas-axis complex is observed; however, an independent basioccipital-exoccipital complex suggests increased mobility at the occipital vertebral junction. While the construction of vertebrae in Tiktaalik is similar to early tetrapodomorphs, its ribs possess a specialized sacral domain. Sacral ribs are expanded and ventrally curved, indicating likely attachment to the expanded iliac blade of the pelvis by ligamentous connection. Thus, the origin of novel rib types preceded major alterations to trunk vertebrae, and linkage between pelvic fins and axial column preceded the origin of limbs. These data reveal an unexpected combination of post-cranial skeletal characters, informing hypotheses of body posture and movement in the closest relatives of limbed vertebrates.
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Affiliation(s)
- Thomas A. Stewart
- Department of Biology, The Pennsylvania State University, State College, PA16802
| | - Justin B. Lemberg
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, IL60637
| | - Emily J. Hillan
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, IL60637
| | - Isaac Magallanes
- Committee on Evolutionary Biology, The University of Chicago, Chicago, IL60637
| | - Edward B. Daeschler
- Department of Vertebrate Zoology, Academy of Natural Sciences of Drexel University, Philadelphia, PA19103
| | - Neil H. Shubin
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, IL60637
- Committee on Evolutionary Biology, The University of Chicago, Chicago, IL60637
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