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Si P, Jayanth A, Andreussi O. Soft-sphere continuum solvation models for nonaqueous solvents. J Comput Chem 2024; 45:719-737. [PMID: 38112395 DOI: 10.1002/jcc.27254] [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: 08/31/2023] [Revised: 10/24/2023] [Accepted: 10/30/2023] [Indexed: 12/21/2023]
Abstract
Solvation effects profoundly influence the characteristics and behavior of chemical systems in liquid solutions. The interaction between solute and solvent molecules intricately impacts solubility, reactivity, stability, and various chemical processes. Continuum solvation models gained prominence in quantum chemistry by implicitly capturing these interactions and enabling efficient investigations of diverse chemical systems in solution. In comparison, continuum solvation models in condensed matter simulation are very recent. Among these, the self-consistent continuum solvation (SCCS) and the soft-sphere continuum solvation models (SSCS) have been among the first to be successfully parameterized and extended to model periodic systems in aqueous solutions and electrolytes. As most continuum approaches, these models depend on a number of parameters that are linked to experimental or theoretical properties of the solvent, or that can be tuned based on reference data. Here, we present a systematic parameterization of the SSCS model for over 100 nonaqueous solvents. We validate the model's efficacy across diverse solvent environments by leveraging experimental solvation-free energies and partition coefficients from comprehensive databases. The average root means square error over all the solvents was calculated as 0.85 kcal/mol which is below the chemical accuracy (1 kcal/mol). Similarly to what has been reported by Hille et al. (J. Chem. Phys. 2019, 150, 041710.) for the SCCS model, a single-parameter model accurately reproduces experimental solvation energies, showcasing the transferability and predictive power of these continuum approaches. Our findings underscore the potential for a unified approach to predict solvation properties, paving the way for enhanced computational studies across various chemical environments.
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Affiliation(s)
- Pradip Si
- Department of Chemistry, University of North Texas, Denton, Texas, USA
| | - Ajay Jayanth
- Texas Academy of Math and Science, University of North Texas, Denton, Texas, USA
| | - Oliviero Andreussi
- Department of Chemistry and Biochemistry, Boise State University, Boise, Idaho, USA
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2
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Liu Y, Hogan JA, Lichstein JW, Guralnick RP, Soltis DE, Soltis PS, Scheiner SM. Biodiversity and productivity in eastern US forests. Proc Natl Acad Sci U S A 2024; 121:e2314231121. [PMID: 38527197 DOI: 10.1073/pnas.2314231121] [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: 08/17/2023] [Accepted: 02/06/2024] [Indexed: 03/27/2024] Open
Abstract
Despite experimental and observational studies demonstrating that biodiversity enhances primary productivity, the best metric for predicting productivity at broad geographic extents-functional trait diversity, phylogenetic diversity, or species richness-remains unknown. Using >1.8 million tree measurements from across eastern US forests, we quantified relationships among functional trait diversity, phylogenetic diversity, species richness, and productivity. Surprisingly, functional trait and phylogenetic diversity explained little variation in productivity that could not be explained by tree species richness. This result was consistent across the entire eastern United States, within ecoprovinces, and within data subsets that controlled for biomass or stand age. Metrics of functional trait and phylogenetic diversity that were independent of species richness were negatively correlated with productivity. This last result suggests that processes that determine species sorting and packing are likely important for the relationships between productivity and biodiversity. This result also demonstrates the potential confusion that can arise when interdependencies among different diversity metrics are ignored. Our findings show the value of species richness as a predictive tool and highlight gaps in knowledge about linkages between functional diversity and ecosystem functioning.
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Affiliation(s)
- Yunpeng Liu
- Institute of Ecology, College of Urban and Environmental Sciences, and Key Laboratory of Earth Surface Processes of Ministry of Education, Peking University, Beijing 100871, China
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611
| | - J Aaron Hogan
- Department of Biology, University of Florida, Gainesville, FL 32611
| | | | - Robert P Guralnick
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611
- Genetics Institute, University of Florida, Gainesville, FL 32610
- Biodiversity Institute, University of Florida, Gainesville, FL 32611
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611
- Department of Biology, University of Florida, Gainesville, FL 32611
- Genetics Institute, University of Florida, Gainesville, FL 32610
- Biodiversity Institute, University of Florida, Gainesville, FL 32611
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611
- Genetics Institute, University of Florida, Gainesville, FL 32610
- Biodiversity Institute, University of Florida, Gainesville, FL 32611
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3
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Neikirk K, Stephens DC, Beasley HK, Marshall AG, Gaddy JA, Damo SM, Hinton AO. Considerations for developing mitochondrial transplantation techniques for individualized medicine. Biotechniques 2024; 76:125-134. [PMID: 38420889 DOI: 10.2144/btn-2023-0072] [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] [Indexed: 03/02/2024] Open
Abstract
Tweetable abstract Mitochondrial transplantation has been used to treat various diseases associated with mitochondrial dysfunction. Here, we highlight the considerations in quality control mechanisms that should be considered in the context of mitochondrial transplantation.
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Affiliation(s)
- Kit Neikirk
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Dominique C Stephens
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN 37232, USA
- Department of Life & Physical Sciences, Fisk University, Nashville, TN 37208, USA
| | - Heather K Beasley
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Andrea G Marshall
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Jennifer A Gaddy
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Steven M Damo
- Department of Life & Physical Sciences, Fisk University, Nashville, TN 37208, USA
| | - Antentor O Hinton
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN 37232, USA
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4
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Su H, Hu YH. Gradient Functional Layer Anode for Carbonate-Superstructured Solid Fuel Cells with Ethane Fuel. Small 2024:e2311684. [PMID: 38533989 DOI: 10.1002/smll.202311684] [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] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/14/2024] [Indexed: 03/28/2024]
Abstract
Carbonate-superstructured solid fuel cells (CSSFCs) are an emerging type of fuel cells with high flexibility of fuels. However, using ethane fuel for solid fuel cells is a great challenge due to serious degradation of their anodes. Herein, this critical issue is solved by creating a novel gradient functional layer anode for CSSFCs. First, a finer-scale anode with a larger surface area is demonstrated to provide more active sites for the internal reforming reaction of ethane, achieving a 60% higher ethane conversion rate and 40% lower polarization resistance than conventional anodes. Second, incorporating a gradient functional layer into the anode results in an additional 50% enhancement in the peak power density of CSSFCs to a record high value (up to 241 mW cm-2) with dry ethane fuel at a low temperature of 550 °C, which is even comparable to the power density of conventional solid oxide fuel cells above 700 °C. Furthermore, the CSSFC with the gradient anode exhibits excellent durability for over 200 h. This finding provides a new strategy to develop efficient anodes for hydrocarbon fuels.
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Affiliation(s)
- Hanrui Su
- Department of Materials Science and Engineering, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931-1295, USA
| | - Yun Hang Hu
- Department of Materials Science and Engineering, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931-1295, USA
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5
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Zipple MN, Vogt CC, Sheehan MJ. Genetically identical mice express alternative reproductive tactics depending on social conditions in the field. Proc Biol Sci 2024; 291:20240099. [PMID: 38503332 PMCID: PMC10950460 DOI: 10.1098/rspb.2024.0099] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 02/19/2024] [Indexed: 03/21/2024] Open
Abstract
In many species, establishing and maintaining a territory is critical to survival and reproduction, and an animal's ability to do so is strongly influenced by the presence and density of competitors. Here we manipulate social conditions to study the alternative reproductive tactics displayed by genetically identical, age-matched laboratory mice competing for territories under ecologically realistic social environmental conditions. We introduced adult males and females of the laboratory mouse strain C57BL/6J into a large, outdoor field enclosure containing defendable resource zones under one of two social conditions. We first created a low-density social environment, such that the number of available territories exceeded the number of males. After males established stable territories, we introduced a pulse of intruder males and observed the resulting defensive and invasive tactics employed. In response to this change in social environment, males with large territories invested more in patrolling but were less effective at excluding intruder males as compared with males with small territories. Intruding males failed to establish territories and displayed an alternative tactic featuring greater exploration as compared with genetically identical territorial males. Alternative tactics did not lead to equal reproductive success-males that acquired territories experienced greater survival and had greater access to females.
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Affiliation(s)
- Matthew N. Zipple
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
| | - Caleb C. Vogt
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
| | - Michael J. Sheehan
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
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6
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Li A, Hulleman J, Wolfe JM. Errors in visual search: Are they stochastic or deterministic? Cogn Res Princ Implic 2024; 9:15. [PMID: 38502280 PMCID: PMC10951178 DOI: 10.1186/s41235-024-00543-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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/07/2024] [Indexed: 03/21/2024] Open
Abstract
In any visual search task in the lab or in the world, observers will make errors. Those errors can be categorized as "deterministic": If you miss this target in this display once, you will definitely miss it again. Alternatively, errors can be "stochastic", occurring randomly with some probability from trial to trial. Researchers and practitioners have sought to reduce errors in visual search, but different types of errors might require different techniques for mitigation. To empirically categorize errors in a simple search task, our observers searched for the letter "T" among "L" distractors, with each display presented twice. When the letters were clearly visible (white letters on a gray background), the errors were almost completely stochastic (Exp 1). An error made on the first appearance of a display did not predict that an error would be made on the second appearance. When the visibility of the letters was manipulated (letters of different gray levels on a noisy background), the errors became a mix of stochastic and deterministic. Unsurprisingly, lower contrast targets produced more deterministic errors. (Exp 2). Using the stimuli of Exp 2, we tested whether errors could be reduced using cues that guided attention around the display but knew nothing about the content of that display (Exp3a, b). This had no effect, but cueing all item locations did succeed in reducing deterministic errors (Exp3c).
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Affiliation(s)
- Aoqi Li
- The University of Manchester, Manchester, UK.
| | | | - Jeremy M Wolfe
- Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
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7
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Ding J, Liu R, Wen H, Tang W, Li Z, Venegas J, Su R, Molho D, Jin W, Wang Y, Lu Q, Li L, Zuo W, Chang Y, Xie Y, Tang J. DANCE: a deep learning library and benchmark platform for single-cell analysis. Genome Biol 2024; 25:72. [PMID: 38504331 PMCID: PMC10949782 DOI: 10.1186/s13059-024-03211-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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 03/05/2024] [Indexed: 03/21/2024] Open
Abstract
DANCE is the first standard, generic, and extensible benchmark platform for accessing and evaluating computational methods across the spectrum of benchmark datasets for numerous single-cell analysis tasks. Currently, DANCE supports 3 modules and 8 popular tasks with 32 state-of-art methods on 21 benchmark datasets. People can easily reproduce the results of supported algorithms across major benchmark datasets via minimal efforts, such as using only one command line. In addition, DANCE provides an ecosystem of deep learning architectures and tools for researchers to facilitate their own model development. DANCE is an open-source Python package that welcomes all kinds of contributions.
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Affiliation(s)
- Jiayuan Ding
- Department of Computer Science and Engineering, Michigan State University, East Lansing, USA.
| | - Renming Liu
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, USA
| | - Hongzhi Wen
- Department of Computer Science and Engineering, Michigan State University, East Lansing, USA
| | - Wenzhuo Tang
- Department of Statistics and Probability, Michigan State University, East Lansing, USA
| | - Zhaoheng Li
- Department of Biostatistics, University of Washington, Seattle, USA
| | - Julian Venegas
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, USA
| | - Runze Su
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, USA
- Department of Statistics and Probability, Michigan State University, East Lansing, USA
| | - Dylan Molho
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, USA
| | - Wei Jin
- Department of Computer Science and Engineering, Michigan State University, East Lansing, USA
| | - Yixin Wang
- Department of Bioengineering, Stanford University, Palo Alto, USA
| | - Qiaolin Lu
- School of Artificial Intelligence, Jilin University, Jilin, China
| | - Lingxiao Li
- Department of Computer Science, Boston University, Boston, USA
| | - Wangyang Zuo
- Department of Computer Science, Zhejiang University of Technology, Zhejiang, China
| | - Yi Chang
- School of Artificial Intelligence, Jilin University, Jilin, China
| | - Yuying Xie
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, USA.
- Department of Statistics and Probability, Michigan State University, East Lansing, USA.
| | - Jiliang Tang
- Department of Computer Science and Engineering, Michigan State University, East Lansing, USA.
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8
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Armour KC, Proistosescu C, Dong Y, Hahn LC, Blanchard-Wrigglesworth E, Pauling AG, Jnglin Wills RC, Andrews T, Stuecker MF, Po-Chedley S, Mitevski I, Forster PM, Gregory JM. Sea-surface temperature pattern effects have slowed global warming and biased warming-based constraints on climate sensitivity. Proc Natl Acad Sci U S A 2024; 121:e2312093121. [PMID: 38466843 PMCID: PMC10962993 DOI: 10.1073/pnas.2312093121] [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: 07/17/2023] [Accepted: 12/15/2023] [Indexed: 03/13/2024] Open
Abstract
The observed rate of global warming since the 1970s has been proposed as a strong constraint on equilibrium climate sensitivity (ECS) and transient climate response (TCR)-key metrics of the global climate response to greenhouse-gas forcing. Using CMIP5/6 models, we show that the inter-model relationship between warming and these climate sensitivity metrics (the basis for the constraint) arises from a similarity in transient and equilibrium warming patterns within the models, producing an effective climate sensitivity (EffCS) governing recent warming that is comparable to the value of ECS governing long-term warming under CO[Formula: see text] forcing. However, CMIP5/6 historical simulations do not reproduce observed warming patterns. When driven by observed patterns, even high ECS models produce low EffCS values consistent with the observed global warming rate. The inability of CMIP5/6 models to reproduce observed warming patterns thus results in a bias in the modeled relationship between recent global warming and climate sensitivity. Correcting for this bias means that observed warming is consistent with wide ranges of ECS and TCR extending to higher values than previously recognized. These findings are corroborated by energy balance model simulations and coupled model (CESM1-CAM5) simulations that better replicate observed patterns via tropospheric wind nudging or Antarctic meltwater fluxes. Because CMIP5/6 models fail to simulate observed warming patterns, proposed warming-based constraints on ECS, TCR, and projected global warming are biased low. The results reinforce recent findings that the unique pattern of observed warming has slowed global-mean warming over recent decades and that how the pattern will evolve in the future represents a major source of uncertainty in climate projections.
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Affiliation(s)
- Kyle C. Armour
- Department of Atmospheric Sciences, University of Washington, Seattle, WA98195
- School of Oceanography, University of Washington, Seattle, WA98195
| | - Cristian Proistosescu
- Department of Climate, Meteorology, and Atmospheric Sciences, University of Illinois, Urbana-Champaign, Champaign, IL61801
- Department of Earth Sciences and Environmental Change, University of Illinois, Urbana-Champaign, Champaign, IL61801
| | - Yue Dong
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO80309
| | - Lily C. Hahn
- Scripps Institution of Oceanography, La Jolla, CA92093
| | | | | | - Robert C. Jnglin Wills
- Department of Atmospheric Sciences, University of Washington, Seattle, WA98195
- Institute for Atmospheric and Climate Science, ETH Zurich, Zurich, CH8092
| | | | - Malte F. Stuecker
- Department of Oceanography and International Pacific Research Center, School of Ocean and Earth Science and Technology, University of Hawai’i at Mānoa, Honolulu, HI96822
| | - Stephen Po-Chedley
- Program for Climate Model Diagnosis and Intercomparison, Lawrence Livermore National Laboratory, Livermore, CA94550
| | - Ivan Mitevski
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY10027
| | - Piers M. Forster
- Priestley International Centre for Climate, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Jonathan M. Gregory
- Met Office Hadley Centre, ExeterEX1 3PB, United Kingdom
- National Centre for Atmospheric Science, University of Reading, ReadingRG6 6ET, United Kingdom
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9
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Samudrala K, Akram MO, Dutton JL, Martin CD, Conley MP. Formation of Strong Boron Lewis Acid Sites on Silica. Inorg Chem 2024; 63:4939-4946. [PMID: 38451151 PMCID: PMC10951953 DOI: 10.1021/acs.inorgchem.3c04121] [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: 11/21/2023] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 03/08/2024]
Abstract
Bis(1-methyl-ortho-carboranyl)borane (HBMeoCb2) is a very strong Lewis acid that reacts with the isolated silanols present on silica partially dehydroxylated at 700 °C (SiO2-700) to form the well-defined Lewis site MeoCb2B(OSi≡) (1) and H2. 11B{1H} magic-angle spinning (MAS) nuclear magnetic resonance (NMR) data of 1 are consistent with that of a three-coordinate boron site. Contacting 1 with O═PEt3 (triethylphosphine oxide TEPO) and measuring 31P{1H} MAS NMR spectra show that 1 preserves the strong Lewis acidity of HBMeoCb2. Hydride ion affinity and fluoride ion affinity calculations using small molecules analogs of 1 also support the strong Lewis acidity of the boron sites in this material. Reactions of 1 with Cp2Hf(13CH3)2 show that the Lewis sites are capable of abstracting methide groups from Hf to form [Cp2Hf-13CH3][H313C-B(MeoCb2)OSi≡], but with a low overall efficiency.
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Affiliation(s)
| | - Manjur O. Akram
- Department
of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Jason L. Dutton
- Department
of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Caleb D. Martin
- Department
of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Matthew P. Conley
- Department
of Chemistry, University of California, Riverside, California 92521, United States
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10
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Pourshaban E, Karkhanis MU, Deshpande A, Banerjee A, Hasan MR, Nikeghbal A, Ghosh C, Kim H, Mastrangelo CH. Power Scavenging Microsystem for Smart Contact Lenses. Small 2024:e2401068. [PMID: 38477701 DOI: 10.1002/smll.202401068] [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] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 03/02/2024] [Indexed: 03/14/2024]
Abstract
On-the-eye microsystems such as smart contacts for vision correction, health monitoring, drug delivery, and displaying information represent a new emerging class of low-profile (≤ 1 mm) wireless microsystems that conform to the curvature of the eyeball surface. The implementation of suitable low-profile power sources for eye-based microsystems on curved substrates is a major technical challenge addressed in this paper. The fabrication and characterization of a hybrid energy generation unit composed of a flexible silicon solar cell and eye-blinking activated Mg-O2 metal-air harvester capable of sustainably supplying electrical power to smart ocular devices are reported. The encapsulated photovoltaic device provides a DC output with a power density of 42.4 µW cm-2 and 2.5 mW cm-2 under indoor and outdoor lighting conditions, respectively. The eye-blinking activated Mg-air harvester delivers pulsed power output with a maximum power density of 1.3 mW cm-2 . A power management circuit with an integrated 11 mF supercapacitor is used to convert the harvesters' pulsed voltages to DC, boost up the voltages, and continuously deliver ≈150 µW at a stable 3.3 V DC output. Uniquely, in contrast to wireless power transfer, the power pack continuously generates electric power and does not require any type of external accessories for operation.
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Affiliation(s)
- Erfan Pourshaban
- Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, UT, 84112, USA
| | - Mohit U Karkhanis
- Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, UT, 84112, USA
| | - Adwait Deshpande
- Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, UT, 84112, USA
| | - Aishwaryadev Banerjee
- Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, UT, 84112, USA
| | - Md Rabiul Hasan
- Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, UT, 84112, USA
| | - Amirali Nikeghbal
- Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, UT, 84112, USA
| | - Chayanjit Ghosh
- Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, UT, 84112, USA
| | - Hanseup Kim
- Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, UT, 84112, USA
| | - Carlos H Mastrangelo
- Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, UT, 84112, USA
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11
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Dube DK, Dube S, Shi H, Benz P, Randhawa S, Fan Y, Wang J, Ma Z, Sanger JW, Sanger JM, Poiesz BJ. Sarcomeric tropomyosin expression during human iPSC differentiation into cardiomyocytes. Cytoskeleton (Hoboken) 2024. [PMID: 38470291 DOI: 10.1002/cm.21850] [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: 11/15/2023] [Revised: 01/31/2024] [Accepted: 02/21/2024] [Indexed: 03/13/2024]
Abstract
Tropomyosin (TPM) is an essential sarcomeric component, stabilizing the thin filament and facilitating actin's interaction with myosin. In mammals, including humans, there are four TPM genes (TPM1, TPM2, TPM3, and TPM4) each of which generates a multitude of TPM isoforms via alternative splicing and using different promoters. In this study, we have examined the expression of transcripts as well as proteins of various sarcomeric TPM isoforms during human inducible pluripotent stem cell differentiation into cardiomyocytes. During the differentiation time course, we harvested cells on Days 0, 5, 10, 15, and 20 to analyze for various sarcomeric TPM transcripts by qRT-PCR and for sarcomeric TPM proteins using two-dimensional Western blot with sarcomeric TPM-specific CH1 monoclonal antibody followed by mass spectra analyses. Our results show increasing levels of total TPM transcripts and proteins during the period of differentiation, but varying levels of specific TPM isoforms during the same period. By Day 20, the rank order of TPM transcripts was TPM1α > TPM1κ > TPM2α > TPM1μ > TPM3α > TPM4α. TPM1α was the dominant protein produced with some TPM2 and much less TPM1κ and μ. Interestingly, small amounts of two lower molecular weight TPM3 isoforms were detected on Day 15. To the best of our knowledge this is the first demonstration of TPM1μ non-muscle isoform protein expression before and during cardiac differentiation.
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Affiliation(s)
- Dipak K Dube
- Department of Medicine, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Syamalima Dube
- Department of Medicine, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Huaiyu Shi
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York, USA
| | - Patricia Benz
- Department of Medicine, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Samender Randhawa
- Department of Medicine, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Yingli Fan
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Jusuo Wang
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Zhen Ma
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York, USA
| | - Joseph W Sanger
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Jean M Sanger
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Bernard J Poiesz
- Department of Medicine, SUNY Upstate Medical University, Syracuse, New York, USA
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12
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Roy K, Rana A, Heil JN, Tackett BM, Dick JE. For Zinc Metal Batteries, How Many Electrons go to Hydrogen Evolution? An Electrochemical Mass Spectrometry Study. Angew Chem Int Ed Engl 2024; 63:e202319010. [PMID: 38168077 DOI: 10.1002/anie.202319010] [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: 12/10/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 01/05/2024]
Abstract
Despite the advantages of aqueous zinc (Zn) metal batteries (AZMB) like high specific capacity (820 mAh g-1 and 5,854 mAh cm-3 ), low redox potential (-0.76 V vs. the standard hydrogen electrode), low cost, water compatibility, and safety, the development of practically relevant batteries is plagued by several issues like unwanted hydrogen evolution reaction (HER), corrosion of Zn substrate (insulating ZnO, Zn(OH)2 , Zn(SO4 )x (OH)y , Zn(ClO4 )x (OH)y etc. passivation layer), and dendrite growth. Controlling and suppressing HER activity strongly correlates with the long-term cyclability of AZMBs. Therefore, a precise quantitative technique is needed to monitor the real-time dynamics of hydrogen evolution during Zn electrodeposition. In this study, we quantify hydrogen evolution using in situ electrochemical mass spectrometry (ECMS). This methodology enables us to determine a correction factor for the faradaic efficiency of this system with unmatched precision. For instance, during the electrodeposition of zinc on a copper substrate at a current density of 1.5 mA/cm2 for 600 seconds, 0.3 % of the total charge is attributed to HER, while the rest contributes to zinc electrodeposition. At first glance, this may seem like a small fraction, but it can be detrimental to the long-term cycling performance of AZMBs. Furthermore, our results provide insights into the correlation between HER and the porous morphology of the electrodeposited zinc, unravelling the presence of trapped H2 and Zn corrosion during the charging process. Overall, this study sets a platform to accurately determine the faradaic efficiency of Zn electrodeposition and provides a powerful tool for evaluating electrolyte additives, salts, and electrode modifications aimed at enhancing long-term stability and suppressing the HER in aqueous Zn batteries.
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Affiliation(s)
- Kingshuk Roy
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Ashutosh Rana
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Joseph N Heil
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Brian M Tackett
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Jeffrey E Dick
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
- Elmore Family School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN 47907, USA
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13
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Sigmund LM, S SS, Albers A, Erdmann P, Paton RS, Greb L. Predicting Lewis Acidity: Machine Learning the Fluoride Ion Affinity of p-Block-Atom-Based Molecules. Angew Chem Int Ed Engl 2024:e202401084. [PMID: 38452299 DOI: 10.1002/anie.202401084] [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: 01/19/2024] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024]
Abstract
"How strong is this Lewis acid?" is a question researchers often approach by calculating its fluoride ion affinity (FIA) with quantum chemistry. Here, we present FIA49k, an extensive FIA dataset with 48,986 data points calculated at the RI-DSD-BLYP-D3(BJ)/def2-QZVPP//PBEh-3c level of theory, including 13 different p-block atoms as the fluoride accepting site. The FIA49k dataset was used to train FIA-GNN, two message-passing graph neural networks, which predict gas and solution phase FIA values of molecules excluded from training with a mean absolute error of 14 kJ mol-1 (r2 =0.93) from the SMILES string of the Lewis acid as the only input. The level of accuracy is notable, given the wide energetic range of 750 kJ mol-1 spanned by FIA49k. The model's value was demonstrated with four case studies, including predictions for molecules extracted from the Cambridge Structural Database and by reproducing results from catalysis research available in the literature. Weaknesses of the model are evaluated and interpreted chemically. FIA-GNN and the FIA49k dataset can be reached via a free web app (www.grebgroup.de/fia-gnn).
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Affiliation(s)
- Lukas M Sigmund
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
- Department of Chemistry, Colorado State University, 1301 Center Avenue, Fort Collins, CO, 80523, USA
| | - Shree Sowndarya S
- Department of Chemistry, Colorado State University, 1301 Center Avenue, Fort Collins, CO, 80523, USA
| | - Andreas Albers
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Philipp Erdmann
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Robert S Paton
- Department of Chemistry, Colorado State University, 1301 Center Avenue, Fort Collins, CO, 80523, USA
| | - Lutz Greb
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
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14
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Yocca A, Akinyuwa M, Bailey N, Cliver B, Estes H, Guillemette A, Hasannin O, Hutchison J, Jenkins W, Kaur I, Khanna RR, Loftin M, Lopes L, Moore-Pollard E, Olofintila O, Oyebode GO, Patel J, Thapa P, Waldinger M, Zhang J, Zhang Q, Goertzen L, Carey SB, Hargarten H, Mattheis J, Zhang H, Jones T, Boston L, Grimwood J, Ficklin S, Honaas L, Harkess A. A chromosome-scale assembly for 'd'Anjou' pear. G3 (Bethesda) 2024; 14:jkae003. [PMID: 38190814 PMCID: PMC10917493 DOI: 10.1093/g3journal/jkae003] [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] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 07/27/2023] [Accepted: 12/01/2023] [Indexed: 01/10/2024]
Abstract
Cultivated pear consists of several Pyrus species with Pyrus communis (European pear) representing a large fraction of worldwide production. As a relatively recently domesticated crop and perennial tree, pear can benefit from genome-assisted breeding. Additionally, comparative genomics within Rosaceae promises greater understanding of evolution within this economically important family. Here, we generate a fully phased chromosome-scale genome assembly of P. communis 'd'Anjou.' Using PacBio HiFi and Dovetail Omni-C reads, the genome is resolved into the expected 17 chromosomes, with each haplotype totaling nearly 540 Megabases and a contig N50 of nearly 14 Mb. Both haplotypes are highly syntenic to each other and to the Malus domestica 'Honeycrisp' apple genome. Nearly 45,000 genes were annotated in each haplotype, over 90% of which have direct RNA-seq expression evidence. We detect signatures of the known whole-genome duplication shared between apple and pear, and we estimate 57% of d'Anjou genes are retained in duplicate derived from this event. This genome highlights the value of generating phased diploid assemblies for recovering the full allelic complement in highly heterozygous crop species.
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Affiliation(s)
- Alan Yocca
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Mary Akinyuwa
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA
| | - Nick Bailey
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Brannan Cliver
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Harrison Estes
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA
| | | | - Omar Hasannin
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Jennifer Hutchison
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Wren Jenkins
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Ishveen Kaur
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | | | - Madelene Loftin
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Lauren Lopes
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Erika Moore-Pollard
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152-3530, USA
| | | | | | - Jinesh Patel
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Parbati Thapa
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA
| | - Martin Waldinger
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Jie Zhang
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Qiong Zhang
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Leslie Goertzen
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Sarah B Carey
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Heidi Hargarten
- Physiology and Pathology of Tree Fruits Research Laboratory, USDA ARS, Wenatchee, WA 98801, USA
| | - James Mattheis
- Physiology and Pathology of Tree Fruits Research Laboratory, USDA ARS, Wenatchee, WA 98801, USA
| | - Huiting Zhang
- Physiology and Pathology of Tree Fruits Research Laboratory, USDA ARS, Wenatchee, WA 98801, USA
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Teresa Jones
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - LoriBeth Boston
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Stephen Ficklin
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Loren Honaas
- Physiology and Pathology of Tree Fruits Research Laboratory, USDA ARS, Wenatchee, WA 98801, USA
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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15
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Massaro I, Poethig RS, Sinha NR, Leichty AR. Chromosome-level genome of the tra nsformable northern wattle, Acacia crassicarpa. G3 (Bethesda) 2024; 14:jkad284. [PMID: 38096217 PMCID: PMC10917515 DOI: 10.1093/g3journal/jkad284] [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] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/01/2023] [Indexed: 03/08/2024]
Abstract
The genus Acacia is a large group of woody legumes containing an enormous amount of morphological diversity in leaf shape. This diversity is at least in part the result of an innovation in leaf development where many Acacia species are capable of developing leaves of both bifacial and unifacial morphologies. While not unique in the plant kingdom, unifaciality is most commonly associated with monocots, and its developmental genetic mechanisms have yet to be explored beyond this group. In this study, we identify an accession of Acacia crassicarpa with high regeneration rates and isolate a clone for genome sequencing. We generate a chromosome-level assembly of this readily transformable clone, and using comparative analyses, confirm a whole-genome duplication unique to Caesalpinoid legumes. This resource will be important for future work examining genome evolution in legumes and the unique developmental genetic mechanisms underlying unifacial morphogenesis in Acacia.
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Affiliation(s)
- Isabelle Massaro
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | | | - Neelima R Sinha
- Department of Plant Biology, University of California Davis, Davis, CA 95616, USA
| | - Aaron R Leichty
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Plant Biology, University of California Davis, Davis, CA 95616, USA
- USDA Plant Gene Expression Center, 800 Buchanan Street, Albany, CA 94710, USA
- 800 Buchanan Street, Albany, CA 94710, USA
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16
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Dunton KL, Hedrick NG, Meamardoost S, Ren C, Howe JR, Wang J, Root CM, Gunawan R, Komiyama T, Zhang Y, Hwang EJ. Divergent Learning-Related Transcriptional States of Cortical Glutamatergic Neurons. J Neurosci 2024; 44:e0302232023. [PMID: 38238073 PMCID: PMC10919205 DOI: 10.1523/jneurosci.0302-23.2023] [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: 03/09/2023] [Revised: 09/30/2023] [Accepted: 11/10/2023] [Indexed: 03/08/2024] Open
Abstract
Experience-dependent gene expression reshapes neural circuits, permitting the learning of knowledge and skills. Most learning involves repetitive experiences during which neurons undergo multiple stages of functional and structural plasticity. Currently, the diversity of transcriptional responses underlying dynamic plasticity during repetition-based learning is poorly understood. To close this gap, we analyzed single-nucleus transcriptomes of L2/3 glutamatergic neurons of the primary motor cortex after 3 d motor skill training or home cage control in water-restricted male mice. "Train" and "control" neurons could be discriminated with high accuracy based on expression patterns of many genes, indicating that recent experience leaves a widespread transcriptional signature across L2/3 neurons. These discriminating genes exhibited divergent modes of coregulation, differentiating neurons into discrete clusters of transcriptional states. Several states showed gene expressions associated with activity-dependent plasticity. Some of these states were also prominent in the previously published reference, suggesting that they represent both spontaneous and task-related plasticity events. Markedly, however, two states were unique to our dataset. The first state, further enriched by motor training, showed gene expression suggestive of late-stage plasticity with repeated activation, which is suitable for expected emergent neuronal ensembles that stably retain motor learning. The second state, equally found in both train and control mice, showed elevated levels of metabolic pathways and norepinephrine sensitivity, suggesting a response to common experiences specific to our experimental conditions, such as water restriction or circadian rhythm. Together, we uncovered divergent transcriptional responses across L2/3 neurons, each potentially linked with distinct features of repetition-based motor learning such as plasticity, memory, and motivation.
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Affiliation(s)
- Katie L Dunton
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston 02881, Rhode Island
| | - Nathan G Hedrick
- Department of Neurobiology, Center for Neural Circuits and Behavior, Department of Neurosciences, and Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla 92093, California
| | - Saber Meamardoost
- Department of Chemical and Biological Engineering, University at Buffalo-SUNY, Buffalo 14260, New York
| | - Chi Ren
- Department of Neurobiology, Center for Neural Circuits and Behavior, Department of Neurosciences, and Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla 92093, California
| | - James R Howe
- Department of Neurobiology, School of Biological Sciences, University of California San Diego, La Jolla 92093, California
- Neurosciences Graduate Program, University of California San Diego, La Jolla 92093, California
| | - Jing Wang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston 02881, Rhode Island
| | - Cory M Root
- Department of Neurobiology, School of Biological Sciences, University of California San Diego, La Jolla 92093, California
| | - Rudiyanto Gunawan
- Department of Chemical and Biological Engineering, University at Buffalo-SUNY, Buffalo 14260, New York
| | - Takaki Komiyama
- Department of Neurobiology, Center for Neural Circuits and Behavior, Department of Neurosciences, and Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla 92093, California
| | - Ying Zhang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston 02881, Rhode Island
| | - Eun Jung Hwang
- Department of Neurobiology, Center for Neural Circuits and Behavior, Department of Neurosciences, and Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla 92093, California
- Cell Biology and Anatomy, Chicago Medical School, Stanson Toshok Center for Brain Function and Repair, Rosalind Franklin University of Medicine and Science, North Chicago 60064, Illinois
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17
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Ostevik KL, Alabady M, Zhang M, Rausher MD. Whole-genome sequence and annotation of Penstemon davidsonii. G3 (Bethesda) 2024; 14:jkad296. [PMID: 38155402 PMCID: PMC10917496 DOI: 10.1093/g3journal/jkad296] [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] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/30/2023]
Abstract
Penstemon is the most speciose flowering plant genus endemic to North America. Penstemon species' diverse morphology and adaptation to various environments have made them a valuable model system for studying evolution. Here, we report the first full reference genome assembly and annotation for Penstemon davidsonii. Using PacBio long-read sequencing and Hi-C scaffolding technology, we constructed a de novo reference genome of 437,568,744 bases, with a contig N50 of 40 Mb and L50 of 5. The annotation includes 18,199 gene models, and both the genome and transcriptome assembly contain over 95% complete eudicot BUSCOs. This genome assembly will serve as a valuable reference for studying the evolutionary history and genetic diversity of the Penstemon genus.
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Affiliation(s)
- Kate L Ostevik
- Department of Evolution, Ecology, and Organismal Biology, University of California Riverside, Riverside, CA 92521, USA
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Magdy Alabady
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Mengrui Zhang
- Department of Statistics, University of Georgia, Athens, GA 30602, USA
| | - Mark D Rausher
- Department of Biology, Duke University, Durham, NC 27708, USA
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18
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Haase MAB, Steenwyk JL, Boeke JD. Gene loss and cis-regulatory novelty shaped core histone gene evolution in the apiculate yeast Hanseniaspora uvarum. Genetics 2024; 226:iyae008. [PMID: 38271560 PMCID: PMC10917516 DOI: 10.1093/genetics/iyae008] [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: 08/28/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
Core histone genes display a remarkable diversity of cis-regulatory mechanisms despite their protein sequence conservation. However, the dynamics and significance of this regulatory turnover are not well understood. Here, we describe the evolutionary history of core histone gene regulation across 400 million years in budding yeasts. We find that canonical mode of core histone regulation-mediated by the trans-regulator Spt10-is ancient, likely emerging between 320 and 380 million years ago and is fixed in the majority of extant species. Unexpectedly, we uncovered the emergence of a novel core histone regulatory mode in the Hanseniaspora genus, from its fast-evolving lineage, which coincided with the loss of 1 copy of its paralogous core histone genes. We show that the ancestral Spt10 histone regulatory mode was replaced, via cis-regulatory changes in the histone control regions, by a derived Mcm1 histone regulatory mode and that this rewiring event occurred with no changes to the trans-regulator, Mcm1, itself. Finally, we studied the growth dynamics of the cell cycle and histone synthesis in genetically modified Hanseniaspora uvarum. We find that H. uvarum divides rapidly, with most cells completing a cell cycle within 60 minutes. Interestingly, we observed that the regulatory coupling between histone and DNA synthesis was lost in H. uvarum. Our results demonstrate that core histone gene regulation was fixed anciently in budding yeasts, however it has greatly diverged in the Hanseniaspora fast-evolving lineage.
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Affiliation(s)
- Max A B Haase
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, 435 E 30th St, New York, NY 10016, USA
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Jacob L Steenwyk
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, 435 E 30th St, New York, NY 10016, USA
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19
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Guo S, Cui H, Agarwal T, Zhang LG. Nanomaterials in 4D Printing: Expanding the Frontiers of Advanced Manufacturing. Small 2024:e2307750. [PMID: 38431939 DOI: 10.1002/smll.202307750] [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] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 02/15/2024] [Indexed: 03/05/2024]
Abstract
As an innovative technology, four-dimentional (4D) printing is built upon the principles of three-dimentional (3D) printing with an additional dimension: time. While traditional 3D printing creates static objects, 4D printing generates "responsive 3D printed structures", enabling them to transform or self-assemble in response to external stimuli. Due to the dynamic nature, 4D printing has demonstrated tremendous potential in a range of industries, encompassing aerospace, healthcare, and intelligent devices. Nanotechnology has gained considerable attention owing to the exceptional properties and functions of nanomaterials. Incorporating nanomaterials into an intelligent matrix enhances the physiochemical properties of 4D printed constructs, introducing novel functions. This review provides a comprehensive overview of current applications of nanomaterials in 4D printing, exploring their synergistic potential to create dynamic and responsive structures. Nanomaterials play diverse roles as rheology modifiers, mechanical enhancers, function introducers, and more. The overarching goal of this review is to inspire researchers to delve into the vast potential of nanomaterial-enabled 4D printing, propelling advancements in this rapidly evolving field.
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Affiliation(s)
- Shengbo Guo
- Department of Mechanical and Aerospace Engineering, The George Washington University, Washington, DC, 20052, USA
| | - Haitao Cui
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Tarun Agarwal
- Department of Mechanical and Aerospace Engineering, The George Washington University, Washington, DC, 20052, USA
| | - Lijie Grace Zhang
- Department of Mechanical and Aerospace Engineering, The George Washington University, Washington, DC, 20052, USA
- Department of Electrical Engineering, The George Washington University, Washington, DC, 20052, USA
- Department of Biomedical Engineering, The George Washington University, Washington, DC, 20052, USA
- Department of Medicine, The George Washington University, Washington, DC, 20052, USA
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20
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Abstract
In recent decades, origami has been explored to aid in the design of engineering structures. These structures span multiple scales and have been demonstrated to be used toward various areas such as aerospace, metamaterial, biomedical, robotics, and architectural applications. Conventionally, origami or deployable structures have been actuated by hands, motors, or pneumatic actuators, which can result in heavy or bulky structures. On the other hand, active materials, which reconfigure in response to external stimulus, eliminate the need for external mechanical loads and bulky actuation systems. Thus, in recent years, active materials incorporated with deployable structures have shown promise for remote actuation of light weight, programmable origami. In this review, active materials such as shape memory polymers (SMPs) and alloys (SMAs), hydrogels, liquid crystal elastomers (LCEs), magnetic soft materials (MSMs), and covalent adaptable network (CAN) polymers, their actuation mechanisms, as well as how they have been utilized for active origami and where these structures are applicable is discussed. Additionally, the state-of-the-art fabrication methods to construct active origami are highlighted. The existing structural modeling strategies for origami, the constitutive models used to describe active materials, and the largest challenges and future directions for active origami research are summarized.
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Affiliation(s)
- Sophie Leanza
- Department of Mechanical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Shuai Wu
- Department of Mechanical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Xiaohao Sun
- The George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - H Jerry Qi
- The George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Ruike Renee Zhao
- Department of Mechanical Engineering, Stanford University, Stanford, CA, 94305, USA
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21
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Mehrab Z, Stundal L, Venkatramanan S, Swarup S, Lewis B, Mortveit HS, Barrett CL, Pandey A, Wells CR, Galvani AP, Singer BH, Leblang D, Colwell RR, Marathe MV. An agent-based framework to study forced migration: A case study of Ukraine. PNAS Nexus 2024; 3:pgae080. [PMID: 38505694 PMCID: PMC10949908 DOI: 10.1093/pnasnexus/pgae080] [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] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 02/06/2024] [Indexed: 03/21/2024]
Abstract
The ongoing Russian aggression against Ukraine has forced over eight million people to migrate out of Ukraine. Understanding the dynamics of forced migration is essential for policy-making and for delivering humanitarian assistance. Existing work is hindered by a reliance on observational data which is only available well after the fact. In this work, we study the efficacy of a data-driven agent-based framework motivated by social and behavioral theory in predicting outflow of migrants as a result of conflict events during the initial phase of the Ukraine war. We discuss policy use cases for the proposed framework by demonstrating how it can leverage refugee demographic details to answer pressing policy questions. We also show how to incorporate conflict forecast scenarios to predict future conflict-induced migration flows. Detailed future migration estimates across various conflict scenarios can both help to reduce policymaker uncertainty and improve allocation and staging of limited humanitarian resources in crisis settings.
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Affiliation(s)
- Zakaria Mehrab
- Biocomplexity Institute & Initiative, University of Virginia, Charlottesville, VA 22904, USA
- Department of Computer Science, University of Virginia, Charlottesville, VA 22904, USA
| | - Logan Stundal
- Biocomplexity Institute & Initiative, University of Virginia, Charlottesville, VA 22904, USA
- Department of Political Science, University of Virginia, Charlottesville, VA 22904, USA
| | | | - Samarth Swarup
- Biocomplexity Institute & Initiative, University of Virginia, Charlottesville, VA 22904, USA
| | - Bryan Lewis
- Biocomplexity Institute & Initiative, University of Virginia, Charlottesville, VA 22904, USA
| | - Henning S Mortveit
- Biocomplexity Institute & Initiative, University of Virginia, Charlottesville, VA 22904, USA
- Department of Systems and Information Engineering, University of Virginia, Charlottesville, VA 22904, USA
| | - Christopher L Barrett
- Biocomplexity Institute & Initiative, University of Virginia, Charlottesville, VA 22904, USA
- Department of Computer Science, University of Virginia, Charlottesville, VA 22904, USA
| | - Abhishek Pandey
- Center for Infectious Disease Modeling and Analysis, Yale School of Public Health, New Haven, CT 06520, USA
| | - Chad R Wells
- Center for Infectious Disease Modeling and Analysis, Yale School of Public Health, New Haven, CT 06520, USA
| | - Alison P Galvani
- Center for Infectious Disease Modeling and Analysis, Yale School of Public Health, New Haven, CT 06520, USA
| | - Burton H Singer
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA
| | - David Leblang
- Department of Political Science, University of Virginia, Charlottesville, VA 22904, USA
| | - Rita R Colwell
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
| | - Madhav V Marathe
- Biocomplexity Institute & Initiative, University of Virginia, Charlottesville, VA 22904, USA
- Department of Computer Science, University of Virginia, Charlottesville, VA 22904, USA
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22
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Jiang Y, Deane CM, Morris GM, O’Brien EP. It is theoretically possible to avoid misfolding into non-covalent lasso entanglements using small molecule drugs. PLoS Comput Biol 2024; 20:e1011901. [PMID: 38470915 PMCID: PMC10931463 DOI: 10.1371/journal.pcbi.1011901] [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: 09/07/2023] [Accepted: 02/08/2024] [Indexed: 03/14/2024] Open
Abstract
A novel class of protein misfolding characterized by either the formation of non-native noncovalent lasso entanglements in the misfolded structure or loss of native entanglements has been predicted to exist and found circumstantial support through biochemical assays and limited-proteolysis mass spectrometry data. Here, we examine whether it is possible to design small molecule compounds that can bind to specific folding intermediates and thereby avoid these misfolded states in computer simulations under idealized conditions (perfect drug-binding specificity, zero promiscuity, and a smooth energy landscape). Studying two proteins, type III chloramphenicol acetyltransferase (CAT-III) and D-alanyl-D-alanine ligase B (DDLB), that were previously suggested to form soluble misfolded states through a mechanism involving a failure-to-form of native entanglements, we explore two different drug design strategies using coarse-grained structure-based models. The first strategy, in which the native entanglement is stabilized by drug binding, failed to decrease misfolding because it formed an alternative entanglement at a nearby region. The second strategy, in which a small molecule was designed to bind to a non-native tertiary structure and thereby destabilize the native entanglement, succeeded in decreasing misfolding and increasing the native state population. This strategy worked because destabilizing the entanglement loop provided more time for the threading segment to position itself correctly to be wrapped by the loop to form the native entanglement. Further, we computationally identified several FDA-approved drugs with the potential to bind these intermediate states and rescue misfolding in these proteins. This study suggests it is possible for small molecule drugs to prevent protein misfolding of this type.
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Affiliation(s)
- Yang Jiang
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Charlotte M. Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles’ Oxford, OX1 3LB United Kingdom
| | - Garrett M. Morris
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles’ Oxford, OX1 3LB United Kingdom
| | - Edward P. O’Brien
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Institute for Computational and Data Sciences, Pennsylvania State University, University Park, Pennsylvania, United States of America
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23
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Niefind F, Mao Q, Nayir N, Kowalik M, Ahn JJ, Winchester AJ, Dong C, Maniyara RA, Robinson JA, van Duin ACT, Pookpanratana S. Watching (De)Intercalation of 2D Metals in Epitaxial Graphene: Insight into the Role of Defects. Small 2024; 20:e2306554. [PMID: 37919862 DOI: 10.1002/smll.202306554] [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] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/06/2023] [Indexed: 11/04/2023]
Abstract
Intercalation forms heterostructures, and over 25 elements and compounds are intercalated into graphene, but the mechanism for this process is not well understood. Here, the de-intercalation of 2D Ag and Ga metals sandwiched between bilayer graphene and SiC are followed using photoemission electron microscopy (PEEM) and atomistic-scale reactive molecular dynamics simulations. By PEEM, de-intercalation "windows" (or defects) are observed in both systems, but the processes follow distinctly different dynamics. Reversible de- and re-intercalation of Ag is observed through a circular defect where the intercalation velocity front is 0.5 nm s-1 ± 0.2 nm s.-1 In contrast, the de-intercalation of Ga is irreversible with faster kinetics that are influenced by the non-circular shape of the defect. Molecular dynamics simulations support these pronounced differences and complexities between the two Ag and Ga systems. In the de-intercalating Ga model, Ga atoms first pile up between graphene layers until ultimately moving to the graphene surface. The simulations, supported by density functional theory, indicate that the Ga atoms exhibit larger binding strength to graphene, which agrees with the faster and irreversible diffusion kinetics observed. Thus, both the thermophysical properties of the metal intercalant and its interaction with defective graphene play a key role in intercalation.
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Affiliation(s)
- Falk Niefind
- Nanoscale Device Characterization Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
- Department of Chemistry & Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Qian Mao
- Department of Mechanical Engineering, Pennsylvania State University, University Park, PA, 16802, USA
| | - Nadire Nayir
- Department of Mechanical Engineering, Pennsylvania State University, University Park, PA, 16802, USA
- Department of Physics, Karamanoglu Mehmetbey University, Karaman, 70000, Turkey
| | - Malgorzata Kowalik
- Department of Mechanical Engineering, Pennsylvania State University, University Park, PA, 16802, USA
| | - Jung-Joon Ahn
- Nanoscale Device Characterization Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
- Department of Physics, Georgetown University, Washington, DC, 20057, USA
| | - Andrew J Winchester
- Nanoscale Device Characterization Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
- Institute for Soft Matter, Georgetown University, Washington, DC, 20057, USA
| | - Chengye Dong
- Department of Materials Science & Engineering, Pennsylvania State University, University Park, PA, 16802, USA
| | - Rinu A Maniyara
- Department of Materials Science & Engineering, Pennsylvania State University, University Park, PA, 16802, USA
| | - Joshua A Robinson
- Department of Materials Science & Engineering, Pennsylvania State University, University Park, PA, 16802, USA
| | - Adri C T van Duin
- Department of Mechanical Engineering, Pennsylvania State University, University Park, PA, 16802, USA
| | - Sujitra Pookpanratana
- Nanoscale Device Characterization Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
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24
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Tian C, Yu J, Zhou D, Ze H, Liu H, Chen Y, Xia R, Ou P, Ni W, Xie K, Sargent EH. Reduction of 5-Hydroxymethylfurfural to 2,5-Bis(hydroxymethyl)Furan at High Current Density using a Ga-Doped AgCu:Cationomer Hybrid Electrocatalyst. Adv Mater 2024:e2312778. [PMID: 38421936 DOI: 10.1002/adma.202312778] [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] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/26/2024] [Indexed: 03/02/2024]
Abstract
Hydrogenation of biomass-derived chemicals is of interest for the production of biofuels and valorized chemicals. Thermochemical processes for biomass reduction typically employ hydrogen as the reductant at elevated temperatures and pressures. Here, the authors investigate the direct electrified reduction of 5-hydroxymethylfurfural (HMF) to a precursor to bio-polymers, 2,5-bis(hydroxymethyl)furan (BHMF). Noting a limited current density in prior reports of this transformation, a hybrid catalyst consisting of ternary metal nanodendrites mixed with a cationic ionomer, the latter purposed to increase local pH and facilitate surface proton diffusion, is investigated. This approach, when implemented using Ga-doped Ag-Cu electrocatalysts designed for p-d orbital hybridization, steered selectivity to BHMF, achieving a faradaic efficiency (FE) of 58% at 100 mA cm-2 and a production rate of 1 mmol cm-2 h-1, the latter a doubling in rate compared to the best prior reports.
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Affiliation(s)
- Cong Tian
- Department of Chemistry, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
| | - Jiaqi Yu
- Department of Chemistry, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
| | - Daojin Zhou
- Department of Chemistry, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
| | - Huajie Ze
- Department of Chemistry, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
| | - Hengzhou Liu
- Department of Chemistry, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
| | - Yuanjun Chen
- Department of Chemistry, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
| | - Rong Xia
- Department of Chemistry, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
| | - Pengfei Ou
- Department of Chemistry, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
| | - Weiyan Ni
- Department of Chemistry, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
| | - Ke Xie
- Department of Chemistry, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
| | - Edward H Sargent
- Department of Chemistry, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Department of Electrical and Computer Engineering, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
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25
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Wu Y, Brust-Mascher I, Gareau MG, De Loera JA, Reardon C. PrestoCell: A persistence-based clustering approach for rapid and robust segmentation of cellular morphology in three-dimensional data. PLoS One 2024; 19:e0299006. [PMID: 38422108 PMCID: PMC10903871 DOI: 10.1371/journal.pone.0299006] [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: 10/20/2023] [Accepted: 02/04/2024] [Indexed: 03/02/2024] Open
Abstract
Light microscopy methods have continued to advance allowing for unprecedented analysis of various cell types in tissues including the brain. Although the functional state of some cell types such as microglia can be determined by morphometric analysis, techniques to perform robust, quick, and accurate measurements have not kept pace with the amount of imaging data that can now be generated. Most of these image segmentation tools are further burdened by an inability to assess structures in three-dimensions. Despite the rise of machine learning techniques, the nature of some biological structures prevents the training of several current day implementations. Here we present PrestoCell, a novel use of persistence-based clustering to segment cells in light microscopy images, as a customized Python-based tool that leverages the free multidimensional image viewer Napari. In evaluating and comparing PrestoCell to several existing tools, including 3DMorph, Omipose, and Imaris, we demonstrate that PrestoCell produces image segmentations that rival these solutions. In particular, our use of cell nuclei information resulted in the ability to correctly segment individual cells that were interacting with one another to increase accuracy. These benefits are in addition to the simplified graphically based user refinement of cell masks that does not require expensive commercial software licenses. We further demonstrate that PrestoCell can complete image segmentation in large samples from light sheet microscopy, allowing quantitative analysis of these large datasets. As an open-source program that leverages freely available visualization software, with minimum computer requirements, we believe that PrestoCell can significantly increase the ability of users without data or computer science expertise to perform complex image analysis.
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Affiliation(s)
- Yue Wu
- Department of Computer Science, UC Davis, Davis, California, United States of America
| | - Ingrid Brust-Mascher
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, UC Davis, Davis, California, United States of America
| | - Melanie G. Gareau
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, UC Davis, Davis, California, United States of America
| | - Jesus A. De Loera
- Department of Mathematics, UC Davis, Davis, California, United States of America
| | - Colin Reardon
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, UC Davis, Davis, California, United States of America
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26
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Berríos KN, Barka A, Gill J, Serrano JC, Bailer PF, Parker JB, Evitt NH, Gajula KS, Shi J, Kohli RM. Cooperativity between Cas9 and hyperactive AID establishes broad and diversifying mutational footprints in base editors. Nucleic Acids Res 2024; 52:2078-2090. [PMID: 38261989 PMCID: PMC10899762 DOI: 10.1093/nar/gkae024] [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: 04/09/2023] [Revised: 12/20/2023] [Accepted: 01/04/2024] [Indexed: 01/25/2024] Open
Abstract
The partnership of DNA deaminase enzymes with CRISPR-Cas nucleases is now a well-established method to enable targeted genomic base editing. However, an understanding of how Cas9 and DNA deaminases collaborate to shape base editor (BE) outcomes has been lacking. Here, we support a novel mechanistic model of base editing by deriving a range of hyperactive activation-induced deaminase (AID) base editors (hBEs) and exploiting their characteristic diversifying activity. Our model involves multiple layers of previously underappreciated cooperativity in BE steps including: (i) Cas9 binding can potentially expose both DNA strands for 'capture' by the deaminase, a feature that is enhanced by guide RNA mismatches; (ii) after strand capture, the intrinsic activity of the DNA deaminase can tune window size and base editing efficiency; (iii) Cas9 defines the boundaries of editing on each strand, with deamination blocked by Cas9 binding to either the PAM or the protospacer and (iv) non-canonical edits on the guide RNA bound strand can be further elicited by changing which strand is nicked by Cas9. Leveraging insights from our mechanistic model, we create novel hBEs that can remarkably generate simultaneous C > T and G > A transitions over >65 bp with significant potential for targeted gene diversification.
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Affiliation(s)
- Kiara N Berríos
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Aleksia Barka
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jasleen Gill
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Juan C Serrano
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Peter F Bailer
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jared B Parker
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Niklaus H Evitt
- Graduate Group in Cell and Molecular Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kiran S Gajula
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Junwei Shi
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rahul M Kohli
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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27
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Goel T, Adams EM, Bialas AL, Tran CM, Rowe T, Martin S, Chandler M, Schubert J, Diamond PH, Collins EMS. Nonlinear elasticity and short-range mechanical coupling govern the rate and symmetry of mouth opening in Hydra. Proc Biol Sci 2024; 291:20232123. [PMID: 38378148 PMCID: PMC10878823 DOI: 10.1098/rspb.2023.2123] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/18/2024] [Indexed: 02/22/2024] Open
Abstract
Hydra has a tubular bilayered epithelial body column with a dome-shaped head on one end and a foot on the other. Hydra lacks a permanent mouth: its head epithelium is sealed. Upon neuronal activation, a mouth opens at the apex of the head which can exceed the body column diameter in seconds, allowing Hydra to ingest prey larger than itself. While the kinematics of mouth opening are well characterized, the underlying mechanism is unknown. We show that Hydra mouth opening is generated by independent local contractions that require tissue-level coordination. We model the head epithelium as an active viscoelastic nonlinear spring network. The model reproduces the size, timescale and symmetry of mouth opening. It shows that radial contractions, travelling inwards from the outer boundary of the head, pull the mouth open. Nonlinear elasticity makes mouth opening larger and faster, contrary to expectations. The model correctly predicts changes in mouth shape in response to external forces. By generating innervated : nerve-free chimera in experiments and simulations, we show that nearest-neighbour mechanical signalling suffices to coordinate mouth opening. Hydra mouth opening shows that in the absence of long-range chemical or neuronal signals, short-range mechanical coupling is sufficient to produce long-range order in tissue deformations.
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Affiliation(s)
- Tapan Goel
- Department of Physics, University of California San Diego, La Jolla, CA 92093, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Ellen M. Adams
- Department of Biology, Swarthmore College, Swarthmore, PA 19081, USA
| | - April L. Bialas
- Department of Biology, Swarthmore College, Swarthmore, PA 19081, USA
| | - Cassidy M. Tran
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Trevor Rowe
- Department of Physics, University of California San Diego, La Jolla, CA 92093, USA
| | - Sara Martin
- Department of Biology, Swarthmore College, Swarthmore, PA 19081, USA
| | - Maia Chandler
- Department of Biology, Swarthmore College, Swarthmore, PA 19081, USA
| | - Johanna Schubert
- Department of Biology, Swarthmore College, Swarthmore, PA 19081, USA
| | - Patrick H. Diamond
- Department of Physics, University of California San Diego, La Jolla, CA 92093, USA
| | - Eva-Maria S. Collins
- Department of Physics, University of California San Diego, La Jolla, CA 92093, USA
- Department of Biology, Swarthmore College, Swarthmore, PA 19081, USA
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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28
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Acharya A, Shrestha S, Chen A, Conte J, Avramovic S, Sikdar S, Anastasopoulos A, Das S. Clinical risk prediction using language models: benefits and considerations. J Am Med Inform Assoc 2024:ocae030. [PMID: 38412328 DOI: 10.1093/jamia/ocae030] [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: 12/02/2023] [Revised: 01/11/2024] [Accepted: 02/03/2024] [Indexed: 02/29/2024] Open
Abstract
OBJECTIVE The use of electronic health records (EHRs) for clinical risk prediction is on the rise. However, in many practical settings, the limited availability of task-specific EHR data can restrict the application of standard machine learning pipelines. In this study, we investigate the potential of leveraging language models (LMs) as a means to incorporate supplementary domain knowledge for improving the performance of various EHR-based risk prediction tasks. METHODS We propose two novel LM-based methods, namely "LLaMA2-EHR" and "Sent-e-Med." Our focus is on utilizing the textual descriptions within structured EHRs to make risk predictions about future diagnoses. We conduct a comprehensive comparison with previous approaches across various data types and sizes. RESULTS Experiments across 6 different methods and 3 separate risk prediction tasks reveal that employing LMs to represent structured EHRs, such as diagnostic histories, results in significant performance improvements when evaluated using standard metrics such as area under the receiver operating characteristic (ROC) curve and precision-recall (PR) curve. Additionally, they offer benefits such as few-shot learning, the ability to handle previously unseen medical concepts, and adaptability to various medical vocabularies. However, it is noteworthy that outcomes may exhibit sensitivity to a specific prompt. CONCLUSION LMs encompass extensive embedded knowledge, making them valuable for the analysis of EHRs in the context of risk prediction. Nevertheless, it is important to exercise caution in their application, as ongoing safety concerns related to LMs persist and require continuous consideration.
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Affiliation(s)
| | | | - Anyi Chen
- Staten Island Performing Provider System, Staten Island, NY, United States
| | - Joseph Conte
- Staten Island Performing Provider System, Staten Island, NY, United States
| | | | | | | | - Sanmay Das
- George Mason University, Fairfax, VA, United States
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29
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Sutton DC, Andrews JC, Dolezal DM, Park YJ, Li H, Eberl DF, Yamamoto S, Groves AK. Comparative exploration of mammalian deafness gene homologues in the Drosophila auditory organ shows genetic correlation between insect and vertebrate hearing. PLoS One 2024; 19:e0297846. [PMID: 38412189 PMCID: PMC10898740 DOI: 10.1371/journal.pone.0297846] [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: 07/21/2023] [Accepted: 01/13/2024] [Indexed: 02/29/2024] Open
Abstract
Johnston's organ, the Drosophila auditory organ, is anatomically very different from the mammalian organ of Corti. However, recent evidence indicates significant cellular and molecular similarities exist between vertebrate and invertebrate hearing, suggesting that Drosophila may be a useful platform to determine the function of the many mammalian deafness genes whose underlying biological mechanisms are poorly characterized. Our goal was a comprehensive screen of all known orthologues of mammalian deafness genes in the fruit fly to better understand conservation of hearing mechanisms between the insect and the fly and ultimately gain insight into human hereditary deafness. We used bioinformatic comparisons to screen previously reported human and mouse deafness genes and found that 156 of them have orthologues in Drosophila melanogaster. We used fluorescent imaging of T2A-GAL4 gene trap and GFP or YFP fluorescent protein trap lines for 54 of the Drosophila genes and found 38 to be expressed in different cell types in Johnston's organ. We phenotypically characterized the function of strong loss-of-function mutants in three genes expressed in Johnston's organ (Cad99C, Msp-300, and Koi) using a courtship assay and electrophysiological recordings of sound-evoked potentials. Cad99C and Koi were found to have significant courtship defects. However, when we tested these genes for electrophysiological defects in hearing response, we did not see a significant difference suggesting the courtship defects were not caused by hearing deficiencies. Furthermore, we used a UAS/RNAi approach to test the function of seven genes and found two additional genes, CG5921 and Myo10a, that gave a statistically significant delay in courtship but not in sound-evoked potentials. Our results suggest that many mammalian deafness genes have Drosophila homologues expressed in the Johnston's organ, but that their requirement for hearing may not necessarily be the same as in mammals.
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Affiliation(s)
- Daniel C. Sutton
- Graduate Program in Genetics & Genomics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jonathan C. Andrews
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, Texas, United States of America
| | - Dylan M. Dolezal
- Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Ye Jin Park
- Graduate Program in Development, Disease Models & Therapeutics, Baylor College of Medicine, Houston, Texas, United States of America
- Huffington Center on Aging, One Baylor Plaza, Houston, Texas, United States of America
| | - Hongjie Li
- Graduate Program in Development, Disease Models & Therapeutics, Baylor College of Medicine, Houston, Texas, United States of America
- Huffington Center on Aging, One Baylor Plaza, Houston, Texas, United States of America
| | - Daniel F. Eberl
- Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Shinya Yamamoto
- Graduate Program in Genetics & Genomics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, Texas, United States of America
- Graduate Program in Development, Disease Models & Therapeutics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, United States of America
| | - Andrew K. Groves
- Graduate Program in Genetics & Genomics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Graduate Program in Development, Disease Models & Therapeutics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, United States of America
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30
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Lionetti D, Suseno S, Shiau AA, de Ruiter G, Agapie T. Redox Processes Involving Oxygen: The Surprising Influence of Redox-Inactive Lewis Acids. JACS Au 2024; 4:344-368. [PMID: 38425928 PMCID: PMC10900226 DOI: 10.1021/jacsau.3c00675] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 03/02/2024]
Abstract
Metalloenzymes with heteromultimetallic active sites perform chemical reactions that control several biogeochemical cycles. Transformations catalyzed by such enzymes include dioxygen generation and reduction, dinitrogen reduction, and carbon dioxide reduction-instrumental transformations for progress in the context of artificial photosynthesis and sustainable fertilizer production. While the roles of the respective metals are of interest in all these enzymatic transformations, they share a common factor in the transfer of one or multiple redox equivalents. In light of this feature, it is surprising to find that incorporation of redox-inactive metals into the active site of such an enzyme is critical to its function. To illustrate, the presence of a redox-inactive Ca2+ center is crucial in the Oxygen Evolving Complex, and yet particularly intriguing given that the transformation catalyzed by this cluster is a redox process involving four electrons. Therefore, the effects of redox inactive metals on redox processes-electron transfer, oxygen- and hydrogen-atom transfer, and O-O bond cleavage and formation reactions-mediated by transition metals have been studied extensively. Significant effects of redox inactive metals have been observed on these redox transformations; linear free energy correlations between Lewis acidity and the redox properties of synthetic model complexes are observed for several reactions. In this Perspective, these effects and their relevance to multielectron processes will be discussed.
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Affiliation(s)
| | - Sandy Suseno
- Division of Chemistry and
Chemical Engineering, California Institute
of Technology, 1200 East California Boulevard, MC 127-72, Pasadena, California 91125, United States
| | - Angela A. Shiau
- Division of Chemistry and
Chemical Engineering, California Institute
of Technology, 1200 East California Boulevard, MC 127-72, Pasadena, California 91125, United States
| | - Graham de Ruiter
- Division of Chemistry and
Chemical Engineering, California Institute
of Technology, 1200 East California Boulevard, MC 127-72, Pasadena, California 91125, United States
| | - Theodor Agapie
- Division of Chemistry and
Chemical Engineering, California Institute
of Technology, 1200 East California Boulevard, MC 127-72, Pasadena, California 91125, United States
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31
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Kültz D, Gardell AM, DeTomaso A, Stoney G, Rinkevich B, Rinkevich Y, Qarri A, Dong W, Luu B, Lin M. Deep quantitative proteomics of North American Pacific coast star tunicate (Botryllus schlosseri). Proteomics 2024:e2300628. [PMID: 38400697 DOI: 10.1002/pmic.202300628] [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: 12/02/2023] [Revised: 01/30/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024]
Abstract
Botryllus schlosseri, is a model marine invertebrate for studying immunity, regeneration, and stress-induced evolution. Conditions for validating its predicted proteome were optimized using nanoElute® 2 deep-coverage LCMS, revealing up to 4930 protein groups and 20,984 unique peptides per sample. Spectral libraries were generated and filtered to remove interferences, low-quality transitions, and only retain proteins with >3 unique peptides. The resulting DIA assay library enabled label-free quantitation of 3426 protein groups represented by 22,593 unique peptides. Quantitative comparisons of single systems from a laboratory-raised with two field-collected populations revealed (1) a more unique proteome in the laboratory-raised population, and (2) proteins with high/low individual variabilities in each population. DNA repair/replication, ion transport, and intracellular signaling processes were distinct in laboratory-cultured colonies. Spliceosome and Wnt signaling proteins were the least variable (highly functionally constrained) in all populations. In conclusion, we present the first colonial tunicate's deep quantitative proteome analysis, identifying functional protein clusters associated with laboratory conditions, different habitats, and strong versus relaxed abundance constraints. These results empower research on B. schlosseri with proteomics resources and enable quantitative molecular phenotyping of changes associated with transfer from in situ to ex situ and from in vivo to in vitro culture conditions.
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Affiliation(s)
- Dietmar Kültz
- Department of Animal Sciences & Genome Center, University of California Davis, Meyer Hall, Davis, California, USA
| | - Alison M Gardell
- School of Interdisciplinary Arts and Sciences, University of Washington Tacoma, Tacoma, Washington, USA
| | - Anthony DeTomaso
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Goleta, California, USA
| | - Greg Stoney
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Goleta, California, USA
| | - Baruch Rinkevich
- Israel Oceanography & Limnological Research, National Institute of Oceanography, Haifa, Israel
| | - Yuval Rinkevich
- Helmholtz Zentrum München, Regenerative Biology and Medicine Institute, Munich, Germany
| | - Andy Qarri
- Israel Oceanography & Limnological Research, National Institute of Oceanography, Haifa, Israel
- Helmholtz Zentrum München, Regenerative Biology and Medicine Institute, Munich, Germany
| | - Weizhen Dong
- Department of Animal Sciences & Genome Center, University of California Davis, Meyer Hall, Davis, California, USA
| | - Brenda Luu
- Department of Animal Sciences & Genome Center, University of California Davis, Meyer Hall, Davis, California, USA
| | - Mandy Lin
- Department of Animal Sciences & Genome Center, University of California Davis, Meyer Hall, Davis, California, USA
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32
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LeBlanc M, Soucy M, Moustafa-Bayoumi M, Soto D, Nessler J. Effect of robotic gait training on muscle and bone characteristics in spinal cord transected rats. J Orthop Res 2024. [PMID: 38374812 DOI: 10.1002/jor.25810] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 12/23/2023] [Accepted: 02/02/2024] [Indexed: 02/21/2024]
Abstract
Osteoporosis and loss of muscle mass are secondary issues with spinal cord injury. Robotic gait training has provided evidence of increasing bone density and muscle mass, but its effect on bone strength is undetermined. The purpose of this study was to determine the effect of a 6-week robotic locomotion training program on skeletal muscle mass and bone characteristics. Twelve female Sprague-Dawley rats received a mid-thoracic spinal cord transection at 5 days old and at 3 weeks old were assigned to a Control or Trained Group. The Trained Group performed 5-min sessions on the Rat Stepper 5 days a week for 6 weeks with 90% of body weight supported. At the end of the 6 weeks, body mass was obtained and right femurs and four lower extremity muscles were harvested. Femur bone mineral density was measured with DXA and mechanical characteristics of the femur were determined via 3-point bending testing. Independent t-tests, effects sizes and percent differences were computed between the two groups (p < 0.05). The Trained Group had significantly larger normalized femur mass (p = 0.007) and normalized soleus muscle mass (p = 0.033) when compared to the Control Group. There was a medium or large effect size with the Trained Groups' femurs having larger mass, bone mineral density, rupture loads, cortical wall thickness, shaft cross sectional area, soleus mass, normalized gastrocnemius mass, and smaller shaft inner diameters compared to the Control Group. These changes may contribute to decreasing osteoporosis and fracture risk in those with spinal cord injuries.
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Affiliation(s)
- Michele LeBlanc
- Exercise Science Department, California Lutheran University, Thousand Oaks, California, USA
| | - Michael Soucy
- Exercise Science Department, California Lutheran University, Thousand Oaks, California, USA
| | | | - Dalziel Soto
- Department of Kinesiology, California State University, San Marcos, USA
| | - Jeff Nessler
- Department of Kinesiology, California State University, San Marcos, USA
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33
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Kang TY, Bocci F, Nie Q, Onuchic JN, Levchenko A. Spatial-temporal order-disorder transition in angiogenic NOTCH signaling controls cell fate specification. eLife 2024; 12:RP89262. [PMID: 38376371 PMCID: PMC10942579 DOI: 10.7554/elife.89262] [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] [Indexed: 02/21/2024] Open
Abstract
Angiogenesis is a morphogenic process resulting in the formation of new blood vessels from pre-existing ones, usually in hypoxic micro-environments. The initial steps of angiogenesis depend on robust differentiation of oligopotent endothelial cells into the Tip and Stalk phenotypic cell fates, controlled by NOTCH-dependent cell-cell communication. The dynamics of spatial patterning of this cell fate specification are only partially understood. Here, by combining a controlled experimental angiogenesis model with mathematical and computational analyses, we find that the regular spatial Tip-Stalk cell patterning can undergo an order-disorder transition at a relatively high input level of a pro-angiogenic factor VEGF. The resulting differentiation is robust but temporally unstable for most cells, with only a subset of presumptive Tip cells leading sprout extensions. We further find that sprouts form in a manner maximizing their mutual distance, consistent with a Turing-like model that may depend on local enrichment and depletion of fibronectin. Together, our data suggest that NOTCH signaling mediates a robust way of cell differentiation enabling but not instructing subsequent steps in angiogenic morphogenesis, which may require additional cues and self-organization mechanisms. This analysis can assist in further understanding of cell plasticity underlying angiogenesis and other complex morphogenic processes.
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Affiliation(s)
- Tae-Yun Kang
- Department of Biomedical Engineering, Yale UniversityNew HavenUnited States
- Yale UniversityNew HavenUnited States
| | - Federico Bocci
- NSF-Simons Center for Multiscale Cell Fate Research, University of California IrvineIrvineUnited States
- Department of Mathematics, University of California IrvineIrvineUnited States
| | - Qing Nie
- NSF-Simons Center for Multiscale Cell Fate Research, University of California IrvineIrvineUnited States
- Department of Mathematics, University of California IrvineIrvineUnited States
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice UniversityHoustonUnited States
| | - Andre Levchenko
- Department of Biomedical Engineering, Yale UniversityNew HavenUnited States
- Yale UniversityNew HavenUnited States
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Brown W, Davidson LA, Deiters A. Expanding the Genetic Code of Xenopus laevis Embryos. ACS Chem Biol 2024; 19:516-525. [PMID: 38277773 PMCID: PMC10877573 DOI: 10.1021/acschembio.3c00686] [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: 11/10/2023] [Revised: 12/20/2023] [Accepted: 12/20/2023] [Indexed: 01/28/2024]
Abstract
The incorporation of unnatural amino acids into proteins through genetic code expansion has been successfully adapted to African claw-toed frog embryos. Six unique unnatural amino acids are incorporated site-specifically into proteins and demonstrate robust and reliable protein expression. Of these amino acids, several are caged analogues that can be used to establish conditional control over enzymatic activity. Using light or small molecule triggers, we exhibit activation and tunability of protein functions in live embryos. This approach was then applied to optical control over the activity of a RASopathy mutant of NRAS, taking advantage of generating explant cultures from Xenopus. Taken together, genetic code expansion is a robust approach in the Xenopus model to incorporate novel chemical functionalities into proteins of interest to study their function and role in a complex biological setting.
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Affiliation(s)
- Wes Brown
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Lance A. Davidson
- Departments
of Bioengineering, Developmental Biology, and Computational and Systems
Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Alexander Deiters
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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35
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Dobbertin da Costa M, Gast RJ, Millette NC. Temporal and spatial variability of constitutive mixotroph abundance and proportion. FEMS Microbiol Ecol 2024; 100:fiae015. [PMID: 38308512 PMCID: PMC10939395 DOI: 10.1093/femsec/fiae015] [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: 11/01/2023] [Revised: 12/19/2023] [Accepted: 02/01/2024] [Indexed: 02/04/2024] Open
Abstract
Mixotrophic plankton can comprise a substantial portion of the plankton community compared to phytoplankton and zooplankton. However, there is a gap in the understanding of conditions that influence mixotroph prevalence and activity in situ because current methods often over- or underestimate mixotroph abundance. A labeled prey-tracer method was utilized to identify active mixotrophs present at two locations in a temperate estuary over a year. The tracer method was combined with light microscopy data to estimate active mixotroph abundance and proportion. This study estimated that actively grazing mixotrophic taxa were more abundant in the spring and autumn compared to summer. Dinoflagellates typically dominated the mixotrophic taxa except during autumn at the low salinity location when cryptophytes dominated. Further analysis suggested that active mixotroph abundances might not be only regulated by environmental conditions favorable to mixotrophy but, instead, environmental conditions favorable to different mixotrophs utilization of phagotrophy. By focusing on mixotrophic taxa that were identified to be actively grazing at time of sampling, this study provided a more nuanced estimation of mixotroph abundance, increasing the understanding of how mixotrophic abundance and proportion in situ are influenced by the planktonic community composition and environmental factors.
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Affiliation(s)
- Marcella Dobbertin da Costa
- Virginia Institute of Marine Science, William & Mary, 1370 Greate Rd., Gloucester Point, VA 23062, United States
| | - Rebecca J Gast
- Woods Hole Oceanographic Institution, 266 Woods Hole Rd, MS #32, Woods Hole, MA 02543, United States
| | - Nicole C Millette
- Virginia Institute of Marine Science, William & Mary, 1370 Greate Rd., Gloucester Point, VA 23062, United States
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36
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Dolfi AC, Kausrud K, Rysava K, Champagne C, Huang YH, Barandongo ZR, Turner WC. Season of death, pathogen persistence and wildlife behaviour alter number of anthrax secondary infections from environmental reservoirs. Proc Biol Sci 2024; 291:20232568. [PMID: 38320613 PMCID: PMC10846954 DOI: 10.1098/rspb.2023.2568] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/09/2024] [Indexed: 02/08/2024] Open
Abstract
An important part of infectious disease management is predicting factors that influence disease outbreaks, such as R, the number of secondary infections arising from an infected individual. Estimating R is particularly challenging for environmentally transmitted pathogens given time lags between cases and subsequent infections. Here, we calculated R for Bacillus anthracis infections arising from anthrax carcass sites in Etosha National Park, Namibia. Combining host behavioural data, pathogen concentrations and simulation models, we show that R is spatially and temporally variable, driven by spore concentrations at death, host visitation rates and early preference for foraging at infectious sites. While spores were detected up to a decade after death, most secondary infections occurred within 2 years. Transmission simulations under scenarios combining site infectiousness and host exposure risk under different environmental conditions led to dramatically different outbreak dynamics, from pathogen extinction (R < 1) to explosive outbreaks (R > 10). These transmission heterogeneities may explain variation in anthrax outbreak dynamics observed globally, and more generally, the critical importance of environmental variation underlying host-pathogen interactions. Notably, our approach allowed us to estimate the lethal dose of a highly virulent pathogen non-invasively from observational studies and epidemiological data, useful when experiments on wildlife are undesirable or impractical.
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Affiliation(s)
- Amélie C. Dolfi
- Wisconsin Cooperative Wildlife Research Unit, Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Kristyna Rysava
- Wisconsin Cooperative Wildlife Research Unit, Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Celeste Champagne
- College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108, USA
| | - Yen-Hua Huang
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
- Institute for Biospheric Studies, Yale University, New Haven, CT 06511, USA
| | - Zoe R. Barandongo
- Wisconsin Cooperative Wildlife Research Unit, Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Wendy C. Turner
- US Geological Survey, Wisconsin Cooperative Wildlife Research Unit, Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI 53706, USA
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37
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González-Gutiérrez C, García-Pons D, Zueco D, Martínez-Pérez MJ. Scanning Spin Probe Based on Magnonic Vortex Quantum Cavities. ACS Nano 2024; 18:4717-4725. [PMID: 38271997 PMCID: PMC10867890 DOI: 10.1021/acsnano.3c06704] [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] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024]
Abstract
Performing nanoscale scanning electron paramagnetic resonance (EPR) requires three essential ingredients: First, a static magnetic field together with field gradients to Zeeman split the electronic energy levels with spatial resolution; second, a radio frequency (rf) magnetic field capable of inducing spin transitions; finally, a sensitive detection method to quantify the energy absorbed by spins. This is usually achieved by combining externally applied magnetic fields with inductive coils or cavities, fluorescent defects, or scanning probes. Here, we theoretically propose the realization of an EPR scanning sensor merging all three characteristics into a single device: the vortex core stabilized in ferromagnetic thin-film discs. On one hand, the vortex ground state generates a significant static magnetic field and field gradients. On the other hand, the precessional motion of the vortex core around its equilibrium position produces a circularly polarized oscillating magnetic field, which is enough to produce spin transitions. Finally, the spin-magnon coupling broadens the vortex gyrotropic frequency, suggesting a direct measure of the presence of unpaired electrons. Moreover, the vortex core can be displaced by simply using external magnetic fields of a few mT, enabling EPR scanning microscopy with large spatial resolution. Our numerical simulations show that, by using low damping magnets, it is theoretically possible to detect single spins located on the disc's surface. Vortex nanocavities could also attain strong coupling to individual spin molecular qubits with potential applications to mediate qubit-qubit interactions or to implement qubit readout protocols.
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Affiliation(s)
- Carlos
A. González-Gutiérrez
- Instituto
de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza ES-50009, Spain
- Department
of Physics and Applied Physics, University
of Massachusetts, Lowell, Massachusetts 01854, United States
- Instituto
de Ciencias Físicas, Universidad
Nacional Autónoma de México, Av. Universidad s/n, Cuernavaca, Morelos 62210, México
| | - David García-Pons
- Instituto
de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza ES-50009, Spain
| | - David Zueco
- Instituto
de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza ES-50009, Spain
| | - María José Martínez-Pérez
- Instituto
de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza ES-50009, Spain
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38
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Thurman HA, Wijegunawardena G, Berthias F, Williamson DL, Wu H, Nagy G, Jensen ON, Shvartsburg AA. Multiplatform High-Definition Ion Mobility Separations of the Largest Epimeric Peptides. Anal Chem 2024; 96:2318-2326. [PMID: 38301112 DOI: 10.1021/acs.analchem.3c03079] [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] [Indexed: 02/03/2024]
Abstract
Ion mobility spectrometry (IMS) coupled to mass spectrometry (MS) has become a versatile tool to fractionate complex mixtures, distinguish structural isomers, and elucidate molecular geometries. Along with the whole MS field, IMS/MS advances to ever larger species. A topical proteomic problem is the discovery and characterization of d-amino acid-containing peptides (DAACPs) that are critical to neurotransmission and toxicology. Both linear IMS and FAIMS previously disentangled d/l epimers with up to ∼30 residues. In the first study using all three most powerful IMS methodologies─trapped IMS, cyclic IMS, and FAIMS─we demonstrate baseline resolution of the largest known d/l peptides (CHH from Homarus americanus with 72 residues) with a dynamic range up to 100. This expands FAIMS analyses of isomeric modified peptides, especially using hydrogen-rich buffers, to the ∼50-100 residue range of small proteins. The spectra for d and l are unprecedentedly strikingly similar except for a uniform shift of the separation parameter, indicating the conserved epimer-specific structural elements across multiple charge states and conformers. As the interepimer resolution tracks the average for smaller DAACPs, the IMS approaches could help search for yet larger DAACPs. The a priori method to calibrate cyclic (including multipass) IMS developed here may be broadly useful.
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Affiliation(s)
- Hayden A Thurman
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Gayani Wijegunawardena
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Francis Berthias
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - David L Williamson
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Haifan Wu
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Gabe Nagy
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Ole N Jensen
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Alexandre A Shvartsburg
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
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Ávila-Lovera E, Haro R, Choudhary M, Acosta-Rangel A, Pratt RB, Santiago LS. The benefits of woody plant stem photosynthesis extend to hydraulic function and drought survival in Parkinsonia florida. Tree Physiol 2024; 44:tpae013. [PMID: 38284819 PMCID: PMC10918054 DOI: 10.1093/treephys/tpae013] [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] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 01/16/2024] [Accepted: 01/21/2024] [Indexed: 01/30/2024]
Abstract
As climate change exacerbates drought stress in many parts of the world, understanding plant physiological mechanisms for drought survival is critical to predicting ecosystem responses. Stem net photosynthesis, which is common in arid environments, may be a drought survival trait, but whether the additional carbon fixed by stems contributes to plant hydraulic function and drought survival in arid land plants is untested. We conducted a stem light-exclusion experiment on saplings of a widespread North American desert tree species, Parkinsonia florida L., and after shading acclimation, we then subjected half of the plants to a drought treatment to test the interaction between light exclusion and water limitation on growth, leaf and stem photosynthetic gas exchange, xylem embolism assessed with micro-computed tomography and gravimetric techniques, and survival. Growth, stem photosynthetic gas exchange, hydraulic function and survival all showed expected reductions in response to light exclusion. However, stem photosynthesis mitigated the drought-induced reductions in gas exchange, xylem embolism (percent loss of conductivity, PLC) and mortality. The highest mortality was in the combined light exclusion and drought treatment, and was related to stem PLC and native sapwood-specific hydraulic conductivity. This research highlights the integration of carbon economy and water transport. Our results show that additional carbon income by photosynthetic stems has an important role in the growth and survival of a widespread desert tree species during drought. This shift in function under conditions of increasing stress underscores the importance of considering stem photosynthesis for predicting drought-induced mortality not only for the additional supply of carbon, but also for its extended benefits for hydraulic function.
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Affiliation(s)
- Eleinis Ávila-Lovera
- School of Biological Sciences, The University of Utah, 257 S 1400 E, Salt Lake City, UT 84112, USA
- Department of Botany and Plant Sciences, University of California, 2150 Batchelor Hall, Riverside, CA 92521, USA
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panama, Republic of Panama
| | - Roxana Haro
- Department of Botany and Plant Sciences, University of California, 2150 Batchelor Hall, Riverside, CA 92521, USA
| | - Manika Choudhary
- Department of Botany and Plant Sciences, University of California, 2150 Batchelor Hall, Riverside, CA 92521, USA
| | - Aleyda Acosta-Rangel
- Department of Botany and Plant Sciences, University of California, 2150 Batchelor Hall, Riverside, CA 92521, USA
| | - R Brandon Pratt
- Department of Biology, California State University, 9001 Stockdale Hwy, Bakersfield, CA 93311, USA
| | - Louis S Santiago
- Department of Botany and Plant Sciences, University of California, 2150 Batchelor Hall, Riverside, CA 92521, USA
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panama, Republic of Panama
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40
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Kinkade JA, Seetharam AS, Sachdev S, Bivens NJ, Phinney BS, Grigorean G, Roberts RM, Tuteja G, Rosenfeld CS. Extracellular vesicles from mouse trophoblast cells: Effects on neural progenitor cells and potential participants in the placenta-brain axis†. Biol Reprod 2024; 110:310-328. [PMID: 37883444 PMCID: PMC10873279 DOI: 10.1093/biolre/ioad146] [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: 01/31/2023] [Revised: 10/12/2023] [Accepted: 10/21/2023] [Indexed: 10/28/2023] Open
Abstract
The fetal brain of the mouse is thought to be dependent upon the placenta as a source of serotonin (5-hydroxytryptamine; 5-HT) and other factors. How factors reach the developing brain remains uncertain but are postulated here to be part of the cargo carried by placental extracellular vesicles (EV). We have analyzed the protein, catecholamine, and small RNA content of EV from mouse trophoblast stem cells (TSC) and TSC differentiated into parietal trophoblast giant cells (pTGC), potential primary purveyors of 5-HT. Current studies examined how exposure of mouse neural progenitor cells (NPC) to EV from either TSC or pTGC affect their transcriptome profiles. The EV from trophoblast cells contained relatively high amounts of 5-HT, as well as dopamine and norepinephrine, but there were no significant differences between EV derived from pTGC and from TSC. Content of miRNA and small nucleolar (sno)RNA, however, did differ according to EV source, and snoRNA were upregulated in EV from pTGC. The primary inferred targets of the microRNA (miRNA) from both pTGC and TSC were mRNA enriched in the fetal brain. NPC readily internalized EV, leading to changes in their transcriptome profiles. Transcripts regulated were mainly ones enriched in neural tissues. The transcripts in EV-treated NPC that demonstrated a likely complementarity with miRNA in EV were mainly up- rather than downregulated, with functions linked to neuronal processes. Our results are consistent with placenta-derived EV providing direct support for fetal brain development and being an integral part of the placenta-brain axis.
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Affiliation(s)
- Jessica A Kinkade
- Biomedical Sciences, University of Missouri, Columbia, MO, USA
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Arun S Seetharam
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Shrikesh Sachdev
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Nathan J Bivens
- Genomics Technology Core Facility, University of Missouri, Columbia, MO, USA
| | - Brett S Phinney
- Proteomics Core UC Davis Genome Center, University of California, Davis, CA, USA
| | - Gabriela Grigorean
- Proteomics Core UC Davis Genome Center, University of California, Davis, CA, USA
| | - R Michael Roberts
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Geetu Tuteja
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Cheryl S Rosenfeld
- Biomedical Sciences, University of Missouri, Columbia, MO, USA
- MU Institute of Data Science and Informatics, University of Missouri, Columbia, MO, USA
- Genetics Area Program, University of Missouri, Columbia, MO, USA
- Thompson Center for Autism and Neurobehavioral Disorders, University of Missouri, Columbia, MO, USA
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41
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Guegler CK, Teodoro GIC, Srikant S, Chetlapalli K, Doering CR, Ghose DA, Laub MT. A phage-encoded RNA-binding protein inhibits the antiviral activity of a toxin-antitoxin system. Nucleic Acids Res 2024; 52:1298-1312. [PMID: 38117986 PMCID: PMC10853763 DOI: 10.1093/nar/gkad1207] [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: 06/23/2023] [Revised: 12/02/2023] [Accepted: 12/06/2023] [Indexed: 12/22/2023] Open
Abstract
Bacteria harbor diverse mechanisms to defend themselves against their viral predators, bacteriophages. In response, phages can evolve counter-defense systems, most of which are poorly understood. In T4-like phages, the gene tifA prevents bacterial defense by the type III toxin-antitoxin (TA) system toxIN, but the mechanism by which TifA inhibits ToxIN remains unclear. Here, we show that TifA directly binds both the endoribonuclease ToxN and RNA, leading to the formation of a high molecular weight ribonucleoprotein complex in which ToxN is inhibited. The RNA binding activity of TifA is necessary for its interaction with and inhibition of ToxN. Thus, we propose that TifA inhibits ToxN during phage infection by trapping ToxN on cellular RNA, particularly the abundant 16S rRNA, thereby preventing cleavage of phage transcripts. Taken together, our results reveal a novel mechanism underlying inhibition of a phage-defensive RNase toxin by a small, phage-encoded protein.
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Affiliation(s)
- Chantal K Guegler
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Gabriella I C Teodoro
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sriram Srikant
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Keerthana Chetlapalli
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christopher R Doering
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Dia A Ghose
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael T Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Niu L, Zhong S, Yang Z, Tan B, Zhao J, Zhou W, Zhang P, Hua L, Sun W, Li H. Mask refinement network for tooth segmentation on panoramic radiographs. Dentomaxillofac Radiol 2024; 53:127-136. [PMID: 38166355 DOI: 10.1093/dmfr/twad012] [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] [Revised: 10/13/2023] [Accepted: 11/12/2023] [Indexed: 01/04/2024] Open
Abstract
OBJECTIVES Instance-level tooth segmentation extracts abundant localization and shape information from panoramic radiographs (PRs). The aim of this study was to evaluate the performance of a mask refinement network that extracts precise tooth edges. METHODS A public dataset which consists of 543 PRs and 16211 labelled teeth was utilized. The structure of a typical Mask Region-based Convolutional Neural Network (Mask RCNN) was used as the baseline. A novel loss function was designed focus on producing accurate mask edges. In addition to our proposed method, 3 existing tooth segmentation methods were also implemented on the dataset for comparative analysis. The average precisions (APs), mean intersection over union (mIoU), and mean Hausdorff distance (mHAU) were exploited to evaluate the performance of the network. RESULTS A novel mask refinement region-based convolutional neural network was designed based on Mask RCNN architecture to extract refined masks for individual tooth on PRs. A total of 3311 teeth were correctly detected from 3382 tested teeth in 111 PRs. The AP, precision, and recall were 0.686, 0.979, and 0.952, respectively. Moreover, the mIoU and mHAU achieved 0.941 and 9.7, respectively, which are significantly better than the other existing segmentation methods. CONCLUSIONS This study proposed an efficient deep learning algorithm for accurately extracting the mask of any individual tooth from PRs. Precise tooth masks can provide valuable reference for clinical diagnosis and treatment. This algorithm is a fundamental basis for further automated processing applications.
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Affiliation(s)
- Li Niu
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu Province 210008, China
| | - Shengwei Zhong
- School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu Province 210094, China
| | - Zhiyu Yang
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu Province 210008, China
| | - Baochun Tan
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu Province 210008, China
| | - Junjie Zhao
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu Province 210008, China
| | - Wei Zhou
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu Province 210008, China
| | - Peng Zhang
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu Province 210008, China
| | - Lingchen Hua
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu Province 210008, China
| | - Weibin Sun
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu Province 210008, China
| | - Houxuan Li
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu Province 210008, China
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Wei R, Ganglberger W, Sun H, Hadar P, Gollub R, Pieper S, Billot B, Au R, Eugenio Iglesias J, Cash SS, Kim S, Shin C, Westover MB, Joseph Thomas R. Linking brain structure, cognition, and sleep: insights from clinical data. Sleep 2024; 47:zsad294. [PMID: 37950486 PMCID: PMC10851868 DOI: 10.1093/sleep/zsad294] [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] [Revised: 10/13/2023] [Indexed: 11/12/2023] Open
Abstract
STUDY OBJECTIVES To use relatively noisy routinely collected clinical data (brain magnetic resonance imaging (MRI) data, clinical polysomnography (PSG) recordings, and neuropsychological testing), to investigate hypothesis-driven and data-driven relationships between brain physiology, structure, and cognition. METHODS We analyzed data from patients with clinical PSG, brain MRI, and neuropsychological evaluations. SynthSeg, a neural network-based tool, provided high-quality segmentations despite noise. A priori hypotheses explored associations between brain function (measured by PSG) and brain structure (measured by MRI). Associations with cognitive scores and dementia status were studied. An exploratory data-driven approach investigated age-structure-physiology-cognition links. RESULTS Six hundred and twenty-three patients with sleep PSG and brain MRI data were included in this study; 160 with cognitive evaluations. Three hundred and forty-two participants (55%) were female, and age interquartile range was 52 to 69 years. Thirty-six individuals were diagnosed with dementia, 71 with mild cognitive impairment, and 326 with major depression. One hundred and fifteen individuals were evaluated for insomnia and 138 participants had an apnea-hypopnea index equal to or greater than 15. Total PSG delta power correlated positively with frontal lobe/thalamic volumes, and sleep spindle density with thalamic volume. rapid eye movement (REM) duration and amygdala volume were positively associated with cognition. Patients with dementia showed significant differences in five brain structure volumes. REM duration, spindle, and slow-oscillation features had strong associations with cognition and brain structure volumes. PSG and MRI features in combination predicted chronological age (R2 = 0.67) and cognition (R2 = 0.40). CONCLUSIONS Routine clinical data holds extended value in understanding and even clinically using brain-sleep-cognition relationships.
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Affiliation(s)
- Ruoqi Wei
- Division of Pulmonary Critical Care & Sleep Medicine, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- McCance Center for Brain Health, Massachusetts General Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Wolfgang Ganglberger
- McCance Center for Brain Health, Massachusetts General Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Department of Neurology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Sleep and Health Zurich, University of Zurich, Zurich, Switzerland
| | - Haoqi Sun
- McCance Center for Brain Health, Massachusetts General Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Department of Neurology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Peter N Hadar
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Randy L Gollub
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, USA
| | | | - Benjamin Billot
- Computer Science and Artificial Intelligence Lab, MIT, Boston, MA, USA
| | - Rhoda Au
- Anatomy& Neurobiology, Neurology, Medicine and Epidemiology, Boston University Chobanian & Avedisian School of Medicine and School of Public Health, Boston University, Boston, MA, USA
| | - Juan Eugenio Iglesias
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, USA
- Isomics, Inc. Cambridge, MA, USA
- Center for Medical Image Computing, University College London, London, UK
| | - Sydney S Cash
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Soriul Kim
- Institute of Human Genomic Study, College of Medicine, Kore University, Seoul, Republic of Korea
| | - Chol Shin
- Institute of Human Genomic Study, College of Medicine, Kore University, Seoul, Republic of Korea
- Biomedical Research Center, Korea University Ansan Hospital, Ansan, Republic of Korea
| | - M Brandon Westover
- McCance Center for Brain Health, Massachusetts General Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Department of Neurology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Robert Joseph Thomas
- Division of Pulmonary Critical Care & Sleep Medicine, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, USA
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Caudron C, Miao Y, Spica ZJ, Wollin C, Haberland C, Jousset P, Yates A, Vandemeulebrouck J, Schmidt B, Krawczyk C, Dahm T. Monitoring underwater volcano degassing using fiber-optic sensing. Sci Rep 2024; 14:3128. [PMID: 38326378 PMCID: PMC10850492 DOI: 10.1038/s41598-024-53444-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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 01/31/2024] [Indexed: 02/09/2024] Open
Abstract
Continuous monitoring of volcanic gas emissions is crucial for understanding volcanic activity and potential eruptions. However, emissions of volcanic gases underwater are infrequently studied or quantified. This study explores the potential of Distributed Acoustic Sensing (DAS) technology to monitor underwater volcanic degassing. DAS converts fiber-optic cables into high-resolution vibration recording arrays, providing measurements at unprecedented spatio-temporal resolution. We conducted an experiment at Laacher See volcano in Germany, immersing a fiber-optic cable in the lake and interrogating it with a DAS system. We detected and analyzed numerous acoustic signals that we associated with bubble emissions in different lake areas. Three types of text-book bubbles exhibiting characteristic waveforms are all found from our detections, indicating different nucleation processes and bubble sizes. Using clustering algorithms, we classified bubble events into four distinct clusters based on their temporal and spectral characteristics. The temporal distribution of the events provided insights into the evolution of gas seepage patterns. This technology has the potential to revolutionize underwater degassing monitoring and provide valuable information for studying volcanic processes and estimating gas emissions. Furthermore, DAS can be applied to other applications, such as monitoring underwater carbon capture and storage operations or methane leaks associated with climate change.
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Affiliation(s)
- Corentin Caudron
- Laboratoire G-Time, Department of Geosciences, Environment, and Society, Université Libre de Bruxelles, Brussels, Belgium
| | - Yaolin Miao
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Zack J Spica
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, USA.
| | - Christopher Wollin
- GFZ German Research Centre for Geosciences, Potsdam, Deutschland, Germany
| | | | - Philippe Jousset
- GFZ German Research Centre for Geosciences, Potsdam, Deutschland, Germany
| | - Alexander Yates
- Laboratoire G-Time, Department of Geosciences, Environment, and Society, Université Libre de Bruxelles, Brussels, Belgium
- ISTerre, Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, IRD, IFSTTAR, 38000, Grenoble, France
| | - Jean Vandemeulebrouck
- ISTerre, Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, IRD, IFSTTAR, 38000, Grenoble, France
| | | | - Charlotte Krawczyk
- GFZ German Research Centre for Geosciences, Potsdam, Deutschland, Germany
- TU Berlin, Institute of Applied Geosciences, Berlin, Deutschland, Germany
| | - Torsten Dahm
- GFZ German Research Centre for Geosciences, Potsdam, Deutschland, Germany
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Graber JH, Hoskinson D, Liu H, Kaczmarek Michaels K, Benson PS, Maki NJ, Wilson CL, McGrath C, Puleo F, Pearson E, Kuehner JN, Moore C. Mutations in yeast Pcf11, a conserved protein essential for mRNA 3' end processing and transcription termination, elicit the Environmental Stress Response. Genetics 2024; 226:iyad199. [PMID: 37967370 PMCID: PMC10847720 DOI: 10.1093/genetics/iyad199] [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: 07/11/2023] [Revised: 10/28/2023] [Accepted: 10/31/2023] [Indexed: 11/17/2023] Open
Abstract
The Pcf11 protein is an essential subunit of the large complex that cleaves and polyadenylates eukaryotic mRNA precursor. It has also been functionally linked to gene-looping, termination of RNA Polymerase II (Pol II) transcripts, and mRNA export. We have examined a poorly characterized but conserved domain (amino acids 142-225) of the Saccharomyces cerevisiae Pcf11 and found that while it is not needed for mRNA 3' end processing or termination downstream of the poly(A) sites of protein-coding genes, its presence improves the interaction with Pol II and the use of transcription terminators near gene promoters. Analysis of genome-wide Pol II occupancy in cells with Pcf11 missing this region, as well as Pcf11 mutated in the Pol II CTD Interacting Domain, indicates that systematic changes in mRNA expression are mediated primarily at the level of transcription. Global expression analysis also shows that a general stress response, involving both activation and suppression of specific gene sets known to be regulated in response to a wide variety of stresses, is induced in the two pcf11 mutants, even though cells are grown in optimal conditions. The mutants also cause an unbalanced expression of cell wall-related genes that does not activate the Cell Wall Integrity pathway but is associated with strong caffeine sensitivity. Based on these findings, we propose that Pcf11 can modulate the expression level of specific functional groups of genes in ways that do not involve its well-characterized role in mRNA 3' end processing.
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Affiliation(s)
- Joel H Graber
- Mount Desert Island Biological Laboratory, Bar Harbor, ME 04609, USA
| | - Derick Hoskinson
- Department of Development, Molecular, and Chemical Biology and School of Graduate Biomedical Science, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Huiyun Liu
- Department of Development, Molecular, and Chemical Biology and School of Graduate Biomedical Science, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Katarzyna Kaczmarek Michaels
- Department of Development, Molecular, and Chemical Biology and School of Graduate Biomedical Science, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Peter S Benson
- Mount Desert Island Biological Laboratory, Bar Harbor, ME 04609, USA
| | - Nathaniel J Maki
- Mount Desert Island Biological Laboratory, Bar Harbor, ME 04609, USA
| | | | - Caleb McGrath
- Department of Biology, Emmanuel College, Boston, MA 02115, USA
| | - Franco Puleo
- Department of Development, Molecular, and Chemical Biology and School of Graduate Biomedical Science, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Erika Pearson
- Department of Development, Molecular, and Chemical Biology and School of Graduate Biomedical Science, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Jason N Kuehner
- Department of Biology, Emmanuel College, Boston, MA 02115, USA
| | - Claire Moore
- Department of Development, Molecular, and Chemical Biology and School of Graduate Biomedical Science, Tufts University School of Medicine, Boston, MA 02111, USA
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Angst P, Dexter E, Stillman JH. Genome assemblies of two species of porcelain crab, Petrolisthes cinctipes and Petrolisthes manimaculis (Anomura: Porcellanidae). G3 (Bethesda) 2024; 14:jkad281. [PMID: 38079165 PMCID: PMC10849366 DOI: 10.1093/g3journal/jkad281] [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] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 11/09/2023] [Indexed: 02/09/2024]
Abstract
Crabs are a large subtaxon of the Arthropoda, the most diverse and species-rich metazoan group. Several outstanding questions remain regarding crab diversification, including about the genomic capacitors of physiological and morphological adaptation, that cannot be answered with available genomic resources. Physiologically and ecologically diverse Anomuran porcelain crabs offer a valuable model for investigating these questions and hence genomic resources of these crabs would be particularly useful. Here, we present the first two genome assemblies of congeneric and sympatric Anomuran porcelain crabs, Petrolisthes cinctipes and Petrolisthes manimaculis from different microhabitats. Pacific Biosciences high-fidelity sequencing led to genome assemblies of 1.5 and 0.9 Gb, with N50s of 706.7 and 218.9 Kb, respectively. Their assembly length difference can largely be attributed to the different levels of interspersed repeats in their assemblies: The larger genome of P. cinctipes has more repeats (1.12 Gb) than the smaller genome of P. manimaculis (0.54 Gb). For obtaining high-quality annotations of 44,543 and 40,315 protein-coding genes in P. cinctipes and P. manimaculis, respectively, we used RNA-seq as part of a larger annotation pipeline. Contrarily to the large-scale differences in repeat content, divergence levels between the two species as estimated from orthologous protein-coding genes are moderate. These two high-quality genome assemblies allow future studies to examine the role of environmental regulation of gene expression in the two focal species to better understand physiological response to climate change, and provide the foundation for studies in fine-scale genome evolution and diversification of crabs.
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Affiliation(s)
- Pascal Angst
- Department of Environmental Sciences, Zoology, University of Basel, 4051 Basel, Switzerland
| | - Eric Dexter
- Department of Environmental Sciences, Zoology, University of Basel, 4051 Basel, Switzerland
| | - Jonathon H Stillman
- Department of Environmental Sciences, Zoology, University of Basel, 4051 Basel, Switzerland
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
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47
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Patterson CW, Bonillas-Monge E, Brennan A, Grether GF, Mendoza-Cuenca L, Tucker R, Vega-Sánchez YM, Drury J. A chromosome-level genome assembly for the smoky rubyspot damselfly (Hetaerina titia). J Hered 2024; 115:103-111. [PMID: 37988159 PMCID: PMC10838124 DOI: 10.1093/jhered/esad070] [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] [Revised: 11/04/2023] [Accepted: 11/09/2023] [Indexed: 11/22/2023] Open
Abstract
Smoky rubyspot damselflies (Hetaerina titia Drury, 1773) are one of the most commonly encountered odonates along streams and rivers on both slopes of Central America and the Atlantic drainages in the United States and southern Canada. Owing to their highly variable wing pigmentation, they have become a model system for studying sexual selection and interspecific behavioral interference. Here, we sequence and assemble the genome of a female smoky rubyspot. Of the primary assembly (i.e. the principle pseudohaplotype), 98.8% is made up of 12 chromosomal pseudomolecules (2N = 22A + X). There are 75 scaffolds in total, an N50 of 120 Mb, a contig-N50 of 0.64 Mb, and a high arthropod BUSCO score [C: 97.6% (S: 97.3%, D: 0.3%), F: 0.8%, M: 1.6%]. We then compare our assembly to that of the blue-tailed damselfly genome (Ischnura elegans), the most complete damselfly assembly to date, and a recently published assembly for an American rubyspot damselfly (Hetaerina americana). Collectively, these resources make Hetaerina a genome-enabled genus for further studies of the ecological and evolutionary forces shaping biological diversity.
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Affiliation(s)
| | | | - Adrian Brennan
- Department of Biosciences, Durham University, Durham, United Kingdom
| | - Gregory F Grether
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, California, LA, United States
| | - Luis Mendoza-Cuenca
- Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, México
| | - Rachel Tucker
- NERC Environmental Omics Facility, University of Sheffield, Sheffield, United Kingdom
| | - Yesenia M Vega-Sánchez
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Morelia, México
| | - Jonathan Drury
- Department of Biosciences, Durham University, Durham, United Kingdom
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Keller A, Bai H, Budinger S, Eliazer S, Hansen M, Konopka AR, Morales-Nebreda L, Najt CP, Prahlad V, Victorelli S, Vorland CJ, Yuan R, Rhoads TW, Mihaylova MM. The Third Annual Symposium of the Midwest Aging Consortium. J Gerontol A Biol Sci Med Sci 2024; 79:glad239. [PMID: 37804247 PMCID: PMC10799755 DOI: 10.1093/gerona/glad239] [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: 08/11/2023] [Indexed: 10/09/2023] Open
Abstract
The geroscience hypothesis suggests that addressing the fundamental mechanisms driving aging biology will prevent or mitigate the onset of multiple chronic diseases, for which the largest risk factor is advanced age. Research that investigates the root causes of aging is therefore of critical importance given the rising healthcare burden attributable to age-related diseases. The third annual Midwest Aging Consortium symposium was convened as a showcase of such research performed by investigators from institutions across the Midwestern United States. This report summarizes the work presented during a virtual conference across topics in aging biology, including immune function in the lung-particularly timely given the Corona Virus Immune Disease-2019 pandemic-along with the role of metabolism and nutrient-regulated pathways in cellular function with age, the influence of senescence on stem cell function and inflammation, and our evolving understanding of the mechanisms underlying observation of sex dimorphism in aging-related outcomes. The symposium focused on early-stage and emerging investigators, while including keynote presentations from leaders in the biology of aging field, highlighting the diversity and strength of aging research in the Midwest.
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Affiliation(s)
- Andrea Keller
- Department of Biological Chemistry and Pharmacology, College of Medicine, Ohio State University, Columbus, Ohio, USA
- Comprehensive Cancer Center, Wexner Medical Center, Arthur G. James Cancer Hospital, Ohio State University, Columbus, Ohio, USA
| | - Hua Bai
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa, USA
| | - Scott Budinger
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Susan Eliazer
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota, USA
| | - Malene Hansen
- Buck Institute for Research on Aging, Novato, California, USA
| | - Adam R Konopka
- Division of Geriatrics and Gerontology, Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Geriatric Research, Education, and Clinical Center, William S. Middleton Memorial Veterans Hospital, Madison, Wisconsin, USA
| | - Luisa Morales-Nebreda
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Charles P Najt
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Veena Prahlad
- Department of Biology, Aging Mind and Brain Initiative; Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa, USA
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Stella Victorelli
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA
| | - Colby J Vorland
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health-Bloomington, Bloomington, Indiana, USA
| | - Rong Yuan
- Geriatric Research Division, Department of Internal Medicine, Southern Illinois University School of Medicine, Springfield, Illinois, USA
| | - Timothy W Rhoads
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Maria M Mihaylova
- Department of Biological Chemistry and Pharmacology, College of Medicine, Ohio State University, Columbus, Ohio, USA
- Comprehensive Cancer Center, Wexner Medical Center, Arthur G. James Cancer Hospital, Ohio State University, Columbus, Ohio, USA
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49
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Matthews ER, Johnson OD, Horn KJ, Gutiérrez JA, Powell SR, Ward MC. Anthracyclines induce cardiotoxicity through a shared gene expression response signature. PLoS Genet 2024; 20:e1011164. [PMID: 38416769 PMCID: PMC10927150 DOI: 10.1371/journal.pgen.1011164] [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: 09/30/2023] [Revised: 03/11/2024] [Accepted: 01/31/2024] [Indexed: 03/01/2024] Open
Abstract
TOP2 inhibitors (TOP2i) are effective drugs for breast cancer treatment. However, they can cause cardiotoxicity in some women. The most widely used TOP2i include anthracyclines (AC) Doxorubicin (DOX), Daunorubicin (DNR), Epirubicin (EPI), and the anthraquinone Mitoxantrone (MTX). It is unclear whether women would experience the same adverse effects from all drugs in this class, or if specific drugs would be preferable for certain individuals based on their cardiotoxicity risk profile. To investigate this, we studied the effects of treatment of DOX, DNR, EPI, MTX, and an unrelated monoclonal antibody Trastuzumab (TRZ) on iPSC-derived cardiomyocytes (iPSC-CMs) from six healthy females. All TOP2i induce cell death at concentrations observed in cancer patient serum, while TRZ does not. A sub-lethal dose of all TOP2i induces limited cellular stress but affects calcium handling, a function critical for cardiomyocyte contraction. TOP2i induce thousands of gene expression changes over time, giving rise to four distinct gene expression response signatures, denoted as TOP2i early-acute, early-sustained, and late response genes, and non-response genes. There is no drug- or AC-specific signature. TOP2i early response genes are enriched in chromatin regulators, which mediate AC sensitivity across breast cancer patients. However, there is increased transcriptional variability between individuals following AC treatments. To investigate potential genetic effects on response variability, we first identified a reported set of expression quantitative trait loci (eQTLs) uncovered following DOX treatment in iPSC-CMs. Indeed, DOX response eQTLs are enriched in genes that respond to all TOP2i. Next, we identified 38 genes in loci associated with AC toxicity by GWAS or TWAS. Two thirds of the genes that respond to at least one TOP2i, respond to all ACs with the same direction of effect. Our data demonstrate that TOP2i induce thousands of shared gene expression changes in cardiomyocytes, including genes near SNPs associated with inter-individual variation in response to DOX treatment and AC-induced cardiotoxicity.
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Affiliation(s)
- E. Renee Matthews
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Omar D. Johnson
- Biochemistry, Cellular and Molecular Biology Graduate Program, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Kandace J. Horn
- John Sealy School of Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - José A. Gutiérrez
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Simon R. Powell
- Neuroscience Graduate Program, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Michelle C. Ward
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
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50
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Liu Z, Luo L, Jin R. Visible to NIR-II Photoluminescence of Atomically Precise Gold Nanoclusters. Adv Mater 2024; 36:e2309073. [PMID: 37922431 DOI: 10.1002/adma.202309073] [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] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/23/2023] [Indexed: 11/05/2023]
Abstract
Atomically precise gold nanoclusters (NCs) have emerged as a new class of precision materials and attracted wide interest in recent years. One of the unique properties of such nanoclusters pertains to their photoluminescence (PL), for it can widely span visible to near-infrared-I and -II wavelengths (NIR-I/II), and even beyond 1700 nm by manipulating the size, structure, and composition. The current research efforts focus on the structure-PL correlation and the development of strategies for raising the PL quantum yields, which is nontrivial when moving from the visible to the near-infrared wavelengths, especially in the NIR-II regions. This review summarizes the recent progress in the field, including i) the types of PL observed in gold NCs such as fluorescence, phosphorescence, and thermally activated delayed fluorescence, as well as dual emission; ii) some effective strategies that are devised to improve the PL quantum yield (QY) of gold NCs, such as heterometal doping, surface rigidification, and core phonon engineering, with double-digit QYs for the NIR PL on the horizons; and iii) the applications of luminescent gold NCs in bioimaging, photosensitization, and optoelectronics. Finally, the remaining challenges and opportunities for future research are highlighted.
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Affiliation(s)
- Zhongyu Liu
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, 15213, USA
| | - Lianshun Luo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, 15213, USA
| | - Rongchao Jin
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, 15213, USA
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