1
|
Sachdev A, Gill K, Sckaff M, Birk AM, Aladesuyi Arogundade O, Brown KA, Chouhan RS, Issagholian-Lewin PO, Patel E, Watry HL, Bernardi MT, Keough KC, Tsai YC, Smith AST, Conklin BR, Clelland CD. Reversal of C9orf72 mutation-induced transcriptional dysregulation and pathology in cultured human neurons by allele-specific excision. Proc Natl Acad Sci U S A 2024; 121:e2307814121. [PMID: 38621131 PMCID: PMC11047104 DOI: 10.1073/pnas.2307814121] [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: 05/09/2023] [Accepted: 03/01/2024] [Indexed: 04/17/2024] Open
Abstract
Efforts to genetically reverse C9orf72 pathology have been hampered by our incomplete understanding of the regulation of this complex locus. We generated five different genomic excisions at the C9orf72 locus in a patient-derived induced pluripotent stem cell (iPSC) line and a non-diseased wild-type (WT) line (11 total isogenic lines), and examined gene expression and pathological hallmarks of C9 frontotemporal dementia/amyotrophic lateral sclerosis in motor neurons differentiated from these lines. Comparing the excisions in these isogenic series removed the confounding effects of different genomic backgrounds and allowed us to probe the effects of specific genomic changes. A coding single nucleotide polymorphism in the patient cell line allowed us to distinguish transcripts from the normal vs. mutant allele. Using digital droplet PCR (ddPCR), we determined that transcription from the mutant allele is upregulated at least 10-fold, and that sense transcription is independently regulated from each allele. Surprisingly, excision of the WT allele increased pathologic dipeptide repeat poly-GP expression from the mutant allele. Importantly, a single allele was sufficient to supply a normal amount of protein, suggesting that the C9orf72 gene is haplo-sufficient in induced motor neurons. Excision of the mutant repeat expansion reverted all pathology (RNA abnormalities, dipeptide repeat production, and TDP-43 pathology) and improved electrophysiological function, whereas silencing sense expression did not eliminate all dipeptide repeat proteins, presumably because of the antisense expression. These data increase our understanding of C9orf72 gene regulation and inform gene therapy approaches, including antisense oligonucleotides (ASOs) and CRISPR gene editing.
Collapse
Affiliation(s)
| | - Kamaljot Gill
- Gladstone Institutes, San Francisco, CA94158
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA94158
| | - Maria Sckaff
- Gladstone Institutes, San Francisco, CA94158
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA94158
| | | | - Olubankole Aladesuyi Arogundade
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA94158
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA94158
| | - Katherine A. Brown
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA94158
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA94158
| | - Runvir S. Chouhan
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA94158
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA94158
| | - Patrick Oliver Issagholian-Lewin
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA94158
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA94158
| | - Esha Patel
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA94158
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA94158
| | | | | | | | | | - Alec Simon Tulloch Smith
- Department of Physiology and Biophysics, University of Washington, Seattle, WA98195
- The Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA98195
| | - Bruce R. Conklin
- Gladstone Institutes, San Francisco, CA94158
- Department of Medicine, University of California San Francisco, San Francisco, CA94143
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA94143
- Department of Pharmacology, University of California San Francisco, San Francisco, CA94158
| | - Claire Dudley Clelland
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA94158
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA94158
| |
Collapse
|
2
|
Brown KA, Donise KR, Cancilliere MK, Aluthge DP, Chen ES. Characterizing Autism Spectrum Disorder and Predicting Suicide Risk for Pediatric Psychiatric Emergency Services Encounters. AMIA Annu Symp Proc 2024; 2023:864-873. [PMID: 38222397 PMCID: PMC10785882] [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] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Individuals diagnosed with autism spectrum disorder (ASD) are at a higher risk for mental health concerns including suicidal thoughts and behaviors (STB). Limited studies have focused on suicidal risk factors that are more prevalent or unique to the population with ASD. This study sought to characterize and classify youth presenting to the psychiatric emergency department (ED) for a chief complaint of STB. The results of this study validated that a high number of patients with ASD present to the ED with STB. There were important differences in clinical characteristics to those with ASD versus those without. Clinical features that showed important impact in predicting high suicide risk in the ASD cases include elements of the mental status exam such as affect, trauma symptoms, abuse history, and auditory hallucinations. Focused attention is needed on these unique differences in ASD cases so that suicide risk level can be appropriately and promptly addressed.
Collapse
Affiliation(s)
| | - Kathleen R Donise
- Department of Psychiatry and Human Behavior at Alpert Medical School, Brown University, Providence RI
- Department of Child and Adolescent Psychiatry, Hasbro Children's Hospital, Providence RI
| | - Mary Kathryn Cancilliere
- Department of Psychiatry and Human Behavior at Alpert Medical School, Brown University, Providence RI
- Department of Child and Adolescent Psychiatry, Hasbro Children's Hospital, Providence RI
| | - Dilum P Aluthge
- Center for Biomedical Informatics, Brown University, Providence RI
| | - Elizabeth S Chen
- Center for Biomedical Informatics, Brown University, Providence RI
| |
Collapse
|
3
|
Salomonsson SE, Maltos AM, Gill K, Aladesuyi Arogundade O, Brown KA, Sachdev A, Sckaff M, Lam KJK, Fisher IJ, Chouhan RS, Van Laar VS, Marley CB, McLaughlin I, Bankiewicz KS, Tsai YC, Conklin BR, Clelland CD. Validated assays for the quantification of C9orf72 human pathology. Sci Rep 2024; 14:828. [PMID: 38191789 PMCID: PMC10774390 DOI: 10.1038/s41598-023-50667-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 12/22/2023] [Indexed: 01/10/2024] Open
Abstract
A repeat expansion mutation in the C9orf72 gene is the leading known genetic cause of FTD and ALS. The C9orf72-ALS/FTD field has been plagued by a lack of reliable tools to monitor this genomic locus and its RNA and protein products. We have validated assays that quantify C9orf72 pathobiology at the DNA, RNA and protein levels using knock-out human iPSC lines as controls. Here we show that single-molecule sequencing can accurately measure the repeat expansion and faithfully report on changes to the C9orf72 locus in what has been a traditionally hard to sequence genomic region. This is of particular value to sizing and phasing the repeat expansion and determining changes to the gene locus after gene editing. We developed ddPCR assays to quantify two major C9orf72 transcript variants, which we validated by selective excision of their distinct transcriptional start sites. Using validated knock-out human iPSC lines, we validated 4 commercially available antibodies (of 9 tested) that were specific for C9orf72 protein quantification by Western blot, but none were specific for immunocytochemistry. We tested 15 combinations of antibodies against dipeptide repeat proteins (DPRs) across 66 concentrations using MSD immunoassay, and found two (against poly-GA and poly-GP) that yielded a 1.5-fold or greater signal increase in patient iPSC-motor neurons compared to knock-out control, and validated them in human postmortem and transgenic mouse brain tissue. Our validated DNA, RNA and protein assays are applicable to discovery research as well as clinical trials.
Collapse
Affiliation(s)
- S E Salomonsson
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - A M Maltos
- Gladstone Institutes, San Francisco, CA, USA
| | - K Gill
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Gladstone Institutes, San Francisco, CA, USA
| | - O Aladesuyi Arogundade
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - K A Brown
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - A Sachdev
- Gladstone Institutes, San Francisco, CA, USA
| | - M Sckaff
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Gladstone Institutes, San Francisco, CA, USA
| | - K J K Lam
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - I J Fisher
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - R S Chouhan
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - V S Van Laar
- Department of Neurological Surgery, The Ohio State University, Columbus, OH, USA
- The Gene Therapy Institute, The Ohio State University, Columbus, OH, USA
| | - C B Marley
- Gladstone Institutes, San Francisco, CA, USA
| | | | - K S Bankiewicz
- Department of Neurological Surgery, The Ohio State University, Columbus, OH, USA
- The Gene Therapy Institute, The Ohio State University, Columbus, OH, USA
| | - Y-C Tsai
- Pacific Biosciences, Menlo Park, CA, USA
| | - B R Conklin
- Gladstone Institutes, San Francisco, CA, USA
- Departments of Medicine, Ophthalmology, and Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - C D Clelland
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA.
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, USA.
| |
Collapse
|
4
|
Pellows LM, Vansuch GE, Chica B, Yang ZY, Ruzicka JL, Willis MA, Clinger A, Brown KA, Seefeldt LC, Peters JW, Dukovic G, Mulder DW, King PW. Low-temperature trapping of N2 reduction reaction intermediates in nitrogenase MoFe protein-CdS quantum dot complexes. J Chem Phys 2023; 159:235102. [PMID: 38117020 DOI: 10.1063/5.0170405] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 11/24/2023] [Indexed: 12/21/2023] Open
Abstract
The biological reduction of N2 to ammonia requires the ATP-dependent, sequential delivery of electrons from the Fe protein to the MoFe protein of nitrogenase. It has been demonstrated that CdS nanocrystals can replace the Fe protein to deliver photoexcited electrons to the MoFe protein. Herein, light-activated electron delivery within the CdS:MoFe protein complex was achieved in the frozen state, revealing that all the electron paramagnetic resonance (EPR) active E-state intermediates in the catalytic cycle can be trapped and characterized by EPR spectroscopy. Prior to illumination, the CdS:MoFe protein complex EPR spectrum was composed of a S = 3/2 rhombic signal (g = 4.33, 3.63, and 2.01) consistent with the FeMo-cofactor in the resting state, E0. Illumination for sequential 1-h periods at 233 K under 1 atm of N2 led to a cumulative attenuation of E0 by 75%. This coincided with the appearance of S = 3/2 and S = 1/2 signals assigned to two-electron (E2) and four-electron (E4) reduced states of the FeMo-cofactor, together with additional S = 1/2 signals consistent with the formation of E6 and E8 states. Simulations of EPR spectra allowed quantification of the different E-state populations, along with mapping of these populations onto the Lowe-Thorneley kinetic scheme. The outcome of this work demonstrates that the photochemical delivery of electrons to the MoFe protein can be used to populate all of the EPR active E-state intermediates of the nitrogenase MoFe protein cycle.
Collapse
Affiliation(s)
- Lauren M Pellows
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, USA
| | - Gregory E Vansuch
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - Bryant Chica
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - Zhi-Yong Yang
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, USA
| | - Jesse L Ruzicka
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, USA
| | - Mark A Willis
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99163, USA
| | - Andrew Clinger
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, USA
| | - Katherine A Brown
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, USA
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99163, USA
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Gordana Dukovic
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, USA
- Materials Science and Engineering, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - David W Mulder
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - Paul W King
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado 80303, USA
| |
Collapse
|
5
|
Wang L, Wong YC, Correira JM, Wancura M, Geiger CJ, Webster SS, Touhami A, Butler BJ, O'Toole GA, Langford RM, Brown KA, Dortdivanlioglu B, Webb L, Cosgriff-Hernandez E, Gordon VD. The accumulation and growth of Pseudomonas aeruginosa on surfaces is modulated by surface mechanics via cyclic-di-GMP signaling. NPJ Biofilms Microbiomes 2023; 9:78. [PMID: 37816780 PMCID: PMC10564899 DOI: 10.1038/s41522-023-00436-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/12/2023] [Indexed: 10/12/2023] Open
Abstract
Attachment of bacteria onto a surface, consequent signaling, and accumulation and growth of the surface-bound bacterial population are key initial steps in the formation of pathogenic biofilms. While recent reports have hinted that surface mechanics may affect the accumulation of bacteria on that surface, the processes that underlie bacterial perception of surface mechanics and modulation of accumulation in response to surface mechanics remain largely unknown. We use thin and thick hydrogels coated on glass to create composite materials with different mechanics (higher elasticity for thin composites; lower elasticity for thick composites) but with the same surface adhesivity and chemistry. The mechanical cue stemming from surface mechanics is elucidated using experiments with the opportunistic human pathogen Pseudomonas aeruginosa combined with finite-element modeling. Adhesion to thin composites results in greater changes in mechanical stress and strain in the bacterial envelope than does adhesion to thick composites with identical surface chemistry. Using quantitative microscopy, we find that adhesion to thin composites also results in higher cyclic-di-GMP levels, which in turn result in lower motility and less detachment, and thus greater accumulation of bacteria on the surface than does adhesion to thick composites. Mechanics-dependent c-di-GMP production is mediated by the cell-surface-exposed protein PilY1. The biofilm lag phase, which is longer for bacterial populations on thin composites than on thick composites, is also mediated by PilY1. This study shows clear evidence that bacteria actively regulate differential accumulation on surfaces of different stiffnesses via perceiving varied mechanical stress and strain upon surface engagement.
Collapse
Affiliation(s)
- Liyun Wang
- Department of Physics, Center for Nonlinear Dynamics, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Yu-Chern Wong
- Department of Physics, Center for Nonlinear Dynamics, The University of Texas at Austin, Austin, TX, 78712, USA
- Department of Mechanical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Joshua M Correira
- Department of Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Megan Wancura
- Department of Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Chris J Geiger
- Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
| | | | - Ahmed Touhami
- Department of Physics and Astronomy University of Texas Rio Grande Valley, One West University Blvd, Brownsville, TX, 78520, USA
| | - Benjamin J Butler
- Surfaces, Microstructure and Fracture Group, Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, UK
| | | | - Richard M Langford
- Surfaces, Microstructure and Fracture Group, Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, UK
| | - Katherine A Brown
- Surfaces, Microstructure and Fracture Group, Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, UK
- Oden Institute for Computational Engineering & Sciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Berkin Dortdivanlioglu
- Department of Civil, Architectural, and Environmental Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Lauren Webb
- Department of Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | | | - Vernita D Gordon
- Department of Physics, Center for Nonlinear Dynamics, The University of Texas at Austin, Austin, TX, 78712, USA.
- LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin, TX, 78712, USA.
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX, 78712, USA.
| |
Collapse
|
6
|
Vansuch G, Mulder DW, Chica B, Ruzicka JL, Yang ZY, Pellows LM, Willis MA, Brown KA, Seefeldt LC, Peters JW, Dukovic G, King PW. Cryo-annealing of Photoreduced CdS Quantum Dot-Nitrogenase MoFe Protein Complexes Reveals the Kinetic Stability of the E 4(2N2H) Intermediate. J Am Chem Soc 2023; 145:21165-21169. [PMID: 37729189 PMCID: PMC10557137 DOI: 10.1021/jacs.3c06832] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Indexed: 09/22/2023]
Abstract
A critical step in the mechanism of N2 reduction to 2NH3 catalyzed by the enzyme nitrogenase is the reaction of the four-electron/four-proton reduced intermediate state of the active-site FeMo-cofactor (E4(4H)). This state is a junction in the catalytic mechanism, either relaxing by the reaction of a metal bound Fe-hydride with a proton forming H2 or going forward with N2 binding coupled to the reductive elimination (re) of two Fe-hydrides as H2 to form the E4(2N2H) state. E4(2N2H) can relax to E4(4H) by the oxidative addition (oa) of H2 and release of N2 or can be further reduced in a series of catalytic steps to release 2NH3. If the H2 re/oa mechanism is correct, it requires that oa of H2 be associative with E4(2N2H). In this report, we have taken advantage of CdS quantum dots in complex with MoFe protein to achieve photodriven electron delivery in the frozen state, with cryo-annealing in the dark, to reveal details of the E-state species and to test the stability of E4(2N2H). Illumination of frozen CdS:MoFe protein complexes led to formation of a population of reduced intermediates. Electron paramagnetic resonance spectroscopy identified E-state signals including E2 and E4(2N2H), as well as signals suggesting the formation of E6 or E8. It is shown that in the frozen state when pN2 is much greater than pH2, the E4(2N2H) state is kinetically stable, with very limited forward or reverse reaction rates. These results establish that the oa of H2 to the E4(2N2H) state follows an associative reaction mechanism.
Collapse
Affiliation(s)
- Gregory
E. Vansuch
- Biosciences
Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - David W. Mulder
- Biosciences
Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Bryant Chica
- Biosciences
Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Jesse L. Ruzicka
- Department
of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Zhi-Yong Yang
- Department
of Chemistry and Biochemistry, Utah State
University, Logan, Utah 84322, United States
| | - Lauren M. Pellows
- Department
of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Mark A. Willis
- Institute
of Biological Chemistry, Washington State
University, Pullman, Washington 99163, United States
| | - Katherine A. Brown
- Biosciences
Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Lance C. Seefeldt
- Department
of Chemistry and Biochemistry, Utah State
University, Logan, Utah 84322, United States
| | - John W. Peters
- Institute
of Biological Chemistry, Washington State
University, Pullman, Washington 99163, United States
- Department
of Chemistry and Biochemistry, University
of Oklahoma, Norman, Oklahoma 73019, United States
| | - Gordana Dukovic
- Department
of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
- Materials
Science and Engineering, University of Colorado
Boulder, Boulder, Colorado 80303, United States
- Renewable
and Sustainable Energy Institute, University
of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Paul W. King
- Biosciences
Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
- Renewable
and Sustainable Energy Institute, University
of Colorado Boulder, Boulder, Colorado 80303, United States
| |
Collapse
|
7
|
Brown KA, Sarkar IN, Crowley KM, Aluthge DP, Chen ES. An Unsupervised Cluster Analysis of Post-COVID-19 Mental Health Outcomes and Associated Comorbidities. AMIA Annu Symp Proc 2023; 2022:289-298. [PMID: 37128434 PMCID: PMC10148293] [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] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The COVID-19 pandemic continues to be widespread, and little is known about mental health impacts from dealing with the disease itself. This retrospective study used a deidentified health information exchange (HIE) dataset of electronic health record data from the state of Rhode Island and characterized different subgroups of the positive COVID-19 population. Three different clustering methods were explored to identify patterns of condition groupings in this population. Increased incidence of mental health conditions was seen post-COVID-19 diagnosis, and these individuals exhibited higher prevalence of comorbidities compared to the negative control group. A self-organizing map cluster analysis showed patterns of mental health conditions in half of the clusters. One mental health cluster revealed a higher comorbidity index and higher severity of COVID-19 disease. The clinical features identified in this study motivate the need for more in-depth analysis to predict and identify individuals at high risk for developing mental illness post-COVID-19 diagnosis.
Collapse
Affiliation(s)
| | - Indra Neil Sarkar
- Center for Biomedical Informatics, Brown University, Providence RI
- Rhode Island Quality Institute, Providence RI
| | - Karen M Crowley
- Center for Biomedical Informatics, Brown University, Providence RI
| | - Dilum P Aluthge
- Center for Biomedical Informatics, Brown University, Providence RI
- Rhode Island Quality Institute, Providence RI
| | - Elizabeth S Chen
- Center for Biomedical Informatics, Brown University, Providence RI
| |
Collapse
|
8
|
Wong YY, Harbison JE, Hope CM, Gundsambuu B, Brown KA, Wong SW, Brown CY, Couper JJ, Breen J, Liu N, Pederson SM, Köhne M, Klee K, Schultze J, Beyer M, Sadlon T, Barry SC. Parallel recovery of chromatin accessibility and gene expression dynamics from frozen human regulatory T cells. Sci Rep 2023; 13:5506. [PMID: 37016052 PMCID: PMC10073253 DOI: 10.1038/s41598-023-32256-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 03/24/2023] [Indexed: 04/06/2023] Open
Abstract
Epigenetic features such as DNA accessibility dictate transcriptional regulation in a cell type- and cell state- specific manner, and mapping this in health vs. disease in clinically relevant material is opening the door to new mechanistic insights and new targets for therapy. Assay for Transposase Accessible Chromatin Sequencing (ATAC-seq) allows chromatin accessibility profiling from low cell input, making it tractable on rare cell populations, such as regulatory T (Treg) cells. However, little is known about the compatibility of the assay with cryopreserved rare cell populations. Here we demonstrate the robustness of an ATAC-seq protocol comparing primary Treg cells recovered from fresh or cryopreserved PBMC samples, in the steady state and in response to stimulation. We extend this method to explore the feasibility of conducting simultaneous quantitation of chromatin accessibility and transcriptome from a single aliquot of 50,000 cryopreserved Treg cells. Profiling of chromatin accessibility and gene expression in parallel within the same pool of cells controls for cellular heterogeneity and is particularly beneficial when constrained by limited input material. Overall, we observed a high correlation of accessibility patterns and transcription factor dynamics between fresh and cryopreserved samples. Furthermore, highly similar transcriptomic profiles were obtained from whole cells and from the supernatants recovered from ATAC-seq reactions. We highlight the feasibility of applying these techniques to profile the epigenomic landscape of cells recovered from cryopreservation biorepositories.
Collapse
Affiliation(s)
- Ying Y Wong
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Jessica E Harbison
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
- Women's and Children's Hospital, North Adelaide, Australia
| | - Christopher M Hope
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
- Women's and Children's Hospital, North Adelaide, Australia
| | | | - Katherine A Brown
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Soon W Wong
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Cheryl Y Brown
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
- Women's and Children's Hospital, North Adelaide, Australia
| | - Jennifer J Couper
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
- Women's and Children's Hospital, North Adelaide, Australia
| | - Jimmy Breen
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Ning Liu
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Stephen M Pederson
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Maren Köhne
- German Center for Neurodegenerative Diseases, University of Bonn, Bonn, Germany
| | - Kathrin Klee
- German Center for Neurodegenerative Diseases, University of Bonn, Bonn, Germany
| | - Joachim Schultze
- German Center for Neurodegenerative Diseases, University of Bonn, Bonn, Germany
| | - Marc Beyer
- German Center for Neurodegenerative Diseases, University of Bonn, Bonn, Germany
| | - Timothy Sadlon
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
- Women's and Children's Hospital, North Adelaide, Australia
| | - Simon C Barry
- Robinson Research Institute, University of Adelaide, Adelaide, Australia.
- Women's and Children's Hospital, North Adelaide, Australia.
| |
Collapse
|
9
|
Wang L, Wong YC, Correira JM, Wancura M, Geiger CJ, Webster SS, Butler BJ, O’Toole GA, Langford RM, Brown KA, Dortdivanlioglu B, Webb L, Cosgriff-Hernandez E, Gordon VD. Bacterial mechanosensing of surface stiffness promotes signaling and growth leading to biofilm formation by Pseudomonas aeruginosa. bioRxiv 2023:2023.01.26.525810. [PMID: 36747833 PMCID: PMC9900894 DOI: 10.1101/2023.01.26.525810] [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] [Indexed: 01/30/2023]
Abstract
The attachment of bacteria onto a surface, consequent signaling, and the accumulation and growth of the surface-bound bacterial population are key initial steps in the formation of pathogenic biofilms. While recent reports have hinted that the stiffness of a surface may affect the accumulation of bacteria on that surface, the processes that underlie bacterial perception of and response to surface stiffness are unknown. Furthermore, whether, and how, the surface stiffness impacts biofilm development, after initial accumulation, is not known. We use thin and thick hydrogels to create stiff and soft composite materials, respectively, with the same surface chemistry. Using quantitative microscopy, we find that the accumulation, motility, and growth of the opportunistic human pathogen Pseudomonas aeruginosa respond to surface stiffness, and that these are linked through cyclic-di-GMP signaling that depends on surface stiffness. The mechanical cue stemming from surface stiffness is elucidated using finite-element modeling combined with experiments - adhesion to stiffer surfaces results in greater changes in mechanical stress and strain in the bacterial envelope than does adhesion to softer surfaces with identical surface chemistry. The cell-surface-exposed protein PilY1 acts as a mechanosensor, that upon surface engagement, results in higher cyclic-di-GMP levels, lower motility, and greater accumulation on stiffer surfaces. PilY1 impacts the biofilm lag phase, which is extended for bacteria attaching to stiffer surfaces. This study shows clear evidence that bacteria actively respond to different stiffness of surfaces where they adhere via perceiving varied mechanical stress and strain upon surface engagement.
Collapse
Affiliation(s)
- Liyun Wang
- Department of Physics, Center for Nonlinear Dynamics, The University of Texas at Austin, Austin, TX 78712, USA
- Present address: Max Planck Institute for Terrestrial Microbiology, Marburg, 35043, Germany
| | - Yu-Chern Wong
- Department of Physics, Center for Nonlinear Dynamics, The University of Texas at Austin, Austin, TX 78712, USA
- Department of Mechanical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Joshua M. Correira
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712 USA
| | - Megan Wancura
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712 USA
| | - Chris J Geiger
- Geisel School of Medicine at Dartmouth, Hanover, NH 03755 USA
| | | | - Benjamin J. Butler
- Surfaces, Microstructure and Fracture Group, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | | | - Richard M. Langford
- Surfaces, Microstructure and Fracture Group, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Katherine A. Brown
- Surfaces, Microstructure and Fracture Group, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
- Oden Institute for Computational Engineering & Sciences, The University of Texas at Austin, Austin, TX 78712
| | - Berkin Dortdivanlioglu
- Department of Civil, Architectural, and Environmental Engineering, The University of Texas at Austin, Austin, TX 78712 USA
| | - Lauren Webb
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712 USA
| | | | - Vernita D. Gordon
- Department of Physics, Center for Nonlinear Dynamics, The University of Texas at Austin, Austin, TX 78712, USA
- LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin, TX 78712, USA
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX 78712, USA
| |
Collapse
|
10
|
Smolinski SL, Lubner CE, Guo Z, Artz JH, Brown KA, Mulder DW, King PW. Correction: The influence of electron utilization pathways on photosystem I photochemistry in Synechocystis sp. PCC 6803. RSC Adv 2022; 13:742. [PMID: 36683772 PMCID: PMC9808578 DOI: 10.1039/d2ra90130g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 01/04/2023] Open
Abstract
[This corrects the article DOI: 10.1039/D2RA01295B.].
Collapse
Affiliation(s)
- Sharon L. Smolinski
- National Renewable Energy Laboratory15013 Denver West ParkwayGoldenCO80401USA
| | - Carolyn E. Lubner
- National Renewable Energy Laboratory15013 Denver West ParkwayGoldenCO80401USA
| | - Zhanjun Guo
- National Renewable Energy Laboratory15013 Denver West ParkwayGoldenCO80401USA
| | - Jacob H. Artz
- National Renewable Energy Laboratory15013 Denver West ParkwayGoldenCO80401USA
| | - Katherine A. Brown
- National Renewable Energy Laboratory15013 Denver West ParkwayGoldenCO80401USA
| | - David W. Mulder
- National Renewable Energy Laboratory15013 Denver West ParkwayGoldenCO80401USA
| | - Paul W. King
- National Renewable Energy Laboratory15013 Denver West ParkwayGoldenCO80401USA
| |
Collapse
|
11
|
Smolinski SL, Lubner CE, Guo Z, Artz JH, Brown KA, Mulder DW, King PW. The influence of electron utilization pathways on photosystem I photochemistry in Synechocystis sp. PCC 6803. RSC Adv 2022; 12:14655-14664. [PMID: 35702219 PMCID: PMC9109680 DOI: 10.1039/d2ra01295b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/06/2022] [Indexed: 01/24/2023] Open
Abstract
The capacity of cyanobacteria to adapt to highly dynamic photon flux and nutrient availability conditions results from controlled management and use of reducing power, and is a major contributing factor to the efficiency of photosynthesis in aquatic environments. The response to changing conditions includes modulating gene expression and protein-protein interactions that serve to adjust the use of electron flux and mechanisms that control photosynthetic electron transport (PET). In this regard, the photochemical activity of photosystem I (PSI) reaction centers can support balancing of cyclic (CEF) and linear electron flow (LEF), and the coupling of redox carriers for use by electron utilization pathways. Therefore, changes in the utilization of reducing power might be expected to result in compensating changes at PSI as a means to support balance of electron flux. To understand this functional relationship, we investigated the properties of PSI and its photochemical activity in cells that lack flavodiiron 1 catalyzed oxygen reduction activity (ORR1). In the absence of ORR1, the oxygen evolution and consumption rates declined together with a shift in the oligomeric form of PSI towards monomers. The effect of these changes on PSI energy and electron transfer properties was examined in isolated trimer and monomer fractions of PSI reaction centers. Collectively, the results demonstrate that PSI photochemistry is modulated through coordination with the depletion of electron demand in the absence of ORR1.
Collapse
Affiliation(s)
- Sharon L. Smolinski
- National Renewable Energy Laboratory15013 Denver West ParkwayGoldenCO80401USA
| | - Carolyn E. Lubner
- National Renewable Energy Laboratory15013 Denver West ParkwayGoldenCO80401USA
| | - Zhanjun Guo
- National Renewable Energy Laboratory15013 Denver West ParkwayGoldenCO80401USA
| | - Jacob H. Artz
- National Renewable Energy Laboratory15013 Denver West ParkwayGoldenCO80401USA
| | - Katherine A. Brown
- National Renewable Energy Laboratory15013 Denver West ParkwayGoldenCO80401USA
| | - David W. Mulder
- National Renewable Energy Laboratory15013 Denver West ParkwayGoldenCO80401USA
| | - Paul W. King
- National Renewable Energy Laboratory15013 Denver West ParkwayGoldenCO80401USA
| |
Collapse
|
12
|
Chica B, Ruzicka J, Pellows LM, Kallas H, Kisgeropoulos E, Vansuch GE, Mulder DW, Brown KA, Svedruzic D, Peters JW, Dukovic G, Seefeldt LC, King PW. Dissecting Electronic-Structural Transitions in the Nitrogenase MoFe Protein P-Cluster during Reduction. J Am Chem Soc 2022; 144:5708-5712. [PMID: 35315658 PMCID: PMC8991001 DOI: 10.1021/jacs.1c13311] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The [8Fe-7S] P-cluster of nitrogenase MoFe protein mediates electron transfer from nitrogenase Fe protein during the catalytic production of ammonia. The P-cluster transitions between three oxidation states, PN, P+, P2+ of which PN↔P+ is critical to electron exchange in the nitrogenase complex during turnover. To dissect the steps in formation of P+ during electron transfer, photochemical reduction of MoFe protein at 231-263 K was used to trap formation of P+ intermediates for analysis by EPR. In complexes with CdS nanocrystals, illumination of MoFe protein led to reduction of the P-cluster P2+ that was coincident with formation of three distinct EPR signals: S = 1/2 axial and rhombic signals, and a high-spin S = 7/2 signal. Under dark annealing the axial and high-spin signal intensities declined, which coincided with an increase in the rhombic signal intensity. A fit of the time-dependent changes of the axial and high-spin signals to a reaction model demonstrates they are intermediates in the formation of the P-cluster P+ resting state and defines how spin-state transitions are coupled to changes in P-cluster oxidation state in MoFe protein during electron transfer.
Collapse
Affiliation(s)
- Bryant Chica
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Jesse Ruzicka
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Lauren M Pellows
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Hayden Kallas
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Effie Kisgeropoulos
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Gregory E Vansuch
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - David W Mulder
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Katherine A Brown
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Drazenka Svedruzic
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99163, United States
| | - Gordana Dukovic
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States.,Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado 80309, United States.,Materials Science and Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Paul W King
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States.,Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado 80309, United States
| |
Collapse
|
13
|
Eisman AS, Brown KA, Chen ES, Sarkar IN. Clinical Note Section Detection Using a Hidden Markov Model of Unified Medical Language System Semantic Types. AMIA Annu Symp Proc 2022; 2021:418-427. [PMID: 35308919 PMCID: PMC8861726] [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] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Clinical notes are a rich source of biomedical data for natural language processing (NLP). The identification of note sections represents a first step in creating portable NLP tools. Here, a system that used a heterogeneous hidden Markov model (HMM) was designed to identify seven note sections: (1) Medical History, (2) Medications, (3) Family and Social History, (4) Physical Exam, (5) Labs and Imaging, (6) Assessment and Plan, and (7) Review of Systems. Unified Medical Language System (UMLS) concepts were identified using MetaMap, and UMLS semantic type distributions for each section type were empirically determined. The UMLS semantic type distributions were used to train the HMM for identifying clinical note sections. The system was evaluated relative to a template boundary model using manually annotated notes from the Medical Information Mart for Intensive Care III. The results show promise for an approach to segment clinical notes into sections for subsequent NLP tasks.
Collapse
Affiliation(s)
- Aaron S Eisman
- Center for Biomedical Informatics, Brown University, Providence RI
- The Warren Alpert Medical School, Brown University, Providence, RI
| | | | - Elizabeth S Chen
- Center for Biomedical Informatics, Brown University, Providence RI
- The Warren Alpert Medical School, Brown University, Providence, RI
- School of Public Health, Brown University, Providence, RI
| | - Indra Neil Sarkar
- Center for Biomedical Informatics, Brown University, Providence RI
- The Warren Alpert Medical School, Brown University, Providence, RI
- School of Public Health, Brown University, Providence, RI
- Rhode Island Quality Institute, Providence, RI
| |
Collapse
|
14
|
Ku JWK, Marsh ST, Nai MH, Robinson KS, Teo DET, Zhong FL, Brown KA, Lim TC, Lim CT, Gan YH. Skin models for cutaneous melioidosis reveal Burkholderia infection dynamics at wound's edge with inflammasome activation, keratinocyte extrusion and epidermal detachment. Emerg Microbes Infect 2021; 10:2326-2339. [PMID: 34821529 PMCID: PMC8654412 DOI: 10.1080/22221751.2021.2011621] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Melioidosis is a serious infectious disease endemic in Southeast Asia, Northern Australia and has been increasingly reported in other tropical and subtropical regions in the world. Percutaneous inoculation through cuts and wounds on the skin is one of the major modes of natural transmission. Despite cuts in skin being a major route of entry, very little is known about how the causative bacterium Burkholderia pseudomallei initiates an infection at the skin and the disease manifestation at the skin known as cutaneous melioidosis. One key issue is the lack of suitable and relevant infection models. Employing an in vitro 2D keratinocyte cell culture, a 3D skin equivalent fibroblast-keratinocyte co-culture and ex vivo organ culture from human skin, we developed infection models utilizing surrogate model organism Burkholderia thailandensis to investigate Burkholderia-skin interactions. Collectively, these models show that the bacterial infection was largely limited at the wound’s edge. Infection impedes wound closure, triggers inflammasome activation and cellular extrusion in the keratinocytes as a potential way to control bacterial infectious load at the skin. However, extensive infection over time could result in the epidermal layer being sloughed off, potentially contributing to formation of skin lesions.
Collapse
Affiliation(s)
- Joanne Wei Kay Ku
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Supatra Tharinee Marsh
- Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
| | - Mui Hoon Nai
- Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
| | | | - Daniel Eng Thiam Teo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Franklin Lei Zhong
- Skin Research Institute of Singapore (SRIS), Immunos, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Katherine A Brown
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.,Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX, USA
| | - Thiam Chye Lim
- Division of Plastic, Reconstructive &Aesthetic Surgery, National University Health System, Singapore, Singapore
| | - Chwee Teck Lim
- Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore.,Institute for Health Innovation and Technology (iHealthtech), National University of Singapore, Singapore, Singapore
| | - Yunn-Hwen Gan
- Department of Biochemistry, National University of Singapore, Singapore, Singapore.,Infectious Diseases Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| |
Collapse
|
15
|
Tiribocchi A, Montessori A, Lauricella M, Bonaccorso F, Brown KA, Succi S. Microscale modelling of dielectrophoresis assembly processes. Philos Trans A Math Phys Eng Sci 2021; 379:20200407. [PMID: 34455845 DOI: 10.1098/rsta.2020.0407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/04/2021] [Indexed: 06/13/2023]
Abstract
This work presents a microscale approach for simulating the dielectrophoresis assembly of polarizable particles under an external electric field. The model is shown to capture interesting dynamical and topological features, such as the formation of chains of particles and their incipient aggregation into hierarchical structures. A quantitative characterization in terms of the number and size of these structures is also discussed. This computational model could represent a viable numerical tool to study the mechanical properties of particle-based hierarchical materials and suggest new strategies for enhancing their design and manufacture. This article is part of the theme issue 'Progress in mesoscale methods for fluid dynamics simulation'.
Collapse
Affiliation(s)
- A Tiribocchi
- Center for Life Nano Science@La Sapienza, Istituto Italiano di Tecnologia, 00161 Roma, Italy
- Istituto per le Applicazioni del Calcolo CNR, via dei Taurini, 19, 00185 Rome, Italy
| | - A Montessori
- Istituto per le Applicazioni del Calcolo CNR, via dei Taurini, 19, 00185 Rome, Italy
| | - M Lauricella
- Istituto per le Applicazioni del Calcolo CNR, via dei Taurini, 19, 00185 Rome, Italy
| | - F Bonaccorso
- Center for Life Nano Science@La Sapienza, Istituto Italiano di Tecnologia, 00161 Roma, Italy
- Istituto per le Applicazioni del Calcolo CNR, via dei Taurini, 19, 00185 Rome, Italy
- Department of Physics and INFN, University of Rome 'Tor Vergata', Via della Ricerca Scientifica, 1 00133 Rome, Italy
| | - K A Brown
- Department of Mechanical Engineering, Boston University, Boston, MA 02215, USA
| | - S Succi
- Center for Life Nano Science@La Sapienza, Istituto Italiano di Tecnologia, 00161 Roma, Italy
- Istituto per le Applicazioni del Calcolo CNR, via dei Taurini, 19, 00185 Rome, Italy
- Institute for Applied Computational Science, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| |
Collapse
|
16
|
Hayes KN, He N, Brown KA, Cheung AM, Juurlink DN, Cadarette SM. Over half of seniors who start oral bisphosphonate therapy are exposed for 3 or more years: novel rolling window approach and patterns of use. Osteoporos Int 2021; 32:1413-1420. [PMID: 33415374 DOI: 10.1007/s00198-020-05794-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/10/2020] [Indexed: 12/17/2022]
Abstract
UNLABELLED Most adherence studies only consider treatment following a first prescription. Using an extended follow-up, we found that 60% of seniors starting oral bisphosphonate therapy were exposed for ≥ 3 years (48% for ≥ 5 years). Studies are needed to examine the benefits and harms of continuing bisphosphonate therapy beyond 3 years. INTRODUCTION The purpose of this study was to identify and describe patterns of long-term oral bisphosphonate use among seniors using a novel methodological approach that considers extended follow-up. METHODS Among Ontarians aged 66 years or older, we identified subjects with a first dispensing of alendronate or risedronate between November 2000 and December 2016. We followed them until death or December 2019 to identify patients with ≥ 3 years of bisphosphonate use, defined as a proportion of days covered ≥ 80%, using 3-year rolling windows. We calculated the proportion of patients with long-term therapy (≥ 3 years of use) using Kaplan-Meier estimates. We described patterns of long-term use and compared patient characteristics between patients with and without long-term therapy. RESULTS We identified 260,784 eligible seniors initiating bisphosphonate therapy. Of these, 60% continued therapy ≥ 3 years (77% women), and 48% continued ≥ 5 years. Characteristics did not meaningfully differ between patients with or without long-term therapy. The median length of long-term therapy was 7.0 (IQR 5.1) years for women and 6.1 (IQR 4.3) years for men. Only 20% experienced a treatment gap before long-term therapy, yet 50% experienced a treatment gap of ≥ 120 days after a median 5.3 years of therapy. Eighty-one percent who returned to therapy following a treatment gap re-initiated an oral bisphosphonate, with 18% switching to denosumab. CONCLUSIONS Among seniors initiating oral bisphosphonates, we found that 60% receive at least 3 years of therapy when using an extended follow-up. Studies are needed to examine the benefits and harms of continuing bisphosphonate therapy beyond 3 years.
Collapse
Affiliation(s)
- K N Hayes
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.
- Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, ON, M5S 3M2, Canada.
| | - N He
- Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, ON, M5S 3M2, Canada
- ICES, Toronto, ON, Canada
| | - K A Brown
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- ICES, Toronto, ON, Canada
- Public Health Ontario, Toronto, ON, Canada
| | - A M Cheung
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- Department of Medicine, University Health Network, University of Toronto, Toronto, ON, Canada
| | - D N Juurlink
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- ICES, Toronto, ON, Canada
- Sunnybrook Research Institute, Toronto, ON, Canada
| | - S M Cadarette
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, ON, M5S 3M2, Canada
- ICES, Toronto, ON, Canada
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| |
Collapse
|
17
|
Clark G, Brown KA, Tripathy MK, Roux SJ. Recent Advances Clarifying the Structure and Function of Plant Apyrases (Nucleoside Triphosphate Diphosphohydrolases). Int J Mol Sci 2021; 22:ijms22063283. [PMID: 33807069 PMCID: PMC8004787 DOI: 10.3390/ijms22063283] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/18/2021] [Accepted: 03/20/2021] [Indexed: 01/22/2023] Open
Abstract
Studies implicating an important role for apyrase (NTPDase) enzymes in plant growth and development began appearing in the literature more than three decades ago. After early studies primarily in potato, Arabidopsis and legumes, especially important discoveries that advanced an understanding of the biochemistry, structure and function of these enzymes have been published in the last half-dozen years, revealing that they carry out key functions in diverse other plants. These recent discoveries about plant apyrases include, among others, novel findings on its crystal structures, its biochemistry, its roles in plant stress responses and its induction of major changes in gene expression when its expression is suppressed or enhanced. This review will describe and discuss these recent advances and the major questions about plant apyrases that remain unanswered.
Collapse
Affiliation(s)
- Greg Clark
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA; (G.C.); (K.A.B.)
| | - Katherine A. Brown
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA; (G.C.); (K.A.B.)
- Cavendish Laboratory, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE, UK
| | | | - Stanley J. Roux
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA; (G.C.); (K.A.B.)
- Correspondence: ; Tel.: +1-512-471-4238
| |
Collapse
|
18
|
Brown KA, Sarkar IN, Chen ES. Mental Health Comorbidity Analysis in Pediatric Patients with Autism Spectrum Disorder Using Rhode Island Medical Claims Data. AMIA Annu Symp Proc 2021; 2020:263-272. [PMID: 33936398 PMCID: PMC8075466] [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] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Identification of comorbidity subgroups linked with Autism Spectrum Disorder (ASD) could provide promising insight into learning more about this disorder. This study sought to use the Rhode Island All-Payer Claims Database to examine mental health conditions linked to ASD. Medical claims data for ASD patients and one or more mental health conditions were analyzed using descriptive statistics, association rule mining (ARM), and sequential pattern mining (SPM). The results indicated that patients with ASD have a higher proportion of mental health diagnoses than the general pediatric population. ARM and SPM methods identified patterns of comorbidities commonly seen among ASD patients. Based on the observed patterns and temporal sequences, suicidal ideation, mood disorders, anxiety, and conduct disorders may need focused attention prospectively. Understanding more about groupings of ASD patients and their comorbidity burden can help bridge gaps in knowledge and make strides toward improved outcomes for patients with ASD.
Collapse
Affiliation(s)
- Katherine A Brown
- Brown Center for Biomedical Informatics, Brown University, Providence RI
| | - Indra Neil Sarkar
- Brown Center for Biomedical Informatics, Brown University, Providence RI
- Rhode Island Quality Institute, Providence RI
| | - Elizabeth S Chen
- Brown Center for Biomedical Informatics, Brown University, Providence RI
| |
Collapse
|
19
|
Butler B, Nguyen TT, Williams A, Tucker A, Proud WG, Brown KA. Use of a Shock Tube Platform in the Replication of Blast Lung Injury. EPJ Web Conf 2021. [DOI: 10.1051/epjconf/202125001024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
War and asymmetrical conflicts are becoming increasingly prevalent in the modern world. Due to improvements in conflict medicine, survivable injuries are now more severe than they once were. Therefore, it is now more important than ever that there exist scientific and engineering methods for replicating wartime injuries in the context of the laboratory. We have developed one such method: a shock tube platform for testing ex vivo samples of the porcine respiratory system. Using this platform, we can, to some extent, simulate the pathophysiological consequences of blast lung. This is a condition commonly present in victims of explosive blasts, both those due to typical armaments and Improvised Explosive Devices (IEDs). Presented here are the results of experiments conducted using porcine bronchiole tissue as ex vivo organ cultures. Data presented show epithelial damage, consistent with known trauma-induced cell injury that can lead to acute respiratory distress syndrome (ARDS).
Collapse
|
20
|
Abstract
Purpose The aim of this study was to examine whether acoustic dysarthria characteristics align with overall motor profile in individuals with Parkinson's disease (PD). Potential speech differences between tremor-dominant and non-tremor-dominant subtypes are theoretically motivated but empirically inconclusive. Method Twenty-seven individuals with dysarthria from PD provided a contextual speech sample. Participants were grouped into non-tremor-dominant (n = 12) and tremor-dominant (n = 15) motor subtypes according to the Unified Parkinson Disease Rating Scale. Dependent speech variables included fundamental frequency range, average pause duration, cepstral peak prominence, stuttering dysfluencies, and maze dysfluencies. Results There were no significant differences between the speech of the tremor-dominant and non-tremor-dominant groups. High within-group variability existed across parameters and motor subtypes. Conclusion Speech characteristics across the areas of phonation, prosody, and fluency did not differ appreciably between PD motor subtypes.
Collapse
Affiliation(s)
- Katherine A Brown
- Department of Speech and Hearing Sciences, University of Washington, Seattle
| | - Kristie A Spencer
- Department of Speech and Hearing Sciences, University of Washington, Seattle
| |
Collapse
|
21
|
Brown KA, Ruzicka J, Kallas H, Chica B, Mulder DW, Peters JW, Seefeldt LC, Dukovic G, King PW. Excitation-Rate Determines Product Stoichiometry in Photochemical Ammonia Production by CdS Quantum Dot-Nitrogenase MoFe Protein Complexes. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02933] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Katherine A. Brown
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Jesse Ruzicka
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Hayden Kallas
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Bryant Chica
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - David W. Mulder
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - John W. Peters
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99163, United States
| | - Lance C. Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Gordana Dukovic
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Paul W. King
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| |
Collapse
|
22
|
Pissarenko A, Yang W, Quan H, Poyer B, Williams A, Brown KA, Meyers MA. The toughness of porcine skin: Quantitative measurements and microstructural characterization. J Mech Behav Biomed Mater 2020; 109:103848. [PMID: 32543412 DOI: 10.1016/j.jmbbm.2020.103848] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 04/14/2020] [Accepted: 05/04/2020] [Indexed: 11/18/2022]
Abstract
An exceptional tear resistance is required of the skin to protect the body from external attacks, environmental damage, and other forms of aggression. To estimate the toughness of juvenile porcine skin, we conduct two types of experiments on pre-notched specimens, placing the tissue under shear (Mode III) by using the classical trouser test with a 25 mm long pre-notch, and opening (Mode I) with an experimental setup with the same pre-notch length. We obtain two distinct average toughness values of JIIIc≈20.4kJ/m2 and JIc=30.4kJ/m2, as a result of differences between these two modes of crack-tip loading and propagation, and collagen alignment. Digital image correlation coupled with single edge notch tests of 10 mm × 30 mm skin samples enables the mapping of the local strains around the tip of the crack. Effects of sample orientation and initial notch size ratio on the strain profile and on the net-section failure stress are discussed. The evaluation of the structure at the crack tip and regions undergoing more uniform states of deformation is conducted by ex situ transmission electron microscopy and in situ environmental scanning electron microscopy. Prior to crack propagation, the stress concentration is decreased by redistributing loads away from the crack tip, illustrated by gradual recruitment of collagen fibers ahead of the crack tip, thus delaying crack growth. After the crack has propagated, collagen fibers are substantially damaged, marked by delamination and recoil of the collagen fibrils.
Collapse
Affiliation(s)
| | - Wen Yang
- University of California, San Diego, CA, USA; Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Boris Poyer
- École Normale Supérieure de Paris-Saclay, Cachan, France
| | | | - Katherine A Brown
- University of Cambridge, Cambridge, UK; University of Texas Austin, Austin, TX, USA
| | | |
Collapse
|
23
|
Chica B, Ruzicka J, Kallas H, Mulder DW, Brown KA, Peters JW, Seefeldt LC, Dukovic G, King PW. Defining Intermediates of Nitrogenase MoFe Protein during N 2 Reduction under Photochemical Electron Delivery from CdS Quantum Dots. J Am Chem Soc 2020; 142:14324-14330. [PMID: 32787260 DOI: 10.1021/jacs.0c06343] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Coupling the nitrogenase MoFe protein to light-harvesting semiconductor nanomaterials replaces the natural electron transfer complex of Fe protein and ATP and provides low-potential photoexcited electrons for photocatalytic N2 reduction. A central question is how direct photochemical electron delivery from nanocrystals to MoFe protein is able to support the multielectron ammonia production reaction. In this study, low photon flux conditions were used to identify the initial reaction intermediates of CdS quantum dot (QD):MoFe protein nitrogenase complexes under photochemical activation using EPR. Illumination of CdS QD:MoFe protein complexes led to redox changes in the MoFe protein active site FeMo-co observed as the gradual decline in the E0 resting state intensity that was accompanied by an increase in the intensity of a new "geff = 4.5" EPR signal. The magnetic properties of the geff = 4.5 signal support assignment as a reduced S = 3/2 state, and reaction modeling was used to define it as a two-electron-reduced "E2" intermediate. Use of a MoFe protein variant, β-188Cys, which poises the P cluster in the oxidized P+ state, demonstrated that the P cluster can function as a site of photoexcited electron delivery from CdS to MoFe protein. Overall, the results establish the initial steps for how photoexcited CdS delivers electrons into the MoFe protein during reduction of N2 to ammonia and the role of electron flux in the photochemical reaction cycle.
Collapse
Affiliation(s)
- Bryant Chica
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Jesse Ruzicka
- Department of Chemistry, University of Colorado-Boulder, Boulder, Colorado 80309, United States
| | - Hayden Kallas
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - David W Mulder
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Katherine A Brown
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99163, United States
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Gordana Dukovic
- Department of Chemistry, University of Colorado-Boulder, Boulder, Colorado 80309, United States
| | - Paul W King
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| |
Collapse
|
24
|
Spencer KA, Paul J, Brown KA, Ellerbrock T, Sohlberg MM. Cognitive Rehabilitation for Individuals With Parkinson's Disease: Developing and Piloting an External Aids Treatment Program. Am J Speech Lang Pathol 2020; 29:1-19. [PMID: 31697899 DOI: 10.1044/2019_ajslp-19-0078] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Purpose Cognitive deficits are common in Parkinson's disease (PD) and can have a detrimental effect on daily activities. To date, most cognitive treatments have had an impairment-based focus with primary outcome measures of formal neuropsychological test scores. Few, if any, studies have focused on functional improvement or patient-centered goals. Method Three individuals with idiopathic PD participated in an 8-week pilot treatment program to train for the use of compensatory external aids to achieve personalized goals. Goal attainment scaling was the primary outcome measure, which was independently judged by multiple raters at baseline, postintervention, and 1 month posttreatment and analyzed via T-score analysis. Descriptive measures, including self-report and spouse-report rating scales of cognitive functioning, were employed. Results All 3 participants improved in the majority of their laboratory and home goals posttreatment, as measured by goal attainment scaling, and maintained gains for the majority of goals 1 month posttreatment. Conclusions This is the 1st known study to implement an external aids treatment program with patient-centered goals for individuals with cognitive deficits from PD. Positive outcomes were likely influenced by 3 factors: (a) a theoretically motivated focus on external aids; (b) a well-documented, systematic approach to instruction; and (c) the personalization of goals. Supplemental Material https://doi.org/10.23641/asha.10093493.
Collapse
Affiliation(s)
- Kristie A Spencer
- Department of Speech and Hearing Sciences, University of Washington, Seattle
| | - Jennifer Paul
- Department of Speech and Hearing Sciences, University of Washington, Seattle
| | - Katherine A Brown
- Department of Speech and Hearing Sciences, University of Washington, Seattle
| | - Taylor Ellerbrock
- Department of Speech and Hearing Sciences, University of Washington, Seattle
| | | |
Collapse
|
25
|
Brown KA, King PW. Coupling biology to synthetic nanomaterials for semi-artificial photosynthesis. Photosynth Res 2020; 143:193-203. [PMID: 31641988 DOI: 10.1007/s11120-019-00670-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 09/04/2019] [Indexed: 06/10/2023]
Abstract
Biohybrid artificial photosynthesis aims to combine the advantages of biological specificity with a range of synthetic nanomaterials to create innovative semi-synthetic systems for solar-to-chemical conversion. Biological systems utilize highly efficient molecular catalysts for reduction-oxidation reactions. They can operate with minimal overpotentials while selectively channeling reductant energy into specific transformation chemistries and product forming pathways. Nanomaterials can be synthesized to have efficient light-absorption capacity and tuneability of charge separation by manipulation of surface chemistries and bulk compositions. These complementary aspects have been combined in a variety of ways, for example, where biological light-harvesting complexes function as antenna for nanoparticle catalysts or where nanoparticles function as light capture, charge separation components for coupling to chemical conversion by redox enzymes and whole cells. The synthetic diversity that is possible with biohybrids is still being explored. The progress arising from creative approaches is generating new model systems to inspire scale-up technologies and generate understanding of the fundamental mechanisms that control energy conversion at the molecular scale. These efforts are leading to discoveries of essential design principles that can enable the development of scalable artificial photosynthesis systems.
Collapse
Affiliation(s)
| | - Paul W King
- National Renewable Energy Laboratory, Golden, CO, 80402, USA
| |
Collapse
|
26
|
Hoogerheide DP, Forsyth VT, Brown KA. Neutron scattering for STRUCTURAL BIOLOGY: Modern neutron sources illuminate the complex functions of living systems. Phys Today 2020; 73:10.1063/pt.3.4498. [PMID: 38487716 PMCID: PMC10938470 DOI: 10.1063/pt.3.4498] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
Modern neutron sources illuminate the complex functions of living systems.
Collapse
Affiliation(s)
- David P Hoogerheide
- National Institute of Standards and Technology Center for Neutron Research in Gaithersburg, Maryland
| | - V Trevor Forsyth
- Institut Laue-Langevin in Grenoble, France; he also holds a chair in biophysics at Keele University in the UK
| | - Katherine A Brown
- Cavendish Laboratory at Cambridge University in the UK and at the University of Texas at Austin
| |
Collapse
|
27
|
Pissarenko A, Yang W, Quan H, Brown KA, Williams A, Proud WG, Meyers MA. Tensile behavior and structural characterization of pig dermis. Acta Biomater 2019; 86:77-95. [PMID: 30660003 DOI: 10.1016/j.actbio.2019.01.023] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 01/10/2019] [Accepted: 01/14/2019] [Indexed: 11/17/2022]
Abstract
Skin, the outermost layer of the body, fulfills a broad range of functions, protecting internal organs from damage and infection, while regulating the body's temperature and water content via the exchange of heat and fluids. It must be able to withstand and recover from extensive deformation and damage that can occur during growth, movement, and potential injuries. A detailed investigation of the evolution of the collagen architecture of the dermis as a function of deformation is conducted, which reveals new aspects that help us to understand the mechanical response of skin. Juvenile pig is used as a model material because of its similarity to human skin. The dermis is found to have a tridimensional woven structure of collagen fibers, which evolves with deformation. After failure, we observe that the fibers have straightened and aligned in the direction of tension. The effects of strain-rate change, cyclic loading, stress relaxation, and orientation are quantitatively established. Digital image correlation techniques are implemented to quantify skin's anisotropy; measurements of the Poisson ratio are reported. This is coupled with transmission electron microscopy which enables obtaining quantitative strain parameters evaluated through the orientation and curvature of the collagen fibers and their changes, for the first time in all three dimensions of the tissue. A model experiment using braided human hair in tension exhibits a similar J-curve response to skin, and we propose that this fiber configuration is at least partially responsible for the monotonic increase of the tangent modulus of skin with strain. The obtained results are intended to serve as a basis for structurally-based models of skin. STATEMENT OF SIGNIFICANCE: Our study reveals a new aspect of the dermis: it is comprised of a tridimensional woven structure of collagen fibers, which evolves with deformation. This is enabled by primarily two techniques, transmission electron microscopy on three perpendicular planes and confocal images with second harmonic generation fluorescence of collagen, captured at different intervals of depth. After failure, the fibers have straightened and aligned in the direction of tension. Digital image correlation techniques are implemented to quantify skin's anisotropy; measurements of the Poisson ratio are reported. A model experiment using braided human hair in tension exhibits a similar J-curve response to skin, and we propose that this fiber configuration is at least partially responsible for the monotonic increase of the tangent modulus of skin with strain.
Collapse
Affiliation(s)
| | - Wen Yang
- University of California, San Diego, CA, USA; Lawrence Berkeley National Laboratory, USA.
| | | | - Katherine A Brown
- Cavendish Laboratory, University of Cambridge, Cambridge, UK; Department of Chemistry, The University of Texas at Austin, Austin, Texas, USA
| | - Alun Williams
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - William G Proud
- Institute of Shock Physics, Imperial College London, London, UK
| | | |
Collapse
|
28
|
Cook GM, Shang P, Li Y, Brown KA, Dinan A, Fang Y, Firth A, Brierley I. Ribosome profiling of porcine reproductive and respiratory syndrome virus. Access Microbiol 2019. [DOI: 10.1099/acmi.ac2019.po0162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Georgia M. Cook
- 1Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Pengcheng Shang
- 2Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, USA
| | - Yanhua Li
- 2Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, USA
| | - Katherine A Brown
- 1Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Adam Dinan
- 1Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Ying Fang
- 2Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, USA
| | - Andrew Firth
- 1Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Ian Brierley
- 1Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
29
|
Kelty ML, Morris W, Gallagher AT, Anderson JS, Brown KA, Mirkin CA, Harris TD. High-throughput synthesis and characterization of nanocrystalline porphyrinic zirconium metal-organic frameworks. Chem Commun (Camb) 2018; 52:7854-7. [PMID: 27247981 DOI: 10.1039/c6cc03264h] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We describe and employ a high-throughput screening method to accelerate the synthesis and identification of pure-phase, nanocrystalline metal-organic frameworks (MOFs). We demonstrate the efficacy of this method through its application to a series of porphyrinic zirconium MOFs, resulting in the isolation of MOF-525, MOF-545, and PCN-223 on the nanoscale.
Collapse
Affiliation(s)
- M L Kelty
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
| | - W Morris
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
| | - A T Gallagher
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
| | - J S Anderson
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
| | - K A Brown
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA. and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - C A Mirkin
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA. and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA and Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, IL 60208, USA
| | - T D Harris
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
| |
Collapse
|
30
|
Abstract
Dysarthria is a common consequence of stroke and can have a detrimental influence on communication and quality of life. Speech-language pathologists (SLPs) play an important role in the evaluation and rehabilitation of stroke survivors who present with dysarthria. An understanding of the physiologic reason behind the altered speech characteristics, such as weakness or incoordination, can facilitate differential diagnosis, guide evaluation strategies, and influence treatment approaches. An initial comprehensive speech evaluation is comprised of examination of the speech mechanism, screening of speech subsystems, perceptual assessment, and intelligibility measurement. Management strategies focus on optimizing communication through compensatory strategies as well as providing physiologic support. The SLP is also responsible for educating family and staff regarding strategies that can facilitate communication.
Collapse
Affiliation(s)
- Kristie A Spencer
- Department of Speech and Hearing Sciences, University of Washington, Seattle, Washington
| | - Katherine A Brown
- Department of Speech and Hearing Sciences, University of Washington, Seattle, Washington
| |
Collapse
|
31
|
Ratzloff MW, Wilker MB, Mulder DW, Lubner CE, Hamby H, Brown KA, Dukovic G, King PW. Activation Thermodynamics and H/D Kinetic Isotope Effect of the Hox to HredH+ Transition in [FeFe] Hydrogenase. J Am Chem Soc 2017; 139:12879-12882. [DOI: 10.1021/jacs.7b04216] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Michael W. Ratzloff
- Biosciences
Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Molly B. Wilker
- Department
of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - David W. Mulder
- Biosciences
Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Carolyn E. Lubner
- Biosciences
Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Hayden Hamby
- Department
of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Katherine A. Brown
- Biosciences
Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Gordana Dukovic
- Department
of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Paul W. King
- Biosciences
Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| |
Collapse
|
32
|
Khanafer N, Daneman N, Greene T, Simor A, Vanhems P, Samore M, Brown KA. Susceptibilities of clinical Clostridium difficile isolates to antimicrobials: a systematic review and meta-analysis of studies since 1970. Clin Microbiol Infect 2017; 24:110-117. [PMID: 28750918 DOI: 10.1016/j.cmi.2017.07.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 07/10/2017] [Accepted: 07/13/2017] [Indexed: 12/29/2022]
Abstract
OBJECTIVES Although exposure to antibiotics can cause Clostridium difficile infection, certain antibiotics are used to treat C. difficile. Measurements of antimicrobial C. difficile activity could help to identify antibiotic risk and emergent resistance. Here, we describe publication patterns relating to C. difficile susceptibilities and estimate minimum inhibitory concentrations (MIC) for antibiotic classes in the published literature between January 1970 and June 2014. METHODS We queried PUBMED and EMBASE for studies reporting antibiotic C. difficile MIC in English or French. We used mixed-effects models to obtain pooled estimates of antibiotic class median MIC (MIC50), 90th percentile of MIC (MIC90), and MIC90:MIC50 ratio. RESULTS Our search identified 182 articles that met our inclusion criteria, of which 27 were retained for meta-analysis. Aminoglycosides (MIC50 120 mg/L, 95% CI 62-250), 3rd (MIC50 75 mg/L, 95% CI 39-130) and 2nd generation cephalosporins (MIC50 64 mg/L, 95% CI 27-140) had the least C. difficile activity. Rifamycins (MIC50 0.034 mg/L, 95% CI 0.012-0.099) and tetracyclines (MIC50 0.29 mg/L, 95% CI 0.054-1.7) had the highest level of activity. The activity of 3rd generation cephalosporins was more than three times lower than that of 1st generation agents (MIC50 19 mg/L, 95% CI 7.0-54). Time-trends in MIC50 were increasing for carbapenems (70% increase per 10 years) while decreasing for tetracyclines (51% decrease per 10 years). CONCLUSIONS We found a 3500-fold variation in antibiotic C. difficile MIC50, with aminoglycosides as the least active agents and rifamycins as the most active. Further research is needed to determine how in vitro measures can help assess patient C. difficile risk and guide antimicrobial stewardship.
Collapse
Affiliation(s)
- N Khanafer
- Service d'Hygiène, Épidémiologie et Prévention, Hôpital Edouard Herriot, Hospices civils de Lyon, Lyon, France; Centre International de Recherche en Infectiologie, Institut national de la santé et de la recherche médicale U1111, Centre National de la Recherche Scientifique UMR5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard 1, Lyon, France.
| | - N Daneman
- Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Canada
| | - T Greene
- Division of Epidemiology, University of Utah, UT, USA
| | - A Simor
- Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Canada
| | - P Vanhems
- Service d'Hygiène, Épidémiologie et Prévention, Hôpital Edouard Herriot, Hospices civils de Lyon, Lyon, France; Centre International de Recherche en Infectiologie, Institut national de la santé et de la recherche médicale U1111, Centre National de la Recherche Scientifique UMR5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard 1, Lyon, France
| | - M Samore
- Division of Epidemiology, University of Utah, UT, USA; Salt Lake City Veterans Affairs Health Care System, Salt Lake City, UT, USA
| | - K A Brown
- Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Canada; Division of Epidemiology, University of Utah, UT, USA; Salt Lake City Veterans Affairs Health Care System, Salt Lake City, UT, USA; Public Health Ontario, Ontario, Canada.
| |
Collapse
|
33
|
Iyengar NM, Brown KA, Zhou XK, Subbaramaiah K, Giri DD, Gucalp A, Howe LR, Zahid H, Bhardwaj P, Wendel NK, Falcone DJ, Morrow M, Wang H, Williams S, Pollak M, Hudis CA, Dannenberg AJ. Abstract PD5-05: Metabolic obesity, adipose inflammation and aromatase: Potential drivers of breast cancer risk in women with normal body mass index. Cancer Res 2017. [DOI: 10.1158/1538-7445.sabcs16-pd5-05] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Elevated body mass index (BMI) is associated with increased risk of postmenopausal breast cancer, which may be partly attributable to an inflammation-aromatase axis. Most individuals with elevated BMI harbor white adipose tissue inflammation (WATi), defined by the presence of crown-like structures in the breast (CLS-B). CLS-B are composed of a dead/dying adipocyte surrounded by CD68+ macrophages. This inflammation is associated with activation of NF-κB and elevated expression of aromatase, which could contribute to tumor development. Additionally, WATi correlates with several circulating changes, including hyperinsulinemia, which increase breast cancer risk. Although breast WATi correlates with rising BMI, it is also present in some normal BMI individuals. Beyond inherited germline syndromes, the etiology of breast cancer in individuals with normal BMI is not well understood. Here we examined the impact of breast WATi on breast aromatase expression and circulating factors in women with normal BMI.
Methods: Non-tumorous breast tissue and fasting blood were collected from 72 women with BMI < 25 kg/m2 undergoing mastectomy at MSKCC. Breast inflammation was detected by the presence of CLS-B using CD68 immunohistochemistry. The primary objective was to determine if breast WATi in normal BMI individuals correlates with elevated aromatase levels in the breast, measured by qPCR, western blotting, immunofluorescence and enzyme activity. Secondary objectives included assessment of breast adipocyte size and circulating metabolic and inflammatory factors.
Results: Breast inflammation was present in 39% of women. Median BMI was 23.0 (range 18.4 to 24.9) in women with breast WATi versus 21.8 (range 17.3 to 24.6) in those without inflammation (P=0.04). Aromatase mRNA expression was positively correlated with WATi (CLS-B/cm2; P=0.002). Those with severe WATi had highest aromatase mRNA levels, compared to those with no or mild WATi (P=0.005). Aromatase protein, assessed by measuring adipose stromal cell-specific immunofluorescence or western blotting, and activity were also higher in CLS-B+ cases compared to CLS-B- (P<0.001). Breast WATi correlated with larger adipocytes (P=0.01) and higher circulating levels of C-reactive protein, leptin, insulin, and triglycerides (P<0.05). Insulin resistance, characterized by the homeostasis model (HOMA2-IR), correlated with breast WATi (P=0.004). Finally, leptin, a known inducer of aromatase and driver of cancer growth, correlated with higher breast aromatase levels (P=0.02) and larger adipocytes (P<0.01).
Conclusions: A metabolically unhealthy state occurs in women with inflamed breast adipose despite having a normal BMI. This subclinical inflammatory state is characterized by elevated aromatase in the breast, insulin resistance, and dysplipidemia. The presence of enlarged adipocytes in the breasts of normal BMI women with inflammation suggests a state of hyperadiposity which could not be predicted based on BMI alone. These findings indicate that normal BMI metabolic obesity may be associated with increased cancer risk. Our results suggest that objective measurements of adiposity rather than BMI may help to identify individuals at increased risk for disease.
Citation Format: Iyengar NM, Brown KA, Zhou XK, Subbaramaiah K, Giri DD, Gucalp A, Howe LR, Zahid H, Bhardwaj P, Wendel NK, Falcone DJ, Morrow M, Wang H, Williams S, Pollak M, Hudis CA, Dannenberg AJ. Metabolic obesity, adipose inflammation and aromatase: Potential drivers of breast cancer risk in women with normal body mass index [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr PD5-05.
Collapse
Affiliation(s)
- NM Iyengar
- Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY; Weill Cornell Medical College, New York, NY; Hudson Institute of Medical Research, Clayton, Victoria, Australia; McGill University, Montreal, QC, Canada
| | - KA Brown
- Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY; Weill Cornell Medical College, New York, NY; Hudson Institute of Medical Research, Clayton, Victoria, Australia; McGill University, Montreal, QC, Canada
| | - XK Zhou
- Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY; Weill Cornell Medical College, New York, NY; Hudson Institute of Medical Research, Clayton, Victoria, Australia; McGill University, Montreal, QC, Canada
| | - K Subbaramaiah
- Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY; Weill Cornell Medical College, New York, NY; Hudson Institute of Medical Research, Clayton, Victoria, Australia; McGill University, Montreal, QC, Canada
| | - DD Giri
- Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY; Weill Cornell Medical College, New York, NY; Hudson Institute of Medical Research, Clayton, Victoria, Australia; McGill University, Montreal, QC, Canada
| | - A Gucalp
- Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY; Weill Cornell Medical College, New York, NY; Hudson Institute of Medical Research, Clayton, Victoria, Australia; McGill University, Montreal, QC, Canada
| | - LR Howe
- Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY; Weill Cornell Medical College, New York, NY; Hudson Institute of Medical Research, Clayton, Victoria, Australia; McGill University, Montreal, QC, Canada
| | - H Zahid
- Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY; Weill Cornell Medical College, New York, NY; Hudson Institute of Medical Research, Clayton, Victoria, Australia; McGill University, Montreal, QC, Canada
| | - P Bhardwaj
- Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY; Weill Cornell Medical College, New York, NY; Hudson Institute of Medical Research, Clayton, Victoria, Australia; McGill University, Montreal, QC, Canada
| | - NK Wendel
- Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY; Weill Cornell Medical College, New York, NY; Hudson Institute of Medical Research, Clayton, Victoria, Australia; McGill University, Montreal, QC, Canada
| | - DJ Falcone
- Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY; Weill Cornell Medical College, New York, NY; Hudson Institute of Medical Research, Clayton, Victoria, Australia; McGill University, Montreal, QC, Canada
| | - M Morrow
- Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY; Weill Cornell Medical College, New York, NY; Hudson Institute of Medical Research, Clayton, Victoria, Australia; McGill University, Montreal, QC, Canada
| | - H Wang
- Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY; Weill Cornell Medical College, New York, NY; Hudson Institute of Medical Research, Clayton, Victoria, Australia; McGill University, Montreal, QC, Canada
| | - S Williams
- Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY; Weill Cornell Medical College, New York, NY; Hudson Institute of Medical Research, Clayton, Victoria, Australia; McGill University, Montreal, QC, Canada
| | - M Pollak
- Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY; Weill Cornell Medical College, New York, NY; Hudson Institute of Medical Research, Clayton, Victoria, Australia; McGill University, Montreal, QC, Canada
| | - CA Hudis
- Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY; Weill Cornell Medical College, New York, NY; Hudson Institute of Medical Research, Clayton, Victoria, Australia; McGill University, Montreal, QC, Canada
| | - AJ Dannenberg
- Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY; Weill Cornell Medical College, New York, NY; Hudson Institute of Medical Research, Clayton, Victoria, Australia; McGill University, Montreal, QC, Canada
| |
Collapse
|
34
|
Yang X, Wang S, King TL, Kerr CJ, Blanchet C, Svergun D, Pal R, Beeby A, Vadivelu J, Brown KA, Jones RA, Zhang L, Huang S. Anisotropic lanthanide-based nano-clusters for imaging applications. Faraday Discuss 2016; 191:465-479. [PMID: 27430046 PMCID: PMC5123638 DOI: 10.1039/c6fd00018e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 03/31/2016] [Indexed: 11/21/2022]
Abstract
We have developed a new class of lanthanide nano-clusters that self-assemble using flexible Schiff base ligands. Cd-Ln and Ni-Ln clusters, [Ln8Cd24(L1)12(OAc)39Cl7(OH)2] (Ln = Nd, Eu), [Eu8Cd24(L1)12(OAc)44], [Ln8Cd24(L2)12(OAc)44] (Ln = Nd, Yb, Sm) and [Nd2Ni4(L3)2(acac)6(NO3)2(OH)2], were constructed using different types of flexible Schiff base ligands. These molecular nano-clusters exhibit anisotropic architectures that differ considerably depending upon the presence of Cd (nano-drum) or Ni (square-like nano-cluster). Structural characterization of the self-assembled particles has been undertaken using crystallography, transmission electron microscopy and small-angle X-ray scattering. Comparison of the metric dimensions of the nano-drums shows a consistency of size using these techniques, suggesting that these molecules may share similar structural features in both solid and solution states. Photophysical properties were studied by excitation of the ligand-centered absorption bands in the solid state and in solution, and using confocal microscopy of microspheres loaded with the compounds. The emissive properties of these compounds vary depending upon the combination of lanthanide and Cd or Ni present in these clusters. The results provide new insights into the construction of novel high-nuclearity nano-clusters and offer a promising foundation for the development of new functional nanomaterials.
Collapse
Affiliation(s)
- Xiaoping Yang
- College of Chemistry and Materials Engineering , Wenzhou University , Zhejiang Key Laboratory of Carbon Materials , Wenzhou 325035 , China . ; Tel: +86 577 88373064
| | - Shiqing Wang
- College of Chemistry and Materials Engineering , Wenzhou University , Zhejiang Key Laboratory of Carbon Materials , Wenzhou 325035 , China . ; Tel: +86 577 88373064
| | - Tyler L. King
- The University of Texas at Austin , Department of Chemistry , Austin , Texas 78712 , USA . ; Tel: +1 512 4711706
| | - Christopher J. Kerr
- European Molecular Biology Laboratory , Hamburg Unit , EMBL c/o DESY , Hamburg , 22607 , Germany
| | - Clement Blanchet
- European Molecular Biology Laboratory , Hamburg Unit , EMBL c/o DESY , Hamburg , 22607 , Germany
| | - Dmitri Svergun
- European Molecular Biology Laboratory , Hamburg Unit , EMBL c/o DESY , Hamburg , 22607 , Germany
| | - Robert Pal
- Department of Chemistry , University of Durham , South Road , Durham , DH1 3LE , UK
| | - Andrew Beeby
- Department of Chemistry , University of Durham , South Road , Durham , DH1 3LE , UK
| | - Jamuna Vadivelu
- Department of Medical Microbiology , University of Malaya , Kuala Lumpur 50603 , Malaysia
| | - Katherine A. Brown
- European Molecular Biology Laboratory , Hamburg Unit , EMBL c/o DESY , Hamburg , 22607 , Germany
- Cavendish Laboratory , Department of Physics , University of Cambridge , Cambridge CB3 0HE , UK .
| | - Richard A. Jones
- European Molecular Biology Laboratory , Hamburg Unit , EMBL c/o DESY , Hamburg , 22607 , Germany
| | - Lijie Zhang
- College of Chemistry and Materials Engineering , Wenzhou University , Zhejiang Key Laboratory of Carbon Materials , Wenzhou 325035 , China . ; Tel: +86 577 88373064
| | - Shaoming Huang
- College of Chemistry and Materials Engineering , Wenzhou University , Zhejiang Key Laboratory of Carbon Materials , Wenzhou 325035 , China . ; Tel: +86 577 88373064
| |
Collapse
|
35
|
Yang X, Wang S, Schipper D, Zhang L, Li Z, Huang S, Yuan D, Chen Z, Gnanam AJ, Hall JW, King TL, Que E, Dieye Y, Vadivelu J, Brown KA, Jones RA. Self-assembly of high-nuclearity lanthanide-based nanoclusters for potential bioimaging applications. Nanoscale 2016; 8:11123-11129. [PMID: 27181930 DOI: 10.1039/c6nr00642f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Two series of Cd-Ln and Ni-Ln clusters [Ln8Cd24L12(OAc)44(48)Cl4(0)] and [Ln8Ni6L6(OAc)24(EtOH)6(H2O)2] were constructed using a flexible ligand. The Cd-Ln clusters exhibit interesting nano-drum-like structures which allows direct visualization by TEM. Luminex MicroPlex Microspheres loaded with the Cd-Sm cluster were visualized using epifluorescence microscopy. Cytotoxicity studies on A549 and AGS cancer cell lines showed that the materials have mild to moderate cytotoxicity.
Collapse
Affiliation(s)
- Xiaoping Yang
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, China
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Brown KA, Harris DF, Wilker MB, Rasmussen A, Khadka N, Hamby H, Keable S, Dukovic G, Peters JW, Seefeldt LC, King PW. Light-driven dinitrogen reduction catalyzed by a CdS:nitrogenase MoFe protein biohybrid. Science 2016; 352:448-50. [PMID: 27102481 DOI: 10.1126/science.aaf2091] [Citation(s) in RCA: 390] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 03/23/2016] [Indexed: 01/24/2023]
Abstract
The splitting of dinitrogen (N2) and reduction to ammonia (NH3) is a kinetically complex and energetically challenging multistep reaction. In the Haber-Bosch process, N2 reduction is accomplished at high temperature and pressure, whereas N2 fixation by the enzyme nitrogenase occurs under ambient conditions using chemical energy from adenosine 5'-triphosphate (ATP) hydrolysis. We show that cadmium sulfide (CdS) nanocrystals can be used to photosensitize the nitrogenase molybdenum-iron (MoFe) protein, where light harvesting replaces ATP hydrolysis to drive the enzymatic reduction of N2 into NH3 The turnover rate was 75 per minute, 63% of the ATP-coupled reaction rate for the nitrogenase complex under optimal conditions. Inhibitors of nitrogenase (i.e., acetylene, carbon monoxide, and dihydrogen) suppressed N2 reduction. The CdS:MoFe protein biohybrids provide a photochemical model for achieving light-driven N2 reduction to NH3.
Collapse
Affiliation(s)
- Katherine A Brown
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Derek F Harris
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322, USA
| | - Molly B Wilker
- Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Andrew Rasmussen
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322, USA
| | - Nimesh Khadka
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322, USA
| | - Hayden Hamby
- Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Stephen Keable
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Gordana Dukovic
- Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - John W Peters
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322, USA
| | - Paul W King
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA.
| |
Collapse
|
37
|
Brown KA, Wilker MB, Boehm M, Hamby H, Dukovic G, King PW. Photocatalytic Regeneration of Nicotinamide Cofactors by Quantum Dot–Enzyme Biohybrid Complexes. ACS Catal 2016. [DOI: 10.1021/acscatal.5b02850] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Katherine A. Brown
- Biosciences Center,
National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Molly B. Wilker
- Department
of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Marko Boehm
- Biosciences Center,
National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Hayden Hamby
- Department
of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Gordana Dukovic
- Department
of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Paul W. King
- Biosciences Center,
National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| |
Collapse
|
38
|
Brown KA, Jones M, Adler F, Leecaster M, Nechodom K, Stevens V, Samore M, Mayer J. The determinants of C. difficile infection in long-term care facilities: a portrait of patient- and facility-level factors across 90 care regions in the veterans affairs health care system. Antimicrob Resist Infect Control 2015. [PMCID: PMC4474708 DOI: 10.1186/2047-2994-4-s1-o36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
39
|
Utterback JK, Wilker MB, Brown KA, King PW, Eaves JD, Dukovic G. Competition between electron transfer, trapping, and recombination in CdS nanorod-hydrogenase complexes. Phys Chem Chem Phys 2015; 17:5538-42. [PMID: 25623885 DOI: 10.1039/c4cp05993j] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electron transfer from photoexcited CdS nanorods to [FeFe]-hydrogenase is a critical step in photochemical H2 production by CdS-hydrogenase complexes. By accounting for the distributions in the numbers of electron traps and enzymes adsorbed, we determine rate constants and quantum efficiencies for electron transfer from transient absorption measurements.
Collapse
Affiliation(s)
- James K Utterback
- Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309, USA.
| | | | | | | | | | | |
Collapse
|
40
|
Hoffmaster AR, AuCoin D, Baccam P, Baggett HC, Baird R, Bhengsri S, Blaney DD, Brett PJ, Brooks TJG, Brown KA, Chantratita N, Cheng AC, Dance DAB, Decuypere S, Defenbaugh D, Gee JE, Houghton R, Jorakate P, Lertmemongkolchai G, Limmathurotsakul D, Merlin TL, Mukhopadhyay C, Norton R, Peacock SJ, Rolim DB, Simpson AJ, Steinmetz I, Stoddard RA, Stokes MM, Sue D, Tuanyok A, Whistler T, Wuthiekanun V, Walke HT. Melioidosis diagnostic workshop, 2013. Emerg Infect Dis 2015; 21. [PMID: 25626057 PMCID: PMC4313648 DOI: 10.3201/eid2102.141045] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Melioidosis is a severe disease that can be difficult to diagnose because of its diverse clinical manifestations and a lack of adequate diagnostic capabilities for suspected cases. There is broad interest in improving detection and diagnosis of this disease not only in melioidosis-endemic regions but also outside these regions because melioidosis may be underreported and poses a potential bioterrorism challenge for public health authorities. Therefore, a workshop of academic, government, and private sector personnel from around the world was convened to discuss the current state of melioidosis diagnostics, diagnostic needs, and future directions.
Collapse
|
41
|
Lewis SM, Treacher DF, Edgeworth J, Mahalingam G, Brown CS, Mare TA, Stacey M, Beale R, Brown KA. Expression of CD11c and EMR2 on neutrophils: potential diagnostic biomarkers for sepsis and systemic inflammation. Clin Exp Immunol 2015; 182:184-94. [PMID: 26153037 DOI: 10.1111/cei.12679] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2015] [Indexed: 12/26/2022] Open
Abstract
There is a need for cellular biomarkers to differentiate patients with sepsis from those with the non-infectious systemic inflammatory response syndrome (SIRS). In this double-blind study we determined whether the expression of known (CD11a/b/c, CD62L) and putative adhesion molecules [CD64, CD97 and epidermal growth factor (EGF)-like molecule containing mucin-like hormone receptor (EMR2)] on blood neutrophils could serve as useful biomarkers of infection and of non-infectious SIRS in critically ill patients. We studied 103 patients with SIRS, 83 of whom had sepsis, and 50 healthy normal subjects, using flow cytometry to characterize neutrophils phenotypically in whole blood samples. Patients with SIRS had an increased prevalence of neutrophils expressing CD11c, CD64 and EMR2 in comparison with healthy subjects (P < 0.001), but normal expression of CD11a, CD11b, CD62L and CD97. An increase in the percentage of neutrophils bearing CD11c was associated with sepsis, EMR2 with SIRS and CD64 with sepsis and SIRS. Neutrophils expressing CD11c had the highest sensitivity (81%) and specificity (80%) for the detection of sepsis, and there was an association between the percentage of neutrophils expressing EMR2 and the extent of organ failure (P < 0.05). Contrary to other reports, we did not observe an abnormal expression of CD11b or CD62L on neutrophils from patients with SIRS, and suggest that this discrepancy is due to differences in cell processing protocols. We propose that blood neutrophils expressing CD11c and EMR2 be considered as potential biomarkers for sepsis and SIRS, respectively.
Collapse
Affiliation(s)
- S M Lewis
- Intensive Care Unit, Guy's and St Thomas' NHS Foundation Trust, London.,Department of Vascular Immunology, Division of Asthma, Allergy and Lung Biology, King's College London
| | - D F Treacher
- Intensive Care Unit, Guy's and St Thomas' NHS Foundation Trust, London
| | - J Edgeworth
- Department of Infection, Guy's and St Thomas' NHS Foundation Trust, University of Leeds, London, UK
| | - G Mahalingam
- Department of Vascular Immunology, Division of Asthma, Allergy and Lung Biology, King's College London
| | - C S Brown
- Intensive Care Unit, Guy's and St Thomas' NHS Foundation Trust, London
| | - T A Mare
- Intensive Care Unit, Guy's and St Thomas' NHS Foundation Trust, London.,Department of Vascular Immunology, Division of Asthma, Allergy and Lung Biology, King's College London
| | - M Stacey
- School of Molecular and Cellular Biology, University of Leeds, London, UK
| | - R Beale
- Intensive Care Unit, Guy's and St Thomas' NHS Foundation Trust, London.,Department of Vascular Immunology, Division of Asthma, Allergy and Lung Biology, King's College London
| | - K A Brown
- Intensive Care Unit, Guy's and St Thomas' NHS Foundation Trust, London.,Department of Vascular Immunology, Division of Asthma, Allergy and Lung Biology, King's College London
| |
Collapse
|
42
|
Butler BJ, Boddy RL, Bo C, Arora H, Williams A, Proud WG, Brown KA. Composite nature of fresh skin revealed during compression. Bioinspired, Biomimetic and Nanobiomaterials 2015. [DOI: 10.1680/bbn.14.00028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
|
43
|
Robles-Rubio CA, Kaczmarek J, Chawla S, Kovacs L, Brown KA, Kearney RE, Sant Anna GM. Automated analysis of respiratory behavior in extremely preterm infants and extubation readiness. Pediatr Pulmonol 2015; 50:479-86. [PMID: 25603969 PMCID: PMC6680183 DOI: 10.1002/ppul.23151] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 11/21/2014] [Indexed: 11/11/2022]
Abstract
BACKGROUND Rates of extubation failure of extremely preterm infants remain high. Analysis of breathing patterns variability during spontaneous breathing under endotracheal tube continuous positive airway pressure (ETT-CPAP) is a potential tool to predict extubation readiness. OBJECTIVE To investigate if automated analysis of respiratory signals would reveal differences in respiratory behavior between infants that were successfully extubated or not. METHODS Respiratory Inductive Plethysmography (RIP) signals were recorded during ETT-CPAP just prior to extubation. Signals were digitized, and analyzed using an Automated Unsupervised Respiratory Event Analysis (AUREA). Extubation failure was defined as reintubation within 72 hr. Statistical differences between infants who were successfully extubated or failed were calculated. RESULTS A total of 56 infants were enrolled and one was excluded due to instability during the ETT-CPAP; 11 out of 55 infants studied failed extubation (20%). No differences in demographics were observed between the success and failure groups. Significant differences on the variability of some respiratory parameters or 'metrics' estimated by AUREA were observed between the 2 groups. Indeed, a simple classification using the variability of two metrics of respiratory behavior predicted extubation failure with high accuracy. CONCLUSION Automated analysis of respiratory behavior during a short ETT-CPAP period may help in the prediction of extubation readiness in extremely preterm infants.
Collapse
Affiliation(s)
- C A Robles-Rubio
- Department of Biomedical Engineering, McGill University, Montreal, Canada
| | | | | | | | | | | | | |
Collapse
|
44
|
Affiliation(s)
- M E Perry
- Division of Anatomy and Cell Biology, Guy's Hospital, UK
| | | | | |
Collapse
|
45
|
Brown KA, Yang X, Schipper D, Hall JW, DePue LJ, Gnanam AJ, Arambula JF, Jones JN, Swaminathan J, Dieye Y, Vadivelu J, Chandler DJ, Marcotte EM, Sessler JL, Ehrlich LIR, Jones RA. A self-assembling lanthanide molecular nanoparticle for optical imaging. Dalton Trans 2015; 44:2667-75. [PMID: 25512085 PMCID: PMC4401500 DOI: 10.1039/c4dt02646b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [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: 11/21/2022]
Abstract
Chromophores that incorporate f-block elements have considerable potential for use in bioimaging applications because of their advantageous photophysical properties compared to organic dye, which are currently widely used. We are developing new classes of lanthanide-based self-assembling molecular nanoparticles as reporters for imaging and as multi-functional nanoprobes or nanosensors for use with biological samples. One class of these materials, which we call lanthanide "nano-drums", are homogeneous 4d-4f clusters approximately 25 to 30 Å in diameter. These are capable of emitting from the visible to near-infrared wavelengths. Here, we present the synthesis, crystal structure, photophysical properties and comparative cytotoxicity data for a 32 metal Eu-Cd nano-drum [Eu(8)Cd(24)L(12)(OAc)(48)] (1). We also explored the imaging capabilities of this nano-drum using epifluorescence, TIRF, and two-photon microscopy platforms.
Collapse
Affiliation(s)
- Katherine A. Brown
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 0HE, UK
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Xiaoping Yang
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, China
| | - Desmond Schipper
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Justin W. Hall
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Lauren J. DePue
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Annie J. Gnanam
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Jonathan F. Arambula
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Jessica N. Jones
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Jagannath Swaminathan
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Yakhya Dieye
- Department of Medical Microbiology, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Jamuna Vadivelu
- Department of Medical Microbiology, University of Malaya, Kuala Lumpur 50603, Malaysia
| | | | - Edward M. Marcotte
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Jonathan L. Sessler
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Lauren I. R. Ehrlich
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Richard A. Jones
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, USA
| |
Collapse
|
46
|
Abstract
Excited state electron transfer (ET) is a fundamental step for the catalytic conversion of solar energy into chemical energy. To understand the properties controlling ET between photoexcited nanoparticles and catalysts, the ET kinetics were measured for solution-phase complexes of CdTe quantum dots and Clostridium acetobutylicum [FeFe]-hydrogenase I (CaI) using time-resolved photoluminescence spectroscopy. Over a 2.0-3.5 nm diameter range of CdTe nanoparticles, the observed ET rate (kET) was sensitive to CaI concentration. To account for diameter effects on CaI binding, a Langmuir isotherm and two geometric binding models were created to estimate maximal CaI affinities and coverages at saturating concentrations. Normalizing the ET kinetics to CaI surface coverage for each CdTe diameter led to k(ET) values that were insensitive to diameter, despite a decrease in the free energy for photoexcited ET (ΔGET) with increasing diameter. The turnover frequency (TOF) of CaI in CdTe-CaI complexes was measured at several molar ratios. Normalization for diameter-dependent changes in CaI coverage showed an increase in TOF with diameter. These results suggest that k(ET) and H2 production for CdTe-CaI complexes are not strictly controlled by ΔG(ET) and that other factors must be considered.
Collapse
Affiliation(s)
- Katherine A Brown
- Biosciences Center, National Renewable Energy Laboratory , Golden, Colorado 80401, United States
| | | | | | | |
Collapse
|
47
|
Gregory AE, Judy BM, Qazi O, Blumentritt CA, Brown KA, Shaw AM, Torres AG, Titball RW. A gold nanoparticle-linked glycoconjugate vaccine against Burkholderia mallei. Nanomedicine 2014; 11:447-56. [PMID: 25194998 DOI: 10.1016/j.nano.2014.08.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 08/18/2014] [Accepted: 08/22/2014] [Indexed: 12/19/2022]
Abstract
UNLABELLED Burkholderia mallei are Gram-negative bacteria, responsible for the disease glanders. B. mallei has recently been classified as a Tier 1 agent owing to the fact that this bacterial species can be weaponised for aerosol release, has a high mortality rate and demonstrates multi-drug resistance. Furthermore, there is no licensed vaccine available against this pathogen. Lipopolysaccharide (LPS) has previously been identified as playing an important role in generating host protection against Burkholderia infection. In this study, we present gold nanoparticles (AuNPs) functionalised with a glycoconjugate vaccine against glanders. AuNPs were covalently coupled with one of three different protein carriers (TetHc, Hcp1 and FliC) followed by conjugation to LPS purified from a non-virulent clonal relative, B. thailandensis. Glycoconjugated LPS generated significantly higher antibody titres compared with LPS alone. Further, they improved protection against a lethal inhalation challenge of B. mallei in the murine model of infection. FROM THE CLINICAL EDITOR Burkholderia mallei is associated with multi-drug resistance, high mortality and potentials for weaponization through aerosol inhalation. The authors of this study present gold nanoparticles (AuNPs) functionalized with a glycoconjugate vaccine against this Gram negative bacterium demonstrating promising results in a murine model even with the aerosolized form of B. Mallei.
Collapse
Affiliation(s)
- Anthony E Gregory
- School of Biosciences, College of Life and Environmental Sciences, University of Exeter, Devon, UK
| | - Barbara M Judy
- Department of Pathology, University of TX Medical Branch, Galveston, USA
| | - Omar Qazi
- Department of Chemistry, University of TX at Austin, Austin, USA
| | - Carla A Blumentritt
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, USA
| | - Katherine A Brown
- Department of Chemistry, University of TX at Austin, Austin, USA; Cavendish Laboratory, Department of Physics, University of Cambridge, UK
| | - Andrew M Shaw
- School of Biosciences, College of Life and Environmental Sciences, University of Exeter, Devon, UK
| | - Alfredo G Torres
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, USA; Department of Pathology, University of TX Medical Branch, Galveston, USA.
| | - Richard W Titball
- School of Biosciences, College of Life and Environmental Sciences, University of Exeter, Devon, UK.
| |
Collapse
|
48
|
Klintmalm GB, Feng S, Lake JR, Vargas HE, Wekerle T, Agnes S, Brown KA, Nashan B, Rostaing L, Meadows-Shropshire S, Agarwal M, Harler MB, García-Valdecasas JC. Belatacept-based immunosuppression in de novo liver transplant recipients: 1-year experience from a phase II randomized study. Am J Transplant 2014; 14:1817-27. [PMID: 25041339 PMCID: PMC4140547 DOI: 10.1111/ajt.12810] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 03/07/2014] [Accepted: 03/23/2014] [Indexed: 01/25/2023]
Abstract
This exploratory phase II study evaluated the safety and efficacy of belatacept in de novo adult liver transplant recipients. Patients were randomized (N = 260) to one of the following immunosuppressive regimens: (i) basiliximab + belatacept high dose [HD] + mycophenolate mofetil (MMF), (ii) belatacept HD + MMF, (iii) belatacept low dose [LD] + MMF, (iv) tacrolimus + MMF, or (v) tacrolimus alone. All received corticosteroids. Demographic characteristics were similar among groups. The proportion of patients who met the primary end point (composite of acute rejection, graft loss, death by month 6) was higher in the belatacept groups (42–48%) versus tacrolimus groups (15–38%), with the highest number of deaths and grafts losses in the belatacept LD group. By month 12, the proportion surviving with a functioning graft was higher with tacrolimus + MMF (93%) and lower with belatacept LD (67%) versus other groups (90%: basiliximab + belatacept HD; 83%: belatacept HD; 88%: tacrolimus). Mean calculated GFR was 15–34 mL/min higher in belatacept-treated patients at 1 year. Two cases of posttransplant lymphoproliferative disease and one case of progressive multifocal leukoencephalopathy occurred in belatacept-treated patients. Follow-up beyond month 12 revealed an increase in death and graft loss in another belatacept group (belatacept HD), after which the study was terminated.
Collapse
Affiliation(s)
- G B Klintmalm
- Annette C. and Harold C. Simmons Transplant Institute, Baylor University Medical CenterDallas, TX,*Corresponding author: Göran B. Klintmalm,
| | - S Feng
- Division of Transplant Surgery, University of California, San FranciscoSan Francisco, CA
| | - J R Lake
- Liver Transplant Program, University of MinnesotaMinneapolis, MN
| | - H E Vargas
- Division of Hepatology, Mayo Clinic ArizonaPhoenix, AZ
| | - T Wekerle
- Division of Transplantation, Medical University of ViennaVienna, Austria
| | - S Agnes
- Department of General and Transplant Surgery, Catholic University, Policlinico “A. Gemelli”Rome, Italy
| | - K A Brown
- Division of Gastroenterology, Henry Ford Health SystemsDetroit, MI
| | - B Nashan
- Department of Hepatobiliary Surgery & Visceral Transplantation, University Medical Center Hamburg-EppendorfHamburg, Germany
| | - L Rostaing
- Department of Nephrology and Organ Transplantation, Toulouse University HospitalToulouse, France,INSERM U1043, IFR-BMT, CHU PurpanToulouse, France
| | | | | | | | | |
Collapse
|
49
|
Butler BJ, Bo C, Tucker AW, Jardine AP, Proud WG, Williams A, Brown KA. Mechanical and histological characterization of trachea tissue subjected to blast-type pressures. ACTA ACUST UNITED AC 2014. [DOI: 10.1088/1742-6596/500/18/182007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
50
|
Wilker MB, Shinopoulos KE, Brown KA, Mulder DW, King PW, Dukovic G. Electron transfer kinetics in CdS nanorod-[FeFe]-hydrogenase complexes and implications for photochemical H₂ generation. J Am Chem Soc 2014; 136:4316-24. [PMID: 24564271 DOI: 10.1021/ja413001p] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This Article describes the electron transfer (ET) kinetics in complexes of CdS nanorods (CdS NRs) and [FeFe]-hydrogenase I from Clostridium acetobutylicum (CaI). In the presence of an electron donor, these complexes produce H2 photochemically with quantum yields of up to 20%. Kinetics of ET from CdS NRs to CaI play a critical role in the overall photochemical reactivity, as the quantum efficiency of ET defines the upper limit on the quantum yield of H2 generation. We investigated the competitiveness of ET with the electron relaxation pathways in CdS NRs by directly measuring the rate and quantum efficiency of ET from photoexcited CdS NRs to CaI using transient absorption spectroscopy. This technique is uniquely suited to decouple CdS→CaI ET from the processes occurring in the enzyme during H2 production. We found that the ET rate constant (k(ET)) and the electron relaxation rate constant in CdS NRs (k(CdS)) were comparable, with values of 10(7) s(-1), resulting in a quantum efficiency of ET of 42% for complexes with the average CaI:CdS NR molar ratio of 1:1. Given the direct competition between the two processes that occur with similar rates, we propose that gains in efficiencies of H2 production could be achieved by increasing k(ET) and/or decreasing k(CdS) through structural modifications of the nanocrystals. When catalytically inactive forms of CaI were used in CdS-CaI complexes, ET behavior was akin to that observed with active CaI, demonstrating that electron injection occurs at a distal iron-sulfur cluster and is followed by transport through a series of accessory iron-sulfur clusters to the active site of CaI. Using insights from this time-resolved spectroscopic study, we discuss the intricate kinetic pathways involved in photochemical H2 generation in CdS-CaI complexes, and we examine how the relationship between the electron injection rate and the other kinetic processes relates to the overall H2 production efficiency.
Collapse
Affiliation(s)
- Molly B Wilker
- Department of Chemistry and Biochemistry, University of Colorado Boulder , Boulder, Colorado 80309, United States
| | | | | | | | | | | |
Collapse
|