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Su B, Palahnuk H, Harbaugh T, Rizk E, Hazard W, Chan A, Bernstein J, Weinsaft JW, Manning KB. Numerical Study on the Impact of Central Venous Catheter Placement on Blood Flow in the Cavo-Atrial Junction. Ann Biomed Eng 2024; 52:1378-1392. [PMID: 38407724 DOI: 10.1007/s10439-024-03463-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 01/30/2024] [Indexed: 02/27/2024]
Abstract
An in silico study is performed to investigate fluid dynamic effects of central venous catheter (CVC) placement within patient-specific cavo-atrial junctions. Prior studies show the CVC infusing a liquid, but this study focuses on the placement without any liquid emerging from the CVC. A 7 or 15-French double-lumen CVC is placed virtually in two patient-specific models; the CVC tip location is altered to understand its effect on the venous flow field. Results show that the CVC impact is trivial on flow in the superior vena cava when the catheter-to-vein ratio ranges from 0.15 to 0.33. Results further demonstrate that when the CVC tip is directly in the right atrium, flow vortices in the right atrium result in elevated wall shear stress near the tip hole. A recirculation region characterizes a spatially variable flow field inside the CVC side hole. Furthermore, flow stagnation is present near the internal side hole corners but an elevated wall shear stress near the curvature of the side hole's exit. These results suggest that optimal CVC tip location is within the superior vena cava, so as to lower the potential for platelet activation due to elevated shear stresses and that CVC geometry and location depth in the central vein significantly influences the local CVC fluid dynamics. A thrombosis model also shows thrombus formation at the side hole and tip hole. After modifying the catheter design, the hemodynamics change, which alter thrombus formation. Future studies are warranted to study CVC design and placement location in an effort to minimize CVC-induced thrombosis incidence.
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Affiliation(s)
- Boyang Su
- Department of Biomedical Engineering, The Pennsylvania State University, 122 Chemical and Biomedical Engineering Building, University Park, PA, 16802-4400, USA
| | - Hannah Palahnuk
- Department of Biomedical Engineering, The Pennsylvania State University, 122 Chemical and Biomedical Engineering Building, University Park, PA, 16802-4400, USA
| | - Thaddeus Harbaugh
- Department of Neurosurgery, Penn State College of Medicine, Hershey, PA, USA
| | - Elias Rizk
- Department of Neurosurgery, Penn State College of Medicine, Hershey, PA, USA
| | - Will Hazard
- Department of Neurosurgery, Penn State College of Medicine, Hershey, PA, USA
| | - Angel Chan
- Department of Medicine (Cardiology), Weill Cornell College, New York, NY, USA
- Department of Medicine (Cardiology), Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jonathan Bernstein
- Division of Pediatric Hematology/Oncology, Penn State Hershey Children's Hospital, Hershey, PA, USA
| | - Jonathan W Weinsaft
- Department of Medicine (Cardiology), Weill Cornell College, New York, NY, USA
- Department of Medicine (Cardiology), Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Radiology (Cardiothoracic Imaging), Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Keefe B Manning
- Department of Biomedical Engineering, The Pennsylvania State University, 122 Chemical and Biomedical Engineering Building, University Park, PA, 16802-4400, USA.
- Department of Surgery, Penn State College of Medicine, Hershey, PA, USA.
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Holbrook JH, Kemper GE, Hummon AB. Quantitative mass spectrometry imaging: therapeutics & biomolecules. Chem Commun (Camb) 2024; 60:2137-2151. [PMID: 38284765 PMCID: PMC10878071 DOI: 10.1039/d3cc05988j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 01/22/2024] [Indexed: 01/30/2024]
Abstract
Mass spectrometry imaging (MSI) has become increasingly utilized in the analysis of biological molecules. MSI grants the ability to spatially map thousands of molecules within one experimental run in a label-free manner. While MSI is considered by most to be a qualitative method, recent advancements in instrumentation, sample preparation, and development of standards has made quantitative MSI (qMSI) more common. In this feature article, we present a tailored review of recent advancements in qMSI of therapeutics and biomolecules such as lipids and peptides/proteins. We also provide detailed experimental considerations for conducting qMSI studies on biological samples, aiming to advance the methodology.
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Affiliation(s)
- Joseph H Holbrook
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA.
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Gabrielle E Kemper
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Amanda B Hummon
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA.
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
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Dolcemascolo R, Heras-Hernández M, Goiriz L, Montagud-Martínez R, Requena-Menéndez A, Ruiz R, Pérez-Ràfols A, Higuera-Rodríguez RA, Pérez-Ropero G, Vranken WF, Martelli T, Kaiser W, Buijs J, Rodrigo G. Repurposing the mammalian RNA-binding protein Musashi-1 as an allosteric translation repressor in bacteria. eLife 2024; 12:RP91777. [PMID: 38363283 PMCID: PMC10942595 DOI: 10.7554/elife.91777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024] Open
Abstract
The RNA recognition motif (RRM) is the most common RNA-binding protein domain identified in nature. However, RRM-containing proteins are only prevalent in eukaryotic phyla, in which they play central regulatory roles. Here, we engineered an orthogonal post-transcriptional control system of gene expression in the bacterium Escherichia coli with the mammalian RNA-binding protein Musashi-1, which is a stem cell marker with neurodevelopmental role that contains two canonical RRMs. In the circuit, Musashi-1 is regulated transcriptionally and works as an allosteric translation repressor thanks to a specific interaction with the N-terminal coding region of a messenger RNA and its structural plasticity to respond to fatty acids. We fully characterized the genetic system at the population and single-cell levels showing a significant fold change in reporter expression, and the underlying molecular mechanism by assessing the in vitro binding kinetics and in vivo functionality of a series of RNA mutants. The dynamic response of the system was well recapitulated by a bottom-up mathematical model. Moreover, we applied the post-transcriptional mechanism engineered with Musashi-1 to specifically regulate a gene within an operon, implement combinatorial regulation, and reduce protein expression noise. This work illustrates how RRM-based regulation can be adapted to simple organisms, thereby adding a new regulatory layer in prokaryotes for translation control.
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Affiliation(s)
- Roswitha Dolcemascolo
- Institute for Integrative Systems Biology (I2SysBio), CSIC – University of ValenciaPaternaSpain
- Department of Biotechnology, Polytechnic University of ValenciaValenciaSpain
| | - María Heras-Hernández
- Institute for Integrative Systems Biology (I2SysBio), CSIC – University of ValenciaPaternaSpain
| | - Lucas Goiriz
- Institute for Integrative Systems Biology (I2SysBio), CSIC – University of ValenciaPaternaSpain
- Department of Applied Mathematics, Polytechnic University of ValenciaValenciaSpain
| | - Roser Montagud-Martínez
- Institute for Integrative Systems Biology (I2SysBio), CSIC – University of ValenciaPaternaSpain
- Department of Biotechnology, Polytechnic University of ValenciaValenciaSpain
| | | | - Raúl Ruiz
- Institute for Integrative Systems Biology (I2SysBio), CSIC – University of ValenciaPaternaSpain
| | - Anna Pérez-Ràfols
- Giotto Biotech SRLSesto FiorentinoItaly
- Magnetic Resonance Center (CERM), Department of Chemistry Ugo Schiff, Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), University of FlorenceSesto FiorentinoItaly
| | - R Anahí Higuera-Rodríguez
- Dynamic Biosensors GmbHPlaneggGermany
- Department of Physics, Technical University of MunichGarchingGermany
| | - Guillermo Pérez-Ropero
- Ridgeview Instruments ABUppsalaSweden
- Department of Chemistry – BMC, Uppsala UniversityUppsalaSweden
| | - Wim F Vranken
- Structural Biology Brussels, Vrije Universiteit BrusselBrusselsBelgium
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles – Vrije Universiteit BrusselBrusselsBelgium
| | | | | | - Jos Buijs
- Ridgeview Instruments ABUppsalaSweden
- Department of Immunology, Genetics, and Pathology, Uppsala UniversityUppsalaSweden
| | - Guillermo Rodrigo
- Institute for Integrative Systems Biology (I2SysBio), CSIC – University of ValenciaPaternaSpain
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Siegel DA, Thanh C, Wan E, Hoh R, Hobbs K, Pan T, Gibson EA, Kroetz DL, Martin J, Hecht F, Pilcher C, Martin M, Carrington M, Pillai S, Busch MP, Stone M, Levy CN, Huang ML, Roychoudhury P, Hladik F, Jerome KR, Kiem HP, Henrich TJ, Deeks SG, Lee SA. Host variation in type I interferon signaling genes (MX1), C-C chemokine receptor type 5 gene, and major histocompatibility complex class I alleles in treated HIV+ noncontrollers predict viral reservoir size. AIDS 2023; 37:477-488. [PMID: 36695358 PMCID: PMC9894159 DOI: 10.1097/qad.0000000000003428] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 10/28/2022] [Indexed: 01/26/2023]
Abstract
OBJECTIVE Prior genomewide association studies have identified variation in major histocompatibility complex (MHC) class I alleles and C-C chemokine receptor type 5 gene (CCR5Δ32) as genetic predictors of viral control, especially in 'elite' controllers, individuals who remain virally suppressed in the absence of therapy. DESIGN Cross-sectional genomewide association study. METHODS We analyzed custom whole exome sequencing and direct human leukocyte antigen (HLA) typing from 202 antiretroviral therapy (ART)-suppressed HIV+ noncontrollers in relation to four measures of the peripheral CD4+ T-cell reservoir: HIV intact DNA, total (t)DNA, unspliced (us)RNA, and RNA/DNA. Linear mixed models were adjusted for potential covariates including age, sex, nadir CD4+ T-cell count, pre-ART HIV RNA, timing of ART initiation, and duration of ART suppression. RESULTS Previously reported 'protective' host genetic mutations related to viral setpoint (e.g. among elite controllers) were found to predict smaller HIV reservoir size. The HLA 'protective' B∗57:01 was associated with significantly lower HIV usRNA (q = 3.3 × 10-3), and among the largest subgroup, European ancestry individuals, the CCR5Δ32 deletion was associated with smaller HIV tDNA (P = 4.3 × 10-3) and usRNA (P = 8.7 × 10-3). In addition, genomewide analysis identified several single nucleotide polymorphisms in MX1 (an interferon stimulated gene) that were significantly associated with HIV tDNA (q = 0.02), and the direction of these associations paralleled MX1 gene eQTL expression. CONCLUSIONS We observed a significant association between previously reported 'protective' MHC class I alleles and CCR5Δ32 with the HIV reservoir size in noncontrollers. We also found a novel association between MX1 and HIV total DNA (in addition to other interferon signaling relevant genes, PPP1CB, DDX3X). These findings warrant further investigation in future validation studies.
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Affiliation(s)
- David A. Siegel
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine
| | | | | | - Rebecca Hoh
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine
| | - Kristen Hobbs
- Department of Medicine, Division of Experimental Medicine
| | - Tony Pan
- Department of Medicine, Division of Experimental Medicine
| | | | | | - Jeffrey Martin
- Department of Biostatistics & Epidemiology, University of California San Francisco, California
| | - Frederick Hecht
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine
| | - Christopher Pilcher
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine
| | - Maureen Martin
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts
| | | | | | - Mars Stone
- Vitalant Blood Bank, San Francisco, California
| | | | - Meei-Li Huang
- Department of Laboratory Medicine and Pathology, University of Washington
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, University of Washington
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Florian Hladik
- Department of Obstetrics and Gynecology
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Keith R. Jerome
- Department of Laboratory Medicine and Pathology, University of Washington
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Hans-Peter Kiem
- Department of Laboratory Medicine and Pathology, University of Washington
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Steven G. Deeks
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine
| | - Sulggi A. Lee
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine
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