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Bell M, Lui H, Lee TK, Kalia S. Validation of medical service insurance claims as a surrogate for ascertaining vitiligo cases. Arch Dermatol Res 2023; 315:541-550. [PMID: 36173455 DOI: 10.1007/s00403-022-02383-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 04/23/2022] [Accepted: 08/02/2022] [Indexed: 11/02/2022]
Abstract
The epidemiology of vitiligo, especially its disease burden on the healthcare system, can be assessed indirectly by analyzing health insurance claims data. Validating this approach is integral to ensuring accurate case identification and cohort characterization. The primary aim of this study was to develop and validate an indirect measure of vitiligo ascertainment using health insurance claims data. These data were used secondarily to identify demographic characteristics, body site involvement, vitiligo subtypes, disease associations, and treatments. This study assessed the validity of identifying vitiligo from billing claims within a Canadian provincial universal health insurance program, versus vitiligo cases accrued from direct medical chart reviews. Claims-based algorithms combining ICD-9-CM diagnostic code 709 with treatment-specific data were derived and tested to identify vitiligo patients. This was compared against cases arising from the manual review of medical records of 606 patient with a diagnostic code for "dyschromia" (ICD-9-CM diagnostic code 709) from January 1 to December 31, 2016. Based on the chart reviews, 204 (33.7%) patients were confirmed to have vitiligo. 42 separate claims-based algorithms combining ICD-9-CM diagnostic code 709 with treatment data specific to vitiligo were modeled and individually tested to evaluate their accuracy for vitiligo ascertainment. One algorithm achieved a sensitivity, specificity, PPV and NPV of 86.8% (95% CI 82.1-91.4), 92.5% (95% CI 90.0-95.1), 85.5% (95% CI 80.7-90.3), and 93.2% (95% CI 90.8-95.7), respectively. There was a 2.2 female-to-male ratio. The most common medical treatments were tacrolimus (74.5%) and topical corticosteroids (54.3%). Hypertension (24.2%) and hypothyroidism (19.6%) were the predominant co-morbidities associated with vitiligo. Health insurance claims data can be used to indirectly ascertain vitiligo for epidemiologic purposes with relatively high diagnostic performance between 85.5 and 93.2%.
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Affiliation(s)
- M Bell
- Department of Dermatology and Skin Science, University of British Columbia, 835 West 10th Avenue, Vancouver, BC, V5Z 4E8, Canada
- Photomedicine Institute, Vancouver Coastal Health Research Institute, Vancouver, Canada
| | - H Lui
- Department of Dermatology and Skin Science, University of British Columbia, 835 West 10th Avenue, Vancouver, BC, V5Z 4E8, Canada
- Photomedicine Institute, Vancouver Coastal Health Research Institute, Vancouver, Canada
- Department of Cancer Control and/or Integrative Oncology and Imaging, BC Cancer, Vancouver, Canada
| | - T K Lee
- Department of Dermatology and Skin Science, University of British Columbia, 835 West 10th Avenue, Vancouver, BC, V5Z 4E8, Canada
- Photomedicine Institute, Vancouver Coastal Health Research Institute, Vancouver, Canada
- Department of Cancer Control and/or Integrative Oncology and Imaging, BC Cancer, Vancouver, Canada
| | - S Kalia
- Department of Dermatology and Skin Science, University of British Columbia, 835 West 10th Avenue, Vancouver, BC, V5Z 4E8, Canada.
- Photomedicine Institute, Vancouver Coastal Health Research Institute, Vancouver, Canada.
- Department of Cancer Control and/or Integrative Oncology and Imaging, BC Cancer, Vancouver, Canada.
- Centre for Clinical Evaluation and Epidemiology, Vancouver Coastal Health Research Institute, Vancouver, Canada.
- Division of Dermatology, BC Children's Hospital Research Institute, Vancouver, Canada.
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2
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Skertich NJ, Lee TK, Grunvald MW, Sivakumar A, Tiglao RM, Madonna MB, Pillai S, Shah AN. The effect of standardized discharge instructions after gastrostomy tube placement on postoperative hospital utilization. J Pediatr Surg 2022; 57:418-423. [PMID: 33867152 DOI: 10.1016/j.jpedsurg.2021.03.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/02/2021] [Accepted: 03/15/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND/PURPOSE Gastrostomy tube (GT) placement is a common pediatric procedure with high postoperative resource utilization. We aimed to determine if standardized discharge instructions (SDI) reduced healthcare utilization rates. METHODS We performed a retrospective cohort study comparing postoperative hospital utilization of patients who underwent initial GT placement pre- and post-SDI protocol implementation from 2014-2019. Statistical analyses included Chi-square tests, multivariable adjusted logistic regression, adjusted Cox proportion hazard regression, and adjusted Poisson regression models when appropriate. RESULTS 197 patients were included, 102 (51.8%) before and 95 (48.2%) after protocol implementation. On primary analysis, SDI patients did not have significantly different total postoperative hospital utilization events at 30-days (48.0% vs. 38.9%, p = 0.25). On secondary analysis, SDI patients had lower rates of ED (8.4% vs. 19.6%, p = 0.026) and office visits (11.6% vs. 25.5%, p = 0.017) at 30-days. Non-SDIs patients had greater odds of ED visits (OR2.7, 95%CI 1.3-5.9, p = 0.01), office visits (OR3.7, 95%CI 1.7-8.1, p = 0.001) and phone calls (OR2.6, 95%CI 1.2-5.7, p = 0.016) at 1-year. The adjusted hazard ratio was 2.0 (95%CI 1.4-3.0, p < 0.001). Incident rate ratio were 1.8 (95%CI 1.2-2.5, p = 0.002) at 30-days and 1.9 (95%CI 1.5-2.4, p < 0.001) at 1-year post-discharge. CONCLUSIONS SDIs post-GT placement may reduce multiple aspects of postoperative hospital utilization.
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Affiliation(s)
- Nicholas J Skertich
- Division of Pediatric Surgery, Department of Surgery, Rush University Medical Center, Chicago, IL, 60612, USA
| | | | - Miles W Grunvald
- Division of Pediatric Surgery, Department of Surgery, Rush University Medical Center, Chicago, IL, 60612, USA
| | | | - Rona M Tiglao
- Division of Pediatric Surgery, Department of Surgery, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Mary Beth Madonna
- Division of Pediatric Surgery, Department of Surgery, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Srikumar Pillai
- Division of Pediatric Surgery, Department of Surgery, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Ami N Shah
- Division of Pediatric Surgery, Department of Surgery, Rush University Medical Center, Chicago, IL, 60612, USA.
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3
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Ovanesov MV, Jackson JW, Golding B, Lee TK. Considerations on activity assay discrepancies in factor VIII and factor IX products. J Thromb Haemost 2021; 19:2102-2111. [PMID: 34145730 DOI: 10.1111/jth.15425] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 05/28/2021] [Accepted: 06/15/2021] [Indexed: 12/13/2022]
Abstract
New modified coagulation factor VIII (FVIII) and factor IX (FIX) products have been designed to improve the treatment of individuals with hemophilia A and B by increasing the interval between dosing. Although these FVIII and FIX molecules have been structurally modified to improve the circulation time, the changes have also influenced their behavior in functional assays in comparison with traditional plasma-derived or recombinant coagulation factors. The assignment of potencies for these products can be problematic because discordance in factor activity values between the commonly used one-stage clotting and chromogenic substrate assays is often observed. Discrepancies in potency assay values also exist when different assay kits and reagents are used in the same assay type. Ideally, all FVIII and FIX products should be calibrated against the World Health Organization (WHO) International Standards (IS) because the assignment of potencies in international units (IU) helps maintain treatment tradition and meaningful references for manufacturers, patients, and clinicians. The discrepant measurements, attributed to the modified structural and functional properties of these products, are manifested in their lack of commutability with the WHO IS for FVIII or FIX. Herein, we discuss the considerations upon which an assay is chosen for potency assignment and postadministration monitoring of a new factor product, which include the validity of the assay calibrated with the IS, the meaning of the potency values in IU, standards of care for patients, clinical relevance between the assigned potency value and recovery value from clinical laboratories, and patient safety.
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Affiliation(s)
- Mikhail V Ovanesov
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Joseph W Jackson
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Basil Golding
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Timothy K Lee
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
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Liang Y, Jackson JW, Woodle SA, Surov SS, Parunov LA, Scott DE, Weinstein M, Lee TK, Ovanesov MV. Detecting factor XIa in immune globulin products: Commutability of international reference materials for traditional and global hemostasis assays. Res Pract Thromb Haemost 2021; 5:211-222. [PMID: 33537546 PMCID: PMC7845073 DOI: 10.1002/rth2.12467] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/21/2020] [Accepted: 11/03/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Activated coagulation factor XIa (FXIa) is an impurity and primary source of procoagulant activity in thrombosis-implicated immune globulin (IG) products. Several assays, of varying quality and precision are used to assess FXIa-like procoagulant activity in units relevant to their respective principles. OBJECTIVES To advance unified reporting, we sought to employ the World Health Organization reference reagents (RRs) to present the results of differing methodologies in units of FXIa activity and rank the sensitivity and robustness of these methodologies. METHODS RR 11/236 served as a calibrator in several FXIa-sensitive blood coagulation tests: two commercial chromogenic FXIa assays (CAs); a nonactivated partial thromboplastin time (NaPTT); an in-house fibrin generation (FG) assay; an in-house thrombin generation (TG) assay; and an assay for FXIa- and kallikrein-like proteolytic activities based on cleavage of substrate SN13a. Some assays were tested in either normal or FXI-deficient plasma. RESULTS Each method demonstrated a sigmoidal dose-response to RRs. NaPTT was the least sensitive to FXIa and the least precise; our in-house TG was the most sensitive; and the two CAs were the most precise. All methods, except for SN13a, which is less specific for thrombotic impurities, gave comparable (within 20% difference) FXIa activity assignments for IG lots. CONCLUSIONS Purified FXIa reference standards support quantitation of FXIa levels in IG products in all tested assay methodologies. This should help to standardize the measurement of thrombotic potentials in IG products and prevent products exhibiting high procoagulant activity from distribution for patient use. Further research is needed to address the effect of IG product-specific matrixes on assay performance.
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Affiliation(s)
- Yideng Liang
- Center for Biologics Evaluation and ResearchU.S. Food and Drug AdministrationSilver SpringMDUSA
| | - Joseph W. Jackson
- Center for Biologics Evaluation and ResearchU.S. Food and Drug AdministrationSilver SpringMDUSA
| | - Samuel A. Woodle
- Center for Biologics Evaluation and ResearchU.S. Food and Drug AdministrationSilver SpringMDUSA
| | - Stepan S. Surov
- Center for Biologics Evaluation and ResearchU.S. Food and Drug AdministrationSilver SpringMDUSA
| | - Leonid A. Parunov
- Center for Biologics Evaluation and ResearchU.S. Food and Drug AdministrationSilver SpringMDUSA
| | - Dorothy E. Scott
- Center for Biologics Evaluation and ResearchU.S. Food and Drug AdministrationSilver SpringMDUSA
| | - Mark Weinstein
- Center for Biologics Evaluation and ResearchU.S. Food and Drug AdministrationSilver SpringMDUSA
| | - Timothy K. Lee
- Center for Biologics Evaluation and ResearchU.S. Food and Drug AdministrationSilver SpringMDUSA
| | - Mikhail V. Ovanesov
- Center for Biologics Evaluation and ResearchU.S. Food and Drug AdministrationSilver SpringMDUSA
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5
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Talaat KR, Porter CK, Bourgeois AL, Lee TK, Duplessis CA, Maciel M, Gutierrez RL, DeNearing B, Adjoodani B, Adkinson R, Testa KJ, Feijoo B, Alcala AN, Brubaker J, Beselman A, Chakraborty S, Sack D, Halpern J, Trop S, Wu H, Jiao J, Sullivan E, Riddle MS, Joseph SS, Poole ST, Prouty MG. Oral delivery of Hyperimmune bovine serum antibodies against CS6-expressing enterotoxigenic Escherichia coli as a prophylactic against diarrhea. Gut Microbes 2020; 12:1732852. [PMID: 32167011 PMCID: PMC7524165 DOI: 10.1080/19490976.2020.1732852] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND . Oral administration of bovine antibodies active against enterotoxigenic Escherichia coli (ETEC) have demonstrated safety and efficacy against diarrhea in human challenge trials. The efficacy of bovine serum immunoglobulins (BSIgG) against recombinant colonization factor CS6 or whole cell ETEC strain B7A was assessed against challenge with the CS6-expressing B7A. METHODS . This was a randomized, double-blind, placebo-controlled trial in which healthy adults received oral hyperimmune BSIgG anti-CS6, anti-B7A whole cell killed or non-hyperimmune BSIgG (placebo) in a 1:1:1 ratio then challenged with ETEC B7A. Two days pre-challenge, volunteers began a thrice daily, seven day course of immunoprophylaxis. On day 3, subjects received 1 × 1010 CFUs of B7A. Subjects were observed for safety and the primary endpoint of moderate-severe diarrhea (MSD). RESULTS . A total of 59 volunteers received product and underwent ETEC challenge. The BSIgG products were well-tolerated across all subjects. Upon challenge, 14/20 (70%) placebo recipients developed MSD, compared to 12/19 (63%; p = .74) receiving anti-CS6 BSIgG and 7/20 (35%; p = .06) receiving anti-B7A BSIgG. Immune responses to the ETEC infection were modest across all groups. CONCLUSIONS . Bovine-derived serum antibodies appear safe and well tolerated. Antibodies derived from cattle immunized with whole cell B7A provided 50% protection against MSD following B7A challenge; however, no protection was observed in subjects receiving serum antibodies targeting CS6. The lack of observed efficacy in this group may be due to low CS6 surface expression on B7A, the high dose challenge inoculum and/or the use of serum derived antibodies versus colostrum-derived antibodies.
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Affiliation(s)
- KR Talaat
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - CK Porter
- Enteric Diseases Department, Naval Medical Research Center, Silver Spring, MD, USA,CONTACT CK Porter Naval Medical Research Center, Silver Spring, MD, USA
| | - AL Bourgeois
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - TK Lee
- Enteric Diseases Department, Naval Medical Research Center, Silver Spring, MD, USA
| | - CA Duplessis
- Enteric Diseases Department, Naval Medical Research Center, Silver Spring, MD, USA
| | - M Maciel
- The Henry M. Jackson Foundation, Bethesda, MD, USA
| | - RL Gutierrez
- Enteric Diseases Department, Naval Medical Research Center, Silver Spring, MD, USA
| | - B DeNearing
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - B Adjoodani
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - R Adkinson
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - KJ Testa
- The Henry M. Jackson Foundation, Bethesda, MD, USA
| | - B Feijoo
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - AN Alcala
- The Henry M. Jackson Foundation, Bethesda, MD, USA
| | - J Brubaker
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - A Beselman
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - S Chakraborty
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - D Sack
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - J Halpern
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - S Trop
- The Henry M. Jackson Foundation, Bethesda, MD, USA
| | - H Wu
- SAB Biotherapeutics Inc, Sioux Falls, SD, USA
| | - J Jiao
- SAB Biotherapeutics Inc, Sioux Falls, SD, USA
| | - E Sullivan
- SAB Biotherapeutics Inc, Sioux Falls, SD, USA
| | - MS Riddle
- Enteric Diseases Department, Naval Medical Research Center, Silver Spring, MD, USA
| | - SS Joseph
- The Henry M. Jackson Foundation, Bethesda, MD, USA
| | - ST Poole
- The Henry M. Jackson Foundation, Bethesda, MD, USA
| | - MG Prouty
- Enteric Diseases Department, Naval Medical Research Center, Silver Spring, MD, USA
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6
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Parunov LA, Surov SS, Chattopadhyay M, Liang Y, Lee TK, Ovanesov MV. Thrombin generation assay modifications needed for its application to monitoring of replacement therapy for haemophilia. Haemophilia 2020; 27:e129-e132. [PMID: 32897618 DOI: 10.1111/hae.14024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/27/2020] [Accepted: 04/15/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Leonid A Parunov
- Center for Biologics Evaluation and Research (CBER), U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Stepan S Surov
- Center for Biologics Evaluation and Research (CBER), U.S. Food and Drug Administration, Silver Spring, Maryland, USA.,Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, Moscow, Russia
| | - Maitreyi Chattopadhyay
- Center for Biologics Evaluation and Research (CBER), U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Yideng Liang
- Center for Biologics Evaluation and Research (CBER), U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Timothy K Lee
- Center for Biologics Evaluation and Research (CBER), U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Mikhail V Ovanesov
- Center for Biologics Evaluation and Research (CBER), U.S. Food and Drug Administration, Silver Spring, Maryland, USA
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7
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Zhang T, Lee TK, Lui H, Dutz J, Dawes M, Lee A, Kalia S. Health insurance claim- and prescription record-based algorithms as a population-based method for eczema ascertainment. J Eur Acad Dermatol Venereol 2020; 34:e466-e468. [PMID: 32103573 DOI: 10.1111/jdv.16315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- T Zhang
- Department of Dermatology and Skin Science, University of British Columbia, Vancouver, BC, Canada.,Photomedicine Institute, Vancouver Coastal Health Research Institute, Vancouver, BC, Canada
| | - T K Lee
- Department of Dermatology and Skin Science, University of British Columbia, Vancouver, BC, Canada.,Photomedicine Institute, Vancouver Coastal Health Research Institute, Vancouver, BC, Canada.,Departments of Cancer Control Research Program and Integrative Oncology - Imaging Unit, BC Cancer, Vancouver, BC, Canada
| | - H Lui
- Department of Dermatology and Skin Science, University of British Columbia, Vancouver, BC, Canada.,Photomedicine Institute, Vancouver Coastal Health Research Institute, Vancouver, BC, Canada.,Departments of Cancer Control Research Program and Integrative Oncology - Imaging Unit, BC Cancer, Vancouver, BC, Canada
| | - J Dutz
- Department of Dermatology and Skin Science, University of British Columbia, Vancouver, BC, Canada.,Division of Dermatology, British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - M Dawes
- Department of Family Practice, University of British Columbia, Vancouver, BC, Canada
| | - A Lee
- Cross Roads Clinics, Vancouver, BC, Canada
| | - S Kalia
- Department of Dermatology and Skin Science, University of British Columbia, Vancouver, BC, Canada.,Photomedicine Institute, Vancouver Coastal Health Research Institute, Vancouver, BC, Canada.,Departments of Cancer Control Research Program and Integrative Oncology - Imaging Unit, BC Cancer, Vancouver, BC, Canada.,Division of Dermatology, British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
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8
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Zhang T, Lee TK, Lui H, Kunimoto B, Han C, Zhou Y, Kalia S. Algorithms for ascertaining keratinocyte carcinomas using health insurance claims and prescription records. J Eur Acad Dermatol Venereol 2019; 33:e275-e276. [PMID: 30762901 DOI: 10.1111/jdv.15490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- T Zhang
- Department of Dermatology and Skin Science, University of British Columbia, Vancouver, BC, Canada.,Photomedicine Institute, Vancouver Coastal Health Research Institute, Vancouver, BC, Canada
| | - T K Lee
- Department of Dermatology and Skin Science, University of British Columbia, Vancouver, BC, Canada.,Photomedicine Institute, Vancouver Coastal Health Research Institute, Vancouver, BC, Canada.,Department of Cancer Control Research Program and Integrative Oncology - BC Cancer, Vancouver, BC, Canada
| | - H Lui
- Department of Dermatology and Skin Science, University of British Columbia, Vancouver, BC, Canada.,Photomedicine Institute, Vancouver Coastal Health Research Institute, Vancouver, BC, Canada.,Department of Cancer Control Research Program and Integrative Oncology - BC Cancer, Vancouver, BC, Canada
| | - B Kunimoto
- Department of Dermatology and Skin Science, University of British Columbia, Vancouver, BC, Canada
| | - C Han
- Department of Dermatology and Skin Science, University of British Columbia, Vancouver, BC, Canada
| | - Y Zhou
- Department of Dermatology and Skin Science, University of British Columbia, Vancouver, BC, Canada
| | - S Kalia
- Department of Dermatology and Skin Science, University of British Columbia, Vancouver, BC, Canada.,Photomedicine Institute, Vancouver Coastal Health Research Institute, Vancouver, BC, Canada
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Chan LH, Zhou L, Ng KY, Wong TL, Lee TK, Ching YP, Yuan YF, Xie D, Richard S, Huen MS, Guan XY, Ma S. Abstract 4479: Protein arginine methyltransferase PRMT6 regulates cancer stemness through CRAF methylation in hepatocellular carcinoma. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-4479] [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] [Indexed: 11/16/2022]
Abstract
Abstract
Arginine methylation is a post-translational modification that plays pivotal roles in signal transduction and gene transcription during cell fate determination. We found protein methyltransferase 6 (PRMT6) to be frequently down-regulated in hepatocellular carcinoma (HCC) cells and its expression to negatively correlate with aggressive cancer features in HCC patients. Silencing of PRMT6 promoted the tumor-initiating, metastasis and therapy resistance potential of HCC cells. Consistently, loss of PRMT6 expression aggravated liver tumorigenesis in a DEN+CCL4 HCC induced PRMT6-/- mouse model. Integrated transcriptome and protein-protein interaction studies revealed an enrichment of genes implicated in RAS signaling and that PRMT6 interacted with CRAF, and likely other RAF family members, and their methylation at conserved arginine 100, negatively regulating its activity, and as a consequence resulting in enhanced MEK/ERK signaling. Our work uncovered a critical repressive function for PRMT6 in maintenance of HCC cells by regulating the MEK/ERK pathway via arginine methylation of RAF, providing a new avenue of molecular mechanism by which ERK mediated stemness in HCC cells are developed.
Citation Format: LH Chan, L Zhou, Kai Yu Ng, TL Wong, TK Lee, YP Ching, YF Yuan, D Xie, S Richard, MS Huen, XY Guan, S Ma. Protein arginine methyltransferase PRMT6 regulates cancer stemness through CRAF methylation in hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4479.
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Affiliation(s)
- LH Chan
- 1The University of Hong Kong, Hong Kong, Hong Kong
| | - L Zhou
- 1The University of Hong Kong, Hong Kong, Hong Kong
| | - Kai Yu Ng
- 1The University of Hong Kong, Hong Kong, Hong Kong
| | - TL Wong
- 1The University of Hong Kong, Hong Kong, Hong Kong
| | - TK Lee
- 2The Hong Kong Polytechnic University, Hong Kong, Hong Kong
| | - YP Ching
- 1The University of Hong Kong, Hong Kong, Hong Kong
| | - YF Yuan
- 3Sun Yat-Sen University Cancer Centre, Guangzhou, China
| | - D Xie
- 3Sun Yat-Sen University Cancer Centre, Guangzhou, China
| | - S Richard
- 4McGill University, Montreal, Quebec, Canada
| | - MS Huen
- 1The University of Hong Kong, Hong Kong, Hong Kong
| | - XY Guan
- 1The University of Hong Kong, Hong Kong, Hong Kong
| | - S Ma
- 1The University of Hong Kong, Hong Kong, Hong Kong
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10
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Kharazmi P, Kalia S, Lui H, Wang ZJ, Lee TK. A feature fusion system for basal cell carcinoma detection through data-driven feature learning and patient profile. Skin Res Technol 2017; 24:256-264. [PMID: 29057507 DOI: 10.1111/srt.12422] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2017] [Indexed: 10/18/2022]
Abstract
BACKGROUND Basal cell carcinoma (BCC) is the most common skin cancer, which is highly damaging in its advanced stages. Computer-aided techniques provide a feasible option for early detection of BCC. However, automated BCC detection techniques immensely rely on handcrafting high-level precise features. Such features are not only computationally complex to design but can also represent a very limited aspect of the lesion characteristics. This paper proposes an automated BCC detection technique that directly learns the features from image data, eliminating the need for handcrafted feature design. METHODS The proposed method is composed of 2 parts. First, an unsupervised feature learning framework is proposed which attempts to learn hidden characteristics of the data including vascular patterns directly from the images. This is done through the design of a sparse autoencoder (SAE). After the unsupervised learning, we treat each of the learned kernel weights of the SAE as a filter. Convolving each filter with the lesion image yields a feature map. Feature maps are condensed to reduce the dimensionality and are further integrated with patient profile information. The overall features are then fed into a softmax classifier for BCC classification. RESULTS On a set of 1199 BCC images, the proposed framework achieved an area under the curve of 91.1%, while the visualization of learned features confirmed meaningful clinical interpretation of the features. CONCLUSION The proposed framework provides a non-invasive fast BCC detection tool that incorporates both dermoscopic lesional features and clinical patient information, without the need for complex handcrafted feature extraction.
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Affiliation(s)
- P Kharazmi
- Biomedical Engineering Program, University of British Columbia, Vancouver, BC, Canada
| | - S Kalia
- Department of Dermatology and Skin Science, University of British Columbia, Vancouver, BC, Canada.,Departments of Cancer Control Research and Integrative Oncology, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - H Lui
- Department of Dermatology and Skin Science, University of British Columbia, Vancouver, BC, Canada.,Departments of Cancer Control Research and Integrative Oncology, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Z J Wang
- Department of Electrical and Computer Engineering, University of British Columbia, Vancouver, BC, Canada
| | - T K Lee
- Biomedical Engineering Program, University of British Columbia, Vancouver, BC, Canada.,Department of Dermatology and Skin Science, University of British Columbia, Vancouver, BC, Canada.,Departments of Cancer Control Research and Integrative Oncology, British Columbia Cancer Agency, Vancouver, BC, Canada
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11
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Hsu YP, Rittichier J, Kuru E, Yablonowski J, Pasciak E, Tekkam S, Hall E, Murphy B, Lee TK, Garner EC, Huang KC, Brun YV, VanNieuwenhze MS. Full color palette of fluorescent d-amino acids for in situ labeling of bacterial cell walls. Chem Sci 2017; 8:6313-6321. [PMID: 28989665 PMCID: PMC5628581 DOI: 10.1039/c7sc01800b] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Accepted: 07/06/2017] [Indexed: 01/01/2023] Open
Abstract
Fluorescent d-amino acids (FDAAs) enable efficient in situ labeling of peptidoglycan in diverse bacterial species. Conducted by enzymes involved in peptidoglycan biosynthesis, FDAA labeling allows specific probing of cell wall formation/remodeling activity, bacterial growth and cell morphology. Their broad application and high biocompatibility have made FDAAs an important and effective tool for studies of peptidoglycan synthesis and dynamics, which, in turn, has created a demand for the development of new FDAA probes. Here, we report the synthesis of new FDAAs, with emission wavelengths that span the entire visible spectrum. We also provide data to characterize their photochemical and physical properties, and we demonstrate their utility for visualizing peptidoglycan synthesis in Gram-negative and Gram-positive bacterial species. Finally, we show the permeability of FDAAs toward the outer-membrane of Gram-negative organisms, pinpointing the probes available for effective labeling in these species. This improved FDAA toolkit will enable numerous applications for the study of peptidoglycan biosynthesis and dynamics.
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Affiliation(s)
- Yen-Pang Hsu
- Department of Molecular and Cellular Biochemistry , Indiana University , Bloomington , IN 47405 , USA .
| | | | - Erkin Kuru
- Department of Molecular and Cellular Biochemistry , Indiana University , Bloomington , IN 47405 , USA .
| | - Jacob Yablonowski
- Department of Molecular and Cellular Biochemistry , Indiana University , Bloomington , IN 47405 , USA .
| | - Erick Pasciak
- Department of Chemistry , Indiana University , Bloomington , IN 47405 , USA
| | - Srinivas Tekkam
- Department of Chemistry , Indiana University , Bloomington , IN 47405 , USA
| | - Edward Hall
- Department of Chemistry , Indiana University , Bloomington , IN 47405 , USA
| | - Brennan Murphy
- Department of Chemistry , Indiana University , Bloomington , IN 47405 , USA
| | - Timothy K Lee
- Department of Bioengineering , Stanford University , Stanford , CA 94305 , USA
| | - Ethan C Garner
- Molecular and Cellular Biology (FAS) Center for Systems Biology , Harvard University , Cambridge , Massachusetts 02138 , USA
| | - Kerwyn Casey Huang
- Department of Bioengineering , Stanford University , Stanford , CA 94305 , USA
- Department of Microbiology and Immunology , Stanford University School of Medicine , Stanford , CA 94305 , USA
| | - Yves V Brun
- Department of Biology , Indiana University , Bloomington , IN 47405 , USA .
| | - Michael S VanNieuwenhze
- Department of Molecular and Cellular Biochemistry , Indiana University , Bloomington , IN 47405 , USA .
- Department of Chemistry , Indiana University , Bloomington , IN 47405 , USA
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12
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Shestopal SA, Hao JJ, Karnaukhova E, Liang Y, Ovanesov MV, Lin M, Kurasawa JH, Lee TK, Mcvey JH, Sarafanov AG. Expression and characterization of a codon-optimized blood coagulation factor VIII. J Thromb Haemost 2017; 15:709-720. [PMID: 28109042 DOI: 10.1111/jth.13632] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Indexed: 08/31/2023]
Abstract
Essentials Recombinant factor VIII (FVIII) is known to be expressed at a low level in cell culture. To increase expression, we used codon-optimization of a B-domain deleted FVIII (BDD-FVIII). This resulted in 7-fold increase of the expression level in cell culture. The biochemical properties of codon-optimized BDD-FVIII were similar to the wild-type protein. SUMMARY Background Production of recombinant factor VIII (FVIII) is challenging because of its low expression. It was previously shown that codon-optimization of a B-domain-deleted FVIII (BDD-FVIII) cDNA resulted in increased protein expression. However, it is well recognized that synonymous mutations may affect the protein structure and function. Objectives To compare biochemical properties of a BDD-FVIII variants expressed from codon-optimized and wild-type cDNAs (CO and WT, respectively). Methods Each variant of the BDD-FVIII was expressed in several independent Chinese hamster ovary (CHO) cell lines, generated using a lentiviral platform. The proteins were purified by two-step affinity chromatography and analyzed in parallel by PAGE-western blot, mass spectrometry, circular dichroism, surface plasmon resonance, and chromogenic, clotting and thrombin generation assays. Results and conclusion The average yield of the CO was 7-fold higher than WT, whereas both proteins were identical in the amino acid sequences (99% coverage) and very similar in patterns of the molecular fragments (before and after thrombin cleavage), glycosylation and tyrosine sulfation, secondary structures and binding to von Willebrand factor and to a fragment of the low-density lipoprotein receptor-related protein 1. The CO preparations had on average 1.5-fold higher FVIII specific activity (activity normalized to protein mass) than WT preparations, which was attributed to better preservation of the CO structure as a result of considerably higher protein concentrations during the production. We concluded that the codon-optimization of the BDD-FVIII resulted in significant increase of its expression and did not affect the structure-function properties.
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Affiliation(s)
- S A Shestopal
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - J-J Hao
- Poochon Scientific, Frederick, MD, USA
| | - E Karnaukhova
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Y Liang
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - M V Ovanesov
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - M Lin
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - J H Kurasawa
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - T K Lee
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - J H Mcvey
- School of Biosciences and Medicine, University of Surrey, Surrey, UK
| | - A G Sarafanov
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
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13
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Zevin M, Coughlin S, Bahaadini S, Besler E, Rohani N, Allen S, Cabero M, Crowston K, Katsaggelos AK, Larson SL, Lee TK, Lintott C, Littenberg TB, Lundgren A, Østerlund C, Smith JR, Trouille L, Kalogera V. Gravity Spy: integrating advanced LIGO detector characterization, machine learning, and citizen science. Class Quantum Gravity 2017; 34:064003. [PMID: 29722360 PMCID: PMC5927381 DOI: 10.1088/1361-6382/aa5cea] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
With the first direct detection of gravitational waves, the advanced laser interferometer gravitational-wave observatory (LIGO) has initiated a new field of astronomy by providing an alternative means of sensing the universe. The extreme sensitivity required to make such detections is achieved through exquisite isolation of all sensitive components of LIGO from non-gravitational-wave disturbances. Nonetheless, LIGO is still susceptible to a variety of instrumental and environmental sources of noise that contaminate the data. Of particular concern are noise features known as glitches, which are transient and non-Gaussian in their nature, and occur at a high enough rate so that accidental coincidence between the two LIGO detectors is non-negligible. Glitches come in a wide range of time-frequency-amplitude morphologies, with new morphologies appearing as the detector evolves. Since they can obscure or mimic true gravitational-wave signals, a robust characterization of glitches is paramount in the effort to achieve the gravitational-wave detection rates that are predicted by the design sensitivity of LIGO. This proves a daunting task for members of the LIGO Scientific Collaboration alone due to the sheer amount of data. In this paper we describe an innovative project that combines crowdsourcing with machine learning to aid in the challenging task of categorizing all of the glitches recorded by the LIGO detectors. Through the Zooniverse platform, we engage and recruit volunteers from the public to categorize images of time-frequency representations of glitches into pre-identified morphological classes and to discover new classes that appear as the detectors evolve. In addition, machine learning algorithms are used to categorize images after being trained on human-classified examples of the morphological classes. Leveraging the strengths of both classification methods, we create a combined method with the aim of improving the efficiency and accuracy of each individual classifier. The resulting classification and characterization should help LIGO scientists to identify causes of glitches and subsequently eliminate them from the data or the detector entirely, thereby improving the rate and accuracy of gravitational-wave observations. We demonstrate these methods using a small subset of data from LIGO's first observing run.
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Affiliation(s)
- M Zevin
- Center for Interdisciplinary Exploration and Research in Astrophysics (CIERA) and Deptartment of Physics and Astronomy, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208, United States of America
| | - S Coughlin
- Center for Interdisciplinary Exploration and Research in Astrophysics (CIERA) and Deptartment of Physics and Astronomy, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208, United States of America
| | - S Bahaadini
- Electrical Engineering and Computer Science, Northwestern University, Evanston, IL 60201, United States of America
| | - E Besler
- Electrical Engineering and Computer Science, Northwestern University, Evanston, IL 60201, United States of America
| | - N Rohani
- Electrical Engineering and Computer Science, Northwestern University, Evanston, IL 60201, United States of America
| | - S Allen
- Adler Planetarium, Chicago, IL 60605, United States of America
| | - M Cabero
- Max-Planck-Institut für Gravitationsphysik, Callinstrasse 38, D-30167 Hannover, Germany
| | - K Crowston
- School of Information Studies, Syracuse University, Syracuse, NY 13210, United States of America
| | - A K Katsaggelos
- Electrical Engineering and Computer Science, Northwestern University, Evanston, IL 60201, United States of America
| | - S L Larson
- Center for Interdisciplinary Exploration and Research in Astrophysics (CIERA) and Deptartment of Physics and Astronomy, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208, United States of America
- Adler Planetarium, Chicago, IL 60605, United States of America
| | - T K Lee
- Department of Communication, University of Utah, Salt Lake City, UT 84112, United States of America
| | - C Lintott
- Department of Physics, University of Oxford, Oxford, United Kingdom
| | - T B Littenberg
- NASA/Marshall Space Flight Center, Huntsville, AL 35812, United States of America
| | - A Lundgren
- Max-Planck-Institut für Gravitationsphysik, Callinstrasse 38, D-30167 Hannover, Germany
| | - C Østerlund
- School of Information Studies, Syracuse University, Syracuse, NY 13210, United States of America
| | - J R Smith
- Department of Physics, California State University Fullerton, Fullerton, CA 92831, United States of America
| | - L Trouille
- Center for Interdisciplinary Exploration and Research in Astrophysics (CIERA) and Deptartment of Physics and Astronomy, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208, United States of America
- Adler Planetarium, Chicago, IL 60605, United States of America
| | - V Kalogera
- Center for Interdisciplinary Exploration and Research in Astrophysics (CIERA) and Deptartment of Physics and Astronomy, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208, United States of America
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14
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Ursell T, Lee TK, Shiomi D, Shi H, Tropini C, Monds RD, Colavin A, Billings G, Bhaya-Grossman I, Broxton M, Huang BE, Niki H, Huang KC. Rapid, precise quantification of bacterial cellular dimensions across a genomic-scale knockout library. BMC Biol 2017; 15:17. [PMID: 28222723 PMCID: PMC5320674 DOI: 10.1186/s12915-017-0348-8] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [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: 08/18/2016] [Accepted: 01/06/2017] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The determination and regulation of cell morphology are critical components of cell-cycle control, fitness, and development in both single-cell and multicellular organisms. Understanding how environmental factors, chemical perturbations, and genetic differences affect cell morphology requires precise, unbiased, and validated measurements of cell-shape features. RESULTS Here we introduce two software packages, Morphometrics and BlurLab, that together enable automated, computationally efficient, unbiased identification of cells and morphological features. We applied these tools to bacterial cells because the small size of these cells and the subtlety of certain morphological changes have thus far obscured correlations between bacterial morphology and genotype. We used an online resource of images of the Keio knockout library of nonessential genes in the Gram-negative bacterium Escherichia coli to demonstrate that cell width, width variability, and length significantly correlate with each other and with drug treatments, nutrient changes, and environmental conditions. Further, we combined morphological classification of genetic variants with genetic meta-analysis to reveal novel connections among gene function, fitness, and cell morphology, thus suggesting potential functions for unknown genes and differences in modes of action of antibiotics. CONCLUSIONS Morphometrics and BlurLab set the stage for future quantitative studies of bacterial cell shape and intracellular localization. The previously unappreciated connections between morphological parameters measured with these software packages and the cellular environment point toward novel mechanistic connections among physiological perturbations, cell fitness, and growth.
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Affiliation(s)
- Tristan Ursell
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.,Department of Physics, University of Oregon, Eugene, OR, 97403, USA
| | - Timothy K Lee
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Daisuke Shiomi
- National Institute of Genetics, Shizuoka, Japan.,Current address: Department of Life Science, Rikkyo University, Tokyo, Japan
| | - Handuo Shi
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Carolina Tropini
- Biophysics Program, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Russell D Monds
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.,Current address: Synthetic Genomics Inc., La Jolla, CA, 92037, USA
| | - Alexandre Colavin
- Biophysics Program, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Gabriel Billings
- Department of Physics, Stanford University, Stanford, CA, 94305, USA
| | | | - Michael Broxton
- Department of Computer Science, Stanford University, Stanford, CA, 94305, USA
| | | | | | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA. .,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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15
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Parunov LA, Surov SS, Liang Y, Lee TK, Ovanesov MV. Can the diagnostic reliability of the thrombin generation test as a global haemostasis assay be improved? The impact of calcium chloride concentration. Haemophilia 2017; 23:466-475. [PMID: 28205396 DOI: 10.1111/hae.13174] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2016] [Indexed: 11/28/2022]
Abstract
BACKGROUND Thrombin generation test (TGT) is a global haemostasis assay with a potential to predict bleeding tendencies and treatment effects in patients with haemophilia. Despite 15 years of clinical research, the diagnostic value of TGT remains controversial, possibly due to suboptimal sensitivity to coagulation deficiencies, robustness and reproducibility. OBJECTIVE The goal of this study was to explore the effect of calcium chloride (CaCl2 ) concentration on the TGT's response to intrinsic coagulation factors (F) VIII, IX and XIa. METHODS Normal and factor-deficient plasmas supplemented with lacking coagulation factor and different CaCl2 levels were tested by calibrated thrombinography assay. RESULTS Thrombin peak height (TPH) was strongly CaCl2 dependent, increasing sharply from no TG at 5 mm to a peak at 13.8 mm of CaCl2 (95% confidence interval [CI]: 13.0, 14.5) in normal and normalized deficient plasmas and at 11.9 mm (CI: 9.7, 14.2) in deficient plasmas, and then decreasing slowly to a complete inhibition at 30-40 mm. In contrast, TG lag time, time to peak and endogenous thrombin potential were nearly insensitive to CaCl2 concentrations between 10 and 20 mm. The maximal difference between the TPH in deficient and supplemented plasmas was observed at 15.5 mm (CI: 12.8, 18.1). CONCLUSION Variations in CaCl2 concentration in the assay mixture and sodium citrate concentrations in patient plasma samples may affect TGT responses, sensitivity and result in increased inter- and intra-laboratory variance. Implementation of TGT by clinical and quality control laboratories may require optimization of CaCl2 concentration.
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Affiliation(s)
- L A Parunov
- Office of Tissues and Advanced Therapies, CBER, US Food and Drug Administration, Silver Spring, MD, USA.,Center for Theoretical Problems of Physicochemical Pharmacology, Moscow, Russia
| | - S S Surov
- Office of Tissues and Advanced Therapies, CBER, US Food and Drug Administration, Silver Spring, MD, USA.,Center for Theoretical Problems of Physicochemical Pharmacology, Moscow, Russia
| | - Y Liang
- Office of Tissues and Advanced Therapies, CBER, US Food and Drug Administration, Silver Spring, MD, USA
| | - T K Lee
- Office of Tissues and Advanced Therapies, CBER, US Food and Drug Administration, Silver Spring, MD, USA
| | - M V Ovanesov
- Office of Tissues and Advanced Therapies, CBER, US Food and Drug Administration, Silver Spring, MD, USA
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16
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Lee TK, Meng K, Shi H, Huang KC. Single-molecule imaging reveals modulation of cell wall synthesis dynamics in live bacterial cells. Nat Commun 2016; 7:13170. [PMID: 27774981 PMCID: PMC5078992 DOI: 10.1038/ncomms13170] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [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: 01/21/2016] [Accepted: 09/08/2016] [Indexed: 12/03/2022] Open
Abstract
The peptidoglycan cell wall is an integral organelle critical for bacterial cell shape and stability. Proper cell wall construction requires the interaction of synthesis enzymes and the cytoskeleton, but it is unclear how the activities of individual proteins are coordinated to preserve the morphology and integrity of the cell wall during growth. To elucidate this coordination, we used single-molecule imaging to follow the behaviours of the two major peptidoglycan synthases in live, elongating Escherichia coli cells and after perturbation. We observed heterogeneous localization dynamics of penicillin-binding protein (PBP) 1A, the synthase predominantly associated with cell wall elongation, with individual PBP1A molecules distributed between mobile and immobile populations. Perturbations to PBP1A activity, either directly through antibiotics or indirectly through PBP1A's interaction with its lipoprotein activator or other synthases, shifted the fraction of mobile molecules. Our results suggest that multiple levels of regulation control the activity of enzymes to coordinate peptidoglycan synthesis. The bacterial cell wall is important for cell shape and stability, but how the activities of the biosynthetic machinery are coordinated are not clear. Here the authors use single-molecule imaging and chemical perturbations to determine factors that affect the localization dynamics of penicillin-binding proteins (PBP)1A and PBP1B.
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Affiliation(s)
- Timothy K Lee
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA.,Program in Biomedical Informatics, Stanford University, Stanford, California 94305, USA
| | - Kevin Meng
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Handuo Shi
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
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17
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Hewagalamulage SD, Lee TK, Clarke IJ, Henry BA. Stress, cortisol, and obesity: a role for cortisol responsiveness in identifying individuals prone to obesity. Domest Anim Endocrinol 2016; 56 Suppl:S112-20. [PMID: 27345309 DOI: 10.1016/j.domaniend.2016.03.004] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 03/14/2016] [Accepted: 03/18/2016] [Indexed: 11/22/2022]
Abstract
There is a strong inter-relationship between activation of the hypothalamo-pituitary-adrenal axis and energy homeostasis. Patients with abdominal obesity have elevated cortisol levels. Furthermore, stress and glucocorticoids act to control both food intake and energy expenditure. In particular, glucocorticoids are known to increase the consumption of foods enriched in fat and sugar. It is well-known that, in all species, the cortisol response to stress or adrenocorticotropin is highly variable. It has now emerged that cortisol responsiveness is an important determinant in the metabolic sequelae to stress. Sheep that are characterized as high-cortisol responders (HRs) have greater propensity to weight gain and obesity than low-cortisol responders (LRs). This difference in susceptibility to become obese is associated with a distinct metabolic, neuroendocrine, and behavioral phenotype. In women and ewes, HR individuals eat more in response to stress than LR. Furthermore, HR sheep have impaired melanocortin signaling and reduced skeletal muscle thermogenesis. High-cortisol responder sheep exhibit reactive coping strategies, whereas LRs exhibit proactive coping strategies. This complex set of traits leads to increased food intake and reduced energy expenditure in HR and thus, predisposition to obesity. We predict that cortisol responsiveness may be used as a marker to identify individuals who are at risk of weight gain and subsequent obesity.
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Affiliation(s)
| | - T K Lee
- Department of Physiology, Monash University, VIC 3800, Australia
| | - I J Clarke
- Department of Physiology, Monash University, VIC 3800, Australia
| | - B A Henry
- Department of Physiology, Monash University, VIC 3800, Australia.
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18
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Auer GK, Lee TK, Rajendram M, Cesar S, Miguel A, Huang KC, Weibel DB. Mechanical Genomics Identifies Diverse Modulators of Bacterial Cell Stiffness. Cell Syst 2016; 2:402-11. [PMID: 27321372 DOI: 10.1016/j.cels.2016.05.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Revised: 02/03/2016] [Accepted: 05/18/2016] [Indexed: 10/21/2022]
Abstract
Bacteria must maintain mechanical integrity to withstand the large osmotic pressure differential across the cell membrane and wall. Although maintaining mechanical integrity is critical for proper cellular function, a fact exploited by prominent cell-wall-targeting antibiotics, the proteins that contribute to cellular mechanics remain unidentified. Here, we describe a high-throughput optical method for quantifying cell stiffness and apply this technique to a genome-wide collection of ∼4,000 Escherichia coli mutants. We identify genes with roles in diverse functional processes spanning cell-wall synthesis, energy production, and DNA replication and repair that significantly change cell stiffness when deleted. We observe that proteins with biochemically redundant roles in cell-wall synthesis exhibit different stiffness defects when deleted. Correlating our data with chemical screens reveals that reducing membrane potential generally increases cell stiffness. In total, our work demonstrates that bacterial cell stiffness is a property of both the cell wall and broader cell physiology and lays the groundwork for future systematic studies of mechanoregulation.
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Affiliation(s)
- George K Auer
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Timothy K Lee
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Manohary Rajendram
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Spencer Cesar
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Amanda Miguel
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Douglas B Weibel
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
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19
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Lee TK, Ewald A. SU-F-J-119: Pilot Study On the Location-Based Lung Motion Assessment. Med Phys 2016. [DOI: 10.1118/1.4956027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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20
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21
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Zhou X, Halladin DK, Rojas ER, Koslover EF, Lee TK, Huang KC, Theriot JA. Bacterial division. Mechanical crack propagation drives millisecond daughter cell separation in Staphylococcus aureus. Science 2015; 348:574-8. [PMID: 25931560 DOI: 10.1126/science.aaa1511] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
When Staphylococcus aureus undergoes cytokinesis, it builds a septum, generating two hemispherical daughters whose cell walls are only connected via a narrow peripheral ring. We found that resolution of this ring occurred within milliseconds ("popping"), without detectable changes in cell volume. The likelihood of popping depended on cell-wall stress, and the separating cells split open asymmetrically, leaving the daughters connected by a hinge. An elastostatic model of the wall indicated high circumferential stress in the peripheral ring before popping. Last, we observed small perforations in the peripheral ring that are likely initial points of mechanical failure. Thus, the ultrafast daughter cell separation in S. aureus appears to be driven by accumulation of stress in the peripheral ring and exhibits hallmarks of mechanical crack propagation.
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Affiliation(s)
- Xiaoxue Zhou
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA. Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA. Howard Hughes Medical Institute (HHMI), Stanford University School of Medicine, Stanford, CA 94305, USA
| | - David K Halladin
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA. Howard Hughes Medical Institute (HHMI), Stanford University School of Medicine, Stanford, CA 94305, USA. Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Enrique R Rojas
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA. Howard Hughes Medical Institute (HHMI), Stanford University School of Medicine, Stanford, CA 94305, USA. Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Elena F Koslover
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA. Howard Hughes Medical Institute (HHMI), Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Timothy K Lee
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Kerwyn Casey Huang
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA. Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Julie A Theriot
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA. Howard Hughes Medical Institute (HHMI), Stanford University School of Medicine, Stanford, CA 94305, USA. Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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22
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Parunov LA, Ataullakhanov FI, Lee TK, Ovanesov MV. Abstract 181: Sub-picomolar Amounts of Coagulation Factor XIa Promote Spatial Clot Growth and Thrombin Generation Inside Propagating Clot. Arterioscler Thromb Vasc Biol 2015. [DOI: 10.1161/atvb.35.suppl_1.181] [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] [Indexed: 11/16/2022]
Abstract
Background:
Activated coagulation factor XI (FXIa) was found in the immunoglobulin products that were associated with higher than usual incidence of thrombotic events (TEs). However, TEs after thrombogenic immunoglobulin administration are very rare and are often recorded as late as 48 hours after administration.
Objective:
This study was aimed to elucidate the mechanisms behind FXIa thrombogenicity. We hypothesized that low amounts of FXIa are not able to activate clotting directly, but can promote on-going coagulation events at a site of vascular lesion.
Materials and methods:
FXIa activity was characterized by kinetic clotting and thrombin generation (TG) assays. Spatial clot growth and thrombin wave propagation in stagnant plasma were studied using thrombodynamics, a time-lapse videomicroscopy-based approach. To model coagulation events at the site of vascular wall lesion, spatial clot growth was initiated by plastic surfaces covered with immobilized tissue factor (TF). Human plasma deficient in various coagulation factors was used to study pathways of FXI activation.
Results:
Low plasma FXIa levels of less than 0.3 pM did not induce thrombin generation or clotting, but increased TG in plasma mixed with TF. Higher FXIa levels (>0.3 pM) activated coagulation directly. In stagnant plasma activated by surface with immobilized TF, sub-picomolar amounts of FXIa were also not able to initiate clotting, but was able to enhance TG inside clots. FXIa-induced TG was localized to the propagating edge of the clot and associated with increased clot growth rate.
Conclusion:
Sub-picomolar amounts of FXIa may promote growth of clot in the vicinity of vascular lesion and have no procoagulant effect in the absence of exposed TF. These in vitro findings suggest that the patient’s condition might contribute to the thrombogenicity of FXIa.
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Affiliation(s)
| | - Fazoil I Ataullakhanov
- Laboratory of Physiology and Cell Biophysics, Cntr for Theoretical Problems of Physicochemical Pharmacology RAS, Moscow, Russian Federation
| | - Timothy K Lee
- Div of Hematology Rsch and Review, FDA, CBER, Silver Spring, MD
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Kurasawa JH, Shestopal SA, Woodle SA, Ovanesov MV, Lee TK, Sarafanov AG. Cluster III of low-density lipoprotein receptor-related protein 1 binds activated blood coagulation factor VIII. Biochemistry 2014; 54:481-9. [PMID: 25486042 DOI: 10.1021/bi5011688] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Low-density lipoprotein receptor-related protein 1 (LRP) mediates clearance of blood coagulation factor VIII (FVIII). In LRP, FVIII binds the complement-type repeats (CRs) of clusters II and IV, which also bind a majority of other LRP ligands. No ligand is known for LRP cluster I, and only three ligands, including the LRP chaperone alpha-2 macroglobulin receptor-associated protein (RAP), bind cluster III. Using surface plasmon resonance, we found that in addition to clusters II and IV, activated FVIII (FVIIIa) binds cluster III. The specificity of this interaction was confirmed using an anti-FVIII antibody fragment, which inhibited the binding. Recombinant fragments of cluster III and its site-directed mutagenesis were used to localize the cluster's site for binding FVIIIa to CR.14-19. The interactive site of FVIIIa was localized within its A1/A3'-C1-C2 heterodimer (HDa), which is a major physiological remnant of FVIIIa. In mice, the clearance of HDa was faster than that of FVIII and prolonged in the presence of RAP, which is known to inhibit interactions of LRP with its ligands. In accordance with this, the cluster III site for RAP (CR.15-19) was found to overlap that for FVIIIa. Altogether, our findings support the involvement of LRP in FVIIIa catabolism and suggest a greater significance of the biological role of cluster III compared to that previously known.
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Affiliation(s)
- James H Kurasawa
- Center for Biologics Evaluation and Research, Food and Drug Administration , Silver Spring, Maryland 20993-0002, United States
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24
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Tropini C, Lee TK, Hsin J, Desmarais SM, Ursell T, Monds RD, Huang KC. Principles of bacterial cell-size determination revealed by cell-wall synthesis perturbations. Cell Rep 2014; 9:1520-7. [PMID: 25456140 PMCID: PMC4254626 DOI: 10.1016/j.celrep.2014.10.027] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 08/21/2014] [Accepted: 10/13/2014] [Indexed: 01/08/2023] Open
Abstract
Although bacterial cell morphology is tightly controlled, the principles of size regulation remain elusive. In Escherichia coli, perturbation of cell-wall synthesis often results in similar morphologies, making it difficult to deconvolve the complex genotype-phenotype relationships underlying morphogenesis. Here we modulated cell width through heterologous expression of sequences encoding the essential enzyme PBP2 and through sublethal treatments with drugs that inhibit PBP2 and the MreB cytoskeleton. We quantified the biochemical and biophysical properties of the cell wall across a wide range of cell sizes. We find that, although cell-wall chemical composition is unaltered, MreB dynamics, cell twisting, and cellular mechanics exhibit systematic large-scale changes consistent with altered chirality and a more isotropic cell wall. This multiscale analysis enabled identification of distinct roles for MreB and PBP2, despite having similar morphological effects when depleted. Altogether, our results highlight the robustness of cell-wall synthesis and physical principles dictating cell-size control.
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Affiliation(s)
- Carolina Tropini
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | - Timothy K Lee
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Jen Hsin
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | - Tristan Ursell
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Russell D Monds
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Biophysics Program, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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25
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Monds RD, Lee TK, Colavin A, Ursell T, Quan S, Cooper TF, Huang KC. Systematic perturbation of cytoskeletal function reveals a linear scaling relationship between cell geometry and fitness. Cell Rep 2014; 9:1528-37. [PMID: 25456141 DOI: 10.1016/j.celrep.2014.10.040] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Revised: 08/18/2014] [Accepted: 10/15/2014] [Indexed: 11/19/2022] Open
Abstract
Diversification of cell size is hypothesized to have occurred through a process of evolutionary optimization, but direct demonstrations of causal relationships between cell geometry and fitness are lacking. Here, we identify a mutation from a laboratory-evolved bacterium that dramatically increases cell size through cytoskeletal perturbation and confers a large fitness advantage. We engineer a library of cytoskeletal mutants of different sizes and show that fitness scales linearly with respect to cell size over a wide physiological range. Quantification of the growth rates of single cells during the exit from stationary phase reveals that transitions between "feast-or-famine" growth regimes are a key determinant of cell-size-dependent fitness effects. We also uncover environments that suppress the fitness advantage of larger cells, indicating that cell-size-dependent fitness effects are subject to both biophysical and metabolic constraints. Together, our results highlight laboratory-based evolution as a powerful framework for studying the quantitative relationships between morphology and fitness.
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Affiliation(s)
- Russell D Monds
- Bio-X Program, Stanford University, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
| | - Timothy K Lee
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | - Tristan Ursell
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Selwyn Quan
- Bio-X Program, Stanford University, Stanford, CA 94305, USA
| | - Tim F Cooper
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
| | - Kerwyn Casey Huang
- Bio-X Program, Stanford University, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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26
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Lee TK, Ewald A, Schultz T, Park SY. SU-E-J-253: Evaluation of 4DCT Images with Correlation of RPM Signals to Tumor Motion for Respiratory-Gated Radiotherapy. Med Phys 2014. [DOI: 10.1118/1.4888307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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27
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Abstract
OBJECTIVE To determine the natural history of deep vein thrombosis in children presented with a first episode in the lower extremity veins. METHODS Children with objective diagnosis of acute deep vein thrombosis were followed up with ultrasound and clinical examination. Risk factors and clinical presentation were prospectively collected. The prevalence of recurrent deep vein thrombosis and the development of signs and symptoms of chronic venous disease were recorded. RESULTS There were 27 children, 15 males and 12 females, with acute deep vein thrombosis, with a mean age of 4 years, range 0.1-16 years. The median follow-up was 23 months, range 8-62 months. The location of thrombosis involved the iliac and common femoral vein in 18 patients and the femoral and popliteal veins in 9. Only one vein was affected in 7 children, two veins in 14 and more than two veins in 6. Recurrent deep vein thrombosis occurred in two patients, while no patient had a clinically significant pulmonary embolism. Signs and symptoms of chronic venous disease were present at last follow-up in 11 patients. There were nine patients with vein collaterals, but no patient developed varicose veins. Reflux was found in 18 veins of 11 patients. Failure of recanalization was seen in 7 patients and partial recanalization in 11. Iliofemoral thrombosis (p = 0.012) and failure to recanalize (p = 0.036) increased significantly the risk for developing signs and symptoms. CONCLUSIONS Children with acute proximal deep vein thrombosis develop mild chronic venous disease signs and symptoms at mid-term follow-up and are closely related with iliofemoral thrombosis and failure to recanalization.
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Affiliation(s)
- G Spentzouris
- Division of Vascular Surgery, Stony Brook University Medical Center, Stony Brook, New York, USA
| | - A Gasparis
- Division of Vascular Surgery, Stony Brook University Medical Center, Stony Brook, New York, USA
| | - R J Scriven
- Section of Pediatric Surgery, Stony Brook University Medical Center, Stony Brook, New York, USA
| | - T K Lee
- Section of Pediatric Surgery, Stony Brook University Medical Center, Stony Brook, New York, USA
| | - N Labropoulos
- Division of Vascular Surgery, Stony Brook University Medical Center, Stony Brook, New York, USA
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28
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Peng Y, Meng J, Mou D, He J, Zhao L, Wu Y, Liu G, Dong X, He S, Zhang J, Wang X, Peng Q, Wang Z, Zhang S, Yang F, Chen C, Xu Z, Lee TK, Zhou XJ. Disappearance of nodal gap across the insulator-superconductor transition in a copper-oxide superconductor. Nat Commun 2014; 4:2459. [PMID: 24051514 DOI: 10.1038/ncomms3459] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 08/18/2013] [Indexed: 11/09/2022] Open
Abstract
The parent compound of the copper-oxide high-temperature superconductors is a Mott insulator. Superconductivity is realized by doping an appropriate amount of charge carriers. How a Mott insulator transforms into a superconductor is crucial in understanding the unusual physical properties of high-temperature superconductors and the superconductivity mechanism. Here we report high-resolution angle-resolved photoemission measurement on heavily underdoped Bi₂Sr₂-xLaxCuO(₆+δ) system. The electronic structure of the lightly doped samples exhibit a number of characteristics: existence of an energy gap along the nodal direction, d-wave-like anisotropic energy gap along the underlying Fermi surface, and coexistence of a coherence peak and a broad hump in the photoemission spectra. Our results reveal a clear insulator-superconductor transition at a critical doping level of ~0.10 where the nodal energy gap approaches zero, the three-dimensional antiferromagnetic order disappears, and superconductivity starts to emerge. These observations clearly signal a close connection between the nodal gap, antiferromagnetism and superconductivity.
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Affiliation(s)
- Yingying Peng
- National Laboratory for Superconductivity, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
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29
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Abstract
Although hydrolysis is known to be as important as synthesis in the growth and development of the bacterial cell wall, the coupling between these processes is not well understood. Bond cleavage can generate deleterious pores, but may also be required for the incorporation of new material and for the expansion of the wall, highlighting the importance of mechanical forces in interpreting the consequences of hydrolysis in models of growth. Critically, minimal essential subsets of hydrolases have now been identified in several model organisms, enabling the reduction of genetic complexity. Recent studies in Bacillus subtilis have provided evidence for both the presence and absence of coupling between synthesis and hydrolysis during sporulation and elongation, respectively. In this review, we discuss strategies for dissecting the relationship between synthesis and hydrolysis using time-lapse imaging, biophysical measurements of cell-wall architecture, and computational modeling.
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Affiliation(s)
- Timothy K Lee
- Department of Bioengineering, Stanford University, Stanford, CA, USA
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30
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Woodle SA, Shibeko AM, Lee TK, Ovanesov MV. Determining the impact of instrument variation and automated software algorithms on the TGT in hemophilia and normalized plasma. Thromb Res 2013; 132:374-80. [PMID: 23953593 DOI: 10.1016/j.thromres.2013.07.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Revised: 07/07/2013] [Accepted: 07/23/2013] [Indexed: 10/26/2022]
Abstract
BACKGROUND Despite increasing recognition as a more precise test of in vivo hemostatic conditions, standardization of the thrombin generation test (TGT) continues to hinder its development as routine clinical practice. Prior efforts largely focused on comparing the effects of experimental conditions and different reagents. Commercialized kits, instruments and software have been introduced to calculate the TG curve and its parameters. However, modified versions of the TGT continue to be used worldwide on a variety of microplate reader instruments and processed using individualized algorithms. No prior study has compared the effect of instrument choice and its inherent noise profile on the processing of the TG curve and its common endpoint parameters. MATERIALS AND METHODS Hemophilia A plasma supplemented with buffer or Factor VIII, mimicking hemophilic or normalized samples respectively, was monitored for thrombin generation after activation with TF on six different fluorescent microplate readers. Each instrument was optimized for TGT signal recording prior to testing. An automated software package containing various mathematical algorithms was utilized to compute the TG curves and parameters, and compare different TG processing approaches. RESULTS Instruments produced unique noise profiles and end-point parameters that were incomparable in absolute signal terms. Similar relative hemophilic responses were obtained across various instruments when the normalized plasma sample was used as an internal standard. Smoothing algorithms corrected destructive instrument noise. CONCLUSIONS Instrument-induced errors from numerical differentiation during TG curve processing cannot be eliminated by external calibrators, and require careful qualification of the instrument and implementation of noise-reducing software algorithms.
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Affiliation(s)
- S A Woodle
- Office of Blood Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Bethesda, MD, USA
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31
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Liang Y, Woodle SA, Shibeko AM, Lee TK, Ovanesov MV. Correction of microplate location effects improves performance of the thrombin generation test. Thromb J 2013; 11:12. [PMID: 23829491 PMCID: PMC3708834 DOI: 10.1186/1477-9560-11-12] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [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: 02/08/2013] [Accepted: 05/11/2013] [Indexed: 11/25/2022] Open
Abstract
Background Microplate-based thrombin generation test (TGT) is widely used as clinical measure of global hemostatic potential and it becomes a useful tool for control of drug potency and quality by drug manufactures. However, the convenience of the microtiter plate technology can be deceiving: microplate assays are prone to location-based variability in different parts of the microtiter plate. Methods In this report, we evaluated the well-to-well consistency of the TGT variant specifically applied to the quantitative detection of the thrombogenic substances in the immune globulin product. We also studied the utility of previously described microplate layout designs in the TGT experiment. Results Location of the sample on the microplate (location effect) contributes to the variability of TGT measurements. Use of manual pipetting techniques and applications of the TGT to the evaluation of procoagulant enzymatic substances are especially sensitive. The effects were not sensitive to temperature or choice of microplate reader. Smallest location effects were observed with automated dispenser-based calibrated thrombogram instrument. Even for an automated instrument, the use of calibration curve resulted in up to 30% bias in thrombogenic potency assignment. Conclusions Use of symmetrical version of the strip-plot layout was demonstrated to help to minimize location artifacts even under the worst-case conditions. Strip-plot layouts are required for quantitative thrombin-generation based bioassays used in the biotechnological field.
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Affiliation(s)
- Yideng Liang
- Office of Blood Research and Review, Center for Biologics Evaluation and Research, U,S, Food and Drug Administration, 29 Lincoln Drive, N29/306, Bethesda, MD 20892, USA.
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32
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Kurasawa JH, Shestopal SA, Karnaukhova E, Struble EB, Lee TK, Sarafanov AG. Mapping the binding region on the low density lipoprotein receptor for blood coagulation factor VIII. J Biol Chem 2013; 288:22033-41. [PMID: 23754288 DOI: 10.1074/jbc.m113.468108] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Low density lipoprotein receptor (LDLR) was shown to mediate clearance of blood coagulation factor VIII (FVIII) from the circulation. To elucidate the mechanism of interaction of LDLR and FVIII, our objective was to identify the region of the receptor necessary for binding FVIII. Using surface plasmon resonance, we found that LDLR exodomain and its cluster of complement-type repeats (CRs) bind FVIII in the same mode. This indicated that the LDLR site for FVIII is located within the LDLR cluster. Similar results were obtained for another ligand of LDLR, α-2-macroglobulin receptor-associated protein (RAP), a common ligand of receptors from the LDLR family. We further generated a set of recombinant fragments of the LDLR cluster and assessed their structural integrity by binding to RAP and by circular dichroism. A number of fragments overlapping CR.2-5 of the cluster were positive for binding RAP and FVIII. The specificity of these interactions was tested by site-directed mutagenesis of conserved tryptophans within the LDLR fragments. For FVIII, the specificity was also tested using a single-chain variable antibody fragment directed against the FVIII light chain as a competitor. Both cases resulted in decreased binding, thus confirming its specificity. The mutagenic study also showed an importance of the conserved tryptophans in LDLR for both ligands, and the competitive binding results showed an involvement of the light chain of FVIII in its interaction with LDLR. In conclusion, the region of CR.2-5 of LDLR was defined as the binding site for FVIII and RAP.
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Affiliation(s)
- James H Kurasawa
- Center for Biologics Evaluation and Research, Food and Drug Administration, Rockville, Maryland 20852, USA
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33
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Choi E, Lee G, Park J, Lee TK, Choi HS, Lee S. Molecular characterization and an infectious clone construction of sweet potato leaf curl virus (SPLCV) isolated from Korea. Acta Virol 2013; 56:187-98. [PMID: 23043598 DOI: 10.4149/av_2012_03_187] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
UNLABELLED Sweet potato leaf curl disease (SPLCD) was primarily identified in sweet potato fields in Korea in 2003, and the complete genomic sequence of sweet potato leaf curl virus (SPLCV) has been cloned. The genome of the Korean SPLCV isolate (SPLCV-KR) comprises 2,828 nucleotides with six open reading frames in DNA-A, similar to a monopartite begomovirus. Additionally, neither the genome B genomic component nor the DNA beta sequence was detected. The results of phylogenetic analysis using the maximum parsimony method showed that SPLCV-KR is more closely related to SPLCV-US (US) than SPLCV-CN (China) and SPLCV-JP (Japan). A tandem repeat dimer of SPLCV-KR was cloned and found to be infectious in sweet potatoes (Ipomoea batatas) via biolistic inoculation. The SPLCV-infected sweet potatoes exhibited mild leaf curl symptoms of SPLCD, and the newly-replicated viral DNA was detected via Southern blot analysis. Results of biotic, molecular, and phylogenetic characterization suggest that SPLCV-KR is a new strain of SPLCV and is importantly placed in the evolutionary progression from curtoviruses to begomoviruses. KEYWORDS sweet potato leaf curl virus; sweet potato leaf curl disease; phylogenetic analysis; infectious clone; biolistic infection.
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Affiliation(s)
- E Choi
- Department of Genetic Engineering, Sungkyunkwan University, Suwon, 440-746, Korea
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34
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Kurasawa JH, Shestopal SA, Jha NK, Ovanesov MV, Lee TK, Sarafanov AG. Insect cell-based expression and characterization of a single-chain variable antibody fragment directed against blood coagulation factor VIII. Protein Expr Purif 2013; 88:201-6. [PMID: 23306063 DOI: 10.1016/j.pep.2012.12.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 12/20/2012] [Accepted: 12/25/2012] [Indexed: 10/27/2022]
Abstract
A recombinant single-chain variable antibody fragment (scFv) KM33 was previously described as a ligand that can inhibit the function of blood coagulation factor VIII (FVIII). This scFv was previously derived from an individual with anti-FVIII antibodies manifested in FVIII functional deficiency (Hemophilia A) and expressed in bacteria. In the present work, we describe an alternative approach for fast and easy production of KM33 in insect cells (Spodoptera frugiperda). The KM33 gene was codon-optimized and expressed in secreted form using a baculovirus system. The protein was isolated using metal-affinity and size-exclusion chromatography to purity of about 96% and yield of 0.4-1.2 mg per 120 mL of culture, based on several independent expression experiments. In a binding assay using surface plasmon resonance, the insect cell-derived KM33 (iKM33) was qualified as a high-affinity ligand for FVIII. Epitope specificity of iKM33 on FVIII (C1 domain) was confirmed by testing the binding with a relevant mutant of FVIII. In several FVIII functional tests (factor Xa generation, APTT clotting, thrombin generation and video microscopy clot growth assays), iKM33 strongly inhibited FVIII activity in accordance with the clinical effect of the parental antibody. Therefore, the expressed protein was concluded to be fully functional and applicable in various assays with FVIII.
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Affiliation(s)
- James H Kurasawa
- Division of Hematology, Office of Blood Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Bethesda, MD 20852, USA
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35
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Fajardo DA, Miyamoto H, Miller JS, Lee TK, Epstein JI. Identification of Gleason pattern 5 on prostatic needle core biopsy: frequency of underdiagnosis and relation to morphology. Int Braz J Urol 2011. [DOI: 10.1590/s1677-55382011000600022] [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: 11/22/2022] Open
Affiliation(s)
| | | | - JS Miller
- The Johns Hopkins Medical Institutions
| | - TK Lee
- The Johns Hopkins Medical Institutions
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36
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Abstract
One of the most exciting developments in signal transduction research has been the proliferation of studies in which a biological discovery was initiated by computational modeling. In this study, we review the major efforts that enable such studies. First, we describe the experimental technologies that are generally used to identify the molecular components and interactions in, and dynamic behavior exhibited by, a network of interest. Next, we review the mathematical approaches that are used to model signaling network behavior. Finally, we focus on three specific instances of 'model-driven discovery': cases in which computational modeling of a signaling network has led to new insights that have been verified experimentally.
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Affiliation(s)
- Jacob J Hughey
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Timothy K Lee
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Markus W Covert
- Department of Bioengineering, Stanford University, Stanford, CA, USA
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37
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Lee TK, Covert MW. High-throughput, single-cell NF-κB dynamics. Curr Opin Genet Dev 2010; 20:677-83. [PMID: 20846851 DOI: 10.1016/j.gde.2010.08.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Revised: 07/23/2010] [Accepted: 08/19/2010] [Indexed: 01/08/2023]
Abstract
Single cells in a population often respond differently to perturbations in the environment. Live-cell microscopy has enabled scientists to observe these differences at the single-cell level. Some advantages of live-cell imaging over population-based methods include better time resolution, higher sensitivity, automation, and richer datasets. One specific area where live-cell microscopy has made a significant impact is the field of NF-κB signaling dynamics, and recent efforts have focused on making live-cell imaging of these dynamics more high-throughput. We highlight the major aspects of increasing throughput and describe a current system that can monitor, image and analyze the NF-κB activation of thousands of single cells in parallel.
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Affiliation(s)
- Timothy K Lee
- Department of Bioengineering, Stanford University, 318 Campus Drive, Stanford, CA 94305, United States
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38
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Tay S, Hughey JJ, Lee TK, Lipniacki T, Quake SR, Covert MW. Single-cell NF-kappaB dynamics reveal digital activation and analogue information processing. Nature 2010; 466:267-71. [PMID: 20581820 DOI: 10.1038/nature09145] [Citation(s) in RCA: 608] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2009] [Accepted: 04/28/2010] [Indexed: 01/19/2023]
Abstract
Cells operate in dynamic environments using extraordinary communication capabilities that emerge from the interactions of genetic circuitry. The mammalian immune response is a striking example of the coordination of different cell types. Cell-to-cell communication is primarily mediated by signalling molecules that form spatiotemporal concentration gradients, requiring cells to respond to a wide range of signal intensities. Here we use high-throughput microfluidic cell culture and fluorescence microscopy, quantitative gene expression analysis and mathematical modelling to investigate how single mammalian cells respond to different concentrations of the signalling molecule tumour-necrosis factor (TNF)-alpha, and relay information to the gene expression programs by means of the transcription factor nuclear factor (NF)-kappaB. We measured NF-kappaB activity in thousands of live cells under TNF-alpha doses covering four orders of magnitude. We find, in contrast to population-level studies with bulk assays, that the activation is heterogeneous and is a digital process at the single-cell level with fewer cells responding at lower doses. Cells also encode a subtle set of analogue parameters to modulate the outcome; these parameters include NF-kappaB peak intensity, response time and number of oscillations. We developed a stochastic mathematical model that reproduces both the digital and analogue dynamics as well as most gene expression profiles at all measured conditions, constituting a broadly applicable model for TNF-alpha-induced NF-kappaB signalling in various types of cells. These results highlight the value of high-throughput quantitative measurements with single-cell resolution in understanding how biological systems operate.
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Affiliation(s)
- Savaş Tay
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA
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39
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Lee TK, Denny EM, Sanghvi JC, Gaston JE, Maynard ND, Hughey JJ, Covert MW. A noisy paracrine signal determines the cellular NF-kappaB response to lipopolysaccharide. Sci Signal 2009; 2:ra65. [PMID: 19843957 DOI: 10.1126/scisignal.2000599] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Nearly identical cells can exhibit substantially different responses to the same stimulus. We monitored the nuclear localization dynamics of nuclear factor kappaB (NF-kappaB) in single cells stimulated with tumor necrosis factor-alpha (TNF-alpha) and lipopolysaccharide (LPS). Cells stimulated with TNF-alpha have quantitative differences in NF-kappaB nuclear localization, whereas LPS-stimulated cells can be clustered into transient or persistent responders, representing two qualitatively different groups based on the NF-kappaB response. These distinct behaviors can be linked to a secondary paracrine signal secreted at low concentrations, such that not all cells undergo a second round of NF-kappaB activation. From our single-cell data, we built a computational model that captures cell variability, as well as population behaviors. Our findings show that mammalian cells can create "noisy" environments to produce diversified responses to stimuli.
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Affiliation(s)
- Timothy K Lee
- Bioengineering Department, Stanford University, 318 Campus Drive West, Stanford, CA 94305-5444, USA
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40
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Ma S, Lee TK, Zheng BJ, Chan KW, Guan XY. CD133+ HCC cancer stem cells confer chemoresistance by preferential expression of the Akt/PKB survival pathway. Oncogene 2007; 27:1749-58. [PMID: 17891174 DOI: 10.1038/sj.onc.1210811] [Citation(s) in RCA: 610] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The recent discovery of cancer stem cells (CSCs) has played a pivotal role in changing our view of carcinogenesis and chemotherapy. Based on this concept, CSCs are responsible for the formation and growth of neoplastic tissue and are naturally resistant to chemotherapy, explaining why traditional chemotherapies can initially shrink a tumor but fails to eradicate it in full, allowing eventual recurrence. Recently, we identified a CSC population in hepatocellular carcinoma (HCC) characterized by their CD133 phenotype. However, the molecular mechanism by which it escapes conventional therapies remains unknown. Here, we examined the sensitivity of these cells to chemotherapeutic agents (doxorubicin and fluorouracil) and the possible mechanistic pathway by which resistance may be regulated. Purified CD133+ HCC cells isolated from human HCC cell line and xenograft mouse models survived chemotherapy in increased proportions relative to most tumor cells which lack the CD133 phenotype; the underlying mechanism of which required the preferential expression of survival proteins involved in the Akt/PKB and Bcl-2 pathway. Treatment of CD133+ HCC cells with an AKT1 inhibitor, specific to the Akt/PKB pathway, significantly reduced the expression of the survival proteins that was normally expressed endogenously. In addition, treatment of unsorted HCC cells with both anticancer drugs in vitro significantly enriched the CD133+ subpopulation. In conclusion, our results show that CD133+ HCC cells contribute to chemoresistance through preferential activation of Akt/PKB and Bcl-2 cell survival response. Targeting of this specific survival signaling pathway in CD133+ HCC CSCs may provide a novel therapeutic model for the disease.
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Affiliation(s)
- S Ma
- Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
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41
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Sun CK, Ng KT, Sun BS, Ho JWY, Lee TK, Ng I, Poon RTP, Lo CM, Liu CL, Man K, Fan ST. The significance of proline-rich tyrosine kinase2 (Pyk2) on hepatocellular carcinoma progression and recurrence. Br J Cancer 2007; 97:50-7. [PMID: 17551499 PMCID: PMC2359657 DOI: 10.1038/sj.bjc.6603827] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Understanding the precise molecular mechanisms that trigger liver cancer cell migration and invasion could develop novel therapeutic strategies targeting cancer cell invasion to increase the sensitivity to current treatment modalities. In the current study, 49 patients with hepatocellular carcinoma (HCC) were included prospectively. Liver tumour and adjacent non-tumour tissues were detected for the expression of Proline-rich tyrosine kinase 2 (Pyk2), focal adhesion kinase (FAK), ezrin and fibronectin at protein and/or gene levels. Correlation between the expressions of Pyk2/FAK with the clinical pathological data was analysed. Protein expression of Pyk2 was also examined in a nude mice orthotopic liver tumour model with higher metastatic potential. There were 59% (29 out of 49) and 57% (28 out of 49) of HCC patients with higher levels of Pyk2 and FAK protein/gene expression, respectively. We observed a positive correlation between the protein and gene expression levels of Pyk2 and FAK (P=0.000, r=0.875). Overexpression of Pyk2 and FAK was significantly correlated with shorter disease-free survival. Patients with higher levels of Pyk2/FAK had larger tumour size and advanced Edmonson grading. In the animal studies, Pyk2 overexpression was found in infiltrative tumour cells and lung metastatic nodules. In conclusion, overexpression of Pyk2 and FAK was found in nearly 60% of HCC patients and was significantly correlated with poor prognosis. The significance of Pyk2 in HCC invasiveness was confirmed by animal studies.
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Affiliation(s)
- C K Sun
- Centre of Cancer Research and Department of Surgery, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - K T Ng
- Centre of Cancer Research and Department of Surgery, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - B S Sun
- Centre of Cancer Research and Department of Surgery, The University of Hong Kong, Pokfulam, Hong Kong, China
- Department of Pathology, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - J W Y Ho
- Centre of Cancer Research and Department of Surgery, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - T K Lee
- Centre of Cancer Research and Department of Surgery, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - I Ng
- Department of Surgery, Yuquan Hospital, Tsinghua University, Beijing, China
| | - R T P Poon
- Centre of Cancer Research and Department of Surgery, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - C M Lo
- Centre of Cancer Research and Department of Surgery, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - C L Liu
- Centre of Cancer Research and Department of Surgery, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - K Man
- Centre of Cancer Research and Department of Surgery, The University of Hong Kong, Pokfulam, Hong Kong, China
- E-mail:
| | - S T Fan
- Centre of Cancer Research and Department of Surgery, The University of Hong Kong, Pokfulam, Hong Kong, China
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Hom EFY, Marchis F, Lee TK, Haase S, Agard DA, Sedat JW. AIDA: an adaptive image deconvolution algorithm with application to multi-frame and three-dimensional data. J Opt Soc Am A Opt Image Sci Vis 2007; 24:1580-600. [PMID: 17491626 PMCID: PMC3166524 DOI: 10.1364/josaa.24.001580] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
We describe an adaptive image deconvolution algorithm (AIDA) for myopic deconvolution of multi-frame and three-dimensional data acquired through astronomical and microscopic imaging. AIDA is a reimplementation and extension of the MISTRAL method developed by Mugnier and co-workers and shown to yield object reconstructions with excellent edge preservation and photometric precision [J. Opt. Soc. Am. A21, 1841 (2004)]. Written in Numerical Python with calls to a robust constrained conjugate gradient method, AIDA has significantly improved run times over the original MISTRAL implementation. Included in AIDA is a scheme to automatically balance maximum-likelihood estimation and object regularization, which significantly decreases the amount of time and effort needed to generate satisfactory reconstructions. We validated AIDA using synthetic data spanning a broad range of signal-to-noise ratios and image types and demonstrated the algorithm to be effective for experimental data from adaptive optics-equipped telescope systems and wide-field microscopy.
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Affiliation(s)
- Erik F Y Hom
- Graduate Group in Biophysics and Department of Biochemistry and Biophysics, University of California, San Francisco 94143-2240, USA.
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Abstract
This study examined the expression of three isoforms of nitric oxide synthase (NOS) in the testes of pigs. Immunohistochemical studies demonstrated the presence of nNOS, eNOS and iNOS in interstitial cells, primary spermatocytes and spermatids. Positive immunoreactions for eNOS and iNOS were detected in peritubular myoid cells. Some vascular endothelial cells were positive for nNOS and eNOS. The expression of nitrotyrosine was detected in interstitial cells. In addition, the histochemical study revealed that all the interstitial cells were stained positively for NADPH-diaphorase, although some spermatids and vascular endothelial cells displayed moderate enzymatic activity. These findings suggest that three isoforms of NOS are expressed in the testis of pig and that they play important roles in the biology of interstitial cells that produce testosterone, as well as in spermatogenesis in the seminiferous tubules.
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Affiliation(s)
- H C Kim
- Department of Veterinary Medicine, Cheju National University, Jeju 690-756, Korea
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Chen YY, Huang PH, Ou MN, Wang CR, Yao YD, Lee TK, Ho MY, Lawrence JM, Booth CH. Kondo interactions and magnetic correlations in CePt2 nanocrystals. Phys Rev Lett 2007; 98:157206. [PMID: 17501380 DOI: 10.1103/physrevlett.98.157206] [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] [Subscribe] [Scholar Register] [Received: 12/07/2006] [Indexed: 05/15/2023]
Abstract
The evolution of the Kondo effect and antiferromagnetic (AF) correlations with size reduction in CePt2 nanoparticles (3.1-26 nm) is studied by analysis of the temperature-dependent specific heat and magnetic susceptibility. The AF correlations diminish with size reduction. The Kondo effect predominates at small particle size with trivalent, small Kondo temperature (TK) magnetic regions coexisting with strongly mixed-valent, large TK nonmagnetic regions. We discuss the role of structural disorder, background density of states and the electronic quantum size effect on the results.
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Affiliation(s)
- Y Y Chen
- Institute of Physics, Academia Sinica, Taipei, Taiwan, Republic of China.
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Rucker D, Johnson JA, Lee TK, Eurich DT, Lewanczuk RZ, Simpson SH, Toth EL, Majumdar SR. The natural history of LDL control in type 2 diabetes: a prospective study of adherence to lipid guidelines. Diabetes Care 2006; 29:2506-8. [PMID: 17065693 DOI: 10.2337/dc06-1205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Diana Rucker
- University of Alberta, 2E3.07 Walter Mackenzie Health Sciences Centre, University of Alberta Hospital, 8440-112th St., Edmonton, Alberta, Canada
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Ng KT, Man K, Sun CK, Lee TK, Poon RT, Lo CM, Fan ST. Clinicopathological significance of homeoprotein Six1 in hepatocellular carcinoma. Br J Cancer 2006; 95:1050-5. [PMID: 17008870 PMCID: PMC2360701 DOI: 10.1038/sj.bjc.6603399] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2006] [Revised: 08/31/2006] [Accepted: 08/31/2006] [Indexed: 01/09/2023] Open
Abstract
Tumour recurrence and metastases of hepatocellular carcinoma (HCC) after hepatectomy are the major obstacles of long-term survival. The present study investigated the clinicopathological significance of a possible metastasis regulator Six1 in HCC patients who were undergone hepatectomy. Seventy-two pairs of RNA and 103 pairs of protein from tumour and adjacent nontumour liver tissues of HCC patients were examined. About 85 and 60% of HCC tumour tissues were found to overexpress Six1 mRNA and protein, respectively, compared with nontumour liver tissues. No Six1 protein was detected in HCC nontumour liver tissues and normal liver tissues. Increased Six1 protein expression in HCC patients was significantly correlated with pathologic tumour-node-metastasis (pTNM) stage (P=0.002), venous infiltration (P=0.004) and poor overall survival (P=0.0423). We concluded that Six1 is frequently overexpressed in HCC patients and elevated Six1 protein in HCC patients may be an indication of advanced stage and poor overall survival after hepatectomy.
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Affiliation(s)
- K T Ng
- Centre for the Study of Liver Disease and Departments of Surgery, The University of Hong Kong, Queen Mary Hospital, L9-55, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong, China
| | - K Man
- Centre for the Study of Liver Disease and Departments of Surgery, The University of Hong Kong, Queen Mary Hospital, L9-55, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong, China
| | - C K Sun
- Centre for the Study of Liver Disease and Departments of Surgery, The University of Hong Kong, Queen Mary Hospital, L9-55, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong, China
| | - T K Lee
- Centre for the Study of Liver Disease and Departments of Surgery, The University of Hong Kong, Queen Mary Hospital, L9-55, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong, China
| | - R T Poon
- Centre for the Study of Liver Disease and Departments of Surgery, The University of Hong Kong, Queen Mary Hospital, L9-55, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong, China
| | - C-M Lo
- Centre for the Study of Liver Disease and Departments of Surgery, The University of Hong Kong, Queen Mary Hospital, L9-55, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong, China
| | - S-T Fan
- Centre for the Study of Liver Disease and Departments of Surgery, The University of Hong Kong, Queen Mary Hospital, L9-55, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong, China
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Abstract
The phospho-Ser/Thr-Pro specific prolyl-isomerase PIN1 is over-expressed in more than 50% of hepatocellular carcinomas (HCCs). To investigate its potential oncogenicity, we over-expressed PIN1 in a non-transformed human liver cell line MIHA. This resulted in up-regulation of beta-catenin and cyclin D1, leading to anchorage-independent growth in soft agar and tumorigenicity in nude mice. To further validate the role of PIN1 in hepatocarcinogenesis, PIN was suppressed by RNA interference (siRNA) in the HCC cell line PLC/PRF/5. siRNA-PIN1 transfection of PLC/PRF/5 cells led to repression of PIN1 expression, resulting in decreased levels of beta-catenin and cyclin D1. siRNA-PIN1 transfectants showed lower cell proliferation rates, reduced colony formation, and retarded cell cycle progression, with an increase in cells residing in G0/G1. Furthermore, soft agar colony formation was depressed, and tumorigenicity in nude mice was abrogated. These findings implicate PIN1 expression as an important step in hepatic carcinogenesis.
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Affiliation(s)
- R W Pang
- Department of Medicine, University of Hong Kong, Queen Mary Hospital, Pokfulam Road, Hong Kong
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Abstract
This paper presents a method for the detection of ketamine in hair. Hair samples (25 mg) were washed, pulverized, and digested in hydrochloric acid (0.5 M) overnight at 45 degrees C. The samples were extracted by an automated solid-phase extraction procedure, and the extracts were subsequently analyzed using gas chromatography-mass spectrometry in selected ion monitoring mode. Linearity up to 120 ng/mg was obtained for both ketamine and norketamine with correlation coefficients of 0.9987 and 0.9985, respectively. Limit of detection was found to be at 0.4 ng/mg for both drugs while the limit of quantitation was found to be 0.6 and 0.8 ng/mg for ketamine and norketamine, respectively. The validated method was used in the analysis of 91 hair segments obtained from 54 ketamine abusers. Based upon the voluntary confession of the ketamine abusers, a correlation between the amount of ketamine detected and the frequency of abuse was observed.
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Affiliation(s)
- H S Leong
- Narcotics II Laboratory, Centre for Forensic Science, Health Sciences Authority, Singapore.
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Abstract
Using the quantum Monte Carlo method, we study, under external magnetic fields, the ground state phase diagram of the two-dimensional spin S=1/2 dimer model with an anisotropic intraplane antiferromagnetic coupling. With the anisotropy 4 greater/approximately Delta greater/approximately 3, a supersolid phase characterized by a nonuniform Bose condensate density that breaks translational symmetry is found. The rich phase diagram also contains a checkerboard solid, an antiferromagnet in the z axis, and a superfluid phase formed by S(z)= +1 spin triplets which has a finite staggered magnetization in the in-plane direction. As we show, the model can be realized as a consequence of including the next nearest neighbor coupling among dimers and our results suggest that spin dimer systems may be an ideal model system to study the supersolid phase.
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Affiliation(s)
- Kwai-Kong Ng
- Institute of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan
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Bainey KR, Kalia N, Carter D, Hrynchyshyn G, Kasza L, Lee TK, Wirzba B, Senaratne MPJ. Right precordial leads and lead aVR at exercise electrocardiography: does it change test results? Ann Noninvasive Electrocardiol 2006; 11:247-52. [PMID: 16846440 PMCID: PMC6932731 DOI: 10.1111/j.1542-474x.2006.00111.x] [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] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND A recent study on exercise testing (ET) suggested that ST-segment changes in the right precordial leads (RPL) may increase its sensitivity substantially. However, this study looked at a highly selected population of patients who all underwent thallium-201 scintigraphy and coronary angiography. The present study evaluated the clinical utility of ST-segment changes in the RPL and lead aVR in an unselected population of patients undergoing ET. METHODS A total of 906 consecutive patients who received ET were included in the study. ET was done using the Bruce Protocol with a 12-lead electrocardiogram (ECG) substituting V(4)R and V(6)R for V(1) and V(6). Leads V(1) and V(6) were selected for omission as these two leads hardly ever manifest changes in isolation. Substituting two leads would obviate the need for a more complex recording system, thus improving clinical utility. RESULTS On the basis of horizontal/downsloping ST-segment depression (STD) of 1.0 mm or more (the usually accepted criterion for a positive ET), 159 (17.5%) patients had a positive ET. In those patients with a negative ET (545 patients), 4 patients (0.7%) manifested STD and 5 patients (0.9%) manifested ST-segment elevation (STE) in leads V(4)R and/or V(6)R, respectively. Of note, 44.7% of the positive ET group had STE in lead aVR. CONCLUSION The use of ST-segment changes in RPL during exercise stress testing does not appreciably change the test results of a standard ET. If one was to consider an additional marker, STE in aVR may be more useful, as it shows a stronger correlation with positive tests and does not require the recording of additional leads.
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Affiliation(s)
- Kevin R Bainey
- Division of Cardiology, Grey Nuns Hospital, Edmonton, Alberta, Canada
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