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Ng DZ, Lee CY, Lam WW, Tong AK, Tan SH, Khoo LP, Tan YH, Chiang J, Chang EW, Chan JY, Poon EY, Somasundaram N, Farid H Rashid M, Tao M, Lim ST, Yang VS. Prognostication of diffuse large B-cell lymphoma patients with Deauville score of 3 or 4 at end-of-treatment PET evaluation: a comparison of the Deauville 5-point scale and the ΔSUVmax method. Leuk Lymphoma 2021; 63:256-259. [PMID: 34665693 DOI: 10.1080/10428194.2021.1992624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Diffuse large B-cell lymphoma is treated with anti-CD 20 and multi-drug chemotherapy for cure. Positron emission tomography (PET) scans are performed at end of treatment (EOT) to assess response. EOT Deauville scores (DS) are equivocal for treatment response in some situations, requiring physicians to determine the need for further investigations or treatment. Studies have suggested the delta maximum standardised uptake value (ΔSUVmax) to be superior to DS for assessment of metabolic response at interim PET, although its use at EOT PET, especially in cases of equivocal response, has yet to be established. We investigated whether ΔSUVmax could better discriminate prognosis than DS 3 or 4 at EOT. ΔSUVmax did not outperform DS. Combination of DS 3 and International Prognostic Index (IPI) <3 selects for patients with extremely low risk of disease progression (HR 0.06, 95% CI 0.01 to 0.62, p 0.018) compared to DS 4 and IPI ≥3.
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Affiliation(s)
- David Z Ng
- Internal Medicine Residency, SingHealth Services, Singapore
| | - Chuan Yaw Lee
- Internal Medicine Residency, SingHealth Services, Singapore
| | - Winnie W Lam
- Department of Nuclear Medicine and Molecular Imaging, Singapore General Hospital, Singapore.,Duke-NUS Medical School, Radiological Sciences Academic Clinical Programme, Singapore
| | - Aaron K Tong
- Department of Nuclear Medicine and Molecular Imaging, Singapore General Hospital, Singapore.,Duke-NUS Medical School, Radiological Sciences Academic Clinical Programme, Singapore
| | - Sze Huey Tan
- Biostatistics Unit, National Cancer Centre Singapore, Singapore
| | - Lay Poh Khoo
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Ya Hwee Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Jianbang Chiang
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Esther W Chang
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Jason Y Chan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore.,Duke-NUS Medical School, Oncology Academic Clinical Programme, Singapore
| | - Eileen Y Poon
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | | | | | - Miriam Tao
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Soon Thye Lim
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore.,Duke-NUS Medical School, Oncology Academic Clinical Programme, Singapore
| | - Valerie S Yang
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore.,Duke-NUS Medical School, Oncology Academic Clinical Programme, Singapore.,Translational Precision Oncology Laboratory, Institute of Molecular & Cell Biology, A*STAR, Singapore
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Yang B, Tang KK, Geng H, Lam WW, Wong YS, Huang CY, Chiu TL, Kong CW, Cheung CW, Cheung KY, Yu SK. Comparison of modeling accuracy between Radixact ®and CyberKnife ®Synchrony ®respiratory tracking system. Biomed Phys Eng Express 2021; 7. [PMID: 34416743 DOI: 10.1088/2057-1976/ac1fa5] [Citation(s) in RCA: 2] [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] [Received: 04/01/2021] [Accepted: 08/20/2021] [Indexed: 11/12/2022]
Abstract
Synchrony Respiratory Tracking system adapted from CyberKnife has been introduced in Radixact to compensate the tumor motion caused by respiration. This study aims to compare the modeling accuracy of the Synchrony system between Radixact and CyberKnife. Two Synchrony plans based on fiducial phantoms were created for CyberKnife and Radixact, respectively. Different respiratory motion traces were used to drive a motion platform to move along the superoinferior and left-right direction. The cycle time and the amplitude of target/surrogate motion of one selected motion trace were scaled to investigate the dependence of modeling accuracy on the motion characteristic. The predicted target position, the correlation error, potential difference (Radixact only) and standard error (CyberKnife only) were extracted from raw data or log files of the two systems. The modeling accuracy was evaluated by calculating the root-mean-square (RMS) error between the predicted target positions and the input motion trace. A threshold T95 within which 95% of the potential difference or the standard error lay was defined and evaluated. Except for the motion trace with a small amplitude and a good (linear) correlation between target and surrogate motion, Radixact showed smaller RMS errors than CyberKnife. The RMS error of both systems increased with the motion amplitude and showed a decreasing trend with the increasing cycle time. No correlation was found between the RMS error and the amplitude of surrogate motion. T95 could be a good estimator of modeling accuracy for CyberKnife rather than Radixact. The correlation error defined in Radixact were largely affected by the number of fiducial markers and the setup error. In general, the modeling accuracy of the Radixact Synchrony system is better than that of the CyberKnife Synchrony system under unfavorable conditions.
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Affiliation(s)
- B Yang
- Medical Physics and Research Department, Hong Kong Sanatorium & Hospital, 2 Village Road, Happy Valley, Hong Kong
| | - K K Tang
- Medical Physics and Research Department, Hong Kong Sanatorium & Hospital, 2 Village Road, Happy Valley, Hong Kong
| | - H Geng
- Medical Physics and Research Department, Hong Kong Sanatorium & Hospital, 2 Village Road, Happy Valley, Hong Kong
| | - W W Lam
- Medical Physics and Research Department, Hong Kong Sanatorium & Hospital, 2 Village Road, Happy Valley, Hong Kong
| | - Y S Wong
- Medical Physics and Research Department, Hong Kong Sanatorium & Hospital, 2 Village Road, Happy Valley, Hong Kong
| | - C Y Huang
- Medical Physics and Research Department, Hong Kong Sanatorium & Hospital, 2 Village Road, Happy Valley, Hong Kong
| | - T L Chiu
- Medical Physics and Research Department, Hong Kong Sanatorium & Hospital, 2 Village Road, Happy Valley, Hong Kong
| | - C W Kong
- Medical Physics and Research Department, Hong Kong Sanatorium & Hospital, 2 Village Road, Happy Valley, Hong Kong
| | - C W Cheung
- Medical Physics and Research Department, Hong Kong Sanatorium & Hospital, 2 Village Road, Happy Valley, Hong Kong
| | - K Y Cheung
- Medical Physics and Research Department, Hong Kong Sanatorium & Hospital, 2 Village Road, Happy Valley, Hong Kong
| | - S K Yu
- Medical Physics and Research Department, Hong Kong Sanatorium & Hospital, 2 Village Road, Happy Valley, Hong Kong
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Nosrati R, Lam WW, Paudel M, Pejović-Milić A, Morton G, Stanisz GJ. Feasibility of using a single MRI acquisition for fiducial marker localization and synthetic CT generation towards MRI-only prostate radiation therapy treatment planning. Biomed Phys Eng Express 2021; 7. [PMID: 34034242 DOI: 10.1088/2057-1976/ac0501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/25/2021] [Indexed: 11/12/2022]
Abstract
Purpose.To investigate the feasibility of using a single MRI acquisition for fiducial marker identification and synthetic CT (sCT) generation towards MRI-only treatment planning for prostate external beam radiation therapy (EBRT).Methods.Seven prostate cancer patients undergoing EBRT, each with three implanted gold fiducial markers, participated in this study. In addition to the planning CT scan, all patients were scanned on a 3 T MR scanner with a 3D double-echo gradient echo (GRE) sequence. Quantitative susceptibility mapping (QSM) was performed for marker localization. QSM-derived marker positions were compared to those from CT. The bulk density assignment technique for sCT generation was adopted. The magnitude GRE images were segmented into muscle, bone, fat, and air using a combination of unsupervised intensity-based classification of soft tissue and convolutional neural networks (CNN) for bone segmentation.Results.All implanted markers were visualized and accurately identified (average error: 0.7 ± 0.5 mm). QSM generated distinctive contrast for hemorrhage, calcifications, and gold fiducial markers. The estimated susceptibility/HU values on QSM/CT for gold and calcifications were 31.5 ± 2.9 ppm/1220 ± 100 HU and 14.6 ± 0.9 ppm/440 ± 100 HU, respectively. The intensity-based soft tissue classification resulted in an average Dice score of 0.97 ± 0.02; bone segmentation using CNN resulted in an average Dice score of 0.93 ± 0.03.Conclusion.This work indicates the feasibility of simultaneous fiducial marker identification and sCT generation using a single MRI acquisition. Future works includes evaluation of the proposed method in a large cohort of patients with optimized acquisition parameters as well as dosimetric evaluations.
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Affiliation(s)
- R Nosrati
- Harvard Medical School, Boston, MA, United States of America.,Boston Children's Hospital, Boston, MA, United States of America
| | - W W Lam
- Sunnybrook Health Sciences Centre, ON, Canada
| | - M Paudel
- Sunnybrook Health Sciences Centre, ON, Canada.,University of Toronto, Toronto, ON, Canada
| | | | - G Morton
- Sunnybrook Health Sciences Centre, ON, Canada.,University of Toronto, Toronto, ON, Canada
| | - G J Stanisz
- Sunnybrook Health Sciences Centre, ON, Canada.,University of Toronto, Toronto, ON, Canada
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Yang B, Wong YS, Lam WW, Geng H, Huang CY, Tang KK, Law WK, Ho CC, Nam PH, Cheung KY, Yu SK. Initial clinical experience of patient-specific QA of treatment delivery in online adaptive radiotherapy using a 1.5 T MR-Linac. Biomed Phys Eng Express 2021; 7. [PMID: 33882471 DOI: 10.1088/2057-1976/abfa80] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 04/21/2021] [Indexed: 11/11/2022]
Abstract
Purpose. This study aims to evaluate the performance of a commercial 1.5 T MR-Linac by analyzing its patient-specific quality assurance (QA) data collected during one full year of clinical operation.Methods and Materials. The patient-specific QA system consisted of offline delivery QA (DQA) and online calculation-based QA. Offline DQA was based on ArcCHECK-MR combined with an ionization chamber. Online QA was performed using RadCalc that calculated and compared the point dose calculation with the treatment planning system (TPS). A total of 24 patients with 189 treatment fractions were enrolled in this study. Gamma analysis was performed and the threshold that encompassed 95% of QA results (T95) was reported. The plan complexity metric was calculated for each plan and compared with the dose measurements to determine whether any correlation existed.Results. All point dose measurements were within 5% deviation. The mean gamma passing rates of the group data were found to be 96.8 ± 4.0% and 99.6 ± 0.7% with criteria of 2%/2mm and 3%/3mm, respectively. T95 of 87.4% and 98.2% was reported for the overall group with the two passing criteria, respectively. No statistically significant difference was found between adaptive treatments with adapt-to-position (ATP) and adapt-to-shape (ATS), whilst the category of pelvis data showed a better passing rate than other sites. Online QA gave a mean deviation of 0.2 ± 2.2%. The plan complexity metric was positively correlated with the mean dose difference whilst the complexity of the ATS cohort had larger variations than the ATP cohort.Conclusions. A patient-specific QA system based on ArcCHECK-MR, solid phantom and ionization chamber has been well established and implemented for validation of treatment delivery of a 1.5 T MR-Linac. Our QA data obtained over one year confirms that good agreement between TPS calculation and treatment delivery was achieved.
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Affiliation(s)
- B Yang
- Medical Physics and Research Department, Hong Kong Sanatorium & Hospital, 2 Village Road, Happy Valley, Hong Kong
| | - Y S Wong
- Medical Physics and Research Department, Hong Kong Sanatorium & Hospital, 2 Village Road, Happy Valley, Hong Kong
| | - W W Lam
- Medical Physics and Research Department, Hong Kong Sanatorium & Hospital, 2 Village Road, Happy Valley, Hong Kong
| | - H Geng
- Medical Physics and Research Department, Hong Kong Sanatorium & Hospital, 2 Village Road, Happy Valley, Hong Kong
| | - C Y Huang
- Medical Physics and Research Department, Hong Kong Sanatorium & Hospital, 2 Village Road, Happy Valley, Hong Kong
| | - K K Tang
- Medical Physics and Research Department, Hong Kong Sanatorium & Hospital, 2 Village Road, Happy Valley, Hong Kong
| | - W K Law
- Medical Physics and Research Department, Hong Kong Sanatorium & Hospital, 2 Village Road, Happy Valley, Hong Kong
| | - C C Ho
- Medical Physics and Research Department, Hong Kong Sanatorium & Hospital, 2 Village Road, Happy Valley, Hong Kong
| | - P H Nam
- Medical Physics and Research Department, Hong Kong Sanatorium & Hospital, 2 Village Road, Happy Valley, Hong Kong
| | - K Y Cheung
- Medical Physics and Research Department, Hong Kong Sanatorium & Hospital, 2 Village Road, Happy Valley, Hong Kong
| | - S K Yu
- Medical Physics and Research Department, Hong Kong Sanatorium & Hospital, 2 Village Road, Happy Valley, Hong Kong
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Lam TP, Lo TL, Chao DVK, Lam KF, Lam WW, Sun KS. Consultation pattern of Hong Kong primary care attenders for psychological distress. Hong Kong Med J 2019; 25 Suppl 2:18-20. [PMID: 30674703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023] Open
Affiliation(s)
- T P Lam
- Department of Family Medicine and Primary Care, The University of Hong Kong
| | - T L Lo
- Department of Family Medicine and Primary Care, The University of Hong Kong
- Kwai Chung Hospital
| | - D V K Chao
- Department of Family Medicine and Primary Care, The University of Hong Kong
- Department of Family Medicine and Primary Health Care, United Christian Hospital and Tseung Kwan O Hospital
| | - K F Lam
- Department of Statistics and Actuarial Science, The University of Hong Kong
| | - W W Lam
- Department of Family Medicine and Primary Care, The University of Hong Kong
| | - K S Sun
- Department of Family Medicine and Primary Care, The University of Hong Kong
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Huang HL, Fong W, Peh WM, Niraj KA, Lam WW. The Utility of FDG PET/CT in IgG4-Related Disease with a Focus on Coronary Artery Involvement. Nucl Med Mol Imaging 2017; 52:53-61. [PMID: 29391913 DOI: 10.1007/s13139-017-0494-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 08/24/2017] [Accepted: 09/03/2017] [Indexed: 11/27/2022] Open
Abstract
Purpose Our case series aims to study the growing use of FDG PET/CT in diagnostic evaluation and follow up of IgG4-RD with emphasis on patients presenting with coronary artery involvement. Methods We conducted a search on the nuclear medicine and rheumatology service databases and identified patients with histologically proven IgG4-RD with FDG PET/CT performed at the Singapore General Hospital. The radiological, clinical, and laboratory findings of these patients were analyzed retrospectively. Results The series included ten male and two female patients. The commonest organ involved (five patients) was the pancreas. In three patients, coronary artery involvement manifested as soft tissue masses surrounding the arterial lumens. In these patients, histological diagnosis was established from alternative biopsy sites with abnormal metabolic activity on FDG PET/CT.Correlation between laboratory and metabolic imaging findings was not statistically significant in our series.Four patients had follow-up FDG PET/CT; three showed interval reduction in metabolic activity to baseline. One showed persistent abnormal metabolic activity before a rise in IgG4 levels. The metabolic imaging response was used to guide steroid dose. Conclusions FDG PET/CT is a useful tool in evaluation and follow-up of IgG4-RD, particularly in identifying alternative biopsy sites in patients who present with coronary artery involvement. Hypermetabolic coronary artery masses on FDG PET/CT should raise clinical suspicion of IgG4-RD. As the coronary artery masses may not show decrease in size after treatment, FDG PET/CT is also useful for metabolic response assessment.
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Affiliation(s)
- Hian L Huang
- 1Department of Nuclear Medicine and Molecular Imaging, Singapore General Hospital, 1 Outram Road, Bukit Merah, 169608 Singapore
- 2Duke-NUS Medical School, Singapore, Singapore
| | - Warren Fong
- 2Duke-NUS Medical School, Singapore, Singapore
- 3Department of Rheumatology and Immunology, Singapore General Hospital, Bukit Merah, Singapore
- 4Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Wee M Peh
- 1Department of Nuclear Medicine and Molecular Imaging, Singapore General Hospital, 1 Outram Road, Bukit Merah, 169608 Singapore
| | - Kasat A Niraj
- 1Department of Nuclear Medicine and Molecular Imaging, Singapore General Hospital, 1 Outram Road, Bukit Merah, 169608 Singapore
| | - Winnie W Lam
- 1Department of Nuclear Medicine and Molecular Imaging, Singapore General Hospital, 1 Outram Road, Bukit Merah, 169608 Singapore
- 2Duke-NUS Medical School, Singapore, Singapore
- 4Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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Yang B, Wong WKR, Geng H, Lam WW, Ho YW, Kwok WM, Cheung KY, Yu SK. Filmless methods for quality assurance of Tomotherapy using ArcCHECK. Med Phys 2017; 44:7-16. [PMID: 28044341 DOI: 10.1002/mp.12009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 05/30/2016] [Revised: 10/15/2016] [Accepted: 11/08/2016] [Indexed: 11/07/2022] Open
Abstract
PURPOSE Tomotherapy delivers an intensity-modulated radiation therapy (IMRT) treatment by the synchronization of gantry rotation, multileaf collimator (MLC), and couch movement. This dynamic nature makes the quality assurance (QA) important and challenging. The purpose of this study is to develop some methodologies using an ArcCHECK for accurate QA measurements of the gantry angle and speed, MLC synchronization and leaf open time, couch translation per gantry rotation, couch speed and uniformity, and constancy of longitudinal beam profile for a Tomotherapy unit. METHODS Four test plans recommended by AAPM Task Group 148 (TG148) and the manufacturer were chosen for this study. Helical and static star shot tests are used for checking the leaves opened at the expected gantry angles. Another helical test is to verify the couch traveled the expected distance per gantry rotation. The final test is for checking the couch speed constancy with a static gantry. ArcCHECK can record the detector signal every 50 ms as a movie file, and has a virtual inclinometer for gantry angle measurement. These features made the measurement of gantry angle and speed, MLC synchronization and leaf open time, and longitudinal beam profile possible. A shaping parameter was defined for facilitating the location of the beam center during the plan delivery, which was thereafter used to calculate the couch translation per gantry rotation and couch speed. The full width at half maximum (FWHM) was calculated for each measured longitudinal beam profile and then used to evaluate the couch speed uniformity. Furthermore, a mean longitudinal profile was obtained for constancy check of field width. The machine trajectory log data were also collected for comparison. Inhouse programs were developed in MATLAB to process both the ArcCHECK and machine log data. RESULTS The deviation of our measurement results from the log data for gantry angle was calculated to be less than 0.4°. The percentage differences between measured and planned leaf open time were found to be within 0.5% in all the tests. Our results showed mean values of MLC synchronization of 0.982, 0.983, and 0.995 at static gantry angle 0°, 45°, and 135°, respectively. The mean value of measured couch translation and couch speed by ArcCHECK had less than 0.1% deviation from the planned values. The variation in the value of FWHM suggested the couch speed uniformity was better than 1%. The mean of measured longitudinal profiles was suitable for constancy check of field width. CONCLUSION Precise and efficient methods for measuring the gantry angle and speed, leaf open time, couch translation per gantry rotation, couch speed and uniformity, and constancy of longitudinal beam profile of Tomotherapy using ArcCHECK have been developed and proven to be accurate compared with machine log data. Estimation of the Tomotherapy binary MLC leaf open time is proven to be precise enough to verify the leaf open time as small as 277.8 ms. Our method also makes the observation and quantification of the synchronization of leaves possible.
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Affiliation(s)
- B Yang
- Medical Physics and Research Department, Hong Kong Sanatorium & Hospital, 2 Village Road, Happy Valley, Hong Kong
| | - W K R Wong
- Medical Physics and Research Department, Hong Kong Sanatorium & Hospital, 2 Village Road, Happy Valley, Hong Kong
| | - H Geng
- Medical Physics and Research Department, Hong Kong Sanatorium & Hospital, 2 Village Road, Happy Valley, Hong Kong
| | - W W Lam
- Medical Physics and Research Department, Hong Kong Sanatorium & Hospital, 2 Village Road, Happy Valley, Hong Kong
| | - Y W Ho
- Medical Physics and Research Department, Hong Kong Sanatorium & Hospital, 2 Village Road, Happy Valley, Hong Kong
| | - W M Kwok
- Biomedical Engineering Department, Hong Kong Sanatorium & Hospital, 2 Village Road, Happy Valley, Hong Kong
| | - K Y Cheung
- Medical Physics and Research Department, Hong Kong Sanatorium & Hospital, 2 Village Road, Happy Valley, Hong Kong
| | - S K Yu
- Medical Physics and Research Department, Hong Kong Sanatorium & Hospital, 2 Village Road, Happy Valley, Hong Kong
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Yang B, Geng H, Kong CW, Lam WW, Cheung KY, Yu SK. Dose rate versus gantry speed test in RapidArc commissioning: a feasibility study using ArcCHECK. Biomed Phys Eng Express 2016. [DOI: 10.1088/2057-1976/aa5196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Large I, Bridge H, Ahmed B, Clare S, Kolasinski J, Lam WW, Miller KL, Dyrby TB, Parker AJ, Smith JET, Daubney G, Sallet J, Bell AH, Krug K. Individual Differences in the Alignment of Structural and Functional Markers of the V5/MT Complex in Primates. Cereb Cortex 2016; 26:3928-3944. [PMID: 27371764 PMCID: PMC5028002 DOI: 10.1093/cercor/bhw180] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Extrastriate visual area V5/MT in primates is defined both structurally by myeloarchitecture and functionally by distinct responses to visual motion. Myelination is directly identifiable from postmortem histology but also indirectly by image contrast with structural magnetic resonance imaging (sMRI). First, we compared the identification of V5/MT using both sMRI and histology in Rhesus macaques. A section-by-section comparison of histological slices with in vivo and postmortem sMRI for the same block of cortical tissue showed precise correspondence in localizing heavy myelination for V5/MT and neighboring MST. Thus, sMRI in macaques accurately locates histologically defined myelin within areas known to be motion selective. Second, we investigated the functionally homologous human motion complex (hMT+) using high-resolution in vivo imaging. Humans showed considerable intersubject variability in hMT+ location, when defined with myelin-weighted sMRI signals to reveal structure. When comparing sMRI markers to functional MRI in response to moving stimuli, a region of high myelin signal was generally located within the hMT+ complex. However, there were considerable differences in the alignment of structural and functional markers between individuals. Our results suggest that variation in area identification for hMT+ based on structural and functional markers reflects individual differences in human regional brain architecture.
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Affiliation(s)
- I Large
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK
| | - H Bridge
- FMRIB Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - B Ahmed
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK
| | - S Clare
- FMRIB Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - J Kolasinski
- FMRIB Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - W W Lam
- FMRIB Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - K L Miller
- FMRIB Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - T B Dyrby
- Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Hvidovre, 2650 Hvidovre, Denmark
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - A J Parker
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK
| | - J E T Smith
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK
| | - G Daubney
- Department of Experimental Psychology, University of Oxford, Oxford, OX1 3UD, UK
| | - J Sallet
- Department of Experimental Psychology, University of Oxford, Oxford, OX1 3UD, UK
| | - A H Bell
- Department of Experimental Psychology, University of Oxford, Oxford, OX1 3UD, UK
- MRC Cognition and Brain Sciences Unit, Cambridge, CB2 7EF, UK
| | - K Krug
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK
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Tan CJ, Thang SP, Lam WW. Unusual mediastinal lymph node uptake and peritoneopleural fistula demonstrated on Technetium-99m macro-aggregated human serum albumin (Tc-99m MAA) peritoneal scintigraphy in a patient with portal hypertension. Med J Malaysia 2016; 71:69-71. [PMID: 27326945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Peritoneal radionuclide scan is an established imaging modality for evaluating peritoneopleural communications. In this case report, unusual mediastinal lymph node radiotracer uptake is seen in a patient with portal hypertension on peritoneal scintigraphy. This was suspected to be due to marked lymphatic enlargement from longstanding portal hypertension since childhood, permitting passage of the large Tc-99m MAA particle. The nodes were morphologically benign on CT. Mediastinal lymph node uptake on peritoneal scintigraphy is rare but should not raise undue clinical concern, particularly in a patient with chronic portal hypertension. Anatomic correlation with SPECT-CT can provide reassurance.
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Affiliation(s)
- C J Tan
- Singapore General Hospital, Department of Nuclear Medicine and PET, Outram Road, Singapore 169508.
| | - S P Thang
- Singapore General Hospital, Department of Nuclear Medicine and PET, Outram Road, Singapore 169508
| | - W W Lam
- Singapore General Hospital, Department of Nuclear Medicine and PET, Outram Road, Singapore 169508
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Das D, Finn RD, Abdubek P, Astakhova T, Axelrod HL, Bakolitsa C, Cai X, Carlton D, Chen C, Chiu HJ, Chiu M, Clayton T, Deller MC, Duan L, Ellrott K, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Lam WW, Marciano D, Miller MD, Morse AT, Nigoghossian E, Nopakun A, Okach L, Puckett C, Reyes R, Tien HJ, Trame CB, van den Bedem H, Weekes D, Wooten T, Xu Q, Yeh A, Zhou J, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. The crystal structure of a bacterial Sufu-like protein defines a novel group of bacterial proteins that are similar to the N-terminal domain of human Sufu. Protein Sci 2011; 19:2131-40. [PMID: 20836087 PMCID: PMC3005784 DOI: 10.1002/pro.497] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Sufu (Suppressor of Fused), a two-domain protein, plays a critical role in regulating Hedgehog signaling and is conserved from flies to humans. A few bacterial Sufu-like proteins have previously been identified based on sequence similarity to the N-terminal domain of eukaryotic Sufu proteins, but none have been structurally or biochemically characterized and their function in bacteria is unknown. We have determined the crystal structure of a more distantly related Sufu-like homolog, NGO1391 from Neisseria gonorrhoeae, at 1.4 Å resolution, which provides the first biophysical characterization of a bacterial Sufu-like protein. The structure revealed a striking similarity to the N-terminal domain of human Sufu (r.m.s.d. of 2.6 Å over 93% of the NGO1391 protein), despite an extremely low sequence identity of ∼15%. Subsequent sequence analysis revealed that NGO1391 defines a new subset of smaller, Sufu-like proteins that are present in ∼200 bacterial species and has resulted in expansion of the SUFU (PF05076) family in Pfam.
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Affiliation(s)
- Debanu Das
- Joint Center for Structural Genomics. http://www.jcsg.org
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12
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Xu Q, Abdubek P, Astakhova T, Axelrod HL, Bakolitsa C, Cai X, Carlton D, Chen C, Chiu HJ, Chiu M, Clayton T, Das D, Deller MC, Duan L, Ellrott K, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Lam WW, Marciano D, Miller MD, Morse AT, Nigoghossian E, Nopakun A, Okach L, Puckett C, Reyes R, Tien HJ, Trame CB, van den Bedem H, Weekes D, Wooten T, Yeh A, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. Structure of the γ-D-glutamyl-L-diamino acid endopeptidase YkfC from Bacillus cereus in complex with L-Ala-γ-D-Glu: insights into substrate recognition by NlpC/P60 cysteine peptidases. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1354-64. [PMID: 20944232 PMCID: PMC2954226 DOI: 10.1107/s1744309110021214] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Accepted: 06/03/2010] [Indexed: 08/10/2023]
Abstract
Dipeptidyl-peptidase VI from Bacillus sphaericus and YkfC from Bacillus subtilis have both previously been characterized as highly specific γ-D-glutamyl-L-diamino acid endopeptidases. The crystal structure of a YkfC ortholog from Bacillus cereus (BcYkfC) at 1.8 Å resolution revealed that it contains two N-terminal bacterial SH3 (SH3b) domains in addition to the C-terminal catalytic NlpC/P60 domain that is ubiquitous in the very large family of cell-wall-related cysteine peptidases. A bound reaction product (L-Ala-γ-D-Glu) enabled the identification of conserved sequence and structural signatures for recognition of L-Ala and γ-D-Glu and, therefore, provides a clear framework for understanding the substrate specificity observed in dipeptidyl-peptidase VI, YkfC and other NlpC/P60 domains in general. The first SH3b domain plays an important role in defining substrate specificity by contributing to the formation of the active site, such that only murein peptides with a free N-terminal alanine are allowed. A conserved tyrosine in the SH3b domain of the YkfC subfamily is correlated with the presence of a conserved acidic residue in the NlpC/P60 domain and both residues interact with the free amine group of the alanine. This structural feature allows the definition of a subfamily of NlpC/P60 enzymes with the same N-terminal substrate requirements, including a previously characterized cyanobacterial L-alanine-γ-D-glutamate endopeptidase that contains the two key components (an NlpC/P60 domain attached to an SH3b domain) for assembly of a YkfC-like active site.
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Affiliation(s)
- Qingping Xu
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Polat Abdubek
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Tamara Astakhova
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Herbert L. Axelrod
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Constantina Bakolitsa
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Xiaohui Cai
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Dennis Carlton
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Connie Chen
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Hsiu-Ju Chiu
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Michelle Chiu
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Thomas Clayton
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Debanu Das
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Marc C. Deller
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Lian Duan
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Kyle Ellrott
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Carol L. Farr
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Julie Feuerhelm
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Joanna C. Grant
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Anna Grzechnik
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Gye Won Han
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Lukasz Jaroszewski
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Kevin K. Jin
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Heath E. Klock
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Mark W. Knuth
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Piotr Kozbial
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - S. Sri Krishna
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Abhinav Kumar
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Winnie W. Lam
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - David Marciano
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Mitchell D. Miller
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Andrew T. Morse
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Edward Nigoghossian
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Amanda Nopakun
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Linda Okach
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Christina Puckett
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Ron Reyes
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Henry J. Tien
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Christine B. Trame
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Henry van den Bedem
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Dana Weekes
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Tiffany Wooten
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Andrew Yeh
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Keith O. Hodgson
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Photon Science, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - John Wooley
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Marc-André Elsliger
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ashley M. Deacon
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Adam Godzik
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Scott A. Lesley
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian A. Wilson
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
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13
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Yeh AP, Abdubek P, Astakhova T, Axelrod HL, Bakolitsa C, Cai X, Carlton D, Chen C, Chiu HJ, Chiu M, Clayton T, Das D, Deller MC, Duan L, Ellrott K, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Lam WW, Marciano D, McMullan D, Miller MD, Morse AT, Nigoghossian E, Nopakun A, Okach L, Puckett C, Reyes R, Tien HJ, Trame CB, van den Bedem H, Weekes D, Wooten T, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. Structure of Bacteroides thetaiotaomicron BT2081 at 2.05 Å resolution: the first structural representative of a new protein family that may play a role in carbohydrate metabolism. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1287-96. [PMID: 20944224 PMCID: PMC2954218 DOI: 10.1107/s1744309110028228] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Accepted: 07/14/2010] [Indexed: 03/06/2023]
Abstract
BT2081 from Bacteroides thetaiotaomicron (GenBank accession code NP_810994.1) is a member of a novel protein family consisting of over 160 members, most of which are found in the different classes of Bacteroidetes. Genome-context analysis lends support to the involvement of this family in carbohydrate metabolism, which plays a key role in B. thetaiotaomicron as a predominant bacterial symbiont in the human distal gut microbiome. The crystal structure of BT2081 at 2.05 Å resolution represents the first structure from this new protein family. BT2081 consists of an N-terminal domain, which adopts a β-sandwich immunoglobulin-like fold, and a larger C-terminal domain with a β-sandwich jelly-roll fold. Structural analyses reveal that both domains are similar to those found in various carbohydrate-active enzymes. The C-terminal β-jelly-roll domain contains a potential carbohydrate-binding site that is highly conserved among BT2081 homologs and is situated in the same location as the carbohydrate-binding sites that are found in structurally similar glycoside hydrolases (GHs). However, in BT2081 this site is partially occluded by surrounding loops, which results in a deep solvent-accessible pocket rather than a shallower solvent-exposed cleft.
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Affiliation(s)
- Andrew P. Yeh
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Polat Abdubek
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Tamara Astakhova
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Herbert L. Axelrod
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Constantina Bakolitsa
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Xiaohui Cai
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Dennis Carlton
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Connie Chen
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Hsiu-Ju Chiu
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Michelle Chiu
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Thomas Clayton
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Debanu Das
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Marc C. Deller
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Lian Duan
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Kyle Ellrott
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Carol L. Farr
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Julie Feuerhelm
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Joanna C. Grant
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Anna Grzechnik
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Gye Won Han
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Lukasz Jaroszewski
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Kevin K. Jin
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Heath E. Klock
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Mark W. Knuth
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Piotr Kozbial
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - S. Sri Krishna
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Abhinav Kumar
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Winnie W. Lam
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - David Marciano
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Daniel McMullan
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Mitchell D. Miller
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Andrew T. Morse
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Edward Nigoghossian
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Amanda Nopakun
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Linda Okach
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Christina Puckett
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Ron Reyes
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Henry J. Tien
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Christine B. Trame
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Henry van den Bedem
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Dana Weekes
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Tiffany Wooten
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Qingping Xu
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Keith O. Hodgson
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Photon Science, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - John Wooley
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Marc-André Elsliger
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ashley M. Deacon
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Adam Godzik
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Scott A. Lesley
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian A. Wilson
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
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14
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Axelrod HL, Das D, Abdubek P, Astakhova T, Bakolitsa C, Carlton D, Chen C, Chiu HJ, Clayton T, Deller MC, Duan L, Ellrott K, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Lam WW, Marciano D, McMullan D, Miller MD, Morse AT, Nigoghossian E, Nopakun A, Okach L, Puckett C, Reyes R, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Wooten T, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. Structures of three members of Pfam PF02663 (FmdE) implicated in microbial methanogenesis reveal a conserved α+β core domain and an auxiliary C-terminal treble-clef zinc finger. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1335-46. [PMID: 20944230 PMCID: PMC2954224 DOI: 10.1107/s1744309110020166] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Accepted: 05/27/2010] [Indexed: 11/29/2022]
Abstract
Examination of the genomic context for members of the FmdE Pfam family (PF02663), such as the protein encoded by the fmdE gene from the methanogenic archaeon Methanobacterium thermoautotrophicum, indicates that 13 of them are co-transcribed with genes encoding subunits of molybdenum formylmethanofuran dehydrogenase (EC 1.2.99.5), an enzyme that is involved in microbial methane production. Here, the first crystal structures from PF02663 are described, representing two bacterial and one archaeal species: B8FYU2_DESHY from the anaerobic dehalogenating bacterium Desulfitobacterium hafniense DCB-2, Q2LQ23_SYNAS from the syntrophic bacterium Syntrophus aciditrophicus SB and Q9HJ63_THEAC from the thermoacidophilic archaeon Thermoplasma acidophilum. Two of these proteins, Q9HJ63_THEAC and Q2LQ23_SYNAS, contain two domains: an N-terminal thioredoxin-like α+β core domain (NTD) consisting of a five-stranded, mixed β-sheet flanked by several α-helices and a C-terminal zinc-finger domain (CTD). B8FYU2_DESHY, on the other hand, is composed solely of the NTD. The CTD of Q9HJ63_THEAC and Q2LQ23_SYNAS is best characterized as a treble-clef zinc finger. Two significant structural differences between Q9HJ63_THEAC and Q2LQ23_SYNAS involve their metal binding. First, zinc is bound to the putative active site on the NTD of Q9HJ63_THEAC, but is absent from the NTD of Q2LQ23_SYNAS. Second, whereas the structure of the CTD of Q2LQ23_SYNAS shows four Cys side chains within coordination distance of the Zn atom, the structure of Q9HJ63_THEAC is atypical for a treble-cleft zinc finger in that three Cys side chains and an Asp side chain are within coordination distance of the zinc.
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Affiliation(s)
- Herbert L. Axelrod
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Debanu Das
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Polat Abdubek
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Tamara Astakhova
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Constantina Bakolitsa
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Dennis Carlton
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Connie Chen
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Hsiu-Ju Chiu
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Thomas Clayton
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Marc C. Deller
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Lian Duan
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Kyle Ellrott
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Carol L. Farr
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Julie Feuerhelm
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Joanna C. Grant
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Anna Grzechnik
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Gye Won Han
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Lukasz Jaroszewski
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Kevin K. Jin
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Heath E. Klock
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Mark W. Knuth
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Piotr Kozbial
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - S. Sri Krishna
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Abhinav Kumar
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Winnie W. Lam
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - David Marciano
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Daniel McMullan
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Therapeutics Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Mitchell D. Miller
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Andrew T. Morse
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Edward Nigoghossian
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Amanda Nopakun
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Linda Okach
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Christina Puckett
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Ron Reyes
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Natasha Sefcovic
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Henry J. Tien
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Christine B. Trame
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Henry van den Bedem
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Dana Weekes
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Tiffany Wooten
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Qingping Xu
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Keith O. Hodgson
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Photon Science, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - John Wooley
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Marc-André Elsliger
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ashley M. Deacon
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Adam Godzik
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Scott A. Lesley
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian A. Wilson
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
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15
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Han GW, Elsliger MA, Yeates TO, Xu Q, Murzin AG, Krishna SS, Jaroszewski L, Abdubek P, Astakhova T, Axelrod HL, Carlton D, Chen C, Chiu HJ, Clayton T, Das D, Deller MC, Duan L, Ernst D, Feuerhelm J, Grant JC, Grzechnik A, Jin KK, Johnson HA, Klock HE, Knuth MW, Kozbial P, Kumar A, Lam WW, Marciano D, McMullan D, Miller MD, Morse AT, Nigoghossian E, Okach L, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Structure of a putative NTP pyrophosphohydrolase: YP_001813558.1 from Exiguobacterium sibiricum 255-15. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1237-44. [PMID: 20944217 PMCID: PMC2954211 DOI: 10.1107/s1744309110025534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Accepted: 06/29/2010] [Indexed: 11/24/2022]
Abstract
The crystal structure of a putative NTPase, YP_001813558.1 from Exiguobacterium sibiricum 255-15 (PF09934, DUF2166) was determined to 1.78 Å resolution. YP_001813558.1 and its homologs (dimeric dUTPases, MazG proteins and HisE-encoded phosphoribosyl ATP pyrophosphohydrolases) form a superfamily of all-α-helical NTP pyrophosphatases. In dimeric dUTPase-like proteins, a central four-helix bundle forms the active site. However, in YP_001813558.1, an unexpected intertwined swapping of two of the helices that compose the conserved helix bundle results in a `linked dimer' that has not previously been observed for this family. Interestingly, despite this novel mode of dimerization, the metal-binding site for divalent cations, such as magnesium, that are essential for NTPase activity is still conserved. Furthermore, the active-site residues that are involved in sugar binding of the NTPs are also conserved when compared with other α-helical NTPases, but those that recognize the nucleotide bases are not conserved, suggesting a different substrate specificity.
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Affiliation(s)
- Gye Won Han
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Marc-André Elsliger
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Todd O. Yeates
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Qingping Xu
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Alexey G. Murzin
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge, England
| | - S. Sri Krishna
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Lukasz Jaroszewski
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Polat Abdubek
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Tamara Astakhova
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Herbert L. Axelrod
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Dennis Carlton
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Connie Chen
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Hsiu-Ju Chiu
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Thomas Clayton
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Debanu Das
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Marc C. Deller
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Lian Duan
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Dustin Ernst
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Julie Feuerhelm
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Joanna C. Grant
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Anna Grzechnik
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Kevin K. Jin
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Hope A. Johnson
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Heath E. Klock
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Mark W. Knuth
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Piotr Kozbial
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Abhinav Kumar
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Winnie W. Lam
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - David Marciano
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Daniel McMullan
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Mitchell D. Miller
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Andrew T. Morse
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Edward Nigoghossian
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Linda Okach
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Ron Reyes
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Christopher L. Rife
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Natasha Sefcovic
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Henry J. Tien
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Christine B. Trame
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Henry van den Bedem
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Dana Weekes
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Keith O. Hodgson
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Photon Science, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - John Wooley
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Ashley M. Deacon
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Adam Godzik
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Scott A. Lesley
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Ian A. Wilson
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
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16
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Xu Q, Abdubek P, Astakhova T, Axelrod HL, Bakolitsa C, Cai X, Carlton D, Chen C, Chiu HJ, Clayton T, Das D, Deller MC, Duan L, Ellrott K, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Lam WW, Marciano D, Miller MD, Morse AT, Nigoghossian E, Nopakun A, Okach L, Puckett C, Reyes R, Tien HJ, Trame CB, van den Bedem H, Weekes D, Wooten T, Yeh A, Zhou J, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. Structure of a membrane-attack complex/perforin (MACPF) family protein from the human gut symbiont Bacteroides thetaiotaomicron. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1297-305. [PMID: 20944225 PMCID: PMC2954219 DOI: 10.1107/s1744309110023055] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Accepted: 06/15/2010] [Indexed: 11/11/2022]
Abstract
Membrane-attack complex/perforin (MACPF) proteins are transmembrane pore-forming proteins that are important in both human immunity and the virulence of pathogens. Bacterial MACPFs are found in diverse bacterial species, including most human gut-associated Bacteroides species. The crystal structure of a bacterial MACPF-domain-containing protein BT_3439 (Bth-MACPF) from B. thetaiotaomicron, a predominant member of the mammalian intestinal microbiota, has been determined. Bth-MACPF contains a membrane-attack complex/perforin (MACPF) domain and two novel C-terminal domains that resemble ribonuclease H and interleukin 8, respectively. The entire protein adopts a flat crescent shape, characteristic of other MACPF proteins, that may be important for oligomerization. This Bth-MACPF structure provides new features and insights not observed in two previous MACPF structures. Genomic context analysis infers that Bth-MACPF may be involved in a novel protein-transport or nutrient-uptake system, suggesting an important role for these MACPF proteins, which were likely to have been inherited from eukaryotes via horizontal gene transfer, in the adaptation of commensal bacteria to the host environment.
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Affiliation(s)
- Qingping Xu
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Polat Abdubek
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Tamara Astakhova
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Herbert L. Axelrod
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Constantina Bakolitsa
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Xiaohui Cai
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Dennis Carlton
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Connie Chen
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Hsiu-Ju Chiu
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Thomas Clayton
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Debanu Das
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Marc C. Deller
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Lian Duan
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Kyle Ellrott
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Carol L. Farr
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Julie Feuerhelm
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Joanna C. Grant
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Anna Grzechnik
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Gye Won Han
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Lukasz Jaroszewski
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Kevin K. Jin
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Heath E. Klock
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Mark W. Knuth
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Piotr Kozbial
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - S. Sri Krishna
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Abhinav Kumar
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Winnie W. Lam
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - David Marciano
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Mitchell D. Miller
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Andrew T. Morse
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Edward Nigoghossian
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Amanda Nopakun
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Linda Okach
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Christina Puckett
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Ron Reyes
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Henry J. Tien
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Christine B. Trame
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Henry van den Bedem
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Dana Weekes
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Tiffany Wooten
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Andrew Yeh
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Jiadong Zhou
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Keith O. Hodgson
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Photon Science, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - John Wooley
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Marc-André Elsliger
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ashley M. Deacon
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Adam Godzik
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Scott A. Lesley
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian A. Wilson
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
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17
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Bakolitsa C, Xu Q, Rife CL, Abdubek P, Astakhova T, Axelrod HL, Carlton D, Chen C, Chiu HJ, Clayton T, Das D, Deller MC, Duan L, Ellrott K, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Lam WW, Marciano D, McMullan D, Miller MD, Morse AT, Nigoghossian E, Nopakun A, Okach L, Puckett C, Reyes R, Tien HJ, Trame CB, van den Bedem H, Weekes D, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. Structure of BT_3984, a member of the SusD/RagB family of nutrient-binding molecules. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1274-80. [PMID: 20944222 PMCID: PMC2954216 DOI: 10.1107/s1744309110032999] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Accepted: 08/16/2010] [Indexed: 11/26/2022]
Abstract
The crystal structure of the Bacteroides thetaiotaomicron protein BT_3984 was determined to a resolution of 1.7 Å and was the first structure to be determined from the extensive SusD family of polysaccharide-binding proteins. SusD is an essential component of the sus operon that defines the paradigm for glycan utilization in dominant members of the human gut microbiota. Structural analysis of BT_3984 revealed an N-terminal region containing several tetratricopeptide repeats (TPRs), while the signature C-terminal region is less structured and contains extensive loop regions. Sequence and structure analysis of BT_3984 suggests the presence of binding interfaces for other proteins from the polysaccharide-utilization complex.
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Affiliation(s)
- Constantina Bakolitsa
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Qingping Xu
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Christopher L. Rife
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Polat Abdubek
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Tamara Astakhova
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Herbert L. Axelrod
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Dennis Carlton
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Connie Chen
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Hsiu-Ju Chiu
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Thomas Clayton
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Debanu Das
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Marc C. Deller
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Lian Duan
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Kyle Ellrott
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Carol L. Farr
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Julie Feuerhelm
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Joanna C. Grant
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Anna Grzechnik
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Gye Won Han
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Lukasz Jaroszewski
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Kevin K. Jin
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Heath E. Klock
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Mark W. Knuth
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Piotr Kozbial
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - S. Sri Krishna
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Abhinav Kumar
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Winnie W. Lam
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - David Marciano
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Daniel McMullan
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Mitchell D. Miller
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Andrew T. Morse
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Edward Nigoghossian
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Amanda Nopakun
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Linda Okach
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Christina Puckett
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Ron Reyes
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Henry J. Tien
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Christine B. Trame
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Henry van den Bedem
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Dana Weekes
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Keith O. Hodgson
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Photon Science, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - John Wooley
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Marc-André Elsliger
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ashley M. Deacon
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Adam Godzik
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Scott A. Lesley
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian A. Wilson
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
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18
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Couch MJ, Lam WW, Ouriadov AV, Santyr GE. Sci-Fri AM: Imaging - 02: Regional Ventilation Mapping of the Rat Lung Using Hyperpolarized 3
He Magnetic Resonance Imaging. Med Phys 2010. [DOI: 10.1118/1.3476181] [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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19
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Chim CS, Wong KY, Loong F, Lam WW, Srivastava G. Frequent epigenetic inactivation of Rb1 in addition to p15 and p16 in mantle cell and follicular lymphoma. Hum Pathol 2007; 38:1849-57. [PMID: 17900658 DOI: 10.1016/j.humpath.2007.05.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [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] [Received: 01/12/2007] [Revised: 05/03/2007] [Accepted: 05/03/2007] [Indexed: 10/22/2022]
Abstract
Dysregulation of cell cycle control is an important mechanism in carcinogenesis. Gene promoter hypermethylation is an alternative mechanism of gene inactivation. We analyzed the methylation status of the tumor suppressor components of the INK4/Rb pathway in mantle cell lymphoma and follicular lymphoma by methylation-specific polymerase chain reaction for p15, p16, p18, and Rb1 in 23 mantle cell lymphoma and 30 follicular lymphoma cases and lymphoma cell lines. The methylation-specific polymerase chain reaction results showed that in mantle cell lymphoma, frequent p16 (82%) but infrequent p15 (8.7%) or Rb1 (17.4%) hypermethylation occurred, with p16 and Rb1 hypermethylation being mutually exclusive (P=.01). In follicular lymphoma, frequent hypermethylation of p15 (36.7%), p16 (56.7%), and Rb1 (43.3%) occurred, with p15 and Rb1 hypermethylation being mutually exclusive (P=.05). Concurrent methylation of p15 and p16 occurred in 26.7% of patients with follicular lymphoma and 8.7% of patients with mantle cell lymphoma. Compared with mantle cell lymphoma, there was more frequent p15 (P=.025) hypermethylation but comparable Rb1 (P=.07) and p16 (P=.07) hypermethylation in follicular lymphoma. In a patient with follicular lymphoma with sequential biopsies, Rb1 was unmethylated and expressed at diagnosis but became methylated and down-regulated at relapse. Moreover, methylation analysis of these 4 genes in an additional 8 patients with grade I follicular lymphoma showed that Rb, but not the other genes, was preferentially methylated in grade II (P=.03). In summary, most patients with mantle cell lymphoma and follicular lymphoma had epigenetic aberrations targeting the INK4/Rb pathway. There is more frequent p16 hypermethylation in mantle cell lymphoma and p15 or Rb1 hypermethylation in follicular lymphoma. The role of Rb methylation in disease or histologic transformation in follicular lymphoma warrants further study.
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Affiliation(s)
- C S Chim
- Department of Medicine, Queen Mary Hospital, The University of Hong Kong, Pokfulam, Hong Kong.
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20
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Abstract
BACKGROUND Radiation-induced carotid stenosis in patients with head and neck tumors can cause significant mortality and morbidity. This study examined the incidence of stenosis in the extracranial carotid arteries of nasopharyngeal carcinoma patients after radiotherapy. METHODS The extracranial carotid arteries of 71 (53 male and 18 female; mean age of 53.6 years) postradiation patients with nasopharyngeal carcinoma were examined with color Doppler ultrasound. The distribution of the arterial stenosis and the degree of stenosis were documented. The results were compared with the control group, which comprised 51 newly diagnosed nasopharyngeal carcinoma patients (35 male and 16 female, mean age of 48.8 years) before radiotherapy. Incidences of risk factors for arterial stenosis such as hypertension, smoking, and hypercholesterolemia also were studied in these two groups. RESULTS There was no significant difference in the incidence of risk factors between the two groups. Arterial stenosis was, however, more common in the postradiation group than the preradiation group (56 of 71 vs. 11 of 51). The common/internal carotid arteries (CCA/ICA) were most commonly involved (55 of 71 vs. 11 of 51; P < 0.01), followed by the external carotid artery (ECA) (32 of 71 vs. 1 of 51; P < 0.01) and vertebral artery (VA; 5 of 71 vs. 0; P = 0.069). Significant stenosis (> 50% reduction of luminal diameter) was only found in the postradiation group (21 of 71 in CCA/ICA, 11 of 71 in ECA, 4 of 71 in VA). CONCLUSIONS This study showed that radiation could cause significant carotid stenosis. Ultrasound examinations for these patients therefore are necessary for early detection and possible intervention of this late radiation-induced complication.
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Affiliation(s)
- W W Lam
- Department of Diagnostic Radiology and Organ Imaging, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR China.
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21
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Abstract
AIM To compare the accuracy of MR-determined cerebral blood volume (CBV) maps with SPECT imaging with thallium-201 in pre-operative grading of intracranial glioma. MATERIAL AND METHODS Nineteen patients (7 female and 12 male, mean age 46.8 years) with intracranial gliomas were examined with MR perfusion imaging pre-operatively. Sixteen of these patients were also examined with SPECT imaging with thallium-201. The tumour to contralateral white matter NI (negative integral) and tracer uptake ratios were evaluated. The ratios in high-grade and low-grade tumours were compared. RESULTS The maximum CBV ratios of grades I and II gliomas (2.958+/-2.217) were significantly lower than the maximum CBV ratio of grades III and IV (9.484+/-4.520), p<0.001. There was no statistical difference when CBV ratios of grades I and II (p=0.381), grades II and III (p=0.229) and grades III and IV (p=0.476) gliomas were compared. Thallium SPECT imaging showed no difference in tumour uptake ratio between low-grade and high-grade gliomas (p=0.299). CONCLUSION MR-determined NI was useful for pre-operative grading of intracranial gliomas but SPECT thallium-201 imaging was not.
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Affiliation(s)
- W W Lam
- Department of Diagnostic Radiology and Organ Imaging, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
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22
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Abstract
This study was undertaken to evaluate the sonographic measurement of subarachnoid spaces in normal children and its relationship with age and to define a normal range in a Chinese population and to differentiate normal variant findings from pathologic dilatation. The subarachnoid spaces in 278 normal term neonates, infants, and children were studied with real-time ultrasound using a 7.5-MHz vector transducer. The craniocortical width, sinocortical width, and interhemispheric width were measured in the coronal plane at the level of the foramen of Monro, on either side of the hemispheres. Correlation of sonographic measurements with age was made. The mean widths were plotted against age. A correlation with age was found in all three spaces, with an increasing trend with age until 28 weeks of gestation. Thereafter, a decreasing trend was noted. The normal upper limit of subarachnoid spaces for children is proposed to be the values on the ninety-fifth percentile of the regression curve. Correlation of measurement with age must be considered to decide whether an increase in subarachnoid space is pathologic or not.
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Affiliation(s)
- W W Lam
- Department of Radiology, Queen Mary Hospital, Hong Kong
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23
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Le SD, Lam WW, Tam PK, Cheng W, Chan FL. H-type tracheo-oesophageal fistula: appearance on three-dimensional computed tomography and virtual bronchoscopy. Pediatr Surg Int 2001; 17:642-3. [PMID: 11727058 DOI: 10.1007/s003830100012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [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] [Accepted: 08/11/2000] [Indexed: 10/27/2022]
Abstract
H-type tracheo-oesophageal fistula (TOF) is a rare type of fistula without oesophageal atresia. The symptoms are usually present at birth, but the diagnosis is often delayed. Traditionally, contrast oesophagography and/or fiberoptic bronchoscopy are used to confirm the diagnosis. We describe the imaging features of a case of H-type TOF seen on three-dimensional computed tomography and virtual bronchoscopy and the usefulness of these techniques in pre-operative evaluation.
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Affiliation(s)
- S D Le
- Department of Diagnostic Radiology, Queen Mary Hospital, 102 Pok Fu Lam Road, Hong Kong
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24
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Abstract
Recovery of liver cell mass following hepatectomy requires a metabolic compromise between differentiated function and organ regrowth. Clinical experience has shown that hepatic failure after resection is more common when the organ is diseased. We have evaluated intracellular hepatic biochemistry in patients with normal and cirrhotic livers undergoing partial hepatectomy, using 31-phosphorus magnetic resonance spectroscopy ((31)P MRS). Eighteen patients were studied, half with normal liver architecture (normal group, n = 9) and half with cirrhotic parenchyma (cirrhosis group, n = 9). Magnetic resonance examinations were performed preoperatively and on postoperative days 2, 4, 6, 14, and 28. Hepatic volume (estimated by magnetic resonance imaging [MRI]) and blood chemistries were measured at the same intervals. Following a comparable reduction in parenchymal volume, the cirrhotic group demonstrated a more sustained fall in adenosine triphosphate (ATP) energy state. Disturbance of membrane phospholipid metabolism and duration of acute-phase reaction were more marked when the liver was diseased. The pattern of derangement of hepatic function, however, was similar in the two groups. Overall, the recovery process was less efficient in the cirrhotic organ, and culminated in a diminished rate and extent of the regenerative response. These outcomes indicate that liver regeneration after partial hepatectomy involves modulation of hepatic energy economy in response to changing work demands. The efficiency of this process is influenced by the histopathologic state of the organ, and in turn governs the physiologic reserve. These findings may explain the mechanism of posthepatectomy liver failure, and offer a rational basis for the assessment of novel hepatic support strategies.
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Affiliation(s)
- D V Mann
- Department of Surgery, Prince of Wales Hospital, Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
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Lam WW, Yuen HY, Wong KS, Leung SF, Liu KH, Metreweli C. Clinically underdetected asymptomatic and symptomatic carotid stenosis as a late complication of radiotherapy in Chinese nasopharyngeal carcinoma patients. Head Neck 2001; 23:780-4. [PMID: 11505489 DOI: 10.1002/hed.1111] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.2] [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: 11/10/2022] Open
Abstract
BACKGROUND Carotid artery stenosis is a late complication of radiotherapy to the neck region. This complication has, however, a significant impact with increased risk of stroke causing mortality and morbidity. Clinicians' awareness of this complication and early detection is therefore important. METHODS Eighty patients with nasopharyngeal carcinoma (NPC) who had received radiotherapy were recruited for color Doppler ultrasonography of the carotid arteries. fifty-eight patients with newly diagnosed NPC who had never received any radiotherapy were recruited as controls. All patients with significant carotid stenosis were referred to the neurology clinic for further assessment. RESULTS Twenty-four patients were found to have more than 50% diameter reduction in the extracranial carotid artery. Clinical assessment by a neurologist showed 9 of 24 patients had a history of transient ischemic attack, amaurosis fugax, or stroke. Seven of these patients had clinically detectable neck bruit. CONCLUSIONS Clinicians attending to patients after radiotherapy for head and neck cancers should be aware of this long-term complication of radiotherapy. A detailed clinical history and incorporation of auscultation of carotid arteries in routine follow-up of postradiotherapy patients are recommended.
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Affiliation(s)
- W W Lam
- Department of Diagnostic Radiology and Organ Imaging, Prince of Wales Hospital, Shatin, New Territories, Hong Kong.
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Lam WW, Tam PK, Ai VH, Chan KL, Chan FL, Leong L. Using gadolinium-infusion MR venography to show the impalpable testis in pediatric patients. AJR Am J Roentgenol 2001; 176:1221-6. [PMID: 11312185 DOI: 10.2214/ajr.176.5.1761221] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
UNLABELLED OBJECTIVE; This study evaluated the adjunctive value of gadolinium-infusion MR venography to locate the impalpable testis. SUBJECTS AND METHODS Routine MR imaging and MR venography were performed in 34 patients presenting with impalpable testis. MR venography was performed by dynamic injection of gadopentetate dimeglumine bismethylamide with images taken at delayed venous phases. The site of the testis was determined by detection of the contrast-enhanced pampiniform venous plexus. RESULTS A total of 44 impalpable testes were examined. Twenty-six hypoplastic canalicular testes, two testes at pelvic skinfold, four atrophic testes in the scrotum, and five intraabdominal testes were detected on both routine MR imaging and MR venography. Five "vanishing" testes in the scrotum and two at the groin region were detected by MR venography but not on MR imaging. CONCLUSION Gadolinium-infusion MR venography is superior to MR imaging in the detection of atrophic testes. The method is a useful adjunct in patients with negative MR imaging findings.
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Affiliation(s)
- W W Lam
- Department of Radiology, Queen Mary Hospital, 102 Pokfulam Rd., Hong Kong
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Abstract
OBJECTIVE There has been limited data on the frequency of microembolic signals in patients with middle cerebral artery (MCA) stenosis, especially during the acute phase of stroke. Using transcranial Doppler, the authors prospectively monitored the MCA segments distal to stenosis in 4 groups of patients for 30 minutes: (1) symptomatic patients with acute ischemic stroke and MCA stenosis, (2) asymptomatic group patients with asymptomatic MCA stenosis, (3) control patients with acute ischemic stroke of undetermined etiology, and (4) normal people. A total of 60 patients completed the study. There were no microembolic signals in the asymptomatic, control, and normal groups. Among 20 patients in the symptomatic group, microembolic signals were detected in 3 patients (15%). The number of emboli ranged from 1 to 6 per 30 minutes. This is the first report of the presence of microembolic signals in acute stroke patients with MCA stenosis.
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Affiliation(s)
- K S Wong
- Department of Medicine and Therapeutics, Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China.
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King AD, Teo P, Lam WW, Leung SF, Metreweli C. Paranasopharyngeal space involvement in nasopharyngeal cancer: detection by CT and MRI. Clin Oncol (R Coll Radiol) 2001; 12:397-402. [PMID: 11202093 DOI: 10.1053/clon.2000.9199] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.3] [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: 11/11/2022]
Abstract
Paranasopharyngeal tumour extension (PTE) from nasopharyngeal carcinoma (NPC) is staged in its own subgroup in the American Joint Committee on Cancer classification. Most large clinical trials use computed tomography (CT) to stage PTE, but diagnosis relies on indirect signs of tumour invasion such as asymmetry of the parapharyngeal fat. Magnetic resonance imaging (MRI) has the advantage of directly revealing PTE because of its ability to depict the complex anatomical structures that form the boundary of the nasopharynx. The aim of this study was to compare CT and MRI in the identification of PTE and to determine whether the imaging modality used influenced staging of the disease. The MRI and CT scans of 78 patients (156 parapharyngeal regions) with NPC were assessed for PTE. On MRI, PTE was considered to be positive when there was tumour invasion through the complex anatomical structures of the nasopharyngeal wall. When using CT, it was considered positive when there was: (1) distortion of the parapharyngeal fat plane; or (2) extension beyond a line drawn from the medial pterygoid plate to the lateral aspect of the carotid artery. CT scanning and MRI were compared. PTE was judged to be present in 28 of 78 (36%) patients by MRI and in 41 of 78 (53%) scanning by CT when using criterion 1 or 2. An analysis of the discordant findings revealed that MRI was positive in three sides of the nasopharynx in early tumour extension through the pharyngobasilar fascia but not identified with CT by using criterion 1 or 2. MRI was negative in 20 and 21 sides of the nasopharynx that were judged to be positive on CT by using criterion 1 and 2 respectively. In these patients MRI revealed that the positive CT scan was caused by a large tumour compressing but not invading the parapharyngeal fat space, a metastatic lateral retropharyngeal node, or a combination of the two. The imaging modality used for staging NPC has an impact on the staging of PTE. CT scanning suggested the presence of PTE more frequently than MRI because of its inability to distinguish the primary tumour from lateral retropharyngeal nodes, and direct tumour invasion of the parapharyngeal region from tumour compression. The imaging modality and criteria used for staging PTE should be taken into consideration when assessing the results of clinical studies.
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Affiliation(s)
- A D King
- Department of Diagnostic Radiology and Organ Imaging, Faculty of Medicine, Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories.
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Wong KS, Huang YN, Gao S, Lam WW, Chan YL. Cerebrovascular disease among Chinese populations--recent epidemiological and neuroimaging studies. Hong Kong Med J 2001; 7:50-7. [PMID: 11406676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023] Open
Abstract
Stroke mortality in individuals of Chinese descent has declined during the past decades, although the absolute number of patients with first-ever stroke is escalating. This review summarises recent epidemiological and imaging studies conducted among Chinese populations. Data indicating differences between Chinese and Caucasian ethnic groups in the pathophysiological mechanisms of stroke are highlighted, and the potential implications of these findings for prevention and management of stroke are discussed.
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Affiliation(s)
- K S Wong
- Division of Neurology, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong
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Wong KS, Li H, Chan YL, Ahuja A, Lam WW, Wong A, Kay R. Use of transcranial Doppler ultrasound to predict outcome in patients with intracranial large-artery occlusive disease. Stroke 2000; 31:2641-7. [PMID: 11062288 DOI: 10.1161/01.str.31.11.2641] [Citation(s) in RCA: 166] [Impact Index Per Article: 6.9] [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: 11/16/2022]
Abstract
BACKGROUND AND PURPOSE Intracranial large-artery occlusive disease is the predominant vascular lesion found in stroke patients of Asian, African, and Hispanic ancestry, making it numerically perhaps the most common vascular cause of stroke in the world. Relatively little is known about the clinical significance of finding such lesions. We investigate whether the presence and the extent of these vascular lesions help predict outcome after stroke. METHODS On the basis of transcranial Doppler of the intracranial arteries with supplementary duplex ultrasound of the carotid arteries, we determined the number of occlusive arteries in the craniocervical circulation of consecutive patients who were hospitalized for acute cerebral ischemia. Patients were followed for 6 months for further vascular events (including transient ischemic attack, stroke, and acute coronary syndrome) or death. RESULTS Among 705 consecutive Chinese patients studied, occlusive arteries were found in 345 patients (49%): 258 patients (37%) had intracranial lesions only, 71 (10%) had both extracranial and intracranial lesions, and 16 (2.3%) had extracranial lesions only. Sixty-three (18%) of the 345 patients with occlusive arteries and 35 (9.7%) of the 360 patients without occlusive arteries had further vascular event or death within 6 months. The risk of vascular events or death increased rapidly with rising numbers of occlusive arteries, after adjustment for vascular risk factors and stroke severity (adjusted odds ratio [OR] 1.25 per occlusive artery, 95% CI 1.12 to 1.39). Other independent risk factors included age (OR 1.03 per year of age, 95% CI 1.01 to 1.05) and atrial fibrillation (OR 3.00, 95% CI 1.40 to 6.69). CONCLUSIONS In patients with predominantly intracranial large-artery occlusive disease, the presence and the total number of occlusive arteries in the craniocervical circulation predict further vascular events or death within 6 months after stroke. Transcranial Doppler ultrasound is an important investigation for the evaluation of patients with stroke in populations at risk of intracranial atherosclerotic disease.
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Affiliation(s)
- K S Wong
- Division of Neurology, Department of Medicine and Therapeutics, the Chinese University of Hong Kong, Shatin, Hong Kong, SAR.
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31
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So NM, Lam WW, Cheng G, Metreweli C, Lam D. Assessment of optic nerve compression in Graves' ophthalmopathy. The usefulness of a quick T1-weighted sequence. Acta Radiol 2000; 41:559-61. [PMID: 11092475 DOI: 10.1080/028418500127346207] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [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: 10/26/2022]
Abstract
PURPOSE Diagnosis of optic nerve compression can be difficult in patients with equivocal clinical signs. We examined the usefulness of a quick coronal MR sequence performed at a predetermined plane as a screening tool for selecting patients at high risk of optic nerve compression. MATERIAL AND METHODS Direct coronal images of the orbit were obtained in 37 patients with Graves' disease in a predetermined plane. The muscular indices (MI) of each orbit were calculated. Mann-Whitney U-Wilcoxon rank sum test was used to assess if there was any statistically significant difference between patients with and without signs of optic nerve compression. The ROC curve was used to identify a value useful for discriminating patients with a higher risk of developing optic nerve compression. RESULTS There was a statistically significant difference (p<0.05) in the MI between patients with and without optic nerve compression. An MI of -0.48 had 100% sensitivity, 89% specificity and 91% accuracy in identifying patients with optic nerve compression. CONCLUSION. A quick coronal MR image obtained at the mid-orbital plane is useful in screening patients with Graves' disease for optic nerve compression.
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Affiliation(s)
- N M So
- Department of Diagnostic Radiology and Organ Imaging, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories
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Chu WC, Lam WW, Metreweli C. Incidence of adverse events after I.V injection of MR contrast agents in a Chinese population. A comparison between gadopentetate and gadodiamide. Acta Radiol 2000; 41:662-6. [PMID: 11092494 DOI: 10.1080/028418500127346108] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [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: 10/26/2022]
Abstract
PURPOSE To study the incidence of adverse events after i.v. injection of MR contrast agents in a Chinese population. A comparison was made between an ionic contrast agent (dimeglumine gadopentetate, Magnevist) and a non-ionic contrast agent (gadodiamide, Omniscan). MATERIAL AND METHODS During a 24-month period, 2,049 Chinese patients who randomly received an i.v. bolus injection of either Magnevist or Omniscan were investigated. All patients were questioned for the presence of any generalized or localized adverse reaction on the following day after the MR examination according to a standardized questionnaire. RESULTS Three hundred and nine out of 2,049 patients (15%) reported an adverse event. There was a higher incidence of adverse events in patients receiving Magnevist as compared to those receiving Omniscan injection. All reported adverse events were clinically mild and required neither treatment nor hospitalization. CONCLUSION There was a higher incidence of adverse reaction in patients receiving Magnevist than in those receiving Omniscan.
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Affiliation(s)
- W C Chu
- Department of Diagnostic Radiology and Organ Imaging, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin
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Khong PL, Peh WC, Lam CH, Chan KL, Cheng W, Lam WW, Ai VH, Saing H, Tam PK, Leong LL, Low LC. Ultrasound-guided hydrostatic reduction of childhood intussusception: technique and demonstration. Radiographics 2000; 20:E1. [PMID: 10992040 DOI: 10.1148/radiographics.20.5.g00see11] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [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: 11/11/2022]
Abstract
The authors review the technique of ultrasound-guided hydrostatic reduction of childhood intussusception and illustrate, in real-time fashion, the treatment of three cases with this technique. Two cases of successful reduction of ileocolic intussusception are demonstrated. The third case is an example of the complex fronded appearance of ileo-ileocolic intussusception and failed reduction. This technique is recommended as an alternative method for the treatment of childhood intussusception, as it does not involve ionizing radiation and is a simple and safe procedure.
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Affiliation(s)
- P L Khong
- Departments of Diagnostic Radiology, Surgery and Pediatrics, The University of Hong Kong and Queen Mary Hospital, Hong Kong
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Yang WT, Lam WW, Yu MY, Cheung TH, Metreweli C. Comparison of dynamic helical CT and dynamic MR imaging in the evaluation of pelvic lymph nodes in cervical carcinoma. AJR Am J Roentgenol 2000; 175:759-66. [PMID: 10954463 DOI: 10.2214/ajr.175.3.1750759] [Citation(s) in RCA: 201] [Impact Index Per Article: 8.4] [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: 11/18/2022]
Abstract
OBJECTIVE This study compares dynamic helical CT with dynamic MR imaging in the evaluation of pelvic lymph nodes in cervical carcinoma. SUBJECTS AND METHODS Women with biopsy-proven cervical carcinoma prospectively underwent dynamic helical CT and MR imaging before surgery. A metastatic node on CT and MR imaging was defined as a rounded soft-tissue structure greater than 10 mm in maximal axial diameter or a node with central necrosis. Imaging results were compared with pathology, and receiver operating characteristic curves for size and shape were plotted on a hemipelvis basis. Nodal density and signal intensity on CT and MR images, respectively, were reviewed for differences between benign and malignant disease. RESULTS A total of 949 lymph nodes were found at pathology in 76 hemipelves in 43 women, of which 69 lymph nodes (7%) in 17 hemipelves (22%) were metastatic. Sensitivity, specificity, positive and negative predictive values, and accuracy of helical CT and MR imaging in the diagnosis of lymph node metastasis on a hemipelvis basis was 64.7%, 96.6%, 84.6%, 90.5%, and 89.5% and 70.6%, 89.8%, 66. 7%, 91.4%, and 85.5%, respectively. Receiver operating characteristic curves for helical CT and MR imaging gave cutoff values of 9 and 12 mm in maximal axial diameter, respectively, in the prediction of metastasis. Central necrosis had a positive predictive value of 100% in the diagnosis of metastasis. Signal intensity on MR imaging and density-enhancement pattern on CT in patients with metastatic nodes did not differ from those in patients with negative nodes. CONCLUSION Helical CT and MR imaging show similar accuracy in the evaluation of pelvic lymph nodes in patients with cervical carcinoma. Central necrosis is useful in the diagnosis of metastasis in pelvic lymph nodes in cervical cancer.
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Affiliation(s)
- W T Yang
- Department of Diagnostic Radiology and Organ Imaging, Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong
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Abstract
AIM To investigate the role of short tau inversion recovery (STIR) sequence in the detection of parametrial invasion in patients with carcinoma of the cervix. MATERIALS AND METHODS Axial magnetic resonance imaging (MRI) images of the cervical region using T1 weighted turbo spin echo (TSE), TSE T2, STIR and T1 weighted dynamic gadolinium enhanced SE sequences were obtained in 38 patients with cervical carcinoma. All the images were assessed for the presence or absence of parametrial invasion using a standard scoring system. The diagnostic confidence, image quality, sensitivity, specificity, positive and negative predictive values and accuracy of each sequence were compared. RESULTS The sensitivity, specificity, positive predictive value, negative predictive value and accuracy for each sequence in the diagnosis of parametrial invasion were: 60%, 80%, 32%, 93% and 78% for unenhanced T1W sequence; 90%, 92%, 64%, 98% and 92% for TSE T2 sequence; 90%, 94%, 69%, 98% and 93% for STIR sequence; and 90%, 80%, 41%, 98% and 82% for dynamic T1W sequence, respectively. Image quality and diagnostic confidence were both better for STIR and T2 compared to the dynamic T1 sequence. CONCLUSION Dynamic T1W imaging is inferior to STIR and TSE T2 sequences. STIR is of similar value in the detection of parametrial invasion in cervical carcinoma as a TSE T2W sequence; their simultaneous use is not justified.
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Affiliation(s)
- W W Lam
- Department of Diagnostic Radiology and Organ Imaging, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong.
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Lam DS, Wong AK, Leung AT, Lam WW, Tam BS, Bhende P. Para-lenticular metallic foreign body missed by high-resolution computed tomography. Eye (Lond) 2000; 14 ( Pt 4):684-5. [PMID: 11040934 DOI: 10.1038/eye.2000.177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Abstract
BACKGROUND To assess the role of staging CT of the thorax in advanced nodal stage nasopharyngeal carcinoma and to examine the hypothesis that contiguous spread of nodal metastases from the supraclavicular region to the upper mediastinal region occurs in this cancer. METHODS Forty-four patients with newly diagnosed nasopharyngeal carcinoma with neck node metastases to the supraclavicular region (ie, AJCC N3b stage) underwent contrast-enhanced CT (CECT) thorax for staging. CT findings and clinical outcome were analyzed. RESULTS No patient was found to have intrathoracic metastasis, although 1 had hepatic metastases on CECT of the thorax, resulting in upstaging in 1 of 44 (2%) of patients. With a median follow-up time of 21 months, 3 patients had lung metastases and 2 had axillary nodal metastases develop without evidence of upper mediastinal nodal metastases. CONCLUSION Staging CECT of the thorax has a very low yield in nasopharyngeal carcinoma, even in advanced nodal disease. The hypothesis that contiguous spread of nodal metastases from the supraclavicular region to the upper mediastinum is not substantiated, and no evidence suggests that radiation therapy for N3b-stage disease needs to encompass the upper mediastinum.
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Affiliation(s)
- S Leung
- Department of Clinical Oncology, Prince of Wales Hospital, Shatin, Hong Kong, China
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Abstract
OBJECTIVE To identify the clinical and radiologic features of intracerebral hemorrhage (ICH) in aspirin users. BACKGROUND Although the benefits of aspirin outweigh its hemorrhagic risks for patients at high risk of vascular diseases, prolonged use of aspirin is associated with an increased risk of ICH. METHODS The authors enrolled consecutive patients with acute stroke who were admitted to a regional hospital from 1993 to 1998 into a stroke registry. From this registry, they identified all stroke patients who had ICH confirmed by CT scan and then selected those taking regular aspirin before ICH as the study group. For each study patient, they selected the immediate next two patients with ICH but not taking aspirin as controls. RESULTS The authors identified 58 aspirin users and 1193 nonusers among all patients hospitalized for ICH. From the group of nonusers, they selected 116 patients as controls. The locations of the hematoma were different (p = 0.002), with more lobar hematoma in the aspirin group (32.8%) than in the control group (10.3%). Prior cerebrovascular disease was the reason for taking aspirin in 37 (64%) patients but five patients had prior ICH. CONCLUSIONS The propensity for lobar hematoma in aspirin-associated ICH suggests its pathology may be somewhat different from spontaneous ICH among nonaspirin users. Further research to examine the risks and benefits of aspirin use in certain subgroups at risk of both thrombotic and hemorrhagic events is needed.
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Affiliation(s)
- K S Wong
- Departments of Medicine & Therapeutics, the Chinese University of Hong Kong, Shatin
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Abstract
BACKGROUND The purpose was to use MR imaging to document the patterns of nodal involvement in the upper neck in nasopharyngeal carcinoma (NPC). METHODS The MR images of 150 patients with newly diagnosed NPC were reviewed retrospectively. Nodes were considered abnormal on MR criteria of size, necrosis, and extracapsular spread. RESULTS Retropharyngeal nodes (RN) were more frequently involved than nonretropharyngeal nodes (NRNs) (94% vs 76% in 115 patients with nodal metastases). NRN involvement without RN was seen in only 7 of 115 patients (6%). Involvement of RN at the level of the oropharynx (82%) was as common as at the nasopharynx (83%) level. Internal jugular nodes were the most frequently involved NRN nodes (72%). Spinal accessory nodal involvement was also common (57%) but seldom in isolation (8%). Submandibular (3%) and parotid (2%) nodal metastases were uncommon and were always associated with advanced nodal metastases in the ipsilateral RN, internal jugular, and spinal accessory regions. CONCLUSION Retropharyngeal nodes are the first echelons of nodal metastases. Direct lymphatic spread to the neck without involvement of the RN nodes is uncommon. RN metastases at the level of the oropharynx are more common than previously suspected, and this should influence radiotherapy planning. NRN outside the internal jugular and spinal accessory chains are rare and only occur when the usual routes of lymphatic spread have already been blocked by tumor.
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Affiliation(s)
- A D King
- Department of Diagnostic Radiology and Organ Imaging, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong
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Lam WW, Tam PK, Chan FL, Chan KL, Cheng W. Esophageal atresia and tracheal stenosis: use of three-dimensional CT and virtual bronchoscopy in neonates, infants, and children. AJR Am J Roentgenol 2000; 174:1009-12. [PMID: 10749240 DOI: 10.2214/ajr.174.4.1741009] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [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: 11/18/2022]
Abstract
OBJECTIVE The objective of this study was to evaluate the use of three-dimensional CT and virtual bronchoscopy in the treatment of neonates, infants, and children with esophageal atresia and tracheal stenosis. CONCLUSION Long-gap (n = 1) and short-gap (n = 5) esophageal atresia, long-segment stenosis (n = 2), patent poststenting trachea (n = 1), normal trachea without fistula (n = 1), and tracheal bronchus (n = 1) were studied. Fistulas between the lower esophagus and carina were noted in all six cases of esophageal atresia. All CT findings correlated with operative or bronchoscopy findings. Sensitivity and specificity were 100%. Three-dimensional CT and virtual bronchoscopy are accurate and useful techniques in the preoperative assessment of esophageal atresia and tracheal stenosis in neonates, infants, and children.
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Affiliation(s)
- W W Lam
- Department of Radiology, Queen Mary Hospital, Hong Kong, China
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Abstract
OBJECTIVE Nasal T-cell/natural killer cell lymphoma is a distinct clinicopathologic entity derived from natural killer cells. The purpose of the study was to describe the MR features of this rare nasal cavity tumor and correlate MR findings with stage of disease. CONCLUSION Nasal T-cell/natural killer cell lymphoma frequently exhibits diffuse invasion of the nasal cavity with necrosis, midline destruction, and extension into the nasopharynx. These features may be seen in both early- and late-stage disease.
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Affiliation(s)
- A D King
- Department of Diagnostic Radiology and Organ Imaging, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR
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Affiliation(s)
- W W Lam
- Department of Diagnostic Radiology and Organ Imaging, Prince of Wales Hospital, Shatin, Hong Kong
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Abstract
BACKGROUND The aim of the study was to use magnetic resonance (MR) imaging to determine the cause of hypoglossal nerve palsy and the sites of injury in patients with nasopharyngeal carcinoma before radiation therapy and during postradiation therapy follow-up. METHODS The clinical records and MR studies of 21 patients with hypoglossal nerve palsy were retrospectively studied. These 21 patients belonged to a cohort of 387 patients with nasopharyngeal carcinoma (153 with newly diagnosed disease and 234 on postradiation follow-up) who underwent MR imaging in a 2.5-year period. RESULTS Four patients had hypoglossal nerve palsy at initial diagnosis and all of them had extensive skull base invasion from tumor extending postero-inferiorly to the level of the foramen magnum. The nerve was invaded in the carotid sheath (3), hypoglossal nerve canal (3), and premedullary cistern (1). In 17 patients developing hypoglossal nerve palsy after radiotherapy, only two (12%) had evidence of tumor recurrence. Radiation-induced neuropathy was the probable cause in 14 patients and 1 case was judged indeterminate. MR evidence of fibrosis was demonstrable along the course the nerve in four patients (29%), involving the carotid sheath (4), hypoglossal nerve canal (2), and premedullary cistern (1). No patient had MR evidence of radiation change in the brain stem. Seven patients had a history of a boost dose of radiation to the parapharyngeal region on one or both sides, and nerve palsy occurred on the boosted side in six of them. CONCLUSION Hypoglossal nerve palsy on presentation was caused by locally advanced nasopharyngeal tumor whereas a palsy arising after radiation therapy was more frequently caused by postradiation damage rather than cancer.
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Affiliation(s)
- A D King
- Department of Diagnostic Radiology and Organ Imaging, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong
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Abstract
Computed tomography (CT) appearances of small bowel malrotation and midgut volvulus (MGV) have rarely been described in paediatric patients. We present spiral CT images of a surgically proven case in a young infant. The literature on imaging techniques to diagnose these conditions is reviewed. Radiation doses of upper gastrointestinal series (UGI) and spiral CT are estimated and compared.
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Affiliation(s)
- V H Ai
- Department of Diagnostic Radiology, Queen Mary Hospital, Hong Kong, Hong Kong
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Peh WC, Khong PL, Lam C, Chan KL, Cheng W, Lam WW, Saing H, Leong LL, Low LC, Tam PK. Reduction of intussusception in children using sonographic guidance. AJR Am J Roentgenol 1999; 173:985-8. [PMID: 10511163 DOI: 10.2214/ajr.173.4.10511163] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- W C Peh
- Department of Diagnostic Radiology, The University of Hong Kong, Queen Mary Hospital, China
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Abstract
OBJECTIVE We report our experience using MR cholangiography and CT cholangiography in pediatric patients with choledochal cysts. SUBJECTS AND METHODS Fourteen patients (two boys, 12 girls; mean age, 7.8 years) with either a preoperative diagnosis of choledochal cyst or a surgical finding of choledochal cyst underwent non-breath-hold MR cholangiography using T2-weighted fat-suppressed fast spin-echo sequences with a 1.5-T magnet, and CT cholangiography with IV infusion of meglumine iodoxamic acid. Radiologic findings were correlated with findings from surgery, operative cholangiography, or percutaneous transhepatic cholangiography. RESULTS The biliary tree was visualized in all 14 patients with MR cholangiography and in 13 patients (92.9%) with CT cholangiography. In the 11 preoperative cases of choledochal cyst, MR cholangiography correctly showed all cysts and CT cholangiography showed 10 cysts (90.9%). The quality of images on CT cholangiography and MR cholangiography was comparable. The sensitivity of CT cholangiography and MR cholangiography in revealing intrahepatic stones was 83.3% and 66.7%, respectively; the specificity for both techniques was 100%. The rate of detecting the pancreatic duct and the common channel by CT cholangiography and MR cholangiography was 63.6% and 45.5% respectively. After surgery, CT cholangiography was superior to MR cholangiography in revealing the location of biliary-enteric anastomosis and the extent of anastomotic narrowing. CONCLUSION Because non-breath-hold MR cholangiography is not invasive and does not use ionizing radiation and potentially toxic contrast agents, it is recommended as the imaging technique of choice in children with choledochal cysts. CT cholangiography can be considered as an adjunct after surgery and in patients in whom MR cholangiography is unsatisfactory.
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Affiliation(s)
- W W Lam
- Department of Diagnostic Radiology, Queen Mary Hospital, University of Hong Kong, China
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Abstract
The purpose was to use MRI to study in detail local tumour extension in patients presenting with nasopharyngeal carcinoma (NPC) and to compare the extent of local disease with the current T-stage classification. MR images of 150 patients with newly diagnosed nasopharyngeal carcinoma were obtained on a 1.5 T unit. 10 extranasopharyngeal sites were analysed for tumour involvement. The number of concurrently involved sites was determined. The extent of tumour invasion was compared with staging as defined by the fifth edition of the AJCC classification. The T-stage distribution was T1 21%, T2 16%, T3 41% and T4 22%. The frequencies of tumour invasion into an individual site, and the mean number of other concurrently involved sites were as follows: skull base 63%, 3.9 sites; parapharyngeal 56%, 3.9 sites; nasal cavity 53%, 4.0 sites; oropharyngeal 17%, 5.2 sites; sphenoid sinus 27%, 5.6 sites; cranium 21%, 5.7 sites; infratemporal fossa 2%, 6.3 sites; ethmoid sinus 14%, 6.5 sites; orbit 5%, 7.0 sites; maxillary sinus 5%, 7.1 sites; and hypopharynx 0%, 0 sites. Extranasopharyngeal extension commonly occurred superiorly into the skull base rather than inferiorly to the oropharynx (p < 0.0001). Anatomical sites defined within the same T-stage category had different frequencies of involvement and different frequencies of concurrently involved sites. Oropharyngeal involvement (T2 stage) was associated with a number of concurrently involved sites comparable to structures in the T3 category. Maxillary and ethmoid sinus involvement (T3 stage) were associated with a number of involved sites comparable to the T4 stage. Invasion of the maxillary antrum and orbit are markers of the most bulky form of NPC.
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Affiliation(s)
- A D King
- Department of Diagnostic Radiology, Faculty of Medicine, Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong
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Lam WW, Hatada I, Ohishi S, Mukai T, Joyce JA, Cole TR, Donnai D, Reik W, Schofield PN, Maher ER. Analysis of germline CDKN1C (p57KIP2) mutations in familial and sporadic Beckwith-Wiedemann syndrome (BWS) provides a novel genotype-phenotype correlation. J Med Genet 1999; 36:518-23. [PMID: 10424811 PMCID: PMC1734395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
Beckwith-Wiedemann syndrome (BWS) is a human imprinting disorder with a variable phenotype. The major features are anterior abdominal wall defects including exomphalos (omphalocele), pre- and postnatal overgrowth, and macroglossia. Additional less frequent complications include specific developmental defects and a predisposition to embryonal tumours. BWS is genetically heterogeneous and epigenetic changes in the IGF2/H19 genes resulting in overexpression of IGF2 have been implicated in many cases. Recently germline mutations in the cyclin dependent kinase inhibitor gene CDKN1C (p57KIP2) have been reported in a variable minority of BWS patients. We have investigated a large series of familial and sporadic BWS patients for evidence of CDKN1C mutations by direct gene sequencing. A total of 70 patients with classical BWS were investigated; 54 were sporadic with no evidence of UPD and 16 were familial from seven kindreds. Novel germline CDKN1C mutations were identified in five probands, 3/7 (43%) familial cases and 2/54 (4%) sporadic cases. There was no association between germline CDKN1C mutations and IGF2 or H19 epigenotype abnormalities. The clinical phenotype of 13 BWS patients with germline CDKN1C mutations was compared to that of BWS patients with other defined types of molecular pathology. This showed a significantly higher frequency of exomphalos in the CDKN1C mutation cases (11/13) than in patients with an imprinting centre defect (associated with biallelic IGF2 expression and H19 silencing) (0/5, p<0.005) or patients with uniparental disomy (0/9, p<0.005). However, there was no association between germline CDKN1C mutations and risk of embryonal tumours. No CDKN1C mutations were identified in six non-BWS patients with overgrowth and Wilms tumour. These findings (1) show that germline CDKN1C mutations are a frequent cause of familial but not sporadic BWS, (2) suggest that CDKN1C mutations probably cause BWS independently of changes in IGF2/H19 imprinting, (3) provide evidence that aspects of the BWS phenotype may be correlated with the involvement of specific imprinted genes, and (4) link genotype-phenotype relationships in BWS and the results of murine experimental models of BWS.
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Affiliation(s)
- W W Lam
- Department of Paediatrics and Child Health, University of Birmingham, UK
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Abstract
The MR features of the denervated tongue have been described following nerve injury from radical neck dissection and tumour invasion. The purpose of the study was to determine whether similar features are present in the tongue following radiation induced neuropathy (RIN). The clinical records and MR images of 12 patients with RIN of the hypoglossal nerve were reviewed retrospectively. T1 weighted SE images were performed in 12, T2 weighted TSE images in 11, fat suppressed images in 10 and contrast enhanced T1 weighted images in nine patients. The denervated tongue revealed "oedemalike" changes in five, fatty infiltration in six, atrophy in 11 and pseudohypertrophy in one patient. Abnormal enhancement was not identified, and in five patients the signal intensity was normal on all sequences. The oedemalike changes, fatty infiltration and normal signal intensity were seen 2-48, 2-48, and 6-63 months, respectively, after the onset of RIN. In conclusion, there was no discernible relationship between the duration of RIN and the MR appearance of the denervated tongue. Oedemalike changes, previously described in the acute/subacute phase of denervation, were also seen in long-standing disease and there was no associated abnormal enhancement in any case. Furthermore, the signal intensity may be normal, the MR diagnosis relying on asymmetry of the size of the tongue. It is postulated that radiation causes incomplete and ongoing damage of the nerve, the course of which is unpredictable.
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Affiliation(s)
- A D King
- Department of Diagnostic Radiology, Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong
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King AD, Kew J, Tong M, Leung SF, Lam WW, Metreweli C, van Hasselt CA. Magnetic resonance imaging of the eustachian tube in nasopharyngeal carcinoma: correlation of patterns of spread with middle ear effusion. Am J Otol 1999; 20:69-73. [PMID: 9918176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
OBJECTIVE The purpose of this study was to use multiplanar high-resolution magnetic resonance imaging (MRI) to detail the patterns of tumor spread in nasopharyngeal carcinoma (NPC) and to correlate the findings with the presence of an effusion in the middle ear and mastoid. MATERIALS AND METHODS Magnetic resonance imaging was performed in 51 patients with newly diagnosed NPC, providing 102 individual sides for analysis. RESULTS Fifty-nine lateral walls of the nasopharynx were involved by NPC. Tumor involved the lateral recess (55), eustachian tube orifice (41), levator palatini (LP) (32), torus tubarius (TT) (21), pharyngobasilar fascia (38), tensor palatini (TP) (17), parapharyngeal fat space (PFS) (19), main body of the cartilaginous eustachian tube (CET) ( 13), bony eustachian tube (0). middle ear (0), and inner ear (0). Effusions were present in 32 (54%) of the 59 involved sides. Effusions were found to be associated with the following patterns of spread: tumor causing major displacement of the CET without invasion (3 of 4), tumor invading TT or LP with minor displacement of the TT (4 of 7) or major displacement of the CET (7 of 7) and advanced invasion involving the TP, PFS, or CET with major displacement of CET (18 of 19). Effusions were not seen in tumors without invasion that were restricted to the lateral recess or eustachian tube orifice either with no displacement (O of I I) or with minor displacement (O of 1 1) of the TT. Effusions were present in 28 of 30 cases with major displacement of the main body of the CET, 4 of 18 with minor displacement of the TT, and 0 of 11 with no displacement. Displacement of the eustachian tube was a significant factor in the production of an effusion (p < 0.00001) and remained significant even after exclusion of all cases of advanced invasion (p < 0.0001). CONCLUSION The cause of an effusion in NPC is multifactorial. Magnetic resonance imaging has shown invasion of the tensor palatini muscle in patients with an effusion, suggesting a functional cause. However, displacement of the eustachian tube is a significant factor in patients with middle ear and mastoid effusions.
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Affiliation(s)
- A D King
- Department of Diagnostic Radiology and Organ Imaging, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories
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