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Hwang DY, Bannon SM, Meurer K, Kubota R, Baskaran N, Kim J, Zhang Q, Reichman M, Fishbein NS, Lichstein K, Motta M, Muehlschlegel S, Reznik ME, Jaffa MN, Creutzfeldt CJ, Fehnel CR, Tomlinson AD, Williamson CA, Vranceanu AM. Thematic Analysis of Psychosocial Stressors and Adaptive Coping Strategies Among Informal Caregivers of Patients Surviving ICU Admission for Coma. Neurocrit Care 2024; 40:674-688. [PMID: 37523110 DOI: 10.1007/s12028-023-01804-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 07/10/2023] [Indexed: 08/01/2023]
Abstract
BACKGROUND Family caregivers of patients with severe acute brain injury (SABI) admitted to intensive care units (ICUs) with coma experience heightened emotional distress stemming from simultaneous stressors. Stress and coping frameworks can inform psychosocial intervention development by elucidating common challenges and ways of navigating such experiences but have yet to be employed with this population. The present study therefore sought to use a stress and coping framework to characterize the stressors and coping behaviors of family caregivers of patients with SABI hospitalized in ICUs and recovering after coma. METHODS Our qualitative study recruited a convenience sample from 14 US neuroscience ICUs. Participants were family caregivers of patients who were admitted with ischemic stroke, intracerebral hemorrhage, subarachnoid hemorrhage, traumatic brain injury, or hypoxic-ischemic encephalopathy; had experienced a comatose state for > 24 h; and completed or were scheduled for tracheostomy and/or gastrostomy tube placement. Participants were recruited < 7 days after transfer out of the neuroscience ICU. We conducted live online video interviews from May 2021 to January 2022. One semistructured interview per participant was recorded and subsequently transcribed. Recruitment was stopped when thematic saturation was reached. We deductively derived two domains using a stress and coping framework to guide thematic analysis. Within each domain, we inductively derived themes to comprehensively characterize caregivers' experiences. RESULTS We interviewed 30 caregivers. We identified 18 themes within the two theory-driven domains, including ten themes describing practical, social, and emotional stressors experienced by caregivers and eight themes describing the psychological and behavioral coping strategies that caregivers attempted to enact. Nearly all caregivers described using avoidance or distraction as an initial coping strategy to manage overwhelming emotions. Caregivers also expressed awareness of more adaptive strategies (e.g., cultivation of positive emotions, acceptance, self-education, and soliciting social and medical support) but had challenges employing them because of their heightened emotional distress. CONCLUSIONS In response to substantial stressors, family caregivers of patients with SABI attempted to enact various psychological and behavioral coping strategies. They described avoidance and distraction as less helpful than other coping strategies but had difficulty engaging in alternative strategies because of their emotional distress. These findings can directly inform the development of additional resources to mitigate the long-term impact of acute psychological distress among this caregiver population.
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Affiliation(s)
- David Y Hwang
- Division of Neurocritical Care, Department of Neurology, University of North Carolina School of Medicine, 170 Manning Drive, CB# 7025, Chapel Hill, NC, 27599-7025, USA.
| | - Sarah M Bannon
- Department of Psychiatry, Center for Health Outcomes and Interdisciplinary Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Kate Meurer
- Division of Neurocritical Care and Emergency Neurology, Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Rina Kubota
- Division of Neurocritical Care and Emergency Neurology, Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Nithyashri Baskaran
- Division of Neurocritical Care and Emergency Neurology, Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Jisoo Kim
- Division of Neurocritical Care and Emergency Neurology, Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Qiang Zhang
- David Geffen School of Medicine at the University of California, Los Angeles, Los Angeles, CA, USA
| | - Mira Reichman
- Department of Psychology, University of Washington, Seattle, WA, USA
| | - Nathan S Fishbein
- Department of Psychiatry, Center for Health Outcomes and Interdisciplinary Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Kaitlyn Lichstein
- Department of Psychiatry, Center for Health Outcomes and Interdisciplinary Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Melissa Motta
- Program in Trauma, Department of Neurology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Susanne Muehlschlegel
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Michael E Reznik
- Department of Neurology, Alpert Medical School, Brown University, Providence, RI, USA
| | - Matthew N Jaffa
- Department of Neurointensive Care, Hartford Hospital, Hartford, CT, USA
| | - Claire J Creutzfeldt
- Department of Neurology, University of Washington and Harborview Medical Center, Seattle, WA, USA
| | - Corey R Fehnel
- Department of Neurology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Amanda D Tomlinson
- Department of Critical Care Medicine, College of Medicine, Mayo Clinic, Jacksonville, FL, USA
| | | | - Ana-Maria Vranceanu
- Department of Psychiatry, Center for Health Outcomes and Interdisciplinary Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
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MacKay M, Afshinnekoo E, Rub J, Hassan C, Khunte M, Baskaran N, Owens B, Liu L, Roboz GJ, Guzman ML, Melnick AM, Wu S, Mason CE. The therapeutic landscape for cells engineered with chimeric antigen receptors. Nat Biotechnol 2020; 38:233-244. [PMID: 31907405 DOI: 10.1038/s41587-019-0329-2] [Citation(s) in RCA: 127] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 10/22/2019] [Indexed: 12/18/2022]
Abstract
Despite the global rapid increase in the number of clinical trials employing chimeric antigen receptors (CARs), no comprehensive survey of their scope, targets and design exists. In this study, we present an interactive CAR clinical trial database, spanning 64 targets deployed in T cells (CAR-T), natural killer cells (CAR-NK) or mixtures (CAR-NK/T) from over 500 clinical trials in 20 countries, encompassing >20,000 patients. By combining these data with transcriptional and proteomic data, we create a 'targetable landscape' for CAR cell therapies based on 13,206 proteins and RNAs across 78 tissues, 124 cell types and 20 cancer types. These data suggest a landscape of over 100 single targets and over 100,000 target pairs using logical switches for CAR cell engineering. Our analysis of the CAR cellular therapeutic landscape may aid the design of future therapies, improve target-to-patient matching, and ultimately help inform our understanding of CAR therapy's safety and efficacy.
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Affiliation(s)
- Matthew MacKay
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional Computational Biology and Medicine Program, Weill Cornell Medicine of Cornell University, New York, NY, USA
| | - Ebrahim Afshinnekoo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Jonathan Rub
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | | | | | | | | | | | - Gail J Roboz
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Monica L Guzman
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ari M Melnick
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Shixiu Wu
- National Cancer Center/National Clinical Research Center for Cancer, Cancer Hospital & Shenzhen Hospital, Shenzhen, China.
- Chinese Academy of Medical Science, Peking Union Medical College, Shenzhen, China.
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
- The Feil Family Brain and Mind Research Institute, New York, NY, USA.
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Baskaran N, Kwoh CK, Hui KM. Comprehensive detection of cancer gene expression profiles and gene networks are impacted by the choice of pre-processing algorithm and gene-selection method. INT J DATA MIN BIOIN 2013; 7:416-35. [PMID: 23798225 DOI: 10.1504/ijdmb.2013.054228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pre-processing algorithms (PPA) and gene-selection methods (GSM) are commonly employed to select Differentially Expressed Genes (DEGs) from microarray data. Previous studies established that different combinations of PPAs and GSMs are intrinsically different in their performance to select biologically relevant DEGs. In this study, we evaluated eight combinations of PPAs and GSMs for their ability to select DEGs for prioritising gene-networks. Although the different combinations yielded dissimilar DEG-lists, all DEG-lists selected could segregate tumour from normal. Nevertheless, the DEG-list selected significantly impacted the prioritisation of cancer-associated gene-networks; hence the initial choice of PPA and GSM is crucial for subsequent interactome investigations.
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Affiliation(s)
- N Baskaran
- Bek Chai Heah Laboratory of Cancer Genomics, Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre, 11 Hospital Drive, Singapore 169610, Singapore.
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Prabhakar MM, Vasudevan K, Karthikeyan S, Baskaran N, Silvan S, Manoharan S. Anti-cell proliferative efficacy of ferulic acid against 7, 12-dimethylbenz(a) anthracene induced hamster buccal pouch carcinogenesis. Asian Pac J Cancer Prev 2013; 13:5207-11. [PMID: 23244136 DOI: 10.7314/apjcp.2012.13.10.5207] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The present study was designed to explore the anti-cell proliferative efficacy of ferulic acid by analysing the expression pattern of cell proliferative markers, proliferating cellular nuclear antigen (PCNA) and cyclin D1, in the buccal mucosa of golden Syrian hamsters treated with 7,12-dimethylbenz(a)anthracene (DMBA). Oral squamous cell carcinomas developed in the buccal pouch of hamsters using topical application of 0.5% DMBA three times a week for 14 weeks. Immunohistochemical (PCNA) and RT-PCR (Cyclin D1) analysis revealed over expression of PCNA and cyclin D1 in the buccal mucosa of hamsters treated with DMBA alone (tumor bearing hamsters). Oral administration of ferulic acid at a dose of 40 mg/kg bw to hamsters treated with DMBA not only completely prevented the tumor formation but also down regulated the expression of PCNA and cyclin D1. The results of the present study thus suggests that ferulic acid might have inhibited tumor formation in the buccal mucosa of hamsters treated with DMBA through its anti-cell proliferative potential as evidenced by decreased expression of PCNA and cyclin D1.
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Affiliation(s)
- M Manoj Prabhakar
- Department of Biochemistry and Biotechnology, Faculty of Science, Annamalai University, Annamalainagar Tamilnadu, India
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Manoharan S, Palanimuthu D, Baskaran N, Silvan S. Modulating Effect of Lupeol on the Expression Pattern of Apoptotic Markers in 7, 12-Dimethylbenz(a)anthracene Induced Oral Carcinogenesis. Asian Pac J Cancer Prev 2012; 13:5753-7. [DOI: 10.7314/apjcp.2012.13.11.5753] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Manoharan S, Singh AK, Suresh K, Vasudevan K, Subhasini R, Baskaran N. Anti-tumor Initiating Potential of Andrographolide in 7,12-dimethylbenz[a]anthracene Induced Hamster Buccal Pouch Carcinogenesis. Asian Pac J Cancer Prev 2012; 13:5701-8. [DOI: 10.7314/apjcp.2012.13.11.5701] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Tan EH, Goh C, Lim WT, Soo KC, Khoo ML, Tan T, Tan DSW, Ang MK, Ng QS, Tan PH, Lim A, Hwang J, Teng YHF, Lim TH, Tan SH, Baskaran N, Hui KM. Gefitinib, cisplatin, and concurrent radiotherapy for locally advanced head and neck cancer: EGFR FISH, protein expression, and mutational status are not predictive biomarkers. Ann Oncol 2011; 23:1010-6. [PMID: 21768327 DOI: 10.1093/annonc/mdr327] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Gefitinib was demonstrated to be synergistic with cisplatin and radiotherapy (RT) in in vitro studies. Biomarkers predictive of response to gefitinib in squamous cell head and neck cancer is still lacking. METHODS Thirty-one patients with locally advanced and easily accessible primary tumor sites for biopsies were recruited. Gefitinib was started 3 weeks before the start of cisplatin/concurrent radiotherapy (CTRT) and continued during the CTRT phase and thereafter for 4 months as consolidation phase. Two baselines and a repeat tumor sample were taken after 2 weeks of gefitinib alone to study its impact on tumor gene expression. Epidermal growth factor receptor (EGFR) protein expression, FISH and mutational status, and matrix metallopeptidase 11 (MMP11) protein expression were correlated with response and survival outcome. RESULTS The overall response rate to gefitinib alone was 9.7%. The survival outcome is as follows: median disease free 1.3 years, median survival time 2.4 years, 3-year disease free 42.9%, and 3-year overall survival 48.4%. EGFR FISH, protein expression, and mutational status did not predict for response nor survival outcome of patients. Although MMP11 overexpression did not predict for response, it predicted significantly for a poorer survival outcome. CONCLUSIONS Gefitinib can be combined safely with cisplatin/RT. More studies are needed to uncover predictive biomarkers of benefit to gefitinib.
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Affiliation(s)
- E-H Tan
- Department of Medical Oncology, National Cancer Centre, Singapore.
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Baskaran N, Senthilkumar K, Saravanan M. A new site record of the Grizzled Giant Squirrel Ratufa macroura (Pennant, 1769) in the Hosur forest division, Eastern Ghats, India and its conservation significance. J Threat Taxa 2011. [DOI: 10.11609/jott.o2632.1837-41] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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9
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Vanitha V, Thiyagesan K, Baskaran N. Prevalence of intestinal parasites among captive Asian Elephants Elephas maximus: effect of season, host demography, and management systems in Tamil Nadu, India. J Threat Taxa 2011. [DOI: 10.11609/jott.o2488.1527-34] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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10
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Baskaran N, Desai AA. Does indigestible food remains in the scats of Sloth Bear Melursus ursinus (Carnivora: Ursidae) represent actual contribution of various diet items? J Threat Taxa 2010. [DOI: 10.11609/jott.o2358.1387-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Silvan S, Manoharan S, Baskaran N, Singh AK. WITHDRAWN: Apigenin: A potent antigenotoxic and anticlastogenic agent. Biomed Pharmacother 2010:S0753-3322(10)00131-9. [PMID: 20863648 DOI: 10.1016/j.biopha.2010.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Accepted: 08/06/2010] [Indexed: 10/19/2022] Open
Abstract
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.
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Affiliation(s)
- S Silvan
- Department of Biochemistry and Biotechnology, Faculty of Science, Annamalai University, Annamalainagar, Tamil Nadu 608002, India
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12
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Baskaran N, Boominathan D. Road kill of animals by highway traffic in the tropical forests of Mudumalai Tiger Reserve, southern India. J Threat Taxa 2010. [DOI: 10.11609/jott.o2101.753-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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13
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Jayashankar B, Lokanath Rai KM, Baskaran N, Sathish HS. Synthesis and pharmacological evaluation of 1,3,4-oxadiazole bearing bis(heterocycle) derivatives as anti-inflammatory and analgesic agents. Eur J Med Chem 2009; 44:3898-902. [PMID: 19423197 DOI: 10.1016/j.ejmech.2009.04.006] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2008] [Revised: 03/30/2009] [Accepted: 04/02/2009] [Indexed: 10/20/2022]
Abstract
A series of novel ether-linked bis(heterocycle)s have been synthesized via [3+2]-cycloaddition reaction of nitrile oxide with allyl alcohol followed by intramolecular 1,3-diploar cycloaddition reaction of nitrile imine with carbonyl group. All the newly synthesized compounds were screened for their anti-inflammatory and analgesic activities. Among the list of compounds (7a-k) studied, 7d, 7g, 7j, and 7k exhibited excellent activity comparable to ibuprofen and aspirin at the similar dosages.
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Affiliation(s)
- B Jayashankar
- Department of Studies in Chemistry, University of Mysore, Manasagangotri, Mysore 570006, India.
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Degar BA, Baskaran N, Hulspas R, Quesenberry PJ, Weissman SM, Forget BG. The homeodomain gene Pitx2 is expressed in primitive hematopoietic stem/progenitor cells but not in their differentiated progeny. Exp Hematol 2001; 29:894-902. [PMID: 11438212 DOI: 10.1016/s0301-472x(01)00661-0] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
OBJECTIVE Hematopoietic stem cells (HSCs) represent a rare and incompletely characterized fraction of marrow cells that are capable of both self-renewal and differentiation into all of the mature cells in the peripheral blood. We undertook to identify genes expressed preferentially by HSCs as an initial step toward better understanding the molecular mechanisms that underlie HSC behavior. METHODS We modified the representational difference analysis technique to isolate gene fragments present in amplified cDNA prepared from highly purified murine hematopoietic stem/progenitor cells (Lin(-)/Hoechst(low)/rhodamine(low)) and absent (or much less abundant) in amplified cDNA prepared from lineage-committed marrow cells. We went on to use one potentially important gene fragment that we isolated in this way, to screen a cDNA library prepared from these cells and to characterize the pattern of expression of the gene in hematopoietic and other cells. RESULTS We isolated a fragment of the homeobox transcription factor Pitx2 from amplified cDNA prepared from murine hematopoietic stem/progenitor cells. From a cDNA library prepared from these cells, a full-length cDNA was isolated that corresponds to one of the three known isoforms of Pitx2 (Pitx2c). Pitx2c is expressed in murine embryonic stem (ES) cells and in hematopoietic stem/progenitor cells but not in more differentiated hematopoietic cells or in a large panel of established murine hematopoietic cell lines. Pitx2c expression was not detected after 48 hours of in vitro cytokine stimulation of hematopoietic stem/progenitor cells. CONCLUSIONS Pitx2c is expressed in hematopoietic stem/progenitor cells but not in their differentiated progeny. The pattern of expression of Pitx2c in primitive hematopoietic stem/progenitor cells suggests that it may play a role in hematopoietic stem-cell biology.
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Affiliation(s)
- B A Degar
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT 06520-8021, USA.
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Affiliation(s)
- M Liu
- Department of Genetics, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06510, USA
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Subrahmanyam YV, Baskaran N, Newburger PE, Weissman SM. A modified method for the display of 3'-end restriction fragments of cDNAs: molecular profiling of gene expression in neutrophils. Methods Enzymol 1999; 303:272-97. [PMID: 10349650 DOI: 10.1016/s0076-6879(99)03018-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Affiliation(s)
- Y V Subrahmanyam
- Department of Genetics, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA
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Ghosh PK, Baskaran N, van den Pol AN. Developmentally regulated gene expression of all eight metabotropic glutamate receptors in hypothalamic suprachiasmatic and arcuate nuclei--a PCR analysis. Brain Res Dev Brain Res 1997; 102:1-12. [PMID: 9298229 DOI: 10.1016/s0165-3806(97)00066-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Previous studies have demonstrated the critical role glutamate plays in the hypothalamus, both in the developing and adult brain. The expression of metabotropic glutamate receptor (mGluR) mRNA (mGluR1-8) was studied in the suprachiasmatic (SCN) and arcuate (ARC) nuclei. Using reverse Northern blots and cDNA-PCR, we found that all eight cloned mGluRs were expressed in these brain regions. Most had not previously been detected here. Surprisingly, this included mGluRs that had previously been thought to be restricted to the retina, such as mGluR6. We also detected, cloned, and sequenced a splice variant of mGluR7 (mGluR7b). Developmentally, the age of maximal expression of mGluRs was dependent on the region. For instance, mGluR5 was more strongly expressed in neonatal ARC than in adult, whereas the opposite was true in the SCN. Compared with P10 neonates, mGluR1, R3, R6, R7a, R7b, and R8 showed a greater expression in adult SCN and ARC.
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Affiliation(s)
- P K Ghosh
- Department of Neurosurgery, Yale University Medical School, New Haven, CT 06520, USA
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Jacob AN, Baskaran N, Kandpal G, Narayan D, Bhargava AK, Kandpal RP. Isolation of human ear specific cDNAs and construction of cDNA libraries from surgically removed small amounts of inner ear tissues. Somat Cell Mol Genet 1997; 23:83-95. [PMID: 9330637 DOI: 10.1007/bf02679968] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We have used representational difference analysis (RDA) for subtractive hybridization of oligo dT primed directionally cloned cDNA libraries from human inner ear tissue and a B-lymphoblast cell line. Two rounds of subtraction-amplification, followed by differential hybridization of selected clones led to the isolation of genes which were specific to the ear. Sequence analysis of randomly chosen clones revealed the presence of a histidine rich Ca2+ binding protein, human dynamin, collagen type 1A1, collagen type 2A1, SPARC, human growth hormone, and several specific genes which had no sequence homology in the data base. Furthermore, to apply these techniques for isolating genes specific to distinct inner ear structures and/or cell types of inner ear for which the starting tissue material is limiting, we have used a modified PCR based protocol to construct representative cDNA libraries. We have characterized a cDNA library constructed from small amounts of inner ear tissues recovered by ablative surgical procedure involving labyrinthectomy. The potential application of these protocols for isolating genes involved in hearing and deafness is discussed.
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Affiliation(s)
- A N Jacob
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania 19140, USA
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Baskaran N, Kandpal RP, Bhargava AK, Glynn MW, Bale A, Weissman SM. Uniform amplification of a mixture of deoxyribonucleic acids with varying GC content. Genome Res 1996; 6:633-8. [PMID: 8796351 DOI: 10.1101/gr.6.7.633] [Citation(s) in RCA: 132] [Impact Index Per Article: 4.7] [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: 02/02/2023]
Abstract
A PCR method for uniform amplification of a mixture of DNA templates differing in GC content is described using the two enzyme approach (Klentaq1 and Pfu DNA polymerase) and a combination of DMSO and betaine. This method was applied to amplify the CGG repeat region from the fragile X region.
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Affiliation(s)
- N Baskaran
- Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA
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Arenstorf HP, Kandpal RP, Baskaran N, Parimoo S, Tanaka Y, Kitajima S, Yasukochi Y, Weissman SM. Construction and characterization of a NotI-BsuE linking library from the human X chromosome. Genomics 1991; 11:115-23. [PMID: 1765370 DOI: 10.1016/0888-7543(91)90108-q] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We describe the construction and characterization of methylation-resistant sequence-tagged NotI linking clones specific for the X chromosome, referred to as NotI-BsuE linking clones. The approach consists of methylating the X-chromosome-specific cloned DNA with BsuE methylase (M. BsuE), an enzyme that methylates the first C residue in the CGCG sequence, followed by selection of the methylation-resistant NotI sites by insertion of a kanamycin-resistance gene in the clones cleavable by NotI. The frequent occurrence of NotI sites in CpG islands is expected to cause methylation of a large number of NotI sites with BsuE methylase, thereby rendering them resistant to NotI cleavage. Thus, the combination of M. BsuE and NotI yields less frequent cutting than the NotI alone. We have isolated, partially sequenced, and characterized 113 NotI-BsuE linking clones, and mapped 50 clones to various regions along the chromosome.
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Affiliation(s)
- H P Arenstorf
- Department of Human Genetics, Yale University School of Medicine, New Haven, Connecticut 06510
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Baskaran N, Prakash V, Savithri HS, Radhakrishnan AN, Appaji Rao N. Mode of interaction of aminooxy compounds with sheep liver serine hydroxymethyltransferase. Biochemistry 1989; 28:9613-7. [PMID: 2611250 DOI: 10.1021/bi00451a010] [Citation(s) in RCA: 12] [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: 01/01/2023]
Abstract
The interaction of aminooxy compounds such as aminooxyacetate (AAA), L-canaline, and hydroxylamine with sheep liver serine hydroxymethyltransferase (EC 2.1.2.1) was studied by absorption spectra and stopped-flow spectrophotometry and compared with the unique feature of interaction of O-amino-D-serine (OADS) with the enzyme [Baskaran, N., Prakash, V., Appu Rao, A. G., Radhakrishnan, A. N., Savithri, H. S., & Appaji Rao, N. (1989) Biochemistry (preceding paper in this issue)]. The reaction of AAA (0.5 mM) with the Schiff base of the enzyme resulted in the formation of pyridoxal 5'-phosphate (PLP) and was biphasic with rate constants of 191 and 19 s-1. The formation of the PLP-AAA oxime measured by decrease in absorbance at 388 nm on interaction of AAA with the enzyme had a rate constant of 5.2 M-1 s-1. On the other hand, the reaction of L-canaline with the enzyme was slower as measured by the disruption of enzyme-Schiff base than the reaction of OADS and AAA. In contrast, the formation of PLP as an intermediate could not be detected upon the interaction of hydroxylamine with the enzyme. The reaction of D-cycloserine with the enzyme was much slower (1.6 x 10(2) M-1 s-1) than the aminooxy compounds. These observations indicate that the aminooxy compounds that are structural analogues of serine (OADS, AAA, and canaline) formed PLP as an intermediate prior to the formation of oxime, whereas with hydroxylamine such an intermediate could not be detected.
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Affiliation(s)
- N Baskaran
- Department of Biochemistry, Indian Institute of Science, Bangalore
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Baskaran N, Prakash V, Appu Rao AG, Radhakrishnan AN, Savithri HS, Appaji Rao N. Mechanism of interaction of O-amino-D-serine with sheep liver serine hydroxymethyltransferase. Biochemistry 1989; 28:9607-12. [PMID: 2514804 DOI: 10.1021/bi00451a009] [Citation(s) in RCA: 13] [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] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The mechanism of interaction of O-amino-D-serine (OADS) with sheep liver serine hydroxymethyltransferase (EC 2.1.2.1) (SHMT) was established by measuring changes in the enzyme activity, absorption spectra, circular dichroism (CD) spectra, and stopped-flow spectrophotometry. OADS was a reversible noncompetitive inhibitor (Ki = 1.8 microM) when serine was the varied substrate. The first step in the interaction of OADS with the enzyme was the disruption of enzyme-Schiff base, characterized by the rapid disappearance of absorbance at 425 nm (6.5 X 10(3) M-1 s-1) and CD intensity at 430 nm. Concomitantly, there was a rapid increase in absorbance and CD intensity at 390 nm. The spectral properties of this intermediate enabled its identification as pyridoxal 5'-phosphate (PLP). These changes were followed by a slow unimolecular step (2 X 10(-3) s-1) leading to the formation of PLP-OADS oxime, which was confirmed by its absorbance and fluorescence spectra and retention time on high-performance liquid chromatography. The PLP-OADS oxime was displaced from the enzyme by the addition of PLP as evidenced by the restoration of complete enzyme activity as well as by the spectral properties. The unique feature of the mechanism proposed for the interaction of OADS with sheep liver SHMT was the formation of PLP as an intermediate.
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Affiliation(s)
- N Baskaran
- Department of Biochemistry, Indian Institute of Science, Bangalore
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