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Pérez-Castaño R, Aranda J, Widner FJ, Kieninger C, Deery E, Warren MJ, Orozco M, Elías-Arnanz M, Padmanabhan S, Kräutler B. The Rhodium Analogue of Coenzyme B 12 as an Anti-Photoregulatory Ligand Inhibiting Bacterial CarH Photoreceptors. Angew Chem Int Ed Engl 2024; 63:e202401626. [PMID: 38416546 DOI: 10.1002/anie.202401626] [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: 01/23/2024] [Revised: 02/23/2024] [Accepted: 02/23/2024] [Indexed: 02/29/2024]
Abstract
Coenzyme B12 (AdoCbl; 5'-deoxy-5'-adenosylcobalamin), the quintessential biological organometallic radical catalyst, has a formerly unanticipated, yet extensive, role in photoregulation in bacteria. The light-responsive cobalt-corrin AdoCbl performs this nonenzymatic role by facilitating the assembly of CarH photoreceptors into DNA-binding tetramers in the dark, suppressing gene expression. Conversely, exposure to light triggers the decomposition of this AdoCbl-bound complex by a still elusive photochemical mechanism, activating gene expression. Here, we have examined AdoRhbl, the non-natural rhodium analogue of AdoCbl, as a photostable isostructural surrogate for AdoCbl. We show that AdoRhbl closely emulates AdoCbl in its uptake by bacterial cells and structural functionality as a regulatory ligand for CarH tetramerization, DNA binding, and repressor activity. Remarkably, we find AdoRhbl is photostable even when bound "base-off/His-on" to CarH in vitro and in vivo. Thus, AdoRhbl, an antivitamin B12, also represents an unprecedented anti-photoregulatory ligand, opening a pathway to precisely target biomimetic inhibition of AdoCbl-based photoregulation, with new possibilities for selective antibacterial applications. Computational biomolecular analysis of AdoRhbl binding to CarH yields detailed structural insights into this complex, which suggest that the adenosyl group of photoexcited AdoCbl bound to CarH may specifically undergo a concerted non-radical syn-1,2-elimination mechanism, an aspect not previously considered for this photoreceptor.
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Affiliation(s)
- Ricardo Pérez-Castaño
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
| | - Juan Aranda
- Institute for Research in Biomedicine, IRB Barcelona), Baldiri Reixac 10-12, 08028, Barcelona, Spain
| | - Florian J Widner
- Institute of Organic Chemistry & Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, A-6020, Innsbruck, Austria
| | - Christoph Kieninger
- Institute of Organic Chemistry & Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, A-6020, Innsbruck, Austria
| | - Evelyne Deery
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Martin J Warren
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Modesto Orozco
- Institute for Research in Biomedicine, IRB Barcelona), Baldiri Reixac 10-12, 08028, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona (Spain); the Joint BSC-IRB Research Program in Computational Biology, and Department of Biochemistry and Biomedicine, University of Barcelona, Baldiri Reixac 10-12, 08028, Barcelona, Spain
| | - Montserrat Elías-Arnanz
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
| | - S Padmanabhan
- Instituto de Química Física Blas Cabrera (IQF-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), 119 c/Serrano, 28006, Madrid, Spain
| | - Bernhard Kräutler
- Institute of Organic Chemistry & Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, A-6020, Innsbruck, Austria
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Iqbal SB, Rao SJ, Pyrgos GJ, Haas CJ, Padmanabhan S. Acute inferior ST-elevation myocardial infarction mimicked by direct lightning strike: a case report. Eur Heart J Case Rep 2023; 7:ytad578. [PMID: 38034938 PMCID: PMC10683038 DOI: 10.1093/ehjcr/ytad578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 11/08/2023] [Accepted: 11/16/2023] [Indexed: 12/02/2023]
Abstract
Background Direct lightning strikes are rare, and multiple organ systems can be involved. Prognosis is dependent on the severity of the injury. Severe myocardial injury associated with transient electrocardiogram changes, which have been previously described, is a hazardous complication. Case summary A 35-year-old man with no known past medical history presented unresponsive following a direct lightning strike while sitting in a portable toilet. High-quality cardiopulmonary resuscitation was started in the field, with return of spontaneous circulation (ROSC) after 1 h. Following ROSC, he received volume resuscitation and was maintained on multiple vasopressors. Electrocardiogram showed significant ST-elevations in inferior leads with elevated troponin I, consistent with inferior ST-elevation myocardial infarction. Labs revealed lactic acidosis, hyperkalaemia, acute kidney, and liver injury. Due to concern for plaque rupture, coronary angiography was performed and revealed no obstructive coronary artery disease. Vasopressor support and volume resuscitation were continued for extensive burns covering greater than 30% body surface area. The patient became progressively hypotensive, eventually precipitating pulseless electrical activity arrest. Emergent labs were notable for severe acidaemia. Despite aggressive interventions, he expired due to severe multi-organ failure. Discussion Direct lightning injuries are rare with serious potential complications. Myocardial damage, either from direct electrical insult or from induced coronary vasospasm, can lead to multi-organ system failure.
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Affiliation(s)
- Shaikh B Iqbal
- Department of Medicine, MedStar Health Internal Medicine Residency Program, 201 E University Pkwy, Baltimore, MD 21218, USA
| | - Shiavax J Rao
- Department of Medicine, MedStar Health Internal Medicine Residency Program, 201 E University Pkwy, Baltimore, MD 21218, USA
| | - George J Pyrgos
- Department of Medicne, MedStar Franklin Square Medical Center, 9000 Franklin Square Dr, Baltimore, MD 21237, USA
| | - Christopher J Haas
- Department of Medicne, MedStar Franklin Square Medical Center, 9000 Franklin Square Dr, Baltimore, MD 21237, USA
| | - Sriram Padmanabhan
- MedStar Heart and Vascular Institute, MedStar Franklin Square Medical Center, 9000 Franklin Square Dr, Baltimore, MD 21237, USA
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Musmade B, Korhale R, Sable M, Lokhande S, Padmanabhan S, Bhope S. Development and validation of stability indicating impurity profiling method for Azelastine Hydrochloride and Fluticasone Propionate in Nasal spray product by using HPLC with UV/PDA detector. J AOAC Int 2023:7079780. [PMID: 36929921 DOI: 10.1093/jaoacint/qsad036] [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] [Received: 03/11/2022] [Revised: 03/09/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023]
Abstract
BACKGROUND This Azelastine HCl (AZ) and Fluticasone propionate (FL) nasal spray drug product is commonly used in the treatment of allergic rhinitis worldwide. The impurity profiling of this product is not reported till date. OBJECTIVE The present study is aimed to develop and validate a novel stability indicating analytical method for the estimation of impurities from Azelastine Hydrochloride and Fluticasone Propionate nasal spray drug product. METHODS A mixture of octane sulfonic acid sodium salt and trifluroacetic acid is used as a mobile phase A. Acetonitrile is used as a mobile phase B. Good separation was achieved on Baker bond phenyl hexyl, 250 x 4.6, 5 µm column at 1 mL/min flow rate in gradient elution mode. The chromatograms were monitored at 239 nm. RESULTS The limit of detection (LOD) and limit of quantitation (LOQ) were found to be 0.006 and 0.019 µg/mL for AZ and 0.010 and 0.030 µg/mL for FL, respectively. The correlation coefficient for all the known impurities and principle analytes was observed 0.999 from LOQ level to 150% of standard concentration. The recovery for all the known impurities was found to be between 90 to 110%. During stress study, 15% degradation was observed in basic condition and 8.7% in acidic condition. No significant degradation was observed in thermal and oxidative conditions. CONCLUSION The impurity profiling method for AZ and FL combination nasal spray product was successfully developed, validated and demonstrated to be accurate, precise, specific, robust and stability indicating. The method can be routinely used for the impurity testing of commercial batches in quality control laboratories in the pharmaceutical industry. HIGHLIGHTS No impurity study has been reported for this combination product till date.
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Affiliation(s)
- Bhaskar Musmade
- Sava Healthcare Limited, (Research and Development center), Chinchwad MIDC, Pune, 411019 India
| | - Rasika Korhale
- Sava Healthcare Limited, (Research and Development center), Chinchwad MIDC, Pune, 411019 India
| | - Mangal Sable
- Sava Healthcare Limited, (Research and Development center), Chinchwad MIDC, Pune, 411019 India
| | - Surbhi Lokhande
- Sava Healthcare Limited, (Research and Development center), Chinchwad MIDC, Pune, 411019 India
| | - Sriram Padmanabhan
- Sava Healthcare Limited, (Research and Development center), Chinchwad MIDC, Pune, 411019 India
| | - Shrinivas Bhope
- Sava Healthcare Limited, (Research and Development center), Chinchwad MIDC, Pune, 411019 India
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Padmanabhan S, Kumar TV, Giridharan K, Stalin B, Nagaprasad N, Jule LT, Ramaswamy K. An analysis of environment effect on ethanol blends with plastic fuel and blend optimization using a full factorial design. Sci Rep 2022; 12:21719. [PMID: 36522376 PMCID: PMC9755122 DOI: 10.1038/s41598-022-26046-9] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
There is a growing amount of plastic waste that needs to be properly disposed of in order to protect the environment from the negative effects of increasing reliance on plastic products. Recent interest has focused on chemical recycling as a means of reducing plastic's negative environmental effects. Converting waste plastics into basic petrochemicals allows them to serve as hydrocarbon feedstock or fuel oil through pyrolysis operations. Scientists have taken a keen interest in the production of bioethanol from renewable feedstocks due to its potential as a source of energy and alternative fuel. Due to its beneficial effects on the environment, ethanol has emerged as a promising biofuel. In this paper, energy recovered from low-density polyethylene and high-density polyethylene waste was converted into an alternative plastic fuel and evaluated for its environmental impact with the blending of ethanol in a diesel engine. Ternary fuel blends with 20%, 30%, and 40% waste plastic fuel and 10%, 15%, and 20% ethanol with standard diesel were tested. The study found that blending 10% ethanol with 20% plastic fuel decreased fuel consumption by around 7.9% compared to base diesel. Carbon monoxide emissions are reduced by about 10.2%, and hydrocarbon emissions are reduced by about 13.43% when using the same ternary blend. The optimum values of fuel consumption and emissions were obtained by full factorial design for a ternary fuel blend of 10% ethanol and 20% plastic fuel at the full load condition.
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Affiliation(s)
- S. Padmanabhan
- grid.464713.30000 0004 1777 5670School of Mechanical and Construction, Vel Tech Rangarajan Dr.Sagunthala R&D Institute of Science and Technology, Chennai, India
| | - T. Vinod Kumar
- grid.412815.b0000 0004 1760 6324Department of Mechanical Engineering, Vels Institute of Science, Technology and Advanced Studies (VISTAS), Chennai, India
| | - K. Giridharan
- grid.252262.30000 0001 0613 6919Department of Mechanical Engineering, Easwari Engineering College, Chennai, India
| | - B. Stalin
- grid.252262.30000 0001 0613 6919Department of Mechanical Engineering, Anna University, Regional Campus Madurai, Madurai, Tamilnadu 625019 India
| | - N. Nagaprasad
- Department of Mechanical Engineering, ULTRA College of Engineering and Technology, Madurai, Tamilnadu 625104 India
| | - Leta Tesfaye Jule
- Centre for Excellence-Indigenous Knowledge, Innovative Technology Transfer and Entrepreneurship, Dambi Dollo University, Dambi Dollo, Ethiopia ,Department of Physics, College of Natural and Computational Science, Dambi Dollo University, Dambi Dollo, Ethiopia
| | - Krishnaraj Ramaswamy
- Centre for Excellence-Indigenous Knowledge, Innovative Technology Transfer and Entrepreneurship, Dambi Dollo University, Dambi Dollo, Ethiopia ,Department of Mechanical Engineering, Dambi Dollo University, Dambi Dollo, Ethiopia
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Shital B. Palghadmal SB, Bhosale RK, Kulkarni PS, Kolhe S, Yewale S, Padmanabhan S. Use of Diaion HP20 Resin to Achieve High Rutin Containing Moringa oleifera Extract: Its Solubility and Anti-Bacterial Properties and Possible Applications in Nebulizer Formulation for COVID Patients. Glob J Health Sci 2022. [DOI: 10.5539/gjhs.v14n10p7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Rutin with several pharmacological properties has been reported to be an effective inhibitor for SARS-COV-2 viral protease. Due to lack of specific drugs available for treatment of covid infection, hunt is on for possible herbal supplements that will impact multiplication of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and also provide immunity to people against such infections. We report a simple and cost-effective method for extraction of rutin from Moringa oleifera, a plant with high nutritive value due to its rich contents in minerals, vitamins and other essential phytochemicals. The solubility of rutin in water was achieved using rutin-arginine mixture (identified as a good water-soluble version of rutin) and tested for its antibacterial activity against Klebsiella pneumoniae and E. coli by MIC studies and compared with rutin solubilized in methanol. Our results demonstrate easy scale of the rutin extraction process and such a process could be applicable to extraction of rutin from other medicinal plants as well. We demonstrate that rutin purified through column chromatography has 20% higher solubility in water and maintains its anti-bacterial properties against Klebsiella pneumoniae and E. coli. Our findings reveal new possibilities of using resin column chromatography for concentrating rutin from plant extracts. Also, potential use of water soluble rutin is envisaged for development of nebulizers for treatment of asthma, hyperglycemia, and pneumonia, seen in COVID-19 affected patients.
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Jayakumar P, Padmanabhan S, Lilly R, Suthendran K. Bio-medical Waste Remediation by Environmental Safe Gelatin Coated Blood Sample Paper and its Effective Utilization. Nat Env Poll Tech 2022. [DOI: 10.46488/nept.2022.v21i03.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sustainability in human development sets exact standards for the management of natural resources, including their extraction, use, and the introduction of waste products into a complex, inventive circuit as a consequence of exploitation. Because of the negative influence that medical waste has on the environment and people, it needs specific handling. Medical waste is increasing in amount all the time and has a wide range of consequences across a wide range of activity domains. This paper discusses various issues of the sustainable management of blood sample bio-medical waste and evaluates the properties of alternative samples which are made of gelatin-coated sample paper. A unique bar-coded paper-based blood sample method has prevented complications during blood tests and is much more environmentally friendly.
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Padmanabhan S, Monera-Girona AJ, Pajares-Martínez E, Bastida-Martínez E, Del Rey Navalón I, Pérez-Castaño R, Galbis-Martínez ML, Fontes M, Elías-Arnanz M. Plasmalogens and Photooxidative Stress Signaling in Myxobacteria, and How it Unmasked CarF/TMEM189 as the Δ1'-Desaturase PEDS1 for Human Plasmalogen Biosynthesis. Front Cell Dev Biol 2022; 10:884689. [PMID: 35646900 PMCID: PMC9131029 DOI: 10.3389/fcell.2022.884689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/25/2022] [Indexed: 11/18/2022] Open
Abstract
Plasmalogens are glycerophospholipids with a hallmark sn-1 vinyl ether bond that endows them with unique physical-chemical properties. They have proposed biological roles in membrane organization, fluidity, signaling, and antioxidative functions, and abnormal plasmalogen levels correlate with various human pathologies, including cancer and Alzheimer’s disease. The presence of plasmalogens in animals and in anaerobic bacteria, but not in plants and fungi, is well-documented. However, their occurrence in the obligately aerobic myxobacteria, exceptional among aerobic bacteria, is often overlooked. Tellingly, discovery of the key desaturase indispensable for vinyl ether bond formation, and therefore fundamental in plasmalogen biogenesis, emerged from delving into how the soil myxobacterium Myxococcus xanthus responds to light. A recent pioneering study unmasked myxobacterial CarF and its human ortholog TMEM189 as the long-sought plasmanylethanolamine desaturase (PEDS1), thus opening a crucial door to study plasmalogen biogenesis, functions, and roles in disease. The findings demonstrated the broad evolutionary sweep of the enzyme and also firmly established a specific signaling role for plasmalogens in a photooxidative stress response. Here, we will recount our take on this fascinating story and its implications, and review the current state of knowledge on plasmalogens, their biosynthesis and functions in the aerobic myxobacteria.
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Affiliation(s)
- S Padmanabhan
- Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Antonio J Monera-Girona
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Elena Pajares-Martínez
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Eva Bastida-Martínez
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Irene Del Rey Navalón
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Ricardo Pérez-Castaño
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - María Luisa Galbis-Martínez
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Marta Fontes
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Montserrat Elías-Arnanz
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain
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Kulkarni P, Padmanabhan S. A novel property of hexokinase inhibition by Favipiravir and proposed advantages over Molnupiravir and 2 Deoxy D glucose in treating COVID-19. Biotechnol Lett 2022; 44:831-843. [PMID: 35608787 PMCID: PMC9128636 DOI: 10.1007/s10529-022-03259-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 05/02/2022] [Indexed: 01/18/2023]
Abstract
PURPOSE In the wake of SARS-CoV-2's global spread, human activities from health to social life to education have been affected. Favipiravir and Molnupiravir exhibited novel hexokinase inhibition and we discuss advantages of this property in their COVID-19 inhibition potential. METHODS This paper describes molecular docking data of human hexokinase II with Favipiravir, Cyan 20, Remdesivir, 2DG, and Molnupiravir along with hexokinase inhibition assays. RESULTS Favipiravir, an antiviral drug previously cleared for treating the flu and ebola, has shown some promise in early trials to treat COVID-19. We observed potent human hexokinase inhibiting potential of Favipiravir (50%) as against 4% and merely 0.3% hexokinase inhibition with Molnupiravir and 2 Deoxy D glucose at 0.1 mM concentration supported by molecular docking studies. CONCLUSION Favipiravir could continue to be part of the COVID-19 treatment regimen due to its resistance to host esterases, hexokinase inhibition potential and proven safety through human trials.
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Affiliation(s)
- Prajakta Kulkarni
- Herbal Division, Sava Healthcare Limited, Research Center, Block D1, Plot No. 17/6, MIDC, Chinchwad, Pune, 411019, India
| | - Sriram Padmanabhan
- Herbal Division, Sava Healthcare Limited, Research Center, Block D1, Plot No. 17/6, MIDC, Chinchwad, Pune, 411019, India.
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Abstract
Photoreceptor proteins enable living organisms to sense light and transduce this signal into biochemical outputs to elicit appropriate cellular responses. Their light sensing is typically mediated by covalently or noncovalently bound molecules called chromophores, which absorb light of specific wavelengths and modulate protein structure and biological activity. Known photoreceptors have been classified into about ten families based on the chromophore and its associated photosensory domain in the protein. One widespread photoreceptor family uses coenzyme B12 or 5'-deoxyadenosylcobalamin, a biological form of vitamin B12, to sense ultraviolet, blue, or green light, and its discovery revealed both a new type of photoreceptor and a novel functional facet of this vitamin, best known as an enzyme cofactor. Large strides have been made in our understanding of how these B12-based photoreceptors function, high-resolution structural descriptions of their functional states are available, as are details of their unusual photochemistry. Additionally, they have inspired notable applications in optogenetics/optobiochemistry and synthetic biology. Here, we provide an overview of what is currently known about these B12-based photoreceptors, their discovery, distribution, molecular mechanism of action, and the structural and photochemical basis of how they orchestrate signal transduction and gene regulation, and how they have been used to engineer optogenetic control of protein activities in living cells.
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Affiliation(s)
- S Padmanabhan
- Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas, Madrid, Spain.
| | - Ricardo Pérez-Castaño
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Lucía Osete-Alcaraz
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - María Carmen Polanco
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Montserrat Elías-Arnanz
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain.
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Pérez-Castaño R, Bastida-Martínez E, Fernández Zapata J, Polanco MDC, Galbis-Martínez ML, Iniesta AA, Fontes M, Padmanabhan S, Elías-Arnanz M. Coenzyme B 12 -dependent and independent photoregulation of carotenogenesis across Myxococcales. Environ Microbiol 2022; 24:1865-1886. [PMID: 35005822 PMCID: PMC9304148 DOI: 10.1111/1462-2920.15895] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/27/2021] [Accepted: 01/01/2022] [Indexed: 11/28/2022]
Abstract
Light-induced carotenogenesis in Myxococcus xanthus is controlled by the B12 -based CarH repressor and photoreceptor, and by a separate intricate pathway involving singlet oxygen, the B12 -independent CarH paralog CarA and various other proteins, some eukaryotic-like. Whether other myxobacteria conserve these pathways and undergo photoregulated carotenogenesis is unknown. Here, comparative analyses across 27 Myxococcales genomes identified carotenogenic genes, albeit arranged differently, with carH often in their genomic vicinity, in all three Myxococcales suborders. However, CarA and its associated factors were found exclusively in suborder Cystobacterineae, with carA-carH invariably in tandem in a syntenic carotenogenic operon, except for Cystobacter/Melittangium, which lack CarA but retain all other factors. We experimentally show B12 -mediated photoregulated carotenogenesis in representative myxobacteria, and a remarkably plastic CarH operator design and DNA binding across Myxococcales. Unlike the two characterized CarH from other phyla, which are tetrameric, Cystobacter CarH (the first myxobacterial homolog amenable to analysis in vitro) is a dimer that combines direct CarH-like B12 -based photoregulation with CarA-like DNA-binding and inhibition by an antirepressor. This study provides new molecular insights into B12 -dependent photoreceptors. It further establishes the B12 -dependent pathway for photoregulated carotenogenesis as broadly prevalent across myxobacteria and its evolution, exclusively in one suborder, into a parallel complex B12 -independent circuit. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Ricardo Pérez-Castaño
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
| | - Eva Bastida-Martínez
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
| | - Jesús Fernández Zapata
- Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas, 28006, Madrid, Spain
| | - María Del Carmen Polanco
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
| | - María Luisa Galbis-Martínez
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
| | - Antonio A Iniesta
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
| | - Marta Fontes
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
| | - S Padmanabhan
- Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas, 28006, Madrid, Spain
| | - Montserrat Elías-Arnanz
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
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11
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Padmanabhan S, Joel C, Joel L, Reddy OY, Harsha KS, Ganesan S. Evaluation of Waste Plastic Pyrolysis Oil Performance with Diethyl Ether Additive on Insulated Piston Diesel Engine. NEPT 2021. [DOI: 10.46488/nept.2021.v20i05.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Considering the amount of waste plastics has risen significantly, energy may be extracted from it. Not only is it possible to dispose of waste plastics by converting them to fuel, but it is also possible to extract energy from them. Our research is motivated by the prospect of using waste plastics as a source of energy through waste plastic pyrolysis oil (WPPO). The innovation of this research is that it will assess the efficiency of plastic pyrolysis oil derived from Low-Density Polyethylene (LDPE) on a Thermal Barrier Coated (TBC) piston engine. The incremental ratio of WPPO to pure diesel with the addition of diethyl ether (DEE) was determined and its output and exhaust emission standards were evaluated using a direct injection single cylinder low heat rejection diesel engine. The results for the WPPO blends were promising as with TBCW20DEE10 demonstrating a 5 to 15% increase in carbon monoxide under different load conditions. TBCW20DEE10 confirmed a greater reduction of hydrocarbons varying from 5 to 12 %. At half load condition, TBCW20DEE10 emits approximately 3.5 % less unit
of smoke.
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12
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Musmade BD, Baraskar ML, Ghodke VN, Bhope SG, Padmanabhan S, Lohar KS. Impurity profiling method development and validation of metformin hydrochloride and teneligliptin hydrobromide hydrate in their combination tablet dosage form by using RP-HPLC with UV/PDA detector. Futur J Pharm Sci 2021. [DOI: 10.1186/s43094-021-00362-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
An accurate, precise and robust analytical method was developed for the impurity profiling in the metformin hydrochloride and teneligliptin hydrobromide hydrate tablet. The gradient was optimized for better separation of impurities by using BDS Hypersil C18 250 × 4.6 mm, 5µ column operated at 35 °C. The octane sulfonic acid and phosphate buffer with triethylamine at pH 3.0 were used as mobile phase A, and acetonitrile was used as mobile phase B. The mobile phase was pumped at 1.0 mL/min. The gradient was optimized for better resolution, and the chromatogram was monitored at 210 nm.
Results
The % recovery of teneligliptin and metformin HCL observed was above 90% from LOQ level to 150%. The correlation coefficient r2 was 0.999 for metformin HCl, teneligliptin, melamine, cyanocobalamin, teneligliptin impurity A and 0.998 for teneligliptin impurity B. The method was found unaffected by change in method variance during the robustness study. During the stress study with acid, base, peroxide and temperature, maximum degradation was observed with peroxide indicating the sensitivity of the molecule toward oxidative stress.
Conclusions
The developed method is precise, accurate, robust and linear and hence can be routinely used for the related substance analysis of metformin hydrochloride and teneligliptin hydrobromide hydrate tablet in the quality control laboratory at manufacturing site during the commercial manufacturing.
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13
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Rao S, Kanwal A, Padmanabhan S. Case report of Barth syndrome: a forgotten cause of cardiomyopathy. Eur Heart J Case Rep 2021; 5:ytab195. [PMID: 34557625 PMCID: PMC8453413 DOI: 10.1093/ehjcr/ytab195] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/01/2020] [Accepted: 03/05/2021] [Indexed: 11/15/2022]
Abstract
Background Barth syndrome (BTHS) is a rare X-linked recessive disorder characterized by clinical features including cardiomyopathy, skeletal myopathy, neutropenia, growth delay, and exercise intolerance. It is often considered to be a paediatric disease, owing to most cases being diagnosed during childhood and mortality being the highest during the first few years of life. Case summary We report a case of dilated cardiomyopathy due to BTHS in a 27-year-old adult male patient, who initially presented with lightheadedness, dyspnoea, orthopnoea, and bilateral lower extremity oedema. Key findings from investigations included leukopenia, prolonged QTc interval, reduced left ventricular ejection fraction (LVEF), global enlargement of all heart chambers, patent coronary arteries, and mild pulmonary hypertension. The patient was diuresed to euvolemia and discharged with a LifeVest. Guideline-directed medical therapy was initiated and uptitrated as an outpatient. A repeat echocardiogram 2 years after initial presentation showed marked improvement in LVEF. Discussion It is possible that there are adult patients with idiopathic cardiomyopathy, which may be attributable to BTHS. In the absence of an obvious underlying cause, with the appropriate historical information, clinical exam, laboratory investigations, and imaging findings, BTHS should be considered as a likely cause of non-ischaemic cardiomyopathy.
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Affiliation(s)
- Shiavax Rao
- Department of Medicine, MedStar Health Internal Medicine Residency Program , 201 E University Pkwy, Baltimore, MD 21218, USA
| | - Arjun Kanwal
- Department of Medicine, MedStar Health Internal Medicine Residency Program , 201 E University Pkwy, Baltimore, MD 21218, USA
| | - Sriram Padmanabhan
- MedStar Heart and Vascular Institute, MedStar Franklin Square Medical Center, 9000 Franklin Square Dr, Baltimore, MD 21237, US A
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14
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Palghadmal SB, Kulkarni PS, Makadia V, Deshmukh MJ, Gondhale PS, Padmanabhan S. Tackling Complications of Coronavirus Infection with Quercetin: Observations and Hypotheses. Exploratory Research and Hypothesis in Medicine 2021; 000:000-000. [DOI: 10.14218/erhm.2021.00015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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15
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Musmade B, Sanatan P, Lokhande S, Kulkarni S, Bhope S, Padmanabhan S, Pachpinde A, Lohar K. Development and validation of stability-indicating RP-HPLC method for the simultaneous estimation of xylometazoline hydrochloride and ipratropium bromide from nasal spray dosage form. Futur J Pharm Sci 2021. [DOI: 10.1186/s43094-021-00247-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
A simple, robust, precise, and an accurate HPLC method was established for simultaneous estimation of xylometazoline hydrochloride and ipratropium bromide from a nasal spray dosage form. The effective separation was obtained by injecting 10 μl of sample and standard solutions on to an Inertsil ODS column, 250 × 4.6, mm, 5 μ at 45 °C using phosphate buffer with 1-pentane sulphonic acid sodium salt at pH 4.7 as a mobile phase A and acetonitrile as the mobile phase B. The gradient was optimized with a flow rate of 1 mL/min and a wavelength of 210.0 nm.
Result
The complete analytical method validation was successfully carried out as per ICH guidelines. The retrieval study was carried out at 50% to 150% level of working concentration, and results were in the range of 99 to 101% for both the analytes. The linearity was proven from 4 to 150% of working concentration with linear regression curve (R2=0.999) for both the analytes. The developed method was robust for different parameters like column temperature, flow rate, mobile phase pH, composition, and gradient.
Conclusion
The developed HPLC method can be successfully used for the estimation of xylometazoline hydrochloride and ipratropium bromide from nasal spray dosage form as a release test in QC department of manufacturing units.
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16
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Griffith N, Walter D, Kumar S, Fahey H, Padmanabhan S, Rweikiza B, Venkatesh R, Vargas J, Srichai-Parsia M. CHARACTERIZATION OF MYOCARDIAL INJURY WITH HIGH-SENSITIVITY TROPONIN. J Am Coll Cardiol 2021. [DOI: 10.1016/s0735-1097(21)01527-8] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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17
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Kanwal A, Rao S, Padmanabhan S. PERICARDIAL METASTASIS FROM RENAL CELL CARCINOMA. J Am Coll Cardiol 2021. [DOI: 10.1016/s0735-1097(21)04015-8] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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18
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Rao SJ, Kanwal A, Rizk S, Padmanabhan S. ACUTE HEPATITIS A CAUSING RECURRENT CARDIAC TAMPONADE. J Am Coll Cardiol 2021. [DOI: 10.1016/s0735-1097(21)03792-x] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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19
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Zinjad P, Gondhale P, Kulkarni S, Musmade B, Bhope S, Padmanabhan S. Development and validation of HPLC-UV method for the quantitative analysis of carcinogenic organic impurities and its isomers in the sodium polystyrene sulfonate polymer. ACTA CHROMATOGR 2021. [DOI: 10.1556/1326.2020.00774] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
AbstractSodium polystyrene sulfonate (SPS) powder is in use for over 50 years for the treatment of hyperkalemia. SPS powder is official in United States Pharmacopoeia, British Pharmacopoeia and European Pharmacopoeia. However, till date, no study has been published on the assessment of organic impurities for this drug. The organic impurities in bulk drug and finished product are associated with their safety, efficacy and stability. A simple, rapid, specific, precise and an accurate HPLC method has been developed for the estimation of toxic organic impurities like styrene, naphthalene, divinyl benzene (DVB) and ethylvinyl benzene (EVB) from SPS bulk drug and finished product. The developed method was validated for specificity, accuracy, precision, linearity, limit of detection (LOD), limit of quantitation (LOQ), solution stability, ruggedness and robustness. The influence of acid, alkali, oxidative stress, photolytic stress, thermal stress and humidity stress conditions on SPS bulk powder and finished product has been studied and reported. The proposed method can be successfully employed for the impurity testing of commercial batches of the bulk drug and finished products of both sodium salt and calcium salt of polystyrene sulfonate.
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Affiliation(s)
- Pushpavati Zinjad
- Sava Healthcare Limited, Research Centre (ADL Dept), Block D1, Plot No. 17/6, MIDC, Chinchwad, Pune, 411019, India
| | - Priyanka Gondhale
- Sava Healthcare Limited, Research Centre (ADL Dept), Block D1, Plot No. 17/6, MIDC, Chinchwad, Pune, 411019, India
| | - Shrikant Kulkarni
- Sava Healthcare Limited, Research Centre (ADL Dept), Block D1, Plot No. 17/6, MIDC, Chinchwad, Pune, 411019, India
| | - Bhaskar Musmade
- Sava Healthcare Limited, Research Centre (ADL Dept), Block D1, Plot No. 17/6, MIDC, Chinchwad, Pune, 411019, India
| | - Shrinivas Bhope
- Sava Healthcare Limited, Research Centre (ADL Dept), Block D1, Plot No. 17/6, MIDC, Chinchwad, Pune, 411019, India
| | - Sriram Padmanabhan
- Sava Healthcare Limited, Research Centre (ADL Dept), Block D1, Plot No. 17/6, MIDC, Chinchwad, Pune, 411019, India
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20
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Yewale S, Farash Z, Kolhe S, Sakkan S, Bhope S, Ambekar P, Padmanabhan S. Benefits of Soleris ® over the Conventional Method for Enumeration of Microbial Load in Salacia Herbal Extract. Pol J Microbiol 2021; 69:453-462. [PMID: 33574873 PMCID: PMC7812356 DOI: 10.33073/pjm-2020-048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 10/02/2020] [Accepted: 10/08/2020] [Indexed: 11/05/2022] Open
Abstract
Stems and roots of Salacia genus plants have been used as a specific remedy for early-stage diabetes, and one of the four sulphonium sulphates, salacinol is the compound responsible for the anti-diabetic activity. Salacia is prone to microbial contamination and insect infestation; hence, methods to estimate the microbial load in such plants will enhance its nutritional value. This paper highlights the novel use of Soleris® to quantify microbes of all types, namely bacteria, yeasts, molds, and coliforms in herbal extracts. The microbial analysis results obtained with Soleris® test vial have been compared with the conventional method, and the results indicate that Soleris® is equally efficient as the conventional method and in fact displays several advantages over the traditional method. The Soleris® method is a real time monitoring system that is highly sensitive, user-friendly, and environmentally friendly since it generates very little biomedical waste and saves a large amount of time. The data presented here demonstrate that for highly contaminated samples, results are available within 24 h. For yeasts and molds, the Soleris® method produces results in 48 h, thus offering considerable time savings compared to other commonly used methods.
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Affiliation(s)
- Sadanand Yewale
- Herbal Division, Sava Healthcare Limited, Research Center, Chinchwad, Pune, India
| | - Zeba Farash
- Analytical Development Laboratory, Sava Healthcare Limited, Research Center, Chinchwad, Pune, India
| | - Sanman Kolhe
- Herbal Division, Sava Healthcare Limited, Research Center, Chinchwad, Pune, India
| | - Sasidharan Sakkan
- QC, Microbiology Division, Sava Healthcare Limited, KIADB Industrial Area, Malur, India
| | - Shrinivas Bhope
- Analytical Development Laboratory, Sava Healthcare Limited, Research Center, Chinchwad, Pune, India
| | - Pradnya Ambekar
- Neogen Food and Animal Security (India) Pvt. Ltd., Kochi, India
| | - Sriram Padmanabhan
- Herbal Division, Sava Healthcare Limited, Research Center, Chinchwad, Pune, India
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21
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Youssef JG, Zahiruddin F, Youssef G, Padmanabhan S, Ensor J, Pingali SR, Zu Y, Sahay S, Iyer SP. G6PD deficiency and severity of COVID19 pneumonia and acute respiratory distress syndrome: tip of the iceberg? Ann Hematol 2021; 100:667-673. [PMID: 33439304 PMCID: PMC7804896 DOI: 10.1007/s00277-021-04395-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 01/03/2021] [Indexed: 01/08/2023]
Abstract
Abstract The severe pneumonia caused by the human coronavirus (hCoV)-SARS-CoV-2 has inflicted heavy casualties, especially among the elderly and those with co-morbid illnesses irrespective of their age. The high mortality in African-Americans and males, in general, raises the concern for a possible X-linked mediated process that could affect the viral pathogenesis and the immune system. We hypothesized that G6PD, the most common X-linked enzyme deficiency, associated with redox status, may have a role in severity of pneumonia. Retrospective chart review was performed in hospitalized patients with COVID19 pneumonia needing supplemental oxygen. A total of 17 patients were evaluated: six with G6PD deficiency (G6PDd) and 11 with normal levels. The two groups (normal and G6PDd) were comparable in terms of age, sex, co-morbidities, and laboratory parameters—LDH, IL-6, CRP, and ferritin, respectively. Thirteen patients needed ventilatory support ; 8 in the normal group and 5 in the G6PDd group (72% vs.83%). The main differences indicating increasing severity in normal vs. G6PDd groups included G6PD levels (12.2 vs. 5.6, P = 0.0002), PaO2/FiO2 ratio (159 vs. 108, P = 0.05), days on mechanical ventilation (10.25 vs. 21 days P = 0.04), hemoglobin level (10 vs. 8.1 P = 0.03), and hematocrit (32 vs. 26 P = 0.015). Only one patient with G6PDd died; 16 were discharged home. Our clinical series ascribes a possible biological role for G6PDd in SARS-CoV2 viral proliferation. It is imperative that further studies are performed to understand the interplay between the viral and host factors in G6PDd that may lead to disparity in outcomes. Key Points • COVID19 studies show higher mortality in men, due to severe pneumonia and ARDS, indicating possible X-linked mediated differences • G6PD, the most common X-linked enzymopathy, highly prevalent in African Americans and Italians, maintains redox homeostasis. • Preclinical studies using G6PD deficient (G6PDd) cells infected with human coronavirus (hCoV), show impaired cellular responses, viral proliferation and worsening oxidative damage. • Retrospective chart review in hospitalized patients with COVID19 pneumonia needing supplemental oxygen shows differences between the two groups (Normal and G6PDd) in hematological indices; the G6PDdgroup demonstrated prolonged PaO2/FiO2 ratio, and longer days on mechanical ventilation indicating the severity of the pneumonia.
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Affiliation(s)
- Jihad G Youssef
- Division of Pulmonary and Critical Care Medicine, Houston Methodist Pulmonary Transplant Center, Houston Methodist Hospital, Houston, TX, USA
| | - Faisal Zahiruddin
- Division of Pulmonary and Critical Care Medicine, Houston Methodist Pulmonary Transplant Center, Houston Methodist Hospital, Houston, TX, USA
| | - George Youssef
- College of Natural Sciences and Mathematics, University of Houston, Houston, TX, USA
| | - Sriram Padmanabhan
- Collaborative Action for SARS-CoV-2 Eradication (CARE), Houston, TX, USA
| | - Joe Ensor
- Houston Methodist Cancer Center, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
| | - Sai Ravi Pingali
- Houston Methodist Cancer Center, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
| | - Youli Zu
- Houston Methodist Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
| | - Sandeep Sahay
- Division of Pulmonary and Critical Care Medicine, Houston Methodist Lung Center, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
| | - Swaminathan P Iyer
- Collaborative Action for SARS-CoV-2 Eradication (CARE), Houston, TX, USA. .,Department of Lymphoma/Myeloma, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, 1400 Unit 429, Holcombe Blvd, Houston, TX, 77030, USA.
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22
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Padmanabhan S, Sposito A, Yeh M, Everitt M, White I, DeVoe DL. Reagent integration and controlled release for multiplexed nucleic acid testing in disposable thermoplastic 2D microwell arrays. Biomicrofluidics 2021; 15:014103. [PMID: 33520047 PMCID: PMC7816768 DOI: 10.1063/5.0039146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/05/2021] [Indexed: 06/12/2023]
Abstract
The seamless integration of reagents into microfluidic devices can serve to significantly reduce assay complexity and cost for disposable diagnostics. In this work, the integration of multiplexed reagents into thermoplastic 2D microwell arrays is demonstrated using a scalable pin spotting technique. Using a simple and low-cost narrow-bore capillary spotting pin, high resolution deposition of concentrated reagents within the arrays of enclosed nanoliter-scale wells is achieved. The pin spotting method is further employed to encapsulate the deposited reagents with a chemically modified wax layer that serves to prevent disruption of the dried assay components during sample introduction through a shared microchannel, while also enabling temperature-controlled release after sample filling is complete. This approach supports the arbitrary patterning and release of different reagents within individual wells without crosstalk for multiplexed analyses. The performance of the in-well spotting technique is characterized using on-chip rolling circle amplification to evaluate its potential for nucleic acid-based diagnostics.
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Affiliation(s)
- S. Padmanabhan
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - A. Sposito
- Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - M. Yeh
- Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - M. Everitt
- Department of Bioengineering, University of Maryland, College Park, Maryland 20742, USA
| | - I. White
- Department of Bioengineering, University of Maryland, College Park, Maryland 20742, USA
| | - D. L. DeVoe
- Author to whom correspondence should be addressed:. Tel.: +1-301-405-8125
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23
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Miller NA, Kaneshiro AK, Konar A, Alonso-Mori R, Britz A, Deb A, Glownia JM, Koralek JD, Mallik L, Meadows JH, Michocki LB, van Driel TB, Koutmos M, Padmanabhan S, Elías-Arnanz M, Kubarych KJ, Marsh ENG, Penner-Hahn JE, Sension RJ. The Photoactive Excited State of the B 12-Based Photoreceptor CarH. J Phys Chem B 2020; 124:10732-10738. [PMID: 33174757 DOI: 10.1021/acs.jpcb.0c09428] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We have used transient absorption spectroscopy in the UV-visible and X-ray regions to characterize the excited state of CarH, a protein photoreceptor that uses a form of B12, adenosylcobalamin (AdoCbl), to sense light. With visible excitation, a nanosecond-lifetime photoactive excited state is formed with unit quantum yield. The time-resolved X-ray absorption near edge structure difference spectrum of this state demonstrates that the excited state of AdoCbl in CarH undergoes only modest structural expansion around the central cobalt, a behavior similar to that observed for methylcobalamin rather than for AdoCbl free in solution. We propose a new mechanism for CarH photoreactivity involving formation of a triplet excited state. This allows the sensor to operate with high quantum efficiency and without formation of potentially dangerous side products. By stabilizing the excited electronic state, CarH controls reactivity of AdoCbl and enables slow reactions that yield nonreactive products and bypass bond homolysis and reactive radical species formation.
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Affiliation(s)
- Nicholas A Miller
- Department of Chemistry, University of Michigan, 930 N University Ave. Ann Arbor, Michigan 48109-1055, United States
| | - April K Kaneshiro
- Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Dr., Ann Arbor, Michigan 48109-0600, United States
| | - Arkaprabha Konar
- Department of Physics, University of Michigan, 450 Church Street, Ann Arbor, Michigan 48109-1040, United States
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Alexander Britz
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States.,Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Aniruddha Deb
- Department of Chemistry, University of Michigan, 930 N University Ave. Ann Arbor, Michigan 48109-1055, United States.,Department of Biophysics, University of Michigan, 930 N University Ave. Ann Arbor, Michigan 48109-1055, United States
| | - James M Glownia
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Jake D Koralek
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Leena Mallik
- Department of Chemistry, University of Michigan, 930 N University Ave. Ann Arbor, Michigan 48109-1055, United States
| | - Joseph H Meadows
- Department of Chemistry, University of Michigan, 930 N University Ave. Ann Arbor, Michigan 48109-1055, United States
| | - Lindsay B Michocki
- Department of Chemistry, University of Michigan, 930 N University Ave. Ann Arbor, Michigan 48109-1055, United States
| | - Tim B van Driel
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Markos Koutmos
- Department of Chemistry, University of Michigan, 930 N University Ave. Ann Arbor, Michigan 48109-1055, United States.,Department of Biophysics, University of Michigan, 930 N University Ave. Ann Arbor, Michigan 48109-1055, United States
| | - S Padmanabhan
- Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas, Madrid 28006, Spain
| | - Montserrat Elías-Arnanz
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas), Facultad de Biología, Universidad de Murcia, Murcia 30100, Spain
| | - Kevin J Kubarych
- Department of Chemistry, University of Michigan, 930 N University Ave. Ann Arbor, Michigan 48109-1055, United States
| | - E Neil G Marsh
- Department of Chemistry, University of Michigan, 930 N University Ave. Ann Arbor, Michigan 48109-1055, United States
| | - James E Penner-Hahn
- Department of Chemistry, University of Michigan, 930 N University Ave. Ann Arbor, Michigan 48109-1055, United States.,Department of Biophysics, University of Michigan, 930 N University Ave. Ann Arbor, Michigan 48109-1055, United States
| | - Roseanne J Sension
- Department of Chemistry, University of Michigan, 930 N University Ave. Ann Arbor, Michigan 48109-1055, United States.,Department of Physics, University of Michigan, 450 Church Street, Ann Arbor, Michigan 48109-1040, United States.,Department of Biophysics, University of Michigan, 930 N University Ave. Ann Arbor, Michigan 48109-1055, United States
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24
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Gallego-García A, Monera-Girona AJ, Pajares-Martínez E, Bastida-Martínez E, Pérez-Castaño R, Iniesta AA, Fontes M, Padmanabhan S, Elías-Arnanz M. A bacterial light response reveals an orphan desaturase for human plasmalogen synthesis. Science 2020; 366:128-132. [PMID: 31604315 DOI: 10.1126/science.aay1436] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 09/04/2019] [Indexed: 01/03/2023]
Abstract
Plasmalogens are glycerophospholipids with a hallmark sn-1 vinyl ether bond. These lipids are found in animals and some bacteria and have proposed membrane organization, signaling, and antioxidant roles. We discovered the plasmanylethanolamine desaturase activity that is essential for vinyl ether bond formation in a bacterial enzyme, CarF, which is a homolog of the human enzyme TMEM189. CarF mediates light-induced carotenogenesis in Myxococcus xanthus, and plasmalogens participate in sensing photooxidative stress through singlet oxygen. TMEM189 and other animal homologs could functionally replace CarF in M. xanthus, and knockout of TMEM189 in a human cell line eliminated plasmalogens. Discovery of the human plasmanylethanolamine desaturase will spur further study of plasmalogen biogenesis, functions, and roles in disease.
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Affiliation(s)
- Aránzazu Gallego-García
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al Instituto de Química Física "Rocasolano," Consejo Superior de Investigaciones Científicas), Facultad de Biología, Universidad de Murcia, Murcia 30100, Spain
| | - Antonio J Monera-Girona
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al Instituto de Química Física "Rocasolano," Consejo Superior de Investigaciones Científicas), Facultad de Biología, Universidad de Murcia, Murcia 30100, Spain
| | - Elena Pajares-Martínez
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al Instituto de Química Física "Rocasolano," Consejo Superior de Investigaciones Científicas), Facultad de Biología, Universidad de Murcia, Murcia 30100, Spain
| | - Eva Bastida-Martínez
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al Instituto de Química Física "Rocasolano," Consejo Superior de Investigaciones Científicas), Facultad de Biología, Universidad de Murcia, Murcia 30100, Spain
| | - Ricardo Pérez-Castaño
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al Instituto de Química Física "Rocasolano," Consejo Superior de Investigaciones Científicas), Facultad de Biología, Universidad de Murcia, Murcia 30100, Spain
| | - Antonio A Iniesta
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al Instituto de Química Física "Rocasolano," Consejo Superior de Investigaciones Científicas), Facultad de Biología, Universidad de Murcia, Murcia 30100, Spain
| | - Marta Fontes
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al Instituto de Química Física "Rocasolano," Consejo Superior de Investigaciones Científicas), Facultad de Biología, Universidad de Murcia, Murcia 30100, Spain
| | - S Padmanabhan
- Instituto de Química Física "Rocasolano," Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain.
| | - Montserrat Elías-Arnanz
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al Instituto de Química Física "Rocasolano," Consejo Superior de Investigaciones Científicas), Facultad de Biología, Universidad de Murcia, Murcia 30100, Spain.
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Mangesh VL, Padmanabhan S, Tamizhdurai P, Narayanan S, Ramesh A. Combustion and emission analysis of hydrogenated waste polypropylene pyrolysis oil blended with diesel. J Hazard Mater 2020; 386:121453. [PMID: 31928791 DOI: 10.1016/j.jhazmat.2019.121453] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/09/2019] [Accepted: 10/09/2019] [Indexed: 05/28/2023]
Abstract
Petroleum-based plastic pyrolysis oil contains unsaturated compounds, and the presence of these compounds makes the produced fuel unsuitable for combustion in diesel engines. Hydrogenation of pyrolysis oil is performed to convert unsaturated compounds to saturated compounds. Past studies have shown that hydrogenation of petroleum-based plastic pyrolysis oil is viable; however, its combustion and emissions analysis in diesel engines has not yet been reported. In this study, we investigated the combustion, performance, and emissions of hydrogenated polypropylene pyrolysis oil (HPPO) blended with diesel. Polypropylene (PP) was converted to pyrolysis oil using ZSM-5 as the catalyst. The hydrogenation of polypropylene pyrolysis oil (PPO) was conducted at pressure of 70 bar, and the reaction temperature was maintained at 350 °C. Ni metal impregnated on the ZSM-5 base support was used as the catalyst of choice. The produced HPPO possessed physicochemical properties that match the EN590 standards(European diesel fuel standards). Gas chromatography-mass spectrometry (GC-MS) studies of PPO and HPPO showed the effectiveness of hydrogenation for the complete conversion of alkenes to alkanes, and hydrocracking resulted in cracking higher carbon number alkanes to lower values. HPPO was blended with diesel in ratios of 10 wt.%, 20 wt.%, 30 wt.%, and 40 wt.%. The diesel engine performance results for the blended fuel showed combustion, performance, and emissions on par with pure diesel fuel for blending ratios up to 20 wt.%. As is known, plastic solid waste (PSW) materials pose serious hazards to the environment. Our HPPO physicochemical properties matched the EN590 standards for diesel fuel. The combustion of HPPO in diesel engines can provide an option for environmentally cleaner disposal of PSW.
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Affiliation(s)
- V L Mangesh
- Sathyabama Institute of Science and Technology, Jeppiar Nagar, Chennai, 600119, India; Department of Marine Engineering, Coimbatore Marine College, Coimbatore, 641032, India.
| | - S Padmanabhan
- Department of Automobile Engineering, Vel Tech Rangarajan Dr Sagunthala R&D Institute of Science and Technology, Avadi, Chennai, 600062, India
| | - P Tamizhdurai
- Environmental and Water Resources Engineering Division, Department of Civil Engineering, Indian Institute of Technology Madras, Chennai, 600036, India
| | - S Narayanan
- Sriram College of Arts and Science, Perumalpattu, Veppampattu, Tiruvallur, Tamilnadu, 602024, India
| | - A Ramesh
- Department of Chemistry, Anna University, Chennai, 600025, India
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Affiliation(s)
- C. Hithaishi
- Division of Nephrology University Health Network and University of Toronto Toronto, Ontario, Canada
| | - T. Lobbedez
- Division of Nephrology University Health Network and University of Toronto Toronto, Ontario, Canada
| | - S. Padmanabhan
- Division of Nephrology University Health Network and University of Toronto Toronto, Ontario, Canada
| | - M.E. Pineda
- Division of Nephrology University Health Network and University of Toronto Toronto, Ontario, Canada
| | - D.G. Oreopoulos
- Division of Nephrology University Health Network and University of Toronto Toronto, Ontario, Canada
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Padmanabhan S. 478 A rare case of right ventricular ischaemia and ventricular tachycardia in neonate caused by intermittent occlusion of origin of the right coronary artery by an echogenic mass. Eur Heart J Cardiovasc Imaging 2020. [DOI: 10.1093/ehjci/jez319.256] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
OnBehalf
Cornwall
A term neonate with poor condition at birth was noted to be markedly bradycardic when crying. ECG showed first degree heart block. Echocardiogram demonstrated poor bi-ventricular function. He was treated for Hypoxic ischemic encephalopathy (HIE).
In the next few hours he developed short episodes of ventricular tachycardia with left bundle branch block and non-conducted P waves suggesting an origin of tachycardia from the right ventricle.
His repeat ECHO suggested that he had right ventricular infarction due to a very rare finding of intermittent occlusion of the origin of the right coronary artery by an echogenic mass.
He was transferred for emergency cardiac surgery to remove a clot of 1.6cm, occluding the right coronary artery. Histology findings were in keeping with a thrombus. Thrombophilia screen for both parents and infant were negative. MRI Brain did not show evidence of HIE suggesting his poor condition at birth was secondary to intermittent coronary ischemia. Discussion: Myocardial infarction (MI) in neonates is a rarely encountered and potentially life-threatening condition, with mortality rate as high as 90%. We present one of the first reported cases of successful surgical management of an acute right coronary artery thrombosis after an early diagnosis. The cause of thrombosis remains unclear in our patient. They were born in poor condition with initial pH 6.9 and lactate of 10, but with a structurally normal heart and negative thrombophilia screen. Perinatal asphyxia is a potential cause; however there is doubt that this may be a symptom rather than cause of the right coronary artery occlusion. Early diagnosis was key in management after a high level of clinical suspicion. He made significant recovery with near normal RV function, and is currently on captopril and carvedilol post-surgery. This is one of the first cases to document near full return of cardiac function following ischaemia to the right ventricle
Abstract 478 Figure. 5
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Affiliation(s)
- S Padmanabhan
- Royal Cornwall Hospitals Trust, Truro, United Kingdom of Great Britain & Northern Ireland
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Abood L, Padmanabhan S. P705 Is chest wall deformity a serious issue? A rare case of TGFBR1 mutation in the paediatric population. Eur Heart J Cardiovasc Imaging 2020. [DOI: 10.1093/ehjci/jez319.378] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
INTRODUCTION
Mutations in the genes encoding transforming growth factor β receptors 1 and 2 (TGFBR1 and TGFBR2) have recently been found in association with a continuum of clinical features.
Mild association – a presentation similar to that of Marfan"s syndrome.
Severe association – a complex phenotype in which aortic dissection or rupture commonly occurs in childhood and at aortic diameters, that ordinarily would not be predictive of these events. Classified as the Loeys–Dietz syndrome.
Is chest wall asymmetry a serious issue? A study of 71 patients with Loeys-Dietz – 9% died from aneurysm rupture or dissection with aortic diameters of less than 4.5cm and as early as 6 months of age.
Genetic variants of unknown clinical significance - how should they be managed?
CASE
History
3-year old girl seen in general paediatric clinic with 5 months history of worsening chest wall deformity.
Examination
Asymmetrical pectus deformity. Spinal asymmetry and soft systolic murmur at the lower left sternal edge.
INVESTIGATION
Chest x-ray: Grossly enlarged and distorted cardiac/mediastinal silhouette.
Echocardiogram
Massive ascending aortic root dilatation (5.5cm) with significant aortic regurgitation.
MRI whole body angiogram
Massively dilated aortic root and ascending aorta to the proximal arch, hugely tortuous and ectatic cerebral vessels, diffuse marked dural ectasia, asymmetrical pectus deformity and a diaphragmatic morgagni hernia in the lower right hemi thorax.
Genetic analysis
Heterozygous missense variant of unknown clinical significance in exon 3 of TGFBR1 gene. The first heterozygous missense variant of its kind in the paediatric population for which its clinical significance remains unknown.
TREATMENT
As risk of dissection, a Bentall procedure was performed.
Family screening - Father has a dilated proximal ascending aorta.
LEARNING POINTS
Chest wall deformity should prompt clinicians to expedite investigations for aortic root dilatation/aneurysm and connective tissue disorders.
The continuum of clinical features of these genetic associations emphasises the importance of early recognition of the phenotype, prophylactic intervention and meticulous surveillance of the distal aorta and vascular tree for optimal management.
A genetic variant of uncertain significance (VUS) should not be used in clinical decision making. Efforts to resolve the classification of the variant as pathogenic or benign should be undertaken with good working relationships with clinical geneticists.
A VUS is difficult for patients and parents to understand and may also cause psychological distress. The importance of careful clinical and molecular characterisation to identify patients and families at risk cannot be overemphasised. This allows the use of a structured approach to intervention, informed counselling regarding the risk of recurrence, concerns related to pregnancy, and guidelines for clinical management.
Abstract P705 Figure. Case Photography and Imaging
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Affiliation(s)
- L Abood
- Royal Cornwall Hospitals Trust, Truro, United Kingdom of Great Britain & Northern Ireland
| | - S Padmanabhan
- Royal Cornwall Hospitals Trust, Truro, United Kingdom of Great Britain & Northern Ireland
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Padmanabhan S, Han JY, Nanayankkara I, Tran K, Ho P, Mesfin N, White I, DeVoe DL. Enhanced sample filling and discretization in thermoplastic 2D microwell arrays using asymmetric contact angles. Biomicrofluidics 2020; 14:014113. [PMID: 32095199 PMCID: PMC7028432 DOI: 10.1063/1.5126938] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 02/09/2020] [Indexed: 05/04/2023]
Abstract
Sample filling and discretization within thermoplastic 2D microwell arrays is investigated toward the development of low cost disposable microfluidics for passive sample discretization. By using a high level of contact angle asymmetry between the filling channel and microwell surfaces, a significant increase in the range of well geometries that can be successfully filled is revealed. The performance of various array designs is characterized numerically and experimentally to assess the impact of contact angle asymmetry and device geometry on sample filling and discretization, resulting in guidelines to ensure robust microwell filling and sample isolation over a wide range of well dimensions. Using the developed design rules, reliable and bubble-free sample filling and discretization is achieved in designs with critical dimensions ranging from 20 μm to 800 μm. The resulting devices are demonstrated for discretized nucleic acid amplification by performing loop-mediated isothermal amplification for the detection of the mecA gene associated with methicillin-resistant Staphylococcus aureus.
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Affiliation(s)
- S. Padmanabhan
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - J. Y. Han
- Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - I. Nanayankkara
- Department of Bioengineering, University of Maryland, College Park, Maryland 20742, USA
| | - K. Tran
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - P. Ho
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - N. Mesfin
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - I. White
- Department of Bioengineering, University of Maryland, College Park, Maryland 20742, USA
| | - D. L. DeVoe
- Author to whom correspondence should be addressed:. Tel.: +1-301-405-8125
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Bernal-Bernal D, Abellón-Ruiz J, Iniesta AA, Pajares-Martínez E, Bastida-Martínez E, Fontes M, Padmanabhan S, Elías-Arnanz M. Multifactorial control of the expression of a CRISPR-Cas system by an extracytoplasmic function σ/anti-σ pair and a global regulatory complex. Nucleic Acids Res 2019; 46:6726-6745. [PMID: 29893914 PMCID: PMC6061681 DOI: 10.1093/nar/gky475] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 05/15/2018] [Indexed: 12/19/2022] Open
Abstract
Expression of CRISPR-Cas systems is a prerequisite for their defensive role against invading genetic elements. Yet, much remains unknown about how this crucial step is regulated. We describe a new mechanism controlling CRISPR-cas expression, which requires an extracytoplasmic function (ECF) σ factor (DdvS), its membrane-bound anti-σ (DdvA) and a global regulatory complex (CarD–CarG). Transcriptomic analyses revealed that the DdvS/CarD/CarG-dependent regulon comprises a type III-B CRISPR-Cas system in Myxococcus xanthus. We mapped four DdvS-driven CarD/CarG-dependent promoters, with one lying immediately upstream of the cas cluster. Consistent with direct action, DdvS and CarD–CarG localize at these promoters in vivo. The cas genes are transcribed as a polycistronic mRNA that reads through the leader into the CRISPR array, a putative σA-dependent promoter in the leader having negligible activity in vivo. Consequently, expression of the entire CRISPR-Cas system and mature CRISPR-RNA (crRNA) production is DdvS/CarD/CarG-dependent. DdvA likely uses its large C-terminal domain to sense and transduce the extracytoplasmic signal triggering CRISPR-cas expression, which we show is not starvation-induced multicellular development. An ECF-σ/anti-σ pair and a global regulatory complex provide an effective mechanism to coordinate signal-sensing with production of precursor crRNA, its processing Cas6 endoribonuclease and other Cas proteins for mature crRNA biogenesis and interference.
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Affiliation(s)
- Diego Bernal-Bernal
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
| | - Javier Abellón-Ruiz
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
| | - Antonio A Iniesta
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
| | - Elena Pajares-Martínez
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
| | - Eva Bastida-Martínez
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
| | - Marta Fontes
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
| | - S Padmanabhan
- Instituto de Química Física 'Rocasolano', Consejo Superior de Investigaciones Científicas (IQFR-CSIC), Serrano 119, 28006 Madrid, Spain
| | - Montserrat Elías-Arnanz
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
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Padmanabhan S, Pérez-Castaño R, Elías-Arnanz M. B12-based photoreceptors: from structure and function to applications in optogenetics and synthetic biology. Curr Opin Struct Biol 2019; 57:47-55. [DOI: 10.1016/j.sbi.2019.01.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 01/22/2019] [Accepted: 01/28/2019] [Indexed: 12/14/2022]
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Babahosseini H, Padmanabhan S, Misteli T, DeVoe DL. A Scalable Random Access Micro-traps Array for Formation, Selective Retrieval and Capturing of Individual Droplets. Annu Int Conf IEEE Eng Med Biol Soc 2019; 2019:1054-1057. [PMID: 31946075 PMCID: PMC8320702 DOI: 10.1109/embc.2019.8857768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Formation, selective retrieval and capturing of individual droplets are key operational capabilities needed for a broad range of droplet microfluidic applications. The membrane displacement trap (MDT) element gives a robust method for uniform discretization and controllable manipulation of aqueous droplets using an enclosed micro-well covered by an elastomer membrane. This capability can be scaled up by combining the modular elements with a system design that requires a minimal number of signal inputs. Incorporation of MDT elements with a pneumatically-controllable multiplexer system can lead to a scalable random access MDT array platform for liquid discretization and selective manipulation. Herein, we report the design and development of a programmable droplet microfluidic platform for liquid sampling and selectively handling up to 32 individual droplets using 10 pneumatic signal inputs. The multiplexer system can logarithmically scale up capacity of the MDT array platform, making it possible to manipulate hundreds droplets.
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Saravanan S, Umesha V, Syed Ali M, Padmanabhan S. Exponential passivity for uncertain neural networks with time-varying delays based on weighted integral inequalities. Neurocomputing 2018. [DOI: 10.1016/j.neucom.2018.07.009] [Citation(s) in RCA: 3] [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: 10/28/2022]
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Fernández-Zapata J, Pérez-Castaño R, Aranda J, Colizzi F, Polanco MC, Orozco M, Padmanabhan S, Elías-Arnanz M. Plasticity in oligomerization, operator architecture, and DNA binding in the mode of action of a bacterial B 12-based photoreceptor. J Biol Chem 2018; 293:17888-17905. [PMID: 30262667 DOI: 10.1074/jbc.ra118.004838] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 07/12/2018] [Revised: 09/20/2018] [Indexed: 11/06/2022] Open
Abstract
Newly discovered bacterial photoreceptors called CarH sense light by using 5'-deoxyadenosylcobalamin (AdoCbl). They repress their own expression and that of genes for carotenoid synthesis by binding in the dark to operator DNA as AdoCbl-bound tetramers, whose light-induced disassembly relieves repression. High-resolution structures of Thermus thermophilus CarHTt have provided snapshots of the dark and light states and have revealed a unique DNA-binding mode whereby only three of four DNA-binding domains contact an operator comprising three tandem direct repeats. To gain further insights into CarH photoreceptors and employing biochemical, spectroscopic, mutational, and computational analyses, here we investigated CarHBm from Bacillus megaterium We found that apoCarHBm, unlike monomeric apoCarHTt, is an oligomeric molten globule that forms DNA-binding tetramers in the dark only upon AdoCbl binding, which requires a conserved W-X 9-EH motif. Light relieved DNA binding by disrupting CarHBm tetramers to dimers, rather than to monomers as with CarHTt CarHBm operators resembled that of CarHTt, but were larger by one repeat and overlapped with the -35 or -10 promoter elements. This design persisted in a six-repeat, multipartite operator we discovered upstream of a gene encoding an Spx global redox-response regulator whose photoregulated expression links photooxidative and general redox responses in B. megaterium Interestingly, CarHBm recognized the smaller CarHTt operator, revealing an adaptability possibly related to the linker bridging the DNA- and AdoCbl-binding domains. Our findings highlight a remarkable plasticity in the mode of action of B12-based CarH photoreceptors, important for their biological functions and development as optogenetic tools.
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Affiliation(s)
- Jesús Fernández-Zapata
- From the Instituto de Química Física "Rocasolano," Consejo Superior de Investigaciones Científicas, 28006 Madrid
| | - Ricardo Pérez-Castaño
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al Instituto de Química Física "Rocasolano," Consejo Superior de Investigaciones Científicas), Facultad de Biología, Universidad de Murcia, Murcia 30100
| | - Juan Aranda
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona; Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona
| | - Francesco Colizzi
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona; Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona
| | - María Carmen Polanco
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al Instituto de Química Física "Rocasolano," Consejo Superior de Investigaciones Científicas), Facultad de Biología, Universidad de Murcia, Murcia 30100
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona; Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona; Department of Biochemistry and Biomedicine, University of Barcelona, 08028 Barcelona, Spain
| | - S Padmanabhan
- From the Instituto de Química Física "Rocasolano," Consejo Superior de Investigaciones Científicas, 28006 Madrid.
| | - Montserrat Elías-Arnanz
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al Instituto de Química Física "Rocasolano," Consejo Superior de Investigaciones Científicas), Facultad de Biología, Universidad de Murcia, Murcia 30100.
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Sundarrajan S, Parambath S, Suresh S, Rao S, Padmanabhan S. Novel properties of recombinant Sso7d-Taq DNA polymerase purified using aqueous two-phase extraction: Utilities of the enzyme in viral diagnosis. Biotechnology Reports 2018; 19:e00270. [PMID: 30197870 PMCID: PMC6127375 DOI: 10.1016/j.btre.2018.e00270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 06/18/2018] [Accepted: 06/19/2018] [Indexed: 11/03/2022]
Abstract
Sso7d-Taq fusion protein purified using a single step of aqueous Two-Phase Extraction (ATPE) is >95% pure and is active. The S-Taq protein has higher thermostability and detergent tolerance over regular Taq polymerase and can be used for PCR's from direct whole blood. The PCR efficiency rate of S-Taq is higher than Taq polymerase and can be used to detect DNA viruses in a clinical setting efficiently. S-Taq can tolerate higher concentrations of magnesium ions and can be used for in-situ PCR’s. S-Taq can be used to carry out PCR’s of bacterial recombinants directly from the overnight culture since it is resistant to inhibition to Luria Bertani broth. This unique property of S-Taq will enable researchers to screen recombinants without the need to isolate the plasmid DNA of recombinants. This would be a huge cost savings for companies engaged in molecular biology research involving PCR’s.
Using Sso7d from Sulfolobus solfataricus as the DNA binding protein fused to Taq DNA polymerase at its amino terminus, we report the hyper-expression and a novel purification methodology of Sso7d-Taq polymerase (S-Taq) using aqueous two-phase extraction system followed by Ni-affinity chromatography. The utility of such a fusion enzyme in carrying out PCR of human genes from whole blood directly and in detecting hepatitis B virus from clinical samples is demonstrated in this article. We present data on the enhanced thermo-stability of S-Taq DNA polymerase over Taq DNA polymerase and also provide evidence of its higher stability with detergents in comparison to Taq polymerase. The purified S-Taq protein showed acceptable limits of host genomic DNA levels without the use of DNases and other DNA precipitating agents and shows promising potential for use in PCR based diagnostics, in-situ PCR’s and forensic science.
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Neduvat AC, Murthy PM, Sundarrajan S, Padmanabhan S. Use of coagulation factor XIII (F13) gene as an internal control for normalization of genomic DNA's for HLA typing. MethodsX 2018; 5:881-889. [PMID: 30151348 PMCID: PMC6107889 DOI: 10.1016/j.mex.2018.07.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 07/27/2018] [Indexed: 11/21/2022] Open
Abstract
Genomic DNA (gDNA) obtained from whole blood samples is a critical element for genomic research and clinical diagnosis. PCR efficiencies of the targeted genes like HLA-A, -B, -C, DPB1 and DRB1 using such isolated gDNAs were variable in spite of having similar amounts of gDNA taken for PCR. We addressed such PCR variabilities by normalizing the gDNA’s using an internal control of human coagulation factor XIII that was found to be variable with all samples and did not correlate with the observed A260 nm readings. The PCR and Q-PCR methodologies for the human coagulation factor XIII have been optimized, and the advantages of normalizing gDNA preparations based on F13 copy numbers have been discussed. This method will serve as a suitable choice to be used in laboratories and research centres, particularly when dealing with a large number of samples for the next-generation sequencing purposes, and in forensic labs with limited sample availability.
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Affiliation(s)
- Anupama Cheleri Neduvat
- Cancyte Technologies Pvt. Ltd, Rangadore Memorial Hospital, 1st Cross, Shankarapuram, Bangalore 560004, India
| | - Prerana Madhusudhana Murthy
- Cancyte Technologies Pvt. Ltd, Rangadore Memorial Hospital, 1st Cross, Shankarapuram, Bangalore 560004, India
| | - Sudarson Sundarrajan
- Cancyte Technologies Pvt. Ltd, Rangadore Memorial Hospital, 1st Cross, Shankarapuram, Bangalore 560004, India
| | - Sriram Padmanabhan
- Cancyte Technologies Pvt. Ltd, Rangadore Memorial Hospital, 1st Cross, Shankarapuram, Bangalore 560004, India
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Guzik B, McCallum L, Zmudka K, Jardine A, Guzik TJ, Dominiczak A, Padmanabhan S. P4783Arterial elastance predicts survival in low risk hypertensive patients. Eur Heart J 2018. [DOI: 10.1093/eurheartj/ehy563.p4783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- B Guzik
- Jagiellonian University, Medical Colledge, Department of Interventional Cardiology, Krakow, Poland
| | - L McCallum
- University of Glasgow, Institute of Cardiovascular and Medical Sciences, Glasgow, United Kingdom
| | - K Zmudka
- Jagiellonian University, Medical Colledge, Department of Interventional Cardiology, Krakow, Poland
| | - A Jardine
- University of Glasgow, Institute of Cardiovascular and Medical Sciences, Glasgow, United Kingdom
| | - T J Guzik
- University of Glasgow, Institute of Cardiovascular and Medical Sciences, Glasgow, United Kingdom
| | - A Dominiczak
- University of Glasgow, Institute of Cardiovascular and Medical Sciences, Glasgow, United Kingdom
| | - S Padmanabhan
- University of Glasgow, Institute of Cardiovascular and Medical Sciences, Glasgow, United Kingdom
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Guzik B, McCallum L, Zmudka K, Jardine A, Guzik TJ, Dominiczak A, Padmanabhan S. P2856Predictors of survival in hypertensive patients with left ventricle hypertrophy. Eur Heart J 2018. [DOI: 10.1093/eurheartj/ehy565.p2856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- B Guzik
- Jagiellonian University, Medical Colledge, Department of Interventional Cardiology, Krakow, Poland
| | - L McCallum
- University of Glasgow, Institute of Cardiovascular and Medical Sciences, Glasgow, United Kingdom
| | - K Zmudka
- Jagiellonian University, Medical Colledge, Department of Interventional Cardiology, Krakow, Poland
| | - A Jardine
- University of Glasgow, Institute of Cardiovascular and Medical Sciences, Glasgow, United Kingdom
| | - T J Guzik
- University of Glasgow, Institute of Cardiovascular and Medical Sciences, Glasgow, United Kingdom
| | - A Dominiczak
- University of Glasgow, Institute of Cardiovascular and Medical Sciences, Glasgow, United Kingdom
| | - S Padmanabhan
- University of Glasgow, Institute of Cardiovascular and Medical Sciences, Glasgow, United Kingdom
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Bernal-Bernal D, Abellón-Ruiz J, Iniesta AA, Pajares-Martínez E, Bastida-Martínez E, Fontes M, Padmanabhan S, Elías-Arnanz M. Multifactorial control of the expression of a CRISPR-Cas system by an extracytoplasmic function σ/anti-σ pair and a global regulatory complex. Nucleic Acids Res 2018. [PMID: 29893914 DOI: 10.1093/nar/gky475.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Expression of CRISPR-Cas systems is a prerequisite for their defensive role against invading genetic elements. Yet, much remains unknown about how this crucial step is regulated. We describe a new mechanism controlling CRISPR-cas expression, which requires an extracytoplasmic function (ECF) σ factor (DdvS), its membrane-bound anti-σ (DdvA) and a global regulatory complex (CarD-CarG). Transcriptomic analyses revealed that the DdvS/CarD/CarG-dependent regulon comprises a type III-B CRISPR-Cas system in Myxococcus xanthus. We mapped four DdvS-driven CarD/CarG-dependent promoters, with one lying immediately upstream of the cas cluster. Consistent with direct action, DdvS and CarD-CarG localize at these promoters in vivo. The cas genes are transcribed as a polycistronic mRNA that reads through the leader into the CRISPR array, a putative σA-dependent promoter in the leader having negligible activity in vivo. Consequently, expression of the entire CRISPR-Cas system and mature CRISPR-RNA (crRNA) production is DdvS/CarD/CarG-dependent. DdvA likely uses its large C-terminal domain to sense and transduce the extracytoplasmic signal triggering CRISPR-cas expression, which we show is not starvation-induced multicellular development. An ECF-σ/anti-σ pair and a global regulatory complex provide an effective mechanism to coordinate signal-sensing with production of precursor crRNA, its processing Cas6 endoribonuclease and other Cas proteins for mature crRNA biogenesis and interference.
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Affiliation(s)
- Diego Bernal-Bernal
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
| | - Javier Abellón-Ruiz
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
| | - Antonio A Iniesta
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
| | - Elena Pajares-Martínez
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
| | - Eva Bastida-Martínez
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
| | - Marta Fontes
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
| | - S Padmanabhan
- Instituto de Química Física 'Rocasolano', Consejo Superior de Investigaciones Científicas (IQFR-CSIC), Serrano 119, 28006 Madrid, Spain
| | - Montserrat Elías-Arnanz
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
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40
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Sundarrajan S, Rao S, Padmanabhan S. Cloning and high-level expression of Thermus thermophilus RecA in E. coli: purification and novel use in HBV diagnostics. Braz J Microbiol 2018; 49:848-855. [PMID: 29691193 PMCID: PMC6175717 DOI: 10.1016/j.bjm.2018.03.007] [Citation(s) in RCA: 2] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 03/08/2018] [Accepted: 03/13/2018] [Indexed: 11/25/2022] Open
Abstract
We studied the role of Thermus thermophilus Recombinase A (RecA) in enhancing the PCR signals of DNA viruses such as Hepatitis B virus (HBV). The RecA gene of a thermophilic eubacterial strain, T. thermophilus, was cloned and hyperexpressed in Escherichia coli. The recombinant RecA protein was purified using a single heat treatment step without the use of any chromatography steps, and the purified protein (>95%) was found to be active. The purified RecA could enhance the polymerase chain reaction (PCR) signals of HBV and improve the detection limit of the HBV diagnosis by real time PCR. The yield of recombinant RecA was ∼35mg/L, the highest yield reported for a recombinant RecA to date. RecA can be successfully employed to enhance detection sensitivity for the diagnosis of DNA viruses such as HBV, and this methodology could be particularly useful for clinical samples with HBV viral loads of less than 10IU/mL, which is interesting and novel.
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Affiliation(s)
- Sudarson Sundarrajan
- Cancyte Technologies Pvt. Ltd., Rangadore Memorial Hospital, Sri Shankara Research Center, Shankarapuram, Bangalore, India
| | - Sneha Rao
- Cancyte Technologies Pvt. Ltd., Rangadore Memorial Hospital, Sri Shankara Research Center, Shankarapuram, Bangalore, India
| | - Sriram Padmanabhan
- Cancyte Technologies Pvt. Ltd., Rangadore Memorial Hospital, Sri Shankara Research Center, Shankarapuram, Bangalore, India.
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Abstract
High quality and sufficient quantity of genomic DNA (gDNA) are the primary requisites of several molecular biologic applications, including clinical studies related to genetics, genomics, gene polymorphism, and DNA fingerprinting. Whole blood is the primary source of gDNA in most of the clinical investigations. Currently, commercial kits are primarily used to achieve these goals. However, the use of kits is limited by the cost and involvement of several centrifugal steps. Other methods reported are either laborious or do not produce high quality or quantity of gDNA or both. Here, we present the data on the development of a centrifugation-free, cost-effective, and user-friendly method for the isolation of human gDNA from the buffy coat of human blood that involves limited numbers of steps with about 15 min of hands-on time per sample.
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Affiliation(s)
- Goutam Mandal
- Cancyte Technologies Pvt. Ltd., Sri Shankara Research Center, Rangadore Memorial Hospital, Bangalore 560004, India
| | - Subhasish Das
- Cancyte Technologies Pvt. Ltd., Sri Shankara Research Center, Rangadore Memorial Hospital, Bangalore 560004, India
| | - Sriram Padmanabhan
- Cancyte Technologies Pvt. Ltd., Sri Shankara Research Center, Rangadore Memorial Hospital, Bangalore 560004, India
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Abstract
An innovative platform enabling complex discretization and manipulation of aqueous droplets is described. The system uses simple membrane displacement trap elements to perform multiple functions including droplet discretization, release, metering, capture, and merging. Multi-layer PDMS devices with membrane displacement trap arrays are used to discretize sample into nanoliter scale droplet volumes, and reliably manipulate individual droplets within the arrays. Performance is characterized for varying capillary number flows, membrane actuation pressures, trap and membrane geometries, and trapped droplet volumes, with operational domains established for each platform function. The novel approach to sample digitization and droplet manipulation is demonstrated through discretization of a dilute bacteria sample, metering of individual traps to generate droplets containing single bacteria, and merging of the resulting droplets to pair the selected bacteria within a single droplet.
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Affiliation(s)
- S Padmanabhan
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland, USA
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Roy A, Kumar P, Bhalla S, Jose A, Poulter N, Padmanabhan S, Prabhakaran D. P4550Building capacity for management of hypertension and its complications in developing country. Eur Heart J 2017. [DOI: 10.1093/eurheartj/ehx504.p4550] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Wigmore EM, Clarke TK, Howard DM, Adams MJ, Hall LS, Zeng Y, Gibson J, Davies G, Fernandez-Pujals AM, Thomson PA, Hayward C, Smith BH, Hocking LJ, Padmanabhan S, Deary IJ, Porteous DJ, Nicodemus KK, McIntosh AM. Do regional brain volumes and major depressive disorder share genetic architecture? A study of Generation Scotland (n=19 762), UK Biobank (n=24 048) and the English Longitudinal Study of Ageing (n=5766). Transl Psychiatry 2017; 7:e1205. [PMID: 28809859 PMCID: PMC5611720 DOI: 10.1038/tp.2017.148] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 05/08/2017] [Accepted: 06/07/2017] [Indexed: 12/23/2022] Open
Abstract
Major depressive disorder (MDD) is a heritable and highly debilitating condition. It is commonly associated with subcortical volumetric abnormalities, the most replicated of these being reduced hippocampal volume. Using the most recent published data from Enhancing Neuroimaging Genetics through Meta-analysis (ENIGMA) consortium's genome-wide association study of regional brain volume, we sought to test whether there is shared genetic architecture between seven subcortical brain volumes and intracranial volume (ICV) and MDD. We explored this using linkage disequilibrium score regression, polygenic risk scoring (PRS) techniques, Mendelian randomisation (MR) analysis and BUHMBOX. Utilising summary statistics from ENIGMA and Psychiatric Genomics Consortium, we demonstrated that hippocampal volume was positively genetically correlated with MDD (rG=0.46, P=0.02), although this did not survive multiple comparison testing. None of the other six brain regions studied were genetically correlated and amygdala volume heritability was too low for analysis. Using PRS analysis, no regional volumetric PRS demonstrated a significant association with MDD or recurrent MDD. MR analysis in hippocampal volume and MDD identified no causal association, however, BUHMBOX analysis identified genetic subgrouping in GS:SFHS MDD cases only (P=0.00281). In this study, we provide some evidence that hippocampal volume and MDD may share genetic architecture in a subgroup of individuals, albeit the genetic correlation did not survive multiple testing correction and genetic subgroup heterogeneity was not replicated. In contrast, we found no evidence to support a shared genetic architecture between MDD and other regional subcortical volumes or ICV.
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Affiliation(s)
- E M Wigmore
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK,Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh EH10 5HF, UK. E-mail:
| | - T-K Clarke
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - D M Howard
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - M J Adams
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - L S Hall
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Y Zeng
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - J Gibson
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - G Davies
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - A M Fernandez-Pujals
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - P A Thomson
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK,Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - C Hayward
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - B H Smith
- Division of Population Health Sciences, University of Dundee, Dundee, UK
| | - L J Hocking
- Division of Applied Medicine, University of Aberdeen, Aberdeen, UK
| | - S Padmanabhan
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - I J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK,Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - D J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - K K Nicodemus
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK,Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - A M McIntosh
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK,Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
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Abstract
Living organisms sense and respond to light, a crucial environmental factor, using photoreceptors, which rely on bound chromophores such as retinal, flavins, or linear tetrapyrroles for light sensing. The discovery of photoreceptors that sense light using 5'-deoxyadenosylcobalamin, a form of vitamin B12 that is best known as an enzyme cofactor, has expanded the number of known photoreceptor families and unveiled a new biological role of this vitamin. The prototype of these B12-dependent photoreceptors, the transcriptional repressor CarH, is widespread in bacteria and mediates light-dependent gene regulation in a photoprotective cellular response. CarH activity as a transcription factor relies on the modulation of its oligomeric state by 5'-deoxyadenosylcobalamin and light. This review surveys current knowledge about these B12-dependent photoreceptors, their distribution and mode of action, and the structural and photochemical basis of how they orchestrate signal transduction and control gene expression.
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Affiliation(s)
- S Padmanabhan
- Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain;
| | - Marco Jost
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158-2140;
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139;
| | - Montserrat Elías-Arnanz
- Departamento de Genética y Microbiología, Área de Genética, Unidad Asociada al Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain;
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46
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Mangesh VL, Padmanabhan S, Ganesan S, PrabhudevRahul D, Kumar Reddy TD. Prospects of pyrolysis oil from plastic waste as fuel for diesel engines: A review. ACTA ACUST UNITED AC 2017. [DOI: 10.1088/1757-899x/197/1/012027] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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47
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Rukshin V, Santos R, Gheorghiu M, Shah PK, Kar S, Padmanabhan S, Azarbal B, Tsang VT, Makkar R, Samuels B, Lepor N, Geft I, Tabak S, Khorsandhi M, Buchbinder N, Eigler N, Cercek B, Hodgson K, Kaul S. A Prospective, Nonrandomized, Open-Labeled Pilot Study Investigating the Use of Magnesium in Patients Undergoing Nonacute Percutaneous Coronary Intervention with Stent Implantation. J Cardiovasc Pharmacol Ther 2016; 8:193-200. [PMID: 14506544 DOI: 10.1177/107424840300800304] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background: Magnesium has recently been shown to inhibit acute stent thrombosis in animal models. This study tested the feasibility of magnesium administration in patients undergoing nonacute percutaneous coronary intervention with stent implantation. Methods: Twenty-one patients undergoing nonemergent percutaneous coronary intervention were enrolled and received intravenous magnesium sulfate (2-g bolus over 20 minutes prepercutaneous coronary intervention, followed by 14 g over 12 hours infusion). Endpoints: safety outcomes-hypotension, bradycardia, bleeding complications and heart block within first 24 hours; angiographic outcomes-acute thrombotic occlusion and need for platelet glycoprotein Ilb/Illa inhibitor bailout; and clinical outcomes-death, myocardial infarction, recurrent ischemia, and need for urgent revascularization at 48 hours and 30 days. Results: No significant effects on heart rate or blood pressure, major bleeding complication, or new electrocardiographic changes were observed. Angiographic thrombus was visualized in two cases, and coronary artery dissection in one case poststent deployment. None of these cases required the use of glycoprotein inhibitors for bailout. Death, myocardial infarction, recurrent ischemia, and need for urgent revascularization were not observed. The serum magnesium level increased from 2.1 ± 0.3 mg/dL at baseline to 3.5 ± 0.8 mg/dL at the end of the infusion (P < .0001). Platelet activation was significantly inhibited at the end of the magnesium sulfate infusion. Conclusion: Intravenous magnesium sulfate has been demonstrated as a feasible and safe agent in patients undergoing nonacute percutaneous coronary intervention with stent implantation. A randomized clinical trial comparing magnesium with glycoprotein inhibitors during percutaneous coronary intervention is warranted.
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Affiliation(s)
- Vladimir Rukshin
- Burns and Allen Research Institute, Department of Medicine, Cedars-Sinai Medical Center, and UCLA School of Medicine, Los Angeles, California, USA
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48
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Abstract
PURPOSE The UK Biobank is a large-scale biomedical resource, containing sociodemographic and medical information, including data on a previous diagnosis of stroke or transient ischaemic attack (TIA). We described these participants and their medication usage. PARTICIPANTS We identified participants who either self-reported or were identified from a nurse-led interview, having suffered a stroke or a TIA and compared them against participants without stroke ort TIA. We assessed their risk factor burden (sex, age, deprivation, waist to hip ratio (WHR), hypertension, smoking, alcohol intake, diabetes, physical exercise and oral contraception use (oral contraceptive pill, OCP)) and medication usage. FINDINGS TO DATE We studied 502,650 people (54.41% women), 6669 (1.23%) participants self-reported a stroke. The nurse-led interview identified 7669 (1.53%) people with stroke and 1781 (0.35%) with TIA. Hypertension, smoking, higher WHR, lower alcohol consumption and diabetes were all more common in people with cerebrovascular disease (p<0.0001 for each). Women with cerebrovascular disease were less likely to have taken the OCP (p=0.0002). People with cerebrovascular disease did more exercise (p=0.03). Antithrombotic medication was taken by 81% of people with stroke (both self-report and nurse-led responders) and 89% with TIA. For self-reported stroke, 63% were taking antithrombotic and cholesterol medications, 54% taking antithrombotic and antihypertensive medications and 46% taking all 3. For the nurse-led interview and TIA, these figures were 65%, 54% and 46%, and 70%, 53% and 45%, respectively. FUTURE PLANS The UK Biobank provides a large, generalisable and contemporary data source in a young population. The characterisation of the UK Biobank cohort with cerebrovascular disease will form the basis for ongoing research using this data source.
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Affiliation(s)
- J Hewitt
- Department of Geriatric Medicine, Division of Population Medicine, Cardiff University, Cardiff, UK
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - M Walters
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - S Padmanabhan
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - J Dawson
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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Clarke TK, Lupton MK, Fernandez-Pujals AM, Starr J, Davies G, Cox S, Pattie A, Liewald DC, Hall LS, MacIntyre DJ, Smith BH, Hocking LJ, Padmanabhan S, Thomson PA, Hayward C, Hansell NK, Montgomery GW, Medland SE, Martin NG, Wright MJ, Porteous DJ, Deary IJ, McIntosh AM. Common polygenic risk for autism spectrum disorder (ASD) is associated with cognitive ability in the general population. Mol Psychiatry 2016; 21:419-25. [PMID: 25754080 PMCID: PMC4759203 DOI: 10.1038/mp.2015.12] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 11/25/2014] [Accepted: 12/19/2014] [Indexed: 12/16/2022]
Abstract
Cognitive impairment is common among individuals diagnosed with autism spectrum disorder (ASD) and attention-deficit hyperactivity disorder (ADHD). It has been suggested that some aspects of intelligence are preserved or even superior in people with ASD compared with controls, but consistent evidence is lacking. Few studies have examined the genetic overlap between cognitive ability and ASD/ADHD. The aim of this study was to examine the polygenic overlap between ASD/ADHD and cognitive ability in individuals from the general population. Polygenic risk for ADHD and ASD was calculated from genome-wide association studies of ASD and ADHD conducted by the Psychiatric Genetics Consortium. Risk scores were created in three independent cohorts: Generation Scotland Scottish Family Health Study (GS:SFHS) (n=9863), the Lothian Birth Cohorts 1936 and 1921 (n=1522), and the Brisbane Adolescent Twin Sample (BATS) (n=921). We report that polygenic risk for ASD is positively correlated with general cognitive ability (beta=0.07, P=6 × 10(-7), r(2)=0.003), logical memory and verbal intelligence in GS:SFHS. This was replicated in BATS as a positive association with full-scale intelligent quotient (IQ) (beta=0.07, P=0.03, r(2)=0.005). We did not find consistent evidence that polygenic risk for ADHD was associated with cognitive function; however, a negative correlation with IQ at age 11 years (beta=-0.08, Z=-3.3, P=0.001) was observed in the Lothian Birth Cohorts. These findings are in individuals from the general population, suggesting that the relationship between genetic risk for ASD and intelligence is partly independent of clinical state. These data suggest that common genetic variation relevant for ASD influences general cognitive ability.
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Affiliation(s)
- T-K Clarke
- Division of Psychiatry, University of Edinburgh, Edinburgh, UK,Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh EH10 5HF, UK. E-mail:
| | - M K Lupton
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | - J Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - G Davies
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - S Cox
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - A Pattie
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - D C Liewald
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - L S Hall
- Division of Psychiatry, University of Edinburgh, Edinburgh, UK
| | - D J MacIntyre
- Division of Psychiatry, University of Edinburgh, Edinburgh, UK
| | - B H Smith
- Division of Applied Health Sciences, University of Aberdeen, Aberdeen, UK
| | - L J Hocking
- Division of Applied Health Sciences, University of Aberdeen, Aberdeen, UK
| | - S Padmanabhan
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - P A Thomson
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK,Division of Applied Health Sciences, University of Aberdeen, Aberdeen, UK,Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK,Medical Genetics Section, Molecular Medicine Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - C Hayward
- Medical Genetics Section, Molecular Medicine Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK,MRC Human Genetics, MRC IGMM, University of Edinburgh, Edinburgh, Scotland, UK
| | - N K Hansell
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - G W Montgomery
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - S E Medland
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - N G Martin
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - M J Wright
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - D J Porteous
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK,Division of Applied Health Sciences, University of Aberdeen, Aberdeen, UK,Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK,Medical Genetics Section, Molecular Medicine Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK,MRC Human Genetics, MRC IGMM, University of Edinburgh, Edinburgh, Scotland, UK,Centre for Genomics and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - I J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK,Division of Applied Health Sciences, University of Aberdeen, Aberdeen, UK,Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK,Medical Genetics Section, Molecular Medicine Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK,MRC Human Genetics, MRC IGMM, University of Edinburgh, Edinburgh, Scotland, UK,Centre for Genomics and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK,Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - A M McIntosh
- Division of Psychiatry, University of Edinburgh, Edinburgh, UK,Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
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50
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Goud A, Padmanabhan S. A rare form of cardiomyopathy: left ventricular non-compaction cardiomyopathy. J Community Hosp Intern Med Perspect 2016; 6:29888. [PMID: 26908378 PMCID: PMC4763555 DOI: 10.3402/jchimp.v6.29888] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Revised: 12/04/2015] [Accepted: 12/18/2015] [Indexed: 11/23/2022] Open
Abstract
Left ventricular non-compaction is a recently recognized, rare form of cardiomyopathy. It is based on the arrest of endomyocardial morphogenesis during embryogenesis. It was first described in 1984 by Engberding who described it as isolated ‘sinusoids’ within the LV. Right now its prevalence is estimated at 0.014 to 1.3 and 3–4% in heart failure patients. Its clinical manifestations are highly variable, ranging from no symptoms to disabling congestive heart failure, arrhythmias, and systemic thromboemboli. Doppler Echocardiogram is considered the diagnostic procedure of choice and treatment is symptomatic management of its symptoms and complications.
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Affiliation(s)
- Aditya Goud
- Department of Internal Medicine, MedStar Franklin Square Medical Center, Baltimore, MD, USA;
| | - Sriram Padmanabhan
- Department of Cardiology, MedStar Franklin Square Medical Center, Baltimore, MD, USA
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