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Yadav MK, Sarma P, Maharana J, Ganguly M, Mishra S, Zaidi N, Dalal A, Singh V, Saha S, Mahajan G, Sharma S, Chami M, Banerjee R, Shukla AK. Structure-guided engineering of biased-agonism in the human niacin receptor via single amino acid substitution. Nat Commun 2024; 15:1939. [PMID: 38431681 PMCID: PMC10908815 DOI: 10.1038/s41467-024-46239-2] [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: 07/31/2023] [Accepted: 02/18/2024] [Indexed: 03/05/2024] Open
Abstract
The Hydroxycarboxylic acid receptor 2 (HCA2), also known as the niacin receptor or GPR109A, is a prototypical GPCR that plays a central role in the inhibition of lipolytic and atherogenic activities. Its activation also results in vasodilation that is linked to the side-effect of flushing associated with dyslipidemia drugs such as niacin. GPR109A continues to be a target for developing potential therapeutics in dyslipidemia with minimized flushing response. Here, we present cryo-EM structures of the GPR109A in complex with dyslipidemia drugs, niacin or acipimox, non-flushing agonists, MK6892 or GSK256073, and recently approved psoriasis drug, monomethyl fumarate (MMF). These structures elucidate the binding mechanism of agonists, molecular basis of receptor activation, and insights into biased signaling elicited by some of the agonists. The structural framework also allows us to engineer receptor mutants that exhibit G-protein signaling bias, and therefore, our study may help in structure-guided drug discovery efforts targeting this receptor.
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Affiliation(s)
- Manish K Yadav
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Parishmita Sarma
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Jagannath Maharana
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Manisankar Ganguly
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Sudha Mishra
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Nashrah Zaidi
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Annu Dalal
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Vinay Singh
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Sayantan Saha
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Gargi Mahajan
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Saloni Sharma
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Mohamed Chami
- BioEM Lab, Biozentrum, Universität Basel, Basel, Switzerland
| | - Ramanuj Banerjee
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India.
| | - Arun K Shukla
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India.
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Maharana J, Sano FK, Sarma P, Yadav MK, Duan L, Stepniewski TM, Chaturvedi M, Ranjan A, Singh V, Saha S, Mahajan G, Chami M, Shihoya W, Selent J, Chung KY, Banerjee R, Nureki O, Shukla AK. Molecular insights into atypical modes of β-arrestin interaction with seven transmembrane receptors. Science 2024; 383:101-108. [PMID: 38175886 PMCID: PMC7615931 DOI: 10.1126/science.adj3347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 11/29/2023] [Indexed: 01/06/2024]
Abstract
β-arrestins (βarrs) are multifunctional proteins involved in signaling and regulation of seven transmembrane receptors (7TMRs), and their interaction is driven primarily by agonist-induced receptor activation and phosphorylation. Here, we present seven cryo-electron microscopy structures of βarrs either in the basal state, activated by the muscarinic receptor subtype 2 (M2R) through its third intracellular loop, or activated by the βarr-biased decoy D6 receptor (D6R). Combined with biochemical, cellular, and biophysical experiments, these structural snapshots allow the visualization of atypical engagement of βarrs with 7TMRs and also reveal a structural transition in the carboxyl terminus of βarr2 from a β strand to an α helix upon activation by D6R. Our study provides previously unanticipated molecular insights into the structural and functional diversity encoded in 7TMR-βarr complexes with direct implications for exploring novel therapeutic avenues.
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Affiliation(s)
- Jagannath Maharana
- Department of Biological Sciences, Indian Institute of Technology Kanpur, Kanpur, India
| | - Fumiya K. Sano
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Parishmita Sarma
- Department of Biological Sciences, Indian Institute of Technology Kanpur, Kanpur, India
| | - Manish K. Yadav
- Department of Biological Sciences, Indian Institute of Technology Kanpur, Kanpur, India
| | - Longhan Duan
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Tomasz M. Stepniewski
- Research Program on Biomedical Informatics, Hospital del Mar Research Institute and Pompeu Fabra University, Barcelona, Spain
| | - Madhu Chaturvedi
- Department of Biological Sciences, Indian Institute of Technology Kanpur, Kanpur, India
| | - Ashutosh Ranjan
- Department of Biological Sciences, Indian Institute of Technology Kanpur, Kanpur, India
| | - Vinay Singh
- Department of Biological Sciences, Indian Institute of Technology Kanpur, Kanpur, India
| | - Sayantan Saha
- Department of Biological Sciences, Indian Institute of Technology Kanpur, Kanpur, India
| | - Gargi Mahajan
- Department of Biological Sciences, Indian Institute of Technology Kanpur, Kanpur, India
| | - Mohamed Chami
- BioEM Lab, Biozentrum, University of Basel, Basel, Switzerland
| | - Wataru Shihoya
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Jana Selent
- Research Program on Biomedical Informatics, Hospital del Mar Research Institute and Pompeu Fabra University, Barcelona, Spain
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Ramanuj Banerjee
- Department of Biological Sciences, Indian Institute of Technology Kanpur, Kanpur, India
| | - Osamu Nureki
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Arun K. Shukla
- Department of Biological Sciences, Indian Institute of Technology Kanpur, Kanpur, India
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Shankar BA, Vaishali, Yadav MK, Kumar M, Burman V. Differential gene expression analysis under salinity stress in the selected turmeric (Curcuma longa L.) cultivars for curcuminoid biosynthesis. Mol Biol Rep 2023; 50:9745-9753. [PMID: 37658929 DOI: 10.1007/s11033-023-08719-4] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 07/28/2023] [Indexed: 09/05/2023]
Abstract
BACKGROUND Curcuminoids are the phenolic compounds found exclusively in turmeric. Their presence is known to increase immunity and resistance against certain cancers and neurological disorders in humans also, protecting the plant itself against salinity stress. METHODS In this experiment, we studied the expression levels of MAPK1 and DCS genes, their curcuminoid biosynthesis under salinity stress conditions so that the impact of individual genes can be understood using semi- quantitative PCR. RESULTS The expressions of the genes with respect to curcuminoid biosynthesis showed fluctuations in their band intensity values due to the production of curcuminoids, which is initiated first in the leaves followed by the rhizomes. Not all the genes responsible for the curcuminoid biosynthesis show positive regulation under salt stress conditions which is observed in response to the severity of the stress imposed on the cultivars. CONCLUSIONS In our findings, both the genes MAPK1 and DCS were down-regulated for curcuminoid biosynthesis compared to their controls in both the cultivars Vallabh Sharad and Selection 1.
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Affiliation(s)
- Bandi Arpitha Shankar
- Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, Uttar Pradesh, India.
| | - Vaishali
- Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, Uttar Pradesh, India
| | - M K Yadav
- Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, Uttar Pradesh, India
| | - Mukesh Kumar
- Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, Uttar Pradesh, India
| | - Vishakha Burman
- Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, Uttar Pradesh, India
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Shankar BA, Vaishali, Yadav MK, Kumar M, Burman V. Correction: Differential gene expression analysis under salinity stress in the selected turmeric (Curcuma longa L.) cultivars for curcuminoid biosynthesis. Mol Biol Rep 2023; 50:9755. [PMID: 37947965 DOI: 10.1007/s11033-023-08907-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Affiliation(s)
- Bandi Arpitha Shankar
- Sardar Vallabhbhai Patel University of Agriculture and Technology,, Meerut, Uttar Pradesh, India.
| | - Vaishali
- Sardar Vallabhbhai Patel University of Agriculture and Technology,, Meerut, Uttar Pradesh, India
| | - M K Yadav
- Sardar Vallabhbhai Patel University of Agriculture and Technology,, Meerut, Uttar Pradesh, India
| | - Mukesh Kumar
- Sardar Vallabhbhai Patel University of Agriculture and Technology,, Meerut, Uttar Pradesh, India
| | - Vishakha Burman
- Sardar Vallabhbhai Patel University of Agriculture and Technology,, Meerut, Uttar Pradesh, India
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Yadav MK, Maharana J, Yadav R, Saha S, Sarma P, Soni C, Singh V, Saha S, Ganguly M, Li XX, Mohapatra S, Mishra S, Khant HA, Chami M, Woodruff TM, Banerjee R, Shukla AK, Gati C. Molecular basis of anaphylatoxin binding, activation, and signaling bias at complement receptors. Cell 2023; 186:4956-4973.e21. [PMID: 37852260 PMCID: PMC7615941 DOI: 10.1016/j.cell.2023.09.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 07/19/2023] [Accepted: 09/20/2023] [Indexed: 10/20/2023]
Abstract
The complement system is a critical part of our innate immune response, and the terminal products of this cascade, anaphylatoxins C3a and C5a, exert their physiological and pathophysiological responses primarily via two GPCRs, C3aR and C5aR1. However, the molecular mechanism of ligand recognition, activation, and signaling bias of these receptors remains mostly elusive. Here, we present nine cryo-EM structures of C3aR and C5aR1 activated by their natural and synthetic agonists, which reveal distinct binding pocket topologies of complement anaphylatoxins and provide key insights into receptor activation and transducer coupling. We also uncover the structural basis of a naturally occurring mechanism to dampen the inflammatory response of C5a via proteolytic cleavage of the terminal arginine and the G-protein signaling bias elicited by a peptide agonist of C3aR identified here. In summary, our study elucidates the innerworkings of the complement anaphylatoxin receptors and should facilitate structure-guided drug discovery to target these receptors in a spectrum of disorders.
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Affiliation(s)
- Manish K Yadav
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Jagannath Maharana
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Ravi Yadav
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA; The Bridge Institute, Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA
| | - Shirsha Saha
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Parishmita Sarma
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Chahat Soni
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Vinay Singh
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Sayantan Saha
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Manisankar Ganguly
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Xaria X Li
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Samanwita Mohapatra
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Sudha Mishra
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Htet A Khant
- USC Center of Excellence for Nano-Imaging, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA
| | - Mohamed Chami
- BioEM Lab, Biozentrum, Universität Basel, Basel, Switzerland
| | - Trent M Woodruff
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Ramanuj Banerjee
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India.
| | - Arun K Shukla
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India.
| | - Cornelius Gati
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA; The Bridge Institute, Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA; Department of Chemistry, Department of Quantitative and Computational Biology, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA.
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6
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Khan MM, Azad AK, Yadav MK, Ahmedullah AK, Hasan MM, Sajib MK, Shabnam N, Islam MN. Digital Gangrene is a Rare Presentation of Takayasu's Arteritis. Mymensingh Med J 2023; 32:1208-1213. [PMID: 37777923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/02/2023]
Abstract
Takayasu's arteritis is a chronic large vessel vasculitis that mainly affects the aorta and its major branches such as brachiocephalic, carotid, subclavian, vertebral, renal, coronary and pulmonary arteries. It most commonly occurs in female at child bearing age and female to male ratio is 8:2. Initial presentations of Takayasu's arteritis may be nonspecific like fever, malaise, weakness, fatigue, arthralgia, myalgia and weight loss but in advanced stage there may be features of vascular inflammation like segmental stenosis, occlusion, dilatation and/or aneurysm. It is a sub acute process over months to years and usually with good collateral formation. So, critical limb ischemia due to acute onset of vascular stenosis is very rare. Here we are reporting a case of a 50-year- old male patient who presented with digital gangrene due to critical limb ischemia. Though the age of onset was at 50 years and the patient lacks clinical features like constitutional symptoms, bruit, claudication, asymmetrical blood pressure, the patient was diagnosed as a case of Takayasus's arteritis. The patient dramatically improved with oral glucocorticoid treatment. Although rare, takayasu's arteritis can presents only with digital gangrene without having other clinical features. The physicians should be aware of this unusual but limb threatening presentation and more studies are needed to find out the exact mechanism of this presentation.
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Affiliation(s)
- M M Khan
- Dr Mohammad Mamun Khan, Resident, Department of Rheumatology, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh; E-mail:
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7
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Maharana J, Sarma P, Yadav MK, Saha S, Singh V, Saha S, Chami M, Banerjee R, Shukla AK. Structural snapshots uncover a key phosphorylation motif in GPCRs driving β-arrestin activation. Mol Cell 2023; 83:2091-2107.e7. [PMID: 37209686 PMCID: PMC7615930 DOI: 10.1016/j.molcel.2023.04.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [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: 10/10/2022] [Revised: 02/22/2023] [Accepted: 04/26/2023] [Indexed: 05/22/2023]
Abstract
Agonist-induced GPCR phosphorylation is a key determinant for the binding and activation of β-arrestins (βarrs). However, it is not entirely clear how different GPCRs harboring divergent phosphorylation patterns impart converging active conformation on βarrs leading to broadly conserved functional responses such as desensitization, endocytosis, and signaling. Here, we present multiple cryo-EM structures of activated βarrs in complex with distinct phosphorylation patterns derived from the carboxyl terminus of different GPCRs. These structures help identify a P-X-P-P type phosphorylation motif in GPCRs that interacts with a spatially organized K-K-R-R-K-K sequence in the N-domain of βarrs. Sequence analysis of the human GPCRome reveals the presence of this phosphorylation pattern in a large number of receptors, and its contribution in βarr activation is demonstrated by targeted mutagenesis experiments combined with an intrabody-based conformational sensor. Taken together, our findings provide important structural insights into the ability of distinct GPCRs to activate βarrs through a significantly conserved mechanism.
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Affiliation(s)
- Jagannath Maharana
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Parishmita Sarma
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Manish K Yadav
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Sayantan Saha
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Vinay Singh
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Shirsha Saha
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Mohamed Chami
- BioEM Lab, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Ramanuj Banerjee
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India.
| | - Arun K Shukla
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India.
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8
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Abstract
The two isoforms of β-arrestins namely β-arrestin 1 and 2 interact with, and regulate a broad repertoire of G protein-coupled receptors (GPCRs). While several protocols have been described in the literature for purification of β-arrestins for biochemical and biophysical studies, some of these protocols involve multiple complicated steps that prolong the process and yield relatively smaller amounts of purified proteins. Here, we describe a simplified and streamlined protocol for expression and purification of β-arrestins using E. coli as an expression host. This protocol is based on N-terminal fusion of GST tag and involves a two-step protocol involving GST-based affinity chromatography and size exclusion chromatography. The protocol described here yields sufficient amounts of high-quality purified β-arrestins suitable for biochemical and structural studies.
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Affiliation(s)
- Manish K Yadav
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, India
| | - Vinay Singh
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, India
| | - Sayantan Saha
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, India
| | - Arun K Shukla
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, India.
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9
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Mehta K, Lee J, Mesic A, Yadav MK, Shrestha R, Poudel K, Gyawali P, Pham TN, Rai S, Stewart BT, Nakarmi KK. 38 Utilizing an Implementation Science Framework to Design a Burn Resuscitation Bundle in a Resource-limited Setting. Journal of Burn Care & Research 2022. [PMCID: PMC8945673 DOI: 10.1093/jbcr/irac012.041] [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] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Introduction
Protocolized burn resuscitation algorithms with hourly, closed loop feedback, have reduced instances of over- and under-resuscitation and improved outcomes in high income countries. However, a “know-do” gap exists as this practice has yet to be adopted in many low- and middle-income countries (LMIC). We aimed to describe the change management process of the development and implementation of a contextually driven protocolized burn resuscitation bundle at a tertiary burn center in an LMIC using an implementation science framework.
Methods
We applied strategies from the Expert Recommendations for Implementing Change (ERIC) for the design and implementation of a burn resuscitation bundle at a major burn center in an LMIC, over a 9-month period. Semi-structured focus group discussions (FGD) were conducted with stakeholders to understand facilitators and barriers to developing and using the protocol, with iterative feedback used to inform and adjust the protocol and documentation tools. Responses were analyzed using content analysis and particularly unique and useful responses were highlighted.
Results
Stakeholders identified resource constraint-related concerns about the feasibility of an hourly IV resuscitation protocol and reached consensus on performing 2-hourly assessments and fluid adjustments. Corresponding documentation tools were developed and iteratively adjusted. Several initial barriers to adoption and institutionalization were encountered. ERIC strategies used to promote intervention uptake included simplification and visualization of the protocol, identification of a project champion, development of educational materials for multiple cadres (e.g., nurses, physicians, health assistants), use of chain of command to enable change and accountability, utilizing institutional branding and ultimately obtaining endorsement by the center’s leadership (Table 1). Post-implementation FGD with stakeholders revealed high levels of acceptance, utilization and adherence of the protocol bundle, with occasional opportunities for improvement identified in protocol completeness and accuracy.
Conclusions
Adoption of change in clinical resuscitation practice in a resource-constrained setting required a contextually driven, multi-faceted approach led by a team of change champions and leaders. The ERIC framework allowed for an iterative approach to prioritize stakeholder engagement and feedback, in order to implement a protocolized IV resuscitation bundle in a LMIC.
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Affiliation(s)
- Kajal Mehta
- University of Washington, Seattle, Washington; Kirtipur Hospital, Kathmandu, Bagmati; University of Washington, Seattle, Washington; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; University of Washington, Seattle, Washington; Kirtipur Ho
| | - Joohee Lee
- University of Washington, Seattle, Washington; Kirtipur Hospital, Kathmandu, Bagmati; University of Washington, Seattle, Washington; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; University of Washington, Seattle, Washington; Kirtipur Ho
| | - Aldina Mesic
- University of Washington, Seattle, Washington; Kirtipur Hospital, Kathmandu, Bagmati; University of Washington, Seattle, Washington; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; University of Washington, Seattle, Washington; Kirtipur Ho
| | - Manish K Yadav
- University of Washington, Seattle, Washington; Kirtipur Hospital, Kathmandu, Bagmati; University of Washington, Seattle, Washington; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; University of Washington, Seattle, Washington; Kirtipur Ho
| | - Raslina Shrestha
- University of Washington, Seattle, Washington; Kirtipur Hospital, Kathmandu, Bagmati; University of Washington, Seattle, Washington; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; University of Washington, Seattle, Washington; Kirtipur Ho
| | - Kiran Poudel
- University of Washington, Seattle, Washington; Kirtipur Hospital, Kathmandu, Bagmati; University of Washington, Seattle, Washington; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; University of Washington, Seattle, Washington; Kirtipur Ho
| | - Prakriti Gyawali
- University of Washington, Seattle, Washington; Kirtipur Hospital, Kathmandu, Bagmati; University of Washington, Seattle, Washington; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; University of Washington, Seattle, Washington; Kirtipur Ho
| | - Tam N Pham
- University of Washington, Seattle, Washington; Kirtipur Hospital, Kathmandu, Bagmati; University of Washington, Seattle, Washington; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; University of Washington, Seattle, Washington; Kirtipur Ho
| | - Shankar Rai
- University of Washington, Seattle, Washington; Kirtipur Hospital, Kathmandu, Bagmati; University of Washington, Seattle, Washington; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; University of Washington, Seattle, Washington; Kirtipur Ho
| | - Barclay T Stewart
- University of Washington, Seattle, Washington; Kirtipur Hospital, Kathmandu, Bagmati; University of Washington, Seattle, Washington; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; University of Washington, Seattle, Washington; Kirtipur Ho
| | - Kiran K Nakarmi
- University of Washington, Seattle, Washington; Kirtipur Hospital, Kathmandu, Bagmati; University of Washington, Seattle, Washington; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; Kirtipur Hospital, Phect-Nepal, Kathmandu, Bagmati; University of Washington, Seattle, Washington; Kirtipur Ho
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Sharanabasav H, Pramesh D, Prasannakumar MK, Chidanandappa E, Yadav MK, Ngangkham U, Parivallal B, Raghavendra BT, Manjunatha C, Sharma SK, Karthik N. Morpho-molecular and mating-type locus diversity of Ustilaginoidea virens: an incitant of false smut of rice from Southern parts of India. J Appl Microbiol 2021; 131:2372-2386. [PMID: 33772985 DOI: 10.1111/jam.15087] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/17/2021] [Accepted: 03/21/2021] [Indexed: 11/30/2022]
Abstract
AIMS To characterize the geo-distinct isolates of Ustilaginoidea virens for morpho-molecular and mating-type locus diversity. METHODS AND RESULTS Sixty-one isolates of U. virens collected from Southern India exhibited significant diversity in mycelial width (3·45-5·50 µm), colony colour (yellow, pale yellow, and white), and growth pattern (thick leather mat, raised-fluffy, flat-fluffy, and raised). Field-borne chlamydospores of each isolate were significantly smaller in size (3·34-5·26 µm2 ) compared to those formed on culture media (18·6-100·89 µm2 ). The phylogenetic study based on internal transcribed sequences revealed two clusters; however, most isolates (n = 54) were grouped in cluster-I, indicating common ancestral origin. We also identified 42 haplotypes; among them, Hap_3 has the highest number of isolates (n = 19). Mating-type locus (MAT1) analysis revealed all sixty-one isolates as heterothallic, wherein 37 and 24 isolates belonging to MAT1-1-1 and MAT1-2-1 heterothallic mating types, respectively. The microsynteny analysis of MAT1 loci of one of the Indian strain (Uv-Gvt) along with Uv-8b (China) strain revealed synteny conservation at MAT1 locus, which is flanked by conserved genes SLA2 and a hypothetical protein in the upstream and APN2, COX12 and APC5 in the downstream of the locus. CONCLUSIONS Morpho-molecular study revealed the significant diversity among geo-distinct isolates, and MAT1 loci analysis indicated the distribution of heterothallic mating types in south Indian paddy fields. And also, complete synteny conservation between Indian and Chinese strain was observed at the MAT1 locus. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first report describing the sexuality of Indian strains of the U. virens, which would help better understand the genetic diversity of the U. virens prevailing in Southern India and aid in developing resistant rice cultivars against this pathogen population.
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Affiliation(s)
- H Sharanabasav
- Rice Pathology Laboratory, All India Coordinated Rice Improvement Programme, University of Agricultural Sciences, Raichur, India
| | - D Pramesh
- Rice Pathology Laboratory, All India Coordinated Rice Improvement Programme, University of Agricultural Sciences, Raichur, India
| | - M K Prasannakumar
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore, India
| | - E Chidanandappa
- Rice Pathology Laboratory, All India Coordinated Rice Improvement Programme, University of Agricultural Sciences, Raichur, India
| | - M K Yadav
- ICAR-National Rice Research Institute, Cuttack, India
| | - U Ngangkham
- ICAR-Research Complex for NEH Region Umia, Meghalaya, India
| | - B Parivallal
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore, India
| | - B T Raghavendra
- Department of Plant Pathology, University of Agricultural Sciences, Raichur, India
| | - C Manjunatha
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington, India
| | - S K Sharma
- ICAR-Research Complex for NEH Region, Imphal Center, Manipur, India
| | - N Karthik
- University of Madras, Chennai, India
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Das D, Yadav MK, Singla L, Kumar A, Karanam M, Dev S, Choudhury AR. Understanding of the Kinetic Stability of
cis‐
Isomer of Azobenzenes through Kinetic and Computational Studies. ChemistrySelect 2020. [DOI: 10.1002/slct.202003275] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Dhiraj Das
- Department of Chemical Sciences Indian Institute of Science Education and Research Mohali, Sector 81, S. A. S. Nagar 140306 Punjab India
| | - Manish K. Yadav
- Department of Chemical Sciences Indian Institute of Science Education and Research Mohali, Sector 81, S. A. S. Nagar 140306 Punjab India
| | - Labhini Singla
- Department of Chemical Sciences Indian Institute of Science Education and Research Mohali, Sector 81, S. A. S. Nagar 140306 Punjab India
| | - Atul Kumar
- Deptartment of Chemistry & Centre of Advanced Studies in Chemistry Panjab University Chandigarh, UT 160014 India
| | - Maheswararao Karanam
- Department of Chemical Sciences Indian Institute of Science Education and Research Mohali, Sector 81, S. A. S. Nagar 140306 Punjab India
| | - Sagarika Dev
- Department of Chemistry MCM DAV College for Women, Sector 36 Chandigarh, Union Territory India. 160036
| | - Angshuman R. Choudhury
- Department of Chemical Sciences Indian Institute of Science Education and Research Mohali, Sector 81, S. A. S. Nagar 140306 Punjab India
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Sood N, Pradhan PK, Verma DK, Yadav MK, Dev AK, Swaminathan TR, Sood NK. Candidatus Actinochlamydia pangasiae sp. nov. (Chlamydiales, Actinochlamydiaceae), a bacterium associated with epitheliocystis in Pangasianodon hypophthalmus. J Fish Dis 2018; 41:281-290. [PMID: 28940578 DOI: 10.1111/jfd.12711] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 08/01/2017] [Accepted: 08/02/2017] [Indexed: 06/07/2023]
Abstract
Chlamydial infections are recognised as causative agent of epitheliocystis, reported from over 90 fish species. In the present study, the farmed striped catfish Pangasianodon hypophthalmus (14-15 cm, 70-90 g) with a history of cumulative mortality of about 23% during June and July 2015, were brought to the laboratory. The histopathological examination of gills from the affected fish revealed presence of granular basophilic intracellular inclusions, mostly at the base of the interlamellar region and in gill filaments. A concurrent infection with Trichodina spp., Ichthyobodo spp. and Dactylogyrus spp. was observed in the gills. The presence of chlamydial DNA in the gills of affected fish was confirmed by amplification and sequencing of 16S rRNA gene. BLAST-n analysis of these amplicons revealed maximum similarity (96%) with Candidatus Actinochlamydia clariae. On the basis of phylogenetic analysis, it was inferred that the epitheliocystis agents from striped catfish were novel and belonged to the taxon Ca. Actinochlamydia. It is proposed that epitheliocystis agents from striped catfish will be named as Ca. Actinochlamydia pangasiae. The 16S rRNA gene amplicons from novel chlamydiae were labelled and linked to inclusions by in situ hybridisation. This is the first report of epitheliocystis from India in a new fish host P. hypophthalmus.
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Affiliation(s)
- N Sood
- ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh, India
| | - P K Pradhan
- ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh, India
| | - D K Verma
- ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh, India
| | - M K Yadav
- ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh, India
| | - A K Dev
- ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh, India
| | - T R Swaminathan
- Peninsular and Marine Fish Genetic Resources Centre, ICAR-NBFGR, Kochi, Kerala
| | - N K Sood
- Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
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13
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Yadav MK, Manoli NM, Vimalraj S, Madhunapantula SV. Unmethylated promoter DNA correlates with p53 expression and apoptotic levels only in Vitamin B9 and B12 deficient megaloblastic anemia but not in non-megaloblastic anemia controls. Int J Biol Macromol 2017; 109:76-84. [PMID: 29246873 DOI: 10.1016/j.ijbiomac.2017.12.070] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 12/08/2017] [Accepted: 12/11/2017] [Indexed: 12/12/2022]
Abstract
Cyanocobalamin (Vitamin B12, VB12) and Folic acid (Vitamin B9, VB9) deficiency leads to anemia in women. We have recently shown low VB12 and VB9 levels in the serum of megaloblastic anemia (MBA) patients. Further, our study demonstrated elevated homocysteine and p53, respectively, in the serum and bone marrow aspirates of MBA patients but not in non-MBA subjects. However, it is unknown whether any gender specific variation in VB12 and VB9 level exists in MBA and non-MBA patients? In addition, it is unclear whether low VB12 and VB9 has a role in the regulation of p53 expression in MBA patients? And whether elevated p53 is functionally active? If so, does bone marrow aspirates of MBA patients show elevated apoptosis. Hence, we have analyzed VB12 and VB9 levels in MBA patients and compared with non-MBA subjects. Next, methylation status of p53 promoter was determined and correlated with p53 expression. Furthermore, the level of apoptosis in bone marrow aspirate paraffin blocks was estimated using TUNEL staining. In conclusion, low VB12 and VB9 in male and female patients directly correlate with p53 promoter unmethylation status, but, inversely correlate with p53 protein expression and its activity, only in MBA cases but not in non-MBA controls.
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Affiliation(s)
- Manish K Yadav
- Center of Excellence in Molecular Biology and Regenerative Medicine (CEMR), Department of Biochemistry, JSS Medical College, Jagadguru Sri Shivarathreeshwara University (Accredited "A" Grade by NAAC and Ranked 45 by National Institutional Ranking Framework (NIRF)-2016, Ministry of Human Resource Development, Government of India), Mysuru, 570015, Karnataka, India
| | - Nandini M Manoli
- Department of Pathology, JSS Medical College, Jagadguru Sri Shivarathreeshwara University (Accredited "A" Grade by NAAC and Ranked 45 by National Institutional Ranking Framework (NIRF)-2016, Ministry of Human Resource Development, Government of India), Mysuru, 570015, Karnataka, India
| | - Selvaraj Vimalraj
- Vascular Biology Lab, AU-KBC Research Centre, MIT campus, Anna University, Chennai, 600044, Tamil Nadu, India.
| | - SubbaRao V Madhunapantula
- Center of Excellence in Molecular Biology and Regenerative Medicine (CEMR), Department of Biochemistry, JSS Medical College, Jagadguru Sri Shivarathreeshwara University (Accredited "A" Grade by NAAC and Ranked 45 by National Institutional Ranking Framework (NIRF)-2016, Ministry of Human Resource Development, Government of India), Mysuru, 570015, Karnataka, India.
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Yadav MK, Manoli NM, Madhunapantula SV. Comparative Assessment of Vitamin-B12, Folic Acid and Homocysteine Levels in Relation to p53 Expression in Megaloblastic Anemia. PLoS One 2016; 11:e0164559. [PMID: 27780269 PMCID: PMC5079580 DOI: 10.1371/journal.pone.0164559] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [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: 09/01/2016] [Accepted: 09/09/2016] [Indexed: 01/03/2023] Open
Abstract
Background Megaloblastic anemia (MBA), also known as macrocytic anemia, is a type of anemia characterized by decreased number of RBCs as well as the presence of unusually large, abnormal and poorly developed erythrocytes (megaloblasts), which fail to enter blood circulation due to their larger size. Lack of vitamin-B12 (VB12) and / or folate (Vitamin-B9, VB9) with elevated homocysteine is the key factor responsible for megaloblastic anemia. Prior studies have demonstrated the induction of apoptosis in these abnormal under-developed erythrocytes. However, it is not clear whether this apoptosis induction is due to elevated p53 level or due to any other mechanism. Furthermore, it is also not fully known whether decreased vitamin-B12 and / or folate are responsible for apoptosis induction mediated by p53 in pre-erythroblasts. Methods Levels of serum VB9, VB12 and homocysteine in 50 patients suffering from MBA were compared with 50 non-megaloblastic anemia control subjects, who were referred by the clinicians for bone marrow examination for medical conditions other than MBA. Next, we have measured the p53 expression in the paraffin embedded blocks prepared from bone marrow biopsy, using immunohistochemistry, and the expression levels correlated with VB9 and VB12 levels. Results Out of 50 MBA patients 40 (80%) and 44 (88%) subjects had very low VB12 and VB9 levels respectively. In contrast, only 2 (4%) and 12 (24%) non-megaloblastic anemia controls, out of 50 subjects, had low VB12 and VB9 respectively. Correlating with low vitamin B9 and B12, the homocysteine levels were high in 80% cases. But, only 20% non-megaloblastic controls exhibited high homocysteine in plasma. Immunohistochemical analysis for p53 expression showed a significantly high level of expression in MBA cases and no—or very low—expression in control subjects. Our correlation studies comparing the VB12 and VB9 levels with p53 expression concludes unusually high p53 levels in patients suffering from VB12 and VB9 deficiency induced MBA compared to control subjects not suffering from MBA. Conclusion Tumor protein p53 is the key protein expressed heavily in the bone marrow biopsies of patients suffering from VB12 and VB9 deficiency induced MBA but not in control subjects. Hence, p53 expression could be used as a surrogate marker for confirming the VB9 and VB12 induced MBA.
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Affiliation(s)
- Manish K Yadav
- Department of Pathology, JSS Medical College, JSS University, Mysuru - 570015, Karnataka, India
| | - Nandini M Manoli
- Department of Pathology, JSS Medical College, JSS University, Mysuru - 570015, Karnataka, India
| | - SubbaRao V Madhunapantula
- Center of Excellence in Molecular Biology and Regenerative Medicine (CEMR), Department of Biochemistry, JSS Medical College, JSS University, Mysuru - 570015, Karnataka, India
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15
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Malviya N, Gupta S, Singh VK, Yadav MK, Bisht NC, Sarangi BK, Yadav D. Genome wide in silico characterization of Dof gene families of pigeonpea (Cajanus cajan (L) Millsp.). Mol Biol Rep 2014; 42:535-52. [PMID: 25344821 DOI: 10.1007/s11033-014-3797-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Accepted: 10/14/2014] [Indexed: 11/24/2022]
Abstract
The DNA binding with One Finger (Dof) protein is a plant specific transcription factor involved in the regulation of wide range of processes. The analysis of whole genome sequence of pigeonpea has identified 38 putative Dof genes (CcDof) distributed on 8 chromosomes. A total of 17 out of 38 CcDof genes were found to be intronless. A comprehensive in silico characterization of CcDof gene family including the gene structure, chromosome location, protein motif, phylogeny, gene duplication and functional divergence has been attempted. The phylogenetic analysis resulted in 3 major clusters with closely related members in phylogenetic tree revealed common motif distribution. The in silico cis-regulatory element analysis revealed functional diversity with predominance of light responsive and stress responsive elements indicating the possibility of these CcDof genes to be associated with photoperiodic control and biotic and abiotic stress. The duplication pattern showed that tandem duplication is predominant over segmental duplication events. The comparative phylogenetic analysis of these Dof proteins along with 78 soybean, 36 Arabidopsis and 30 rice Dof proteins revealed 7 major clusters. Several groups of orthologs and paralogs were identified based on phylogenetic tree constructed. Our study provides useful information for functional characterization of CcDof genes.
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Affiliation(s)
- N Malviya
- Department of Biotechnology, D.D.U. Gorakhpur University, Gorakhpur, 273 009, Uttar Pradesh, India
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Tacchi S, Grånäs O, Stollo A, Madami M, Gubbiotti G, Carlotti G, Marangolo M, Eddrief M, Etgens VH, Yadav MK, Nordström L, Sanyal B. Epitaxial Fe films on ZnSe(001): effect of the substrate surface reconstruction on the magnetic anisotropy. J Phys Condens Matter 2012; 24:236006. [PMID: 22576333 DOI: 10.1088/0953-8984/24/23/236006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
It is well known that Fe films deposited on a c(2 × 2)-reconstructed ZnSe(001) surface show a strong in-plane uniaxial magnetic anisotropy. Here, the effect of the substrate reconstruction on the magnetic anisotropy of Fe has been studied by in situ Brillouin light scattering. We found that the in-plane uniaxial anisotropy is strongly reduced for Fe films grown on a (1 × 1)-unreconstructed ZnSe substrate while the in-plane biaxial one is nearly unaffected by the substrate reconstruction. Calculations of magnetic anisotropy energies within the framework of ab initio density functional theory reveal that the strong suppression of anisotropy at the (1 × 1) interface occurs due to complex atomic relaxations as well as the competing effects originating from magnetocrystalline anisotropy and dipole-dipole interactions. For both sharp and intermixed c(2 × 2) interfaces, the magnetic anisotropy is enhanced compared to the (1 × 1) case due to the further lowering of symmetry. The theoretical results are in agreement with the experimental findings.
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Affiliation(s)
- S Tacchi
- CNISM, Unità di Perugia-Dipartimento di Fisica and Università di Perugia, Perugia, Italy.
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Yadav MK, Kwon SK, Huh HJ, Chae SW, Song JJ. Detection of methicillin-resistant Staphylococcus aureus (MRSA) from nasal samples by multiplex real-time PCR based on dual priming AT-rich primers. Folia Microbiol (Praha) 2011; 57:37-45. [PMID: 22187362 DOI: 10.1007/s12223-011-0085-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 10/25/2011] [Indexed: 10/14/2022]
Abstract
In this study, we reported on the design of a multiplex real-time PCR assay based on SYBR Green I, incorporating dual priming adenine-thymine (AT)-rich primers for direct detection of MRSA from nasal samples. The multiplex real-time polymerase chain reaction (RT-PCR) assay reported in this study is based on SYBR Green I with incorporation of six dual priming AT-rich primers designed from the SCCmec/orf junction. A string (4-6 bp) of low-melting bases, such as adenine and thymine, was incorporated into the primers, which virtually divided a single primer in two functional regions, thus decreasing non-specific PCR products. The analytical sensitivity and specificity of the RT-PCR assay was determined with genomic DNA of reference strains (MRSA, MSSA, and MRCoNS). RT-PCR assay was performed for analysis of 72 nasal swab specimens, and the results were confirmed by use of a culture method. Furthermore, the results of RT-PCR were compared with LightCycler MRSA advance test. The multiplex RT-PCR assay reproducibly detected a minimum of 1 pg genomic DNA (31.5 copy of genome) of MRSA reference strains and clinical isolates, with a specific melting peak at 83.5 ± 1.5°C, and neither fluorescence nor a melting peak was detected in non-target isolates. The concordance rate between RT-PCR assay and culture method was 87.5% with Cohen's kappa value (κ) 0.75, which showed good agreement between the two assays. The sensitivity, specificity, positive predictive value, and negative predictive value of the assay were 93.5%, 82.9%, 80.5%, and 94.4%, respectively. In a comparative study for the detection of 72 nasal samples, the sensitivity, specificity, positive predictive value, and negative predictive value of the multiplex RT-PCR assay with respect to LightCycler MRSA advance test was 84.2%, 88.2%, 89%, and, 83.3%, respectively. The results of RT-PCR assay demonstrated high specificity (88.2%) and positive predictive value (89%) for the direct detection of MRSA from nasal samples.
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Affiliation(s)
- M K Yadav
- Department of Otorhinolaryngology-Head and Neck Surgery, Dongguk University Ilsan Hospital, Goyang, Gyeonggi, South Korea
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Yadav MK, Mittal P, Rishi JP, Agarwal K. Disseminated abdominal hydatidosis. J Assoc Physicians India 2007; 55:875-876. [PMID: 18405141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
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Yadav MK, Leeneshwar H, Jai RP. Pulseless cardiomyopathy. J Assoc Physicians India 2006; 54:814-6. [PMID: 17214280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Takayasu arteritis can have myriads of presentation, depending on site and extent of disease. As no age is immune for this disease, it is important to keep a high index of suspicion, otherwise the diagnosis can be missed. We hereby describe a case of Takayasu arteritis, which presented as dilated cardiomyopathy.
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Affiliation(s)
- M K Yadav
- Department of Medicine, Head Allergy and Repiratory Medicine, SMS Medical College, Jaipur
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