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Nandi NB, Purkayastha A, Kłak J, Ganguly R, Ghanta S, Misra TK. Copper(II) complexes of 1,3-dimethyl-5-(4′/3′-pyridylazo)-6-aminouracil: Structures, redox, magnetic and protein binding properties. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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2
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Nandi NB, Purkayastha A, Roy S, Kłak J, Ganguly R, Alkorta I, Misra TK. Tetranuclear copper( ii) cubane complexes derived from self-assembled 1,3-dimethyl-5-( o-phenolate-azo)-6-aminouracil: structures, non-covalent interactions and magnetic property. NEW J CHEM 2021. [DOI: 10.1039/d0nj05232a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new doubly opened 4 + 2 Cu4O4 cubane cluster exhibits strong antiferromagnetic exchange coupling with J1 = −110.1 cm−1, and J2 = −27.1 cm−1.
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Affiliation(s)
| | - Atanu Purkayastha
- Department of Chemistry
- National Institute of Technology
- Agartala 799046
- India
| | - Shaktibrata Roy
- Department of Chemistry
- National Institute of Technology
- Agartala 799046
- India
| | - Julia Kłak
- Faculty of Chemistry
- University of Wroclaw
- Wroclaw 50383
- Poland
| | | | - Ibon Alkorta
- Instituto de Química Médica
- CSIC
- 28006 Madrid
- Spain
| | - Tarun Kumar Misra
- Department of Chemistry
- National Institute of Technology
- Agartala 799046
- India
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3
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Mulay A, Konda B, Garcia G, Yao C, Beil S, Sen C, Purkayastha A, Kolls JK, Pociask DA, Pessina P, de Aja JS, Garcia-de-Alba C, Kim CF, Gomperts B, Arumugaswami V, Stripp B. SARS-CoV-2 infection of primary human lung epithelium for COVID-19 modeling and drug discovery. bioRxiv 2020:2020.06.29.174623. [PMID: 32637946 PMCID: PMC7337376 DOI: 10.1101/2020.06.29.174623] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is the latest respiratory pandemic resulting from zoonotic transmission of severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2). Severe symptoms include viral pneumonia secondary to infection and inflammation of the lower respiratory tract, in some cases causing death. We developed primary human lung epithelial infection models to understand responses of proximal and distal lung epithelium to SARS-CoV-2 infection. Differentiated air-liquid interface cultures of proximal airway epithelium and 3D organoid cultures of alveolar epithelium were readily infected by SARS-CoV-2 leading to an epithelial cell-autonomous proinflammatory response. We validated the efficacy of selected candidate COVID-19 drugs confirming that Remdesivir strongly suppressed viral infection/replication. We provide a relevant platform for studying COVID-19 pathobiology and for rapid drug screening against SARS-CoV-2 and future emergent respiratory pathogens. ONE SENTENCE SUMMARY A novel infection model of the adult human lung epithelium serves as a platform for COVID-19 studies and drug discovery.
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Affiliation(s)
- A. Mulay
- Lung and Regenerative Medicine Institutes, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - B. Konda
- Lung and Regenerative Medicine Institutes, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - G. Garcia
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA
| | - C. Yao
- Lung and Regenerative Medicine Institutes, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - S. Beil
- Lung and Regenerative Medicine Institutes, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - C. Sen
- UCLA Children’s Discovery and Innovation Institute, Mattel Children’s Hospital UCLA, Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - A. Purkayastha
- UCLA Children’s Discovery and Innovation Institute, Mattel Children’s Hospital UCLA, Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - J. K. Kolls
- Tulane School of Medicine, New Orleans, 70112
| | | | - P. Pessina
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary & Respiratory Diseases, Boston Children’s Hospital, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - J. Sainz de Aja
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary & Respiratory Diseases, Boston Children’s Hospital, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - C. Garcia-de-Alba
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary & Respiratory Diseases, Boston Children’s Hospital, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - C. F. Kim
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary & Respiratory Diseases, Boston Children’s Hospital, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - B. Gomperts
- UCLA Children’s Discovery and Innovation Institute, Mattel Children’s Hospital UCLA, Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, 90095, USA
- li and Edythe Broad, Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA 90095, USA
| | - V. Arumugaswami
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA
- li and Edythe Broad, Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA 90095, USA
| | - B.R. Stripp
- Lung and Regenerative Medicine Institutes, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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Mulay A, Konda B, Garcia G, Yao C, Beil S, Sen C, Purkayastha A, Kolls JK, Pociask DA, Pessina P, Sainz de Aja J, Garcia-de-Alba C, Kim CF, Gomperts B, Arumugaswami V, Stripp BR. SARS-CoV-2 infection of primary human lung epithelium for COVID-19 modeling and drug discovery. bioRxiv 2020. [PMID: 32637946 DOI: 10.1101/2020.06.29.174623.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is the latest respiratory pandemic resulting from zoonotic transmission of severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2). Severe symptoms include viral pneumonia secondary to infection and inflammation of the lower respiratory tract, in some cases causing death. We developed primary human lung epithelial infection models to understand responses of proximal and distal lung epithelium to SARS-CoV-2 infection. Differentiated air-liquid interface cultures of proximal airway epithelium and 3D organoid cultures of alveolar epithelium were readily infected by SARS-CoV-2 leading to an epithelial cell-autonomous proinflammatory response. We validated the efficacy of selected candidate COVID-19 drugs confirming that Remdesivir strongly suppressed viral infection/replication. We provide a relevant platform for studying COVID-19 pathobiology and for rapid drug screening against SARS-CoV-2 and future emergent respiratory pathogens. One Sentence Summary A novel infection model of the adult human lung epithelium serves as a platform for COVID-19 studies and drug discovery.
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5
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Purkayastha A, Dhar S, Mondal SP, Franconetti A, Frontera A, Ganguly R, Kirillov AM, Misra TK. Metal–organic architectures driven by a multifunctional 6-aminouracil spacer: structures, noncovalent interactions, and conductivity. CrystEngComm 2020. [DOI: 10.1039/c9ce01437c] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Three new coordination polymers were assembled from a multifunctional 6-aminouracil building block and their structural features & functional properties were investigated.
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Affiliation(s)
- Atanu Purkayastha
- Department of Chemistry
- National Institute of Technology Agartala
- India
| | - Sourab Dhar
- Department of Physics
- National Institute of Technology Agartala
- India
| | | | | | | | - Rakesh Ganguly
- Division of Chemistry & Biological Chemistry
- Nanyang Technology University
- Singapore
| | - Alexander M. Kirillov
- Centro de Química Estrutural
- Instituto Superior Técnico
- Universidade de Lisboa
- Lisbon
- Portugal
| | - Tarun Kumar Misra
- Department of Chemistry
- National Institute of Technology Agartala
- India
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Purkayastha A, Debnath D, Majumder M, Ortega-Castro J, Kirillov AM, Ganguly R, Klak J, Frontera A, Misra TK. Nickel(II) based homo- vs heterometallic 1D coordination polymers derived from a novel 6-aminouracil building block: Structures, topologies, non-covalent interactions, magnetism, and antibacterial activity. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2018.06.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Debnath D, Purkayastha A, Kirillov A, Ganguly R, Misra TK. Study of an efficient conversion of 1,3-dimethyl-5-(Arylazo)-6-Amino-Uracils to 1,3-dimethyl-8-(Aryl)-Azapurin-2,6-Diones. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.08.087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Debnath D, Roy S, Purkayastha A, Bauzá A, Choudhury R, Ganguly R, Frontera A, Misra TK. Synthesis and structure of 1,3-dimethyl-5-( p -sulfonamide-phenylazo)-6-aminouracil and its Ni(II) complex: Topological insights and investigation for noncovalent interactions. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.03.121] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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9
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Choudhury R, Purkayastha A, Debnath D, Misra TK. Synthesis and study of aggregation kinetics of fluorescence active N -(1-Naphthyl)ethylenediammonium cations functionalized silver nanoparticles for a chemo-sensor probe. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.04.121] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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10
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Purkayastha A, Debnath D, Roy S, Bauzá A, Choudhury R, Frontera A, Misra TK. Synthesis and Investigation of Solid‐ and Solution‐State Structures of Nickel(II) Complexes with 1,3‐Dimethyl‐5‐(arylazo)‐6‐aminouracil. Eur J Inorg Chem 2016. [DOI: 10.1002/ejic.201601021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Atanu Purkayastha
- Department of Chemistry National Institute of Technology (NIT) Agartala 799046 Tripura India
| | - Diptanu Debnath
- Department of Chemistry National Institute of Technology (NIT) Agartala 799046 Tripura India
| | - Subhadip Roy
- Department of Chemistry National Institute of Technology (NIT) Agartala 799046 Tripura India
| | - Antonio Bauzá
- Departament de Quimica Universitat de les Illes Balears Crta. de Valldemossa km 7.5 07122 Palma de Mallorca (Baleares) Spain
| | - Rupasree Choudhury
- Department of Chemistry National Institute of Technology (NIT) Agartala 799046 Tripura India
| | - Antonio Frontera
- Departament de Quimica Universitat de les Illes Balears Crta. de Valldemossa km 7.5 07122 Palma de Mallorca (Baleares) Spain
| | - Tarun Kumar Misra
- Department of Chemistry National Institute of Technology (NIT) Agartala 799046 Tripura India
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11
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Debnath D, Purkayastha A, Choudhury R, Misra TK. Conversion of 1,3-Dimethyl-5-(Arylazo)-6-Amino-Uracils to 1,3-Dimethyl-5-(Arylazo)-Barbituric Acids: Spectroscopic Characterization, Photophysical Property and Determination of pKaof the Products. J CHIN CHEM SOC-TAIP 2016. [DOI: 10.1002/jccs.201600007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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12
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Choudhury R, Purkayastha A, Debnath D, Misra TK. Recognition of silver nanoparticles surface-adsorbed citrate anions by macrocyclic polyammonium cations: a spectrophotometric approach to study aggregation kinetics and evaluation of association constant. J Mol Recognit 2016; 29:452-61. [DOI: 10.1002/jmr.2544] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 02/08/2016] [Accepted: 03/16/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Rupasree Choudhury
- Department of Chemistry; National Institute of Technology; Agartala Tripura 799046 India
| | - Atanu Purkayastha
- Department of Chemistry; National Institute of Technology; Agartala Tripura 799046 India
| | - Diptanu Debnath
- Department of Chemistry; National Institute of Technology; Agartala Tripura 799046 India
| | - Tarun Kumar Misra
- Department of Chemistry; National Institute of Technology; Agartala Tripura 799046 India
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13
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Roy S, Bauza A, Frontera A, Schaper F, Banik R, Purkayastha A, Reddy BM, Sridhar B, Drew MG, Das SK, Das S. Structural diversity and non-covalent interactions in Cd(II) and Zn(II) complexes derived from 3,5-dinitrobenzoic acid and pyridine: Experimental and theoretical aspects. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2015.10.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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14
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Roy S, Bauza A, Frontera A, Banik R, Purkayastha A, Drew MGB, Reddy BM, Sridhar B, Das SK, Das S. Experimental observation and theoretical investigation of a novel Cd(ii) complex with π-hole interactions involving nitro groups. CrystEngComm 2015. [DOI: 10.1039/c5ce00453e] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A cadmium(ii) complex, which represents a novel example of supramolecular system bearing a network of π-hole interactions, has been synthesized.
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Affiliation(s)
- Subhadip Roy
- Department of Chemistry
- National Institute of Technology (NIT) Agartala
- Tripura, India
| | - Antonio Bauza
- Departament de Quimica
- Universitat de les Illes Balears
- 07122 Palma de Mallorca, Spain
| | - Antonio Frontera
- Departament de Quimica
- Universitat de les Illes Balears
- 07122 Palma de Mallorca, Spain
| | - Rupak Banik
- Department of Chemistry
- National Institute of Technology (NIT) Agartala
- Tripura, India
| | - Atanu Purkayastha
- Department of Chemistry
- National Institute of Technology (NIT) Agartala
- Tripura, India
| | | | - Benjaram M. Reddy
- Inorganic and Physical Chemistry Division
- Indian Institute of Chemical Technology
- Hyderabad, India
| | | | - Saroj Kr. Das
- Department of Chemistry
- National Institute of Technology (NIT) Agartala
- Tripura, India
| | - Subrata Das
- Department of Chemistry
- National Institute of Technology (NIT) Patna
- Ashok Rajpath
- Patna-800005, India
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Yan Q, Purkayastha A, Singh AP, Li H, Li A, Ramanujan RV, Ramanath G. High-coercivity FePt nanoparticle assemblies embedded in silica thin films. Nanotechnology 2009; 20:025609. [PMID: 19417278 DOI: 10.1088/0957-4484/20/2/025609] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The ability to process assemblies using thin film techniques in a scalable fashion would be a key to transmuting the assemblies into manufacturable devices. Here, we embed FePt nanoparticle assemblies into a silica thin film by sol-gel processing. Annealing the thin film composite at 650 degrees C transforms the chemically disordered fcc FePt phase into the fct phase, yielding magnetic coercivity values H(c)>630 mT. The positional order of the particles is retained due to the protection offered by the silica host. Such films with assemblies of high-coercivity magnetic particles are attractive for realizing new types of ultra-high-density data storage devices and magneto-composites.
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Affiliation(s)
- Q Yan
- Department of Materials Science and Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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Affiliation(s)
- A. Purkayastha
- a Department of Chemistry , Indian Institute of Technology , Guwahati 781 001
- b Department of Chemistry , Indian Institute of Technology , Guwahati 781 001
| | - J.B. Baruah
- a Department of Chemistry , Indian Institute of Technology , Guwahati 781 001
- b Department of Chemistry , Indian Institute of Technology , Guwahati 781 001
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17
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Yu G, Snyder E, Boyle S, Crasta O, Czar M, Mane S, Purkayastha A, Sobral B, Setubal J. A versatile computational pipeline for bacterial genome annotation improvement and comparative analysis, with Brucella as a use case. Nucleic Acids Res 2007; 35:3953-62. [PMID: 17553834 PMCID: PMC1919506 DOI: 10.1093/nar/gkm377] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We present a bacterial genome computational analysis pipeline, called GenVar. The pipeline, based on the program GeneWise, is designed to analyze an annotated genome and automatically identify missed gene calls and sequence variants such as genes with disrupted reading frames (split genes) and those with insertions and deletions (indels). For a given genome to be analyzed, GenVar relies on a database containing closely related genomes (such as other species or strains) as well as a few additional reference genomes. GenVar also helps identify gene disruptions probably caused by sequencing errors. We exemplify GenVar's capabilities by presenting results from the analysis of four Brucella genomes. Brucella is an important human pathogen and zoonotic agent. The analysis revealed hundreds of missed gene calls, new split genes and indels, several of which are species specific and hence provide valuable clues to the understanding of the genome basis of Brucella pathogenicity and host specificity.
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Affiliation(s)
- G.X. Yu
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, Department of Biology and Department of Computer Science, Boise State University, Boise, ID 83726 and Center for Molecular Medicine and Infectious Diseases, Virginia–Maryland Regional College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, USA
| | - E.E. Snyder
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, Department of Biology and Department of Computer Science, Boise State University, Boise, ID 83726 and Center for Molecular Medicine and Infectious Diseases, Virginia–Maryland Regional College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, USA
| | - S.M. Boyle
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, Department of Biology and Department of Computer Science, Boise State University, Boise, ID 83726 and Center for Molecular Medicine and Infectious Diseases, Virginia–Maryland Regional College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, USA
| | - O.R. Crasta
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, Department of Biology and Department of Computer Science, Boise State University, Boise, ID 83726 and Center for Molecular Medicine and Infectious Diseases, Virginia–Maryland Regional College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, USA
| | - M. Czar
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, Department of Biology and Department of Computer Science, Boise State University, Boise, ID 83726 and Center for Molecular Medicine and Infectious Diseases, Virginia–Maryland Regional College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, USA
| | - S.P. Mane
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, Department of Biology and Department of Computer Science, Boise State University, Boise, ID 83726 and Center for Molecular Medicine and Infectious Diseases, Virginia–Maryland Regional College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, USA
| | - A. Purkayastha
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, Department of Biology and Department of Computer Science, Boise State University, Boise, ID 83726 and Center for Molecular Medicine and Infectious Diseases, Virginia–Maryland Regional College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, USA
| | - B. Sobral
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, Department of Biology and Department of Computer Science, Boise State University, Boise, ID 83726 and Center for Molecular Medicine and Infectious Diseases, Virginia–Maryland Regional College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, USA
| | - J.C. Setubal
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, Department of Biology and Department of Computer Science, Boise State University, Boise, ID 83726 and Center for Molecular Medicine and Infectious Diseases, Virginia–Maryland Regional College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, USA
- *To whom correspondence should be addressed. +1 540 231 9464+1 540 231 2606
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Snyder EE, Kampanya N, Lu J, Nordberg EK, Karur HR, Shukla M, Soneja J, Tian Y, Xue T, Yoo H, Zhang F, Dharmanolla C, Dongre NV, Gillespie JJ, Hamelius J, Hance M, Huntington KI, Jukneliene D, Koziski J, Mackasmiel L, Mane SP, Nguyen V, Purkayastha A, Shallom J, Yu G, Guo Y, Gabbard J, Hix D, Azad AF, Baker SC, Boyle SM, Khudyakov Y, Meng XJ, Rupprecht C, Vinje J, Crasta OR, Czar MJ, Dickerman A, Eckart JD, Kenyon R, Will R, Setubal JC, Sobral BWS. PATRIC: the VBI PathoSystems Resource Integration Center. Nucleic Acids Res 2006; 35:D401-6. [PMID: 17142235 PMCID: PMC1669763 DOI: 10.1093/nar/gkl858] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The PathoSystems Resource Integration Center (PATRIC) is one of eight Bioinformatics Resource Centers (BRCs) funded by the National Institute of Allergy and Infection Diseases (NIAID) to create a data and analysis resource for selected NIAID priority pathogens, specifically proteobacteria of the genera Brucella, Rickettsia and Coxiella, and corona-, calici- and lyssaviruses and viruses associated with hepatitis A and E. The goal of the project is to provide a comprehensive bioinformatics resource for these pathogens, including consistently annotated genome, proteome and metabolic pathway data to facilitate research into counter-measures, including drugs, vaccines and diagnostics. The project's curation strategy has three prongs: ‘breadth first’ beginning with whole-genome and proteome curation using standardized protocols, a ‘targeted’ approach addressing the specific needs of researchers and an integrative strategy to leverage high-throughput experimental data (e.g. microarrays, proteomics) and literature. The PATRIC infrastructure consists of a relational database, analytical pipelines and a website which supports browsing, querying, data visualization and the ability to download raw and curated data in standard formats. At present, the site warehouses complete sequences for 17 bacterial and 332 viral genomes. The PATRIC website () will continually grow with the addition of data, analysis and functionality over the course of the project.
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Affiliation(s)
- E E Snyder
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
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Vafaei S, Borca-Tasciuc T, Podowski MZ, Purkayastha A, Ramanath G, Ajayan PM. Effect of nanoparticles on sessile droplet contact angle. Nanotechnology 2006; 17:2523-2527. [PMID: 21727499 DOI: 10.1088/0957-4484/17/10/014] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
This paper investigates the change in contact angle of droplets of fluid containing dispersed nanoparticles (nanofluid) functionalized with thioglycolic acid molecules as a function of the concentration and size of nanoparticles, and the quality and composition of the substrate material. Bismuth telluride nanoparticles with an average size ranging from 2.5 to 10.4 nm and functionalized with thioglycolic acid groups were grown by a microemulsion method and dispersed in water. Experimental measurements of the contact angle of nanofluid droplets cast on smooth glass and silicon substrates show that the contact angle depends strongly on nanoparticle concentration. Moreover, smaller size nanoparticles lead to larger changes in contact angle at the same mass concentration. These findings contribute to understanding the role of functionalized nanoparticles in surface wettability.
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Affiliation(s)
- S Vafaei
- Department of Mechanical, Aerospace and Nuclear Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA
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Rowland B, Purkayastha A, Monserrat C, Casart Y, Takiff H, McDonough KA. Fluorescence-based detection of lacZ reporter gene expression in intact and viable bacteria including Mycobacterium species. FEMS Microbiol Lett 1999; 179:317-25. [PMID: 10518732 DOI: 10.1111/j.1574-6968.1999.tb08744.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
A variety of fluorescein di-beta-D-galactopyranoside (FDG)-based substrates were evaluated for measuring beta-galactosidase expression in bacteria. One substrate, 5-acetylamino-FDG (C2FDG), performed well in all bacteria tested, including the slow growing mycobacterium, Mycobacterium bovis BCG. The sensitivity of C2FDG in intact, viable BCG was similar to that of o-nitrophenyl-beta-D-galactopyranoside in cell lysates when used to measure lacZ reporter gene activity. C2FDG was approximately 70-fold more sensitive than green fluorescent protein (GFP) in BCG when assayed in a fluorescence plate reader, and comparable to GFP when measured by flow cytometry. These assays provide an important new alternative for the rapid measurement of reporter gene expression in viable bacteria.
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Affiliation(s)
- B Rowland
- David Axelrod Institute, Wadsworth Center, New York State Department of Health, P.O. Box 22002, 120 New Scotland Ave, Albany, NY 12208, USA
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Bhattacharjee D, Purkayastha A, Misra TN. Raman spectral study of vibrational relaxation in acetophenone. J CHEM SCI 1997. [DOI: 10.1007/bf02872564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Cui J, O'Shea KS, Purkayastha A, Saunders TL, Ginsburg D. Fatal haemorrhage and incomplete block to embryogenesis in mice lacking coagulation factor V. Nature 1996; 384:66-8. [PMID: 8900278 DOI: 10.1038/384066a0] [Citation(s) in RCA: 175] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Coagulation factor V is a critical cofactor for the activation of prothrombin to thrombin, the penultimate step in the generation of a fibrin blood clot. Genetic deficiency of factor V results in a congenital bleeding disorder (parahaemophilia), whereas inheritance of a mutation rendering factor V resistant to inactivation is an important risk factor for thrombosis. We report here that approximately half of homozygous embryos deficient in factor V (Fv-/-), which have been generated by gene targeting, die at embryonic day (E) 9-10, possibly as a result of an abnormality in the yolk-sac vasculature. The remaining Fv-/- mice progress normally to term, but die from massive haemorrhage within 2 hours of birth. Considered together with the milder phenotypes generally associated with deficiencies of other clotting factors, our findings demonstrate the primary role of the common coagulation pathway and the absolute requirement for functional factor V for prothrombinase activity. They also provide direct evidence for the existence of other critical haemostatic functions for thrombin in addition to fibrin clot formation, and identify a previously unrecognized role for the coagulation system in early mammalian development.
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Affiliation(s)
- J Cui
- Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, USA
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Purkayastha A, DeWitt W, Koberlein N. Foreign body in a Meckel's diverticulum. JAMA 1984; 251:2659. [PMID: 6716595 DOI: 10.1001/jama.1984.03340440019011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Purkayastha A, Saran M, Gerfin E. An unusual case of gallbladder disease. JAMA 1980; 243:2031. [PMID: 7373741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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