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Tyagi M, Shah U, Patel G, Toshniwal V, Bhongade R, Sharma P. THE IMPACT OF SLEEP ON PHYSICAL AND MENTAL HEALTH: IMPORTANCE OF HEALTHY SLEEP HABITS. Georgian Med News 2023:89-94. [PMID: 37522781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 08/01/2023]
Abstract
Sleep is an important part of health, and when you go to sleep, how long you sleep, and how well you sleep all have a big impact on your health. Sleep may be required for regulating the body's metabolism, feelings, function, memory storage, brain recovery, and learning. Because of how important these processes are, sleep should be seen as just as important to health as what you eat and how much you exercise. Adults' sleep generally gets shorter and less restful, their sleep starts later and is more broken up, they have more sleep problems, and their rest-activity rhythms get weaker. In addition to receiving enough sleep (quality), healthy sleep habits also include maintaining a consistent sleep schedule. Ninety male college students with varying sleep schedules were analyzed for their physical and emotional well-being. By using factor analysis to categorize individuals' sleeping patterns across three dimensions regularity, quality, and quantity. We were able to develop sleep-habit measures. Clustering identified four distinct patterns of sleep behavior: good sleep was defined by regular, high-quality sleep despite being of comparatively brief duration; long sleep was predictable, fairly lengthy, but of minimal quality; short sleep was of excellent quality despite being short and irregular; and poor sleep was erratic, low-quality, and relatively long. The excellent sleepers also had reduced diastolic and systolic and a smaller means waist measurement. In addition, the poor sleepers had the lowest average MCS scores of all of the study groups. Poor sleepers also had the lowest mean scores on the Subjective Depression Scale (SDS). Issues involving glucose or lipid absorption were also more common in the short-term and long poor-sleep categories. Without restful sleep and a regular bedtime routine, it is impossible to maintain excellent mental and physical wellness, even if time and sleep are maintained constantly. Therefore, to produce suitable sleep recommendations for enhanced mental and physical health, we evaluated not only the quantity of sleep but also its consistency and high quality.
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Affiliation(s)
- M Tyagi
- 1Department of Psychitary, Teerthanker Mahaveer University, Moradabad, Uttar Pradesh, India
| | - U Shah
- 2Department of Genetics, School of Sciences, JAIN (Deemed-to-be University), Karnataka, India
| | - G Patel
- 3Department of Community Medicine, Parul University, PO Limda, Tal. Waghodia, District Vadodara, Gujarat, India
| | - V Toshniwal
- 4Department of Nursing, IIMT University, Meerut, Uttar Pradesh, India
| | - R Bhongade
- 5Department of Ayurveda, Sanskriti University, Mathura, Uttar Pradesh, India
| | - P Sharma
- 6Department of Pharmacy, Vivekananda Global University, Jaipur, India
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Takahashi N, Tlemsani C, Pongor L, Rajapakse V, Tyagi M, Wen X, Fasaye G, Schmidt K, Kim C, Rajan A, Swift S, Sciuto L, Vilimas R, Webb S, Nichols S, Figg W, Pommier Y, Calzone K, Steinberg S, Wei J, Guha U, Turner C, Khan J, Thomas A. OA11.05 Whole Exome Sequencing Reveals the Potential Role of Hereditary Predisposition in Small Cell Lung Cancer, a Tobacco-Related Cancer. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.01.315] [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: 10/21/2022]
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Abstract
It is known that the organic units in hybrid halide perovskites are free to rotate, but it is not clear if this freedom is of any relevance to the structure-property relationship of these compounds. We have employed quasi-elastic neutron scattering using two different spectrometers, thus providing a wide dynamic range to investigate the cation dynamics in methylammonium lead bromide (MAPbBr3) and formamidinium lead bromide (FAPbBr3) over a large temperature range covering all known crystallographic phases of these two compounds. Our results establish a plastic crystal-like phase forming above 30 K within the orthorhombic phase of MAPbBr3 related to 3-fold rotations of MA units around the C-N axis with an activation energy, Ea, of ∼27 meV, which has no counterpart in the FA compound. MA exhibits an additional 4-fold orientational motion of the whole molecule via rotation of the C-N axis itself with an Ea of ∼68 meV common for the high-temperature tetragonal and cubic phases. In contrast, the FA compound exhibits only an isotropic orientational motion of the whole FA unit with Ea ≈ 106 meV within the orthorhombic phase and a substantially reduced common Ea of ∼62 meV for the high-temperature tetragonal and cubic phases. Our results suggest that the rotational dynamics of the organic units, crystallographic phases, and physical properties of these compounds are intimately connected.
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Affiliation(s)
- V K Sharma
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
| | - R Mukhopadhyay
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
| | - A Mohanty
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, India
| | - M Tyagi
- National Institute of Standards and Technology, Center for Neutron Research, Gaithersburg, Maryland 20899, United States
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - J P Embs
- Laboratory for Neutron Scattering and Imaging, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - D D Sarma
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, India
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Sharma V, Mamontov E, Tyagi M. Effects of NSAIDs on the nanoscopic dynamics of lipid membrane. Biochimica et Biophysica Acta (BBA) - Biomembranes 2020; 1862:183100. [DOI: 10.1016/j.bbamem.2019.183100] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 08/16/2019] [Accepted: 09/19/2019] [Indexed: 01/30/2023]
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Verma TR, Painuly NK, Tyagi M, Johny D, Gupta R, Bhatt MLB. Validation of the Gel & Wax Boluses and Comparison of their Dosimetric Performance with Virtual Bolus. J Biomed Phys Eng 2019; 9:629-636. [PMID: 32039093 PMCID: PMC6943845 DOI: 10.31661/jbpe.v0i0.1177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 06/15/2019] [Indexed: 11/16/2022]
Abstract
Background In general, radiotherapy treatment planning is performed using the virtual bolus. It is necessary to investigate physical bolus in comparison to virtual one. Objectives In the present study, first, radiological properties of superflab Gel bolus and Paraffin wax bolus was investigated in terms of their relative electron density. Then, dosimetric performance of both the bolus (i.e. Gel and Parafin wax) was compared with Virtual bolus. Material and Methods In This experimental study, the radiological property of Wax and Gel boluses was investigated using two methods. In one, the relative electron density of both the Gel and Wax boluses was calculated by measuring their linear attenuation coefficient where in another method relative electron density was calculated by recording their CT No directly from their CT scan. Later CT scan of solid water slab phantom (dimension 30x30x15 cm3), with physical boluses (i.e. Gel and Wax bolus) of appropriate thicknesses required to deliver a dose of 200 cGy at Dmax using 4 MV, 6 MV and 15 MV photon beams, was taken. These CT data sets were retrieved to TPS. A plan was done to deliver a dose of 200 cGy at Dmax using Single 4 MV, 6 MV and 15 MV photon beams. Dose at depths Dmax, 1 cm, 2 cm, 3 cm, 4 cm and 5 cm was recorded. Using this similar method, doses at depths viz Dmax, 1 cm, 2 cm, 3 cm, 4 cm and 5 cm was recorded for the Gel and Wax boluses. The differences in dose of gel and wax bolus from virtual bolus were recorded for comparison of their dosimetric performance. Results The measured (calculated) relative electron density of wax and Gel bolus was found to be 0.958 (0.926) and 0.923 (0.907), respectively. Variation in dosimetric performance of Gel and Wax with reference to Virtual bolus was studied. However, on average, Gel bolus was more consistent with virtual bolus. Conclusion To avoid any dose difference between, delivered (using physical bolus) and planned (using virtual bolus), the physical boluses should be investigated for their dosimetric performance in comparison to virtual bolus. The results obtained and methodology used in this study can be applied in routine radiotherapy practices.
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Affiliation(s)
- T R Verma
- PhD, Department of Radiotherapy, King George's Medical University, UP, Lucknow, India
| | - N K Painuly
- PhD, Department of Radiotherapy, King George's Medical University, UP, Lucknow, India
| | - M Tyagi
- MSc, Department of Radiology &
| | - D Johny
- MSc, Department of Radiotherapy, King George's Medical University, UP, Lucknow, India
| | - R Gupta
- MD, Department of Radiotherapy, King George's Medical University, UP, Lucknow, India
| | - M L B Bhatt
- MD, Department of Radiotherapy, King George's Medical University, UP, Lucknow, India
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Affiliation(s)
| | | | | | | | - M. Tyagi
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-6100, United States
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, United States
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Tyagi M, Khan A, Husain M, Husain S. Analytical and computational studies of the nonlinear vibrations of SWCNTs embedded in viscous elastic matrix using KBM method. Chaos 2019; 29:023134. [PMID: 30823744 DOI: 10.1063/1.5079700] [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] [Received: 11/02/2018] [Accepted: 02/05/2019] [Indexed: 06/09/2023]
Abstract
The forced vibration analysis of single wall carbon nanotubes (SWCNTs) embedded in the viscous elastic matrix subjected to axial parametric excitation has been investigated. The Euler Bernoulli beam model of the non-local continuum theory is used. The resonant and non-resonant solutions are analytically studied using the Krylov Bogoliubov and Mitropolsky method. It has been seen that the amplitude remains constant up to the second order of approximation. The resonant solutions are also found to analyze the possibility of chaos in the neighborhood of resonance. The computational techniques are used, and plots of time series, phase plot, and Poincaré surface of section are also drawn to confirm the chaotic behavior for certain values of parameters of SWCNTs, which may lead the aging process in the SWCNTs after a long time.
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Affiliation(s)
- M Tyagi
- Centre for Nanoscience and Nanotechnology, Jamia Millia Islamia (A Central University), New Delhi 110025, India
| | - A Khan
- Department of Mathematics, Jamia Millia Islamia (A Central University), New Delhi 110025, India
| | - M Husain
- Department of Physics, Jamia Millia Islamia (A Central University), New Delhi 110025, India
| | - S Husain
- Centre for Nanoscience and Nanotechnology, Jamia Millia Islamia (A Central University), New Delhi 110025, India
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Buck ZN, Torres J, Miskowiec A, Mamontov E, Kaiser H, Hansen FY, Taub H, Tyagi M, Collins L, Herwig KW. Effect of melittin on water diffusion and membrane structure in DMPC lipid bilayers. ACTA ACUST UNITED AC 2018. [DOI: 10.1209/0295-5075/123/18002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Tyagi M, Sonia Z, Sun L, Dubrovsky L, Bukrinsky M. DNA-PK regulates HIV transcription and latency by supporting the activity of RNA polymerase II and the recruitment of transcription machinery at HIV LTR. J Virus Erad 2017. [DOI: 10.1016/s2055-6640(20)30591-4] [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: 10/23/2022] Open
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Sharma VK, Hayes DG, Urban VS, O'Neill HM, Tyagi M, Mamontov E. Nanoscopic dynamics of bicontinous microemulsions: effect of membrane associated protein. Soft Matter 2017. [PMID: 28631792 DOI: 10.1039/c7sm00875a] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Bicontinous microemulsions (BμE) generally consist of nanodomains formed by surfactant in a mixture of water and oil at nearly equal proportions and are potential candidates for the solubilization and purification of membrane proteins. Here we present the first time report of nanoscopic dynamics of surfactant monolayers within BμEs formed by the anionic surfactant sodium dodecyl sulfate (SDS) measured on the nanosecond to picosecond time scale using quasielastic neutron scattering (QENS). BμEs investigated herein consisted of middle phases isolated from Winsor-III microemulsion systems that were formed by mixing aqueous and oil solutions under optimal conditions. QENS data indicates that surfactants undergo two distinct motions, namely (i) lateral motion along the surface of the oil nanodomains and (ii) localized internal motion. Lateral motion can be described using a continuous diffusion model, from which the lateral diffusion coefficient is obtained. Internal motion of surfactant is described using a model which assumes that a fraction of the surfactants' hydrogens undergoes localized translational diffusion that could be considered confined within a spherical volume. The effect of cytochrome c, an archetypal membrane-associated protein known to strongly partition near the surfactant head groups in BμEs (a trend supported by small-angle X-ray scattering [SAXS] analysis), on the dynamics of BμE has also been investigated. QENS results demonstrated that cytochrome c significantly hindered both the lateral and the internal motions of surfactant. The lateral motion was more strongly affected: a reduction of the lateral diffusion coefficient by 33% was measured. This change is mainly attributable to the strong association of cytochrome c with oppositely charged SDS. In contrast, analysis of SAXS data suggested that thermal fluctuations (for a longer length and slower time scale compared to QENS) were increased upon incorporation of cytochrome c. This study demonstrates the utility of QENS for evaluating dynamics of BμEs in nanoscopic region, and that proteins directly affect the microscopic dynamics, which is of relevance for evaluating release kinetics of encapsulated drugs from BμE delivery systems and the use of BμEs as biomembrane mimetic systems for investigating membrane protein-biomembrane interactions.
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Affiliation(s)
- V K Sharma
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India.
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Abstract
ABSTRACT
The dynamics of polypropylene glycol, both neat and attached to silica nanoparticles, were investigated using elastic neutron backscattering and dielectric spectroscopy. The mean square displacement measured by the former is suppressed by the particles at temperatures corresponding to a dielectric secondary relaxation (that involves only a portion of the repeat unit) and the segmental relaxation (glass transition). Despite the suppression of the displacements, the motions are faster in the nanocomposite, primarily due to poorer packing (lower density) at the particle interface. At very low temperatures we discovered a new dynamic process in the polymer. Reflecting its very local nature, this process is unaffected by attachment of the chains to the silica.
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Affiliation(s)
- M. Tyagi
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899-6102
- Department of Materials Science, University of Maryland, College Park, MD 20742
| | - R. Casalini
- Naval Research Laboratory, Chemistry Division, Washington, DC 20375-5342
| | - C. M. Roland
- Naval Research Laboratory, Chemistry Division, Washington, DC 20375-5342
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Miskowiec A, Buck ZN, Hansen FY, Kaiser H, Taub H, Tyagi M, Diallo SO, Mamontov E, Herwig KW. On the structure and dynamics of water associated with single-supported zwitterionic and anionic membranes. J Chem Phys 2017; 146:125102. [DOI: 10.1063/1.4978677] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- A. Miskowiec
- Department of Physics and Astronomy and University of Missouri Research Reactor, University of Missouri, Columbia, Missouri 65211, USA
| | - Z. N. Buck
- Department of Physics and Astronomy and University of Missouri Research Reactor, University of Missouri, Columbia, Missouri 65211, USA
| | - F. Y. Hansen
- Department of Chemistry, Technical University of Denmark, IK 207 DTU, DK-2800 Lyngby, Denmark
| | - H. Kaiser
- Department of Physics and Astronomy and University of Missouri Research Reactor, University of Missouri, Columbia, Missouri 65211, USA
| | - H. Taub
- Department of Physics and Astronomy and University of Missouri Research Reactor, University of Missouri, Columbia, Missouri 65211, USA
| | - M. Tyagi
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-6102, USA
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - S. O. Diallo
- Spallation Neutron Source, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - E. Mamontov
- Spallation Neutron Source, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - K. W. Herwig
- Spallation Neutron Source, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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Sharma VK, Mamontov E, Ohl M, Tyagi M. Incorporation of aspirin modulates the dynamical and phase behavior of the phospholipid membrane. Phys Chem Chem Phys 2017; 19:2514-2524. [DOI: 10.1039/c6cp06202d] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Effect of aspirin on the microscopic dynamics of a membrane has been investigated using quasielastic neutron scattering and neutron spin echo techniques.
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Affiliation(s)
- V. K. Sharma
- Solid State Physics Division
- Bhabha Atomic Research Centre
- Mumbai 400085
- India
| | - E. Mamontov
- Chemical and Engineering Materials Division
- Neutron Sciences Directorate
- Oak Ridge National Laboratory
- Oak Ridge
- USA
| | - M. Ohl
- Jülich Center for Neutron Science
- Oak Ridge
- USA
| | - M. Tyagi
- National Institute of Standards and Technology Center for Neutron Research
- Gaithersburg
- USA
- Department of Materials Science and Engineering
- University of Maryland
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Osti NC, Etampawala TN, Shrestha UM, Aryal D, Tyagi M, Diallo SO, Mamontov E, Cornelius CJ, Perahia D. Water dynamics in rigid ionomer networks. J Chem Phys 2016; 145:224901. [PMID: 27984911 DOI: 10.1063/1.4971209] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- N. C. Osti
- Department of Chemistry, Clemson University, Clemson, South Carolina 29634, USA
| | - T. N. Etampawala
- Department of Chemistry, Clemson University, Clemson, South Carolina 29634, USA
| | - U. M. Shrestha
- Department of Chemistry, Clemson University, Clemson, South Carolina 29634, USA
| | - D. Aryal
- Department of Chemistry, Clemson University, Clemson, South Carolina 29634, USA
| | - M. Tyagi
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - S. O. Diallo
- Chemical and Engineering Materials Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - E. Mamontov
- Chemical and Engineering Materials Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - C. J. Cornelius
- Chemical and Biomolecular Engineering Department, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
| | - D. Perahia
- Department of Chemistry, Clemson University, Clemson, South Carolina 29634, USA
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Sharma VK, Mamontov E, Tyagi M, Qian S, Rai DK, Urban VS. Dynamical and Phase Behavior of a Phospholipid Membrane Altered by an Antimicrobial Peptide at Low Concentration. J Phys Chem Lett 2016; 7:2394-401. [PMID: 27232190 DOI: 10.1021/acs.jpclett.6b01006] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The mechanism of action of antimicrobial peptides is traditionally attributed to the formation of pores in the lipid cell membranes of pathogens, which requires a substantial peptide to lipid ratio. However, using incoherent neutron scattering, we show that even at a concentration too low for pore formation, an archetypal antimicrobial peptide, melittin, disrupts the regular phase behavior of the microscopic dynamics in a phospholipid membrane, dimyristoylphosphatidylcholine (DMPC). At the same time, another antimicrobial peptide, alamethicin, does not exert a similar effect on the DMPC microscopic dynamics. The melittin-altered lateral motion of DMPC at physiological temperature no longer resembles the fluid-phase behavior characteristic of functional membranes of the living cells. The disruptive effect demonstrated by melittin even at low concentrations reveals a new mechanism of antimicrobial action relevant in more realistic scenarios, when peptide concentration is not as high as would be required for pore formation, which may facilitate treatment with antimicrobial peptides.
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Affiliation(s)
- V K Sharma
- Biology and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
- Solid State Physics Division, Bhabha Atomic Research Centre , Mumbai 400085, India
| | - E Mamontov
- Chemical and Engineering Materials Division, Neutron Sciences Directorate, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - M Tyagi
- National Institute of Standards and Technology Center for Neutron Research , Gaithersburg, Maryland 20899, United States
- Department of Materials Science and Engineering, University of Maryland , College Park, Maryland 20742, United States
| | - S Qian
- Biology and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - D K Rai
- Biology and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - V S Urban
- Biology and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
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Patra G, Singh S, Tiwari B, Singh A, Desai D, Tyagi M, Sen S, Gadkari S. Optically stimulated luminescence in Ag doped Li2B4O7 single crystal and its sensitivity to neutron detection and dosimetry in OSL mode. RADIAT MEAS 2016. [DOI: 10.1016/j.radmeas.2016.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Mamontov E, Sharma VK, Borreguero JM, Tyagi M. Protein-Style Dynamical Transition in a Non-Biological Polymer and a Non-Aqueous Solvent. J Phys Chem B 2016; 120:3232-9. [DOI: 10.1021/acs.jpcb.6b00866] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- E. Mamontov
- Chemical
and Engineering Materials Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - V. K. Sharma
- Biology
and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Solid
State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - J. M. Borreguero
- Neutron
Data Analysis and Visualization Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - M. Tyagi
- National Institute of Standards and Technology Center for Neutron Research, Gaithersburg, Maryland 20899, United States
- Department
of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, United States
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Tyagi M, Vishwanadh B, Bhattacharyya K, Ghosh SK, Tewari R. A study on reaction kinetics and development of silicide coatings on Nb–1Zr–0.1C alloy by molten salt technique. RSC Adv 2016. [DOI: 10.1039/c6ra08280g] [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] [Indexed: 11/21/2022] Open
Abstract
In this study a molten salt technique has been used to produce silicide coating on Nb–1Zr–0.1C alloy using a NaCl–KCl–NaF–Na2SiF6–Si melt.
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Affiliation(s)
- M. Tyagi
- Homi Bhabha National Institute
- Mumbai 400094
- India
| | - B. Vishwanadh
- Materials Science Division
- Bhabha Atomic Research Centre
- Mumbai 400085
- India
| | - K. Bhattacharyya
- Chemistry Division
- Bhabha Atomic Research Centre
- Mumbai 400085
- India
| | - S. K. Ghosh
- Homi Bhabha National Institute
- Mumbai 400094
- India
- Materials Processing Division
- Bhabha Atomic Research Centre
| | - R. Tewari
- Homi Bhabha National Institute
- Mumbai 400094
- India
- Materials Science Division
- Bhabha Atomic Research Centre
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Sharma VK, Mamontov E, Tyagi M, Urban VS. Effect of α-Tocopherol on the Microscopic Dynamics of Dimyristoylphosphatidylcholine Membrane. J Phys Chem B 2015; 120:154-63. [DOI: 10.1021/acs.jpcb.5b10417] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- V. K. Sharma
- Biology
and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Solid
State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - E. Mamontov
- Chemical
and Engineering Materials Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - M. Tyagi
- National Institute of Standards and Technology Center for Neutron Research, Gaithersburg, Maryland 20899, United States
- Department
of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - V. S. Urban
- Biology
and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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Tyagi M, Sharma S, Dewan A, Tandon S, Yadav G, Wadhwan G, Bhushan M, Kumar L, Bandyopadhyay H. EP-1617: Assessment of set-up errors in frameless fractionated SRT of cranial lesions with CBCT and immobilization cast. Radiother Oncol 2015. [DOI: 10.1016/s0167-8140(15)41609-3] [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: 11/30/2022]
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Dhawan AK, Singh S, Tyagi M, Arora V. Scar with recurrent serosanguinous discharge. Clin Exp Dermatol 2014; 40:213-5. [PMID: 25251614 DOI: 10.1111/ced.12462] [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] [Accepted: 04/03/2014] [Indexed: 10/24/2022]
Affiliation(s)
- A K Dhawan
- Department of Dermatology, UCMS and GTB Hospital, Delhi, India
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22
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23
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Affiliation(s)
- C. Chukwudozie
- The Craft and Hawkins Dept. of Petroleum Engineering; Louisiana State University and A & M College; Baton Rouge LA 70803
| | - M. Tyagi
- The Craft and Hawkins Dept. of Petroleum Engineering, Center for Computation and Technology (CCT); Louisiana State University and A & M College; Baton Rouge LA 70803
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24
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Roh JH, Tyagi M, Hogan TE, Roland CM. Effect of binding to carbon black on the dynamics of 1,4-polybutadiene. J Chem Phys 2013; 139:134905. [DOI: 10.1063/1.4822476] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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25
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Affiliation(s)
- J. H. Roh
- Chemistry Division, Code 6120, Naval Research Laboratory, Washington, D.C. 20375-5342,
United States
| | - M. Tyagi
- Center for
Neutron Research, National Institute of Standards and Technology, Gaithersburg,
Maryland 20899-6100, United States
- Department of Materials
Science
and Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - T. E. Hogan
- Center for Research and Technology, Bridgestone Americas, Akron, Ohio 44317-0001, United
States
| | - C. M. Roland
- Chemistry Division, Code 6120, Naval Research Laboratory, Washington, D.C. 20375-5342,
United States
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Abstract
An aqueous methanol solution (x(MeOH) = 0.30) has been studied by quasielastic neutron scattering. The single-particle water dynamics were effectively isolated by employing deuterated methanol. A smooth dynamic transition to a sub-Arrhenius temperature dependence has been observed in the relaxation times. We associate this behavior with the formation of small crystallites in the system. These findings are compared with molecular dynamics simulations and previous nuclear magnetic resonance measurements. We discuss possible dynamic signatures of structuring in the mixture.
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Affiliation(s)
- C E Bertrand
- Department of Nuclear Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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27
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Clenathous S, Tyagi M, Isenberg D, Newman S. THU0479-HPR What do we know about self-reported fatigue in systemic lupus erythematosus? Ann Rheum Dis 2013. [DOI: 10.1136/annrheumdis-2012-eular.2444] [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: 11/04/2022]
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28
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Abstract
Fatigue is one of the most complex and ill understood symptoms of chronic illness often reported as the number one complaint by patients with systemic lupus erythematosus (SLE). This paper aims to provide a comprehensive review of the literature on fatigue in SLE. A pool of 55 relevant articles was retrieved via electronic searches of six databases including MEDLINE, EMBASE, CINAHL, AMED, PsychINFO and PubMed. Fatigue in the studies reviewed was assessed by a range of self-report instruments, the content of which is varied. The results displayed a consensus on the high prevalence of fatigue in SLE, which is significantly higher when compared with controls. The aetiology of fatigue appears to be multifactorial. Disease activity is not always significantly associated with fatigue, in comparison with other secondary features of SLE and psychological variables. The literature is limited by the cross-sectional nature of most of the studies, which does not permit for any firm conclusion regarding the direction of causal relationships to be made. The high prevalence of fatigue in SLE emphasizes the need for further detailed prospective research to inform the understanding of its aetiology, course and management.
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Affiliation(s)
- S Cleanthous
- Centre for Rheumatology Research, University College London, UK
| | - M Tyagi
- Health Services Research, City University, London, UK
| | - DA Isenberg
- Centre for Rheumatology Research, University College London, UK
| | - SP Newman
- Health Services Research, City University, London, UK
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30
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31
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Kapoor N, Tyagi M, Kumar H, Arya A, Siddiqui M, Amir A, Malik A. Production of Cellulase Enzyme by Chaetomium sp. using Wheat Straw in Solid State Fermentation. ACTA ACUST UNITED AC 2010. [DOI: 10.3923/jm.2010.1199.1206] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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32
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Khodadadi S, Roh JH, Kisliuk A, Mamontov E, Tyagi M, Woodson SA, Briber RM, Sokolov AP. Dynamics of biological macromolecules: not a simple slaving by hydration water. Biophys J 2010; 98:1321-6. [PMID: 20371332 DOI: 10.1016/j.bpj.2009.12.4284] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Revised: 11/24/2009] [Accepted: 12/04/2009] [Indexed: 11/29/2022] Open
Abstract
We studied the dynamics of hydrated tRNA using neutron and dielectric spectroscopy techniques. A comparison of our results with earlier data reveals that the dynamics of hydrated tRNA is slower and varies more strongly with temperature than the dynamics of hydrated proteins. At the same time, tRNA appears to have faster dynamics than DNA. We demonstrate that a similar difference appears in the dynamics of hydration water for these biomolecules. The results and analysis contradict the traditional view of slaved dynamics, which assumes that the dynamics of biological macromolecules just follows the dynamics of hydration water. Our results demonstrate that the dynamics of biological macromolecules and their hydration water depends strongly on the chemical and three-dimensional structures of the biomolecules. We conclude that the whole concept of slaving dynamics should be reconsidered, and that the mutual influence of biomolecules and their hydration water must be taken into account.
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Affiliation(s)
- S Khodadadi
- Department of Polymer Science, University of Akron, Akron, Ohio, USA
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33
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34
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Inoue R, Kanaya T, Nishida K, Tsukushi I, Telling MTF, Gabrys BJ, Tyagi M, Soles C, Wu WL. Glass transition and molecular mobility in polymer thin films. Phys Rev E Stat Nonlin Soft Matter Phys 2009; 80:031802. [PMID: 19905138 DOI: 10.1103/physreve.80.031802] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Indexed: 05/28/2023]
Abstract
Extensive studies on polymer thin films to date have revealed their interesting but unusual properties such as film thickness dependence of glass transition temperature Tg and thermal expansivity. Recent studies have shown that the lower Tg is not always related to the higher mobility in polymer thin films, which contradicts our current understanding of the glass transition process. In this work, we report the results of inelastic neutron-scattering measurements on polystyrene thin films using two spectrometers with different energy resolutions as well as ellipsometry measurements. The results are interpreted in terms of cooperatively rearranging region and motional slowing down due to the surface effect that explain plausibly the anomalous relationship between the glass transition temperature Tg and the molecular mobility in thin films.
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Affiliation(s)
- R Inoue
- Institute for Chemical Research, Kyoto University, Uji, Kyoto-fu 611-0011, Japan
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35
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Chandra S, Gautam A, Tyagi M. Synthesis, structural characterization, and antibacterial studies of a tetradentate macrocyclic ligand and Its Co(II), Ni(II), and Cu(II) complexes. RUSS J COORD CHEM+ 2009. [DOI: 10.1134/s1070328409010060] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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36
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Tyagi M, Arbe A, Alvarez F, Colmenero J, González MA. Short-range order and collective dynamics of poly(vinyl acetate): A combined study by neutron scattering and molecular dynamics simulations. J Chem Phys 2008; 129:224903. [DOI: 10.1063/1.3028210] [Citation(s) in RCA: 26] [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: 11/14/2022] Open
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37
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38
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Abstract
We present a comprehensive evaluation of a new structure mining method called PB-ALIGN. It is based on the encoding of protein structure as 1D sequence of a combination of 16 short structural motifs or protein blocks (PBs). PBs are short motifs capable of representing most of the local structural features of a protein backbone. Using derived PB substitution matrix and simple dynamic programming algorithm, PB sequences are aligned the same way amino acid sequences to yield structure alignment. PBs are short motifs capable of representing most of the local structural features of a protein backbone. Alignment of these local features as sequence of symbols enables fast detection of structural similarities between two proteins. Ability of the method to characterize and align regions beyond regular secondary structures, for example, N and C caps of helix and loops connecting regular structures, puts it a step ahead of existing methods, which strongly rely on secondary structure elements. PB-ALIGN achieved efficiency of 85% in extracting true fold from a large database of 7259 SCOP domains and was successful in 82% cases to identify true super-family members. On comparison to 13 existing structure comparison/mining methods, PB-ALIGN emerged as the best on general ability test dataset and was at par with methods like YAKUSA and CE on nontrivial test dataset. Furthermore, the proposed method performed well when compared to flexible structure alignment method like FATCAT and outperforms in processing speed (less than 45 s per database scan). This work also establishes a reliable cut-off value for the demarcation of similar folds. It finally shows that global alignment scores of unrelated structures using PBs follow an extreme value distribution. PB-ALIGN is freely available on web server called Protein Block Expert (PBE) at http://bioinformatics.univ-reunion.fr/PBE/.
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Affiliation(s)
- M Tyagi
- Laboratoire de Biochimie et Génétique Moléculaire, Bioinformatics Team, Université de La Réunion, BP 7151, 15 avenue René Cassin, 97715 Saint Denis Messag Cedex 09, La Réunion, France
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39
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Bartos J, Alegría A, Sausa O, Tyagi M, Gómez D, Kristiak J, Colmenero J. Positron-annihilation-lifetime response and broadband dielectric relaxation spectroscopy: diethyl phthalate. Phys Rev E Stat Nonlin Soft Matter Phys 2007; 76:031503. [PMID: 17930247 DOI: 10.1103/physreve.76.031503] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Indexed: 05/25/2023]
Abstract
We report the results of a combined phenomenological analysis of the data from positron-annihilation-lifetime spectroscopy (PALS) and the relaxation data from broadband dielectric spectroscopy (BDS) on diethyl phthalate (DEP). The ortho-positronium (o-Ps) lifetime, tau3, as a function of temperature over a temperature range from 67 K up to 300 K is compared with the spectral features and the relaxation parameters of the BDS spectra decomposed into the primary alpha and the secondary beta processes in the temperature range from 140 K up to 380 K by using the Williams-Watts scheme. Phenomenological model-free analysis of the tau3-T plot provides the three characteristic PALS temperatures, where the two most pronounced ones at TgPALS=185 K and Tb2=245 K=1.32TgPALS are related to the glass-liquid transition and the onset of a quasiplateau region, respectively. In the case of a weaker bend effect at Tb1=210 K=1.14TgPALS, a number of new coincidences with changes in the dielectric beta process have been found. They concern the changes in width parameter of the distribution function for the beta relaxation time and the activation energy of the betaeff process, a crossover from the Arrhenius to the non-Arrhenius type of temperature dependence as well as with the onset of a short-time tail of the beta relaxation time distribution and finally, with changes in the relaxation strength of the alpha and betaeff processes. All these findings indicate a close connection of the o -Ps annihilation parameters and relaxation characteristics of BDS response for the DEP matrix.
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Affiliation(s)
- J Bartos
- Polymer Institute of SAS, Dúbravská cesta 9, 842 36 Bratislava, Slovakia
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40
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Tyagi M, Arbe A, Alegría A, Colmenero J, Frick B. Dynamic Confinement Effects in Polymer Blends. A Quasielastic Neutron Scattering Study of the Slow Component in the Blend Poly(vinyl acetate)/Poly(ethylene oxide). Macromolecules 2007. [DOI: 10.1021/ma070539i] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M. Tyagi
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, 20018 San Sebastián, Spain, Centro de Física de Materiales (CSIC−UPV/EHU), Apartado 1072, 20080 San Sebastián, Spain, Departamento de Física de Materiales UPV/EHU, Apartado 1072, 20080 San Sebastián, Spain, and Institut Laue−Langevin, BP 156, 38042 Grenoble Cedex 9, France
| | - A. Arbe
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, 20018 San Sebastián, Spain, Centro de Física de Materiales (CSIC−UPV/EHU), Apartado 1072, 20080 San Sebastián, Spain, Departamento de Física de Materiales UPV/EHU, Apartado 1072, 20080 San Sebastián, Spain, and Institut Laue−Langevin, BP 156, 38042 Grenoble Cedex 9, France
| | - A. Alegría
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, 20018 San Sebastián, Spain, Centro de Física de Materiales (CSIC−UPV/EHU), Apartado 1072, 20080 San Sebastián, Spain, Departamento de Física de Materiales UPV/EHU, Apartado 1072, 20080 San Sebastián, Spain, and Institut Laue−Langevin, BP 156, 38042 Grenoble Cedex 9, France
| | - J. Colmenero
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, 20018 San Sebastián, Spain, Centro de Física de Materiales (CSIC−UPV/EHU), Apartado 1072, 20080 San Sebastián, Spain, Departamento de Física de Materiales UPV/EHU, Apartado 1072, 20080 San Sebastián, Spain, and Institut Laue−Langevin, BP 156, 38042 Grenoble Cedex 9, France
| | - B. Frick
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, 20018 San Sebastián, Spain, Centro de Física de Materiales (CSIC−UPV/EHU), Apartado 1072, 20080 San Sebastián, Spain, Departamento de Física de Materiales UPV/EHU, Apartado 1072, 20080 San Sebastián, Spain, and Institut Laue−Langevin, BP 156, 38042 Grenoble Cedex 9, France
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41
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Hernández CJ, Ortíz T, Rosa C, Foster K, Tyagi M, Lugo N, Albrecht R, Chinapen S. Substance P and acetylcholine are co-localized in the pathway mediating mucociliary activity in Rana pipiens. Comp Biochem Physiol B Biochem Mol Biol 2007; 146:477-81. [PMID: 17276713 PMCID: PMC1876671 DOI: 10.1016/j.cbpb.2006.11.012] [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: 07/04/2006] [Revised: 11/10/2006] [Accepted: 11/11/2006] [Indexed: 10/23/2022]
Abstract
Mucociliary activity is an important clearance mechanism in the respiratory system of air breathing vertebrates. Substance P (SP) and acetylcholine play a key role in the stimulation of the mucociliary transport in the frog palate. In this study, retrograde neuronal tracing was combined with immunocytochemistry for SP and choline acetyl transferase (ChAT) in the trigeminal ganglion and for neurokinin-1 receptor (NK1R) in the palate of Rana pipiens. The cells of origin of the palatine nerve were identified in the trigeminal ganglion using the retrograde tracer Fluorogold (FG). Optimal labeling of FG cells in the trigeminal ganglion was obtained at 96 h of exposure. Immunoflorescent shows that SP and acetylcholine are co-localized in 92% of the cells labeled with FG in the trigeminal ganglion. NK1 receptors were found in the membrane of epithelial and goblet cells of the palate. Ultrastructural study of the palate showed axonal-like endings with vesicles in connection with epithelial and goblet cells. These results further support the concerted action of both neurotransmitters in the regulation of mucociliary activity in the frog palate.
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Affiliation(s)
- C J Hernández
- Department of Biology, University of Puerto Rico at Humacao, Humacao 00791, Puerto Rico.
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42
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Tyagi M, Sharma P, Swamy CS, Cadet F, Srinivasan N, de Brevern AG, Offmann B. Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet. Nucleic Acids Res 2006; 34:W119-23. [PMID: 16844973 PMCID: PMC1538797 DOI: 10.1093/nar/gkl199] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [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: 11/13/2022] Open
Abstract
Encoding protein 3D structures into 1D string using short structural prototypes or structural alphabets opens a new front for structure comparison and analysis. Using the well-documented 16 motifs of Protein Blocks (PBs) as structural alphabet, we have developed a methodology to compare protein structures that are encoded as sequences of PBs by aligning them using dynamic programming which uses a substitution matrix for PBs. This methodology is implemented in the applications available in Protein Block Expert (PBE) server. PBE addresses common issues in the field of protein structure analysis such as comparison of proteins structures and identification of protein structures in structural databanks that resemble a given structure. PBE-T provides facility to transform any PDB file into sequences of PBs. PBE-ALIGNc performs comparison of two protein structures based on the alignment of their corresponding PB sequences. PBE-ALIGNm is a facility for mining SCOP database for similar structures based on the alignment of PBs. Besides, PBE provides an interface to a database (PBE-SAdb) of preprocessed PB sequences from SCOP culled at 95% and of all-against-all pairwise PB alignments at family and superfamily levels. PBE server is freely available at .
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Affiliation(s)
- M. Tyagi
- Laboratoire de Biochimie et Génétique Moléculaire, Bioinformatics Team, Université de La RéunionBP 7151, 15 avenue René Cassin, 97715 Saint Denis Messag Cedex 09, La Réunion, France
| | - P. Sharma
- Laboratoire de Biochimie et Génétique Moléculaire, Bioinformatics Team, Université de La RéunionBP 7151, 15 avenue René Cassin, 97715 Saint Denis Messag Cedex 09, La Réunion, France
| | - C. S. Swamy
- Molecular Biophysics Unit, Indian Institute of ScienceBangalore 560 012, India
| | - F. Cadet
- Laboratoire de Biochimie et Génétique Moléculaire, Bioinformatics Team, Université de La RéunionBP 7151, 15 avenue René Cassin, 97715 Saint Denis Messag Cedex 09, La Réunion, France
| | - N. Srinivasan
- Laboratoire de Biochimie et Génétique Moléculaire, Bioinformatics Team, Université de La RéunionBP 7151, 15 avenue René Cassin, 97715 Saint Denis Messag Cedex 09, La Réunion, France
- Molecular Biophysics Unit, Indian Institute of ScienceBangalore 560 012, India
| | - A. G. de Brevern
- INSERM, U726, Equipe de Bioinformatique et Génomique Moléculaire (EBGM), Université Paris 7—Denis Diderotcase 7113, 2, place Jussieu, 75251 Paris Cedex 05, France
| | - B. Offmann
- Laboratoire de Biochimie et Génétique Moléculaire, Bioinformatics Team, Université de La RéunionBP 7151, 15 avenue René Cassin, 97715 Saint Denis Messag Cedex 09, La Réunion, France
- To whom correspondence should be addressed. Tel: +262 262 93 8641; Fax: +262 262 93 8237;
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Tyagi M, Arbe A, Colmenero J, Frick B, Stewart JR. Dynamic Confinement Effects in Polymer Blends. A Quasielastic Neutron Scattering Study of the Dynamics of Poly(ethylene oxide) in a Blend with Poly(vinyl acetate). Macromolecules 2006. [DOI: 10.1021/ma052642i] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- M. Tyagi
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, 20018 San Sebastián, Spain; Unidad Física de Materiales (CSIC−UPV/EHU), Apartado 1072, 20080 San Sebastián, Spain; Departamento de Física de Materiales, UPV/EHU, Apartado 1072, 20080 San Sebastián, Spain; and Institut Laue-Langevin, BP 156, 38042 Grenoble Cedex 9, France
| | - A. Arbe
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, 20018 San Sebastián, Spain; Unidad Física de Materiales (CSIC−UPV/EHU), Apartado 1072, 20080 San Sebastián, Spain; Departamento de Física de Materiales, UPV/EHU, Apartado 1072, 20080 San Sebastián, Spain; and Institut Laue-Langevin, BP 156, 38042 Grenoble Cedex 9, France
| | - J. Colmenero
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, 20018 San Sebastián, Spain; Unidad Física de Materiales (CSIC−UPV/EHU), Apartado 1072, 20080 San Sebastián, Spain; Departamento de Física de Materiales, UPV/EHU, Apartado 1072, 20080 San Sebastián, Spain; and Institut Laue-Langevin, BP 156, 38042 Grenoble Cedex 9, France
| | - B. Frick
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, 20018 San Sebastián, Spain; Unidad Física de Materiales (CSIC−UPV/EHU), Apartado 1072, 20080 San Sebastián, Spain; Departamento de Física de Materiales, UPV/EHU, Apartado 1072, 20080 San Sebastián, Spain; and Institut Laue-Langevin, BP 156, 38042 Grenoble Cedex 9, France
| | - J. R. Stewart
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, 20018 San Sebastián, Spain; Unidad Física de Materiales (CSIC−UPV/EHU), Apartado 1072, 20080 San Sebastián, Spain; Departamento de Física de Materiales, UPV/EHU, Apartado 1072, 20080 San Sebastián, Spain; and Institut Laue-Langevin, BP 156, 38042 Grenoble Cedex 9, France
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44
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Marcello A, Cinelli RA, Ferrari A, Signorelli A, Tyagi M, Pellegrini V, Beltram F, Giacca M. Visualization of in vivo direct interaction between HIV-1 TAT and human cyclin T1 in specific subcellular compartments by fluorescence resonance energy transfer. J Biol Chem 2001; 276:39220-5. [PMID: 11504720 DOI: 10.1074/jbc.m104830200] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human cyclin T1, a component of the P-TEFb kinase complex, was originally identified through its biochemical interaction with the Tat transactivator protein of human immunodeficiency virus type 1 (HIV-1). Current understanding suggests that binding of Tat to P-TEFb is required to promote efficient transcriptional elongation of viral RNAs. However, the dynamics and the subnuclear localization of this process are still largely unexplored in vivo. Here we exploit high resolution fluorescence resonance energy transfer (FRET) to visualize and quantitatively analyze the direct interaction between Tat and cyclin T1 inside the cells. We observed that cyclin T1 resides in specific subnuclear foci which are in close contact with nuclear speckles and that Tat determines its redistribution outside of these compartments. Consistent with this observation, strong FRET was observed between the two proteins both in the cytoplasm and in regions of the nucleus outside of cyclin T1 foci and overlapping with Tat localization. These results are consistent with a model by which Tat recruits cyclin T1 outside of the nuclear compartments where the protein resides to promote transcriptional activation.
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Affiliation(s)
- A Marcello
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34012 Trieste, Italy
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45
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Abstract
Film cooling flows are characterized by a row of jets injected at an angle from the blade surface or endwalls into the heated crossflow. The resulting flowfield is quite complex, and accurate predictions of the flow and heat transfer have been difficult to obtain, particularly in the near field of the injected jet. The flowfield is characterized by a spectrum of vortical structures including the dominant kidney vortex, the horse-shoe vortex, the wake vortices and the shear layer vortices. These anisotropic and unsteady structures are not well represented by empirical or ad-hoc turbulence models, and lead to inaccurate predictions in the near field of the jet. In this paper, a variety of modeling approaches have been reviewed, and the limitations of these approaches are identified. Recent emergence of Direct Numerical Simulation (DNS) and Large Eddy Simulation (LES) tools allow the resolution of the coherent structure dynamics, and it is shown in this paper, that such approaches provide improved predictions over that obtained with turbulence models.
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Affiliation(s)
- S Acharya
- Mechanical Engineering Department, Louisiana State University, Baton Rouge, LA 70803, USA
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46
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Cinelli RA, Tozzini V, Pellegrini V, Beltram F, Cerullo G, Zavelani-Rossi M, De Silvestri S, Tyagi M, Giacca M. Coherent dynamics of photoexcited green fluorescent proteins. Phys Rev Lett 2001; 86:3439-3442. [PMID: 11327990 DOI: 10.1103/physrevlett.86.3439] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2000] [Indexed: 05/23/2023]
Abstract
The coherent dynamics of vibronic wave packets in the green fluorescent protein is reported. At room temperature the nonstationary dynamics following impulsive photoexcitation displays an oscillating optical transmissivity pattern with components at 67 fs (497 cm(-1)) and 59 fs (593 cm(-1)). Our results are complemented by ab initio calculations of the vibrational spectrum of the chromophore. This analysis shows the interplay between the dynamics of the aminoacidic structure and the electronic excitation in the primary optical events of green fluorescent proteins.
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Affiliation(s)
- R A Cinelli
- Scuola Normale Superiore and Istituto Nazionale per la Fisica della Materia, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
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Abstract
Tat, the transactivator protein of human immunodeficiency virus-1, has the unusual capacity of being internalized by cells when present in the extracellular milieu. This property can be exploited for the cellular delivery of heterologous proteins fused to Tat both in cell culture and in living animals. Here we provide genetic and biochemical evidence that cell membrane heparan sulfate (HS) proteoglycans act as receptors for extracellular Tat uptake. Cells genetically defective in the biosynthesis of fully sulfated HS are selectively impaired in the internalization of recombinant Tat fused to the green fluorescent protein, as evaluated by both flow cytometry and functional assays. In wild type cells, Tat uptake is competitively inhibited by soluble heparin and by treatment with glycosaminoglycan lyases specifically degrading HS chains. Cell surface HS proteoglycans also mediate physiological internalization of Tat green fluorescent protein released from neighboring producing cells. In contrast to extracellular Tat uptake, both wild type cells and cells genetically impaired in proteoglycan synthesis are equally proficient in the extracellular release of Tat, thus indicating that proteoglycans are not required for this process. The ubiquitous distribution of HS proteoglycans is consistent with the efficient intracellular delivery of heterologous proteins fused with Tat to different mammalian cell types.
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Affiliation(s)
- M Tyagi
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), 34012 Trieste, Italy
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48
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Tyagi M, Singh S, Singh H. Iodinated natural rubber latex: preparation, characterisation & antibacterial activity assessment. Artif Cells Blood Substit Immobil Biotechnol 2000; 28:521-33. [PMID: 11063093] [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: 04/15/2023]
Abstract
Natural Rubber (NR) in both its latex and dried form was treated with iodine to make it antibacterial in nature. The NR latex was dried and washed, dissolved in toluene, iodinated and cast into films. In a different approach, NR in its latex form (emulsion) was blended with aqueous solution of povidone-iodine complex (PVP-I) and films were cast. Phase separation of PVP-I was observed in the films prepared using NR latex; whereas the film prepared using NR solution in toluene and molecular iodine were homogeneous, transparent light brown. Solubility assessment of the films revealed that unlike pure NR, the iodinated NR failed to go into solution completely. The films obtained from both the approaches were evaluated for release of iodide ions. On immersion in water, PVP-I blended latex did not retain iodine while sustained release of iodide ion was observed in case of dried NR dissolved in toluene and treated with iodine. The FT-IR spectra of the iodinated films revealed that iodine attaches covalently to the double bonds in the isoprene units of NR. The films were also evaluated for their antibacterial properties and it was observed that the films prepared from both the approaches, acquired antimicrobial properties.
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Affiliation(s)
- M Tyagi
- Centre for Biomedical Engineering, Indian Institute of Technology, New Delhi
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49
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Rusnati M, Taraboletti G, Urbinati C, Tulipano G, Giuliani R, Molinari-Tosatti MP, Sennino B, Giacca M, Tyagi M, Albini A, Noonan D, Giavazzi R, Presta M. Thrombospondin-1/HIV-1 tat protein interaction: modulation of the biological activity of extracellular Tat. FASEB J 2000; 14:1917-30. [PMID: 11023976 DOI: 10.1096/fj.99-0902com] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Tat protein, a trans-activating factor of the human immunodeficiency virus type 1, acts also as an extracellular molecule modulating gene expression, cell survival, growth, transformation, and angiogenesis. Here we demonstrate that human thrombospondin-1 (TSP), a plasma glycoprotein and constituent of the extracellular matrix, binds to glutathione-S-transferase (GST)-Tat protein but not to GST. Scatchard plot analysis of the binding of free GST-Tat to immobilized TSP reveals a high-affinity interaction (Kd equal to 25 nM). Accordingly, TSP inhibits cell internalization and HIV-1 LTR trans-activating activity of extracellular Tat in HL3T1 cells with ID50 equal to 10-30 nM. Also, TSP inhibits cell interaction and mitogenic activity of extracellular Tat in T53 Tat-less cells. TSP is instead ineffective when administered after the interaction of Tat with cell surface heparan-sulfate proteoglycans has occurred, in keeping with its ability to prevent but not disrupt Tat/heparin interaction in vitro. Finally, TSP inhibits the autocrine loop of stimulation exerted by endogenous Tat in parental T53 cells. Accordingly, TSP overexpression inhibits cell proliferation, angiogenic activity, and tumorigenic capacity of stable T53 transfectants. Our data demonstrate the ability of TSP to bind to Tat protein and to affect its LTR trans-activating, mitogenic, angiogenic, and tumorigenic activity. These findings suggest that TSP may be implicated in the progression of AIDS and in AIDS-associated pathologies by modulating the bioavailability and biological activity of extracellular Tat.
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Affiliation(s)
- M Rusnati
- Chair of General Pathology and Immunology, University of Brescia, Brescia, Italy
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50
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Cinelli RA, Ferrari A, Pellegrini V, Tyagi M, Giacca M, Beltram F. The enhanced green fluorescent protein as a tool for the analysis of protein dynamics and localization: local fluorescence study at the single-molecule level. Photochem Photobiol 2000; 71:771-6. [PMID: 10857375 DOI: 10.1562/0031-8655(2000)071<0771:tegfpa>2.0.co;2] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The green fluorescent protein (GFP) has emerged, in recent years, as a powerful reporter molecule for monitoring gene expression, protein localization and protein-protein interaction. Several mutant variants are now available differing in absorption, emission spectra and quantum yield. Here we present a detailed study of the fluorescence properties of the Phe-64-->Leu, Ser-65-->Thr mutant down to the single molecule level in order to assess its use in quantitative fluorescence microscopy and single-protein trafficking. This enhanced GFP (EGFP) is being used extensively as it offers higher-intensity emission after blue-light excitation with respect to wild-type GFP. By means of fluorescence spectroscopy we demonstrate the absence of the neutral form of the chromophore and the lack of photobleaching recovery after ultraviolet light irradiation. Furthermore, we show that the EGFP spectral properties from isolated to densely packed molecules are highly conserved. From these experiments EGFP emerges as an ideal molecule for quantitative studies of intra and intercellular tagged-protein dynamics and fluorescence-activated cell sorting, but not for monitoring single-protein trafficking over extended periods of time.
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