1
|
Sahoo GR, Roy AS, Srivastava M. Time-Frequency Analysis of Two-Dimensional Electron Spin Resonance Signals. J Phys Chem A 2023; 127:7793-7801. [PMID: 37699569 PMCID: PMC10529365 DOI: 10.1021/acs.jpca.3c02708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
Two-dimensional electron spin resonance (2D ESR) spectroscopy is a unique experimental technique for probing protein structure and dynamics, including processes that occur at the microsecond time scale. While it provides significant resolution enhancement over the one-dimensional experimental setup, spectral broadening and noise make extraction of spectral information highly challenging. Traditionally, two-dimensional Fourier transform (2D FT) is applied for the analysis of 2D ESR signals, although its efficiency is limited to stationary signals. In addition, it often fails to resolve overlapping peaks in 2D ESR. In this work, we propose a time-frequency analysis of 2D time-domain signals, which identifies all frequency peaks by decoupling a signal into its distinct constituent components via projection on the time-frequency plane. The method utilizes 2D undecimated discrete wavelet transform (2D UDWT) as an intermediate step in the analysis, followed by signal reconstruction and 2D FT. We have applied the method to a simulated 2D double quantum coherence (DQC) signal for validation and a set of experimental 2D ESR signals, demonstrating its efficiency in resolving overlapping peaks in the frequency domain, while displaying frequency evolution with time in case of non-stationary data.
Collapse
Affiliation(s)
- Gyana Ranjan Sahoo
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Aritro Sinha Roy
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- National Biomedical Resources for Advanced ESR Technologies (ACERT), Ithaca, New York 14853, United States
| | - Madhur Srivastava
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- National Biomedical Resources for Advanced ESR Technologies (ACERT), Ithaca, New York 14853, United States
| |
Collapse
|
2
|
Roy AS, Freed JH, Srivastava M. Differentiating Unimodal and Multimodal Distributions in Pulsed Dipolar Spectroscopy Using Wavelet Transforms. Res Sq 2023:rs.3.rs-3216615. [PMID: 37577617 PMCID: PMC10418556 DOI: 10.21203/rs.3.rs-3216615/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Site directed spin labeling has enabled protein structure determination using electron spin resonance (ESR) pulsed dipolar spectroscopy (PDS). Small details in a distance distribution can be key to understanding important protein structure-function relationships. A major challenge has been to differentiate unimodal and overlapped multimodal distance distributions. They often yield similar distributions and dipolar signals. Current model-free distance reconstruction techniques such as Srivastava-Freed Singular Value Decomposition (SF-SVD) and Tikhonov regularization can suppress these small features in uncertainty and/or error bounds, despite being present. In this work, we demonstrate that continuous wavelet transform (CWT) can distinguish PDS signals from unimodal and multimodal distance distributions. We show that periodicity in CWT representation reflects unimodal distributions, which is masked for multimodal cases. This work is meant as a precursor to a cross-validation technique, which could indicate the modality of the distance distribution.
Collapse
Affiliation(s)
- Aritro Sinha Roy
- Department of Chemistry and Chemical Biology, Cornell University, Baker Laboratory, Ithaca, 14853, NY, USA
- National Biomedical Resource for Advanced ESR Spectroscopy, Cornell University, Baker Laboratory, Ithaca, 14853, NY, USA
| | - Jack H. Freed
- Department of Chemistry and Chemical Biology, Cornell University, Baker Laboratory, Ithaca, 14853, NY, USA
- National Biomedical Resource for Advanced ESR Spectroscopy, Cornell University, Baker Laboratory, Ithaca, 14853, NY, USA
| | - Madhur Srivastava
- Department of Chemistry and Chemical Biology, Cornell University, Baker Laboratory, Ithaca, 14853, NY, USA
- National Biomedical Resource for Advanced ESR Spectroscopy, Cornell University, Baker Laboratory, Ithaca, 14853, NY, USA
- Cornell Atkinson Center for Sustainability, Cornell University, 340 Tower Road, Ithaca, 14853, NY, USA
| |
Collapse
|
3
|
Roy AS, Dzikovski B, Dolui D, Makhlynets O, Dutta A, Srivastava M. A Simulation Independent Analysis of Single- and Multi-Component cw ESR Spectra. Magnetochemistry 2023; 9:112. [PMID: 37476293 PMCID: PMC10357894 DOI: 10.3390/magnetochemistry9050112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
The accurate analysis of continuous-wave electron spin resonance (cw ESR) spectra of biological or organic free-radicals and paramagnetic metal complexes is key to understanding their structure-function relationships and electrochemical properties. The current methods of analysis based on simulations often fail to extract the spectral information accurately. In addition, such analyses are highly sensitive to spectral resolution and artifacts, users' defined input parameters and spectral complexity. We introduce a simulation-independent spectral analysis approach that enables broader application of ESR. We use a wavelet packet transform-based method for extracting g values and hyperfine (A) constants directly from cw ESR spectra. We show that our method overcomes the challenges associated with simulation-based methods for analyzing poorly/partially resolved and unresolved spectra, which is common in most cases. The accuracy and consistency of the method are demonstrated on a series of experimental spectra of organic radicals and copper-nitrogen complexes. We showed that for a two-component system, the method identifies their individual spectral features even at a relative concentration of 5% for the minor component.
Collapse
Affiliation(s)
- Aritro Sinha Roy
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
- National Biomedical Resource for Advanced ESR Spectroscopy, Cornell University, Ithaca, NY 14853, USA
| | - Boris Dzikovski
- National Biomedical Resource for Advanced ESR Spectroscopy, Cornell University, Ithaca, NY 14853, USA
| | - Dependu Dolui
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Olga Makhlynets
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, USA
| | - Arnab Dutta
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Madhur Srivastava
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
- National Biomedical Resource for Advanced ESR Spectroscopy, Cornell University, Ithaca, NY 14853, USA
| |
Collapse
|
4
|
Sinha Roy A, Srivastava M. Analysis of Small-Molecule Mixtures by Super-Resolved 1H NMR Spectroscopy. J Phys Chem A 2022; 126:9108-9113. [PMID: 36413171 DOI: 10.1021/acs.jpca.2c06858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Analysis of small molecules is essential to metabolomics, natural products, drug discovery, food technology, and many other areas of interest. Current barriers preclude from identifying the constituent molecules in a mixture as overlapping clusters of NMR lines pose a major challenge in resolving signature frequencies for individual molecules. While homonuclear decoupling techniques produce much simplified pure shift spectra, they often affect sensitivity. Conversion of typical NMR spectra to pure shift spectra by signal processing without a priori knowledge about the coupling patterns is essential for accurate analysis. We developed a super-resolved wavelet packet transform based 1H NMR spectroscopy that can be used in high-throughput studies to reliably decouple individual constituents of small molecule mixtures. We demonstrate the efficacy of the method on the model mixtures of saccharides and amino acids in the presence of significant noise.
Collapse
Affiliation(s)
- Aritro Sinha Roy
- Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-0001,United States
| | - Madhur Srivastava
- Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-0001,United States.,National Biomedical Resources for Advanced ESR Technologies (ACERT), Ithaca, New York 14853, United States
| |
Collapse
|
5
|
Rittmeyer A, Felip E, Altorki N, Vallieres E, Zhou C, Martinez-Marti A, Csoszi T, Reck M, Teixeira M, Deng Y, Huang M, McNally V, Bennett E, Gitlitz B, Srivastava M, Wakelee H. 123P IMpower010: Exploratory overall survival (OS) with adjuvant atezolizumab (atezo) vs best supportive care (BSC) in stage II-IIIA NSCLC with high PD-L1 expression. Immuno-Oncology and Technology 2022. [DOI: 10.1016/j.iotech.2022.100235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
6
|
Sawalgi V, Amin D, Arora AJ, Srivastava M, Uppin M. A Rare Case of Systemic Cystic Angiomatosis Involving the Bones, Spleen, Liver, and Lungs. Cureus 2022; 14:e30414. [DOI: 10.7759/cureus.30414] [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] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
|
7
|
Frings VG, Jopp L, Srivastava M, Presser D, Goebeler M, Schmidt M. Stress signaling and STAT1 activation characterize the keratinocytic gene expression pattern in Hidradenitis suppurativa. J Eur Acad Dermatol Venereol 2022; 36:2488-2498. [PMID: 35881108 DOI: 10.1111/jdv.18465] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 07/11/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND The pathogenetic factors generating the innate immune signal necessary for T cell activation, initiation and chronification of Hidradenitis suppurativa (HS, also known as Acne inversa) are still poorly understood. Emerging evidence suggests that a defective keratinocyte function critically contributes to HS disease development and progression. OBJECTIVES To elucidate the role of keratinocytes in HS lesion formation, we compared the transcriptomes of lesional and perilesional epidermis isolated from HS patients by RNA sequencing (RNA Seq). METHODS Pairwise-matched lesional and perilesional HS skin samples of five different donors were obtained and epidermal keratinocytes freshly isolated and processed for RNA extraction and RNA seq. Lesionally regulated genes were analyzed by large scale promotor analysis and functional annotation clustering to identify epidermally overrepresented transcription factor binding sites and functionally related gene groups. Results were experimentally validated with independent epidermal isolates of patient-matched lesional and perilesional HS skin employing qRT-PCR, cell culture, immunoblot, and immunostaining. RESULTS We show that HS is characterized by a strong epidermal stress state evident by a significant overrepresentation of an AP-1-driven gene signature and a substantial activation of the stress-activated cJun N-terminal kinase (JNK) pathway in lesional epidermis. Additionally, our data reveal a strong induction of STAT1 activation in lesional HS epidermis that likely results from IFNγ production and triggered expression of key inflammatory genes coordinating innate immune activation and the adaptive T cell response in HS. CONCLUSIONS Our data implicate a key role of stress signaling and JAK/STAT1 activation in disease progression of HS and suggest interference with JAK/STAT1 signaling as a potentially promising therapeutic approach for HS.
Collapse
Affiliation(s)
- V G Frings
- Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, Germany
| | - L Jopp
- Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, Germany
| | - M Srivastava
- Core Unit Systemmedizin (SysMed), Medical Faculty, University of Würzburg, Würzburg, Germany
| | - D Presser
- Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, Germany
| | - M Goebeler
- Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, Germany
| | - M Schmidt
- Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, Germany
| |
Collapse
|
8
|
Lavanya V, Malik IM, Nallapareddy K, Srivastava M, Valiyaveettil D, Ahmed SF. Correlation of Target Volumes on Magnetic Resonance Imaging and Prostate-Specific Membrane Antigen Brain Scans in the Treatment Planning of Glioblastomas. Indian J Nucl Med 2022; 37:245-248. [PMID: 36686310 PMCID: PMC9855252 DOI: 10.4103/ijnm.ijnm_189_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/08/2022] [Accepted: 02/23/2022] [Indexed: 11/05/2022] Open
Abstract
Background Imaging of gliomas/glioblastomas has always been challenging. Many magnetic resonance imaging (MRI) techniques are available for imaging glioblastomas. MRI cannot always differentiate tumor from nonspecific changes and postoperative changes in brain tissue. Among the new positron emission tomography-computed tomography (PET-CT) tracers, gallium-68 prostate-specific membrane antigen (Ga-68 PSMA-11 PET-CT) appears to be the most promising one. The absence of uptake by normal brain parenchyma leads to high tumor-to-background ratio leading to better visualization of the tumor. Objective The aim of this study was to assess the correlation of target volumes on MRI and PSMA brain scans in the treatment planning of glioblastomas. Materials and Methods Twenty-four patients in the age group of 5-75 years with histologically proven glioblastoma were included in the study following maximum safe resection. Simulation for treatment planning was done with Ga-68 PSMA PET-CT brain with IV iodine-based contrast. The pre- and postoperative MRI images were fused with PSMA simulation images. Gross tumor volumes (GTVs) contoured on T1-contrast MRI and on PSMA scans were compared. Results GTV contoured on MRI and PSMA brain scans showed complete overlap in 17 patients. In seven patients, the target volumes drawn on Ga-68 PSMA brain scans were slightly smaller than the target volumes drawn on MRI brain scans. This difference in volumes could be due to postoperative changes which showed enhancement on the MRI scan. Conclusion Ga-68 PSMA PET-CT shows good correlation with MRI brain in the evaluation and RT planning in glioblastomas. Tumor necrosis and postoperative changes did not show PSMA uptake. Precise target delineation on PSMA PET-CT can potentially result in smaller and more accurate GTVs, which in turn would result in less RT-induced side effects.
Collapse
Affiliation(s)
- Vutkuri Lavanya
- Department of Radiation Oncology, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India
| | - Irukulla Monica Malik
- Department of Radiation Oncology, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India
| | - Kavitha Nallapareddy
- Department of Nuclear Medicine, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India
| | - Madhur Srivastava
- Department of Nuclear Medicine, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India
| | - Deepthi Valiyaveettil
- Department of Radiation Oncology, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India
| | - Syed Fayaz Ahmed
- Department of Radiation Oncology, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India
| |
Collapse
|
9
|
Bekerman W, Srivastava M. Enabling dynamics studies of proteins at low concentrations using electron spin resonance. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.731] [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] Open
|
10
|
Srivastava M. Revisiting signal analysis in the big data era. Nat Comput Sci 2022; 2:70-71. [PMID: 37274540 PMCID: PMC10238072 DOI: 10.1038/s43588-022-00210-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A fast and accurate time-frequency analysis is challenging for many applications, especially in the current big data era. A recent work introduces a fast continuous wavelet transform that effectively boosts the analysis speed without sacrificing the resolution of the result.
Collapse
Affiliation(s)
- Madhur Srivastava
- National Biomedical Center for Advanced ESR Technology, Cornell University, Ithaca, NY, USA
- Department of Chemistry and Chemical Biology, Ithaca, NY, USA
| |
Collapse
|
11
|
Schmidt T, Freed JH, Clore GM, Srivastava M. Studying structure evolution of proteins using pulsed dipolar spectroscopy. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.735] [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: 11/02/2022] Open
|
12
|
Abstract
Noise impedes experimental studies by reducing signal resolution and/or suppressing weak signals. Signal averaging and filtering are the primary methods used to reduce noise, but they have limited effectiveness and lack capabilities to recover signals at low signal-to-noise ratios (SNRs). We utilize a wavelet transform-based approach to effectively remove noise from spectroscopic data. The wavelet denoising method we use is a significant improvement on standard wavelet denoising approaches. We demonstrate its power in extracting signals from noisy spectra on a variety of signal types ranging from hyperfine lines to overlapped peaks to weak peaks overlaid on strong ones, drawn from electron-spin-resonance spectroscopy. The results show that one can accurately extract details of complex spectra, including retrieval of very weak ones. It accurately recovers signals at an SNR of ∼1 and improves the SNR by about 3 orders of magnitude with high fidelity. Our examples show that one is now able to address weaker SNR signals much better than by previous methods. This new wavelet approach can be successfully applied to other spectroscopic signals.
Collapse
Affiliation(s)
- Madhur Srivastava
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca 14853, United States.,National Biomedical Center for Advanced Electron Spin Resonance Technology, Cornell University, Ithaca 14853, United States
| | - Boris Dzikovski
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca 14853, United States
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca 14853, United States.,National Biomedical Center for Advanced Electron Spin Resonance Technology, Cornell University, Ithaca 14853, United States
| |
Collapse
|
13
|
Manning LK, Srivastava M, Bingham J, Curran GC, Westermann T, Cook RW. Neuronal inclusions resembling Negri bodies in the thalamus of a red kangaroo (Macropus rufus). Aust Vet J 2021; 99:178-180. [PMID: 33559148 DOI: 10.1111/avj.13057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/15/2020] [Accepted: 01/10/2021] [Indexed: 11/30/2022]
Abstract
Eosinophilic intracytoplasmic neuronal inclusions resembling Negri bodies, but not associated with lyssaviral infection, were detected in the ventrolateral thalamus of a young-adult, male red kangaroo (Macropus rufus). Similar neuronal inclusions, also with a regional distribution in the brain, have been reported as an incidental, possibly age-related finding in other animal species.
Collapse
Affiliation(s)
- L K Manning
- Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales, 2568, Australia
| | - M Srivastava
- Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales, 2568, Australia
| | - J Bingham
- CSIRO Australian Centre for Disease Preparedness, East Geelong, Victoria, 3219, Australia
| | - G C Curran
- Animal and Climate Investigations, Broken Hill, New South Wales, 2880, Australia
| | - T Westermann
- Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales, 2568, Australia
| | - R W Cook
- Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales, 2568, Australia
| |
Collapse
|
14
|
Muok AR, Chua TK, Srivastava M, Yang W, Maschmann Z, Borbat PP, Chong J, Zhang S, Freed JH, Briegel A, Crane BR. Engineered chemotaxis core signaling units indicate a constrained kinase-off state. Sci Signal 2020; 13:13/657/eabc1328. [PMID: 33172954 DOI: 10.1126/scisignal.abc1328] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Bacterial chemoreceptors, the histidine kinase CheA, and the coupling protein CheW form transmembrane molecular arrays with remarkable sensing properties. The receptors inhibit or stimulate CheA kinase activity depending on the presence of attractants or repellants, respectively. We engineered chemoreceptor cytoplasmic regions to assume a trimer of receptor dimers configuration that formed well-defined complexes with CheA and CheW and promoted a CheA kinase-off state. These mimics of core signaling units were assembled to homogeneity and investigated by site-directed spin-labeling with pulse-dipolar electron-spin resonance spectroscopy (PDS), small-angle x-ray scattering, targeted protein cross-linking, and cryo-electron microscopy. The kinase-off state was especially stable, had relatively low domain mobility, and associated the histidine substrate and docking domains with the kinase core, thus preventing catalytic activity. Together, these data provide an experimentally restrained model for the inhibited state of the core signaling unit and suggest that chemoreceptors indirectly sequester the kinase and substrate domains to limit histidine autophosphorylation.
Collapse
Affiliation(s)
- Alise R Muok
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.,Institute for Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Teck Khiang Chua
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Madhur Srivastava
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.,National Biomedical Center for Advanced ESR Technologies (ACERT), Cornell University, Ithaca, NY 14853, USA
| | - Wen Yang
- Institute for Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Zach Maschmann
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Petr P Borbat
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.,National Biomedical Center for Advanced ESR Technologies (ACERT), Cornell University, Ithaca, NY 14853, USA
| | - Jenna Chong
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Sheng Zhang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.,National Biomedical Center for Advanced ESR Technologies (ACERT), Cornell University, Ithaca, NY 14853, USA
| | - Ariane Briegel
- Institute for Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
| |
Collapse
|
15
|
Badea CT, Clark DP, Holbrook M, Srivastava M, Mowery Y, Ghaghada KB. Functional imaging of tumor vasculature using iodine and gadolinium-based nanoparticle contrast agents: a comparison of spectral micro-CT using energy integrating and photon counting detectors. Phys Med Biol 2019; 64:065007. [PMID: 30708357 PMCID: PMC6607440 DOI: 10.1088/1361-6560/ab03e2] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Advances in computed tomography (CT) hardware have propelled the development of novel CT contrast agents. In particular, the spectral capabilities of x-ray CT can facilitate simultaneous imaging of multiple contrast agents. This approach is particularly useful for functional imaging of solid tumors by simultaneous visualization of multiple targets or architectural features that govern cancer development and progression. Nanoparticles are a promising platform for contrast agent development. While several novel imaging moieties based on high atomic number elements are being explored, iodine (I) and gadolinium (Gd) are particularly attractive because of their existing approval for clinical use. In this work, we investigate the in vivo discrimination of I and Gd nanoparticle contrast agents using both dual energy micro-CT with energy integrating detectors (DE-EID) and photon counting detector (PCD)-based spectral micro-CT. Simulations and phantom experiments were performed using varying concentrations of I and Gd to determine the imaging performance with optimized acquisition parameters. Quantitative spectral micro-CT imaging using liposomal-iodine (Lip-I) and liposomal-Gd (Lip-Gd) nanoparticle contrast agents was performed in sarcoma bearing mice for anatomical and functional imaging of tumor vasculature. Iterative reconstruction provided high sensitivity to detect and discriminate relatively low I and Gd concentrations. According to the Rose criterion applied to the experimental results, the detectability limits for I and Gd were approximately 2.5 mg ml-1 for both DE-EID CT and PCD micro-CT, even if the radiation dose was approximately 3.8 times lower with PCD micro-CT. The material concentration maps confirmed expected biodistributions of contrast agents in the blood, liver, spleen and kidneys. The PCD provided lower background signal and better simultaneous visualization of tumor vasculature and intratumoral distribution patterns of nanoparticle contrast agent compared to DE-EID decompositions. Preclinical spectral CT systems such as this could be useful for functional characterization of solid tumors, simultaneous quantitative imaging of multiple targets and for identifying clinically-relevant applications that benefit from the use of spectral imaging. Additionally, it could aid in the development nanoparticles that show promise in the developing field of cancer theranostics (therapy and diagnostics) by measuring vascular tumor biomarkers such as fractional blood volume and the delivery of liposomal chemotherapeutics.
Collapse
Affiliation(s)
- C T Badea
- Department of Radiology, Center for In Vivo Microscopy, Duke University, Durham, NC 27710, United States of America.,http://civm.duhs.duke.edu/.,Author to whom any correspondence should be addressed
| | - D P Clark
- Department of Radiology, Center for In Vivo Microscopy, Duke University, Durham, NC 27710, United States of America
| | - M Holbrook
- Department of Radiology, Center for In Vivo Microscopy, Duke University, Durham, NC 27710, United States of America
| | - M Srivastava
- Singleton Department of Pediatric Radiology, Texas Children's Hospital, Houston, TX 77030, United States of America
| | - Y Mowery
- Department of Radiation Oncology, Duke University, Durham, NC 27710, United States of America
| | - K B Ghaghada
- Singleton Department of Pediatric Radiology, Texas Children's Hospital, Houston, TX 77030, United States of America
| |
Collapse
|
16
|
Bera A, Eidelman O, Russ E, Landa A, Karaian J, Eklund M, Hu H, Pollard HB, Shriver CD, Srivastava M. Abstract P4-01-26: Circulating cell-free DNA in serum as a marker for the early detection of tumor recurrence in breast cancer patients. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p4-01-26] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Quantitative estimation of circulating cell-free DNA (cfDNA) isolated from serum by noninvasive procedures can serve as a potential biomarker for the early detection of many cancers. However, a simple, straightforward technique is unavailable to estimate the cfDNA in clinical labs. Moreover, the prognostic value of cfDNA in patients with breast cancer (BrCa) is currently under debate. The aim of this study was to develop a simple yet effective quantitative method for measuring the cfDNA in serum and to eventually investigate the relationship between cfDNA and the occurrence of recurrence in BrCa patients.
Methods: A total of 240 patient cases (n=240) were selected and are comprised of different subtypes of breast cancer patients and control individuals. We selected 21 serum samples from patients which showed recurrence after 4-7 years of disease-free survival. For the compare studies, each of the recurrent and non-recurrent serum samples was incubated with the SYBR Green I (2 μM). A standard graph was also made with known DNA concentration to calculate the amount of cfDNA in these recurrent and non-recurrent serum samples. Additionally, a comparative study was also performed with the serum of patients with non-recurrent BrCa versus healthy patients.
Results: We develop a simple fluorescent based measuring technique which can easily estimate the cfDNA in one step. SYBR Green binds to DNA, and as a result, the fluorescence of SYBR Green increases substantially. Global Wilcoxon analyses were performed to compare the cfDNA amount between non-recurrent and recurrent patients. There is a significant difference in fluorescent intensities between recurrent patients' samples versus non-recurrent patients which are directly proportional to the cfDNA levels. The amount of cfDNA is higher in recurrent patient (ratio is 1.3 up; p= 0.03; AUC=0.76) compared to similar non-recurrent patients. While we compared the fluorescence data between normal/healthy patients versus non-recurrent is turned out as non-significant (healthy to non-recurrent ratio = 1.03; p= 0.20, AUC=0.61).
Conclusion: In this current study, we developed a straightforward one-step technique to measure the amount of cfDNA in serum, which can easily translate into a clinical diagnostic tool. To the best of our knowledge, this is the first report which demonstrates serum cfDNA as an early detection marker for recurrent breast cancer patients. The relatively high level of cfDNA in the serum of recurrent breast cancer patients compared to non-recurrent breast cancer patients indicates an uncovered circulating genetic information which triggers the cancer recurrence pathway to relapse cancer in the near future.
Citation Format: Bera A, Eidelman O, Russ E, Landa A, Karaian J, Eklund M, Hu H, Pollard HB, Shriver CD, Srivastava M. Circulating cell-free DNA in serum as a marker for the early detection of tumor recurrence in breast cancer patients [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-01-26.
Collapse
Affiliation(s)
- A Bera
- Uniformed Services University, Bethesda, MD; Walter Reed National Military Medical Center, Bethesda, MD; Chan Soon-Shiong Institute of Molecular Medicine, Windber, PA
| | - O Eidelman
- Uniformed Services University, Bethesda, MD; Walter Reed National Military Medical Center, Bethesda, MD; Chan Soon-Shiong Institute of Molecular Medicine, Windber, PA
| | - E Russ
- Uniformed Services University, Bethesda, MD; Walter Reed National Military Medical Center, Bethesda, MD; Chan Soon-Shiong Institute of Molecular Medicine, Windber, PA
| | - A Landa
- Uniformed Services University, Bethesda, MD; Walter Reed National Military Medical Center, Bethesda, MD; Chan Soon-Shiong Institute of Molecular Medicine, Windber, PA
| | - J Karaian
- Uniformed Services University, Bethesda, MD; Walter Reed National Military Medical Center, Bethesda, MD; Chan Soon-Shiong Institute of Molecular Medicine, Windber, PA
| | - M Eklund
- Uniformed Services University, Bethesda, MD; Walter Reed National Military Medical Center, Bethesda, MD; Chan Soon-Shiong Institute of Molecular Medicine, Windber, PA
| | - H Hu
- Uniformed Services University, Bethesda, MD; Walter Reed National Military Medical Center, Bethesda, MD; Chan Soon-Shiong Institute of Molecular Medicine, Windber, PA
| | - HB Pollard
- Uniformed Services University, Bethesda, MD; Walter Reed National Military Medical Center, Bethesda, MD; Chan Soon-Shiong Institute of Molecular Medicine, Windber, PA
| | - CD Shriver
- Uniformed Services University, Bethesda, MD; Walter Reed National Military Medical Center, Bethesda, MD; Chan Soon-Shiong Institute of Molecular Medicine, Windber, PA
| | - M Srivastava
- Uniformed Services University, Bethesda, MD; Walter Reed National Military Medical Center, Bethesda, MD; Chan Soon-Shiong Institute of Molecular Medicine, Windber, PA
| |
Collapse
|
17
|
Srivastava M, Freed JH. Revealing Multiple Conformations of Proteins at Long Distances by using Singular Value Decomposition Method in Pulsed Dipolar ESR Spectroscopy. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.935] [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: 11/27/2022] Open
|
18
|
Srivastava M, Freed JH. Singular Value Decomposition Method To Determine Distance Distributions in Pulsed Dipolar Electron Spin Resonance: II. Estimating Uncertainty. J Phys Chem A 2018; 123:359-370. [PMID: 30525624 DOI: 10.1021/acs.jpca.8b07673] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This paper is a continuation of the method introduced by Srivastava and Freed (2017) that is a new method based on truncated singular value decomposition (TSVD) for obtaining physical results from experimental signals without any need for Tikhonov regularization or other similar methods that require a regularization parameter. We show here how to estimate the uncertainty in the SVD-generated solutions. The uncertainty in the solution may be obtained by finding the minimum and maximum values over which the solution remains converged. These are obtained from the optimum range of singular value contributions, where the width of this region depends on the solution point location (e.g., distance) and the signal-to-noise ratio (SNR) of the signal. The uncertainty levels typically found are very small with substantial SNR of the (denoised) signal, emphasizing the reliability of the method. With poorer SNR, the method is still satisfactory but with greater uncertainty, as expected. Pulsed dipolar electron spin resonance spectroscopy experiments are used as an example, but this TSVD approach is general and thus applicable to any similar experimental method wherein singular matrix inversion is needed to obtain the physically relevant result. We show that the Srivastava-Freed TSVD method along with the estimate of uncertainty can be effectively applied to pulsed dipolar electron spin resonance signals with SNR > 30, and even for a weak signal (e.g., SNR ≈ 3) reliable results are obtained by this method, provided the signal is first denoised using wavelet transforms (WavPDS).
Collapse
|
19
|
Merz GE, Borbat PP, Muok AR, Srivastava M, Bunck DN, Freed JH, Crane BR. Site-Specific Incorporation of a Cu 2+ Spin Label into Proteins for Measuring Distances by Pulsed Dipolar Electron Spin Resonance Spectroscopy. J Phys Chem B 2018; 122:9443-9451. [PMID: 30222354 DOI: 10.1021/acs.jpcb.8b05619] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Pulsed dipolar electron spin resonance spectroscopy (PDS) is a powerful tool for measuring distances in solution-state macromolecules. Paramagnetic metal ions, such as Cu2+, are used as spin probes because they can report on metalloprotein features and can be spectroscopically distinguished from traditional nitroxide (NO)-based labels. Here, we demonstrate site-specific incorporation of Cu2+ into non-metalloproteins through the use of a genetically encodable non-natural amino acid, 3-pyrazolyltyrosine (PyTyr). We first incorporate PyTyr in cyan fluorescent protein to measure Cu2+-to-NO distances and examine the effects of solvent conditions on Cu2+ binding and protein aggregation. We then apply the method to characterize the complex formed by the histidine kinase CheA and its target response regulator CheY. The X-ray structure of CheY-PyTyr confirms Cu labeling at PyTyr but also reveals a secondary Cu site. Cu2+-to-NO and Cu2+-to-Cu2+ PDS measurements of CheY-PyTyr with nitroxide-labeled CheA provide new insights into the conformational landscape of the phosphotransfer complex and have implications for kinase regulation.
Collapse
Affiliation(s)
- Gregory E Merz
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
| | - Peter P Borbat
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
| | - Alise R Muok
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
| | - Madhur Srivastava
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
| | - David N Bunck
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
| | - Jack H Freed
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
| | - Brian R Crane
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
| |
Collapse
|
20
|
Srivastava M, Gupta A, Ojha B, Kumar D, Mishra S, Yadav G. Effect of fluoroscopically guided caudal epidural steroid injection in degenerative lumbar spinal stenosis–A randomized controlled trial. Ann Phys Rehabil Med 2018. [DOI: 10.1016/j.rehab.2018.05.035] [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: 10/28/2022]
|
21
|
Srivastava M, Freed JH. A New Wavelet Approach to Remove Noise from Experimental Signals: Reducing Signal Acquisition Times and Improving Resolution in Biophysical Methods. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.2047] [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: 10/18/2022] Open
|
22
|
Bera A, Leighton XM, Pollard H, Srivastava M. Cyclin E and FGF8 are downstream cell growth regulators in distinct tumor suppressor effects of ANXA7 in hormone-resistant cancer cells of breast versus prostate origin. Trends Cancer Res 2018; 13:55-62. [PMID: 30369774 PMCID: PMC6200414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Tumor suppressor function of Annexin-A7 (ANXA7) was demonstrated by cancer-prone phenotype in Anxa7(+/-) mice and ANXA7 profiling in human cancers including prostate and breast. Consistent with its more evident in vivo tumor suppressor role in prostate cancer, wild-type(wt)-ANXA7 in vitro induced similar G2-arrests, but reduced survival more drastically in prostate cancer cells compared to breast cancer cells (DU145 versus MDA-MB-231 and -435). In all three hormone-resistant cancer cell lines, wt-ANXA7 abolished the expression of the oncogenic low-molecular weight (LMW) cyclin E which was for the first time encountered in prostate cancer cells. Dominant-negative nMMM-ANXA7 (which lacks phosphatidylserine liposome aggregation properties) failed to abrogate LMW-cyclin E and simultaneously induced fibroblast growth factor 8 (FGF8) in DU145 that was consistent with the continuing cell cycle progression and reduced cell death. Adenoviral vector alone induced FGF8 in MDA-MB-231/435 cell lines, but not in DU145 cells. Our data indicated that the LMW-Cyclin E expressions in breast cancer and prostate cancer cell-lines were differentially regulated by wild-type and dominant-negative ANXA7 isoforms, demonstrating a different survival mechanism utilized by breast cancer cells. Conventional tumor suppressor p53 failed to completely abolish FGF8 and LMW-cyclin E in breast cancer cells, which were eventually translated into their survival. Thus, ANXA7 tumor suppression could modulate FGF8 and cyclin E expression, and control implying more specific associations with the annexin properties of ANXA7 in prostate tumorigenesis.
Collapse
|
23
|
Srivastava M, Alla SK, Meena SS, Gupta N, Mandal RK, Prasad NK. ZnxFe3−xO4 (0.01 ≤ x ≤ 0.8) nanoparticles for controlled magnetic hyperthermia application. NEW J CHEM 2018. [DOI: 10.1039/c8nj00547h] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [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
Stable temperature was attained during magnetic hyperthermia by Zn substituted magnetite nanoparticles.
Collapse
Affiliation(s)
- M. Srivastava
- Department of Metallurgical Engineering, Indian Institute of Technology (Banaras Hindu University)
- Varanasi
- India
| | - S. K. Alla
- Department of Metallurgical Engineering, Indian Institute of Technology (Banaras Hindu University)
- Varanasi
- India
| | - Sher Singh Meena
- Solid State Physics Division
- Bhabha Atomic Research Centre
- Mumbai
- India
| | - Nidhi Gupta
- Technical Physics Division
- Bhabha Atomic Research Centre
- Mumbai
- India
| | - R. K. Mandal
- Department of Metallurgical Engineering, Indian Institute of Technology (Banaras Hindu University)
- Varanasi
- India
| | - N. K. Prasad
- Department of Metallurgical Engineering, Indian Institute of Technology (Banaras Hindu University)
- Varanasi
- India
| |
Collapse
|
24
|
Abstract
Regularization is often utilized to elicit the desired physical results from experimental data. The recent development of a denoising procedure yielding about 2 orders of magnitude in improvement in SNR obviates the need for regularization, which achieves a compromise between canceling effects of noise and obtaining an estimate of the desired physical results. We show how singular value decomposition (SVD) can be employed directly on the denoised data, using pulse dipolar electron spin resonance experiments as an example. Such experiments are useful in measuring distances and their distributions, P(r) between spin labels on proteins. In noise-free model cases exact results are obtained, but even a small amount of noise (e.g., SNR = 850 after denoising) corrupts the solution. We develop criteria that precisely determine an optimum approximate solution, which can readily be automated. This method is applicable to any signal that is currently processed with regularization of its SVD analysis.
Collapse
Affiliation(s)
- Madhur Srivastava
- National Biomedical Center for Advanced ESR Technology, Cornell University, Ithaca, New York 14853, United States
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Jack H. Freed
- National Biomedical Center for Advanced ESR Technology, Cornell University, Ithaca, New York 14853, United States
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Corresponding Author:
| |
Collapse
|
25
|
Singh RK, Srivastava M, Prasad NK, Shetty PH, Kannan S. Hyperthermia effect and antibacterial efficacy of Fe
3+
/Co
2+
co‐substitutions in β‐Ca
3
(PO
4
)
2
for bone cancer and defect therapy. J Biomed Mater Res B Appl Biomater 2017; 106:1317-1328. [DOI: 10.1002/jbm.b.33921] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 04/11/2017] [Accepted: 04/22/2017] [Indexed: 01/16/2023]
Affiliation(s)
- Ram Kishore Singh
- Centre for Nanoscience and Technology, Pondicherry UniversityPuducherry605 014 India
| | - M. Srivastava
- Department of Metallurgical EngineeringIndian Institute of Technology (Banaras Hindu University)Varanasi221005 Uttar Pradesh India
| | - N. K. Prasad
- Department of Metallurgical EngineeringIndian Institute of Technology (Banaras Hindu University)Varanasi221005 Uttar Pradesh India
| | - P. H. Shetty
- Department of Food Science and TechnologyPondicherry UniversityPuducherry605 014 India
| | - S. Kannan
- Centre for Nanoscience and Technology, Pondicherry UniversityPuducherry605 014 India
| |
Collapse
|
26
|
Singh RK, Srivastava M, Prasad NK, Awasthi S, Dhayalan A, Kannan S. Iron doped β-Tricalcium phosphate: Synthesis, characterization, hyperthermia effect, biocompatibility and mechanical evaluation. Mater Sci Eng C Mater Biol Appl 2017; 78:715-726. [PMID: 28576042 DOI: 10.1016/j.msec.2017.04.130] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 04/20/2017] [Accepted: 04/21/2017] [Indexed: 01/22/2023]
Abstract
The ability of β-Tricalcium phosphate [β-TCP, β-Ca3(PO4)2] to host iron at its structural lattice and its associated magnetic susceptibility, hyperthermia effect, biocompatibility and mechanical characteristics is investigated. The studies revealed the ability of β-Ca3(PO4)2 to host 5.02mol% of Fe3+ at its Ca2+(5) site. Excess Fe3+ additions led to the formation of trigonal Ca9Fe(PO4)7 and moreover a minor amount of CaFe3(PO4)3O crystallization was also observed. A gradual increment in the iron content at β-Ca3(PO4)2 results in the simultaneous effect of pronounced hyperthermia effect and mechanical stability. However, the presence of CaFe3(PO4)3O contributes for the reduced hyperthermia effect and mechanical stability of iron substituted β-Ca3(PO4)2. Haemolytic tests, cytotoxicity tests and ALP gene expression analysis confirmed the biocompatibility of the investigated systems.
Collapse
Affiliation(s)
- Ram Kishore Singh
- Centre for Nanoscience and Technology, Pondicherry University, Puducherry 605 014, India
| | - M Srivastava
- Department of Metallurgical Engineering, Indian Institute of Technology, Banaras Hindu University, India
| | - N K Prasad
- Department of Metallurgical Engineering, Indian Institute of Technology, Banaras Hindu University, India
| | - Sharad Awasthi
- Department of Biotechnology, Pondicherry University, Puducherry 605 014, India
| | - Arunkumar Dhayalan
- Department of Biotechnology, Pondicherry University, Puducherry 605 014, India
| | - S Kannan
- Centre for Nanoscience and Technology, Pondicherry University, Puducherry 605 014, India.
| |
Collapse
|
27
|
Srivastava M, Georgieva ER, Freed JH. A New Wavelet Denoising Method for Experimental Time-Domain Signals: Pulsed Dipolar Electron Spin Resonance. J Phys Chem A 2017; 121:2452-2465. [PMID: 28257206 DOI: 10.1021/acs.jpca.7b00183] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We adapt a new wavelet-transform-based method of denoising experimental signals to pulse-dipolar electron-spin resonance spectroscopy (PDS). We show that signal averaging times of the time-domain signals can be reduced by as much as 2 orders of magnitude, while retaining the fidelity of the underlying signals, in comparison with noiseless reference signals. We have achieved excellent signal recovery when the initial noisy signal has an SNR ≳ 3. This approach is robust and is expected to be applicable to other time-domain spectroscopies. In PDS, these time-domain signals representing the dipolar interaction between two electron spin labels are converted into their distance distribution functions P(r), usually by regularization methods such as Tikhonov regularization. The significant improvements achieved by using denoised signals for this regularization are described. We show that they yield P(r)'s with more accurate detail and yield clearer separations of respective distances, which is especially important when the P(r)'s are complex. Also, longer distance P(r)'s, requiring longer dipolar evolution times, become accessible after denoising. In comparison to standard wavelet denoising approaches, it is clearly shown that the new method (WavPDS) is superior.
Collapse
Affiliation(s)
- Madhur Srivastava
- National Biomedical Center for Advanced ESR Technology, ‡Meinig School of Biomedical Engineering, and §Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Elka R Georgieva
- National Biomedical Center for Advanced ESR Technology, ‡Meinig School of Biomedical Engineering, and §Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Jack H Freed
- National Biomedical Center for Advanced ESR Technology, ‡Meinig School of Biomedical Engineering, and §Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| |
Collapse
|
28
|
Wright S, Amzel A, Ikoro N, Srivastava M, Leclerc-Madlala S, Bowsky S, Miller H, Phelps BR. Talking to children about their HIV status: a review of available resources, tools, and models for improving and promoting pediatric disclosure. AIDS Care 2017; 29:1019-1025. [PMID: 28081616 DOI: 10.1080/09540121.2016.1273471] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
As children living with HIV (CLHIV) grow into adolescence and adulthood, caregivers and healthcare providers are faced with the sensitive challenge of when to disclose to a CLHIV his or her HIV status. Despite WHO recommendations for CLHIV to know their status, in countries most affected by HIV, effective resources are often limited, and national guidance on disclosure is often lacking. To address the need for effective resources, gray and scientific literature was searched to identify existing tools and resources that can aid in the disclosure process. From peer-reviewed literature, seven disclosure models from six different countries were identified. From the gray literature, 23 resources were identified including children's books (15), job aides to assist healthcare providers (5), and videos (3). While these existing resources can be tailored to reflect local norms and used to aid in the disclosure process, careful consideration must be taken in order to avoid damaging disclosure practices.
Collapse
Affiliation(s)
- S Wright
- a U.S. Agency for International Development, Office of HIV/AIDS , Washington , DC , USA
| | - A Amzel
- a U.S. Agency for International Development, Office of HIV/AIDS , Washington , DC , USA
| | - N Ikoro
- a U.S. Agency for International Development, Office of HIV/AIDS , Washington , DC , USA
| | - M Srivastava
- a U.S. Agency for International Development, Office of HIV/AIDS , Washington , DC , USA
| | - S Leclerc-Madlala
- a U.S. Agency for International Development, Office of HIV/AIDS , Washington , DC , USA
| | - S Bowsky
- b Futures Group International , Washington , USA
| | - H Miller
- a U.S. Agency for International Development, Office of HIV/AIDS , Washington , DC , USA
| | - B R Phelps
- a U.S. Agency for International Development, Office of HIV/AIDS , Washington , DC , USA
| |
Collapse
|
29
|
Singh R, Srivastava M, Prasad NK, Awasthi S, Kumar Dhayalan A, Kannan S. Structural analysis and magnetic induced hyperthermia of Fe3+and Mn2+substituted β-Ca3(PO4)2. NEW J CHEM 2017. [DOI: 10.1039/c7nj01228d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Fe3+/Mn2+co-substitutions in β-Ca3(PO4)2elicit a good hyperthermia effect and biocompatible features.
Collapse
Affiliation(s)
- Ramkishore Singh
- Centre for Nanoscience and Technology
- Pondicherry University
- Puducherry-605 014
- India
| | - M. Srivastava
- Department of Metallurgical Engineering
- Indian Institute of Technology (Banaras Hindu University)
- Varanasi-221005
- India
| | - N. K. Prasad
- Department of Metallurgical Engineering
- Indian Institute of Technology (Banaras Hindu University)
- Varanasi-221005
- India
| | - Sharad Awasthi
- Department of Biotechnology
- Pondicherry University
- Puducherry-605 014
- India
| | | | - S. Kannan
- Centre for Nanoscience and Technology
- Pondicherry University
- Puducherry-605 014
- India
| |
Collapse
|
30
|
Prasad NK, Srivastava M, Alla SK, Danda JR, Aditya D, Mandal RK. ZrxFe3−xO4 (0.01 ≤ x ≤ 1.0) nanoparticles: a possible magnetic in vivo switch. RSC Adv 2016. [DOI: 10.1039/c6ra04815c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AC field controlled temperature during magnetic hyperthermia for ZrxFe3−xO4 (0.01 ≤ x ≤ 1.0) based ferrofluids. The unexpected behavior observed despite their high magnetization (~50 Am2 kg−1) and Curie temperature (TC > 300 °C).
Collapse
Affiliation(s)
- N. K. Prasad
- Department of Metallurgical Engineering
- Indian Institute of Technology
- Banaras Hindu University
- Varanasi
- India
| | - M. Srivastava
- Department of Metallurgical Engineering
- Indian Institute of Technology
- Banaras Hindu University
- Varanasi
- India
| | - S. K. Alla
- Department of Metallurgical Engineering
- Indian Institute of Technology
- Banaras Hindu University
- Varanasi
- India
| | - J. R. Danda
- Department of Metallurgical Engineering
- Indian Institute of Technology
- Banaras Hindu University
- Varanasi
- India
| | - D. Aditya
- Department of Metallurgical Engineering
- Indian Institute of Technology
- Banaras Hindu University
- Varanasi
- India
| | - R. K. Mandal
- Department of Metallurgical Engineering
- Indian Institute of Technology
- Banaras Hindu University
- Varanasi
- India
| |
Collapse
|
31
|
Abstract
A new method is presented to denoise 1-D experimental signals using wavelet transforms. Although the state-of- the-art wavelet denoising methods perform better than other denoising methods, they are not very effective for experimental signals. Unlike images and other signals, experimental signals in chemical and biophysical applications for example, are less tolerant to signal distortion and under-denoising caused by the standard wavelet denoising methods. The new method 1) provides a method to select the number of decomposition levels to denoise, 2) uses a new formula to calculate noise thresholds that does not require noise estimation, 3) uses separate noise thresholds for positive and negative wavelet coefficients, 4) applies denoising to the Approximation component, and 5) allows the flexibility to adjust the noise thresholds. The new method is applied to continuous wave electron spin resonance (cw-ESR) spectra and it is found that it increases the signal-to-noise ratio (SNR) by more than 32 dB without distorting the signal, whereas standard denoising methods improve the SNR by less than 10 dB and with some distortion. Also, its computation time is more than 6 times faster.
Collapse
Affiliation(s)
- Madhur Srivastava
- National Biomedical Center for Advanced ESR Technology (ACERT) and the Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853 USA
| | - C. Lindsay Anderson
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, 14853 USA
| | - Jack H. Freed
- National Biomedical Center for Advanced ESR Technology (ACERT) and the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853 USA
| |
Collapse
|
32
|
AbuRahma A, Srivastava M, Stone P. Effects of Statins on Early and Late Clinical Outcomes of Carotid Endarterectomy and the Rate of Post-Carotid Endarterectomy Restenosis. J Vasc Surg 2015. [DOI: 10.1016/j.jvs.2015.10.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
33
|
Sharma S, Javadekar SM, Pandey M, Srivastava M, Kumari R, Raghavan SC. Homology and enzymatic requirements of microhomology-dependent alternative end joining. Cell Death Dis 2015; 6:e1697. [PMID: 25789972 PMCID: PMC4385936 DOI: 10.1038/cddis.2015.58] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 12/24/2014] [Accepted: 02/09/2015] [Indexed: 01/19/2023]
Abstract
Nonhomologous DNA end joining (NHEJ) is one of the major double-strand break (DSB) repair pathways in higher eukaryotes. Recently, it has been shown that alternative NHEJ (A-NHEJ) occurs in the absence of classical NHEJ and is implicated in chromosomal translocations leading to cancer. In the present study, we have developed a novel biochemical assay system utilizing DSBs flanked by varying lengths of microhomology to study microhomology-mediated alternative end joining (MMEJ). We show that MMEJ can operate in normal cells, when microhomology is present, irrespective of occurrence of robust classical NHEJ. Length of the microhomology determines the efficiency of MMEJ, 5 nt being obligatory. Using this biochemical approach, we show that products obtained are due to MMEJ, which is dependent on MRE11, NBS1, LIGASE III, XRCC1, FEN1 and PARP1. Thus, we define the enzymatic machinery and microhomology requirements of alternative NHEJ using a well-defined biochemical system.
Collapse
Affiliation(s)
- S Sharma
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - S M Javadekar
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - M Pandey
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - M Srivastava
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - R Kumari
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - S C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| |
Collapse
|
34
|
Singh A, Bajpai V, Srivastava M, Arya KR, Kumar B. Rapid profiling and structural characterization of bioactive compounds and their distribution in different parts of Berberis petiolaris Wall. ex G. Don applying hyphenated mass spectrometric techniques. Rapid Commun Mass Spectrom 2014; 28:2089-2100. [PMID: 25156599 DOI: 10.1002/rcm.7001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2013] [Revised: 07/23/2014] [Accepted: 07/27/2014] [Indexed: 06/03/2023]
Abstract
RATIONALE Berberis petiolaris Wall. is a lesser known medicinal plant, belonging to the family Berberidaceae. The genus Berberis is known for many biological activities such as anti-microbial, anti-inflammatory and anti-diarrheal, etc. There are not many reports of the isolation of components from Berberis petiolaris. This study aims to seek identification, characterization and quantification of components. METHODS A method was developed for rapid screening of phytochemicals using high-pressure liquid chromatography hyphenated with quadrupole time-of-flight mass spectrometry (HPLC/ESI-QTOF-MS/MS). Suitable collision-induced dissociation mass spectrometry (CID-MS/MS) methods were developed for structural investigation of alkaloids, flavanoids and other classes of compounds using nine reference standards for authentication. Multiple reaction monitoring (MRM) methods were developed for quantitative study of five constituents using triple quadrupole-linear ion trap mass spectrometry (UPLC/QqLIT-MS/MS). RESULTS On the basis of HPLC retention behavior and fragmentation pathways obtained by high-resolution MS and MS/MS, 32 compounds were identified and characterized in different parts of Berberis petiolaris. Quantitative studies of chlorogenic acid, magnoflorine, jatrorrhizine, palmatine and berberine were also completed successfully. CONCLUSIONS Rapid and accurate HPLC/ESI-QTOF-MS/MS and UPLC/ESI-QqLIT-MS/MS methods were established for identification, characterization and quantification of phytochemicals in the ethanolic extract of Berberis petiolaris. These methods, therefore, can be used for studies on phytochemical variation in different parts of the plant. Principle components analysis (PCA) may be used for plant part discrimination.
Collapse
Affiliation(s)
- A Singh
- CSIR - Central Drug Research Institute (CDRI), SAIF Division, Lucknow, 226031, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110025, India
| | | | | | | | | |
Collapse
|
35
|
Jain S, Mahajan S, Srivastava M. Pure chondrosarcomas of the uterus: a rare uterine tumour. J OBSTET GYNAECOL 2014; 34:752-4. [PMID: 24921947 DOI: 10.3109/01443615.2014.923820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- S Jain
- Department of Pathology, Sir Ganga Ram Hospital , New Delhi , India
| | | | | |
Collapse
|
36
|
Abstract
The aim of the present study was to formulate and evaluate in situ gelling syringeable nanoemulgels (NEGs) of ketoprofen for periodontal delivery. Application of 3-factor 3-level design was employed using the Box-Behnken experimental design for the optimization of nanoemulsion using three independent variables such as percent concentration (v/v) of oil (X1), S mix (mixture of surfactant and cosurfactant) (X2) and water (X3); while the particle size (nm) (Y1), polydispersity index (Y2) and zeta potential (mV) (Y3) were used as dependent variables. The NEG was evaluated based on their drug content, pH measurement, mucoadhesion on the goat buccal mucosa, syringeability and inverted sol-gel transition temperature. The drug release data were analyzed for curve fitting based on the Korsmeyer-Peppas law, and the n-values of optimized A5 and A8 formulations were found 0.3721 and 0.3932, respectively, confirmed that both the formulations followed pseudo Fickian diffusion (n < 0.43). The formulation A8 with the optimal drug release was identified as the best NEG formulation. Results of rheological, mucoadhesion and syringeability studies showed the suitability of desired sol-gel property for periodontal drug delivery. The Herschel-Bulkley model was the best fit model to explain the flow behavior of optimized formulation. Using the HET-CAM method, significantly lower in vitro toxicity was indicated the suitability of developed NEG for intra-pocket delivery.
Collapse
Affiliation(s)
- M Srivastava
- a Department of Pharmaceutics, Faculty of Pharmacy , Jamia Hamdard University , New Delhi , India
| | - K Kohli
- a Department of Pharmaceutics, Faculty of Pharmacy , Jamia Hamdard University , New Delhi , India
| | - M Ali
- a Department of Pharmaceutics, Faculty of Pharmacy , Jamia Hamdard University , New Delhi , India
| |
Collapse
|
37
|
Gsponer JR, Braun M, Scheble VJ, Zellweger T, Bachmann A, Perner S, Vlajnic T, Srivastava M, Tan SH, Dobi A, Sesterhenn IA, Srivastava S, Bubendorf L, Ruiz C. ERG rearrangement and protein expression in the progression to castration-resistant prostate cancer. Prostate Cancer Prostatic Dis 2014; 17:126-31. [PMID: 24469092 DOI: 10.1038/pcan.2013.62] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 12/02/2013] [Accepted: 12/17/2013] [Indexed: 12/21/2022]
Abstract
BACKGROUND Approximately half of the prostate carcinomas are characterized by a chromosomal rearrangement fusing the androgen-regulated gene TMPRSS2 to the oncogenic ETS transcription factor ERG. Aim of this study was to comprehensively analyze the role and impact of the ERG rearrangement and protein expression on the progression to castration-resistant (CR) disease. METHODS We used a tissue microarray (TMA) constructed from 114 hormone naive (HN) and 117 CR PCs. We analyzed the ERG rearrangement status by fluorescence in situ hybridization and the expression profiles of ERG, androgen receptor (AR) and the proliferation marker Ki67 by immunohistochemistry. RESULTS Nearly half of the PC tissue specimens (HN: 38%, CR: 46%) harbored a TMPRSS2-ERG gene fusion. HN PCs with positive translocation status showed increased tumor cell proliferation (P<0.05). As expected, TMPRSS2-ERG gene fusion was strongly associated with increased ERG protein expression in HN and CR PCs (both P<0.0001). Remarkably, the study revealed a subgroup (26%) of CR PCs with ERG rearrangement but without any detectable ERG protein expression. This subgroup showed significantly lower levels of AR protein expression and androgen-regulated serum PSA (both P<0.05). CONCLUSIONS In this study, we identified a subgroup of ERG-rearranged CR PCs without detectable ERG protein expression. Our results suggest that this subgroup could represent CR PCs with a dispensed AR pathway. These tumors might represent a thus far unrecognized subset of patients with AR-independent CR PC who may not benefit from conventional therapy directed against the AR pathway.
Collapse
Affiliation(s)
- J R Gsponer
- Institute for Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - M Braun
- Department of Prostate Cancer Research, Institute of Pathology, University Hospital of Bonn, Bonn, Germany
| | - V J Scheble
- Institute of Pathology, Comprehensive Cancer Center, University Hospital Tuebingen, Tuebingen, Germany
| | - T Zellweger
- Division of Urology, St Claraspital, Basel, Switzerland
| | - A Bachmann
- Department of Urology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - S Perner
- Department of Prostate Cancer Research, Institute of Pathology, University Hospital of Bonn, Bonn, Germany
| | - T Vlajnic
- Institute for Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - M Srivastava
- Department of Anatomy, Physiology, and Genetics, and Institute for Molecular Medicine, Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD, USA
| | - S H Tan
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - A Dobi
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | | | - S Srivastava
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - L Bubendorf
- Institute for Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - C Ruiz
- Institute for Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| |
Collapse
|
38
|
Smitharani JA, Sowmyashree ML, Vasantha KM, Srivastava M, Sashidhar VR. (22)Na influx is significantly lower in salt tolerant groundnut (Arachis hypogaea) varieties. Physiol Mol Biol Plants 2014; 20:49-55. [PMID: 24554838 PMCID: PMC3925480 DOI: 10.1007/s12298-013-0202-6] [Citation(s) in RCA: 4] [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] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 07/30/2013] [Accepted: 08/16/2013] [Indexed: 05/25/2023]
Abstract
Distinct varieties differing in salt tolerance were initially identified from two separate green house experiments using two systems; solution as well as soil culture. The first screening involved a diverse group of 27 cultivars. Several physiological traits; Chlorophyll Stability Index (CSI), Salt Tolerance Index (STI) and ion content were determined to screen the cultivars for differences in salt tolerance using solution culture in the first experiment. A set of six varieties (three tolerant and three susceptible) were selected from this experiment and then subjected again to salt stress adopting a natural soil system in the second experiment which involved a screening approach essentially similar to that of the first experiment. In the third experiment using two distinct cultivars differing in salt tolerance selected from experiment II, (22)Na influx rate was determined in the root and shoot at the end of a 24 h salt imposition in Hoagland's nutrient system containing 180 KBq of (22)Na. The results suggested that there were distinct differences in (22)Na influx rate into root and concurrently in the shoot. The salt tolerant Spanish improved and one of the moderately tolerant Trombay variety TAG 24, showed good regulation of (22)Na influx resulting in low (22)Na concentration. The salt susceptible variety JSP39 had nearly 7-8 fold higher root (22)Na content as compared to the tolerant and moderately tolerant cultivars. The results have highlighted the importance of Na exclusion as an important determinant of salt tolerance in groundnut.
Collapse
Affiliation(s)
- J. A. Smitharani
- />Department of Crop Physiology, Stress Physiology Lab, University of Agricultural Sciences, GKVK, Bangalore, 560 065 India
| | - M. L. Sowmyashree
- />Department of Crop Physiology, Stress Physiology Lab, University of Agricultural Sciences, GKVK, Bangalore, 560 065 India
| | - K. M. Vasantha
- />Department of Crop Physiology, Stress Physiology Lab, University of Agricultural Sciences, GKVK, Bangalore, 560 065 India
| | | | - V. R. Sashidhar
- />Department of Crop Physiology, Stress Physiology Lab, University of Agricultural Sciences, GKVK, Bangalore, 560 065 India
| |
Collapse
|
39
|
Ingersoll S, Ahmad S, Ahmed H, Mohiuddin Y, Srivastava M, Oyer J, Banks R, Finkler N, Edwards J, Holloway R. Interleukin-stimulated cellular therapy: Effectiveness against ovarian cancer using in vitro and in vivo models. Gynecol Oncol 2013. [DOI: 10.1016/j.ygyno.2013.04.144] [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: 10/26/2022]
|
40
|
Gabor M, Gabor LJ, Peacock L, Srivastava M, Rosenwax A, Phalen D. Psittacid herpesvirus 3 infection in the eclectus parrot (Eclectus roratus) in Australia. Vet Pathol 2013; 50:1053-7. [PMID: 23697483 DOI: 10.1177/0300985813490753] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Psittacid herpesvirus 3 (PsHV-3) has recently been implicated as the cause of a severe respiratory disease in Bourke's parrots (Neopsephotus bourkii) in the United States. In this report, the clinical manifestations and gross and microscopic lesions of PsHV-3 infection in 2 eclectus parrots (Eclectus roratus) in Australia are described. The presence of a PsHV-3 infection was confirmed by polymerase chain reaction amplification and sequencing of PsHV-3 DNA using degenerate and PsHV-3 primers. Electron microscopy of infected cells demonstrated the assembly of herpesvirus virions as well as intranuclear tubular structures. The detection of PsHV-3 in Australia in 2 eclectus parrots broadens the list of known affected species and confirms the presence of this virus in Australia.
Collapse
Affiliation(s)
- M Gabor
- State Veterinary Diagnostic Laboratory, EMAI, PMB 8, Camden, Sydney, 2570, Australia.
| | | | | | | | | | | |
Collapse
|
41
|
Sachan R, Agarwal R, Patel M, Natu S, Srivastava M. O590 SERUM SOLUBLE FAS (sFAS) CONCENTRATIONS IN PATIENTS WITH PREINVASIVE, INVASIVE CERVICAL CANCER AND VAGINAL CANCER - A HOSPITAL BASED STUDY IN NORTH INDIAN POPULATION. Int J Gynaecol Obstet 2012. [DOI: 10.1016/s0020-7292(12)61020-0] [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: 11/28/2022]
|
42
|
Joseph S, Verma S, Sahoo M, Sharma A, Srivastava M, Reddy M, Murthy P. IgG subclass responses to proinflammatory fraction of Brugia malayi in human filariasis. Indian J Med Res 2012; 135:650-5. [PMID: 22771594 PMCID: PMC3401695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2010] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND & OBJECTIVES Earlier we demonstrated that immunization with F6, a proinflammatory molecular fraction isolated from the human filarial parasite Brugia malayi, protected the host and eliminated the infection in Mastomys coucha by a Th1/Th2 response including IgG2a antibody response. Whether F6 molecules become accessible to human host during natural course of infection and elicit similar response is not known. The present study was undertaken to determine the profile of IgG subclasses specifically reactive to F6 in different categories of bancroftian filariasis cases to infer any relationship between the levels of a particular F6-specific IgG subclass and the infection or disease status. METHODS Serum samples of normal individuals from filariasis non-endemic regions of India like Jammu & Kashmir, Uttarakhand, and Chandigarh [(NEN-W; n=10), healthy subjects from USA (NEN-U; n=10) and three categories of bancroftian filariasis cases from endemic areas: endemic normals (EN; n=10) with no symptoms and no microfilariae, asymptomatic microfilaremics (ASM; n=10) and chronic symptomatic amicrofilaremics (CL; n=10) were assayed for F6-specific IgG1, IgG2, IgG3 and IgG4 by ELISA using SDS-PAGE-isolated F6 fraction of B. malayi adult worms. RESULTS Significantly high levels of F6-specific IgG1, IgG2 and IgG3 were found in CL (P<0.001) and EN (P<0.01-0.001) bancroftian filariasis cases compared to NEN-U. Significant levels of F6-specific IgG1 (P<0.01) and IgG2 (P<0.01) but not IgG3 were found in ASM cases compared to NEN-U. The most abundant was IgG2 which when compared to NEN-U, was significantly high in CL (P<0.001) and EN cases (P<0.001), followed by ASM (P<0.01). F6-specific IgG4 response in EN, ASM and CL subjects was not significantly different from the levels of NEN-U. Among the non-endemic normals, the NEN-W subjects showed significant reactivity with IgG2 (P<0.001) but not with IgG1, IgG3 and IgG4 as compared to NEN-U subjects. IgG subclass levels were different in different categories. INTERPRETATION & CONCLUSIONS The high levels of F6 reactive IgG1, IgG2 and IgG3 in endemic normals and chronic symptomatic bancroftian patients, and IgG1 and IgG2 in asymptomatic microfilaraemics, suggest that F6 molecules of parasite are accessible in these subjects for IgG subclass-specific immune response and IgG2 may be related to pathogenesis. Studies using individual F6 molecules will be done to identify the molecule(s) involved in infection and protective immunity.
Collapse
Affiliation(s)
- S.K. Joseph
- Division of Parasitology, CSIR-Central Drug Research Institute, Lucknow, India
| | - S.K. Verma
- Division of Parasitology, CSIR-Central Drug Research Institute, Lucknow, India
| | - M.K. Sahoo
- Division of Parasitology, CSIR-Central Drug Research Institute, Lucknow, India
| | - A. Sharma
- Division of Parasitology, CSIR-Central Drug Research Institute, Lucknow, India
| | - M. Srivastava
- Division of Biometry & Statistics, CSIR-Central Drug Research Institute, Lucknow, India
| | - M.V.R. Reddy
- Department of Biochemistry & JB Tropical Disease Research Centre, Mahatma Gandhi Institute of Medical Sciences, Sevagram, India
| | - P.K. Murthy
- Division of Parasitology, CSIR-Central Drug Research Institute, Lucknow, India
| |
Collapse
|
43
|
Sindhwani G, Verma A, Biswas D, Srivastava M, Rawat J. A pilot study on domiciliary pulmonary rehabilitation programme in the management of severe chronic obstructive pulmonary disease. Singapore Med J 2011; 52:689-693. [PMID: 21947149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
INTRODUCTION Pulmonary rehabilitation is now an accepted modality of care in the management of chronic obstructive pulmonary disease (COPD) patients. However, in resource-limited settings, conventional pulmonary rehabilitation may not be feasible due to the high cost involved and the extensive infrastructure requirement. In view of these constraints, we designed a domiciliary pulmonary rehabilitation programme and evaluated its usefulness in the management of severe COPD. METHODS A total of 20 patients suffering from severe COPD (ten patients each in the experimental and control groups) were enrolled in the study. The experimental group was subjected to domiciliary pulmonary rehabilitation along with medical management, while the control group underwent only conventional medical management. During the six-month study period, both groups were assessed for quality of life (clinical COPD questionnaire), exercise capacity (six-minute walk distance) and spirometry values (forced expiratory volume in one second and forced vital capacity). RESULTS Statistically significant differences were observed in clinical COPD questionnaire scores in both groups from the fourth month (p-value is 0.002 and 0.001 at the end of four and six months, respectively). The results of the six-minute walk distance showed a similar trend (p-value is 0.009 and 0.001 at the end of four and six months, respectively). No significant difference was observed in either of the spirometry values. CONCLUSION The domiciliary pulmonary rehabilitation programme improves the quality of life and exercise endurance of patients with severe COPD, and thereby acts as a substitute for conventional pulmonary rehabilitation programmes in resource-limited situations.
Collapse
Affiliation(s)
- G Sindhwani
- Department of Pulmonary Medicine, Himalayan Institute of Medical Sciences, Swami Ram Nagar, Jolly Grant, Dehradun 248140, Uttarakhand, India.
| | | | | | | | | |
Collapse
|
44
|
|
45
|
Srivastava S, Singh V, Kumar R, Srivastava M, Sinha A, Simon S. In vitro Evaluation of Carbendazim 50% WP, Antagonists and Botanicals Against Fusarium oxysporum f. sp. psidii Associated with Rhizosphere Soil of Guava. ACTA ACUST UNITED AC 2010. [DOI: 10.3923/ajppaj.2011.46.53] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
46
|
Hadi R, Kumar S, Srivastava M, Pant MC, Srivastava PK, Jamal N. Quantitative tumor volume VS TNM staging: the impact on prognosis in head and neck cancer. Gulf J Oncolog 2010:28-34. [PMID: 20601336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2010] [Indexed: 05/29/2023]
Abstract
OBJECTIVES To evaluate the prognostic value of tumor volume (TV) by clinical method (CM) and Computerized Tomography (CT) scan in head and neck (H and N) cancer. MATERIALS AND METHODS Total 25 patients' (pts) pretreatment tumor volume (PT TV) was assessed clinically by cuboid volume method. Afterwards contrast enhanced computerized tomography (CECT) images of the pts were transferred to workstation by DICOM software. The computerized tomography tumor volume (CT TV) was obtained on Radworks 6.0, using mouse control cursor. After assessment, the patients were given 3 cycles of neoadjuvant chemotherapy followed by radiotherapy by conventional method on Co-60 Theratron 780 C. After 1 month of treatment, TV was again measured. STATISTICAL METHOD Statistical analysis was done on MSTAT statistical analysis software. Two-tailed student t test, chi square test and test for two proportions for significance had been used. RESULTS Large variations in tumor volume were found both in intra as well as inter T-stages. As the tumor size increases with T stages, the difference in measurement of TV by both methods decreases. CT TV results pre as well as post-treatment were more consistent than clinical method. CONCLUSION The use of TV as a prognostic factor by CT scan seems to be more useful parameter than the CM. TV should be included in the TNM (tumor, node, and metastasis) classification after setting the strict guidelines for tumor delineation, to solve the discrepancy of treatment outcome in the same clinical stage.
Collapse
Affiliation(s)
- R Hadi
- Department of Radiation Oncology, Regional Cancer Centre, JIPMER, Pudducherry, India
| | | | | | | | | | | |
Collapse
|
47
|
|
48
|
Torosyan Y, Dobi A, Glasman M, Mezhevaya K, Naga S, Huang W, Paweletz C, Leighton X, Pollard HB, Srivastava M. Role of multi-hnRNP nuclear complex in regulation of tumor suppressor ANXA7 in prostate cancer cells. Oncogene 2010; 29:2457-66. [PMID: 20190808 DOI: 10.1038/onc.2010.2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Annexin-A7 (ANXA7) tumor suppressor role has been shown in various tumors, and ANXA7 expression has been particularly lost in androgen-resistant prostate cancers. In this study, we studied ANXA7 regulation in normal prostate versus androgen-sensitive and -resistant prostate cancer cells. Deletion mapping analysis showed lowest ANXA7-promoter activities in androgen-sensitive LNCaP prostate cancer cells. Genomatix analysis of ANXA7 promoter identified a cluster of steroid nuclear hormone receptor elements, including V$GREF (V$GRE.02/ARE.02). Gelshift analysis clearly indicated distinct nuclear protein occupancy at this ANXA7-promoter site (-1086/-890) in prostate cancer (LNCaP, DU145, and PC3) versus normal prostate (PrEC) cells. In matrix-assisted laser desorption time-of-flight mass spectrometry-based search for ANXA7 nuclear regulators, we identified several heterogeneous nuclear ribonucleoproteins (hnRNPs) (A1, A2/B1 and K) attached to the steroid-associated ANXA7-promoter site in the androgen-resistant PC3 prostate cancer cells with high ANXA7 gene copy number, but not in PrEC. The hnPNP role in ANXA7 regulation (that was validated by hnRNPA2/B1 antibody interference) resulted in multiple ANXA7 cDNA and protein products in PC3, but not in PrEC. Ingenuity pathways analysis showed plausible molecular paths between ANXA7 and the hnRNP-associated network in prostate cancer progression. Thus, a multi-hnRNP complex can be responsible for aberrant ANXA7 transcription and splicing, thereby affecting ANXA7 expression pattern and tumor suppressor function in prostate cancer.
Collapse
Affiliation(s)
- Y Torosyan
- Department of Anatomy, Physiology and Genetics, Institute for Molecular Medicine, Uniformed Services University School of Medicine (USUHS), Bethesda, MD 20814, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Steinwede K, Walter K, Aly S, Bohling J, Maus R, Schreiber O, Srivastava M, Länger F, Welte T, Ehlers S, Maus UA. Role of cathepsin G and neutrophil elastase in the lung host defense against mycobacterial infections. Pneumologie 2010. [DOI: 10.1055/s-0030-1251391] [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: 10/19/2022]
|
50
|
Philip AK, Srivastava M, Pathak K. Buccoadhesive gels of glibenclamide: A means for achieving enhanced bioavailability. Drug Deliv 2009; 16:405-15. [DOI: 10.1080/10717540903126314] [Citation(s) in RCA: 11] [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: 10/20/2022] Open
|