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Loya-Lopez SI, Allen HN, Duran P, Calderon-Rivera A, Gomez K, Kumar U, Shields R, Zeng R, Dwivedi A, Saurabh S, Korczeniewska OA, Khanna R. Intranasal CRMP2-Ubc9 inhibitor regulates Na V 1.7 to alleviate trigeminal neuropathic pain. Pain 2024; 165:573-588. [PMID: 37751532 PMCID: PMC10922202 DOI: 10.1097/j.pain.0000000000003053] [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: 07/11/2023] [Accepted: 07/25/2023] [Indexed: 09/28/2023]
Abstract
ABSTRACT Dysregulation of voltage-gated sodium Na V 1.7 channels in sensory neurons contributes to chronic pain conditions, including trigeminal neuropathic pain. We previously reported that chronic pain results in part from increased SUMOylation of collapsin response mediator protein 2 (CRMP2), leading to an increased CRMP2/Na V 1.7 interaction and increased functional activity of Na V 1.7. Targeting this feed-forward regulation, we developed compound 194 , which inhibits CRMP2 SUMOylation mediated by the SUMO-conjugating enzyme Ubc9. We further demonstrated that 194 effectively reduces the functional activity of Na V 1.7 channels in dorsal root ganglia neurons and alleviated inflammatory and neuropathic pain. Here, we used a comprehensive array of approaches, encompassing biochemical, pharmacological, genetic, electrophysiological, and behavioral analyses, to assess the functional implications of Na V 1.7 regulation by CRMP2 in trigeminal ganglia (TG) neurons. We confirmed the expression of Scn9a , Dpysl2 , and UBE2I within TG neurons. Furthermore, we found an interaction between CRMP2 and Na V 1.7, with CRMP2 being SUMOylated in these sensory ganglia. Disrupting CRMP2 SUMOylation with compound 194 uncoupled the CRMP2/Na V 1.7 interaction, impeded Na V 1.7 diffusion on the plasma membrane, and subsequently diminished Na V 1.7 activity. Compound 194 also led to a reduction in TG neuron excitability. Finally, when intranasally administered to rats with chronic constriction injury of the infraorbital nerve, 194 significantly decreased nociceptive behaviors. Collectively, our findings underscore the critical role of CRMP2 in regulating Na V 1.7 within TG neurons, emphasizing the importance of this indirect modulation in trigeminal neuropathic pain.
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Affiliation(s)
- Santiago I. Loya-Lopez
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, New York, United States of America
- NYU Pain Research Center, 433 First Avenue, New York, NY 10010, United States of America
| | - Heather N. Allen
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, New York, United States of America
- NYU Pain Research Center, 433 First Avenue, New York, NY 10010, United States of America
| | - Paz Duran
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, New York, United States of America
- NYU Pain Research Center, 433 First Avenue, New York, NY 10010, United States of America
| | - Aida Calderon-Rivera
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, New York, United States of America
- NYU Pain Research Center, 433 First Avenue, New York, NY 10010, United States of America
| | - Kimberly Gomez
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, New York, United States of America
- NYU Pain Research Center, 433 First Avenue, New York, NY 10010, United States of America
| | - Upasana Kumar
- Center for Orofacial Pain and Temporomandibular Disorders, Department of Diagnostic Sciences, Rutgers School of Dental Medicine, Newark, NJ 07101, United States of America
| | - Rory Shields
- Rutgers School of Graduate Studies, Newark Health Science Campus, Newark, NJ 07101, United States of America
| | - Rui Zeng
- Department of Chemistry, College of Arts and Sciences, New York University, 100 Washington Square East, New York, NY 10003, United States of America
| | - Akshat Dwivedi
- Department of Chemistry, College of Arts and Sciences, New York University, 100 Washington Square East, New York, NY 10003, United States of America
| | - Saumya Saurabh
- Department of Chemistry, College of Arts and Sciences, New York University, 100 Washington Square East, New York, NY 10003, United States of America
| | - Olga A. Korczeniewska
- Center for Orofacial Pain and Temporomandibular Disorders, Department of Diagnostic Sciences, Rutgers School of Dental Medicine, Newark, NJ 07101, United States of America
- Rutgers School of Graduate Studies, Newark Health Science Campus, Newark, NJ 07101, United States of America
| | - Rajesh Khanna
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, New York, United States of America
- NYU Pain Research Center, 433 First Avenue, New York, NY 10010, United States of America
- Department of Neuroscience and Physiology and Neuroscience Institute, School of Medicine, New York University, New York, NY, 10010, USA
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Chong TN, Panjalingam M, Saurabh S, Shapiro L. Phosphatase to kinase switch of a critical enzyme contributes to timing of cell differentiation. mBio 2024; 15:e0212523. [PMID: 38055339 PMCID: PMC10790692 DOI: 10.1128/mbio.02125-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/20/2023] [Indexed: 12/08/2023] Open
Abstract
IMPORTANCE The process of cell differentiation is highly regulated in both prokaryotic and eukaryotic organisms. The aquatic bacterium, Caulobacter crescentus, undergoes programmed cell differentiation from a motile swarmer cell to a stationary stalked cell with each cell cycle. This critical event is regulated at multiple levels. Kinase activity of the bifunctional enzyme, PleC, is limited to a brief period when it initiates the molecular signaling cascade that results in cell differentiation. Conversely, PleC phosphatase activity is required for pili formation and flagellar rotation. We show that PleC is localized to the flagellar pole by the scaffold protein, PodJ, which is known to suppress PleC kinase activity in vitro. PleC mutants that are unable to bind PodJ have increased kinase activity in vivo, resulting in premature differentiation. We propose a model in which PodJ regulation of PleC's enzymatic activity contributes to the robust timing of cell differentiation during the Caulobacter cell cycle.
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Affiliation(s)
- Trisha N. Chong
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Mayura Panjalingam
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Saumya Saurabh
- Department of Chemistry, New York University, New York, New York, USA
| | - Lucy Shapiro
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
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Saurabh S, Khushboo S, Gouranga D, Rupnarayan B. Evaluation of Gastrocnemius Muscle Flap in Post-Burn Flexion Knee Contracture. Ann Burns Fire Disasters 2023; 36:251-256. [PMID: 38680430 PMCID: PMC11042073] [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] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 02/05/2022] [Indexed: 05/01/2024]
Abstract
Burn injury and consequent contracture is not a new problem for humans. It is severely disabling for the patients, especially if it involves a large joint like the knee. The objective of the study was to evaluate the usefulness of the gastrocnemius flap and improvement in knee joint function following the use of the flap in post-burn flexion knee contracture. This prospective study was performed from January 2016 to December 2017. Twenty-five patients with flexion knee contracture were treated with incisional or excisional release of contracture and coverage with gastrocnemius muscle flap. The post operative improvement in knee function was evaluated. There was improvement in range of motion of the knee in all the operated patients and the patients were able to maintain unassisted bipedal locomotion. There was no flap loss in any case. In post-burn knee contracture with limited local fascio cutaneous flap options, gastrocnemius flap gives very good functional and aesthetic outcome with no major complication.
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Affiliation(s)
- S. Saurabh
- Rajendra Institute of Medical Sciences, Ranchi, India
| | - S. Khushboo
- Rajendra Institute of Medical Sciences, Ranchi, India
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Loya-Lopez SI, Allen HN, Duran P, Calderon-Rivera A, Gomez K, Kumar U, Shields R, Zeng R, Dwivedi A, Saurabh S, Korczeniewska OA, Khanna R. Intranasal CRMP2-Ubc9 Inhibitor Regulates Na V 1.7 to Alleviate Trigeminal Neuropathic Pain. bioRxiv 2023:2023.07.16.549195. [PMID: 37502910 PMCID: PMC10370107 DOI: 10.1101/2023.07.16.549195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Dysregulation of voltage-gated sodium Na V 1.7 channels in sensory neurons contributes to chronic pain conditions, including trigeminal neuropathic pain. We previously reported that chronic pain results in part from increased SUMOylation of collapsin response mediator protein 2 (CRMP2), leading to an increased CRMP2/Na V 1.7 interaction and increased functional activity of Na V 1.7. Targeting this feed-forward regulation, we developed compound 194 , which inhibits CRMP2 SUMOylation mediated by the SUMO-conjugating enzyme Ubc9. We further demonstrated that 194 effectively reduces the functional activity of Na V 1.7 channels in dorsal root ganglia neurons and alleviated inflammatory and neuropathic pain. Here, we employed a comprehensive array of investigative approaches, encompassing biochemical, pharmacological, genetic, electrophysiological, and behavioral analyses, to assess the functional implications of Na V 1.7 regulation by CRMP2 in trigeminal ganglia (TG) neurons. We confirmed the expression of Scn9a , Dpysl2 , and UBE2I within TG neurons. Furthermore, we found an interaction between CRMP2 and Na V 1.7, with CRMP2 being SUMOylated in these sensory ganglia. Disrupting CRMP2 SUMOylation with compound 194 uncoupled the CRMP2/Na V 1.7 interaction, impeded Na V 1.7 diffusion on the plasma membrane, and subsequently diminished Na V 1.7 activity. Compound 194 also led to a reduction in TG neuron excitability. Finally, when intranasally administered to rats with chronic constriction injury of the infraorbital nerve (CCI-ION), 194 significantly decreased nociceptive behaviors. Collectively, our findings underscore the critical role of CRMP2 in regulating Na V 1.7 within TG neurons, emphasizing the importance of this indirect modulation in trigeminal neuropathic pain.
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Maiti A, Buffalo CZ, Saurabh S, Montecinos-Franjola F, Hachey JS, Conlon WJ, Tran GN, Hassan B, Walters KJ, Drobizhev M, Moerner WE, Ghosh P, Matsuo H, Tsien RY, Lin JY, Rodriguez EA. Structural and photophysical characterization of the small ultra-red fluorescent protein. Nat Commun 2023; 14:4155. [PMID: 37438348 PMCID: PMC10338489 DOI: 10.1038/s41467-023-39776-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 06/29/2023] [Indexed: 07/14/2023] Open
Abstract
The small Ultra-Red Fluorescent Protein (smURFP) represents a new class of fluorescent protein with exceptional photostability and brightness derived from allophycocyanin in a previous directed evolution. Here, we report the smURFP crystal structure to better understand properties and enable further engineering of improved variants. We compare this structure to the structures of allophycocyanin and smURFP mutants to identify the structural origins of the molecular brightness. We then use a structure-guided approach to develop monomeric smURFP variants that fluoresce with phycocyanobilin but not biliverdin. Furthermore, we measure smURFP photophysical properties necessary for advanced imaging modalities, such as those relevant for two-photon, fluorescence lifetime, and single-molecule imaging. We observe that smURFP has the largest two-photon cross-section measured for a fluorescent protein, and that it produces more photons than organic dyes. Altogether, this study expands our understanding of the smURFP, which will inform future engineering toward optimal FPs compatible with whole organism studies.
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Affiliation(s)
- Atanu Maiti
- Cancer Innovation Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Cosmo Z Buffalo
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Saumya Saurabh
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | | | - Justin S Hachey
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - William J Conlon
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - Geraldine N Tran
- Department of Radiology, Boston University, Boston, MA, 02118, USA
| | - Bakar Hassan
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Kylie J Walters
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Mikhail Drobizhev
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, 59717, USA
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Partho Ghosh
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Hiroshi Matsuo
- Cancer Innovation Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Roger Y Tsien
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
- Howard Hughes Medical Institute, La Jolla, CA, 92093, USA
| | - John Y Lin
- Tasmanian School of Medicine, University of Tasmania, Hobart, Tasmania, 7000, Australia
| | - Erik A Rodriguez
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA.
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Saurabh S, Chong TN, Bayas C, Dahlberg PD, Cartwright HN, Moerner WE, Shapiro L. ATP-responsive biomolecular condensates tune bacterial kinase signaling. Sci Adv 2022; 8:eabm6570. [PMID: 35171683 PMCID: PMC8849385 DOI: 10.1126/sciadv.abm6570] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Biomolecular condensates formed via liquid-liquid phase separation enable spatial and temporal organization of enzyme activity. Phase separation in many eukaryotic condensates has been shown to be responsive to intracellular adenosine triphosphate (ATP) levels, although the consequences of these mechanisms for enzymes sequestered within the condensates are unknown. Here, we show that ATP depletion promotes phase separation in bacterial condensates composed of intrinsically disordered proteins. Enhanced phase separation promotes the sequestration and activity of a client kinase enabling robust signaling and maintenance of viability under the stress posed by nutrient scarcity. We propose that a diverse repertoire of condensates can serve as control knobs to tune enzyme sequestration and reactivity in response to the metabolic state of bacterial cells.
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Affiliation(s)
- Saumya Saurabh
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Corresponding author. (S.S.); (L.S.)
| | - Trisha N. Chong
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Camille Bayas
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | | | | | - W. E. Moerner
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Lucy Shapiro
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Corresponding author. (S.S.); (L.S.)
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Affiliation(s)
- S Saurabh
- From the Department of Community Medicine and Family Medicine, All India Institute of Medical Sciences (AIIMS), Basni, Jodhpur, Rajasthan 342005, India
- Address correspondence to S. Saurabh, Department of Community Medicine and Family Medicine, All India Institute of Medical Sciences (AIIMS), Basni, Jodhpur, Rajasthan 342005, India. ;
| | - C Vohra
- All India Institute of Medical Sciences (AIIMS), Basni, Jodhpur, Rajasthan 342005, India
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Gupta MK, Bhardwaj P, Goel A, Saurabh S, Misra S. COVID-19 appropriate behavior in India: Time to invest for the benefits in future. J Family Med Prim Care 2021; 10:1818-1822. [PMID: 34195109 PMCID: PMC8208203 DOI: 10.4103/jfmpc.jfmpc_2382_20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/18/2021] [Accepted: 02/24/2021] [Indexed: 11/18/2022] Open
Abstract
The COVID-19 pandemic gave an opportunity to adopt many appropriate changes in the behavior of the people in India. The major gears of those behavior changes were the enforcement by the government, fear, motivation (self and induced), and self-experiences or realizations with time. If those changes are fitted in the Trans-Theoretical Model, Indian people have passed through the “Pre-Contemplation” to “Action” stage of behavior changes during different phases of this pandemic. Frequent hand hygiene, maintaining physical distancing, use of face mask, cough etiquettes, avoid greetings through physical contacts, fear in spitting and urination at public places, refrain from gatherings and avoiding outside food are some of the examples of those appropriate behaviors which were enforced or learnt during the COVID pandemic. The continuous lockdown made people understand the difference between “want” and “need,” the importance of local production, and the significance of social media and technology in routine life. The work-from-home strategy gave a chance to appreciate the work--life balance in a more applied way. The first-ever lifetime experience of unbelievable rejuvenating nature because of lack of human play taught people to appreciate nature. Although the current focus is on responding to the pandemic and on coping with its immediate effects, yet this is the time when there is an urgent need to create an enabling environment to support and sustain these COVID-19 appropriate behaviors (maintenance stage) to reap the maximum benefits out of them. Sustaining these appropriate behaviors is also important considering the bimodal distribution of the COVID-19 and possibility of advent of the second wave of COVID-19 in near future.
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Affiliation(s)
- Manoj Kumar Gupta
- Department of Community Medicine and Family Medicine, AIIMS, Jodhpur, Rajasthan, India
| | - P Bhardwaj
- Department of Community Medicine and Family Medicine, AIIMS, Jodhpur, Rajasthan, India
| | - A Goel
- Department of Community Medicine and Family Medicine, AIIMS, Jodhpur, Rajasthan, India
| | - S Saurabh
- Department of Community Medicine and Family Medicine, AIIMS, Jodhpur, Rajasthan, India
| | - S Misra
- Department of Director and CEO, AIIMS, Jodhpur, Rajasthan, India
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Gu B, Comerci CJ, McCarthy DG, Saurabh S, Moerner WE, Wysocka J. Opposing Effects of Cohesin and Transcription on CTCF Organization Revealed by Super-resolution Imaging. Mol Cell 2020; 80:699-711.e7. [PMID: 33091336 PMCID: PMC7725164 DOI: 10.1016/j.molcel.2020.10.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/30/2020] [Accepted: 09/30/2020] [Indexed: 12/21/2022]
Abstract
CCCTC-binding factor (CTCF) and cohesin play critical roles in organizing mammalian genomes into topologically associating domains (TADs). Here, by combining genetic engineering with quantitative super-resolution stimulated emission depletion (STED) microscopy, we demonstrate that in living cells, CTCF forms clusters typically containing 2-8 molecules. A fraction of CTCF clusters, enriched for those with ≥3 molecules, are coupled with cohesin complexes with a characteristic physical distance suggestive of a defined molecular interaction. Acute degradation of the cohesin unloader WAPL or transcriptional inhibition (TI) result in increased CTCF clustering. Furthermore, the effect of TI on CTCF clusters is alleviated by the acute loss of the cohesin subunit SMC3. Our study provides quantitative characterization of CTCF clusters in living cells, uncovers the opposing effects of cohesin and transcription on CTCF clustering, and highlights the power of quantitative super-resolution microscopy as a tool to bridge the gap between biochemical and genomic methodologies in chromatin research.
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Affiliation(s)
- Bo Gu
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Colin J Comerci
- Department of Chemistry, Stanford University, Stanford, CA, USA; Biophysics Program, Stanford University, Stanford, CA, USA
| | | | - Saumya Saurabh
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA, USA; Biophysics Program, Stanford University, Stanford, CA, USA.
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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Saurabh S, Kumar R, Gupta MK, Bhardwaj P, Nag VL, Garg MK, Misra S. Prolonged persistence of SARS-CoV-2 in the upper respiratory tract of asymptomatic infected individuals. QJM 2020; 113:556-560. [PMID: 32609360 PMCID: PMC7337859 DOI: 10.1093/qjmed/hcaa212] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 06/18/2020] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Duration of persistence of SARS-CoV-2 in the upper respiratory tract of infected individuals has important clinical and epidemiological implications. AIM We aimed to establish the duration and risk factors for persistence of SARS-CoV-2 in the upper respiratory tract of asymptomatic infected individuals. METHODS Data of repeat rRT-PCR (real-time reverse transcription-polymerase chain reaction) test done for SARS-CoV-2 infected individuals at our institute at Jodhpur, India were analysed from 19 March to 21 May 2020. Duration of virus persistence was estimated with parametric regression models based on weibull, log-normal, log-logistic, gamma and generalized gamma distributions. Factors associated with prolonged viral persistence were analysed with the best-fitting model. RESULTS Fifty-one SARS-CoV-2 infected individuals with repeat rRT-PCR test were identified with 44 asymptomatics. The asymptomatic individuals had median virus persistence duration of 8.87 days (95% CI: 7.65-10.27) and 95 percentile duration of 20.70 days (95% CI: 16.08-28.20). The overall median virus persistence including both symptomatic and asymptomatic individuals was found to be 9.18 days (95% CI: 8.04-10.48). Around one-fourth asymptomatics (10/44) demonstrated SARS-CoV-2 persistence beyond 2 weeks. Age <60 years and local transmission were found to be significantly associated with longer virus persistence among asymptomatic individuals on univariate regression but not in multivariate analysis. CONCLUSION Recommended home isolation duration for SARS-CoV-2 infected individuals in India should be extended from 17 days to at least 3 weeks. Prolonged persistence of SARS-CoV-2 in a considerable proportion of asymptomatic individuals merits attention with regard to ensuring universal infection prevention precautions irrespective of symptomatic status.
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Affiliation(s)
- S Saurabh
- Department of Community Medicine and Family Medicine, All India Institute of Medical Sciences (AIIMS), Jodhpur 342005, India
| | - R Kumar
- Engineering Science Laboratory - Central Scientific Instruments Organization (CSIO), Council for Scientific and Industrial Research (CSIR), Chandigarh 160030, India
| | - M K Gupta
- Department of Community Medicine and Family Medicine, All India Institute of Medical Sciences (AIIMS), Jodhpur 342005, India
| | - P Bhardwaj
- Department of Community Medicine and Family Medicine, All India Institute of Medical Sciences (AIIMS), Jodhpur 342005, India
| | | | | | - S Misra
- Director, All India Institute of Medical Sciences (AIIMS), Jodhpur 342005, India
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11
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Dahlberg PD, Saurabh S, Sartor AM, Wang J, Mitchell PG, Chiu W, Shapiro L, Moerner WE. Cryogenic single-molecule fluorescence annotations for electron tomography reveal in situ organization of key proteins in Caulobacter. Proc Natl Acad Sci U S A 2020; 117:13937-13944. [PMID: 32513734 PMCID: PMC7321984 DOI: 10.1073/pnas.2001849117] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Superresolution fluorescence microscopy and cryogenic electron tomography (CET) are powerful imaging methods for exploring the subcellular organization of biomolecules. Superresolution fluorescence microscopy based on covalent labeling highlights specific proteins and has sufficient sensitivity to observe single fluorescent molecules, but the reconstructions lack detailed cellular context. CET has molecular-scale resolution but lacks specific and nonperturbative intracellular labeling techniques. Here, we describe an imaging scheme that correlates cryogenic single-molecule fluorescence localizations with CET reconstructions. Our approach achieves single-molecule localizations with an average lateral precision of 9 nm, and a relative registration error between the set of localizations and CET reconstruction of ∼30 nm. We illustrate the workflow by annotating the positions of three proteins in the bacterium Caulobacter crescentus: McpA, PopZ, and SpmX. McpA, which forms a part of the chemoreceptor array, acts as a validation structure by being visible under both imaging modalities. In contrast, PopZ and SpmX cannot be directly identified in CET. While not directly discernable, PopZ fills a region at the cell poles that is devoid of electron-dense ribosomes. We annotate the position of PopZ with single-molecule localizations and confirm its position within the ribosome excluded region. We further use the locations of PopZ to provide context for localizations of SpmX, a low-copy integral membrane protein sequestered by PopZ as part of a signaling pathway that leads to an asymmetric cell division. Our correlative approach reveals that SpmX localizes along one side of the cell pole and its extent closely matches that of the PopZ region.
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Affiliation(s)
- Peter D Dahlberg
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Saumya Saurabh
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Annina M Sartor
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Jiarui Wang
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Patrick G Mitchell
- Division of Cryo-EM and Bioimaging, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Wah Chiu
- Division of Cryo-EM and Bioimaging, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
- Department of Bioengineering, Stanford University, Stanford, CA 94305
| | - Lucy Shapiro
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA 94305;
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12
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Antoniou C, Burnette K, Christensen-Quick A, Lewinska M, Ji Y, Khalifa MM, Nikolaou A, Srivastava P, Hollingsworth BA, van Rhijn N, Saurabh S, Konstantinides N, Heim AB, Moore EB, Strong M, Kosanic A, Kirshner SN, Halder A, Waiho K. Seeking career clarity. Science 2020; 368:26-28. [PMID: 32241935 DOI: 10.1126/science.abb6859] [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: 11/02/2022]
Affiliation(s)
- Chloe Antoniou
- Department of Basic and Clinical Sciences, University of Nicosia Medical School, Nicosia, Cyprus.
| | - Katie Burnette
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA.
| | | | - Monika Lewinska
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, 2200, Denmark. Twitter: @LewinskaMonika
| | - Yongsheng Ji
- Department of Human Parasitology, Anhui Medical University, Hefei, Anhui, 230032, China.
| | - Muhammad M Khalifa
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, WI 53703, USA.
| | | | - Pragya Srivastava
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA. Twitter: @pragya_srivas
| | - Brynn Anne Hollingsworth
- American Association for the Advancement of Science (AAAS) Science and Technology Policy Fellow, Rockville, MD 20850, USA.
| | - Norman van Rhijn
- Manchester Fungal Infection Group, University of Manchester, Manchester, Lancashire, M13 9XX, UK. Twitter: @NormanRhijn
| | - Saumya Saurabh
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA. Twitter: @saumya_s
| | - Nikos Konstantinides
- Department of Biology, New York University, New York, NY 10003, USA. Twitter: @nkonst4
| | - Ashley Barbara Heim
- School of Biological Sciences, University of Northern Colorado, Greeley, CO 80631, USA.
| | - Eric Britt Moore
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA.
| | - Michael Strong
- Center for Genes, Environment, and Health, National Jewish Health and University of Colorado, Anschutz Medical Campus, Denver, CO 80206, USA.
| | - Aleksandra Kosanic
- Zukunftskolleg, University of Konstanz, Konstanz, D 78457, Germany. Twitter: @SashaKosanic
| | - Samuel Nathan Kirshner
- School of Information Systems and Technology Management, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Antarip Halder
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru, Karnataka, 560012, India.
| | - Khor Waiho
- Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, 21030, Malaysia.
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13
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Dahlberg PD, Saurabh S, Wang J, Sartor AM, Chiu W, Shapiro L, Moerner WE. Cryogenic Superresolution Fluorescence Correlated with Cryogenic Electron Tomography: Combining Specific Labeling and High Resolution. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.293] [Citation(s) in RCA: 1] [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: 11/29/2022] Open
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14
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Fujii K, Susanto TT, Saurabh S, Barna M. Decoding the Function of Expansion Segments in Ribosomes. Mol Cell 2019; 72:1013-1020.e6. [PMID: 30576652 DOI: 10.1016/j.molcel.2018.11.023] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [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: 09/17/2018] [Revised: 10/30/2018] [Accepted: 11/15/2018] [Indexed: 10/27/2022]
Abstract
Expansion segments (ESs) are enigmatic insertions within the eukaryotic ribosome, the longest of which resemble tentacle-like extensions that vary in length and sequence across evolution, with a largely unknown function. By selectively engineering rRNA in yeast, we find that one of the largest ESs, ES27L, has an unexpected function in translation fidelity. Ribosomes harboring a deletion in the distal portion of ES27L have increased amino acid misincorporation, as well as readthrough and frameshifting errors. By employing quantitative mass spectrometry, we further find that ES27L acts as an RNA scaffold to facilitate binding of a conserved enzyme, methionine amino peptidase (MetAP). We show that MetAP unexpectedly controls the accuracy of ribosome decoding, which is coupled to an increase in its enzymatic function through its interaction with ES27L. These findings reveal that variable ESs of the ribosome serve important functional roles and act as platforms for the binding of proteins that modulate translation across evolution.
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Affiliation(s)
- Kotaro Fujii
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Teodorus Theo Susanto
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Saumya Saurabh
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Maria Barna
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA.
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15
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Saurabh S, Shapiro L. Dissection of Protein Function Within a Bacterial Biomolecular Condensate by In Vitro Reconstitution. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.2475] [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] Open
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16
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Gopalakrishnan M, Vinod KV, Dutta TK, Shaha KK, Sridhar MG, Saurabh S. Exploring circulatory shock and mortality in viper envenomation: a prospective observational study from India. QJM 2018; 111:799-806. [PMID: 30107433 DOI: 10.1093/qjmed/hcy175] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Viper envenomation contributes to nearly 50% of snake-bite deaths in India, chiefly due to circulatory shock. The mechanisms leading to circulatory shock include bleeding, capillary leak syndrome (CLS) and myocardial depression. Pituitary-adrenal axis involvement in circulatory shock, though described, has not been fully elucidated. AIM To identify predictors of circulatory shock and mortality in viper envenomation and explore the role of pituitary-adrenal axis in circulatory shock. DESIGN Prospective hospital-based observational study. METHODS Once a syndromic diagnosis of viper envenomation was made, relevant clinical and laboratory data were collected. Serum cortisol was estimated in those with circulatory shock. Post-mortem examination of pituitary, kidneys and adrenals was performed. Adjusted odds-ratios were calculated for respective risk-factors for shock and mortality using multivariable logistic regression with backward elimination strategy. RESULTS Of 248 patients of viper envenomation treated at our hospital, circulatory shock was present in 19% and in-hospital mortality was 23%. CLS, circulatory shock, bleeding and requirement of > 20 vials of antivenom predicted mortality. Ischaemic and haemorrhagic necrosis of pituitary or adrenals was present in 51% of post-mortem specimens. Disseminated intravascular coagulation (DIC) and CLS were strong predictors of pituitary haemorrhage. CONCLUSION Predictors of mortality - bleeding, CLS and requirement of high antivenom doses are warning signs which can alert clinicians to patients who may have poor outcomes. Our study points to a definite role of pituitary-adrenal axis in circulatory shock supports the hypothesis that pituitary involvement in viper envenomation closely resembles Sheehan syndrome. The mechanism of pituitary involvement appears to be a result of increased susceptibility of the swollen gland secondary to CLS and micro thrombi deposition in DIC.
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Affiliation(s)
- M Gopalakrishnan
- Department of Medicine, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Dhanvantari Nagar, Puducherry, India
| | - K V Vinod
- Department of Medicine, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Dhanvantari Nagar, Puducherry, India
| | - T K Dutta
- Department of Medicine, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Dhanvantari Nagar, Puducherry, India
| | - K K Shaha
- Department of Forensic Medicine and Toxicology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Dhanvantari Nagar, Puducherry, India
| | - M G Sridhar
- Department of Biochemistry, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Dhanvantari Nagar, Puducherry, India
| | - S Saurabh
- Department of Preventive and Social Medicine, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Dhanvantari Nagar, Puducherry, India
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17
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Dahlberg P, Sartor AM, Wang J, Saurabh S, Shapiro L, Moerner WE. Identification of PAmKate as a Red Photoactivatable Fluorescent Protein for Cryogenic Super-Resolution Imaging. J Am Chem Soc 2018; 140:12310-12313. [PMID: 30222332 PMCID: PMC6174896 DOI: 10.1021/jacs.8b05960] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Indexed: 11/30/2022]
Abstract
Single-molecule super-resolution fluorescence microscopy conducted in vitrified samples at cryogenic temperatures offers enhanced localization precision due to reduced photobleaching rates, a chemical-free and rapid fixation method, and the potential of correlation with cryogenic electron microscopy. Achieving cryogenic super-resolution microscopy requires the ability to control the sparsity of emissive labels at cryogenic temperatures. Obtaining this control presents a key challenge for the development of this technique. In this work, we identify a red photoactivatable protein, PAmKate, which remains activatable at cryogenic temperatures. We characterize its activation as a function of temperature and find that activation is efficient at cryogenic and room temperatures. We perform cryogenic super-resolution experiments in situ, labeling PopZ, a protein known to assemble into a microdomain at the poles of the model bacterium Caulobacter crescentus. We find improved localization precision at cryogenic temperatures compared to room temperature by a factor of 4, attributable to reduced photobleaching.
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Affiliation(s)
- Peter
D. Dahlberg
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Annina M. Sartor
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Jiarui Wang
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Department
of Developmental Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
| | - Saumya Saurabh
- Department
of Developmental Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
| | - Lucy Shapiro
- Department
of Developmental Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
| | - W. E. Moerner
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
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18
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Gotrik M, Sekhon G, Saurabh S, Nakamoto M, Eisenstein M, Soh HT. Direct Selection of Fluorescence-Enhancing RNA Aptamers. J Am Chem Soc 2018; 140:3583-3591. [PMID: 29505267 DOI: 10.1021/jacs.7b10724] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
RNA aptamers that generate a strong fluorescence signal upon binding a nonfluorescent small-molecule dye offer a powerful means for the selective imaging of individual RNA species. Unfortunately, conventional in vitro discovery methods are not efficient at generating such fluorescence-enhancing aptamers, because they primarily exert selective pressure based on target affinity-a characteristic that correlates poorly with fluorescence enhancement. Thus, only a handful of fluorescence-enhancing aptamers have been reported to date. In this work, we describe a method for converting DNA libraries into "gene-linked RNA aptamer particles" (GRAPs) that each display ∼105 copies of a single RNA sequence alongside the DNA that encodes it. We then screen large libraries of GRAPs in a high-throughput manner using the FACS instrument based directly on their fluorescence-enhancing properties. Using this strategy, we demonstrate the capability to generate fluorescence-enhancing aptamers that produce a variety of different emission wavelengths upon binding the dye of interest.
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Affiliation(s)
- Michael Gotrik
- Materials Department , University of California - Santa Barbara , Santa Barbara , California 93108 , United States.,Department of Electrical Engineering and Department of Radiology , Stanford University , Stanford , California 94305 , United States
| | - Gurpreet Sekhon
- Department of Electrical Engineering and Department of Radiology , Stanford University , Stanford , California 94305 , United States
| | - Saumya Saurabh
- Department of Developmental Biology , Stanford University , Stanford , California 94305 , United States
| | - Margaret Nakamoto
- Department of Electrical Engineering and Department of Radiology , Stanford University , Stanford , California 94305 , United States
| | - Michael Eisenstein
- Department of Electrical Engineering and Department of Radiology , Stanford University , Stanford , California 94305 , United States
| | - H Tom Soh
- Department of Electrical Engineering and Department of Radiology , Stanford University , Stanford , California 94305 , United States
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19
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Perkins LA, Yan Q, Schmidt BF, Kolodieznyi D, Saurabh S, Larsen MB, Watkins SC, Kremer L, Bruchez MP. Genetically Targeted Ratiometric and Activated pH Indicator Complexes (TRApHIC) for Receptor Trafficking. Biochemistry 2018; 57:861-871. [PMID: 29283245 DOI: 10.1021/acs.biochem.7b01135] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fluorescent protein-based pH sensors are useful tools for measuring protein trafficking through pH changes associated with endo- and exocytosis. However, commonly used pH-sensing probes are ubiquitously expressed with their protein of interest throughout the cell, hindering our ability to focus on specific trafficking pools of proteins. We developed a family of excitation ratiometric, activatable pH responsive tandem dyes, consisting of a pH sensitive Cy3 donor linked to a fluorogenic malachite green acceptor. These cell-excluded dyes are targeted and activated upon binding to a genetically expressed fluorogen-activating protein and are suitable for selective labeling of surface proteins for analysis of endocytosis and recycling in live cells using both confocal and superresolution microscopy. Quantitative profiling of the endocytosis and recycling of tagged β2-adrenergic receptor (B2AR) at a single-vesicle level revealed differences among B2AR agonists, consistent with more detailed pharmacological profiling.
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Affiliation(s)
| | - Qi Yan
- Sharp Edge Laboratories , Pittsburgh, Pennsylvania 15203, United States
| | | | | | - Saumya Saurabh
- Department of Developmental Biology, Stanford University , Stanford, California 94305, United States
| | - Mads Breum Larsen
- Center for Biologic Imaging, Department of Cell Biology and Physiology, School of Medicine, University of Pittsburgh , Pittsburgh, Pennsylvania 15213, United States
| | - Simon C Watkins
- Center for Biologic Imaging, Department of Cell Biology and Physiology, School of Medicine, University of Pittsburgh , Pittsburgh, Pennsylvania 15213, United States
| | - Laura Kremer
- Institute of Human Genetics, Helmholtz Zentrum München , Munich, Germany
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20
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Meyer C, Becker A, Blaum K, Breitenfeldt C, George S, Göck J, Grieser M, Grussie F, Guerin EA, von Hahn R, Herwig P, Krantz C, Kreckel H, Lion J, Lohmann S, Mishra PM, Novotný O, O'Connor AP, Repnow R, Saurabh S, Schwalm D, Schweikhard L, Spruck K, Sunil Kumar S, Vogel S, Wolf A. Radiative Rotational Lifetimes and State-Resolved Relative Detachment Cross Sections from Photodetachment Thermometry of Molecular Anions in a Cryogenic Storage Ring. Phys Rev Lett 2017; 119:023202. [PMID: 28753369 DOI: 10.1103/physrevlett.119.023202] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Indexed: 06/07/2023]
Abstract
Photodetachment thermometry on a beam of OH^{-} in a cryogenic storage ring cooled to below 10 K is carried out using two-dimensional frequency- and time-dependent photodetachment spectroscopy over 20 min of ion storage. In equilibrium with the low-level blackbody field, we find an effective radiative temperature near 15 K with about 90% of all ions in the rotational ground state. We measure the J=1 natural lifetime (about 193 s) and determine the OH^{-} rotational transition dipole moment with 1.5% uncertainty. We also measure rotationally dependent relative near-threshold photodetachment cross sections for photodetachment thermometry.
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Affiliation(s)
- C Meyer
- Max-Planck-Institut für Kernphysik, D-69117 Heidelberg, Germany
| | - A Becker
- Max-Planck-Institut für Kernphysik, D-69117 Heidelberg, Germany
| | - K Blaum
- Max-Planck-Institut für Kernphysik, D-69117 Heidelberg, Germany
| | - C Breitenfeldt
- Max-Planck-Institut für Kernphysik, D-69117 Heidelberg, Germany
- Institut für Physik, Ernst-Moritz-Arndt-Universität Greifswald, D-17487 Greifswald, Germany
| | - S George
- Max-Planck-Institut für Kernphysik, D-69117 Heidelberg, Germany
| | - J Göck
- Max-Planck-Institut für Kernphysik, D-69117 Heidelberg, Germany
| | - M Grieser
- Max-Planck-Institut für Kernphysik, D-69117 Heidelberg, Germany
| | - F Grussie
- Max-Planck-Institut für Kernphysik, D-69117 Heidelberg, Germany
| | - E A Guerin
- Max-Planck-Institut für Kernphysik, D-69117 Heidelberg, Germany
| | - R von Hahn
- Max-Planck-Institut für Kernphysik, D-69117 Heidelberg, Germany
| | - P Herwig
- Max-Planck-Institut für Kernphysik, D-69117 Heidelberg, Germany
| | - C Krantz
- Max-Planck-Institut für Kernphysik, D-69117 Heidelberg, Germany
| | - H Kreckel
- Max-Planck-Institut für Kernphysik, D-69117 Heidelberg, Germany
| | - J Lion
- Max-Planck-Institut für Kernphysik, D-69117 Heidelberg, Germany
| | - S Lohmann
- Max-Planck-Institut für Kernphysik, D-69117 Heidelberg, Germany
| | - P M Mishra
- Max-Planck-Institut für Kernphysik, D-69117 Heidelberg, Germany
| | - O Novotný
- Max-Planck-Institut für Kernphysik, D-69117 Heidelberg, Germany
| | - A P O'Connor
- Max-Planck-Institut für Kernphysik, D-69117 Heidelberg, Germany
| | - R Repnow
- Max-Planck-Institut für Kernphysik, D-69117 Heidelberg, Germany
| | - S Saurabh
- Max-Planck-Institut für Kernphysik, D-69117 Heidelberg, Germany
| | - D Schwalm
- Max-Planck-Institut für Kernphysik, D-69117 Heidelberg, Germany
- Weizmann Institute of Science, Rehovot 76100, Israel
| | - L Schweikhard
- Institut für Physik, Ernst-Moritz-Arndt-Universität Greifswald, D-17487 Greifswald, Germany
| | - K Spruck
- Max-Planck-Institut für Kernphysik, D-69117 Heidelberg, Germany
- Institut für Atom- und Molekülphysik, Justus-Liebig-Universität Gießen, D-35392 Gießen, Germany
| | - S Sunil Kumar
- Max-Planck-Institut für Kernphysik, D-69117 Heidelberg, Germany
| | - S Vogel
- Max-Planck-Institut für Kernphysik, D-69117 Heidelberg, Germany
| | - A Wolf
- Max-Planck-Institut für Kernphysik, D-69117 Heidelberg, Germany
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21
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Saurabh S, Perez AM, Comerci CJ, Shapiro L, Moerner WE. Super-Resolution Microscopy and Single-Protein Tracking in Live Bacteria Using a Genetically Encoded, Photostable Fluoromodule. ACTA ACUST UNITED AC 2017. [PMID: 28627757 DOI: 10.1002/cpcb.21] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Visualization of dynamic protein structures in live cells is crucial for understanding the mechanisms governing biological processes. Fluorescence microscopy is a sensitive tool for this purpose. In order to image proteins in live bacteria using fluorescence microscopy, one typically genetically fuses the protein of interest to a photostable fluorescent tag. Several labeling schemes are available to accomplish this. Particularly, hybrid tags that combine a fluorescent or fluorogenic dye with a genetically encoded protein (such as enzymatic labels) have been used successfully in multiple cell types. However, their use in bacteria has been limited due to challenges imposed by a complex bacterial cell wall. Here, we describe the use of a genetically encoded photostable fluoromodule that can be targeted to cytosolic and membrane proteins in the Gram negative bacterium Caulobacter crescentus. Additionally, we summarize methods to use this fluoromodule for single protein imaging and super-resolution microscopy using stimulated emission depletion. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Saumya Saurabh
- Department of Chemistry, Stanford University, Stanford, California
| | - Adam M Perez
- Department of Developmental Biology, Beckman Center for Molecular and Genetic Medicine, Stanford University School of Medicine, Stanford, California.,Department of Biology, Stanford University, Stanford, California
| | - Colin J Comerci
- Biophysics Program, Stanford University, Stanford, California
| | - Lucy Shapiro
- Department of Developmental Biology, Beckman Center for Molecular and Genetic Medicine, Stanford University School of Medicine, Stanford, California
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, California
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22
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Saurabh S, Perez AM, Comerci CJ, Shapiro L, Moerner WE. Super-resolution Imaging of Live Bacteria Cells Using a Genetically Directed, Highly Photostable Fluoromodule. J Am Chem Soc 2016; 138:10398-401. [PMID: 27479076 DOI: 10.1021/jacs.6b05943] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The rapid development in fluorescence microscopy and imaging techniques has greatly benefited our understanding of the mechanisms governing cellular processes at the molecular level. In particular, super-resolution microscopy methods overcome the diffraction limit to observe nanoscale cellular structures with unprecedented detail, and single-molecule tracking provides precise dynamic information about the motions of labeled proteins and oligonucleotides. Enhanced photostability of fluorescent labels (i.e., maximum emitted photons before photobleaching) is a critical requirement for achieving the ultimate spatio-temporal resolution with either method. While super-resolution imaging has greatly benefited from highly photostable fluorophores, a shortage of photostable fluorescent labels for bacteria has limited its use in these small but relevant organisms. In this study, we report the use of a highly photostable fluoromodule, dL5, to genetically label proteins in the Gram-negative bacterium Caulobacter crescentus, enabling long-time-scale protein tracking and super-resolution microscopy. dL5 imaging relies on the activation of the fluorogen Malachite Green (MG) and can be used to label proteins sparsely, enabling single-protein detection in live bacteria without initial bleaching steps. dL5-MG complexes emit 2-fold more photons before photobleaching compared to organic dyes such as Cy5 and Alexa 647 in vitro, and 5-fold more photons compared to eYFP in vivo. We imaged fusions of dL5 to three different proteins in live Caulobacter cells using stimulated emission depletion microscopy, yielding a 4-fold resolution enhancement compared to diffraction-limited imaging. Importantly, dL5 fusions to an intermediate filament protein CreS are significantly less perturbative compared to traditional fluorescent protein fusions. To the best of our knowledge, this is the first demonstration of the use of fluorogen activating proteins for super-resolution imaging in live bacterial cells.
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Affiliation(s)
- Saumya Saurabh
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Adam M Perez
- Department of Developmental Biology, Stanford University School of Medicine , Stanford, California 94305, United States.,Department of Biology, Stanford University , Stanford, California 94305, United States
| | - Colin J Comerci
- Biophysics Program, Stanford University , Stanford, California 94305, United States
| | - Lucy Shapiro
- Department of Developmental Biology, Stanford University School of Medicine , Stanford, California 94305, United States
| | - W E Moerner
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
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23
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von Hahn R, Becker A, Berg F, Blaum K, Breitenfeldt C, Fadil H, Fellenberger F, Froese M, George S, Göck J, Grieser M, Grussie F, Guerin EA, Heber O, Herwig P, Karthein J, Krantz C, Kreckel H, Lange M, Laux F, Lohmann S, Menk S, Meyer C, Mishra PM, Novotný O, O'Connor AP, Orlov DA, Rappaport ML, Repnow R, Saurabh S, Schippers S, Schröter CD, Schwalm D, Schweikhard L, Sieber T, Shornikov A, Spruck K, Sunil Kumar S, Ullrich J, Urbain X, Vogel S, Wilhelm P, Wolf A, Zajfman D. The cryogenic storage ring CSR. Rev Sci Instrum 2016; 87:063115. [PMID: 27370434 DOI: 10.1063/1.4953888] [Citation(s) in RCA: 16] [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] [Indexed: 06/06/2023]
Abstract
An electrostatic cryogenic storage ring, CSR, for beams of anions and cations with up to 300 keV kinetic energy per unit charge has been designed, constructed, and put into operation. With a circumference of 35 m, the ion-beam vacuum chambers and all beam optics are in a cryostat and cooled by a closed-cycle liquid helium system. At temperatures as low as (5.5 ± 1) K inside the ring, storage time constants of several minutes up to almost an hour were observed for atomic and molecular, anion and cation beams at an energy of 60 keV. The ion-beam intensity, energy-dependent closed-orbit shifts (dispersion), and the focusing properties of the machine were studied by a system of capacitive pickups. The Schottky-noise spectrum of the stored ions revealed a broadening of the momentum distribution on a time scale of 1000 s. Photodetachment of stored anions was used in the beam lifetime measurements. The detachment rate by anion collisions with residual-gas molecules was found to be extremely low. A residual-gas density below 140 cm(-3) is derived, equivalent to a room-temperature pressure below 10(-14) mbar. Fast atomic, molecular, and cluster ion beams stored for long periods of time in a cryogenic environment will allow experiments on collision- and radiation-induced fragmentation processes of ions in known internal quantum states with merged and crossed photon and particle beams.
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Affiliation(s)
- R von Hahn
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - A Becker
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - F Berg
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - K Blaum
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - C Breitenfeldt
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - H Fadil
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - F Fellenberger
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - M Froese
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - S George
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - J Göck
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - M Grieser
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - F Grussie
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - E A Guerin
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - O Heber
- Weizmann Institute of Science, Rehovot 76100, Israel
| | - P Herwig
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - J Karthein
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - C Krantz
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - H Kreckel
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - M Lange
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - F Laux
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - S Lohmann
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - S Menk
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - C Meyer
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - P M Mishra
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - O Novotný
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - A P O'Connor
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - D A Orlov
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - M L Rappaport
- Weizmann Institute of Science, Rehovot 76100, Israel
| | - R Repnow
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - S Saurabh
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - S Schippers
- I. Physikalisches Institut, Justus-Liebig-Universität Gießen, 35392 Gießen, Germany
| | - C D Schröter
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - D Schwalm
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - L Schweikhard
- Institut für Physik, Ernst-Moritz-Arndt-Universität, 17487 Greifswald, Germany
| | - T Sieber
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - A Shornikov
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - K Spruck
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - S Sunil Kumar
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - J Ullrich
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - X Urbain
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - S Vogel
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - P Wilhelm
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - A Wolf
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - D Zajfman
- Weizmann Institute of Science, Rehovot 76100, Israel
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24
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O'Connor AP, Becker A, Blaum K, Breitenfeldt C, George S, Göck J, Grieser M, Grussie F, Guerin EA, von Hahn R, Hechtfischer U, Herwig P, Karthein J, Krantz C, Kreckel H, Lohmann S, Meyer C, Mishra PM, Novotný O, Repnow R, Saurabh S, Schwalm D, Spruck K, Sunil Kumar S, Vogel S, Wolf A. Photodissociation of an Internally Cold Beam of CH^{+} Ions in a Cryogenic Storage Ring. Phys Rev Lett 2016; 116:113002. [PMID: 27035300 DOI: 10.1103/physrevlett.116.113002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Indexed: 06/05/2023]
Abstract
We have studied the photodissociation of CH^{+} in the Cryogenic Storage Ring at ambient temperatures below 10 K. Owing to the extremely high vacuum of the cryogenic environment, we were able to store CH^{+} beams with a kinetic energy of ∼60 keV for several minutes. Using a pulsed laser, we observed Feshbach-type near-threshold photodissociation resonances for the rotational levels J=0-2 of CH^{+}, exclusively. In comparison to updated, state-of-the-art calculations, we find excellent agreement in the relative intensities of the resonances for a given J, and we can extract time-dependent level populations. Thus, we can monitor the spontaneous relaxation of CH^{+} to its lowest rotational states and demonstrate the preparation of an internally cold beam of molecular ions.
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Affiliation(s)
- A P O'Connor
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - A Becker
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - K Blaum
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - C Breitenfeldt
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
- Institut für Physik, Ernst-Moritz-Arndt Universität, 17487 Greifswald, Germany
| | - S George
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - J Göck
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - M Grieser
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - F Grussie
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - E A Guerin
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - R von Hahn
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - U Hechtfischer
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - P Herwig
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - J Karthein
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - C Krantz
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - H Kreckel
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - S Lohmann
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - C Meyer
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - P M Mishra
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - O Novotný
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - R Repnow
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - S Saurabh
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - D Schwalm
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
- Department of Particle Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - K Spruck
- Institut für Atom- und Molekülphysik, Universität Gießen, 35392 Gießen, Germany
| | - S Sunil Kumar
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - S Vogel
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - A Wolf
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
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25
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Seshadri KS, Singal R, Priti H, Ravikanth G, Vidisha MK, Saurabh S, Pratik M, Gururaja KV. Microhyla laterite sp. nov., A New Species of Microhyla Tschudi, 1838 (Amphibia: Anura: Microhylidae) from a Laterite Rock Formation in South West India. PLoS One 2016; 11:e0149727. [PMID: 26960208 PMCID: PMC4784882 DOI: 10.1371/journal.pone.0149727] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 01/27/2016] [Indexed: 11/26/2022] Open
Abstract
In recent times, several new species of amphibians have been described from India. Many of these discoveries are from biodiversity hotspots or from within protected areas. We undertook amphibian surveys in human dominated landscapes outside of protected areas in south western region of India between years 2013-2015. We encountered a new species of Microhyla which is described here as Microhyla laterite sp. nov. It was delimited using molecular, morphometric and bioacoustics comparisons. Microhyla laterite sp. nov. appears to be restricted to areas of the West coast of India dominated by laterite rock formations. The laterite rock formations date as far back as the Cretaceous-Tertiary boundary and are considered to be wastelands in-spite of their intriguing geological history. We identify knowledge gaps in our understanding of the genus Microhyla from the Indian subcontinent and suggest ways to bridge them.
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Affiliation(s)
- K. S. Seshadri
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Block S3, Singapore, Singapore
| | - Ramit Singal
- Independent Researcher, B-14, Law Apartments, Karkardooma, Delhi, India
| | - H. Priti
- Manipal University, Manipal, India
- Suri Sehgal Centre for Biodiversity and Conservation, Ashoka Trust for Research in Ecology and the Environment (ATREE), Royal Enclave, Sriramapura, Jakkur (P.O), Bengaluru, India
| | - G. Ravikanth
- Suri Sehgal Centre for Biodiversity and Conservation, Ashoka Trust for Research in Ecology and the Environment (ATREE), Royal Enclave, Sriramapura, Jakkur (P.O), Bengaluru, India
| | - M. K. Vidisha
- Science Media Center, Gubbi Labs LLP, WS-5, I Floor, Entrepreneurship Center, Society for Innovation and Development, Indian Institute of Science Campus, Bengaluru, India
| | - S. Saurabh
- Independent Researcher, A/103, Gokul, B. P. Road, Dahisar (W), Mumbai, India
| | - M. Pratik
- Independent Researcher, 3C/704, Whispering Palms, Lokhandwala Township, Kandivali East, Mumbai, India
| | - Kotambylu Vasudeva Gururaja
- Science Media Center, Gubbi Labs LLP, WS-5, I Floor, Entrepreneurship Center, Society for Innovation and Development, Indian Institute of Science Campus, Bengaluru, India
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Backlund MP, Arbabi A, Petrov PN, Arbabi E, Saurabh S, Faraon A, Moerner WE. Removing Orientation-Induced Localization Biases in Single-Molecule Microscopy Using a Broadband Metasurface Mask. Nat Photonics 2016; 10:459-462. [PMID: 27574529 PMCID: PMC5001689 DOI: 10.1038/nphoton.2016.93] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 04/11/2016] [Indexed: 05/21/2023]
Abstract
Nanoscale localization of single molecules is a crucial function in several advanced microscopy techniques, including single-molecule tracking and wide-field super-resolution imaging 1. To date, a central consideration of such techniques is how to optimize the precision of molecular localization. However, as these methods continue to push toward the nanometre size scale, an increasingly important concern is the localization accuracy. In particular, single fluorescent molecules emit with an anisotropic radiation pattern of an oscillating electric dipole, which can cause significant localization biases using common estimators 2-5. Here we present the theory and experimental demonstration of a solution to this problem based on azimuthal filtering in the Fourier plane of the microscope. We do so using a high efficiency dielectric metasurface polarization/phase device composed of nanoposts with sub-wavelength spacing 6. The method is demonstrated both on fluorophores embedded in a polymer matrix, and in dL5 protein complexes that bind Malachite green 7, 8.
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Affiliation(s)
- Mikael P. Backlund
- Department of Chemistry, Stanford University, 375 North-South Mall, Stanford, CA 94305
| | - Amir Arbabi
- T. J. Watson Laboratory of Applied Physics, California Institute of Technology, 1200 E California Blvd., Pasadena, CA 91125
| | - Petar N. Petrov
- Department of Chemistry, Stanford University, 375 North-South Mall, Stanford, CA 94305
| | - Ehsan Arbabi
- T. J. Watson Laboratory of Applied Physics, California Institute of Technology, 1200 E California Blvd., Pasadena, CA 91125
| | - Saumya Saurabh
- Department of Chemistry, Stanford University, 375 North-South Mall, Stanford, CA 94305
| | - Andrei Faraon
- T. J. Watson Laboratory of Applied Physics, California Institute of Technology, 1200 E California Blvd., Pasadena, CA 91125
- A.F. for questions regarding the metasurface mask. Contact:
| | - W. E. Moerner
- Department of Chemistry, Stanford University, 375 North-South Mall, Stanford, CA 94305
- Correspondence should be directed to W.E.M. for questions regarding the experiment, Contact:
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27
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Yan Q, Schmidt BF, Perkins LA, Naganbabu M, Saurabh S, Andreko SK, Bruchez MP. Near-instant surface-selective fluorogenic protein quantification using sulfonated triarylmethane dyes and fluorogen activating proteins. Org Biomol Chem 2015; 13:2078-86. [PMID: 25520058 DOI: 10.1039/c4ob02309a] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Agonist-promoted G-protein coupled receptor (GPCR) endocytosis and recycling plays an important role in many signaling events in the cell. However, the approaches that allow fast and quantitative analysis of such processes still remain limited. Here we report an improved labeling approach based on the genetic fusion of a fluorogen activating protein (FAP) to a GPCR and binding of a sulfonated analog of the malachite green (MG) fluorogen to rapidly and selectively label cell surface receptors. Fluorescence microscopy and flow cytometry demonstrate that this dye does not cross the plasma membrane, binds with high affinity to a dL5** FAP-GPCR fusion construct, activating tagged surface receptors within seconds of addition. The ability to rapidly and selectively label cell surface receptors with a fluorogenic genetically encoded tag allows quantitative imaging and analysis of highly dynamic processes like receptor endocytosis and recycling.
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Affiliation(s)
- Qi Yan
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA.
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Zhang M, Chakraborty SK, Sampath P, Rojas JJ, Hou W, Saurabh S, Thorne SH, Bruchez MP, Waggoner AS. Fluoromodule-based reporter/probes designed for in vivo fluorescence imaging. J Clin Invest 2015; 125:3915-27. [PMID: 26348895 DOI: 10.1172/jci81086] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 07/30/2015] [Indexed: 12/26/2022] Open
Abstract
Optical imaging of whole, living animals has proven to be a powerful tool in multiple areas of preclinical research and has allowed noninvasive monitoring of immune responses, tumor and pathogen growth, and treatment responses in longitudinal studies. However, fluorescence-based studies in animals are challenging because tissue absorbs and autofluoresces strongly in the visible light spectrum. These optical properties drive development and use of fluorescent labels that absorb and emit at longer wavelengths. Here, we present a far-red absorbing fluoromodule-based reporter/probe system and show that this system can be used for imaging in living mice. The probe we developed is a fluorogenic dye called SC1 that is dark in solution but highly fluorescent when bound to its cognate reporter, Mars1. The reporter/probe complex, or fluoromodule, produced peak emission near 730 nm. Mars1 was able to bind a variety of structurally similar probes that differ in color and membrane permeability. We demonstrated that a tool kit of multiple probes can be used to label extracellular and intracellular reporter-tagged receptor pools with 2 colors. Imaging studies may benefit from this far-red excited reporter/probe system, which features tight coupling between probe fluorescence and reporter binding and offers the option of using an expandable family of fluorogenic probes with a single reporter gene.
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29
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Saurabh S, Zhang M, Mann VR, Costello AM, Bruchez MP. Kinetically Tunable Photostability of Fluorogen-Activating Peptide-Fluorogen Complexes. Chemphyschem 2015; 16:2974-80. [PMID: 26310607 DOI: 10.1002/cphc.201500587] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Indexed: 11/09/2022]
Abstract
Ease of genetic encoding, labeling specificity, and high photostability are the most sought after qualities in a fluorophore for biological detection. Furthermore, many applications can gain from the fluorogenic nature of fluoromodules and the ability to turn on the same fluoromodules multiple times. Fluorogen-activating peptides (FAPs) bind noncovalently to their cognate fluorogens and exhibit enhanced photostability. Herein, the photostabilities of malachite green (MG)-binding and thiazole-orange-binding FAPs are compared under limiting- and excess-fluorogen conditions to establish distinct mechanisms for photostability that correspond to the dissociation rate of the FAP-fluorogen complex. FAPs with slow dissociation show evidence of dye encapsulation and protection from photo or environmental degradation and single-step bleaching at the single molecule level, whereas those with rapid dissociation show repeated cycles of binding and enhanced photostability by exchange of bleached fluorogen with a new dye. A combination of generalizable selection pressure based on bleaching, flow cytometry, and site-specific amino acid mutagenesis is used to obtain a modified FAP with enhanced photostability, due to rapid dissociation of the MG fluorogen. These studies shed light on the basic mechanisms by which noncovalent association can effect photostable labeling, and demonstrate novel reagents for photostable and intermittent labeling of biological targets.
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Affiliation(s)
- Saumya Saurabh
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213 (USA).,Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA 15213 (USA)
| | - Ming Zhang
- Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA 15213 (USA).,Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213 (USA)
| | - Victor R Mann
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213 (USA)
| | - Andrea M Costello
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213 (USA)
| | - Marcel P Bruchez
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213 (USA). .,Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA 15213 (USA).
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Saurabh S, Beck LE, Maji S, Baty CJ, Wang Y, Yan Q, Watkins SC, Bruchez MP. Multiplexed modular genetic targeting of quantum dots. ACS Nano 2014; 8:11138-46. [PMID: 25380615 PMCID: PMC4246007 DOI: 10.1021/nn5044367] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 11/07/2014] [Indexed: 05/19/2023]
Abstract
While DNA-directed nanotechnology is now a well-established platform for bioinspired nanoscale assembly in vitro, the direct targeting of various nanomaterials in living biological systems remains a significant challenge. Hybrid biological systems with integrated and targeted nanomaterials may have interesting and exploitable properties, so methods for targeting various nanomaterials to precise biological locations are required. Fluorescence imaging has benefited from the use of nanoparticles with superior optical properties compared to fluorescent organic dyes or fluorescent proteins. While single-particle tracking (SPT) in living cells with genetically encoded proteins is limited to very short trajectories, the high photon output of genetically targeted and multiplexed quantum dots (QDs) would enable long-trajectory analysis of multiple proteins. However, challenges with genetic targeting of QDs limit their application in these experiments. In this report, we establish a modular method for targeting QD nanoparticles selectively to multiple genetically encoded tags by precomplexing QD-streptavidin conjugates with cognate biotinylated hapten molecules. This approach enables labeling and SPT of multiple genetically encoded proteins on living cells at high speed and can label expressed proteins in the cytosol upon microinjection into living cells. While we demonstrate labeling with three distinct QD conjugates, the approach can be extended to other specific hapten-affinity molecule interactions and alternative nanoparticles, enabling precise directed targeting of nanoparticles in living biological systems.
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Affiliation(s)
- Saumya Saurabh
- Department of Chemistry, Molecular Biosensor and Imaging Center, Department of Physics, Lane Center for Computational Biology, and Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States
| | - Lauren E. Beck
- Department of Chemistry, Molecular Biosensor and Imaging Center, Department of Physics, Lane Center for Computational Biology, and Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States
| | - Suvrajit Maji
- Department of Chemistry, Molecular Biosensor and Imaging Center, Department of Physics, Lane Center for Computational Biology, and Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States
| | - Catherine J. Baty
- Department of Cell Biology, Center for Biological Imaging, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Yi Wang
- Department of Chemistry, Molecular Biosensor and Imaging Center, Department of Physics, Lane Center for Computational Biology, and Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States
| | - Qi Yan
- Department of Chemistry, Molecular Biosensor and Imaging Center, Department of Physics, Lane Center for Computational Biology, and Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States
| | - Simon C. Watkins
- Department of Cell Biology, Center for Biological Imaging, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Marcel P. Bruchez
- Department of Chemistry, Molecular Biosensor and Imaging Center, Department of Physics, Lane Center for Computational Biology, and Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States
- Address correspondence to
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Tan C, Saurabh S, Bruchez MP, Schwartz R, LeDuc P. Reply to 'Complexity of molecular crowding in cell-free enzymatic reaction networks'. Nat Nanotechnol 2014; 9:407-408. [PMID: 24894472 DOI: 10.1038/nnano.2014.111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Affiliation(s)
- Cheemeng Tan
- Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Saumya Saurabh
- 1] Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA [2] Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Marcel P Bruchez
- 1] Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA [2] Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA [3] Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Russell Schwartz
- 1] Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA [2] Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Philip LeDuc
- 1] Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA [2] Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA [3] Department of Mechanical Engineering and Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
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Saurabh S, Mann VR, Beck LE, Zhang M, Costello A, Bruchez MP. Exploiting Binding Kinetics of Fluorogen Activating Peptides to Enhance Photostability: Applications to Live Cell Single Molecule Imaging. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.3331] [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] Open
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Tan C, Saurabh S, Bruchez M, Schwartz R, LeDuc P. Molecular crowding shapes gene expression in synthetic cellular nanosystems. Nat Nanotechnol 2013; 8:602-8. [PMID: 23851358 PMCID: PMC3951305 DOI: 10.1038/nnano.2013.132] [Citation(s) in RCA: 170] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Accepted: 06/10/2013] [Indexed: 05/16/2023]
Abstract
The integration of synthetic and cell-free biology has made tremendous strides towards creating artificial cellular nanosystems using concepts from solution-based chemistry, where only the concentrations of reacting species modulate gene expression rates. However, it is known that macromolecular crowding, a key feature in natural cells, can dramatically influence biochemical kinetics via volume exclusion effects, which reduce diffusion rates and enhance binding rates of macromolecules. Here, we demonstrate that macromolecular crowding can increase the robustness of gene expression by integrating synthetic cellular components of biological circuits and artificial cellular nanosystems. Furthermore, we reveal how ubiquitous cellular modules, including genetic components, a negative feedback loop and the size of the crowding molecules can fine-tune gene circuit response to molecular crowding. By bridging a key gap between artificial and living cells, our work has implications for efficient and robust control of both synthetic and natural cellular circuits.
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Affiliation(s)
- Cheemeng Tan
- Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Saumya Saurabh
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Marcel Bruchez
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Russell Schwartz
- Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Department of Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Correspondence and requests for materials should be addressed to Philip Leduc & Russell Schwartz. ; . Tel: 412-268-2504. Fax: 412-268-3348
| | - Philip LeDuc
- Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Correspondence and requests for materials should be addressed to Philip Leduc & Russell Schwartz. ; . Tel: 412-268-2504. Fax: 412-268-3348
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Bhattacharya S, Sharma DK, Saurabh S, De S, Sain A, Nandi A, Chowdhury A. Plasticization of poly(vinylpyrrolidone) thin films under ambient humidity: insight from single-molecule tracer diffusion dynamics. J Phys Chem B 2013; 117:7771-82. [PMID: 23777572 DOI: 10.1021/jp401704e] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Studies on diffusion dynamics of single molecules (SMs) have been useful in revealing inhomogeneity of polymer thin films near and above the glass-transition temperature (T(g)). However, despite several applications of polymer thin films where exposure to solvent (or vapor) is common, the effect of absorbed solvent molecules on local morphology and rigidity of polymer matrices is yet to be explored in detail. High-T(g) hydrophilic polymers such as poly(vinylpyrrolidone) (PVP) are used as pharmaceutical coatings for drug release in aqueous medium, as they readily absorb moisture, which results in effective lowering of the T(g) and thereby leads to plasticization. The effect of moisture absorption on swelling and softening of PVP thin films was investigated by visualizing the diffusion dynamics of rhodamine 6G (Rh6G) tracer molecules at various ambient relative humidities (RH). Wide-field epifluorescence microscopy, in conjunction with high-resolution SM tracking, was used to monitor the spatiotemporal evolution of individual tracers under varied moisture contents of the matrix. In the absence of atmospheric moisture, Rh6G molecules in dry PVP films are translationally inactive, suggestive of rigid local environments. Under low moisture contents (RH 30-50%), translational mobility remains arrested but rotational motion is augmented, indicating slight swelling of the polymer network which marks the onset of plasticization. The translational mobility of Rh6G was found to be triggered only at a threshold ambient RH, beyond which a large proportion of tracers exhibit extensive diffusion dynamics. Interestingly, SM tracking data at higher moisture contents of the film (RH ≥ 60%) reveal that the distributions of dynamic parameters (such as diffusivity) are remarkably broad, spanning several orders of magnitude. Furthermore, Rh6G molecules display a wide variety of translational motion even at a fixed ambient RH, clearly pointing out the extremely inhomogeneous environment of plasticized PVP network. Intriguingly, it is observed that a majority of tracers undergo anomalous subdiffusion even under high moisture contents of the matrix. Analyses of SM trajectories using velocity autocorrelation function reveal that subdiffusive behaviors of Rh6G are likely to originate from fractional Brownian motion, a signature of tracer dynamics in viscoelastic medium.
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Affiliation(s)
- Sukanya Bhattacharya
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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Saurabh S, Strobos EH, Patankar S, Zinkin L, Kassir A, Snyder M. The argon beam coagulator: a more effective and expeditious way to address presacral bleeding. Tech Coloproctol 2012; 18:73-6. [PMID: 23111401 DOI: 10.1007/s10151-012-0915-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 10/01/2012] [Indexed: 12/20/2022]
Abstract
Presacral bleeding is a dreaded complication of pelvic surgery. Rapid and effective control of such bleeding is important to avoid potentially life-threatening outcomes. Various methods for controlling presacral bleeding, all with only limited success, have been described in the literature. We report the alternative technique of using the argon beam coagulator (ABC) to control presacral bleeding. We demonstrate its efficacious use in both open surgery and a laparoscopic case. Our approach involved applying an argon beam at bone setting directly to the bleeders and using a "point and shoot" technique. We found that ABC is a simpler, equally effective and expeditious way of addressing presacral bleeding. To the best of our knowledge, there has been only one previously reported case in the literature of the use of ABC to control presacral bleeding.
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Affiliation(s)
- S Saurabh
- General Surgery Resident (PGY4), Drexel University College of Medicine, Philadelphia, PA, 19102, USA,
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Saurabh S, Maji S, Bruchez MP. Evaluation of sCMOS cameras for detection and localization of single Cy5 molecules. Opt Express 2012; 20:7338-49. [PMID: 22453414 PMCID: PMC3500109 DOI: 10.1364/oe.20.007338] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Revised: 02/23/2012] [Accepted: 03/05/2012] [Indexed: 05/25/2023]
Abstract
The ability to detect single molecules over the electronic noise requires high performance detector systems. Electron Multiplying Charge-Coupled Device (EMCCD) cameras have been employed successfully to image single molecules. Recently, scientific Complementary Metal Oxide Semiconductor (sCMOS) based cameras have been introduced with very low read noise at faster read out rates, smaller pixel sizes and a lower price compared to EMCCD cameras. In this study, we have compared the two technologies using two EMCCD and three sCMOS cameras to detect single Cy5 molecules. Our findings indicate that the sCMOS cameras perform similar to EMCCD cameras for detecting and localizing single Cy5 molecules.
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Affiliation(s)
- Saumya Saurabh
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Ave, Pittsburgh, Pennsylvania 15213,
USA
| | - Suvrajit Maji
- Lane Center for Computational Biology, Carnegie Mellon University, 4400 Fifth Ave, Pittsburgh, Pennsylvania 15213,
USA
| | - Marcel P. Bruchez
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Ave, Pittsburgh, Pennsylvania 15213,
USA
- Lane Center for Computational Biology, Carnegie Mellon University, 4400 Fifth Ave, Pittsburgh, Pennsylvania 15213,
USA
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Ave, Pittsburgh, Pennsylvania 15213,
USA
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Abstract
Fitz-Hugh-Curtis syndrome is a condition characterized by inflammation of the liver capsule with concomitant pelvic inflammation without involvement of liver parenchyma. It is classically seen in young women who present with sharp, pleuritic right upper quadrant pain, usually but not always accompanied by symptoms of pelvic inflammatory disease (PID) and is frequently confused with biliary tract disease. Rarely the syndrome has been reported in males, hematogenous and lymphatic spread to liver is thought to be the underlying mechanism. Serological tests and computed tomography (CT) scan may aid in diagnosis of Fitz-Hugh-Curtis syndrome. Definitive diagnosis is made by laparoscopy, which provides both diagnostic and therapeutic benefits. We report a case of Fitz-Hugh-Curtis syndrome in a young male patient, which was diagnosed and treated by laparoscopy. We also include a review of the literature.
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Affiliation(s)
- S Saurabh
- Hahnemann University Hospital, Philadelphia, USA
| | - E Unger
- Hahnemann University Hospital, Philadelphia, USA
| | - C Pavlides
- Hahnemann University Hospital, Philadelphia, USA
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Saurabh S, Bruchez MP. Fluorogen Activating Peptides that Enhance Photostability through Encapsulation of the Fluorogen. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.2103] [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: 10/14/2022] Open
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Swain P, Dash S, Bal J, Routray P, Sahoo PK, Sahoo SK, Saurabh S, Gupta SD, Meher PK. Passive transfer of maternal antibodies and their existence in eggs, larvae and fry of Indian major carp, Labeo rohita (Ham.). Fish Shellfish Immunol 2006; 20:519-27. [PMID: 16157486 DOI: 10.1016/j.fsi.2005.06.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2004] [Revised: 05/25/2005] [Accepted: 06/28/2005] [Indexed: 05/04/2023]
Abstract
Lack of immune competence in the early stages of life leads to severe mortality in larval stages of different fish species including Indian major carp (IMC). Investigation through indirect enzyme linked immunosorbent assay (ELISA) and agglutination test revealed a significant increase in specific serum antibody response in the brood fish of Indian major carp, Labeo rohita (Ham.) following immunisation with a virulent Aeromonas hydrophila bacterin 1 month prior to breeding, which was transferred to larvae through the egg. No significant differences (P > 0.05) in mean antibody levels in larvae at the 1st and 2nd weeks post-hatch was recorded while a slight rise in antibody level was observed in 3-week-old fry, perhaps due to exposure to A. hydrophila present in the aquatic environment. Immunised brood fish serum, egg and larval extracts in non-reducing sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) and subsequent western blot analysis revealed an antibody molecule of approximate molecular weight 210 kDa. On challenge with virulent A. hydrophila, a significant reduction in mortality was recorded in immunised larvae and fry (58.0, 43.75 and 37.14% in the 1st, 2nd and 3rd week, respectively) relative to control fish (87.0, 79.0 and 76.4% in 1st, 2nd and 3rd week, respectively). The present study indicated the role of maternally derived antibody in protection of hatchlings of Indian major carp against specific pathogens.
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Affiliation(s)
- P Swain
- Aquatic Animal Health Division, Central Institute of Freshwater Aquaculture, Kausalyaganga-751002, Bhubaneswar, Orissa, India.
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