93 results on '"Somnath Dutta"'
Search Results
2. ALMASOP. The Localized and Chemically Rich Features near the Bases of the Protostellar Jet in HOPS 87
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Shih-Ying Hsu, Chin-Fei Lee, Sheng-Yuan Liu, Doug Johnstone, Tie Liu, Satoko Takahashi, Leonardo Bronfman, Huei-Ru Vivien Chen, Somnath Dutta, David J. Eden, Neal J. Evans II, Naomi Hirano, Mika Juvela, Yi-Jehng Kuan, Woojin Kwon, Chang Won Lee, Jeong-Eun Lee, Shanghuo Li, Chun-Fan Liu, Xunchuan Liu, Qiuyi Luo, Sheng-Li Qin, Dipen Sahu, Patricio Sanhueza, Hsien Shang, Kenichi Tatematsu, and Yao-Lun Yang
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Radio astronomy ,Star formation ,Astrochemistry ,Complex organic molecules ,Protostars ,Astrophysics ,QB460-466 - Abstract
HOPS 87 is a Class 0 protostellar core known to harbor an extremely young bipolar outflow and a hot corino. We report the discovery of localized, chemically rich regions near the bases of the two-lobe bipolar molecular outflow in HOPS 87 containing molecules such as H _2 CO, ^13 CS, H _2 S, OCS, and CH _3 OH, the simplest complex organic molecule (COM). The locations and kinematics suggest that these localized features are due to jet-driven shocks rather than being part of the hot-corino region encasing the protostar. The COM compositions of the molecular gas in these jet-localized regions are relatively simpler than those in the hot-corino zone. We speculate that this simplicity is due to either the liberation of ice with a less complex chemical history or the effects of shock chemistry. Our study highlights the dynamic interplay between the protostellar bipolar outflow, disk, inner-core environment, and the surrounding medium, contributing to our understanding of molecular complexity in solar-like young stellar objects.
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- 2024
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3. The First Ka-band (26.1–35 GHz) Blind Line Survey toward Orion KL
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Xunchuan Liu, Tie Liu, Zhiqiang Shen, Sheng-Li Qin, Qiuyi Luo, Yan Gong, Yu Cheng, Christian Henkel, Qilao Gu, Fengyao Zhu, Tianwei Zhang, Rongbing Zhao, Yajun Wu, Bin Li, Juan Li, Zhang Zhao, Jinqing Wang, Weiye Zhong, Qinghui Liu, Bo Xia, Li Fu, Zhen Yan, Chao Zhang, Lingling Wang, Qian Ye, Aiyuan Yang, Fengwei Xu, Somnath Dutta, Shanghuo Li, Meizhu Liu, Dongting Yang, Chuanshou Li, and Li Chen
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Single-dish antennas ,Millimeter astronomy ,Radio spectroscopy ,Star formation ,Young stellar objects ,OB stars ,Astrophysics ,QB460-466 - Abstract
We conducted a Ka -band (26.1–35 GHz) line survey toward Orion KL using the TianMa 65 m Radio Telescope (TMRT). It is the first blind line survey in the Ka band and achieves a sensitivity at the mK level (1–3 mK at a spectral resolution of ∼1 km s ^−1 ). In total, 592 Gaussian features are extracted. Among them, 257 radio recombination lines (RRLs) are identified. The maximum Δ n of RRLs of H, He, and C are 20, 15, and 5, respectively. Through stacking, we have detected the β lines of ion RRLs (RRLs of C ^+ with the possible contribution of other ions like O ^+ ) for the first time, and a tentative signal of the γ lines of ion RRLs can also be seen on the stacked spectrum. Besides this, 318 other line features were assigned to 37 molecular species, and 10 of these species were not detected in the Q -band survey of TMRT. The vibrationally excited states of nine species were also detected. The emission of most species can be modeled under LTE. A number of transitions of E-CH3OH ( J _2 − J _1 ) display maser effects, which are confirmed by our modeling, and besides the bumping peak at J ∼ 6, there is another peak at J ∼ 13. Methylcyanoacetylene (CH _3 C _3 N) is detected in Orion KL for the first time. This work emphasizes that the Ka band, which was long ignored for spectral line surveys, is very useful for surveying RRLs and molecular lines simultaneously.
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- 2024
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4. ALMA Survey of Orion Planck Galactic Cold Clumps (ALMASOP): Molecular Jets and Episodic Accretion in Protostars
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Somnath Dutta, Chin-Fei Lee, Doug Johnstone, Jeong-Eun Lee, Naomi Hirano, James Di Francesco, Anthony Moraghan, Tie Liu, Dipen Sahu, Sheng-Yuan Liu, Ken’ichi Tatematsu, Paul F. Goldsmith, Chang Won Lee, Shanghuo Li, David Eden, Mika Juvela, Leonardo Bronfman, Shih-Ying Hsu, Kee-Tae Kim, Woojin Kwon, Patricio Sanhueza, Xunchuan Liu, Jesús Alejandro López-Vázquez, Qiuyi Luo, and Hee-Weon Yi
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Star formation ,Protostars ,Stellar jets ,Stellar winds ,Stellar accretion ,Submillimeter astronomy ,Astronomy ,QB1-991 - Abstract
Protostellar outflows and jets are almost ubiquitous characteristics during the mass accretion phase and encode the history of stellar accretion, complex organic molecule (COM) formation, and planet formation. Episodic jets are likely connected to episodic accretion through the disk. Despite the importance, studies on episodic accretion and ejection links have not been done yet in a systematic fashion using high-sensitivity and high-resolution observations. To explore episodic accretion mechanisms and the chronologies of episodic events, we investigated 39 fields containing protostars with Atacama Large Millimeter/submillimeter Array observations of CO, SiO, and 1.3 mm continuum emission. We detected SiO emission in 19 fields, where 17 sources are driving molecular jets. Jet velocities, mass-loss rates, mass accretion rates, and periods of accretion events appear to have some dependence on the driving forces of the jet (e.g., bolometric luminosity, envelope mass). Next, velocities and mass-loss rates appear to be somewhat correlated with the surrounding envelope mass, suggesting that the presence of high mass around protostars increases the ejection–accretion activity. We determine mean periods of ejection events of 20–175 yr for our sample, which could be associated with perturbation zones of ∼2−25 au extent around the protostars. In addition, mean ejection periods show an apparent anticorrelation with the envelope mass, where high accretion rates may trigger more frequent ejection events. The observed periods of outburst/ejection are much shorter than the freezeout timescale of the simplest COMs like CH _3 OH, suggesting that episodic events could affect the ice–gas balance inside and around the snowline.
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- 2024
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5. ALMA Survey of Orion Planck Galactic Cold Clumps (ALMASOP): Discovery of an Extremely Dense and Compact Object Embedded in the Prestellar Core G208.68-19.92-N2
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Naomi Hirano, Dipen Sahu, Sheng-Yaun Liu, Tie Liu, Ken’ichi Tatematsu, Somnath Dutta, Shanghuo Li, Chin-Fei Lee, Pak Shing Li, Shih-Ying Hsu, Sheng-Jun Lin, Doug Johnstone, Leonardo Bronfman, Huei-Ru Vivien Chen, David J. Eden, Yi-Jehng Kuan, Woojin Kwon, Chang Won Lee, Hong-Li Liu, Mark G. Rawlings, Isabelle Ristorcelli, and Alessio Traficante
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Molecular clouds ,Collapsing clouds ,Star forming regions ,Star formation ,Astrochemistry ,Early stellar evolution ,Astrophysics ,QB460-466 - Abstract
The internal structure of the prestellar core G208.68-19.02-N2 (G208-N2) in the Orion Molecular Cloud 3 (OMC-3) region has been studied with the Atacama Large Millimeter/submillimeter Array. The dust continuum emission revealed a filamentary structure with a length of ∼5000 au and an average H _2 volume density of ∼6 × 10 ^7 cm ^−3 . At the tip of this filamentary structure, there is a compact object, which we call a nucleus , with a radius of ∼150–200 au and a mass of ∼0.1 M _⊙ . The nucleus has a central density of ∼2 × 10 ^9 cm ^−3 with a radial density profile of r ^−1.87±0.11 . The density scaling of the nucleus is ∼3.7 times higher than that of the singular isothermal sphere (SIS). This as well as the very low virial parameter of 0.39 suggests that the gravity is dominant over the pressure everywhere in the nucleus. However, there is no sign of CO outflow localized to this nucleus. The filamentary structure is traced by the N _2 D ^+ 3–2 emission, but not by the C ^18 O 2–1 emission, implying the significant CO depletion due to high density and cold temperature. Toward the nucleus, the N _2 D ^+ also shows the signature of depletion. This could imply either the depletion of the parent molecule, N _2 , or the presence of the embedded very-low luminosity central source that could sublimate the CO in the very small area. The nucleus in G208-N2 is considered to be a prestellar core on the verge of first hydrostatic core (FHSC) formation or a candidate for the FHSC.
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- 2024
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6. ALMA Survey of Orion Planck Galactic Cold Clumps (ALMASOP): A Forming Quadruple System with Continuum 'Ribbons' and Intricate Outflows
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Qiu-yi Luo, Tie Liu, Aaron T. Lee, Stella S. R. Offner, James di Francesco, Doug Johnstone, Mika Juvela, Paul F. Goldsmith, Sheng-Li Qin, Xiaofeng Mai, Xun-chuan Liu, Patricio Sanhueza, Feng-Wei Xu, Ken’ichi Tatematsu, Somnath Dutta, Huei-Ru Vivien Chen, Shanghuo Li, Aiyuan Yang, Sheng-Yuan Liu, Chin-Fei Lee, Naomi Hirano, Chang Won Lee, Dipen Sahu, Hsien Shang, Shih-Ying Hsu, Leonardo Bronfman, Woojin Kwon, M. G. Rawlings, David Eden, Xing Lu, Qi-lao Gu, Zhiyuan Ren, D. Ward-Thompson, and Zhi-Qiang Shen
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Star formation ,Star forming regions ,Multiple stars ,Interstellar medium ,Protostars ,Astrophysics ,QB460-466 - Abstract
One of the most poorly understood aspects of low-mass star formation is how multiple-star systems are formed. Here we present the results of Atacama Large Millimeter/submillimeter Array (ALMA) Band 6 observations toward a forming quadruple protostellar system, G206.93-16.61E2, in the Orion B molecular cloud. ALMA 1.3 mm continuum emission reveals four compact objects, of which two are Class I young stellar objects and the other two are likely in prestellar phase. The 1.3 mm continuum emission also shows three asymmetric ribbon-like structures that are connected to the four objects, with lengths ranging from ∼500 to ∼2200 au. By comparing our data with magnetohydrodynamic simulations, we suggest that these ribbons trace accretion flows and also function as gas bridges connecting the member protostars. Additionally, ALMA CO J = 2−1 line emission reveals a complicated molecular outflow associated with G206.93-16.61E2, with arc-like structures suggestive of an outflow cavity viewed pole-on.
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- 2023
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7. Multiple nanocages of a cyanophage small heat shock protein with icosahedral and octahedral symmetries
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Sreeparna Biswas, Priyanka Garg, Somnath Dutta, and Kaza Suguna
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Medicine ,Science - Abstract
Abstract The structures of a cyanophage small heat shock protein (sHSP) were determined as octahedrons of 24-mers and 48-mers and as icosahedrons of 60-mers. An N-terminal deletion construct of an 18 kDa sHSP of Synechococcus sp. phage S-ShM2 crystallized as a 24-mer and its structure was determined at a resolution of 7 Å. The negative stain electron microscopy (EM) images showed that the full-length protein is a mixture of a major population of larger and a minor population of smaller cage-like particles. Their structures have been determined by electron cryomicroscopy 3D image reconstruction at a resolution of 8 Å. The larger particles are 60-mers with icosahedral symmetry and the smaller ones are 48-mers with octahedral symmetry. These structures are the first of the viral/phage origin and the 60-mer is the largest and the first icosahedral assembly to be reported for sHSPs.
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- 2021
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8. Comparative Immunogenicity of Bacterially Expressed Soluble Trimers and Nanoparticle Displayed Influenza Hemagglutinin Stem Immunogens
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Uddipan Kar, Sara Khaleeq, Priyanka Garg, Madhuraj Bhat, Poorvi Reddy, Venkada Subramanian Vignesh, Aditya Upadhyaya, Mili Das, Ghadiyaram Chakshusmathi, Suman Pandey, Somnath Dutta, and Raghavan Varadarajan
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protein design ,stabilization ,thermal tolerance ,competition assay ,oligomer ,antibody response ,Immunologic diseases. Allergy ,RC581-607 - Abstract
Current influenza vaccines need to be updated annually due to mutations in the globular head of the viral surface protein, hemagglutinin (HA). To address this, vaccine candidates have been designed based on the relatively conserved HA stem domain and have shown protective efficacy in animal models. Oligomerization of the antigens either by fusion to oligomerization motifs or display on self-assembling nanoparticle scaffolds, can induce more potent immune responses compared to the corresponding monomeric antigen due to multivalent engagement of B-cells. Since nanoparticle display can increase manufacturing complexity, and often involves one or more mammalian cell expressed components, it is important to characterize and compare various display and oligomerization scaffolds. Using a structure guided approach, we successfully displayed multiple copies of a previously designed soluble, trimeric influenza stem domain immunogen, pH1HA10, on the ferritin like protein, MsDps2 (12 copies), Ferritin (24 copies) and Encapsulin (180 copies). All proteins were expressed in Escherichia coli. The nanoparticle fusion immunogens were found to be well folded and bound to the influenza stem directed broadly neutralizing antibodies with high affinity. An 8.5 Å Cryo-EM map of Msdps2-pH1HA10 confirmed the successful design of the nanoparticle fusion immunogen. Mice immunization studies with the soluble trimeric stem and nanoparticle fusion constructs revealed that all of them were immunogenic, and protected mice against homologous (A/Belgium/145-MA/2009) and heterologous (A/Puerto Rico/8/1934) challenge with 10MLD50 mouse adapted virus. Although nanoparticle display conferred a small but statistically significant improvement in protection relative to the soluble trimer in a homologous challenge, heterologous protection was similar in both nanoparticle-stem immunized and trimeric stem immunized groups. Such rapidly producible, bacterially expressed antigens and nanoparticle scaffolds are useful modalities to tackle future influenza pandemics.
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- 2022
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9. One-step sequence and structure-guided optimization of HIV-1 envelope gp140
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Sameer Kumar Malladi, David Schreiber, Ishika Pramanick, Malavika Abhineshababu Sridevi, Adi Goldenzweig, Somnath Dutta, Sarel Jacob Fleishman, and Raghavan Varadarajan
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Rosetta ,Protein stability ,Protein design ,Vaccine ,Immunogen ,Virus ,Biology (General) ,QH301-705.5 - Abstract
Stabilization of the metastable envelope glycoprotein (Env) of HIV-1 is hypothesized to improve induction of broadly neutralizing antibodies. We improved the expression yield and stability of the HIV-1 envelope glycoprotein BG505SOSIP.664 gp140 by means of a previously described automated sequence and structure-guided computational thermostabilization approach, PROSS. This combines sequence conservation information with computational assessment of mutant stabilization, thus taking advantage of the extensive natural sequence variation present in HIV-1 Env. PROSS is used to design three gp140 variants with 17–45 mutations relative to the parental construct. One of the designs is experimentally observed to have a fourfold improvement in yield and a 4 °C increment in thermostability. In addition, the designed immunogens have similar antigenicity profiles to the native flexible linker version of wild type, BG505SOSIP.664 gp140 (NFL Wt) to major epitopes targeted by broadly neutralizing antibodies. PROSS eliminates the laborious process of screening many variants for stability and functionality, providing a proof of principle of the method for stabilization and improvement of yield without compromising antigenicity for next generation complex, highly glycosylated vaccine candidates.
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- 2020
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10. ALMA Survey of Orion Planck Galactic Cold Clumps (ALMASOP): The Warm-envelope Origin of Hot Corinos
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Shih-Ying Hsu, Sheng-Yuan Liu, Doug Johnstone, Tie Liu, Leonardo Bronfman, Huei-Ru Vivien Chen, Somnath Dutta, David J. Eden, Neal J. Evans II, Naomi Hirano, Mika Juvela, Yi-Jehng Kuan, Woojin Kwon, Chin-Fei Lee, Chang Won Lee, Jeong-Eun Lee, Shanghuo Li, Chun-Fan Liu, Xunchuan Liu, Qiuyi Luo, Sheng-Li Qin, Mark G. Rawlings, Dipen Sahu, Patricio Sanhueza, Hsien Shang, Ken'ichi Tatematsu, and Yao-Lun Yang
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Astrochemistry ,Interstellar molecules ,Star forming regions ,Low mass stars ,Protostars ,Astrophysics ,QB460-466 - Abstract
Hot corinos are of great interest due to their richness in interstellar complex organic molecules (COMs) and the consequent potential prebiotic connection to solar-like planetary systems. Recent surveys have reported an increasing number of detected hot corinos in Class 0/I protostars; however, the relationships between their physical properties and the hot-corino signatures remain elusive. In this study, our objective is to establish a general picture of the detectability of hot corinos by identifying the origins of the hot-corino signatures in the sample of young stellar objects (YSOs) obtained from the Atacama Large Millimeter/submillimeter Array Survey of Orion Planck Galactic Cold Clumps project. We apply spectral energy distribution modeling to our sample and identify the physical parameters of the modeled YSOs directly, linking the detection of hot-corino signatures to the envelope properties of the YSOs. Imaging simulations of the methanol emission further support this scenario. We therefore posit that the observed COM emission originates from the warm inner envelopes of the sample YSOs, based on both the warm region size and the envelope density profile. The former is governed by the source luminosity and is additionally affected by the disk and cavity properties, while the latter is related to the evolutionary stages. This scenario provides a framework for detecting hot-corino signatures toward luminous Class 0 YSOs, with fewer detections being observed toward similarly luminous Class I sources.
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- 2023
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11. ALMA Survey of Orion Planck Galactic Cold Clumps (ALMASOP): Density Structure of Centrally Concentrated Prestellar Cores from Multiscale Observations
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Dipen Sahu, Sheng-Yuan Liu, Doug Johnstone, Tie Liu, Neal J. Evans II, Naomi Hirano, Ken’ichi Tatematsu, James Di Francesco, Chin-Fei Lee, Kee-Tae Kim, Somnath Dutta, Shih-Ying Hsu, Shanghuo Li, Qiu-Yi Luo, Patricio Sanhueza, Hsien Shang, Alessio Traficante, Mika Juvela, Chang Won Lee, David J. Eden, Paul F. Goldsmith, Leonardo Bronfman, Woojin Kwon, Jeong-Eun Lee, Yi-Jehng Kuan, and Isabelle Ristorcelli
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Molecular clouds ,Collapsing clouds ,Infrared dark clouds ,Star formation ,Astronomical methods ,Astronomy data modeling ,Astrophysics ,QB460-466 - Abstract
Starless cores represent the initial stage of evolution toward (proto)star formation, and a subset of them, known as prestellar cores, with high density (∼ 10 ^6 cm ^−3 or higher) and being centrally concentrated are expected to be embryos of (proto)stars. Determining the density profile of prestellar cores therefore provides an important opportunity to gauge the initial conditions of star formation. In this work, we perform rigorous modeling to estimate the density profiles of three nearly spherical prestellar cores among a sample of five highly dense cores detected by our recent observations. We employed multiscale observational data of the (sub)millimeter dust continuum emission, including those obtained by SCUBA-2 on the James Clerk Maxwell Telescope with a resolution of ∼ 5600 au and by multiple Atacama Large Millimeter/submillimeter Array observations with a resolution as high as ∼ 480 au. We are able to consistently reproduce the observed multiscale dust continuum images of the cores with a simple prescribed density profile, which bears an inner region of flat density and an r ^−2 profile toward the outer region. By utilizing the peak density and the size of the inner flat region as a proxy for the dynamical stage of the cores, we find that the three modeled cores are most likely unstable and prone to collapse. The sizes of the inner flat regions, as compact as ∼ 500 au, signify them as being the highly evolved prestellar cores rarely found to date.
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- 2023
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12. Neutralizing Efficacy of Encapsulin Nanoparticles against SARS-CoV2 Variants of Concern
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Sara Khaleeq, Nayanika Sengupta, Sahil Kumar, Unnatiben Rajeshbhai Patel, Raju S. Rajmani, Poorvi Reddy, Suman Pandey, Randhir Singh, Somnath Dutta, Rajesh P. Ringe, and Raghavan Varadarajan
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SpyTag ,SpyCatcher ,SWE adjuvant ,Omicron ,encapsulin ,thermotolerant ,Microbiology ,QR1-502 - Abstract
Rapid emergence of the SARS-CoV-2 variants has dampened the protective efficacy of existing authorized vaccines. Nanoparticle platforms offer a means to improve vaccine immunogenicity by presenting multiple copies of desired antigens in a repetitive manner which closely mimics natural infection. We have applied nanoparticle display combined with the SpyTag–SpyCatcher system to design encapsulin–mRBD, a nanoparticle vaccine displaying 180 copies of the monomeric SARS-CoV-2 spike receptor-binding domain (RBD). Here we show that encapsulin–mRBD is strongly antigenic and thermotolerant for long durations. After two immunizations, squalene-in-water emulsion (SWE)-adjuvanted encapsulin–mRBD in mice induces potent and comparable neutralizing antibody titers of 105 against wild-type (B.1), alpha, beta, and delta variants of concern. Sera also neutralizes the recent Omicron with appreciable neutralization titers, and significant neutralization is observed even after a single immunization.
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- 2023
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13. Protective Efficacy of Recombinant Influenza Hemagglutinin Ectodomain Fusions
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Nidhi Mittal, Nayanika Sengupta, Sameer Kumar Malladi, Poorvi Reddy, Madhuraj Bhat, Raju S. Rajmani, Koen Sedeyn, Xavier Saelens, Somnath Dutta, and Raghavan Varadarajan
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influenza virus ,hemagglutinin ,immunogen ,mouse immunization ,neutralization ,linker ,Microbiology ,QR1-502 - Abstract
In current seasonal influenza vaccines, neutralizing antibody titers directed against the hemagglutinin surface protein are the primary correlate of protection. These vaccines are, therefore, quantitated in terms of their hemagglutinin content. Adding other influenza surface proteins, such as neuraminidase and M2e, to current quadrivalent influenza vaccines would likely enhance vaccine efficacy. However, this would come with increased manufacturing complexity and cost. To address this issue, as a proof of principle, we have designed genetic fusions of hemagglutinin ectodomains from H3 and H1 influenza A subtypes. These recombinant H1-H3 hemagglutinin ectodomain fusions could be transiently expressed at high yield in mammalian cell culture using Expi293F suspension cells. Fusions were trimeric, and as stable in solution as their individual trimeric counterparts. Furthermore, the H1-H3 fusion constructs were antigenically intact based on their reactivity with a set of conformation-specific monoclonal antibodies. H1-H3 hemagglutinin ectodomain fusion immunogens, when formulated with the MF59 equivalent adjuvant squalene-in-water emulsion (SWE), induced H1 and H3-specific humoral immune responses equivalent to those induced with an equimolar mixture of individually expressed H1 and H3 ectodomains. Mice immunized with these ectodomain fusions were protected against challenge with heterologous H1N1 (Bel/09) and H3N2 (X-31) mouse-adapted viruses with higher neutralizing antibody titers against the H1N1 virus. Use of such ectodomain-fused immunogens would reduce the number of components in a vaccine formulation and allow for the inclusion of other protective antigens to increase influenza vaccine efficacy.
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- 2021
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14. Conformational Sensors and Domain Swapping Reveal Structural and Functional Differences between β-Arrestin Isoforms
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Eshan Ghosh, Hemlata Dwivedi, Mithu Baidya, Ashish Srivastava, Punita Kumari, Tomek Stepniewski, Hee Ryung Kim, Mi-Hye Lee, Jaana van Gastel, Madhu Chaturvedi, Debarati Roy, Shubhi Pandey, Jagannath Maharana, Ramon Guixà-González, Louis M. Luttrell, Ka Young Chung, Somnath Dutta, Jana Selent, and Arun K. Shukla
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Biology (General) ,QH301-705.5 - Abstract
Summary: Desensitization, signaling, and trafficking of G-protein-coupled receptors (GPCRs) are critically regulated by multifunctional adaptor proteins, β-arrestins (βarrs). The two isoforms of βarrs (βarr1 and 2) share a high degree of sequence and structural similarity; still, however, they often mediate distinct functional outcomes in the context of GPCR signaling and regulation. A mechanistic basis for such a functional divergence of βarr isoforms is still lacking. By using a set of complementary approaches, including antibody-fragment-based conformational sensors, we discover structural differences between βarr1 and 2 upon their interaction with activated and phosphorylated receptors. Interestingly, domain-swapped chimeras of βarrs display robust complementation in functional assays, thereby linking the structural differences between receptor-bound βarr1 and 2 with their divergent functional outcomes. Our findings reveal important insights into the ability of βarr isoforms to drive distinct functional outcomes and underscore the importance of integrating this aspect in the current framework of biased agonism. : Ghosh et al. discover structural differences between β-arrestin isoforms (β-arrestin 1 and 2), which are universal regulators of signaling and trafficking of G-protein-coupled receptors (GPCRs). These findings have direct implications for understanding the regulatory and signaling paradigms of GPCRs and designing novel therapeutics targeting this important class of receptors. Keywords: GPCRs, β-arrestins, cellular signaling, antibody fragments, biosensors, biased agonism, desensitization, negative staining, electron microscopy
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- 2019
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15. Simplified Approach for Preparing Graphene Oxide TEM Grids for Stained and Vitrified Biomolecules
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Anil Kumar, Nayanika Sengupta, and Somnath Dutta
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TEM ,graphene oxide ,Cryo-EM ,SEM ,AFM ,MsDps ,Chemistry ,QD1-999 - Abstract
In this manuscript, we report the application of graphene oxide (GO) in the preparation of cryo-electron microscopy (cryo-EM) and transmission electron microscopy (TEM) grids. We treated GO with water and organic solvents, such as, methanol, ethanol and isopropanol separately to isolate significantly large GO monolayer flake to fabricate the grids for cryo-EM and TEM study. We implemented a simplified approach to isolate flakes of GO monolayer for constructing the TEM grids, independent of expensive heavy equipment (Langmuir–Blodgett trough, glow-discharge system, carbon-evaporator or plasma-cleaner or peristaltic pumps). We employed confocal microscopy, SEM and TEM to characterize the flake size, stability and transparency of the GO monolayer and atomic force microscopy (AFM) to probe the depth of GO coated grids. Additionally, GO grids are visualized at cryogenic condition for suitability of GO monolayer for cryo-EM study. In addition, GO-Met-H2O grids reduce the effect of preferred orientation of biological macromolecules within the amorphous ice. The power-spectrum and contrast-transfer-function unequivocally suggest that GO-Met-H2O fabricated holey grids have excellent potential for application in high-resolution structural characterization of biomolecules. Furthermore, only 200 movies and ~8000 70S ribosome particles are selected on GO-coated grids for cryo-EM reconstruction to achieve high-resolution structure.
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- 2021
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16. Crystal Structure of the Pre-fusion Nipah Virus Fusion Glycoprotein Reveals a Novel Hexamer-of-Trimers Assembly.
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Kai Xu, Yee-Peng Chan, Birgit Bradel-Tretheway, Zeynep Akyol-Ataman, Yongqun Zhu, Somnath Dutta, Lianying Yan, YanRu Feng, Lin-Fa Wang, Georgios Skiniotis, Benhur Lee, Z Hong Zhou, Christopher C Broder, Hector C Aguilar, and Dimitar B Nikolov
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Immunologic diseases. Allergy ,RC581-607 ,Biology (General) ,QH301-705.5 - Abstract
Nipah virus (NiV) is a paramyxovirus that infects host cells through the coordinated efforts of two envelope glycoproteins. The G glycoprotein attaches to cell receptors, triggering the fusion (F) glycoprotein to execute membrane fusion. Here we report the first crystal structure of the pre-fusion form of the NiV-F glycoprotein ectodomain. Interestingly this structure also revealed a hexamer-of-trimers encircling a central axis. Electron tomography of Nipah virus-like particles supported the hexameric pre-fusion model, and biochemical analyses supported the hexamer-of-trimers F assembly in solution. Importantly, structure-assisted site-directed mutagenesis of the interfaces between F trimers highlighted the functional relevance of the hexameric assembly. Shown here, in both cell-cell fusion and virus-cell fusion systems, our results suggested that this hexamer-of-trimers assembly was important during fusion pore formation. We propose that this assembly would stabilize the pre-fusion F conformation prior to cell attachment and facilitate the coordinated transition to a post-fusion conformation of all six F trimers upon triggering of a single trimer. Together, our data reveal a novel and functional pre-fusion architecture of a paramyxoviral fusion glycoprotein.
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- 2015
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17. On-the-Fly Acquisition and Rendering with Low Cost LiDAR and RGB Cameras for Marine Navigation.
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Somnath Dutta, Fabio Ganovelli, and Paolo Cignoni
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- 2023
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18. Dynamic Real-Time Spatio-Temporal Acquisition and Rendering in Adverse Environments.
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Somnath Dutta, Fabio Ganovelli, and Paolo Cignoni
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- 2023
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19. 3D Point Set Registration based on Hierarchical Descriptors.
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Somnath Dutta, Benjamin Russig, and Stefan Gumhold
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- 2022
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20. Optical photometric variable stars towards Cygnus OB7
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Somnath Dutta, Soumen Mondal, Santosh Joshi, and Ramkrishna Das
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- 2019
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21. Cryo-EM-based structural insights into supramolecular assemblies of γ-hemolysin from S. aureus reveal the pore formation mechanism
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Suman Mishra, Anupam Roy, and Somnath Dutta
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Structural Biology ,Molecular Biology - Published
- 2023
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22. A dimeric proteomimetic prevents SARS-CoV-2 infection by dimerizing the spike protein
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Bhavesh Khatri, Ishika Pramanick, Sameer Kumar Malladi, Raju S. Rajmani, Sahil Kumar, Pritha Ghosh, Nayanika Sengupta, R. Rahisuddin, Narender Kumar, S. Kumaran, Rajesh P. Ringe, Raghavan Varadarajan, Somnath Dutta, and Jayanta Chatterjee
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SARS-CoV-2 ,Spike Glycoprotein, Coronavirus ,COVID-19 ,Humans ,Angiotensin-Converting Enzyme 2 ,Cell Biology ,Peptidyl-Dipeptidase A ,Peptides ,Dimerization ,Molecular Biology ,Protein Binding - Abstract
Protein tertiary structure mimetics are valuable tools to target large protein–protein interaction interfaces. Here, we demonstrate a strategy for designing dimeric helix-hairpin motifs from a previously reported three-helix-bundle miniprotein that targets the receptor-binding domain (RBD) of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). Through truncation of the third helix and optimization of the interhelical loop residues of the miniprotein, we developed a thermostable dimeric helix-hairpin. The dimeric four-helix bundle competes with the human angiotensin-converting enzyme 2 (ACE2) in binding to RBD with 2:2 stoichiometry. Cryogenic-electron microscopy revealed the formation of dimeric spike ectodomain trimer by the four-helix bundle, where all the three RBDs from either spike protein are attached head-to-head in an open conformation, revealing a novel mechanism for virus neutralization. The proteomimetic protects hamsters from high dose viral challenge with replicative SARS-CoV-2 viruses, demonstrating the promise of this class of peptides that inhibit protein–protein interaction through target dimerization.
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- 2022
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23. Serendipitous Discovery of a Highly Active and Selective Resistance-Modifying Agent for Colistin-Resistant Gram-Negative Bacteria
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Yuefeng Gao, Somnath Dutta, and Xiang Wang
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General Chemical Engineering ,General Chemistry - Abstract
Antibiotic resistance is a growing global health concern. Colistin is one of the last-resort antibiotics that treats multidrug-resistant (MDR) Gram-negative bacterial infection. However, bacteria resistant to colistin have become increasingly prevalent. Using a bacterial whole-cell screen of a fragment-based library, one compound was discovered to resensitize MDR
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- 2022
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24. Recognition determinants of broad and potent HIV-1 neutralization by an affinity matured antibody from a pediatric elite-neutralizer
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Sanjeev Kumar, Swarandeep Singh, Arnab Chatterjee, Prashant Bajpai, Shaifali Sharma, Sanket Katpara, Rakesh Lodha, Somnath Dutta, and Kalpana Luthra
- Abstract
The structural and characteristic features of HIV-1 broadly neutralizing antibodies (bnAbs) from chronically infected pediatric donors are currently unknown. Herein, we characterized a heavy chain matured HIV-1 bnAb 44m, identified from a pediatric elite-neutralizer. Interestingly, in comparison to its wild-type AIIMS-P01 bnAb, 44m exhibited moderately higher level of somatic hypermutations (SHM) of 15.2%. 44m neutralized 79% of HIV-1 heterologous viruses tested, with a geometric mean IC50titer of 0.36 μg/ml. The cryoEM structure of 44m Fab in complex with fully-cleaved glycosylated native-like BG505.SOSIP envelope trimer at 4.4 Å resolution revealed that 44m targets the V3-glycan N332-supersite and GDIR motif to neutralize HIV-1 with improved potency and breadth, plausibly attributed by a matured heavy chain as compared to that of wild-type AIIMS-P01 bnAb. This study improves our understanding on pediatric HIV-1 bnAbs and structural basis of broad HIV-1 neutralization by 44m may be useful blueprint for vaccine design in future.
- Published
- 2023
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25. Cryo-EM reveals the mechanism of DNA compaction byMycobacterium smegmatisDps2
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Priyanka Garg, Thejas Satheesh, Mahipal Ganji, and Somnath Dutta
- Abstract
DNA-binding protein under starvation (Dps), is a miniature ferritin complex which plays a vital role in protecting bacterial DNA during starvation for maintaining the integrity of bacteria from hostile conditions.Mycobacterium smegmatisis one such bacteria that express MsDps2, which binds DNA to protect it under oxidative and nutritional stress conditions. Several approaches, including cryo-electron tomography (Cryo-ET), were implemented to identify the structure of the Dps protein that is bound to DNA. However, none of the structures of the Dps-DNA complex was resolved to high resolution to be able to identify the DNA binding residues. In this study, we implemented various biochemical and biophysical studies to characterize the DNA protein interactions of Dps protein. We employed single-particle cryo-EM-based structural analysis of MsDps2-DNA and identify that the region close to N-terminal confers the DNA binding property. Based on cryo-EM data, we performed mutations of several arginine residues proximal to DNA binding region, which dramatically reduced the MsDps2-DNA interaction. In addition, we demonstrated the proposed model for DNA compaction during lattice formation. We also pinpointed arginine residues, which are responsible for DNA binding in lattice arrangement of MsDps2. We performed single-molecule imaging experiments of MsDps2-DNA interactions that corroborate well with our structural studies.
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- 2023
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26. ATOMS: ALMA Three-millimeter Observations of Massive Star-forming regions – V. Hierarchical fragmentation and gas dynamics in IRDC G034.43+00.24
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Ken'ichi Tatematsu, Eswaraiah Chakali, Feng-Wei Xu, Mika Juvela, E. Mannfors, Qiu-Yi Luo, Qizhou Zhang, S. N. Zhang, Sheng-Li Qin, Lokesh K. Dewangan, Ke Wang, L. Viktor Tóth, Junzhi Wang, Tie Liu, Rong Liu, Zhiyuan Ren, Leonardo Bronfman, Paul F. Goldsmith, T. Baug, Jin-Zeng Li, Shanghuo Li, Pak Shing Li, Jianwen Zhou, X.-W. Liu, Xi Chen, Chang Won Lee, Somnath Dutta, Hong-Li Liu, Yong Zhang, Di Li, Anandmayee Tej, Chao Zhang, Archana Soam, Yuefang Wu, Anindya Saha, Amelia M. Stutz, Namitha Issac, Mengyao Tang, Department of Physics, and Particle Physics and Astrophysics
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ISM: individual objects: G034.43+00.24 ,Astrophysics::High Energy Astrophysical Phenomena ,stars: kinematics and dynamics ,Continuum (design consultancy) ,FOS: Physical sciences ,Astrophysics::Cosmology and Extragalactic Astrophysics ,Astrophysics ,Star (graph theory) ,ISM: clouds ,01 natural sciences ,MAGNETIC-FIELDS ,Virial theorem ,CLUMPS ,0103 physical sciences ,Astrophysics::Solar and Stellar Astrophysics ,DENSE ,Infrared dark cloud ,ACCRETION ,COLLAPSE ,010303 astronomy & astrophysics ,Astrophysics::Galaxy Astrophysics ,Physics ,stars: formation ,010308 nuclear & particles physics ,Star formation ,Fragmentation (computing) ,PROTOSTARS ,Astronomy and Astrophysics ,DRIVEN ,115 Astronomy, Space science ,Astrophysics - Astrophysics of Galaxies ,Accretion (astrophysics) ,13. Climate action ,Space and Planetary Science ,Astrophysics of Galaxies (astro-ph.GA) ,Millimeter ,MOLECULAR OUTFLOWS - Abstract
We present new 3-mm continuum and molecular lines observations from the ATOMS survey towards the massive protostellar clump, MM1, located in the filamentary infrared dark cloud (IRDC), G034.43+00.24 (G34). The lines observed are the tracers of either dense gas (e.g. HCO+/H13CO+ J = 1-0) or outflows (e.g. CS J = 2-1). The most complete picture to date of seven cores in MM1 is revealed by dust continuum emission. These cores are found to be gravitationally bound, with virial parameter, $\alpha_{vir}, Comment: 14 pages with 6 figures, and in press
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- 2021
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27. Multiple nanocages of a cyanophage small heat shock protein with icosahedral and octahedral symmetries
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Kaza Suguna, Sreeparna Biswas, Priyanka Garg, and Somnath Dutta
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Models, Molecular ,Materials science ,Icosahedral symmetry ,Cryo-electron microscopy ,Protein Conformation ,Science ,Population ,Biophysics ,Article ,Protein Aggregates ,Structure-Activity Relationship ,Viral Proteins ,Nanocages ,Bacteriophages ,Amino Acid Sequence ,education ,Conserved Sequence ,education.field_of_study ,Multidisciplinary ,Octahedral symmetry ,Resolution (electron density) ,Cryoelectron Microscopy ,Cyanophage ,Negative stain ,Heat-Shock Proteins, Small ,Molecular Weight ,Crystallography ,Mutation ,Medicine ,Protein Multimerization ,Structural biology ,Molecular Chaperones ,Protein Binding - Abstract
The structures of a cyanophage small heat shock protein (sHSP) were determined as octahedrons of 24-mers and 48-mers and as icosahedrons of 60-mers. An N-terminal deletion construct of an 18 kDa sHSP of Synechococcus sp. phage S-ShM2 crystallized as a 24-mer and its structure was determined at a resolution of 7 Å. The negative stain electron microscopy (EM) images showed that the full-length protein is a mixture of a major population of larger and a minor population of smaller cage-like particles. Their structures have been determined by electron cryomicroscopy 3D image reconstruction at a resolution of 8 Å. The larger particles are 60-mers with icosahedral symmetry and the smaller ones are 48-mers with octahedral symmetry. These structures are the first of the viral/phage origin and the 60-mer is the largest and the first icosahedral assembly to be reported for sHSPs.
- Published
- 2021
28. High resolution cryo-EM structures of two potently SARS-CoV-2 neutralizing monoclonal antibodies of same donor origin that vary in neutralizing Omicron variants
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Clayton Fernando Rencilin, Mohammad Yousuf Ansari, Arnab Chatterjee, Suprit Deshpande, Sohini Mukherjee, Randhir Singh, Sowrabha Jayatheertha, Poorvi M. Reddy, Payel Das, Nitin Hingankar, Deepak Rathore, Raghavan Varadarajan, Jayanta Bhattacharya, and Somnath Dutta
- Abstract
While vaccines have by large been found to effective against the evolving SARS-CoV-2 variants, the profound and rapid effectivity of monoclonal antibodies (mAbs) in significantly reducing hospitalization to severe disease outcomes have also been demonstrated. In the present study, by high resolution cryo-electron microscopy (cryo-EM), we examined the structural insights of two trimeric spike (S) protein bound mAbs isolated from an Indian convalescent individual infected with ancestral SARS-CoV-2 which we recently reported to potently neutralize SARS-CoV-2 from its ancestral form through highly virulent Delta form however different in their ability to neutralize Omicron variants. Our findings showed binding and conformational heterogeneities of both the mAbs (THSC20.HVTR04 and THSC20.HVTR26) bound to S trimer in its apo and hACE-2 bound forms. Additionally, cryo-EM resolved structure assisted modeling highlighted key residues associated with the ability of these two mAbs to neutralize Omicron variants. Our findings highlighted key interacting features modulating antigen-antibody interacting that can further aid in structure guided antibody engineering to enhance their breadth and potency.HighlightsTwo potent human mAbs obtained from a single donor differ binding to Omicron spikesPattern of binding and conformation of these mAbs bound to full length spike differsAntibody binding alters the conformational states of S trimer in its apo and hACE-2 bound forms.Cryo-EM structure guided modeling highlighted correlates of interacting residues associated with resistance and sensitivity of BA.1, BA.2, BA.4/BA.5 resistance and sensitivity against these mAbs.
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- 2022
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29. Cryo-EM reveals the membrane binding phenomenon of EspB, a virulence factor of the Mycobacterial Type VII secretion system
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Nayanika Sengupta, Surekha P., and Somnath Dutta
- Abstract
Mycobacterium tuberculosis utilizes sophisticated machinery called the type VII secretion system to translocate virulence factors across its complex lipid membrane. ESX-1 is one of the essential and well-studied secretion systems which transport various virulence factors, including EspB. EspB, a ~36 kDa secreted substrate, has been implicated to play vital role in protecting the bacteria from hostile environment within the host cell phagosome. It is also involved in bacterial pathogenesis and has been shown to bind phospholipids. Recently, two cryo-EM structures of EspB full-length and the secreted isoforms were resolved. Despite the availability of multiple high-resolution structures of EspB, the physiological relevance and mechanism of virulence of this secreted substrate remains poorly characterized. In this current work, we implemented cryo-EM-based structural studies, including various functional assays, TEM imaging, and biophysical approach to demonstrate the interaction of EspB with lipids and bio-membrane. Our findings also indicated that EspB may play a crucial role in binding to and rupturing host mitochondrial membrane. Through cryo-EM studies we were able to show the possible membrane-binding region of EspB. Our study sheds light on host-pathogen interactions and bacterial pathogenesis mediated by EspB.
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- 2022
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30. Cryo-EM-based structural insights into supramolecular assemblies of γ-Hemolysin from Staphylococcus aureus reveal the pore formation mechanism
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Suman Mishra, ANUPAM ROY, and Somnath Dutta
- Abstract
γ-hemolysin (γ-HL) is a hemolytic and leukotoxic bicomponent β-pore-forming toxin (β-PFT), a potent virulence factor from Staphylococcus aureus Newman strain. In this study, we performed single particle cryo-EM of γ-HL in a lipid environment. We observed clustering and square lattice packing of octameric HlgAB pores upon membrane bilayer, and an octahedral superassembly of octameric pore complexes, that we resolved at resolution 3.5 Å. Our atomic model further demonstrated the key residues involved in hydrophobic zipping between the rim domains of adjacent octameric pore complexes, thus providing first evidence of additional structural stability in PFTs upon membrane lysis. We also observed lipid densities at the octahedral and octameric interfaces, providing critical insights into the lipid-binding residues involved for both HlgA and HlgB components. Furthermore, the hitherto elusive N-terminal region of HlgA has also been resolved in our cryo-EM map and an overall mechanism of pore formation for bicomponent β-PFTs is proposed.
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- 2022
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31. Structural insights into thermostable direct hemolysin of Vibrio parahaemolyticus using single-particle cryo-EM
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Suman Mishra, Nidhi Kundu, Ishika Pramanick, Anil Kumar, Kausik Chattopadhyay, and Somnath Dutta
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Hemolysin Proteins ,Structural Biology ,Cryoelectron Microscopy ,Bacterial Toxins ,Vibrio parahaemolyticus ,Molecular Biology ,Biochemistry - Abstract
Thermostable direct hemolysin (TDH) is a ~19 kDa, hemolytic pore-forming toxin from the gram-negative marine bacterium Vibrio parahaemolyticus, one of the causative agents of seafood-borne acute gastroenteritis and septicemia. Previous studies have established that TDH exists as a tetrameric assembly in physiological state; however, there is limited knowledge regarding the molecular arrangement of its disordered N-terminal region (NTR)-the absence of which has been shown to compromise TDH's hemolytic and cytotoxic abilities. In our current study, we have employed single-particle cryo-electron microscopy to resolve the solution-state structures of wild-type TDH and a TDH construct with deletion of the NTR (NTD), in order to investigate structural aspects of NTR on the overall tetrameric architecture. We observed that both TDH and NTD electron density maps, resolved at global resolutions of 4.5 and 4.2 Å, respectively, showed good correlation in their respective oligomeric architecture. Additionally, we were able to locate extra densities near the pore opening of TDH which might correspond to the disordered NTR. Surprisingly, under cryogenic conditions, we were also able to observe novel supramolecular assemblies of TDH tetramers, which we were able to resolve to 4.3 Å. We further investigated the tetrameric and inter-tetrameric interaction interfaces to elaborate upon the key residues involved in both TDH tetramers and TDH super assemblies. Our current structural study will aid in understanding the mechanistic aspects of this pore-forming toxin and the role of its disordered NTR in membrane interaction.
- Published
- 2022
32. Author response for 'Structural insights into Thermostable Direct Hemolysin of Vibrio parahaemolyticus using single particle cryo‐EM'
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null Suman Mishra, null Nidhi Kundu, null Ishika Pramanick, null Anil Kumar, null Kausik Chattopadhyay, and null Somnath Dutta
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- 2022
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33. Cryo-EM reveals the membrane-binding phenomenon of EspB, a virulence factor of the mycobacterial type VII secretion system
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Nayanika Sengupta, Surekha Padmanaban, and Somnath Dutta
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Cell Biology ,Molecular Biology ,Biochemistry - Published
- 2023
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34. S-Adenosylmethionine–responsive cystathionine β-synthase modulates sulfur metabolism and redox balance inMycobacteriumtuberculosis
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Parijat Bandyopadhyay, Ishika Pramanick, Rupam Biswas, Sabarinath PS, Sreesa Sreedharan, Shalini Singh, Raju S. Rajmani, Sunil Laxman, Somnath Dutta, and Amit Singh
- Subjects
Multidisciplinary - Abstract
Methionine and cysteine metabolisms are important for the survival and pathogenesis ofMycobacterium tuberculosis(Mtb). The transsulfuration pathway converts methionine to cysteine and represents an important link between antioxidant and methylation metabolism in diverse organisms. Using a combination of biochemistry and cryo–electron microscopy, we characterized the first enzyme of the transsulfuration pathway, cystathionine β-synthase (MtbCbs) inMtb. We demonstrated thatMtbCbs is a heme-less, pyridoxal-5′-phosphate–containing enzyme, allosterically activated byS-adenosylmethionine (SAM). The atomic model ofMtbCbs in its native and SAM-bound conformations revealed a unique mode of SAM-dependent allosteric activation. Further, SAM stabilizedMtbCbs by sterically occluding proteasomal degradation, which was crucial for supporting methionine and redox metabolism inMtb. Genetic deficiency ofMtbCbs reducedMtbsurvival upon homocysteine overload in vitro, inside macrophages, and in mice coinfected with HIV. Thus, theMtbCbs-SAM axis constitutes an important mechanism of coordinating sulfur metabolism inMtb.
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- 2022
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35. Glu289 residue in the pore-forming motif of Vibrio cholerae cytolysin is important for efficient β-barrel pore formation
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Anish Kumar Mondal, Nayanika Sengupta, Mahendra Singh, Rupam Biswas, Kusum Lata, Indrajit Lahiri, Somnath Dutta, and Kausik Chattopadhyay
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Pore Forming Cytotoxic Proteins ,Bacterial Proteins ,Cytotoxins ,Virulence Factors ,Cell Membrane ,Amino Acid Motifs ,Mutation ,Glutamic Acid ,Cell Biology ,Molecular Biology ,Biochemistry ,Vibrio cholerae - Abstract
Vibrio cholerae cytolysin (VCC) is a potent membrane-damaging β-barrel pore-forming toxin. Upon binding to the target membranes, VCC monomers first assemble into oligomeric prepore intermediates and subsequently transform into transmembrane β-barrel pores. VCC harbors a designated pore-forming motif, which, during oligomeric pore formation, inserts into the membrane and generates a transmembrane β-barrel scaffold. It remains an enigma how the molecular architecture of the pore-forming motif regulates the VCC pore-formation mechanism. Here, we show that a specific pore-forming motif residue, E289, plays crucial regulatory roles in the pore-formation mechanism of VCC. We find that the mutation of E289A drastically compromises pore-forming activity, without affecting the structural integrity and membrane-binding potential of the toxin monomers. Although our single-particle cryo-EM analysis reveals WT-like oligomeric β-barrel pore formation by E289A-VCC in the membrane, we demonstrate that the mutant shows severely delayed kinetics in terms of pore-forming ability that can be rescued with elevated temperature conditions. We find that the pore-formation efficacy of E289A-VCC appears to be more profoundly dependent on temperature than that of the WT toxin. Our results suggest that the E289A mutation traps membrane-bound toxin molecules in the prepore-like intermediate state that is hindered from converting into the functional β-barrel pores by a large energy barrier, thus highlighting the importance of this residue for the pore-formation mechanism of VCC.
- Published
- 2022
36. Structure-activity relationship studies of [1,2,5]oxadiazolo[3,4-b]pyrazine-containing polymyxin-selective resistance-modifying agents
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Somnath Dutta, Nianzi Liu, Yuefeng Gao, Lily Beck, and Xiang Wang
- Subjects
Organic Chemistry ,Clinical Biochemistry ,Pharmaceutical Science ,Microbial Sensitivity Tests ,Biochemistry ,Article ,Anti-Bacterial Agents ,Structure-Activity Relationship ,Drug Resistance, Multiple, Bacterial ,Pyrazines ,Drug Discovery ,Gram-Negative Bacteria ,Molecular Medicine ,Humans ,Polymyxins ,Gram-Negative Bacterial Infections ,Molecular Biology - Abstract
Multidrug-resistant (MDR) Gram-negative bacteria are an urgent and rapidly spreading threat to human health with limited treatment options. Previously, we discovered a novel [1,2,5]oxadiazolo[3,4-b]pyrazine-containing compound (1) that selectively re-sensitized a variety of MDR Gram-negative bacteria to colistin, one of the last-resort antibiotic. Herein, we report the structure–activity relationship studies of compound 1 that led to the discovery of several more potent and/or less toxic resistance-modifying agents (RMAs). Further evaluation of these RMAs showed that they were effective in a wide range of MDR bacteria. These results demonstrated these compounds as a novel class of RMAs and may be further developed as therapeutic agents.
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- 2022
37. Tyrosine in the hinge region of the pore‐forming motif regulates oligomeric β‐barrel pore formation by Vibrio cholerae cytolysin
- Author
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Somnath Dutta, Shashi Bhushan Pandit, Anish Kumar Mondal, Paras Verma, Kausik Chattopadhyay, and Nayanika Sengupta
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Protein Conformation ,Amino Acid Motifs ,Molecular Dynamics Simulation ,Biology ,medicine.disease_cause ,Microbiology ,Cell Line ,03 medical and health sciences ,Protein structure ,Bacterial Proteins ,Microscopy, Electron, Transmission ,medicine ,Humans ,Tyrosine ,Vibrio cholerae ,Molecular Biology ,Cells, Cultured ,030304 developmental biology ,0303 health sciences ,Pore-forming toxin ,Cytotoxins ,Perforin ,030306 microbiology ,Toxin ,Cell Membrane ,Recombinant Proteins ,Transmembrane protein ,Cell biology ,Membrane ,Mutation ,Cytolysin ,Protein Multimerization - Abstract
β-barrel pore-forming toxins perforate cell membranes by forming oligomeric β-barrel pores. The most crucial step is the membrane-insertion of the pore-forming motifs that create the transmembrane β-barrel scaffold. Molecular mechanism that regulates structural reorganization of these pore-forming motifs during β-barrel pore-formation still remains elusive. Using Vibrio cholerae cytolysin as an archetypical example of the β-barrel pore-forming toxin, we show that a key tyrosine residue (Y321) in the hinge region of the pore-forming motif plays crucial role in this process. Mutation of Y321 abrogates oligomerization of the membrane-bound toxin protomers, and blocks subsequent steps of pore-formation. Our study suggests that the presence of Y321 in the hinge region of the pore-forming motif is crucial for the toxin molecule to sense membrane-binding, and to trigger essential structural rearrangements required for the subsequent oligomerization and pore-formation process. Such a regulatory mechanism of pore-formation by V. cholerae cytolysin has not been documented earlier in the structurally related β-barrel pore-forming toxins.
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- 2020
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38. One-step sequence and structure-guided optimization of HIV-1 envelope gp140
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Adi Goldenzweig, Ishika Pramanick, Raghavan Varadarajan, Sarel J. Fleishman, Somnath Dutta, Malavika Abhineshababu Sridevi, Sameer Kumar Malladi, and David Schreiber
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Automated ,Antigenicity ,Immunogen ,Chemistry ,Protein design ,Mutant ,Wild type ,Computational biology ,Article ,Epitope ,Virus ,lcsh:Biology (General) ,Structural Biology ,Rosetta ,Protein stability ,Molecular Biology ,Linker ,Vaccine ,lcsh:QH301-705.5 ,Sequence (medicine) - Abstract
Stabilization of the metastable envelope glycoprotein (Env) of HIV-1 is hypothesized to improve induction of broadly neutralizing antibodies. We improved the expression yield and stability of the HIV-1 envelope glycoprotein BG505SOSIP.664 gp140 by means of a previously described automated sequence and structure-guided computational thermostabilization approach, PROSS. This combines sequence conservation information with computational assessment of mutant stabilization, thus taking advantage of the extensive natural sequence variation present in HIV-1 Env. PROSS is used to design three gp140 variants with 17-45 mutations relative to the parental construct. One of the designs is experimentally observed to have a fourfold improvement in yield and a 4 °C increment in thermostability. In addition, the designed immunogens have similar antigenicity profiles to the native flexible linker version of wild type, BG505SOSIP.664 gp140 (NFL Wt) to major epitopes targeted by broadly neutralizing antibodies. PROSS eliminates the laborious process of screening many variants for stability and functionality, providing a proof of principle of the method for stabilization and improvement of yield without compromising antigenicity for next generation complex, highly glycosylated vaccine candidates.
- Published
- 2020
39. A Q-band line survey towards Orion KL using the Tianma radio telescope
- Author
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Xunchuan Liu, Tie Liu, Zhiqiang Shen, Sheng-Li Qin, Qiuyi Luo, Yu Cheng, Qilao Gu, Tianwei Zhang, Feng-Yao Zhu, Sheng-Yuan Liu, Xing Lu, Rongbing Zhao, Weiye Zhong, Yajun Wu, Juan Li, Zhang Zhao, Jinqing Wang, Qinghui Liu, Bo Xia, Bin Li, Li Fu, Zhen Yan, Chao Zhang, Lingling Wang, Qian Ye, Ken’ichi Tatematsu, Hongli Liu, Hsien Shang, Fengwei Xu, Chin-Fei Lee, and Somnath Dutta
- Subjects
Space and Planetary Science ,Astrophysics of Galaxies (astro-ph.GA) ,FOS: Physical sciences ,Astronomy and Astrophysics ,Astrophysics - Astrophysics of Galaxies - Abstract
We have conducted a line survey towards Orion KL using the Q-band receiver of Tianma 65 m radio telescope (TMRT), covering 34.8--50 GHz with a velocity resolution between 0.79 km s$^{-1}$ and 0.55 km s$^{-1}$ respectively. The observations reach a sensitivity on the level of 1-8 mK, proving that the TMRT is sensitive for conducting deep line surveys. In total, 597 Gaussian features are extracted. Among them, 177 radio recombination lines (RRLs) are identified, including 126, 40 and 11 RRLs of hydrogen, helium and carbon, with a maximum $\Delta n$ of 16, 7, and 3, respectively. The carbon RRLs are confirmed to originate from photodissociation regions with a $V_{\rm LSR}\sim$9 km s$^{-1}$. In addition, 371 molecular transitions of 53 molecular species are identified. Twenty-one molecular species of this survey were not firmly detected in the Q band by Rizzo et al. (2017), including species such as H$_2$CS, HCOOH, C$_2$H$_5$OH, H$_2^{13}$CO, H$_2$CCO, CH$_3$CHO, CH$_2$OCH$_2$, HCN $v_2=1$, and CH$_3$OCHO $v_t=1$. In particular, the vibrationally excited states of ethyl cyanide (C$_2$H$_5$CN $v$13/$v$21) are for the first time firmly detected in the Q band. NH$_3$ (15,15) and (16,16) are identified, and they are so far the highest transitions of the NH$_3$ inversion lines detected towards Orion KL. All the identified lines can be reproduced by a radiative transfer model., Comment: 51 pages, 18 figures, accepted by ApJS
- Published
- 2022
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40. The JCMT Transient Survey: Four-year Summary of Monitoring the Submillimeter Variability of Protostars
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Jonathan M. C. Rawlings, Helen Kirk, Dipen Sahu, Oscar Morata, Samuel Pearson, Yuri Aikawa, James Lane, Aashish Gupta, Jaehan Bae, Fujun Du, Shu-ichiro Inutsuka, Daniel Harsono, Geumsook Park, Giseon Baek, Yi-Jehng Kuan, Geoffrey C. Bower, Gregory J. Herczeg, Spencer Plovie, Aleks Scholz, Doug Johnstone, Chin-Fei Lee, Zhen Guo, Hsien Shang, Hyunju Yoo, Graham S. Bell, Jeong-Eun Lee, Yong-Hee Lee, Carlos Contreras-Peña, Woojin Kwon, Paula S. Teixeira, Sheng-Yuan Liu, Gerald H. Moriarty-Schieven, Bhavana Lalchand, Somnath Dutta, Jan Forbrich, Ziyan Xu, Shih-Yun Tang, Huei-Ru Vivien Chen, Dimitris Stamatellos, Jennifer Hatchell, Colton Broughton, Tim Naylor, Wen Ping Chen, Yao-Te Wang, Tanvi Sharma, Tyler L. Bourke, Andy Pon, Steve Mairs, Shih-Ping Lai, Logan Francis, Miju Kang, Scott Chapman, Tie Liu, University of St Andrews. School of Physics and Astronomy, and University of St Andrews. St Andrews Centre for Exoplanet Science
- Subjects
Variable stars ,FOS: Physical sciences ,01 natural sciences ,0103 physical sciences ,QB Astronomy ,Protostar ,FU Orionis stars ,14. Life underwater ,Pre-main sequence stars ,010303 astronomy & astrophysics ,Solar and Stellar Astrophysics (astro-ph.SR) ,QC ,QB ,Physics ,010308 nuclear & particles physics ,Star formation ,F510 ,Astronomy ,Astronomy and Astrophysics ,3rd-DAS ,Astrophysics - Astrophysics of Galaxies ,Young stellar objects ,Protostars ,QC Physics ,Astrophysics - Solar and Stellar Astrophysics ,13. Climate action ,Space and Planetary Science ,Astrophysics of Galaxies (astro-ph.GA) ,Transient (oscillation) ,Submillimeter astronomy - Abstract
We present the four-year survey results of monthly submillimeter monitoring of eight nearby ($< 500 $pc) star-forming regions by the JCMT Transient Survey. We apply the Lomb-Scargle Periodogram technique to search for and characterize variability on 295 submillimeter peaks brighter than 0.14 Jy beam$^{-1}$, including 22 disk sources (Class II), 83 protostars (Class 0/I), and 190 starless sources. We uncover 18 secular variables, all of them protostars. No single-epoch burst or drop events and no inherently stochastic sources are observed. We classify the secular variables by their timescales into three groups: Periodic, Curved, and Linear. For the Curved and Periodic cases, the detectable fractional amplitude, with respect to mean peak brightness, is $\sim4$ % for sources brighter than $\sim$ 0.5 Jy beam$^{-1}$. Limiting our sample to only these bright sources, the observed variable fraction is 37 % (16 out of 43). Considering source evolution, we find a similar fraction of bright variables for both Class 0 and Class I. Using an empirically motivated conversion from submillimeter variability to variation in mass accretion rate, six sources (7 % of our full sample) are predicted to have years-long accretion events during which the excess mass accreted reaches more than 40 % above the total quiescently accreted mass: two previously known eruptive Class I sources, V1647 Ori and EC 53 (V371 Ser), and four Class 0 sources, HOPS 356, HOPS 373, HOPS 383, and West 40. Considering the full protostellar ensemble, the importance of episodic accretion on few years timescale is negligible, only a few percent of the assembled mass. However, given that this accretion is dominated by events of order the observing time-window, it remains uncertain as to whether the importance of episodic events will continue to rise with decades-long monitoring., Accepted for publication in the Astrophysical Journal
- Published
- 2021
41. Single-particle cryo-EM reveals conformational variability of the oligomeric VCC β-barrel pore in a lipid bilayer
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Nayanika Sengupta, Somnath Dutta, Suman Mishra, Anish Kumar Mondal, and Kausik Chattopadhyay
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Models, Molecular ,Conformational change ,genetic structures ,Perforin ,Cryo-electron microscopy ,Vesicle ,Cell Membrane ,Cryoelectron Microscopy ,Lipid Bilayers ,Cell Biology ,Biology ,medicine.disease_cause ,Protein Structure, Secondary ,eye diseases ,Transmembrane protein ,Barrel ,Bacterial Proteins ,Vibrio cholerae ,Biophysics ,medicine ,sense organs ,Cytolysin ,Protein Multimerization ,Lipid bilayer - Abstract
Vibrio cholerae cytolysin (VCC) is a water-soluble, membrane-damaging, pore-forming toxin (PFT) secreted by pathogenic V. cholerae, which causes eukaryotic cell death by altering the plasma membrane permeability. VCC self-assembles on the cell surface and undergoes a dramatic conformational change from prepore to heptameric pore structure. Over the past few years, several high-resolution structures of detergent-solubilized PFTs have been characterized. However, high-resolution structural characterization of small β-PFTs in a lipid environment is still rare. Therefore, we used single-particle cryo-EM to characterize the structure of the VCC oligomer in large unilamellar vesicles, which is the first atomic-resolution cryo-EM structure of VCC. From our study, we were able to provide the first documented visualization of the rim domain amino acid residues of VCC interacting with lipid membrane. Furthermore, cryo-EM characterization of lipid bilayer–embedded VCC suggests interesting conformational variabilities, especially in the transmembrane channel, which could have a potential impact on the pore architecture and assist us in understanding the pore formation mechanism.
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- 2021
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42. User-friendly, High-throughput, and Fully Automated Data Acquisition Software for Single-particle Cryo-electron Microscopy
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Somnath Dutta, Anil Kumar, P Surekha, and Sahil Gulati
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General Immunology and Microbiology ,Computer science ,business.industry ,SARS-CoV-2 ,General Chemical Engineering ,General Neuroscience ,Detector ,Cryoelectron Microscopy ,COVID-19 ,macromolecular substances ,Pipeline (software) ,General Biochemistry, Genetics and Molecular Biology ,Domain (software engineering) ,Data acquisition ,Workflow ,Software ,Spike Glycoprotein, Coronavirus ,Image Processing, Computer-Assisted ,Humans ,business ,Protocol (object-oriented programming) ,Throughput (business) ,Computer hardware - Abstract
In the past several years, technological and methodological advancements in single-particle cryo-electron microscopy (cryo-EM) have paved a new avenue for the high-resolution structure determination of biological macromolecules. Despite the remarkable advances in cryo-EM, there is still scope for improvement in various aspects of the single-particle analysis workflow. Single-particle analysis demands a suitable software package for high-throughput automatic data acquisition. Several automatic data acquisition software packages were developed for automatic imaging for single-particle cryo-EM in the last eight years. This paper presents an application of a fully automated image acquisition pipeline for vitrified biomolecules under low-dose conditions. It demonstrates a software package, which can collect cryo-EM data fully, automatically, and precisely. Additionally, various microscopic parameters are easily controlled by this software package. This protocol demonstrates the potential of this software package in automated imaging of the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) spike protein with a 200 keV cryo-electron microscope equipped with a direct electron detector (DED). Around 3,000 cryo-EM movie images were acquired in a single session (48 h) of data collection, yielding an atomic-resolution structure of the spike protein of SARS-CoV-2. Furthermore, this structural study indicates that the spike protein adopts two major conformations, 1-RBD (receptor-binding domain) up open and all RBD down closed conformations.
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- 2021
43. Immunogenicity and Protective Efficacy of a Highly Thermotolerant, Trimeric SARS-CoV-2 Receptor Binding Domain Derivative
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Shashank Tripathi, Somnath Dutta, Nagendrakumar Balasubramanian Singanallur, Ishika Pramanick, Sujeet Jha, Aditya Upadhyaya, Unnatiben Rajeshbhai Patel, Sankar Bhattacharyya, Parismita Kalita, Rajesh P. Ringe, Akansha Tyagi, Nidhi Girish, Shane Riddell, Sara Khaleeq, Debajyoti Chakraborty, Poorvi Reddy, Mohammad Suhail Khan, Raghavan Varadarajan, Samreen Siddiqui, Nupur Agarwal, Sameer Kumar Malladi, Kawkab Kanjo, Madhuraj Bhat, Shailendra Mani, Sarah Goldie, Savitha Gayathri, Suman Pandey, R. S. Rajmani, Sahil Kumar, Rajesh Pandey, Randhir Singh, Petrus Jansen van Vuren, Alexander J. McAuley, and Seshadri S. Vasan
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Thermotolerance ,Glycan ,Glycosylation ,Guinea Pigs ,Heterologous ,Antibodies, Viral ,Virus ,Neutralization ,chemistry.chemical_compound ,Mice ,Animals ,Humans ,COVID-19 Serotherapy ,biology ,Chemistry ,SARS-CoV-2 ,Immunogenicity ,Immunization, Passive ,COVID-19 ,Transfection ,Molecular biology ,Infectious Diseases ,HEK293 Cells ,Cell culture ,Spike Glycoprotein, Coronavirus ,biology.protein ,Antibody - Abstract
The Receptor Binding Domain (RBD) of SARS-CoV-2 is the primary target of neutralizing antibodies. We designed a trimeric, highly thermotolerant glycan engineered RBD by fusion to a heterologous, poorly immunogenic disulfide linked trimerization domain derived from cartilage matrix protein. The protein expressed at a yield of ∼80-100 mg/liter in transiently transfected Expi293 cells, as well as CHO and HEK293 stable cell lines and formed homogeneous disulfide-linked trimers. When lyophilized, these possessed remarkable functional stability to transient thermal stress of upto 100 °C and were stable to long term storage of over 4 weeks at 37 °C unlike an alternative RBD-trimer with a different trimerization domain. Two intramuscular immunizations with a human-compatible SWE adjuvanted formulation, elicited antibodies with pseudoviral neutralizing titers in guinea pigs and mice that were 25-250 fold higher than corresponding values in human convalescent sera. Against the beta (B.1.351) variant of concern (VOC), pseudoviral neutralization titers for RBD trimer were ∼ three-fold lower than against wildtype B.1 virus. RBD was also displayed on a designed ferritin-like Msdps2 nanoparticle. This showed decreased yield and immunogenicity relative to trimeric RBD. Replicative virus neutralization assays using mouse sera demonstrated that antibodies induced by the trimers neutralized all four VOC to date, namely B.1.1.7, B.1.351, P.1 and B.1.617.2 without significant differences. Trimeric RBD immunized hamsters were protected from viral challenge. The excellent immunogenicity, thermotolerance, and high yield of these immunogens suggest that they are a promising modality to combat COVID-19, including all SARS-CoV-2 VOC to date.
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- 2021
44. N-Terminal Region of Vibrio parahemolyticus Thermostable Direct Hemolysin Regulates the Membrane-Damaging Action of the Toxin
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Vinica Dhar, Anil Kumar, Pratima Verma, Nidhi Kundu, Somnath Dutta, and Kausik Chattopadhyay
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0303 health sciences ,Toxin ,Chemistry ,030302 biochemistry & molecular biology ,Cell ,food and beverages ,medicine.disease_cause ,Biochemistry ,Cell biology ,03 medical and health sciences ,Cytolysis ,Membrane ,medicine.anatomical_structure ,Tetramer ,Covalent bond ,medicine ,Cytotoxic T cell ,Function (biology) - Abstract
Thermostable direct hemolysin (TDH) of Vibrio parahemolyticus is a membrane-damaging pore-forming toxin with potent cytolytic/cytotoxic activity. TDH exists as a tetramer consisting of protomers with a core β-sandwich domain, flanked by an 11-amino acid long N-terminal region (NTR). This NTR could not be modeled in the previously determined crystal structure of TDH. Moreover, the functional implication of NTR for the membrane-damaging action of TDH remains unknown. In the present study, we have explored the implications of NTR for the structure-function mechanism of TDH. Our data show that the presence of NTR modulates the physicochemical property of TDH in terms of augmenting the amyloidogenic propensity of the protein. Deletion of NTR compromises the binding of TDH toward target cell membranes and drastically affects the membrane-damaging cytolytic/cytotoxic activity of the toxin. Mutations of aromatic/hydrophobic residues within NTR also confer compromised cell-killing activity. Moreover, covalent trapping of NTR, via an engineered disulfide bond, against the core β-sandwich domain also abrogates the cytolytic/cytotoxic activity of TDH. This observation suggests that an unrestrained configuration of NTR is crucial for the membrane-damaging action of TDH. On the basis of our study, we propose a model explaining the role of NTR in the membrane-damaging function of TDH.
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- 2019
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45. Development of mCherry tagged UdgX as a highly sensitive molecular probe for specific detection of uracils in DNA
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Shashanka Aroli, Kapudeep Karmakar, Dipshikha Chakravortty, Umesh Varshney, Somnath Dutta, and Madhurima Datta
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0301 basic medicine ,Recombinant Fusion Proteins ,Mycobacterium smegmatis ,Biophysics ,Oxocarbenium ,Biochemistry ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Bacterial Proteins ,Uracil ,Molecular Biology ,Gene ,biology ,DNA ,Cell Biology ,biology.organism_classification ,Luminescent Proteins ,030104 developmental biology ,chemistry ,Deoxyribose ,Molecular Probes ,030220 oncology & carcinogenesis ,Molecular probe ,mCherry ,Genome, Bacterial - Abstract
Uracil is not always a mistakenly occurring base in DNA. Uracils in DNA genomes are known to be important in the life cycles of Bacillus subtilis phages (PBS1/2) and the malarial parasite, Plasmodium falciparum; and have been implicated in the development of fruit fly and antibody maturation in B-lymphocytes. Availability of a sensitive, specific and robust technique for the detection uracils in genes/genomes is essential to understand its varied biological roles. Mycobacterium smegmatis UdgX (MsmUdgX), identified and characterised in our laboratory, forms covalent complexes with the uracil sites in DNA in a specific manner. MsmUdgX cleaves the glycosidic bond between uracil and the deoxyribose sugar in DNA to produce uracilate and oxocarbenium ions. The oxocarbenium ion is then captured into a covalent complex by the nucleophilic attack of a histidine side chain of MsmUdgX. Here, we describe the use of a fusion protein, mCherry tagged MsmUdgX (mChUdgX), which combines the property of MsmUdgX to covalently and specifically bind the uracil sites in the genome, with the sensitivity of fluorescent detection of mCherry as a reporter. We show that both the purified mChUdgX and the Escherichia coli cell-extracts overexpressing mChUdgX provide high sensitivity and specificity of detecting uracils in DNA.
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- 2019
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46. Structural insights into the activation of metabotropic glutamate receptors
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Tong Sun Kobilka, Yan Zhang, William I. Weis, Michael J. Robertson, Matthew Ling-Hon Chu, Brian K. Kobilka, Toon Laermans, Hongli Hu, Somnath Dutta, Georgios Skiniotis, Jesper Mosolff Mathiesen, Dan Feng, Antoine Koehl, Jeffrey T. Tarrasch, Rasmus Fonseca, Jan Steyaert, Bingfa Sun, Structural Biology Brussels, and Department of Bio-engineering Sciences
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0301 basic medicine ,Agonist ,Multidisciplinary ,Chemistry ,medicine.drug_class ,Protein domain ,Allosteric regulation ,3. Good health ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,Membrane protein ,general ,Metabotropic glutamate receptor ,Extracellular ,Biophysics ,medicine ,Signal transduction ,Receptor ,030217 neurology & neurosurgery - Abstract
Metabotropic glutamate receptors are family C G-protein-coupled receptors. They form obligate dimers and possess extracellular ligand-binding Venus flytrap domains, which are linked by cysteine-rich domains to their 7-transmembrane domains. Spectroscopic studies show that signalling is a dynamic process, in which large-scale conformational changes underlie the transmission of signals from the extracellular Venus flytraps to the G protein-coupling domains-the 7-transmembrane domains-in the membrane. Here, using a combination of X-ray crystallography, cryo-electron microscopy and signalling studies, we present a structural framework for the activation mechanism of metabotropic glutamate receptor subtype 5. Our results show that agonist binding at the Venus flytraps leads to a compaction of the intersubunit dimer interface, thereby bringing the cysteine-rich domains into close proximity. Interactions between the cysteine-rich domains and the second extracellular loops of the receptor enable the rigid-body repositioning of the 7-transmembrane domains, which come into contact with each other to initiate signalling.
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- 2019
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47. Comparative immunogenicity of bacterially expressed soluble trimers and nanoparticle displayed influenza hemagglutinin stem immunogens
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Uddipan Kar, Sara Khaleeq, Priyanka Garg, Madhuraj Bhat, Poorvi Reddy, Venkada Subramanian Vignesh, Aditya Upadhyaya, Mili Das, Ghadiyaram Chakshusmathi, Suman Pandey, Somnath Dutta, and Raghavan Varadarajan
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Immunogen ,T cell ,Immunology ,Hemagglutinin Glycoproteins, Influenza Virus ,Virus ,Mice ,Immune system ,CR6261 ,Influenza, Human ,medicine ,Animals ,Humans ,Immunology and Allergy ,Avidity ,B cell ,Mammals ,biology ,Chemistry ,Fusion protein ,Virology ,Hemagglutinins ,medicine.anatomical_structure ,Influenza Vaccines ,Ferritins ,biology.protein ,Nanoparticles - Abstract
Current influenza vaccines need to be updated annually due to mutations in the globular head of the viral surface protein, hemagglutinin (HA). To address this, vaccine candidates have been designed based on the relatively conserved HA stem domain and have shown protective efficacy in animal models. Oligomerization of the antigens either by fusion to oligomerization motifs or display on self-assembling nanoparticle scaffolds, can induce more potent immune responses compared to the corresponding monomeric antigen due to multivalent engagement of B-cells. Since nanoparticle display can increase manufacturing complexity, and often involves one or more mammalian cell expressed components, it is important to characterize and compare various display and oligomerization scaffolds. Using a structure guided approach, we successfully displayed multiple copies of a previously designed soluble, trimeric influenza stem domain immunogen, pH1HA10, on the ferritin like protein, MsDps2 (12 copies), Ferritin (24 copies) and Encapsulin (180 copies). All proteins were expressed in Escherichia coli. The nanoparticle fusion immunogens were found to be well folded and bound to the influenza stem directed broadly neutralizing antibodies with high affinity. An 8.5 Å Cryo-EM map of Msdps2-pH1HA10 confirmed the successful design of the nanoparticle fusion immunogen. Mice immunization studies with the soluble trimeric stem and nanoparticle fusion constructs revealed that all of them were immunogenic, and protected mice against homologous (A/Belgium/145-MA/2009) and heterologous (A/Puerto Rico/8/1934) challenge with 10MLD50 mouse adapted virus. Although nanoparticle display conferred a small but statistically significant improvement in protection relative to the soluble trimer in a homologous challenge, heterologous protection was similar in both nanoparticle-stem immunized and trimeric stem immunized groups. Such rapidly producible, bacterially expressed antigens and nanoparticle scaffolds are useful modalities to tackle future influenza pandemics.
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- 2021
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48. Simplified Approach for Preparing Graphene Oxide TEM Grids for Stained and Vitrified Biomolecules
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Somnath Dutta, Nayanika Sengupta, and Anil Kumar
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Materials science ,Cryo-electron microscopy ,General Chemical Engineering ,Oxide ,Nanotechnology ,02 engineering and technology ,Article ,law.invention ,lcsh:Chemistry ,03 medical and health sciences ,chemistry.chemical_compound ,law ,Monolayer ,Microscopy ,General Materials Science ,030304 developmental biology ,Cryo-EM ,chemistry.chemical_classification ,0303 health sciences ,Graphene ,Biomolecule ,021001 nanoscience & nanotechnology ,chemistry ,lcsh:QD1-999 ,Transmission electron microscopy ,Amorphous ice ,SEM ,TEM ,graphene oxide ,MsDps ,AFM ,0210 nano-technology ,apoferritin - Abstract
In this manuscript, we report the application of graphene oxide (GO) in the preparation of cryo-electron microscopy (cryo-EM) and transmission electron microscopy (TEM) grids. We treated GO with water and organic solvents, such as, methanol, ethanol and isopropanol separately to isolate significantly large GO monolayer flake to fabricate the grids for cryo-EM and TEM study. We implemented a simplified approach to isolate flakes of GO monolayer for constructing the TEM grids, independent of expensive heavy equipment (Langmuir–Blodgett trough, glow-discharge system, carbon-evaporator or plasma-cleaner or peristaltic pumps). We employed confocal microscopy, SEM and TEM to characterize the flake size, stability and transparency of the GO monolayer and atomic force microscopy (AFM) to probe the depth of GO coated grids. Additionally, GO grids are visualized at cryogenic condition for suitability of GO monolayer for cryo-EM study. In addition, GO-Met-H2O grids reduce the effect of preferred orientation of biological macromolecules within the amorphous ice. The power-spectrum and contrast-transfer-function unequivocally suggest that GO-Met-H2O fabricated holey grids have excellent potential for application in high-resolution structural characterization of biomolecules. Furthermore, only 200 movies and ~8000 70S ribosome particles are selected on GO-coated grids for cryo-EM reconstruction to achieve high-resolution structure.
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- 2021
49. Spectroscopic and photometric monitoring of a poorly known high-luminous OH/IR star: IRAS 18278+0931
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Supriyo Ghosh, Ramkrishna Das, Somnath Dutta, and Soumen Mondal
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Physics ,FOS: Physical sciences ,Astronomy and Astrophysics ,Astrophysics ,Astrophysics::Cosmology and Extragalactic Astrophysics ,Astrophysics - Astrophysics of Galaxies ,Observational astronomy ,Astrophysics - Solar and Stellar Astrophysics ,Space and Planetary Science ,Astrophysics of Galaxies (astro-ph.GA) ,Astrophysics::Solar and Stellar Astrophysics ,OH/IR star ,Astrophysics::Earth and Planetary Astrophysics ,Spectroscopy ,Solar and Stellar Astrophysics (astro-ph.SR) ,Astrophysics::Galaxy Astrophysics - Abstract
We present the time-dependent properties of a poorly known OH/IR star $-$ IRAS 18278+0931 (hereafter, IRAS 18+09) towards the Ophiuchus constellation. We have carried out long-term optical/near-infrared (NIR) photometric and spectroscopic observations to study the object. From optical $R$- and $I$-band light curves, the period of IRAS 18+09 is estimated to be 575 $\pm$ 30 days and the variability amplitudes range from $\Delta$R $\sim$ 4.0 mag to $\Delta$I $\sim$ 3.5 mag. From the standard Period-Luminosity (PL) relations, the distance ($D$) to the object, 4.0 $\pm$ 1.3 kpc, is estimated. Applying this distance in the radiative transfer model, the spectral energy distribution (SED) are constructed from multi-wavelength photometric and IRAS-LRS spectral data which provides the luminosity, optical depth, and gas mass-loss rate (MLR) of the object to be 9600 $\pm$ 500 $L_{\odot}$, 9.1 $\pm$ 0.6 at 0.55 $\mu$m and 1.0$\times$10$^{-6}$ M$_\odot$ yr$^{-1}$, respectively. The current mass of the object infers in the range 1.0 $-$ 1.5 $M_\odot$ assuming solar metallicity. Notably, the temporal variation of atomic and molecular features (e.g., TiO, Na I, Ca I, CO, H$_2$O) over the pulsation cycle of the OH/IR star illustrates the sensitivity of the spectral features to the dynamical atmosphere as observed in pulsating AGB stars., Comment: 14 pages, 7 figures, 5 tables. Accepted for publication in AJ
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- 2021
50. ALMA survey of orion planck galactic cold clumps (ALMASOP): Detection of extremely high-density compact structure of prestellar cores and multiple substructures within
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Gwanjeong Kim, Zhi-Qiang Shen, Jeong-Eun Lee, Sheng-Li Qin, V. M. Pelkonen, Archana Soam, J. Montillaud, Jinhua He, Naomi Hirano, D. Alina, Leonardo Bronfman, Jianjun Zhou, Maria Cunningham, Mika Juvela, Sheng-Yuan Liu, David Eden, Anthony Moraghan, Isabelle Ristorcelli, Neal J. Evans, Doug Johnstone, Yi-Jehng Kuan, Chang Won Lee, Qizhou Zhang, Shih-Ying Hsu, Paul F. Goldsmith, Yuefang Wu, Chin-Fei Lee, Somnath Dutta, Shanghuo Li, Hsien Shang, Tie Liu, Pak Shing Li, Woojin Kwon, Qiu Yi Luo, Dipen Sahu, Kee-Tae Kim, Guido Garay, Patricio Sanhueza, Ken'ichi Tatematsu, Kai Syun Jhan, Di Li, National Natural Science Foundation of China, National Research Council of Canada, Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), National Research Foundation of Korea, National Aeronautics and Space Administration (US), Japan Society for the Promotion of Science, Chinese Academy of Sciences, Academia Sinica Institute of Astronomy and Astrophysics (ASIAA), Academia Sinica, Shanghai Astronomical Observatory [Shanghai] (SHAO), Chinese Academy of Sciences [Beijing] (CAS), University of Texas at Austin [Austin], Nazarbayev University [Kazakhstan], Universidad de Chile = University of Chile [Santiago] (UCHILE), University of New South Wales [Sydney] (UNSW), Liverpool John Moores University (LJMU), Jet Propulsion Laboratory (JPL), NASA-California Institute of Technology (CALTECH), Yunnan Observatories, Chinese Academy of Sciences [Changchun Branch] (CAS), National Astronomical Observatories [Beijing] (NAOC), NRC Herzberg Astronomy and Astrophysics, Conseil National de Recherches Canada (CNRC), University of Victoria [Canada] (UVIC), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, University of KwaZulu-Natal [Durban, Afrique du Sud] (UKZN), University of California [Berkeley] (UC Berkeley), University of California (UC), Korea Astronomy and Space Science Institute (KASI), Univers, Transport, Interfaces, Nanostructures, Atmosphère et environnement, Molécules (UMR 6213) (UTINAM), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Institut de Ciencies del Cosmos (ICCUB), Universitat de Barcelona (UB), Institut de recherche en astrophysique et planétologie (IRAP), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), National Astronomical Observatory of Japan (NAOJ), Graduate University for Advanced Studies [Hayama] (SOKENDAI), NASA Ames Research Center (ARC), Peking University [Beijing], Harvard-Smithsonian Center for Astrophysics (CfA), Harvard University-Smithsonian Institution, Xinjiang Astronomical Observatory, and Department of Physics
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Research program ,010504 meteorology & atmospheric sciences ,Library science ,High density ,FOS: Physical sciences ,MASS ,01 natural sciences ,STAR-FORMATION ,Star forming regions ,0103 physical sciences ,Molecular clouds ,Collapsing clouds ,Star-forming regions ,China ,010303 astronomy & astrophysics ,ComputingMilieux_MISCELLANEOUS ,0105 earth and related environmental sciences ,Physics ,Star formation ,CLOUDS ,International partnership ,Astronomy and Astrophysics ,115 Astronomy, Space science ,Chinese academy of sciences ,Astrophysics - Astrophysics of Galaxies ,Protostars ,State agency ,Space and Planetary Science ,Astrophysics of Galaxies (astro-ph.GA) ,Christian ministry ,FRAGMENTATION ,[PHYS.ASTR]Physics [physics]/Astrophysics [astro-ph] ,SYSTEM - Abstract
Prestellar cores are self-gravitating dense and cold structures within molecular clouds where future stars are born. They are expected, at the stage of transitioning to the protostellar phase, to harbor centrally concentrated dense (sub)structures that will seed the formation of a new star or the binary/multiple stellar systems. Characterizing this critical stage of evolution is key to our understanding of star formation. In this work, we report the detection of high-density (sub)structures on the thousand-astronomical-unit (au) scale in a sample of dense prestellar cores. Through our recent ALMA observations toward the Orion Planck Galactic Cold Clumps, we have found five extremely dense prestellar cores, which have centrally concentrated regions of ∼2000 au in size, and several 107 cm-3 in average density. Masses of these centrally dense regions are in the range of 0.30 to 6.89M⊙. For the first time, our higher resolution observations (0.8' ∼ 320 au) further reveal that one of the cores shows clear signatures of fragmentation; such individual substructures/fragments have sizes of 800-1700 au, masses of 0.08 to 0.84M⊙, densities of 2 - 8 × 107 cm-3, and separations of ∼1200 au. The substructures are massive enough (≳0.1M⊙) to form young stellar objects and are likely examples of the earliest stage of stellar embryos that can lead to widely (∼1200 au) separated multiple systems., L. acknowledges the support from the international partnership program of the Chinese Academy of Sciences through grant No.114231KYSB20200009, National Natural Science Foundation of China (NSFC) through grant NSFC No.12073061, and Shanghai Pujiang Program 20PJ1415500. N.H. acknowledges MoST 108-2112-M-001-017 and MoST 109-2112-M-001-023 grants. G.G. acknowledges support from ANID project AFB 170002. L.B. acknowledges support from ANID project AFB-170002. S.L.Q. is supported by the National Natural Science Foundation of China under grant No. U1631237. D.J. is supported by NRC Canada and by an NSERC Discovery Grant. V.M.P. acknowledges support by the Spanish MINECO under project AYA2017-88754-P, and financial support from the State Agency for Research of the Spanish Ministry of Science and Innovation through the “Unit of Excellence María de Maeztu 2020-2023” award to the Institute of Cosmos Sciences (CEX2019-000918-M). C.W.L. is supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology (NRF-2019R1A2C1010851). A.S. acknowledges financial support from the NSF through grant AST-1715876. The research was carried out in part at the Jet Propulsion Laboratory, which is operated for NASA by the California Institute of Technology. D. L. acknowledges support from NSFC No. 11911530226 and 11725313. K.T. was supported by JSPS KAKENHI grant No. 20H05645. J.H. thanks the NSFC grant No. 11873086 and Yunnan Province of China (No. 2017HC018).This work is sponsored (in part) by the Chinese Academy of Sciences (CAS), through a grant to the CAS South America Center for Astronomy (CASSACA) in Santiago, Chile.
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- 2021
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