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Shityakov S, Kravtsov V, Skorb EV, Nosonovsky M. Ergodicity Breaking and Self-Destruction of Cancer Cells by Induced Genome Chaos. ENTROPY (BASEL, SWITZERLAND) 2023; 26:37. [PMID: 38248163 PMCID: PMC10814486 DOI: 10.3390/e26010037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/25/2023] [Accepted: 12/28/2023] [Indexed: 01/23/2024]
Abstract
During the progression of some cancer cells, the degree of genome instability may increase, leading to genome chaos in populations of malignant cells. While normally chaos is associated with ergodicity, i.e., the state when the time averages of relevant parameters are equal to their phase space averages, the situation with cancer propagation is more complex. Chromothripsis, a catastrophic massive genomic rearrangement, is observed in many types of cancer, leading to increased mutation rates. We present an entropic model of genome chaos and ergodicity and experimental evidence that increasing the degree of chaos beyond the non-ergodic threshold may lead to the self-destruction of some tumor cells. We study time and population averages of chromothripsis frequency in cloned rhabdomyosarcomas from rat stem cells. Clones with frequency above 10% result in cell apoptosis, possibly due to mutations in the BCL2 gene. Potentially, this can be used for suppressing cancer cells by shifting them into a non-ergodic proliferation regime.
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Affiliation(s)
- Sergey Shityakov
- Infochemistry Scientific Center (ISC), ITMO University, 9 Lomonosova St., 191002 St. Petersburg, Russia;
| | - Viacheslav Kravtsov
- Infochemistry Scientific Center (ISC), ITMO University, 9 Lomonosova St., 191002 St. Petersburg, Russia;
| | - Ekaterina V. Skorb
- Infochemistry Scientific Center (ISC), ITMO University, 9 Lomonosova St., 191002 St. Petersburg, Russia;
| | - Michael Nosonovsky
- Infochemistry Scientific Center (ISC), ITMO University, 9 Lomonosova St., 191002 St. Petersburg, Russia;
- College of Engineering and Applied Science, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
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2
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Niazi S, Groth R, Morawska L, Spann K, Ristovski Z. Dynamics and Viability of Airborne Respiratory Syncytial Virus under Various Indoor Air Conditions. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:21558-21569. [PMID: 38084588 DOI: 10.1021/acs.est.3c03455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
The factors governing the viability of airborne viruses embedded within respiratory particles are not well understood. This study aimed to investigate the relative humidity (RH)-dependent viability of airborne respiratory syncytial virus (RSV) in simulated respiratory particles suspended in various indoor air conditions. We tested airborne RSV viability in three static indoor air conditions, including sub-hysteresis (RH < 39%), hysteresis (39% < RH < 65%), and super-hysteresis (RH > 65%) air as well as in three dynamic indoor air conditions, including the transitions between the static conditions. The dynamic conditions were hysteresis → super-hysteresis → hysteresis, sub-hysteresis → hysteresis, and super-hysteresis → hysteresis. We found that after 45 min of particle aging in static conditions, the viability of RSV in sub-hysteresis, hysteresis, and super-hysteresis air was 0.72% ± 0.06%, 0.03% ± 0.006%, and 0.27% ± 0.008%, respectively. After 45 min of aging in dynamic conditions, the RSV viability decreased for particles that remained in a liquid (deliquesced) state during aging when compared with particles in a solid (effloresced) state. The decreased viability of airborne RSV for deliquesced particles is consistent with prolonged exposure to elevated aqueous solutes. These results represent the first measurements of the survival of airborne RSV over particle aging time, with equal viability in low, intermediate, and high RHs at 5 and 15 min and a V-shaped curve after 45 min.
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Affiliation(s)
- Sadegh Niazi
- International Laboratory for Air Quality and Health (ILAQH), School of Earth and Atmospheric Sciences, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Robert Groth
- International Laboratory for Air Quality and Health (ILAQH), School of Earth and Atmospheric Sciences, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Lidia Morawska
- International Laboratory for Air Quality and Health (ILAQH), School of Earth and Atmospheric Sciences, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Kirsten Spann
- Centre for Immunology and Infection Control (CIIC), School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD 4006, Australia
| | - Zoran Ristovski
- International Laboratory for Air Quality and Health (ILAQH), School of Earth and Atmospheric Sciences, Queensland University of Technology, Brisbane, QLD 4000, Australia
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Kong ZM, Sandhu HS, Qiu L, Wu J, Tian WJ, Chi XJ, Tao Z, Yang CFJ, Wang XJ. Virus Dynamics and Decay in Evaporating Human Saliva Droplets on Fomites. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:17737-17750. [PMID: 35904357 DOI: 10.1021/acs.est.2c02311] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The transmission of most respiratory pathogens, including SARS-CoV-2, occurs via virus-containing respiratory droplets, and thus, factors that affect virus viability in droplet residues on surfaces are of critical medical and public health importance. Relative humidity (RH) is known to play a role in virus survival, with a U-shaped relationship between RH and virus viability. The mechanisms affecting virus viability in droplet residues, however, are unclear. This study examines the structure and evaporation dynamics of virus-containing saliva droplets on fomites and their impact on virus viability using four model viruses: vesicular stomatitis virus, herpes simplex virus 1, Newcastle disease virus, and coronavirus HCoV-OC43. The results support the hypothesis that the direct contact of antiviral proteins and virions within the "coffee ring" region of the droplet residue gives rise to the observed U-shaped relationship between virus viability and RH. Viruses survive much better at low and high RH, and their viability is substantially reduced at intermediate RH. A phenomenological theory explaining this phenomenon and a quantitative model analyzing and correlating the experimentally measured virus survivability are developed on the basis of the observations. The mechanisms by which RH affects virus viability are explored. At intermediate RH, antiviral proteins have optimal influence on virions because of their largest contact time and overlap area, which leads to the lowest level of virus activity.
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Affiliation(s)
- Zi-Meng Kong
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Harpal Singh Sandhu
- Department of Ophthalmology and Visual Sciences, School of Medicine, University of Louisville, Louisville, Kentucky 40202, United States
- Department of Bioengineering, J.B. Speed School of Engineering, University of Louisville, Louisville, Kentucky 40292, United States
| | - Lu Qiu
- School of Energy and Power Engineering, Beihang University, Beijing 100191, China
| | - Jicheng Wu
- School of Energy and Power Engineering, Beihang University, Beijing 100191, China
| | - Wen-Jun Tian
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Xiao-Jing Chi
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Zhi Tao
- School of Energy and Power Engineering, Beihang University, Beijing 100191, China
| | - Chi-Fu Jeffrey Yang
- Department of Surgery, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Xiao-Jia Wang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
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Pezzotti G, Ohgitani E, Imamura H, Ikegami S, Shin-Ya M, Adachi T, Adachi K, Yamamoto T, Kanamura N, Marin E, Zhu W, Higasa K, Yasukochi Y, Okuma K, Mazda O. Raman Multi-Omic Snapshot and Statistical Validation of Structural Differences between Herpes Simplex Type I and Epstein-Barr Viruses. Int J Mol Sci 2023; 24:15567. [PMID: 37958551 PMCID: PMC10647490 DOI: 10.3390/ijms242115567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023] Open
Abstract
Raman spectroscopy was applied to study the structural differences between herpes simplex virus Type I (HSV-1) and Epstein-Barr virus (EBV). Raman spectra were first collected with statistical validity on clusters of the respective virions and analyzed according to principal component analysis (PCA). Then, average spectra were computed and a machine-learning approach applied to deconvolute them into sub-band components in order to perform comparative analyses. The Raman results revealed marked structural differences between the two viral strains, which could mainly be traced back to the massive presence of carbohydrates in the glycoproteins of EBV virions. Clear differences could also be recorded for selected tyrosine and tryptophan Raman bands sensitive to pH at the virion/environment interface. According to the observed spectral differences, Raman signatures of known biomolecules were interpreted to link structural differences with the viral functions of the two strains. The present study confirms the unique ability of Raman spectroscopy for answering structural questions at the molecular level in virology and, despite the structural complexity of viral structures, its capacity to readily and reliably differentiate between different virus types and strains.
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Affiliation(s)
- Giuseppe Pezzotti
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-Ku, Matsugasaki, Kyoto 606-8585, Japan; (H.I.); (S.I.); (W.Z.)
- Department of Molecular Genetics, Institute of Biomedical Science, Kansai Medical University, 2-5-1 Shin-Machi, Hirakata 573-1010, Japan
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-Ku, 465 Kajii-Cho, Kyoto 602-8566, Japan; (E.O.); (M.S.-Y.); (T.A.); (O.M.)
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-Ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
- Department of Orthopedic Surgery, Tokyo Medical University, 6-7-1 Nishi-Shinjuku, Shinjuku-Ku, Tokyo 160-0023, Japan
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
- Department of Molecular Science and Nanosystems, Ca’ Foscari University of Venice, Via Torino 155, 30172 Venice, Italy
| | - Eriko Ohgitani
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-Ku, 465 Kajii-Cho, Kyoto 602-8566, Japan; (E.O.); (M.S.-Y.); (T.A.); (O.M.)
| | - Hayata Imamura
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-Ku, Matsugasaki, Kyoto 606-8585, Japan; (H.I.); (S.I.); (W.Z.)
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-Ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
| | - Saki Ikegami
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-Ku, Matsugasaki, Kyoto 606-8585, Japan; (H.I.); (S.I.); (W.Z.)
| | - Masaharu Shin-Ya
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-Ku, 465 Kajii-Cho, Kyoto 602-8566, Japan; (E.O.); (M.S.-Y.); (T.A.); (O.M.)
| | - Tetsuya Adachi
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-Ku, 465 Kajii-Cho, Kyoto 602-8566, Japan; (E.O.); (M.S.-Y.); (T.A.); (O.M.)
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-Ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
- Department of Microbiology, School of Medicine, Kansai Medical University, 2-5-1 Shinmachi, Hirakata 573-1010, Japan;
| | - Keiji Adachi
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-Ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
| | - Toshiro Yamamoto
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-Ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
| | - Narisato Kanamura
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-Ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
| | - Elia Marin
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-Ku, Matsugasaki, Kyoto 606-8585, Japan; (H.I.); (S.I.); (W.Z.)
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-Ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
| | - Wenliang Zhu
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-Ku, Matsugasaki, Kyoto 606-8585, Japan; (H.I.); (S.I.); (W.Z.)
| | - Koichiro Higasa
- Genome Analysis, Institute of Biomedical Science, Kansai Medical University, 2-3-1 Shinmachi, Hirakata 573-1191, Japan; (K.H.); (Y.Y.)
| | - Yoshiki Yasukochi
- Genome Analysis, Institute of Biomedical Science, Kansai Medical University, 2-3-1 Shinmachi, Hirakata 573-1191, Japan; (K.H.); (Y.Y.)
| | - Kazu Okuma
- Department of Microbiology, School of Medicine, Kansai Medical University, 2-5-1 Shinmachi, Hirakata 573-1010, Japan;
| | - Osam Mazda
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-Ku, 465 Kajii-Cho, Kyoto 602-8566, Japan; (E.O.); (M.S.-Y.); (T.A.); (O.M.)
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Choi J, Poudel K, Nam KS, Piri A, Rivera-Piza A, Ku SK, Hwang J, Kim JO, Byeon JH. Aero-manufacture of nanobulges for an in-place anticoronaviral on air filters. JOURNAL OF HAZARDOUS MATERIALS 2023; 445:130458. [PMID: 36444810 DOI: 10.1016/j.jhazmat.2022.130458] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/09/2022] [Accepted: 11/20/2022] [Indexed: 06/16/2023]
Abstract
The interest in removing contagious viruses from indoor air using ventilation and filtration systems is increasing rapidly because people spend most of the day indoors. The development of an effective platform to regenerate the antiviral function of air filters during use and safe abrogation of used filters containing infectious viruses is a challenging task, because an on-demand safe-by-design manufacture system is essential for in-place antiviral coatings, but it has been rarely investigated. With these considerations, an electrically operable dispenser was prepared for decorating continuous ultrafine Fe-Zn, Fe-Ag, or Fe-Cu particles (<5 nm) onto SiO2 nanobeads (ca. 130 nm) to form nanobulges (i.e., nanoroughness for engaging coronavirus spikes) in the aerosol state for 3 min direct deposition on the air filter surfaces. The resulting nanobulges were exposed to human coronaviruses (HCoV; surrogates of SARS-CoV-2) to assess antiviral function. The results were compared with similar-sized individual Zn, Ag, and Cu particles. The nanobulges exhibited comparable antiviral activity to Zn, Ag, and Cu particles while retaining biosafety in both in vitro and in vivo models because of the significantly smaller metallic fractions. This suggests that the bimetallic bulge structures generate reactive oxygen species and Fenton-mediated hydroxyl radicals for inactivating HCoV.
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Affiliation(s)
- Jisoo Choi
- School of Mechanical Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Kishwor Poudel
- College of Pharmacy, Yeungnam University, Gyeongsan 38511, Republic of Korea; Wellman Center for Photomedicine, Department of Dermatology, Meassachusetts General Hospital, Harvard Medical School, MA 02114, USA
| | - Kang Sik Nam
- School of Mechanical Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Amin Piri
- School of Mechanical Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Adriana Rivera-Piza
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Sae Kwang Ku
- College of Korean Medicine, Daegu Haany University, Gyeongsan 38610 Republic of Korea
| | - Jungho Hwang
- School of Mechanical Engineering, Yonsei University, Seoul 03722, Republic of Korea.
| | - Jong Oh Kim
- College of Pharmacy, Yeungnam University, Gyeongsan 38511, Republic of Korea.
| | - Jeong Hoon Byeon
- School of Mechanical Engineering, Yeungnam University, Gyeongsan 38541, Republic of Korea.
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Sun W, Chen H, Tao S, Li N, Xu Y, Fang Y, Chen L, Liang W, Cao G. Detection rate of SARS-CoV-2 RNA in relation to isolation time and environmental surface type. Front Public Health 2022; 10:957827. [PMID: 36187635 PMCID: PMC9515418 DOI: 10.3389/fpubh.2022.957827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/11/2022] [Indexed: 01/24/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV-2) causes environmental contamination via respiratory droplets and persists on contaminants and environmental surfaces for anywhere from a few hours to 6 days. Therefore, it is particularly important to understand the transmission and containment of SARS-CoV-2 on the surface of objects within isolated environments. In this study, 356 environmental surface samples were collected and 79 tested positive, with the highest contamination rate (56.96%) in the wood category (bedside tables, wood floors, and walls). This study revealed differences in the detection rates of environmental surfaces in hospitalized and discharged rooms of patients with confirmed COVID-19 in 2 isolated settings (A: p = 0.001; B: p = 0.505) and suggested that environmental contamination may be an important route of virus transmission, providing a reference to guide the enhancement of ventilation, the use of hotel isolation model, the advocacy of cotton masks, and the effective suppression of virus transmission.
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Affiliation(s)
- Weijie Sun
- Department of Clinical Laboratory, Ningbo First Hospital, Ningbo, China
| | - Huimin Chen
- School of Medicine, Medical School of Jiangsu University, Zhenjiang, China
| | - Shuan Tao
- School of Medicine, Medical School of Jiangsu University, Zhenjiang, China
| | - Na Li
- Laboratory Medical School, Bengbu Medical College, Bengbu, China
| | - Yao Xu
- School of Medicine, Medical School of Ningbo University, Ningbo, China
| | - Yewei Fang
- School of Medicine, Medical School of Ningbo University, Ningbo, China
| | - Luyan Chen
- School of Medicine, Medical School of Ningbo University, Ningbo, China
| | - Wei Liang
- Department of Clinical Laboratory, Ningbo First Hospital, Ningbo, China,*Correspondence: Wei Liang
| | - Gang Cao
- Department of Pain Clinic, Ningbo First Hospital, Ningbo, China,Gang Cao
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Basak M, Mitra S, Bandyopadhyay D. Pathways to community transmission of COVID-19 due to rapid evaporation of respiratory virulets. J Colloid Interface Sci 2022; 619:229-245. [PMID: 35397458 PMCID: PMC8986321 DOI: 10.1016/j.jcis.2022.03.098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 03/06/2022] [Accepted: 03/21/2022] [Indexed: 12/16/2022]
Abstract
HYPOTHESIS The formation of virus-laden colloidal respiratory microdroplets - the sneeze or cough virulets and their evaporation driven miniaturization in the open air are found to have a significant impact on the community transmission of COVID-19 pandemic. SIMULATION DETAILS We simulate the motions and trajectories of virulets by employing laminar fluid flow coupled with droplet tracing physics. A force field analysis has been included considering the gravity, drag, and inertial forces to unleash some of the finer features of virulet trajectories leading to the droplet and airborne transmissions of the virus. Furthermore, an analytical model corroborates temperature (T) and relative humidity (RH) controlled droplet miniaturization. RESULTS The study elucidates that the tiny (1-50 µm) and intermediate (60-100 µm) size ranged virulets tend to form bioaerosol and facilitate an airborne transmission while the virulets of larger dimensions (300 to 500 µm) are more prone to gravity dominated droplet transmission. Subsequently, the mapping between the T and RH guided miniaturization of virulets with the COVID-19 cases for six different cities across the globe justifies the significant contribution of miniaturization-based bioaerosol formation for community transmission of the pandemic.
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Affiliation(s)
- Mitali Basak
- Centre for Nanotechnology, Indian Institute of Technology Guwahati, Assam 781039, India
| | - Shirsendu Mitra
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Assam 781039, India
| | - Dipankar Bandyopadhyay
- Centre for Nanotechnology, Indian Institute of Technology Guwahati, Assam 781039, India; Department of Chemical Engineering, Indian Institute of Technology Guwahati, Assam 781039, India; School of Health Sciences and Technology,Indian Institute of Technology Guwahati, Assam 781039, India.
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Shityakov S, Skorb EV, Nosonovsky M. Topological bio-scaling analysis as a universal measure of protein folding. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220160. [PMID: 35845855 PMCID: PMC9277272 DOI: 10.1098/rsos.220160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 06/14/2022] [Indexed: 05/24/2023]
Abstract
Scaling relationships for polymeric molecules establish power law dependencies between the number of molecular segments and linear dimensions, such as the radius of gyration. They also establish spatial topological properties of the chains, such as their dimensionality. In the spatial domain, power exponents α = 1 (linear stretched molecule), α = 0.5 (the ideal chain) and α = 0.333 (compact globule) are significant. During folding, the molecule undergoes the transition from the one-dimensional linear to the three-dimensional globular state within a very short time. However, intermediate states with fractional dimensions can be stabilized by modifying the solubility (e.g. by changing the solution temperature). Topological properties, such as dimension, correlate with the interaction energy, and thus by tuning the solubility one can control molecular interaction. We investigate these correlations using the example of a well-studied short model of Trp-cage protein. The radius of gyration is used to estimate the fractal dimension of the chain at different stages of folding. It is expected that the same principle is applicable to much larger molecules and that topological (dimensional) characteristics can provide insights into molecular folding and interactions.
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Affiliation(s)
- Sergey Shityakov
- Infochemistry Scientific Center (ISC), ITMO University, 9 Lomonosova St., St Petersburg 191002, Russia
| | - Ekaterina V. Skorb
- Infochemistry Scientific Center (ISC), ITMO University, 9 Lomonosova St., St Petersburg 191002, Russia
| | - Michael Nosonovsky
- Infochemistry Scientific Center (ISC), ITMO University, 9 Lomonosova St., St Petersburg 191002, Russia
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9
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Abstract
The debate over whether viruses are living organisms tends to be paradigmatically determined. The metabolic paradigm denies that they are, while new research evidences the opposite. The purpose of this paper is to deliver a generic model for viral contexts that explains why viruses are alive. It will take a systems biology approach, with a qualitative part (using metacybernetics) to provide deeper explanations of viral contexts, and a quantitative part (using Fisher Information deriving from the variational principle of Extreme Physical Information) which is in principle able to take measurements and predict outcomes. The modelling process provides an extended view of the epigenetic processes of viruses. The generic systems biology model will depict viruses as autonomous entities with metaphysical processes of autopoietic self-organisation and adaptation, enabling them to maintain their physical viability and hence, within their populations, mutate and evolve. The autopoietic epigenetic processes are shown to describe their capability to change, and these are both qualitatively and quantitatively explored, the latter providing an approach to make measurements of physical phenomena under uncertainty. Viruses maintain their fitness when they are able to maintain their stability, and this is indicated by information flow efficacy. A brief case study is presented on the COVID-19 virus from the perspective that it is a living system, and this includes outcome predictions given Fisher Information conditions for known contexts.
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Jarvis MC. Drying of virus-containing particles: modelling effects of droplet origin and composition. JOURNAL OF ENVIRONMENTAL HEALTH SCIENCE & ENGINEERING 2021; 19:1987-1996. [PMID: 34754455 PMCID: PMC8569499 DOI: 10.1007/s40201-021-00750-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 10/17/2021] [Indexed: 05/13/2023]
Abstract
BACKGROUND AND PURPOSE Virus-containing aerosol droplets emitted by breathing, speech or coughing dry rapidly to equilibrium with ambient relative humidity (RH), increasing in solute concentration with effects on virus survival and decreasing in diameter with effects on sedimentation and respiratory uptake. The aim of this paper is to model the effect of ionic and macromolecular solutes on droplet drying and solute concentration. METHODS Deliquescence-efflorescence concepts and Kohler theory were used to simulate the evolution of solute concentrations and water activity in respiratory droplets, starting from efflorescence data on mixed NaCl/KCl aerosols and osmotic pressure data on respiratory macromolecules. RESULTS In NaCl/KCl solutions total salt concentrations were shown to reach 10-13 M at the efflorescence RH of 40-55%, depending on the K:Na ratio. Dependence on K:Na ratio implies that the evaporation curves differ between aerosols derived from saliva and from airway surfaces. The direct effect of liquid droplet size through the Kelvin term was shown to be smaller and restricted to the evolution of breath emissions. Modelling the effect of proteins and glycoproteins showed that salts determine drying equilibria down to the efflorescence RH, and macromolecules at lower RH. CONCLUSION Differences in solute composition between airway surfaces and saliva are predicted to lead to different drying behaviour of droplets emitted by breathing, speech and coughing. These differences may influence the inactivation of viruses.
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Affiliation(s)
- Michael C. Jarvis
- School of Chemistry, Glasgow University, Glasgow, Scotland G12 8QQ UK
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Atamas N, Gavryushenko D, Yablochkova K, Lazarenko M, Taranyik G. Temperature and temporal heterogeneities of water dynamics in the physiological temperature range. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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