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Li Y, Bao Q, Yang S, Yang M, Mao C. Bionanoparticles in cancer imaging, diagnosis, and treatment. VIEW 2022. [DOI: 10.1002/viw.20200027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Yan Li
- Institute of Applied Bioresource Research College of Animal Science Zhejiang University Hangzhou Zhejiang China
| | - Qing Bao
- School of Materials Science and Engineering Zhejiang University Hangzhou Zhejiang China
| | - Shuxu Yang
- Department of Neurosurgery Sir Run Run Shaw Hospital School of Medicine Zhejiang University Hangzhou Zhejiang China
| | - Mingying Yang
- Institute of Applied Bioresource Research College of Animal Science Zhejiang University Hangzhou Zhejiang China
| | - Chuanbin Mao
- School of Materials Science and Engineering Zhejiang University Hangzhou Zhejiang China
- Department of Chemistry and Biochemistry Stephenson Life Science Research Center University of Oklahoma Norman Oklahoma USA
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2
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Meyer A, Greene M, Kimmelshue C, Cademartiri R. Stabilization of T4 bacteriophage at acidic and basic pH by adsorption on paper. Colloids Surf B Biointerfaces 2017; 160:169-176. [PMID: 28926767 DOI: 10.1016/j.colsurfb.2017.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 07/24/2017] [Accepted: 09/01/2017] [Indexed: 12/30/2022]
Abstract
Bacteriophages find applications in agriculture, medicine, and food safety. Many of these applications can expose bacteriophages to stresses that inactivate them including acidic and basic pH. Bacteriophages can be stabilized against these stresses by materials including paper, a common material in packaging and consumer products. Combining paper and bacteriophages creates antibacterial materials, which can reduce the use of antibiotics. Here we show that adsorption on paper protects T4, T5, and T7 bacteriophage from acidic and basic pH. We added bacteriophages to filter paper functionalized with carboxylic acid (carboxyl methyl cellulose) or amine (chitosan) groups, and exposed them to pH from 5.6 to 14. We determined the number of infective bacteriophages after exposure directly on the paper. All papers extended the lifetime of infective bacteriophage by at least a factor of four with some papers stabilizing bacteriophages for up to one week. The degree of stabilization depended on five main factors (i) the family of the bacteriophage, (ii) the charge of the paper and bacteriophages, (iii) the location of the bacteriophages within the paper, (iv) the ability of the paper to prevent bacteriophage-bacteriophage aggregation, and (v) the sensitivity of the bacteriophage proteins to the tested pH. Even when adsorbed on paper the bacteriophages were able to remove E. coli in milk. Choosing the right paper modification or material will protect bacteriophages adsorbed on that material against detrimental pH and other environmental challenges increasing the range of applications of bacteriophages on materials.
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Affiliation(s)
- Abigail Meyer
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA
| | - Melissa Greene
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA
| | - Chad Kimmelshue
- Department of Agronomy, Iowa State University, Ames, IA, USA
| | - Rebecca Cademartiri
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA; Department of Materials Science and Engineering, Iowa State University, Ames, IA, USA.
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3
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Lin TY. Simple sequence repeat variations expedite phage divergence: Mechanisms of indels and gene mutations. Mutat Res 2016; 789:48-56. [PMID: 27133219 DOI: 10.1016/j.mrfmmm.2016.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 03/26/2016] [Accepted: 04/11/2016] [Indexed: 12/27/2022]
Abstract
Phages are the most abundant biological entities and influence prokaryotic communities on Earth. Comparing closely related genomes sheds light on molecular events shaping phage evolution. Simple sequence repeat (SSR) variations impart over half of the genomic changes between T7M and T3, indicating an important role of SSRs in accelerating phage genetic divergence. Differences in coding and noncoding regions of phages infecting different hosts, coliphages T7M and T3, Yersinia phage ϕYeO3-12, and Salmonella phage ϕSG-JL2, frequently arise from SSR variations. Such variations modify noncoding and coding regions; the latter efficiently changes multiple amino acids, thereby hastening protein evolution. Four classes of events are found to drive SSR variations: insertion/deletion of SSR units, expansion/contraction of SSRs without alteration of genome length, changes of repeat motifs, and generation/loss of repeats. The categorization demonstrates the ways SSRs mutate in genomes during phage evolution. Indels are common constituents of genome variations and human diseases, yet, how they occur without preexisting repeat sequence is less understood. Non-repeat-unit-based misalignment-elongation (NRUBME) is proposed to be one mechanism for indels without adjacent repeats. NRUBME or consecutive NRUBME may also change repeat motifs or generate new repeats. NRUBME invoking a non-Watson-Crick base pair explains insertions that initiate mononucleotide repeats. Furthermore, NRUBME successfully interprets many inexplicable human di- to tetranucleotide repeat generations. This study provides the first evidence of SSR variations expediting phage divergence, and enables insights into the events and mechanisms of genome evolution. NRUBME allows us to emulate natural evolution to design indels for various applications.
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Affiliation(s)
- Tiao-Yin Lin
- Department of Biological Science and Technology, Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsin Chu, Taiwan.
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4
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Rapid detection of bacteriophages in starter culture using water-in-oil-in-water emulsion microdroplets. Appl Microbiol Biotechnol 2014; 98:8347-55. [DOI: 10.1007/s00253-014-6018-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 08/04/2014] [Accepted: 08/09/2014] [Indexed: 01/30/2023]
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5
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Lin TY, Lo YH, Tseng PW, Chang SF, Lin YT, Chen TS. A T3 and T7 recombinant phage acquires efficient adsorption and a broader host range. PLoS One 2012; 7:e30954. [PMID: 22347414 PMCID: PMC3276506 DOI: 10.1371/journal.pone.0030954] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 12/27/2011] [Indexed: 11/19/2022] Open
Abstract
It is usually thought that bacteriophage T7 is female specific, while phage T3 can propagate on male and female Escherichia coli. We found that the growth patterns of phages T7M and T3 do not match the above characteristics, instead showing strain dependent male exclusion. Furthermore, a T3/7 hybrid phage exhibits a broader host range relative to that of T3, T7, as well as T7M, and is able to overcome the male exclusion. The T7M sequence closely resembles that of T3. T3/7 is essentially T3 based, but a DNA fragment containing part of the tail fiber gene 17 is replaced by the T7 sequence. T3 displays inferior adsorption to strains tested herein compared to T7. The T3 and T7 recombinant phage carries altered tail fibers and acquires better adsorption efficiency than T3. How phages T3 and T7 recombine was previously unclear. This study is the first to show that recombination can occur accurately within only 8 base-pair homology, where four-way junction structures are identified. Genomic recombination models based on endonuclease I cleavages at equivalent and nonequivalent sites followed by strand annealing are proposed. Retention of pseudo-palindromes can increase recombination frequency for reviving under stress.
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Affiliation(s)
- Tiao-Yin Lin
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, People's Republic of China.
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6
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Fraikin JL, Teesalu T, McKenney CM, Ruoslahti E, Cleland AN. A high-throughput label-free nanoparticle analyser. NATURE NANOTECHNOLOGY 2011; 6:308-13. [PMID: 21378975 DOI: 10.1038/nnano.2011.24] [Citation(s) in RCA: 156] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 02/04/2011] [Indexed: 05/11/2023]
Abstract
Synthetic nanoparticles and genetically modified viruses are used in a range of applications, but high-throughput analytical tools for the physical characterization of these objects are needed. Here we present a microfluidic analyser that detects individual nanoparticles and characterizes complex, unlabelled nanoparticle suspensions. We demonstrate the detection, concentration analysis and sizing of individual synthetic nanoparticles in a multicomponent mixture with sufficient throughput to analyse 500,000 particles per second. We also report the rapid size and titre analysis of unlabelled bacteriophage T7 in both salt solution and mouse blood plasma, using just ~1 × 10⁻⁶ l of analyte. Unexpectedly, in the native blood plasma we discover a large background of naturally occurring nanoparticles with a power-law size distribution. The high-throughput detection capability, scalable fabrication and simple electronics of this instrument make it well suited for diverse applications.
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Affiliation(s)
- Jean-Luc Fraikin
- Department of Physics, University of California Santa Barbara, California 93106, USA
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7
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Role of structure-proteins in the porphyrin-DNA interaction. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2009; 96:207-15. [PMID: 19604705 DOI: 10.1016/j.jphotobiol.2009.06.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2009] [Revised: 06/17/2009] [Accepted: 06/18/2009] [Indexed: 11/22/2022]
Abstract
We studied the complexation of meso-tetrakis(4-N-methylpyridyl)porphyrin (TMPyP) with HeLa nucleosomes and compared it to our earlier results on T7 phage nucleoprotein complex (NP) and isolated DNA. To identify binding modes and relative concentrations of the bound TMPyP forms, the porphyrin absorption spectra were analyzed at various base pair/porphyrin ratios. Spectral decomposition and circular dichroism measurements proved that the two main binding modes of TMPyP, i.e., external binding and intercalation occur also in the nucleosomes. The DNA superstructure maintained by the proteins decreases its accessibility for TMPyP similarly in both nucleoproteins. A difference is observed between the partitioning of the two binding modes: in the case of nucleosome the ratio of intercalation to groove-binding is changed from 60/40 to 40/60 as determined for T7 NP and for isolated DNA-s. Using UV and CD melting studies, we revealed that TMPyP destabilizes the DNA-protein interaction in the nucleosomes but not in the T7 phage. Lastly, photoinduced reaction of bound TMPyP caused alterations in DNA structures and DNA-protein interactions within both nucleoprotein complexes; the nucleosomes were found to be more sensitive to the photoreaction.
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Zupán K, Egyeki M, Tóth K, Fekete A, Herényi L, Módos K, Csík G. Comparison of the efficiency and the specificity of DNA-bound and free cationic porphyrin in photodynamic virus inactivation. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2007; 90:105-12. [PMID: 18222092 DOI: 10.1016/j.jphotobiol.2007.11.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2007] [Revised: 11/28/2007] [Accepted: 11/28/2007] [Indexed: 10/22/2022]
Abstract
The risk of transmitting infections by blood transfusion has been substantially reduced. However, alternative methods for inactivation of pathogens in blood and its components are needed. Application of photoactivated cationic porphyrins can offer an approach to remove non-enveloped viruses from aqueous media. Here we tested the virus inactivation capability of meso-Tetrakis(4-N-methylpyridyl)porphyrin (TMPyP) and meso-Tri-(4-N-methylpyridyl)monophenylporphyrin (TMPyMPP) in the dark and upon irradiation. T7 bacteriophage, as a surrogate on non-enveloped viruses was selected as a test system. TMPyP and TMPyMPP reduce the viability of T7 phage already in the dark, which can be explained by their selective binding to nucleic acid. Both compounds proved to be efficient photosensitizers of virus inactivation. The binding of porphyrin to phage DNA was not a prerequisite of phage photosensitization, moreover, photoinactivation was more efficiently induced by free than by DNA bound porphyrin. As optical melting studies and agarose gel electrophoresis of T7 nucleoprotein revealed, photoreactions of TMPyP and TMPyMPP affect the structural integrity of DNA and also of viral proteins, despite their selective DNA binding.
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Affiliation(s)
- Kristóf Zupán
- Institute of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary.
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9
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Egyeki M, Tóth K, Waldeck W, Schmezer P, Langowski J, Csík G. DNA damaging capability of hematoporphyrin towards DNAs of various accessibilities. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2006; 84:119-27. [PMID: 16549364 DOI: 10.1016/j.jphotobiol.2006.02.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2005] [Revised: 01/17/2006] [Accepted: 02/06/2006] [Indexed: 11/16/2022]
Abstract
In this work we wanted to verify that photoactivation of DNA-non-binding porphyrin derivative hematoporphyrin IX (Hp) is able to induce damages in DNAs of various accessibilities such as B-conformation and superhelical isolated DNA, nucleoprotein complex and intracellular DNAs. It was found that photodynamic reaction of Hp results significant changes in thermal stability of isolated T7 DNA and induces single strand breaks in supercoiled Bluescript plasmid isolated from Escherichia coli cells. As optical melting measurements revealed, the irradiation of photosensitized T7 nucleoprotein complex leads to a destabilization of the protein capsid. The photodynamic reaction affected both the protein structure and DNA-protein interaction, however, the parameters corresponding to the DNA denaturation are not influenced. The accumulation of Hp in HeLa cells was followed by laser scanning confocal microscopy. The picture received is typical for lipophilic dyes. When Hp loaded cells were irradiated, a reduction of viability could be observed in a concentration and a light dose dependent manner; 12microM porphyrin induced almost complete cell killing after 30min irradiation. After similar treatment, alkaline agarose gel electrophoresis of isolated nuclear DNA did not show the presence of single strand breaks. The alkaline comet assay also failed to demonstrate any DNA damage in HeLa cells. We also considered the possibility of the generation of damages in intracellular SV40 DNA. According to the electropherograms there was no difference between the patterns of DNAs from treated and control samples.
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Affiliation(s)
- M Egyeki
- Institute of Biophysics and Radiation Biology, Semmelweis University, Hungarian Academy of Science, P.O. Box 263, H-1444 Budapest, Hungary
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10
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DAVISON PF, FREIFELDER D. The physical properties of the deoxyribonucleic acid from T7 bacteriophage. J Mol Biol 1998; 5:643-9. [PMID: 14025541 DOI: 10.1016/s0022-2836(62)80092-8] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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11
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DAVISON PF, FREIFELDER D, HOLLOWAY BW. INTERRUPTIONS IN THE POLYNUCLEOTIDE STRANDS IN BACTERIOPHAGE DNA. J Mol Biol 1996; 8:1-10. [PMID: 14149959 DOI: 10.1016/s0022-2836(64)80142-x] [Citation(s) in RCA: 105] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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12
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13
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Chung YB, Hinkle DC. Bacteriophage T7 DNA packaging. I. Plasmids containing a T7 replication origin and the T7 concatemer junction are packaged into transducing particles during phage infection. J Mol Biol 1990; 216:911-26. [PMID: 2266562 DOI: 10.1016/s0022-2836(99)80010-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Bacteriophage T7 DNA is a linear duplex molecule with a 160 base-pair direct repeat (terminal redundancy) at its ends. During replication, large DNA concatemers are formed, which are multimers of the T7 genome linked head to tail through recombination at the terminal redundancy. We define the sequence that results from this recombination, a mature right end joined to the left end of T7 DNA, as the concatemer junction. To study the processing and packaging of T7 concatemers into phage particles, we have cloned the T7 concatemer junction into a plasmid vector. This plasmid is efficiently (at least 15 particles/infected cell) packaged into transducing particles during a T7 infection. These transducing particles can be separated from T7 phage by sedimentation to equilibrium in CsCl. The packaged plasmid DNA is a linear concatemer of about 40 x 10(3) base-pairs with ends at the expected T7 DNA sequences. Thus, the T7 concatemer junction sequence on the plasmid is recognized for processing and packaging by the phage system. We have identified a T7 DNA replication origin near the right end of the T7 genome that is necessary for efficient plasmid packaging. The origin, which is associated with a T7 RNA polymerase promoter, causes amplification of the plasmid DNA during T7 infection. The amplified plasmid DNA sediments very rapidly and contains large concatemers, which are expected to be good substrates for the packaging reaction. When cloned in pBR322, a sequence containing only the mature right end of T7 DNA is sufficient for efficient packaging. Since this sequence does not contain DNA to the right of the site where a mature T7 right end is formed, it was expected that right ends would not form on this DNA. In fact, with this plasmid the right end does not form at the normal T7 sequence but is instead formed within the vector. Apparently, the T7 packaging system can also recognize a site in pBR322 DNA to produce an end for packaging. This site is not recognized solely by a "headful" mechanism, since there can be considerable variation in the amount of DNA packaged (32 x 10(3) to 42 x 10(3) base-pairs). Furthermore, deletion of this region from the vector DNA prevents packaging of the plasmid. The end that is formed in vector DNA is somewhat heterogeneous. About one-third of the ends are at a unique site (nucleotide 1712 of pBR322), which is followed by the sequence 5'-ATCTGT-3'. This sequence is also found adjacent to the cut made in a T7 DNA concatemer to produce a normal T7 right end.
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Affiliation(s)
- Y B Chung
- Department of Biology, University of Rochester, NY 14627
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14
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Tóth K, Csik G, Rontó G. Dark and photoreactivity of 4'-aminomethyl-4,5',8-trimethylpsoralen with T7 phage. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 1990; 5:167-78. [PMID: 2111396 DOI: 10.1016/1011-1344(90)80004-h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The dark and photoreactions of 4'-aminomethyl-4,5',8-trimethylpsoralen (AMT) with T7 phage were investigated from biological and structural points of view. The dark reaction leads to the structural destabilization of the double helix of the DNA as is shown by optical melting measurements. The genotoxicity of AMT in the dark is comparable with that of known genotoxic drugs as determined by phage inactivation. The photoreaction with UVA light leads to the formation of mono- and di-adducts depending on the wavelength and dose used. Mono- and di-adducts influence DNA stability differently; biologically both types of adducts are genotoxic as measured by action spectra.
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Affiliation(s)
- K Tóth
- Institute of Biophysics, Semmelweis Medical University, Budapest, Hungary
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15
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Tóth K, Bolard J, Rontó G, Aslanian D. UV-induced small structural changes in the T7 bacteriophage studied by melting methods. BIOPHYSICS OF STRUCTURE AND MECHANISM 1983; 10:229-39. [PMID: 6722280 DOI: 10.1007/bf00535551] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
UV optical absorption and circular dichroism (CD) properties (spectra and melting curves) of T7 bacteriophage were investigated to detect "in situ" structural damages which can be related to the biological inactivation due to UV irradiation. UV doses (0.2-1.2 kJ/m2 at 254 nm) near to the biologically effective minimal dose were applied where the initial genetic damage (approximately 10 events/phage) was observed. The decrease of the melting temperature of the helix-coil transition and the broadening of the transition range indicate the destabilization of the intraphage structure due to the presence of about 0.1-0.6% damaged base concentration.
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16
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Jarrell KF, Kropinski AM. Isolation and characterization of a bacteriophage specific for the lipopolysaccharide of rough derivatives of Pseudomonas aeruginosa strain PAO. J Virol 1981; 38:529-38. [PMID: 6787214 PMCID: PMC171183 DOI: 10.1128/jvi.38.2.529-538.1981] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
A lipopolysaccharide (LPS)-defective (rough) mutant of Pseudomonas aeruginosa PAO was isolated by selection for resistance to the LPS-specific phage E79. The LPS of this mutant, AK-1012, lacked the O-antigenic side chain-specific amino sugar fucosamine as well as the core-specific sugars glucose and rhamnose. Using this strain, we isolated and characterized a phage, phi PLS27, which is specifically inactivated upon incubation with LPS extracted from rough mutants of P. aeruginosa PAO. phi PLS27 was found to be a Bradley type C phage and was very similar to coliphage T7 in a number of properties, including size, buoyant density, mass, and the number of structural proteins.
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Abstract
High resolution "low-loss" scanning electron microscopy is a relatively new technique which permits an investigator to examine structures that were formerly visualized exclusively by transmission electron microscopy [1]. This paper presents some images of intact bacterial virus T7, viewed at the ultrastructural level. Due to the high resolution capibility of this technique, and the demanding physical prerequisites for visualization of the specimen, current specimen preparation techniques were modified in order to permit 1--2 nm resolution in surface mode. Using this method of microscopy, it is possible to view clearly this small bacteriophage (the smallest of the T-coliphages), adsorbed to its host bacterium, in a scanning mode at magnification (and resolution) comparable to TEM without resorting to the use of replicas, or reconstruction of a two-dimensional image.
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19
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Hawkins RB. Quantitative determination of cross-linkage of bacteriophage DNA and protein by ionizing radiation. INTERNATIONAL JOURNAL OF RADIATION BIOLOGY AND RELATED STUDIES IN PHYSICS, CHEMISTRY, AND MEDICINE 1978; 33:425-41. [PMID: 306977 DOI: 10.1080/09553007814550351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Coliphage T7 was dissolved in tryptone broth and exposted to 60C gamma-radiation. Cross-linkage of DNA and protein of the virion was assayed using phenol-water countercurrent distribution. The results are interpreted in terms of a statistical model of cross-linkage and double-strand breaks. It was found that protein--DNA cross-links accumulate linearly with dose at a rate of o.74 X 10(-11) cross-links per rad per nucleotide pair, which is of the order of 5 per cent of the formation rate of double-strand breaks.
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20
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21
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Bleichrodt JF, Roos AL, Roos-Verheij WS. Induction of mutations in bacteriophage T7 by gamma-rays: independence of host-repair mechanisms. Mutat Res 1977; 43:313-26. [PMID: 331092 DOI: 10.1016/0027-5107(77)90055-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Amber mutants of bacteriophage T7 are reverted by gamma-rays to pseudo wild-type particles, i.e. particles able to propagate in a suppressorless host. The yield of revertants is much higher when the phage is irradiated in the presence of oxygen than when irradiated anoxically. Under particular gas conditions the efficiency of mutation induction differs by less than a factor of ten among six different amber codons in cistrons 1, 5, 6, 12, 17 and 19. The induction of mutations is not dependent on error-prone repair involving the recA or lexA genes of the host cell. It is estimated that of the damages that may be inflicted by gamma-rays upon an amber codon, fewer than 1 out of 85 results in reversion of the codon to pseudo wild-type.
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22
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de Groot G, Greve J, Blok J. Transient electric birefringence of the bacteriophages T3 and T7. Biopolymers 1977; 16:639-54. [PMID: 843608 DOI: 10.1002/bip.1977.360160313] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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23
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Roeder GS, Sadowski PD. Bacteriophage T7 morphogenesis: phage-related particles in cells infected with wild-type and mutant T7 phage. Virology 1977; 76:263-85. [PMID: 319595 DOI: 10.1016/0042-6822(77)90302-6] [Citation(s) in RCA: 79] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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24
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Doly J, Anagnostopoulos C. Isolation, subunit structure and properties of the ATP-dependent deoxyribonuclease of Bacillus subtilis. State of the protein in a mutant devoid of activity. EUROPEAN JOURNAL OF BIOCHEMISTRY 1976; 71:309-16. [PMID: 12960 DOI: 10.1111/j.1432-1033.1976.tb11117.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A prodcedure was developed for the purification of the ATP-dependent deoxyribonuclease of Bacillus subtilis 168. It comprises ammonium sulphate fractionation, Sephadex gel filtration, DEAE-cellulose chromatography and gel electrophoresis on a discontinuous polyacrylamide gradient. The enzyme has been obtained in a homogeneous state. Its molecular weight was estimated to be 270000 by disc electrophoresis. Dodecylsulfate-polyacrylamide gel electrophoresis showed the presence of five nonidentical subunits of the following molecular weights: 81000, 70000, 62000, 52500 and 42500. These values give 308000 as the molecular weight of the native enzyme. The pH optimum of the purified enzyme is 9.6. The optimal concentrations of Mg2+ and ATP for exonuclease activity on native B. subtilis DNA were determined. ATP-requirement for hydrolysis of single-stranded DNA is less strigent. The enzyme also possesses high DNA-dependent ATPase activity. The purification procedure was applied to extracts of a mutant devoid of activity for this enzyme (strain GSY 1290). A protein was isolated which is very similar to the active DNAase as regards electrophoretic mobility, reaction with specific antisera and size of four of the subunits. One subunit is missing (Mr 70000) and is replaced by a smaller polypeptide (Mr 565000). The latter results suggest that the mutant is affected in the genetic locus coding for the 70000-Mr subunit.
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25
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26
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Wakem LP, Ebisuzaki K. Pathways of DNA repair in T4 phage. II. Sedimentation analysis of intracellular DNA in repair-defective mutants. Virology 1976; 73:155-64. [PMID: 960557 DOI: 10.1016/0042-6822(76)90069-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Karska-Wysocki B, Thibodeau L, Verly WG. Inactivation of the T7 coliphage by monofunctional alkylating agents. Action of phage adsorption and injection of its DNA. BIOCHIMICA ET BIOPHYSICA ACTA 1976; 435:184-91. [PMID: 181068 DOI: 10.1016/0005-2787(76)90249-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Alkylation by ethyl or methyl methanesulfonate to an extent that inactivates more than 99.5% of T7 coliphages has no effect on phage adsorption on Escherichia coli B cells, but decreases the amount of phage DNA injected into the host cells. Depurination interferes with the injection of the phage DNA. Failure to inject the whole phage genome thus appears to be a cause of the immediate as well as of the delayed inactivation of the T7 coliphage treated by monofunctional alkylating agents; the hypothesis that it is the only cause of inactivation, although not very likely, cannot be excluded at the present time.
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28
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West D, Lagenaur C, Agabian N. Isolation and characterization of Caulobacter crecentus bacteriophage phi Cd1. J Virol 1976; 17:568-75. [PMID: 1255848 PMCID: PMC515447 DOI: 10.1128/jvi.17.2.568-575.1976] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
A DNA-containing bacteriophage, phiCd1, was isolated from sewage and shown to infect both stalked and swarmer cells of Caulobacter crescentus strain CB13B1a. phiCd1 is a small, icosohedral bacteriophage, 60 nm in diameter, which possesses a short, noncontractile tail, 10 to 12 nm in length. The bacteriophage particle is composed of at least eight structural proteins. phiCd1 nucleic acid exists as a linear duplex of DNA as judged by: (i) thermal denaturation (Tm), (ii) CsCl density gradient centrifugation, and (iii) chemical analysis of its base composition. The DNA is 61% guanosine plus cytosine, has a buoyant density in CsCl of 1.721 +/- 0.001 g/cm3, and denatures sharply at 78.5 C in 0.1 SSC (standard saline citrate) buffer. The S20, w value for the DNA is 34.3 +/- 0.1S as compared with T7 DNA, indicating a molecular weight of about 29 x 10(6).
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29
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Aksiyote-Benbasat J, Bloomfield VA. Joining of bacteriophage T4D heads and tails: a kinetic study by inelastic light scattering. J Mol Biol 1975; 95:335-57. [PMID: 1097715 DOI: 10.1016/0022-2836(75)90195-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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31
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Matsuo-Kato H, Fujisawa H. Studies on Bacteriophage T3. III. Characterization of capsids as intermediates of the T3 head assembly. Virology 1975; 63:105-14. [PMID: 1089334 DOI: 10.1016/0042-6822(75)90375-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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32
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King J, Lenk EV, Botstein D. Mechanism of head assembly and DNA encapsulation in Salmonella phage P22. II. Morphogenetic pathway. J Mol Biol 1973; 80:697-731. [PMID: 4773027 DOI: 10.1016/0022-2836(73)90205-2] [Citation(s) in RCA: 178] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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33
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Chan VL, Ebisuzaki K. Intergenic suppression of amber polynucleotide ligase mutation in bacteriophage T4. II. Virology 1973; 53:60-74. [PMID: 4574877 DOI: 10.1016/0042-6822(73)90465-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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34
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Reinert KE, Triebel H, Strassburger J. Hydrodynamic behavior and molecular weight of homogeneous and of polydisperse native DNA. BIOCHIMICA ET BIOPHYSICA ACTA 1972; 287:367-75. [PMID: 4641250 DOI: 10.1016/0005-2787(72)90280-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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35
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Shooter KV, Howse R, Merrifield RK, Robins AB. The interaction of plantinum II compounds with bacteriophages T7 and R17. Chem Biol Interact 1972; 5:289-307. [PMID: 4643763 DOI: 10.1016/0009-2797(72)90069-5] [Citation(s) in RCA: 83] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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36
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Burnotte J, Verly WG. Fluorimetric determination of DNA interstrand crosslinks. BIOCHIMICA ET BIOPHYSICA ACTA 1972; 269:370-5. [PMID: 5039542 DOI: 10.1016/0005-2787(72)90124-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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37
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Burnotte J, Verly WG. Crosslinking of methylated DNA by moderate heating at neutral pH. BIOCHIMICA ET BIOPHYSICA ACTA 1972; 262:449-52. [PMID: 5019068 DOI: 10.1016/0005-2787(72)90488-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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38
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Gampel-Jobbagy Z, Van de Walle C, Powers EL. Modification of the radiation sensitivity of bacteriophage T7 by O 2 and N 2 O. INTERNATIONAL JOURNAL OF RADIATION BIOLOGY AND RELATED STUDIES IN PHYSICS, CHEMISTRY, AND MEDICINE 1972; 21:115-25. [PMID: 4536891 DOI: 10.1080/09553007214550141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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39
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Abstract
The efficiencies of the various methods used for phage concentration have been compared. The two-phase concentration method (with polyethylene glycol and dextran sulfate) gave maximal recoveries of infectivity for coliphages of the T-even and T-odd series and for ribonucleic acid phages and single-stranded deoxyribonucleic acid phages. Precipitation of phages by acid gave high yields when applied to T2 and T4 phages but not with T3 and T7 coliphages. Differential centrifugation was efficient when sedimented phages were gently dispersed before repeating the centrifugation cycle. The efficiencies of the various methods have also been confirmed by electron microscope studies, which also show that the two-phase concentration method gave rise to intact phages. Zone centrifugations in sucrose gradients (12.5 to 52.5%) indicated that coliphages of the T-even series sediment faster than T-odd coliphages; they may thus be separated from each other and from empty ghosts by centrifugation at 100,000 x g for 40 min. Equilibrium centrifugation in preformed cesium chloride gradients was also useful for phage concentration and purification. This study also deals with some optical properties of purified phages; optical cross sections and absorbance ratios (at 260 and 280 nm) of the various preparations are given.
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41
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Burnotte J, Verly W. A Kinetic Approach to the Mechanism of Deoxyribonucleic Acid Cross-Linking by HNO2. J Biol Chem 1971. [DOI: 10.1016/s0021-9258(18)61813-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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42
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Pesce A, Schito GC. Physicochemical properties of N4 coliphage protein ghosts. BIOCHIMICA ET BIOPHYSICA ACTA 1971; 236:450-7. [PMID: 4936430 DOI: 10.1016/0005-2795(71)90225-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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43
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Reinert KE, Strassburger J, Triebel H. Molecular weights and hydrodynamic properties for homogeneous native DNA, derived from diffusion, sedimentation, and viscosity measurements on polydisperse samples. Biopolymers 1971; 10:285-307. [PMID: 5545524 DOI: 10.1002/bip.360100206] [Citation(s) in RCA: 46] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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44
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Bancroft FC, Freifelder D. Molecular weights of coliphages and coliphage DNA. I. Measurement of the molecular weight of bacteriophage T7 by high-speed equilibrium centrifugation. J Mol Biol 1970; 54:537-46. [PMID: 4923668 DOI: 10.1016/0022-2836(70)90124-5] [Citation(s) in RCA: 87] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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45
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Dubin SB, Benedek GB, Bancroft FC, Freifelder D. Molecular weights of coliphages and colip- hage DNA. II. Measurement of diffusion coefficients using optical mixing spectroscopy, and measurement of sedimentation coefficients. J Mol Biol 1970; 54:547-56. [PMID: 5492019 DOI: 10.1016/0022-2836(70)90125-7] [Citation(s) in RCA: 96] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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46
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Brakier L, Verly WG. The lethal action of ehtyl methanesulfonate, nitrogen mustard and myleran on the T7 coliphage. BIOCHIMICA ET BIOPHYSICA ACTA 1970; 213:296-311. [PMID: 4927486 DOI: 10.1016/0005-2787(70)90038-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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47
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Dussault P, Bourgault JM, Verly WG. T7 coliphage inactivation by nitrous acid. BIOCHIMICA ET BIOPHYSICA ACTA 1970; 213:312-9. [PMID: 4927487 DOI: 10.1016/0005-2787(70)90039-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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48
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Abstract
Polyoma and Shope papilloma viruses were purified and analyzed by chemical and physical methods. Disc electrophoresis of degraded virions indicated the presence, in both cases, of only one major species of polypeptide subunit. The weight of the peptide chain of polyoma virus was estimated in 8 m urea to be about 45,000 avograms, based on the sedimentation rate in a sucrose-urea gradient and the diffusion coefficient estimated from the differential migration in electrophoresis in gels of different pore size. The presence of a minor peptide of smaller size was suggested by carboxyl-terminal and sedimentation analyses. The amino acid composition of polyoma capsid protein was reported. Chemical analyses showed that polyoma virus and Shope papilloma virus contained 16 and 17.5% deoxyribonucleic acid, respectively. Light scattering by the polyoma virion showed it to have a molecular weight of 22 x 10(6) and a diameter of 54 nm.
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50
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Sargeant K. Large-Scale Bacteriophage Production. ADVANCES IN APPLIED MICROBIOLOGY 1970. [DOI: 10.1016/s0065-2164(08)70402-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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