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Kajsikova M, Kajsik M, Bocanova L, Papayova K, Drahovska H, Bukovska G. Endolysin EN572-5 as an alternative to treat urinary tract infection caused by Streptococcus agalactiae. Appl Microbiol Biotechnol 2024; 108:79. [PMID: 38189950 PMCID: PMC10774192 DOI: 10.1007/s00253-023-12949-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/13/2023] [Accepted: 11/26/2023] [Indexed: 01/09/2024]
Abstract
Streptococcus agalactiae (Group B Streptococcus, GBS) is an opportunistic pathogen causing urinary tract infection (UTI). Endolysin EN572-5 was identified in prophage KMB-572-E of the human isolate Streptococcus agalactiae KMB-572. The entire EN572-5 gene was cloned into an expression vector and the corresponding recombinant protein EN572-5 was expressed in Escherichia coli in a soluble form, isolated by affinity chromatography, and characterized. The isolated protein was highly active after 30 min incubation in a temperature range of - 20 °C to 37 °C and in a pH range of 5.5-8.0. The endolysin EN572-5 lytic activity was tested on different Streptococcus spp. and Lactobacillus spp. The enzyme lysed clinical GBS (n = 31/31) and different streptococci (n = 6/8), and also exhibited moderate lytic activity against UPEC (n = 4/4), but no lysis of beneficial vaginal lactobacilli (n = 4) was observed. The ability of EN572-5 to eliminate GBS during UTI was investigated using an in vitro model of UPSA. After the administration of 3 μM EN572-5, a nearly 3-log decrease of urine bacterial burden was detected within 3 h. To date, no studies have been published on the use of endolysins against S. agalactiae during UTI. KEY POINTS: • A lytic protein, EN572-5, from a prophage of a human GBS isolate has been identified. • This protein is easily produced, simple to prepare, and stable after lyophilization. • The bacteriolytic activity of EN572-5 was demonstrated for the first time in human urine.
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Affiliation(s)
- Maria Kajsikova
- Department of Genomics and Biotechnology, Institute of Molecular Biology SAS, Dubravska cesta 21, 845 51, Bratislava, Slovakia
| | - Michal Kajsik
- Comenius University Science Park, Ilkovicova 8, 841 04, Bratislava, Slovakia
| | - Lucia Bocanova
- Department of Genomics and Biotechnology, Institute of Molecular Biology SAS, Dubravska cesta 21, 845 51, Bratislava, Slovakia
| | - Kristina Papayova
- Department of Genomics and Biotechnology, Institute of Molecular Biology SAS, Dubravska cesta 21, 845 51, Bratislava, Slovakia
| | - Hana Drahovska
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 841 15, Bratislava, Slovakia
| | - Gabriela Bukovska
- Department of Genomics and Biotechnology, Institute of Molecular Biology SAS, Dubravska cesta 21, 845 51, Bratislava, Slovakia.
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Stevens RH, Zhang H, Kajsik M, Płoski R, Rydzanicz M, Sabaka P, Šutovský S. Successful use of a phage endolysin for treatment of chronic pelvic pain syndrome/chronic bacterial prostatitis. Front Med (Lausanne) 2023; 10:1238147. [PMID: 37649979 PMCID: PMC10462781 DOI: 10.3389/fmed.2023.1238147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 07/26/2023] [Indexed: 09/01/2023] Open
Abstract
Chronic prostatitis (CP) is a common inflammatory condition of the prostate that is estimated to effect 2%-10% of the world's male population. It can manifest as perineal, suprapubic, or lower back pain and urinary symptoms occurring with either recurrent bacterial infection [chronic bacterial prostatitis (CBP)] or in the absence of evidence of bacterial infection [chronic pelvic pain syndrome (CPPS)]. Here, in the case of a 39 years-old CBP patient, we report the first successful use of a bacteriophage-derived muralytic enzyme (endolysin) to treat and resolve the disease. Bacteriological analysis of the patient's prostatic secretion and semen samples revealed a chronic Enterococcus faecalis prostate infection, supporting a diagnosis of CBP. The patient's E. faecalis strain was resistant to several antibiotics and developed resistance to others during the course of treatment. Previous treatment with multiple courses of antibiotics, bacteriophages, probiotics, and immunologic stimulation had failed to achieve long term eradication of the infection or lasting mitigation of the symptoms. A cloned endolysin gene, encoded by E. faecalis bacteriophage ϕEf11, was expressed, and the resulting gene product was purified to electrophoretic homogeneity. A seven-day course of treatment with the endolysin resulted in the elimination of the E. faecalis infection to below culturally detectable levels, and the abatement of symptoms to near normal levels. Furthermore, during the endolysin treatment, the patient experienced no untoward reactions. The present report demonstrates the effectiveness of an endolysin as a novel modality in managing a recalcitrant infection that could not be controlled by conventional antibiotic therapy.
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Affiliation(s)
- Roy H. Stevens
- Laboratory of Oral Infectious Diseases, Kornberg School of Dentistry, Temple University, Philadelphia, PA, United States
| | - Hongming Zhang
- Laboratory of Oral Infectious Diseases, Kornberg School of Dentistry, Temple University, Philadelphia, PA, United States
| | - Michal Kajsik
- Department of Bacteriology, Comenius University Science Park, Bratislava, Slovakia
- Department of Molecular Biology, Comenius University Faculty of Natural Sciences, Bratislava, Slovakia
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | | | - Peter Sabaka
- Department of Infectiology and Geographical Medicine, Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | - Stanislav Šutovský
- 1st Department of Neurology, Faculty of Medicine, Comenius University and University Hospital, Bratislava, Slovakia
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Baláž A, Kajsik M, Budiš J, Szemes T, Turňa J. PHERI-Phage Host ExploRation Pipeline. Microorganisms 2023; 11:1398. [PMID: 37374901 DOI: 10.3390/microorganisms11061398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Antibiotic resistance is becoming a common problem in medicine, food, and industry, with multidrug-resistant bacterial strains occurring in all regions. One of the possible future solutions is the use of bacteriophages. Phages are the most abundant form of life in the biosphere, so we can highly likely purify a specific phage against each target bacterium. The identification and consistent characterization of individual phages was a common form of phage work and included determining bacteriophages' host-specificity. With the advent of new modern sequencing methods, there was a problem with the detailed characterization of phages in the environment identified by metagenome analysis. The solution to this problem may be to use a bioinformatic approach in the form of prediction software capable of determining a bacterial host based on the phage whole-genome sequence. The result of our research is the machine learning algorithm-based tool called PHERI. PHERI predicts the suitable bacterial host genus for the purification of individual viruses from different samples. In addition, it can identify and highlight protein sequences that are important for host selection.
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Affiliation(s)
- Andrej Baláž
- Geneton Ltd., Ilkovicova 8, 841 04 Bratislava, Slovakia
- Department of Applied Informatics, Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynska dolina F1, 842 48 Bratislava, Slovakia
| | - Michal Kajsik
- Science Park, Comenius University, Ilkovicova 8, 841 04 Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 841 04 Bratislava, Slovakia
- Medirex Group Academy n.o., Novozamocka 1, 949 05 Nitra, Slovakia
| | - Jaroslav Budiš
- Geneton Ltd., Ilkovicova 8, 841 04 Bratislava, Slovakia
- Science Park, Comenius University, Ilkovicova 8, 841 04 Bratislava, Slovakia
- Slovak Centre of Scientific and Technical Information (SCSTI), Lamacska Cesta 8/A, 811 04 Bratislava, Slovakia
| | - Tomáš Szemes
- Geneton Ltd., Ilkovicova 8, 841 04 Bratislava, Slovakia
- Science Park, Comenius University, Ilkovicova 8, 841 04 Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 841 04 Bratislava, Slovakia
| | - Ján Turňa
- Science Park, Comenius University, Ilkovicova 8, 841 04 Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 841 04 Bratislava, Slovakia
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Kajsik M, Durovka P, Kajsikova M, Bohmer M, Szemes T, Drahovska H. Complete Genome Sequence of Cronobacter dublinensis Bacteriophage vB_Cdu_VP8. Microbiol Resour Announc 2023:e0029623. [PMID: 37195201 DOI: 10.1128/mra.00296-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023] Open
Abstract
Cronobacter dublinensis is a Gram-negative pathogen that is capable of causing infection in humans. In this announcement, we describe the characterization of bacteriophage vB_Cdu_VP8, which is able to lyse a Cronobacter dublinensis strain. Related to phages belonging to the genus Muldoonvirus, such as Muldoon and SP1, vB_Cdu_VP8 contains 264 predicted protein-coding genes and 3 tRNAs.
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Affiliation(s)
- Michal Kajsik
- Medirex Group Academy n.o., Nitra, Slovakia
- Comenius University Science Park, Bratislava, Slovakia
| | | | - Maria Kajsikova
- Comenius University Science Park, Bratislava, Slovakia
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | | | - Tomas Szemes
- Comenius University Science Park, Bratislava, Slovakia
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Kajsik M, Durovka P, Kajsikova M, Rusnakova D, Szemes T, Drahovska H. Complete Genome Sequence of New Cronobacter-Specific Bacteriophage Dev_CS701. Microbiol Resour Announc 2023; 12:e0003423. [PMID: 36995218 PMCID: PMC10112128 DOI: 10.1128/mra.00034-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023] Open
Abstract
Cronobacter is a ubiquitous Gram-negative bacterium linked with serious infections. In this report, we describe the characterization of Cronobacter phage Dev_CS701, which was isolated from wastewater. Related to phages belonging to the Straboviridae family and Pseudotevenvirus genus, such as vB_CsaM_IeB, Dev_CS701 contains 257 predicted protein-coding genes and a tRNA gene.
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Affiliation(s)
- Michal Kajsik
- Medirex Group Academy n.o., Nitra, Slovakia
- Comenius University Science Park, Bratislava, Slovakia
| | | | | | | | - Tomas Szemes
- Comenius University Science Park, Bratislava, Slovakia
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Andrezal M, Oravcova L, Kadličekova V, Ozaee E, Elnwrani S, Bugala J, Markuskova B, Kajsik M, Drahovska H. Characterization and the host specificity of Pet-CM3-4, a new phage infecting Cronobacter and Enterobacter strains. Virus Res 2023; 324:199025. [PMID: 36528171 DOI: 10.1016/j.virusres.2022.199025] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 12/09/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
Bacteria belonging to Cronobacter and Enterobacter genera are opportunistic pathogens responsible for infections in immunocompromised patients including neonates. Phage therapy offers a safe method for pathogen elimination, however, phages must be well characterized before application. In the present study we isolated four closely related bacteriophages from the subfamily Tevenvirinae infecting Cronobacter and Enterobacter strains. Bacteriophage Pet-CM3-4 which was isolated on C. malonaticus strain possessed broader host specificity than other three phages with primary Enterobacter hosts. Based on genome sequences all these phages have been assigned to the genus Karamvirus. We also studied factors influencing the host specificity of Pet-CM3-4 phage and its host range mutant Pet-CM3-1 and observed that a lysine to glutamine substitution in the long tail fiber adhesin was the reason of the Pet-CM3-1 reduced host specificity. By characterization of phage-resistant mutants from transposon library of C. malonaticus KMB-72 strain we identified that LPS is the receptor of both phages. C. malonaticus O:3 antigen is the receptor of Pet-CM3-1 phage and the Pet-CM3-4 phage binds to structures of the LPS core region. Obtained results will contribute to our understanding of biology and evolution of Tevenvirinae phages.
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Affiliation(s)
- Michal Andrezal
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 84104 Bratislava, Slovakia
| | - Lucia Oravcova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 84104 Bratislava, Slovakia
| | - Veronika Kadličekova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 84104 Bratislava, Slovakia
| | - Elham Ozaee
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 84104 Bratislava, Slovakia
| | - Sulafa Elnwrani
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 84104 Bratislava, Slovakia
| | - Juraj Bugala
- Comenius University Science Park, Ilkovičova 8, 84104 Bratislava, Slovakia
| | - Barbora Markuskova
- Comenius University Science Park, Ilkovičova 8, 84104 Bratislava, Slovakia
| | - Michal Kajsik
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 84104 Bratislava, Slovakia; Comenius University Science Park, Ilkovičova 8, 84104 Bratislava, Slovakia; Medirex group academy n.o., Novozámocká 1/67, 949 05 Nitra, Slovakia
| | - Hana Drahovska
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 84104 Bratislava, Slovakia; Comenius University Science Park, Ilkovičova 8, 84104 Bratislava, Slovakia.
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Strieskova L, Gazdaricova I, Kajsik M, Soltys K, Budis J, Pos O, Lickova M, Klempa B, Szemes T. Ultracentrifugation enrichment protocol followed by total RNA sequencing allows assembly of the complete mitochondrial genome. J Biotechnol 2019; 299:8-12. [PMID: 31022426 DOI: 10.1016/j.jbiotec.2019.04.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/18/2019] [Accepted: 04/20/2019] [Indexed: 12/23/2022]
Abstract
The mitochondrial genome is an independent genetic system in each eukaryotic cell outside the nuclear genome. Mitochondrial DNA (mtDNA) appears in high copy number within one cell, unlike nuclear DNA, which exists in two copies. But nevertheless, mtDNA represent only small part of total cellular DNA what causes problematic analysis and identification of relevant mutations. While most researchers tend to overlook it because of its small size, the mitochondrial genome contains genes that are essential for cellular energetics and survival. Because of the increased awareness on the importance of metabolism and bioenergetics in a wide variety of human diseases, more and more mtDNA studies were performed. Mitochondrial genome research has established the connection between mtDNA and a wide variety of diseases such as cancer or neurodegenerative disorders. At the present time, several methods are known, that allow sequencing of mtDNA. However, genomic analysis is often complicated due to the low content of mtDNA compared to nuclear DNA. For this reason, we have designed a new approach to obtaining the genomic mitochondrial sequence. We chose RNA based sequencing. Since human mtDNA does not contain introns, the reconstruction of whole mitochondrial genome through RNA sequencing seems to be effective. Our method is based on total RNA sequencing coupled with simple ultracentrifugation protocol and de novo assembly. Following our protocol, we were able to assemble a complete mammalian mitochondrial genome with a length of 16,505 bp and an average coverage of 156. The method is a relatively simple and inexpensive which could help in the further research or diagnostics of mtDNA-based diseases.
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Affiliation(s)
| | - Iveta Gazdaricova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Michal Kajsik
- Comenius University Science Park, Bratislava, Slovakia
| | - Katarina Soltys
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia; Comenius University Science Park, Bratislava, Slovakia
| | - Jaroslav Budis
- Geneton Ltd., Bratislava, Slovakia; Comenius University Science Park, Bratislava, Slovakia; Slovak Centre of Scientific and Technical Information, Bratislava, Slovakia
| | - Ondrej Pos
- Geneton Ltd., Bratislava, Slovakia; Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia.
| | - Martina Lickova
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Boris Klempa
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Tomas Szemes
- Geneton Ltd., Bratislava, Slovakia; Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia; Comenius University Science Park, Bratislava, Slovakia
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Orieskova M, Kajsik M, Szemes T, Holy O, Forsythe S, Turna J, Drahovska H. Contribution of the thermotolerance genomic island to increased thermal tolerance in Cronobacter strains. Antonie van Leeuwenhoek 2016; 109:405-14. [DOI: 10.1007/s10482-016-0645-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 01/02/2016] [Indexed: 11/29/2022]
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Chaturvedi N, Kajsik M, Forsythe S, Pandey PN. Protein sequences insight into heavy metal tolerance in Cronobacter sakazakii BAA-894 encoded by plasmid pESA3. Arch Microbiol 2015; 197:1141-9. [PMID: 26384977 DOI: 10.1007/s00203-015-1147-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 08/14/2015] [Accepted: 09/07/2015] [Indexed: 01/10/2023]
Abstract
The recently annotated genome of the bacterium Cronobacter sakazakii BAA-894 suggests that the organism has the ability to bind heavy metals. This study demonstrates heavy metal tolerance in C. sakazakii, in which proteins with the heavy metal interaction were recognized by computational and experimental study. As the result, approximately one-fourth of proteins encoded on the plasmid pESA3 are proposed to have potential interaction with heavy metals. Interaction between heavy metals and predicted proteins was further corroborated using protein crystal structures from protein data bank database and comparison of metal-binding ligands. In addition, a phylogenetic study was undertaken for the toxic heavy metals, arsenic, cadmium, lead and mercury, which generated relatedness clustering for lead, cadmium and arsenic. Laboratory studies confirmed the organism's tolerance to tellurite, copper and silver. These experimental and computational study data extend our understanding of the genes encoding for proteins of this important neonatal pathogen and provide further insights into the genotypes associated with features that can contribute to its persistence in the environment. The information will be of value for future environmental protection from heavy toxic metals.
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Affiliation(s)
- Navaneet Chaturvedi
- Department of Biochemistry and Molecular Biology, Tel Aviv University, 69978, Tel Aviv, Israel.
| | - Michal Kajsik
- Pathogen Research Group, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK
| | - Stephen Forsythe
- Pathogen Research Group, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK
| | - Paras Nath Pandey
- Department of Mathematics, University of Allahabad, Allahabad, 211002, India
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Siqueira Santos RF, da Silva N, Amstalden Junqueira VC, Kajsik M, Forsythe S, Pereira JL. Screening for Cronobacter species in powdered and reconstituted infant formulas and from equipment used in formula preparation in maternity hospitals. Ann Nutr Metab 2013; 63:62-8. [PMID: 23941974 DOI: 10.1159/000353137] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 05/15/2013] [Indexed: 11/19/2022]
Abstract
BACKGROUND/AIMS Cronobacter spp. have been identified as being of considerable risk to neonates. The occurrence of organisms in infant formulas is therefore of considerable interest. METHODS The occurrence of Cronobacter spp. in infant feeds (formulas and fortified cow's milk) was determined using most probable number (MPN) analysis, and from formula preparation utensils. Ninety-nine samples were analyzed, of which 42 were unopened cans of powdered infant formula (PIF), 25 reconstituted infant formulas in feeding bottles, 27 utensils used in the preparation of infant formula and 5 samples of fortified cow's milk. Presumptive Cronobacter spp. isolates were identified using the 7 allele multilocus sequence typing (MLST) scheme. RESULTS C. sakazakii, C. malonaticus and C. muytjensii were recovered from PIF. Although the incidence of Cronobacter in PIF was 29% (12/42), the level was low with an average of 0.54 MPN/100 g. According to MLST profiling, C. sakazakii was the most frequently isolated Cronobacter species, and C. sakazakii ST4 (associated with neonatal meningitis) was recovered from 2/42 PIF samples at 0.51 and 0.92 MPN/100 g. CONCLUSIONS Cronobacter spp. can be isolated from PIF and therefore strict hygienic practices during PIF preparation are important to minimize neonate exposure and reduce the risk of severe infections.
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Drahovska H, Kajsik M, Orieskova M, Oslanecova L, Kaclikova E, Turna J. Characterization of Cronobacter bacteriophages as tools in food protection. Curr Opin Biotechnol 2013. [DOI: 10.1016/j.copbio.2013.05.273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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