Русская версия English version   
О журнале
Редакционная коллегия
Правила для авторов
Информация для читателей и авторов
Оглавление текущего номера
Архив
Контакты
Поиск

Отправить статью
 


Том 19   Выпуск 2   Год 2024
Список литературы

  1. Ventola C.L. The antibiotic resistance crisis: part 1: causes and threats. Pharmacy and Therapeutics. 2015;40(4):277–283.
  2. Ventola C.L. The antibiotic resistance crisis: part 2: management strategies and new agents. Pharmacy and Therapeutics. 2015;40(5):344–352.
  3. Górski A., Międzybrodzki R., Weber-Dąbrowska B., Fortuna W., Letkiewicz S., Rogóż P., Jończyk-Matysiak E., Dąbrowska K., Majewska J., Borysowski J. Phage Therapy: Combating Infections with Potential for Evolving from Merely a Treatment for Complications to Targeting Diseases. Front. Microbiol. 2016;7. Article No. 1515. doi: 10.3389/fmicb.2016.01515
  4. Golkar Z., Bagasra O., Pace D.G. Bacteriophage therapy: a potential solution for the antibiotic resistance crisis. J. Infect. Dev. Ctries. 2014;8(2):129–136. doi: 10.3855/jidc.3573
  5. Nikulin N., Nikulina A., Zimin A., Aminov R. Phages for treatment of Escherichia coli infections. Prog. Mol. Biol. Transl. Sci. 2023;200:171–206. doi: 10.1016/bs.pmbts.2023.03.011
  6. Łusiak-Szelachowska M., Międzybrodzki R., Drulis-Kawa Z., Cater K., Knežević P., Winogradow C., Amaro K., Jończyk-Matysiak E., Weber-Dąbrowska B., Rękas J. et al. Bacteriophages and antibiotic interactions in clinical practice: What we have learned so far. J. Biomed. Sci. 2022;29. Article No. 23. doi: 10.1186/s12929-022-00806-1
  7. Romero-Calle D., Guimarães Benevides R., Góes-Neto A., Billington C. Bacteriophages as alternatives to antibiotics in clinical care. Antibiotics. 2019;8. Article No. 138. doi: 10.3390/antibiotics8030138
  8. Hankin E.H. L'action bactericide des eaux de la Jumna et du Gange sur le vibrion du cholera. Annales de l'Institut Pasteur. 1896;10:511–523 (in French).
  9. Gamaleya N.F. Bacteriolysins – enzymes that destroy bacteria. Russian archive of pathology. 1898;6:607–613 (in Russ.).
  10. Twort F.W. An investigation on the nature of ultra-microscopic viruses. Lancet. 1915;186:1241–1243. doi: 10.1016/S0140-6736(01)20383-3
  11. d'Herelle F. Sur un microbe invisible antagoniste des bacilles dysentériques. C. R. Hebd. Seances Acad. Sci. 1917;165(11):373–375 (in French).
  12. Moelling K., Broecker F., Willy C. A wake-up call: we need phage therapy now. Viruses. 2018;10. Article No. 688. doi: 10.3390/v10120688
  13. Abedon S., Danis-Wlodarczyk K., Alves D. Phage therapy in the 21st century: is there modern, clinical evidence of phage-mediated efficacy? Pharmaceuticals. 2021;14. Article No. 1157. doi: 10.3390/ph14111157
  14. Kamel M., Aleya S., Alsubih M., Aleya L. Microbiome dynamics: a paradigm shift in combatting infectious diseases. J. Pers. Med. 2024;14(2). Article No. 217. doi: 10.3390/jpm14020217
  15. Chang C., Yu X., Guo W., Guo C., Guo X., Li Q., Zhu Y. Bacteriophage-mediated control of biofilm: a promising new dawn for the future. Front. Microbiol. 2022;13. Article No. 825828. doi: 10.3389/fmicb.2022.825828
  16. Merril C.R., Biswas B., Carlton R., Jensen N.C., Creed G.J., Zullo S., Adhya S. Long-circulating bacteriophage as antibacterial agents. Proc. Natl Acad. Sci. USA. 1996;93:3188–3192. doi: 10.1073/pnas.93.8.3188
  17. Zimin A., Butanaev A.M., Suzina N.E., Skoblikov N.E., Sakhabutdinova L.R., Prisyazhnaya N.V., Коnоnеnко S.I., Koshchaev A.G. Construction of mutants of bacteriophage T4 with reduced antigenicity. Scientific Journal of KubSAU. 2017;134(10). Article No.34. doi: 10.21515/1990-4665-134-034
  18. Nikulin N., Коnоnеnко S., Koshchayev A., Zimin A. Design of therapeutic phage cocktails based on T4-type bacteriophages: advantages and disadvantages. Polythematic Online Scientific Journal of Kuban State Agrarian University. 2017;133(9). Article No. 63. doi: 10.21515/1990-4665-133-063
  19. Kiryanova O.Yu., Kiryanov I.I., Kuluev B.R., Garafutdinov R.R., Chemeris A.V., Gubaydullin I.M. Multiplex in silico RAPD-Analysis for Genome Barcoding. Mathematical Biology and Bioinformatics. 2022;17(2):208–229. doi: 10.17537/2022.17.208
  20. Kiryanova O.Yu., Garafutdinov R.R., Chemeris D.A., Gerashchenkov G.A., Giniyatov Y.R., Gubaydullin I.M., Chemeris A.V. DNA polymorphism of dogs (Canis Familiaris L.). VI. Genomic in silico barcoding of canine genomes and genomes of their wild relatives. Biomics. 2022;14(1):59–67. doi: 10.31301/2221-6197.bmcs.2022-4
  21. Kiryanova O.Yu., Kuluev B.R., Kuluev A.R., Mardanshin I.S., Gubaydullin I.M., Chemeris A.V. Multiplex in silico RAPD-analysis of several related plants with different genome sizes and prospects for this approach for DNA-cataloguing of agricultural plant varieties. Biomics. 2020;12(2):194–210. doi: 10.31301/2221-6197.bmcs.2020-10
  22. Nikulin N.A., Zimin A.A. Influence of non-canonical DNA bases on the genomic diversity of Tevenvirinae. Front. Microbiol. 2021;12. doi: 10.3389/fmicb.2021.632686
  23. Brettin T., Davis J., Disz T., Edwards R.A., Gerdes S., Olsen G.J., Olson R., Overbeek R., Parrello B., Pusch G.D., Shukla M. et al. RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci. Rep. 2015;5. Article No. 8365. doi: 10.1038/srep08365
  24. Wattam A.R., Davis J.J., Assaf R., Boisvert S., Brettin T., Bun C., Conrad N., Dietrich E.M., Disz T., Gabbard J.L. et al. Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. Nucleic Acids Res. 2017;45(D1):D535–D542. doi: 10.1093/nar/gkw1017
  25. Kristensen D.M., Kannan L., Coleman M.K., Wolf Y.I., Sorokin A., Koonin E.V., Mushegian A. A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches. Bioinformatics. 2010;26(12):1481–1487. doi: 10.1093/bioinformatics/btq229
  26. Contreras-Moreira B., Vinuesa P. GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. Appl. Environ. Microbiol. 2013;79(24):7696-7701. doi: 10.1128/AEM.02411-13
  27. Petrov V.M., Ratnayaka S., Nolan J.M., Miller E.S., Karam J.D. Genomes of the T4-related bacteriophages as windows on microbial genome evolution. Virol. J. 2010;7. Article No. 292. doi: 10.1186/1743-422X-7-292
  28. Miller E.S., Kutter E., Mosig G., Arisaka F., Kunisawa T., Rüger W. Bacteriophage T4 genome. Microbiol. Mol. Biol. Rev. 2003;67(1):86–156. doi: 10.1128/MMBR.67.1.86-156.2003
  29. Kumar S., Stecher G., Li M., Knyaz C., Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol. Biol. Evol. 2018;35(6):1547–1549. doi: 10.1093/molbev/msy096
  30. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution. 1987;4(4):406–425. doi: 10.1093/oxfordjournals.molbev.a040454
  31. Nikulin N.A., Kiselev S.S., Panyukov V.V., Lu Y., Zimin A.A. Comparative analysis of Actinobacteria phage-plasmids and their transduction potential. Mathematical Biology and Bioinformatics. 2023;18:323–346. doi: 10.17537/2023.18.323
  32. Sorensen T. A method of establishing groups of equal amplitudes in plant sociology based on similarity of species content and its application to analyses of the vegetation on danish commons. Kongelige Danske Videnskabernes Selskab, Biologiske Skrifter. 1948;5:1–34.
  33. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 1981;17:368–376. doi: 10.1007/BF01734359
  34. Edgar R.C. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–1797. doi: 10.1093/nar/gkh340
  35. Schwarz G. Estimating the dimension of a model. Ann. Stat. 1978;6:461–464. doi: 10.1214/aos/1176344136
  36. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 1985;39:783–791. doi: 10.1111/j.1558-5646.1985.tb00420.x
  37. Kiryanova O.Yu., Kiryanov I.I., Garafutdinov R.R., Chemeris A.V., Gubaidullin I.M. Computer program #2021667097 (2021667097 GATCGgenerator). https://onlinepatent.ru/software/2021667097/ (дата регистрации 25.10.2021) (in Russ.).
  38. Tavare S. Some probabilistic and statistical problems in the analysis of DNA sequences. Lect. Mathem. Life Sci. 1986;17:57–86.
  39. Gu X., Fu Y.X., Li W.H. Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Mol. Biol. Evol. 1995;12:546–557. doi: 10.1093/oxfordjournals.molbev.a040235
  40. Whelan S., Goldman N. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol. Biol. Evol. 2001;18:691–699. doi: 10.1093/oxfordjournals.molbev.a003851
  41. Church D.L., Cerutti L., Gürtler A., Griener T., Zelazny A., Emler S. Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory. Clin. Microbiol. Rev. 2020;33. Article No. e00053-19. doi: 10.1128/CMR.00053-19
  42. Ludwig W., Schleifer K.H. Bacterial phylogeny based on 16S and 23S rRNA sequence analysis. FEMS Microbiol. Rev. 1994;15(2-3):155–173. doi: 10.1111/j.1574-6976.1994.tb00132.x
  43. Guo M., Yuan C., Tao L., Cai Y., Zhang W. Life barcoded by DNA barcodes. Conserv. Genet. Resour. 2022;14(4):351–365. doi: 10.1007/s12686-022-01291-2
  44. Regueira-Iglesias A., Balsa-Castro C., Blanco-Pintos T., Tomás I. Critical review of 16S rRNA gene sequencing workflow in microbiome studies: From primer selection to advanced data analysis. Mol. Oral Microbiol. 2023;38(5):347–399. doi: 10.1111/omi.12434
  45. Morsli M., Salipante F., Magnan C., Dunyach-Remy C., Sotto A., Lavigne J.P. Direct metagenomics investigation of non-surgical hard-to-heal wounds: a review. Ann. Clin. Microbiol. Antimicrob. 2024;23(1). Article No. 39. doi: 10.1186/s12941-024-00698-z
  46. Kuo M.T., Chen J.L., Hsu S.L., Chen A., You H.L. An Omics Approach to Diagnosing or Investigating Fungal Keratitis. Int. J. Mol. Sci. 2019;20(15). Article No. 3631. doi: 10.3390/ijms20153631
  47. Drevinek P., Hollweck R., Lorenz M.G., Lustig M., Bjarnsholt T. Direct 16S/18S rRNA Gene PCR Followed by Sanger Sequencing as a Clinical Diagnostic Tool for Detection of Bacterial and Fungal Infections: a Systematic Review and Meta-Analysis. J. Clin. Microbiol. 2023;61(9). Article No. e0033823. doi: 10.1128/jcm.00338-23
  48. Poulsen S.H., Søgaard K.K., Fuursted K., Nielsen H.L. Evaluating the diagnostic accuracy and clinical utility of 16S and 18S rRNA gene targeted next-generation sequencing based on five years of clinical experience. Infect. Dis. (Lond.). 2023;55(11):767–775. doi: 10.1080/23744235.2023.2241550
  49. Hebert P.D., Cywinska A., Ball S.L., deWaard J.R. Biological identifications through DNA barcodes. Proc. Biol. Sci. 2003;270(1512):313–321. doi: 10.1098/rspb.2002.2218
  50. Zhu Y., Shang J., Peng C., Sun Y. Phage family classification under Caudoviricetes: A review of current tools using the latest ICTV classification framework. Front. Microbiol. 2022;13. Article No. 1032186. doi: 10.3389/fmicb.2022.1032186
  51. Turner D., Adriaenssens E.M., Lehman S.M., Moraru C., Kropinski A.M. Bacteriophage Taxonomy: A Continually Evolving Discipline. Methods Mol. Biol. 2024;2734:27-45. doi: 10.1007/978-1-0716-3523-0_3
  52. Krupovic M., Turner D., Morozova V., Dyall-Smith M., Oksanen H.M., Edwards R., Dutilh B.E., Lehman S.M., Reyes A., Baquero D.P. et al. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021. Arch. Virol. 2021;166(11):3239–3244. doi: 10.1007/s00705-021-05205-9
  53. Zerbini F.M., Siddell S.G., Lefkowitz E.J., Mushegian A.R., Adriaenssens E.M., Alfenas-Zerbini P., Dempsey D.M., Dutilh B.E., García M.L., Hendrickson R.C. et al. Changes to virus taxonomy and the ICTV Statutes ratified by the International Committee on Taxonomy of Viruses (2023). Arch. Virol. 2023;168(7). Article No. 175. doi: 10.1007/s00705-023-05797-4
  54. Adriaenssens E., Brister J.R. How to Name and Classify Your Phage: An Informal Guide. Viruses. 2017;9(4). Article No. 70. doi: 10.3390/v9040070
  55. Lin R.C.Y., Iredell J., Khatami A. After the Paper: Australian Phage Network. https://communities.springernature.com/posts/after-the-paper-australian-phage-network (accessed 18.10.2024).
  56. Onsea J., Soentjens P., Djebara S., Merabishvili M., Depypere M., Spriet I., De Munter P., Debaveye Y., Nijs S., Vanderschot P. et al. Bacteriophage Application for Difficult-to-treat Musculoskeletal Infections: Development of a Standardized Multidisciplinary Treatment Protocol. Viruses. 2019;11(10). Article No. 891. doi: 10.3390/v11100891
  57. Pirnay J.P., Verbeken G., Ceyssens P.J., Huys I., De Vos D., Ameloot C., Fauconnier A. The Magistral Phage. Viruses. 2018;10(2). Article No. 64. doi: 10.3390/v10020064
  58. Gibson S.B., Green S.I., Liu C.G., Salazar K.C., Clark J.R., Terwilliger A.L., Kaplan H.B., Maresso A.W., Trautner B.W., Ramig R.F. Constructing and Characterizing Bacteriophage Libraries for Phage Therapy of Human Infections. Frontiers in Microbiology. 2019;10. Article No. 2537. doi: 10.3389/fmicb.2019.02537
Содержание
Оригинальная статья
Кирьянова О.Ю., Киселев С.С., Панюков В.В., Никулин Н.А., Назипова Н.Н., Чемерис А.В., Зимин А.А. Использование мультиплексной виртуальной ПЦР для генетического штрихкодирования бактериофагов рода Tequatrovirus. Математическая биология и биоинформатика. 2024;19(2):369-392. doi: 10.17537/2024.19.369
(опубликована на рус. яз.)

Аннотация (рус.)
Аннотация (англ.)
Полный текст (рус., pdf)
Список литературы
Перевод на англ. яз.

Kiryanova O.Yu., Kiselev S.S., Panyukov V.V., Nikulin N.A., Nazipova N.N., Chemeris A.V., Zimin A.A. Using Multiplex Virtual PCR for Genetic Barcoding of Tequatrovirus Bacteriophages. Маthematical biology and bioinformatics. 2024, 19(Suppl.):t1-t21. doi: 10.17537/2024.19.t1

Полный текст (англ., pdf)

 
  Copyright ИМПБ РАН © 2005-2026