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Труды сотрудников ИБФ СО РАН

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Каталог книг и продолжающихся изданий библиотеки Института биофизики СО РАН (6)

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The comparative redundancy of genes of various organisms and viruses / A. N. Gorban [и др.] // Genetika. - 1993. - Vol. 29, Is. 9. - P. 1413-1419 . - ISSN 0016-6758
Кл.слова (ненормированные):
article -- dna content -- evolution -- genome -- nonhuman -- restriction mapping -- virus -- amino acid sequence -- comparative study -- gene frequency -- human -- molecular genetics -- nucleotide sequence -- restriction mapping -- virus gene -- Amino Acid Sequence -- Base Sequence -- Comparative Study -- English Abstract -- Gene Frequency -- Genes, Viral -- Human -- Molecular Sequence Data -- Restriction Mapping

Scopus
Держатели документа:
Institute of Biophysics, Siberian Division, Russian Academy of Sciences, Krasnoyarsk, Russian Federation : 660036, Красноярск, Академгородок, д. 50, стр. 50

Доп.точки доступа:
Gorban, A.N.; Mirkes, E.M.; Popova, T.G.; Sadovsky, M.G.

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THE COMPARATIVE REDUNDANCY OF GENES OF VARIOUS ORGANISMS AND VIRUSES [Текст] / A. N. GORBAN [и др.] // Genetika. - 1993. - Vol. 29, Is. 9. - P. 1413-1419. - Cited References: 20 . - ISSN 0016-6758

РУБ Genetics & Heredity
Рубрики:
CODON
Аннотация: This paper is devoted to the comparative stude of redundancy of genetic texts of various organisms and viruses. To determine the tedundance of a gene, we have introduced the strict measure for that latter. The measure for a text's redundance is the length of restriction of Frequence/Correlation Dictionary of a given genetic text. Frequence/Correlation Dictionary is the ser of all subsequences belang to a given genetic text, accompanied by the frequencies of their occurrence. The restriction length is defined as that one, for which all the subsequences (of that length) are unique. We have found, that genes of human viruses are less redundant, in comparison to those of human genes. Other aspects of a comparative redundance invastigations of the genes are discussed. The problem of the determination of truet intron could be treated by this methodology, as well, as the evolution of genome.

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Держатели документа:
RUSSIAN ACAD SCI,CTR COMP,KRASNOYARSK,RUSSIA
ИВМ СО РАН : 660036, Красноярск, Академгородок, д. 50, стр. 50

Доп.точки доступа:
GORBAN, A.N.; MIRKES, E.M.; POPOVA, T.G.; SADOVSKY, M.G.

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CORRELATION APPROACH TO COMPARING NUCLEOTIDE-SEQUENCES [Текст] / A. N. GORBAN, T. G. POPOVA, M. G. SADOVSKY // Zhurnal Obshchei Biol. - 1994. - Vol. 55, Is. 04.05.2013. - P. 420-430. - Cited References: 22 . - ISSN 0044-4596

РУБ Biology

Аннотация: A new method of evaluation of similarity between two nucleotide sequences is proposed. It is based on comparing frequency/correlation dictionaries of the sequences under investigation. The dictionary is a set of all strings of various length occurring within the sequences accompanied by their frequencies. The method proposed allows to compare sequences of arbitrary lengths, its advantage is absence of necessity of informal (expert) choice of the best fit. Efficiency of the method is demonstrated by comparison of several human genes and viruses.

WOS : 660036, Красноярск, Академгородок, д. 50, стр. 50

Доп.точки доступа:
GORBAN, A.N.; POPOVA, T.G.; SADOVSKY, M.G.

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Human virus genes are less redundant than human genes [Текст] / A. N. Gorban, T. G. Popova, M. G. Sadovskii // Genetika. - 1996. - Vol. 32, Is. 2. - P. 289-294. - Cited References: 8 . - ISSN 0016-6758

РУБ Genetics & Heredity

Аннотация: Statistical parameters of nucleotide sequences of mature human RNAs and those of human viruses were compared. The redundancy values of the appropriate genes were compared. The redundancy of virus genes was shown to be, on the average, less than that of human genes. The distribution of human genes according to redundancy values is bimodal, and that of human virus gene's is trimodal. This fact suggests possibility of a novel gene classification according to statistical characteristics of nucleotide sequences.

WOS : 660036, Красноярск, Академгородок, д. 50, стр. 50

Доп.точки доступа:
Gorban, A.N.; Popova, T.G.; Sadovskii, M.G.

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On the problem of genome redundancy in viruses and prokaryotes [Text] / M. G. Sadovsky // Russ. J. Genet. - 2002. - Vol. 38, Is. 5. - P. 575-581, DOI 10.1023/A:1015503617023. - Cited References: 10 . - ISSN 1022-7954

РУБ Genetics & Heredity

Аннотация: A specific index of nucleotide sequence redundancy, the specific restriction length of a finite frequency dictionary, was determined for a complete set of genes in some viral genomes and a genome of a bacterium, Bacillus subtilis. The distribution of the gene number over the specific restriction length was shown to be bimodal for viral genomes and unimodal for the Bac. subtilis genome. These results agree with earlier data.

WOS
Держатели документа:
Russian Acad Sci, Inst Biophys, Krasnoyarsk 660036, Russia
ИБФ СО РАН : 660036, Красноярск, Академгородок, д. 50, стр. 50

Доп.точки доступа:
Sadovsky, M.G.

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Bioluminescent detection of tick-borne encephalitis virus in native ticks / A. N. Kudryavtsev, L. P. Burakova, L. A. Frank // Anal. Methods. - 2017. - Vol. 9, Is. 15. - P2252-2255, DOI 10.1039/c7ay00535k . - ISSN 1759-9660
Кл.слова (ненормированные):
Proteins -- Recombinant proteins -- Viruses -- Binding proteins -- Bioluminescence
Аннотация: A one-step bioluminescent immunoassay for tick-borne encephalitis virus (TBEV) in natural ticks based on the hybrid protein 14D5a-Rm7 was developed. Recombinant Ca2+-dependent coelenterazine-binding protein was shown to be a more convenient substrate form for the Rm7 domain than coelenterazine. Over 600 samples of natural ticks were analyzed and shown to have essential differences in the discrimination factor D for TBEV-positive (2.77 ± 0.81) and TBEV-negative (1.15 ± 0.28) samples. © The Royal Society of Chemistry.

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Держатели документа:
Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, Krasnoyarsk, Russian Federation
Siberian Federal University, Krasnoyarsk, Russian Federation

Доп.точки доступа:
Kudryavtsev, A. N.; Burakova, L. P.; Frank, L. A.

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Comprehensive Insights Into Composition, Metabolic Potentials, and Interactions Among Archaeal, Bacterial, and Viral Assemblages in Meromictic Lake Shunet in Siberia / Y. T. Wu [et al.] // Front. Microbiol. - 2018. - Vol. 9. - Ст. 1763, DOI 10.3389/fmicb.2018.01763. - Cited References:103. - This research was supported by the Ministry of Science and Technology in Taiwan through the Taiwan-Russia Joint Project Grant NSC 99-2923-B-001-001-MY3 and NSC 102-2923-B-001-004 and the Russian Foundation for Basic Research, Grant No. 16-05-00091-a. The research was partially supported by the Council on grants from the President of the Russian Federation for support of leading scientific schools (grant NSh-9249.2016.5). . - ISSN 1664-302X

РУБ Microbiology
Рубрики:
BACTERIOPLANKTON COMMUNITY COMPOSITION
RIBOSOMAL-RNA GENES
ANTARCTIC
Кл.слова (ненормированные):
Lake Shunet -- metagenomics -- archaeal -- bacterial and viral assemblages -- meromictic lake
Аннотация: Microorganisms are critical to maintaining stratified biogeochemical characteristics in meromictic lakes; however, their community composition and potential roles in nutrient cycling are not thoroughly described. Both metagenomics and metaviromics were used to determine the composition and capacity of archaea, bacteria, and viruses along the water column in the landlocked meromictic Lake Shunet in Siberia. Deep sequencing of 265 Gb and high-quality assembly revealed a near-complete genome corresponding to Nonlabens sp. sh3vir. in a viral sample and 38 bacterial bins (0.2-5.3 Mb each). The mixolimnion (3.0 m) had the most diverse archaeal, bacterial, and viral communities, followed by the monimolimnion (5.5 m) and chemocline (5.0 m). The bacterial and archaeal communities were dominated by Thiocapsa and Methanococcoides, respectively, whereas the viral community was dominated by Siphoviridae. The archaeal and bacterial assemblages and the associated energy metabolism were significantly related to the various depths, in accordance with the stratification of physicochemical parameters. Reconstructed elemental nutrient cycles of the three layers were interconnected, including co-occurrence of denitrification and nitrogen fixation in each layer and involved unique processes due to specific biogeochemical properties at the respective depths. According to the gene annotation, several pre-dominant yet unknown and uncultured bacteria also play potentially important roles in nutrient cycling. Reciprocal BLAST analysis revealed that the viruses were specific to the host archaea and bacteria in the mixolimnion. This study provides insights into the bacterial, archaeal, and viral assemblages and the corresponding capacity potentials in Lake Shunet, one of the three meromictic lakes in central Asia. Lake Shunet was determined to harbor specific and diverse viral, bacterial, and archaeal communities that intimately interacted, revealing patterns shaped by indigenous physicochemical parameters.

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Scopus
Держатели документа:
Natl Pingtung Univ Sci & Technol, Dept Forestry, Neipu, Taiwan.
Acad Sinica, Biodivers Res Ctr, Taipei, Taiwan.
Germark Biotechnol Co Ltd, Taichung, Taiwan.
Univ Melbourne, Melbourne Sch Engn, Optimisat & Pattern Recognit Grp, Melbourne, Vic, Australia.
Acad Sinica, Taiwan Int Grad Program, Mol & Biol Agr Sci, Taipei, Taiwan.
Natl Chung Hsing Univ, Grad Inst Biotechnol, Dept Life Sci, Taichung, Taiwan.
Russian Acad Sci, Inst Biophys, Siberian Div, Krasnoyarsk, Russia.
Siberian Fed Univ, Krasnoyarsk, Russia.

Доп.точки доступа:
Wu, Yu-Ting; Yang, Cheng-Yu; Chiang, Pei-Wen; Tseng, Ching-Hung; Chiu, Hsiu-Hui; Saeed, Isaam; Baatar, Bayanmunkh; Rogozin, Denis; Halgamuge, Saman; Degermendzhi, Andrei; Tang, Sen-Lin; Ministry of Science and Technology in Taiwan [NSC 99-2923-B-001-001-MY3, NSC 102-2923-B-001-004]; Russian Foundation for Basic Research [16-05-00091-a]; Russian Federation [NSh-9249.2016.5]

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Study of the immunogenicity of the VP2 protein of canine parvovirus produced using an improved Baculovirus expression system / D. Chang, Y. Liu, Y. Chen [et al.] // BMC Vet. Res. - 2020. - Vol. 16, Is. 1. - Ст. 202, DOI 10.1186/s12917-020-02422-3 . - ISSN 1746-6148
Кл.слова (ненормированные):
Baculovirus expression system -- Canine parvovirus -- VP2 protein -- canine parvovirus vaccine -- protein VP2 -- recombinant protein -- unclassified drug -- virus antibody -- virus vaccine -- affinity chromatography -- animal experiment -- antibody titer -- Article -- baculovirus expression system -- Canine parvovirus -- controlled study -- DNA transposition -- enzyme linked immunosorbent assay -- female -- fluorescence microscopy -- gene expression level -- hemagglutination inhibition -- hemagglutination inhibition test -- immunogenicity -- mouse -- nonhuman -- parvovirus infection -- protein expression -- Sf9 cell line -- vaccination -- Western blotting
Аннотация: Background: Canine parvovirus (CPV) is now recognized as a serious threat to the dog breeding industry worldwide. Currently used CPV vaccines all have their specific drawbacks, prompting a search for alternative safe and effective vaccination strategies such as subunit vaccine. VP2 protein is the major antigen targeted for developing CPV subunit vaccine, however, its production in baculovirus expression system remains challenging due to the insufficient yield. Therefore, our study aims to increase the VP2 protein production by using an improved baculovirus expression system and to evaluate the immunogenicity of the purified VP2 protein in mice. Results: The results showed that high-level expression of the full length VP2 protein was achieved using our modified baculovirus expression system. The recombinant virus carrying two copies of VP2 gene showed the highest expression level, with a productivity of 186 mg/L, which is about 1.4-1.6 fold that of the recombinant viruses carrying only one copy. The purified protein reacted with Mouse anti-His tag monoclonal antibody and Rabbit anti-VP2 polyclonal antibody. BALB/c mice were intramuscularly immunized with purified VP2 protein twice at 2 week intervals. After vaccination, VP2 protein could induce the mice produce high level of hemagglutination inhibition antibodies. Conclusions: Full length CPV VP2 protein was expressed at high level and purified efficiently. Moreover, it stimulated mice to produce high level of antibodies with hemmaglutination inhibition properties. The VP2 protein expressed in this study could be used as a putative economic and efficient subunit vaccine against CPV infection. © 2020 The Author(s).

Scopus
Держатели документа:
Henan Provincal Engineering and Technology Center of Health Products for Livestock and Poultry, Key Laboratory of Ecological Security, Collab. Innov. Ctr. of Water Secty. for Water Src. Reg. of Mid-line of S.-to-N. Diversion Proj. of Henan Prov., School of Agricultural Engineering, Nanyang Normal University, Nanyang, 473061, China
Institute of Biophysics, Siberian Branch, Russian Academy of Science, Federal Research Center Krasnoyarsk Science Center SB RAS, Krasnoyarsk, 660036, Russian Federation

Доп.точки доступа:
Chang, D.; Liu, Y.; Chen, Y.; Hu, X.; Burov, A.; Puzyr, A.; Bondar, V.; Yao, L.

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Study of the immunogenicity of the VP2 protein of canine parvovirus produced using an improved Baculovirus expression system / D. Chang, Y. K. Liu, Y. Y. Chen [et al.] // BMC Vet. Res. - 2020. - Vol. 16, Is. 1. - Ст. 202, DOI 10.1186/s12917-020-02422-3. - Cited References:30. - This work was financially supported by the National Natural Science Foundation of China (No. 31870917), The program for Innovative Research Team of Science and Technology in University of Henan Province (No. 20IRTSTHN024) and Key Scientific Research Projects of Colleges and Universities in Henan Province of China (No. 18B230008). The funding bodies played no role in the design of the study, the collection, analysis, and interpretation of data and in writing the manuscript. . - ISSN 1746-6148

РУБ Veterinary Sciences
Рубрики:
VIRUS-LIKE PARTICLES
   ESCHERICHIA-COLI
   GENETIC-ANALYSIS
   CPV-VP2
Кл.слова (ненормированные):
Canine parvovirus -- VP2 protein -- Baculovirus expression system
Аннотация: Background Canine parvovirus (CPV) is now recognized as a serious threat to the dog breeding industry worldwide. Currently used CPV vaccines all have their specific drawbacks, prompting a search for alternative safe and effective vaccination strategies such as subunit vaccine. VP2 protein is the major antigen targeted for developing CPV subunit vaccine, however, its production in baculovirus expression system remains challenging due to the insufficient yield. Therefore, our study aims to increase the VP2 protein production by using an improved baculovirus expression system and to evaluate the immunogenicity of the purified VP2 protein in mice. Results The results showed that high-level expression of the full length VP2 protein was achieved using our modified baculovirus expression system. The recombinant virus carrying two copies of VP2 gene showed the highest expression level, with a productivity of 186 mg/L, which is about 1.4-1.6 fold that of the recombinant viruses carrying only one copy. The purified protein reacted with Mouse anti-His tag monoclonal antibody and Rabbit anti-VP2 polyclonal antibody. BALB/c mice were intramuscularly immunized with purified VP2 protein twice at 2 week intervals. After vaccination, VP2 protein could induce the mice produce high level of hemagglutination inhibition antibodies. Conclusions Full length CPV VP2 protein was expressed at high level and purified efficiently. Moreover, it stimulated mice to produce high level of antibodies with hemmaglutination inhibition properties. The VP2 protein expressed in this study could be used as a putative economic and efficient subunit vaccine against CPV infection.

WOS
Держатели документа:
Nanyang Normal Univ, Sch Agr Engn, Henan Provincal Engn & Technol Ctr Hlth Prod Live, Nanyang 473061, Peoples R China.
Nanyang Normal Univ, Sch Agr Engn, Key Lab Ecol Secur, Nanyang 473061, Peoples R China.
Nanyang Normal Univ, Sch Agr Engn, Collaborat Innovat Ctr Water Secur Water Source R, Nanyang 473061, Peoples R China.
Russian Acad Sci, Fed Res Ctr, Krasnoyarsk Sci Ctr, Inst Biophys,Siberian Branch, Krasnoyarsk 660036, Russia.

Доп.точки доступа:
Chang, Dao; Liu, Yangkun; Chen, Yangyang; Hu, Xiaomin; Burov, Andrey; Puzyr, Alexey; Bondar, Vladimir; Yao, Lunguang; National Natural Science Foundation of ChinaNational Natural Science Foundation of China [31870917]; program for Innovative Research Team of Science and Technology in University of Henan Province [20IRTSTHN024]; Key Scientific Research Projects of Colleges and Universities in Henan Province of China [18B230008]

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10.

Positive feedback between acidosis and hypoxia during the transition of COVID-19 to a severe form of the disease / D. Lagutkin, D. Semyonov, Y. E. Yegorov [et al.] // FEBS Open Bio. - 2021. - Vol. 11. - P450-450. - Cited References:0 . - ISSN 2211-5463

РУБ Biochemistry & Molecular Biology

Аннотация: SARSCoV2 virus causes disease that has several distinctive characteristics compared to diseases caused by other viruses. We have put forward a hypothesis that relates COVID19 pathogenesis with acidosis, which frequently characterizes severe cases of this disease. It has been shown that hypoxia and acidosis affect the progression of severe COVID19 at various physiological levels such as organs, tissues, and cells. The physiological effects of acidosis and hypoxia range from the level of compensatory capabilities of the whole organism to the functioning of a single hemoglobin molecule. In our work, we consider several mechanisms that link the damaging factors of COVID19 with acidosis. These mechanisms reveal stepbystep processes with a pronounced positive feedback. In accordance with the well known Bohr effect, a decrease in blood pH leads to a drop in blood oxygen saturation. At the same time, this drop in saturation contributes to the further development of acidosis. This indicates a depletion of the body's compensatory capabilities to regulate acidosis and leads to deterioration of the patient's condition. In addition, a decrease in pH can cause conformational changes in the viral Sprotein, followed by changes in ability of some antibodies to recognize the virus. This might lead to the decrease in antibodies affinity and avidity, negatively affecting virus clearance. Low levels of pH and hypoxia in blood and tissues can induce a proinflammatory innate response even in the absence of antigen stimulation. Therefore, hypoxia and acidosis can lead to a restructuring of the immune system and multidirectional pro and antiinflammatory responses, which often, instead of recovery, lead to the disease aggravation.

WOS
Держатели документа:
Russian Acad Sci, Engelhardt Inst Mol Biol, Moscow, Russia.
Voyno Yasenetsky Krasnoyarsk State Med Univ, Krasnoyarsk, Russia.
Russian Acad Sci, Siberian Branch, Inst Biophys, Krasnoyarsk, Russia.
Voronezh State Univ, Voronezh, Russia.
Lomonosov Moscow State Univ, Fac Phys, 1-2 Leninskie Gory, Moscow 119991, Russia.
Russian Acad Sci, Inst Analyt Instrumentat, Moscow, Russia.
Sendai Viralyt LLC, Acton, MA USA.

Доп.точки доступа:
Lagutkin, D.; Semyonov, D.; Yegorov, Y. E.; Lavrinenko, I.; Generalov, E.; Zaitceva, A. Y.; Matveeva, O.; Nechipurenko, Y. D.

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