Vadim Fomin

Mr. Vadim Fomin

Moscow Institute of Physics and Technology
orcid

Research Focus & Metrics

Academic Career Length

6Years (2021-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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23 May 2021 in Biosensors
Verified
Journal Article
Open access
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SBSergey Vladimirovich Bazhenov
Sergey Vladimirovich Bazhenov
UNUliana Novoyatlova
Uliana Novoyatlova
ESEkaterina Scheglova
Ekaterina Scheglova
VFVadim Fomin
Vadim Fomin
SKSvetlana Khrulnova
Svetlana Khrulnova
IMIlya Vladimirovich Manukhov
Ilya Vladimirovich Manukhov
Aliivibrio fischeri LuxR and Aliivibrio logei LuxR1 and LuxR2 regulatory proteins are quorum sensing transcriptional (QS) activators, inducing promoters of luxICDABEG genes in the presence of an autoinducer (3-oxo-hexanoyl-l-homoserine lactone). In the Aliivibrio cells, luxR genes are regulated by HNS, CRP, LitR, etc. Here we investigated the role of the luxR expression level in LuxI/R QS system functionality and improved the whole-cell biosensor for autoinducer detection. Escherichia coli-based bacterial lux-biosensors were used, in which Photorhabdus luminescensluxCDABE genes were controlled by LuxR-dependent promoters and luxR, luxR1, or luxR2 regulatory genes. We varied either the dosage of the regulatory gene in the cells using additional plasmids, or the level of the regulatory gene expression using the lactose operon promoter. It was shown that an increase in expression level, as well as dosage of the regulatory gene in biosensor cells, leads to an increase in sensitivity (the threshold concentration of AI is reduced by one order of magnitude) and to a two to threefold reduction in response time. The best parameters were obtained for a biosensor with an increased dosage of luxRA. fischeri (sensitivity to 3-oxo-hexanoyl-l-homoserine lactone reached 30–100 pM).

6 August 2024 in Biology
Verified
Journal Article
Open access
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RERahaf Al Ebrahim
Rahaf Al Ebrahim
MAMaria G. Alekseeva
Maria G. Alekseeva
SBSergey Vladimirovich Bazhenov
Sergey Vladimirovich Bazhenov
VFVadim Fomin
Vadim Fomin
DMDilara Mavletova
Dilara Mavletova
IMIlya Vladimirovich Manukhov
Ilya Vladimirovich Manukhov
The L. fermentum U-21 strain, known for secreting chaperones into the extracellular milieu, emerges as a promising candidate for the development of novel therapeutics termed disaggregases for Parkinson’s disease. Our study focuses on characterizing the secreted protein encoded by the C0965_000195 locus in the genome of this strain. Through sequence analysis and structural predictions, the protein encoded by C0965_000195 is identified as ClpL, homologs of which are known for their chaperone functions. The chaperone activity of ClpL from L. fermentum U-21 is investigated in vivo by assessing the refolding of luciferases with varying thermostabilities from Aliivibrio fischeri and Photorhabdus luminescens within Escherichia coli cells. The results indicate that the clpL gene from L. fermentum U-21 can compensate for the absence of the clpB gene, enhancing the refolding capacity of thermodenatured proteins in clpB-deficient cells. In vitro experiments demonstrate that both spent culture medium containing proteins secreted by L. fermentum U-21 cells, including ClpL, and purified heterologically expressed ClpL partially prevent the thermodenaturation of luciferases. The findings suggest that the ClpL protein from L. fermentum U-21, exhibiting disaggregase properties against aggregating proteins, may represent a key component contributing to the pharmabiotic attributes of this strain.

11 March 2023 in Heliyon
Verified
Journal Article
Open access
VFVadim Fomin
Vadim Fomin
SBS.V. Bazhenov
S.V. Bazhenov
OKO.V. Kononchuk
O.V. Kononchuk
VMV.O. Matveeva
V.O. Matveeva
AZA.P. Zarubina
A.P. Zarubina
IMIlya Vladimirovich Manukhov
Ilya Vladimirovich Manukhov
For decades, transcription of Photorhabdus luminescens lux-operon was considered being constitutive. Therefore, this lux-operon has been used for measurements in non-specific bacterial luminescent biosensors. Here, the expression of Photorhabdus lux-operon under high temperature was studied. The expression was researched in the natural strain Photorhabdus temperata and in the heterologous system of Escherichia coli. P. temperata FV2201 bacterium was isolated from soil in the Moscow region (growth optimum 28 °C). We showed that its luminescence significantly increases when the temperature rises to 34 °C. The increase in luminescence is associated with an increase in the transcription of luxCDABE genes, which was confirmed by RT-PCR. The promoter of the lux-operon of the related bacterium P. luminescens ZM1 from the forests of Moldova, being cloned in the heterologous system of E. coli, is activated when the temperature rises from room temperature to 42 °C. When heat shock is caused by ethanol addition, transcription of lux-operon increases only in the natural strain of P. temperata, but not in the heterologous system of E. coli cells. In addition, the activation of the lux-operon of P. luminescens persists in E. coli strains deficient in both the rpoH and rpoE genes. These results indicate the presence of sigma 32 and sigma 24 independent heat-shock-like mechanism of regulation of the lux-operon of P. luminescens in the heterologous E. coli system.

5 September 2024 in Biosensors
Verified
Journal Article
Open access
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UNUliana Novoyatlova
Uliana Novoyatlova
AKAnna Kudryavtseva
Anna Kudryavtseva
SBSergey Vladimirovich Bazhenov
Sergey Vladimirovich Bazhenov
AUAnna A. Utkina
Anna A. Utkina
VFVadim Fomin
Vadim Fomin
IMIlya Vladimirovich Manukhov
Ilya Vladimirovich Manukhov
The ability of aquatic mesofauna representatives involved in trophic chains to sorb and accumulate toxicants is important for understanding the functioning of aquatic ecosystems and for fishing industry. This study investigated the capacity of marine amphipod Gammarus oceanicus and freshwater amphipods Eulimnogammarus vittatus and Gammarus lacustris to absorb the DNA-alkylating agent methyl methanesulfonate (MMS). The presence of alkylating agents in the environment and in the tissues of the amphipods was determined using whole-cell lux-biosensor Escherichia coli MG1655 pAlkA-lux, in which the luxCDABE genes from Photorhabdus luminescens, enabling the luminescence of the cell culture, are controlled by the PalkA promoter of DNA glycosylase. It was shown that within one day of incubation in water containing MMS at a concentration above 10 μM, the amphipods absorbed the toxicant and their tissues produce more alkylation damage to biosensor cells than the surrounding water. Concentrations of MMS above 1 mM in the environment caused the death of the amphipods before the toxicant could be significantly concentrated in their tissues. The sensitivity and the capacity to absorb MMS were found to be approximately the same for the marine amphipod G. oceanicus and the freshwater amphipods E. vittatus and G. lacustris.

27 May 2024 in Preprints.org
Verified
Preprint
Open access
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RERahaf Al Ebrahim
Rahaf Al Ebrahim
MAMaria G. Alekseeva
Maria G. Alekseeva
SBSergey Vladimirovich Bazhenov
Sergey Vladimirovich Bazhenov
VFVadim Fomin
Vadim Fomin
DMDilara Mavletova
Dilara Mavletova
IMIlya Vladimirovich Manukhov
Ilya Vladimirovich Manukhov
Strain L. fermentum U-21 secretes chaperones into the medium and it is considered as the candidate for the development of drugs, so-called disaggregases, for Parkinson’s disease therapy. This study is devoted to characterization of secreted protein encoded by C0965_000195 locus. Analysis of sequence and predicted structure of the protein encoded by C0965_000195 allows us to attribute it to the ClpL, homologs of which are known to be chaperones. The chaperone activity of ClpL L. fermentum U-21 was evaluated in vivo by refolding of differing in thermostability luciferases from Aliivibrio fischeri and Photorhabdus luminescens in Escherichia coli cells. It was observed that clpL from L. fermentum U-21 can compensate for the deficiency in the clpB gene and enhance the ability to refold thermodenatured proteins in clpB- cells. In vitro experiments have demonstrated the ability of a spent culture medium containing proteins secreted by L. fermentum U-21 cells, including ClpL, to prevent thermodenaturation of luciferases partially.We suggest that the ClpL protein from L. fermentum U-21 strain, which exhibits disaggregase properties against aggregating proteins, may be one of the clue components that play a role in the pharmabiotic properties of this strain.

21 April 2025 in Journal of Basic Microbiology
Verified
Journal Article
Closed access
VMValeriia Olegovna Matveeva
Valeriia Olegovna Matveeva
AGAnna Dmitrievna Grebennikova
Anna Dmitrievna Grebennikova
DSDaniil Igorevich Sakharov
Daniil Igorevich Sakharov
VFVadim Fomin
Vadim Fomin
IMIlya Vladimirovich Manukhov
Ilya Vladimirovich Manukhov
SBSergey Vladimirovich Bazhenov
Sergey Vladimirovich Bazhenov