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Article ; Online: Spatial structure favors microbial coexistence except when slower mediator diffusion weakens interactions.

Lobanov, Alexander / Dyckman, Samantha / Kurkjian, Helen / Momeni, Babak

2023 Volume 12

Abstract: Microbes often exist in spatially structured environments and many of their interactions are mediated through diffusible metabolites. How does such a context affect microbial coexistence? To address this question, we use a model in which the spatial ... ...

Abstract	Microbes often exist in spatially structured environments and many of their interactions are mediated through diffusible metabolites. How does such a context affect microbial coexistence? To address this question, we use a model in which the spatial distributions of species and diffusible interaction mediators are explicitly included. We simulate the enrichment process, examining how microbial species spatially reorganize and how eventually a subset of them coexist. In our model, we find that slower motility of cells promotes coexistence by allowing species to co-localize with their facilitators and avoid their inhibitors. We additionally find that a spatially structured environment is more influential when species mostly facilitate each other, rather than when they are mostly competing. More coexistence is observed when species produce many mediators and consume some (not many or few) mediators, and when overall consumption and production rates are balanced. Interestingly, coexistence appears to be disfavored when mediators are diffusing slowly because that leads to weaker interaction strengths. Overall, our results offer new insights into how production, consumption, motility, and diffusion intersect to determine microbial coexistence in a spatially structured environment.
MeSH term(s)	Models, Biological ; Ecosystem ; Microbial Interactions
Language	English
Publishing date	2023-06-23
Publishing country	England
Document type	Journal Article
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.82504
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Article ; Online: Reply to Wang et al., "Assessment of the Abundance and Potential Function of Human Papillomavirus Type 16 Circular E7 RNA".

Yu, Lulu / Lobanov, Alexei / Zheng, Zhi-Ming

mBio

2022 Volume 13, Issue 3, Page(s) e0075822

MeSH term(s)	Human papillomavirus 16/genetics ; Humans ; Papillomavirus Infections ; RNA, Circular
Chemical Substances	RNA, Circular
Language	English
Publishing date	2022-05-17
Publishing country	United States
Document type	Research Support, N.I.H., Intramural ; Letter ; Comment
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mbio.00758-22
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Article ; Online: A combined pH and temperature precipitation step facilitates the purification of tobacco-derived recombinant proteins that are sensitive to extremes of either parameter

Opdensteinen, P. / Lobanov, A. / Buyel, J.F.

2021

Abstract: Art. 2000340, 10 S. ... Incubation at pH 4.0 or blanching at ∼65°C facilitates the purification of biopharmaceutical proteins from plants by precipitating most of the host cell proteins (HCPs) before chromatography. However, both methods are compatible ... ...

Abstract	Art. 2000340, 10 S. Incubation at pH 4.0 or blanching at ∼65°C facilitates the purification of biopharmaceutical proteins from plants by precipitating most of the host cell proteins (HCPs) before chromatography. However, both methods are compatible only with pH or thermostable target proteins whereas many target proteins may irreversibly denature, e.g., at pH < 4.0. Here, we developed a combined pH/temperature treatment for clarified tobacco extracts and intact leaves. The latter were subjected to a blanching procedure, i.e., the submersion into a hot buffer. Using a design of experiments approach we identified conditions that remove ∼70% of HCPs at ∼55°C, using the thermosensitive antibody 2G12 and the pH-sensitive DsRed as model proteins. We found that pH and temperature exerted a combined effect during the precipitation of HCPs in the pH range 5.0-7.0 at 35°C-60°C. For clarified extracts, the temperature required to achieve a DsRed purity threshold of 20% total soluble protein (TSP) increased from 54°C to 63°C when the pH was increased from 6.4 to 7.3. The pH-stable antibody 2G12 was less responsive to the combined treatment, but the purity of 1% TSP was achieved at 35°C instead of 44°C when the pH was reduced from 6.3 to 5.8. When blanching intact leaves, product losses were not exacerbated at pH 4.0. Indeed, the highest DsRed purity (58% TSP) was achieved at this pH, combined with a temperature of 60°C and an incubation time of 30 min. In contrast, the highest 2G12 purity (0.7% TSP) was achieved at pH 5.1 and 40°C with an incubation time of 20 min. Our data suggest that a combined pH/temperature regime can avoid extreme values of either parameter; therefore, broadening the applicability of these simple purification techniques to other recombinant proteins. 16 Nr.4
Keywords	540 ; 660 ; 571 ; 572
Subject code	580
Language	English
Publishing country	de
Document type	Article ; Online
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Article ; Online: Two-parameter landscape of transport efficiency in mesoscopic networks: transitions from the Braess to normal regimes without a congestion relaxation.

Lobanov, A D / Lobanova, A D / Pupasov-Maksimov, A M

Journal of physics. Condensed matter : an Institute of Physics journal

2022 Volume 34, Issue 32

Abstract: This paper deals with the Braess paradox in quantum transport. The scattering matrix formalism is used to consider a two-parameter family of mesoscopic conductors with the topology of the classical Braess transport network. The study investigates the ... ...

Abstract	This paper deals with the Braess paradox in quantum transport. The scattering matrix formalism is used to consider a two-parameter family of mesoscopic conductors with the topology of the classical Braess transport network. The study investigates the mutual influence of the congestion and smoothness of the system on the Braess behavior. Both the Braess paradox and normal transport regimes coexist within the two-parametric landscape under the same congestion.
Language	English
Publishing date	2022-06-14
Publishing country	England
Document type	Journal Article
ZDB-ID	1472968-4
ISSN	1361-648X ; 0953-8984
ISSN (online)	1361-648X
ISSN	0953-8984
DOI	10.1088/1361-648X/ac6472
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Article ; Online: Reusable Single Cell for Iterative Epigenomic Analyses.

Ohnuki, Hidetaka / Venzon, David J / Lobanov, Alexei / Tosato, Giovanna

Journal of visualized experiments : JoVE

2022 , Issue 180

Abstract: Current single-cell epigenome analyses are designed for single use. The cell is discarded after a single use, preventing analysis of multiple epigenetic marks in a single cell and requiring data from other cells to distinguish signal from experimental ... ...

Abstract	Current single-cell epigenome analyses are designed for single use. The cell is discarded after a single use, preventing analysis of multiple epigenetic marks in a single cell and requiring data from other cells to distinguish signal from experimental background noise in a single cell. This paper describes a method to reuse the same single cell for iterative epigenomic analyses. In this experimental method, cellular proteins are first anchored to a polyacrylamide polymer instead of crosslinking them to protein and DNA, alleviating structural bias. This critical step allows repeated experiments with the same single cell. Next, a random primer with a scaffold sequence for proximity ligation is annealed to the genomic DNA, and the genomic sequence is added to the primer by extension using a DNA polymerase. Subsequently, an antibody against an epigenetic marker and control IgG, each labeled with different DNA probes, are bound to the respective targets in the same single cell. Proximity ligation is induced between the random primer and the antibody by adding a connector DNA with complementary sequences to the scaffold sequence of the random primer and the antibody-DNA probe. This approach integrates antibody information and nearby genome sequences in a single DNA product of proximity ligation. By enabling repeated experiments with the same single cell, this method allows an increase in data density from a rare cell and statistical analysis using only IgG and antibody data from the same cell. The reusable single cells prepared by this method can be stored for at least a few months and reused later to broaden epigenetic characterization and increase data density. This method provides flexibility to researchers and their projects.
MeSH term(s)	DNA/genetics ; DNA Probes ; DNA-Directed DNA Polymerase/genetics ; Epigenome ; Epigenomics/methods
Chemical Substances	DNA Probes ; DNA (9007-49-2) ; DNA-Directed DNA Polymerase (EC 2.7.7.7)
Language	English
Publishing date	2022-02-11
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural ; Video-Audio Media
ZDB-ID	2259946-0
ISSN	1940-087X ; 1940-087X
ISSN (online)	1940-087X
ISSN	1940-087X
DOI	10.3791/63456
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Article ; Online: A combined pH and temperature precipitation step facilitates the purification of tobacco-derived recombinant proteins that are sensitive to extremes of either parameter.

Opdensteinen, Patrick / Lobanov, Aleksandr / Buyel, Johannes Felix

Biotechnology journal

2021 Volume 16, Issue 4, Page(s) e2000340

Abstract: Incubation at pH 4.0 or blanching at ∼65°C facilitates the purification of biopharmaceutical proteins from plants by precipitating most of the host cell proteins (HCPs) before chromatography. However, both methods are compatible only with pH or ... ...

Abstract	Incubation at pH 4.0 or blanching at ∼65°C facilitates the purification of biopharmaceutical proteins from plants by precipitating most of the host cell proteins (HCPs) before chromatography. However, both methods are compatible only with pH or thermostable target proteins whereas many target proteins may irreversibly denature, e.g., at pH < 4.0. Here, we developed a combined pH/temperature treatment for clarified tobacco extracts and intact leaves. The latter were subjected to a blanching procedure, i.e., the submersion into a hot buffer. Using a design of experiments approach we identified conditions that remove ∼70% of HCPs at ∼55°C, using the thermosensitive antibody 2G12 and the pH-sensitive DsRed as model proteins. We found that pH and temperature exerted a combined effect during the precipitation of HCPs in the pH range 5.0-7.0 at 35°C-60°C. For clarified extracts, the temperature required to achieve a DsRed purity threshold of 20% total soluble protein (TSP) increased from 54°C to 63°C when the pH was increased from 6.4 to 7.3. The pH-stable antibody 2G12 was less responsive to the combined treatment, but the purity of 1% TSP was achieved at 35°C instead of 44°C when the pH was reduced from 6.3 to 5.8. When blanching intact leaves, product losses were not exacerbated at pH 4.0. Indeed, the highest DsRed purity (58% TSP) was achieved at this pH, combined with a temperature of 60°C and an incubation time of 30 min. In contrast, the highest 2G12 purity (0.7% TSP) was achieved at pH 5.1 and 40°C with an incubation time of 20 min. Our data suggest that a combined pH/temperature regime can avoid extreme values of either parameter; therefore, broadening the applicability of these simple purification techniques to other recombinant proteins.
MeSH term(s)	Hydrogen-Ion Concentration ; Plant Leaves ; Recombinant Proteins/genetics ; Temperature ; Nicotiana
Chemical Substances	Recombinant Proteins
Language	English
Publishing date	2021-01-25
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2221885-3
ISSN	1860-7314 ; 1860-6768
ISSN (online)	1860-7314
ISSN	1860-6768
DOI	10.1002/biot.202000340
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Article: Kinetics and Mechanism of Epinephrine Autoxidation in the Presence of Plant Superoxide Inhibitors: A New Look at the Methodology of Using a Model System in Biological and Chemical Research.

Volkov, Vladimir / Lobanov, Anton / Voronkov, Mikhail / Baygildiev, Timur / Misin, Vyacheslav / Tsivileva, Olga

Antioxidants (Basel, Switzerland)

2023 Volume 12, Issue 8

Abstract: Superoxide is the primary active oxygen form produced in living organisms. Because of superoxide anion radical formation during epinephrine oxidation in alkaline medium, this system is offered in some works for antioxidant activity analysis, however, ... ...

Abstract	Superoxide is the primary active oxygen form produced in living organisms. Because of superoxide anion radical formation during epinephrine oxidation in alkaline medium, this system is offered in some works for antioxidant activity analysis, however, without enough physicochemical justification. Therefore, the task of developing reliable methods for analyzing the superoxide inhibition activity of various objects is very urgent. In this work, a kinetic model of epinephrine autoxidation in an alkaline medium in the presence of antioxidants of plant origin is proposed. The participation of chain reactions with long oxidation chains in this process is revealed. The limiting stage of the process is a one-electron reduction of oxygen by the anionic forms of the phenolic hydroxyls of epinephrine. The appearance of the absorption maximum at a wavelength of 347 nm during epinephrine autoxidation is associated with adrenolutin formation, which is confirmed by HPLC/UV/MS. No adduct formation between phenolic antioxidants and epinephrine oxidation products was found. The complex U-shaped character of epinephrine autoxidation rate dependence on the content of antioxidants in the reaction system was shown. The study of the kinetics of epinephrine autoxidation in the presence of an individual phenolic plant superoxide inhibitor, chlorogenic acid, was carried out for the first time. The inhibitory effect of yarrow, chamomile, and bur beggar-ticks plant extracts in the adrenaline system was examined.
Language	English
Publishing date	2023-07-30
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2704216-9
ISSN	2076-3921
ISSN	2076-3921
DOI	10.3390/antiox12081530
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Article: KSHV promotes oncogenic FOS to inhibit nuclease AEN and transactivate RGS2 for AKT phosphorylation.

Majerciak, Vladimir / Alvarado-Hernandez, Beatriz / Ma, Yanping / Duduskar, Shivalee / Lobanov, Alexei / Cam, Maggie / Zheng, Zhi-Ming

bioRxiv : the preprint server for biology

2024

Abstract: Kaposi's sarcoma-associated herpesvirus (KSHV) ORF57 is a lytic RNA-binding protein. We applied BCBL-1 cells in lytic KSHV infection and performed UV cross-linking immunoprecipitation (CLIP) followed by RNA-seq of the CLIPed RNA fragments (CLIP-seq). We ... ...

Abstract	Kaposi's sarcoma-associated herpesvirus (KSHV) ORF57 is a lytic RNA-binding protein. We applied BCBL-1 cells in lytic KSHV infection and performed UV cross-linking immunoprecipitation (CLIP) followed by RNA-seq of the CLIPed RNA fragments (CLIP-seq). We identified ORF57-bound transcripts from 544 host protein-coding genes. By comparing with the RNA-seq profiles from BCBL-1 cells with latent and lytic KSHV infection and from HEK293T cells with and without ORF57 expression, we identified FOS and CITED2 RNAs being two common ORF57-specific RNA targets. FOS dimerizes with JUN as a transcription factor AP-1 involved in cell proliferation, differentiation, and transformation. Knockout of the ORF57 gene from the KSHV genome led BAC16-iSLK cells incapable of FOS expression in KSHV lytic infection. The dysfunctional KSHV genome in FOS expression could be rescued by Lenti-ORF57 virus infection. ORF57 protein does not regulate FOS translation but binds to the 13-nt RNA motif near the FOS RNA 5' end and prolongs FOS mRNA half-life 7.7 times longer than it is in the absence of ORF57. This binding of ORF57 to FOS RNA is competitive to the binding of a host nuclease AEN (also referred to as ISG20L1). KSHV infection inhibits the expression of AEN, but not exosomal RNA helicase MTR4. FOS expression mediated by ORF57 inhibits
Language	English
Publishing date	2024-01-28
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.01.27.577582
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Book ; Online: Predicting Tags For Programming Tasks by Combining Textual And Source Code Data

Lobanov, Artyom / Bogomolov, Egor / Golubev, Yaroslav / Mirzayanov, Mikhail / Bryksin, Timofey

2023

Abstract: Competitive programming remains a very popular activity that combines both software engineering and education. In order to prepare and to practice, contestants use extensive archives of problems from past contents available on various competitive ... ...

Abstract	Competitive programming remains a very popular activity that combines both software engineering and education. In order to prepare and to practice, contestants use extensive archives of problems from past contents available on various competitive programming platforms. One way to make this process more effective is to provide an automatic tag system for the tasks. Prior works do that by either using the tasks' problem statements or the code of their solutions. In this study, we investigate which information source is more valuable for tag prediction. To answer that question, we compare existing approaches of both types on the same dataset and with the same set of tags. Then, we propose a novel approach, which is an ensemble of the Gated Graph Neural Network model for analyzing solutions and the Bidirectional Encoder Representations from Transformers model for processing statements. Our experiments show that our approach outperforms previously proposed models by 0.175 of the PR-AUC metric. Comment: The work was carried out at the end of 2020. 7 pages, 2 figures
Keywords	Computer Science - Software Engineering
Subject code	006
Publishing date	2023-01-11
Publishing country	us
Document type	Book ; Online
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Article ; Online: Effect of the Hemin Molecular Complexes on the Structure and Properties of the Composite Electrospun Materials Based on Poly(3-hydroxybutyrate).

Tyubaeva, Polina / Varyan, Ivetta / Lobanov, Anton / Olkhov, Anatoly / Popov, Anatoly

Polymers

2021 Volume 13, Issue 22

Abstract: The creation of innovative fibrous materials based on biodegradable semicrystalline polymers and modifying additives is an urgent scientific problem. In particular, the development of biomedical materials based on molecular complexes and biopolymers with ...

Abstract	The creation of innovative fibrous materials based on biodegradable semicrystalline polymers and modifying additives is an urgent scientific problem. In particular, the development of biomedical materials based on molecular complexes and biopolymers with controlled properties is of great interest. The paper suggests an approach to modifying the structure and properties of the composite materials based on poly(3-hydroxybutyrate) (PHB) obtained by the electrospinning method using molecular complexes of hemin. The introduction of 1-5 wt. % of hemin has a significant effect on the supramolecular structure, morphology and properties of PHB-based fibers. Changes in the supramolecular structure intensified with the increasing hemin concentration. On the one hand, a decrease in the fraction of the crystalline phase by 8-10% was observed. At the same time, there is a decrease in the density of the amorphous phase by 15-70%. Moreover, the addition of hemin leads to an improvement in the strength characteristics of the material: the elongation at break increased by 1.5 times, and in the tensile strength, it increased by 3 times. The antimicrobial activity of the hemin-containing composite materials against
Language	English
Publishing date	2021-11-21
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527146-5
ISSN	2073-4360 ; 2073-4360
ISSN (online)	2073-4360
ISSN	2073-4360
DOI	10.3390/polym13224024
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