Alexander Ivanov - Academia.edu (original) (raw)

Papers by Alexander Ivanov

Photosynthesis research, Jan 3, 2018

The high-light-induced alterations in photosynthetic performance of photosystem II (PSII) and pho... more The high-light-induced alterations in photosynthetic performance of photosystem II (PSII) and photosystem I (PSI) as well as effectiveness of dissipation of excessive absorbed light during illumination for different periods of time at room (22 °C) and low (8-10 °C) temperature of leaves of Arabidopsis thaliana, wt and lut2, were followed with the aim of unraveling the role of lutein in the process of photoinhibition. Photosynthetic parameters of PSII and PSI were determined on whole leaves by PAM fluorometer and oxygen evolving activity-by a Clark-type electrode. In thylakoid membranes, isolated from non-illuminated and illuminated for 4.5 h leaves of wt and lut2 the photochemical activity of PSII and PSI and energy interaction between the main pigment-protein complexes was determined. Results indicate that in non-illuminated leaves of lut2 the maximum rate of oxygen evolution and energy utilization in PSII is lower, excitation pressure of PSII is higher and cyclic electron transpor...

ACS central science, Jan 27, 2018

Fundamental understanding of the selective recognition and separation of -block metal ions by che... more Fundamental understanding of the selective recognition and separation of -block metal ions by chelating agents is of crucial importance for advancing sustainable energy systems. Current investigations in this area are mostly focused on the study of inner-sphere interactions between metal ions and donor groups of ligands, while the effects on the selectivity resulting from molecular interactions in the outer-sphere region have been largely overlooked. Herein, we explore the fundamental origins of the selectivity of the solvating extractant ,,','-tetraoctyl diglycolamide (TODGA) for adjacent lanthanides in a liquid-liquid extraction system, which is of relevance to nuclear fuel reprocessing and rare-earth refining technologies. Complementary investigations integrating distribution studies, quantum mechanical calculations, and classical molecular dynamics simulations establish a relationship between coextracted water and lanthanide extraction by TODGA across the series, pointin...

Inorganic chemistry, Jan 5, 2018

The novel metal chelator N-2-(pyridylmethyl)diethylenetriamine-N,N',N″,N″-tetraacetic acid (D... more The novel metal chelator N-2-(pyridylmethyl)diethylenetriamine-N,N',N″,N″-tetraacetic acid (DTTA-PyM) was designed to replace a single oxygen-donor acetate group of the well-known aminopolycarboxylate complexant diethylenetriamine-N,N,N',N″,N″-pentaacetic acid (DTPA) with a nitrogen-donor 2-pyridylmethyl. Potentiometric, spectroscopic, computational, and radioisotope distribution methods show distinct differences for the 4f and 5f coordination environments and enhanced actinide binding due to the nitrogen-bearing heterocyclic moiety. The Am, Cm, and Lncomplexation studies for DTTA-PyM reveal an enhanced preference, relative to DTPA, for trivalent actinide binding. Fluorescence studies indicate no changes to the octadentate coordination of trivalent curium, while evidence of heptadentate complexation of trivalent europium is found in mixtures containing EuHLcomplexes at the same aqueous acidity. The denticity change observed for Eusuggests that complex protonation occurs on t...

PloS one, 2018

Hypermethylation is observed in the promoter regions of suppressor genes in the tumor cancer cell... more Hypermethylation is observed in the promoter regions of suppressor genes in the tumor cancer cells. Reactivation of these genes by demethylation of their promoters is a prospective strategy of the anticancer therapy. Previous experiments have shown that symmetric dimeric bisbenzimidazoles DBP(n) are able to block DNA methyltransferase activities. It was also found that DBP(n) produces a moderate effect on the activation of total gene expression in HeLa-TI population containing epigenetically repressed avian sarcoma genome. It is shown that DBP(n) are able to penetrate the cellular membranes and accumulate in breast carcinoma cell MCF-7, mainly in the mitochondria and in the nucleus, excluding the nucleolus. The DBP(n) are non-toxic to the cells and have a weak overall demethylation effect on genomic DNA. DBP(n) demethylate the promoter regions of the tumor suppressor genes PTEN and RARB. DBP(n) promotes expression of the genes RARB, PTEN, CDKN2A, RUNX3, Apaf-1 and APC "silent&q...

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Plant, cell & environment, Jan 7, 2018

High latitude forests will experience large changes in temperature and COconcentrations this cent... more High latitude forests will experience large changes in temperature and COconcentrations this century. We evaluated the effects of future climate conditions on two dominant boreal tree species, Pinus sylvestris L. and Picea abies (L.) H. Karst, exposing seedlings to three seasons of ambient (430 ppm) or elevated CO(750 ppm) and ambient temperatures, a +4 °C warming, or a +8 °C warming. Pinus sylvestris responded positively to warming: seedlings developed a larger canopy, maintained high net COassimilation rates (A) and acclimated dark respiration (R). In contrast, carbon fluxes in Picea abies were negatively impacted by warming: maximum rates of Adecreased, electron transport was redirected to alternative electron acceptors, and thermal acclimation of Rwas weak. Elevated COtended to exacerbate these effects in warm-grown Picea abies, and by the end of the experiment Picea abies from the +8 °C, high COtreatment produced fewer buds than they had three years earlier. Treatments had litt...

Microbiological research, 2018

DNA sequence-specific fluorescent dimeric bisbenzimidazoles DBP(n) and DBPA(n), noncovalently int... more DNA sequence-specific fluorescent dimeric bisbenzimidazoles DBP(n) and DBPA(n), noncovalently interacting with A-T pairs in the minor groove of double-stranded DNA were used for studying and monitoring the expression of histone-like H-NS-dependent promoters. Histone-like H-NS selectively binds to AT-rich segments of DNA and silences a large number of genes in bacterial chromosomes. The H-NS-dependent promoters of Quorum Sensing (QS)-regulated lux operons of the marine bacteria mesophilic Aliivibrio fischeri, psychrophilic Aliivibrio logei were used. Escherichia coli lux biosensors were constructed by cloning fragments bearing QS-regulated promoters into the vector, thereby placing each fragment upstream of the promoterless Photorhabdus luminescens luxCDABE genes. It was shown that the dimeric bisbenzimidazoles DBP(n) and DBPA(n) counteract the H-NS silencing activity. Thus, the presence of DBP(n) or DBPA(n) in the medium leads to an approximately 10-100-fold increase in the level of...

Nature chemical biology, Jan 14, 2018

Despite decades of accumulated knowledge about proteins and their post-translational modification... more Despite decades of accumulated knowledge about proteins and their post-translational modifications (PTMs), numerous questions remain regarding their molecular composition and biological function. One of the most fundamental queries is the extent to which the combinations of DNA-, RNA- and PTM-level variations explode the complexity of the human proteome. Here, we outline what we know from current databases and measurement strategies including mass spectrometry-based proteomics. In doing so, we examine prevailing notions about the number of modifications displayed on human proteins and how they combine to generate the protein diversity underlying health and disease. We frame central issues regarding determination of protein-level variation and PTMs, including some paradoxes present in the field today. We use this framework to assess existing data and to ask the question, "How many distinct primary structures of proteins (proteoforms) are created from the 20,300 human genes?&quot...

Plant biology (Stuttgart, Germany), Jan 22, 2017

The abundance of calcareous soils makes bicarbonate-induced iron (Fe) deficiency a major problem ... more The abundance of calcareous soils makes bicarbonate-induced iron (Fe) deficiency a major problem for plant growth and crop yield. Therefore, Fe-efficient plants may constitute a solution for calcareous soil use. In the present work, we investigated the ability of the forage legume Sulla carnosa (Desf.) to maintain the integrity of its photosynthetic apparatus under iron deficiency conditions. Three treatments were applied: control, direct iron deficiency and bicarbonate-induced iron deficiency. At the harvest, all organs of deficient plants showed severe growth inhibition, the effect being less pronounced under indirect iron deficiency. Pigment analysis of fully-expanded leaves revealed a reduction in the concentrations of chlorophyll a, chlorophyll b, and carotenoids under iron deficiency conditions. Electron transport rate (ETR), maximal and effective quantum yield of photosystem II (PSII), photochemical quenching (qP), non-photochemical quenching (qN) as well as P700 activity wer...

Mathematische Zeitschrift

Bulletin of Mathematical Sciences

We study a possible Majorana representation R of the alternating group A 6 of degree 6 such that ... more We study a possible Majorana representation R of the alternating group A 6 of degree 6 such that for some involutions s and t in A 6 , generating a D 6 -subgroup, the corresponding Majorana axes a s and a t generate a subalgebra of type 3C. We show that there exists at most one such representation R and that its dimension is at most 70. The representation R does not correspond to a subalgebra in the Monster algebra generated by a subset of the Majorana axes canonically indexed by the involutions of an A 6 -subgroup in the Monster.

Fibre Chemistry

Ways of finding the relative error of spectral measurements as a function of the methods of photo... more Ways of finding the relative error of spectral measurements as a function of the methods of photometric evaluation are examined. The errors of measurements in estimating the orientation factor with the dichroism and ratio of optical densities in analytical bands and bands of the internal standard in the spectra of fibreforming compounds are found.

Talanta, 2017

Actinium-225 is a potential Targeted Alpha Therapy (TAT) isotope. It can be generated with high e... more Actinium-225 is a potential Targeted Alpha Therapy (TAT) isotope. It can be generated with high energy (≥ 100MeV) proton irradiation of thorium targets. The main challenge in the chemical recovery of (225)Ac lies in the separation from thorium and many fission by-products most importantly radiolanthanides. We recently developed a separation strategy based on a combination of cation exchange and extraction chromatography to isolate and purify (225)Ac. In this study, actinium and lanthanide equilibrium distribution coefficients and column elution behavior for both TODGA (N,N,N',N'-tetra-n-octyldiglycolamide) and TEHDGA (N,N,N',N'-tetrakis-2-ethylhexyldiglycolamide) were determined. Density functional theory (DFT) calculations were performed and were in agreement with experimental observations providing the foundation for understanding of the selectivity for Ac and lanthanides on different DGA (diglycolamide) based resins. The results of Gibbs energy (ΔGaq) calculations...

Journal of proteome research, Jul 4, 2017

Cannabinoid 2 receptor (CB2R), a Class A G-protein coupled receptor (GPCR), is a promising drug t... more Cannabinoid 2 receptor (CB2R), a Class A G-protein coupled receptor (GPCR), is a promising drug target in a wide array of pathological conditions. Rational drug design has been hindered due to our poor understanding of the structural features involved in ligand binding. Binding of a high-affinity biarylpyrazole inverse agonist AM1336 to a library of the human CB2 receptor (hCB2R) cysteine-substituted mutants provided indirect evidence that two cysteines in transmembrane helix-7 (H7) were critical for the covalent attachment. Here, we used proteomics analysis of the hCB2R with bound AM1336 to directly identify peptides with covalently attached ligand and applied in-silico modeling for visualization of the ligand-receptor interactions. The hCB2R, with affinity tags (FlaghCB2His6), was produced in a baculovirus-insect cell expression system and purified as a functional receptor using immunoaffinity chromatography. Using mass spectrometry-based bottom-up proteomic analysis of the hCB2R-...

Inorganic chemistry, Jan 15, 2017

We report a new family of preorganized bis-lactam-1,10-phenanthroline (BLPhen) complexants that p... more We report a new family of preorganized bis-lactam-1,10-phenanthroline (BLPhen) complexants that possess both hard and soft donor atoms within a convergent cavity and show unprecedented extraction strength for the trivalent f-block metal ions. BLPhen ligands with saturated and unsaturated δ-lactam rings have notable differences in their affinity and selectivity for Am(III) over Eu(III), with the latter being the most selective mixed N,O-donor extractant of Am(III) reported to date. Saturated BLPhen was crystallized with five Ln(III) nitrates to form charge-neutral 1:1 complexes in the solid state. DFT calculations further elaborate on the variety of effects that dictate the performance of these preorganized compounds.

Photosynthesis research, Jan 8, 2017

Temperature is one of the main factors controlling the formation, development, and functional per... more Temperature is one of the main factors controlling the formation, development, and functional performance of the photosynthetic apparatus in all photoautotrophs (green plants, algae, and cyanobacteria) on Earth. The projected climate change scenarios predict increases in air temperature across Earth's biomes ranging from moderate (3-4 °C) to extreme (6-8 °C) by the year 2100 (IPCC in Climate change 2007: The physical science basis: summery for policymakers, IPCC WG1 Fourth Assessment Report 2007; Climate change 2014: Mitigation of Climate Change, IPCC WG3 Fifth Assessment Report 2014). In some areas, especially of the Northern hemisphere, even more extreme warm seasonal temperatures may occur, which possibly will cause significant negative effects on the development, growth, and yield of important agricultural crops. It is well documented that high temperatures can cause direct damages of the photosynthetic apparatus and photosystem II (PSII) is generally considered to be the pr...

Analytical chemistry, Jan 26, 2017

Host cell proteins (HCPs) are process-related impurities of biopharmaceuticals that remain at tra... more Host cell proteins (HCPs) are process-related impurities of biopharmaceuticals that remain at trace levels despite multiple stages of downstream purification. Currently, there is interest in implementing LC-MS in biopharmaceutical HCP profiling alongside conventional ELISA, because individual species can be identified and quantitated. Conventional data dependent LC-MS is hampered by the low concentration of HCP-derived peptides, which are 5-6 orders of magnitude less abundant than the biopharmaceutical-derived peptides. In this paper, we present a novel data independent acquisition (DIA)-MS workflow to identify HCP peptides using automatically combined targeted and untargeted data processing, followed by verification and quantitation using parallel reaction monitoring (PRM). Untargeted data processing with DIA-Umpire provided a means of identifying HCPs not represented in the assay library used for targeted, peptide-centric, data analysis. An IgG1 monoclonal antibody (mAb) purified ...

Inorganic chemistry, Jan 6, 2017

The subtle energetic differences underpinning adjacent lanthanide discrimination are explored wit... more The subtle energetic differences underpinning adjacent lanthanide discrimination are explored with diglycolamide ligands. Our approach converges liquid-liquid extraction experiments with solution-phase X-ray absorption spectroscopy (XAS) and density functional theory (DFT) simulations, spanning the lanthanide series. The homoleptic [(DGA)3Ln](3+) complex was confirmed in the organic extractive solution by XAS, and this was modeled using DFT. An interplay between steric strain and coordination energies apparently gives rise to a nonlinear trend in discriminatory lanthanide ion complexation across the series. Our results highlight the importance of optimizing chelate molecular geometry to account for both coordination interactions and strain energies when designing new ligands for efficient adjacent lanthanide separation for rare-earth refining.

Inorganic chemistry, Jan 30, 2016

Studies of the complexation of new promising ligands with uranyl (UO2(2+)) and other seawater cat... more Studies of the complexation of new promising ligands with uranyl (UO2(2+)) and other seawater cations can aid the development of more efficient, selective, and robust sorbents for the recovery of uranium from seawater. In this work, we propose that the ligand design principles based on structural preorganization can be successfully applied to obtain a dramatic enhancement in UO2(2+) ion binding affinity and selectivity. This concept is exemplified through the investigation of the complexes of UO2(2+), VO2(+), and VO(2+) with the highly preorganized ligand 1,10-phenanthroline-2,9-dicarboxylic acid (PDA) using a combination of fluorescence and absorbance techniques, along with density functional theory (DFT) calculations. The measured stability constant value, log K1, of 16.5 for the UO2(2+)/PDA complex is very high compared to uranyl complexes with other dicarboxylic ligands. Moreover, PDA exhibits strong selectivity for uranyl over vanadium ions, since the determined stability const...

Journal of Proteome Research, 2016

Conventional TopN data-dependent acquisition (DDA) LC-MS/MS analysis identifies only a limited fr... more Conventional TopN data-dependent acquisition (DDA) LC-MS/MS analysis identifies only a limited fraction of all detectable precursors because the ion-sampling rate of contemporary mass spectrometers is insufficient to target each precursor in a complex sample. TopN DDA preferentially targets high-abundance precursors with limited sampling of low-abundance precursors and repeated analyses only marginally improve sample coverage due to redundant precursor sampling. In this work, advanced precursor ion selection algorithms were developed and applied in the bottom-up analysis of HeLa cell lysate to overcome the above deficiencies. Precursors fragmented in previous runs were efficiently excluded using an automatically aligned exclusion list, which reduced overlap of identified peptides to ∼10% between replicates. Exclusion of previously fragmented high-abundance peptides allowed deeper probing of the HeLa proteome over replicate LC-MS runs, resulting in the identification of 29% more peptides beyond the saturation level achievable using conventional TopN DDA. The gain in peptide identifications using the developed approach translated to the identification of several hundred low-abundance protein groups, which were not detected by conventional TopN DDA. Exclusion of only identified peptides compared with the exclusion of all previously fragmented precursors resulted in an increase of 1000 (∼10%) additional peptide identifications over four runs, suggesting the potential for further improvement in the depth of proteomic profiling using advanced precursor ion selection algorithms.

Northern Sakhalin is a region of the intensive oil and gas transportation by oil-pipe lines. In J... more Northern Sakhalin is a region of the intensive oil and gas transportation by oil-pipe lines. In July 2, 1997, the oil spill has happened at the oil-pipe line 'Okha-Komsomolsk-on- Amur.' Oil pollution spread over the basin of Tengi Rive (Amur estuary). The Tengi River is a spawning area for endemic and important commercial fish. There is a reserve on the