Doctor of Philosophy

dissertationThe multivesicular body (MVB) is a late endosomal compartment containing intralumenal vesicles enriched with a subset of transmembrane cargoes that form as a result of the inward budding of the endosomal limiting membrane. In Sacchoromyces cerevisiae ESCRT (endosomal sorting complexes required for transport) machinery, consisting of distinct protein complexes ESCRT-0, I, II and III, together with the AAA+ (ATPases associate with the variety of cellular activities) Vps4 (vacuolar protein sorting 4) ATPase are responsible for the MVB sorting. Solubilization of ESCRTs by the active Vps4 oligomer is thought to be the final step in the biogenesis of MVB. Vps4 consists of N-terminal ESCRT-III-interacting MIT (microtubule interaction and trafficking) domain, C-terminal nucleotide ATPase domain and the linker region that connects them. Function of the Vps4 is regulated through its recruitment from the cytoplasm through a complex network of interactions with ESCRT-III-associtaed proteins Did2, Ist1, Vta1 and Vps60 to the endosomeassociated ESCRT-III consisting of Vps20, Snf7, Vps2 and Vps24 where Vps4 assembles into an active oligomer. ATPase domains of Vps4 subunits promote oligomerization into closed rings and two stacked rings form an active Vps4 oligomer that contains a functionally important central cavity. Position of the MIT domains in the oligomer varies, suggesting that function of the active Vps4 oligomer might require flexibility in movement of the MIT domains. In Chapter 2, we have perfomed a detailed in vivo analysis of the interactions that mediate recruitment of Vps4 to ESCRT-III. Our data revealed a high degree of redundancy in the Vps4 interaction network. In our model, we propose that interactions with Did2 and Ist1 recruit Vps4 from cytoplasm to ESCRT-III and subsequent interaction with Vta1 promotes formation of an active Vps4 ATPase. We speculate that two rings that comprise active Vps4 oligomer have different functions - one ring is important for the ATP hydrolysis and substrate processing by Vps4, whereas the second ring is not directly involved in the ATP hydrolysis and serves a regulatory role. In Chapter 3, we have investigated if MIT domains need to be tucked away from the central cavity of the active Vps4 oligomer to allow processing of a substrate. We performed detailed functional and biochemical analysis of the serial deletions within the linker region. In our model, we propose that MIT domains are positioned around the central cavity region and cooperate together in solubilization of a substrate

Evaluating the Influence of Musical and Monetary Rewards on Decision Making through Computational Modelling

A central question in behavioural neuroscience is how different rewards modulate learning. While the role of monetary rewards is well-studied in decision-making research, the influence of abstract rewards like music remains poorly understood. This study investigated the dissociable effects of these two reward types on decision making. Forty participants completed two decision-making tasks, each characterised by probabilistic associations between stimuli and rewards, with probabilities changing over time to reflect environmental volatility. In each task, choices were reinforced either by monetary outcomes (win/lose) or by the endings of musical melodies (consonant/dissonant). We applied the Hierarchical Gaussian Filter, a validated hierarchical Bayesian framework, to model learning under these two conditions. Bayesian statistics provided evidence for similar learning patterns across both reward types, suggesting individuals’ similar adaptability. However, within the musical task, individual preferences for consonance over dissonance explained some aspects of learning. Specifically, correlation analyses indicated that participants more tolerant of dissonance behaved more stochastically in their belief-to-response mappings and were less likely to choose the response associated with the current prediction for a consonant ending, driven by higher volatility estimates. By contrast, participants averse to dissonance showed increased tonic volatility, leading to larger updates in reward tendency beliefs

Interaction of the conserved oligomeric Golgi complex with t-SNARE Syntaxin5a/Sed5 enhances intra-Golgi SNARE complex stability

Tethering factors mediate initial interaction of transport vesicles with target membranes. Soluble N-ethylmaleimide–sensitive fusion protein attachment protein receptors (SNAREs) enable consequent docking and membrane fusion. We demonstrate that the vesicle tether conserved oligomeric Golgi (COG) complex colocalizes and coimmunoprecipitates with intra-Golgi SNARE molecules. In yeast cells, the COG complex preferentially interacts with the SNARE complexes containing yeast Golgi target (t)-SNARE Sed5p. In mammalian cells, hCog4p and hCog6p interact with Syntaxin5a, the mammalian homologue of Sed5p. Moreover, fluorescence resonance energy transfer reveals an in vivo interaction between Syntaxin5a and the COG complex. Knockdown of the mammalian COG complex decreases Golgi SNARE mobility, produces an accumulation of free Syntaxin5, and decreases the steady-state levels of the intra-Golgi SNARE complex. Finally, overexpression of the hCog4p N-terminal Syntaxin5a-binding domain destabilizes intra-Golgi SNARE complexes, disrupting the Golgi. These data suggest that the COG complex orchestrates vesicular trafficking similarly in yeast and mammalian cells by binding to the t-SNARE Syntaxin5a/Sed5p and enhancing the stability of intra-Golgi SNARE complexes

Neuromodulation of choice-induced preference changes: the tDCS study of cognitive dissonance

IntroductionDifficult choices between two equally attractive options result in a cognitive discrepancy between dissonant cognitions such as preferences and actions often followed by a sense of psychological discomfort known as cognitive dissonance. It can lead to changes in the desirability of options: the chosen option becomes more desirable, whereas the rejected option is devalued. Despite the ample experimental evidence to show this effect, the neural mechanisms and timing of such choice-induced preference changes are not fully understood.MethodsIn this study, we used transcranial direct current stimulation (tDCS) to modulate the activity of the posterior medial frontal cortex (pMFC), which has been associated with conflict monitoring and choice-induced preference changes in neuroimaging studies. Prior to a revised version of Brehm’s free-choice paradigm, participants in two experiments underwent cathodal (inhibitory) or anodal (excitatory) tDCS of the pMFC compared to sham (placebo) stimulation prior to the choice phase.ResultsOur results showed that cathodal tDCS significantly decreased the choice-induced preference change relative to a sham, but only in direct comparisons of rejected options. No significant effect of anodal tDCS in comparison with sham was observed.DiscussionThis study replicates the general behavioral effect of cognitive dissonance and provide partial support for the theory of the pMFC contribution to choice-related cognitive dissonance and subsequent preference changes, with possible limitations of an under-sampling for the obtained effect size and an asymmetry in the inhibitory-excitatory effects of non-invasive tDCS

Infusion extraction and measurement on CT images based on computer vision and neural network

This paper presents a new approach to the automated detection and quantification of pulmonary emphysema and pneumoconiosis using computed tomography images. The proposed method employs computer vision and neural network algorithms to improve the accuracy and speed of lung diagnosis, as well as the monitoring of emphysema and its changes over time. The study analyzes existing approaches and demonstrates the novelty of the proposed method. The paper reports high accuracy of emphysema extraction and size measurements based on three different patient cases, as evaluated by an expert, and the successful segmentation of pneumosclerosis. The proposed method has the potential to significantly improve medical image segmentation, particularly in the detection and diagnosis of diseases such as Chronic Obstructive Pulmonary Disease (COPD) and COVID-19. The study concludes that the proposed method may also be useful in other areas of medical imaging, contributing to the ongoing effort to develop new and improved methods for medical image analysis and interpretation

Screening of proteases produced by Aspergillus micromycetes active against proteins of the hemostasis system

Background and Purpose: The primary cause of death is cardiovascular disease, hence accurate diagnosis and treatment are urgently required. For these intents, proteases are regarded as perspective agents. High substrate specificity is a need for an effective enzyme, which makes Aspergillus micromycetes—known for producing proteases with precise action—biotechnologically promising. This study's major goal was to look at the possibilities of Aspergillus species, which had never been mentioned in terms of general proteolytics. Materials and Methods: Every species was cultivated in two-stages submerged conditions with two different nitrogen sources, whereupon, proteolytic activity in culture fluid was determined. Using chromogenic peptide substrates and fibrin plates, these species' thrombin, plasmin, factor Xa, urokinase, protein C-like, and activating activities towards hemostasis proteins, as well as fibrinolytic and plasminogen-activating activities, were evaluated. Results: It was shown that A. aureolatus and A. tennesseensis are active proteolytics exhibiting plasmin-like activity (116.17 and 87.09 U×10-3, respectively), factor Xa-like activity (76.27 and 77.92 U×10-3, respectively) and urokinase activity (85.99 and 59.91 U×10-3, respectively). The thrombin-like activity was found for A. tabacinus (50.37 U×10-3), and protein C-like activity was noticeable for A. creber, A. jensenii, A. protuberus, and A. ruber (62.90, 65.51, 73.37, and 111.85 U×10-3, respectively). Additionally, more than half of species have the ability to directly activate plasminogen or operate as fibrinolytics.Conclusion: New proteolytic strains were discovered, offering hope for the therapy of cardiovascular disorders. Fungal enzymes' high specificity and activity make them useful in a variety of fields, including medicine and diagnostics

Some ways to wildlife research in a megalopolis (on the example of the city of Nizhny Novgorod)

The paper is aimed to characterize the abundance of wildlife species listed in the Red Data Books of Russia and the Nizhny Novgorod Oblast on the territory of the city of Nizhny Novgorod, a megalopolis located in the geographical center of European Russia, to identify particular areas as habitats of rare species, to justify the need for protection of these areas. The analysis was based on the results of the authors’ surveys, published data, stock information (since the end of the XIX century), facts collected by the methods of citizen science. We have been developed the database containing 938 units of information about the registrations of 119 rare wildlife species in the city and identified 37 areas as the most important habitats of rare wildlife species, the human transformation of which should be avoided or requires special attention to the conservation of rare wildlife species and their habitats. We have proposed the matrix to estimate the degree of protection of urban habitats of rare wildlife species. Today, the habitats of a third of rare species are not protected by law. If all 37 identified natural areas are adopted as protected, more than 82% of rare urban species will be provided with territorial protection in full or at a high level

National Projects in the Arctic Zone of the Russian Federation

In 2021, the Russian Federation will assume the chairmanship of the Arctic Council. This fact confirms the special attention of the country’s leadership to the unique geostrategic region. In December 2020, President of the Russian Federation Vladimir Putin, at an online meeting with volunteers and finalists of the contest “Volunteer of Russia”, noted that Russia would grow with the Arctic and the territories of the North. Many Russian citizens’ lives and the state’s success in the international arena depend on this territory’s development. One of the most important mechanisms for achieving the stated goals is national projects (NP), which should make a significant contribution to the development of the country’s territory. The purpose of the study is to assess NP in the subjects that are entirely related to the Arctic zone: Murmansk oblast, Nenets Autonomous Okrug (NAO), Yamalo-Nenets Autonomous Okrug (YANAO), and Chukotka Autonomous Okrug (CHAO). In the course of the work, general scientific research methods were applied: comparative analysis, data comparison, induction, deduction, etc. The study results showed that, despite all the differences in economic and geographical position, financial condition, population, and regional development priorities, all Arctic regions have similar problems that hinder the effective development of territories. Without solving the problems indicated in the work, it is impossible to expect a qualitative «break-through» and implement the NP’s goals