Yeast as a Versatile Tool in Biotechnology

Yeasts represent a very diverse group of microorganisms, and even strains that are classified as the same species often show a high level of genetic divergence. Yeasts biodiversity is closely related to their applicability. Biotechnological importance of yeast is almost immeasurable. For centuries, people have exploited its enzymatic potential to produce fermented food as bread or alcoholic beverages. Admittedly, yeasts application was initially instinctual, but with science and technology development, these microorganisms got the object of thorough scientific investigations. It must be recognized that yeast represents an excellent scientific model because of its eukaryotic origin and knowledge of genetics of yeast cells as well as metabolism examined in detail. In 1996, the genome of baker yeast Saccharomyces cerevisiae has been elucidated, what opened the opportunity for the global study of the expression and functioning of the eukaryotic genome. Also, currently, an international team is working on the synthesis of the 16 yeast chromosomes by synthetic biology tools, and the results are expected till the end of the year. Nowadays, yeast is regarded as a versatile tool for biotechnological purposes

Task-dependent fractal patterns of information processing in working memory

We applied detrended fluctuation analysis, power spectral density, and eigenanalysis of detrended cross-correlations to investigate fMRI data representing a diurnal variation of working memory in four visual tasks: two verbal and two nonverbal. We show that the degree of fractal scaling is regionally dependent on the engagement in cognitive tasks. A particularly apparent difference was found between memorisation in verbal and nonverbal tasks. Furthermore, the detrended cross-correlations between brain areas were predominantly indicative of differences between resting state and other tasks, between memorisation and retrieval, and between verbal and nonverbal tasks. The fractal and spectral analyses presented in our study are consistent with previous research related to visuospatial and verbal information processing, working memory (encoding and retrieval), and executive functions, but they were found to be more sensitive than Pearson correlations and showed the potential to obtain other subtler results. We conclude that regionally dependent cognitive task engagement can be distinguished based on the fractal characteristics of BOLD signals and their detrended cross-correlation structure

Non-linear Functional Brain Co-activations in Short-Term Memory Distortion Tasks

Recent works shed light on the neural correlates of true and false recognition and the influence of time of day on cognitive performance. The current study aimed to investigate the modulation of the false memory formation by the time of day using a non-linear correlation analysis originally designed for fMRI resting-state data. Fifty-four young and healthy participants (32 females, mean age: 24.17 ± 3.56 y.o.) performed in MRscanner the modified Deese-Roediger-McDermott paradigm in short-term memory during one session in the morning and another in the evening. Subjects’ responses were modeled with a general linear model, which includes as a predictor the nonlinear correlations of regional BOLD activity with the stimuli, separately for encoding and retrieval phases. The results show the dependence of the non-linear correlations measures with the time of day and the type of the probe. In addition, the results indicate differences in the correlations measures with hippocampal regions between positive and lure probes. Besides confirming previous results on the influence of time-of-day on cognitive performance, the study demonstrates the effectiveness of the non-linear correlation analysis method for the characterization of fMRI task paradigms.Fil: Ceglarek, Anna. Jagiellonian University; PoloniaFil: Ochab, Jeremi K.. Jagiellonian University; PoloniaFil: Cifre, Ignacio. Universitat Ramon Llull; EspañaFil: Fafrowicz, Magdalena. Jagiellonian University; PoloniaFil: Sikora Wachowicz, Barbara. Jagiellonian University; PoloniaFil: Lewandowska, Koryna. Jagiellonian University; PoloniaFil: Bohaterewicz, Bartosz. Jagiellonian University; PoloniaFil: Marek, Tadeusz. Jagiellonian University; PoloniaFil: Chialvo, Dante Renato. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Ciencias Físicas. - Universidad Nacional de San Martín. Instituto de Ciencias Físicas; Argentin

Observing changes in human functioning during induced sleep deficiency and recovery periods

Prolonged periods of sleep restriction seem to be common in the contemporary world. Sleep loss causes perturbations of circadian rhythmicity and degradation of waking alertness as reflected in attention, cognitive efficiency and memory. Understanding whether and how the human brain recovers from chronic sleep loss is important not only from a scientific but also from a public health perspective. In this work we report on behavioral, motor, and neurophysiological correlates of sleep loss in healthy adults in an unprecedented study conducted in natural conditions and comprising 21 consecutive days divided into periods of 4 days of regular life (a baseline), 10 days of chronic partial sleep restriction (30% reduction relative to individual sleep need) and 7 days of recovery. Throughout the whole experiment we continuously measured the spontaneous locomotor activity by means of actigraphy with 1-minute resolution. On a daily basis the subjects were undergoing EEG measurements (64-electrodes with 500 Hz sampling frequency): resting state with eyes open and closed (8 minutes long each) followed by Stroop task lasting 22 minutes. Altogether we analyzed actigraphy (distributions of rest and activity durations), behavioral measures (reaction times and accuracy from Stroop task) and EEG (amplitudes, latencies and scalp maps of event-related potentials from Stroop task and power spectra from resting states). We observed unanimous deterioration in all the measures during sleep restriction. Further results indicate that a week of recovery subsequent to prolonged periods of sleep restriction is insufficient to recover fully. Only one measure (mean reaction time in Stroop task) reverted to baseline values, while the others did not.Fil: Ochab, Jeremi K.. Jagiellonian University. Marian Smoluchowski Institute of Physics; Polonia. Jagiellonian University. Mark Kac Complex Systems Research Centre; PoloniaFil: Szwed, Jerzy. Jagiellonian University. Marian Smoluchowski Institute of Physics; Polonia. Jagiellonian University. Mark Kac Complex Systems Research Centre; PoloniaFil: Oles, Katarzyna. Jagiellonian University. Marian Smoluchowski Institute of Physics; PoloniaFil: Beres, Anna. Jagiellonian University. Department of Cognitive Neuroscience and Neuroergonomics; PoloniaFil: Chialvo, Dante Renato. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de San Martin. Escuela de Ciencia y Tecnologia. Centro de Estudios Multidisciplinarios En Sistemas Complejos y Ciencias del Cerebro.; ArgentinaFil: Domagalik, Aleksandra. Jagiellonian University. Department of Cognitive Neuroscience and Neuroergonomics; PoloniaFil: Frafrowicz, Magdalena. Jagiellonian University. Department of Cognitive Neuroscience and Neuroergonomics; PoloniaFil: Oginska, Halszka. Jagiellonian University. Department of Cognitive Neuroscience and Neuroergonomics; PoloniaFil: Gudowska-Nowak, Ewa. Jagiellonian University. Marian Smoluchowski Institute of Physics; Polonia. Jagiellonian University. Małopolska Center of Biotechnology ; PoloniaFil: Marek, Tadeusz. Jagiellonian University. Department of Cognitive Neuroscience and Neuroergonomic; Polonia. Jagiellonian University. Małopolska Center of Biotechnology; ArgentinaFil: Nowak, Maciej A.. Jagiellonian University. Marian Smoluchowski Institute of Physics; Polonia. Jagiellonian University. Mark Kac Complex Systems Research Centre; Poloni

Pandemic chronicles 2020-2021

Kroniki pandemii to zbiór 27 stanowisk opublikowanych przez interdyscyplinarny Zespół doradczy ds. COVID-19 przy Prezesie Polskiej Akademii Nauk, działający od lipca 2020 roku. Jest to już drugie po Zrozumieć COVID-19 obszerniejsze opracowanie naszego zespołu porządkujące wiadomości dotyczące wirusa SARS-CoV-2 i powodowanej przez niego choroby COVID-19. Wydane we wrześniu 2020 roku Zrozumieć COVID-19 miało na celu podsumowanie przebiegu pierwszych miesięcy pandemii i przygotowanie społeczeństwa w Polsce do ciężkiego sezonu jesienno-zimowego 2020/2021. Niniejsze opracowanie powstaje po dwóch latach trwania pandemii, która rozpoczęła się w Wuhan w grudniu 2019 roku. Mamy nadzieję, że dzięki na bieżąco tworzonym tekstom raportującym przebieg pandemii i dylematy, przed którymi stawało społeczeństwo, w przypadku kolejnych podobnych wyzwań skorzystamy z tych trudnych i ważnych doświadczeń

Comparative study of fungal cell disruption—scope and limitations of the methods

Simple and effective protocols of cell wall disruption were elaborated for tested fungal strains: Penicillium citrinum, Aspergillus fumigatus, Rhodotorula gracilis. Several techniques of cell wall disintegration were studied, including ultrasound disintegration, homogenization in bead mill, application of chemicals of various types, and osmotic shock. The release of proteins from fungal cells and the activity of a cytosolic enzyme, glucose-6-phosphate dehydrogenase, in the crude extracts were assayed to determine and compare the efficacy of each method. The presented studies allowed adjusting the particular method to a particular strain. The mechanical methods of disintegration appeared to be the most effective for the disintegration of yeast, R. gracilis, and filamentous fungi, A. fumigatus and P. citrinum. Ultrasonication and bead milling led to obtaining fungal cell-free extracts containing high concentrations of soluble proteins and active glucose-6-phosphate dehydrogenase systems

Influence of parameter perturbations on the reachability of therapeutic target in systems with switchings

Abstract Background Examination of physiological processes and the influences of the drugs on them can be efficiently supported by mathematical modeling. One of the biggest problems is related to the exact fitting of the parameters of a model. Conditions inside the organism change dynamically, so the rates of processes are very difficult to estimate. Perturbations in the model parameters influence the steady state so a desired therapeutic goal may not be reached. Here we investigate the effect of parameter deviation on the steady state in three simple models of the influence of a therapeutic drug on its target protein. Two types of changes in the model parameters are taken into account: small perturbations in the system parameter values, and changes in the switching time of a specific parameter. Additionally, we examine the systems response in case of a drug concentration decreasing with time. Results The models which we analyze are simplified, because we want to avoid influences of complex dynamics on the results. A system with a negative feedback loop is the most robust and the most rapid, so it requires the largest drug dose but the effects are observed very quickly. On the other hand a system with positive feedback is very sensitive to changes, so small drug doses are sufficient to reach a therapeutic target. In systems without feedback or with positive feedback, perturbations in the model parameters have a bigger influence on the reachability of the therapeutic target than in systems with negative feedback. Drug degradation or inactivation in biological systems enforces multiple drug applications to maintain the level of a drug’s target under the desired threshold. The frequency of drug application should be fitted to the system dynamics, because the response velocity is tightly related to the therapeutic effectiveness and the time for achieving the goal. Conclusions Systems with different types of regulation vary in their dynamics and characteristic features. Depending on the feedback loop, different types of therapy may be the most appropriate, and deviations in the model parameters have different influences on the reachability of the therapeutic target

Multiple epidemic waves as the outcome of stochastic SIR epidemics with behavioral responses : a hybrid modeling approach

In the behavioral epidemiology (BE) of infectious diseases, little theoretical effort seems to have been devoted to understand the possible effects of individuals' behavioral responses during an epidemic outbreak in small populations. To fill this gap, here we first build general, behavior implicit, SIR epidemic models including behavioral responses and set them within the framework of nonlinear feedback control theory. Second, we provide a thorough investigation of the effects of different types of agents' behavioral responses for the dynamics of hybrid stochastic SIR outbreak models. In the proposed model, the stochastic discrete dynamics of infection spread is combined with a continuous model describing the agents' delayed behavioral response. The delay reflects the memory mechanisms with which individuals enact protective behavior based on past data on the epidemic course. This results in a stochastic hybrid system with time-varying transition probabilities. To simulate such system, we extend Gillespie's classic stochastic simulation algorithm by developing analytical formulas valid for our classes of models. The algorithm is used to simulate a number of stochastic behavioral models and to classify the effects of different types of agents' behavioral responses. In particular this work focuses on the effects of the structure of the response function and of the form of the temporal distribution of such response. Among the various results, we stress the appearance of multiple, stochastic epidemic waves triggered by the delayed behavioral response of individuals