Instytut Podstawowych Problemów Techniki
Polskiej Akademii Nauk

Pracownicy

lic. Frederic Grabowski

Zakład Biosystemów i Miękkiej Materii (ZBiMM)
doktorant
telefon: (+48) 22 826 12 81 wewn.: 450
pokój: 310
e-mail:
ORCID: 0000-0003-4070-9500

Ostatnie publikacje
1.  Grabowski F., Preibisch G., Giziński S., Kochańczyk M., Lipniacki T., SARS-CoV-2 variant of concern 202012/01 has about twofold replicative advantage and acquires concerning mutations, Viruses, ISSN: 1999-4915, DOI: 10.3390/v13030392, Vol.13, No.3, pp.392-1-16, 2021

Streszczenie:
The novel SARS-CoV-2 Variant of Concern (VOC)-202012/01 (also known as B.1.1.7), first collected in United Kingdom on 20 September 2020, is a rapidly growing lineage that in January 2021 constituted 86% of all SARS-CoV-2 genomes sequenced in England. The VOC has been detected in 40 out of 46 countries that reported at least 50 genomes in January 2021. We have estimated that the replicative advantage of the VOC is in the range 1.83–2.18 [95% CI: 1.71–2.40] with respect to the 20A.EU1 variant that dominated in England in November 2020, and in range 1.65–1.72 [95% CI: 1.46–2.04] in Wales, Scotland, Denmark, and USA. As the VOC strain will likely spread globally towards fixation, it is important to monitor its molecular evolution. We have estimated growth rates of expanding mutations acquired by the VOC lineage to find that the L18F substitution in spike has initiated a fast growing VOC substrain. The L18F substitution is of significance because it has been found to compromise binding of neutralizing antibodies. Of concern are immune escape mutations acquired by the VOC: E484K, F490S, S494P (in the receptor binding motif of spike) and Q677H, Q675H (in the proximity of the polybasic cleavage site at the S1/S2 boundary). These mutants may hinder efficiency of existing vaccines and expand in response to the increasing after-infection or vaccine-induced seroprevalence.

Słowa kluczowe:
COVID-19 pandemic, SARS-CoV-2, spike protein, VOC-202012/01, spike L18F, genome sequencing, mutation

Afiliacje autorów:
Grabowski F. - IPPT PAN
Preibisch G. - inna afiliacja
Giziński S. - inna afiliacja
Kochańczyk M. - IPPT PAN
Lipniacki T. - IPPT PAN
100p.
2.  Kochańczyk M., Grabowski F., Lipniacki T., Super-spreading events initiated the exponential growth phase of COVID-19 with R-0 higher than initially estimated, Royal Society Open Science, ISSN: 2054-5703, DOI: 10.1098/rsos.200786, Vol.7, No.9, pp.200786-1-9, 2020

Streszczenie:
The basic reproduction number R0 of the coronavirus disease 2019 has been estimated to range between 2 and 4. Here, we used an SEIR model that properly accounts for the distribution of the latent period and, based on empirical estimates of the doubling time in the near-exponential phases of epidemic progression in China, Italy, Spain, France, UK, Germany, Switzerland and New York State, we estimated that R0 lies in the range 4.7-11.4. We explained this discrepancy by performing stochastic simulations of model dynamics in a population with a small proportion of super-spreaders. The simulations revealed two-phase dynamics, in which an initial phase of relatively slow epidemic progression diverts to a faster phase upon appearance of infectious super-spreaders. Early estimates obtained for this initial phase may suggest lower R0.

Słowa kluczowe:
COVID-19, reproduction number

Afiliacje autorów:
Kochańczyk M. - IPPT PAN
Grabowski F. - inna afiliacja
Lipniacki T. - IPPT PAN
100p.
3.  Kochańczyk M., Grabowski F., Lipniacki T., Dynamics of COVID-19 pandemic at constant and time-dependent contact rates, MATHEMATICAL MODELLING OF NATURAL PHENOMENA, ISSN: 0973-5348, DOI: 10.1051/mmnp/2020011, Vol.15, pp.28-1-12, 2020

Streszczenie:
We constructed a simple Susceptible−Exposed–Infectious–Removed model of the spread of COVID-19. The model is parametrised only by the average incubation period, τ, and two rate parameters: contact rate, β, and exclusion rate, γ. The rates depend on nontherapeutic interventions and determine the basic reproduction number, R0 = β/γ, and, together with τ, the daily multiplication coefficient in the early exponential phase, θ. Initial R0 determines the reduction of β required to contain the spread of the epidemic. We demonstrate that introduction of a cascade of multiple exposed states enables the model to reproduce the distributions of the incubation period and the serial interval reported by epidemiologists. Using the model, we consider a hypothetical scenario in which β is modulated solely by anticipated changes of social behaviours: first, β decreases in response to a surge of daily new cases, pressuring people to self-isolate, and then, over longer time scale, β increases as people gradually accept the risk. In this scenario, initial abrupt epidemic spread is followed by a plateau and slow regression, which, although economically and socially devastating, grants time to develop and deploy vaccine or at least limit daily cases to a manageable number.

Słowa kluczowe:
basic reproduction number, novel coronavirus

Afiliacje autorów:
Kochańczyk M. - IPPT PAN
Grabowski F. - inna afiliacja
Lipniacki T. - IPPT PAN
40p.
4.  Grabowski F., Czyż P., Kochańczyk M., Lipniacki T., Limits to the rate of information transmission through the MAPK pathway, JOURNAL OF THE ROYAL SOCIETY INTERFACE, ISSN: 1742-5689, DOI: 10.1098/rsif.2018.0792, Vol.16, No.152, pp.20180792-1-10, 2019

Streszczenie:
Two important signalling pathways of NF-κB and ERK transmit merely 1 bit of information about the level of extracellular stimulation. It is thus unclear how such systems can coordinate complex cell responses to external cues. We analyse information transmission in the MAPK/ERK pathway that converts both constant and pulsatile EGF stimulation into pulses of ERK activity. Based on an experimentally verified computational model, we demonstrate that, when input consists of sequences of EGF pulses, transmitted information increases nearly linearly with time. Thus, pulse-interval transcoding allows more information to be relayed than the amplitude–amplitude transcoding considered previously for the ERK and NF-κB pathways. Moreover, the information channel capacity C, or simply bitrate, is not limited by the bandwidth B = 1/τ, where τ ≈ 1 h is the relaxation time. Specifically, when the input is provided in the form of sequences of short binary EGF pulses separated by intervals that are multiples of τ/n (but not shorter than τ), then for n = 2, C ≈ 1.39 bit/h^-1; and for n = 4, C ≈ 1.86 bit/h^-1. The capability to respond to random sequences of EGF pulses enables cells to propagate spontaneous ERK activity waves across tissue.

Słowa kluczowe:
cellular signal transduction, pulsatile stimulation, pulse-interval transcoding, bandwidth, representation problem

Afiliacje autorów:
Grabowski F. - inna afiliacja
Czyż P. - University of Oxford (GB)
Kochańczyk M. - IPPT PAN
Lipniacki T. - IPPT PAN
100p.

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