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Article ; Online: Transcriptogram analysis reveals relationship between viral titer and gene sets responses during Corona-virus infection.

de Almeida, Rita M C / Thomas, Gilberto L / Glazier, James A

NAR genomics and bioinformatics

2022 Volume 4, Issue 1, Page(s) lqac020

Abstract: To understand the difference between benign and severe outcomes after Coronavirus infection, we urgently need ways to clarify and quantify the time course of tissue and immune responses. Here we re-analyze 72-hour time-series microarrays generated in ... ...

Abstract	To understand the difference between benign and severe outcomes after Coronavirus infection, we urgently need ways to clarify and quantify the time course of tissue and immune responses. Here we re-analyze 72-hour time-series microarrays generated in 2013 by Sims and collaborators for SARS-CoV-1
Language	English
Publishing date	2022-03-15
Publishing country	England
Document type	Journal Article
ISSN	2631-9268
ISSN (online)	2631-9268
DOI	10.1093/nargab/lqac020
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Article: Transcriptogram analysis reveals relationship between viral titer and gene sets responses during Corona-virus infection.

de Almeida, Rita M C / Thomas, Gilberto L / Glazier, James A

bioRxiv : the preprint server for biology

2021

Abstract	To understand the difference between benign and severe outcomes after Coronavirus infection, we urgently need ways to clarify and quantify the time course of tissue and immune responses. Here we re-analyze 72-hour time-series microarrays generated in 2013 by Sims and collaborators for SARS-CoV-1
Keywords	covid19
Language	English
Publishing date	2021-02-25
Publishing country	United States
Document type	Preprint
DOI	10.1101/2020.06.16.155267
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Book ; Online: CompuCell3D Model of Cell Migration Reproduces Chemotaxis

Dal-Castel, Pedro C. / Thomas, Gilberto L. / Perrone, Gabriel C. / de Almeida, Rita M. C.

2023

Abstract: Chemotaxis combines three processes: directional sensing, polarity reorientation and migration. Directed migration plays an important role in immune response, metastasis, wound healing and development. To describe chemotaxis, we extend a previously ... ...

Abstract	Chemotaxis combines three processes: directional sensing, polarity reorientation and migration. Directed migration plays an important role in immune response, metastasis, wound healing and development. To describe chemotaxis, we extend a previously published computational model of a 3D single cell, that presents three compartments (lamellipodium, nucleus and cytoplasm), whose migration on a flat surface quantitatively describes experiments. The simulation is built in the framework of CompuCell3D, an environment based on the Cellular Potts Model. In our extension, we treat chemotaxis as a compound process rather than a response to a potential force. We propose robust protocols to measure cell persistence, drift speed, terminal speed, chemotactic efficiency, taxis time, and we analyse cell migration dynamics in the cell reference frame from position and polarization recordings through time. Our metrics can be applied to experimental results and allow quantitative comparison between simulations and experiments. We found that our simulated cells exhibit a trade-off between polarization stability and chemotactic efficiency. Specifically, we found that cells with lower protrusion forces and smaller lamellipodia exhibit an increased ability to undergo chemotaxis. We also noticed no significant change in cell movement due to external chemical gradient when analysing cell displacement in the cell reference frame. Our results demonstrate the importance of measuring cell polarity throughout the entire cell trajectory, and treating velocity quantities carefully when cell movement is diffusive at short time intervals. The simulation we developed is adequate to the development of new measurement protocols, and it helps paving the way to more complex multicellular simulations to model collective migration and their interaction with external fields, which are under development on this date. Comment: Download and run (in CompuCell3D version 4) the simulation at https://github.com/pdalcastel/Single_Cell_Chemotaxis_2.3 . See the ...
Keywords	Physics - Biological Physics
Subject code	612
Publishing date	2023-12-01
Publishing country	us
Document type	Book ; Online
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Book ; Online: Velocities of Mesenchymal Cells May be Ill-Defined

Giardini, Guilherme S. Y. / Thomas, Gilberto L. / da Cunha, Carlo R. / de Almeida, Rita M. C.

2023

Abstract: The dynamics of single cell migration on flat surfaces is usually modeled by a Langevin-like problem consisting of ballistic motion for short periods and random walk. for long periods. Conversely, recent studies have revealed a previously neglected ... ...

Abstract	The dynamics of single cell migration on flat surfaces is usually modeled by a Langevin-like problem consisting of ballistic motion for short periods and random walk. for long periods. Conversely, recent studies have revealed a previously neglected random motion at very short intervals, what would rule out the possibility of defining the cell instantaneous velocity and a robust measurement procedure. A previous attempt to address this issue considered an anisotropic migration model, which takes into account a polarization orientation along which the velocity is well-defined, and a direction orthogonal to the polarization vector that describes the random walk. Although the numerically and analytically calculated mean square displacement and auto-correlation agree with experimental data for that model, the velocity distribution peaks at zero, which contradicts experimental observations of a constant drift in the polarization direction. Moreover, Potts model simulations indicate that instantaneous velocity cannot be measured for any direction. Here, we consider dynamical equations for cell polarization, which is measurable and introduce a polarization-dependent displacement, circumventing the problem of ill defined instantaneous velocity. Polarization is a well-defined quantity, preserves memory for short intervals, and provides a robust measurement procedure for characterizing cell migration. We consider cell polarization dynamics to follow a modified Langevin equation that yields cell displacement distribution that peaks at positive values, in agreement with experiments and Potts model simulations. Furthermore, displacement autocorrelation functions present two different time scales, improving the agreement between theoretical fits and experiments or simulations.
Keywords	Physics - Biological Physics ; Quantitative Biology - Cell Behavior
Subject code	612
Publishing date	2023-11-28
Publishing country	us
Document type	Book ; Online
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Article ; Online: Epigenetic reprogramming by TET enzymes impacts co-transcriptional R-loops.

Sabino, João C / de Almeida, Madalena R / Abreu, Patrícia L / Ferreira, Ana M / Caldas, Paulo / Domingues, Marco M / Santos, Nuno C / Azzalin, Claus M / Grosso, Ana Rita / de Almeida, Sérgio Fernandes

eLife

2022 Volume 11

Abstract: DNA oxidation by ten-eleven translocation (TET) family enzymes is essential for epigenetic reprogramming. The conversion of 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) initiates developmental and cell-type-specific transcriptional programs ...

Abstract	DNA oxidation by ten-eleven translocation (TET) family enzymes is essential for epigenetic reprogramming. The conversion of 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) initiates developmental and cell-type-specific transcriptional programs through mechanisms that include changes in the chromatin structure. Here, we show that the presence of 5hmC in the transcribed gene promotes the annealing of the nascent RNA to the template DNA strand, leading to the formation of an R-loop. Depletion of TET enzymes reduced global R-loops in the absence of gene expression changes, whereas CRISPR-mediated tethering of TET to an active gene promoted the formation of R-loops. The genome-wide distribution of 5hmC and R-loops shows a positive correlation in mouse and human stem cells and overlap in half of all active genes. Moreover, R-loop resolution leads to differential expression of a subset of genes that are involved in crucial events during stem cell proliferation. Altogether, our data reveal that epigenetic reprogramming via TET activity promotes co-transcriptional R-loop formation, disclosing new mechanisms of gene expression regulation.
MeSH term(s)	5-Methylcytosine/metabolism ; Animals ; Cytosine ; DNA/metabolism ; DNA Methylation ; Dioxygenases/genetics ; Epigenesis, Genetic ; Epigenomics ; Humans ; Mice ; R-Loop Structures
Chemical Substances	5-Methylcytosine (6R795CQT4H) ; Cytosine (8J337D1HZY) ; DNA (9007-49-2) ; Dioxygenases (EC 1.13.11.-)
Language	English
Publishing date	2022-02-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.69476
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Article: Exact solution for the Anisotropic Ornstein-Uhlenbeck process.

de Almeida, Rita M C / Giardini, Guilherme S Y / Vainstein, Mendeli / Glazier, James A / Thomas, Gilberto L

Physica A

2021 Volume 587

Abstract: Active-Matter models commonly consider particles with overdamped dynamics subject to a force (speed) with constant modulus and random direction. Some models also include random noise in particle displacement (a Wiener process), resulting in diffusive ... ...

Abstract	Active-Matter models commonly consider particles with overdamped dynamics subject to a force (speed) with constant modulus and random direction. Some models also include random noise in particle displacement (a Wiener process), resulting in diffusive motion at short time scales. On the other hand, Ornstein-Uhlenbeck processes apply Langevin dynamics to the particles' velocity and predict motion that is not diffusive at short time scales. Experiments show that migrating cells have gradually varying speeds at intermediate and long time scales, with short-time diffusive behavior. While Ornstein-Uhlenbeck processes can describe the moderate-and long-time speed variation, Active-Matter models for over-damped particles can explain the short-time diffusive behavior. Isotropic models cannot explain both regimes, because short-time diffusion renders instantaneous velocity ill-defined, and prevents the use of dynamical equations that require velocity time-derivatives. On the other hand, both models correctly describe some of the different temporal regimes seen in migrating biological cells and must, in the appropriate limit, yield the same observable predictions. Here we propose and solve analytically an Anisotropic Ornstein-Uhlenbeck process for polarized particles, with Langevin dynamics governing the particle's movement in the polarization direction and a Wiener process governing displacement in the orthogonal direction. Our characterization provides a theoretically robust way to compare movement in dimensionless simulations to movement in experiments in which measurements have meaningful space and time units. We also propose an approach to deal with inevitable finite-precision effects in experiments and simulations.
Language	English
Publishing date	2021-10-19
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1466577-3
ISSN	1873-2119 ; 0378-4371
ISSN (online)	1873-2119
ISSN	0378-4371
DOI	10.1016/j.physa.2021.126526
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Article ; Online: Anticonvulsant activity of Tetrahydrolinalool: behavioral, electrophysiological, and molecular docking approaches.

Fonsêca, Diogo V / da Silva, Pablo R / Pires, Hugo F O / Rocha, Juliana S / de Oliveira, Leandra Eugênia G / Reis, Flavia M S / Cavalho, Erika B M / Pazos, Natalia D N / de Sousa, Natália F / Guedes, Erika C / Ribeiro, Leandro R / Sá, Rita de Cassia S / Salvadori, Mirian G S S / Sousa, Damião P / Scotti, Marcus T / Felipe, Cicero F B / de Almeida, Reinaldo N / Scotti, Luciana

ChemMedChem

2024 , Page(s) e202400135

Abstract: Tetrahydrolinalool (THL) is an acyclic monoterpene alcohol, produced during linalol metabolism and also a constituent of essential oils. As described in the literature, many monoterpenes present anticonvulsant properties, and thus we became interested in ...

Abstract	Tetrahydrolinalool (THL) is an acyclic monoterpene alcohol, produced during linalol metabolism and also a constituent of essential oils. As described in the literature, many monoterpenes present anticonvulsant properties, and thus we became interested in evaluating the anticonvulsant activity of Tetrahydrolinalool using in mice model as well as in silico approaches. Our results demonstrated that THL increased latency to seizure onset and also reduced the mortality, in picrotoxin induced seizure tests. The results may be related to GABAergic regulation, which was also suggested in seizure testing induced by 3-mercapto-propionic acid. In the strychnine-induced seizure testing, none of the groups pretreated with THL modulated the parameters indicative of anticonvulsant effect. The electrophysiological results revealed that THL treatment reduces seizures induced by pentylenetetrazole. The in silico molecular docking studies showed that the interaction between THL and a GABAA receptor model formed a stable complex, in comparison to the crystaligraphic structure of diazepam, a structurally related ligand. In conclusion, all the evidences showed that THL presents effective anticonvulsant activity related to the GABAergic pathway, being a candidate for treatment of epileptic syndromes.
Language	English
Publishing date	2024-04-30
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2218496-X
ISSN	1860-7187 ; 1860-7179
ISSN (online)	1860-7187
ISSN	1860-7179
DOI	10.1002/cmdc.202400135
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Article ; Online: Epigenetic reprogramming by TET enzymes impacts co-transcriptional R-loops

João C Sabino / Madalena R de Almeida / Patrícia L Abreu / Ana M Ferreira / Paulo Caldas / Marco M Domingues / Nuno C Santos / Claus M Azzalin / Ana Rita Grosso / Sérgio Fernandes de Almeida

eLife, Vol

2022 Volume 11

Abstract	DNA oxidation by ten-eleven translocation (TET) family enzymes is essential for epigenetic reprogramming. The conversion of 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) initiates developmental and cell-type-specific transcriptional programs through mechanisms that include changes in the chromatin structure. Here, we show that the presence of 5hmC in the transcribed gene promotes the annealing of the nascent RNA to the template DNA strand, leading to the formation of an R-loop. Depletion of TET enzymes reduced global R-loops in the absence of gene expression changes, whereas CRISPR-mediated tethering of TET to an active gene promoted the formation of R-loops. The genome-wide distribution of 5hmC and R-loops shows a positive correlation in mouse and human stem cells and overlap in half of all active genes. Moreover, R-loop resolution leads to differential expression of a subset of genes that are involved in crucial events during stem cell proliferation. Altogether, our data reveal that epigenetic reprogramming via TET activity promotes co-transcriptional R-loop formation, disclosing new mechanisms of gene expression regulation.
Keywords	R-loops ; DNA hydroxymethylation ; TET enzymes ; gene expression ; stem cells ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2022-02-01T00:00:00Z
Publisher	eLife Sciences Publications Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Global Ban on Plastic and What Next? Are Consumers Ready to Replace Plastic with the Second-Generation Bioplastic? Results of the Snowball Sample Consumer Research in China, Western and Eastern Europe, North America and Brazil.

Kochanska, Ewa / Wozniak, Katarzyna / Nowaczyk, Agnieszka / Piedade, Patrícia J / de Almeida Lavorato, Marilena Lino / Almeida, Alexandre Marcelo / Morais, Ana Rita C / Lukasik, Rafal M

International journal of environmental research and public health

2022 Volume 19, Issue 21

Abstract: Plastic can be used for many things and at the same time is the most versatile material in our modern world. However, the uncontrolled and unprecedented use of plastic comes to its end. The global ban on plastic brings significant changes in technology ... ...

Abstract	Plastic can be used for many things and at the same time is the most versatile material in our modern world. However, the uncontrolled and unprecedented use of plastic comes to its end. The global ban on plastic brings significant changes in technology but even more so in civil perception-changes taking place before our eyes. The aim of this study was to find answers to the questions about the readiness of consumers for a global ban on plastic. Within the research, the differences in consumer acceptance in countries in Europe, South and North America and Asia and the expression of social readiness to change attitudes towards plastic food packaging were analyzed. This work sketches the legal framework related to limiting the use of one-use food packaging made of fossil raw materials at the level of the European Union, Poland and Portugal but also at the level of the two largest economies in the world, China and the United States, as well as lower-income countries, e.g., Ukraine and Brazil. The survey results were analyzed using descriptive and inferential statistics. The performed study demonstrates that, in in all the surveyed countries, appropriate legal acts related to the reduction of plastic in everyday life are already in place. Furthermore, this work demonstrates the full understanding of plastic banning in all surveyed countries. Consumers are aware that every effort should be made to prevent the world from drowning in plastic waste. Society is, in general, open to the use of bioplastics produced from the second-generation resource if second-generation bioplastics contribute to environmental and pollution reduction targets.
MeSH term(s)	Plastics ; Brazil ; North America ; Europe ; China ; Poland
Chemical Substances	Plastics
Language	English
Publishing date	2022-10-27
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2175195-X
ISSN	1660-4601 ; 1661-7827
ISSN (online)	1660-4601
ISSN	1661-7827
DOI	10.3390/ijerph192113970
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Article ; Online: Effect of dietary advanced glycation end-products restriction on type 2 diabetes mellitus control: a systematic review.

Oliveira, Julia S / de Almeida, Carolina / de Souza, Ângela M N / da Cruz, Luciana D / Alfenas, Rita C G

Nutrition reviews

2021 Volume 80, Issue 2, Page(s) 294–305

Abstract: Context: Reducing dietary advanced glycation end-products (AGEs) may favor diabetes control.: Objective: Critically analyze studies about the effect of dietary AGEs restriction on inflammation, oxidative stress, and glycemic control in patients with ... ...

Abstract	Context: Reducing dietary advanced glycation end-products (AGEs) may favor diabetes control. Objective: Critically analyze studies about the effect of dietary AGEs restriction on inflammation, oxidative stress, and glycemic control in patients with type 2 diabetes mellitus (DM2). Data source: This systematic review was conducted according to PRISMA methodology. The PubMed, Web of Science, LILACS, and Cochrane Library databases were searched, using the terms "type 2 diabetes," "advanced glycation end products" and "diet." Data extraction: Seven original studies were included in this review. The duration of the studies ranged from 1 day to 16 weeks. All extracted data were compiled, compared, and critically analyzed. Data analysis: Glycemic variables were considered the primary outcomes. The secondary outcomes were glycation, inflammatory, and oxidative stress markers. Conclusion: Although serum insulin, homeostasis model assessment of insulin resistance, and glycated hemoglobin values were lower after the consumption of AGEs restricted diets in most studies, there was a lack of unanimity regarding dietary AGEs' positive effect on inflammation, oxidative stress, and blood glucose. Systematic review registration: PROSPERO registration no. CRD42020152640.
MeSH term(s)	Blood Glucose ; Diabetes Mellitus, Type 2 ; Glycated Hemoglobin A ; Glycation End Products, Advanced ; Humans ; Insulin Resistance
Chemical Substances	Blood Glucose ; Glycated Hemoglobin A ; Glycation End Products, Advanced
Language	English
Publishing date	2021-05-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Systematic Review
ZDB-ID	82067-2
ISSN	1753-4887 ; 0029-6643
ISSN (online)	1753-4887
ISSN	0029-6643
DOI	10.1093/nutrit/nuab020
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