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Bio Systems

Igor Goychuk
Multiple experiments show that various submicron particles such as magnetosomes, RNA messengers, viruses, and even much smaller nanoparticles such as globular proteins diffuse anomalously slow in viscoelastic cytosol of living cells. Hence, their sufficiently fast directional transport by molecular motors such as kinesins is crucial for the cell operation. It has been shown recently that the traditional flashing Brownian ratchet models of molecular motors are capable to describe both normal and anomalous transport of such subdiffusing cargos by molecular motors with a very high efficiency...
November 9, 2018: Bio Systems
Katarzyna Walczewska-Szewc, Wieslaw Nowak
Mutations in gene KCNJ11 encoding the Kir6.2 subunit of the ATP-sensitive potassium channel (KATP), a representative of a quite complex biosystem, may affect insulin release from pancreatic beta-cells. Both gain and loss of channel activity are observed, which lead to varied clinical phenotypes ranging from neonatal diabetes to congenital hyperinsulinism. In order to understand the mechanisms of the channel function better we mapped, based on the literature review, known medically relevant Kir6.2/SUR1 mutations into recently (2017) determined CryoEM 3D structures of this complex...
November 2, 2018: Bio Systems
Garrison W Greenwood, Hussein A Abbass, Eleni Petraki
It is not fully understood how cooperation emerges in a population of individuals with no connections or prior experience with each other. Strategy selection that is purely based on accumulated payoffs promotes free riders who put their self interests above that of any group. How could cooperation persist in these settings? Researchers have posited direct or indirect reciprocity as possible explanations but these theories fail if interactions are not repeated or reputations are ignored. Altruistic punishment may provide an answer...
November 1, 2018: Bio Systems
Malgorzata Domino, Krzysztof Domino, Zdzislaw Gajewski
The analysis of the uterine contraction have become a general practice in an effort to improve the clinical management of uterine contractions during pregnancy and labour in human beings. The fluctuations in uterine activity may occur without affecting progress of gestation, however the painful and fashion contractions may be the first threat of miscarriage. While pigs were considered as an referential preclinical model, the computational modelling of spontaneous myoelectrical activity of complex systems of porcine myometrium in peri-fertilization period has been proposed...
November 1, 2018: Bio Systems
Katarzyna Jesionek, Marcin Kostur
We demonstrate how low-density lipoproteins (LDL) are transported and accumulated through walls of the coronary artery. The result of modeling is a map of the LDL concentration on the patient specific vessel. It identifies places at high risk for plague growth. Using the geometry of the same patient we compare the results of two-layer and four-layer models of LDL transport.
October 31, 2018: Bio Systems
Zenon Pawlak, Aleksandra Mrela, Mariusz Kaczmarek, Mieczyslaw Cieszko, Wieslaw Urbaniak
Lipid profiles of injured and healthy knees' synovial fluids show significant differences. The paper shows that osteoporosis changes the SF content and the lipid profile substantially. It is observed an increase in phospholipids over the fractured ones, and in the lysophosphatidylcholine levels because of the probable release of phospholipases from osteoporosis tissues. To estimate the implication of the lipid environment in case the AC changes, we measured friction coefficient normal samples, e-OA, and l-OA...
October 30, 2018: Bio Systems
A E Filippov, R Guillermo-Ferreira, S N Gorb
Tree trunks and other cylindrical objects, where aggregated insects live, represent a very specific world for predator-prey interactions, which must differ from the situation on a 2D plane. In the present paper, in order to gain a better understanding of the specificity of predator-prey interaction in a cylindrical space, we applied a theoretical approach. Here we introduce a numerical model that allows us to test the effect of different interaction properties between predator and aggregated prey on the plane (2D) and on a cylinder (3D), taking into consideration different abilities of predators to visually detect the prey in these two types of space...
October 30, 2018: Bio Systems
Gopal Dila, J Michel Christian, Olivier Poch, Raymond Ripp, D Thompson Julie
A set X of 20 trinucleotides has been found to have the highest average occurrence in the reading frame, compared to the two shifted frames, of genes of bacteria, archaea, eukaryotes, plasmids and viruses (Michel, 2017, 2015; Arquès and Michel, 1996). This set X has an interesting mathematical property, since X is a maximal C3 self-complementary trinucleotide circular code (Arquès and Michel, 1996). Furthermore, any motif obtained from this circular code X has the capacity to retrieve, maintain and synchronize the reading frame in genes...
October 24, 2018: Bio Systems
Lev V Beloussov
We start by comparing two explicatory approaches, which we call law-centered and "instructivistic". Although the latter dominates in modern biology, we find it inappropriate for treating developmental problems, especially those related to morphogenesis. As an example of a law-centered approach we suggest a simple morphomechanical rule based upon the idea of the hyper-restoration of mechanical stresses. We show that this rule not only provides a general framework for morphogenesis, but can also reproduce, via parametric modulations, quite specific developmental events...
October 16, 2018: Bio Systems
Natalia N Luchinskaia, Vladimir G Cherdantsev, Alexander S Ermakov, Nadezhda S Glagoleva, Lev V Beloussov
Reactions of embryonic tissues to a distributed and concentrated stretching are described and compared with the mechanics of the normal gastrulation movements. A role of mechanically stressed dynamic cell structures in the gastrulation, demarcation of notochord borders and in providing proportionality of the axial rudiments is demonstrated. A morphomechanical scheme of amphibian gastrulation is presented.
October 12, 2018: Bio Systems
Richard Gordon
No abstract text is available yet for this article.
October 12, 2018: Bio Systems
Alexander S Ermakov
The first explanations of the mechanisms of development of living organisms were proposed in antiquity. At that time two competing ideas existed, about the strict determination of embryonic structures (we call it the "Hippocrates line") and about the possible formation of structures from the unstructured condition ("Aristotle line"). We can trace the opposition between the "Hippocrates line" and "Aristotle line" from antiquity till the present time. At the end of the XIX century, experimental investigation of the mechanisms of integrity of development had started...
October 10, 2018: Bio Systems
Svetlana Surkova, Elena Golubkova, Ludmila Mamon, Maria Samsonova
Here, we review the latest publications on dynamics and interpretation of morphogen gradients in Drosophila early embryo. The instructive cues provided by these gradients are further interpreted by target genes to enable correct cell fate specification. Moreover, recent studies point on the dynamic and active input from gradients themselves. Latest research has demonstrated that the decay of maternal gradients affects the positional dynamics of target gap gene expression. Study of temporal interpretation of the Bicoid (Bcd) morphogen signal revealed that the Bcd-dependent cell fate specification proceeds sequentially from the posterior towards the anterior...
October 10, 2018: Bio Systems
Sara Barbosa, Bastian Niebel, Sebastian Wolf, Klaus Mauch, Ralf Takors
The study of biological systems at a system level has become a reality due to the increasing powerful computational approaches able to handle increasingly larger datasets. Uncovering the dynamic nature of gene regulatory networks in order to attain a system level understanding and improve the predictive power of biological models is an important research field in systems biology. The task itself presents several challenges, since the problem is of combinatorial nature and highly depends on several biological constraints and also the intended application...
October 9, 2018: Bio Systems
Zbigniew J Grzywna, Przemyslaw Borys
Using the results from previous modeling of the ball and chain inactivation of the potassium channels we try to model the inactivation of the NaV 1.5 sodium channels in adult and neonatal form. The (fast) inactivation of sodium channels differs from the inactivation of the potassium channels by the use of a inactivating hinge rather than a ball on a chain. The adult and neonatal variants of the channel differ mostly in a charged amino acid residue located on the extracellular side. We show that a drift caused by this residue is sufficient to describe the differences in inactivation between the two forms of the NaV 1...
October 9, 2018: Bio Systems
L V Beloussov, T G Troshina, N S Glagoleva, S V Kremnyov
Several important morphogenetic processes belong to the category of collective cell movements (CCM), by which we mean coordinated rearrangements of many neighboring cells. The causes of the dynamic order established during CCM are still unclear. We performed statistical studies of rates and angular orientations of cell rearrangements in two kinds of embryonic tissues, which we categorized as "committed" (in the sense of being capable of autonomous CCM) as opposed to "naïve" tissues, which are those that require external forces in order to exhibit full scale CCM...
October 6, 2018: Bio Systems
Andrei Lipchinsky
One of the most challenging questions in cell and developmental biology is how molecular signals are translated into mechanical forces that ultimately drive cell growth and motility. Despite an impressive body of literature demonstrating the importance of cytoskeletal and motor proteins as well as osmotic stresses for cell developmental mechanics, a host of dissenting evidence strongly suggests that these factors per se cannot explain growth mechanics even at the level of a single tip-growing cell. The present study addresses this issue by exploring fundamental interrelations between electrical and mechanical fields operating in cells...
October 6, 2018: Bio Systems
Denis Bredov, Ilya Volodyaev
The article is devoted to physical views on embryo development as a combination of structurally stable dynamics and symmetry-breaking events in the general process of self-organization. The first corresponds to the deterministic aspect of embryo development. The second type of processes is associated with sudden increase of variability in the periods of symmetry-breaking, which manifests unstable dynamics. The biological basis under these considerations includes chemokinetics (a system of inductors, repressors, and interaction with their next surrounding) and morphomechanics (i...
October 4, 2018: Bio Systems
Catharine J Roussel, Marc R Roussel
The expression of the TGF-β protein Nodal on the left side of vertebrate embryos is a determining event in the development of internal-organ asymmetry. We present a mathematical model for the control of the expression of Nodal and its antagonist Lefty consisting entirely of realistic elementary reactions. We analyze the model in the absence of Lefty and find a wide range of parameters over which bistability (two stable steady states) is observed, with one stable steady state a low-Nodal state corresponding to the right-hand developmental fate, and the other a high-Nodal state corresponding to the left...
October 4, 2018: Bio Systems
Mikhail A Shishkin
Evolution of living systems is a succession of historical changes in their equilibrium states. In the individual life cycle, every such state is realized as an equilibrium of developmental system, i.e. as its adult organizational norm. A trigger for a switching the system to a search for a new equilibrium is the loss under critical conditions of effective regulation of normal development towards uniform final state. This is manifested by replacement of the adult norm by its individual deviations. Thus, the organizational change begins with its adult state, which is the first to undergo the disturbance under new conditions...
October 3, 2018: Bio Systems
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