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Bio Systems

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https://www.readbyqxmd.com/read/28735035/the-lamin-code
#1
Nadir M Maraldi
Unicellular eukaryotes and metazoa present a nuclear envelope (NE) and metazoa express in it one or more lamins that give rise to the nuclear lamina. The expression of different types of lamins is related to the complexity of the organism and the expression of type-A lamins is related to the initial steps of tissue-specific cell differentiation. Several posttranslational modifications characterize the expression of lamin A in the course of cell differentiation, and the alteration of this expression pattern leads to impressive phenotypic diseases that are collectively referred to as laminopathies...
July 19, 2017: Bio Systems
https://www.readbyqxmd.com/read/28735034/language-a-fresh-concept-to-integrate-syntactic-and-semantic-information-in-life-sciences
#2
Rémi Tournebize, Cédric Gaucherel
Several fields in biology tend to view the concept of information from one or the other of two extreme positions. Exclusionists base their stance of total rejection on gene-centrism and gene-determinism, typified by the recently-established endo-Darwinist school of life sciences. At the other end of the spectrum, there is total acceptance, as in the newly developed information-centred paradigms that populate biosemiotics. We propose in this paper to split the informational concepts into two irreducible (but linked) poles: the syntactic (concerned with the quantification of the information structure or complexity in a system), and the semantic (concerned with the organization rules and causality weights of interactions in a system)...
July 19, 2017: Bio Systems
https://www.readbyqxmd.com/read/28733249/dna-based-random-key-generation-and-management-for-otp-encryption
#3
Yunpeng Zhang, Xin Liu, Manhui Sun
One-time pad (OTP) is a principle of key generation applied to the stream ciphering method which offers total privacy. The OTP encryption scheme has proved to be unbreakable in theory, but difficult to realize in practical applications. Because OTP encryption specially requires the absolute randomness of the key, its development has suffered from dense constraints. DNA cryptography is a new and promising technology in the field of information security. DNA chromosomes storing capabilities can be used as one-time pad structures with pseudo-random number generation and indexing in order to encrypt the plaintext messages...
July 18, 2017: Bio Systems
https://www.readbyqxmd.com/read/28720508/to-swim-or-not-to-swim-a-population-level-model-of-xenopus-tadpole-decision-making-and-locomotor-behaviour
#4
Roman Borisyuk, Robert Merrison-Hort, Steve R Soffe, Stella Koutsikou, Wen-Chang Li
We present a detailed computational model of interacting neuronal populations that mimic the hatchling Xenopus tadpole nervous system. The model includes four sensory pathways, integrators of sensory information, and a central pattern generator (CPG) network. Sensory pathways of different modalities receive inputs from an "environment"; these inputs are then processed and integrated to select the most appropriate locomotor action. The CPG populations execute the selected action, generating output in motor neuron populations...
July 15, 2017: Bio Systems
https://www.readbyqxmd.com/read/28709805/effect-of-diseases-on-symbiotic-systems
#5
Pankaj Kumar Tiwari, Sourav Kumar Sasmal, Amar Sha, Ezio Venturino, Joydev Chattopadhyay
There are many species living in symbiotic communities. In this study, we analyzed models in which populations are in the mutualism symbiotic relations subject to a disease spreading among one of the species. The main goal is the characterization of symbiotic relations of coexisting species through their mutual influences on their respective carrying capacities, taking into account that this influence can be quite strong. The functional dependence of the carrying capacities reflects the fact that the correlations between populations cannot be realized merely through direct interactions, as in the usual predator-prey Lotka-Volterra model, but also through the influence of each species on the carrying capacities of the other one...
July 12, 2017: Bio Systems
https://www.readbyqxmd.com/read/28709806/the-sugar-code-why-glycans-are-so-important
#6
REVIEW
Hans-Joachim Gabius
The cell surface is the platform for presentation of biochemical signals that are required for intercellular communication. Their profile necessarily needs to be responsive to internal and external factors in a highly dynamic manner. The structural features of the signals must meet the criterion of high-density information coding in a minimum of space. Thus, only biomolecules that can generate many different oligomers ('words') from few building blocks ('letters') qualify to meet this challenge. Examining the respective properties of common biocompounds that form natural oligo- and polymers comparatively, starting with nucleotides and amino acids (the first and second alphabets of life), comes up with sugars as clear frontrunner...
July 11, 2017: Bio Systems
https://www.readbyqxmd.com/read/28698018/carrying-pieces-of-information-in-organocatalytic-bytes-semiopoiesis-a-new-theory-of-life-and-its-origins
#7
Wanderley Dantas Dos Santos
Living beings have been classically described as autopoietic machines: chemical systems, which maintain a reproducible steady state by producing their components and boundaries. On the other hand, very simple autopoietic micelles have been produced in laboratory. They consist in micelles able to catalyse the production of their own surfactants. However is very clear that these autopoietic systems are unable to evolve. In this way, these autopoietic micelles cannot be associated to living organisms, which are always linked by evolutionary relationships...
July 8, 2017: Bio Systems
https://www.readbyqxmd.com/read/28684284/adaptive-evolution-of-body-size-subject-to-indirect-effect-in-trophic-cascade-system
#8
Xin Wang, Meng Fan, Lina Hao
Trophic cascades represent a classic example of indirect effect and are wide-spread in nature. Their ecological impact are well established, but the evolutionary consequences have received even less theoretical attention. We theoretically and numerically investigate the trait (i.e., body size of consumer) evolution in response to indirect effect in a trophic cascade system. By applying the quantitative trait evolutionary theory and the adaptive dynamic theory, we formulate and explore two different types of eco-evolutionary resource-consumer-predator trophic cascade model...
July 3, 2017: Bio Systems
https://www.readbyqxmd.com/read/28684283/efficiency-of-rate-and-latency-coding-with-respect-to-metabolic-cost-and-time
#9
Marie Levakova
Recent studies on the theoretical performance of latency and rate code in single neurons have revealed that the ultimate accuracy is affected in a nontrivial way by aspects such as the level of spontaneous activity of presynaptic neurons, amount of neuronal noise or the duration of the time window used to determine the firing rate. This study explores how the optimal decoding performance and the corresponding conditions change when the energy expenditure of a neuron in order to spike and maintain the resting membrane potential is accounted for...
July 3, 2017: Bio Systems
https://www.readbyqxmd.com/read/28676239/elucidation-of-the-molecular-mechanism-of-heat-shock-proteins-and-its-correlation-with-k722q-mutations-in-lon-protease
#10
Sanchari Bhattacharjee, Rakhi Dasgupta, Angshuman Bagchi
Cells withstand the effects of temperature change with the help of small heat shock proteins IbpA and IbpB. The IbpAB protein complex interacts with Lon protease in their free form and gets degraded at physiological temperature when there is no temperature stress. However, the proteolytic degradation of IbpAB is diminished when Lon is mutated. The mutation K722Q in Lon brings about some structural changes so that the proteolytic interactions between the heat shock proteins with that of the mutated Lon protease are lost...
July 1, 2017: Bio Systems
https://www.readbyqxmd.com/read/28625482/equalizing-the-information-amounts-of-protein-and-mrna-by-information-theory
#11
Y Adiguzel
Based on the Shannon's information communication theory, information amount of the entire length of a polymeric macromolecule can be calculated in bits through adding the entropies of each building block. Proteins, DNA and RNA are such macromolecules. When only the building blocks' variation is considered as the source of entropy, there is seemingly lower information in case of the protein if this approach is applied directly on a protein of specific size and the coding sequence size of the mRNA corresponding to the particular length of the protein...
June 15, 2017: Bio Systems
https://www.readbyqxmd.com/read/28602731/energy-conservation-and-maximal-entropy-production-in-enzyme-reactions
#12
Andrej Dobovišek, Marko Vitas, Milan Brumen, Aleš Fajmut
A procedure for maximization of the density of entropy production in a single stationary two-step enzyme reaction is developed. Under the constraints of mass conservation, fixed equilibrium constant of a reaction and fixed products of forward and backward enzyme rate constants the existence of maximum in the density of entropy production is demonstrated. In the state with maximal density of entropy production the optimal enzyme rate constants, the stationary concentrations of the substrate and the product, the stationary product yield as well as the stationary reaction flux are calculated...
June 7, 2017: Bio Systems
https://www.readbyqxmd.com/read/28571930/hokf-high-order-kalman-filter-for-epilepsy-forecasting-modeling
#13
Ngoc Anh Thi Nguyen, Hyung-Jeong Yang, Sunhee Kim
Epilepsy forecasting has been extensively studied using high-order time series obtained from scalp-recorded electroencephalography (EEG). An accurate seizure prediction system would not only help significantly improve patients' quality of life, but would also facilitate new therapeutic strategies to manage epilepsy. This paper thus proposes an improved Kalman Filter (KF) algorithm to mine seizure forecasts from neural activity by modeling three properties in the high-order EEG time series: noise, temporal smoothness, and tensor structure...
May 30, 2017: Bio Systems
https://www.readbyqxmd.com/read/28535929/genetic-coding-and-united-hypercomplex-systems-in-the-models-of-algebraic-biology
#14
REVIEW
Sergey V Petoukhov
Structured alphabets of DNA and RNA in their matrix form of representations are connected with Walsh functions and a new type of systems of multidimensional numbers. This type generalizes systems of complex numbers and hypercomplex numbers, which serve as the basis of mathematical natural sciences and many technologies. The new systems of multi-dimensional numbers have interesting mathematical properties and are called in a general case as "systems of united-hypercomplex numbers" (or briefly "U-hypercomplex numbers")...
May 20, 2017: Bio Systems
https://www.readbyqxmd.com/read/28506827/how-tumor-growth-can-be-influenced-by-delayed-interactions-between-cancer-cells-and-the-microenvironment
#15
Dibakar Ghosh, Subhas Khajanchi, Sylvain Mangiarotti, Fabrice Denis, Syamal K Dana, Christophe Letellier
Although recent advances in oncology emphasized the role of microenvironment in tumor growth, the role of delays for modeling tumor growth is still uncertain. In this paper, we considered a model, describing the interactions of tumor cells with their microenvironment made of immune cells and host cells, in which we inserted, as suggested by the clinicians, two time delays, one in the interactions between tumor cells and immune cells and, one in the action of immune cells on tumor cells. We showed analytically that the singular point associated with the co-existence of the three cell populations loses its stability via a Hopf bifurcation...
May 12, 2017: Bio Systems
https://www.readbyqxmd.com/read/28495292/the-living-organism-strengthening-the-basis
#16
Roland Cazalis, Timoteo Carletti, Ron Cottam
In spite of the considerable amount of literature dedicated to the living organism, it retains its mysteries. One of the most discussed aspects nowadays is whether the term "cognition" can be attributed to all classes of organisms, or whether it only refers to a metaphoric use of one human reality. Our approach consists of retaining the term "cognition" and making it a technical term, in order to propose a generic model. In this way, cognition becomes what finally characterises an organism as an autonomous agent...
May 7, 2017: Bio Systems
https://www.readbyqxmd.com/read/28479110/boredom-begets-creativity-a-solution-to-the-exploitation-exploration-trade-off-in-predictive-coding
#17
Jaime Gomez-Ramirez, Tommaso Costa
Here we investigate whether systems that minimize prediction error e.g. predictive coding, can also show creativity, or on the contrary, prediction error minimization unqualifies for the design of systems that respond in creative ways to non recurrent problems. We argue that there is a key ingredient that has been overlooked by researchers that needs to be incorporated to understand intelligent behavior in biological and technical systems. This ingredient is boredom. We propose a mathematical model based on the Black-Scholes-Merton equation which provides mechanistic insights into the interplay between boredom and prediction pleasure as the key drivers of behavior...
May 4, 2017: Bio Systems
https://www.readbyqxmd.com/read/28465242/in-vitro-molecular-machine-learning-algorithm-via-symmetric-internal-loops-of-dna
#18
Ji-Hoon Lee, Seung Hwan Lee, Christina Baek, Hyosun Chun, Je-Hwan Ryu, Jin-Woo Kim, Russell Deaton, Byoung-Tak Zhang
Programmable biomolecules, such as DNA strands, deoxyribozymes, and restriction enzymes, have been used to solve computational problems, construct large-scale logic circuits, and program simple molecular games. Although studies have shown the potential of molecular computing, the capability of computational learning with DNA molecules, i.e., molecular machine learning, has yet to be experimentally verified. Here, we present a novel molecular learning in vitro model in which symmetric internal loops of double-stranded DNA are exploited to measure the differences between training instances, thus enabling the molecules to learn from small errors...
April 29, 2017: Bio Systems
https://www.readbyqxmd.com/read/28344109/phylogenomic-proximity-and-metabolic-discrepancy-of-methanosarcina-mazei-go1-across-methanosarcinal-genomes
#19
M Bharathi, P Chellapandi
Methanosarcina mazei Go1 is a heterotrophic methanogenic archaean contributing a significant role in global methane cycling and biomethanation process. Phylogenomic relatedness and metabolic discrepancy of this genome were described herein by comparing its whole genome sequence, intergenomic distance, genome function, synteny homologs and origin of replication, and marker genes with very closely related genomes, Methanosarcina acetivorans and Methanosarcina barkeri. Phylogenomic analysis of this study revealed that genome functional feature and metabolic core of M...
May 2017: Bio Systems
https://www.readbyqxmd.com/read/28300609/a-binary-representation-of-the-genetic-code
#20
Louis R Nemzer
This article introduces a novel binary representation of the canonical genetic code based on both the structural similarities of the nucleotides, as well as the physicochemical properties of the encoded amino acids. Each of the four mRNA bases is assigned a unique 2-bit identifier, so that the 64 triplet codons are each indexed by a 6-bit label. The ordering of the bits reflects the hierarchical organization manifested by the DNA replication/repair and tRNA translation systems. In this system, transition and transversion mutations are naturally expressed as binary operations, and the severities of the different point mutations can be analyzed...
May 2017: Bio Systems
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