scholarly journals Biological information

2020 ◽  
Vol 139 (4) ◽  
pp. 361-370
Author(s):  
Jürgen Jost
Keyword(s):  
Computer Science ◽  
Genetic Information ◽  
Spatial Organization ◽  
Environmental Information ◽  
External Factors ◽  
Biological Information ◽  
Cellular Processes ◽  
Theory Of Information ◽  
Concept Of Information

AbstractIn computer science, we can theoretically neatly separate transmission and processing of information, hardware and software, and programs and their inputs. This is much more intricate in biology. Nevertheless, I argue that Shannon’s concept of information is useful in biology, although its application is not as straightforward as many people think. In fact, the recently developed theory of information decomposition can shed much light on the complementarity between coding and regulatory, or internal and environmental information. The key challenge that we formulate in this contribution is to understand how genetic information and external factors combine to create an organism, and conversely how the genome has learned in the course of evolution how to harness the environment, and analogously how coding, regulation and spatial organization interact in cellular processes.

scholarly journals Epigenetic Methylations on N6-Adenine and N6-Adenosine with the same Input but Different Output

2019 ◽  
Vol 20 (12) ◽  
pp. 2931 ◽  
Author(s):  
Zhiqing Li ◽  
Ping Zhao ◽  
Qingyou Xia
Keyword(s):  
Genetic Information ◽  
Target Genes ◽  
Technological Development ◽  
Wide Spectrum ◽  
Functional Identification ◽  
Methyl Group ◽  
Cellular Processes ◽  
Dna And Rna ◽  
Future Challenges ◽  
Detection Strategies

Epigenetic modifications on individual bases in DNA and RNA can encode inheritable genetic information beyond the canonical bases. Among the nucleic acid modifications, DNA N6-methadenine (6mA) and RNA N6-methyladenosine (m6A) have recently been well-studied due to the technological development of detection strategies and the functional identification of modification enzymes. The current findings demonstrate a wide spectrum of 6mA and m6A distributions from prokaryotes to eukaryotes and critical roles in multiple cellular processes. It is interesting that the processes of modification in which the methyl group is added to adenine and adenosine are the same, but the outcomes of these modifications in terms of their physiological impacts in organisms are quite different. In this review, we summarize the latest progress in the study of enzymes involved in the 6mA and m6A methylation machinery, including methyltransferases and demethylases, and their functions in various biological pathways. In particular, we focus on the mechanisms by which 6mA and m6A regulate the expression of target genes, and we highlight the future challenges in epigenetic regulation.

scholarly journals Chromatin dynamics during interphase and cell division: similarities and differences between model and crop plants

2019 ◽  
Vol 71 (17) ◽  
pp. 5205-5222 ◽  
Author(s):  
Ales Pecinka ◽  
Christian Chevalier ◽  
Isabelle Colas ◽  
Kriton Kalantidis ◽  
Serena Varotto ◽  
...  
Keyword(s):  
Genetic Information ◽  
Molecular Mechanisms ◽  
Current Knowledge ◽  
Crop Plants ◽  
Regulatory Proteins ◽  
Abiotic And Biotic Stresses ◽  
Chromatin Dynamics ◽  
Biotic Stresses ◽  
Cellular Processes ◽  
Organismal Development

Abstract Genetic information in the cell nucleus controls organismal development and responses to the environment, and finally ensures its own transmission to the next generations. To achieve so many different tasks, the genetic information is associated with structural and regulatory proteins, which orchestrate nuclear functions in time and space. Furthermore, plant life strategies require chromatin plasticity to allow a rapid adaptation to abiotic and biotic stresses. Here, we summarize current knowledge on the organization of plant chromatin and dynamics of chromosomes during interphase and mitotic and meiotic cell divisions for model and crop plants differing as to genome size, ploidy, and amount of genomic resources available. The existing data indicate that chromatin changes accompany most (if not all) cellular processes and that there are both shared and unique themes in the chromatin structure and global chromosome dynamics among species. Ongoing efforts to understand the molecular mechanisms involved in chromatin organization and remodeling have, together with the latest genome editing tools, potential to unlock crop genomes for innovative breeding strategies and improvements of various traits.

scholarly journals Signal co-operation between integrins and other receptor systems

2009 ◽  
Vol 418 (3) ◽  
pp. 491-506 ◽  
Author(s):  
Charles H. Streuli ◽  
Nasreen Akhtar
Keyword(s):  
Cell Fate ◽  
Tyrosine Kinases ◽  
Spatial Organization ◽  
Growth Factor Receptor ◽  
Cellular Processes ◽  
Extracellular Signals ◽  
Β1 Integrins ◽  
Α6β4 Integrin ◽  
Epidermal Growth ◽  
Adhesive Interactions

The multicellular nature of metazoans means that all cellular processes need to be tuned by adhesive interactions between cells and their local microenvironment. The spatial organization of cells within tissues requires sophisticated networks of extracellular signals to control their survival and proliferation, movements and positioning, and differentiated function. These cellular characteristics are mediated by multiple inputs from adhesion systems in combination with soluble and developmental signals. In the present review we explore how one class of adhesion receptor, the integrins, co-operate with other types of receptor to control diverse aspects of cell fate. In particular we discuss: (i) how β3 and β1 integrins work together with growth factors to control angiogenesis; (ii) how α6β4 integrin co-operates with receptor tyrosine kinases in normal epithelial function and cancer; (iii) the interplay between β1 integrins and EGF (epidermal growth factor) receptor; (iv) signal integration connecting integrins and cytokine receptors for interleukins, prolactin and interferons; and (v) how integrins and syndecans co-operate in cell migration.

scholarly journals Padlock and Proximity Probes forIn Situand Array-Based Analyses: Tools for the Post-Genomic Era

2003 ◽  
Vol 4 (5) ◽  
pp. 525-530 ◽  
Author(s):  
Ulf Landegren ◽  
Fredrik Dahl ◽  
Mats Nilsson ◽  
Simon Fredriksson ◽  
Johan Banér ◽  
...  
Keyword(s):  
Full Advantage ◽  
High Throughput ◽  
General Problem ◽  
Genetic Information ◽  
Biological Systems ◽  
Biological Information ◽  
Dna Ligation ◽  
Health And Disease ◽  
Macromolecular Composition ◽  
Detection Specificity

Highly specific high-throughput assays will be required to take full advantage of the accumulating information about the macromolecular composition of cells and tissues, in order to characterize biological systems in health and disease. We discuss the general problem of detection specificity and present the approach our group has taken, involving the reformatting of analogue biological information to digital reporter segments of genetic information via a series of DNA ligation assays. The assays enable extensive, coordinated analyses of the numbers and locations of genes, transcripts and protein.

scholarly journals LIVING BEINGS AS INFORMED SYSTEMS: TOWARDS A PHYSICAL THEORY OF INFORMATION

1996 ◽  
Vol 04 (04) ◽  
pp. 565-584
Author(s):  
ANTONIO LEÓN
Keyword(s):  
Physical Theory ◽  
Point Of View ◽  
Physical Point ◽  
Absolute Measure ◽  
Functional Measure ◽  
Physical Information ◽  
Physical Effects ◽  
Theory Of Information ◽  
Concept Of Information ◽  
Physical Laws

I propose here a new concept of information based on two relevant aspects of its expression. The first refers to the undeniable fact that the expression of information modifies the physical state of its receiver. The second, to that the said changes are arbitrary, not deducible from physical laws but from a code established arbitrarily. Thus, physical information is proposed here as the capacity of producing arbitrary changes. Once defined information from this physical point of view, I deduce some basic physical properties of informed systems. These properties (renewal, self-reproducing, evolution, diversification) are immediately recognisable as the attributes most characteristic of living beings, the only natural informed systems we know. Although no new attribute of living beings has been discovered here, the formal way used to obtain them is a significant novelty. I also propose here a double evaluation of information. The former is an absolute measure of the physical effects of its expression based on Einstein’s probability. The latter is a functional measure based on the probability that an informed system attain a given objective as consequence of the expression of its information.

scholarly journals Infusing Autopoietic and Cognitive Behaviors into Digital Automata to Improve Their Sentience, Resilience, and Intelligence

2022 ◽  
Vol 6 (1) ◽  
pp. 7
Author(s):  
Rao Mikkilineni
Keyword(s):  
General Theory ◽  
Computer Science ◽  
Common Knowledge ◽  
Physical World ◽  
Cognitive Behaviors ◽  
Symbolic Computing ◽  
New Science ◽  
Theory Of Information ◽  
Living Organisms ◽  
Classical Computer

All living beings use autopoiesis and cognition to manage their “life” processes from birth through death. Autopoiesis enables them to use the specification in their genomes to instantiate themselves using matter and energy transformations. They reproduce, replicate, and manage their stability. Cognition allows them to process information into knowledge and use it to manage its interactions between various constituent parts within the system and its interaction with the environment. Currently, various attempts are underway to make modern computers mimic the resilience and intelligence of living beings using symbolic and sub-symbolic computing. We discuss here the limitations of classical computer science for implementing autopoietic and cognitive behaviors in digital machines. We propose a new architecture applying the general theory of information (GTI) and pave the path to make digital automata mimic living organisms by exhibiting autopoiesis and cognitive behaviors. The new science, based on GTI, asserts that information is a fundamental constituent of the physical world and that living beings convert information into knowledge using physical structures that use matter and energy. Our proposal uses the tools derived from GTI to provide a common knowledge representation from existing symbolic and sub-symbolic computing structures to implement autopoiesis and cognitive behaviors.

scholarly journals Information: Concept Clarification and Theoretical Representation

2011 ◽  
Vol 9 (2) ◽  
pp. 347-357 ◽  
Author(s):  
Mark Burgin
Keyword(s):  
Information Theory ◽  
General Theory ◽  
Mathematical Models ◽  
Synthetic Approach ◽  
Conceptual Level ◽  
Theoretical Level ◽  
Information Operations ◽  
Theory Of Information ◽  
Concept Of Information ◽  
Information Concept

The general theory of information is a synthetic approach, which organizes and encompasses all main directions in information theory. It is developed on three levels: conceptual, methodological and theoretical. On the conceptual level, the concept of information is purified and information operations are separated and described. On the methodological level, it is formulated as system of principles, explaining what information is and how to measure information. On the theoretical level, mathematical models of information are constructed and studied. The goal of this paper is to clarify the concept of information and discuss its mathematical models, establishing relations with physics as the most developed science.

Towards the General Theory of Information Asymmetry

2015 ◽  
pp. 124-135 ◽  
Author(s):  
Waseem Afzal
Keyword(s):  
Literature Review ◽  
General Theory ◽  
Information Asymmetry ◽  
Information Asymmetries ◽  
Different Types ◽  
Theory Of Information ◽  
Concept Of Information

Information imperfections of various kinds are present around us and information asymmetry is one such kind. The phrase “information imperfection” indicates information which is less than ideal for many conceivable reasons. The concept of “information asymmetry” is different, and indicates the presence of more information at one end of an informational distribution. The purpose of this chapter is not to provide a literature review of information asymmetry but to (1) build on previous work, (2) suggest a set of concepts, and (3) describe examples of information asymmetries in order to propose a framework for a general theory of information asymmetry. To this end, this chapter provides a brief overview of the concepts of information asymmetry and information imperfection. It also proposes a set of four concepts considered to be of importance in understanding information asymmetry; describes two major categories of information asymmetries; discusses different types of informational disturbances; and finally discusses the potential effects of information asymmetries.

scholarly journals The meaning of biological information

2016 ◽  
Vol 374 (2063) ◽  
pp. 20150065 ◽  
Author(s):  
Eugene V. Koonin
Keyword(s):  
Entire Range ◽  
Evolutionary Conservation ◽  
Amino Acid Sequences ◽  
Biological Information ◽  
Biological Functions ◽  
Biologically Relevant ◽  
Functional Roles ◽  
Biological Meaning ◽  
Concept Of Information ◽  
Single Sequence

Biological information encoded in genomes is fundamentally different from and effectively orthogonal to Shannon entropy. The biologically relevant concept of information has to do with ‘meaning’, i.e. encoding various biological functions with various degree of evolutionary conservation. Apart from direct experimentation, the meaning, or biological information content, can be extracted and quantified from alignments of homologous nucleotide or amino acid sequences but generally not from a single sequence, using appropriately modified information theoretical formulae. For short, information encoded in genomes is defined vertically but not horizontally. Informally but substantially, biological information density seems to be equivalent to ‘meaning’ of genomic sequences that spans the entire range from sharply defined, universal meaning to effective meaninglessness. Large fractions of genomes, up to 90% in some plants, belong within the domain of fuzzy meaning. The sequences with fuzzy meaning can be recruited for various functions, with the meaning subsequently fixed, and also could perform generic functional roles that do not require sequence conservation. Biological meaning is continuously transferred between the genomes of selfish elements and hosts in the process of their coevolution. Thus, in order to adequately describe genome function and evolution, the concepts of information theory have to be adapted to incorporate the notion of meaning that is central to biology.

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