scholarly journals Replication is Recursion; or, Lambda: the Biological Imperative

2015 ◽  
Author(s):  
Scott Federhen
Keyword(s):  
Living Cell ◽  
Mathematical Theory ◽  
Replication Fork ◽  
Computer Programs ◽  
Biological Processes ◽  
Theory Of Computation ◽  
Biological Replication ◽  
New Perspective ◽  
Living Organisms ◽  
Computational Systems

There is a striking visual symmetry between the 'paradoxical combinator' (which implements recursion in the mathematical theory of computation) and the biological replication fork (which implements reproduction in the living cell). Can this mean anything? Living organisms are information processors – the genome encodes instructions for the process of life much as computer programs encode instructions for a computer. Replication in biological systems is intuitively similar to recursion in computational systems. The following discussion will present enough of the mathematics to allow biologists to make sense of the symmetries in the logo. Mathematicians will learn nothing new about biology, but may be encouraged to look at biological processes from a new perspective.

Environmental significance of atrazine in aqueous systems and its removal by biological processes: an overview

2013 ◽  
Vol 8 (2) ◽  
pp. 159-178 ◽  
Keyword(s):  
Drinking Water ◽  
Ground Water ◽  
Water Environment ◽  
Biological Processes ◽  
Biological Degradation ◽  
Environmental Significance ◽  
Carbon And Nitrogen ◽  
Carbon Nitrogen Ratio ◽  
Nitrogen Ratio ◽  
Living Organisms

Atrazine, a chlorinated s-triazine group of herbicide is one of the most widely used pesticides in the World. Due to its extensive use, long half-life and various toxic properties, it has very high environmental significance. Up to 22 mg l-1 of atrazine was found in ground water whereas permissible limit of atrazine is in ppb level in drinking water. As per Indian standard there should not be any pesticide present in drinking water. Among many other treatment processes available, Incineration, adsorption, chemical treatment, phytoremediation and biodegradation are the most commonly used ones. Biological degradation of atrazine depends upon various factors like the operating environment, external carbon and nitrogen sources, carbon/ nitrogen ratio (C/N), water content and the bacterial strain. Although, general atrazine degradation pathways are available, the specific pathways in specific conditions are not yet clearly defined. In this paper extensive review has been made on the occurrence of atrazine in surface and ground water bodies, probable sources and causes of its occurrence in water environment, the toxicity of atrazine on various living organisms and its removal by biological processes.

scholarly journals The Etiology and Pathophysiology Genesis of Benign Prostatic Hyperplasia and Prostate Cancer: A New Perspective

Medicines ◽  
2021 ◽  
Vol 8 (6) ◽  
pp. 30
Author(s):  
Teow J. Phua
Keyword(s):  
Prostate Cancer ◽  
Benign Prostatic Hyperplasia ◽  
Cell Biology ◽  
Cancer Biology ◽  
Cost Savings ◽  
Prostatic Hyperplasia ◽  
Biological Processes ◽  
New Perspective ◽  
Prostatic Diseases

Background: The etiology of benign prostatic hyperplasia and prostate cancer are unknown, with ageing being the greatness risk factor. Methods: This new perspective evaluates the available interdisciplinary evidence regarding prostate ageing in terms of the cell biology of regulation and homeostasis, which could explain the timeline of evolutionary cancer biology as degenerative, inflammatory and neoplasm progressions in these multifactorial and heterogeneous prostatic diseases. Results: This prostate ageing degeneration hypothesis encompasses the testosterone-vascular-inflamm-ageing triad, along with the cell biology regulation of amyloidosis and autophagy within an evolutionary tumorigenesis microenvironment. Conclusions: An understanding of these biological processes of prostate ageing can provide potential strategies for early prevention and could contribute to maintaining quality of life for the ageing individual along with substantial medical cost savings.

Influence of sterilization conditions on sulfate-functionalized polyGGE

2021 ◽  
pp. 1-12
Author(s):  
Shuo Zhou ◽  
Xun Xu ◽  
Nan Ma ◽  
Friedrich Jung ◽  
Andreas Lendlein
Keyword(s):  
Microbial Contamination ◽  
Gamma Ray ◽  
Glycidyl Ether ◽  
Biological Processes ◽  
Chain Mobility ◽  
Functionalized Materials ◽  
Polymeric Implants ◽  
Gamma Ray Irradiation ◽  
Group Density ◽  
Living Organisms

Sulfated biomolecules are known to influence numerous biological processes in all living organisms. Particularly, they contribute to prevent and inhibit the hypercoagulation condition. The failure of polymeric implants and blood contacting devices is often related to hypercoagulation and microbial contamination. Here, bioactive sulfated biomacromolecules are mimicked by sulfation of poly(glycerol glycidyl ether) (polyGGE) films. Autoclaving, gamma-ray irradiation and ethylene oxide (EtO) gas sterilization techniques were applied to functionalized materials. The sulfate group density and hydrophilicity of sulfated polymers were decreased while chain mobility and thermal degradation were enhanced post autoclaving when compared to those after EtO sterilization. These results suggest that a quality control after sterilization is mandatory to ensure the amount and functionality of functionalized groups are retained.

scholarly journals Characterization of an Insoluble and Soluble Form of Melanin Produced by Streptomyces cavourensis SV 21, a Sea Cucumber Associated Bacterium

Marine Drugs ◽  
2022 ◽  
Vol 20 (1) ◽  
pp. 54
Author(s):  
Joko Tri Wibowo ◽  
Matthias Y. Kellermann ◽  
Lars-Erik Petersen ◽  
Yustian R. Alfiansah ◽  
Colleen Lattyak ◽  
...  
Keyword(s):  
Biological Properties ◽  
Water Soluble ◽  
Soluble Form ◽  
Wide Range ◽  
Biological Form ◽  
Insoluble Form ◽  
New Perspective ◽  
Living Organisms ◽  
Purification Protocol

Melanin is a widely distributed and striking dark-colored pigment produced by countless living organisms. Although a wide range of bioactivities have been recognized, there are still major constraints in using melanin for biotechnological applications such as its fragmentary known chemical structure and its insolubility in inorganic and organic solvents. In this study, a bacterial culture of Streptomyces cavourensis SV 21 produced two distinct forms of melanin: (1) a particulate, insoluble form as well as (2) a rarely observed water-soluble form. The here presented novel, acid-free purification protocol of purified particulate melanin (PPM) and purified dissolved melanin (PDM) represents the basis for an in-depth comparison of their physicochemical and biological properties, which were compared to the traditional acid-based precipitation of melanin (AM) and to a synthetic melanin standard (SM). Our data show that the differences in solubility between PDM and PPM in aqueous solutions may be a result of different adjoining cation species, since the soluble PDM polymer is largely composed of Mg2+ ions and the insoluble PPM is dominated by Ca2+ ions. Furthermore, AM shared most properties with SM, which is likely attributed to a similar, acid-based production protocol. The here presented gentler approach of purifying melanin facilitates a new perspective of an intact form of soluble and insoluble melanin that is less chemical altered and thus closer to its original biological form.

Glycan Labeling and Analysis in Cells and In Vivo

2021 ◽  
Vol 14 (1) ◽  
pp. 363-387
Author(s):  
Bo Cheng ◽  
Qi Tang ◽  
Che Zhang ◽  
Xing Chen
Keyword(s):  
Chemical Modification ◽  
Biological Function ◽  
Biological Processes ◽  
Affinity Tags ◽  
Functional Roles ◽  
Antibody Conjugates ◽  
Living Organisms ◽  
In Cells

As one of the major types of biomacromolecules in the cell, glycans play essential functional roles in various biological processes. Compared with proteins and nucleic acids, the analysis of glycans in situ has been more challenging. Herein we review recent advances in the development of methods and strategies for labeling, imaging, and profiling of glycans in cells and in vivo. Cellular glycans can be labeled by affinity-based probes, including lectin and antibody conjugates, direct chemical modification, metabolic glycan labeling, and chemoenzymatic labeling. These methods have been applied to label glycans with fluorophores, which enables the visualization and tracking of glycans in cells, tissues, and living organisms. Alternatively, labeling glycans with affinity tags has enabled the enrichment of glycoproteins for glycoproteomic profiling. Built on the glycan labeling methods, strategies enabling cell-selective and tissue-specific glycan labeling and protein-specific glycan imaging have been developed. With these methods and strategies, researchers are now better poised than ever to dissect the biological function of glycans in physiological or pathological contexts.

scholarly journals Treating Senescence like Cancer: Novel Perspectives in Senotherapy of Chronic Diseases

2020 ◽  
Vol 21 (21) ◽  
pp. 7984
Author(s):  
Alessia Mongelli ◽  
Sandra Atlante ◽  
Veronica Barbi ◽  
Tiziana Bachetti ◽  
Fabio Martelli ◽  
...  
Keyword(s):  
Chronic Diseases ◽  
Cell Senescence ◽  
Biological Processes ◽  
Social Relevance ◽  
Chemical Agents ◽  
Age Related ◽  
Living Organisms ◽  
Specific Pathway

The WHO estimated around 41 million deaths worldwide each year for age-related non-communicable chronic diseases. Hence, developing strategies to control the accumulation of cell senescence in living organisms and the overall aging process is an urgently needed problem of social relevance. During aging, many biological processes are altered, which globally induce the dysfunction of the whole organism. Cell senescence is one of the causes of this modification. Nowadays, several drugs approved for anticancer therapy have been repurposed to treat senescence, and others are under scrutiny in vitro and in vivo to establish their senomorphic or senolytic properties. In some cases, this research led to a significant increase in cell survival or to a prolonged lifespan in animal models, at least. Senomorphics can act to interfere with a specific pathway in order to restore the appropriate cellular function, preserve viability, and to prolong the lifespan. On the other hand, senolytics induce apoptosis in senescent cells allowing the remaining non–senescent population to preserve or restore tissue function. A large number of research articles and reviews recently addressed this topic. Herein, we would like to focus attention on those chemical agents with senomorphic or senolytic properties that perspectively, according to literature, suggest a potential application as senotherapeutics for chronic diseases.

Computational Knowledge Representation in Cognitive Science

2019 ◽  
Vol 56 (3) ◽  
pp. 138-152
Author(s):  
Igor F. Mikhailov ◽  
Keyword(s):  
Knowledge Representation ◽  
Cognitive Science ◽  
Network Architecture ◽  
Mathematical Theory ◽  
Computational Approach ◽  
Formal Epistemology ◽  
The Social ◽  
Parallel Network ◽  
Substrate Independent ◽  
Computational Systems

Cognitive research can contribute to the formal epistemological study of knowledge representation inasmuch as, firstly, it may be regarded as a descriptive science of the very same subject as that, of which formal epistemology is a normative one. And, secondly, the notion of representation plays a constitutive role in both disciplines, though differing therein in shades of its meaning. Representation, in my view, makes sense only being paired with computation. A process may be viewed as computational if it adheres to some algorithm and is substrate-independent. Traditionally, psychology is not directly determined by neuroscience, sticking to functional or dynamical analyses in the what-level and skipping mechanistic explanations in the how-level. Therefore, any version of computational approach in psychology is a very promising move in connecting the two scientific realms. On the other hand, the digital and linear computational approach of the classical cognitive science is of little help in this way, as it is not biologically realistic. Thus, what is needed there on the methodological level, is a shift from classical Turing-style computationalism to a generic computational theory that would comprehend the complicated architecture of neuronal computations. To this end, the cutting-edge cognitive neuroscience is in need of а satisfactory mathematical theory applicable to natural, particularly neuronal, computations. Computational systems may be construed as natural or artificial devices that use some physical processes on their lower levels as atomic operations for algorithmic processes on their higher levels. A cognitive system is a multi-level mechanism, in which linguistic, visual and other processors are built on numerous levels of more elementary operations, which ultimately boil down to atomic neural spikes. The hypothesis defended in this paper is that knowledge derives not only from an individual computational device, such as a brain, but also from the social communication system that, in its turn, may be presented as a kind of supercomputer of the parallel network architecture. Therefore, a plausible account of knowledge production and exchange must base on some mathematical theory of social computations, along with that of natural, particularly neuronal, ones.

scholarly journals New perspective in the assessment of total intracellular magnesium

2014 ◽  
Vol 87 (1) ◽  
Author(s):  
Azzurra Sargenti ◽  
Lucia Merolle ◽  
Giulia Andreani ◽  
Concettina Cappadone ◽  
Giovanna Farruggia ◽  
...  
Keyword(s):  
Quantitative Determination ◽  
Atomic Absorption Spectroscopy ◽  
Biological Processes ◽  
Intracellular Magnesium ◽  
Qualitative And Quantitative ◽  
High Affinity ◽  
New Family ◽  
New Perspective ◽  
Good Agreement

Magnesium (Mg) is essential for biological processes, but its cellular homeostasis has not been thoroughly elucidated, mainly because of the inadequacy of the available techniques to map intracellular Mg distribution. Recently, particular interest has been raised by a new family of fluorescent probes, diaza-18-crown-hydroxyquinoline (DCHQ), that shows remarkably high affinity and specificity for Mg, thus permitting the detection of the total intracellular Mg. The data obtained by fluori- metric and cytofluorimetric assays performed with DCHQ5 are in good agreement with atomic absorption spectroscopy, confirming that DCHQ5 probe allows both qualitative and quantitative determination of total intracellular Mg.

Information and Meaning

2020 ◽  
Author(s):  
Wendy Wheeler
Keyword(s):  
Information Technology ◽  
Mathematical Theory ◽  
Single Cells ◽  
Feedback Loops ◽  
Learning Systems ◽  
Evolutionary Learning ◽  
Bell Laboratory ◽  
Living Organisms ◽  
Do So ◽  
The Way

Since the publication of Claude Shannon’s groundbreaking paper, “A Mathematical Theory of Communication,” in two parts in the Bell Laboratory journal in 1948, understanding and research concerning communication and information has received a technicized treatment. As biosemiotics has been at the forefront in arguing, all living organisms communicate, but they do not do so in the digital mode used in information technology (IT) engineering. Life communicates in inherited, evolutionary ways that are traceable from single cells all the way to complex humans. What IT engineers call “redundancy” those studying living organisms call “meaning.” The trade between individual organisms and their environment takes place in the circulation, interpretation, and feedback loops of semiosis. In this way, organisms are able to maintain the features of adaptive, creative, and evolutionary learning systems by modeling their worlds in open, receptive fashion via the use of iconic and indexical signs. In other words, organisms make use of natural, then cultural metaphors and metonyms.

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