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Baverstock K. The Gene: An appraisal. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024; 186:e73-e88. [PMID: 38044248 DOI: 10.1016/j.pbiomolbio.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The gene can be described as the foundational concept of modern biology. As such, it has spilled over into daily discourse, yet it is acknowledged among biologists to be ill-defined. Here, following a short history of the gene, I analyse critically its role in inheritance, evolution, development, and morphogenesis. Wilhelm Johannsen's genotype-conception, formulated in 1910, has been adopted as the foundation stone of genetics, giving the gene a higher degree of prominence than is justified by the evidence. An analysis of the results of the Long-Term Evolution Experiment (LTEE) with E. coli bacteria, grown over 60,000 generations, does not support spontaneous gene mutation as the source of variance for natural selection. From this it follows that the gene is not Mendel's unit of inheritance: that must be Johannsen's transmission-conception at the gamete phenotype level, a form of inheritance that Johannsen did not consider. Alternatively, I contend that biology viewed on the bases of thermodynamics, complex system dynamics, and self-organisation, provides a new framework for the foundations of biology. In this framework, the gene plays a passive role as a vital information store: it is the phenotype that plays the active role in inheritance, evolution, development, and morphogenesis.
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Affiliation(s)
- Keith Baverstock
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio Campus, Kuopio, Finland.
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2
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Cuevas-Zuviría B, Fer E, Adam ZR, Kaçar B. The modular biochemical reaction network structure of cellular translation. NPJ Syst Biol Appl 2023; 9:52. [PMID: 37884541 PMCID: PMC10603163 DOI: 10.1038/s41540-023-00315-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
Translation is an essential attribute of all living cells. At the heart of cellular operation, it is a chemical information decoding process that begins with an input string of nucleotides and ends with the synthesis of a specific output string of peptides. The translation process is interconnected with gene expression, physiological regulation, transcription, and responses to signaling molecules, among other cellular functions. Foundational efforts have uncovered a wealth of knowledge about the mechanistic functions of the components of translation and their many interactions between them, but the broader biochemical connections between translation, metabolism and polymer biosynthesis that enable translation to occur have not been comprehensively mapped. Here we present a multilayer graph of biochemical reactions describing the translation, polymer biosynthesis and metabolism networks of an Escherichia coli cell. Intriguingly, the compounds that compose these three layers are distinctly aggregated into three modes regardless of their layer categorization. Multimodal mass distributions are well-known in ecosystems, but this is the first such distribution reported at the biochemical level. The degree distributions of the translation and metabolic networks are each likely to be heavy-tailed, but the polymer biosynthesis network is not. A multimodal mass-degree distribution indicates that the translation and metabolism networks are each distinct, adaptive biochemical modules, and that the gaps between the modes reflect evolved responses to the functional use of metabolite, polypeptide and polynucleotide compounds. The chemical reaction network of cellular translation opens new avenues for exploring complex adaptive phenomena such as percolation and phase changes in biochemical contexts.
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Affiliation(s)
- Bruno Cuevas-Zuviría
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Evrim Fer
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Zachary R Adam
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Geosciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Betül Kaçar
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
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Richardson K. Genes and knowledge: Response to Baverstock, K. the gene an appraisal. https://doi.org/10.1016/j.pbiomolbio.2021.04.005. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 167:12-17. [PMID: 34736965 DOI: 10.1016/j.pbiomolbio.2021.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 09/21/2021] [Accepted: 10/26/2021] [Indexed: 06/13/2023]
Abstract
This response aims to expand on some of the issues raised by Keith Baverstock's The Gene: An Appraisal, especially on the evolution and nature of knowledge in living things. In contrast to the simple associationism envisaged in "genetic information", it emphasises the dynamic complexity and changeability of most natural environments, and, therefore, predictability based on underlying statistical structures. That seems to be the basis of the "cognitive" functions increasingly being reported about cellular, as well as more evolved, functions, and of the autonomous agency of organisms thriving creatively in complex environments.
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4
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Silva MP, Rodrigues CG, Varanda WA, Nogueira RA. Memory in Ion Channel Kinetics. Acta Biotheor 2021; 69:697-722. [PMID: 34043104 DOI: 10.1007/s10441-021-09415-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 05/20/2021] [Indexed: 12/21/2022]
Abstract
Ion channels are transport proteins present in the lipid bilayers of biological membranes. They are involved in many physiological processes, such as the generation of nerve impulses, hormonal secretion, and heartbeat. Conformational changes in the ion channel-forming protein allow the opening or closing of pores to control the ionic flux through the cell membranes. The opening and closing of the ion channel have been classically treated as a random kinetic process, known as a Markov process. Here the time the channel remains in a given state is assumed to be independent of the condition it had in the previous state. More recently, however, several studies have shown that this process is not random but a deterministic one, where both the open and closed dwell-times and the ionic current flowing through the channel are history-dependent. This property is called long memory or long-range correlation. However, there is still much controversy regarding how this memory originates, which region of the channel is responsible for this property, and which models could best reproduce the memory effect. In this article, we provide a review of what is, where it is, its possible origin, and the mathematical methods used to analyze the long-term memory present in the kinetic process of ion channels.
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Affiliation(s)
- M P Silva
- Department of Animal Morphology and Physiology, Federal Rural University of Pernambuco, Recife, Pernambuco, Brazil
| | - C G Rodrigues
- Department of Biophysics and Radiobiology, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | - W A Varanda
- Department of Physiology-Faculty of Medicine of Ribeirão Preto, University of São Paulo (Retired), Ribeirão Preto, São Paulo, Brazil
| | - R A Nogueira
- Department of Animal Morphology and Physiology, Federal Rural University of Pernambuco, Recife, Pernambuco, Brazil.
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Correspondence insights into the role of genes in cell functionality. Comments on "The gene: An appraisal" by K. Baverstock. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 167:152-160. [PMID: 34624359 DOI: 10.1016/j.pbiomolbio.2021.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 11/21/2022]
Abstract
One of the most important goals of the post-genomic era is to understand the different sources of molecular information that regulate the functional and structural architecture of cells. In this regard, Prof. K. Baverstock underscores in his recent article "The gene: An appraisal" (Baverstock, 2021) that genes are not the leading elements in cellular functionality, inheritance and evolution. As a consequence, the theory of evolution based on the Neo-Darwinian synthesis, is inadequate for today's scientific evidence. Conversely, the author contends that life processes viewed on the basis of thermodynamics, complex system dynamics and self-organization provide a new framework for the foundations of Biology. I consider it necessary to comment on some essential aspects of this relevant work, and here I present a short overview of the main non-genetic sources of biomolecular order and complexity that underline the molecular dynamics and functionality of cells. These sources generate different processes of complexity, which encompasses from the most elementary levels of molecular activity to the emergence of systemic behaviors, and the information necessary to sustain them is not contained in the genome.
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Baverstock K. The gene: An appraisal. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 164:46-62. [PMID: 33979646 DOI: 10.1016/j.pbiomolbio.2021.04.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/14/2021] [Accepted: 04/22/2021] [Indexed: 11/29/2022]
Abstract
The gene can be described as the foundational concept of modern biology. As such, it has spilled over into daily discourse, yet it is acknowledged among biologists to be ill-defined. Here, following a short history of the gene, I analyse critically its role in inheritance, evolution, development, and morphogenesis. Wilhelm Johannsen's genotype-conception, formulated in 1910, has been adopted as the foundation stone of genetics, giving the gene a higher degree of prominence than is justified by the evidence. An analysis of the results of the Long-Term Evolution Experiment (LTEE) with E. coli bacteria, grown over 60,000 generations, does not support spontaneous gene mutation as the source of variance for natural selection. From this it follows that the gene is not Mendel's unit of inheritance: that must be Johannsen's transmission-conception at the gamete phenotype level, a form of inheritance that Johannsen did not consider. Alternatively, I contend that biology viewed on the bases of thermodynamics, complex system dynamics and self-organisation, provides a new framework for the foundations of biology. In this framework, the gene plays a passive role as a vital information store: it is the phenotype that plays the active role in inheritance, evolution, development, and morphogenesis.
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Affiliation(s)
- Keith Baverstock
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio Campus, Kuopio, Finland.
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Carrasco-Pujante J, Bringas C, Malaina I, Fedetz M, Martínez L, Pérez-Yarza G, Dolores Boyano M, Berdieva M, Goodkov A, López JI, Knafo S, De la Fuente IM. Associative Conditioning Is a Robust Systemic Behavior in Unicellular Organisms: An Interspecies Comparison. Front Microbiol 2021; 12:707086. [PMID: 34349748 PMCID: PMC8327096 DOI: 10.3389/fmicb.2021.707086] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 06/22/2021] [Indexed: 11/17/2022] Open
Abstract
The capacity to learn new efficient systemic behavior is a fundamental issue of contemporary biology. We have recently observed, in a preliminary analysis, the emergence of conditioned behavior in some individual amoebae cells. In these experiments, cells were able to acquire new migratory patterns and remember them for long periods of their cellular cycle, forgetting them later on. Here, following a similar conceptual framework of Pavlov's experiments, we have exhaustively studied the migration trajectories of more than 2000 individual cells belonging to three different species: Amoeba proteus, Metamoeba leningradensis, and Amoeba borokensis. Fundamentally, we have analyzed several relevant properties of conditioned cells, such as the intensity of the responses, the directionality persistence, the total distance traveled, the directionality ratio, the average speed, and the persistence times. We have observed that cells belonging to these three species can modify the systemic response to a specific stimulus by associative conditioning. Our main analysis shows that such new behavior is very robust and presents a similar structure of migration patterns in the three species, which was characterized by the presence of conditioning for long periods, remarkable straightness in their trajectories and strong directional persistence. Our experimental and quantitative results, compared with other studies on complex cellular responses in bacteria, protozoa, fungus-like organisms and metazoans that we discus here, allow us to conclude that cellular associative conditioning might be a widespread characteristic of unicellular organisms. This new systemic behavior could be essential to understand some key principles involved in increasing the cellular adaptive fitness to microenvironments.
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Affiliation(s)
- Jose Carrasco-Pujante
- Department of Physiology and Cell Biology, Faculty of Health Sciences, The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Carlos Bringas
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Iker Malaina
- Department of Mathematics, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Maria Fedetz
- Department of Cell Biology and Immunology, CSIC, Institute of Parasitology and Biomedicine “López-Neyra”, Granada, Spain
| | - Luis Martínez
- Department of Mathematics, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
- Basque Center of Applied Mathematics, Bilbao, Spain
| | - Gorka Pérez-Yarza
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - María Dolores Boyano
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Mariia Berdieva
- Laboratory of Cytology of Unicellular Organisms, Institute of Cytology Russian Academy of Science, Saint Petersburg, Russia
| | - Andrew Goodkov
- Laboratory of Cytology of Unicellular Organisms, Institute of Cytology Russian Academy of Science, Saint Petersburg, Russia
| | - José I. López
- Department of Pathology, Cruces University Hospital, Biocruces-Bizkaia Health Research Institute, Barakaldo, Spain
| | - Shira Knafo
- Department of Physiology and Cell Biology, Faculty of Health Sciences, The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beersheba, Israel
- Biophysics Institute, CSIC-UPV/EHU, University of the Basque Country (UPV/EHU) and Ikerbasque - Basque Foundation for Science, Bilbao, Spain
| | - Ildefonso M. De la Fuente
- Department of Mathematics, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
- Department of Nutrition, CEBAS-CSIC Institute, Espinardo University Campus, Murcia, Spain
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De la Fuente IM, Martínez L, Carrasco-Pujante J, Fedetz M, López JI, Malaina I. Self-Organization and Information Processing: From Basic Enzymatic Activities to Complex Adaptive Cellular Behavior. Front Genet 2021; 12:644615. [PMID: 34093645 PMCID: PMC8176287 DOI: 10.3389/fgene.2021.644615] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/16/2021] [Indexed: 11/13/2022] Open
Abstract
One of the main aims of current biology is to understand the origin of the molecular organization that underlies the complex dynamic architecture of cellular life. Here, we present an overview of the main sources of biomolecular order and complexity spanning from the most elementary levels of molecular activity to the emergence of cellular systemic behaviors. First, we have addressed the dissipative self-organization, the principal source of molecular order in the cell. Intensive studies over the last four decades have demonstrated that self-organization is central to understand enzyme activity under cellular conditions, functional coordination between enzymatic reactions, the emergence of dissipative metabolic networks (DMN), and molecular rhythms. The second fundamental source of order is molecular information processing. Studies on effective connectivity based on transfer entropy (TE) have made possible the quantification in bits of biomolecular information flows in DMN. This information processing enables efficient self-regulatory control of metabolism. As a consequence of both main sources of order, systemic functional structures emerge in the cell; in fact, quantitative analyses with DMN have revealed that the basic units of life display a global enzymatic structure that seems to be an essential characteristic of the systemic functional metabolism. This global metabolic structure has been verified experimentally in both prokaryotic and eukaryotic cells. Here, we also discuss how the study of systemic DMN, using Artificial Intelligence and advanced tools of Statistic Mechanics, has shown the emergence of Hopfield-like dynamics characterized by exhibiting associative memory. We have recently confirmed this thesis by testing associative conditioning behavior in individual amoeba cells. In these Pavlovian-like experiments, several hundreds of cells could learn new systemic migratory behaviors and remember them over long periods relative to their cell cycle, forgetting them later. Such associative process seems to correspond to an epigenetic memory. The cellular capacity of learning new adaptive systemic behaviors represents a fundamental evolutionary mechanism for cell adaptation.
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Affiliation(s)
- Ildefonso M. De la Fuente
- Department of Nutrition, CEBAS-CSIC Institute, Murcia, Spain
- Department of Mathematics, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Luis Martínez
- Department of Mathematics, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, Leioa, Spain
- Basque Center of Applied Mathematics (BCAM), Bilbao, Spain
| | - Jose Carrasco-Pujante
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Maria Fedetz
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine “López-Neyra”, CSIC, Granada, Spain
| | - José I. López
- Department of Pathology, Cruces University Hospital, Biocruces-Bizkaia Health Research Institute, Barakaldo, Spain
| | - Iker Malaina
- Department of Mathematics, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, Leioa, Spain
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De la Fuente IM, López JI. Cell Motility and Cancer. Cancers (Basel) 2020; 12:E2177. [PMID: 32764365 PMCID: PMC7464129 DOI: 10.3390/cancers12082177] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/03/2020] [Accepted: 08/03/2020] [Indexed: 02/07/2023] Open
Abstract
Cell migration is an essential systemic behavior, tightly regulated, of all living cells endowed with directional motility that is involved in the major developmental stages of all complex organisms such as morphogenesis, embryogenesis, organogenesis, adult tissue remodeling, wound healing, immunological cell activities, angiogenesis, tissue repair, cell differentiation, tissue regeneration as well as in a myriad of pathological conditions. However, how cells efficiently regulate their locomotion movements is still unclear. Since migration is also a crucial issue in cancer development, the goal of this narrative is to show the connection between basic findings in cell locomotion of unicellular eukaryotic organisms and the regulatory mechanisms of cell migration necessary for tumor invasion and metastases. More specifically, the review focuses on three main issues, (i) the regulation of the locomotion system in unicellular eukaryotic organisms and human cells, (ii) how the nucleus does not significantly affect the migratory trajectories of cells in two-dimension (2D) surfaces and (iii) the conditioned behavior detected in single cells as a primitive form of learning and adaptation to different contexts during cell migration. New findings in the control of cell motility both in unicellular organisms and mammalian cells open up a new framework in the understanding of the complex processes involved in systemic cellular locomotion and adaptation of a wide spectrum of diseases with high impact in the society such as cancer.
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Affiliation(s)
- Ildefonso M. De la Fuente
- Department of Nutrition, CEBAS-CSIC Institute, Espinardo University Campus, 30100 Murcia, Spain
- Department of Mathematics, Faculty of Science and Technology, University of the Basque Country, 48940 Leioa, Spain
| | - José I. López
- Department of Pathology, Cruces University Hospital, Biocruces-Bizkaia Health Research Institute, 48903 Barakaldo, Spain
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De la Fuente IM, Bringas C, Malaina I, Fedetz M, Carrasco-Pujante J, Morales M, Knafo S, Martínez L, Pérez-Samartín A, López JI, Pérez-Yarza G, Boyano MD. Evidence of conditioned behavior in amoebae. Nat Commun 2019; 10:3690. [PMID: 31417086 PMCID: PMC6695432 DOI: 10.1038/s41467-019-11677-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 07/26/2019] [Indexed: 01/05/2023] Open
Abstract
Associative memory is the main type of learning by which complex organisms endowed with evolved nervous systems respond efficiently to certain environmental stimuli. It has been found in different multicellular species, from cephalopods to humans, but never in individual cells. Here we describe a motility pattern consistent with associative conditioned behavior in the microorganism Amoeba proteus. We use a controlled direct-current electric field as the conditioned stimulus, and a specific chemotactic peptide as the unconditioned stimulus. The amoebae are capable of linking two independent past events, generating persistent locomotion movements that can prevail for 44 min on average. We confirm a similar behavior in a related species, Metamoeba leningradensis. Thus, our results indicate that unicellular organisms can modify their behavior during migration by associative conditioning.
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Affiliation(s)
- Ildefonso M De la Fuente
- Department of Nutrition, CEBAS-CSIC Institute, Espinardo University Campus, Murcia, 30100, Spain.
- Department of Mathematics, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, Leioa, 48940, Spain.
| | - Carlos Bringas
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of the Basque Country, UPV/EHU, Leioa, 48940, Spain
| | - Iker Malaina
- Department of Mathematics, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, Leioa, 48940, Spain
| | - María Fedetz
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine "López-Neyra", CSIC, Granada, 18016, Spain
| | - Jose Carrasco-Pujante
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of the Basque Country, UPV/EHU, Leioa, 48940, Spain
| | - Miguel Morales
- Biophysics Institute, CSIC-UPV/EHU, University of the Basque Country (UPV/EHU), Leioa, 48940, Spain
| | - Shira Knafo
- Biophysics Institute, CSIC-UPV/EHU, University of the Basque Country (UPV/EHU), Leioa, 48940, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, 48013, Spain
- Department of Physiology and Cell Biology, Faculty of Health Sciences, and The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Luis Martínez
- Department of Mathematics, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, Leioa, 48940, Spain
- Basque Center of Applied Mathematics (BCAM), Bilbao, 48009, Spain
| | - Alberto Pérez-Samartín
- Department of Neurosciences, Faculty of Medicine and Nursing, University of the Basque Country, UPV/EHU, Leioa, 48940, Spain
| | - José I López
- Department of Pathology, Cruces University Hospital, Biocruces-Bizkaia Health Research Institute, University of the Basque Country (UPV/EHU), Barakaldo, 48903, Spain
| | - Gorka Pérez-Yarza
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of the Basque Country, UPV/EHU, Leioa, 48940, Spain
| | - María Dolores Boyano
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of the Basque Country, UPV/EHU, Leioa, 48940, Spain
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Csermely P. The Wisdom of Networks: A General Adaptation and Learning Mechanism of Complex Systems: The Network Core Triggers Fast Responses to Known Stimuli; Innovations Require the Slow Network Periphery and Are Encoded by Core-Remodeling. Bioessays 2017; 40. [PMID: 29168203 DOI: 10.1002/bies.201700150] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 10/12/2017] [Indexed: 12/30/2022]
Abstract
I hypothesize that re-occurring prior experience of complex systems mobilizes a fast response, whose attractor is encoded by their strongly connected network core. In contrast, responses to novel stimuli are often slow and require the weakly connected network periphery. Upon repeated stimulus, peripheral network nodes remodel the network core that encodes the attractor of the new response. This "core-periphery learning" theory reviews and generalizes the heretofore fragmented knowledge on attractor formation by neural networks, periphery-driven innovation, and a number of recent reports on the adaptation of protein, neuronal, and social networks. The core-periphery learning theory may increase our understanding of signaling, memory formation, information encoding and decision-making processes. Moreover, the power of network periphery-related "wisdom of crowds" inventing creative, novel responses indicates that deliberative democracy is a slow yet efficient learning strategy developed as the success of a billion-year evolution. Also see the video abstract here: https://youtu.be/IIjP7zWGjVE.
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Affiliation(s)
- Peter Csermely
- Department of Medical Chemistry, Semmelweis University, Budapest, Hungary
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12
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Multisite tumor sampling: a new tumor selection method to enhance intratumor heterogeneity detection. Hum Pathol 2017; 64:1-6. [DOI: 10.1016/j.humpath.2017.02.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 01/14/2017] [Accepted: 02/09/2017] [Indexed: 01/20/2023]
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13
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M De la Fuente I, Malaina I, Pérez-Samartín A, Boyano MD, Pérez-Yarza G, Bringas C, Villarroel Á, Fedetz M, Arellano R, Cortes JM, Martínez L. Dynamic properties of calcium-activated chloride currents in Xenopus laevis oocytes. Sci Rep 2017; 7:41791. [PMID: 28198817 PMCID: PMC5304176 DOI: 10.1038/srep41791] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 12/30/2016] [Indexed: 11/18/2022] Open
Abstract
Chloride is the most abundant permeable anion in the cell, and numerous studies in the last two decades highlight the great importance and broad physiological role of chloride currents mediated anion transport. They participate in a multiplicity of key processes, as for instance, the regulation of electrical excitability, apoptosis, cell cycle, epithelial secretion and neuronal excitability. In addition, dysfunction of Cl− channels is involved in a variety of human diseases such as epilepsy, osteoporosis and different cancer types. Historically, chloride channels have been of less interest than the cation channels. In fact, there seems to be practically no quantitative studies of the dynamics of chloride currents. Here, for the first time, we have quantitatively studied experimental calcium-activated chloride fluxes belonging to Xenopus laevis oocytes, and the main results show that the experimental Cl− currents present an informational structure characterized by highly organized data sequences, long-term memory properties and inherent “crossover” dynamics in which persistent correlations arise at short time intervals, while anti-persistent behaviors become dominant in long time intervals. Our work sheds some light on the understanding of the informational properties of ion currents, a key element to elucidate the physiological functional coupling with the integrative dynamics of metabolic processes.
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Affiliation(s)
- Ildefonso M De la Fuente
- Department of Nutrition, CEBAS-CSIC Institute, Espinardo University Campus, Murcia, Spain.,Department of Mathematics, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Iker Malaina
- Department of Mathematics, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Alberto Pérez-Samartín
- Department of Neurosciences, Faculty of Medicine and Dentistry, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - María Dolores Boyano
- Department of Cell Biology and Histology, Faculty of Medicine and Dentistry, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Gorka Pérez-Yarza
- Department of Cell Biology and Histology, Faculty of Medicine and Dentistry, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Carlos Bringas
- Department of Cell Biology and Histology, Faculty of Medicine and Dentistry, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Álvaro Villarroel
- Biophysics Unit, CSIC, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - María Fedetz
- Department of Biochemistry and Pharmacology, Institute of Parasitology and Biomedicine "López-Neyra", CSIC, Granada, Spain
| | - Rogelio Arellano
- Laboratory of Cellular Neurophysiology, Neurobiology Institute, UNAM, Querétaro, México
| | - Jesus M Cortes
- Department of Cell Biology and Histology, Faculty of Medicine and Dentistry, University of the Basque Country, UPV/EHU, Leioa, Spain.,BioCruces Health Research Institute, Cruces University Hospital, Barakaldo, Spain.,IKERBASQUE: The Basque Foundation for Science, Bilbao, Spain
| | - Luis Martínez
- Department of Mathematics, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, Leioa, Spain
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Zakhartsev M, Yang X, Reuss M, Pörtner HO. Metabolic efficiency in yeast Saccharomyces cerevisiae in relation to temperature dependent growth and biomass yield. J Therm Biol 2015; 52:117-29. [PMID: 26267506 DOI: 10.1016/j.jtherbio.2015.05.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 05/29/2015] [Accepted: 05/29/2015] [Indexed: 11/16/2022]
Abstract
Canonized view on temperature effects on growth rate of microorganisms is based on assumption of protein denaturation, which is not confirmed experimentally so far. We develop an alternative concept, which is based on view that limits of thermal tolerance are based on imbalance of cellular energy allocation. Therefore, we investigated growth suppression of yeast Saccharomyces cerevisiae in the supraoptimal temperature range (30-40°C), i.e. above optimal temperature (Topt). The maximal specific growth rate (μmax) of biomass, its concentration and yield on glucose (Yx/glc) were measured across the whole thermal window (5-40°C) of the yeast in batch anaerobic growth on glucose. Specific rate of glucose consumption, specific rate of glucose consumption for maintenance (mglc), true biomass yield on glucose (Yx/glc(true)), fractional conservation of substrate carbon in product and ATP yield on glucose (Yatp/glc) were estimated from the experimental data. There was a negative linear relationship between ATP, ADP and AMP concentrations and specific growth rate at any growth conditions, whilst the energy charge was always high (~0.83). There were two temperature regions where mglc differed 12-fold, which points to the existence of a 'low' (within 5-31°C) and a 'high' (within 33-40°C) metabolic mode regarding maintenance requirements. The rise from the low to high mode occurred at 31-32°C in step-wise manner and it was accompanied with onset of suppression of μmax. High mglc at supraoptimal temperatures indicates a significant reduction of scope for growth, due to high maintenance cost. Analysis of temperature dependencies of product formation efficiency and Yatp/glc revealed that the efficiency of energy metabolism approaches its lower limit at 26-31°C. This limit is reflected in the predetermined combination of Yx/glc(true), elemental biomass composition and degree of reduction of the growth substrate. Approaching the limit implies a reduction of the safety margin of metabolic efficiency. We hypothesize that a temperature increase above Topt (e.g. >31°C) triggers both an increment in mglc and suppression of μmax, which together contribute to an upshift of Yatp/glc from the lower limit and thus compensate for the loss of the safety margin. This trade-off allows adding 10 more degrees to Topt and extends the thermal window up to 40°C, sustaining survival and reproduction in supraoptimal temperatures. Deeper understanding of the limits of thermal tolerance can be practically exploited in biotechnological applications.
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Affiliation(s)
- Maksim Zakhartsev
- Alfred Wegener Institute for Marine and Polar Research (AWI), Bremerhaven, Germany; Institute of Biochemical Engineering (IBVT), University of Stuttgart, Stuttgart, Germany; Institute of Pharmacy and Molecular Biotechnology (IPMB), University of Heidelberg, Germany.
| | - Xuelian Yang
- Institute of Biochemical Engineering (IBVT), University of Stuttgart, Stuttgart, Germany; Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University, Beijing, China
| | - Matthias Reuss
- Institute of Biochemical Engineering (IBVT), University of Stuttgart, Stuttgart, Germany
| | - Hans Otto Pörtner
- Alfred Wegener Institute for Marine and Polar Research (AWI), Bremerhaven, Germany
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15
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De la Fuente IM. Elements of the cellular metabolic structure. Front Mol Biosci 2015; 2:16. [PMID: 25988183 PMCID: PMC4428431 DOI: 10.3389/fmolb.2015.00016] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 04/12/2015] [Indexed: 12/19/2022] Open
Abstract
A large number of studies have demonstrated the existence of metabolic covalent modifications in different molecular structures, which are able to store biochemical information that is not encoded by DNA. Some of these covalent mark patterns can be transmitted across generations (epigenetic changes). Recently, the emergence of Hopfield-like attractor dynamics has been observed in self-organized enzymatic networks, which have the capacity to store functional catalytic patterns that can be correctly recovered by specific input stimuli. Hopfield-like metabolic dynamics are stable and can be maintained as a long-term biochemical memory. In addition, specific molecular information can be transferred from the functional dynamics of the metabolic networks to the enzymatic activity involved in covalent post-translational modulation, so that determined functional memory can be embedded in multiple stable molecular marks. The metabolic dynamics governed by Hopfield-type attractors (functional processes), as well as the enzymatic covalent modifications of specific molecules (structural dynamic processes) seem to represent the two stages of the dynamical memory of cellular metabolism (metabolic memory). Epigenetic processes appear to be the structural manifestation of this cellular metabolic memory. Here, a new framework for molecular information storage in the cell is presented, which is characterized by two functionally and molecularly interrelated systems: a dynamic, flexible and adaptive system (metabolic memory) and an essentially conservative system (genetic memory). The molecular information of both systems seems to coordinate the physiological development of the whole cell.
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Affiliation(s)
- Ildefonso M. De la Fuente
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine “López-Neyra,” Consejo Superior de Investigaciones CientíficasGranada, Spain
- Department of Mathematics, University of the Basque Country, UPV/Euskal Herriko UnibertsitateaLeioa, Spain
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López JI, Larrinaga G, Kuroda N, Angulo JC. The normal and pathologic renal medulla: A comprehensive overview. Pathol Res Pract 2015; 211:271-80. [DOI: 10.1016/j.prp.2014.12.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 11/26/2014] [Accepted: 12/09/2014] [Indexed: 01/13/2023]
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17
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Lewis DD, Villarreal FD, Wu F, Tan C. Synthetic biology outside the cell: linking computational tools to cell-free systems. Front Bioeng Biotechnol 2014; 2:66. [PMID: 25538941 PMCID: PMC4260521 DOI: 10.3389/fbioe.2014.00066] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 11/23/2014] [Indexed: 12/22/2022] Open
Abstract
As mathematical models become more commonly integrated into the study of biology, a common language for describing biological processes is manifesting. Many tools have emerged for the simulation of in vivo synthetic biological systems, with only a few examples of prominent work done on predicting the dynamics of cell-free synthetic systems. At the same time, experimental biologists have begun to study dynamics of in vitro systems encapsulated by amphiphilic molecules, opening the door for the development of a new generation of biomimetic systems. In this review, we explore both in vivo and in vitro models of biochemical networks with a special focus on tools that could be applied to the construction of cell-free expression systems. We believe that quantitative studies of complex cellular mechanisms and pathways in synthetic systems can yield important insights into what makes cells different from conventional chemical systems.
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Affiliation(s)
- Daniel D. Lewis
- Integrative Genetics and Genomics, University of California Davis, Davis, CA, USA
- Department of Biomedical Engineering, University of California Davis, Davis, CA, USA
| | | | - Fan Wu
- Department of Biomedical Engineering, University of California Davis, Davis, CA, USA
| | - Cheemeng Tan
- Department of Biomedical Engineering, University of California Davis, Davis, CA, USA
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18
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Zaldumbide L, Erramuzpe A, Guarch R, Cortés JM, López JI. Large (>3.8 cm) clear cell renal cell carcinomas are morphologically and immunohistochemically heterogeneous. Virchows Arch 2014; 466:61-6. [DOI: 10.1007/s00428-014-1673-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 09/10/2014] [Accepted: 10/13/2014] [Indexed: 12/21/2022]
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De la Fuente IM, Cortés JM, Valero E, Desroches M, Rodrigues S, Malaina I, Martínez L. On the dynamics of the adenylate energy system: homeorhesis vs homeostasis. PLoS One 2014; 9:e108676. [PMID: 25303477 PMCID: PMC4193753 DOI: 10.1371/journal.pone.0108676] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 09/03/2014] [Indexed: 11/20/2022] Open
Abstract
Biochemical energy is the fundamental element that maintains both the adequate turnover of the biomolecular structures and the functional metabolic viability of unicellular organisms. The levels of ATP, ADP and AMP reflect roughly the energetic status of the cell, and a precise ratio relating them was proposed by Atkinson as the adenylate energy charge (AEC). Under growth-phase conditions, cells maintain the AEC within narrow physiological values, despite extremely large fluctuations in the adenine nucleotides concentration. Intensive experimental studies have shown that these AEC values are preserved in a wide variety of organisms, both eukaryotes and prokaryotes. Here, to understand some of the functional elements involved in the cellular energy status, we present a computational model conformed by some key essential parts of the adenylate energy system. Specifically, we have considered (I) the main synthesis process of ATP from ADP, (II) the main catalyzed phosphotransfer reaction for interconversion of ATP, ADP and AMP, (III) the enzymatic hydrolysis of ATP yielding ADP, and (IV) the enzymatic hydrolysis of ATP providing AMP. This leads to a dynamic metabolic model (with the form of a delayed differential system) in which the enzymatic rate equations and all the physiological kinetic parameters have been explicitly considered and experimentally tested in vitro. Our central hypothesis is that cells are characterized by changing energy dynamics (homeorhesis). The results show that the AEC presents stable transitions between steady states and periodic oscillations and, in agreement with experimental data these oscillations range within the narrow AEC window. Furthermore, the model shows sustained oscillations in the Gibbs free energy and in the total nucleotide pool. The present study provides a step forward towards the understanding of the fundamental principles and quantitative laws governing the adenylate energy system, which is a fundamental element for unveiling the dynamics of cellular life.
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Affiliation(s)
- Ildefonso M. De la Fuente
- Institute of Parasitology and Biomedicine “López-Neyra”, CSIC, Granada, Spain
- Department of Mathematics, University of the Basque Country UPV/EHU, Leioa, Spain
- Unit of Biophysics (CSIC, UPV/EHU), and Department of Biochemistry and Molecular Biology University of the Basque Country, Bilbao, Spain
- Biocruces Health Research Institute, Hospital Universitario de Cruces, Barakaldo, Spain
| | - Jesús M. Cortés
- Biocruces Health Research Institute, Hospital Universitario de Cruces, Barakaldo, Spain
- Ikerbasque: The Basque Foundation for Science, Bilbao, Basque Country, Spain
| | - Edelmira Valero
- Department of Physical Chemistry, School of Industrial Engineering, University of Castilla-La Mancha, Albacete, Spain
| | | | - Serafim Rodrigues
- School of Computing and Mathematics, University of Plymouth, Plymouth, United Kingdom
| | - Iker Malaina
- Biocruces Health Research Institute, Hospital Universitario de Cruces, Barakaldo, Spain
- Department of Physiology, University of the Basque Country UPV/EHU, Bilbao, Spain
| | - Luis Martínez
- Department of Mathematics, University of the Basque Country UPV/EHU, Leioa, Spain
- Biocruces Health Research Institute, Hospital Universitario de Cruces, Barakaldo, Spain
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20
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Baffy G, Loscalzo J. Complexity and network dynamics in physiological adaptation: An integrated view. Physiol Behav 2014; 131:49-56. [DOI: 10.1016/j.physbeh.2014.04.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 04/08/2014] [Indexed: 10/25/2022]
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21
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Larrinaga G, Perez I, Ariz U, Sanz B, Beitia M, Errarte P, Etxezarraga C, Candenas ML, Pinto FM, López JI. Clinical impact of aspartyl aminopeptidase expression and activity in colorectal cancer. Transl Res 2013; 162:297-308. [PMID: 23948443 DOI: 10.1016/j.trsl.2013.07.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 07/09/2013] [Accepted: 07/23/2013] [Indexed: 12/12/2022]
Abstract
Aspartyl aminopeptidase (ASP; EC 3.4.11.21) is a widely distributed and abundant cytosolic enzyme that regulates bioactive peptides such as angiotensin II. It has been demonstrated that the expression and activity of this enzyme is modified in tissue and serum of patients with several types of cancer. However, the involvement of ASP in the neoplastic development and survival of patients with colorectal cancer (CRC) has not been analyzed to date. The activity and messenger RNA expression of ASP in tumor tissue (n = 71) and plasma (n = 40) of patients with CRC was analyzed prospectively using fluorometric and quantitative real-time polymerase chain reaction methods. Data obtained from tumor tissue were compared with those from the surrounding normal mucosa. Classic pathologic parameters (grade, stage, nodal invasion, distant metastases and perineural, lymphatic, and vascular invasion) were stratified following ASP data and analyzed for 5-year survival. ASP was upregulated in CRC tissues, and greater activity correlated significantly with the absence of lymph node metastases and with better overall survival. Inversely, greater plasmatic ASP activity was associated with worse overall and disease-free survival. Data suggest that ASP is involved in colorectal neoplasia and point to this enzyme as a potential useful diagnostic tool in clinical practice.
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Affiliation(s)
- Gorka Larrinaga
- Department of Nursing I, School of Nursing, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain; Department of Physiology, Faculty of Medicine and Dentistry, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain; BioCruces Health Research Institute, Barakaldo, Bizkaia, Spain.
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