Biosystems最新文献_第10页

The epoch-making importance of Ervin Bauer's theoretical biology 埃尔文-鲍尔的理论生物学具有划时代的重要意义。

IF 1.6 4区生物学

Biosystems Pub Date : 2024-04-01 DOI: 10.1016/j.biosystems.2024.105179

Attila Grandpierre

{"title":"The epoch-making importance of Ervin Bauer's theoretical biology","authors":"Attila Grandpierre","doi":"10.1016/j.biosystems.2024.105179","DOIUrl":"10.1016/j.biosystems.2024.105179","url":null,"abstract":"<div><p>Ervin Bauer was the only biologist who recognized that the best way to develop theoretical biology on an equal footing with theoretical physics was to follow the method that has ensured the great successes of modern theoretical physics: the general method of science. Following this method, he succeeded to find the universal principle of biology. From this principle he managed to derive all the basic equations of biology, that of metabolism, reproduction, growth, responsiveness and successfully explained all the fundamental phenomena of life. In this paper, I introduce Bauer's theoretical biology and discuss whether he understood it within the framework of the modern physical worldview, or in a broader framework. I point out that the theoretical biology of Ervin Bauer is the first to go beyond the physical worldview, to establish a deeper, biological worldview, and thus to represent a major advance in our understanding of the nature of life, with a significance even greater than that of the Copernican turn. Clarifying the difference between the living and the non-living, it is important to consider the difference between machines and living organisms. It is well known that machines are the manifestations of a dual control; globally, their behavior is controlled by their given structure, while locally, their behavior is governed by the physical laws. Based on Bauer's theoretical biology, it is pointed out that living organisms manifest a three-level causality; the ‘additional’, biological level corresponds to the autonomous, time-dependent control of their structures.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140141065","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

An integrated approach to understand the regulatory role of miR-27 family in breast cancer metastasis 了解 miR-27 家族在乳腺癌转移中调控作用的综合方法

IF 1.6 4区生物学

Biosystems Pub Date : 2024-04-01 DOI: 10.1016/j.biosystems.2024.105200

Sohini Chakraborty , Utpalendu Paul , Subhadeep Banerjee, Debanjan Saha, Satarupa Banerjee

{"title":"An integrated approach to understand the regulatory role of miR-27 family in breast cancer metastasis","authors":"Sohini Chakraborty , Utpalendu Paul , Subhadeep Banerjee, Debanjan Saha, Satarupa Banerjee","doi":"10.1016/j.biosystems.2024.105200","DOIUrl":"https://doi.org/10.1016/j.biosystems.2024.105200","url":null,"abstract":"<div><p>One of the prime reasons of increasing breast cancer mortality is metastasizing cancer cells. Owing to the side effects of clinically available drugs to treat breast cancer metastasis, it is of utmost importance to understand the underlying biogenesis of breast cancer tumorigenesis. In-silico identification of potential RNAs might help in utilizing the miR-27 family as a therapeutic target in breast cancer. The experimentally verified common interacting mRNAs for miR27 family are retrieved from three publicly available databases- TargetScan, miRDB and miRTarBase. Finally on comparing the common genes with HCMDB and GEPIA data, four breast cancer-associated differentially expressed metastatic mRNAs (GATA3, ENAH, ITGA2 and SEMA4D) are obtained. Corresponding to the miR27 family and associated mRNAs, interacting drugs are retrieved from Sm2mir and CTDbase, respectively. The interaction network-based approach was utilized to obtain the hub RNAs and triad modules by employing the ‘Cytohubba’ and ‘MClique’ plugins, respectively in Cytoscape. Further, sample-, subclass- and promoter methylation-based expression analyses reveals GATA3 and ENAH to be the most significant mRNAs in breast cancer metastasis having >10% genetic alteration in both METABRIC Vs TCGA datasets as per their oncoprint analysis via cBioPortal. Additionally, survival analysis in Oncolnc reveals SEMA4D as survival biomarker. Interactions among the miR27 family, their target mRNAs and drugs interacting with miRNAs and mRNAs can be extensively explored in both in-vivo and in-vitro setups to assess their therapeutic potential in the diminution of breast cancer.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140342356","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The sensual cell: Feeling and affect in unicellular species 感性细胞：单细胞物种的感觉和情感

IF 1.6 4区生物学

Biosystems Pub Date : 2024-03-29 DOI: 10.1016/j.biosystems.2024.105197

Arthur S. Reber , František Baluška , William B. Miller , Predrag Slijepčević

{"title":"The sensual cell: Feeling and affect in unicellular species","authors":"Arthur S. Reber , František Baluška , William B. Miller , Predrag Slijepčević","doi":"10.1016/j.biosystems.2024.105197","DOIUrl":"https://doi.org/10.1016/j.biosystems.2024.105197","url":null,"abstract":"<div><p>Our previous efforts to probe the complex, rich experiential lives of unicellular species have focused on the origins of consciousness (Reber, 2019) and the biomolecular processes that underlie sentience (Reber et al., 2023). Implied, but unexplored, was the assumption that these cognitive functions and associated unicellular organismal behaviors were linked with and often driven by affect, feelings, sensual experiences. In this essay we dig more deeply into these valenced (We're using the term <em>valence</em> here to cover the aspects of sensory experiences that have evaluative elements, are experienced as positive or negative ─ those where this affective, internal representation is an essential element in how the input is interpreted and responded to.) self-referencing features. In the first part, we examine the empirical evidence for various sensual experiences that have been identified. In the second part, we look at other features of prokaryote life that appear to also have affective, valenced elements but where the data to support the proposition aren't as strong. We engage in some informed speculation about these phenomena.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140328576","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A multi-cell model for the C4 photosynthetic pathway in developing wheat grains based upon tissue-specific transcriptome data 基于组织特异性转录组数据的发育中麦粒的 C4 光合途径多细胞模型

IF 1.6 4区生物学

Biosystems Pub Date : 2024-03-29 DOI: 10.1016/j.biosystems.2024.105195

Parimalan Rangan , Agnelo Furtado , Viswanathan Chinnusamy , Robert Henry

{"title":"A multi-cell model for the C4 photosynthetic pathway in developing wheat grains based upon tissue-specific transcriptome data","authors":"Parimalan Rangan , Agnelo Furtado , Viswanathan Chinnusamy , Robert Henry","doi":"10.1016/j.biosystems.2024.105195","DOIUrl":"https://doi.org/10.1016/j.biosystems.2024.105195","url":null,"abstract":"<div><p>A non-Kranz C<sub>4</sub> photosynthesis of the NAD-ME subtype, specifically in developing wheat grains (14 dpa, days post-anthesis) was originally demonstrated using transcriptome-based RNA-seq. Here we present a re-examination of evidence for C<sub>4</sub> photosynthesis in the developing grains of wheat and, more broadly, the Pooideae and an investigation of the evolutionary processes and implications. The expression profiles for the genes associated with C<sub>4</sub> photosynthesis (C<sub>4</sub>- and C<sub>3</sub>-specific) were evaluated using published transcriptome data for the outer pericarp, inner pericarp, and endosperm tissues of the developing wheat grains. The expression of the C<sub>4</sub>-specific genes across these three tissues revealed the involvement of all three tissues in an orderly fashion to accomplish the non-Kranz NAD-ME-dependent C<sub>4</sub> photosynthesis. Based on their expression levels in RPKM (reads per kilobase per million mapped reads) values, a model involving multiple cell- and tissue-types is proposed for C<sub>4</sub> photosynthesis involved in the refixation of the respired CO<sub>2</sub> from the endosperm tissues in the developing wheat grains. This multi-cell C<sub>4</sub> model, proposed to involve more than two cell types, requires further biochemical validation.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140328577","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Variation in base composition, structure-function relationships, and origins of structural repetition in bacterial rpsA gene 细菌 rpsA 基因碱基组成的变异、结构-功能关系和结构重复的起源。

IF 1.6 4区生物学

Biosystems Pub Date : 2024-03-25 DOI: 10.1016/j.biosystems.2024.105196

Andrey V. Machulin , Evgeniya I. Deryusheva , Oxana V. Galzitskaya

{"title":"Variation in base composition, structure-function relationships, and origins of structural repetition in bacterial rpsA gene","authors":"Andrey V. Machulin , Evgeniya I. Deryusheva , Oxana V. Galzitskaya","doi":"10.1016/j.biosystems.2024.105196","DOIUrl":"10.1016/j.biosystems.2024.105196","url":null,"abstract":"<div><p>Protein domain repeats are known to arise due to tandem duplications of internal genes. However, the understanding of the underlying mechanisms of this process is incomplete. The goal of this work was to investigate the mechanism of occurrence of repeat expansion based on studying the sequences of 1324 <em>rpsA</em> genes of bacterial S1 ribosomal proteins containing different numbers of S1 structural domains. The <em>rpsA</em> gene encodes ribosomal S1 protein, which is essential for cell viability as it interacts with both mRNA and proteins. Gene ontology (GO) analysis of S1 domains in ribosomal S1 proteins revealed that bacterial protein sequences in S1 mainly have 3 types of molecular functions: RNA binding activity, nucleic acid activity, and ribosome structural component. Our results show that the maximum value of <em>rpsA</em> gene identity for full-length proteins was found for S1 proteins containing six structural domains (58%). Analysis of consensus sequences showed that parts of the <em>rpsA</em> gene encoding separate S1 domains have no a strictly repetitive structure between groups containing different numbers of S1 domains. At the same time, gene regions encoding some conserved residues that form the RNA-binding site remain conserved. The detected phylogenetic similarity suggests that the proposed fold of the <em>rpsA</em> translation initiation region of <em>Escherichia coli</em> has functional value and is important for translational control of <em>rpsA</em> gene expression in other bacterial phyla, but not only in gamma Proteobacteria.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140307616","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Stress-induced failure of embodied cognition: A general model 压力导致的具身认知失败：一般模型

IF 1.6 4区生物学

Biosystems Pub Date : 2024-03-24 DOI: 10.1016/j.biosystems.2024.105193

Rodrick Wallace, Gregory Fricchione

{"title":"Stress-induced failure of embodied cognition: A general model","authors":"Rodrick Wallace, Gregory Fricchione","doi":"10.1016/j.biosystems.2024.105193","DOIUrl":"10.1016/j.biosystems.2024.105193","url":null,"abstract":"<div><p>We derive the classic, ubiquitous, but enigmatic Yerkes–Dodson effect of applied stress on real-world performance in a highly natural manner from fundamental assumptions on cognition and its dynamics, as constrained by the asymptotic limit theorems of information and control theories. We greatly extend the basic approach by showing how differences in an underlying probability model can affect the dynamics of decision across a broad range of cognitive enterprise. Most particularly, however, this development may help inform our understanding of the different expressions of human psychopathology. A ‘thin tailed’ underlying distribution appears to characterize expression of ‘ordinary’ situational depression/anxiety symptoms of conditions like burnout induced by toxic stress. A ‘fat tailed’ underlying distribution appears to be associated with brain structure and function abnormalities leading to serious mental illness and poor decision making where symptoms are not only emerging in the setting of severe stress but may also appear in a highly punctuated manner at relatively lower levels of stress. A simple hierarchical optimization shows how environmental ‘shadow price’ constraints can buffer or aggravate the effects of stress and arousal. Extension of the underlying theory to other patterns of pathology, like immune disorders and premature aging, seems apt. Applications to the punctuated dynamics of institutional cognition under stress also appear possible. Ultimately, the probability models studied here can be converted to new statistical tools for the analysis of observational and experimental data.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140208112","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Structural analyzes suggest that MiSSP13 and MiSSP16.5 may act as proteases inhibitors during ectomycorrhiza establishment in Laccaria bicolor 结构分析表明，MiSSP13和MiSSP16.5可能是Laccaria bicolor建立外生菌根过程中的蛋白酶抑制剂

IF 1.6 4区生物学

Biosystems Pub Date : 2024-03-19 DOI: 10.1016/j.biosystems.2024.105194

Ariadne N.M. Furtado , Sávio Torres de Farias , Mayara dos Santos Maia

{"title":"Structural analyzes suggest that MiSSP13 and MiSSP16.5 may act as proteases inhibitors during ectomycorrhiza establishment in Laccaria bicolor","authors":"Ariadne N.M. Furtado , Sávio Torres de Farias , Mayara dos Santos Maia","doi":"10.1016/j.biosystems.2024.105194","DOIUrl":"https://doi.org/10.1016/j.biosystems.2024.105194","url":null,"abstract":"<div><p>•The signaling process during mycorrhiza establishment involves intense molecular communication between symbionts. It has been suggested that a group of protein effectors, the so-called MiSSPs, plays a broader function in the symbiosis metabolism, however, many of these remain uncharacterized structurally and functionally.</p><p>•Herein we used three-dimensional protein structure modeling methods, ligand analysis, and molecular docking to structurally characterize and describe two protein effectors, MiSSP13 and MiSSP16.5, with enhanced expression during the mycorrhizal process in <em>Laccaria bicolor</em>.</p><p>•MiSSP13 and MiSSP16.5 show structural homology with the cysteine and aspartate protease inhibitor, cocaprin (CCP1). Through structural analysis, it was observed that MiSSP13 and MiSSP16.5 have an active site similar to that observed in CCP1. The protein-protein docking data showed that MiSSP13 and MiSSP16.5 interact with the papain and pepsin proteases at sites that are near to where CCP1 interacts with these same targets, suggesting a function as inhibitor of cysteine and aspartate proteases. The interaction of MiSSP13 with papain and MiSSP16.5 with pepsin was stronger than the interaction of CCP1 with these proteases, suggesting that the MiSSPs had a greater activity in inhibiting these classes of proteases. Based on the data supplied, a model is proposed for the function of MiSSPs 13 and 16.5 during the symbiosis establishment. Our findings, while derived from <em>in silico</em> analyses, enable us formulate intriguing hypothesis on the function of MiSSPs in ectomycorrhization, which will require experimental validation.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140180368","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Life and fate of Ervin Bauer (1890–1938), the eminent scholar and foundational theoretical biologist 著名学者、理论生物奠基人埃尔文-鲍尔（1890-1938 年）的生平与命运。

IF 1.6 4区生物学

Biosystems Pub Date : 2024-03-18 DOI: 10.1016/j.biosystems.2024.105191

Svetlana M. Bauer

引用次数: 0

Flock members experience gas pressures higher than lone individuals 羊群成员所承受的气体压力要高于孤独的个体。

IF 1.6 4区生物学

Biosystems Pub Date : 2024-03-16 DOI: 10.1016/j.biosystems.2024.105192

Arturo Tozzi

引用次数: 0

Unraveling power-law scaling through exponential cell division dynamics 通过指数细胞分裂动力学揭示幂律缩放规律

IF 1.6 4区生物学

Biosystems Pub Date : 2024-03-15 DOI: 10.1016/j.biosystems.2024.105190

Jia-Xu Han , Zhuangdong Bai , Rui-Wu Wang

{"title":"Unraveling power-law scaling through exponential cell division dynamics","authors":"Jia-Xu Han , Zhuangdong Bai , Rui-Wu Wang","doi":"10.1016/j.biosystems.2024.105190","DOIUrl":"https://doi.org/10.1016/j.biosystems.2024.105190","url":null,"abstract":"<div><p>A primary objective of biology is the development of universal laws that define how organic form develops and how it evolves as a function of size, both ontogenetically and across evolutionary time. Scaling theory has been essential in reaching this goal by giving a complete perspective point, particularly in illuminating the fundamental biological features produced within scaling exponents defining families of equations. Nonetheless, the theoretical basis of the allometric equation within scaling theory are inadequately explained, particularly when it comes to establishing links between micro-level processes at the cellular level and macro-level phenomena. We proposed an unlimited cell bipartition, resulting in an exponential growth in cell numbers during an individual’s lifespan, to bridge this conceptual gap between cellular processes and allometric scaling. The power-law scaling between body mass and organ weight was produced by the synchronous exponential increments and the allometric exponent is rate of logarithmic cell proliferation rate. Substituting organ weight for erythrocyte weight aided in the development of a power-law scaling relationship between body mass and metabolic rate. Furthermore, it is critical to understand how cell size affects the exponent in power-law scaling. We find that a bigger exponent will result from an increase in the average weight of organ cells or a decrease in the average weight of all cells. Furthermore, cell proliferation dynamics showed a complex exponential scaling between body mass and longevity, defying the previously reported power-law scaling. We discovered a quadratic link between longevity and logarithmic body mass. Notably, all of the parameters included in these relationships are explained by indices linked to cell division and embryonic development. This research adds to our understanding of the complex interaction between cellular processes and overarching scaling phenomena in biology.</p></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140138046","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0