Progress in Biophysics & Molecular Biology最新文献_第9页

A landscape of consciousness: Toward a taxonomy of explanations and implications 意识的景观：意识的景观：解释和影响的分类法。

IF 3.8 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2024-08-01 Epub Date: 2024-01-26 DOI: 10.1016/j.pbiomolbio.2023.12.003

Robert Lawrence Kuhn

{"title":"A landscape of consciousness: Toward a taxonomy of explanations and implications","authors":"Robert Lawrence Kuhn","doi":"10.1016/j.pbiomolbio.2023.12.003","DOIUrl":"10.1016/j.pbiomolbio.2023.12.003","url":null,"abstract":"<div><p>Diverse explanations or theories of consciousness are arrayed on a roughly physicalist-to-nonphysicalist landscape of essences and mechanisms. Categories: Materialism Theories (philosophical, neurobiological, electromagnetic field, computational and informational, homeostatic and affective, embodied and enactive, relational, representational, language, phylogenetic evolution); Non-Reductive Physicalism; Quantum Theories; Integrated Information Theory; Panpsychisms; Monisms; Dualisms; Idealisms; Anomalous and Altered States Theories; Challenge Theories. There are many subcategories, especially for Materialism Theories. Each explanation is self-described by its adherents, critique is minimal and only for clarification, and there is no attempt to adjudicate among theories. The implications of consciousness explanations or theories are assessed with respect to: meaning/purpose/value (if any); AI consciousness; virtual immortality; and survival beyond death. A Landscape of Consciousness, I suggest, offers perspective.</p></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"190 ","pages":"Pages 28-169"},"PeriodicalIF":3.8,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0079610723001128/pdfft?md5=e1401856928d55a631d4e6e91b35ae72&pid=1-s2.0-S0079610723001128-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139570972","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Modelling DNA damage-repair and beyond DNA 损伤修复建模及其他

IF 3.8 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2024-08-01 Epub Date: 2024-05-14 DOI: 10.1016/j.pbiomolbio.2024.05.002

Hooshang Nikjoo , Shirin Rahmanian , Reza Taleei

{"title":"Modelling DNA damage-repair and beyond","authors":"Hooshang Nikjoo , Shirin Rahmanian , Reza Taleei","doi":"10.1016/j.pbiomolbio.2024.05.002","DOIUrl":"10.1016/j.pbiomolbio.2024.05.002","url":null,"abstract":"<div><p>The paper presents a review of mechanistic modelling studies of DNA damage and DNA repair, and consequences to follow in mammalian cell nucleus. We hypothesize DNA deletions are consequences of repair of double strand breaks leading to the modifications of genome that play crucial role in long term development of genetic inheritance and diseases. The aim of the paper is to review formation mechanisms underlying naturally occurring DNA deletions in the human genome and their potential relevance for bridging the gap between induced DNA double strand breaks and deletions in damaged human genome from endogenous and exogenous events. The model of the cell nucleus presented enables simulation of DNA damage at molecular level identifying the spectrum of damage induced in all chromosomal territories and loops. Our mechanistic modelling of DNA repair for double stand breaks (DSB), single strand breaks (SSB) and base damage (BD), shows the complexity of DNA damage is responsible for the longer repair times and the reason for the biphasic feature of mammalian cells repair curves. In the absence of experimentally determined data, the mechanistic model of repair predicts the in vivo rate constants for the proteins involved in the repair of DSB, SSB, and of BD.</p></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"190 ","pages":"Pages 1-18"},"PeriodicalIF":3.8,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141037463","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Appreciation of Sir Tom Blundell 汤姆-布伦德尔爵士赏析。

IF 3.2 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2024-08-01 Epub Date: 2024-05-31 DOI: 10.1016/j.pbiomolbio.2024.05.004

Denis Noble (Editor in Chief), Delphine Dean (Editor in Chief)

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Cooperative genes in smart systems: Toward an inclusive new synthesis in evolution 智能系统中的合作基因：进化中的包容性新合成

IF 3.8 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2024-07-01 Epub Date: 2024-04-07 DOI: 10.1016/j.pbiomolbio.2024.04.001

Peter A. Corning

引用次数: 0

Exploring gene regulation and biological processes in insects: Insights from omics data using gene regulatory network models 探索昆虫的基因调控和生物过程：利用基因调控网络模型从全微观数据中获得启示

IF 3.8 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2024-07-01 Epub Date: 2024-04-09 DOI: 10.1016/j.pbiomolbio.2024.04.002

Fong Ting Chee , Sarahani Harun , Kauthar Mohd Daud , Suhaila Sulaiman , Nor Azlan Nor Muhammad

引用次数: 0

Tumour-regulatory role of long non-coding RNA HOXA-AS3 长非编码 RNA HOXA-AS3 的肿瘤调节作用

IF 3.8 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2024-07-01 Epub Date: 2024-04-07 DOI: 10.1016/j.pbiomolbio.2024.04.003

Zhi Xiong Chong , Wan Yong Ho , Swee Keong Yeap

{"title":"Tumour-regulatory role of long non-coding RNA HOXA-AS3","authors":"Zhi Xiong Chong , Wan Yong Ho , Swee Keong Yeap","doi":"10.1016/j.pbiomolbio.2024.04.003","DOIUrl":"https://doi.org/10.1016/j.pbiomolbio.2024.04.003","url":null,"abstract":"<div><p>Dysregulation of long non-coding RNA (lncRNA) HOXA-AS3 has been shown to contribute to the development of multiple cancer types. Several studies have presented the tumour-modulatory role or prognostic significance of this lncRNA in various kinds of cancer. Overall, HOXA-AS3 can act as a competing endogenous RNA (ceRNA) that inhibits the activity of seven microRNAs (miRNAs), including miR-29a-3p, miR-29 b-3p, miR-29c, miR-218–5p, miR-455–5p, miR-1286, and miR-4319. This relieves the downstream messenger RNA (mRNA) targets of these miRNAs from miRNA-mediated translational repression, allowing them to exert their effect in regulating cellular activities. Examples of the pathways regulated by lncRNA HOXA-AS3 and its associated downstream targets include the WNT/β-catenin and epithelial-to-mesenchymal transition (EMT) activities. Besides, HOXA-AS3 can interact with other cellular proteins like homeobox HOXA3 and HOXA6, influencing the oncogenic signaling pathways associated with these proteins. Generally, HOXA-AS3 is overexpressed in most of the discussed human cancers, making this lncRNA a potential candidate to diagnose cancer or predict the clinical outcomes of cancer patients. Hence, targeting HOXA-AS3 could be a new therapeutic approach to slowing cancer progression or as a potential biomarker and therapeutic target. A drawback of using lncRNA HOXA-AS3 as a biomarker or therapeutic target is that most of the studies that have reported the tumour-regulatory roles of lncRNA HOXA-AS3 are single observational, <em>in vitro</em>, or <em>in vivo</em> studies. More in-depth mechanistic and large-scale clinical trials must be conducted to confirm the tumour-modulatory roles of lncRNA HOXA-AS3 further. Besides, no lncRNA HOXA-AS3 inhibitor has been tested preclinically and clinically, and designing such an inhibitor is crucial as it may potentially slow cancer progression.</p></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"189 ","pages":"Pages 13-25"},"PeriodicalIF":3.8,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140633275","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Modelling DNA Damage-Repair and Beyond. DNA 损伤修复建模及其他

IF 3.8 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2024-05-14 DOI: 10.1016/j.pbiomolbio.2024.05.002

Hooshang Nikjoo, Shirin Rahmanian, Reza Taleei

{"title":"Modelling DNA Damage-Repair and Beyond.","authors":"Hooshang Nikjoo, Shirin Rahmanian, Reza Taleei","doi":"10.1016/j.pbiomolbio.2024.05.002","DOIUrl":"https://doi.org/10.1016/j.pbiomolbio.2024.05.002","url":null,"abstract":"<p><p>The paper presents a review of mechanistic modelling studies of DNA damage and DNA repair, and consequences to follow in mammalian cell nucleus. We hypothesise DNA deletions are consequences of repair of double strand breaks leading to the modifications of genome that play crucial role in long term development of genetic inheritance and diseases. The aim of the paper is to review formation mechanisms underlying naturally occurring DNA deletions in the human genome and their potential relevance for bridging the gap between induced DNA double strand breaks and deletions in damaged human genome from endogenous and exogenous events. The model of the cell nucleus presented enables simulation of DNA damage at molecular level identifying the spectrum of damage induced in all chromosomal territories and loops. Our mechanistic modelling of DNA repair for double stand breaks (DSB), single strand breaks (SSB) and base damage (BD), shows the complexity of DNA damage is responsible for the longer repair times and the reason for the biphasic feature of mammalian cells repair curves. In the absence of experimentally determined data, the mechanistic model of repair predicts the in vivo rate constants for the proteins involved in the repair of DSB, SSB, and of BD.</p>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140960934","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Responses to commentaries on “The gene: An appraisal” 对 "基因 "评论的回应：评价 "的评论。

IF 3.8 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2024-05-01 Epub Date: 2024-02-14 DOI: 10.1016/j.pbiomolbio.2024.02.002

Keith Baverstock

{"title":"Responses to commentaries on “The gene: An appraisal”","authors":"Keith Baverstock","doi":"10.1016/j.pbiomolbio.2024.02.002","DOIUrl":"10.1016/j.pbiomolbio.2024.02.002","url":null,"abstract":"<div><p>The central conclusions of “The Gene: An Appraisal” are that genetic variance does not underpin biological evolution, and, therefore, that genes are not Mendel's units of inheritance. In this response, I will address the criticisms I have received via commentaries on that paper by defending the following statements:</p><p>1. Epistasis does not explain the power-law fitness profile of the Long-Term Evolution Experiment (LTEE). The data from the evolution of <em>natural systems</em> displays the power-law form ubiquitously. Epistasis plays no role in evolution.</p><p>2. The common characteristics of living things (natural systems) are described by the principle of least action in de Maupertuis's original form, which is synonymous with the 2nd law of thermodynamics and Newton's 2nd law of motion in its complete form, i.e., F = dp/dt. Organisms strive to achieve free energy balance with their environments.</p><p>3. Based on an appraisal of the scientific environment between 1880 and 1911, I conclude that Johannsen's genotype conception was perhaps, the only option available to him.</p><p>4. The power-law fitness profile of the LTEE falsifies Fisher's Genetical Theory of Natural Selection, Johannsen's genotype conception, and the idea that ‘Darwinian evolution’ is an exception to the generic thermodynamic process of evolution in natural systems.</p><p>5. The use of the technique of genome-wide association to identify the causes and the likelihoods of inherited common diseases and behavioural traits is a ‘wild goose chase’ because genes are not the units of inheritance.</p></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"188 ","pages":"Pages 31-42"},"PeriodicalIF":3.8,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S007961072400018X/pdfft?md5=e7aa3c3acf34cfb11fa23fbe39cdab86&pid=1-s2.0-S007961072400018X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139742707","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Research progress on the role of reactive oxygen species in the initiation, development and treatment of breast cancer 关于活性氧在乳腺癌的发生、发展和治疗中的作用的研究进展

IF 3.8 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2024-05-01 Epub Date: 2024-02-20 DOI: 10.1016/j.pbiomolbio.2024.02.005

Jing Zhong, Yan Tang

{"title":"Research progress on the role of reactive oxygen species in the initiation, development and treatment of breast cancer","authors":"Jing Zhong, Yan Tang","doi":"10.1016/j.pbiomolbio.2024.02.005","DOIUrl":"10.1016/j.pbiomolbio.2024.02.005","url":null,"abstract":"<div><p>According to international cancer data, breast cancer (BC) is the leading type of cancer in women. Although significant progress has been made in treating BC, metastasis and drug resistance continue to be the primary causes of mortality for many patients. Reactive oxygen species (ROS) play a dual role in vivo: normal levels can maintain the body's normal physiological function; however, high levels of ROS below the toxicity threshold can lead to mtDNA damage, activation of proto-oncogenes, and inhibition of tumor suppressor genes, which are important causes of BC. Differences in the production and regulation of ROS in different BC subtypes have important implications for the development and treatment of BC. ROS can also serve as an important intracellular signal transduction factor by affecting the antioxidant system, activating MAPK and PI3K/AKT, and other signal pathways to regulate cell cycle and change the relationship between cells and the activity of metalloproteinases, which significantly impacts the metastasis of BC. Hypoxia in the BC microenvironment increases ROS production levels, thereby inducing the expression of hypoxia inducible factor-1α (HIF-1α) and forming “ROS- HIF-1α-ROS” cycle that exacerbates BC development. Many anti-BC therapies generate sufficient toxic ROS to promote cancer cell apoptosis, but because the basal level of ROS in BC cells exceeds that of normal cells, this leads to up-regulation of the antioxidant system, drug efflux, and apoptosis inhibition, rendering BC cells resistant to the drug. ROS crosstalks with tumor vessels and stromal cells in the microenvironment, increasing invasiveness and drug resistance in BC.</p></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"188 ","pages":"Pages 1-18"},"PeriodicalIF":3.8,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139918105","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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 synchronic, diachronic cell as the holism of consciousness 作为意识整体性的同步、异步细胞。

IF 3.8 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2024-05-01 Epub Date: 2024-02-24 DOI: 10.1016/j.pbiomolbio.2024.02.006

John S. Torday

{"title":"The synchronic, diachronic cell as the holism of consciousness","authors":"John S. Torday","doi":"10.1016/j.pbiomolbio.2024.02.006","DOIUrl":"10.1016/j.pbiomolbio.2024.02.006","url":null,"abstract":"<div><p>The cell is both synchronic and diachronic, based on ontogeny and phylogeny, respectively. As experimental evidence for this holism, absent gravitational force, differentiated lung and bone cells devolve, losing their phenotypes, losing their evolutionary status, reverting to their nonlocal status. Thus, when evolution is seen as serial homeostasis, it is homologous with Quantum Entanglement as the nonlocal means of maintaining homeostatic balance between particles. This monadic perspective on consciousness is one-hundred and eighty degrees out of synch with the conventional way of thinking about consciousness as a diad, or mind and brain. There have been many attempts to explain consciousness, virtually all of them based on the brain as mind. The working hypothesis is that consciousness is a holism constituted by the unicell, the lipid cell membrane forming a barrier between inside and outside of the cell's environment as a topology. Conceptually, both the unicell and ‘two hands clapping’ are holisms, but because the cell is constituted by the ambiguity of negative entropy, and ‘one hand clapping’ requires two hands, they are both pseudo-holisms, constantly striving to be whole again. In the case of the cell, it is incomplete in the sense that there are factors in the ever-changing environment that can homeostatically complete it. That process results in biochemical modification of specific DNA codes in the egg or sperm so that the offspring is able to adapt in subsequent generations epigenetically. The opportunity to trace the evolution of the breath from humans to fish opens up to the further revelation of the interplay between evolution and geological change, tracing it back to invertebrates, sponges, and ultimately to unicellular organisms. And therein is evidence that the Cosmos itself ‘breathes’, providing the ultimate celestial fundament for this trail of holisms.</p></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"188 ","pages":"Pages 19-23"},"PeriodicalIF":3.8,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139974578","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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