Progress in Biophysics & Molecular Biology最新文献_第5页

In vitro study of the expression of autophagy genes ATG101, mTOR and AMPK in breast cancer with treatment of lactoferrin and in silico study of their communication networks and protein interactions 体外研究乳铁蛋白治疗乳腺癌时自噬基因 ATG101、mTOR 和 AMPK 的表达情况，并对它们的通讯网络和蛋白质相互作用进行硅学研究。

IF 3.8 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2024-05-21 DOI: 10.1016/j.pbiomolbio.2024.05.003

Atefeh Mashhadi Kholerdi , Fatemeh Moradian , Havva Mehralitabar

{"title":"In vitro study of the expression of autophagy genes ATG101, mTOR and AMPK in breast cancer with treatment of lactoferrin and in silico study of their communication networks and protein interactions","authors":"Atefeh Mashhadi Kholerdi , Fatemeh Moradian , Havva Mehralitabar","doi":"10.1016/j.pbiomolbio.2024.05.003","DOIUrl":"10.1016/j.pbiomolbio.2024.05.003","url":null,"abstract":"<div><p>Autophagy is a new window of science that has been noticed due to the importance of specific therapies in cancer. In this study, the effect of lactoferrin (Lf) on the expression level of ATG101, mTOR and AMPK genes in breast cancer cell line MCF7, as well as the interaction between lactoferrin protein and their protein were investigated. The expression level of the genes was measured using a real-time PCR method. PDB, UniProt, KEGG, and STRING databases and ClusPro webserver and PyMol software were used <em>in silico</em> study. The results showed that the expression level of the ATG101 gene in treatment with concentrations of 100, 400, 600, and 800 μg/ml Lf decreased by 0.05, 0.13, 0.54 and 0.77, respectively. The expression level of the mTOR gene in treatment with concentrations of 100, 400, 600, and 800 μg/ml Lf decreased by 0.07, 0.05, 0.13, and 0.49 times respectively. The level of the AMPK gene expression in treatment with concentrations of 100, 400, 600, and 800 μg/ml Lf decreased by 0.05, 0.01, 0.06, and 0.03, respectively. Virtualization of the interaction of Lf protein with ATG101, mTOR and AMPK proteins by Pymol software showed that the N lobe region of Lf interacted with the HORMA domain of ATG101 protein, the fat domain of mTOR protein, and the CTD domain of AMPK protein. Although Lf was not able to increase the expression of autophagy-inducing genes, it may be able to induce autophagy through protein interaction by activating or inhibiting proteins related to autophagy regulation.</p></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"190 ","pages":"Pages 19-27"},"PeriodicalIF":3.8,"publicationDate":"2024-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141088780","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

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":"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":"2024-05-14","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

Biology in the 21st century: Natural selection is cognitive selection 21 世纪的生物学：自然选择就是认知选择。

IF 3.8 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2024-05-11 DOI: 10.1016/j.pbiomolbio.2024.05.001

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

{"title":"Biology in the 21st century: Natural selection is cognitive selection","authors":"William B. Miller Jr. , František Baluška , Arthur S. Reber , Predrag Slijepčević","doi":"10.1016/j.pbiomolbio.2024.05.001","DOIUrl":"10.1016/j.pbiomolbio.2024.05.001","url":null,"abstract":"<div><p>Natural selection has a formal definition as the natural process that results in the survival and reproductive success of individuals or groups best adjusted to their environment, leading to the perpetuation of those genetic qualities best suited to that organism's environmental niche. Within conventional Neo-Darwinism, the largest source of those variations that can be selected is presumed to be secondary to random genetic mutations. As these arise, natural selection sustains adaptive traits in the context of a 'struggle for existence'. Consequently, in the 20th century, natural selection was generally portrayed as the primary evolutionary driver. The 21st century offers a comprehensive alternative to Neo-Darwinian dogma within Cognition-Based Evolution. The substantial differences between these respective evolutionary frameworks have been most recently articulated in a revision of Crick's Central Dogma, a former centerpiece of Neo-Darwinism. The argument is now advanced that the concept of natural selection should also be comprehensively reappraised. Cognitive selection is presented as a more precise term better suited to 21st century biology. Since cognition began with life's origin, natural selection represents cognitive selection.</p></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"190 ","pages":"Pages 170-184"},"PeriodicalIF":3.8,"publicationDate":"2024-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140917551","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

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 : 2024-04-09 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

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 : 2024-04-07 DOI: 10.1016/j.pbiomolbio.2024.04.001

Peter A. Corning

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 : 2024-04-07 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":"2024-04-07","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

A hypothesis of teleological evolution, via endogenous acetylcholine, nitric oxide, and calmodulin pathways 通过内源性乙酰胆碱、一氧化氮和钙调素途径进行目的论进化的假说。

IF 3.8 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2024-03-28 DOI: 10.1016/j.pbiomolbio.2024.03.003

Amelia Lewis

{"title":"A hypothesis of teleological evolution, via endogenous acetylcholine, nitric oxide, and calmodulin pathways","authors":"Amelia Lewis","doi":"10.1016/j.pbiomolbio.2024.03.003","DOIUrl":"10.1016/j.pbiomolbio.2024.03.003","url":null,"abstract":"<div><p>The Extended Evolutionary Synthesis (EES) addresses the issues in evolutionary biology which cannot be explained by neo-Darwinian theory. The EES paradigm recognises teleology and agency in living systems, and identifies that organisms can directly affect their evolutionary trajectory in a goal-directed manner, yet the physiological pathways via which this occurs remain unidentified. Here, I propose a physiological pathway via which organisms can alter their genotype and phenotype by making behavioural decisions with respect their activity levels, partitioning of resources either toward growth, defence against disease, or their behavioural response to stressors. Specifically, I hypothesize that agential, teleological decisions mediated by acetylcholine result in induced nitric oxide (NO) activity, which regulates metabolism, blood flow, and immune response. Nitric oxide, however, is also a key epigenetic molecule, being involved in DNA acetylation, methylation, and de-methylation. Further, NO alters the histone complexes which scaffold nuclear DNA strands, and is thus a good candidate in identifying a system which allows an organisms to make teleological genetic changes. The proposed mechanisms of inheritance of these genetic changes is via the paternal line, whereby epigenetic changes in the somatic Sertoli cells in animals are transcribed by mRNA and included in the germline cells – the male gametes. The microsporangium in plants, and the sporophore cells in fungi, meanwhile, are proposed to form similar systems in response to sensory detection of stressors. Whilst the hypothesis is presented as a simplified model for future testing, it opens new avenues for study in evolutionary biology.</p></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"188 ","pages":"Pages 68-76"},"PeriodicalIF":3.8,"publicationDate":"2024-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140327424","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

WITHDRAWN: The dysregulated autophagy in osteoarthritis: Revisiting molecular profile. 骨关节炎中失调的自噬：重新审视分子特征

IF 3.2 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2024-03-24 DOI: 10.1016/j.pbiomolbio.2024.03.004

Liang Liu, Jie Wang, Lu Liu, Wenling Shi, Huajie Gao, Lun Liu

引用次数: 0

The role of photobiomodulation in accelerating bone repair 光生物调节在加速骨修复中的作用。

IF 3.8 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2024-03-16 DOI: 10.1016/j.pbiomolbio.2024.03.002

Ping Lu , Jinfeng Peng , Jie Liu , Lili Chen

引用次数: 0