首页 > 最新文献

IEEE life sciences letters最新文献

英文 中文
Circadian Gating of the Mammalian Cell Cycle Restriction Point: A Mathematical Analysis 哺乳动物细胞周期限制点的昼夜节律门控:一个数学分析
Pub Date : 2015-07-13 DOI: 10.1109/LLS.2015.2449511
Jing Su, M. A. Henson
A critical decision in the mammalian cell cycle is whether to pass through the restriction point (R-point) or enter the cell cycle. In this letter, we modeled the decision-making system of the mammalian cell cycle entry and the simulated circadian regulation of the R-point driven by external epithelial growth factor (EGF) patterns. Our conceptual model replicated key signaling behaviors observed experimentally, suggesting that the proposed network captured the essential system features. The model revealed the dramatic importance of the EGF dynamics on promoting cell proliferation, showed that the EGF signal duration was more important than the signal strength for driving cells past the R-point, and suggested that the loss of circadian control of the cell cycle entry could be associated with cancer development.
哺乳动物细胞周期的一个关键决策是通过限制点(r点)还是进入细胞周期。在这封信中,我们模拟了哺乳动物细胞周期进入的决策系统,并模拟了由外部上皮生长因子(EGF)模式驱动的r点的昼夜节律调节。我们的概念模型复制了实验观察到的关键信号行为,表明所提出的网络捕获了基本的系统特征。该模型揭示了EGF动力学对促进细胞增殖的巨大重要性,表明EGF信号持续时间比信号强度对驱动细胞超过r点更重要,并表明细胞周期进入的昼夜节律控制的丧失可能与癌症的发展有关。
{"title":"Circadian Gating of the Mammalian Cell Cycle Restriction Point: A Mathematical Analysis","authors":"Jing Su, M. A. Henson","doi":"10.1109/LLS.2015.2449511","DOIUrl":"https://doi.org/10.1109/LLS.2015.2449511","url":null,"abstract":"A critical decision in the mammalian cell cycle is whether to pass through the restriction point (R-point) or enter the cell cycle. In this letter, we modeled the decision-making system of the mammalian cell cycle entry and the simulated circadian regulation of the R-point driven by external epithelial growth factor (EGF) patterns. Our conceptual model replicated key signaling behaviors observed experimentally, suggesting that the proposed network captured the essential system features. The model revealed the dramatic importance of the EGF dynamics on promoting cell proliferation, showed that the EGF signal duration was more important than the signal strength for driving cells past the R-point, and suggested that the loss of circadian control of the cell cycle entry could be associated with cancer development.","PeriodicalId":87271,"journal":{"name":"IEEE life sciences letters","volume":"1 1","pages":"11-14"},"PeriodicalIF":0.0,"publicationDate":"2015-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1109/LLS.2015.2449511","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"62509608","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Exploiting Ordinal Class Structure in Multiclass Classification: Application to Ovarian Cancer 多类分类中序类结构的开发:在卵巢癌中的应用
Pub Date : 2015-06-30 DOI: 10.1109/LLS.2015.2451291
Burook Misganaw, M. Vidyasagar
In multiclass machine learning problems, one needs to distinguish between the nominal labels that do not have any natural ordering and the ordinal labels that are ordered. Ordinal labels are pervasive in biology, and some examples are given here. In this note, we point out the importance of making use of the order information when it is inherent to the problem. We demonstrate that algorithms that use this additional information outperform the algorithms that do not, on a case study of assigning one of four labels to the ovarian cancer patients on the basis of their time of progression-free survival. As an aside, it is also pointed out that the algorithms that make use of ordering information require fewer data normalizations. This aspect is important in biological applications, where data are plagued by variations in platforms and protocols, batch effects, and so on.
在多类机器学习问题中,人们需要区分没有任何自然排序的标称标签和有序的有序标签。序数标签在生物学中普遍存在,这里给出一些例子。在本文中,我们指出了当订单信息是问题的固有属性时,使用订单信息的重要性。我们证明,使用这些额外信息的算法优于不使用这些信息的算法,在一个案例研究中,根据卵巢癌患者的无进展生存时间为其分配四种标签之一。此外,还指出,利用排序信息的算法需要较少的数据规范化。这方面在生物应用程序中很重要,因为在生物应用程序中,数据受到平台和协议、批处理效果等变化的困扰。
{"title":"Exploiting Ordinal Class Structure in Multiclass Classification: Application to Ovarian Cancer","authors":"Burook Misganaw, M. Vidyasagar","doi":"10.1109/LLS.2015.2451291","DOIUrl":"https://doi.org/10.1109/LLS.2015.2451291","url":null,"abstract":"In multiclass machine learning problems, one needs to distinguish between the nominal labels that do not have any natural ordering and the ordinal labels that are ordered. Ordinal labels are pervasive in biology, and some examples are given here. In this note, we point out the importance of making use of the order information when it is inherent to the problem. We demonstrate that algorithms that use this additional information outperform the algorithms that do not, on a case study of assigning one of four labels to the ovarian cancer patients on the basis of their time of progression-free survival. As an aside, it is also pointed out that the algorithms that make use of ordering information require fewer data normalizations. This aspect is important in biological applications, where data are plagued by variations in platforms and protocols, batch effects, and so on.","PeriodicalId":87271,"journal":{"name":"IEEE life sciences letters","volume":"1 1","pages":"15-18"},"PeriodicalIF":0.0,"publicationDate":"2015-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1109/LLS.2015.2451291","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"62509637","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 10
Exploiting Ordinal Class Structure in Multiclass Classification: Application to Ovarian Cancer 多类分类中序类结构的开发:在卵巢癌中的应用
Pub Date : 2015-06-30 DOI: 10.1109/LLS.2015.2451291
Burook Misganaw;Mathukumalli Vidyasagar
In multiclass machine learning problems, one needs to distinguish between the nominal labels that do not have any natural ordering and the ordinal labels that are ordered. Ordinal labels are pervasive in biology, and some examples are given here. In this note, we point out the importance of making use of the order information when it is inherent to the problem. We demonstrate that algorithms that use this additional information outperform the algorithms that do not, on a case study of assigning one of four labels to the ovarian cancer patients on the basis of their time of progression-free survival. As an aside, it is also pointed out that the algorithms that make use of ordering information require fewer data normalizations. This aspect is important in biological applications, where data are plagued by variations in platforms and protocols, batch effects, and so on.
在多类机器学习问题中,人们需要区分没有任何自然排序的标称标签和有序的有序标签。序数标签在生物学中普遍存在,这里给出一些例子。在本文中,我们指出了当订单信息是问题的固有属性时,使用订单信息的重要性。我们证明,使用这些额外信息的算法优于不使用这些信息的算法,在一个案例研究中,根据卵巢癌患者的无进展生存时间为其分配四种标签之一。此外,还指出,利用排序信息的算法需要较少的数据规范化。这方面在生物应用程序中很重要,因为在生物应用程序中,数据受到平台和协议、批处理效果等变化的困扰。
{"title":"Exploiting Ordinal Class Structure in Multiclass Classification: Application to Ovarian Cancer","authors":"Burook Misganaw;Mathukumalli Vidyasagar","doi":"10.1109/LLS.2015.2451291","DOIUrl":"https://doi.org/10.1109/LLS.2015.2451291","url":null,"abstract":"In multiclass machine learning problems, one needs to distinguish between the nominal labels that do not have any natural ordering and the ordinal labels that are ordered. Ordinal labels are pervasive in biology, and some examples are given here. In this note, we point out the importance of making use of the order information when it is inherent to the problem. We demonstrate that algorithms that use this additional information outperform the algorithms that do not, on a case study of assigning one of four labels to the ovarian cancer patients on the basis of their time of progression-free survival. As an aside, it is also pointed out that the algorithms that make use of ordering information require fewer data normalizations. This aspect is important in biological applications, where data are plagued by variations in platforms and protocols, batch effects, and so on.","PeriodicalId":87271,"journal":{"name":"IEEE life sciences letters","volume":"1 1","pages":"15-18"},"PeriodicalIF":0.0,"publicationDate":"2015-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1109/LLS.2015.2451291","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49908372","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 10
A Compartmental Lateral Inhibition System to Generate Contrasting Patterns 产生对比模式的隔室侧抑制系统
Pub Date : 2015-06-16 DOI: 10.1109/LLS.2015.2446211
Ana Sofia Rufino Ferreira;Justin Hsia;Murat Arcak
We propose a lateral inhibition system and analyze contrasting patterns of gene expression. The system consists of a set of compartments interconnected by channels. Each compartment contains a colony of cells that produce diffusible molecules to be detected by the neighboring colonies. Each cell is equipped with an inhibitory circuit that reduces its production when the detected signal is sufficiently strong. We characterize the parameter range in which steady-state patterns emerge.
我们提出了一个侧抑制系统,并分析了基因表达的对比模式。该系统由一组通过通道相互连接的隔间组成。每个隔室包含一群细胞,这些细胞产生可扩散的分子,以便被邻近的菌落检测到。每个细胞都配备了抑制回路,当检测到的信号足够强时,抑制回路会减少其产生。我们描述了出现稳态模式的参数范围。
{"title":"A Compartmental Lateral Inhibition System to Generate Contrasting Patterns","authors":"Ana Sofia Rufino Ferreira;Justin Hsia;Murat Arcak","doi":"10.1109/LLS.2015.2446211","DOIUrl":"https://doi.org/10.1109/LLS.2015.2446211","url":null,"abstract":"We propose a lateral inhibition system and analyze contrasting patterns of gene expression. The system consists of a set of compartments interconnected by channels. Each compartment contains a colony of cells that produce diffusible molecules to be detected by the neighboring colonies. Each cell is equipped with an inhibitory circuit that reduces its production when the detected signal is sufficiently strong. We characterize the parameter range in which steady-state patterns emerge.","PeriodicalId":87271,"journal":{"name":"IEEE life sciences letters","volume":"1 1","pages":"7-10"},"PeriodicalIF":0.0,"publicationDate":"2015-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1109/LLS.2015.2446211","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49908370","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
A Compartmental Lateral Inhibition System to Generate Contrasting Patterns 产生对比模式的隔室侧抑制系统
Pub Date : 2015-06-16 DOI: 10.1109/LLS.2015.2446211
Ana Sofia Rufino Ferreira, Justin Hsia, M. Arcak
We propose a lateral inhibition system and analyze contrasting patterns of gene expression. The system consists of a set of compartments interconnected by channels. Each compartment contains a colony of cells that produce diffusible molecules to be detected by the neighboring colonies. Each cell is equipped with an inhibitory circuit that reduces its production when the detected signal is sufficiently strong. We characterize the parameter range in which steady-state patterns emerge.
我们提出了一个侧抑制系统,并分析了基因表达的对比模式。该系统由一组通过通道相互连接的隔间组成。每个隔室包含一群细胞,这些细胞产生可扩散的分子,以便被邻近的菌落检测到。每个细胞都配备了抑制回路,当检测到的信号足够强时,抑制回路会减少其产生。我们描述了出现稳态模式的参数范围。
{"title":"A Compartmental Lateral Inhibition System to Generate Contrasting Patterns","authors":"Ana Sofia Rufino Ferreira, Justin Hsia, M. Arcak","doi":"10.1109/LLS.2015.2446211","DOIUrl":"https://doi.org/10.1109/LLS.2015.2446211","url":null,"abstract":"We propose a lateral inhibition system and analyze contrasting patterns of gene expression. The system consists of a set of compartments interconnected by channels. Each compartment contains a colony of cells that produce diffusible molecules to be detected by the neighboring colonies. Each cell is equipped with an inhibitory circuit that reduces its production when the detected signal is sufficiently strong. We characterize the parameter range in which steady-state patterns emerge.","PeriodicalId":87271,"journal":{"name":"IEEE life sciences letters","volume":"1 1","pages":"7-10"},"PeriodicalIF":0.0,"publicationDate":"2015-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1109/LLS.2015.2446211","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"62509598","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
A Coupled Stochastic Model Explains Differences in Cry Knockout Behavior 一个耦合的随机模型解释了哭击行为的差异
Pub Date : 2015-06-04 DOI: 10.1109/LLS.2015.2439498
John H. Abel;Lukas A. Widmer;Peter C. St. John;Jörg Stelling;Francis J. Doyle
In the mammalian suprachiasmatic nucleus (SCN), a population of noisy cell-autonomous oscillators synchronizes to generate robust circadian rhythms at the organism level. Within these cells, two isoforms of Cryptochrome, Cry1 and Cry2, participate in a negative feedback loop driving oscillation. Previous work has shown that single, dissociated SCN neurons respond differently to Cry1 and Cry2 knockouts. These differences have led to speculation that CRY1 and CRY2 may play different functional roles in the oscillator. To address this proposition, we have developed a new coupled, stochastic model focused on the Period (Per) and Cry feedback loop, and incorporating intercellular coupling via vasoactive intestinal peptide. We show that single dissociated Cry1 knockouts display partially rhythmic behavior. Additionally, intrinsic molecular noise and differences in relative abundance, rather than differing functions, are sufficient to explain the range of rhythmicity encountered in Cry knockouts in the SCN. The results further highlight the essential role of stochastic behavior in understanding and accurately modeling the circadian network.
在哺乳动物视交叉上核(SCN)中,一群嘈杂的细胞自主振荡器在生物体水平上同步产生强大的昼夜节律。在这些细胞中,Cry1和Cry2这两种隐色素的同工异构体参与了一个驱动振荡的负反馈回路。先前的研究表明,单个分离的SCN神经元对Cry1和Cry2敲除的反应不同。这些差异导致推测CRY1和CRY2可能在振荡器中发挥不同的功能作用。为了解决这一问题,我们开发了一个新的耦合随机模型,重点关注周期(Per)和哭声反馈回路,并通过血管活性肠肽纳入细胞间耦合。我们发现单个分离的Cry1敲除表现出部分节律性行为。此外,固有的分子噪声和相对丰度的差异,而不是不同的功能,足以解释SCN中Cry敲除所遇到的节律性范围。这些结果进一步强调了随机行为在理解和准确建模昼夜节律网络中的重要作用。
{"title":"A Coupled Stochastic Model Explains Differences in Cry Knockout Behavior","authors":"John H. Abel;Lukas A. Widmer;Peter C. St. John;Jörg Stelling;Francis J. Doyle","doi":"10.1109/LLS.2015.2439498","DOIUrl":"https://doi.org/10.1109/LLS.2015.2439498","url":null,"abstract":"In the mammalian suprachiasmatic nucleus (SCN), a population of noisy cell-autonomous oscillators synchronizes to generate robust circadian rhythms at the organism level. Within these cells, two isoforms of Cryptochrome, \u0000<italic>Cry1</i>\u0000 and \u0000<italic>Cry2</i>\u0000, participate in a negative feedback loop driving oscillation. Previous work has shown that single, dissociated SCN neurons respond differently to \u0000<italic>Cry1</i>\u0000 and \u0000<italic>Cry2</i>\u0000 knockouts. These differences have led to speculation that CRY1 and CRY2 may play different functional roles in the oscillator. To address this proposition, we have developed a new coupled, stochastic model focused on the \u0000<italic>Period</i>\u0000 (\u0000<italic>Per</i>\u0000) and \u0000<italic>Cry</i>\u0000 feedback loop, and incorporating intercellular coupling via vasoactive intestinal peptide. We show that single dissociated \u0000<italic>Cry1</i>\u0000 knockouts display partially rhythmic behavior. Additionally, intrinsic molecular noise and differences in relative abundance, rather than differing functions, are sufficient to explain the range of rhythmicity encountered in \u0000<italic>Cry</i>\u0000 knockouts in the SCN. The results further highlight the essential role of stochastic behavior in understanding and accurately modeling the circadian network.","PeriodicalId":87271,"journal":{"name":"IEEE life sciences letters","volume":"1 1","pages":"3-6"},"PeriodicalIF":0.0,"publicationDate":"2015-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1109/LLS.2015.2439498","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49908369","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 7
A Coupled Stochastic Model Explains Differences in Cry Knockout Behavior 一个耦合的随机模型解释了哭击行为的差异
Pub Date : 2015-06-04 DOI: 10.1109/LLS.2015.2439498
John H. Abel, L. Widmer, Peter C. St. John, J. Stelling, F. Doyle
In the mammalian suprachiasmatic nucleus (SCN), a population of noisy cell-autonomous oscillators synchronizes to generate robust circadian rhythms at the organism level. Within these cells, two isoforms of Cryptochrome, Cry1 and Cry2, participate in a negative feedback loop driving oscillation. Previous work has shown that single, dissociated SCN neurons respond differently to Cry1 and Cry2 knockouts. These differences have led to speculation that CRY1 and CRY2 may play different functional roles in the oscillator. To address this proposition, we have developed a new coupled, stochastic model focused on the Period (Per) and Cry feedback loop, and incorporating intercellular coupling via vasoactive intestinal peptide. We show that single dissociated Cry1 knockouts display partially rhythmic behavior. Additionally, intrinsic molecular noise and differences in relative abundance, rather than differing functions, are sufficient to explain the range of rhythmicity encountered in Cry knockouts in the SCN. The results further highlight the essential role of stochastic behavior in understanding and accurately modeling the circadian network.
在哺乳动物视交叉上核(SCN)中,一群嘈杂的细胞自主振荡器在生物体水平上同步产生强大的昼夜节律。在这些细胞中,Cry1和Cry2这两种隐色素的同工异构体参与了一个驱动振荡的负反馈回路。先前的研究表明,单个分离的SCN神经元对Cry1和Cry2敲除的反应不同。这些差异导致推测CRY1和CRY2可能在振荡器中发挥不同的功能作用。为了解决这一问题,我们开发了一个新的耦合随机模型,重点关注周期(Per)和哭声反馈回路,并通过血管活性肠肽纳入细胞间耦合。我们发现单个分离的Cry1敲除表现出部分节律性行为。此外,固有的分子噪声和相对丰度的差异,而不是不同的功能,足以解释SCN中Cry敲除所遇到的节律性范围。这些结果进一步强调了随机行为在理解和准确建模昼夜节律网络中的重要作用。
{"title":"A Coupled Stochastic Model Explains Differences in Cry Knockout Behavior","authors":"John H. Abel, L. Widmer, Peter C. St. John, J. Stelling, F. Doyle","doi":"10.1109/LLS.2015.2439498","DOIUrl":"https://doi.org/10.1109/LLS.2015.2439498","url":null,"abstract":"In the mammalian suprachiasmatic nucleus (SCN), a population of noisy cell-autonomous oscillators synchronizes to generate robust circadian rhythms at the organism level. Within these cells, two isoforms of Cryptochrome, <italic>Cry1</italic> and <italic>Cry2</italic>, participate in a negative feedback loop driving oscillation. Previous work has shown that single, dissociated SCN neurons respond differently to <italic>Cry1</italic> and <italic>Cry2</italic> knockouts. These differences have led to speculation that CRY1 and CRY2 may play different functional roles in the oscillator. To address this proposition, we have developed a new coupled, stochastic model focused on the <italic>Period</italic> (<italic>Per</italic>) and <italic>Cry</italic> feedback loop, and incorporating intercellular coupling via vasoactive intestinal peptide. We show that single dissociated <italic>Cry1</italic> knockouts display partially rhythmic behavior. Additionally, intrinsic molecular noise and differences in relative abundance, rather than differing functions, are sufficient to explain the range of rhythmicity encountered in <italic>Cry</italic> knockouts in the SCN. The results further highlight the essential role of stochastic behavior in understanding and accurately modeling the circadian network.","PeriodicalId":87271,"journal":{"name":"IEEE life sciences letters","volume":"39 1","pages":"3-6"},"PeriodicalIF":0.0,"publicationDate":"2015-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1109/LLS.2015.2439498","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"62509560","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 7
Circadian Gating of the Mammalian Cell Cycle Restriction Point: A Mathematical Analysis 哺乳动物细胞周期限制点的昼夜节律门控:一个数学分析
Pub Date : 2015-06-01 DOI: 10.1109/LLS.2015.2449511
Jing Su;Michael A. Henson
A critical decision in the mammalian cell cycle is whether to pass through the restriction point (R-point) or enter the cell cycle. In this letter, we modeled the decision-making system of the mammalian cell cycle entry and the simulated circadian regulation of the R-point driven by external epithelial growth factor (EGF) patterns. Our conceptual model replicated key signaling behaviors observed experimentally, suggesting that the proposed network captured the essential system features. The model revealed the dramatic importance of the EGF dynamics on promoting cell proliferation, showed that the EGF signal duration was more important than the signal strength for driving cells past the R-point, and suggested that the loss of circadian control of the cell cycle entry could be associated with cancer development.
哺乳动物细胞周期的一个关键决策是通过限制点(r点)还是进入细胞周期。在这封信中,我们模拟了哺乳动物细胞周期进入的决策系统,并模拟了由外部上皮生长因子(EGF)模式驱动的r点的昼夜节律调节。我们的概念模型复制了实验观察到的关键信号行为,表明所提出的网络捕获了基本的系统特征。该模型揭示了EGF动力学对促进细胞增殖的巨大重要性,表明EGF信号持续时间比信号强度对驱动细胞超过r点更重要,并表明细胞周期进入的昼夜节律控制的丧失可能与癌症的发展有关。
{"title":"Circadian Gating of the Mammalian Cell Cycle Restriction Point: A Mathematical Analysis","authors":"Jing Su;Michael A. Henson","doi":"10.1109/LLS.2015.2449511","DOIUrl":"https://doi.org/10.1109/LLS.2015.2449511","url":null,"abstract":"A critical decision in the mammalian cell cycle is whether to pass through the restriction point (R-point) or enter the cell cycle. In this letter, we modeled the decision-making system of the mammalian cell cycle entry and the simulated circadian regulation of the R-point driven by external epithelial growth factor (EGF) patterns. Our conceptual model replicated key signaling behaviors observed experimentally, suggesting that the proposed network captured the essential system features. The model revealed the dramatic importance of the EGF dynamics on promoting cell proliferation, showed that the EGF signal duration was more important than the signal strength for driving cells past the R-point, and suggested that the loss of circadian control of the cell cycle entry could be associated with cancer development.","PeriodicalId":87271,"journal":{"name":"IEEE life sciences letters","volume":"1 1","pages":"11-14"},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1109/LLS.2015.2449511","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49908371","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Displacement of Bacterial Plasmids by Engineered Unilateral Incompatibility 利用工程单侧不相容性置换细菌质粒
Pub Date : 2015-06-01 DOI: 10.1109/LLS.2015.2465839
Robert Gooding-Townsend;Steven Ten Holder;Brian Ingalls
Bacterial plasmids employ copy number control systems to ensure that they do not overburden their hosts. Plasmid incompatibility is caused by shared components of copy number control systems, resulting in mutual inhibition of replication. Incompatible plasmids cannot be stably maintained within a host cell. Unilateral incompatibility, in which the plasmid replicons are compatible but one plasmid encodes for the replication inhibitor of the other, leads to rapid displacement of the inhibited plasmid. Thus, we propose that the unilateral incompatibility can be used to eradicate an undesirable plasmid from a population. To investigate this process, we developed deterministic and stochastic models of plasmid dynamics. An analysis of these models provides predictions about the efficacy of plasmid displacement.
细菌质粒采用拷贝数控制系统,以确保它们不会使宿主负担过重。质粒不亲和性是由拷贝数控制系统的共享组分引起的,从而导致复制的相互抑制。不相容的质粒不能在宿主细胞内稳定地维持。单侧不相容,即质粒复制子是相容的,但其中一个质粒编码另一个质粒的复制抑制剂,导致被抑制的质粒快速位移。因此,我们提出单侧不亲和性可用于从种群中根除不需要的质粒。为了研究这一过程,我们开发了质粒动力学的确定性和随机模型。对这些模型的分析提供了质粒置换效果的预测。
{"title":"Displacement of Bacterial Plasmids by Engineered Unilateral Incompatibility","authors":"Robert Gooding-Townsend;Steven Ten Holder;Brian Ingalls","doi":"10.1109/LLS.2015.2465839","DOIUrl":"https://doi.org/10.1109/LLS.2015.2465839","url":null,"abstract":"Bacterial plasmids employ copy number control systems to ensure that they do not overburden their hosts. Plasmid incompatibility is caused by shared components of copy number control systems, resulting in mutual inhibition of replication. Incompatible plasmids cannot be stably maintained within a host cell. Unilateral incompatibility, in which the plasmid replicons are compatible but one plasmid encodes for the replication inhibitor of the other, leads to rapid displacement of the inhibited plasmid. Thus, we propose that the unilateral incompatibility can be used to eradicate an undesirable plasmid from a population. To investigate this process, we developed deterministic and stochastic models of plasmid dynamics. An analysis of these models provides predictions about the efficacy of plasmid displacement.","PeriodicalId":87271,"journal":{"name":"IEEE life sciences letters","volume":"1 1","pages":"19-21"},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1109/LLS.2015.2465839","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49908373","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
IEEE Life Sciences Letters Inaugural Editorial IEEE生命科学通讯首期社论
Pub Date : 2015-06-01 DOI: 10.1109/LLS.2015.2476536
Francis J. Doyle;Mathukumalli Vidyasagar
We, the editors of the IEEE Life Sciences Letters (LSL), take pleasure in welcoming readers to this, the Inaugural Issue of the journal. LSL is intended to facilitate the rapid review and publication of high-quality contemporary research in the broad areas of personalized medicine, pharmaceutical engineering, synthetic biology, and systems biology. We are fortunate to have four outstanding individuals as Senior Editors, one for each theme area, as well as several Associate Editors.
我们,IEEE生命科学快报(LSL)的编辑们,很高兴欢迎读者们来到杂志的创刊号。LSL旨在促进个性化医学、制药工程、合成生物学和系统生物学等广泛领域的高质量当代研究的快速审查和出版。幸运的是,我们有四位杰出的高级编辑,每个主题领域一位,以及几位副编辑。
{"title":"IEEE Life Sciences Letters Inaugural Editorial","authors":"Francis J. Doyle;Mathukumalli Vidyasagar","doi":"10.1109/LLS.2015.2476536","DOIUrl":"https://doi.org/10.1109/LLS.2015.2476536","url":null,"abstract":"We, the editors of the \u0000<italic>IEEE Life Sciences Letters</i>\u0000 (LSL), take pleasure in welcoming readers to this, the Inaugural Issue of the journal. LSL is intended to facilitate the rapid review and publication of high-quality contemporary research in the broad areas of personalized medicine, pharmaceutical engineering, synthetic biology, and systems biology. We are fortunate to have four outstanding individuals as Senior Editors, one for each theme area, as well as several Associate Editors.","PeriodicalId":87271,"journal":{"name":"IEEE life sciences letters","volume":"1 1","pages":"1-2"},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1109/LLS.2015.2476536","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49908368","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
期刊
IEEE life sciences letters
全部 Acc. Chem. Res. ACS Applied Bio Materials ACS Appl. Electron. Mater. ACS Appl. Energy Mater. ACS Appl. Mater. Interfaces ACS Appl. Nano Mater. ACS Appl. Polym. Mater. ACS BIOMATER-SCI ENG ACS Catal. ACS Cent. Sci. ACS Chem. Biol. ACS Chemical Health & Safety ACS Chem. Neurosci. ACS Comb. Sci. ACS Earth Space Chem. ACS Energy Lett. ACS Infect. Dis. ACS Macro Lett. ACS Mater. Lett. ACS Med. Chem. Lett. ACS Nano ACS Omega ACS Photonics ACS Sens. ACS Sustainable Chem. Eng. ACS Synth. Biol. Anal. Chem. BIOCHEMISTRY-US Bioconjugate Chem. BIOMACROMOLECULES Chem. Res. Toxicol. Chem. Rev. Chem. Mater. CRYST GROWTH DES ENERG FUEL Environ. Sci. Technol. Environ. Sci. Technol. Lett. Eur. J. Inorg. Chem. IND ENG CHEM RES Inorg. Chem. J. Agric. Food. Chem. J. Chem. Eng. Data J. Chem. Educ. J. Chem. Inf. Model. J. Chem. Theory Comput. J. Med. Chem. J. Nat. Prod. J PROTEOME RES J. Am. Chem. Soc. LANGMUIR MACROMOLECULES Mol. Pharmaceutics Nano Lett. Org. Lett. ORG PROCESS RES DEV ORGANOMETALLICS J. Org. Chem. J. Phys. Chem. J. Phys. Chem. A J. Phys. Chem. B J. Phys. Chem. C J. Phys. Chem. Lett. Analyst Anal. Methods Biomater. Sci. Catal. Sci. Technol. Chem. Commun. Chem. Soc. Rev. CHEM EDUC RES PRACT CRYSTENGCOMM Dalton Trans. Energy Environ. Sci. ENVIRON SCI-NANO ENVIRON SCI-PROC IMP ENVIRON SCI-WAT RES Faraday Discuss. Food Funct. Green Chem. Inorg. Chem. Front. Integr. Biol. J. Anal. At. Spectrom. J. Mater. Chem. A J. Mater. Chem. B J. Mater. Chem. C Lab Chip Mater. Chem. Front. Mater. Horiz. MEDCHEMCOMM Metallomics Mol. Biosyst. Mol. Syst. Des. Eng. Nanoscale Nanoscale Horiz. Nat. Prod. Rep. New J. Chem. Org. Biomol. Chem. Org. Chem. Front. PHOTOCH PHOTOBIO SCI PCCP Polym. Chem.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1