发布求助
文献互助 智能选刊 最新文献

Systems and Synthetic Biology最新文献

筛选
英文 中文
A computational study of dsDNA pairs and vibrational resonance in separating water. dsDNA对及其在分离水中振动共振的计算研究。
Systems and Synthetic Biology Pub Date : 2014-12-01 Epub Date: 2014-11-05 DOI: 10.1007/s11693-014-9157-3
Richard J Calloway, Michael D Proctor, Victor M Boyer, Samantha Napier
{"title":"A computational study of dsDNA pairs and vibrational resonance in separating water.","authors":"Richard J Calloway,&nbsp;Michael D Proctor,&nbsp;Victor M Boyer,&nbsp;Samantha Napier","doi":"10.1007/s11693-014-9157-3","DOIUrl":"https://doi.org/10.1007/s11693-014-9157-3","url":null,"abstract":"<p><p>This article investigates the relationship between molecular sequence and dependent interacting behavior of molecular segment pairs and secondly, sequence dependent, vibrational resonance in surrounding normal saline, protein-free water. The development of a molecular model to explore these systems phenomena, the results of several nanoscale molecular dynamics simulations, and analysis of behavior of interacting ΦX174 double-stranded DNA segment pair models in various configurations are presented. Fourier analysis revealed intriguing vibration frequencies within the solvent plane between the segments, while subsequent frequency domain transformation of the time domain waveforms revealed statistically significant resonating harmonic signals in the THz range. </p>","PeriodicalId":22161,"journal":{"name":"Systems and Synthetic Biology","volume":"8 4","pages":"329-35"},"PeriodicalIF":0.0,"publicationDate":"2014-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s11693-014-9157-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34094486","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Information processing in the adaptation of Saccharomyces cerevisiae to osmotic stress: an analysis of the phosphorelay system. 酿酒酵母菌适应渗透胁迫的信息处理:磷接力系统的分析。
Systems and Synthetic Biology Pub Date : 2014-12-01 Epub Date: 2014-04-19 DOI: 10.1007/s11693-014-9146-6
Friedemann Uschner, Edda Klipp
{"title":"Information processing in the adaptation of Saccharomyces cerevisiae to osmotic stress: an analysis of the phosphorelay system.","authors":"Friedemann Uschner,&nbsp;Edda Klipp","doi":"10.1007/s11693-014-9146-6","DOIUrl":"https://doi.org/10.1007/s11693-014-9146-6","url":null,"abstract":"<p><p>Cellular signaling is key for organisms to survive immediate stresses from fluctuating environments as well as relaying important information about external stimuli. Effective mechanisms have evolved to ensure appropriate responses for an optimal adaptation process. For them to be functional despite the noise that occurs in biochemical transmission, the cell needs to be able to infer reliably what was sensed in the first place. For example Saccharomyces cerevisiae are able to adjust their response to osmotic shock depending on the severity of the shock and initiate responses that lead to near perfect adaptation of the cell. We investigate the Sln1-Ypd1-Ssk1-phosphorelay as a module in the high-osmolarity glycerol pathway by incorporating a stochastic model. Within this framework, we can imitate the noisy perception of the cell and interpret the phosphorelay as an information transmitting channel in the sense of C.E. Shannon's \"Information Theory\". We refer to the channel capacity as a measure to quantify and investigate the transmission properties of this system, enabling us to draw conclusions on viable parameter sets for modeling the system. </p>","PeriodicalId":22161,"journal":{"name":"Systems and Synthetic Biology","volume":"8 4","pages":"297-306"},"PeriodicalIF":0.0,"publicationDate":"2014-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s11693-014-9146-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34094481","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 9
Statistical approach for lysosomal membrane proteins (LMPs) identification. 溶酶体膜蛋白（LMPs）鉴定的统计方法。
Systems and Synthetic Biology Pub Date : 2014-12-01 Epub Date: 2014-08-02 DOI: 10.1007/s11693-014-9153-7
Vijay Tripathi, Pooja Tripathi, Dwijendra Gupta
{"title":"Statistical approach for lysosomal membrane proteins (LMPs) identification.","authors":"Vijay Tripathi, Pooja Tripathi, Dwijendra Gupta","doi":"10.1007/s11693-014-9153-7","DOIUrl":"10.1007/s11693-014-9153-7","url":null,"abstract":"<p><p>Discrimination of Lysosomal membrane proteins (LMP's) from folding types of globular (GPs) and other membrane proteins (OtMPs) is an important task both for identifying LMPs from genomic sequences and for the successful prediction of their secondary and tertiary structures. We have systematically analyzed the amino acid frequencies as well as dipeptide count of GPs, LMPs and OtMPs. Based on the above calculated single amino acid frequency combined with dipeptide count information, we statistically discriminated LMPs from GPs and OtMPs. This approach correctly classified the LMPs with an accuracy of 95 %. On the other hand, the amino acid frequency alone can discriminate LMPs with an accuracy of only 79 %. Similarly dipeptide count alone has an accuracy of 87 % for the discrimination of LMPs. Thus the combined information of both amino acid frequencies and dipeptide composition gives us significant high accurate results. </p>","PeriodicalId":22161,"journal":{"name":"Systems and Synthetic Biology","volume":"8 4","pages":"313-9"},"PeriodicalIF":0.0,"publicationDate":"2014-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4571724/pdf/11693_2014_Article_9153.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34094483","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Virus proteins similar to human proteins as possible disturbance on human pathways. 病毒蛋白质与人类蛋白质相似，可能干扰人类途径。
Systems and Synthetic Biology Pub Date : 2014-12-01 Epub Date: 2014-05-24 DOI: 10.1007/s11693-014-9141-y
Zhao Jin, Masaaki Kotera, Susumu Goto
{"title":"Virus proteins similar to human proteins as possible disturbance on human pathways.","authors":"Zhao Jin,&nbsp;Masaaki Kotera,&nbsp;Susumu Goto","doi":"10.1007/s11693-014-9141-y","DOIUrl":"https://doi.org/10.1007/s11693-014-9141-y","url":null,"abstract":"<p><p>Cancer is not rare anywhere in the world now, and the global burden of cancer continues to increase largely every year. Previous research on infections and cancers reported that, about 17.8 % of the cancers worldwide, which are over 1.9 million cases of cancer, are related to viral infections. At least six oncoviruses, cancer-causing viruses, have been known so far, which include hepatitis B virus, hepatitis C virus, Epstein-Barr virus (EBV or HHV-4), human papillomavirus, human T lymphotropic virus type 1, Kaposi's sarcoma-associated herpesvirus (KSHV or HHV-8), but the pathogenic mechanism is far from being completely understood. In this study, assuming that finding human proteins significantly similar to viral oncoproteins leads to a categorization of the cancer-related pathways that are currently not clearly known, we analyzed different types of virus-caused cancers based on their similarity in order to clarify the unknown cancer mechanisms. As a result, we obtained several potential tumor pathways that may be significant and essential in oncogenic cancer process, which will be helpful for further study on cancer mechanisms and the development of new drug targets. </p>","PeriodicalId":22161,"journal":{"name":"Systems and Synthetic Biology","volume":"8 4","pages":"283-95"},"PeriodicalIF":0.0,"publicationDate":"2014-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s11693-014-9141-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34198120","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
Recent advances and opportunities in synthetic logic gates engineering in living cells. 活细胞合成逻辑门工程的最新进展与机遇。
Systems and Synthetic Biology Pub Date : 2014-12-01 Epub Date: 2014-08-28 DOI: 10.1007/s11693-014-9154-6
Vijai Singh
{"title":"Recent advances and opportunities in synthetic logic gates engineering in living cells.","authors":"Vijai Singh","doi":"10.1007/s11693-014-9154-6","DOIUrl":"https://doi.org/10.1007/s11693-014-9154-6","url":null,"abstract":"<p><p>Recently, a number of synthetic biologic gates including AND, OR, NOR, NOT, XOR and NAND have been engineered and characterized in a wide range of hosts. The hope in the emerging synthetic biology community is to construct an inventory of well-characterized parts and install distinct gene and circuit behaviours that are externally controllable. Though the field is still growing and major successes are yet to emerge, the payoffs are predicted to be significant. In this review, we highlight specific examples of logic gates engineering with applications towards fundamental understanding of network complexity and generating a novel socially useful applications. </p>","PeriodicalId":22161,"journal":{"name":"Systems and Synthetic Biology","volume":"8 4","pages":"271-82"},"PeriodicalIF":0.0,"publicationDate":"2014-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s11693-014-9154-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34198119","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 57
Cartoons on bacterial balloons: scientists' opinion on the popularization of synthetic biology. 细菌气球上的漫画：科学家对普及合成生物学的看法。
Systems and Synthetic Biology Pub Date : 2014-12-01 Epub Date: 2014-10-08 DOI: 10.1007/s11693-014-9155-5
Martí Domínguez, Anna Mateu, Helge Torgersen, Manuel Porcar
{"title":"Cartoons on bacterial balloons: scientists' opinion on the popularization of synthetic biology.","authors":"Martí Domínguez, Anna Mateu, Helge Torgersen, Manuel Porcar","doi":"10.1007/s11693-014-9155-5","DOIUrl":"10.1007/s11693-014-9155-5","url":null,"abstract":"<p><p>How do scientists perceive the media coverage of synthetic biology (SB)? In this paper, we approach this question by studying a set of cartoons devoted to SB. Based on a categorization of the cartoons into five large thematic groups an international survey was carried out to assess the opinion of SB research groups on science communication with regard to the public image of their discipline. The 101 responses obtained indicate that in general, their perception of the communication is not negative, although many respondents raised concerns on the media's inclination to sensationalism and over-simplification. However, the results also suggest that (in the light of the unfortunate experiences with GMO communication) scientists should think twice before proposing metaphorical interpretations of their research. </p>","PeriodicalId":22161,"journal":{"name":"Systems and Synthetic Biology","volume":"8 4","pages":"321-8"},"PeriodicalIF":0.0,"publicationDate":"2014-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4571726/pdf/11693_2014_Article_9155.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34094484","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Mechanisms of cell division as regulators of acute immune response. 细胞分裂作为急性免疫反应调节器的机制。
Systems and Synthetic Biology Pub Date : 2014-09-01 Epub Date: 2014-04-29 DOI: 10.1007/s11693-014-9149-3
Andrey Kan, Philip D Hodgkin
{"title":"Mechanisms of cell division as regulators of acute immune response.","authors":"Andrey Kan, Philip D Hodgkin","doi":"10.1007/s11693-014-9149-3","DOIUrl":"10.1007/s11693-014-9149-3","url":null,"abstract":"<p><p>The acute adaptive immune response is complex, proceeding through phases of activation of quiescent lymphocytes, rapid expansion by cell division and cell differentiation, cessation of division and eventual death of greater than 95 % of the newly generated population. Control of the response is not central but appears to operate as a distributed process where global patterns reliably emerge as a result of collective behaviour of a large number of autonomous cells. In this review, we highlight evidence that competing intracellular timed processes underlie the distribution of individual fates and control cell proliferation, cessation and loss. These principles can be captured in a mathematical model to illustrate consistency with previously published experimentally observed data. </p>","PeriodicalId":22161,"journal":{"name":"Systems and Synthetic Biology","volume":"8 3","pages":"215-21"},"PeriodicalIF":0.0,"publicationDate":"2014-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4127173/pdf/11693_2014_Article_9149.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32596096","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Swinging a sword: how microtubules search for their targets. 挥剑:微管如何寻找它们的目标。
Systems and Synthetic Biology Pub Date : 2014-09-01 Epub Date: 2014-02-16 DOI: 10.1007/s11693-014-9134-x
Nenad Pavin, Iva M Tolić-Nørrelykke
{"title":"Swinging a sword: how microtubules search for their targets.","authors":"Nenad Pavin,&nbsp;Iva M Tolić-Nørrelykke","doi":"10.1007/s11693-014-9134-x","DOIUrl":"https://doi.org/10.1007/s11693-014-9134-x","url":null,"abstract":"<p><p>The cell interior is in constant movement, which is to a large extent determined by microtubules, thin and long filaments that permeate the cytoplasm. To move large objects, microtubules need to connect them to the site of their destination. For example, during cell division, microtubules connect chromosomes with the spindle poles via kinetochores, protein complexes on the chromosomes. A general question is how microtubules, while being bound to one structure, find the target that needs to be connected to this structure. Here we review the mechanisms of how microtubules search for kinetochores, with emphasis on the recently discovered microtubule feature to explore space by pivoting around the spindle pole. In addition to accelerating the search for kinetochores, pivoting helps the microtubules to search for cortical anchors, as well as to self-organize into parallel arrays and asters to target specific regions of the cell. Thus, microtubule pivoting constitutes a mechanism by which they locate targets in different cellular contexts. </p>","PeriodicalId":22161,"journal":{"name":"Systems and Synthetic Biology","volume":"8 3","pages":"179-86"},"PeriodicalIF":0.0,"publicationDate":"2014-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s11693-014-9134-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32596671","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 24
Experiments inside a box lead to out-of-the-box ideas on cellular organization. 盒子里的实验带来了关于细胞组织的不同寻常的想法。
Systems and Synthetic Biology Pub Date : 2014-09-01 Epub Date: 2014-03-26 DOI: 10.1007/s11693-014-9139-5
Liedewij Laan
{"title":"Experiments inside a box lead to out-of-the-box ideas on cellular organization.","authors":"Liedewij Laan","doi":"10.1007/s11693-014-9139-5","DOIUrl":"https://doi.org/10.1007/s11693-014-9139-5","url":null,"abstract":"<p><p>Microtubules are biopolymers that assemble from tubulin dimers into hollow tubes and play an important role in cellular organization. Their fascinating properties and variety of functions, like for example chromosome segregation, sperm propagation and polarity establishment, have made them a popular subject of study. In this perspective I focus on the contribution of minimal in vitro systems to our understanding of microtubule organization within the physical confinement of a cell. </p>","PeriodicalId":22161,"journal":{"name":"Systems and Synthetic Biology","volume":"8 3","pages":"223-6"},"PeriodicalIF":0.0,"publicationDate":"2014-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s11693-014-9139-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32596097","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Role and regulation of kinesin-8 motors through the cell cycle. 激酶-8马达在细胞周期中的作用和调控。
Systems and Synthetic Biology Pub Date : 2014-09-01 Epub Date: 2014-03-23 DOI: 10.1007/s11693-014-9140-z
Liam J Messin, Jonathan B A Millar
{"title":"Role and regulation of kinesin-8 motors through the cell cycle.","authors":"Liam J Messin,&nbsp;Jonathan B A Millar","doi":"10.1007/s11693-014-9140-z","DOIUrl":"https://doi.org/10.1007/s11693-014-9140-z","url":null,"abstract":"<p><p>Members of the kinesin-8 motor family play a central role in controlling microtubule length throughout the eukaryotic cell cycle. Inactivation of kinesin-8 causes defects in cell polarity during interphase and astral and mitotic spindle length, metaphase chromosome alignment, timing of anaphase onset and accuracy of chromosome segregation. Although the biophysical mechanism by which kinesin-8 molecules influence microtubule dynamics has been studied extensively in a variety of species, a consensus view has yet to emerge. One reason for this might be that some members of the kinesin-8 family can associate to other microtubule-associated proteins, cell cycle regulatory proteins and other kinesin family members. In this review we consider how cell cycle specific modification and its association to other regulatory proteins may modulate the function of kinesin-8 to enable it to function as a master regulator of microtubule dynamics. </p>","PeriodicalId":22161,"journal":{"name":"Systems and Synthetic Biology","volume":"8 3","pages":"205-13"},"PeriodicalIF":0.0,"publicationDate":"2014-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s11693-014-9140-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32596095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 20
首页 上一页 下一页 尾页
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
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
请完成安全验证×
相关产品
×
本文献相关产品
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 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号：481959085
Book学术官方微信