Systems and Synthetic Biology最新文献_第5页

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

引用次数: 20

Systems and synthetic biology approaches to cell division. 细胞分裂的系统和合成生物学方法。

Systems and Synthetic Biology Pub Date : 2014-09-01 Epub Date: 2014-01-30 DOI: 10.1007/s11693-014-9132-z

Alireza Mashaghi, Cees Dekker

引用次数: 7

When genome integrity and cell cycle decisions collide: roles of polo kinases in cellular adaptation to DNA damage. 当基因组完整性和细胞周期决定发生冲突:polo激酶在细胞适应DNA损伤中的作用。

Systems and Synthetic Biology Pub Date : 2014-09-01 Epub Date: 2014-07-27 DOI: 10.1007/s11693-014-9151-9

Diego Serrano, Damien D'Amours

{"title":"When genome integrity and cell cycle decisions collide: roles of polo kinases in cellular adaptation to DNA damage.","authors":"Diego Serrano, Damien D'Amours","doi":"10.1007/s11693-014-9151-9","DOIUrl":"https://doi.org/10.1007/s11693-014-9151-9","url":null,"abstract":"The drive to proliferate and the need to maintain genome integrity are two of the most powerful forces acting on biological systems. When these forces enter in conflict, such as in the case of cells experiencing DNA damage, feedback mechanisms are activated to ensure that cellular proliferation is stopped and no further damage is introduced while cells repair their chromosomal lesions. In this circumstance, the DNA damage response dominates over the biological drive to proliferate, and may even result in programmed cell death if the damage cannot be repaired efficiently. Interestingly, the drive to proliferate can under specific conditions overcome the DNA damage response and lead to a reactivation of the proliferative program in checkpoint-arrested cells. This phenomenon is known as adaptation to DNA damage and is observed in all eukaryotic species where the process has been studied, including normal and cancer cells in humans. Polo-like kinases (PLKs) are critical regulators of the adaptation response to DNA damage and they play key roles at the interface of cell cycle and checkpoint-related decisions in cells. Here, we review recent progress in defining the specific roles of PLKs in the adaptation process and how this conserved family of eukaryotic kinases can integrate the fundamental need to preserve genomic integrity with effective cellular proliferation. ","PeriodicalId":22161,"journal":{"name":"Systems and Synthetic Biology","volume":"8 3","pages":"195-203"},"PeriodicalIF":0.0,"publicationDate":"2014-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s11693-014-9151-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32596094","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

Getting into shape: How do rod-like bacteria control their geometry? 塑形:棒状细菌如何控制它们的几何形状?

Systems and Synthetic Biology Pub Date : 2014-09-01 Epub Date: 2014-04-22 DOI: 10.1007/s11693-014-9143-9

Ariel Amir, Sven van Teeffelen

引用次数: 20

Microtubule networks for plant cell division. 植物细胞分裂的微管网络。

Systems and Synthetic Biology Pub Date : 2014-09-01 Epub Date: 2014-04-02 DOI: 10.1007/s11693-014-9142-x

Jeroen de Keijzer, Bela M Mulder, Marcel E Janson

{"title":"Microtubule networks for plant cell division.","authors":"Jeroen de Keijzer, Bela M Mulder, Marcel E Janson","doi":"10.1007/s11693-014-9142-x","DOIUrl":"https://doi.org/10.1007/s11693-014-9142-x","url":null,"abstract":"During cytokinesis the cytoplasm of a cell is divided to form two daughter cells. In animal cells, the existing plasma membrane is first constricted and then abscised to generate two individual plasma membranes. Plant cells on the other hand divide by forming an interior dividing wall, the so-called cell plate, which is constructed by localized deposition of membrane and cell wall material. Construction starts in the centre of the cell at the locus of the mitotic spindle and continues radially towards the existing plasma membrane. Finally the membrane of the cell plate and plasma membrane fuse to form two individual plasma membranes. Two microtubule-based cytoskeletal networks, the phragmoplast and the pre-prophase band (PPB), jointly control cytokinesis in plants. The bipolar microtubule array of the phragmoplast regulates cell plate deposition towards a cortical position that is templated by the ring-shaped microtubule array of the PPB. In contrast to most animal cells, plants do not use centrosomes as foci of microtubule growth initiation. Instead, plant microtubule networks are striking examples of self-organizing systems that emerge from physically constrained interactions of dispersed microtubules. Here we will discuss how microtubule-based activities including growth, shrinkage, severing, sliding, nucleation and bundling interrelate to jointly generate the required ordered structures. Evidence mounts that adapter proteins sense the local geometry of microtubules to locally modulate the activity of proteins involved in microtubule growth regulation and severing. Many of the proteins and mechanisms involved have roles in other microtubule assemblies as well, bestowing broader relevance to insights gained from plants. ","PeriodicalId":22161,"journal":{"name":"Systems and Synthetic Biology","volume":"8 3","pages":"187-94"},"PeriodicalIF":0.0,"publicationDate":"2014-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s11693-014-9142-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32596672","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: 22

Toward the assembly of a minimal divisome. 组装最小的分裂体。

Systems and Synthetic Biology Pub Date : 2014-09-01 Epub Date: 2014-04-27 DOI: 10.1007/s11693-014-9150-x

Zohreh Nourian, Andrew Scott, Christophe Danelon

{"title":"Toward the assembly of a minimal divisome.","authors":"Zohreh Nourian, Andrew Scott, Christophe Danelon","doi":"10.1007/s11693-014-9150-x","DOIUrl":"10.1007/s11693-014-9150-x","url":null,"abstract":"The construction of an irreducible minimal cell having all essential attributes of a living system is one of the biggest challenges facing synthetic biology. One ubiquitous task accomplished by any living systems is the division of the cell envelope. Hence, the assembly of an elementary, albeit sufficient, molecular machinery that supports compartment division, is a crucial step towards the realization of self-reproducing artificial cells. Looking backward to the molecular nature of possible ancestral, supposedly more rudimentary, cell division systems may help to identify a minimal divisome. In light of a possible evolutionary pathway of division mechanisms from simple lipid vesicles toward modern life, we define two approaches for recapitulating division in primitive cells: the membrane deforming protein route and the lipid biosynthesis route. Having identified possible proteins and working mechanisms participating in membrane shape alteration, we then discuss how they could be integrated into the construction framework of a programmable minimal cell relying on gene expression inside liposomes. The protein synthesis using recombinant elements (PURE) system, a reconstituted minimal gene expression system, is conceivably the most versatile synthesis platform. As a first step towards the de novo synthesis of a divisome, we showed that the N-BAR domain protein produced from its gene could assemble onto the outer surface of liposomes and sculpt the membrane into tubular structures. We finally discuss the remaining challenges for building up a self-reproducing minimal cell, in particular the coupling of the division machinery with volume expansion and genome replication. ","PeriodicalId":22161,"journal":{"name":"Systems and Synthetic Biology","volume":"8 3","pages":"237-47"},"PeriodicalIF":0.0,"publicationDate":"2014-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4127181/pdf/11693_2014_Article_9150.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32596099","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

Divided we stand: splitting synthetic cells for their proliferation. 我们分裂了:分裂合成细胞使其增殖。

Systems and Synthetic Biology Pub Date : 2014-09-01 Epub Date: 2014-05-27 DOI: 10.1007/s11693-014-9145-7

Yaron Caspi, Cees Dekker

{"title":"Divided we stand: splitting synthetic cells for their proliferation.","authors":"Yaron Caspi, Cees Dekker","doi":"10.1007/s11693-014-9145-7","DOIUrl":"https://doi.org/10.1007/s11693-014-9145-7","url":null,"abstract":"With the recent dawn of synthetic biology, the old idea of man-made artificial life has gained renewed interest. In the context of a bottom-up approach, this entails the de novo construction of synthetic cells that can autonomously sustain themselves and proliferate. Reproduction of a synthetic cell involves the synthesis of its inner content, replication of its information module, and growth and division of its shell. Theoretical and experimental analysis of natural cells shows that, whereas the core synthesis machinery of the information module is highly conserved, a wide range of solutions have been realized in order to accomplish division. It is therefore to be expected that there are multiple ways to engineer division of synthetic cells. Here we survey the field and review potential routes that can be explored to accomplish the division of bottom-up designed synthetic cells. We cover a range of complexities from simple abiotic mechanisms involving splitting of lipid-membrane-encapsulated vesicles due to physical or chemical principles, to potential division mechanisms of synthetic cells that are based on prokaryotic division machineries. ","PeriodicalId":22161,"journal":{"name":"Systems and Synthetic Biology","volume":"8 3","pages":"249-69"},"PeriodicalIF":0.0,"publicationDate":"2014-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s11693-014-9145-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32596101","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: 37

Can systems biology approach help in finding more effective treatment for acute myeloid leukemia? 系统生物学方法能帮助找到更有效的治疗急性髓系白血病的方法吗?

Systems and Synthetic Biology Pub Date : 2014-06-01 Epub Date: 2014-04-16 DOI: 10.1007/s11693-014-9147-5

Anuradha Vaidya

{"title":"Can systems biology approach help in finding more effective treatment for acute myeloid leukemia?","authors":"Anuradha Vaidya","doi":"10.1007/s11693-014-9147-5","DOIUrl":"https://doi.org/10.1007/s11693-014-9147-5","url":null,"abstract":"Acute myeloid leukemia (AML) is a hematological cancer comprising of cancer stem cells (CSCs) that are responsible for the disease progression, drug resistance and post treatment relapses. Advances in genomic technologies have identified AML as a genetically heterogenous disease with dysregulated gene expression networks. Furthermore, observation of intracellular signaling in individual CSCs by mass cytometry has demonstrated the dysregulation of the mitogen associated protein kinase (MAPK) pathways. It has been envisaged that the future treatment for AML would entail upon formulating individualized treatment plans leading to decreased drug related toxicities for patients. However the emerging role of signaling pathways as dynamic molecular switches influencing the cell cycle process, thereby leading to varying stages of cell differentiation, is making community rethink about the current strategies used for the treatment of AML. This commentary will focus on discovering novel biomarkers and identifying new therapeutic targets, to analyze and treat AML, on a platform enabled by systems biology approach. ","PeriodicalId":22161,"journal":{"name":"Systems and Synthetic Biology","volume":"8 2","pages":"165-7"},"PeriodicalIF":0.0,"publicationDate":"2014-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s11693-014-9147-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32319377","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: 5

Identifying pseudogenes from hypothetical proteins for making synthetic proteins. 从假设的蛋白质中识别假基因以制造合成蛋白质。

Systems and Synthetic Biology Pub Date : 2014-06-01 Epub Date: 2014-04-20 DOI: 10.1007/s11693-014-9148-4

P R Shidhi, Achuthsankar S Nair, Prashanth Suravajhala

引用次数: 6

Designing synthetic drugs against Plasmodium falciparum: a computational study of histone-lysine N-methyltransferase (PfHKMT). 设计抗恶性疟原虫的合成药物:组蛋白赖氨酸n -甲基转移酶(PfHKMT)的计算研究。

Systems and Synthetic Biology Pub Date : 2014-06-01 Epub Date: 2014-04-08 DOI: 10.1007/s11693-014-9144-8

Monal Sharma, Chhaya Dhiman, Poonam Dangi, Shailja Singh

{"title":"Designing synthetic drugs against Plasmodium falciparum: a computational study of histone-lysine N-methyltransferase (PfHKMT).","authors":"Monal Sharma, Chhaya Dhiman, Poonam Dangi, Shailja Singh","doi":"10.1007/s11693-014-9144-8","DOIUrl":"https://doi.org/10.1007/s11693-014-9144-8","url":null,"abstract":"Histone lysine methyltransferase (HKMT) are histone-modifying enzymes that catalyze the transfer of methyl groups to lysine and arginine residues of histone protein. HKMTs have been involved in transcriptional regulation of various proteins in organisms. Malaria parasite also has HKMT, which plays a major role in parasite development and pathogenesis and also in regulation of various biological process and pathways. Our aim is to study fundamental biology of key molecules involved in the survival of Plasmodium falciparum and use these to develop efficient synthetic peptides and chemical compounds. As a first step in this direction, we computationally predicted the three-dimensional structure of HKMT of P. falciparum (PfHKMT) by using iterative threading assembly refinement. The PfHKMT three-dimensional model was validated using PROCHECK and docked with known HKMT inhibitor Bix01294 using Autodock. Our initial results are encouraging and indicate that structural analysis of PfHKMT could be important in developing novel synthetic molecules against malaria. ","PeriodicalId":22161,"journal":{"name":"Systems and Synthetic Biology","volume":"8 2","pages":"155-60"},"PeriodicalIF":0.0,"publicationDate":"2014-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s11693-014-9144-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32319375","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: 7