Cellular logistics最新文献

Vps34 and the Armus/TBC-2 Rab GAPs: Putting the brakes on the endosomal Rab5 and Rab7 GTPases. Vps34和Armus/TBC-2 Rab gap:抑制内体Rab5和Rab7 gtpase

Cellular logistics Pub Date : 2017-12-19 eCollection Date: 2017-01-01 DOI: 10.1080/21592799.2017.1403530

Fiona Law, Christian E Rocheleau

引用次数: 8

Integrative biological simulation praxis: Considerations from physics, philosophy, and data/model curation practices. 综合生物模拟实践:从物理学、哲学和数据/模型管理实践的考虑。

Cellular logistics Pub Date : 2017-11-29 eCollection Date: 2017-01-01 DOI: 10.1080/21592799.2017.1392400

Gopal P Sarma, Victor Faundez

{"title":"Integrative biological simulation praxis: Considerations from physics, philosophy, and data/model curation practices.","authors":"Gopal P Sarma, Victor Faundez","doi":"10.1080/21592799.2017.1392400","DOIUrl":"https://doi.org/10.1080/21592799.2017.1392400","url":null,"abstract":"Integrative biological simulations have a varied and controversial history in the biological sciences. From computational models of organelles, cells, and simple organisms, to physiological models of tissues, organ systems, and ecosystems, a diverse array of biological systems have been the target of large-scale computational modeling efforts. Nonetheless, these research agendas have yet to prove decisively their value among the broader community of theoretical and experimental biologists. In this commentary, we examine a range of philosophical and practical issues relevant to understanding the potential of integrative simulations. We discuss the role of theory and modeling in different areas of physics and suggest that certain sub-disciplines of physics provide useful cultural analogies for imagining the future role of simulations in biological research. We examine philosophical issues related to modeling which consistently arise in discussions about integrative simulations and suggest a pragmatic viewpoint that balances a belief in philosophy with the recognition of the relative infancy of our state of philosophical understanding. Finally, we discuss community workflow and publication practices to allow research to be readily discoverable and amenable to incorporation into simulations. We argue that there are aligned incentives in widespread adoption of practices which will both advance the needs of integrative simulation efforts as well as other contemporary trends in the biological sciences, ranging from open science and data sharing to improving reproducibility.","PeriodicalId":72547,"journal":{"name":"Cellular logistics","volume":"7 4","pages":"e1392400"},"PeriodicalIF":0.0,"publicationDate":"2017-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21592799.2017.1392400","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35704507","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: 4

Agents and networks to model the dynamic interactions of intracellular transport. 模拟细胞内运输的动态相互作用的代理和网络。

Cellular logistics Pub Date : 2017-11-29 eCollection Date: 2017-01-01 DOI: 10.1080/21592799.2017.1392401

Luis S Mayorga, Meghna Verma, Raquel Hontecillas, Stefan Hoops, Josep Bassaganya-Riera

引用次数: 7

How can biological modeling help cell biology? 生物建模如何帮助细胞生物学?

Cellular logistics Pub Date : 2017-11-14 eCollection Date: 2017-01-01 DOI: 10.1080/21592799.2017.1404780

Elizabeth Sztul

引用次数: 2

Amino acid and small GTPase regulation of mTORC1. 氨基酸和小GTPase对mTORC1的调控。

Cellular logistics Pub Date : 2017-09-29 eCollection Date: 2017-01-01 DOI: 10.1080/21592799.2017.1378794

Thu P Nguyen, Anderson R Frank, Jenna L Jewell

引用次数: 24

Finding your inner modeler: An NSF-sponsored workshop to introduce cell biologists to modeling/computational approaches. 寻找你内在的建模者:一个nsf赞助的研讨会，向细胞生物学家介绍建模/计算方法。

Cellular logistics Pub Date : 2017-09-25 eCollection Date: 2017-01-01 DOI: 10.1080/21592799.2017.1382669

David E Stone, Elizabeth S Haswell, Elizabeth Sztul

{"title":"Finding your inner modeler: An NSF-sponsored workshop to introduce cell biologists to modeling/computational approaches.","authors":"David E Stone, Elizabeth S Haswell, Elizabeth Sztul","doi":"10.1080/21592799.2017.1382669","DOIUrl":"https://doi.org/10.1080/21592799.2017.1382669","url":null,"abstract":"In classical Cell Biology, fundamental cellular processes are revealed empirically, one experiment at a time. While this approach has been enormously fruitful, our understanding of cells is far from complete. In fact, the more we know, the more keenly we perceive our ignorance of the profoundly complex and dynamic molecular systems that underlie cell structure and function. Thus, it has become apparent to many cell biologists that experimentation alone is unlikely to yield major new paradigms, and that empiricism must be combined with theory and computational approaches to yield major new discoveries. To facilitate those discoveries, three workshops will convene annually for one day in three successive summers (2017-2019) to promote the use of computational modeling by cell biologists currently unconvinced of its utility or unsure how to apply it. The first of these workshops was held at the University of Illinois, Chicago in July 2017. Organized to facilitate interactions between traditional cell biologists and computational modelers, it provided a unique educational opportunity: a primer on how cell biologists with little or no relevant experience can incorporate computational modeling into their research. Here, we report on the workshop and describe how it addressed key issues that cell biologists face when considering modeling including: (1) Is my project appropriate for modeling? (2) What kind of data do I need to model my process? (3) How do I find a modeler to help me in integrating modeling approaches into my work? And, perhaps most importantly, (4) why should I bother?","PeriodicalId":72547,"journal":{"name":"Cellular logistics","volume":"7 4","pages":"e1382669"},"PeriodicalIF":0.0,"publicationDate":"2017-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21592799.2017.1382669","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35704505","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

Intermolecular interactions involving an acidic patch on immunoglobulin variable domain and the γ2 constant region mediate crystalline inclusion body formation in the endoplasmic reticulum. 免疫球蛋白可变区和γ - 2恒定区酸性斑块的分子间相互作用介导了内质网晶体包涵体的形成。

Cellular logistics Pub Date : 2017-08-08 eCollection Date: 2017-01-01 DOI: 10.1080/21592799.2017.1361499

Haruki Hasegawa, Mei Geng, Randal R Ketchem, Ling Liu, Kevin Graham, Frederick Jacobsen

{"title":"Intermolecular interactions involving an acidic patch on immunoglobulin variable domain and the γ2 constant region mediate crystalline inclusion body formation in the endoplasmic reticulum.","authors":"Haruki Hasegawa, Mei Geng, Randal R Ketchem, Ling Liu, Kevin Graham, Frederick Jacobsen","doi":"10.1080/21592799.2017.1361499","DOIUrl":"https://doi.org/10.1080/21592799.2017.1361499","url":null,"abstract":"Full-length immunoglobulins (Igs) are widely considered difficult to crystallize because of their large size, N-linked glycosylation, and flexible hinge region. However, numerous cases of intracellular Ig crystallization are reported in plasma cell dyscrasias. What makes some Ig clones more prone to crystallize during biosynthesis as well as the biochemical and cell biological requirements for this cryptic event are poorly understood. To investigate the underlying process of intracellular Ig crystallization we searched for model IgGs that can induce crystalline inclusions during recombinant overexpression. By testing various subunit combinations through mixing and matching of individual subunit chains derived from a panel of human IgG clones, we identified one secretion competent IgG2λ that induced needle-like crystalline inclusions in transfected HEK293 cells. Ig crystallization rarely occurred at steady-state cell growth conditions but was easily induced when ER-to-Golgi transport was pharmacologically blocked. Homology modeling revealed the presence of a prominent negatively-charged patch on the variable domain surface. The patch was composed of eight aspartic acids, of which five were in the heavy chain variable region and three were in the light chain. Crystallization occurred only when the two subunits were co-transfected and the intracellular crystals co-localized with ER resident proteins. Furthermore, subtype switching from IgG2 to IgG1 and stepwise neutralization of the acidic patch independently abrogated Ig crystallization events. The evidence supported that the formation of needle-like crystalline inclusions in the ER was underscored by multivalent intermolecular interactions between the acidic patch and undefined determinants present on the γ2 subunit constant region.","PeriodicalId":72547,"journal":{"name":"Cellular logistics","volume":"7 3","pages":"e1361499"},"PeriodicalIF":0.0,"publicationDate":"2017-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21592799.2017.1361499","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35442259","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: 2

The ARL2 GTPase regulates mitochondrial fusion from the intermembrane space. ARL2 GTPase 可调节线粒体与膜间隙的融合。

Cellular logistics Pub Date : 2017-06-23 eCollection Date: 2017-01-01 DOI: 10.1080/21592799.2017.1340104

Laura E Newman, Cara R Schiavon, Rachel E Turn, Richard A Kahn

{"title":"The ARL2 GTPase regulates mitochondrial fusion from the intermembrane space.","authors":"Laura E Newman, Cara R Schiavon, Rachel E Turn, Richard A Kahn","doi":"10.1080/21592799.2017.1340104","DOIUrl":"10.1080/21592799.2017.1340104","url":null,"abstract":"Mitochondria are essential, dynamic organelles that regularly undergo both fusion and fission in response to cellular conditions, though mechanisms of the regulation of their dynamics are incompletely understood. We provide evidence that increased activity of the small GTPase ARL2 is strongly correlated with an increase in fusion, while loss of ARL2 activity results in a decreased rate of mitochondrial fusion. Strikingly, expression of activated ARL2 can partially restore the loss of fusion resulting from deletion of either mitofusin 1 (MFN1) or mitofusin 2 (MFN2), but not deletion of both. We only observe the full effects of ARL2 on mitochondrial fusion when it is present in the intermembrane space (IMS), as constructs driven to the matrix or prevented from entering mitochondria are essentially inactive in promoting fusion. Thus, ARL2 is the first regulatory (small) GTPase shown to act inside mitochondria or in the fusion pathway. Finally, using high-resolution, structured illumination microscopy (SIM), we find that ARL2 and mitofusin immunoreactivities present as punctate staining along mitochondria that share a spatial convergence in fluorescence signals. Thus, we propose that ARL2 plays a regulatory role in mitochondrial fusion, acting from the IMS and requiring at least one of the mitofusins in their canonical role in fusion of the outer membranes.","PeriodicalId":72547,"journal":{"name":"Cellular logistics","volume":"7 3","pages":"e1340104"},"PeriodicalIF":0.0,"publicationDate":"2017-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5602422/pdf/kcll-07-03-1340104.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35442260","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

Ypt4 and lvs1 regulate vacuolar size and function in Schizosaccharomyces pombe. Ypt4和lvs1调节裂糖菌液泡大小和功能。

Cellular logistics Pub Date : 2017-06-09 eCollection Date: 2017-01-01 DOI: 10.1080/21592799.2017.1335270

Addison Rains, Yorisha Bryant, Kaitlyn A Dorsett, Austin Culver, Jamal Egbaria, Austin Williams, Matt Barnes, Raeann Lamere, Austin R Rossi, Stephanie C Waldrep, Caroline Wilder, Elliot Kliossis, Melanie L Styers

{"title":"Ypt4 and lvs1 regulate vacuolar size and function in Schizosaccharomyces pombe.","authors":"Addison Rains, Yorisha Bryant, Kaitlyn A Dorsett, Austin Culver, Jamal Egbaria, Austin Williams, Matt Barnes, Raeann Lamere, Austin R Rossi, Stephanie C Waldrep, Caroline Wilder, Elliot Kliossis, Melanie L Styers","doi":"10.1080/21592799.2017.1335270","DOIUrl":"https://doi.org/10.1080/21592799.2017.1335270","url":null,"abstract":"The yeast vacuole plays key roles in cellular stress responses. Here, we show that deletion of lvs1, the fission yeast homolog of the Chediak-Higashi Syndrome CHS1/LYST gene, increases vacuolar size, similar to deletion of the Rab4 homolog ypt4. Overexpression of lvs1-YFP rescued vacuolar size in ypt4Δ cells, but ypt4-YFP did not rescue lvs1Δ, suggesting that lvs1 may act downstream of ypt4. Vacuoles were capable of hypotonic shock-induced fusion and recovery in both ypt4Δ and lvs1Δ cells, although recovery may be slightly delayed in ypt4Δ. Endocytic and secretory trafficking were not affected, but ypt4Δ and lvs1Δ strains were sensitive to neutral pH and CaCl2, consistent with vacuolar dysfunction. In addition to changes in vacuolar size, deletion of ypt4 also dramatically increased cell size, similar to tor1 mutants. These results implicate ypt4 and lvs1 in maintenance of vacuolar size and suggest that ypt4 may link vacuolar homeostasis to cell cycle progression.","PeriodicalId":72547,"journal":{"name":"Cellular logistics","volume":"7 3","pages":"e1335270"},"PeriodicalIF":0.0,"publicationDate":"2017-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21592799.2017.1335270","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35442258","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

Yeast chemotropism: A paradigm shift in chemical gradient sensing. 酵母的趋化性:化学梯度传感的范式转变。

Cellular logistics Pub Date : 2017-04-11 eCollection Date: 2017-01-01 DOI: 10.1080/21592799.2017.1314237

Amber Ismael, David E Stone

引用次数: 8