123 results match your criteria Cellular logistics[Journal]


How can biological modeling help cell biology?

Authors:
Elizabeth Sztul

Cell Logist 2017 14;7(4):e1404780. Epub 2017 Nov 14.

Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA.

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http://dx.doi.org/10.1080/21592799.2017.1404780DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5739094PMC
November 2017
1 Read

Vps34 and the Armus/TBC-2 Rab GAPs: Putting the brakes on the endosomal Rab5 and Rab7 GTPases.

Cell Logist 2017 19;7(4):e1403530. Epub 2017 Dec 19.

Division of Endocrinology and Metabolism, Department of Medicine and the Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada.

Rab5 and Rab7 GTPases are key regulators of endosome maturation and lysosome fusion. They activate the class III phosphoinositide 3-kinase (PI3K) Vps34 to generate pools of phosphatidylinositol-3 phosphate [PI(3)P] on endosomes. Together PI(3)P and the GTP-bound Rabs coordinate the recruitment of endosomal regulators to drive early to late endosome maturation and ultimately lysosome fusion. Read More

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http://dx.doi.org/10.1080/21592799.2017.1403530DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5739090PMC
December 2017
1 Read

Agents and networks to model the dynamic interactions of intracellular transport.

Cell Logist 2017 29;7(4):e1392401. Epub 2017 Nov 29.

Nutritional Immunology and Molecular Medicine Laboratory, Biocomplexity Institute, Virginia Tech, Blacksburg, VA, USA.

Cell biology is increasingly evolving to become a more formal and quantitative science. The field of intracellular transport is no exception. However, it is extremely challenging to formulate mathematical and computational models for processes that involve dynamic structures that continuously change their shape, position and composition, leading to information transfer and functional outcomes. Read More

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http://dx.doi.org/10.1080/21592799.2017.1392401DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5739099PMC
November 2017
4 Reads

Integrative biological simulation praxis: Considerations from physics, philosophy, and data/model curation practices.

Cell Logist 2017 29;7(4):e1392400. Epub 2017 Nov 29.

School of Medicine, Emory University, Atlanta, GA, USA.

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. Read More

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http://dx.doi.org/10.1080/21592799.2017.1392400DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5739097PMC
November 2017
2 Reads

Finding your inner modeler: An NSF-sponsored workshop to introduce cell biologists to modeling/computational approaches.

Cell Logist 2017 25;7(4):e1382669. Epub 2017 Sep 25.

Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA.

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. Read More

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http://dx.doi.org/10.1080/21592799.2017.1382669DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5739093PMC
September 2017

Amino acid and small GTPase regulation of mTORC1.

Cell Logist 2017 29;7(4):e1378794. Epub 2017 Sep 29.

Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX USA.

The mammalian target of rapamycin (mTOR) is an evolutionarily conserved serine/threonine kinase that belongs to the phosphatidylinositol 3-kinase-related kinase (PIKK) family. mTOR is the catalytic subunit of mTOR complex 1 (mTORC1), which integrates multiple environmental signals to control cell growth and metabolism. Nutrients, specifically amino acids, are the most potent stimuli for mTORC1 activation. Read More

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http://dx.doi.org/10.1080/21592799.2017.1378794DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5739091PMC
September 2017
20 Reads

Intermolecular interactions involving an acidic patch on immunoglobulin variable domain and the γ2 constant region mediate crystalline inclusion body formation in the endoplasmic reticulum.

Cell Logist 2017 8;7(3):e1361499. Epub 2017 Aug 8.

Department of Therapeutic Discovery, Amgen Inc., Thousand Oaks, CA, USA.

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. Read More

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http://dx.doi.org/10.1080/21592799.2017.1361499DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5602423PMC
August 2017
54 Reads

The ARL2 GTPase regulates mitochondrial fusion from the intermembrane space.

Cell Logist 2017 23;7(3):e1340104. Epub 2017 Jun 23.

Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA.

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. Read More

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http://dx.doi.org/10.1080/21592799.2017.1340104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5602422PMC
June 2017
3 Reads

and regulate vacuolar size and function in .

Cell Logist 2017 9;7(3):e1335270. Epub 2017 Jun 9.

Department of Biology, Birmingham-Southern College, Birmingham, AL, USA.

The yeast vacuole plays key roles in cellular stress responses. Here, we show that deletion of , the fission yeast homolog of the Chediak-Higashi Syndrome / gene, increases vacuolar size, similar to deletion of the Rab4 homolog . Overexpression of lvs1-YFP rescued vacuolar size in cells, but ypt4-YFP did not rescue , suggesting that may act downstream of . Read More

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http://dx.doi.org/10.1080/21592799.2017.1335270DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5602425PMC
June 2017
29 Reads

Yeast chemotropism: A paradigm shift in chemical gradient sensing.

Cell Logist 2017 11;7(2):e1314237. Epub 2017 Apr 11.

Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA.

The ability of cells to direct their movement and growth in response to shallow chemical gradients is essential in the life cycles of all eukaryotic organisms. The signaling mechanisms underlying directional sensing in chemotactic cells have been well studied; however, relatively little is known about how chemotropic cells interpret chemical gradients. Recent studies of chemotropism in budding and fission yeast have revealed 2 quite different mechanisms-biased wandering of the polarity complex, and differential internalization of the receptor and G protein. Read More

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http://dx.doi.org/10.1080/21592799.2017.1314237DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5501219PMC
April 2017
2 Reads

The Arf activator GBF1 localizes to plasma membrane sites involved in cell adhesion and motility.

Cell Logist 2017 20;7(2):e1308900. Epub 2017 Mar 20.

Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA.

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http://dx.doi.org/10.1080/21592799.2017.1308900DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5501194PMC
March 2017
58 Reads

A plasmid library of full-length zebrafish rab proteins for cell biology.

Cell Logist 2017 1;7(1):e1301151. Epub 2017 Mar 1.

Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia; Centre for Microscopy and Microanalysis, University of Queensland, Brisbane, Queensland, Australia.

The zebrafish is an emerging model for highly sophisticated medium-throughput experiments such as genetic and chemical screens. However, studies of entire protein families within this context are often hampered by poor genetic resources such as clone libraries. Here we describe a complete collection of 76 full-length open reading frame clones for the zebrafish rab protein family. Read More

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https://www.tandfonline.com/doi/full/10.1080/21592799.2017.1
Publisher Site
http://dx.doi.org/10.1080/21592799.2017.1301151DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5383215PMC
March 2017
4 Reads

Rab11-FIP1 phosphorylation by MARK2 regulates polarity in MDCK cells.

Cell Logist 2017 9;7(1):e1271498. Epub 2017 Jan 9.

Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, TN, USA; Department of Cell & Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA; Section of Surgical Sciences, Vanderbilt University School of Medicine, Nashville, TN, USA; Nashville VA Medical Center, Nashville, TN, USA; Vanderbilt Ingram Cancer Center, Nashville, TN, USA.

MARK2/Par1b/EMK1, a serine/threonine kinase, is required for correct apical/basolateral membrane polarization in epithelial cells. However, the specific substrates mediating MARK2 action are less well understood. We have now found that MARK2 phosphorylates Rab11-FIP1B/C at serine 234 in a consensus site similar to that previously identified in Rab11-FIP2. Read More

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http://dx.doi.org/10.1080/21592799.2016.1271498DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5383218PMC
January 2017
2 Reads

Plasmids for variable expression of proteins targeted to the mitochondrial matrix or intermembrane space.

Cell Logist 2016 13;6(4):e1247939. Epub 2016 Oct 13.

Department of Biochemistry, Emory University School of Medicine , Atlanta, GA, USA.

We describe the construction and uses of a series of plasmids for directing expression to varied levels of exogenous proteins targeted to the mitochondrial matrix or intermembrane space. We found that the level of protein expression achieved, the kinetics of expression and mitochondrial import, and half-life after import can each vary with the protein examined. These factors should be considered when directing localization of an exogenous protein to mitochondria for rescue, proteomics, or other approaches. Read More

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http://dx.doi.org/10.1080/21592799.2016.1247939DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5190143PMC
October 2016
5 Reads

Neo1 and phosphatidylethanolamine contribute to vacuole membrane fusion in .

Cell Logist 2016 Jul-Sep;6(3):e1228791. Epub 2016 Aug 25.

Department of Biological Sciences, Vanderbilt University , Nashville, TN, USA.

is an essential gene in budding yeast and belongs to a highly conserved subfamily of P-type ATPase genes that encode phospholipid flippases. Inactivation of temperature sensitive alleles produces pleiomorphic defects in the secretory and endocytic pathways, including fragmented vacuoles. A screen for multicopy suppressors of growth defects yielded , which encodes a Rab7 homolog involved in SNARE-dependent vacuolar fusion. Read More

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http://dx.doi.org/10.1080/21592799.2016.1228791DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5058351PMC
August 2016
3 Reads

An improved reversibly dimerizing mutant of the FK506-binding protein FKBP.

Cell Logist 2016 Jul-Sep;6(3):e1204848. Epub 2016 Jun 24.

Department of Molecular Genetics and Cell Biology, University of Chicago , Chicago, IL, USA.

FK506-binding protein (FKBP) is a monomer that binds to FK506, rapamycin, and related ligands. The F36M substitution, in which Phe36 in the ligand-binding pocket is changed to Met, leads to formation of antiparallel FKBP dimers, which can be dissociated into monomers by ligand binding. This FKBP(M) mutant has been employed in the mammalian secretory pathway to generate aggregates that can be dissolved by ligand addition to create cargo waves. Read More

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http://dx.doi.org/10.1080/21592799.2016.1204848DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5058350PMC
June 2016
3 Reads

Allosteric properties of PH domains in Arf regulatory proteins.

Cell Logist 2016 Apr-Jun;6(2):e1181700. Epub 2016 Apr 26.

Laboratory of Structural Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health , Bethesda, MD, USA.

Pleckstrin Homology (PH) domains bind phospholipids and proteins. They are critical regulatory elements of a number enzymes including guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs) for Ras-superfamily guanine nucleotide binding proteins such as ADP-ribosylation factors (Arfs). Recent studies have indicated that many PH domains may bind more than one ligand cooperatively. Read More

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http://dx.doi.org/10.1080/21592799.2016.1181700DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4878581PMC
April 2016
8 Reads

Small GTPases in trafficking - a family approach: Introducing a rolling series focused on groups or families of small GTPases in trafficking.

Authors:
Jennifer L Stow

Cell Logist 2016 Jan-Mar;6(1):e1178036. Epub 2016 Apr 21.

Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD, Australia.

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http://dx.doi.org/10.1080/21592799.2016.1178036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4861589PMC
April 2016
2 Reads

Degradation elements coincide with cofactor binding sites in a short-lived transcription factor.

Cell Logist 2016 Jan-Mar;6(1):e1157664. Epub 2016 Mar 8.

Department of Molecular Biophysics and Biochemistry, Yale University , New Haven, CT, USA.

Elaborate control of gene expression by transcription factors is common to all kingdoms of life. In eukaryotes, transcription factor abundance and activity are often regulated by targeted proteolysis via the ubiquitin-proteasome system (UPS). The yeast MATα2 (α2) cell type regulator has long served as a model for UPS-dependent transcription factor degradation. Read More

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http://dx.doi.org/10.1080/21592799.2016.1157664DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4861582PMC
March 2016
1 Read

Sequential recruitment of Rab GTPases during early stages of phagocytosis.

Cell Logist 2016 Jan-Mar;6(1):e1140615. Epub 2016 Jan 29.

Institute for Molecular Bioscience, The University of Queensland , Brisbane, Queensland, Australia.

The phagocytosis and destruction of pathogens and dead cells by macrophages is important for innate immunity and tissue maintenance. Multiple Rab family GTPases engage effector molecules to coordinate the early stages of phagocytosis, which include rapid changes in actin polymerization, membrane phospholipids, trafficking and the activation of receptors. Defining the spatiotemporal, sequential recruitment of these Rabs is critical for insights into how phagocytosis is initiated and coordinated. Read More

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http://dx.doi.org/10.1080/21592799.2016.1140615DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4861590PMC
January 2016
2 Reads

Tool box: Plasmids for the expression or knockdown of human ARF Family GTPases (ARF/ARL/SAR) and their co-expression in bacteria with N-myristoyltransferases.

Cell Logist 2015 Jul-Sep;5(3):e1090523. Epub 2015 Sep 21.

Department of Biochemistry; Emory University School of Medicine ; Atlanta, GA USA.

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http://dx.doi.org/10.1080/21592799.2015.1090523DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4820815PMC
September 2015
4 Reads

Arf-like GTPase Arl8: Moving from the periphery to the center of lysosomal biology.

Cell Logist 2015 Jul-Sep;5(3):e1086501. Epub 2015 Sep 21.

Department of Biological Sciences; Indian Institute of Science Education and Research-Mohali (IISERM) ; Mohali, India.

Lysosomes are dynamic organelles that not only mediate degradation of cellular substrates but also play critical roles in processes such as cholesterol homeostasis, plasma membrane repair, antigen presentation, and cell migration. The small GTPase Arl8, a member of Arf-like (Arl) family of proteins, has recently emerged as a crucial regulator of lysosome positioning and membrane trafficking toward lysosomes. Through interaction with its effector SKIP, the human Arl8 paralog (Arl8b) mediates kinesin-1 dependent motility of lysosomes on microtubule tracks toward the cell periphery. Read More

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http://dx.doi.org/10.1080/21592799.2015.1086501DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4820812PMC
September 2015
16 Reads

Diacylglycerol kinases in membrane trafficking.

Cell Logist 2015 Apr-Jun;5(2):e1078431. Epub 2015 Aug 3.

Department of Biochemistry and Molecular Biology and the Fred and Pamela Buffett Cancer Center; University of Nebraska Medical Center ; Omaha, NE USA.

Diacylglycerol kinases (DGKs) belong to a family of cytosolic kinases that regulate the phosphorylation of diacylglycerol (DAG), converting it into phosphatidic acid (PA). There are 10 known mammalian DGK isoforms, each with a different tissue distribution and substrate specificity. These differences allow regulation of cellular responses by fine-tuning the delicate balance of cellular DAG and PA. Read More

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http://dx.doi.org/10.1080/21592799.2015.1078431DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4820814PMC
August 2015
5 Reads

Role of the epithelial cell-specific clathrin adaptor complex AP-1B in cell polarity.

Authors:
Heike Fölsch

Cell Logist 2015 Apr-Jun;5(2):e1074331. Epub 2015 Jul 30.

Department of Cell and Molecular Biology; Northwestern University; Feinberg School of Medicine ; Chicago, IL USA.

Epithelial cells are important for organ development and function. To this end, they polarize their plasma membrane into biochemically and physically distinct membrane domains. The apical membrane faces the luminal site of an organ and the basolateral domain is in contact with the basement membrane and neighboring cells. Read More

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http://dx.doi.org/10.1080/21592799.2015.1074331DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4820817PMC
July 2015
3 Reads

Plasma membrane regulates Ras signaling networks.

Cell Logist 2015 Oct-Dec;5(4):e1136374. Epub 2016 Feb 18.

Department of Biochemistry and Molecular Genetics; University of Illinois at Chicago ; Chicago, IL USA.

Ras GTPases activate more than 20 signaling pathways, regulating such essential cellular functions as proliferation, survival, and migration. How Ras proteins control their signaling diversity is still a mystery. Several pieces of evidence suggest that the plasma membrane plays a critical role. Read More

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http://dx.doi.org/10.1080/21592799.2015.1136374DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4820813PMC
February 2016
41 Reads

ROCK1 and ROCK2 inhibition alters dendritic spine morphology in hippocampal neurons.

Cell Logist 2015 Oct-Dec;5(4):e1133266. Epub 2016 Jan 19.

Center for Neurodegeneration and Experimental Therapeutics; University of Alabama at Birmingham; Birmingham, AL USA; Department of Neurology; University of Alabama at Birmingham; Birmingham, AL USA.

Communication among neurons is mediated through synaptic connections between axons and dendrites, and most excitatory synapses occur on actin-rich protrusions along dendrites called dendritic spines. Dendritic spines are structurally dynamic, and synapse strength is closely correlated with spine morphology. Abnormalities in the size, shape, and number of dendritic spines are prevalent in neurologic diseases, including autism spectrum disorders, schizophrenia, and Alzheimer disease. Read More

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http://dx.doi.org/10.1080/21592799.2015.1133266DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4820816PMC
January 2016
14 Reads

Role of tetanus neurotoxin insensitive vesicle-associated membrane protein in membrane domains transport and homeostasis.

Cell Logist 2015 Jan-Mar;5(1):e1025182. Epub 2015 Apr 29.

INSERM; U950; Membrane Traffic in Health and Disease ; Paris, France ; Univ Paris Diderot ; Sorbonne Paris Cité; ERL U950 ; Paris, France ; CNRS; UMR 7592; Institut Jacques Monod ; Paris, France.

Biological membranes in eukaryotes contain a large variety of proteins and lipids often distributed in domains in plasma membrane and endomembranes. Molecular mechanisms responsible for the transport and the organization of these membrane domains along the secretory pathway still remain elusive. Here we show that vesicular SNARE TI-VAMP/VAMP7 plays a major role in membrane domains composition and transport. Read More

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http://dx.doi.org/10.1080/21592799.2015.1025182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4501207PMC
April 2015
46 Reads
3 Citations

An optimized TALEN application for mutagenesis and screening in .

Cell Logist 2015 Jan-Mar;5(1):e1023423. Epub 2015 Feb 27.

Department of Biochemistry and Molecular Biology; Mayo Clinic ; Rochester, MN, USA ; Division of Gastroenterology and Hepatology; Mayo Clinic ; Rochester, MN, USA.

Transcription activator-like effector nucleases (TALENs) emerged as powerful tools for locus-specific genome engineering. Due to the ease of TALEN assembly, the key to streamlining TALEN-induced mutagenesis lies in identifying efficient TALEN pairs and optimizing TALEN mRNA injection concentrations to minimize the effort to screen for mutant offspring. Here we present a simple methodology to quantitatively assess bi-allelic TALEN cutting, as well as approaches that permit accurate measures of somatic and germline mutation rates in . Read More

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http://dx.doi.org/10.1080/21592799.2015.1023423DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4501208PMC
February 2015
44 Reads

Interaction with the effector dynamin-related protein 1 (Drp1) is an ancient function of Rab32 subfamily proteins.

Cell Logist 2014 Oct-Dec;4(4):e986399. Epub 2014 Oct 2.

Faculty of Medicine and Dentistry; Department of Cell Biology; University of Alberta ; Edmonton, Alberta, Canada.

The mitochondria-associated membrane (MAM) is an endoplasmic reticulum (ER) domain that forms contacts with mitochondria and accommodates Ca transfer between the two organelles. The GTPase Rab32 regulates this function of the MAM via determining the localization of the Ca regulatory transmembrane protein calnexin to the MAM. Another function of the MAM is the regulation of mitochondrial dynamics mediated by GTPases such as dynamin-related protein 1 (Drp1). Read More

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http://dx.doi.org/10.4161/21592799.2014.986399DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4355727PMC
October 2014
77 Reads

The Vps39-like TRAP1 is an effector of Rab5 and likely the missing Vps3 subunit of human CORVET.

Cell Logist 2014 Oct-Dec;4(4):e970840. Epub 2014 Oct 2.

Department of Biology/Chemistry; Biochemistry Section; University of Osnabruck ; Osnabrück, Germany .

Membrane fusion in the endocytic pathway is mediated by a protein machinery consistent of Rab GTPases, tethering factors and SNAREs. In yeast, the endosomal CORVET and lysosomal HOPS tethering complexes share 4 of their 6 subunits. The 2 additional subunits in each complex - Vps3 and Vps8 for CORVET, and the homologous Vps39 and Vps41 for HOPS - bind directly to Rab5 and Rab7, respectively. Read More

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http://dx.doi.org/10.4161/21592780.2014.970840DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4325178PMC
October 2014
11 Reads

Ypt/Rab GTPases regulate two intersections of the secretory and the endosomal/lysosomal pathways.

Cell Logist 2014 Jul-Sep;4(3):e954870. Epub 2014 Jul 3.

Department of Biochemistry and Molecular Genetics; University of Illinois at Chicago ; Chicago, IL USA.

A prevailing question in the Ypt/Rab field is whether these conserved GTPases are specific to cellular compartments. The established role for Ypt1 and its human homolog Rab1 is in endoplasmic reticulum (ER)-to-Golgi transport. More recently these regulators were implicated also in autophagy. Read More

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http://www.tandfonline.com/doi/abs/10.4161/21592780.2014.954
Publisher Site
http://dx.doi.org/10.4161/21592780.2014.954870DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4279804PMC
July 2014
7 Reads

TGN exit of the cation-independent mannose 6-phosphate receptor does not require acid hydrolase binding.

Cell Logist 2014 Jul-Sep;4(3):e954441. Epub 2014 Jul 3.

Department of Cell Biology; University Medical Center Utrecht ; Utrecht, The Netherlands.

The cation-independent mannose 6-phosphate (Man-6-P) receptor (CI-MPR) binds newly synthesized, Man-6-P-containing lysosomal acid hydrolases in the trans-Golgi network (TGN) for clathrin-mediated transport to endosomes. It has remained unresolved, however, whether acid hydrolase binding is required for exit of the CI-MPR from the TGN. To address this question we used a B cell line derived from a Mucolipidosis type II (MLII)/I-cell disease patient. Read More

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http://dx.doi.org/10.4161/21592780.2014.954441DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4292573PMC
July 2014
8 Reads

AKAP350C targets to mitochondria via a novel amphipathic alpha helical domain.

Cell Logist 2014 Jul-Sep;4(3):e943597. Epub 2014 Jul 3.

Epithelial Biology Center; Vanderbilt University Medical Center ; Nashville, TN USA ; Department of Surgery; Vanderbilt University Medical Center ; Nashville, TN USA.

Mitochondria regulate metabolism and homeostasis within cells. Mitochondria are also very dynamic organelles, constantly undergoing fission and fusion. The importance of maintaining proper mitochondrial dynamics is evident in the various diseases associated with defects in these processes. Read More

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http://dx.doi.org/10.4161/21592780.2014.943597DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4279805PMC
July 2014
2 Reads

Class C ABC transporters and vacuole fusion.

Cell Logist 2014 Jul-Sep;4(3):e943588. Epub 2014 Jul 3.

Department of Biochemistry; University of Illinois at Urbana-Champaign ; Urbana, IL USA.

Membrane fusion is carried out by core machinery that is conserved throughout eukaryotes. This is comprised of Rab GTPases and their effectors, and SNARE proteins, which together are sufficient to drive the fusion of reconstituted proteoliposomes. However, an outer layer of factors that are specific to individual trafficking pathways regulates the spatial and temporal occurrence of fusion. Read More

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http://dx.doi.org/10.4161/21592780.2014.943588DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4292212PMC
July 2014
14 Reads

Spatial and temporal control of Rho GTPase functions.

Cell Logist 2014 Apr-Jun;4(2):e943618. Epub 2014 May 1.

Yale Cardiovascular Research Center and Departments of Medicine (Cardiology); Cell Biology and Biomedical Engineering; Yale School of Medicine ; New Haven, CT USA.

Rho family GTPases control almost every aspect of cell physiology and, since their discovery, a wealth of knowledge has accumulated about their biochemical regulation and function. However, each Rho GTPase distributes between multiple cellular compartments, even within the same cell, where they are controlled by multiple regulators and signal to multiple effectors. Thus, major questions about spatial and temporal aspects of regulation remain unanswered. Read More

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http://www.tandfonline.com/doi/abs/10.4161/21592780.2014.943
Publisher Site
http://dx.doi.org/10.4161/21592780.2014.943618DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4279778PMC
May 2014
6 Reads

GEF-effector interactions.

Cell Logist 2014 Apr-Jun;4(2):e943616. Epub 2014 May 1.

Institut Jacques Monod, CNRS; Université Paris Diderot; Sorbonne Paris Cité ; Paris, France.

Members of the Arf family of small GTP-binding proteins, or GTPases, are activated by guanine nucleotide exchange factors (GEFs) that catalyze GDP release from their substrate Arf, allowing GTP to bind. In the secretory pathway, Arf1 is first activated by GBF1 at the -Golgi, then by BIG1 and BIG2 at the -Golgi and -Golgi network (TGN). Upon activation, Arf1-GTP interacts with effectors such as coat complexes, and is able to recruit different coat complexes to different membrane sites in cells. Read More

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http://dx.doi.org/10.4161/21592780.2014.943616DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4279777PMC
May 2014
17 Reads

Is the model of signal amplification by GPCRs/GEFs activating multiple GTPases relevant to a broad spectrum of heterotrimeric and RAS superfamily GTPases?

Authors:
Richard A Kahn

Cell Logist 2014 Jun 1;4(2):e943602. Epub 2014 May 1.

Department of Biochemistry; Emory University School of Medicine ; Atlanta, GA USA.

Concepts or models of biological processes shape how we think about them, discuss them, and design experiments to test aspects of them. Because of the importance of our models of cell signaling by regulatory GTPases and the desire to extend those models to related signaling modules, I have throughout my career been fascinated by the similarities and differences between the modeling of heterotrimeric G protein and monomeric RAS superfamily GTPases. Recent discussions with colleagues led me to conclude that there is a growing divergence in how researchers model the activation and signaling processes of monomeric and trimeric GTPases and also a surprising lack of consensus within each camp. Read More

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http://dx.doi.org/10.4161/21592780.2014.943602DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4276334PMC
June 2014
68 Reads

G protein coupled receptor signaling complexes in live cells.

Authors:
John R Hepler

Cell Logist 2014 4;4:e29392. Epub 2014 Jun 4.

Department of Pharmacology; Emory University School of Medicine; Atlanta, GA USA.

Classical models of receptor (GPCR) and G protein (Gαβγ) signaling based on biochemical studies have proposed that receptor stimulation results in G protein activation (Gα-GTP) and dissociation of the heterotrimer (Gα-GTP + Gβγ) to regulate downstream signaling events. Unclear is whether or not there exists freely diffusible, activated Gα-GTP on cellular membranes capable of catalytic signal amplification. Recent studies in live cells indicate that GPCRs serve as platforms for the assembly of macromolecular signaling complexes that include G proteins to support a highly efficient and spatially restricted signaling event, with no requirement for full Gα-GTP and Gβγ dissociation and lateral diffusion within the plasma membrane. Read More

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http://dx.doi.org/10.4161/cl.29392DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4160338PMC
June 2014
3 Reads

G Protein-coupled receptors: Multi-turnover GDP/GTP exchange catalysis on heterotrimeric G proteins.

Authors:
Elliott M Ross

Cell Logist 2014 4;4:e29391. Epub 2014 Jun 4.

Department of Pharmacology and Green Center for Systems Biology; University of Texas Southwestern Medical Center; Dallas, TX USA.

G protein-coupled receptors and heterotrimeric G proteins can diffuse laterally in the plasma membrane such that one receptor can catalyze the activation (GDP/GTP exchange) of multiple G proteins. In some cases, these processes are fast enough to support molecular signal amplification, where a single receptor maintains the activation of multiple G proteins at steady-state. Amplification in cells is probably highly regulated. Read More

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http://dx.doi.org/10.4161/cl.29391DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4160333PMC
June 2014
2 Reads

Current understanding of signal amplification in phototransduction.

Cell Logist 2014 4;4:e29390. Epub 2014 Jun 4.

Departments of Cell Biology and Human Anatomy and Ophthalmology and Vision Science; University of California; Davis, CA USA.

The studies of visual signal transduction, or phototransduction, have played a pivotal role in elucidating the most general principles of G protein signaling, particularly in regards to the concept of signal amplification, i.e., the process by which activation of a relatively small number of G protein coupled receptors is transformed into a robust downstream signaling event. Read More

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http://dx.doi.org/10.4161/cl.29390DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4160332PMC
June 2014
8 Reads

A historical perspective on the lateral diffusion model of GTPase activation and related coupling of membrane signaling proteins.

Authors:
Paul A Liebman

Cell Logist 2014 4;4:e29389. Epub 2014 Jun 4.

Department of Biochemistry and Biophysics; University of Pennsylvania; Philadelphia, PA USA.

Aspects of our discovery of lateral diffusion of the G protein coupled receptor (GPCR) rhodopsin and that a single activated rhodopsin can non-covalently catalyze GTP binding to thousands of GTPases per second on rod disk membranes via this diffusion are summarized herein. Rapid GTPase coupling to membrane-bound phosphodiesterase (PDE) further amplifies the signal via cGMP hydrolysis, essential to visual transduction. Important generalizations from this work are that biomembranes can uniquely concentrate, orient for reaction and provide a solvent appropriate to rapid, powerful and appropriately controlled sequential interaction of signaling proteins. Read More

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http://dx.doi.org/10.4161/cl.29389DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4160331PMC
June 2014
2 Reads

Tracking of the dynamic localization of the Rab-specific HOPS subunits reveal their distinct interaction with Ypt7 and vacuoles.

Cell Logist 2014 12;4:e29191. Epub 2014 May 12.

Biochemistry section; Department of Biology/Chemistry; University of Osnabrück; Osnabrück, Germany.

Endosomal and vacuole fusion depends on the two homologous tethering complexes CORVET and HOPS. HOPS binds the activated Rab GTPase Ypt7 via two distinct subunits, Vps39 and Vps41. To understand the participation and possible polarity of Vps41 and Vps39 during tethering, we used an in vivo approach. Read More

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http://www.tandfonline.com/doi/abs/10.4161/cl.29191
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http://dx.doi.org/10.4161/cl.29191DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4156483PMC
May 2014
6 Reads

An investigation of the effect of membrane curvature on transmembrane-domain dependent protein sorting in lipid bilayers.

Cell Logist 2014 6;4:e29087. Epub 2014 May 6.

CNRS-Institut Curie; UMR144; Paris, France.

Sorting of membrane proteins within the secretory pathway of eukaryotic cells is a complex process involving discrete sorting signals as well as physico-chemical properties of the transmembrane domain (TMD). Previous work demonstrated that tail-anchored (TA) protein sorting at the interface between the Endoplasmic Reticulum (ER) and the Golgi complex is exquisitely dependent on the length and hydrophobicity of the transmembrane domain, and suggested that an imbalance between TMD length and bilayer thickness (hydrophobic mismatch) could drive long TMD-containing proteins into curved membrane domains, including ER exit sites, with consequent export of the mismatched protein out of the ER. Here, we tested a possible role of curvature in TMD-dependent sorting in a model system consisting of Giant Unilamellar Vesicles (GUVs) from which narrow membrane tubes were pulled by micromanipulation. Read More

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http://dx.doi.org/10.4161/cl.29087DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4156485PMC
May 2014
25 Reads

Distinct patterns of phosphatidylserine localization within the Rab11a-containing recycling system.

Cell Logist 2014 3;4:e28680. Epub 2014 Apr 3.

Section of Surgical Sciences and the Epithelial Biology Center; Vanderbilt University Medical Center; Nashville, TN ; Department of Cell & Developmental Biology; Vanderbilt University School of Medicine; Nashville, TN ; Vanderbilt-Ingram Cancer Center; Vanderbilt University Medical Center; Nashville, TN ; Nashville Veterans Affairs Medical Center; Nashville, TN.

The Rab11 GTPases and Rab11 family-interacting proteins (Rab11-FIPs) define integrated yet distinct compartments within the slow recycling pathway. The lipid content of these compartments is less well understood, although past studies have indicated phosphatidylserine (PS) is an integral component of recycling membranes. We sought to identify key differences in the presence of PS within Rab and Rab11-FIP containing membranes. Read More

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http://dx.doi.org/10.4161/cl.28680DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4156484PMC
April 2014
2 Reads

Altered trafficking of mutated growth factor receptors and their associated molecules: implication for human cancers.

Cell Logist 2014 18;4:e28461. Epub 2014 Mar 18.

Institute of Development, Aging and Cancer, Tohoku University; Sendai, Japan.

Ligand-stimulated receptor tyrosine kinases (RTKs) are phosphorylated/ubiquitinated, endocytosed and transported to the lysosomes via endosomes/multivesicular bodies, resulting in the attenuation of signal transmission. If this physiological mechanism of RTK signal downregulation is perturbed, signal transduction persists and may contribute to cellular transformation. This article presents several such examples. Read More

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http://dx.doi.org/10.4161/cl.28461DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4156482PMC
March 2014
4 Reads

Kinesin-2 mediates apical endosome transport during epithelial lumen formation.

Cell Logist 2014 Jan 6;4(1):e28928. Epub 2014 May 6.

Department of Cell and Developmental Biology; School of Medicine; Anschutz Medical Campus; University of Colorado Denver; Aurora, CO USA.

Apical lumen formation is a key step during epithelial morphogenesis of tubular organs. Appropriate transport and targeting of apical proteins to the apical membrane initiation site (AMIS) plays a crucial role in establishing a solitary, central lumen. FIP5, a Rab11-interacting protein, is an important regulator that directs apical endosome trafficking along microtubules toward the AMIS during cytokinesis. Read More

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http://dx.doi.org/10.4161/cl.28928DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4024058PMC
January 2014
10 Reads

From all to (nearly) none: Tracing adaptin evolution in Fungi.

Cell Logist 2014 Jan 21;4(1):e28114. Epub 2014 Feb 21.

Department of Cell Biology; Faculty of Medicine and Dentistry; University of Alberta; Edmonton, Alberta, Canada.

The five adaptor protein (AP) complexes function in cargo-selection and coat-recruitment stages of vesicular transport in eukaryotic cells. Much of what we know about AP complex function has come from experimental work using as a model. Here, using a combination of comparative genomic and phylogenetic approaches we provide evolutionary context for the knowledge gained from this model system by searching the genomes of diverse fungi as well as a member of the sister group to all fungi, for presence of AP subunits. Read More

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http://dx.doi.org/10.4161/cl.28114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4022609PMC
January 2014
15 Reads

The proteolytic landscape of the yeast vacuole.

Cell Logist 2014 Jan 12;4(1):e28023. Epub 2014 Feb 12.

Department of Biological Sciences; University of Pittsburgh; Pittsburgh, PA USA.

The vacuole in the yeast plays a number of essential roles, and to provide some of these required functions the vacuole harbors at least seven distinct proteases. These proteases exhibit a range of activities and different classifications, and they follow unique paths to arrive at their ultimate, common destination in the cell. This review will first summarize the major functions of the yeast vacuole and delineate how proteins are targeted to this organelle. Read More

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http://dx.doi.org/10.4161/cl.28023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4022603PMC
January 2014
2 Reads

Novel effects of Brefeldin A (BFA) in signaling through the insulin receptor (IR) pathway and regulating FoxO1-mediated transcription.

Cell Logist 2014 Jan 9;4(1):e27732. Epub 2014 Jan 9.

Department of Cell, Developmental and Integrative Biology; University of Alabama at Birmingham; Birmingham, AL USA.

Brefeldin A (BFA) is a fungal metabolite best known for its ability to inhibit activation of ADP-ribosylation factor (Arf) and thereby inhibit secretory traffic. BFA also appears to regulate the trafficking of the GLUT4 glucose transporter by inducing its relocation from intracellular stores to the cell surface. Such redistribution of GLUT4 is normally regulated by insulin-mediated signaling. Read More

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http://dx.doi.org/10.4161/cl.27732DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4022606PMC
January 2014
13 Reads

Unique and conserved features of the plant ER-shaping GTPase RHD3.

Cell Logist 2014 Jan 28;4(1):e28217. Epub 2014 Feb 28.

MSU-DOE Plant Research Lab; Michigan State University; East Lansing, MI USA.

The architectural integrity of the endoplasmic reticulum (ER) network depends on the function of membrane-associated dynamin-like GTPases that include metazoan atlastins, plant RHD3 and yeast Sey1p. The evidence that these proteins are sufficient to drive membrane fusion of reconstituted proteoliposomes, and that loss-of-function mutations lead to conspicuous ER shape defects indicates that atlastins, RHD3 and Sey1p promote ER membrane fusion. However, complementation experiments in reciprocal loss-of-function backgrounds have also suggested that RHD3 and Sey1p may be not functionally equivalent, supporting that ER fusion mechanisms may be not entirely conserved in eukaryotes. Read More

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https://ai2-s2-pdfs.s3.amazonaws.com/141b/ed742608b95ed33dd0
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http://www.tandfonline.com/doi/abs/10.4161/cl.28217
Publisher Site
http://dx.doi.org/10.4161/cl.28217DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4013103PMC
January 2014
3 Reads