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1.  Protein Kinase D family kinases 
Bioarchitecture  2014;4(3):111-115.
Highly invasive pancreatic tumors are often recognized in late stages due to a lack of clear symptoms and pose major challenges for treatment and disease management. Broad-band Protein Kinase D (PKD) inhibitors have recently been proposed as additional treatment option for this disease. PKDs are implicated in the control of cancer cell motility, angiogenesis, proliferation and metastasis. In particular, PKD2 expression is elevated in pancreatic cancer, whereas PKD1 expression is comparably lower. In our recent study we report that both kinases control PDAC cell invasive properties in an isoform-specific, but opposing manner. PKD1 selectively mediates anti-migratory/anti-invasive features by preferential regulation of the actin-regulatory Cofilin-phosphatase Slingshot1L (SSH1L). PKD2, on the other hand enhances invasion and angiogenesis of PDAC cells in 3D-ECM cultures and chorioallantois tumor models by stimulating expression and secretion of matrix-metalloproteinase 7 and 9 (MMP7/9). MMP9 also enhances PKD2-mediated tumor angiogenesis releasing extracellular matrix-bound VEGF-A. We thus suggest high PKD2 expression and loss of PKD1 may be beneficial for tumor cells to enhance their matrix-invading abilities. In our recent study we demonstrate for the first time PKD1 and 2 isoform-selective effects on pancreatic cancer cell invasion, in-vitro and in-vivo, defining isoform-specific regulation of PKDs as a major future issue.
PMCID: PMC4201600  PMID: 24847910
PKD1; PKD2; MMP7; MMP9; invasion; angiogenesis; isoform specificity
2.  0.1 kilopascal difference for mechanophenotyping 
Bioarchitecture  2014;4(3):116-118.
Current knowledge understands the mesenchymal cell invasion in a 3D matrix as a combined process of cell-to-matrix adhesion based cell migration and matrix remodeling. Excluding cell invasion stimulated by cytokines and chemokines, the basal cell invasion itself is a complicated process that can be regulated by matrix ligand type, density, geometry, and stiffness, etc. Understanding such a complicated biological process requires delicate dissections into simplified model studies by altering only one or two elements at a time. Past cell motility studies focusing on matrix stiffness have revealed that a stiffer matrix promotes 2D X-Y axis lateral cell motility. Here, we comment on two recent studies that report, instead of stiffer matrix, a softer matrix promotes matrix proteolysis and the formation of invadosome-like protrusions (ILPs) along the 3D Z axis. These studies also reveal that soft matrix precisely regulates such ILPs formation in the stiffness scale range of 0.1 kilopascal in normal cells. In contrast, malignant cells such as cancer cells can form ILPs in response to a much wider range of matrix stiffness. Further, different cancer cells respond to their own favorable range of matrix stiffness to spontaneously form ILPs. Thus, we hereby propose the idea of utilizing the matrix stiffness to precisely regulate ILP formation as a mechanophenotyping tool for cancer metastasis prediction and pathological diagnosis.
PMCID: PMC4201601  PMID: 25029598
cell migration; cell invasion; cancer metastasis; invadosomes; invadopodia; podosomes; matrix stiffness; mechanophenotyping; cellular architecture; soft matrix
3.  Filamin A and Big2: A shared endocytic pathway 
Bioarchitecture  2014;4(2):53-57.
Neural proliferation, migration and differentiation require reorganization of the actin cytoskeleton and regulation of vesicle trafficking to provide stability in maintaining cell adhesions, allow for changes in cell shape, and establishing cell polarity. Human disorders involving the actin-binding Filamin A (FLNA) and vesicle trafficking Brefeldin-associated guanine exchange factor 2 (BIG2 is encoded by the ARFGEF2 gene) proteins are implicated in these various developmental processes, resulting in a malformation of cortical development called periventricular heterotopia (nodules along the ventricular lining) and microcephaly (small brain). Here we discuss several recent reports from our laboratory that demonstrate a shared role for both proteins in actin-associated vesicle trafficking, which is required to maintain the expression and stability of cell adhesion and cell cycle associated molecules during cortical development. While changes in FLNA and BIG2 have first been linked to disorders involving the central nervous system, increasing reports suggest they are associated with aberrant development of various other organ systems in the body. These studies suggest that vesicle trafficking defects in FLN-GEF dependent pathways may contribute to a much broader phenotype than previously realized.
PMCID: PMC4199812  PMID: 24709996
actin; filamin; brefeldin inhibited guanine exchange factor 2; RhoGTPase
4.  The marriage of quantitative genetics and cell biology 
Bioarchitecture  2014;4(2):58-61.
Microtubules play a central role in many essential cellular processes, including chromosome segregation, intracellular transport, and cell polarity. As these dynamic polymers are crucial components of eukaryotic cellular architecture, we were surprised by our recent discovery that a common human genetic difference leads to variation in microtubule stability in cells from different people. A single nucleotide polymorphism (SNP) near the TUBB6 gene, encoding class V β-tubulin, is associated with the expression level of this protein, which reduces microtubule stability at higher levels of expression. We discuss the novel cellular GWAS (genome-wide association study) platform that led to this discovery of natural, common variation in microtubule stability and the implications this finding may have for human health and disease, including cancer and neurological disorders. Furthermore, our generalizable approach provides a gateway for cell biologists to help interpret the functional consequences of human genetic variation.
PMCID: PMC4199813  PMID: 24618686
microtubule; genome-wide association; TUBB6; genetic variation; pyroptosis; Salmonella; cellular GWAS; lymphoblastoid
5.  Coordinating the cytoskeleton and endocytosis for regulated plasma membrane growth in the early Drosophila embryo 
Bioarchitecture  2014;4(2):68-74.
Plasma membrane organization is under the control of cytoskeletal networks and endocytic mechanisms, and a growing literature is showing how closely these influences are interconnected. Here, we review how plasma membranes are formed around individual nuclei of the syncytial Drosophila embryo. Specifically, we outline the pathways that promote and maintain the growth of pseudocleavage and cellularization furrows, as well as specific pathways that keep furrow growth in check. This system has become important for studies of actin regulators, such as Rho1, Diaphanous, non-muscle myosin II and Arp2/3, and endocytic regulators, such as a cytohesin Arf-GEF (Steppke), clathrin, Amphiphysin and dynamin. More generally, it provides a model for understanding how cytoskeletal-endocytic cross-talk regulates the assembly of a cell.
PMCID: PMC4199814  PMID: 24874871
cytoskeleton; endocytosis; plasma membrane; actin; Rho1; cytohesin; Steppke; Amphiphysin; Drosophila; cellularization
6.  Cytoskeletal self-organization in neuromorphogenesis 
Bioarchitecture  2014;4(2):75-80.
Self-organization of dynamic microtubules via interactions with associated motors plays a critical role in spindle formation. The microtubule-based mechanisms underlying other aspects of cellular morphogenesis, such as the formation and development of protrusions from neuronal cells is less well understood. In a recent study, we investigated the molecular mechanism that underlies the massive reorganization of microtubules induced in non-neuronal cells by expression of the neuronal microtubule stabilizer MAP2c. In that study we directly observed cortical dynein complexes and how they affect the dynamic behavior of motile microtubules in living cells. We found that stationary dynein complexes transiently associate with motile microtubules near the cell cortex and that their rapid turnover facilitates efficient microtubule transport. Here, we discuss our findings in the larger context of cellular morphogenesis with specific focus on self-organizing principles from which cellular shape patterns such as the thin protrusions of neurons can emerge.
PMCID: PMC4199815  PMID: 24847718
self-organization; cortical dynein; cytoplasmic dynein; cellular morphogenesis; neuromorphogenesis; neurite; microtubules
7.  Tribolium embryo morphogenesis 
Bioarchitecture  2014;4(1):16-21.
Development of multicellular organisms depends on patterning and growth mechanisms encoded in the genome, but also on the physical properties and mechanical interactions of the constituent cells that interpret these genetic cues. This fundamental biological problem requires integrated studies at multiple levels of biological organization: from genes, to cell behaviors, to tissue morphogenesis. We have recently combined functional genetics with live imaging approaches in embryos of the insect Tribolium castaneum, in order to understand their remarkable transformation from a uniform single-layered blastoderm into a condensed multi-layered embryo covered by extensive extra-embryonic tissues. We first developed a quick and reliable methodology to fluorescently label various cell components in entire Tribolium embryos. Live imaging of labeled embryos at single cell resolution provided detailed descriptions of cell behaviors and tissue movements during normal embryogenesis. We then compared cell and tissue dynamics between wild-type and genetically perturbed embryos that exhibited altered relative proportions of constituent tissues. This systematic comparison led to a qualitative model of the molecular, cellular and tissue interactions that orchestrate the observed epithelial rearrangements. We expect this work to establish the Tribolium embryo as a powerful and attractive model system for biologists and biophysicists interested in the molecular, cellular and mechanical control of tissue morphogenesis.
PMCID: PMC4199798  PMID: 24451992
Tribolium castaneum; Drosophila melanogaster; arthropods; fluorescence live imaging; functional genetics; embryo morphogenesis; extraembryonic development; cell shape; cell intercalation; convergence and extension
8.  Stabilization of neuronal connections and the axonal cytoskeleton 
Bioarchitecture  2014;4(1):22-24.
Stabilization of axonal connections is an underappreciated, but critical, element in development and maintenance of neuronal functions. The ability to maintain the overall architecture of the brain for decades is essential for our ability to process sensory information efficiently, coordinate motor activity, and retain memories for a lifetime. While the importance of the neuronal cytoskeleton in this process is acknowledged, little has been known about specializations of the axonal cytoskeleton needed to stabilize neuronal architectures. A novel post-translational modification of tubulin that stabilizes normally dynamic microtubules in axons has now been identified. Polyamination appears to be enriched in axons and is developmentally regulated with a time course that correlates with increased microtubule stabilization. Identifying one of the molecular mechanisms for maintaining neuronal connections creates new research avenues for understanding the role of stabilizing neuronal architecture in neuronal function and in neuropathology.
PMCID: PMC4199799  PMID: 24492417
axonal cytoskeleton; microtubule stability; plasticity; post-translational modification; neuronal function
9.  Microtubules CLASP to Adherens Junctions in epidermal progenitor cells 
Bioarchitecture  2014;4(1):25-30.
Cadherin-mediated cell adhesion at Adherens Junctions (AJs) and its dynamic connections with the microtubule (MT) cytoskeleton are important regulators of cellular architecture. However, the functional relevance of these interactions and the molecular players involved in different cellular contexts and cellular compartments are still not completely understood. Here, we comment on our recent findings showing that the MT plus-end binding protein CLASP2 interacts with the AJ component p120-catenin (p120) specifically in progenitor epidermal cells. Absence of either protein leads to alterations in MT dynamics and AJ functionality. These findings represent a novel mechanism of MT targeting to AJs that may be relevant for the maintenance of proper epidermal progenitor cell homeostasis. We also discuss the potential implication of other MT binding proteins previously associated to AJs in the wider context of epithelial tissues. We hypothesize the existence of adaptation mechanisms that regulate the formation and stability of AJs in different cellular contexts to allow the dynamic behavior of these complexes during tissue homeostasis and remodeling.
PMCID: PMC4199800  PMID: 24522006
microtubules; Adherens Junctions; p120-catenin; CLASP2; cadherins; epidermis; keratinocytes
10.  Dynamin-dependent maintenance of epithelial integrity is essential for zebrafish epiboly 
Bioarchitecture  2014;4(1):31-34.
Epiboly, the thinning and spreading of one tissue over another, is a widely employed morphogenetic movement that is essential for the development of many organisms. In the zebrafish embryo, epiboly describes the coordinated vegetal movement of the deep cells, enveloping layer (EVL) and yolk syncytial layer (YSL) to engulf the yolk cell. Recently, we showed that the large GTPase Dynamin plays a fundamental role in epiboly in the early zebrafish embryo. Because Dynamin plays a well-described role in vesicle scission during endocytosis, we predicted that Dynamin might regulate epiboly through participating in bulk removal of the yolk cell membrane ahead of the advancing margin, a proposed part of the epiboly motor. Unexpectedly, we found that Dynamin function was dispensable in the yolk cell and instead, it was required to maintain the epithelial integrity of the EVL during epiboly. Here, we present a model describing the maintenance of EVL integrity, which is required for the proper generation and transmission of tension during epiboly. Furthermore, we discuss the role of Dynamin-mediated regulation of ezrin-radixin-moesin (ERM) family proteins in the maintenance of epithelial integrity.
PMCID: PMC4199801  PMID: 24522009
zebrafish; epiboly; dynamin; enveloping layer; endocytosis; epithelial integrity; ERM proteins; synaptotagmin
11.  Getting myosin-V on the right track 
Bioarchitecture  2014;4(1):35-38.
Recent studies have revealed a novel mechanism of myosin regulation in which the actin-binding protein tropomyosin converts atypical type-V myosins into processive cargo transporters. To achieve this, tropomyosin's primary role appears to lie in its ability to influence myosin's enzyme kinetics, prolonging the strong actin-bound ADP/apo state to enable hand-over-hand walking of myosin-V dimers along actin tracks. Activation of myosin-V mediated transport by tropomyosin underscores its function in helping to direct cargos to specific actin tracks and subcellular destinations. This type of regulation supports the broader notion that tropomyosin plays a key role in actomyosin sorting.
PMCID: PMC4199802  PMID: 24531330
actin; tropomyosin; myosin-V; duty ratio; processivity; intracellular transport; actomyosin sorting
12.  Coiled coil cytoskeletons collaborate in polar growth of Streptomyces 
Bioarchitecture  2013;3(4):110-112.
Streptomyces is a multicellular mycelial bacterium, which exhibits pronounced cell polarity and grows by extension of the hyphal tips. Similarly to other polarly growing walled cells, such as filamentous fungi or pollen tubes, Streptomyces hyphae face an intrinsic problem: addition of new cell wall material causes structural weakness of the elongating tip. Cellular strategies employed by walled cells to cope with this problem are not well understood. We have identified a coiled coil protein FilP, with properties similar to those of animal intermediate filament (IF) proteins, which somehow confers rigidity and elasticity to the Streptomyces hyphae. In a recent publication we showed that FilP forms extensive cis-interconnected networks, which likely explain its biological function in determining the mechanical properties of the cells. Surprisingly, the intrinsically non-dynamic cytoskeletal network of FilP exhibits a dynamic behavior in vivo and assembles into growth-dependent polar gradients. We show that apical accumulation of FilP is dependent on its interaction with the main component of the Streptomyces polarisome, DivIVA. Thus, the same polarisome complex that orchestrates cell elongation, also recruits an additional stress-bearing structure to the growing tips with an intrinsically weak cell wall. Similar strategy might be used by all polarly growing walled cells.
PMCID: PMC4201604  PMID: 24002529
intermediate filament; cytoskeleton; polar growth; Streptomyces; coiled coil; FilP
13.  MicroRNA-23b regulates cellular architecture and impairs motogenic and invasive phenotypes during cancer progression 
Bioarchitecture  2013;3(4):119-124.
The cytoskeleton is a dynamic three dimensional structure contained within the cytoplasm of a cell, and is important in cell shape and movement, and in metastatic progression during carcinogenesis. Members of the Rho family of small GTPases, RHO, RAC and cell cycle division 42 (Cdc42) proteins regulate cytoskeletal dynamics, through the control of a panel of genes. We have recently shown that the microRNA (miRNA) miR-23b represents a central effector of cytoskeletal remodelling. It increases cell-cell interactions, modulates focal adhesion and reduces cell motility and invasion by directly regulating several genes involved in these processes.
PMCID: PMC4201606  PMID: 24002530
miR-23b; microRNAs; miRNAs; cytoskeleton; motility; metastasis; adhesion; focal adhesion; tumor growth
14.  New insights on vertebrate olivo-cerebellar climbing fibers from computerized morphological reconstructions 
Bioarchitecture  2013;3(2):38-41.
Characterization of neuronal connectivity is essential to understanding the architecture of the animal nervous system. Specific labeling and imaging techniques can visualize axons and dendrites of single nerve cells. Two-dimensional manual drawing has long been used to describe the morphology of labeled neuronal elements. However, quantitative morphometry, which is essential to understanding functional significance, cannot be readily extracted unless the detailed neuronal geometry is comprehensively reconstructed in three-dimensional space. We have recently applied an accurate and robust digital reconstruction system to cerebellar climbing fibers, which form highly dense and complex terminal arbors as one of the strongest presynaptic endings in the vertebrate nervous system. Resulting statistical analysis has shown how climbing fibers morphology is special in comparison to other axonal terminals. While thick primary branches may convey excitation quickly and faithfully to the far ends, thin tendril branches, which have a larger bouton density, form the majority of presynaptic outputs. This data set, now publicly available from NeuroMorpho.Org for further modeling and analysis, may constitute the first detailed and comprehensive digital reconstruction of the complete axonal terminal field with identified branch types and full accounting of boutons for any neuronal class in the vertebrate brain.
PMCID: PMC3715541  PMID: 23756373
axon; terminal arbor; bouton; branches; tendril; cerebellar cortex; molecular layer; biotinylated dextran amine; rat
15.  Dickkopf-3 function in the prostate 
Bioarchitecture  2013;3(2):42-44.
The tumor suppressor Dickkopf-3 (Dkk-3) is rather a unique molecule. Although it is related to the Dickkopf family of secreted Wnt antagonists, it does not directly inhibit Wnt signaling, and its function and mechanism of action are unknown. Endogenous Dkk-3 was recently found to be required to limit cell proliferation both in the developing mouse prostate and in 3D cultures of human prostate epithelial cells. Dkk-3 was further shown to modulate the response of normal prostate epithelial cells to transforming growth factor-β (TGF-β). These studies are consistent with a model in which Dkk-3 is required by normal cells to prevent the TGF-β switch from tumor suppressor to tumor promoter. Here, we discuss these findings and their potential impact on the development and progression of prostate cancer.
PMCID: PMC3715542  PMID: 23765605
Dkk-3; TGF-β; acinar morphogenesis; prostate
16.  Supracellular actomyosin assemblies during development 
Bioarchitecture  2013;3(2):45-49.
Changes in cell shape are one of the driving forces of tissue morphogenesis. Contractile cytoskeletal assemblies based on actomyosin networks have emerged as a main player that can drive these changes. Different types of actomyosin networks have been identified, with distinct subcellular localizations, including apical junctional and apicomedial actomyosin. A further specialization of junctional actomyosin are so-called actomyosin ‘cables’, supracellular arrangements that appear to stretch over many cell diameters. Such actomyosin cables have been shown to serve several important functions, in processes such as wound healing, epithelial morphogenesis and maintenance of compartment identities during development. In the Drosophila embryo, we have recently identified a function for a circumferential actomyosin cable in assisting tube formation. Here, I will briefly summarize general principles that have emerged from the analysis of such cables.
PMCID: PMC3715543  PMID: 23760352
Actomyosin; morphogenesis; cable; wound healing; Drosophila; anisotropy; development
17.  Human fronto-parietal and parieto-hippocampal pathways represent behavioral priorities in multiple spatial reference frames 
Bioarchitecture  2013;3(5):147-152.
We represent behaviorally relevant information in different spatial reference frames in order to interact effectively with our environment. For example, we need an egocentric (e.g., body-centered) reference frame to specify limb movements and an allocentric (e.g., world-centered) reference frame to navigate from one location to another. Posterior parietal cortex (PPC) is vital for performing transformations between these different coordinate systems. Here, we review evidence for multiple pathways in the human brain, from PPC to motor, premotor, and supplementary motor areas, as well as to structures in the medial temporal lobe. These connections are important for transformations between egocentric reference frames to facilitate sensory-guided action, or from egocentric to allocentric reference frames to facilitate spatial navigation.
PMCID: PMC3907462  PMID: 24322829
parietal cortex; frontal cortex; spatial attention; coordinate transformation; connectivity; saccade; grasp; reach; navigation
18.  Axonal trafficking of NMNAT2 and its roles in axon growth and survival in vivo 
Bioarchitecture  2013;3(5):133-140.
The NAD-synthesizing enzyme NMNAT2 is critical for axon survival in primary culture and its depletion may contribute to axon degeneration in a variety of neurodegenerative disorders. Here we discuss several recent reports from our laboratory that establish a critical role for NMNAT2 in axon growth in vivo in mice and shed light on the delivery and turnover of this survival factor in axons. In the absence of NMNAT2, axons fail to extend more than a short distance beyond the cell body during embryonic development, implying a requirement for NMNAT2 in axon maintenance even during development. Furthermore, we highlight findings regarding the bidirectional trafficking of NMNAT2 in axons on a vesicle population that undergoes fast axonal transport in primary culture neurites and in mouse sciatic nerve axons in vivo. Surprisingly, loss of vesicle association boosts the axon protective capacity of NMNAT2, an effect that is at least partially mediated by a longer protein half-life of cytosolic NMNAT2 variants. Analysis of wild-type and variant NMNAT2 in mouse sciatic nerves and Drosophila olfactory receptor neuron axons supports the existence of a similar mechanism in vivo, highlighting the potential for regulation of NMNAT2 stability and turnover as a mechanism to modulate axon degeneration in vivo.
PMCID: PMC3907460  PMID: 24284888
NMNAT2; Wallerian degeneration; axon growth; axon survival; axonal transport; neurodegeneration; palmitoylation; ubiquitin proteasome
19.  Spatiotemporal regulation of meiotic recombination by Liaisonin 
Bioarchitecture  2013;3(1):20-24.
Sexual reproduction involves diversification of genetic information in successive generations. Meiotic recombination, which substantially contributes to the increase in genetic diversity, is initiated by programmed DNA double-strand breaks (DSBs) catalyzed by the evolutionarily conserved Spo11 protein. Spo11 requires additional partner proteins for its DNA cleavage reaction. DSBs are preferentially introduced at defined chromosomal sites called “recombination hotspots.” Recent studies have revealed that meiotically established higher-order chromosome structures, such as chromosome axes and loops, are also crucial in the control of DSB formation. Most of the DSB sites are located within chromatin loop regions, while many of the proteins involved in DSB formation reside on chromosomal axes. Hence, DSB proteins and DSB sites seem to be distantly located.
To resolve this paradox, we conducted comprehensive proteomics and ChIP-chip analyses on Spo11 partners in Schizosaccharomyces pombe, in combination with mutant studies. We identified two distinct DSB complexes, the “DSBC (DSB Catalytic core)“ and “SFT (Seven-Fifteen-Twenty four; Rec7-Rec15-Rec24)” subcomplexes. The DSBC subcomplex contains Spo11 and functions as the catalytic core for the DNA cleavage reaction. The SFT subcomplex is assumed to execute regulatory functions. To activate the DSBC subcomplex, the SFT subcomplex tethers hotspots to axes via its interaction with Mde2, which can interact with proteins in both DSBC and SFT subcomplexes. Thus, Mde2 is likely to bridge these two subcomplexes, forming a “tethered loop-axis complex.” It should be noted that Mde2 expression is strictly regulated by S phase checkpoint monitoring of the completion of DNA replication. From these observations, we proposed that Mde2 is a central coupler for meiotic recombination initiation to establish a tethered loop-axis complex in liaison with the S phase checkpoint.
PMCID: PMC3639241  PMID: 23572041
Meiotic recombination; Spo11; DNA double-strand break formation; higher-order chromosome structure; S phase checkpoint
20.  The role of the cofilin-actin rod stress response in neurodegenerative diseases uncovers potential new drug targets 
Bioarchitecture  2012;2(6):204-208.
The cofilin-actin rod stress response is an actin cytoskeletal dynamic arrest that occurs in cells under a variety of stress conditions. Upon stress, the rapidly activated cofilin saturates actin filaments causing them to bundle into rod structures in either the nucleus or cytoplasm, halting actin polymerization and thus freeing ATP. Importantly, these rods dissociate quickly following relief of the transient stress. The rods form inappropriately in neurons involved in the progression of Alzheimer disease (AD) and we have linked dysfunctional dynamics of the nuclear rod response to Huntington disease (HD). Cofilin levels are also perturbed in Parkinson disease (PD), and profilin, an actin binding protein with opposite action to cofilin, is mutated in Amyotrophic Lateral Sclerosis (ALS). The persistence of the rods post-stress suggests that critical molecular switches to turn this response both on and off are being affected in neurodegeneration. We have recently shown that the cofilin protein is regulated by highly conserved nuclear import and export signals and that these signals are required to be functional for an appropriate rod formation during stress. The ability of cofilin to form rods is required in a cell culture model for cells to be resistant to apoptosis under stress conditions, indicating that a normal cofilin-actin rod response is likely integral to proper cell health in higher order organisms. Here we hypothesize on the potential physiological function of nuclear cofilin-actin rods and why the dysregulation of this response could lead to the selective vulnerability of the most susceptible populations of cells in HD. We further suggest that learning more about this cytoskeletal cell stress response will open up new avenues for drug target discovery in neurodegenerative disorders.
PMCID: PMC3527314  PMID: 23267414
Huntington disease; actin; cofilin; cofilin rods; cytoskeleton; nuclear transport signals; profilin
21.  Akirin 
Bioarchitecture  2012;2(6):209-213.
Embryonic patterning relies upon an exquisitely timed program of gene regulation. While the regulation of this process via the action of transcription factor networks is well understood, new lines of study have highlighted the importance of a concurrently regulated program of chromatin remodeling during development. Chromatin remodeling refers to the manipulation of the chromatin architecture through rearrangement, repositioning, or restructuring of nucleosomes to either favor or hinder the expression of associated genes. While the role of chromatin remodeling pathways during tumor development and cancer progression are beginning to be clarified, the roles of these pathways in the course of tissue specification, morphogenesis and patterning remains relatively unknown. Further, relatively little is understood as to the mechanism whereby developmentally critical transcription factors coordinate with chromatin remodeling factors to optimize target gene loci for gene expression. Such a mechanism might involve direct transcription factor/chromatin remodeling factor interactions, or could likely be mediated via an unknown intermediary. Our group has identified the relatively unknown protein Akirin as a putative member of this latter group: a secondary cofactor that serves as an interface between a developmentally critical transcription factor and the chromatin remodeling machinery. This role for the Akirin protein suggests a novel regulatory mode for regulating gene expression during development.
PMCID: PMC3527315  PMID: 23242134
Akirin; Twist; SWI/SNF; chromatin; transcription; muscle; Drosophila
22.  Competition and compensation 
Bioarchitecture  2012;2(5):171-174.
Stereocilia are actin protrusions with remarkably well-defined lengths and organization. A flurry of recent papers has reported multiple myosin motor proteins involved in regulating stereocilia structures by transporting actin-regulatory cargo to the tips of stereocilia.1-13 In our recent paper, we show that two paralogous class 3 myosins — Myo3a and Myo3b — both transport the actin-regulatory protein Espin 1 (Esp1) to stereocilia and filopodia tips in a remarkably similar, albeit non-identical fashion.1 Here we present experimental and computational data that suggests that subtle differences between these two proteins’ biophysical and biochemical properties can help us understand how these myosin species target and regulate the lengths of actin protrusions.
PMCID: PMC3696061  PMID: 22954581
myosin; actin; filopodia; cytoskeleton; motor proteins; stereocilia; deafness
23.  Tethering factor P115 
Bioarchitecture  2012;2(5):175-180.
The membrane tethering factor p115 has been shown to have important functions in ER to Golgi traffic and Golgi biogenesis. The multidomain structure of p115 allows for interactions with a diverse array of proteins that govern cargo movement at the ER-Golgi interface. Within its C-terminal region p115 contains four coiled-coil domains (CC1-CC4). Of the four coiled-coils, only CC1 has been shown to be required for p115 function, presumably by its ability to bind numerous SNARE proteins as well as the small GTPase Rab1. Recently, we showed that CC4 also interacts with SNARE proteins and that CC4 is required for p115 function in Golgi homeostasis and the trafficking of transmembrane but not soluble cargo. Here, we propose a novel model wherein p115 facilitates membrane tethering and fusion by simultaneously engaging its CC1 and CC4 domains with distinct SNARE proteins to promote formation of SNARE complexes.
PMCID: PMC3696062  PMID: 22992751
p115; SNARE; tethering; Golgi; coiled-coil domain
24.  Evolutionary conservation of neocortical neurogenetic program in the mammals and birds 
Bioarchitecture  2012;2(4):124-129.
The unique innovation of the layered neocortex in mammalian evolution is believed to facilitate adaptive radiation of mammalian species to various ecological environments by furnishing high information processing ability. There are no transitional states from the non-mammalian simple brain to the mammalian multilayered neocortex, and thus it is totally a mystery so far how this brain structure has been acquired during evolution. In our recent study, we found the evidence showing that the evolutionary origin of the neocortical neuron subtypes predates the actual emergence of layer structure. Our comparative developmental analysis of the chick pallium, homologous to the mammalian neocortex, revealed that mammals and avians fundamentally share the neocortical neuron subtypes and their production mechanisms, suggesting that their common ancestor already possessed a similar neuronal repertory. We further demonstrated that the neocortical layer-specific neuron subtypes are arranged as mediolaterally separated domains in the chick, but not as layers in the mammalian neocortex. These animal group-specific neuronal arrangements are accomplished by spatial modulation of the neurogenetic program, suggesting an evolutionary hypothesis that the regulatory changes in the neurogenetic program innovated the mammalian specific layered neocortex.
PMCID: PMC3675072  PMID: 22960728
bird; brain patterning; evolution; layer; mammal; neocortex; neural progenitor; neuron subtype; pallium; stem cell
25.  p21-activated kinase 4 regulates mitotic spindle positioning and orientation 
Bioarchitecture  2012;2(4):130-133.
During mitosis, microtubules (MTs) are massively rearranged into three sets of highly dynamic MTs that are nucleated from the centrosomes to form the mitotic spindle. Tight regulation of spindle positioning in the dividing cell and chromosome alignment at the center of the metaphase spindle are required to ensure perfect chromosome segregation and to position the cytokinetic furrow that will specify the two daughter cells. Spindle positioning requires regulation of MT dynamics, involving depolymerase activities together with cortical and kinetochore-mediated pushing and pulling forces acting on astral MTs and kinetochore fibres. These forces rely on MT motor activities. Cortical pulling forces exerted on astral MTs depend upon dynein/dynactin complexes and are essential in both symmetric and asymmetric cell division. A well-established spindle positioning pathway regulating the cortical targeting of dynein/dynactin involves the conserved LGN (Leu-Gly-Asn repeat-enriched-protein) and NuMA (microtubule binding nuclear mitotic apparatus protein) complex.1 Spindle orientation is also regulated by integrin-mediated cell adhesion2 and actin retraction fibres that respond to mechanical stress and are influenced by the microenvironment of the dividing cell.3 Altering the capture of astral MTs or modulating pulling forces affects spindle position, which can impair cell division, differentiation and embryogenesis.
In this general scheme, the activity of mitotic kinases such as Auroras and Plk1 (Polo-like kinase 1) is crucial.4 Recently, the p21-activated kinases (PAKs) emerged as novel important players in mitotic progression. In our recent article, we demonstrated that PAK4 regulates spindle positioning in symmetric cell division.5 In this commentary, and in light of recent published studies, we discuss how PAK4 could participate in the regulation of mechanisms involved in spindle positioning and orientation.
PMCID: PMC3675073  PMID: 22960742
astral microtubules; dynein; p21-activated kinase; spindle orientation and positioning

Results 1-25 (31)