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1.  Myo19 Ensures Symmetric Partitioning of Mitochondria and Coupling of Mitochondrial Segregation to Cell Division 
Current Biology  2014;24(21):2598-2605.
During animal cell division, an actin-based ring cleaves the cell into two. Problems with this process can cause chromosome missegregation and defects in cytoplasmic inheritance and the partitioning of organelles, which in turn are associated with human diseases [1–3]. Although much is known about how chromosome segregation is coupled to cell division, the way organelles coordinate their inheritance during partitioning to daughter cells is less well understood. Here, using a high-content live-imaging small interfering RNA screen, we identify Myosin-XIX (Myo19) as a novel regulator of cell division. Previously, this actin-based motor was shown to control the interphase movement of mitochondria [4]. Our analysis shows that Myo19 is indeed localized to mitochondria and that its silencing leads to defects in the distribution of mitochondria within cells and in mitochondrial partitioning at division. Furthermore, many Myo19 RNAi cells undergo stochastic division failure—a phenotype that can be mimicked using a treatment that blocks mitochondrial fission and rescued by decreasing mitochondrial fusion, implying that mitochondria can physically interfere with cytokinesis. Strikingly, using live imaging we also observe the inappropriate movement of mitochondria to the poles of spindles in cells depleted for Myo19 as they enter anaphase. Since this phenocopies the results of an acute loss of actin filaments in anaphase, these data support a model whereby the Myo19 actin-based motor helps to control mitochondrial movement to ensure their faithful segregation during division. The presence of DNA within mitochondria makes their inheritance an especially important aspect of symmetrical cell division.
•RNAi screen identifies Myo19 as novel regulator of cell division•Myo19 ensures fair mitochondrial inheritance at division•Division requires coupled mitochondrial segregation and cytokinesis
It is not known how animal cells partition mitochondria at division. Rohn et al. identify the unconventional myosin Myo19 as a novel actin-based regulator of this process. Myo19 depletion alters the distribution of mitochondria at mitotic exit, leading to unequal mitochondrial segregation at division and, occasionally, to division failure.
PMCID: PMC4228054  PMID: 25447992
2.  An inside-out origin for the eukaryotic cell 
BMC Biology  2014;12(1):76.
Although the origin of the eukaryotic cell has long been recognized as the single most profound change in cellular organization during the evolution of life on earth, this transition remains poorly understood. Models have always assumed that the nucleus and endomembrane system evolved within the cytoplasm of a prokaryotic cell.
Drawing on diverse aspects of cell biology and phylogenetic data, we invert the traditional interpretation of eukaryotic cell evolution. We propose that an ancestral prokaryotic cell, homologous to the modern-day nucleus, extruded membrane-bound blebs beyond its cell wall. These blebs functioned to facilitate material exchange with ectosymbiotic proto-mitochondria. The cytoplasm was then formed through the expansion of blebs around proto-mitochondria, with continuous spaces between the blebs giving rise to the endoplasmic reticulum, which later evolved into the eukaryotic secretory system. Further bleb-fusion steps yielded a continuous plasma membrane, which served to isolate the endoplasmic reticulum from the environment.
The inside-out theory is consistent with diverse kinds of data and provides an alternative framework by which to explore and understand the dynamic organization of modern eukaryotic cells. It also helps to explain a number of previously enigmatic features of cell biology, including the autonomy of nuclei in syncytia and the subcellular localization of protein N-glycosylation, and makes many predictions, including a novel mechanism of interphase nuclear pore insertion.
PMCID: PMC4210606  PMID: 25350791
Archaea; Cell topology; Cytoplasmic continuity; ER and endomembrane organization; Evolution of eukaryotes; Mitochondria; Nuclear pore insertion; Origin of the nucleus; Vesicle trafficking
3.  The Role of Chromosome Missegregation in Cancer Development: A Theoretical Approach Using Agent-Based Modelling 
PLoS ONE  2013;8(8):e72206.
Many cancers are aneuploid. However, the precise role that chromosomal instability plays in the development of cancer and in the response of tumours to treatment is still hotly debated. Here, to explore this question from a theoretical standpoint we have developed an agent-based model of tissue homeostasis in which to test the likely effects of whole chromosome mis-segregation during cancer development. In stochastic simulations, chromosome mis-segregation events at cell division lead to the generation of a diverse population of aneuploid clones that over time exhibit hyperplastic growth. Significantly, the course of cancer evolution depends on genetic linkage, as the structure of chromosomes lost or gained through mis-segregation events and the level of genetic instability function in tandem to determine the trajectory of cancer evolution. As a result, simulated cancers differ in their level of genetic stability and in their growth rates. We used this system to investigate the consequences of these differences in tumour heterogeneity for anti-cancer therapies based on surgery and anti-mitotic drugs that selectively target proliferating cells. As expected, simulated treatments induce a transient delay in tumour growth, and reveal a significant difference in the efficacy of different therapy regimes in treating genetically stable and unstable tumours. These data support clinical observations in which a poor prognosis is correlated with a high level of chromosome mis-segregation. However, stochastic simulations run in parallel also exhibit a wide range of behaviours, and the response of individual simulations (equivalent to single tumours) to anti-cancer therapy prove extremely variable. The model therefore highlights the difficulties of predicting the outcome of a given anti-cancer treatment, even in cases in which it is possible to determine the genotype of the entire set of cells within the developing tumour.
PMCID: PMC3753339  PMID: 23991060
4.  Changes in Ect2 Localization Couple Actomyosin-Dependent Cell Shape Changes to Mitotic Progression 
Developmental Cell  2012;23(2):371-383.
As they enter mitosis, animal cells undergo profound actin-dependent changes in shape to become round. Here we identify the Cdk1 substrate, Ect2, as a central regulator of mitotic rounding, thus uncovering a link between the cell-cycle machinery that drives mitotic entry and its accompanying actin remodeling. Ect2 is a RhoGEF that plays a well-established role in formation of the actomyosin contractile ring at mitotic exit, through the local activation of RhoA. We find that Ect2 first becomes active in prophase, when it is exported from the nucleus into the cytoplasm, activating RhoA to induce the formation of a mechanically stiff and rounded metaphase cortex. Then, at anaphase, binding to RacGAP1 at the spindle midzone repositions Ect2 to induce local actomyosin ring formation. Ect2 localization therefore defines the stage-specific changes in actin cortex organization critical for accurate cell division.
► Ect2 drives dynamic changes in cell shape throughout mitosis ► Ect2 induces actin-dependent changes in cortical mechanics at mitotic onset ► Ect2's distinct functions are achieved through changes in subcellular localization ► Actin remodeling for animal cell division begins at mitotic entry
Cell division is accompanied by dramatic changes in cell shape, which Matthews et al. show are regulated by the Cdk1 substrate Ect2. At mitotic onset, Ect2 leaves the nucleus to activate RhoA and cortical actomyosin, driving mitotic rounding. It is then repositioned at mitotic exit to drive actomyosin ring formation.
PMCID: PMC3763371  PMID: 22898780
5.  FMNL2 Drives Actin-Based Protrusion and Migration Downstream of Cdc42 
Current Biology  2012;22(11):1005-1012.
Cell migration entails protrusion of lamellipodia, densely packed networks of actin filaments at the cell front. Filaments are generated by nucleation, likely mediated by Arp2/3 complex and its activator Scar/WAVE [1]. It is unclear whether formins contribute to lamellipodial actin filament nucleation or serve as elongators of filaments nucleated by Arp2/3 complex [2]. Here we show that the Diaphanous-related formin FMNL2, also known as FRL3 or FHOD2 [3], accumulates at lamellipodia and filopodia tips. FMNL2 is cotranslationally modified by myristoylation and regulated by interaction with the Rho-guanosine triphosphatase Cdc42. Abolition of myristoylation or Cdc42 binding interferes with proper FMNL2 activation, constituting an essential prerequisite for subcellular targeting. In vitro, C-terminal FMNL2 drives elongation rather than nucleation of actin filaments in the presence of profilin. In addition, filament ends generated by Arp2/3-mediated branching are captured and efficiently elongated by the formin. Consistent with these biochemical properties, RNAi-mediated silencing of FMNL2 expression decreases the rate of lamellipodia protrusion and, accordingly, the efficiency of cell migration. Our data establish that the FMNL subfamily member FMNL2 is a novel elongation factor of actin filaments that constitutes the first Cdc42 effector promoting cell migration and actin polymerization at the tips of lamellipodia.
► FMNL2 is a novel Cdc42 effector accumulating at lamellipodial and filopodial tips ► FMNL2 is regulated but not localized by N-terminal myristoylation and Cdc42 binding ► FMNL2 processively elongates actin filaments in the presence of profilin ► FMNL2 drives cell migration by increasing the efficiency of lamellipodia protrusion
PMCID: PMC3765947  PMID: 22608513
6.  A Biomechanical Analysis of Ventral Furrow Formation in the Drosophila Melanogaster Embryo 
PLoS ONE  2012;7(4):e34473.
The article provides a biomechanical analysis of ventral furrow formation in the Drosophila melanogaster embryo. Ventral furrow formation is the first large-scale morphogenetic movement in the fly embryo. It involves deformation of a uniform cellular monolayer formed following cellularisation, and has therefore long been used as a simple system in which to explore the role of mechanics in force generation. Here we use a quantitative framework to carry out a systematic perturbation analysis to determine the role of each of the active forces observed. The analysis confirms that ventral furrow invagination arises from a combination of apical constriction and apical–basal shortening forces in the mesoderm, together with a combination of ectodermal forces. We show that the mesodermal forces are crucial for invagination: the loss of apical constriction leads to a loss of the furrow, while the mesodermal radial shortening forces are the primary cause of the internalisation of the future mesoderm as the furrow rises. Ectodermal forces play a minor but significant role in furrow formation: without ectodermal forces the furrow is slower to form, does not close properly and has an aberrant morphology. Nevertheless, despite changes in the active mesodermal and ectodermal forces lead to changes in the timing and extent of furrow, invagination is eventually achieved in most cases, implying that the system is robust to perturbation and therefore over-determined.
PMCID: PMC3325263  PMID: 22511944
7.  Comparative RNAi screening identifies a conserved core metazoan actinome by phenotype 
The Journal of Cell Biology  2011;194(5):789-805.
RNAi Screens in Drosophila and human cells for novel actin regulators revealed conserved roles for proteins involved in nuclear actin export, RNA splicing, and ubiquitination.
Although a large number of actin-binding proteins and their regulators have been identified through classical approaches, gaps in our knowledge remain. Here, we used genome-wide RNA interference as a systematic method to define metazoan actin regulators based on visual phenotype. Using comparative screens in cultured Drosophila and human cells, we generated phenotypic profiles for annotated actin regulators together with proteins bearing predicted actin-binding domains. These phenotypic clusters for the known metazoan “actinome” were used to identify putative new core actin regulators, together with a number of genes with conserved but poorly studied roles in the regulation of the actin cytoskeleton, several of which we studied in detail. This work suggests that although our search for new components of the core actin machinery is nearing saturation, regulation at the level of nuclear actin export, RNA splicing, ubiquitination, and other upstream processes remains an important but unexplored frontier of actin biology.
PMCID: PMC3171124  PMID: 21893601
8.  Dynamics of adherens junctions in epithelial establishment, maintenance, and remodeling 
The Journal of Cell Biology  2011;192(6):907-917.
The epithelial cadherin (E-cadherin)–catenin complex binds to cytoskeletal components and regulatory and signaling molecules to form a mature adherens junction (AJ). This dynamic structure physically connects neighboring epithelial cells, couples intercellular adhesive contacts to the cytoskeleton, and helps define each cell’s apical–basal axis. Together these activities coordinate the form, polarity, and function of all cells in an epithelium. Several molecules regulate AJ formation and integrity, including Rho family GTPases and Par polarity proteins. However, only recently, with the development of live-cell imaging, has the extent to which E-cadherin is actively turned over at junctions begun to be appreciated. This turnover contributes to junction formation and to the maintenance of epithelial integrity during tissue homeostasis and remodeling.
PMCID: PMC3063136  PMID: 21422226
9.  Identification and characterization of a set of conserved and new regulators of cytoskeletal organization, cell morphology and migration 
BMC Biology  2011;9:54.
Cell migration is essential during development and in human disease progression including cancer. Most cell migration studies concentrate on known or predicted components of migration pathways.
Here we use data from a genome-wide RNAi morphology screen in Drosophila melanogaster cells together with bioinformatics to identify 26 new regulators of morphology and cytoskeletal organization in human cells. These include genes previously implicated in a wide range of functions, from mental retardation, Down syndrome and Huntington's disease to RNA and DNA-binding genes. We classify these genes into seven groups according to phenotype and identify those that affect cell migration. We further characterize a subset of seven genes, FAM40A, FAM40B, ARC, FMNL3, FNBP3/FBP11, LIMD1 and ZRANB1, each of which has a different effect on cell shape, actin filament distribution and cell migration. Interestingly, in several instances closely related isoforms with a single Drosophila homologue have distinct phenotypes. For example, FAM40B depletion induces cell elongation and tail retraction defects, whereas FAM40A depletion reduces cell spreading.
Our results identify multiple regulators of cell migration and cytoskeletal signalling that are highly conserved between Drosophila and humans, and show that closely related paralogues can have very different functions in these processes.
PMCID: PMC3201212  PMID: 21834987
10.  The importance of structured noise in the generation of self-organizing tissue patterns through contact-mediated cell–cell signalling 
Lateral inhibition provides the basis for a self-organizing patterning system in which distinct cell states emerge from an otherwise uniform field of cells. The development of the microchaete bristle pattern on the notum of the fruitfly, Drosophila melanogaster, has long served as a popular model of this process. We recently showed that this bristle pattern depends upon a population of dynamic, basal actin-based filopodia, which span multiple cell diameters. These protrusions establish transient signalling contacts between non-neighbouring cells, generating a type of structured noise that helps to yield a well-ordered and spaced pattern of bristles. Here, we develop a general model of protrusion-based patterning to analyse the role of noise in this process. Using a simple asynchronous cellular automata rule-based model we show that this type of structured noise drives the gradual refinement of lateral inhibition-mediated patterning, as the system moves towards a stable configuration in which cells expressing the inhibitory signal are near-optimally packed. By analysing the effects of introducing thresholds required for signal detection in this model of lateral inhibition, our study shows how filopodia-mediated cell–cell communication can generate complex patterns of spots and stripes, which, in the presence of signalling noise, align themselves across a patterning field. Thus, intermittent protrusion-based signalling has the potential to yield robust self-organizing tissue-wide patterns without the need to invoke diffusion-mediated signalling.
PMCID: PMC3104346  PMID: 21084342
patterning; lateral inhibition; noise; filopodia; signalling; cellular automata
11.  A Polarised Population of Dynamic Microtubules Mediates Homeostatic Length Control in Animal Cells 
PLoS Biology  2010;8(11):e1000542.
An analysis of cells grown on micro-patterned lines, and of cells during zebrafish development, identifies a population of microtubules that align along the long axis of cells to mediate homeostatic length control.
Because physical form and function are intimately linked, mechanisms that maintain cell shape and size within strict limits are likely to be important for a wide variety of biological processes. However, while intrinsic controls have been found to contribute to the relatively well-defined shape of bacteria and yeast cells, the extent to which individual cells from a multicellular animal control their plastic form remains unclear. Here, using micropatterned lines to limit cell extension to one dimension, we show that cells spread to a characteristic steady-state length that is independent of cell size, pattern width, and cortical actin. Instead, homeostatic length control on lines depends on a population of dynamic microtubules that lead during cell extension, and that are aligned along the long cell axis as the result of interactions of microtubule plus ends with the lateral cell cortex. Similarly, during the development of the zebrafish neural tube, elongated neuroepithelial cells maintain a relatively well-defined length that is independent of cell size but dependent upon oriented microtubules. A simple, quantitative model of cellular extension driven by microtubules recapitulates cell elongation on lines, the steady-state distribution of microtubules, and cell length homeostasis, and predicts the effects of microtubule inhibitors on cell length. Together this experimental and theoretical analysis suggests that microtubule dynamics impose unexpected limits on cell geometry that enable cells to regulate their length. Since cells are the building blocks and architects of tissue morphogenesis, such intrinsically defined limits may be important for development and homeostasis in multicellular organisms.
Author Summary
Because many physical processes change with scale, size control is a fundamental problem for living systems. While in some instances the size of a structure is directly determined by the dimensions of its individual constituents, many biological structures are dynamic, self-organising assemblies of relatively small component parts. How such assemblies are maintained within defined size limits remains poorly understood. Here, by confining cells to spread on lines, we show that animal cells reach a defined length that is independent of their volume and width. In searching for a “ruler” that might determine this axial limit to cell spreading, we identified a population of dynamic microtubule polymers that become oriented along the long axis of cells. This growing population of oriented microtubules drives extension of the spreading cell margin while, conversely, interactions with the cell margin promote microtubule depolymerisation, leading to cell shortening. Using a mathematical model we show that this coupling of dynamic microtubule polymerisation and depolymerisation with directed cell elongation is sufficient to explain the limit to cell spreading and cell length homeostasis. Because microtubules appear to regulate cell length in a similar way in the developing zebrafish neural tube, we suggest that this microtubule-dependent mechanism is likely to be of widespread importance for the regulation of cell and tissue geometry.
PMCID: PMC2982804  PMID: 21103410
12.  The FLIGHT Drosophila RNAi database 
Fly  2010;4(4):344-348.
FLIGHT ( is an online resource compiling data from high-throughput Drosophila in vivo and in vitro RNAi screens. FLIGHT includes details of RNAi reagents and their predicted off-target effects, alongside RNAi screen hits, scores and phenotypes, including images from high-content screens. The latest release of FLIGHT is designed to enable users to upload, analyze, integrate and share their own RNAi screens. Users can perform multiple normalizations, view quality control plots, detect and assign screen hits and compare hits from multiple screens using a variety of methods including hierarchical clustering. FLIGHT integrates RNAi screen data with microarray gene expression as well as genomic annotations and genetic/physical interaction datasets to provide a single interface for RNAi screen analysis and datamining in Drosophila.
PMCID: PMC3174485  PMID: 20855970
RNAi; database; integration; bioinformatics; phenotype
13.  A Role for p38 Stress-Activated Protein Kinase in Regulation of Cell Growth via TORC1▿ †  
Molecular and Cellular Biology  2009;30(2):481-495.
The target of rapamycin (TOR) complex 1 (TORC1) signaling pathway is a critical regulator of translation and cell growth. To identify novel components of this pathway, we performed a kinome-wide RNA interference (RNAi) screen in Drosophila melanogaster S2 cells. RNAi targeting components of the p38 stress-activated kinase cascade prevented the cell size increase elicited by depletion of the TOR negative regulator TSC2. In mammalian and Drosophila tissue culture, as well as in Drosophila ovaries ex vivo, p38-activating stresses, such as H2O2 and anisomycin, were able to activate TORC1. This stress-induced TORC1 activation could be blocked by RNAi against mitogen-activated protein kinase kinase 3 and 6 (MKK3/6) or by the overexpression of dominant negative Rags. Interestingly, p38 was also required for the activation of TORC1 in response to amino acids and growth factors. Genetic ablation either of p38b or licorne, its upstream kinase, resulted in small flies consisting of small cells. Mutants with mutations in licorne or p38b are nutrition sensitive; low-nutrient food accentuates the small-organism phenotypes, as well as the partial lethality of the p38b null allele. These data suggest that p38 is an important positive regulator of TORC1 in both mammalian and Drosophila systems in response to certain stresses and growth factors.
PMCID: PMC2798466  PMID: 19917724
14.  Parallel RNAi screens across different cell lines identify generic and cell type-specific regulators of actin organization and cell morphology 
Genome Biology  2009;10(3):R26.
Parallel RNA interference screens and gene expression arrays in six Drosophila cell lines identified regulators of cell morphology, including a neuronal function for the kinase minibrain/DYRK1A in the regulation of protrusion morphology.
In recent years RNAi screening has proven a powerful tool for dissecting gene functions in animal cells in culture. However, to date, most RNAi screens have been performed in a single cell line, and results then extrapolated across cell types and systems.
Here, to dissect generic and cell type-specific mechanisms underlying cell morphology, we have performed identical kinome RNAi screens in six different Drosophila cell lines, derived from two distinct tissues of origin. This analysis identified a core set of kinases required for normal cell morphology in all lines tested, together with a number of kinases with cell type-specific functions. Most significantly, the screen identified a role for minibrain (mnb/DYRK1A), a kinase associated with Down's syndrome, in the regulation of actin-based protrusions in CNS-derived cell lines. This cell type-specific requirement was not due to the peculiarities in the morphology of CNS-derived cells and could not be attributed to differences in mnb expression. Instead, it likely reflects differences in gene expression that constitute the cell type-specific functional context in which mnb/DYRK1A acts.
Using parallel RNAi screens and gene expression analyses across cell types we have identified generic and cell type-specific regulators of cell morphology, which include mnb/DYRK1A in the regulation of protrusion morphology in CNS-derived cell lines. This analysis reveals the importance of using different cell types to gain a thorough understanding of gene function across the genome and, in the case of kinases, the difficulties of using the differential gene expression to predict function.
PMCID: PMC2690997  PMID: 19265526
15.  PDGF/VEGF signaling controls cell size in Drosophila 
Genome Biology  2009;10(2):R20.
Pvr and its ligands, Pvf 2 and 3, which are upstream of Ras and PI3kinase, are identified from a genome-wide screen in Drosophila cells, as regulators of cell growth.
In multicellular animals, cell size is controlled by a limited set of conserved intracellular signaling pathways, which when deregulated contribute to tumorigenesis by enabling cells to grow outside their usual niche. To delineate the pathways controlling this process, we screened a genome-scale, image-based Drosophila RNA interference dataset for double-stranded RNAs that reduce the average size of adherent S2R+ cells.
Automated analysis of images from this RNA interference screen identified the receptor tyrosine kinase Pvr, Ras pathway components and several novel genes as regulators of cell size. Significantly, Pvr/Ras signaling also affected the size of other Drosophila cell lines and of larval hemocytes. A detailed genetic analysis of this growth signaling pathway revealed a role for redundant secreted ligands, Pvf2 and Pvf3, in the establishment of an autocrine growth signaling loop. Downstream of Ras1, growth signaling was found to depend on parallel mitogen-activated protein kinase (MAPK) and phospho-inositide-3-kinase (PI3K) signaling modules, as well as the Tor pathway.
This automated genome-wide screen identifies autocrine Pvf/Pvr signaling, upstream of Ras, MAPK and PI3K, as rate-limiting for the growth of immortalized fly cells in culture. Since, Pvf2/3 and Pvr show mutually exclusive in vivo patterns of gene expression, these data suggest that co-expression of this receptor-ligand pair plays a key role in driving cell autonomous growth during the establishment of Drosophila cell lines, as has been suggested to occur during tumor development.
PMCID: PMC2688285  PMID: 19216764
16.  A Genome-Wide RNAi Screen to Dissect Centriole Duplication and Centrosome Maturation in Drosophila 
PLoS Biology  2008;6(9):e224.
Centrosomes comprise a pair of centrioles surrounded by an amorphous pericentriolar material (PCM). Here, we have performed a microscopy-based genome-wide RNA interference (RNAi) screen in Drosophila cells to identify proteins required for centriole duplication and mitotic PCM recruitment. We analysed 92% of the Drosophila genome (13,059 genes) and identified 32 genes involved in centrosome function. An extensive series of secondary screens classified these genes into four categories: (1) nine are required for centriole duplication, (2) 11 are required for centrosome maturation, (3) nine are required for both functions, and (4) three genes regulate centrosome separation. These 32 hits include several new centrosomal components, some of which have human homologs. In addition, we find that the individual depletion of only two proteins, Polo and Centrosomin (Cnn) can completely block centrosome maturation. Cnn is phosphorylated during mitosis in a Polo-dependent manner, suggesting that the Polo-dependent phosphorylation of Cnn initiates centrosome maturation in flies.
Author Summary
A major goal of the cell cycle is to accurately separate the duplicated chromosomes between two daughter cells. To achieve this, a pair of centrosomes organise a bipolar spindle made of microtubules; the chromosomes line up on the spindle and are then separated to the two spindle poles. Centrosomes are also required for the formation of cilia and flagella, which are present in many eukaryotic cells; centrosome dysfunction is a common feature of many human cancers and several neurological disorders, whereas mutations in genes that affect cilia function give rise to several human diseases. Here, we perform a genome-wide screen using RNA interference to try to identify all of the proteins required for centrosome function in the model organism Drosophila melanogaster (a fruitfly). We identified all 16 of the centrosomal proteins that were already known to be required for centrosome function in Drosophila, as well as 16 new centrosomal components or regulators. We confirmed the centrosomal location of several of the components and performed some analysis of their functions. We believe we are approaching a complete inventory of the proteins required for centrosome function in flies.
An RNAi screen identifies 16 new centrosomal components or regulators inDrosophila, and molecular dissection of their function addresses the role of Polo kinase in the maturation of pericentriolar material.
PMCID: PMC2535660  PMID: 18798690
17.  The Evolution of Robust Development and Homeostasis in Artificial Organisms 
PLoS Computational Biology  2008;4(3):e1000030.
During embryogenesis, multicellular animals are shaped via cell proliferation, cell rearrangement, and apoptosis. At the end of development, tissue architecture is then maintained through balanced rates of cell proliferation and loss. Here, we take an in silico approach to look for generic systems features of morphogenesis in multicellular animals that arise as a consequence of the evolution of development. Using artificial evolution, we evolved cellular automata-based digital organisms that have distinct embryonic and homeostatic phases of development. Although these evolved organisms use a variety of strategies to maintain their form over time, organisms of different types were all found to rapidly recover from environmental damage in the form of wounds. This regenerative response was most robust in an organism with a stratified tissue-like architecture. An evolutionary analysis revealed that evolution itself contributed to the ability of this organism to maintain its form in the face of genetic and environmental perturbation, confirming the results of previous studies. In addition, the exceptional robustness of this organism to surface injury was found to result from an upward flux of cells, driven in part by cell divisions with a stable niche at the tissue base. Given the general nature of the model, our results lead us to suggest that many of the robust systems properties observed in real organisms, including scar-free wound-healing in well-protected embryos and the layered tissue architecture of regenerating epithelial tissues, may be by-products of the evolution of morphogenesis, rather than the direct result of selection.
Author Summary
During development, multicellular animals are shaped by cell proliferation, cell rearrangement, and cell death to generate an adult whose form is maintained over time. Disruption of this finely balanced state can have devastating consequences, including aging, psoriasis, and cancer. Typically, however, development is robust, so that animals achieve the same final form even when challenged by environmental damage such as wounding. To see how morphogenetic robustness arises, we have taken an in silico approach to evolve digital organisms that exhibit distinct phases of growth and homeostasis. During the homeostasis period, organisms were found to use a variety of strategies to maintain their form. Remarkably, however, all recovered from severe wounds, despite having evolved in the absence of selection pressure to do so. This ability to regenerate was most striking in an organism with a tissue-like architecture, where it was enhanced by a directional flux of cells that drives tissue turnover. This identifies a stratified architecture, like that seen in human skin and gut, as an evolutionarily accessible and robust form of tissue organisation, and suggests that wound-healing may be a general feature of evolved morphogenetic systems. Both may therefore contribute to homeostasis, wound-healing, and regeneration in real animals.
PMCID: PMC2274883  PMID: 18369424
18.  FLIGHT: database and tools for the integration and cross-correlation of large-scale RNAi phenotypic datasets 
Nucleic Acids Research  2005;34(Database issue):D479-D483.
FLIGHT () is a new database designed to help researchers browse and cross-correlate data from large-scale RNAi studies. To date, the majority of these functional genomic screens have been carried out using Drosophila cell lines. These RNAi screens follow 100 years of classical Drosophila genetics, but have already revealed their potential by ascribing an impressive number of functions to known and novel genes. This has in turn given rise to a pressing need for tools to simplify the analysis of the large amount of phenotypic information generated. FLIGHT aims to do this by providing users with a gene-centric view of screen results and by making it possible to cluster phenotypic data to identify genes with related functions. Additionally, FLIGHT provides microarray expression data for many of the Drosophila cell lines commonly used in RNAi screens. This, together with information about cell lines, protocols and dsRNA primer sequences, is intended to help researchers design their own cell-based screens. Finally, although the current focus of FLIGHT is Drosophila, the database has been designed to facilitate the comparison of functional data across species and to help researchers working with other systems navigate their way through the fly genome.
PMCID: PMC1347401  PMID: 16381916

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