The Saccharomyces cerevisiae BNI1 gene product (Bni1p) is a member of the formin family proteins, which participate in cell polarization, cytokinesis, and vertebrate limb formation. During mating pheromone response, bni1 mutants showed defects both polarized morphogenesis reorganization underlying actin cytoskeleton. In two-hybrid experiments, Bni1p formed complexes with activated form Rho-related guanosine triphosphatase Cdc42p, actin, two actin-associated profilin Bud6p (Aip3p). Both (like...

During mitosis in budding yeast the nucleus first moves to mother-bud neck and then into neck. Both movements depend on interactions of cytoplasmic microtubules with cortex. We investigated mechanism these living cells using video analysis GFP-labeled wild-type EB1 Arp1 mutants, which are defective second steps, respectively. found that nuclear movement is largely mediated by capture microtubule ends at one cortical region incipient bud site or tip, followed depolymerization. Efficient...

The Saccharomyces cerevisiae AXL1 gene product Axl1p shares homology with the insulin-degrading enzyme family of endoproteases. Yeast axl1 mutants showed a defect in a-factor pheromone secretion, and probable site processing by was identified within precursor. In addition, appears to function as morphogenetic determinant for axial bud selection. Amino acid substitutions presumptive active caused defects propheromone but failed perturb Thus, has been shown participate dual regulation distinct...

The spindle position checkpoint in Saccharomyces cerevisiae delays mitotic exit until the has moved into mother–bud neck, ensuring that each daughter cell inherits a nucleus. small G protein Tem1p is critical promoting and concentrated at pole destined for bud. presumed nucleotide exchange factor Tem1p, Lte1p, These findings suggested hypothesis movement of through neck allows to interact with GTP loading exit. However, we report deletion LTE1 had little effect on timing We also examined...

The cell cycle is composed of bistable molecular switches that govern the transitions between gap phases (G1 and G2) in which DNA replicated (S) partitioned daughter cells (M). Many details budding yeast G1-S transition (Start) have been elucidated recent years, especially with regard to its switch-like behavior due positive feedback mechanisms. These results led us reevaluate expand a previous mathematical model cycle. new incorporates Whi3 inhibition Cln3 activity, Whi5 SBF MBF...

Networks have become ubiquitous in systems biology. Visualization is a crucial component their analysis. However, collaborations within research teams network biology are hampered by software that either specific to computational algorithm, create visualizations not biologically meaningful, or limited features for sharing networks and visualizations. We present GraphSpace, web-based platform fosters team science allowing collaborating groups easily store, interact with, layout share...

Synthetic biologists rely on databases of biological parts to design genetic devices and systems. The sequences descriptions are often derived from features previously described plasmids using ad hoc, error-prone time-consuming curation processes because existing loosely organized. These lack consistency in the way they identify describe sequences. Furthermore, legacy bioinformatics file formats like GenBank do not provide enough information about purpose features. We have analyzed...

Fifty years of genetic and molecular experiments have revealed a wealth interactions involved in the control cell division. In light complexity this system, mathematical modeling has proved useful analyzing biochemical hypotheses that can be tested experimentally. Stochastic been especially understanding intrinsic variability cycle events, but stochastic hampered by lack reliable data on absolute numbers mRNA molecules per for genes. To fill void, we used fluorescence situ hybridization...

The use of microfluidics in live cell imaging allows the acquisition dense time-series from individual cells that can be perturbed through computer-controlled changes growth medium. Systems and synthetic biologists frequently perform gene expression studies require conditions to characterize stability switches, transfer function a genetic device, or oscillations networks. It is rarely possible know priori at what times various should made, success experiment unknown until all image...

Abstract Laboratory strains, cell lines, and other genetic materials change hands frequently in the life sciences. Despite evidence that such are subject to mix-ups, contamination, accumulation of secondary mutations, verification strains samples is not an established part many experimental workflows. With plummeting cost next generation technologies, it conceivable whole genome sequencing (WGS) could be applied routine strain sample future. To demonstrate need for validation by WGS, we...

We reported previously that Ca2+ depletion of Dictyostelium discoideum cells severely inhibits extracellular cyclic nucleotide phosphodiesterase (PD) synthesis at a post-transcriptional step. In this study, further experiments were performed to learn more about the nature phenomenon. Examination polysomal distribution PD transcripts in control and depleted by incubation with EGTA A23187 (EA) suggested inhibition production does not involve translational control. Kinetic analysis inhibitory...

In addition to their role in regulating transport across the nuclear envelope, increasing evidence suggests pore complexes (NPCs) function gene expression. For example, induction of certain genes (e.g., yeast INO1) is accompanied by movement from interior NPCs. As sumoylation has been linked regulation chromatin spatial organization and transcriptional activity, we investigated expression NPC recruitment INO1 gene. We observed that both increased decreased proteins associated with specific...

Abstract Over the last 30 years, computational biologists have developed increasingly realistic mathematical models of regulatory networks controlling division eukaryotic cells. These capture data resulting from two complementary experimental approaches: low-throughput experiments aimed at extensively characterizing functions small numbers genes, and large-scale genetic interaction screens that provide a systems-level perspective on cell process. The former is insufficient to...

Abstract Motivation Mathematical models of cellular processes can systematically predict the phenotypes novel combinations multi-gene mutations. Searching for informative predictions and prioritizing them experimental validation is challenging since number possible grows exponentially in Moreover, keeping track crosses needed to make new mutants planning sequences experiments unmanageable when experimenter deluged by hundreds potentially test. Results We present CrossPlan, a methodology...

Abstract Laboratory strains, cell lines, and other genetic materials change hands frequently in the life sciences. Despite evidence that such are subject to mix-ups, contamination, accumulation of secondary mutations, verification strains samples is not an established part many experimental workflows. With plummeting cost next generation technologies, it conceivable whole genome sequencing (WGS) could be applied routine strain sample future. To demonstrate need for validation by WGS, we...

To divide replicated chromosomes equally between daughter cells, kinetochores must attach to microtubules emanating from opposite poles of the mitotic spindle (biorientation). An error correction mechanism facilitates this process by destabilizing erroneous kinetochore-microtubule attachments. Here we present a stochastic model attachments, via an essential protein Ndc80 in budding yeast, Saccharomyces cerevisiae. Using model, calculate dynamics pair sister as they transition among different...

Mathematical models of cellular processes can systematically predict the phenotypes novel combinations multi-gene mutations. Searching for informative predictions and prioritizing them experimental validation is challenging since number possible grows exponentially in Moreover, keeping track crosses needed to make new mutants planning sequences experiments unmanageable when experimenter deluged by hundreds potentially test. We present CrossPlan, a methodology genetic set target from source...