Advances in genome-wide RNAi cellular screens: a case study using the Drosophila JAK/STAT pathway

BACKGROUND: Genome-scale RNA-interference (RNAi) screens are becoming ever more common gene discovery tools. However, whilst every screen identifies interacting genes, less attention has been given to how factors such as library design and post-screening bioinformatics may be effecting the data generated. RESULTS: Here we present a new genome-wide RNAi screen of the Drosophila JAK/STAT signalling pathway undertaken in the Sheffield RNAi Screening Facility (SRSF). This screen was carried out using a second-generation, computationally optimised dsRNA library and analysed using current methods and bioinformatic tools. To examine advances in RNAi screening technology, we compare this screen to a biologically very similar screen undertaken in 2005 with a first-generation library. Both screens used the same cell line, reporters and experimental design, with the SRSF screen identifying 42 putative regulators of JAK/STAT signalling, 22 of which verified in a secondary screen and 16 verified with an independent probe design. Following reanalysis of the original screen data, comparisons of the two gene lists allows us to make estimates of false discovery rates in the SRSF data and to conduct an assessment of off-target effects (OTEs) associated with both libraries. We discuss the differences and similarities between the resulting data sets and examine the relative improvements in gene discovery protocols. CONCLUSIONS: Our work represents one of the first direct comparisons between first- and second-generation libraries and shows that modern library designs together with methodological advances have had a significant influence on genome-scale RNAi screens

A theoretical framework for planar polarity establishment through interpretation of graded cues by molecular bridges

Planar polarity is a widespread phenomenon found in many tissues, allowing cells to coordinate morphogenetic movements and function. A common feature of animal planar polarity systems is the formation of molecular bridges between cells, which become polarised along a tissue axis. We propose that these bridges provide a general mechanism by which cells interpret different forms of tissue gradients to coordinate directional information. We illustrate this using a generalised and consistent modelling framework, providing a conceptual basis for understanding how different mechanisms of gradient function can generate planar polarity. We make testable predictions of how different gradient mechanisms can influence polarity direction

Low frequency response of a collectively pinned vortex manifold

A low frequency dynamic response of a vortex manifold in type-II superconductor can be associated with thermally activated tunneling of large portions of the manifold between pairs of metastable states (two-level systems). We suggest that statistical properties of these states can be verified by using the same approach for the analysis of thermal fluctuations the behaviour of which is well known. We find the form of the response for the general case of vortex manifold with non-dispersive elastic moduli and for the case of thin superconducting film for which the compressibility modulus is always non-local.Comment: 8 pages, no figures, ReVTeX, the final version. Text strongly modified, all the results unchange

Flux Creep and Flux Jumping

We consider the flux jump instability of the Bean's critical state arising in the flux creep regime in type-II superconductors. We find the flux jump field, $B_j$, that determines the superconducting state stability criterion. We calculate the dependence of $B_j$ on the external magnetic field ramp rate, $\dot B_e$. We demonstrate that under the conditions typical for most of the magnetization experiments the slope of the current-voltage curve in the flux creep regime determines the stability of the Bean's critical state, {\it i.e.}, the value of $B_j$. We show that a flux jump can be preceded by the magneto-thermal oscillations and find the frequency of these oscillations as a function of $\dot B_e$.Comment: 7 pages, ReVTeX, 2 figures attached as postscript file

QuantifyPolarity, a new tool-kit for measuring planar polarized protein distributions and cell properties in developing tissues

The coordination of cells or structures within the plane of a tissue is known as planar polarization. It is often governed by the asymmetric distribution of planar polarity proteins within cells. A number of quantitative methods have been developed to provide a readout of planar polarized protein distributions. However, previous planar polarity quantification methods can be affected by variation in cell geometry. Hence, we developed a novel planar polarity quantification method based on Principal Component Analysis (PCA) that is shape insensitive. Here, we compare this method with other state-of-the-art methods on simulated models and biological datasets. We found that the PCA method performs robustly in quantifying planar polarity independently of variation in cell geometry and other image conditions. We designed a user-friendly graphical user interface called QuantifyPolarity, equipped with three polarity methods for automated quantification of polarity. QuantifyPolarity also provides tools to quantify cell morphology and packing geometry, allowing the relationship of these characteristics to planar polarization to be investigated. This tool enables experimentalists with no prior computational expertise to perform high-throughput cell polarity and shape analysis automatically and efficiently

Spin-Glass State in CuGa2O4\rm CuGa_2O_4

Magnetic susceptibility, magnetization, specific heat and positive muon spin relaxation (\musr) measurements have been used to characterize the magnetic ground-state of the spinel compound $\rm CuGa_2O_4$. We observe a spin-glass transition of the S=1/2 $\rm Cu^{2+}$ spins below $\rm T_f=2.5K$ characterized by a cusp in the susceptibility curve which suppressed when a magnetic field is applied. We show that the magnetization of $\rm CuGa_2O_4$ depends on the magnetic histo Well below $\rm T_f$, the muon signal resembles the dynamical Kubo-Toyabe expression reflecting that the spin freezing process in $\rm CuGa_2O_4$ results Gaussian distribution of the magnetic moments. By means of Monte-Carlo simulati we obtain the relevant exchange integrals between the $\rm Cu^{2+}$ spins in this compound.Comment: 6 pages, 16 figure

Ground-state clusters of two-, three- and four-dimensional +-J Ising spin glasses

A huge number of independent true ground-state configurations is calculated for two-, three- and four-dimensional +- J spin-glass models. Using the genetic cluster-exact approximation method, system sizes up to N=20^2,8^3,6^4 spins are treated. A ``ballistic-search'' algorithm is applied which allows even for large system sizes to identify clusters of ground states which are connected by chains of zero-energy flips of spins. The number of clusters n_C diverges with N going to infinity. For all dimensions considered here, an exponential increase of n_C appears to be more likely than a growth with a power of N. The number of different ground states is found to grow clearly exponentially with N. A zero-temperature entropy per spin of s_0=0.078(5)k_B (2d), s_0=0.051(3)k_B (3d) respectively s_0=0.027(5)k_B (4d) is obtained.Comment: large extensions, now 12 pages, 9 figures, 27 reference

Quantum field theory of metallic spin glasses

We introduce an effective field theory for the vicinity of a zero temperature quantum transition between a metallic spin glass (``spin density glass'') and a metallic quantum paramagnet. Following a mean field analysis, we perform a perturbative renormalization-group study and find that the critical properties are dominated by static disorder-induced fluctuations, and that dynamic quantum-mechanical effects are dangerously irrelevant. A Gaussian fixed point is stable for a finite range of couplings for spatial dimensionality $d > 8$, but disorder effects always lead to runaway flows to strong coupling for $d \leq 8$. Scaling hypotheses for a {\em static\/} strong-coupling critical field theory are proposed. The non-linear susceptibility has an anomalously weak singularity at such a critical point. Although motivated by a perturbative study of metallic spin glasses, the scaling hypotheses are more general, and could apply to other quantum spin glass to paramagnet transitions.Comment: 16 pages, REVTEX 3.0, 2 postscript figures; version contains reference to related work in cond-mat/950412

Calculation of ground states of four-dimensional +or- J Ising spin glasses

Ground states of four-dimensional (d=4) EA Ising spin glasses are calculated for sizes up to 7x7x7x7 using a combination of a genetic algorithm and cluster-exact approximation. The ground-state energy of the infinite system is extrapolated as e_0=-2.095(1). The ground-state stiffness (or domain wall) energy D is calculated. A D~L^{\Theta} behavior with \Theta=0.65(4) is found which confirms that the d=4 model has an equilibrium spin-glass-paramagnet transition for non-zero T_c.Comment: 5 pages, 3 figures, 31 references, revtex; update of reference