Genome surveyor 2.0: cis-regulatory analysis in Drosophila

Genome Surveyor 2.0 is a web-based tool for discovery and analysis of cis-regulatory elements in Drosophila, built on top of the GBrowse genome browser for convenient visualization. Genome Surveyor was developed as a tool for predicting transcription factor (TF) binding targets and cis-regulatory modules (CRMs/enhancers), based on motifs representing experimentally determined DNA binding specificities. Since its first publication, we have added substantial new functionality (e.g. phylogenetic averaging of motif scores from multiple species, and a novel CRM discovery technique), increased the number of supported motifs about 4-fold (from approximately 100 to approximately 400), added provisions for evolutionary comparison across many more Drosophila species (from 2 to 12), and improved the user-interface. The server is free and open to all users, and there is no login requirement. Address: http://veda.cs.uiuc.edu/gs

Asystole following Reintubation during Suspension Laryngoscopy

Transient increase in heart rate and mean arterial pressure commonly occur during manipulation of the airway via direct laryngoscopy. This phenomenon is understood to be due to a sympathetic nervous system reflex causing an increase in plasma catecholamines. Rarely, severe bradycardia and possible asystole can occur following laryngoscopy. One previous report described asystole during suspension laryngoscopy after uneventful direct laryngoscopy. Here we report a case of asystole occurring at the time of reinsertion and cuff inflation of an endotracheal tube in a patient who had been hemodynamically stable during initial direct laryngoscopy and the ensuing suspension laryngoscopy. The asystole was immediately recognized and successful cardiopulmonary resuscitation was performed with the patient returning to baseline sinus rhythm. Cardiac arrest following laryngoscopy is rare. This case highlights the importance of continued vigilance even after the initial manipulations of the airway by both direct laryngoscopy and suspension laryngoscopy are to be performed. Identifying patients who may benefit from premedication with a vagolytic drug may prevent adversity. Preoperative heart rate analysis can identify patients with strong vagal tone

Three Structure-Selective Endonucleases Are Essential in the Absence of BLM Helicase in Drosophila

DNA repair mechanisms in mitotically proliferating cells avoid generating crossovers, which can contribute to genome instability. Most models for the production of crossovers involve an intermediate with one or more four-stranded Holliday junctions (HJs), which are resolved into duplex molecules through cleavage by specialized endonucleases. In vitro studies have implicated three nuclear enzymes in HJ resolution: MUS81–EME1/Mms4, GEN1/Yen1, and SLX4–SLX1. The Bloom syndrome helicase, BLM, plays key roles in preventing mitotic crossover, either by blocking the formation of HJ intermediates or by removing HJs without cleavage. Saccharomyces cerevisiae mutants that lack Sgs1 (the BLM ortholog) and either Mus81–Mms4 or Slx4–Slx1 are inviable, but mutants that lack Sgs1 and Yen1 are viable. The current view is that Yen1 serves primarily as a backup to Mus81–Mms4. Previous studies with Drosophila melanogaster showed that, as in yeast, loss of both DmBLM and MUS81 or MUS312 (the ortholog of SLX4) is lethal. We have now recovered and analyzed mutations in Drosophila Gen. As in yeast, there is some redundancy between Gen and mus81; however, in contrast to the case in yeast, GEN plays a more predominant role in responding to DNA damage than MUS81–MMS4. Furthermore, loss of DmBLM and GEN leads to lethality early in development. We present a comparison of phenotypes occurring in double mutants that lack DmBLM and either MUS81, GEN, or MUS312, including chromosome instability and deficiencies in cell proliferation. Our studies of synthetic lethality provide insights into the multiple functions of DmBLM and how various endonucleases may function when DmBLM is absent

Integrating motif, DNA accessibility and gene expression data to build regulatory maps in an organism

Characterization of cell type specific regulatory networks and elements is a major challenge in genomics, and emerging strategies frequently employ high-throughput genome-wide assays of transcription factor (TF) to DNA binding, histone modifications or chromatin state. However, these experiments remain too difficult/expensive for many laboratories to apply comprehensively to their system of interest. Here, we explore the potential of elucidating regulatory systems in varied cell types using computational techniques that rely on only data of gene expression, low-resolution chromatin accessibility, and TF-DNA binding specificities (\u27motifs\u27). We show that static computational motif scans overlaid with chromatin accessibility data reasonably approximate experimentally measured TF-DNA binding. We demonstrate that predicted binding profiles and expression patterns of hundreds of TFs are sufficient to identify major regulators of approximately 200 spatiotemporal expression domains in the Drosophila embryo. We are then able to learn reliable statistical models of enhancer activity for over 70 expression domains and apply those models to annotate domain specific enhancers genome-wide. Throughout this work, we apply our motif and accessibility based approach to comprehensively characterize the regulatory network of fruitfly embryonic development and show that the accuracy of our computational method compares favorably to approaches that rely on data from many experimental assays. Acids Research

Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development

Regulation of eukaryotic gene transcription is often combinatorial in nature, with multiple transcription factors (TFs) regulating common target genes, often through direct or indirect mutual interactions. Many individual examples of cooperative binding by directly interacting TFs have been identified, but it remains unclear how pervasive this mechanism is during animal development. Cooperative TF binding should be manifest in genomic sequences as biased arrangements of TF-binding sites. Here, we explore the extent and diversity of such arrangements related to gene regulation during Drosophila embryogenesis. We used the DNA-binding specificities of 322 TFs along with chromatin accessibility information to identify enriched spacing and orientation patterns of TF-binding site pairs. We developed a new statistical approach for this task, specifically designed to accurately assess inter-site spacing biases while accounting for the phenomenon of homotypic site clustering commonly observed in developmental regulatory regions. We observed a large number of short-range distance preferences between TF-binding site pairs, including examples where the preference depends on the relative orientation of the binding sites. To test whether these binding site patterns reflect physical interactions between the corresponding TFs, we analyzed 27 TF pairs whose binding sites exhibited short distance preferences. In vitro protein-protein binding experiments revealed that \u3e65% of these TF pairs can directly interact with each other. For five pairs, we further demonstrate that they bind cooperatively to DNA if both sites are present with the preferred spacing. This study demonstrates how DNA-binding motifs can be used to produce a comprehensive map of sequence signatures for different mechanisms of combinatorial TF action

Epigenetic Telomere Protection by Drosophila DNA Damage Response Pathways

Analysis of terminal deletion chromosomes indicates that a sequence-independent mechanism regulates protection of Drosophila telomeres. Mutations in Drosophila DNA damage response genes such as atm/tefu, mre11, or rad50 disrupt telomere protection and localization of the telomere-associated proteins HP1 and HOAP, suggesting that recognition of chromosome ends contributes to telomere protection. However, the partial telomere protection phenotype of these mutations limits the ability to test if they act in the epigenetic telomere protection mechanism. We examined the roles of the Drosophila atm and atr-atrip DNA damage response pathways and the nbs homolog in DNA damage responses and telomere protection. As in other organisms, the atm and atr-atrip pathways act in parallel to promote telomere protection. Cells lacking both pathways exhibit severe defects in telomere protection and fail to localize the protection protein HOAP to telomeres. Drosophila nbs is required for both atm- and atr-dependent DNA damage responses and acts in these pathways during DNA repair. The telomere fusion phenotype of nbs is consistent with defects in each of these activities. Cells defective in both the atm and atr pathways were used to examine if DNA damage response pathways regulate telomere protection without affecting telomere specific sequences. In these cells, chromosome fusion sites retain telomere-specific sequences, demonstrating that loss of these sequences is not responsible for loss of protection. Furthermore, terminally deleted chromosomes also fuse in these cells, directly implicating DNA damage response pathways in the epigenetic protection of telomeres. We propose that recognition of chromosome ends and recruitment of HP1 and HOAP by DNA damage response proteins is essential for the epigenetic protection of Drosophila telomeres. Given the conserved roles of DNA damage response proteins in telomere function, related mechanisms may act at the telomeres of other organisms

The Two-Loop Scale Dependence of the Static QCD Potential including Quark Masses

The interaction potential V(Q^2) between static test charges can be used to define an effective charge $\alpha_V(Q^2)$ and a physically-based renormalization scheme for quantum chromodynamics and other gauge theories. In this paper we use recent results for the finite-mass fermionic corrections to the heavy-quark potential at two-loops to derive the next-to-leading order term for the Gell Mann-Low function of the V-scheme. The resulting effective number of flavors $N_F(Q^2/m^2)$ in the $\alpha_V$ scheme is determined as a gauge-independent and analytic function of the ratio of the momentum transfer to the quark pole mass. The results give automatic decoupling of heavy quarks and are independent of the renormalization procedure. Commensurate scale relations then provide the next-to-leading order connection between all perturbatively calculable observables to the analytic and gauge-invariant $\alpha_V$ scheme without any scale ambiguity and a well defined number of active flavors. The inclusion of the finite quark mass effects in the running of the coupling is compared with the standard treatment of finite quark mass effects in the $\bar{MS}$ scheme.Comment: 27 pages, 13 figure

Renormalization-Scale-Invariant PQCD Predictions for R_e+e- and the Bjorken Sum Rule at Next-to-Leading Order

We discuss application of the physical QCD effective charge $\alpha_V$, defined via the heavy-quark potential, in perturbative calculations at next-to-leading order. When coupled with the Brodsky-Lepage-Mackenzie prescription for fixing the renormalization scales, the resulting series are automatically and naturally scale and scheme independent, and represent unambiguous predictions of perturbative QCD. We consider in detail such commensurate scale relations for the $e^+e^-$ annihilation ratio $R_{e^+e^-}$ and the Bjorken sum rule. In both cases the improved predictions are in excellent agreement with experiment.Comment: 13 Latex pages with 5 figures; to be published in Physical Review

Odd C-P contributions to diffractive processes

We investigate contributions to diffractive scattering, which are odd under C- and P-parity. Comparison of p-$\bar p$ and p-p scattering indicates that these odderon contributions are very small and we show how a diquark clustering in the proton can explain this effect. A good probe for the odderon exchange is the photo- and electroproduction of pseudo-scalar mesons. We concentrate on the pi^0 and show that the quasi elastic pi^0-production is again strongly suppressed for a diquark structure of the proton whereas the cross sections for diffractive proton dissociation are larger by orders of magnitude and rather independent of the proton structure.Comment: 18 pages, LaTex2e, graphicx package, 14 eps figures include