C-terminal motif prediction in eukaryotic proteomes using comparative genomics and statistical over-representation across protein families

Abstract Background The carboxy termini of proteins are a frequent site of activity for a variety of biologically important functions, ranging from post-translational modification to protein targeting. Several short peptide motifs involved in protein sorting roles and dependent upon their proximity to the C-terminus for proper function have already been characterized. As a limited number of such motifs have been identified, the potential exists for genome-wide statistical analysis and comparative genomics to reveal novel peptide signatures functioning in a C-terminal dependent manner. We have applied a novel methodology to the prediction of C-terminal-anchored peptide motifs involving a simple z-statistic and several techniques for improving the signal-to-noise ratio. Results We examined the statistical over-representation of position-specific C-terminal tripeptides in 7 eukaryotic proteomes. Sequence randomization models and simple-sequence masking were applied to the successful reduction of background noise. Similarly, as C-terminal homology among members of large protein families may artificially inflate tripeptide counts in an irrelevant and obfuscating manner, gene-family clustering was performed prior to the analysis in order to assess tripeptide over-representation across protein families as opposed to across all proteins. Finally, comparative genomics was used to identify tripeptides significantly occurring in multiple species. This approach has been able to predict, to our knowledge, all C-terminally anchored targeting motifs present in the literature. These include the PTS1 peroxisomal targeting signal (SKL*), the ER-retention signal (K/HDEL*), the ER-retrieval signal for membrane bound proteins (KKxx*), the prenylation signal (CC*) and the CaaX box prenylation motif. In addition to a high statistical over-representation of these known motifs, a collection of significant tripeptides with a high propensity for biological function exists between species, among kingdoms and across eukaryotes. Motifs of note include a serine-acidic peptide (DSD*) as well as several lysine enriched motifs found in nearly all eukaryotic genomes examined. Conclusion We have successfully generated a high confidence representation of eukaryotic motifs anchored at the C-terminus. A high incidence of true-positives in our results suggests that several previously unidentified tripeptide patterns are strong candidates for representing novel peptide motifs of a widely employed nature in the C-terminal biology of eukaryotes. Our application of comparative genomics, statistical over-representation and the adjustment for protein family homology has generated several hypotheses concerning the C-terminal topology as it pertains to sorting and potential protein interaction signals. This approach to background reduction could be expanded for application to protein motif prediction in the protein interior. A parallel N-terminal analysis is presented as supplementary data.</p

Coherent Anti-Stokes Raman Spectroscopy (CARS) Measurements in Supersonic Combustors at NASA Langley Research Center

This paper describes the recent use of coherent anti-Stokes Raman spectroscopy (CARS) to study supersonic combustion at NASA Langley Research Center. CARS is a nonlinear optical measurement technique used to measure temperature and species mole fractions remotely in harsh environments. A CARS system has been applied to two different combustor geometries at NASA Langley. Both experiments used the same vitiated wind-tunnel facility to create an air flow that simulates flight at Mach numbers of 6 and 7 for the combustor inlet and both experiments used hydrogen fuel. In the first experiment, the hydrogen was injected supersonically at a 30-degree angle with respect to the incoming flow. In the second experiment, the hydrogen was injected sonically at normal incidence. While these injection schemes produced significantly different flow features, the CARS method provided mean temperature, N2, O2 and H2 maps at multiple downstream locations for both. The primary aim of these measurements was to provide detailed flowfield information for computational fluid dynamics (CFD) code validation

Molecular-Based Optical Diagnostics for Hypersonic Nonequilibrium Flows

This manuscript describes Molecular-Based Optical Diagnostics for Hypersonic Nonequilibrium Flows. This is a book chapter and has no formal abstract

The Mock LISA Data Challenges: from Challenge 3 to Challenge 4

The Mock LISA Data Challenges are a program to demonstrate LISA data-analysis capabilities and to encourage their development. Each round of challenges consists of one or more datasets containing simulated instrument noise and gravitational waves from sources of undisclosed parameters. Participants analyze the datasets and report best-fit solutions for the source parameters. Here we present the results of the third challenge, issued in Apr 2008, which demonstrated the positive recovery of signals from chirping Galactic binaries, from spinning supermassive--black-hole binaries (with optimal SNRs between ~ 10 and 2000), from simultaneous extreme-mass-ratio inspirals (SNRs of 10-50), from cosmic-string-cusp bursts (SNRs of 10-100), and from a relatively loud isotropic background with Omega_gw(f) ~ 10^-11, slightly below the LISA instrument noise.Comment: 12 pages, 2 figures, proceedings of the 8th Edoardo Amaldi Conference on Gravitational Waves, New York, June 21-26, 200

ACCERBATIN, a small molecule at the intersection of auxin and reactive oxygen species homeostasis with herbicidal properties

The volatile two-carbon hormone ethylene acts in concert with an array of signals to affect etiolated seedling development. From a chemical screen, we isolated a quinoline carboxamide designated ACCERBATIN (AEX) that exacerbates the 1-aminocyclopropane-1-carboxylic acid-induced triple response, typical for ethylene-treated seedlings in darkness. Phenotypic analyses revealed distinct AEX effects including inhibition of root hair development and shortening of the root meristem. Mutant analysis and reporter studies further suggested that AEX most probably acts in parallel to ethylene signaling. We demonstrated that AEX functions at the intersection of auxin metabolism and reactive oxygen species (ROS) homeostasis. AEX inhibited auxin efflux in BY-2 cells and promoted indole-3-acetic acid (IAA) oxidation in the shoot apical meristem and cotyledons of etiolated seedlings. Gene expression studies and superoxide/hydrogen peroxide staining further revealed that the disrupted auxin homeostasis was accompanied by oxidative stress. Interestingly, in light conditions, AEX exhibited properties reminiscent of the quinoline carboxylate-type auxin-like herbicides. We propose that AEX interferes with auxin transport from its major biosynthesis sites, either as a direct consequence of poor basipetal transport from the shoot meristematic region, or indirectly, through excessive IAA oxidation and ROS accumulation. Further investigation of AEX can provide new insights into the mechanisms connecting auxin and ROS homeostasis in plant development and provide useful tools to study auxin-type herbicides

Building a Field: The Future of Astronomy with Gravitational Waves

Harnessing the sheer discovery potential of GW Astronomy will require bold, deliberate,and sustained efforts to train and develop the requisite workforce. The next decaderequires a strategic plan to build - from the ground up - a robust, open, andwell-connected GW Astronomy community with deep participation from traditionalastronomers, physicists, data scientists, and instrumentalists. This basic infrastructure issorely needed as an enabling foundation for research. We outline a set ofrecommendations for funding agencies, universities, and professional societies to helpbuild a thriving, diverse, and inclusive new field

Improving and Standardizing Pediatric Asthma Care Across MaineHealth Using the Validated Hospital Asthma Severity Scoring (HASS) Tool

Objective: To assess if an inter-professional educational intervention can improve the accuracy and inter-rater reliability of the HASS.https://knowledgeconnection.mainehealth.org/lambrew-retreat-2024/1011/thumbnail.jp

Lipid metabolic perturbation is an early-onset phenotype in adult spinster mutants: a Drosophila model for lysosomal storage disorders

Intracellular accumulation of lipids and swollen dysfunctional lysosomes are linked to several neurodegenerative diseases, including lysosomal storage disorders (LSD). Detailed characterization of lipid metabolic changes in relation to the onset and progression of neurodegeneration is currently missing. We systematically analyzed lipid perturbations in spinster (spin) mutants, a Drosophila model of LSD-like neurodegeneration. Our results highlight an imbalance in brain ceramide and sphingosine in the early stages of neurodegeneration, preceding the accumulation of endomembranous structures, manifestation of altered behavior, and buildup of lipofuscin. Manipulating levels of ceramidase and altering these lipids in spin mutants allowed us to conclude that ceramide homeostasis is the driving force in disease progression and is integral to spin function in the adult nervous system. We identified 29 novel physical interaction partners of Spin and focused on the lipid carrier protein, Lipophorin (Lpp). A subset of Lpp and Spin colocalize in the brain and within organs specialized for lipid metabolism (fat bodies and oenocytes). Reduced Lpp protein was observed in spin mutant tissues. Finally, increased levels of lipid metabolites produced by oenocytes in spin mutants allude to a functional interaction between Spin and Lpp, underscoring the systemic nature of lipid perturbation in LSD

Laser Interferometer Space Antenna

Following the selection of The Gravitational Universe by ESA, and the successful flight of LISA Pathfinder, the LISA Consortium now proposes a 4 year mission in response to ESA's call for missions for L3. The observatory will be based on three arms with six active laser links, between three identical spacecraft in a triangular formation separated by 2.5 million km. LISA is an all-sky monitor and will offer a wide view of a dynamic cosmos using Gravitational Waves as new and unique messengers to unveil The Gravitational Universe. It provides the closest ever view of the infant Universe at TeV energy scales, has known sources in the form of verification binaries in the Milky Way, and can probe the entire Universe, from its smallest scales near the horizons of black holes, all the way to cosmological scales. The LISA mission will scan the entire sky as it follows behind the Earth in its orbit, obtaining both polarisations of the Gravitational Waves simultaneously, and will measure source parameters with astrophysically relevant sensitivity in a band from below $10^{-4}\,$Hz to above $10^{-1}\,$Hz.Comment: Submitted to ESA on January 13th in response to the call for missions for the L3 slot in the Cosmic Vision Programm