Unravelling an Extra Neutral Gauge Boson at the LHC using Third Generation Fermions

We study the potential to use measurements of extra neutral gauge bosons (Z') properties in pp collisions at the Large Hadron Collider to unravel the underlying physics. We focus on the usefulness of third generation final states (tau, b, t) in distinguishing between models with non-universal Z'-fermion couplings. We present an update of discovery limits of Z's including the 2010-2011 LHC run and include models with non-universal couplings. We show how ratios of sigma(pp -> Z' -> ttbar), sigma(pp -> Z' -> bbbar), and sigma(pp -> Z' -> tau^+tau^-) to sigma(pp -> Z' -> mu^+mu^-) can be used to distinguish between models and measure parameters of the models. Of specific interest are models with preferential couplings, such as models with generation dependent couplings. We also find that forward-backward asymmetry measurements with third generation fermions in the final state could provide important input to understanding the nature of the Z'. Understanding detector resolution and efficiencies will be crucial for extracting results

Using Final State Pseudorapidities to Improve s-channel Resonance Observables at the LHC

We study the use of final state particle pseudorapidity for measurements of s-channel resonances at the LHC. Distinguishing the spin of an s-channel resonance can, in principle, be accomplished using angular distributions in the centre-of-mass frame, possibly using a centre-edge asymmetry measurement, A_CE. In addition, forward-backward asymmetry measurements, A_FB, can be used to distinguish between models of extra neutral gauge bosons. In this note we show how these measurements can be improved by using simple methods based on the pseudorapidity of the final state particles and present the expected results for A_FB and A_CE for several representative models.Comment: 6 pages, 4 figures, 1 table; typos fixed, improved visibility of figures for greyscale printin

General and Specific Promotion of Flagellar Assembly by a Flagellar Nucleoside Diphosphate Kinase

Nucleoside diphosphate kinases (NDKs) play a central role in diverse cellular processes using the canonical NDK activity or alternative mechanisms that remain poorly defined. Our study of dimeric NDK5 in a flagellar motility control complex, the radial spoke (RS), has revealed new modalities. The flagella in Chlamydomonas ndk5 mutant were paralyzed, albeit only deficient in three RS subunits. RS morphology appeared severely changed in averaged cryo-electron tomograms, suggesting that NDK5 is crucial for the intact spokehead formation as well as RS structural stability. Intriguingly, ndk5’s flagella were also short, resembling those of an allelic spoke-less mutant. All ndk5’s phenotypes were rescued by expressions of NDK5 or a mutated NDK5 lacking the canonical kinase activity. Importantly, the mutated NDK5 that appeared fully functional in ndk5 cells elicited a dominant-negative effect in wild-type cells, causing paralyzed short flagella with hypophosphorylated, less abundant, but intact RSs, and accumulated hypophosphorylated NDK5 in the cell body. We propose that NDK5 dimer is an RS structural subunit with an additional mechanism that uses cross-talk between the two NDK monomers to accelerate phosphorylation-related assembly of RSs and entire flagella

Constraining Extra Neutral Gauge Bosons with Atomic Parity Violation Measurements

The discovery of a new neutral gauge boson, $Z'$, could provide the first concrete evidence of physics beyond the standard model. We explore how nuclear weak charge measurements in atomic parity violation (APV) experiments can be used to constrain $Z'$ bosons. We use the recent measurement of the $^{133}$Cs nuclear weak charge to estimate lower bounds on the mass of $Z'$ bosons for a number of representative models and to put constraints on the couplings of a newly discovered $Z'$ boson. We also consider how these constraints might be improved by future APV experiments that will measure nuclear weak charges of multiple isotopes. We show how measurements of a single isotope, and combining measurements into ratios and differences, can be used to constrain the couplings of a $Z'$ and discriminate between models. We find that current and future APV experiments could potentially play an important role in unravelling new physics if a $Z'$ were discovered.Comment: 7 pages, 1 figure, Revised versio

Radial Spoke Proteins of \u3cem\u3eChlamydomonas\u3c/em\u3e Flagella

The radial spoke is a ubiquitous component of `9+2\u27 cilia and flagella, and plays an essential role in the control of dynein arm activity by relaying signals from the central pair of microtubules to the arms. The Chlamydomonas reinhardtii radial spoke contains at least 23 proteins, only 8 of which have been characterized at the molecular level. Here, we use mass spectrometry to identify 10 additional radial spoke proteins. Many of the newly identified proteins in the spoke stalk are predicted to contain domains associated with signal transduction, including Ca2+-, AKAP- and nucleotide-binding domains. This suggests that the spoke stalk is both a scaffold for signaling molecules and itself a transducer of signals. Moreover, in addition to the recently described HSP40 family member, a second spoke stalk protein is predicted to be a molecular chaperone, implying that there is a sophisticated mechanism for the assembly of this large complex. Among the 18 spoke proteins identified to date, at least 12 have apparent homologs in humans, indicating that the radial spoke has been conserved throughout evolution. The human genes encoding these proteins are candidates for causing primary ciliary dyskinesia, a severe inherited disease involving missing or defective axonemal structures, including the radial spokes

The role of transposable element clusters in genome evolution and loss of synteny in the rice blast fungus Magnaporthe oryzae

BACKGROUND: Transposable elements are abundant in the genomes of many filamentous fungi, and have been implicated as major contributors to genome rearrangements and as sources of genetic variation. Analyses of fungal genomes have also revealed that transposable elements are largely confined to distinct clusters within the genome. Their impact on fungal genome evolution is not well understood. Using the recently available genome sequence of the plant pathogenic fungus Magnaporthe oryzae, combined with additional bacterial artificial chromosome clone sequences, we performed a detailed analysis of the distribution of transposable elements, syntenic blocks, and other features of chromosome 7. RESULTS: We found significant levels of conserved synteny between chromosome 7 and the genomes of other filamentous fungi, despite more than 200 million years of divergent evolution. Transposable elements are largely restricted to three clusters located in chromosomal segments that lack conserved synteny. In contradiction to popular evolutionary models and observations from other model organism genomes, we found a positive correlation between recombination rate and the distribution of transposable element clusters on chromosome 7. In addition, the transposable element clusters are marked by more frequent gene duplications, and genes within the clusters have greater sequence diversity to orthologous genes from other fungi. CONCLUSION: Together, these data suggest that transposable elements have a profound impact on the M. oryzae genome by creating localized segments with increased rates of chromosomal rearrangements, gene duplications and gene evolution

Alkahest NuclearBLAST : a user-friendly BLAST management and analysis system

BACKGROUND -: Sequencing of EST and BAC end datasets is no longer limited to large research groups. Drops in per-base pricing have made high throughput sequencing accessible to individual investigators. However, there are few options available which provide a free and user-friendly solution to the BLAST result storage and data mining needs of biologists. RESULTS -: Here we describe NuclearBLAST, a batch BLAST analysis, storage and management system designed for the biologist. It is a wrapper for NCBI BLAST which provides a user-friendly web interface which includes a request wizard and the ability to view and mine the results. All BLAST results are stored in a MySQL database which allows for more advanced data-mining through supplied command-line utilities or direct database access. NuclearBLAST can be installed on a single machine or clustered amongst a number of machines to improve analysis throughput. NuclearBLAST provides a platform which eases data-mining of multiple BLAST results. With the supplied scripts, the program can export data into a spreadsheet-friendly format, automatically assign Gene Ontology terms to sequences and provide bi-directional best hits between two datasets. Users with SQL experience can use the database to ask even more complex questions and extract any subset of data they require. CONCLUSION -: This tool provides a user-friendly interface for requesting, viewing and mining of BLAST results which makes the management and data-mining of large sets of BLAST analyses tractable to biologists

Non-invasive vagus nerve stimulation for primary headache: A clinical update.

Background Non-invasive vagus nerve stimulation (nVNS) is a proven treatment for cluster headache and migraine. Several possible mechanisms of action by which nVNS mitigates headache have been identified. Methods We conducted a narrative review of recent scientific and clinical research into nVNS for headache, including findings from mechanistic studies and their possible relationships to the clinical effects of nVNS. Results Findings from animal and human studies have provided possible mechanistic explanations for nVNS efficacy in headache involving four core areas: Autonomic nervous system functions; cortical spreading depression inhibition; neurotransmitter regulation; and nociceptive modulation. We discuss how overlap and interplay among these areas may underlie the utility of nVNS in the context of clinical evidence supporting its safety and efficacy as acute and preventive therapy for both cluster headache and migraine. Possible future nVNS applications are also discussed. Conclusion Significant progress over the past several years has yielded valuable mechanistic and clinical evidence that, combined with the excellent safety and tolerability profile of nVNS, suggests that it should be considered a first-line treatment for both acute and preventive treatment of cluster headache, an effective option for acute treatment of migraine, and a highly relevant, practical option for migraine prevention