The Morphology of the Rat Vibrissal Array: A Model for Quantifying Spatiotemporal Patterns of Whisker-Object Contact

In all sensory modalities, the data acquired by the nervous system is shaped by the biomechanics, material properties, and the morphology of the peripheral sensory organs. The rat vibrissal (whisker) system is one of the premier models in neuroscience to study the relationship between physical embodiment of the sensor array and the neural circuits underlying perception. To date, however, the three-dimensional morphology of the vibrissal array has not been characterized. Quantifying array morphology is important because it directly constrains the mechanosensory inputs that will be generated during behavior. These inputs in turn shape all subsequent neural processing in the vibrissal-trigeminal system, from the trigeminal ganglion to primary somatosensory (“barrel”) cortex. Here we develop a set of equations for the morphology of the vibrissal array that accurately describes the location of every point on every whisker to within ±5% of the whisker length. Given only a whisker's identity (row and column location within the array), the equations establish the whisker's two-dimensional (2D) shape as well as three-dimensional (3D) position and orientation. The equations were developed via parameterization of 2D and 3D scans of six rat vibrissal arrays, and the parameters were specifically chosen to be consistent with those commonly measured in behavioral studies. The final morphological model was used to simulate the contact patterns that would be generated as a rat uses its whiskers to tactually explore objects with varying curvatures. The simulations demonstrate that altering the morphology of the array changes the relationship between the sensory signals acquired and the curvature of the object. The morphology of the vibrissal array thus directly constrains the nature of the neural computations that can be associated with extraction of a particular object feature. These results illustrate the key role that the physical embodiment of the sensor array plays in the sensing process

Predikin and PredikinDB: a computational framework for the prediction of protein kinase peptide specificity and an associated database of phosphorylation sites

Background: We have previously described an approach to predicting the substrate specificity of serine-threonine protein kinases. The method, named Predikin, identifies key conserved substrate-determining residues in the kinase catalytic domain that contact the substrate in the region of the phosphorylation site and so determine the sequence surrounding the phosphorylation site. Predikin was implemented originally as a web application written in Javascript

Observation of an Excited Bc+ State

Using pp collision data corresponding to an integrated luminosity of 8.5 fb-1 recorded by the LHCb experiment at center-of-mass energies of s=7, 8, and 13 TeV, the observation of an excited Bc+ state in the Bc+π+π- invariant-mass spectrum is reported. The observed peak has a mass of 6841.2±0.6(stat)±0.1(syst)±0.8(Bc+) MeV/c2, where the last uncertainty is due to the limited knowledge of the Bc+ mass. It is consistent with expectations of the Bc∗(2S31)+ state reconstructed without the low-energy photon from the Bc∗(1S31)+→Bc+γ decay following Bc∗(2S31)+→Bc∗(1S31)+π+π-. A second state is seen with a global (local) statistical significance of 2.2σ (3.2σ) and a mass of 6872.1±1.3(stat)±0.1(syst)±0.8(Bc+) MeV/c2, and is consistent with the Bc(2S10)+ state. These mass measurements are the most precise to date

Functional Analysis of the Kinome of the Wheat Scab Fungus Fusarium graminearum

As in other eukaryotes, protein kinases play major regulatory roles in filamentous fungi. Although the genomes of many plant pathogenic fungi have been sequenced, systematic characterization of their kinomes has not been reported. The wheat scab fungus Fusarium graminearum has 116 protein kinases (PK) genes. Although twenty of them appeared to be essential, we generated deletion mutants for the other 96 PK genes, including 12 orthologs of essential genes in yeast. All of the PK mutants were assayed for changes in 17 phenotypes, including growth, conidiation, pathogenesis, stress responses, and sexual reproduction. Overall, deletion of 64 PK genes resulted in at least one of the phenotypes examined, including three mutants blocked in conidiation and five mutants with increased tolerance to hyperosmotic stress. In total, 42 PK mutants were significantly reduced in virulence or non-pathogenic, including mutants deleted of key components of the cAMP signaling and three MAPK pathways. A number of these PK genes, including Fg03146 and Fg04770 that are unique to filamentous fungi, are dispensable for hyphal growth and likely encode novel fungal virulence factors. Ascospores play a critical role in the initiation of wheat scab. Twenty-six PK mutants were blocked in perithecia formation or aborted in ascosporogenesis. Additional 19 mutants were defective in ascospore release or morphology. Interestingly, F. graminearum contains two aurora kinase genes with distinct functions, which has not been reported in fungi. In addition, we used the interlog approach to predict the PK-PK and PK-protein interaction networks of F. graminearum. Several predicted interactions were verified with yeast two-hybrid or co-immunoprecipitation assays. To our knowledge, this is the first functional characterization of the kinome in plant pathogenic fungi. Protein kinase genes important for various aspects of growth, developmental, and infection processes in F. graminearum were identified in this study

Observation of CP Violation in Charm Decays

A search for charge-parity (CP) violation in D-0 -> K-K+ and D-0 -> pi(-)pi(+) decays is reported, using pp collision data corresponding to an integrated luminosity of 5.9 fb(-1) collected at a center-of-mass energy of 13 TeV with the LHCb detector. The flavor of the charm meson is inferred from the charge of the pion in D* (2010)(+) -> D-0 pi(+) decays or from the charge of the muon in (B) over bar -> D-0 mu(-)(nu) over bar X-mu decays. The difference between the CP asymmetries in D-0 -> K-K+ and D-0 -> pi(-)pi(+) decays is measured to be Delta A(CP) = [-18.2 +/- 3.2(stat) +/- 0.9(syst)] x 10(-4) for pi-tagged and Delta A(CP) = [-9 +/- 8(stat) +/- 5(syst)] x 10(-4) for mu-tagged D-0 mesons. Combining these with previous LHCb results leads to Delta A(CP) = (-15.4 +/- 2.9) x 10(-4), where the uncertainty includes both statistical and systematic contributions. The measured value differs from zero by more than 5 standard deviations. This is the first observation of CP violation in the decay of charm hadrons

Observation of a narrow pentaquark state, P-c(4312)(+), and of the two-peak structure of the P-c(4450)(+)

A narrow pentaquark state, P-c(4312)(+), decaying to J/psi p, is discovered with a statistical significance of 7.3 sigma in a data sample of Lambda(0)(b) -> J/psi pK(-) decays, which is an order of magnitude larger than that previously analyzed by the LHCb Collaboration. The P-c(4450)(+) pentaquark structure formerly reported by LHCb is confirmed and observed to consist of two narrow overlapping peaks, P-c(4440)(+) and P-c(4457)(+), where the statistical significance of this two-peak interpretation is 5.4 sigma. The proximity of the Sigma(+)(c)(D) over bar (0) and Sigma(+)(c)(D) over bar (*0) thresholds to the observed narrow peaks suggests that they play an important role in the dynamics of these states

Observation of an Excited Bc⁺ state

Using p p collision data corresponding to an integrated luminosity of 8.5     fb − 1 recorded by the LHCb experiment at center-of-mass energies of √ s = 7 , 8, and 13 TeV, the observation of an excited B + c state in the B + c π + π − invariant-mass spectrum is reported. The observed peak has a mass of 6841.2 ± 0.6 ( stat ) ± 0.1 ( syst ) ± 0.8 ( B + c )     MeV / c 2 , where the last uncertainty is due to the limited knowledge of the B + c mass. It is consistent with expectations of the B ∗ c ( 2 3 S 1 ) + state reconstructed without the low-energy photon from the B ∗ c ( 1 3 S 1 ) + → B + c γ decay following B ∗ c ( 2 3 S 1 ) + → B ∗ c ( 1 3 S 1 ) + π + π − . A second state is seen with a global (local) statistical significance of 2.2 σ ( 3.2 σ ) and a mass of 6872.1 ± 1.3 ( stat ) ± 0.1 ( syst ) ± 0.8 ( B + c )     MeV / c 2 , and is consistent with the B c ( 2 1 S 0 ) + state. These mass measurements are the most precise to date

Observation of the doubly charmed baryon decay Ξcc++→Ξc′+π+

The Ξcc++→Ξc′+π+ decay is observed using proton-proton collisions collected by the LHCb experiment at a centre-of-mass energy of 13 TeV, corresponding to an integrated luminosity of 5.4 fb−1. The Ξcc++→Ξc′+π+ decay is reconstructed partially, where the photon from the Ξc′+→Ξc+γ decay is not reconstructed and the pK−π+ final state of the Ξc+ baryon is employed. The Ξcc++→Ξc′+π+branching fraction relative to that of the Ξcc++→Ξc+π+ decay is measured to be 1.41 ± 0.17 ± 0.10, where the first uncertainty is statistical and the second systematic. [Figure not available: see fulltext.