julilili42/papers huggingface dataset:
Comparison of gene activation by two TAL effectors from X anthomonas axonopodis pv. manihotis reveals candidate host susceptibility genes in cassava
2015-11-17

Summary Xanthomonas axonopodis pv. manihotis ( Xam ) employs transcription activator‐like (TAL) effectors to promote bacterial growth and symptom formation during infection of cassava. TAL effectors are secreted via the bacterial type III secretion system into plant cells, where they are directed to the nucleus, bind DNA in plant promoters and activate the expression of downstream genes. The DNA‐binding activity of TAL effectors is carried out by a central domain which contains a series of repeat variable diresidues (RVDs) that dictate the sequence of bound nucleotides. TAL14 Xam668 promotes virulence in Xam strain Xam668 and has been shown to activate multiple cassava genes. In this study, we used RNA sequencing to identify the full target repertoire of TAL14 Xam668 in cassava, which includes over 50 genes. A subset of highly up‐regulated genes was tested for activation by TAL14 CIO151 from Xam strain CIO151. Although TAL14 CIO151 and TAL14 Xam668 differ by only a single RVD, they display differential activation of gene targets. TAL14 CIO151 complements the TAL14 Xam668 mutant defect, implying that shared target genes are important for TAL14 Xam668 ‐mediated disease susceptibility. Complementation with closely related TAL effectors is a novel approach to the narrowing down of biologically relevant susceptibility genes of TAL effectors with multiple targets. This study provides an example of how TAL effector target activation by two strains within a single species of Xanthomonas can be dramatically affected by a small change in RVD–nucleotide affinity at a single site, and reflects the parameters of RVD–nucleotide interaction determined using designer TAL effectors in transient systems.
Kinesin Kip2 enhances microtubule growth in vitro through length-dependent feedback on polymerization and catastrophe
2015-11-18

The size and position of mitotic spindles is determined by the lengths of their constituent microtubules. Regulation of microtubule length requires feedback to set the balance between growth and shrinkage. Whereas negative feedback mechanisms for microtubule length control, based on depolymerizing kinesins and severing proteins, have been studied extensively, positive feedback mechanisms are not known. Here, we report that the budding yeast kinesin Kip2 is a microtubule polymerase and catastrophe inhibitor in vitro that uses its processive motor activity as part of a feedback loop to further promote microtubule growth. Positive feedback arises because longer microtubules bind more motors, which walk to the ends where they reinforce growth and inhibit catastrophe. We propose that positive feedback, common in biochemical pathways to switch between signaling states, can also be used in a mechanical signaling pathway to switch between structural states, in this case between short and long polymers.
Ontogenetic Tooth Reduction in Stenopterygius quadriscissus (Reptilia: Ichthyosauria): Negative Allometry, Changes in Growth Rate, and Early Senescence of the Dental Lamina
2015-11-18

We explore the functional, developmental, and evolutionary processes which are argued to produce tooth reduction in the extinct marine reptile Stenopterygius quadriscissus (Reptilia: Ichthyosauria). We analyze the relationship between mandible growth and tooth size, shape, and count, to establish an ontogenetic trend. The pattern in S. quadriscissus is consistent with hypotheses of tooth size reduction by neutral selection, and this unusual morphology (a functionally edentulous rostrum) was produced by a series of different evolutionary developmental changes that are known for other taxa showing tooth reduction and loss. Specifically, this species evolved functional edentulism by evolutionary changes in the growth allometry of the dentition and by altering growth rates through ontogeny. This observation supports previous hypotheses that S. quadriscissus underwent ontogenetic tooth reduction. Tooth reduction in S. quadriscissus may be caused by unique selective pressures resulting from prey choice and feeding behavior, expanding our current understanding of the mechanisms producing tooth reduction.
High-velocity gas toward the LMC resides in the Milky Way\\n halo
2015-11-18

\\n Aims. To explore the origin of high-velocity gas in the direction of the\\n Large Magellanic Cloud, (LMC) we analyze absorption lines in the ultraviolet spectrum of a\\n Galactic halo star that is located in front of the LMC at d =\\n 9.2+4.1-7.2 \\n kpc distance. \\n Methods. We study the velocity-component structure of low and\\n intermediate metal ions (C <sc>ii</sc>, Si <sc>ii</sc>, Si <sc>iii</sc>) in the spectrum\\n of RX J0439.8−6809, as\\n obtained with the Cosmic Origins Spectrograph (COS) onboard the Hubble\\n Space Telescope (HST), and measure equivalent widths and column densities for\\n these ions. We supplement our COS data with a Far-Ultraviolet Spectroscopic Explorer\\n (FUSE) spectrum of the nearby LMC star Sk −69 59 and with H <sc>i </sc>21 cm data from the Leiden-Argentina-Bonn\\n (LAB) survey. \\n Results. Metal absorption toward RX J0439.8−6809 is unambiguously detected in three\\n different velocity components near vLSR = 0, + 60, and + 150 km s-1. The presence of absorption\\n proves that all three gas components are situated in front of the star, thus located in\\n the disk and inner halo of the Milky Way. For the high-velocity cloud (HVC) at\\n vLSR = +\\n 150 km s-1, we derive an oxygen abundance of [O/H] =−0.63 (~0.2 solar) from the neighboring\\n Sk −69 59 sight line, in\\n accordance with previous abundance measurements for this HVC. From the observed kinematics\\n we infer that the HVC hardly participates in the Galactic rotation. \\n Conclusions. Our study shows that the HVC toward the LMC represents a\\n Milky Way halo cloud that traces low column density gas with relatively low metallicity.\\n We rule out scenarios in which the HVC represents material close to the LMC that stems\\n from a LMC outflow. \\n
Generalization of the Van Cittert–Zernike theorem: observers moving with respect to sources
2015-11-18

The use of the Van Cittert--Zernike theorem for the formulation of the\\nvisibility function in satellite-based Earth observation with passive\\nradiometers does not take into account the relative motion of the observer (the\\nsatellite antenna) with respect to sources of the electro-magnetic fields at\\nthe surface of the Earth. The motion of the observer leads on the one hand to a\\nmore complex signal due to a pixel-dependent Doppler shift that is neglected in\\nthe standard derivation of the Van Cittert--Zernike theorem, but on the other\\nhand one may hope that it could be employed for a temporal aperture synthesis,\\nwhere virtual baselines are created through the motion of the satellite. Here,\\nwe generalize the formulation of the aperture synthesis concept to the case of\\nobservers moving with respect to the sources, and to the correlation of fields\\nmeasured at times that differ by the travel time of the observer along a\\nvirtual baseline. Our derivation is based on first principles, starting with\\nthe wave propagation in the Earth reference frame of electro-magnetic fields\\narising from incoherent current sources, and Lorentz transforming the fields\\ninto the reference frame of the satellite. Our detailed study leads to the\\nremarkable conclusion that the delay time due to observer motion cancels\\nexactly the Doppler effect. This justifies the neglect of the Doppler effect in\\nexisting imaging systems based on the standard Van Cittert--Zernike theorem.\\n
Retraction for Hantke et al., Escherichia coli Exports Cyclic AMP via TolC
2015-11-18

Volume 193, no. 5, p. [1086–1089][1], 2011. We were informed by Kevin Young and Gang Li (Microbiology 160: 2079–2088, 2014) that strain H41 is not a tolC mutant as we had described. We have sequenced strain H41 and confirm that it is not a tolC mutant. Rather, the observed phenotype is due to a
Hypergroups Related to a Pair of Compact Hypergroups
2015-11-18

The purpose of the present paper is to investigate a hypergroup associated with irreducible characters of a compact hypergroup H and a closed subhypergroup H0 of H with |H/H0|&lt;+∞. The convolution of this hypergroup is introduced by inducing irreducible characters of H0 to H and by restricting irreducible characters of H to H0. The method of proof relies on the notion of an induced character and an admissible hypergroup pair.
Platelet-derived CXCL12 regulates monocyte function, survival, differentiation into macrophages and foam cells through differential involvement of CXCR4–CXCR7
2015-11-19

Abstract Platelets store and release CXCL12 (SDF-1), which governs differentiation of hematopoietic progenitors into either endothelial or macrophage-foam cells. CXCL12 ligates CXCR4 and CXCR7 and regulates monocyte/macrophage functions. This study deciphers the relative contribution of CXCR4–CXCR7 in mediating the effects of platelet-derived CXCL12 on monocyte function, survival, and differentiation. CXCL12 and macrophage migration inhibitory factor (MIF) that ligate CXCR4–CXCR7 induced a dynamic bidirectional trafficking of the receptors, causing CXCR4 internalization and CXCR7 externalization during chemotaxis, thereby influencing relative receptor availability, unlike MCP-1. In vivo we found enhanced accumulation of platelets and platelet-macrophage co-aggregates in peritoneal fluid following induction of peritonitis in mice. The relative surface expression of CXCL12, CXCR4, and CXCR7 among infiltrated monocytes was also enhanced as compared with peripheral blood. Platelet-derived CXCL12 from collagen-adherent platelets and recombinant CXCL12 induced monocyte chemotaxis specifically through CXCR4 engagement. Adhesion of monocytes to immobilized CXCL12 and CXCL12-enriched activated platelet surface under static and dynamic arterial flow conditions were mediated primarily through CXCR7 and were counter-regulated by neutralizing platelet-derived CXCL12. Monocytes and culture-derived-M1–M2 macrophages phagocytosed platelets, with the phagocytic potential of culture-derived-M1 macrophages higher than M2 involving CXCR4–CXCR7 participation. CXCR7 was the primary receptor in promoting monocyte survival as exerted by platelet-derived CXCL12 against BH3-mimetic induced apoptosis (phosphatidylserine exposure, caspase-3 activation, loss of mitochondrial transmembrane potential). In co-culture experiments with platelets, monocytes predominantly differentiated into CD163 + macrophages, which was attenuated upon CXCL12 neutralization and CXCR4/CXCR7 blocking antibodies. Moreover, OxLDL uptake by platelets induced platelet apoptosis, like other platelet agonists TRAP and collagen-related peptide (CRP). CXCL12 facilitated phagocytosis of apoptotic platelets by monocytes and M1–M2 macrophages, also promoted their differentiation into foam cells via CXCR4 and CXCR7. Thus, platelet-derived CXCL12 could regulate monocyte-macrophage functions through differential engagement of CXCR4 and CXCR7, indicating an important role in inflammation at site of platelet accumulation.
Tracking potential source areas of Central European loess:examples from Tokaj (HU), Nussloch (D) and Grub (AT)
2015-11-19

Abstract There are several competing hypotheses for theorigin of loess in Europe but quantitative evidence is stillrare. Here, Sr-Nd isotopic and bulk elemental compositionof loess from Marine Isotope Stages 2 and 3 fromthree study regions in Central Europe – Nussloch (Germany),Grub (Austria) and Tokaj (Hungary) - are analyzed.This study aims at examining differences and similaritiesof loess deposits throughout Europe, correlating loesswith potential source rocks from major mountain rangesand comparing loess with floodplain sediments from mainrivers as integrated samples of the drainage areas. The resultsshow that European loess deposits are largely uniformand that sediment sources have been rather stablein the Southern and Eastern parts of Central Europeand more variable in West Central Europe. However, themethods used are not sufficient to unequivocally confirmand reject potential sediment sources but, in combination,help to identify the most likely sediment origins. While adirect correlation of loess and potential source rocks is dif-ficult, the comparison with floodplain sediments is mostpromising and confirms previous hypotheses. Loess fromTokaj and Grub is most likely a mix of material transportedby the Danube River and sediments from the surroundingmountains. Rhine River sediments are probably the mainsource of loess at Nussloch.
The ASYMMETRIC LEAVES Complex Employs Multiple Modes of Regulation to Affect Adaxial-Abaxial Patterning and Leaf Complexity
2015-11-20

Abstract Flattened leaf architecture is not a default state but depends on positional information to precisely coordinate patterns of cell division in the growing primordium. This information is provided, in part, by the boundary between the adaxial (top) and abaxial (bottom) domains of the leaf, which are specified via an intricate gene regulatory network whose precise circuitry remains poorly defined. Here, we examined the contribution of the ASYMMETRIC LEAVES (AS) pathway to adaxial-abaxial patterning in Arabidopsis thaliana and demonstrate that AS1-AS2 affects this process via multiple, distinct regulatory mechanisms. AS1-AS2 uses Polycomb-dependent and -independent mechanisms to directly repress the abaxial determinants MIR166A, YABBY5, and AUXIN RESPONSE FACTOR3 (ARF3), as well as a nonrepressive mechanism in the regulation of the adaxial determinant TAS3A. These regulatory interactions, together with data from prior studies, lead to a model in which the sequential polarization of determinants, including AS1-AS2, explains the establishment and maintenance of adaxial-abaxial leaf polarity. Moreover, our analyses show that the shared repression of ARF3 by the AS and trans-acting small interfering RNA (ta-siRNA) pathways intersects with additional AS1-AS2 targets to affect multiple nodes in leaf development, impacting polarity as well as leaf complexity. These data illustrate the surprisingly multifaceted contribution of AS1-AS2 to leaf development showing that, in conjunction with the ta-siRNA pathway, AS1-AS2 keeps the Arabidopsis leaf both flat and simple.
Submicron-Scale Heterogeneities in Nickel Sorption of Various Cell–Mineral Aggregates Formed by Fe(II)-Oxidizing Bacteria
2015-11-20

Fe(II)-oxidizing bacteria form biogenic cell-mineral aggregates (CMAs) composed of microbial cells, extracellular organic compounds, and ferric iron minerals. CMAs are capable of immobilizing large quantities of heavy metals, such as nickel, via sorption processes. CMAs play an important role for the fate of heavy metals in the environment, particularly in systems characterized by elevated concentrations of dissolved metals, such as mine drainage or contaminated sediments. We applied scanning transmission (soft) X-ray microscopy (STXM) spectrotomography for detailed 3D chemical mapping of nickel sorbed to CMAs on the submicron scale. We analyzed different CMAs produced by phototrophic or nitrate-reducing microbial Fe(II) oxidation and, in addition, a twisted stalk structure obtained from an environmental biofilm. Nickel showed a heterogeneous distribution and was found to be preferentially sorbed to biogenically precipitated iron minerals such as Fe(III)-(oxyhydr)oxides and, to a minor extent, associated with organic compounds. Some distinct nickel accumulations were identified on the surfaces of CMAs. Additional information obtained from scatter plots and angular distance maps, showing variations in the nickel-iron and nickel-organic carbon ratios, also revealed a general correlation between nickel and iron. Although a high correlation between nickel and iron was observed in 2D maps, 3D maps revealed this to be partly due to projection artifacts. In summary, by combining different approaches for data analysis, we unambiguously showed the heterogeneous sorption behavior of nickel to CMAs.
Whisking Control by Motor Cortex
2015-11-21

The rodent whiskers (the so-called vibrissae) are an active scanning sensorimotor system with major perceptual functions. Apart from tactile perception, the whisker motor system also has important contributions to the animals' navigation and orientation capabilities. The whisker motor system is highly modular with circuits processing basic motor commands, rhythmic whisking, and modulating the motor actions using information from incoming tactile signals. The vibrissaVibrissa l primary motor cortex (vM1) reflects these functional divisions by displaying a distinct set of sub-areas with different functions. Like the primate fingertip system, vM1 displays direct cortico-motoneurons (CM) cells, in principle compatible with the notion that vM1 is involved in directly computing patterns of muscle activity. There is strong evidence, however, that vM1 action on the muscles is rather indirect with important brainstem premotor networks bearing the responsibility of computing muscle activity patterns. The connectivity of the different vM1 modules to central pattern generators (CPGs), generating the basic rhythmic movement patterns and the trigeminal brainstem loop (TBL), the brainstem sensorimotor reflex arc, representing the lowest hierarchy of sensorimotor interactions, are being unearthed by current investigations.
Gravitational wave afterglow in binary neutron star mergers
2015-11-23

We study in detail the f-mode secular instability for rapidly rotating\\nneutron stars, putting emphasis on supermassive models which do not have a\\nstable nonrotating counterpart. Such neutron stars are thought to be the\\ngeneric outcome of the merger of two standard mass neutron stars. In addition\\nwe take into account the effects of strong magnetic field and r-mode\\ninstability, that can drain a substantial amount of angular momentum. We find\\nthat the gravitational wave signal emitted by supramassive neutron stars can\\nreach above the Advance LIGO sensitivity at distance of about 20Mpc and the\\ndetectability is substantially enhanced for the Einstein Telescope. The event\\nrate will be of the same order as the merging rates, while the analysis of the\\nsignal will carry information for the equation of state of the post-merging\\nneutron stars and the strength of the magnetic fields.\\n
Site-Directed RNA Editing in Vivo Can Be Triggered by the Light-Driven Assembly of an Artificial Riboprotein
2015-11-23

Site-directed RNA editing allows for the manipulation of RNA and protein function by reprogramming genetic information at the RNA level. For this we assemble artificial RNA-guided editases and demonstrate their transcript repair activity in cells and in developing embryos of the annelid Platynereis dumerilii. A hallmark of our assembly strategy is the covalent attachment of guideRNA and editing enzyme by applying the SNAP-tag technology, a process that we demonstrate here to be readily triggered by light in vitro, in mammalian cell culture, and also in P. dumerilii. Lacking both sophisticated chemistry and extensive genetic engineering, this technology provides a convenient route for the light-dependent switching of protein isoforms. The presented strategy may also serve as a blue-print for the engineering of addressable machineries that apply tailored nucleic acid analogues to manipulate RNA or DNA site-specifically in living organisms.
Associative learning rapidly establishes neuronal representations of upcoming behavioral choices in crows
2015-11-23

Significance Corvid songbirds show remarkable cognitive abilities. The executive brain area nidopallium caudolaterale (NCL) is thought to mediate flexible behavior and cognition in birds, similar to the independently evolved prefrontal cortex in mammals. Here, we show that NCL neurons in crows change their responses during associative learning tasks to signal which stimuli belong together. NCL activity mapped distinct visual stimuli to a common associated response by grouping them according to their meaning. During association learning, such goal-oriented prospective representations are rapidly established within minutes of encountering previously unknown stimuli. By enabling a common, behaviorally meaningful code for both novel and highly familiar stimuli based on their required responses, NCL neuronal activity is ideally suited for executive control of flexible, goal-driven behavior.
Sequential modulation of backward crosstalk and task-shielding in dual-tasking.
2015-11-23

In dual-task studies, Task 1 performance is often improved when Task 2 requires a spatially compatible response (i.e., 1 on the same side)-the backward crosstalk effect (BCE). This BCE is taken as evidence that at least some of the tasks' central processing related to response selection occurs in parallel, and the size of the BCE has been interpreted as an index of how well Task 1 is shielded against influences from the concurrent Task 2 processing. In 3 experiments, it is investigated whether the compatibility status of the previous trial influences the BCE similar to the Gratton effect observed for conflict tasks. In all experiments, the BCE was large after a compatible trial but absent (or reversed) after an incompatible trial, thus a Gratton-like sequential modulation of the BCE. This result suggests rapid bottom-up adjustments as a consequence of just-experienced incompatibility of responses. One explanation is that the degree of allowed parallel processing during Task 1 response selection is adjusted according to recent experience.
Mass-Spectrometry-Based Proteomics Reveals Organ-Specific Expression Patterns To Be Used as Forensic Evidence
2015-11-23

Standard forensic procedures to examine bullets after an exchange of fire include a mechanical or ballistic reconstruction of the event. While this is routine to identify which projectile hit a subject by DNA analysis of biological material on the surface of the projectile, it is rather difficult to determine which projectile caused the lethal injury--often the crucial point with regard to legal proceedings. With respect to fundamental law it is the duty of the public authority to make every endeavor to solve every homicide case. To improve forensic examinations, we present a forensic proteomic method to investigate biological material from a projectile's surface and determine the tissues traversed by it. To obtain a range of relevant samples, different major bovine organs were penetrated with projectiles experimentally. After tryptic "on-surface" digestion, mass-spectrometry-based proteome analysis, and statistical data analysis, we were able to achieve a cross-validated organ classification accuracy of >99%. Different types of anticipated external variables exhibited no prominent influence on the findings. In addition, shooting experiments were performed to validate the results. Finally, we show that these concepts could be applied to a real case of murder to substantially improve the forensic reconstruction.