MaizeGDB becomes ‘sequence-centric’

MaizeGDB is the maize research community’s central repository for genetic and genomic information about the crop plant and research model Zea mays ssp. mays. The MaizeGDB team endeavors to meet research needs as they evolve based on researcher feedback and guidance. Recent work has focused on better integrating existing data with sequence information as it becomes available for the B73, Mo17 and Palomero Toluqueño genomes. Major endeavors along these lines include the implementation of a genome browser to graphically represent genome sequences; implementation of POPcorn, a portal ancillary to MaizeGDB that offers access to independent maize projects and will allow BLAST similarity searches of participating projects’ data sets from a single point; and a joint MaizeGDB/PlantGDB project to involve the maize community in genome annotation. In addition to summarizing recent achievements and future plans, this article also discusses specific examples of community involvement in setting priorities and design aspects of MaizeGDB, which should be of interest to other database and resource providers seeking to better engage their users. MaizeGDB is accessible online at http://www.maizegdb.org

Multisensory information facilitates reaction speed by enlarging activity difference between superior colliculus hemispheres in rats

Animals can make faster behavioral responses to multisensory stimuli than to unisensory stimuli. The superior colliculus (SC), which receives multiple inputs from different sensory modalities, is considered to be involved in the initiation of motor responses. However, the mechanism by which multisensory information facilitates motor responses is not yet understood. Here, we demonstrate that multisensory information modulates competition among SC neurons to elicit faster responses. We conducted multiunit recordings from the SC of rats performing a two-alternative spatial discrimination task using auditory and/or visual stimuli. We found that a large population of SC neurons showed direction-selective activity before the onset of movement in response to the stimuli irrespective of stimulation modality. Trial-by-trial correlation analysis showed that the premovement activity of many SC neurons increased with faster reaction speed for the contraversive movement, whereas the premovement activity of another population of neurons decreased with faster reaction speed for the ipsiversive movement. When visual and auditory stimuli were presented simultaneously, the premovement activity of a population of neurons for the contraversive movement was enhanced, whereas the premovement activity of another population of neurons for the ipsiversive movement was depressed. Unilateral inactivation of SC using muscimol prolonged reaction times of contraversive movements, but it shortened those of ipsiversive movements. These findings suggest that the difference in activity between the SC hemispheres regulates the reaction speed of motor responses, and multisensory information enlarges the activity difference resulting in faster responses

Experiments on conduit flow and eruption behavior of basaltic volcanic eruptions

Multiphase flow in basaltic volcanic conduits is investigated using analog experiments and theoretical approaches. Depending on gas supply, large gas bubbles (gas slugs) may rise through basaltic magma in regimes of distinct fluid‐dynamical behavior: ascent of single slugs, supplied slugs fed from the gas source during ascent, and periodic slug flow. An annular flow regime commences at the highest gas supply rates. A first set of experiments demonstrates that the growth of gas slugs due to hydrostatic decompression does not affect their ascent velocity and that excess pressure in the slugs remain negligible. The applicability of theoretical formulae describing slug ascent velocity as a function of liquid and conduit properties is evaluated in a second set of experiments. A third set of experiments with continuous gas supply into a cylindrical conduit are scaled to basaltic conditions over Morton, Eotvös, Reynolds, and Froude numbers. Gas flow rate and liquid viscosity are varied over the whole range of flow regimes to observe flow dynamics and to measure gas and liquid eruption rates. Foam generation by slug bursting at the surface and partial slug disruption by wake turbulence can modify the bubble content and size distribution of the magma. At the transition from slug to annular flow, when the liquid bridges between the gas slugs disappear, pressure at the conduit entrance drops by ∼60% from the hydrostatic value to the dynamic‐flow resistance of the annular flow, which may trigger further degassing in a stored magma to maintain the annular flow regime until the gas supply is exhausted and the eruption ends abruptly. Magma discharge may also terminate when magma ascent is hindered by wall friction in long volcanic conduits and the annular gas flow erodes all magma from the conduit. Supplied slugs are found to reach much higher rise velocities than unsupplied slugs and to collapse to turbulent annular flow upon bursting at the surface. A fourth set of experiments uses a conduit partially blocked by built‐in obstacles providing traps for gas pockets. Once gas pockets are filled, rising gas slugs deform but remain intact as they move around obstacles without coalescence or significant velocity changes. Bursting of bubbles coalescing with trapped gas pockets causes pressure signals at least 3 orders of magnitude more powerful than gas pocket oscillation induced by passing liquid. Our experiments suggest a refined classification of Strombolian and Hawaiian eruptions according to time‐dependant behavior into sporadically pulsating lava fountains (driven by stochastic rise of single slugs), periodically pulsating lava fountains (resulting from slug flow), and quasi‐steady lava fountains (oscillating at the frequency of annular‐flow turbulence)

Challenging claims in the study of migratory birds and climate change

Recent shifts in phenology in response to climate change are well established but often poorly understood. Many animals integrate climate change across a spatially and temporally dispersed annual life cycle, and effects are modulated by ecological interactions, evolutionary change and endogenous control mechanisms. Here we assess and discuss key statements emerging from the rapidly developing study of changing spring phenology in migratory birds. These well-studied organisms have been instrumental for understanding climate-change effects, but research is developing rapidly and there is a need to attack the big issues rather than risking affirmative science. Although we agree poorly on the support for most claims, agreement regarding the knowledge basis enables consensus regarding broad patterns and likely causes. Empirical data needed for disentangling mechanisms are still scarce, and consequences at a population level and on community composition remain unclear. With increasing knowledge, the overall support (‘consensus view’) for a claim increased and between-researcher variability in support (‘expert opinions') decreased, indicating the importance of assessing and communicating the knowledge basis. A proper integration across biological disciplines seems essential for the field's transition from affirming patterns to understanding mechanisms and making robust predictions regarding future consequences of shifting phenologies

The influence of vibrissal somatosensory processing in rat superior colliculus on prey capture

The lateral part of intermediate layer of superior colliculus (SCl) is a critical substrate for successful predation by rats. Hunting-evoked expression of the activity marker Fos is concentrated in SCl while prey capture in rats with NMDA lesions in SCl is impaired. Particularly affected are rapid orienting and stereotyped sequences of actions associated with predation of fast moving prey. Such deficits are consistent with the view that the deep layers of SC are important for sensory guidance of movement. Although much of the relevant evidence involves visual control of movement, less is known about movement guidance by somatosensory input from vibrissae. Indeed, our impression is that prey contact with whiskers is a likely stimulus to trigger predation. Moreover, SCl receives whisker and orofacial somatosensory information directly from trigeminal complex, and indirectly from zona incerta, parvicelular reticular formation and somatosensory barrel cortex. To better understand sensory guidance of predation by vibrissal information we investigated prey capture by rats after whisker removal and the role of superior colliculus (SC) by comparing Fos expression after hunting with and without whiskers. Rats were allowed to hunt cockroaches, after which their whiskers were removed. Two days later they were allowed to hunt cockroaches again. Without whiskers the rats were less able to retain the cockroaches after capture and less able to pursue them in the event of the cockroach escaping. The predatory behaviour of rats with re-grown whiskers returned to normal. In parallel, Fos expression in SCl induced by predation was significantly reduced in whiskerless animals. We conclude that whiskers contribute to the efficiency of rat prey capture and that the loss of vibrissal input to SCl, as reflected by reduced Fos expression, could play a critical role in predatory deficits of whiskerless rats

A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale

In this era of complete genomes, our knowledge of neuroanatomical circuitry remains surprisingly sparse. Such knowledge is however critical both for basic and clinical research into brain function. Here we advocate for a concerted effort to fill this gap, through systematic, experimental mapping of neural circuits at a mesoscopic scale of resolution suitable for comprehensive, brain-wide coverage, using injections of tracers or viral vectors. We detail the scientific and medical rationale and briefly review existing knowledge and experimental techniques. We define a set of desiderata, including brain-wide coverage; validated and extensible experimental techniques suitable for standardization and automation; centralized, open access data repository; compatibility with existing resources, and tractability with current informatics technology. We discuss a hypothetical but tractable plan for mouse, additional efforts for the macaque, and technique development for human. We estimate that the mouse connectivity project could be completed within five years with a comparatively modest budget.Comment: 41 page

Pest risk assessment of Spodoptera frugiperda for the European Union

EFSA was asked for a partial risk assessment of Spodoptera frugiperda for the territory of the EU focussing on the main pathways for entry, factors affecting establishment, risk reduction options and pest management. As a polyphagous pest, five commodity pathways were examined in detail. Aggregating across these and other pathways, we estimate that tens of thousands to over a million individual larvae could enter the EU annually on host commodities. Instigating risk reduction options on sweetcorn, a principal host, reduces entry on that pathway 100-fold. However, sweetcorn imports are a small proportion of all S. frugiperda host imports, several of which are already regulated and further regulation is estimated to reduce the median number entering over all pathways by approximately 10%. Low temperatures limit the area for establishment but small areas of Spain, Italy and Greece can provide climatic conditions suitable for establishment. If infested imported commodities are distributed across the EU in proportion to consumer population, a few hundreds to a few thousands of individuals would reach NUTS 2 regions within which suitable conditions for establishment exist. Although S. frugiperda is a known migrant, entry directly into the EU from extant populations in sub-Saharan Africa is judged not feasible. However, if S. frugiperda were to establish in North Africa, in the range of thousands to over two million adults could seasonally migrate into the southern EU. Entry into suitable NUTS2 areas via migration will be greater than via commercial trade but is contingent on the establishment of S. frugiperda in North Africa. The likelihood of entry of the pest via natural dispersal could only be mitigated via control of the pest in Africa. If S. frugiperda were to arrive and become a pest of maize in the EU, Integrated Pest Management (IPM) or broad spectrum insecticides currently used against existing pests could be applied

Transthyretin Protects against A-Beta Peptide Toxicity by Proteolytic Cleavage of the Peptide: A Mechanism Sensitive to the Kunitz Protease Inhibitor

Alzheimer's disease (AD) is a neurodegenerative disorder characterized by the deposition of amyloid β-peptide (A-Beta) in the brain. Transthyretin (TTR) is a tetrameric protein of about 55 kDa mainly produced in the liver and choroid plexus of the brain. The known physiological functions of TTR are the transport of thyroid hormone T4 and retinol, through binding to the retinol binding protein. TTR has also been established as a cryptic protease able to cleave ApoA-I in vitro. It has been described that TTR is involved in preventing A-Beta fibrilization, both by inhibiting and disrupting A-Beta fibrils, with consequent abrogation of toxicity. We further characterized the nature of the TTR/A-Beta interaction and found that TTR, both recombinant or isolated from human sera, was able to proteolytically process A-Beta, cleaving the peptide after aminoacid residues 1, 2, 3, 10, 13, 14,16, 19 and 27, as determined by mass spectrometry, and reversed phase chromatography followed by N-terminal sequencing. A-Beta peptides (1–14) and (15–42) showed lower amyloidogenic potential than the full length counterpart, as assessed by thioflavin binding assay and ultrastructural analysis by transmission electron microscopy. A-Beta cleavage by TTR was inhibited in the presence of an αAPP peptide containing the Kunitz Protease Inhibitor (KPI) domain but not in the presence of the secreted αAPP derived from the APP isoform 695 without the KPI domain. TTR was also able to degrade aggregated forms of A-Beta peptide. Our results confirmed TTR as a protective molecule in AD, and prompted A-Beta proteolysis by TTR as a protective mechanism in this disease. TTR may prove to be a useful therapeutic agent for preventing or retarding the cerebral amyloid plaque formation implicated in AD pathology

Underplating of the Hawaiian Swell : evidence from teleseismic receiver functions

Author Posting. © The Authors, 2010. This article is posted here by permission of John Wiley & Sons for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 183 (2010): 313-329, doi:10.1111/j.1365-246X.2010.04720.x.The Hawaiian Islands are the canonical example of an age-progressive island chain, formed by volcanism long thought to be fed from a hotspot source that is more or less fixed in the mantle. Geophysical data, however, have so far yielded contradictory evidence on subsurface structure. The substantial bathymetric swell is supportive of an anomalously hot upper mantle, yet seafloor heat flow in the region does not appear to be enhanced. The accumulation of magma beneath pre-existing crust (magmatic underplating) has been suggested to add chemical buoyancy to the swell, but to date the presence of underplating has been constrained only by local active-source experiments. In this study, teleseismic receiver functions derived from seismic events recorded during the PLUME project were analysed to obtain a regional map of crustal structure for the Hawaiian Swell. This method yields results that compare favourably with those from previous studies, but permits a much broader view than possible with active-source seismic experiments. Our results indicate that the crustal structure of the Hawaiian Islands is quite complicated and does not conform to the standard model of sills fed from a central source. We find that a shallow P-to-s conversion, previously hypothesized to result from the volcano-sediment interface, corresponds more closely to the boundary between subaerial and subaqueous extrusive material. Correlation between uplifted bathymetry at ocean-bottom-seismometer locations and presence of underplating suggests that much of the Hawaiian Swell is underplated, whereas a lack of underplating beneath the moat surrounding the island of Hawaii suggests that underplated crust outward of the moat has been fed from below by dykes through the lithosphere rather than by sills spreading from the island centre. Local differences in underplating may reflect focusing of magma-filled dykes in response to stress from volcanic loading. Finally, widespread underplating adds chemical buoyancy to the swell, reducing the amplitude of a mantle thermal anomaly needed to match bathymetry and supporting observations of normal heat flow.We are grateful to the Ocean Sciences Division of the U.S. National Science Foundation for their support of this project under grants OCE-0002470, OCE-0002552 and OCE-0002819