The complex polyploid genome architecture of sugarcane.

Sugarcane, the world's most harvested crop by tonnage, has shaped global history, trade and geopolitics, and is currently responsible for 80% of sugar production worldwide1. While traditional sugarcane breeding methods have effectively generated cultivars adapted to new environments and pathogens, sugar yield improvements have recently plateaued2. The cessation of yield gains may be due to limited genetic diversity within breeding populations, long breeding cycles and the complexity of its genome, the latter preventing breeders from taking advantage of the recent explosion of whole-genome sequencing that has benefited many other crops. Thus, modern sugarcane hybrids are the last remaining major crop without a reference-quality genome. Here we take a major step towards advancing sugarcane biotechnology by generating a polyploid reference genome for R570, a typical modern cultivar derived from interspecific hybridization between the domesticated species (Saccharum officinarum) and the wild species (Saccharum spontaneum). In contrast to the existing single haplotype ('monoploid') representation of R570, our 8.7 billion base assembly contains a complete representation of unique DNA sequences across the approximately 12 chromosome copies in this polyploid genome. Using this highly contiguous genome assembly, we filled a previously unsized gap within an R570 physical genetic map to describe the likely causal genes underlying the single-copy Bru1 brown rust resistance locus. This polyploid genome assembly with fine-grain descriptions of genome architecture and molecular targets for biotechnology will help accelerate molecular and transgenic breeding and adaptation of sugarcane to future environmental conditions.

Overview of the Langmuir probe system on the Mega Ampere Spherical Tokamak (MAST) Upgrade.

A detailed description of the Langmuir probe system on Mega Ampere Spherical Tokamak Upgrade is presented. The system features 850 tile-embedded probes and 40 bespoke electronic modules that each have the capability to drive and acquire data from up to 16 probes in a time-multiplexed manner. The system provides spatiotemporal-resolved measurements (1 cm and ∼1 ms, respectively) in the divertor region of ion saturation current, electron temperature, and floating potential. The standard interpretation of current-voltage (IV) characteristics is to apply a four-parameter fit, based on unmagnetized probe theory, which includes a linear model for the ion saturation region. To mitigate the effect of the magnetic field, analysis is restricted to the region of the IV characteristic, which is sensitive to only the tail of the electron energy distribution function.

Overview and first measurements of the MAST Upgrade bolometer diagnostic.

A suite of multi-channel resistive bolometers has been implemented to measure the total radiation from Mega Amp Spherical Tokamak Upgrade plasmas, with cameras covering the core plasma and lower divertor chamber. Data are digitized and processed using novel field-programmable gate array-based electronics, offering improved compactness and new operational capabilities. A synthetic diagnostic has been developed to explore the quality of 2D reconstructions available from the system and to quantify the uncertainty on quantities such as the total radiated power. Measurements in the first campaign have demonstrated correct functioning of the diagnostic while also highlighting issues with electrical noise and some failure mechanisms of the detectors, as well as significant neutral beam fast-particle losses.

Methods to determine the radiated power in SPI-mitigated disruptions in JET.

This paper presents techniques for evaluating the radiated power in JET disruptions. Disrupting plasmas are shown to have non-axisymmetric radiation profiles, motivating the re-evaluation of the standard techniques for calculating the total radiated power at JET using bolometry. Four single-channel bolometers at different toroidal locations are exploited to quantify the radiation asymmetry. Toroidal radiation peaking factors integrated over the entire disruption of up to 1.5 have been observed when varying the quantity of neon in pellets used in disruptions mitigated by shattered pellet injection. Using synthetic bolometer diagnostics developed with the Cherab spectroscopy modeling framework, we can estimate the systematic error on total power calculations for relevant radiation profiles and improve estimates of the total radiated power. We show that the component of the systematic error on the total power due to the poloidal radiation profile can be reduced from 70% to 10% with suitable assumptions about the structure of the poloidal profile.

The digital mirror Langmuir probe: Field programmable gate array implementation of real-time Langmuir probe biasing.

High bandwidth, high spatial resolution measurements of electron temperature, density, and plasma potential are valuable for resolving turbulence in the boundary plasma of tokamaks. While conventional Langmuir probes can provide such measurements, either their temporal or spatial resolution is limited: the former by the sweep rate necessary for obtaining I-V characteristics and the latter by the need to use multiple electrodes, as is the case in triple and double probe configurations. The Mirror Langmuir Probe (MLP) bias technique overcomes these limitations by rapidly switching the voltage on a single electrode cycling between three bias states, each dynamically optimized for the local plasma conditions. The MLP system on Alcator C-Mod used analog circuitry to perform this function, measuring Te, VF, and Isat at 1.1 MSPS. Recently, a new prototype digital MLP controller has been implemented on a Red Pitaya Field Programmable Gate Array (FPGA) board which reproduces the functionality of the original controller and performs all data acquisition. There is also the potential to provide the plasma parameters externally for use with feedback control systems. The use of FPGA technology means the system is readily customizable at a fraction of the development time and implementation cost. A second Red Pitaya was used to test the MLP by simulating the current response of a physical probe using C-Mod experimental measurements. This project is available as a git repository to facilitate extensibility (e.g., real-time control outputs and more voltage states) and scalability through collaboration.

The AUSTRAL VLBI observing program.

The AUSTRAL observing program was started in 2011, performing geodetic and astrometric very long baseline interferometry (VLBI) sessions using the new Australian AuScope VLBI antennas at Hobart, Katherine, and Yarragadee, with contribution from the Warkworth (New Zealand) 12 m and Hartebeesthoek (South Africa) 15 m antennas to make a southern hemisphere array of telescopes with similar design and capability. Designed in the style of the next-generation VLBI system, these small and fast antennas allow for a new way of observing, comprising higher data rates and more observations than the standard observing sessions coordinated by the International VLBI Service for Geodesy and Astrometry (IVS). In this contribution, the continuous development of the AUSTRAL sessions is described, leading to an improvement of the results in terms of baseline length repeatabilities by a factor of two since the start of this program. The focus is on the scheduling strategy and increased number of observations, aspects of automated operation, and data logistics, as well as results of the 151 AUSTRAL sessions performed so far. The high number of the AUSTRAL sessions makes them an important contributor to VLBI end-products, such as the terrestrial and celestial reference frames and Earth orientation parameters. We compare AUSTRAL results with other IVS sessions and discuss their suitability for the determination of baselines, station coordinates, source coordinates, and Earth orientation parameters.

Isolation and RFLP genotyping of Toxoplasma gondii from the mongoose (Herpestes auropunctatus) in Grenada, West Indies.

Little is known of the genetic diversity and epidemiology of Toxoplasma gondii infection in wildlife in Caribbean Islands. The prevalence and genetic diversity of T. gondii in mongooses (Herpestes auropunctatus) was investigated. During 2011 and 2012, 91 mongooses were trapped in different parts of Grenada, bled, euthanized, and examined at necropsy. Antibodies to T. gondii were found in 27 mongooses tested by the modified agglutination test (cut-off titer 25). Muscles (heart, tongue, neck) of 25 of the seropositive mongooses were bioassayed for T. gondii infection in mice. Viable T. gondii was isolated by bioassay in mice from four mongooses with MAT titers of 1:50 in two, 1:200 for one, and 1:400 for one mongoose. The four T. gondii isolates were further propagated in cell culture. Strain typing of T. gondii DNA extracted from cell-cultured tachyzoites using the 10 PCR-restriction fragment length polymorphism (RFLP) markers SAG1, SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, and Apico revealed one isolate belongs to the Type III (ToxoDB #2) lineage, two to ToxoDB#7 lineage, and one to the ToxoDB #216 lineage. This is the first report of T. gondii isolation and genotyping in H. auropunctatus worldwide.

Estimating forest LAI profiles and structural parameters using a ground-based laser called 'Echidna'.

There are many techniques for measuring leaf area index (LAI) and forest canopy foliage profiles but their accuracy is questionable. This paper briefly reviews current methods of estimating forest LAI and presents a novel, ground-based laser system, Echidna that can make a wide range of measurements of forest structure, including LAI. Here, use of the system to provide field data and derived gap probabilities in the form of a 'hemispherical photograph with range' is demonstrated. The results show consistency and reproducibility and do not depend on special conditions for the natural light field.

The morphology of the inner ear from the domestic pig (Sus scrofa).

The morphology of the hair cells of the inner ear end organs from the domestic pig (Sus scrofa) have been studied using a combination of Scanning and Transmission Electron Microscopy (SEM and TEM), revealing hair cells from the cochlea and vestibule using a novel surgical and technical approach. This is the first time that the inner ear hair cells from S. scrofa have been studied, thus providing useful anatomical information on the morphology of the hair cells from the cochlea, saccule and utricle from a large mammal. Anatomical information in relation to the morphology of the inner ear is of considerable importance, both in the pathological diagnosis of trauma and in the development of cochlea implants and other biotechnological systems associated with the enhancement of hearing. Standard fixation protocols using cardiac perfusion was not employed in this study as this method cannot always be applied, such as the pathological examination of the human ear, or the study of animals protected by endangered species legislation. With the exception of a very few countries, cetaceans cannot be killed for research purposes, yet physiological information on the inner ear from these species is urgently required for ecological assessment reasons. Supporting the use of S. scrofa as a model for cetacean hearing research is that this animal is a member of the order Artiodactyla, which includes both the hippopotamus and cetaceans. Being of a similar size, the pig is an ideal subject for developing protocols and surgical techniques required to investigate both the human and small cetacean auditory systems.

The relationship between body size and evoked potentials from the statocysts of the prawn Palaemon serratus.

The organisation of the statocyst hair cells and auditory evoked potentials (AEPs) generated by the afferents in three body size classes of prawn (Palaemon serratus) have been studied using a combination of anatomical, electron microscopic and electrophysiological approaches. The statistical examination of the relationship between the sensory setae and body size showed an increase in both the length and number of statocyst hair cells as the animal grows. In view of this finding, the response of the statocyst organ to a 500 Hz tone burst was recorded from four specimens from each size class using two subcutaneous electrodes, positioned in the carapace close to the supraoesophageal ganglion and statocyst. Neither body size nor the number of afferents in the statocyst has any significant impact on the amplitude of AEPs in response to the 500 Hz tone burst. The findings of this study show that P. serratus is capable of hearing a 500 Hz tone regardless of body size, a finding that is of ecological importance when considering the effect of anthropogenic sound on crustaceans.

The inner ear ultrastructure from the paddlefish (Polyodon spathula) using transmission electron microscopy.

The structure of the hair cells on each sensory macula from the inner ear of the paddlefish (Polyodon spathula) was studied using scanning and transmission electron microscopy, revealing the nucleated cell bodies and peripheral nerve fibres of the saccule utricle and lagena. Examination of the structures within the cell body revealed comparable features with those found in the inner ear hair cells from bony fish species, although in P. spathula the afferent cell body is almost twice the size. This is the first time that the inner ear hair cells from an Acipenseriform fish have been studied using transmission microscopy, thus providing benchmark anatomical information in relation to the cellular morphology of the afferent receptors from a 'healthy' P. spathula ear. Structural information is of assistance in the study of aquatic animal hearing for environmental monitoring purposes, as morphological data can be used to confirm if evidence of raised hearing thresholds from animals exposed to intense anthropogenic noise or other destructive agents (determined using electrophysiological or behavioural techniques) are a direct result of damage to the ultrastructure of the inner ear.

Magnetic versus manual guidewire manipulation in neuroradiology: in vitro results.

INTRODUCTION: Standard microguidewires used in interventional neuroradiology have a predefined shape of the tip that cannot be changed while the guidewire is in the vessel. We evaluated a novel magnetic navigation system (MNS) that generates a magnetic field to control the deflection of a microguidewire that can be used to reshape the guidewire tip in vivo without removing the wire from the body, thereby potentially facilitating navigation along tortuous paths or multiple acute curves. METHOD: The MNS consists of two permanent magnets positioned on either side of the fluoroscopy table that create a constant precisely controlled magnetic field in the defined region of interest. This field enables omnidirectional rotation of a 0.014-inch magnetic microguidewire (MG). Speed of navigation, accuracy in a tortuous vessel anatomy and the potential for navigating into in vitro aneurysms were tested by four investigators with differing experience in neurointervention and compared to navigation with a standard, manually controlled microguidewire (SG). RESULTS: Navigation using MG was faster (P=0.0056) and more accurate (0.2 mistakes per trial vs. 2.6 mistakes per trial) only in less-experienced investigators. There were no statistically significant differences between the MG and the SG in the hands of experienced investigators. One aneurysm with an acute angulation from the carrier vessel could be navigated only with the MG while the SG failed, even after multiple reshaping manoeuvres. CONCLUSION: Our findings suggest that magnetic navigation seems to be easier, more accurate and faster in the hands of less-experienced investigators. We consider that the features of the MNS may improve the efficacy and safety of challenging neurointerventional procedures.

The hearing abilities of the silver carp (Hypopthalmichthys molitrix) and bighead carp (Aristichthys nobilis).

Concern regarding the spread of silver carp (Hypopthalmichthys molitrix) and bighead carp (Aristichthys nobilis) through the Illinois River has prompted the development of a Bio-acoustic Fish Fence (BAFF) to act as an acoustic fish deterrent. The application of this technology has resulted in a need to understand the auditory physiology of the target species, in order to maximise the effect of the barrier in preventing the migration of the non-indigenous carp species into Lake Michigan, whilst minimising the effect on indigenous fish populations. Therefore, the hearing thresholds of 12 H. molitrix and 12 A. nobilis were defined using the Auditory Brainstem Response (ABR) technique, in a pressure-dominated sound field generated by submerged transducers of the type used in the construction of the BAFF system. The results clearly show that these fish are most sensitive to sounds in a frequency bandwidth of between 750 Hz and 1500 Hz, with higher thresholds below 300 Hz and above 2000 Hz.

The inner ear morphology and hearing abilities of the Paddlefish (Polyodon spathula) and the Lake Sturgeon (Acipenser fulvescens).

Concern regarding the spread of silver carp (Hypopthalmichthys molitrix) and bighead carp (Aristichthysc nobilis) through the Illinois River has prompted the development of an Acoustic Fish Deterrent (AFD) system. The application of this technology has resulted in a need to understand the auditory physiology of fish other than the target species, in order to minimise the effect of the AFD barrier on the ecology of indigenous fish populations. To this end, both the structures involved in sound reception and the hearing abilities of the paddlefish (Polyodon spathula) and the lake sturgeon (Acipenser fulvescens) are studied here using a combination of morphological and physiological approaches, revealing that both fish are responsive to sounds ranging in frequency from 100 to 500 Hz. The lowest hearing thresholds from both species were acquired from frequencies in a bandwidth of between 200 and 300 Hz, with higher thresholds at 100 and 500 Hz. The rationale for studying hearing in P. spathula and A. fulvescens in particular, is the value placed on them by both the commercial caviar producing industry and by the recreational fisheries sector. The hearing abilities of twelve P. spathula and twelve A. fulvescens were tested in sound fields dominated by either sound pressure or particle motion, with the results showing that acipenseriform fish are responsive to the motion of water particles in a sound field, rather than the sound pressure component. In this study, we measure the intensity of the sound field required to evoke threshold responses using a pressure sensitive hydrophone, as pressure dominated sound fields are the most audible acoustic condition for specialists like H. molitrix and A. nobilis (the target species). The results of the auditory examination clearly show that P. spathula and A. fulvescens are not sensitive to sound pressure, and will therefore have a significantly higher deterrent threshold than H. molitrix and A. nobilis in a pressure dominated sound field.

The polarisation of hair cells from the ear of the European bass (Dicentrarchus labrax).

The polarisation of ciliary bundles on the macula of the saccule in the European bass (Dicentrarchus labrax L) has been studied using a scanning electron microscope (SEM). These data show that D. labrax possesses ciliary bundles arranged in four dichotomous quadrants with a standard orientation, comparable to hearing generalists from the order Perciformes. The spacing between ciliary bundles was investigated in three size classes of fish, with the results indicating that the addition of receptor cells in the ear of D. labrax continues for at least the first 2 years of development. The lengths of the kinocilia from ciliary bundles in each quadrant of the macula were also studied, and found to be of uniform length. In addition, we look at the internal structure of the afferent using transmission electron microscopy (TEM), revealing the nucleated cell body and peripheral nerve fibres of the saccule consistent with other TEM examinations of saccular ultrastructure. This information is required to gain an insight into the inner ear of D. labrax, as part of a larger study of the morphology and physiology of the hearing systems of both vertebrate and invertebrate marine animals.

The hearing abilities of the prawn Palaemon serratus.

The mechanism of sound reception and the hearing abilities of the prawn (Palaemon serratus) have been studied using a combination of anatomical, electron microscopic and electrophysiological approaches, revealing that P. serratus is responsive to sounds ranging in frequency from 100 to 3000 Hz. It is the first time that the Auditory Brainstem Response (ABR) recording technique has been used on invertebrates, and the acquisition of hearing ability data from the present study adds valuable information to the inclusion of an entire sub-phylum of animals when assessing the potential impact of anthropogenic underwater sounds on marine organisms. Auditory evoked potentials were acquired from P. serratus, using two subcutaneous electrodes positioned in the carapace close to the supraesophageal ganglion and the statocyst (a small gravistatic organ located below the eyestalk on the peduncle of the bilateral antennules). The morphology of the statocyst receptors and the otic nerve pathways to the brain have also been studied, and reveal that P. serratus possesses an array of sensory hairs projecting from the floor of the statocyst into a mass of sand granules embedded in a gelatinous substance. It is the purpose of this work to show that the statocyst is responsive to sounds propagated through water from an air mounted transducer. The fundamental measure of the hearing ability of any organism possessing the appropriate receptor mechanism is its audiogram, which presents the lowest level of sound that the species can hear as a function of frequency. The statocyst of P. serratus is shown here to be sensitive to the motion of water particles displaced by low-frequency sounds ranging from 100 Hz up to 3000 Hz, with a hearing acuity similar to that of a generalist fish. Also, recorded neural waveforms were found to be similar in both amplitude and shape to those acquired from fish and higher vertebrates, when stimulated with low-frequency sound, and complete ablation of the electrophysiological response was achieved by removal of the statocyst.

The cosmic ray ground level enhancement of 6 November 1997.

The relativistic solar proton event of 6 November 1997 resulted in the first ground-level enhancement (GLE) of solar cycle 23. The earliest onset was around 1215 UT but was up to 15 minutes later at some neutron monitor locations. The time of maximum intensity also varied significantly over the world-wide neutron monitor network. The modeled particle distributions and spectra are presented. The apparent particle arrival direction is found to be largely consistent with propagation outward from the sun along interplanetary magnetic field lines.

Effect of aging on the substance P receptor, NK-1, in the spinal cord of rats with peripheral nerve injury.

Substance P (SP) levels in the spinal cords of very old rats are less than the levels in younger rats (Bergman et al., 1996). After injury to a peripheral nerve in young rats, immunoreactivity (ir) to the SP receptor, NK-1 (neurokinin-1), increases in the spinal cord ipsilateral to the injury and the increases are correlated with the development of thermal hyperalgesia (Goff et al., 1998). Thus we postulated that aged rats might display an increased sensitivity to thermal stimulation before peripheral nerve injury and that they might respond differently to injury than do younger rats. To test this hypothesis, we used the Bennett and Xie model (1988) of chronic constriction injury (CCI) to the sciatic nerve to induce a neuropathic pain condition. We investigated the effect of age on changes in NK-1 ir in superficial layers of the dorsal horn and on numbers of NK ir cells in deeper laminae at the L4-L5 levels of the spinal cord after CCI. NK-1 receptors were tagged immunohistochemically and their distribution quantified by use of computer-assisted image analysis. NK-1 ir changes were related to alterations in thermal and tactile sensitivity that developed after CCI in young, mature and aged (4-6, 14-16, and 24-26 months) Fischer F344 BNF1 hybrid rats. No differences in thermal or tactile sensitivity of young and aged rats were seen in the absence of nerve injury. After injury, aged rats developed thermal hyperalgesia and tactile allodynia more slowly than did the younger rats. NK-1 receptor ir and numbers of NK-1 ir cells in the dorsal horn increased with time post-injury in all three groups. NK-1 ir increases were correlated with the development of thermal hyperalgesia in those rats that displayed hyperalgesia. However, some rats developed an increased threshold to thermal stimuli (analgesia) and that also was correlated with increases in NK-1 ir. Thus NK-1 ir extent, while correlated with thermal sensitivity in the absence of injury, is not a specific marker for disturbances in one particular sensory modality; rather it increases with peripheral nerve injury per se.

Neuropathic pain in aged rats: behavioral responses and astrocytic activation.

We used the Bennett and Xie (1988) model of chronic neuropathic pain to study the effect of age on thermal and tactile sensitivity and on astrocytic activation in the dorsal horn of the spinal cord after nerve injury. Fischer 344 FBNF1 hybrid rats in three age groups, 4-6, 14-16, and 24-26 months, were studied. Rats were either unligated (day 0, control) or the left sciatic nerve was loosely ligated to cause a chronic constriction injury (CCI). CCI causes a neuropathic pain condition characterized by tactile allodynia and thermal hyperalgesia. Rats were behaviorally assessed for tactile and thermal sensitivity of their ligated and unligated hind paws up to 35 days postligation. Rats were sacrificed before or at various days postligation, and activated astrocytes were identified at the L4-L5 levels of their spinal cords by use of an antibody to glial fibrillary acid protein (GFAP). The number of GFAP-ir astrocytes in the dorsal horn of the spinal cord in the control, uninjured condition decreased with age (P < or = 0.001) but increased after CCI in all three age groups. After CCI, astrocytic activation in the cord was less robust in aged rats than in younger ones (P < or = 0.01). Not all the CCI rats displayed hyperalgesia to touch and to heat. Rats with an increased sensitivity to heat had increased levels of GFAP-ir in their cords; however, rats with decreased thermal sensitivity also displayed increased GFAP-ir. Thus the presence of activated astrocytes was not correlated with a single behavioral manifestation of neuropathic pain.

Pitfalls in homozygosity mapping.

There is much interest in use of identity-by-descent (IBD) methods to map genes, both in Mendelian and in complex disorders. Homozygosity mapping provides a rapid means of mapping autosomal recessive genes in consanguineous families by identifying chromosomal regions that show homozygous IBD segments in pooled samples. In this report, we point out some potential pitfalls that arose during the course of homozygosity mapping of the enhanced S-cone syndrome gene, resulting from (1) unexpected allelic heterogeneity, so that the region containing the disease locus was missed as a result of pooling; (2) identification of a homozygous IBD region unrelated to the disease locus; and (3) the potential for inflation of LOD scores as a result of underestimation of the extent of inbreeding, which Broman and Weber suggest may be quite common.