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.

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.

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.

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.

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.

Fusogenic domains of golgi membranes are sequestered into specialized regions of the stack that can be released by mechanical fragmentation.

A well-characterized cell-free assay that reconstitutes Golgi transport is shown to require physically fragmented Golgi fractions for maximal activity. A Golgi fraction containing large, highly stacked flattened cisternae associated with coatomer-rich components was inactive in the intra-Golgi transport assay. In contrast, more fragmented hepatic Golgi fractions of lower purity were highly active in this assay. Control experiments ruled out defects in glycosylation, the presence of excess coatomer or inhibitory factors, as well as the lack or consumption of limiting diffusible factors as responsible for the lower activity of intact Golgi fractions. Neither Brefeldin A treatment, preincubation with KCl (that completely removed associated coatomer) or preincubation with imidazole buffers that caused unstacking, activated stacked fractions for transport. Only physical fragmentation promoted recovery of Golgi fractions active for transport in vitro. Rate-zonal centrifugation partially separated smaller transport-active Golgi fragments with a unique v-SNARE pattern, away from the bulk of Golgi-derived elements identified by their morphology and content of Golgi marker enzymes (N-acetyl glucosaminyl and galactosyl transferase activities). These fragments released during activation likely represent intra-Golgi continuities involved in maintaining the dynamic redistribution of resident enzymes during rapid anterograde transport of secretory cargo through the Golgi in vivo.

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 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.

Effects of methylglyoxal on rat pancreatic beta-cells.

The addition of the alpha-ketoaldehyde methylglyoxal (0.5 or 1 mmol/L) to single isolated rat pancreatic beta-cells caused a rapid, marked depolarization resulting in electrical activity. This effect of methylglyoxal on beta-cell was reversible upon removal of the alpha-ketoaldehyde, and could be inhibited by the anion channel blockers 4,4'-diisothiocyanatostilbene-2,2'-disulphonic acid (DIDS) and 5-nitro-2-(3-phenylpropylamino) benzoic acid (NPPB). Methylglyoxal also resulted in elevated cytosolic [Ca2+] and an intracellular acidification in intact rat islets. In perifused islets, methylglyoxal provoked a modest, transient stimulation of secretion but inhibited glucose-induced insulin release. Incubation of islets with methylglyoxal resulted in the formation of large quantities of D-lactate, indicating metabolism of the alpha-ketoaldehyde via the glyoxalase pathway. The effects of methylglyoxal on beta-cell membrane potential, cytosolic [Ca2+] and intracellular pH were also observed in response to phenylglyoxal which is also effectively metabolized via the glyoxalase pathway. However, t-butylglyoxal which is poorly metabolized via the glyoxalase pathway, caused neither depolarization of the membrane potential nor intracellular acidification, but did inhibit glucose-induced insulin release. These findings suggests that the depolarization and acidification evoked by methyl- and phenylglyoxal are dependent upon their metabolism via the glyoxalase pathway. The possible mechanisms coupling alpha-ketoaldehyde metabolism via the glyoxalase pathway with membrane depolarization are discussed.

Aging and neuropathic pain.

Although chronic neuropathic pain disorders are more prevalent in the senescent population, little is known about how the aging process alters the thermal hyperalgesic sensitivity to peripheral nerve injury. In this study, neuropathic pain was induced in young, mature and aged FBNF1 hybrid rats via unilateral ligation of the left sciatic nerve. The extent to which the aging process affects the thermal hyperalgesic responsiveness of these animals was investigated. The results demonstrate that the aging process differentially alters nociceptive processing.

Microglial proliferation in the spinal cord of aged rats with a sciatic nerve injury.

Nerve injury may lead to chronic neuropathic pain syndromes. We determined whether the extent of central nervous system microglial activation that accompanies nerve injury is age dependent and correlated with behavioral manifestations of pain. We used the Bennett and Xie sciatic nerve chronic constriction injury model (Bennett, G.J., Xie, Y.-K., A peripheral mononeuropathy in rat that produces disorders of pain sensation like those seen in man, Pain, 33 (1998) 87-107) to induce neuropathic pain in three age cohorts of Fischer 344 FBNF1 hybrid rats (4-6, 14-16, and 24-26 months). Rats were assessed for thermal sensitivity (hyperalgesia) of their hind paws pre-injury (day 0) and up to 35 days post injury. On various days post injury, the L4-L5 levels of their spinal cords were reacted for localization of an antibody to OX-42, a marker for microlgia. OX-42 immunoreactivity (ir) was quantified by use of a Bioquant density analysis system. OX-42 ir was heavy in areas of sciatic nerve primary afferent terminations and in the motor columns of its neurons. Aging increases OX-42 ir in the absence of injury. After injury, OX-42 ir increased further, but the increases over control levels decreased with age. Ligation-induced analgesia and hyperalgesia were both correlated with the increases in OX-42 ir, regardless of age.

Pre-mortem diagnosis of Creutzfeldt-Jakob disease by detection of abnormal cerebrospinal fluid proteins.

Creutzfeldt-Jakob disease (CJD) may be difficult to diagnose early or when it has an atypical presentation. We describe two patients with progressive dementia in whom the results of diagnostic brain biopsies were unhelpful. Spinal fluid from these patients, analyzed by two-dimensional electrophoresis, contained two abnormal proteins (Nos. 130 and 131, with relative molecular masses of 26,000 and 29,000 daltons and isoelectric points of 5.2 and 5.1). These findings suggested a provisional diagnosis of Creutzfeldt-Jakob disease, which was confirmed in both patients at autopsy. Detection of these abnormal cerebrospinal fluid proteins appears to be a valuable laboratory adjunct in evaluating patients with an unexplained progressive dementia.

Strain differences in neuropathic hyperalgesia.

The purpose of this study was to investigate strain-related differences in the onset and maintenance of thermal hyperalgesia following the induction of peripheral nerve injury in two inbred strains of rats (Fischer 344 and Lewis) and two outbred strains of rats (Sprague-Dawley and Wistar). Neuropathic pain was induced via unilateral ligation of the left sciatic nerve with chromic gut sutures. A plantar analgesia meter was used to measure paw-withdrawal latency from the ligated vs. unligated hind paws of inbred vs. outbred strains of rats to investigate strain-related differences in nerve injury-induced thermal hyperalgesia. The results demonstrated no significant effects of animal strain on presurgical paw-withdrawal latency values. Following the sciatic nerve ligation (SNL) surgery, a significant hyperalgesic response was elicited from the Sprague-Dawley and Wistar rats (outbred strains) for at least 28 days. Conversely, data analyses from the inbred strains failed to demonstrate significant hyperalgesic responses to peripheral nerve injury, with the exception of postsurgical day 10. These data emphasize the importance of considering the strain of the rat being investigated before extrapolating the results from animals experiments to treatment strategies for humans with chronic neuropathic pain.

Changes in spinal serotonin turnover mediate age-related differences in the behavioral manifestations of peripheral nerve injury.

The Bennett and Xie model of peripheral nerve injury was used to study the effects of aging on the onset and progression of sciatic nerve ligation (SNL)-induced thermal hyperalgesia and tactile-evoked allodynia in young, mature, and aged Fischer 344 FBNF1 male rats (4-6, 14-16, and 24-26 months old, respectively). A plantar analgesia meter and calibrated von Frey pressure filaments were employed as the analgesiometric assays. In the absence of nerve injury, aged rats were found to be more sensitive than younger animals to noxious thermal stimuli. Following the SNL surgery, thermal hyperalgesia was observed in all three age groups within 3 days. On post-SNL day 35, the paw-withdrawal latency values of the young and mature animals returned to presurgical baseline levels, while the aged rats continued to exhibit thermal hyperalgesia. Tactile-evoked allodynia was apparent within 3 days following peripheral nerve injury in the oldest cohort, but was delayed in the younger animals. On post-SNL days 0 (control), 3, 21, and 35, young, mature, and aged rats were sacrificed and high-performance liquid chromatography and electrochemical detection (HPLC/ECD) methods were used for neurochemical analyses of spinal serotonin (5-HT), norepinephrine (NE), and 5-hydroxyindoleacetic acid (5-HIAA). Spinal 5-HT and NE levels were not significantly altered by the aging process, nor were they affected by peripheral nerve injury. However, spinal 5-HT turnover from the aged animals was greater than that detected in spinal tissue from the younger counterparts. Differences in spinal 5-HT turnover may contribute to age-related variability in spinal nociceptive processing.

Hair follicle cycle and shedding in male beagle dogs.

Skin biopsy samples were collected from the thoracolumbar region of 9 male Beagle dogs ranging in age from 2 weeks to 32 months. The highest percentages of anagen hair follicles were present in samples collected during the winter and the summer seasons, and highest percentages of telogen hair follicles were present in samples collected during the fall and the spring seasons. Catagen, never exceeding 7% of the follicles, was found during a brief transitory stage. Peak shedding of hairs combed from the coats of dogs occurred in the spring and fall--these peaks appearing simultaneously with peak percentages of hair follicles in the telogen phase. Dogs younger than 1 year of age had 10% fewer follicles in the telogen stage than did older dogs. In dogs 2 weeks of age, 12 to 16% of the hair follicles were in the telogen stage.

Histology of the hair cycle in male beagle dogs.

A detailed histologic study of the hair follicles of male Beagle dogs was made to determine changes in microscopic structure associated with the three stages in the hair cycle. Observed changes are that the bulbs of hair follicles in anagen are more closely associated with adipose tissue than they are in telogen. This is due to the deeper penetration of the follicles into the subcutaneous tissue during anagen. The hair germ cells of telogen were presumed to arise from the stratum basale of the matrix cells rather than from the outer root sheath cells. During telogen, the dermal papilla is separated from the club hair, but remains in close proximity to it. There is no connecting stalk as is reported for other animals.

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.

Maternal attitudes toward circumcision.

Two hundred questionnaires were completed anonymously by mothers to determine the nature of their attitudes and knowledge of neonatal circumcision. Neonatal circumcision had been performed on 95 percent of the sons. A wide variety of reasons were given for circumcising newborns; few were medically valid. Eighty-seven percent of mothers considered circumcision to be without risk, and 80 percent of mothers stated that the risks of circumcision had not been explained to them. This retrospective study revealed a lack of maternal understanding regarding neonatal circumcision.

Alcohol and the nervous system.

Alcoholism is regarded as a multifactorial disorder, but the causes of alcoholism are poorly understood. The most important part of dealing with this widespread health and social problem is a prevention and early identification and treatment of those at risk. Therapeutic intervention should take place before development of cognitive impairment and physical dependence, otherwise treatment of developed alcoholism is notoriously unsatisfactory.