Updated guidelines for gene nomenclature in wheat.

KEY MESSAGE: Here, we provide an updated set of guidelines for naming genes in wheat that has been endorsed by the wheat research community. The last decade has seen a proliferation in genomic resources for wheat, including reference- and pan-genome assemblies with gene annotations, which provide new opportunities to detect, characterise, and describe genes that influence traits of interest. The expansion of genetic information has supported growth of the wheat research community and catalysed strong interest in the genes that control agronomically important traits, such as yield, pathogen resistance, grain quality, and abiotic stress tolerance. To accommodate these developments, we present an updated set of guidelines for gene nomenclature in wheat. These guidelines can be used to describe loci identified based on morphological or phenotypic features or to name genes based on sequence information, such as similarity to genes characterised in other species or the biochemical properties of the encoded protein. The updated guidelines provide a flexible system that is not overly prescriptive but provides structure and a common framework for naming genes in wheat, which may be extended to related cereal species. We propose these guidelines be used henceforth by the wheat research community to facilitate integration of data from independent studies and allow broader and more efficient use of text and data mining approaches, which will ultimately help further accelerate wheat research and breeding.

Genetic Relationship of Stripe Rust Resistance Genes Yr34 and Yr48 in Wheat and Identification of Linked KASP Markers.

The Australian continent was free from wheat stripe rust caused by Puccinia striiformis f. sp. tritici until exotic incursions occurred in 1979 and 2002. The 2002 incursion enabled the identification of a new stripe rust resistance gene (Yr34) in the advanced breeding line WAWHT2046. In this study, we developed and validated markers closely linked with Yr34, which is located in the distal region in the long arm of chromosome 5A. Four kompetitive allele-specific polymerase chain reaction (KASP) and three sequence-tagged site (STS) markers derived from the International Wheat Genome Sequencing Consortium RefSeq v1.0 scaffold-77836 cosegregated with Yr34. Markers sun711, sun712, sun725, sunKASP_109, and sunKASP_112 were shown to be suitable for marker-assisted selection in a validation panel of 71 Australian spring wheat genotypes, with the exception of cultivar Orion that carried the Yr34-linked alleles for sunKASP_109 and sunKASP_112. Markers previously reported to be linked with adult plant stripe rust resistance gene Yr48 also cosegregated with Yr34. Wheat genotypes carrying Yr34 and Yr48 produced identical haplotypes for the Yr34-linked markers identified in this study and those previously reported to be linked with Yr48. Phenotypic testing of genotypes carrying Yr34 and Yr48 showed that both genes conferred similar seedling responses to pre-2002 and post-2002 P. striiformis f. sp. tritici pathotypes. Further testing of 600 F2 plants from a cross between WAWHT2046 and RIL143 (Yr48) with P. striiformis f. sp. tritici pathotype 134 E16A+Yr17+Yr27+ failed to reveal any susceptible segregants. Our results strongly suggest that Yr34 and Yr48 are the same gene, and that Yr48 should be considered a synonym of Yr34.

Generation of Paramoeba perurans clonal cultures using flow cytometry and confirmation of virulence.

Amoebic gill disease (AGD) in farmed Atlantic salmon is caused by the amoeba Paramoeba perurans. The recent establishment of in vitro culture techniques for P. perurans has provided a valuable tool for studying the parasite in detail. In this study, flow cytometry was used to generate clonal cultures from single-sorted amoeba, and these were used to successfully establish AGD in experimental Atlantic salmon. The clonal cultures displayed differences in virulence, based on gill scores. The P. perurans load on gills, determined by qPCR analysis, showed a positive relationship with gill score, and with clonal virulence, indicating that the ability of amoebae to proliferate and/or remain attached on gills may play a role in virulence. Gill scores based on gross signs and histopathological analysis were in agreement. No association between level of gill score and specific gill arch was observed. It was found that for fish with lower gill scores based on histopathological examination, gross examination and qPCR analysis of gills from the same fish were less successful in detecting lesions and amoebae, respectively.

A mortality event in wrasse species (Labridae) associated with the presence of viral haemorrhagic septicaemia virus.

Viral haemorrhagic septicaemia (VHS) is an infectious disease of farmed and wild fish and has an extensive host range in both freshwater and marine environments. In December 2012, a wrasse population consisting of ballan, Labrus bergylta (Ascanius), corkwing, Symphodus melops (L.), cuckoo, Labrus mixtus L., goldsinny, Ctenolabrus rupestris (L.), and rock cook, Centrolabrus exoletus (L.), held at a marine hatchery in the Shetland Isles, Scotland, experienced a mortality event. Approximately 10 000 wrasse were being held at the facility on behalf of an Atlantic salmon, Salmo salar L., aquaculture company prior to being deployed for the biological control of parasites on marine pen Atlantic salmon, aquaculture sites. Fish Health Inspectors from Marine Scotland Science initiated a diagnostic investigation, and subsequent diagnostic testing confirmed the site to be VHSV positive by qRT-PCR and virus isolation followed by ELISA. A VHSV genotype-specific qRT-PCR assay revealed that the isolates belonged to genotype III, the European marine strain of the virus. The virus genotype was further confirmed by nucleic acid sequencing of the partial nucleoprotein (N) and glycoprotein (G) genes followed by BLAST nucleotide searches. This study reports for the first time the detection of VHSV within multiple wrasse species and highlights the need for a comprehensive risk-based approach to the use of wrasse and other finfish species as biological controls within the aquaculture industry.

I know why the caged bird sings: Distress tolerant individuals show greater resting state connectivity between ventromedial prefrontal cortex and right amygdala as a function of higher vagal tone.

BACKGROUND: Intolerance to psychological distress is associated with various forms of psychopathology, ranging from addiction to mood disturbance. The capacity to withstand aversive affective states is often explained by individual differences in cardiovagal tone as well as resting state connectivity of the ventromedial prefrontal cortex (vmPFC), a region involved in the regulation of emotions and cardio-autonomic tone. However, it is unclear which brain regions involved in distress tolerance show greater resting state functional connectivity (rsFC) as a function of resting heart rate variability (HRV). METHODS: One-hundred and twenty-six adults, aged 20 to 83.5 years, were selected from a lifespan cohort at the Nathan Kline Institute-Rockland Sample. Participants' distress tolerance levels were assessed based upon performance on the Behavioral Indicator of Resiliency to Distress (BIRD) task. Artifact-free resting-state functional brain scans collected during separate sessions were used. While inside the scanner, a pulse oximeter was used to record beat-to-beat intervals to derive high-frequency heart rate variability (HF-HRV). The relationship between HF-HRV and vmPFC to whole brain functional connectivity was compared between distress tolerant (BIRD completers) and distress intolerant (BIRD non-completers). RESULTS: Groups did not differ in their history of psychiatric diagnosis. Higher resting HF-HRV was associated with longer total time spent on the BIRD task for the entire sample (r = 0.255, p = 0.004). After controlling for age, gender, body mass index, head motion, and gray matter volume. Distress tolerant individuals showed greater rsFC (p < 0.005 (uncorrected), k = 20) between the vmPFC and default-mode network (DMN) hubs including posterior cingulate cortex/precuneus, medial temporal lobes, and the parahippocampal cortex. As a function of higher resting HF-HRV greater vmPFC connectivity was observed with sub-threshold regions in the right amygdala and left anterior prefrontal cortex, with the former passing small volume correction, in distress tolerant versus distress intolerant individuals. CONCLUSION: In a lifespan sample of community-dwelling adults, distress tolerant individuals showed greater vmPFC connectivity with anterior and posterior hubs of the DMN compared to distress intolerant individuals. As a function of greater HF-HRV, distress tolerant individuals evidenced greater vmPFC with salience and executive control network hubs. These findings are consistent with deficits in neural resource allocation within a triple network resting amongst persons exhibiting behavioral intolerance to psychological distress.

Functional effects of CCL3L1 copy number.

Copy number variation (CNV) is becoming increasingly important as a feature of human variation in disease susceptibility studies. However, the consequences of CNV are not so well understood. Here, we present data exploring the functional consequences of CNV of CCL3L1 in 55 independent UK samples with no known clinical phenotypes. The copy number of CCL3L1 was determined by the paralogue ratio test, and expression levels of macrophage inflammatory protein-1α (MIP-1α) and mRNA from stimulated monocytes were measured and analysed. The data show no statistically significant association of MIP-1α protein levels with copy number. However, there was a significant correlation between copy number and CCL3L1:CCL3 mRNA ratio. The data also provide evidence that expression of CCL3 predominates in both protein and mRNA, and therefore the observed variation of CCL3 is potentially more important biologically than that of CNV of CCL3L1.

Development and validation of a range of endogenous controls to support the implementation of practical Taqman real-time PCR-based surveillance for fish diseases within aquaculture.

The use of Taqman real-time PCR-based technology has recently become more frequent in the detection of pathogens in the aquaculture industry. This interest has necessitated the development of robust and reliable pathogen-detection assays. The development of a range of endogenous control assays to be run alongside these diagnostic assays works to further increase confidence in the latter. This study describes the design of a range of endogenous control assays based on the elongation factor 1-α (EF1-α) gene specific to a range of fish species including Atlantic salmon, Salmo salar; rainbow trout, Oncorhynchus mykiss; brown trout, Salmo trutta; cod, Gadus morhua; haddock, Melanogrammus aeglefinus; saithe, Pollachius virens; whiting, Merlangius merlangus; Norway pout, Trisopterus esmarkii; carp (family Cyprinidae), roach, Rutilus rutilus; European eel, Anguilla anguilla; and herring, Clupea harengus, as well as a number of fish cell lines. Evidence is provided of the validation of these assays for specific species, a range of tissue types and cell lines as well as an example of the potential uses of these assays.

A multiple resistance locus on chromosome arm 3BS in wheat confers resistance to stem rust (Sr2), leaf rust (Lr27) and powdery mildew.

Sr2 is the only known durable, race non-specific adult plant stem rust resistance gene in wheat. The Sr2 gene was shown to be tightly linked to the leaf rust resistance gene Lr27 and to powdery mildew resistance. An analysis of recombinants and mutants suggests that a single gene on chromosome arm 3BS may be responsible for resistance to these three fungal pathogens. The resistance functions of the Sr2 locus are compared and contrasted with those of the adult plant resistance gene Lr34.

Detection of salmonid alphavirus RNA in wild marine fish: implications for the origins of salmon pancreas disease in aquaculture.

Salmonid alphaviruses (SAVs), which include the aetiological agents of salmon pancreas disease (SPD) in farmed Atlantic salmon Salmo salar L. and sleeping disease (SD) in rainbow trout Oncorhynchus mykiss (Walbaum), are significant viral pathogens of European salmonid aquaculture. SAV is horizontally transmitted and the virus can survive for extended periods in seawater. A lack of convincing evidence for vertical transmission coupled to the fact that the SPD virus (SPDV) occurs in historically infected sites irrespective of fallow period duration suggests that a substantial reservoir of infection exists in the marine environment. We used a highly sensitive real-time PCR (qPCR) assay targeting a region of the SAV nsP1 gene to screen wild marine fish species for the presence of SAV in an attempt to identify such a potential reservoir. Screened fish species were caught in the vicinity of aquaculture activity in an area with a previous history of SAV infection (Shetland Isles, Scotland). SAV RNA was detected in internal organs (kidney and heart) from the flatfish species common dab Limanda limanda, long rough dab Hippoglossoides platessoides, and plaice Pleuronectes platessa. Based on these findings, sampling was extended to an area remote from aquaculture activity (Stonehaven Bay, NE coast of Scotland) from where heart tissues obtained from common dab also tested positive. While no virus could be cultivated from these samples, qPCR detections were shown to be SAV-specific by sequencing of an alternative gene region (E2) to that targeted by the qPCR assay. Analysis of these nucleotide sequences revealed minor differences to those previously obtained from farmed salmon, and subsequent phylogenetic analysis of an E2 dataset demonstrated a subtype V-like sequence.

Take my breath away: Neural activation at breath-hold differentiates individuals with panic disorder from healthy controls.

There is neuroanatomical evidence of an "extended fear network" of brain structures involved in the etiology of panic disorder (PD). Although ventilatory distrubance is a primary symptom of PD these sensations may also trigger onset of a panic attack (PA). Here, a voluntary breath-holding paradigm was used to mimic the hypercapnia state in order to compare blood oxygen level-dependent (BOLD) response, at the peak of a series of 18 s breath-holds, of 21 individuals with PD to 21 low anxiety matched controls. Compared to the rest condition, BOLD activity at the peak (12 - 18 s) of the breath-hold was greater for PD versus controls within a number of structures implicated in the extended fear network, including hippocampus, thalamus, and brainstem. Activation was also observed in cortical structures that are shown to be involved in interoceptive and self-referential processing, such as right insula, middle frontal gyrus, and precuneus/posterior cingulate. In lieu of amygdala activation, our findings show elevated activity throughout an extended network of cortical and subcortical structures involved in contextual, interoceptive and self-referential processing when individuals with PD engage in voluntary breath-holding.

The disengage deficit in hemispatial neglect is restricted to between-object shifts and is abolished by prism adaptation.

We sought to determine the effects of prism adaptation on peripherally cued visual attention shifting in patients with spatial neglect, using a task devised by Egly et al. (J Exp Psychol Gen 123:161-177, 1994) based on the classic Posner paradigm. This task allowed a comparison of "within-object" versus "between-object" attention shifts. A display was presented containing two parallel outline rectangles, and subjects were asked to make rapid responses to a target, which would appear at one end of one of the rectangles. The target location was pre-cued with 75% validity: on invalid trials attention was directed either to the other end of the same rectangle, or to the other rectangle. Healthy subjects and right-hemisphere patients without neglect showed a left-right symmetrical pattern, with a larger validity effect when required to shift attention between rectangles, thus indicating a greater difficulty of attention-shifting between than within the respective shapes. The neglect patients showed the typical leftward "disengage deficit" previously observed in neglect, but only for attention shifts between objects, indicating that the effect is object-based rather than purely spatial. A comparison of vertical and horizontal shift costs showed that this attention-shifting deficit for left-hemifield target stimuli was directional rather than hemifield-based: it was absent for vertical shifts of attention within the left hemifield. Finally, we found that prism adaptation abolished the disengage deficit. We found no effects of prism adaptation in the control subjects. We argue that prism adaptation has a powerful effect on one of the fundamental manifestations of the neglect syndrome.

Tools and constraints in monitoring interactions between marine litter and megafauna: Insights from case studies around the world.

Adverse impacts of marine litter is documented on >1400 species, including marine megafauna (fish, birds, sea turtles and mammals). The primary impacts include ingestion and entanglement, and there is increasing concern about chemical contamination via ingestion. Numerous survey approaches and monitoring programs have been developed and implemented around the world. They may aim to provide data about parameters such as species distribution and interactions with anthropogenic activities. During the Sixth International Marine Debris Conference, a session was dedicated to the tools and constraints in monitoring interactions between litter and megafauna. In the present paper, we summarize 7 case studies which discuss entanglement and ingestion including macro- and micro-debris in several taxa and across multiple geographic regions. We then discusses the importance of tools and standardizing methods for assessment and management purposes, in the context of international environmental policies and marine litter strategies.

Grasping the past. delay can improve visuomotor performance.

"Optic ataxia" is caused by damage to the human posterior parietal cortex (PPC). It disrupts all components of a visually guided prehension movement, not only the transport of the hand toward an object's location, but also the in-flight finger movements pretailored to the metric properties of the object. Like previous cases, our patient (I.G.) was quite unable to open her handgrip appropriately when directly reaching out to pick up objects of different sizes. When first tested, she failed to do this even when she had previewed the target object 5 s earlier. Yet despite this deficit in "real" grasping, we found, counterintuitively, that I.G. showed good grip scaling when "pantomiming" a grasp for an object seen earlier but no longer present. We then found that, after practice, I.G. became able to scale her handgrip when grasping a real target object that she had previewed earlier. By interposing catch trials in which a different object was covertly substituted for the original object during the delay between preview and grasp, we found that I.G. was now using memorized visual information to calibrate her real grasping movements. These results provide new evidence that "off-line" visuomotor guidance can be provided by networks independent of the PPC.

Changes in Nutritional and Functional Status in Longer Stay Patients Admitted to a Geriatric Evaluation and Management Unit.

OBJECTIVES: Malnutrition and functional decline are common in older inpatients admitted to subacute care settings. However the association between changes in nutritional status and relevant functional outcomes remains under-researched. This study examined changes in nutritional status, function and mobility in patients admitted to a Geriatric Evaluation and Management (GEM) unit who had a length of stay (LOS) longer than 21 days. DESIGN: A prospective, observational study. SETTING: Two GEM units at St Vincent's Hospital Melbourne, Australia. PARTICIPANTS: Patients admitted to the GEM units who stayed longer than 21 days were included in the study. MEASUREMENTS: Patients were assessed on admission and prior to discharge using the Subjective Global Assessment (SGA), Functional Independence Measure (FIM) motor domain and the Modified Elderly Mobility Scale (MEMS). RESULTS: Fifty-nine patients (Mean age 84.0 ± 7 years) met the required length of stay and were included in the study. Fifty-four per cent (n=32) were malnourished on admission (SGA B/C) and 44% (n=26) were malnourished on discharge. Twenty-two per cent (n=13) improved SGA category, 75% remained stable (n=44) and 3% deteriorated (n=2) from admission to discharge. Total Motor FIM scores significantly increased from admission to discharge in both the improved (p<0.001) and stable or deteriorated (p<0.001) nutritional status groups. Subjects who improved in nutritional status had a significantly higher MEMS score at discharge (p<0.001). CONCLUSION: On admission to the GEM unit, just over half the included patients were rated as malnourished defined by SGA category. Nearly one quarter of the sample had improved their nutritional status at the time of discharge. Improvement in nutritional status was associated with greater improvement in mobility scores. Further studies are required to investigate the effectiveness of nutrition interventions, which will inform models of care aiming to optimise nutritional, functional, and associated clinical outcomes in patients admitted to GEM units.

Reaching errors in optic ataxia are linked to eye position rather than head or body position.

When reaching towards a visual stimulus, spatial information about the target must be transformed into an appropriate motor command. Visual information is coded initially in retinotopic coordinates, while the reaching movement ultimately requires the specification of the target position in limb-centred coordinates. It is well established that the posterior parietal cortex (PPC) plays an important role in transforming visual target information into motor commands. Lesions in the PPC can result in optic ataxia, a condition in which the visual guidance of goal-directed movements is impaired. Here, we present evidence from two patients with unilateral optic ataxia following right PPC lesions, that the pattern of reaching errors is linked to an eye-centred frame of reference. Both patients made large errors when reaching to visual targets on the left side of space, while facing and fixating straight ahead. By varying the location of fixation and the orientation of the head and body, we were able to establish that these large errors were made specifically to targets to the left of eye-fixation, rather than to the left of head-, body-, or limb-relative space. These data support the idea that visual targets for reaching movements are coded in eye-centred coordinates within the posterior parietal cortex.

Anticipatory breeding for resistance to rust diseases in wheat.

Anticipatory resistance breeding is the process of predicting future pathotypes and producing resistant germplasm to avert future losses. It is made possible by a national pathotype surveillance program and knowledge that new pathotypes arise predominantly from mutation in existing pathotypes. This is supported by genetic analyses to catalogue the identity and distribution of resistance genes in current cultivars. A national germplasm enhancement program ensuring that both currently effective and potentially new sources of resistance are available in a wide range of adapted genotypes enables rapid cultivar replacement before or soon after the occurrence of new pathotypes. The policy of recommending only rust-resistant cultivars in the more rust-prone areas has resulted in significant reductions in pathogen population size and variability. With increased and more rapid international human travel and transport, there is an increased threat of exotic pathotypes, the effects of which are more difficult to predict. As the frequency and magnitude of epidemics decline, public awareness programs will be required to achieve and maintain the use of rust resistance by the entire wheat industry.

Coherent quantum transport features in carbon superlattice structures.

Whilst resonant transmission is well understood and can be fully harnessed for crystalline superlattices, a complete picture has not yet emerged for disordered superlattices. It has proven difficult to tune resonant transmission in disordered diamond-like carbon (DLC) superlattices as conventional models are not equipped to incorporate significant structural disorder. In this work, we present concurrent experimental and theoretical analysis which addresses resonant transmission in DLC superlattices. Devices were fabricated by growing alternate layers of DLC with different percentages of sp3 hybridized carbon.Coherent quantum transport effects were demonstrated in these structurally disordered DLC superlattices through distinct current modulation with negative differential resistance (NDR) in the current-voltage (I-V) measurements. A model was developed using tight-binding calculations assuming a random variation of the hopping integral to simulate structural (bond-length) disorder. Calculations of the I-V characteristics compliment the interpretation of the measurements and illustrate that while DLC superlattice structures are unlike their classical counterparts, the near-field structural order will help with the confinement of quantised states. The present model provides an empirical guide for tailoring the properties of future devices, giving rise to much hope that carbon electronics operating at high frequencies over large areas can now be developed.

Fluorescence depolarization in a model system: carbonic anhydrase-dansyl sulphonamide.

The model system, carbonic anhydrase to which dansyl sulphonamide is specifically adsorbed, was chosen to test the fundamentals of the fluorescence depolarisation method. Fluorescence decay was shown to be satisfactorily represented by a single exponential decay term and the derived lifetime did not seem to vary significantly with mean excitation or emission wavelength. Depolarisation measurements were quite reproducible and those made with varying temperature were consistent with those performed with varying solution viscosity, thus excluding localised dye rotation. The calculated relaxation time, which was independent of wavelength of excitation or emission, was in conformity with a rigid spherical molecule of molecular weight 29 000 with 30% hydration.

Cloning and analysis of IgM anti-thyroglobulin autoantibodies from patients with Hashimoto's thyroiditis.

Hashimoto's thyroiditis is an autoimmune disease in which autoantibodies reactive to a number of thyroid antigens are made. In order to investigate the autoantibody repertoire in this disease, B cells from four patients with Hashimoto's thyroiditis were immortalised and, after limiting dilution, screened for reactivity to thyroid antigens. After a second limiting dilution, one anti-thyroglobulin IgM-secreting clone from three patients, and four clones from one patient, were analysed. The Ig heavy and light chain genes from each clone were amplified using the polymerase chain reaction and sequenced. The resulting heavy and light chain sequences were heterogeneous, although the four clones from one patient and the clone from a second patient shared a germline VH sequence. All antibodies had similar functional affinity, comparable to serum IgG from Hashimoto's patients. The cross-reactivity of the antibodies was analysed against bovine and rat thyroglobulin, histones, cardiolipin and human skeletal muscle. The antibodies were polyreactive, indicating that they are probably natural autoantibodies of unknown pathogenic significance.