QUANTITATIVE TRAIT LOCI FOR AGRONOMIC AND END-USE QUALITY PERFORMANCE AND THE EFFECT OF SOILBORNE WHEAT MOSAIC VIRUS IN A HARD WINTER WHEAT POPULATION IN NEBRASKA

To better understand agronomic and end-use quality in wheat (Triticum aestivum L.) we developed a population containing 154 F6:8 recombinant inbred lines (RILs) from the cross TAM107-R7/Arlin. The parental lines and RILs were phenotyped at six environments in Nebraska and differed for resistance to Wheat soilborne mosaic virus (WSBMV), morphological, agronomic, and end-use quality traits. Additionally, a 2300 cM genome-wide linkage map was created for quantitative trait loci (QTL) analysis. Based on our results across multiple environments, the best RILs could be used for cultivar improvement. The population and marker data are publicly available for interested researchers for future research. The population was used to determine the effect of WSBMV on agronomic and end-use quality and for the mapping of a resistance locus. Results from two infected environments showed that all but two agronomic traits were significantly affected by the disease. Specifically, the disease reduced grain yield by 30% of susceptible RILs and they flowered 5 d later and were 11 cm shorter. End-use quality traits were not negatively affected but flour protein content was increased in susceptible RILs. The resistance locus SbmTmr1 mapped to 27.1 cM near marker wPt-5870 on chromosome 5DL using ELISA data. Finally, we investigated how WSBMV affected QTL detection in the population. QTLs were mapped at two WSBMV infected environments, four uninfected environments, and in the resistant and susceptible RIL subpopulations in the infected environments. Fifty-two significant (LOD≥3) QTLs were mapped in RILs at uninfected environments. Many of the QTLs were pleiotropic or closely linked at 6 chromosomal regions. Forty-seven QTLs were mapped in RILs at WSBMV infected environments. Comparisons between uninfected and infected environments identified 20 common QTLs and 21 environmentally specific QTLs. Finally, 24 QTLs were determined to be affected by WSBMV by comparing the subpopulations in QTL analyses within the same environment. The comparisons were statistically validated using marker by disease interactions. These results showed that QTLs can be affected by WSBMV and careful interpretation of QTL results is needed where biotic stresses are present. Finally, beneficial QTLs not affected by WSBMV or the environment are candidates for marker-assisted selection.

Taking an Endemically Infected Bovine Tb Area Through to Livestock Clearance. A Case Study of West Taupo, New Zealand

The Pest Management Strategy for Bovine Tuberculosis (Tb) in New Zealand aims to achieve efficient freedom from Tb by 2013 and to eradicate the disease from livestock and wildlife. The West Taupo area, in the central North Island of New Zealand, was chronically infected with Tb in both domestic livestock herds (cattle and deer) and within wildlife populations (brushtail possum, ferret, feral deer and pigs). Through the development and implementation of a technically innovative management plan, this area is now approaching Tb free status. The case study / management plan reported here discusses the operational techniques and strategies that were implemented to achieve Tb clearance in the livestock herds and the possibilities of eradication from wildlife species. It particularly identifies the variations in control strategies that are required as population densities reduce and the challenges of maintaining strong effective control at low densities of some wildlife species, whilst not needing to control other species that were initially clinically diagnosed with Tb control. Use of diagnostic tools and education as an area moves through the cycle towards Tb freedom are as essential as the physical control activities. The use of intensive monitoring of both livestock and wildlife species as trend and performance indicators and the need to educate farmers, hunters and other land use groups become increasingly important.

DEVELOPMENTAL STATUS OF N-(3-CHLORO-4-METHYLPHENYL) ACETAMIDE AS A CANDIDATE BLACKBIRD/STARLING ROOST TOXICANT

Large winter roosts of blackbirds (Icteridae) and starlings (Sturnus vulgaris) often cause conflicts, both real and imagined, between the birds and local human popula- tions. These conflicts may range from objections to the noise and odor engendered by thousands or millions of birds, to fear of epidemic human and livestock diseases, and the possibility of economic losses from crop depredations. Many people believe the most direct way to combat these conflicts is to reduce local roosting populations by kill- ing the birds. In response to this perceived need for a roost toxicant, the U.S. Fish and Wildlife Service (FWS) developed PA-14, a surfactant which can be aerially applied to problem roosts for population reduction (Lefebvre and Seubert 1970). Successful use of this material, however, requires concurrent rainfall and low temperatures, conditions which may not occur sufficiently often to permit roost treatment at desired times or places. Because of this difficulty, and continued pressures from management person- nel and the agricultural community, the Service has continued its search for a safe, ef- fective roost toxicant usable without severe weather restrictions. One of the current candidate materials is N-(3-chloro-4-methylphenyl)acetamide (CAT, DRC-2698), a derivative of StarlicideR (DRC-1339). This compound was initially developed by S.A. Peoples of the University of California-Davis (Peoples et al. 1976). California researchers are still investigating the avicidal potential of CAT, mainly on baits and in wick perches, while FWS interest has centered thus far on its possible utility as an aerially applied roost treatment. This report is a summary of our investigations to date.

Measuring Aeolian Saltation: A Comparison of Sensors

SHERMAN, D.J.; LI, B.; FERRELL E.J.; ELLIS, J.T.; COX, W.D.; MAIA, L.P., and SOUSA, P.H.G.O., 2011. Measuring Aeolian Saltation: A Comparison of Sensors. In: Roberts, T.M., Rosati, J.D., and Wang, P. (eds.), Proceedings, Symposium to Honor Dr. Nicholas C. Kraus, Journal of Coastal Research, Special Issue, No. 59, pp. 280-290. West Palm Beach (Florida), ISSN 0749-0208. We report the results of field experiments designed to compare four types of aeolian saltation sensors: the Safire; the Wenglor (R) Particle Counter; the Miniphone; and the Buzzer Disc. Sets of sensors were deployed in tight spatial arrays and sampled at rates as fast as 20 kHz. In two of the three trials, the data from the sensors are compared to data obtained from sand traps. The Miniphone and the Buzzer Disc, based on microphone and piezoelectric technologies, respectively, produced grain impact counts comparable to those derived from the trap data. The Satire and the Wenglor (R) Particle Counter produce count rates that were an order of magnitude too slow. Satires undercount because of their large momentum threshold and because its signal is saturated at relatively slow transport rates. We conclude that the Miniphone and the Buzzer Disc are appropriate for deployment as grain counters because their small size allows them to be installed in closely-spaced sets.

Lectotypification of the name Helianthus dentatus Cav., basionym of Viguiera dentata (Cav.) Spreng. (Asteraceae: Heliantheae)

A recent molecular phylogenetic analysis (Schilling & Panero 2011) proposed to narrow the concept of the paraphyletic genus Viguiera Kunth (1818: 176; Asteraceae: Heliantheae) to embrace only the type, V. dentata (Cavanilles 1794: 10) Sprengel (1826: 615). Robinson (1977) emphasized the peculiarities of Viguiera dentata as the "distinctive and unique" presence of hairs on the filaments of the anther, the disk corollas throat less than twice as long as the lobes and densely scabrous below, a combination of features that differs from most member of the genus. During taxonomic studies of Viguiera and related genera, it was discovered that V. dentata has never been typified. The basionym, Helianthus dentatus, was described by Antonio Jose Cavanilles in Icones et Descriptiones Plantarum based on plants grown in the Real Jardin Botanico from seed sent by Martin Sesse from Mexico (Blanco 2000). Previous workers including Blake (1918) and Robinson (1977) have accepted the plate in Cavanilles as the type for Helianthus dentatus Cav.

Whole genome sequencing analysis of Plasmodium vivax using whole genome capture

Background: Malaria caused by Plasmodium vivax is an experimentally neglected severe disease with a substantial burden on human health. Because of technical limitations, little is known about the biology of this important human pathogen. Whole genome analysis methods on patient-derived material are thus likely to have a substantial impact on our understanding of P. vivax pathogenesis and epidemiology. For example, it will allow study of the evolution and population biology of the parasite, allow parasite transmission patterns to be characterized, and may facilitate the identification of new drug resistance genes. Because parasitemias are typically low and the parasite cannot be readily cultured, on-site leukocyte depletion of blood samples is typically needed to remove human DNA that may be 1000X more abundant than parasite DNA. These features have precluded the analysis of archived blood samples and require the presence of laboratories in close proximity to the collection of field samples for optimal pre-cryopreservation sample preparation. Results: Here we show that in-solution hybridization capture can be used to extract P. vivax DNA from human contaminating DNA in the laboratory without the need for on-site leukocyte filtration. Using a whole genome capture method, we were able to enrich P. vivax DNA from bulk genomic DNA from less than 0.5% to a median of 55% (range 20%-80%). This level of enrichment allows for efficient analysis of the samples by whole genome sequencing and does not introduce any gross biases into the data. With this method, we obtained greater than 5X coverage across 93% of the P. vivax genome for four P. vivax strains from Iquitos, Peru, which is similar to our results using leukocyte filtration (greater than 5X coverage across 96% of the genome). Conclusion: The whole genome capture technique will enable more efficient whole genome analysis of P. vivax from a larger geographic region and from valuable archived sample collections.

RNA Interference of Endochitinases in the Sugarcane Endophyte Trichoderma virens 223 Reduces Its Fitness as a Biocontrol Agent of Pineapple Disease

The sugarcane root endophyte Trichoderma virens 223 holds enormous potential as a sustainable alternative to chemical pesticides in the control of sugarcane diseases. Its efficacy as a biocontrol agent is thought to be associated with its production of chitinase enzymes, including N-acetyl-beta-D-glucosaminidases, chitobiosidases and endochitinases. We used targeted gene deletion and RNA-dependent gene silencing strategies to disrupt N-acetyl-beta-D-glucosaminidase and endochitinase activities of the fungus, and to determine their roles in the biocontrol of soil-borne plant pathogens. The loss of N-acetyl-beta-D-glucosaminidase activities was dispensable for biocontrol of the plurivorous damping-off pathogens Rhizoctonia solani and Sclerotinia sclerotiorum, and of the sugarcane pathogen Ceratocystis paradoxa, the causal agent of pineapple disease. Similarly, suppression of endochitinase activities had no effect on R. solani and S. sclerotiorum disease control, but had a pronounced effect on the ability of T. virens 223 to control pineapple disease. Our work demonstrates a critical requirement for T. virens 223 endochitinase activity in the biocontrol of C. paradoxa sugarcane disease, but not for general antagonism of other soil pathogens. This may reflect its lifestyle as a sugarcane root endophyte.

Identification of Novel Interaction between ADAM17 (a Disintegrin and Metalloprotease 17) and Thioredoxin-1

ADAM17, which is also known as TNF alpha-converting enzyme, is the major sheddase for the EGF receptor ligands and is considered to be one of the main proteases responsible for the ectodomain shedding of surface proteins. How a membrane-anchored proteinase with an extracellular catalytic domain can be activated by inside-out regulation is not completely understood. We characterized thioredoxin-1 (Trx-1) as a partner of the ADAM17 cytoplasmic domain that could be involved in the regulation of ADAM17 activity. We induced the overexpression of the ADAM17 cytoplasmic domain in HEK293 cells, and ligands able to bind this domain were identified by MS after protein immunoprecipitation. Trx-1 was also validated as a ligand of the ADAM17 cytoplasmic domain and full-length ADAM17 recombinant proteins by immunoblotting, immunolocalization, and solid phase binding assay. In addition, using nuclear magnetic resonance, it was shown in vitro that the titration of the ADAM17 cytoplasmic domain promotes changes in the conformation of Trx-1. The MS analysis of the cross-linked complexes showed cross-linking between the two proteins by lysine residues. To further evaluate the functional role of Trx-1, we used a heparin-binding EGF shedding cell model and observed that the overexpression of Trx-1 in HEK293 cells could decrease the activity of ADAM17, activated by either phorbol 12-myristate 13-acetate or EGF. This study identifies Trx-1 as a novel interaction partner of the ADAM17 cytoplasmic domain and suggests that Trx-1 is a potential candidate that could be involved in ADAM17 activity regulation.

Hypoellipticity in spaces of ultradistributions-Study of a model case

In this work we study C (a)-hypoellipticity in spaces of ultradistributions for analytic linear partial differential operators. Our main tool is a new a-priori inequality, which is stated in terms of the behaviour of holomorphic functions on appropriate wedges. In particular, for sum of squares operators satisfying Hormander's condition, we thus obtain a new method for studying analytic hypoellipticity for such a class. We also show how this method can be explicitly applied by studying a model operator, which is constructed as a perturbation of the so-called Baouendi-Goulaouic operator.

Influence of HAART on Alternative Reading Frame Immune Responses over the Course of HIV-1 Infection

Background: Translational errors can result in bypassing of the main viral protein reading frames and the production of alternate reading frame (ARF) or cryptic peptides. Within HIV, there are many such ARFs in both sense and the antisense directions of transcription. These ARFs have the potential to generate immunogenic peptides called cryptic epitopes (CE). Both antiretroviral drug therapy and the immune system exert a mutational pressure on HIV-1. Immune pressure exerted by ARF CD8(+) T cells on the virus has already been observed in vitro. HAART has also been described to select HIV-1 variants for drug escape mutations. Since the mutational pressure exerted on one location of the HIV-1 genome can potentially affect the 3 reading frames, we hypothesized that ARF responses would be affected by this drug pressure in vivo. Methodology/Principal findings: In this study we identified new ARFs derived from sense and antisense transcription of HIV-1. Many of these ARFs are detectable in circulating viral proteins. They are predominantly found in the HIV-1 env nucleotide region. We measured T cell responses to 199 HIV-1 CE encoded within 13 sense and 34 antisense HIV-1 ARFs. We were able to observe that these ARF responses are more frequent and of greater magnitude in chronically infected individuals compared to acutely infected patients, and in patients on HAART, the breadth of ARF responses increased. Conclusions/Significance: These results have implications for vaccine design and unveil the existence of potential new epitopes that could be included as vaccine targets.

Segmental dataset and whole body expression data do not support the hypothesis that non-random movement is an intrinsic property of Drosophila retrogenes

Background: Several studies in Drosophila have shown excessive movement of retrogenes from the X chromosome to autosomes, and that these genes are frequently expressed in the testis. This phenomenon has led to several hypotheses invoking natural selection as the process driving male-biased genes to the autosomes. Metta and Schlotterer (BMC Evol Biol 2010, 10:114) analyzed a set of retrogenes where the parental gene has been subsequently lost. They assumed that this class of retrogenes replaced the ancestral functions of the parental gene, and reported that these retrogenes, although mostly originating from movement out of the X chromosome, showed female-biased or unbiased expression. These observations led the authors to suggest that selective forces (such as meiotic sex chromosome inactivation and sexual antagonism) were not responsible for the observed pattern of retrogene movement out of the X chromosome. Results: We reanalyzed the dataset published by Metta and Schlotterer and found several issues that led us to a different conclusion. In particular, Metta and Schlotterer used a dataset combined with expression data in which significant sex-biased expression is not detectable. First, the authors used a segmental dataset where the genes selected for analysis were less testis-biased in expression than those that were excluded from the study. Second, sex-biased expression was defined by comparing male and female whole-body data and not the expression of these genes in gonadal tissues. This approach significantly reduces the probability of detecting sex-biased expressed genes, which explains why the vast majority of the genes analyzed (parental and retrogenes) were equally expressed in both males and females. Third, the female-biased expression observed by Metta and Schltterer is mostly found for parental genes located on the X chromosome, which is known to be enriched with genes with female-biased expression. Fourth, using additional gonad expression data, we found that autosomal genes analyzed by Metta and Schlotterer are less up regulated in ovaries and have higher chance to be expressed in meiotic cells of spermatogenesis when compared to X-linked genes. Conclusions: The criteria used to select retrogenes and the sex-biased expression data based on whole adult flies generated a segmental dataset of female-biased and unbiased expressed genes that was unable to detect the higher propensity of autosomal retrogenes to be expressed in males. Thus, there is no support for the authors' view that the movement of new retrogenes, which originated from X-linked parental genes, was not driven by selection. Therefore, selection-based genetic models remain the most parsimonious explanations for the observed chromosomal distribution of retrogenes.

Head & neck optical diagnostics: vision of the future of surgery

Review paper and Proceedings of the Inaugural Meeting of the Head and Neck Optical Diagnostics Society (HNODS) on March 14th 2009 at University College London.

At the frontiers of surgery: review

The complete surgical removal of disease is a desirable outcome particularly in oncology. Unfortunately much disease is microscopic and difficult to detect causing a liability to recurrence and worsened overall prognosis with attendant costs in terms of morbidity and mortality. It is hoped that by advances in optical diagnostic technology we could better define our surgical margin and so increase the rate of truly negative margins on the one hand and on the other hand to take out only the necessary amount of tissue and leave more unaffected non-diseased areas so preserving function of vital structures. The task has not been easy but progress is being made as exemplified by the presentations at the 2nd Scientific Meeting of the Head and Neck Optical Diagnostics Society (HNODS) in San Francisco in January 2010. We review the salient advances in the field and propose further directions of investigation.

The future of medical diagnostics: review paper

While histopathology of excised tissue remains the gold standard for diagnosis, several new, non-invasive diagnostic techniques are being developed. They rely on physical and biochemical changes that precede and mirror malignant change within tissue. The basic principle involves simple optical techniques of tissue interrogation. Their accuracy, expressed as sensitivity and specificity, are reported in a number of studies suggests that they have a potential for cost effective, real-time, in situ diagnosis.

Development of replication-defective lymphocytic choriomeningitis virus vectors for the induction of potent CD8+ T cell immunity

Lymphocytic choriomeningitis virus (LCMV) exhibits natural tropism for dendritic cells and represents the prototypic infection that elicits protective CD8(+) T cell (cytotoxic T lymphocyte (CTL)) immunity. Here we have harnessed the immunobiology of this arenavirus for vaccine delivery. By using producer cells constitutively synthesizing the viral glycoprotein (GP), it was possible to replace the gene encoding LCMV GP with vaccine antigens to create replication-defective vaccine vectors. These rLCMV vaccines elicited CTL responses that were equivalent to or greater than those elicited by recombinant adenovirus 5 or recombinant vaccinia virus in their magnitude and cytokine profiles, and they exhibited more effective protection in several models. In contrast to recombinant adenovirus 5, rLCMV failed to elicit vector-specific antibody immunity, which facilitated re-administration of the same vector for booster vaccination. In addition, rLCMV elicited T helper type 1 CD4+ T cell responses and protective neutralizing antibodies to vaccine antigens. These features, together with low seroprevalence in humans, suggest that rLCMV may show utility as a vaccine platform against infectious diseases and cancer.