Analysis of the bread wheat genome using whole-genome shotgun sequencing

Bread wheat (Triticum aestivum) is a globally important crop, accounting for 20 per cent of the calories consumed by humans. Major efforts are underway worldwide to increase wheat production by extending genetic diversity and analysing key traits, and genomic resources can accelerate progress. But so far the very large size and polyploid complexity of the bread wheat genome have been substantial barriers to genome analysis. Here we report the sequencing of its large, 17-gigabase-pair, hexaploid genome using 454 pyrosequencing, and comparison of this with the sequences of diploid ancestral and progenitor genomes. We identified between 94,000 and 96,000 genes, and assigned two-thirds to the three component genomes (A, B and D) of hexaploid wheat. High-resolution synteny maps identified many small disruptions to conserved gene order. We show that the hexaploid genome is highly dynamic, with significant loss of gene family members on polyploidization and domestication, and an abundance of gene fragments. Several classes of genes involved in energy harvesting, metabolism and growth are among expanded gene families that could be associated with crop productivity. Our analyses, coupled with the identification of extensive genetic variation, provide a resource for accelerating gene discovery and improving this major crop.

SU-E-T-01: Applications of 6MV FFF Photon Beams in Optimizing Radiobiological Response for Respiratory-Gated Liver SBRT

PURPOSE

To establish a radiobiological basis for gated stereotactic body radiotherapy of primary and metastatic liver cancers using volumetric arc radiotherapy in a flattening filter free (FFF) mode.

METHODS

Human cervical carcinoma, SiHa, non-small cell lung carcinoma, H460, and Chinese hamster V79 cells were irradiated in a water bath with 6MV photons from a Varian TrueBeam linear accelerator. To establish dose-response and its sensitivity to dose rate following acute irradiation, doses of 2, 4, 6, 8 and 10 Gy were delivered in FFF mode at 400 and 1200 MU/min. To investigate whether removal of the flattening filter affects cell response, doses of 5 and 10 Gy were delivered to SiHa and H460 cells in FFF and filtered modes at 400 MU/min. Finally, to assess the effect of protracting dose delivery by gating, a dose of 10 Gy was delivered to SiHa and H460 cells acutely and also over 15, 30 and 60 min.

RESULTS

Dose-response over doses examined was independent of dose rate in FFF mode. Differences in cell survival following irradiation in FFF and filtered modes were not significant. However a significant increase in survival for both H460 and SiHa cells was observed for 15 min split-dose irradiation compared to acute irradiation but further increase in irradiation time to 60 min did not affect cell survival.

CONCLUSIONS

Dose rate and presence of a flattening filter showed no effect on cell survival, however, survival was significantly affected when dose delivery time was protracted to that typical of conformal field therapy. Volumetric arc based gated SBRT may be beneficial for tumor cell kill, though the gating window and duty cycle have to be balanced against the effect of dose delivery protraction. Research Support (Varian Medical Systems).

Development and characterization of wheat-Ae. searsii Robertsonian translocations and a recombinant chromosome conferring resistance to stem rust

The emergence of a new highly virulent race of stem rust (Puccinia graminis tritici), Ug99, rapid evolution of new Ug99 derivative races overcoming resistance of widely deployed genes, and spread towards important wheat growing areas now potentially threaten world food security. Exploiting novel genes effective against Ug99 from wild relatives of wheat is one of the most promising strategies for the protection of the wheat crop. A new source of resistance to Ug99 was identified in the short arm of the Aegilops searsii chromosome 3S(s) by screening wheat- Ae. searsii introgression libraries available as individual chromosome and chromosome arm additions to the wheat genome. For transferring this resistance gene into common wheat, we produced three double-monosomic chromosome populations (3A/3S(s), 3B/3S(s) and 3D/3S(s)) and then applied integrated stem rust screening, molecular maker analysis, and cytogenetic analysis to identify resistant wheat-Ae. searsii Robertsonian translocation. Three Robertsonian translocations (T3AL·3S(s)S, T3BL·3S(s)S and T3DL·3S(s)S) and one recombinant (T3DS-3S(s)S·3S(s)L) with stem rust resistance were identified and confirmed to be genetically compensating on the basis of genomic in situ hybridization, analysis of 3A, 3B, 3D and 3S(s)S-specific SSR/STS-PCR markers, and C-banding. In addition, nine SSR/STS-PCR markers of 3S(s)S-specific were developed for marker-assisted selection of the resistant gene. Efforts to reduce potential linkage drag associated with 3S(s)S of Ae. searsii are currently under way.

Circumferential resection margin (CRM) in esophageal (OC) and gastroesophageal (GOJ) cancers

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Background: We hypothesized that CRM size affect survival and local recurrence for OC and GOJ cancer. We also assessed the utility of CT in predicting margin status.

Methods: A retrospective analysis of a prospective database was carried out on all patients who had esophagectomy between January 2000 and July 2008. Patients diagnosed with OC and GOJ tumors on final pathologic examination were included. Distance from the CRM was assessed by a specialist upper GI pathologist. Two radiologists, blinded to postoperative margin status, reviewed preoperative CT scans using 16 separate parameters, comparing them to measured CRM status.

Results: 419 patients were assessed. 223 pts had OC or GOJ type 1 tumors, average age 62 years (range 36–80), mean follow-up 5.8 years (2-9.5). There were 125 deaths and median overall survival (OS) 3.33 years (95% CI 2.76-6.24). 76 patients had recurrence at a median of 1.3 years (0.1-4.7). For 144 patients had OC or GOJ type 1 T3 tumors. Selected results are presented in the Table. There was no CRM size above which there was no further reduction in recurrence. Postoperative chemoradiation did not improve OS (p=0.79) or recurrence (p=0.96) in patients with CRM of 0-1 mm. In 50 patients the CT parameters significantly correlated with margin status were largest axial diameter (p=0.003) and contact with adjacent structures (p=0.005). A complete statistical review with multivariate and subgroup analyses will be presented.

Conclusions: CRM size is strongly correlated with survival and recurrence in OC and type 1 GOJ tumors. Prediction of a close CRM could be used to select for more intensive therapy prior to undergoing radical surgery, such as chemoradiation. Preoperative CT can help in this prediction.

[Table: see text]

No significant financial relationships to disclose.

Complexity and accuracy of image registration methods in SPECT-guided radiation therapy

The use of functional imaging in radiotherapy treatment (RT) planning requires accurate co-registration of functional imaging scans to CT scans. We evaluated six methods of image registration for use in SPECT-guided radiotherapy treatment planning. Methods varied in complexity from 3D affine transform based on control points to diffeomorphic demons and level set non-rigid registration. Ten lung cancer patients underwent perfusion SPECT-scans prior to their radiotherapy. CT images from a hybrid SPECT/CT scanner were registered to a planning CT, and then the same transformation was applied to the SPECT images. According to registration evaluation measures computed based on the intensity difference between the registered CT images or based on target registration error, non-rigid registrations provided a higher degree of accuracy than rigid methods. However, due to the irregularities in some of the obtained deformation fields, warping the SPECT using these fields may result in unacceptable changes to the SPECT intensity distribution that would preclude use in RT planning. Moreover, the differences between intensity histograms in the original and registered SPECT image sets were the largest for diffeomorphic demons and level set methods. In conclusion, the use of intensity-based validation measures alone is not sufficient for SPECT/CT registration for RTTP. It was also found that the proper evaluation of image registration requires the use of several accuracy metrics.

Feasibility of physical map construction from fingerprinted bacterial artificial chromosome libraries of polyploid plant species

BACKGROUND

The presence of closely related genomes in polyploid species makes the assembly of total genomic sequence from shotgun sequence reads produced by the current sequencing platforms exceedingly difficult, if not impossible. Genomes of polyploid species could be sequenced following the ordered-clone sequencing approach employing contigs of bacterial artificial chromosome (BAC) clones and BAC-based physical maps. Although BAC contigs can currently be constructed for virtually any diploid organism with the SNaPshot high-information-content-fingerprinting (HICF) technology, it is currently unknown if this is also true for polyploid species. It is possible that BAC clones from orthologous regions of homoeologous chromosomes would share numerous restriction fragments and be therefore included into common contigs. Because of this and other concerns, physical mapping utilizing the SNaPshot HICF of BAC libraries of polyploid species has not been pursued and the possibility of doing so has not been assessed. The sole exception has been in common wheat, an allohexaploid in which it is possible to construct single-chromosome or single-chromosome-arm BAC libraries from DNA of flow-sorted chromosomes and bypass the obstacles created by polyploidy.

RESULTS

The potential of the SNaPshot HICF technology for physical mapping of polyploid plants utilizing global BAC libraries was evaluated by assembling contigs of fingerprinted clones in an in silico merged BAC library composed of single-chromosome libraries of two wheat homoeologous chromosome arms, 3AS and 3DS, and complete chromosome 3B. Because the chromosome arm origin of each clone was known, it was possible to estimate the fidelity of contig assembly. On average 97.78% or more clones, depending on the library, were from a single chromosome arm. A large portion of the remaining clones was shown to be library contamination from other chromosomes, a feature that is unavoidable during the construction of single-chromosome BAC libraries.

CONCLUSIONS

The negligibly low level of incorporation of clones from homoeologous chromosome arms into a contig during contig assembly suggested that it is feasible to construct contigs and physical maps using global BAC libraries of wheat and almost certainly also of other plant polyploid species with genome sizes comparable to that of wheat. Because of the high purity of the resulting assembled contigs, they can be directly used for genome sequencing. It is currently unknown but possible that equally good BAC contigs can be also constructed for polyploid species containing smaller, more gene-rich genomes.

Monte Carlo calculation of dose distribution in early stage NSCLC patients planned for accelerated hypofractionated radiation therapy in the NCIC-BR25 protocol

The dosimetric consequences of plans optimized using a commercial treatment planning system (TPS) for hypofractionated radiation therapy are evaluated by re-calculating with Monte Carlo (MC). Planning guidelines were in strict accordance with the Canadian BR25 protocol which is similar to the RTOG 0236 and 0618 protocols in patient eligibility and total dose, but has a different hypofractionation schedule (60 Gy in 15 fractions versus 60 Gy in 3 fractions). A common requirement of the BR25 and RTOG protocols is that the dose must be calculated by the TPS without tissue heterogeneity (TH) corrections. Our results show that optimizing plans using the pencil beam algorithm with no TH corrections does not ensure that the BR25 planning constraint of 99% of the PTV receiving at least 95% of the prescription dose would be achieved as revealed by MC simulations. This is due to poor modelling of backscatter and lateral electronic equilibrium by the TPS. MC simulations showed that as little as 75% of the PTV was actually covered by the 95% isodose line. The under-dosage of the PTV was even more pronounced if plans were optimized with the TH correction applied. In the most extreme case, only 23% of the PTV was covered by the 95% isodose.

Cytogenetics in the age of molecular genetics

From the beginning of the 20th Century, we have seen tremendous advances in knowledge and understanding in almost all biological disciplines, including genetics, molecular biology, structural and functional genomics, and biochemistry. Among these advances, cytogenetics has played an important role. This paper details some of the important milestones of modern cytogenetics. Included are the historical role of cytogenetics in genetic studies in general and the genetics stocks produced using cytogenetic techniques. The basic biological questions cytogenetics can address and the important role and practical applications of cytogenetics in applied sciences, such as in agriculture and in breeding for disease resistance in cereals, are also discussed. The goal of this paper is to show that cytogenetics remains important in the age of molecular genetics, because it is inseparable from overall genome analysis. Cytogenetics complements studies in other disciplines within the field of biology and provides the basis for linking genetics, molecular biology and genomics research.

Development and mapping of EST-derived simple sequence repeat markers for hexaploid wheat

Expressed sequence tags (ESTs) are a valuable source of molecular markers. To enhance the resolution of an existing linkage map and to identify putative functional polymorphic gene loci in hexaploid wheat (Triticum aestivum L.), over 260,000 ESTs from 5 different grass species were analyzed and 5418 SSR-containing sequences were identified. Using sequence similarity analysis, 156 cross-species superclusters and 138 singletons were used to develop primer pairs, which were then tested on the genomic DNA of barley (Hordeum vulgare), maize (Zea mays), rice (Oryza sativa), and wheat. Three-hundred sixty-eight primer pairs produced PCR amplicons from at least one species and 227 primer pairs amplified DNA from two or more species. EST-SSR sequences containing dinucleotide motifs were significantly more polymorphic (74%) than those containing trinucleotides (56%), and polymorphism was similar for markers in both coding and 5' untranslated (UTR) regions. Out of 112 EST-SSR markers, 90 identified 149 loci that were integrated into a reference wheat genetic map. These loci were distributed on 19 of the 21 wheat chromosomes and were clustered in the distal chromosomal regions. Multiple-loci were detected by 39% of the primer pairs. Of the 90 mapped ESTs, putative functions for 22 were identified using BLASTX queries. In addition, 80 EST-SSR markers (104 loci) were located to chromosomes using nullisomic-tetrasomic lines. The enhanced map from this study provides a basis for comparative mapping using orthologous and PCR-based markers and for identification of expressed genes possibly affecting important traits in wheat.

The National Psychiatric Morbidity Surveys of Great Britain--initial findings from the household survey

This paper describes the Household Survey from the National Survey of Psychiatric Morbidity. This covered a sample drawn at random from the population of Britain, with the exception of the Highlands and Islands of Scotland. The Postcode Address File was used as the sampling frame. Nearly 13,000 adults aged 16-65 were selected for interview, of which 10,108 (79.4%) were successfully interviewed. Eight percent could not be contacted and 13% refused interview. Psychiatric assessment was carried out by lay interviewers using the CIS-R. Subjects were also screened for psychosis, and screen-positive individuals were examined by psychiatrists using SCAN. Sixteen per cent of subjects scored above the standard cut-off of 12 on the CIS-R. The overall one-week prevalence of neurotic disorder was 12.3% in males and 19.5% in females. Unmarried and post-marital groups had high rates of disorder, as did single parents and people living on their own. Respondents in Social Class I had notably lower rates of neurotic disorder than the remainder of the sample. Unemployment was strongly associated with disorder. Subjects living in urban areas had a higher overall prevalence, but there was no significant variation by region. Black respondents had higher rates of disorders that were entirely explained by their age, family type, and social class. Individual neurotic disorders were all significantly commoner in women, with the exception of panic disorder. The one-year prevalence of functional psychoses was four per 1000, with no sex difference. Alcohol and drug dependence was considerably more prevalent in men. For the first time, the survey provides data on the prevalence and correlates of psychiatric disorder on a nationwide sample that can be used to inform equitable and effective national psychiatric services.

Socio-economic status, standard of living, and neurotic disorder

Evidence on the association between socio-economic status and the prevalence of neurotic disorder is contradictory. We studied the association between three elements of socio-economic status and the prevalence of neurotic psychiatric disorder in a representative sample of adults aged 16-64 living in private households in the UK. A cross-sectional survey of 10,108 adults aged 16-65 resident in private households in the UK was selected by a multi-stage, clustered, random-sampling design. Neurotic disorders were defined using a standardised interview, the revised clinical interview schedule (CIS-R). Data for 9570 people were available for this study. We used housing tenure and access to cars as measures of standard of living; both were associated with the prevalence of neurotic disorder even after adjustment for other socio-economic and demographic variables, including the Registrar General's Social Class and educational attainment. Those people with no access to a car had an odds ratio for neurotic disorder of 1.4 (95% CI 1.1-1.7), compared with those who had access to two or more cars. People who rented their homes were also at increased risk (1.3 [1.1-1.5]). We estimated that about 10% of the neurotic disorder in the UK could be attributed to the increased prevalence of those without cars who rented their homes. There was a complex interaction between the Registrar General's Social Class and sex, and there was no independent association with educational attainment. There is an independent association between low standard of living and the prevalence of neurotic psychiatric disorder. The UK has experienced one of the largest increases in income inequality within western market economies over the past 20 years, and this inequality may have had adverse consequences for the mental health of the population.

The prevalence of psychiatric morbidity among adults living in institutions

This paper presents prevalence data from the 1994 OPCS survey of psychiatric morbidity among adults permanently resident in institutions catering for people with mental health problems in Great Britain. It describes briefly the survey methods used, and how diagnoses of psychiatric morbidity were derived. Its main aim is to show the prevalence of psychiatric morbidity in different types of institutional settings. Residents were eligible for the survey if they were aged 16 to 64 at the date of sampling and were permanently resident at the establishment. Residents were defined as permanently resident if they had been living in the sampled establishment for six months or more, or had no other permanent address, or were likely to stay in the establishment for the foreseeable future. In 1994, about 33,200 adults aged 16 to 64 were permanently resident in accommodation for people with mental health problems. About a third of residents were in NHS hospitals, while about two-thirds were in residential care facilities. About two-thirds of adults interviewed suffered from schizophrenia, delusional and schizoaffective disorders. About 8% suffered from neurotic disorders and 8% suffered from affective psychoses (mainly bipolar affective disorder). The prevalence of schizophrenia, delusional, and schizoaffective disorders was higher in hospitals than in residential care, while the prevalence of neurotic and related disorders was higher in residential accommodation. The prevalence of schizophrenia, delusional, and schizoaffective disorders was higher in NHS psychiatric hospitals and general hospital units than in private hospitals, clinics or nursing homes.