QTL analysis of malting quality traits in two barley populations

Selection for malting quality traits is a major breeding objective for barley breeding programs. With molecular markers linked to loci affecting these traits, this selection can be undertaken at an earlier stage of the breeding program than is possible using conventional tests. Quantitative trait loci (QTLs) associated with malting quality traits were mapped in 2 populations derived from parents with elite malting quality. Progeny from an Arapiles/Franklin population grown in 4 environments and an Alexis/Sloop population grown in 5 environments were tested for grain protein percentage, α-amylase activity, diastatic power, hot water extract, wort viscosity, wort β-glucan, β-glucanase, and free α-amino acids. QTL analysis was performed using a one-stage approach, which allowed for modelling of spatial variation in the field, and in each phase of the malting quality analysis in the laboratory. QTLs for malting quality traits were detected on all chromosomes and for both populations. Few of these QTLs were significant in all of the environments, indicating that QTL × environment interactions were important. There were many coincident QTLs for traits that are expected to be related such as diastatic power and α-amylase activity, wort β-glucan and wort viscosity and for some traits that are not expected to be related such as hot water extract and malt viscosity.

[Echocardiography and mechanical complications of recent myocardial infarction]

The constantly advancing technology of echocardiography and its widespread usage in the intensive care unit has made it a routine examination in patients with acute myocardial infarction. It has become the reference method for diagnosis and monitoring of certain complications such as pericardial effusion, intra-ventricular thrombosis, ventricular aneurysm and mitral regurgitation. The echocardiographic description of these complications dates back to the 1980s during which prospective studies accurately described the principal abnormalities. These descriptions have not been much improved upon with the advent of new technology. On the other hand, the frequency of these complications assessed in an era when reperfusion by thrombolysis or primary angioplasty was much less common than today, has considerably decreased.

The incidence and patterns of BCR/ABL rearrangements in chronic myeloid leukaemia (CML) using fluorescence in situ hybridisation (FISH)

INTRODUCTION

Chronic myeloid leukaemia (CML) is characterised by the formation of the BCR/ABL fusion gene, usually as a result of the Philadelphia (Ph) translocation between chromosomes 9 and 22.

MATERIALS AND METHODS

The incidence of both typical and atypical BCR/ ABL gene rearrangements was determined in 110 patients suspected of CML using dual fusion fluorescence in situ hybridisation (DF-FISH) probes.

RESULTS

Eighty-seven per cent of CML patients showed Ph translocation while 13% were negative for the Ph chromosome. About 71.9% of Ph-positive patients displayed the typical DF-FISH signal pattern. Atypical patterns among the Ph-positive patients included the concurrent loss of residual proximal 9q and distal 22q (10.4%), complex translocation with additional partners (9.4%), supernumerary Ph (3.1%), loss of residual 9q sequences proximal to breakpoint (3.1%), and deletion of distal derivative 22q signal (2.1%). Cryptic genetic alterations with loss of proximal 9q sequences were found in 13.5% of CML Ph-positive patients, which is associated with poor prognosis. Fusion signals were detected in 57.1% of CML Ph-negative patients, indicating cryptic BCR/ABL rearrangements (i.e., masked Ph).

CONCLUSION

FISH is able to detect BCR/ABL fusion in CML with masked or variant Ph not apparent with conventional karyotyping. Establishment of signal patterns with FISH is important as atypical patterns may have clinical prognostic implications.

Evidence for deletion of 9q as a two-step process in chronic myeloid leukemia

Evidence for deletion of 9q as a two-step process in chronic myeloid leukemia. Chronic myeloid leukemia (CML) is characterized by the Philadelphia translocation t(9;22)(q34;q11) resulting in the BCR/ABL fusion gene. Submicroscopic deletion of the derivative chromosome 9 occurs in a subset of these patients and is associated with poor prognosis. In the current study, we present two unusual cases of CML selected from a series of 54 consecutive cases. A detailed study using classical cytogenetics and fluorescence in situ hybridization (FISH) analysis was done using dual color extra signal FISH and whole chromosome paint in order to elucidate the mechanism of 9q deletion. One case had two clones on interphase FISH, one with and one without chromosome 9q deletion. The other case had two clones on both cytogenetic and FISH analyses, one with and one without a marker chromosome carrying chromosome 9q sequences. In this latter case, the clone with deletion of the derivative chromosome 9 comprised 21.1% at diagnosis, increasing to 36.8% after 11 months, suggesting a growth advantage. We report here evidence that deletions on 9q in CML may occur through breakage and rearrangement of chromosomes resulting in derivative chromosomes and either a marker chromosome or fragment/episome, followed by loss of chromosome material from the cell.

Assessment of left ventricular contraction by parametric analysis of main motion (PAMM): theory and application for echocardiography

The computerized study of the regional contraction of the left ventricle has undergone numerous developments, particularly in relation to echocardiography. A new method, parametric analysis of main motion (PAMM), is proposed in order to synthesize the information contained in a cine loop of images in parametric images. PAMM determines, for the intensity variation time curves (IVTC) observed in each pixel, two amplitude coefficients characterizing the continuous component and the alternating component; the variable component is generated from a mother curve by introducing a time shift coefficient and a scale coefficient. Two approaches, a PAMM data driven and a PAMM model driven (simpler and faster), are proposed. On the basis of the four coefficients, an amplitude image and an image of mean contraction time are synthesized and interpreted by a cardiologist. In all cases, both PAMM methods allow better IVTC adjustment than the other methods of parametric imaging used in echocardiography. A preliminary database comprising 70 segments is scored and compared with the visual analysis, taken from a consensus of two expert interpreters. The levels of absolute and relative concordance are 79% and 97%. PAMM model driven is a promising method for the rapid detection of abnormalities in left ventricle contraction.

Qualité des eaux de trois bras morts de la Garonne variabilité spatio-temporelle)

Pendant deux années, des mesures et analyses d'eau ont été faites mensuellement sur une station de la Garonne et sur trois bras morts différant par leur communication avec le fleuve. La variabilité spatio-temporelle a été dressée à partir de 14 variables physico-chimiques susceptibles d'influer les équilibres chimiques de l'eau et la vie aquatique. Les données ont fait l'objet d'une Analyse en Composantes principales précédée par une analyse de variance entre saisons et entre stations de mesures afin de déterminer l'importance des hétérogénéités spatiale et temporelle des données.

L'eau du fleuve est soumise à un cycle climatique annuel de température et de débit. De brèves fortes eaux de printemps alternent avec de longues périodes de débits stables et inférieurs aux moyennes établies sur plusieurs décennies. Par rapport aux charges de sulfates et de chlorures prises comme référence du drainage du bassin versant, les flux de nitrates ont un pic accentué au printemps, résultant des activités agricoles. Les phosphates présentent aussi un accroissement automnal qui pourrait traduire un cycle annuel de minéralisation-déminéralisation. Les matières organiques s'élèvent en rapport au taux de chlorophylle a. L'eau de Garonne est de bonne qualité et conforme à la typologie habituelle, hormis des taux déclassants d'ammoniaque provenant de l'agglomération toulousaine et dont l'autoépuration est souvent incomplète. Par rapport à la Garonne, les trois bras morts sont caractérisés par un cycle thermique accentué en été. Mise en évidence par l'ACP, la minéralisation des eaux de ces trois bras morts évolue selon un cycle saisonnier parallèlement aux fluctuations de débit de la Garonne. Elle indique un gradient de minéralisation croissante de l'hiver au printemps. La qualité de l'eau lors des fortes eaux printanières est homogénéisée et imposée par le fleuve. En phases de faibles débits, la qualité de l'eau évolue parallèlement à celle de la Garonne (concentrations des substances) pour un bras mort ventilé par une communication amont et aval. En revanche, les deux bras morts en simple communication aval présentent un retard à la concentration de l'eau d'autant plus évident que la communication est étroite. Les substances fertilisantes (nitrates, phosphates, ...) augmentant de l'amont vers l'aval dans ces deux derniers bras morts, sont en été en concentration inférieure par rapport au fleuve, en raison : 1) du remplissage printanier par des eaux diluées, puis du retard estival à l’équilibrage par simple communication aval et 2) de la consommation par les organismes végétaux aquatiques. L'élude des différences spatio-temporelles met ainsi en évidence un gradient saisonnier de minéralisation, un gradient aval-amont de productivité et un gradient aval-amont de réchauffement estival. La productivité apparaît donc liée au réchauffement estival plutôt qu'à la minéralisation ou aux teneurs en substances fertilisantes.

Radiation fields in gynecologic oncology: correlation of soft tissue (surgical) to radiologic landmarks

OBJECTIVES

(1). To determine if radiation fields defined by bony structure landmarks correlate to anatomic boundaries of lymph node dissection marked intraoperatively; and (2). to determine if a patient's body mass index (BMI) correlates with these anatomic or radiographic boundaries.

METHODS

One hundred patients undergoing exploratory laparotomy with pelvic and paraaortic lymph node dissection had three medium hemoclips placed at vascular junctions considered of clinical significance to lymph node dissection: insertion of the left ovarian vein into the renal vein, insertion of the right ovarian vein into the vena cava, inferior mesenteric artery (IMA), bifurcation of the aorta, bifurcation of the common iliacs (bilateral), and the insertion of the deep circumflex vein (DCV) in to the external iliac vein (bilateral). Postoperatively, an abdominal X-ray was obtained. Comparisons were made between these eight major vascular landmarks and radiographic bony landmarks that are used to define radiation field boundaries. The percentage of vascular landmarks that were encompassed or fell outside of traditional radiation fields was determined with a 1-cm margin considered an adequate boundary for radiation. These measurements were also compared to patient BMIs.

RESULTS

Radiation fields defined by traditional bony landmarks would adequately encompass the paraaortic lymph nodes in the majority of patients (91%). For pelvic radiation fields, there was a significant "miss" (39%) of common iliac lymph nodes. Approximately one quarter (26%) of patients would receive inadequate coverage of one or both of the lateral boundaries of pelvic radiation. There was no apparent correlation of BMI to vascular or bony landmarks.

CONCLUSIONS

Radiation fields determined by traditional bony landmarks do not adequately reflect the anatomic (surgical) landmarks associated with the lymphatic drainage of the female reproductive organs. Although the majority of tertiary care centers now use advanced imaging techniques (e.g. computed tomography) to plan their radiation treatments, the historical guidelines of radiographic landmarks are still used in smaller institutions and continue to be referenced in Gynecologic Oncology Group protocols. For centers still using radiographic landmarks, the application of hemoclips with X-ray identification is a low-cost modality that is easily reproducible and may be clinically useful in guiding treatment.

Small-cell carcinoma of the cervix: fourteen years of experience at a single institution using a combined-modality regimen of involved-field irradiation and platinum-based combination chemotherapy

PURPOSE

To determine the efficacy and toxicity of a combined-modality regimen of irradiation with platinum-based combination chemotherapy in small-cell carcinoma of the cervix (SCCC).

PATIENTS AND METHODS

Thirty-four patients with SCCC were seen and treated at the British Columbia Cancer Agency between May 1988 and November 2002. Two protocols were used, SMCC (May 1988 to December 1995) and SMCC2 (January 1996 to November 2002). Both protocols used cisplatin, etoposide, and involved-field irradiation (essentially pelvis plus or minus para-aortics) with concurrent chemotherapy. In addition, SMCC2 included carboplatin and paclitaxel, and the para-aortics were irradiated routinely.

RESULTS

Thirty-one patients received either SMCC (n = 17) or SMCC2 (n = 14), and three patients did not (disease too extensive, n = 1; patient refusal, n = 1; and alternative regimen, n = 1). For the 31 patients treated on one of the protocols, the 3-year overall and failure-free survival (FFS) rates were 60% and 57%, respectively. The results were equivalent for SMCC and SMCC2. Radiologic stage was the only independent predictor for FFS (80% at 3 years for stage I and II patients v 38% at 3 years for stage III and IV patients). Distant failure (28%) was the most common cause of failure, with local failure occurring in 13% of patients. The switch to SMCC2 did not improve efficacy but did lessen the toxicity.

CONCLUSION

SCCC can be successfully treated in approximately 55% of patients with a combination of irradiation and platinum-based chemotherapy. Disease extent predicts for chance of curability.

The atherogenic lipid profile is associated with type 2 diabetes and some of its treatment modalities

BACKGROUND

Since diabetes is strongly linked to cardiovascular disease, we tested whether: 1) diabetic patients have a high prevalence of the atherogenic lipid profile and 2) the drugs used to treat hyperglycemia are related to the atherogenic lipid profile.

METHODS

Seventy-two diabetic patients were retrospectively studied for lipids using the Lipid Research Clinic methods and LDL and HDL gel electrophoreses.

RESULTS

Despite normal mean levels of total LDL- and HDL-cholesterol (HDL-c), diabetic patients had abnormal mean levels and an unusually high prevalence of lipid abnormalities not apparent on routine lipid blood tests. Thus, mean LDL peak particle diameter (PPD) was 258 +/- 11A and values < 263A occurred in 57% of diabetic patients; HDL2 < 40% in 61% and Lp(a) > 25 mg/dl occurred in 36% of patients, despite good glycemic control. Mean HbA1c [Diabetes Control and Complications Trial (DCCT) formatted] was 6.5 +/- 1.4%. In contrast to patients using sulfonylureas or metformin, diabetic patients using insulin had significantly larger mean LDL PPD (261 vs 254A, p < 0.006), lower triglycerides (115 vs 215 mg/dl,p < 0.0001), higher HDL-c (53 vs 40 mg/dl,p < 0.0001) and higher HDL2 levels (43 vs 29%, p < 0.0001).

CONCLUSIONS

In this diabetic group, traditional guidelines fail to identify patients with high dyslipidemic prevalence rates (84%). Further, certain oral hypoglycemic treatments are associated with less favorable atherogenic lipid profiles when compared to insulin treatment.

Mapping and QTL analysis of the barley population Chebec × Harrington

A doubled haploid population of 120 individuals was produced from the parents Chebec, an Australian 2-row barley of feed quality with resistance to the cereal cyst nematode, and Harrington, a 2-rowed, Canadian variety of premium malting quality. This paper describes 18 field and laboratory experiments conducted with the population and summarises the traits mapped and analysed. The genomic location of 25 traits and genes is described and marker–trait associations for 5 traits (malt extract, diastatic power, resistance to cereal cyst nematode, early flowering, resistance to pre-harvest sprouting) important to Australian efforts to improve malting barley varieties have been used in practical breeding programs. Detailed maps for these populations are shown in this paper, while a consensus map incorporating these maps and further experiments on the populations are described elsewhere in this issue.

Mapping and QTL analysis of the barley population Mundah × Keel

The barley mapping population Mundah × Keel was devised to characterise and map chromosome regions associated with improved growth and grain yield on sandy soils of low fertility. A low level of polymorphism between the parents proved problematic for the construction of a detailed linkage map of this population. Despite this, significant quantitative trait loci (QTLs) for specific traits were detected, providing an insight into the probable chromosome regions associated with sand adaptation. In addition, this population is being employed to identify loci associated with the expression of traits for moisture stress and frost tolerance, and resistance to spot form of net blotch and leaf scald.

Potential of SSR markers for plant breeding and variety identification in Australian barley germplasm

SSR markers closely linked to 18 loci that control 16 important barley traits were assessed for their applicability in Australian barley breeding programs. A panel of 40 genotypes routinely used by the South Australian Barley Improvement Program (SABIP) was used to examine the usefulness of these SSR markers for marker assisted selection (MAS). The success of monitoring a trait locus from donor to recipient lines ranged from 10 to 98%, depending on the marker. SSRs with a high polymorphic information content (PIC) value were found to be the most useful for application in MAS. The assessment also indicated that SSRs derived from genomic sequences were more successful for MAS than those designed from expressed sequence tags. A total of 130 SSR markers were screened among 2 panels of Australian barley genotypes to determine which markers would be the most useful for discriminating Australian germplasm. PIC values generated by this screening were also compared with those generated using a panel of European barley genotypes. Using ordinary correlations (parametric), rank correlations (non-parametric), and partial correlations (multi-variate), a strong association was found between the 2 Australian panels, but no or weak correlation was observed between the 2 Australian panels and the European dataset. It can therefore be concluded that PIC values generated by SSR markers screened with European genotypes cannot be used to predict the usefulness of an SSR marker for discriminating Australian genotypes. From PIC values generated in this study, 36 SSR markers have been selected for the discrimination of Australian genotypes. These markers all show high and/or consistent PIC values among Australian and European barley genotypes.

Barley malting quality: are we selecting the best?

This paper presents an analysis of several key barley malting traits from 2 mapping populations grown as a series of multi-environment field trials. The analysis is based on a mixed model that includes terms for all sources of variation in the trait data, namely varieties, variety by trial interaction, variation between plots in the field, and variation between samples in the laboratory processes required to measure the traits. The base-line model is extended to accommodate variance heterogeneity and correlated effects for many of the terms in the model. The results show that accounting for these phenomena may cause substantial changes in variety rankings. The methods of design and analysis proposed in this paper for barley quality trait data do not have common usage so if adopted in future there is an opportunity for substantial improvements in response to selection.

Mapping and QTL analysis of the barley population Alexis × Sloop

Two populations between the German malting variety Alexis and the Australian malting variety Sloop were constructed, mapped, phenotyped, and subjected to quantitative trait loci analysis. One population consisted of 153 F4-derived recombinant inbred lines and the other of 111 doubled haploid lines. This paper describes 18 field and laboratory experiments conducted with the populations and summarises the traits mapped and analysed. The genetic basis of 5 traits (malt extract, resistance to leaf rust, resistance to powdery mildew, early flowering, plant stature) important to Australian efforts to improve malting barley varieties was elucidated. Detailed maps for these populations are shown in this paper, while a consensus map incorporating these maps and further experiments on the populations are described elsewhere in this issue.

Does prophylactic endoscopic sphincterotomy prevent recurrent biliary problems in patients with gallstones and a normal cholangiogram?

BACKGROUND

Endoscopic sphincterotomy (ES) is indicated in patients with confirmed bile duct stones at endoscopic retrograde cholangiopancreatography (ERCP). The role of ES in patients with suspected bile duct stones but a normal cholangiogram, in the prevention of recurrent biliary symptoms, when cholecystectomy is not planned, is unclear.

AIM

To determine if prophylactic ES prevents further biliary problems in such patients.

METHODS

Patients were identified with gallbladder stones presenting with jaundice, abnormal liver function tests (LFTs) or dilated bile ducts on ultrasound, in whom cholecystectomy was not planned and who had a normal cholangiogram at ERCP. Patients were followed-up to determine the frequency of recurrent biliary problems or repeat investigations.

RESULTS

Forty-one patients were included, of whom 20 had an ES. The frequency of pre-ERCP features did not differ between the two groups. Median follow-up was 32 months (range 15-66). Post-ERCP recurrent abdominal pain (5 vs 3; p=0.39), jaundice (3 vs 1; p=0.28), pancreatitis (0 vs 1; p=0.32), and repeat ultrasound (2 vs 1; p=0.52), ERCP (1 vs 1; p=0.97) or cholecystectomy (2 vs 3, p=0.82) did not differ between the two groups.

CONCLUSIONS

Patients with gallstones, suspected common bile duct (CBD) stones and a normal cholangiogram need not have a prophylactic sphincterotomy since there is no reduction in recurrent biliary problems and this potentially increases the morbidity.

Paclitaxel and carboplatin, alone or with irradiation, in advanced or recurrent endometrial cancer: a phase II study

PURPOSE

To evaluate the efficacy of carboplatin plus paclitaxel in primarily advanced or recurrent endometrial cancers.

PATIENTS AND METHODS

Four distinct patient groups received carboplatin (area under the curve, 5 to 7) plus paclitaxel 175 mg/m(2) for 3 hours at 4-week intervals: group 1 (n = 21), patients with primarily advanced, nonpapillary serous cancers; group 2 (n = 20), the same as group 1 but with papillary serous cancers; group 3 (n = 18), recurrent, nonpapillary serous cancers; and group 4 (n = 4), recurrent, papillary serous cancers. Involved-field irradiation was used in groups 1 and 2 for those with radioencompassable disease.

RESULTS

Sixty-three patients were treated. Response rates to chemotherapy in the assessable patients in the four groups were 78% (95% confidence interval [CI], 51% to 100%); 60% (95% CI, 35% to 85%), 56% (95% CI, 34% to 78%), and 50%, respectively. Nineteen patients (90%) in group 1 also were irradiated, and the median failure-free survival time for all 21 patients was 23 months, with a 62% 3-year overall survival rate. Eleven patients (55%) in group 2 were irradiated, and the median failure-free survival time for all 18 patients was 18 months, with a 39% 3-year overall survival rate. The median failure-free interval in the patients in group 3 was 6 months, with a 15-month median overall survival time. Toxicity was manageable, reversible, and predominantly hematologic. Two patients developed neutropenic fever, and three patients, including these two, were hospitalized for complications.

CONCLUSION

Carboplatin-paclitaxel is an efficacious, low-toxicity regimen for managing primarily advanced or recurrent endometrial cancers.

Early stage uterine papillary serous carcinoma of the endometrium: effect of adjuvant whole abdominal radiotherapy and pathologic parameters on outcome

BACKGROUND

Uterine papillary serous carcinoma (UPSC) is an aggressive subtype of endometrial cancer, behaving like ovarian epithelial cancers and having a predilection for transperitoneal relapse. Within this subtype of uterine cancers, predictors of outcome and the role of adjuvant therapies have not been firmly established, to the authors' knowledge.

METHODS

Between 1985-1995, 78 patients who had International Federation of Gynecology and Obstetrics (FIGO) Stage I, II, or IIIa UPSC (based on positive washings only) were seen at the British Columbia Cancer Agency. During this time, the authors had a policy of offering adjuvant pelvic, paraaortic and whole-abdominal radiotherapy (WART) to these patients. Fifty-eight patients received adjuvant WART, and 20 received lesser or no adjuvant therapy. The authors undertook a retrospective analysis of pathology with quantification of the percentage of papillary serous component (% PSC) and p53 expression. Pathology was retrieved and reviewed on 62 patients; p53 staining was performed on blocks from the hysterectomy specimen in 46 cases. Pathologic parameters, stage, and adjuvant therapy were correlated with clinical outcome in a multivariate analysis.

RESULTS

Median follow-up was 52 months (3-139 mos) and the 5-year disease-specific survival rate was 66.2%. The 58 patients who received adjuvant WART had a significantly better 5-year disease-specific survival than those 20 patients who did not, 74.9% versus 41.3% (P = 0.04). Multivariate analysis showed that % PSC and p53 were not significant predictors of outcome for early stage UPSC. Of the factors examined, only FIGO stage and WART significantly predicted improved outcome (P = 0.02 and 0.04, respectively).

CONCLUSIONS

The current study demonstrated a significant difference in the outcomes of patients who had FIGO Stage I compared with Stage II UPSC. In the current series of patients, the authors were not able to predict outcome based on % PSC or p53 expression. The current study results with WART were promising, and WART merits further study.