Multispectral and thermal infrared data, visual scores for severity of common rust symptoms, and genotypic single nucleotide polymorphism data of three F2-derived biparental doubled-haploid maize populations

Three F2-derived biparental doubled haploid (DH) maize populations were generated for genetic mapping of resistance to common rust. Each of the three populations has the same susceptible parent, but a different resistance donor parent. Population 1 and 3 consist of 320 lines each, population 2 consists of 260 lines. The DH lines were evaluated for their susceptibility to common rust in two years and with two replications in each year. For phenotyping, a visual score (VS) for susceptibility was assigned. Additionally, unmanned aerial vehicle (UAV) derived multispectral and thermal infrared data was recorded and combined in different vegetation indices ("remote sensing", RS). The DH lines were genotyped with the DarTseq method, to obtain data on single nucleotide polymorphisms (SNPs). After quality control, 9051 markers remained. Missing values were "imputed" by the empirical mean of the marker scores of the respective locus. We used the data for comparison of genome-wide association studies and genomic prediction when based on different phenotyping methods, that is either VS or RS data. The data may be interesting for reuse for instance for benchmarking genomic prediction models, for phytopathological studies addressing common rust, or for specifications of vegetation indices.

Use of remote sensing for linkage mapping and genomic prediction for common rust resistance in maize

Breeding for disease resistance is a central component of strategies implemented to mitigate biotic stress impacts on crop yield. Conventionally, genotypes of a plant population are evaluated through a labor-intensive process of assigning visual scores (VS) of susceptibility (or resistance) by specifically trained staff, which limits manageable volumes and repeatability of evaluation trials. Remote sensing (RS) tools have the potential to streamline phenotyping processes and to deliver more standardized results at higher through-put. Here, we use a two-year evaluation trial of three newly developed biparental populations of maize doubled haploid lines (DH) to compare the results of genomic analyses of resistance to common rust (CR) when phenotyping is either based on conventional VS or on RS-derived (vegetation) indices. As a general observation, for each population × year combination, the broad sense heritability of VS was greater than or very close to the maximum heritability across all RS indices. Moreover, results of linkage mapping as well as of genomic prediction (GP), suggest that VS data was of a higher quality, indicated by higher - log p values in the linkage studies and higher predictive abilities for genomic prediction. Nevertheless, despite the qualitative differences between the phenotyping methods, each successfully identified the same genomic region on chromosome 10 as being associated with disease resistance. This region is likely related to the known CR resistance locus Rp1. Our results indicate that RS technology can be used to streamline genetic evaluation processes for foliar disease resistance in maize. In particular, RS can potentially reduce costs of phenotypic evaluations and increase trialing capacities.

Radiative transfer model inversion using high-resolution hyperspectral airborne imagery - Retrieving maize LAI to access biomass and grain yield

Mapping crop within-field yield variability provide an essential piece of information for precision agriculture applications. Leaf Area Index (LAI) is an important parameter that describes maize growth, vegetation structure, light absorption and subsequently maize biomass and grain yield (GY). The main goal for this study was to estimate maize biomass and GY through LAI retrieved from hyperspectral aerial images using a PROSAIL model inversion and compare its performance with biomass and GY estimations through simple vegetation index approaches. This study was conducted in two separate maize fields of 12 and 20 ha located in north-west Mexico. Both fields were cultivated with the same hybrid. One field was irrigated by a linear pivot and the other by a furrow irrigation system. Ground LAI data were collected at different crop growth stages followed by maize biomass and GY at the harvesting time. Through a weekly/biweekly airborne flight campaign, a total of 19 mosaics were acquired between both fields with a micro-hyperspectral Vis-NIR imaging sensor ranging from 400 to 850 nanometres (nm) at different crop growth stages. The PROSAIL model was calibrated and validated for retrieving maize LAI by simulating maize canopy spectral reflectance based on crop-specific parameters. The model was used to retrieve LAI from both fields and to subsequently estimate maize biomass and GY. Additionally, different vegetation indices were calculated from the aerial images to also estimate maize yield and compare the indices with PROSAIL based estimations. The PROSAIL validation to retrieve LAI from hyperspectral imagery showed a R² value of 0.5 against ground LAI with RMSE of 0.8 m²/m². Maize biomass and GY estimation based on NDRE showed the highest accuracies, followed by retrieved LAI, GNDVI and NDVI with R² value of 0.81, 0.73, 0.73 and 0.65 for biomass, and 0.83, 0.69, 0.73 and 0.62 for GY estimation, respectively. Furthermore, the late vegetative growth stage at V16 was found to be the best stage for maize yield prediction for all studied indices.

The 14q22.2 colorectal cancer variant rs4444235 shows cis-acting regulation of BMP4

Common genetic variation at human 14q22.2 tagged by rs4444235 is significantly associated with colorectal cancer (CRC) risk. Re-sequencing was used to comprehensively annotate the 17kb region of strong linkage disequilibrium encompassing rs4444235. Through bioinformatic analyses using H3K4Me1, H3K4Me3, and DNase-I hypersensitivity chromatin signatures and evolutionary conservation we identified seven candidate disease-causing single-nucleotide polymorphisms mapping to six regions within the 17-kb region predicted to have regulatory potential. Reporter gene studies of these regions demonstrated that the element to which rs4444235 maps acts as an allele-specific transcriptional enhancer. Allele-specific expression studies in CRC cell lines heterozygous for rs4444235 showed significantly increased expression of bone morphogenetic protein-4 (BMP4) associated with the risk allele (P<0.001). These data provide evidence for a functional basis for the non-coding risk variant rs4444235 at 14q22.2 and emphasizes the importance of genetic variation in the BMP pathway genes as determinants of CRC risk.

Early outcome after single vs bilateral lung transplantation in older recipients

BACKGROUND

Lung transplantation (LT) has been increasingly performed in patients older than 60 years. The outcome of LT in this recipient age group has not been extensively analyzed. The purpose of this study was to evaluate the early death (30 days) in LT recipients older than 60 years according to the type of procedure, that is, single vs bilateral LT.

METHODS

We retrospectively reviewed our experience with older recipients between January 1999 and August 2007. Probability of survival was compared using the two-tailed Fisher exact test. The odds ratio for death at 30 days was estimated using multiple logistic regression.

RESULTS

During the study, 167 LT procedures were performed in 164 patients, of whom 51 (30.5%) were aged 60 years or older (age range, 60-70 years; mean [SD], 63.3 [2.4] years). Thirty-seven recipients aged 60 years or older underwent single LT, and 14 underwent bilateral LT. The 30-day survival was 81% (95% confidence interval [CI], 65%-92%) in patients who underwent single LT, and 92% (95% CI, 64%-100%) in patients who underwent bilateral LT. No differences were observed in the survival probability between the two groups (P = .42). Logistic regression analysis for death at 30 days showed an odds ratio of 1.10 (95% CI, 0.08-14.5; P = .94) in the unilateral LT group.

CONCLUSIONS

Early survival in LT recipients aged 60 years or older who underwent bilateral LT was comparable with that in who underwent single LT. The type of procedure is not a predictor of death in this age group. Recipients older than 60 years should not be excluded from consideration for bilateral LT.

A clinical evaluation of trichomoniasis in San Jose, Costa Rica using the InPouch TV test

OBJECTIVE

to determine the prevalence of trichomoniasis in San Jose, Costa Rica, comparing two methods, the InPouch TV test and the saline wet mount.

METHODS

One hundred symptomatic and asymptomatic female patients at two hospitals and at a sexually transmitted disease (STD) clinic were evaluated. Vaginal discharge was the most prevalent genitourinary abnormality among symptomatic patients. The patients were between 18 and 70 years old. Fifty-seven were from the STD clinic, 43 from the two hospitals. A saline wet mount and a culture were taken from each patient. The culture employed a new procedure for diagnosis of trichomonads, the InPouch TV test (BioMed Diagnostics, San Jose, CA).

RESULTS

Thirteen of the 100 patients were culture positive, two of whom were wet mount positive. No wet mount positives were culture negative. Eleven of the positive tests were from the STD clinic and two were from the hospitals.

CONCLUSIONS

The results of this initial epidemiologic study indicate a prevalence of 19% for trichomoniasis in the STD clinic population and 4.6% in the hospitals group. Trichomonas vaginalis was not diagnosed by laboratory methods prior to this study. The InPouch TV test has a selective fungicidal and bactericidal, enriched proteose-peptone medium which provides a sensitivity of 4 organisms per ml and a 1 year shelf life at room temperature. This in vitro culture test demonstrated unique capabilities as a transport and culture medium. Its procedure offers simplicity in application and an excellent visualisation of trichomonads.