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.

Identification of the first homozygous intragenic deletion in the YY1AP1 gene in a consanguineous family: New insights into the phenotypic variability associated with Grange syndrome

Grange syndrome (GRNG-MIM#135580) is a rare recessive disorder associating variable features including diffuse vascular stenosis, brachysyndactyly, osteopenia with increased bone fragility, cardiac malformations, and variable developmental delay. Since its first description in 1998, only 15 individuals from 10 families have been reported, carrying homozygous or compound heterozygous frameshift or nonsense variants in YY1AP1. In a patient with cutaneous and bone syndactyly and a hemorrhagic stroke at the age of 16 months, consistent with a clinical diagnosis of GRNG, we performed exome sequencing after negative array-CGH and congenital limb malformation panel results. Copy number variant analysis from exome data identified a homozygous intragenic out-of-frame deletion of 1.84 kb encompassing exons seven and eight of YY1AP1, confirming a molecular diagnosis of GRNG. Genetic counseling led to the identification of additional family members compatible with GRNG. Here, we provide new insights into the phenotypic variability associated with GRNG and highlight the utility of the detection of small copy number variants to identify the molecular causes of heterogeneous malformative genetic disorders.

Cost of exome analysis in patients with intellectual disability: a micro-costing study in a French setting

BACKGROUND

With the development of next generation sequencing technologies in France, exome sequencing (ES) has recently emerged as an opportunity to improve the diagnosis rate of patients presenting an intellectual disability (ID). To help French policy makers determine an adequate tariff for ES, we aimed to assess the unit cost per ES diagnostic test for ID from the preparation of the pre-analytical step until the report writing step and to identify its main cost drivers.

METHODS

A micro-costing bottom-up approach was conducted for the year 2018 in a French setting as part of the DISSEQ study, a cost-effectiveness study funded by the Ministry of Health and performed in collaboration with the GAD (Génétique des Anomalies du Développement), a genetic team from the Dijon University Hospital, and a public sequencing platform, the Centre National de Recherche en Génomique Humaine (CNRGH). The analysis was conducted from the point of view of these two ES stakeholders. All of the resources (labor, equipment, disposables and reagents, reusable material) required to analyze blood samples were identified, collected and valued. Several sensitivity analyses were performed.

RESULTS

The unit nominal cost per ES diagnostic test for ID was estimated to be €2,019.39. Labor represented 50.7% of the total cost. The analytical step (from the preparation of libraries to the analysis of sequences) represented 88% of the total cost. Sensitivity analyses suggested that a simultaneous price decrease of 20% for the capture kit and 50% for the sequencing support kit led to an estimation of €1,769 per ES diagnostic test for ID.

CONCLUSION

This is the first estimation of ES cost to be done in the French setting of ID diagnosis. The estimation is especially influenced by the price of equipment kits, but more generally by the organization of the centers involved in the different steps of the analysis and the time period in which the study was conducted. This information can now be used to define an adequate tariff and assess the efficiency of ES.

TRIAL REGISTRATION

ClinicalTrials.gov identifier NCT03287206 on September 19, 2017.

High-responsivity operation of quantum cascade detectors at 9 µm

Quantum cascade detectors (QCDs) are devices operating at zero external bias with a low dark-current. They show linear detection and high saturation intensities, making them suitable candidates for heterodyne detection in long-wave infrared (LWIR) free space optical communication systems. We present an approach to mitigate the performance limitation at long wavelengths, by a comparison of similar single and multi-period QCDs for optimizing their responsivity and noise behaviour. Our InGaAs/InAlAs/InP ridge QCDs are designed for operation at λ = 9.124 µm. Optical waveguide simulations support the accurate optical characterization. A detailed device analysis reveals room-temperature responsivities of 111 mA/W for the 15-period and 411 mA/W for the single-period device.

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.

Optical parametric generation in OP-GaAs waveguides pumped by a femtosecond fluoride fiber laser

We report on mid-infrared optical parametric generation in the 4-5 μm and 9-12 μm bands by pumping custom-designed orientation-patterned gallium arsenide (OP-GaAs) rib waveguides with an ultrafast femtosecond fiber laser system. This pump source is seeded by a mode-locked fluoride fiber laser with 59 MHz repetition rate and can be tuned between 2.8 and 3.2 μm using a soliton self-frequency shifting stage. The single TE and TM modes OP-GaAs crystals feature quasi-phase-matched grating periods of 85 and 90 μm and different transverse sizes thus allowing a wide spectral tunability.

Increased ranking change in wheat breeding under climate change

The International Maize and Wheat Improvement Center develops and annually distributes elite wheat lines to public and private breeders worldwide. Trials have been created in multiple sites over many years to assess the lines' performance for use in breeding and release as varieties, and to provide iterative feedback on refining breeding strategies¹. The collaborator test sites are experiencing climate change, with new implications for how wheat genotypes are bred and selected². Using a standard quantitative genetic model to analyse four International Maize and Wheat Improvement Center global spring wheat trial datasets, we examine how genotype-environment interactions have changed over recent decades. Notably, crossover interactions-a critical indicator of changes in the ranking of cultivar performance in different environments-have increased over time. Climatic factors explained over 70% of the year-to-year variability in crossover interactions for yield. Yield responses of all lines in trial environments from 1980 to 2018 revealed that climate change has increased the ranking change in breeding targeted to favourable environments by ~15%, while it has maintained or reduced the ranking change in breeding targeted to heat and drought stress by up to 13%. Genetic improvement has generally increased crossover interactions, particularly for wheat targeted to high-yielding environments. However, the latest wheat germplasm developed under heat stress was better adapted and more stable, partly offsetting the increase in ranking changes under the warmer climate.

Indian agriculture, air pollution, and public health in the age of COVID

Emerging evidence supports the intuitive link between chronic health conditions associated with air pollution and the vulnerability of individuals and communities to COVID-19. Poor air quality already imposes a highly significant public health burden in Northwest India, with pollution levels spiking to hazardous levels in November and early December when rice crop residues are burned. The urgency of curtailing the COVID-19 pandemic and mitigating a potential resurgence later in the year provides even more justification for accelerating efforts to dramatically reduce open agricultural burning in India.

Agricultural labor, COVID-19, and potential implications for food security and air quality in the breadbasket of India

To contain the COVID-19 pandemic, India imposed a national lockdown at the end of March 2020, a decision that resulted in a massive reverse migration as many workers across economic sectors returned to their home regions. Migrants provide the foundations of the agricultural workforce in the 'breadbasket' states of Punjab and Haryana in Northwest India.There are mounting concerns that near and potentially longer-term reductions in labor availability may jeopardize agricultural production and consequently national food security. The timing of rice transplanting at the beginning of the summer monsoon season has a cascading influence on productivity of the entire rice-wheat cropping system. To assess the potential for COVID-related reductions in the agriculture workforce to disrupt production of the dominant rice-wheat cropping pattern in these states, we use a spatial ex ante modelling framework to evaluate four scenarios representing a range of plausible labor constraints on the timing of rice transplanting. Averaged over both states, results suggest that rice productivity losses under all delay scenarios would be low as compare to those for wheat, with total system productivity loss estimates ranging from 9%, to 21%, equivalent to economic losses of USD $674 m to $1.48 billion. Late rice transplanting and harvesting can also aggravate winter air pollution with concomitant health risks. Technological options such as direct seeded rice, staggered nursery transplanting, and crop diversification away from rice can help address these challenges but require new approaches to policy and incentives for change.

Re-designing irrigated intensive cereal systems through bundling precision agronomic innovations for transitioning towards agricultural sustainability in North-West India

A study was conducted to design productive, profitable, irrigation water¸ nitrogen and energy use efficient intensive cereal systems (rice-wheat; RW and maize-wheat; MW) in North-West India. Bundling of conservation agriculture (CA) with sub-surface drip irrigation termed as CA⁺ were compared with CA alone and conventional tillage based and flood irrigated RW rotation (farmer’s practice; ScI). In contrast to conventional till RW rotation which consumed 1889 mm ha⁻¹ irrigation water (2-yr mean), CA⁺ system saved 58.4 and 95.5% irrigation water in RW and MW rotations, respectively. CA⁺ practices saved 45.8 and 22.7% of irrigation water in rice and maize, respectively compared to CA with flood irrigation. On a system basis, CA⁺ practices saved 46.7 and 44.7% irrigation water under RW (ScV) and MW (ScVI) systems compared to their respective CA-based systems with flood irrigation (ScIII and ScIV). CA⁺ in RW system recorded 11.2% higher crop productivity and improved irrigation water productivity by 145% and profitability by 29.2% compared to farmers’ practice. Substitution of rice with maize (MW system; ScVI) recorded 19.7% higher productivity, saved 84.5% of irrigation water and increased net returns by 48.9% compared to farmer’s practice. CA⁺ RW and MW system improved energy productivity by 75 and 169% and partial factor productivity of N by 44.6 and 49.6%, respectively compared to ScI. The sub-surface drip irrigation system saved the fertilizer N by 20% under CA systems. CA⁺ in RW and MW systems recorded ~13 and 5% (2-yr mean) higher profitability with 80% subsidy on installing sub-surface drip irrigation system and similar profitability without subsidy scenario compared with their respective flood irrigated CA-based systems.

MED13L-related intellectual disability: involvement of missense variants and delineation of the phenotype

Molecular anomalies in MED13L, leading to haploinsufficiency, have been reported in patients with moderate to severe intellectual disability (ID) and distinct facial features, with or without congenital heart defects. Phenotype of the patients was referred to "MED13L haploinsufficiency syndrome." Missense variants in MED13L were already previously described to cause the MED13L-related syndrome, but only in a limited number of patients. Here we report 36 patients with MED13L molecular anomaly, recruited through an international collaboration between centers of expertise for developmental anomalies. All patients presented with intellectual disability and severe language impairment. Hypotonia, ataxia, and recognizable facial gestalt were frequent findings, but not congenital heart defects. We identified seven de novo missense variations, in addition to protein-truncating variants and intragenic deletions. Missense variants clustered in two mutation hot-spots, i.e., exons 15-17 and 25-31. We found that patients carrying missense mutations had more frequently epilepsy and showed a more severe phenotype. This study ascertains missense variations in MED13L as a cause for MED13L-related intellectual disability and improves the clinical delineation of the condition.

Genetic mitigation strategies to tackle agricultural GHG emissions: The case for biological nitrification inhibition technology

Accelerated soil-nitrifier activity and rapid nitrification are the cause of declining nitrogen-use efficiency (NUE) and enhanced nitrous oxide (N₂O) emissions from farming. Biological nitrification inhibition (BNI) is the ability of certain plant roots to suppress soil-nitrifier activity, through production and release of nitrification inhibitors. The power of phytochemicals with BNI-function needs to be harnessed to control soil-nitrifier activity and improve nitrogen-cycling in agricultural systems. Transformative biological technologies designed for genetic mitigation are needed, so that BNI-enabled crop-livestock and cropping systems can rein in soil-nitrifier activity, to help reduce greenhouse gas (GHG) emissions and globally make farming nitrogen efficient and less harmful to environment. This will reinforce the adaptation or mitigation impact of other climate-smart agriculture technologies.

140 W peak power laser system tunable in the LWIR

We present a high peak power rapidly tunable laser system in the long-wave infrared comprising an external-cavity quantum cascade laser (EC-QCL) broadly tunable from 8 to 10 µm and an optical parametric amplifier (OPA) based on quasi phase-matching in orientation-patterned gallium arsenide (OP-GaAs) of fixed grating period. The nonlinear crystal is pumped by a pulsed fiber laser system to achieve efficient amplification in the OPA. Quasi phase-matching remains satisfied when the EC-QCL wavelength is swept from 8 to 10 µm with a crystal of fixed grating period through tuning the pump laser source around 2 µm. The OPA demonstrates parametric amplification from 8 µm to 10 µm and achieves output peak powers up to 140 W with spectral linewidths below 3.5 cm^-1. The beam profile quality (M²) remains below 3.4 in both horizontal and vertical directions. Compared to the EC-QCL, the linewidth broadening is attributed to a coupling with the OPA.

Integrating crops and livestock in subtropical agricultural systems

As the demand for livestock products increases, and is expected to continue to increase over the next few decades, especially in developing countries, smallholder mixed systems are becoming more intensive. However, with limited land and water resources and concern about the environmental impact of agricultural practices and climate change, the challenge is to find ways of increasing productivity that do not compromise household food security, but rather increase incomes equitably and sustain or enhance the natural resource base. In developed countries there has been increased specialisation of crop and livestock production. In contrast, the majority of livestock in developing countries is kept in mixed crop/livestock systems. Crops (cereal grains and pulses) and crop residues provide the basis of the diet for animals, e.g. cereal straw fed to dairy cattle or sweet potato vines fed to pigs. Animal manure can provide significant nutrient inputs to crops. Water productivity is higher in mixed crop/livestock systems compared with growing crops alone. Mixed systems allow for a more flexible and profitable use of family labour where employment opportunities are limited. They also spread risks across several enterprises, a consideration in smallholder systems that may become even more important under certain climate change scenarios. Integrated crop/livestock systems can play a significant role in improving global food security but will require appropriate technological developments, institutional arrangements and supportive policy environments if they are to fulfil that potential in the coming decades.

Genotype-phenotype relationship in 2 SMA III patients with novel mutations in the Tudor domain

OBJECTIVE

We report the cases of 2 patients with late-onset spinal muscular atrophy (SMA) type III, who were hemizygous for SMN1 deletion and carriers of novel SMN1 intragenic missense mutations, and we investigate the genotype-phenotype relationship.

METHODS

Patients were tested for SMN1 deletions with standard methodology. Sequencing of all exons, exon-intron junctions, and flanking sequences of SMN1 by nested PCR was used to detect intragenic point mutations. SMN1 and SMN2 quantification was undertaken to investigate the genotype-phenotype relationship.

RESULTS

Two novel point mutations were identified in exon 3 of SMN1 (p.Tyr130Cys and p.Tyr130His) in the highly conserved Tudor domain of the Smn protein.

CONCLUSIONS

The genetic basis of SMA in the rare cases of compound heterozygous carriers of SMN1 deletions is complex. Small intragenic SMN1 mutations often lead to severe SMA phenotypes, especially if the point mutations lie in exon 3 that codes for the highly conserved Tudor domain of the Smn protein. Although both our patients were carriers of intragenic SMN1 mutations in the coding region of the Tudor domain, they presented with a mild SMA phenotype despite a low SMN2 copy number. We discuss the possible determinant role of these novel missense mutations in the phenotypic outcome and compensatory mechanisms that may account for the genotype-phenotype discrepancy.

Smart investments in sustainable food production: revisiting mixed crop-livestock systems

Farmers in mixed crop-livestock systems produce about half of the world's food. In small holdings around the world, livestock are reared mostly on grass, browse, and nonfood biomass from maize, millet, rice, and sorghum crops and in their turn supply manure and traction for future crops. Animals act as insurance against hard times and supply farmers with a source of regular income from sales of milk, eggs, and other products. Thus, faced with population growth and climate change, small-holder farmers should be the first target for policies to intensify production by carefully managed inputs of fertilizer, water, and feed to minimize waste and environmental impact, supported by improved access to markets, new varieties, and technologies.

Expanding the clinical and neuroradiologic phenotype of primary microcephaly due to ASPM mutations

OBJECTIVE

To determine the spectrum of clinical, neuropsychological, and neuroradiologic features in patients with autosomal recessive primary microcephaly (MCPH) due to ASPM gene mutations.

METHODS

ASPM was sequenced in 52 unrelated MCPH probands. In patients with ASPM mutations, we evaluated the clinical phenotype, cognition, behavior, brain MRI, and family.

RESULTS

We found homozygous or compound heterozygous ASPM loss-of-function mutations in 11 (22%) probands and 5 siblings. The probands harbored 18 different mutations, of which 16 were new. Microcephaly was severe after 1 year of age in all 16 patients, although in 4 patients the occipital-frontal circumference (OFC) at birth was decreased by only 2 SD. The OFC Z score consistently decreased after birth. Late-onset seizures occurred in 3 patients and significant pyramidal tract involvement in 1 patient. Intellectual quotients ranged from borderline-normal to severe mental retardation. Mild motor delay was noted in 7/16 patients. Language development was delayed in all patients older than 3 years. Brain MRI (n = 12) showed a simplified gyral pattern in 9 patients and several malformations including ventricle enlargement (n = 7), partial corpus callosum agenesis (n = 3), mild cerebellar hypoplasia (n = 1), focal cortical dysplasia (n = 1), and unilateral polymicrogyria (n = 1). Non-neurologic abnormalities consisted of short stature (n = 1), idiopathic premature puberty (n = 1), and renal dysplasia (n = 1).

CONCLUSIONS

We provide a detailed description of features associated with ASPM mutations. Borderline microcephaly at birth, borderline-normal intellectual efficiency, and brain malformations can occur in ASPM-related primary hereditary microcephaly.

Niger-wide assessment of in situ sorghum genetic diversity with microsatellite markers

Understanding the geographical, environmental and social patterns of genetic diversity on different spatial scales is key to the sustainable in situ management of genetic resources. However, few surveys have been conducted on crop genetic diversity using exhaustive in situ germplasm collections on a country scale and such data are missing for sorghum in sub-Saharan Africa, its centre of origin. We report here a genetic analysis of 484 sorghum varieties collected in 79 villages evenly distributed across Niger, using 28 microsatellite markers. We found a high level of SSR diversity in Niger. Diversity varied between eastern and western Niger, and allelic richness was lower in the eastern part of the country. Genetic differentiation between botanical races was the first structuring factor (Fst = 0.19), but the geographical distribution and the ethnic group to which farmers belonged were also significantly associated with genetic diversity partitioning. Gene pools are poorly differentiated among climatic zones. The geographical situation of Niger, where typical western African (guinea), central African (caudatum) and eastern Sahelian African (durra) sorghum races converge, explained the high observed genetic diversity and was responsible for the interactions among the ethnic, geographical and botanical structure revealed in our study. After correcting for the structure of botanical races, spatial correlation of genetic diversity was still detected within 100 km, which may hint at limited seed exchanges between farmers. Sorghum domestication history, in relation to the spatial organisation of human societies, is therefore key information for sorghum in situ conservation programs in sub-Saharan Africa.

Supplementation with groundnut haulms for sheep fattening in the West African Sahel

Groundnut haulms along with cowpea hay are major crop residues used for animal fattening in the West African Sahel. In traditional sheep fattening, feeds are always provided ad-hoc and in an unregulated fashion, which is rather wasteful. As a preliminary study to establish the optimal feeding levels of groundnut haulms for profitable sheep fattening, a feeding trial was conducted for 70 days with four levels of groundnut haulms (0, 150, 300 and 450 g/day) and a basal diet of bush hay. The effects of supplementation with groundnut haulms on feed intake, water consumption, live weight changes and economic return were determined. Twenty-four Peuhl Oudah rams with average initial weight of 28.6 kg (SD = 1.4) were randomly allocated to four treatments defined by the four levels of groundnut haulms in the diet. Faeces and urine were collected in weeks 5 and 9 of the trial. Digestible organic matter intake (g/(kg LW)0.75) and nitrogen intake (g/day) increased linearly with the level of groundnut haulms offered. Sheep that were fed only bush hay lost 18.4 g/day, while those that were offered 150, 300 and 450 g of groundnut haulms gained 1.4, 19.3 and 40.2 g/day, respectively. The gross return ranged from 1883 to 4946 FCFA per ram. Net benefit, after removing the feed and veterinary costs from the gross return, ranged from 368 to 1400 FCFA per ram.

Diversity of wild and cultivated pearl millet accessions (Pennisetum glaucum [L.] R. Br.) in Niger assessed by microsatellite markers

Genetic diversity of crop species in sub-Sahelian Africa is still poorly documented. Among such crops, pearl millet is one of the most important staple species. In Niger, pearl millet covers more than 65% of the total cultivated area. Analyzing pearl millet genetic diversity, its origin and its dynamics is important for in situ and ex situ germplasm conservation and to increase knowledge useful for breeding programs. We developed new genetic markers and a high-throughput technique for the genetic analysis of pearl millet. Using 25 microsatellite markers, we analyzed genetic diversity in 46 wild and 421 cultivated accessions of pearl millet in Niger. We showed a significantly lower number of alleles and lower gene diversity in cultivated pearl millet accessions than in wild accessions. This result contrasts with a previous study using iso-enzyme markers showing similar genetic diversity between cultivated and wild pearl millet populations. We found a strong differentiation between the cultivated and wild groups in Niger. Analyses of introgressions between cultivated and wild accessions showed modest but statistically supported evidence of introgressions. Wild accessions in the central region of Niger showed introgressions of cultivated alleles. Accessions of cultivated pearl millet showed introgressions of wild alleles in the western, central, and eastern parts of Niger.

PTCH mutations and deletions in patients with typical nevoid basal cell carcinoma syndrome and in patients with a suspected genetic predisposition to basal cell carcinoma: a French study

The patched (PTCH) mutation rate in nevoid basal cell carcinoma syndrome (NBCCS) reported in various studies ranges from 40 to 80%. However, few studies have investigated the role of PTCH in clinical conditions suggesting an inherited predisposition to basal cell carcinoma (BCC), although it has been suggested that PTCH polymorphisms could predispose to multiple BCC (MBCC). In this study, we therefore performed an exhaustive analysis of PTCH (mutations detection and deletion analysis) in 17 patients with the full complement of criteria for NBCCS (14 sporadic and three familial cases), and in 48 patients suspected of having a genetic predisposition to BCC (MBCC and/or age at diagnosis ⩽40 years and/or familial BCC). Eleven new germline alterations of the PTCH gene were characterised in 12 out of 17 patients harbouring the full complement of criteria for the syndrome (70%). These were frameshift mutations in five patients, nonsense mutations in five patients, a small inframe deletion in one patient, and a large germline deletion in another patient. Only one missense mutation (G774R) was found, and this was in a patient affected with MBCC, but without any other NBCCS criterion. We therefore suggest that patients harbouring the full complement of NBCCS criteria should as a priority be screened for PTCH mutations by sequencing, followed by a deletion analysis if no mutation is detected. In other clinical situations that suggest genetic predisposition to BCC, germline mutations of PTCH are not common.

Dasatinib (D) vs high dose imatinib (IM) in patients (pts) with chronic phase chronic myeloid leukemia (CP-CML) resistant to imatinib. Results of CA180017 START-R randomized trial

6507

Background: High dose imatinib (800 mg/day) has been shown to have efficacy in a subset of CML patients with resistance to IM, although the durability of responses is not well-established. Dasatinib (BMS-354825) is a novel, highly potent, oral multi-targeted kinase inhibitor of BCR-ABL and SRC with activity against 18/19 imatinib resistant BCR-ABL mutants tested in vitro. Methods: START-R is a multicenter randomized (2:1 ratio) trial of D 70 mg twice daily (bid) and IM 800 mg/day in pts with CP-CML resistant to prior IM 400 to 600 mg/day. Cross-over was allowed for lack of response or intolerance (grade 3–4 non hematologic toxicity). D dose escalation to 90 mg bid was allowed for inadequate response at 12 wks, and dose reduction to 50 or 40 mg bid for drug toxicity. IM dose reduction to 600 mg/day was allowed. Evaluations consisted of weekly blood counts for the first 12 wks, bone marrow cytology and cytogenetics every 12 wks. The primary endpoint was major cytogenetic response (MCyR) rate at wk 12. Results: From February 2005 to November 2005, 150 pts were randomized of whom the first 36 pts (D 22, IM 14) are reported. Median age was 57 yrs, with 12 males and 24 females. Treatment groups were balanced with respect to CML characteristics; median time from initial diagnosis was 61 months for D and IM; prior interferon 64% and 79%; no prior CyR on IM 36% and 57%. BCR-ABL mutations were documented in 10 D pts and 1 IM pt. Dose reductions were required in 8 D pts and 1 IM pt. Complete hematologic response was documented in 21 D and 13 IM pts. MCyR rate at 12 wks was 45% for D and 21% for IM (7 complete for D and 1 for IM). With a 95% CI on the difference between D and IM was - 9.9 to +51.2. Two (9%) D and 11 (79%) IM pts crossed over for intolerance (1 D and 6 IM) or no MCyR (1 D and 5 IM). Grade 3–4 neutropenia or thrombopenia occurred in 8 and 9 dasatinib pts and in 8 and 2 IM pts. Most common grade 1–2 non-hematologic toxicities in D and IM groups were diarrhea (7 and 1 pts), nausea (7 and 7 pts), and facial/peripheral edema (8 and 7 pts). Conclusions: Dasatinib was effective in pts with CP-CML resistant to IM 400 to 600 mg/day. Preliminary data suggest that D is more effective and better tolerated than high dose IM. An updated analysis of all randomized pts will be presented.

[Table: see text]

Optical parametric oscillation in quasi-phase-matched GaAs

We demonstrate an optical parametric oscillator (OPO) based on GaAs. The OPO utilizes an all-epitaxially-grown orientation-patterned GaAs crystal that is 0.5 mm thick, 5 mm wide, and 11 mm long, with a domain reversal period of 61.2 microm. Tuning either the near-IR pump wavelength between 1.8 and 2 microm or the temperature of the GaAs crystal allows the mid-IR output to be tuned between 2.28 and 9.14 microm, which is limited only by the spectral range of the OPO mirrors. The pump threshold of the singly resonant OPO is 16 microJ for the 6-ns pump pulses, and the photon conversion slope efficiency reaches 54%. We also show experimentally the possibility of pump-polarization-independent frequency conversion in GaAs.

Difference frequency generation of 8-microm radiation in orientation- patterned GaAs

First-order quasi-phase-matched difference frequency generation of narrowband tunable mid-infrared light is demonstrated in orientation-patterned GaAs. The all-epitaxial orientation-patterned crystal is fabricated by a combination of molecular beam epitaxy and hydride vapor phase epitaxy. Lasers at 1.3 and 1.55 microm were mixed to give an idler output at 8 microm, with power and wavelength tuning consistent with theoretical estimates, indicating excellent material uniformity over the 19-mm-long and 500-microm-thick device.

Clinical phase I and pharmacokinetic study of S 16020, a new olivacine derivative: report on three infusion schedules

S 16020, a new 9-OH olivacine derivative, is a novel topoisomerase II inhibitor with activity in cell lines presenting the classical multidrug resistance phenotype. This report summarizes, in addition to pharmacokinetic data, the whole phase I clinical experience of S 16020 using three different infusion schedules. Asthenia and skin toxicity were the main side effects. In an attempt to understand the skin toxicity mechanism, experiments in animals were performed, the results of which are reported. S 16020 showed rapid tumor necrotizing activity in some patients, with soft tissue metastases of epidermoïd tumors and pain at the tumor site. To document the side effects of S 16020 and tumor site reactions (pain, edema, inflammatory signs), inflammatory parameters and some cytokines were measured. In our patients there was no hemolysis and no detection of anti-S 16020 antibodies, confirming the absence of immunogenicity of the compound. Based on the overall data of the three infusion schedules of S 16020, the dose of 100 mg/m(2) over 3 h every 3 weeks was selected for phase II studies.

Measurement of the nonlinear coefficient of orientation-patterned GaAs and demonstration of highly efficient second-harmonic generation

Quasi-phase-matched (QPM) GaAs structures, 0.5 mm thick, 10 mm long, and with 61-mum grating periods, were grown by a combination of molecular-beam epitaxy and hydride vapor phase epitaxy. These were characterized by use of mid-IR second-harmonic generation (SHG) with a ZnGeP(2) (ZGP) optical parametric oscillator as a pump source. The SHG efficiencies of QPM GaAs and QPM LiNbO(3) were directly compared, and a ratio of nonlinear coefficients d(14)(GaAs)/d(33) (LiNbO(3))=5.01+/-0.3 was found at 4.1-mum fundamental wavelength. For input pulse energies as low as 50muJ and approximately 60-ns pulse duration, an internal SHG conversion efficiency of 33% was measured in QPM GaAs.

Composition, structure and size distribution of suspended particulates from the Rhine River

Fluvial suspended particulates collected from the Rhine River were investigated in terms of composition, structure and size distribution. Elemental analysis and Diffuse Reflectance Infrared Spectroscopy reveal that most particulate organic matter is formed from material derived from microorganisms. Transmission Electron Microscopy observations on resin-embedded samples and structural characterization from break-up experiments, show that fluvial particulate matter should be viewed as fractal aggregates organized by bacterial exopolymeric substances. The shape of particulate size distribution suggests that the formation and dynamics of suspended particulate matter are controlled mainly by physical processes. Finally, particulate growth and structure are consistent with a cluster-cluster aggregation scheme.

Upper extremity pain after spinal cord injury

OBJECTIVE

Patients with spinal cord injury (SCI) may complain of upper extremity (UE) pain. The purpose of this study was to determine the frequency and severity of UE pain as well as its association with functional activities. Types of treatments that SCI patients received for UE pain and the benefits of these treatments were also identified.

STUDY DESIGN AND METHODS

A questionnaire of demographic variables and measures of UE pain intensity, location, treatment, and interference with functional activities was mailed to 170 persons with SCI. Data was analyzed by descriptive and comparative statistics.

RESULTS

Of the 130 persons who responded, 76 (58.5%) (38 paraplegic, 38 tetraplegic patients) reported UE pain: 71% had shoulder pain, 53% wrist pain, 43% hand pain, and 35% elbow pain. Pain interfered with transfers in 65% (36/55) of the patients who were doing them. Of ten functional activities, pain was more likely to be associated with pressure reliefs, transfers, and wheelchair mobility. Sixty-three per cent sought medical treatment for pain, and of those, 90% received either physical therapy, pharmacological treatment or massage. Although only 27% had wheelchair or home modification or joint protection education, these approaches were helpful for almost all and very helpful or extremely helpful in 26.6% and 63.6% of the patients, respectively.

CONCLUSION

UE pain is a common problem in individuals with SCI and has impact on daily activities. UE pain prevention and management programs are needed for SCI patients.

Clinical experience of fotemustine, cisplatin and high dose tamoxifen in patients with metastatic malignant melanoma

Inspired by the high response rates achieved with the DBCT regimen (dacarbazine [DTIC], carmustine [BCNU], cisplatin and tamoxifen [TAM]), we administered the nitrosourea compound fotemustine, cisplatin and TAM (FCT regimen) to 69 patients with metastatic melanoma. Fotemustine (100 mg/m2) and cisplatin (100 mg/m2) were administered every 4 weeks, preceded by TAM 160 mg daily for 7 days from the second course onwards. Pharmacokinetic blood sampling was performed in 14 patients during the initial two cycles to compare the pharmacokinetic behaviour of fotemustine with or without TAM. Previous chemo- or radiotherapy was allowed, and patients with brain metastases or concomitant other malignancies were included. Four complete and 11 partial responders were observed among 66 evaluable patients, yielding a response rate of 22.7% (95% confidence interval 12.9 32.5%). The median survival time was 6.4 months (range 0.1-52+ months). The main toxicities were thrombocytopenia, protracted nausea/vomiting and ototoxicity. Renal toxicity was generally mild, but possibly contributed to two deaths. Seven patients experienced deep venous thrombosis during the study. TAM had no influence on the pharmacokinetics of fotemustine. The activity of the FCT regimen was clearly inferior to that initially reported with DBCT treatment. However, a recent publication concludes that the latter achieves a considerably lower response rate when administered to a larger patient group. We believe our results reflect the true activity of FCT and similar regimens when administered routinely to unselected patients. Considering the number of potentially serious side effects, we cannot recommend the moderately active FCT regimen as a palliative treatment option for melanoma patients.

Ventricular arrhythmia and torsade de pointe: dose limiting toxicities of the MDR-modulator S9788 in a phase I trial

BACKGROUND

S9788 is a triazineaminopiperidine derivative capable of reversing multidrug resistance (MDR) in vitro. In preclinical models S9788 was several fold more potent MDR inhibitor than verapamil or cyclosporine. At P-glycoprotein (Pgp) blocking concentrations, S9788 appeared to have only very little toxicity.

PATIENTS AND METHODS

In a two step phase I trial we treated 39 patients with refractory cancer with S9788 and bolus doxorubicin. The steps differed mainly in the S9788 infusion duration; in the first part 23 patients received the MDR-reversing drug S9788 over 30 minutes, in the second step of the study 16 patients were administered S9788 over 150 minutes. The doses of S9788 were escalated in cohorts of three patients up to a dose level (DL) of 96 mg/m2 on the 30 minutes infusion, and to 144 mg/m2 on the 150 minutes infusion. The pharmacokinetics of S9788 were determined.

RESULTS

With the 30-minute infusion schedule symptomatic cardiac arrhythmia were found to be dose limiting. In all patients at the highest DL transient cardiac repolarization prolongation with a long QT-interval on ECG was demonstrated. With the 150-minute administration schedule, S9788 could be escalated up to 144 mg/m2 without subjective toxicity. However, transient QT prolongation was present in all patients. A third degree AV-block and a QT increase of about 40% occurred at the highest DL. Asymptomatic torsade de pointe (DL 96 mg/m2) was demonstrated on Holter recording in one patient. Theses repolarization disturbances with QT increase were considered dose limiting toxicity and the trial was closed. No arrhythmia related death was noted. Pharmacokinetics were similar with both infusion schedules with a mean alpha half life of 11.3 and 13.2 minutes, for the 30-minute and 150-minute infusion, and a terminal half life of 13.5 and 15 hours, respectively. QTc prolongation duration appeared to be dose-dependent.

CONCLUSIONS

With the tested infusion schedules, cardiac toxicity, in particular AV-blocks and QT prolongation, leading to ventricular arrhythmia and torsade de pointe, are the dose limiting toxicities of S9788. Our experience together with the observation of asymptomatic torsade de pointe in two other phase 1 trials of S9788 infused over six hours precluded the further clinical development of S9788.

Oxaliplatin combined to 5-fluorouracil and folinic acid: an effective therapy in patients with advanced colorectal cancer

Patients with colorectal carcinoma progressing after a 5-fluorouracil (5-FU)-containing regimen were eligible. One treatment cycle consisted of repeated administrations of 5-FU combined to folinic acid for six times and to oxaliplatin for three times over 50 days. 5-FU was given at the dose of 2.6 g/m2 as a continuous infusion over 24 h on days 1, 8, 22, 29 and 43 preceded by i.v. folinic acid (FA) at a dose of 500 mg/m2 over 1 h. Oxaliplatin was given 1 h after 5-FU at the dose of 130 mg/m2 over a 2 h infusion on days 1, 22 and 43. A total of 37 patients were treated according to this schedule. The rates of objective responses after the first and second treatment cycles were 28 and 17%, respectively, with rates of tumor growth control, i.e. including the stabilizations, of 55 and 28%. The median duration of response was 10 months and the median duration of stabilizations was 6 months. The median survival time from initiation of oxaliplatin-containing therapy is 10 months (2-28+). The median survival time from the diagnosis of metastatic disease is 24 months (2-40+). The main toxicities were leucopenia, diarrhea, fatigue and paresthesias. The combination of 5-FU/FA/oxaliplatin was well tolerated and appears as a meaningful therapy after failure of a previous 5-FU-containing treatment.

Medical care for mass gatherings at collegiate football games

BACKGROUND

Many articles have reviewed medical care at mass gatherings, but few have specifically looked at care provided during football games. Some of the largest gatherings occur at various stadiums during football season.

METHODS

We analyzed the medical care provided for the spectators at Williams-Brice Stadium for the University of South Carolina 1995 football season. The average attendance per game was 69,427; seven home games were played. Six physician/nurse/paramedic/paramedic teams provided medical care using prehospital equipment.

RESULTS

Medical care was given to 526 individuals, an average of 1.08 +/- 0.37 per 1,000 spectators per game. Records of 465 persons (88%) were available for review. The most common complaints were headache (48%), trauma (16%), gastrointestinal distress (10%), and environmental (7%). Nineteen patients (4%) required transport to nearby hospitals for further evaluation.

CONCLUSIONS

These results reflect patients with medical complaints seen during one collegiate football season in South Carolina. We believe this information can be used in planning medical care needs at other mass gatherings.

[Role of radiotherapy in cancers of the stomach]

The rational bases for using radiotherapy in gastric cancer are strong since most of the patients will finally die from locoregional recurrence and/or distant metastases. The review of the randomized studies investigating that question failed to demonstrate a benefit from using radiotherapy. Inappropriate methodology could explain the lack of results: the number of patients in the series is too small, the treatment modalities are not standardized, the patients populations are inhomogeneous. Well conceived clinical trials are still required in order to answer that question.

[Colorectal cancer: a controllable disease]

Colorectal cancer is one of the most frequent cancers in western countries. Five years after curative surgery and adjuvant chemotherapy, about 10% more patients with Dukes C colon cancer are free of disease compared to the control group. Several regimens using 5-fluorouracil with folinic acid (5FU/FA) or levamisole are available. For patients with disseminated disease. 5FU/FA based treatments allows a doubling in survival as compared to best supportive care. Moreover, quality of life is significantly improved. New agents are upcoming. Tomudex seems to be equivalent to 5FU/FA but easier to administer. CPT-11 or oxaliplatin have been investigated in second line after failure of 5FU/FA. The available data suggest that median survival is prolonged by ten months, in addition to what was already obtained in first line with 5FU/FA. Colorectal cancer must be revisited. An active approach of our patients should allow to reduce the incidence of the disease, to increase the number of disease free patients 5 years after surgery, to prolong survival and improve the quality of life of those who will develop metastatic disease.

[Non surgical treatment of pancreatic cancers]

Pancreatic cancer is a disease difficult to treat. Diagnosis is late, cancer remaining clinically unapparent even if locally advanced or metastatic. Few patients can be submitted to curative surgery. Even if resection is possible, 5-year survival varies from 0% to 18% according to series. Some data suggest that chemotherapy with or without radiotherapy could influence disease free survival but a benefit on overall survival has not been demonstrated. For locally advanced disease, the results of a trial published in 1968, showed that a combination of radiotherapy and 5-Fluorouracil (5FU) improved median survival as compared to radiotherapy alone (5.5 versus 10 months). Since then, no progress has been achieved. At the present time, survival of patients with metastatic pancreatic cancer cannot be improved. Very recently, a new agent, gemcitabine, has been compared to 5FU. Criteria for activity were based on clinical improvement analgesia consumption, performance status and weight gain. Twenty-four percent of the patients treated with gemcitabine had a clinical benefit as compared to 5% for those treated with 5FU. Other studies comparing chemotherapy to best supportive care show a significant decrease of depression and anxiety as well as an improvement in quality of life for patients being treated.

Gastrointestinal Tract Cancer Liaison Office: an attempt to organise clinical research in Europe

The Gastrointestinal Tract Cancer Liaison Office (GITCLO) was developed in an attempt to organise the increasing body of clinical research in gastrointestinal tumours in Europe. This paper represents an analysis, by tumour localisation, of the trials collected for the second edition of the GITCLO booklet. The list of cooperative groups, chairmen and study coordinators is given with their respective telephone and telefax numbers. A total of 84 trials were collected, conducted by 46 co-operative groups in 14 countries. For each organ and stage of disease, a summary of concepts investigated is given with the references of the study co-ordinator. Obviously, too many questions are raised at the same time. In colorectal cancer, for example, a total of 41 trials exploring 22 concepts are currently open for patients' registration. We hope that the present attempt to clarify the situation of clinical research in the field of gastrointestinal cancers in Europe will speed up therapeutic progress in the best interest of the patients.

Analysis of ETV6 and ETV6-AML1 proteins in acute lymphoblastic leukaemia

The t(12;21) is a recurring chromosomal abnormality in acute lymphoblastic leukaemias (ALLs) which results in the production of an ETV6-AML1 fusion gene. The association between t(12;21) and the deletion of the untranslocated allele of ETV6 is among the most frequent abnormalities observed in B-lineage ALLs in children. In order to study the proteins encoded by ETV6 and ETV6-AML1, we raised polyclonal antibodies directed against a recombinant peptide corresponding to the junctional region of ETV6-AML1. Cell lysates from various leukaemic cell lines, and from children with B- and T-lineage ALLs, were studied by Western blot. Two isoforms of ETV6 protein were detected in normal bone marrow cells and in leukaemic cells without 12p alteration: a major form (apparent m.w. 63 kD) and a minor one (apparent m.w. 53 kD). In the REH cell line, which expresses the ETV6-AML1 fusion transcript and no normal ETV6 mRNA, the ETV6 isoforms were absent and two new bands were detected corresponding to ETV6-AML1 protein products (apparent m.w. 95 and 105 kD). A similar pattern was obtained with blast cells from patients with a t(12;21) and a deletion of ETV6. In two patients with a t(12;21) but no deletion of ETV6, four bands were detected corresponding to both the normal ETV6 and ETV6-AML1 proteins, suggesting that in these cases the second ETV6 allele was not inactivated. Surprisingly, the expression pattern of ETV6 differed widely from patient to patient. In three out of 13 patients without t(12;21), the relative intensity of the bands corresponding to ETV6 isoforms in blast cells from patients was completely different from normal cells, with a marked predominance of the 53 kD isoform. The pattern of ETV6 expression was normal in bone marrow from the same patients during remission. These finding suggest that ETV6 abnormalities are not restricted to patients with translocations or deletions involving this gene.

Phase IB study of doxorubicin in combination with the multidrug resistance reversing agent S9788 in advanced colorectal and renal cell cancer

S9788 is a new triazineaminopiperidine derivate capable of reversing multidrug resistance (MDR) in cells resistant to chemotherapeutic agents such as doxorubicin. It does not belong to a known class of MDR revertants, but its action involves the binding of P-glycoprotein. Thirty-eight evaluable patients with advanced colorectal or renal cell cancer were treated with doxorubicin alone (16 patients) followed after disease progression with combination treatment of doxorubicin plus S9788 (12 patients) or upfront with the combination of doxorubicin plus S9788 (22 patients). S9788 was given i.v. as a loading dose of 56 mg m-2 over 30 min followed by doxorubicin given at 50 mg m-2 as a bolus infusion. Thereafter, a 2-h infusion of S9788 was administered at escalating doses ranging from 24 to 120 mg m-2 in subsequent cohorts of 4-10 patients. Pharmacokinetic analysis demonstrated that concentrations of S9788 that are known to reverse MDR in vitro were achieved in patients at non-toxic doses. Compared with treatment with doxorubicin alone, treatment with the combination of doxorubicin and S9788 produced a significant increase in the occurrence of WHO grade 3-4 granulocytopenia. Treatment with S9788 was cardiotoxic as it caused a dose-dependent and reversible increase in corrected QT intervals as well as clinically non-significant arrhythmias on 24- or 48-h Holter recordings. Although clinically relevant cardiac toxicities did not occur, the study was terminated as higher doses of S9788 may increase the risk of severe cardiac arrhythmias. Twenty-nine patients treated with S9788 plus doxorubicin were evaluable for response, and one patient, who progressed after treatment with doxorubicin alone, achieved a partial response. We conclude that S9788 administered at the doses and schedule used in this study results in relevant plasma concentrations in humans and can safely be administered in combination with doxorubicin.

Fotemustine in patients with advanced gastric cancer, a phase II trial from the EORTC-GITCCG (European Organization for Research and Treatment of Cancer, Gastrointestinal Tract Cancer Cooperative Group)

Fotemustine activity was evaluated in 26 patients, mostly pretreated, with advanced gastric cancer. Its main toxicity was haematological with grade 3-4 neutropenia in 32% and grade 3-4 thrombocytopenia in 50% of the patients, complicated by 2 toxicity-related deaths due to haemorrhage. No complete or partial responses were observed in the 26 eligible patients and median survival was only 11 weeks. Fotemustine therefore has no activity in advanced gastric cancer.

Duodenal expression of NF-E2 in mouse models of altered iron metabolism

This study investigated the relationship between duodenal mucosal mRNA levels of the transcription factor, NF-E2, H-ferritin (a putative NF-E2 regulated gene) and iron absorption in mice. CD1-strain mice with normal and altered iron metabolism (hypoxic, iron-deficient, iron-loaded) and animals with genetic defects of iron metabolism (hypotransferrinaemia, beta-thalassaemia) were studied. Tissue RNA from these mouse models was subjected to reverse transcription and PCR amplification for NF-E2 and a stable ribosomal protein (S14) and the products analysed with an automated laser fluorescent sequencer. Duodenal NF-E2 mRNA levels were generally low and decreased in the hypoxic and iron-deficient groups, both of which exhibited elevated iron absorption as compared to controls. A modest increase in the NF-E2 mRNA level was seen in the iron-loaded mice, whose iron absorption was decreased. In contrast, both the genetic strains showed elevated NF-E2 mRNA levels in conjunction with raised iron absorption values. Only the iron-deficient group exhibited an alteration in the duodenal mucosal H/L ferritin ratio. Hence, no relationship was evident between the NF-E2 mRNA levels and the H/L ferritin ratio. These data indicate that NF-E2 is not the primary regulator of intestinal iron absorption.