An Efficient Method to Prepare Barcoded cDNA Libraries from Plant Callus for Long-Read Sequencing.

Long-read sequencing methods allow a comprehensive analysis of transcriptomes in identifying full-length transcripts. This revolutionary method represents a considerable breakthrough for non-model species since it allows enhanced gene annotation and gene expression studies when compared to former sequencing methods. However, woody plant tissues are challenging to the successful preparation of cDNA libraries, thus, impairing further cutting-edge sequencing analyses. Here, a detailed protocol for preparing cDNA libraries suitable for high throughput RNA sequencing using Oxford Nanopore Technologies® is described. This method was used to prepare eight barcoded cDNA libraries from two Solanum betaceum cell lines: one with compact morphology and embryogenic competency (EC) and another with friable and non-embryogenic (NEC). The libraries were successfully sequenced, and data quality assessment showed high mean quality scores. Using this method, long-read sequencing will allow a comprehensive analysis of plant transcriptomes.

Evaluation of comparative scenarios from different sites of chestnut production using life cycle assessment (LCA): Case study in the Beira Interior region of Portugal.

The evaluation of the environmental impacts of chestnut production in the Beira Interior region (Portugal) is accessed. The comparative life cycle assessment (LCA) was performed with the use of openLCA software with 16 Environmental Footprint (EF) impact categories retrieved from the AGRIBALYSE database. The system boundary was from "cradle-to-farm gate" and the functional unit was 1 ton of chestnut delivered to consumers (only wholesale buyers). The processes model for the production of agricultural machinery, pesticides, fertilizers, and materials was modeled based on surveys and existing literature. The data was gathered from four different production areas: Serra da Estrela, Malcata, Gardunha, and Plateau area. Each site has two selected representative producers inner 250 km2 square radius environment. The results showed that the average GHG emissions in the low-input group (Estrela and Gardunha) were 1.83 kg CO2-eq/ton with the energy burden (80-89%) as main contribution emissions and in the intensive-input group (Malcata and Plateau) were 2.61 kg CO2-eq/ton with the main contribution source of emissions are fertilizer (76-83%). Sensitivity analysis results indicate shift input material and cultivation activities in chestnut production systems can be possible for all study areas without reducing yield production. The suggestions in this article can be used by farmers, policymakers, and other stakeholders to adopt new alternative production scenarios.

Urinary cotinine assessment of maternal smoking and environmental tobacco smoke exposure status and its associations with perinatal outcomes: a cross-sectional birth study.

Tobacco consumption and environmental tobacco smoke (ETS) exposure remains an important public health concern. Pregnant women require particular attention as active and passive smoking during pregnancy are associated with multiple adverse perinatal outcomes. This study aimed to biochemically validate self-reported smoking and ETS exposure status among pregnant women, to more precisely ascertain its association with adverse perinatal outcomes. Data refers to 595 pregnant women who sought prenatal care in a public hospital in Porto, Portugal. A standard questionnaire on smoking and ETS-related variables was completed. Urinary cotinine (UC) concentrations were assessed by solid-phase competitive ELISA, in maternal urine samples collected on the day of delivery. The results showed that the optimal UC cut-off value to distinguish smokers from non-smokers and within non-smokers those who were exposed to ETS from those non-exposed in the third trimester of pregnancy was 74.1 ng/mL (sensitivity and specificity of 96.7% and 98.0%, respectively) and 1.6 ng/mL (sensitivity of 66.2% and specificity of 75.7%, respectively). The agreement between maternal self-reported and UC-based smoking status was very good (κ=0.919, p<0.001), but much lower for ETS exposure (κ=0.386, p<0.001). Maternal active smoking in the third trimester of pregnancy was associated with a significant decrease in birth weight, length and head circumference of 157.66 g (95% CI: -245.81, -69.52; p<0.001), 0.78 cm (95% CI: -1.22, -0.34; p=0.001) and 0.39 cm (95% CI: -0.70, -0.07; p=0.016), respectively. Maternal ETS exposure in the third trimester of pregnancy was associated with a non-significant increase in birth weight of 38.37 g (95% CI: -28.91, 105.64; p=0.263). Furthermore, maternal smoking cessation was associated with the increase of approximately 172 g in birth weight (95% CI: 50.00, 293.19). As such, there is an urgent need for increased public health awareness campaigns to encourage smoking cessation during pregnancy, in order to improve perinatal outcomes.

The importance of socioeconomic position in smoking, cessation and environmental tobacco smoke exposure during pregnancy.

Tobacco is still a leading cause of premature death and morbidity. Particular attention has been given to pregnant women due to the scientific evidence on the importance of early life exposures for disease onset later in life. The purpose of this study was to assess smoking prevalence, smoking cessation rate and environmental tobacco smoke (ETS) exposure, and the role of socioeconomic position (SEP) on these behaviors among pregnant women. Cross-sectional data of 619 pregnant women, aged between 18 and 46 years, from Porto Metropolitan Area, Portugal, on current smoking, ETS exposure and SEP indicators was collected, face-to-face, using a questionnaire filled in during a personal interview at the postpartum hospital stay. The smoking prevalence, and ETS exposure among non-smokers before pregnancy was 27.6% and 57.4%, respectively. 4.1% of the participants reported to have stopped smoking before pregnancy, whereas about 41% quitted along pregnancy, resulting in a smoking prevalence at birth of 14.6%. Exposure to ETS also decreased throughout pregnancy to 49.8% at birth. Lower educational level was significantly associated with both higher smoking prevalence and exposure to ETS and lower smoking cessation. This study demonstrates that smoking and ETS exposure during pregnancy remains high, and that there are still significant socioeconomic inequalities in smoking; thus tobacco-focused preventive interventions need to be reinforced.