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 smoking cessation during pregnancy and its association with perinatal outcomes

 

In utero exposure to tobacco smoke is associated with an increased risk of multiple adverse perinatal outcomes. Smoking cessation during pregnancy has been related to the improvement of these outcomes, but often relies on self-reporting, impairing an accurate assessment of smoking cessation impact on newborńs health. Building on data obtained in the frame of the NEOGENE project, this work aimed to estimate the association between smoking cessation among pregnant women, confirmed by maternal urinary cotinine concentrations, and perinatal outcomes. The study population included 595 pregnant women who sought prenatal care in a public hospital in Porto (Portugal), from April 2017 to July 2018. Data on tobacco consumption and cessation was obtained in a face-to-face interview, during the hospital stay. Perinatal outcomes, namely birth weight (BW), length (BL) and head circumference (HC) were retrieved from the hospital medical records. Maternal self-reported tobacco use was validated by urinary cotinine concentrations, using the solid-phase competitive ELISA technique. Maternal active smoking was associated with a significant decrease in BW, BL and HC of 157.66 g (p &lt; 0.001), 0.78 cm (p = 0.001) and 0.39 cm (p = 0.016). Notably, maternal smoking cessation led to a significant increase in BW of approximately 172 g (p = 0.006), when compared to mothers who have not ceased. Increases in BL and HC did not reach significance. This study upholds that tobacco consumption is still an important public health threat in Portugal and that smoking cessation during pregnancy reverses smoking-associated deficits in perinatal outcomes, emphasizing the crucial need for awareness campaigns to promote smoking cessation during pregnancy.

Acknowledgments: This work was supported by FCT and FAPESP (FAPESP/19914/2014). AIS, JM and CC also acknowledge FCT for individual funding (SFRH/BD/145101/2019, SFRH/BPD/115112/2016 and SFRH/BPD/96196/2013 grants, respectively).

Key messages

Maternal active smoking was significantly associated with lower birth weight, length and head circumference. Maternal smoking cessation reverses the smoking-associated deficits in birth weight.

Postharvest changes in water status and chlorophyll content of lettuce (Lactuca sativa L.) and their relationship with overall visual quality

The purpose of this study was to evaluate water status, chlorophyll content (C), and overall visual quality (OVQ) of fresh butter lettuce (Lactuca sativa var. Lores) as well as these indexes' evolution during storage and their relationships, if any. Whole lettuce plants were stored at optimal postharvest conditions (0 to 2 degrees C and 97% to 99% relative humidity). Measured parameters during each sampling day were relative water content (RWC), water content (WC), free water (FW), bound water (BW), free water to total water ratio (FW/TW), C, and OVQ. All parameters were evaluated in the external, middle, and internal zones of lettuce heads. The external zone had higher initial values of RWC, WC, and FW than the internal zone. The external zone yielded the highest FW/TW ratio (85%), indicating that external leaves had more water available to be used in degradation reactions and were more perishable, with the lowest shelf life if compared with the other lettuce zones. During storage, water status index evolution differed from zone to zone. An increase in BW and a decrease in FW were detected in all lettuce zones. RWC turned out to be a more sensitive measurement than WC. Yet RWC showed no significant correlation with any index. The OVQ parameter correlates with FW directly, or indirectly through FW/TW in all lettuce zones; therefore, FW is an objective and quantitative measurement, which impacts on the visual quality of butter lettuce. The decrease in chlorophyll content observed in the external leaves strongly correlated with the decrease in OVQ.