Cell-free methylated DNA immunoprecipitation and high throughput sequencing technology: diagnostic value in patients with renal cell carcinoma.

Background CfmeDNA is a promising biomarker for non-invasive assessment of solid tumors: i) MeDNA is tissue- and tumor-specific ii) cfDNA methylation changes are stable unlike DNA alterations iii) \u2018methylation target size\u2019 is larger than identifying specific genomic alterations and, therefore, more sensitive. CfMeDIP-seq is a sensitive assay for genome-wide bisulfite-free cfMeDNA profiling, that requires 1-10 ng input DNA. We tested the feasibility of cfMeDIP-seq to detect ccRCC across TNM stages Methods We evaluated plasma cfDNA collected prior to nephrectomy in 46 pts with ccRCC: 25 stage I, 7 stage II, 6 stage III, 8 stage IV. cfMeDIP-seq involves four steps: 1) cfDNA end-repair, A-tailing, and adapter ligation, 2) cfMeDNA immunoprecipitation and enrichment using an Ab targeting 5-methylcytosine (quality control by qPCR to ensure 99% reaction specificity), 3) adapter-mediated PCR to amplify cfMeDNA, and 4) high-throughput NGS for cfMeDNA data. A previously-derived model (Shen et al, Nature, 2018) was used to classify pts as having ccRCC or not based on cfMeDNA. cfMeDIP-seq paired end data was reduced to 300 bp windows of the genome that map to CpG islands, shores, shelves, and FANTOM5 enhancers; a classifier was then built using the top 1,000 most variable fragments between pts with ccRCC and cancer-free controls. Statistical comparisons were performed in the R statistical environment, with the caret package being used for classifier construction and evaluation Results The average amount of cfDNA isolated from 1 ml of ccRCC plasma was 19.8\ub139.8 ng/\u3bcL [1.95-260]. Greater than 99% specificity of reaction and <1% of unMeDNA was achieved in 46/46 samples (100%). The previously-derived classifier of ccRCC correctly predicted 46/46 pts (100%) as having ccRCC. Across 3 rounds of 5-fold cross-validation, the classifier performed with a Cohen\u2019s Kappa of 0.93 Conclusion CfMeDIP-seq is a non-invasive, cost-effective, and sensitive assay to detect cancer-specific cfmeDNA in ccRCC pts prior to nephrectomy. With further validation, cfmeDNA may detect minimal residual disease after nephrectomy for \u2018precision\u2019 adjuvant therapy

Soil water availability and relationship between canopy and roots in young olive trees (cv Coratina).

Trials were carried out in the Basilicata region (41°03’ N, 15°42’ E, Southern Italy) using ownrooted plants of the cultivar Coratina planted in 1992 at distances of 6 x 3 m. During 1992, the whole plot (about 7000 m2) was irrigated. From 1993 onwards, irrigation was suspended in part of the plot. A representative number of plants during 1992, 1993, 1994 and 1998 was destroyed in order to carry out dry weight measurements on roots and canopy. The ratio between root and leaf dry weight was always greater in nonirrigated plants compared to irrigated ones. Roots explored a soil volume ranged from 0.5 m3 in the first year to 16.8 m3 in the seventh year for irrigated plants and from 0.5 m3 to 13.4 m3 for non-irrigated ones. The study showed that in deep soil, with a greater capacity for water storage during the rainfall season, limited water supply (220-1350 m3 ha-1) during the first seven years from planting increased canopy growth by 79% compared to nonirrigated plants, but made little difference to root growth. In non-irrigated plants, canopy growth (but not root growth) was drastically reduced, as a defence strategy against water deficit, making for a better root/leaf ratio and consequently greater water availability for leaves

Preliminary investigations on sunburn in Chardonnay grapevine variety

The aim of this investigation was to determine if a temperature response curve can be used to describe sunburn in grape berries. Trials were carried out at the Viticulture and Enology Department (University of California, Davis) on cv Chardonnay (clone 29) grown under both field and greenhouse conditions. Greenhouse plants were two years old, grown in 5 L pots, and watered daily with a modified Hoagland’s nutrient solution. The vines were pruned to two shoots with one or two clusters per shoot, and the shoots were vertically trained to approximately 1.5 m. Field-grown vines were clone 29 grafted onto 101-14 rootstock, planted at 2.5 x 3.7 m spacing, cane pruned, and VSP trained. Rows were north-south oriented. In order to increase the temperature of the berry surface, solar radiation was concentrated using a normal reading lens with different magnifications degrees. Temperature was measured with a copper-constantan thermocouples attached to the berry surface. Experiments were performed just before harvest. Sunburn was caused by using different ranges of temperatures held constant for 2 or 5 minutes in the case of greenhouse plants and 5, 10, and 15 minutes in the case of field-grown plants. The effects of treatments were rated on visual basis by a panel of 3 people at one day intervals for three or four consecutive days after the treatments. On the last day, treated berries were harvested and analyzed for cell viability and membrane integrity using the fluorescein diacetate (FDA) technique. In greenhouse grown vines, a temperature of 38-40 °C for 5 minutes was sufficient to cause visual symptoms of sunburn two days after the treatments, even if no cells were permanently damaged. In field-grown vines, 5 minutes at 40-43 °C caused 12.4% cell mortality and permanent surface deformation. In conclusion, exposure of berries to a surface temperature of 40-43 °C appears to be effective in causing sunburn in greenhouse and field-grown plants. The radiation regime experienced by the cluster during the growing season may be important to determine the critical level of temperature causing sunburn

Carbon Fluxes in Sustainable Tree Crops: Field, Ecosystem and Global Dimension

Carbon (C) budget at cropping systems has not only agronomic but also environmental relevance because of their contribution to both emissions and removals of greenhouse gases (GHGs). Ideally, sustainable orchards are expected to remove atmospheric CO2 at a rate greater than that of the emissions because of (i) optimized biology of the system and (ii) reduced on-site/offsite inputs sourced by the technosphere. However, such a computation might produce inconsistent results and in turn biased communication on sustainability of the cropping systems because C accounting framework(s) are used under unclear context. This study examined the sustainability of orchards in terms of impact on GHGs focusing its significance at the field, ecosystem and global dimension analyzing some operational aspects and limitations of existing frameworks (e.g., net ecosystem carbon balance (NECB), life cycle assessment (LCA)). Global relevance of sustainable orchard was also discussed considering the C sequestration at cropland as instructed by Intergovernmental Panel on Climate Change (IPCC). The uniqueness of olive tree lifespan duration and C sequestration is discussed within the Product Environmental Footprint of agrifood product. The paper also highlighted overlapping components among the NECB, LCA and IPCC frameworks and the need for an integrated C accounting scheme for a more comprehensive and detailed mapping of sustainability in agriculture

Postharvest regulated deficit irrigation in peach tree in a Mediterranean environment: effect on vegetative growth and yield

The aim of this paper was to verify the possibility to reduce irrigation water requirements by applying regulated deficit irrigation (RDI) during phenological stages less sensitive to water deficit. The effects of two different levels of RDI were studied in a peach orchard (cv Springcrest). From bud break to harvest, irrigation was managed by applying 100% ETc, while from harvest to early autumn, irrigation was equivalent to 100%, 50% and 25% ETc. During the trial, no significant reductions in yield or quality were found for the 50% ETc treatment, whereas about 1,000, 1,800 and 2,400 m3 ha-1 of water were saved in the first, the second and the third year. The 25% treatment did reduce quality and yield significantly. Under scarce water supply conditions, a clear benefit can be obtained through the use of 50% RDI during the post-harvest period, especially for early harvest peache

Variability of total soil respiration in a Mediterranean vineyard

Total soil respiration (TSR) is the major component of the CO2 global flux. The knowledge of the temporal-spatial variability of TSR allows for a better interpretation of a critical component of global greenhouse gas flux measurements. The objective of the research was to evaluate the TSR dynamic over a long measurement period in a vineyard in the South of Italy. A static home-made automatic system was used to measure TSR for a three year period. A portable gas analyser (Li-Cor 6400-09) was used to study TSR spatial variability. A non-invasive geophysical technique (Electromagnetic Induction – EMI) was applied to search for a significant relationship between apparent soil electrical conductivity (ECa), the EMI signal and TSR. Long-term measurements of TSR enabled to study its temporal dynamics. CO2 rates ranged from 0.78 to 43.7 g CO2 m–2 day–1. TSR increased during spring and decreased by 45–50% during the mid-summer. The daily trend of TSR showed differences between the seasons studied reporting a clearly variation among TSR measured on row and inter-row positions. The supplemental irrigation significantly affected (P &lt; 0.001) CO2 soil effluxes which showed a weekly mean increase of 300%. Significant inverse relationships were found by interpolating TSR values and ECa (coefficient of correlation ranging from –0.43 to –0.83 at P &lt; 0.001). The spatialisation of TSR at field scale was performed using the linear regression between TSR values and EMI signals. TSR spatialisation gave a more detailed view of CO2 emissions distribution within the vineyard. EMI technique could be a useful tool to compute accurately the global CO2 emissions which are a complex and hard to measure component of the agrosystem carbon balance

Effects of limited irrigation water volumes on near-isohydric ‘Montepulciano’ vines trained to overhead trellis system

The thermal increase, due to the changed climatic context, is leading to marked variations in the yield and quality of the grapes and causing an increase in the use of water resources in several viticultural areas. Nevertheless, in some environments, rainfalls are scarce and there is no water availability. In this study, we compared the impact of low water irrigation volumes (DI, replacement of 70% of crop evapotranspiration) with respect to non-irrigated vines (NI), on the physiological, yield and qualitative performances of near-isohydric variety ‘Montepulciano’, trained to overhead trellis system, which requires a high-water supply. The stomatal conductance and photosynthesis values, in basal and median leaves, were higher in DI vines. All NI leaves sufered water stress, showing in the youngest leaves (position 20 and 25 along the main shoot) higher carbon isotope discrimination (δ13C) (− 25.38‰ and 25–25.77‰, respectively). At harvest, DI vines showed yield higher of 30% and 33% than NI vines in 2005 and 2006, respectively, and 18% in 2007. In environments with prolonged water shortage and low water resource, near-isohydric ‘Montepulciano’ vines, trained to overhead trellis system and irrigated with limited volumes, determined a signifcant improvement of ‘vineyard efciency’ with a yield of 19.2 t/ha with respect to 13.4 t/ha of NI vines, ensuring also more sugar content (+31%), anthocyanin concentration (+13%) and polyphenolic substances (+8%) than NI vines

Pamidronate improves the quality of life and induces clinical remission of bone metastases in patients with thyroid cancer

Skeletal metastases from thyroid cancer are poorly responsive to medical or radioiodine treatment. Bone destruction in skeletal metastases results from osteoclast-induced bone resorption. Therefore, a new approach in the therapy of bone metastases consists in using aminobisphosphonates, such as pamidronate, which are potent inhibitors of osteoclastic activity. In the present study, 10 thyroid cancer patients with painful osteolytic bone metastases were administered pamidronate (90 mg, as a 2 hour intravenous infusion) monthly for 12 consecutive cycles. Bone pain, quality of life, performance status, analgesic consumption and disease staging were evaluated before and during the trial. The patients who had been administered pamidronate showed a significant decrease in bone pain (P = 0.0052). Performance status improved nearly significantly (P = 0.051), while the quality of life showed a remarkable amelioration. However, no significant decrease in analgesic consumption was recorded. Partial radiographic response of bone lesions was observed in 2/10 patients. The side effects of pamidronate were mild and transient. In conclusion, monthly infusion of pamidronate is a well-tolerated treatment that induces significant relief from bone pain and improves the quality of life of thyroid cancer patients with symptomatic and osteolytic bone metastases. © 2001 Cancer Research Campaign http://www.bjcancer.co

Innovation in grapevine water status monitoring and drought adaptation: leaf angle and temperature regulation

Increase of frequency, duration, and intensity of drought and heatwave and related water and heat crops stress are among the principal effects of climate change. This paper reports: (i) the effect of calcite particle film (CaPF) as a mitigation strategy against heat stress in well-watered (WW) or in drought-stress (D) conditions; and (ii) response of leaf angle variation to stomatal conductance changes induced by drought stress of Aleatico grapevine cultivar. Results have showed that CaPF, under WW conditions, reduced leaf temperature, and increased gas exchange, but, under very severe water stress, CaPF treatment was ineffective. Leaf angle ranged from 70° (WW vines) to 100° (drought stressed vines) and showed a good fit (R2 =0.81) with stomatal conductance within the range of 0.25 – 0.05 mol m-2 s–1 proving it might be a reliable proxy of vine water status