Onions Selected for Reduced Symptom Expression of Iris Yellow Spot Have Higher Photosynthetic Rates

Bulb onion (Allium cepa L.) is an economically valuable vegetable crop in the United States. Onion production is threatened by onion thrips, which are the vector for Iris yellow spot virus, which is the causal agent of Iris yellow spot (IYS). New Mexico State University (NMSU) breeding lines 12-236, 12-238, 12-243, and 12-337 have exhibited fewer IYS disease symptoms in the field; however, little is known about the effects of the disease on the photosynthesis rate (Pn). We hypothesized that these NMSU breeding lines would have a higher Pn than IYS-susceptible cultivars Rumba and Stockton Early Yellow. To test this hypothesis, a field study was conducted for 3 years at NMSU, and Pn was measured five times throughout each season at 2-week intervals. During bulb development and maturation, which occurred at 10 and 12 weeks after transplanting, all NMSU breeding lines exhibited a higher Pn when compared with that of an IYS-susceptible cultivar. Pn was highest at the end of the vegetative growth stage and decreased as bulbs approached maturation for all cultivars. Additionally, a high Pn at 10 and 12 weeks after transplanting coincided with high bulb weight at harvest. NMSU breeding lines have increased Pn compared with that of IYS-susceptible cultivars and resulted in larger and more marketable bulbs. These results indicate that maintaining Pn may be related to reduced IYS symptom expression of onion

Pecan (<i>Carya illinoinensis</i>) and Dairy Waste Stream Utilization: Properties and Economics of On-Farm Windrow Systems

Improper management of organic waste can lead to unnecessary carbon dioxide and methane emissions, and groundwater contamination. In this study, organic waste materials from two of New Mexico’s (U.S.A.) top agricultural industries, pecan (Carya illinoinensis) and dairy cattle dairy manure, were used to evaluate the feasibility of an on-farm compost program. Pecan woody residues (P) served as the primary carbon source; regional cattle dairy manure (M) served as the primary nitrogen source. Additional (A) inputs from a compost consulting company (PM/A) and green waste from community landscaping and on-farm harvested legumes (PMG/A) were employed, both of which required additional labor and material inputs. Finished composts were analyzed for selected macro, secondary and micronutrients, pH, sodium adsorption ratio (SAR), electrical conductivity (EC), total carbon (TC) and organic matter (OM) content, bulk density (bd), and microbial biomass. The PM alone treatment showed similar or significantly higher amounts of macro, secondary and micronutrients compared to the PM/A and PMG/A treatments. Total microbial biomass and total salinity were highest for the PM treatment. The total cost of the PM treatment was around 1/6 of the cost of the lowest-cost addition compost production scheme, indicating that simpler, lower-input production methods may be more advantageous for on-farm compost program development

Comparative transcriptome analyses reveal insights into catkin bloom patterns in pecan protogynous and protandrous cultivars.

In perennial plants such as pecan, once reproductive maturity is attained, there are genetic switches that are regulated and required for flower development year after year. Pecan trees are heterodichogamous with both pistillate and staminate flowers produced on the same tree. Therefore, defining genes exclusively responsible for pistillate inflorescence and staminate inflorescence (catkin) initiation is challenging at best. To understand these genetic switches and their timing, this study analyzed catkin bloom and gene expression of lateral buds collected from a protogynous (Wichita) and a protandrous (Western) pecan cultivar in summer, autumn and spring. Our data showed that pistillate flowers in the current season on the same shoot negatively impacted catkin production on the protogynous 'Wichita' cultivar. Whereas fruit production the previous year on 'Wichita' had a positive effect on catkin production on the same shoot the following year. However, fruiting the previous year nor current year pistillate flower production had no significant effect on catkin production on 'Western' (protandrous cultivar) cultivar. The RNA-Seq results present more significant differences between the fruiting and non-fruiting shoots of the 'Wichita' cultivar compared to the 'Western' cultivar, revealing the genetic signals likely responsible for catkin production. Our data presented here, indicates the genes showing expression for the initiation of both types of flowers the season before bloom

Lenalidomide consolidation benefits patients with CLL receiving chemoimmunotherapy: results for CALGB 10404 (Alliance).

Prior to novel targeted agents for chronic lymphocytic leukemia (CLL), the best chemoimmunotherapy regimen in patients with non-del(11q) disease was unclear. The role of lenalidomide was also not defined. This phase 2 study randomized 342 untreated patients with non-del(11q) CLL requiring therapy to fludarabine plus rituximab (FR; n = 123), FR plus lenalidomide consolidation (FR+L; n = 109), or FR plus cyclophosphamide (FCR; n = 110) and compared 2-year progression-free survival (PFS) rates of each to the historical control rate with FC (60%). Patients with del(11q) in at least 20% of pretreatment cells continued with FCR (n = 27) or were reassigned to FCR+L (n = 31) and excluded from the primary analysis. Among non-del(11q) patients, 2-year PFS rates were 64% (90% confidence interval [CI], 57-71; FR), 72% (90% CI, 65-79; FR+L), and 74% (90% CI, 66-80; FCR); FR+L and FCR had rates significantly greater than historical control. Median PFS was significantly shorter with FR compared with FR+L

Extended Treatment with Single-Agent Ibrutinib at the 420 mg Dose Leads to Durable Responses in Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma

Purpose: Ibrutinib, a first-in-class, once-daily, oral inhibitor of Bruton tyrosine kinase, promotes apoptosis, and inhibits B-cell proliferation, adhesion, and migration. Ibrutinib has demonstrated single-agent efficacy and acceptable tolerability at doses of 420 and 840 mg in patients with chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL) who were treatment-naïve (TN) or had relapsed/refractory (R/R) CLL after ≥1 prior therapy in a phase Ib/II study (PCYC-1102). Subsequently, the ibrutinib 420 mg dose was approved in CLL.Experimental Design: We report data with 44 months of follow-up on 94 patients with TN and R/R CLL/SLL receiving ibrutinib 420 mg once-daily in PCYC-1102 and the long-term extension study PCYC-1103.Results: Ninety-four CLL/SLL patients (27 TN, 67 R/R) were treated with ibrutinib (420 mg/day). Patients with R/R disease had received a median of four prior therapies (range, 1-12). Responses were rapid and durable and median duration of response was not reached. Best overall response was 91% [85% TN (complete response, CR 26%) and 94% R/R (9% CR)]. Median progression-free survival (PFS) was not reached in either group. The 30-month PFS rate was 96% and 76% for TN and R/R patients, respectively. Ibrutinib was well tolerated with extended follow-up; rates of grade ≥3 cytopenias and fatigue, as well as discontinuations due to toxicities decreased over time.Conclusions: Single-agent ibrutinib at 420 mg once-daily resulted in durable responses and was well tolerated with up to 44 months follow-up in patients with TN and R/R CLL/SLL. Currently, 66% of patients continue on ibrutinib. Clin Cancer Res; 23(5); 1149-55. ©2017 AACR

Quantitative DNA methylation analysis identifies a single CpG dinucleotide important for ZAP-70 expression and predictive of prognosis in chronic lymphocytic leukemia

PURPOSE: Increased ZAP-70 expression predicts poor prognosis in chronic lymphocytic leukemia (CLL). Current methods for accurately measuring ZAP-70 expression are problematic, preventing widespread application of these tests in clinical decision making. We therefore used comprehensive DNA methylation profiling of the ZAP-70 regulatory region to identify sites important for transcriptional control. PATIENTS AND METHODS: High-resolution quantitative DNA methylation analysis of the entire ZAP-70 gene regulatory regions was conducted on 247 samples from patients with CLL from four independent clinical studies. RESULTS: Through this comprehensive analysis, we identified a small area in the 5′ regulatory region of ZAP-70 that showed large variability in methylation in CLL samples but was universally methylated in normal B cells. High correlation with mRNA and protein expression, as well as activity in promoter reporter assays, revealed that within this differentially methylated region, a single CpG dinucleotide and neighboring nucleotides are particularly important in ZAP-70 transcriptional regulation. Furthermore, by using clustering approaches, we identified a prognostic role for this site in four independent data sets of patients with CLL using time to treatment, progression-free survival, and overall survival as clinical end points. CONCLUSION: Comprehensive quantitative DNA methylation analysis of the ZAP-70 gene in CLL identified important regions responsible for transcriptional regulation. In addition, loss of methylation at a specific single CpG dinucleotide in the ZAP-70 5′ regulatory sequence is a highly predictive and reproducible biomarker of poor prognosis in this disease. This work demonstrates the feasibility of using quantitative specific ZAP-70 methylation analysis as a relevant clinically applicable prognostic test in CLL

Quantitative DNA Methylation Analysis Identifies a Single CpG Dinucleotide Important for ZAP-70 Expression and Predictive of Prognosis in Chronic Lymphocytic Leukemia

PURPOSE: Increased ZAP-70 expression predicts poor prognosis in chronic lymphocytic leukemia (CLL). Current methods for accurately measuring ZAP-70 expression are problematic, preventing widespread application of these tests in clinical decision making. We therefore used comprehensive DNA methylation profiling of the ZAP-70 regulatory region to identify sites important for transcriptional control. PATIENTS AND METHODS: High-resolution quantitative DNA methylation analysis of the entire ZAP-70 gene regulatory regions was conducted on 247 samples from patients with CLL from four independent clinical studies. RESULTS: Through this comprehensive analysis, we identified a small area in the 5′ regulatory region of ZAP-70 that showed large variability in methylation in CLL samples but was universally methylated in normal B cells. High correlation with mRNA and protein expression, as well as activity in promoter reporter assays, revealed that within this differentially methylated region, a single CpG dinucleotide and neighboring nucleotides are particularly important in ZAP-70 transcriptional regulation. Furthermore, by using clustering approaches, we identified a prognostic role for this site in four independent data sets of patients with CLL using time to treatment, progression-free survival, and overall survival as clinical end points. CONCLUSION: Comprehensive quantitative DNA methylation analysis of the ZAP-70 gene in CLL identified important regions responsible for transcriptional regulation. In addition, loss of methylation at a specific single CpG dinucleotide in the ZAP-70 5′ regulatory sequence is a highly predictive and reproducible biomarker of poor prognosis in this disease. This work demonstrates the feasibility of using quantitative specific ZAP-70 methylation analysis as a relevant clinically applicable prognostic test in CLL