The relationship of drought-related gene expression in Arabidopsis thaliana to hormonal and environmental factors

Almost 2000 drought-responsive genes were identified in Arabidopsis thaliana under progressive soil drought stress using whole-genome oligonucleotide microarrays. Most of the drought-regulated genes recovered to normal expression levels by 3 h after rewatering. It has previously been shown that the abscisic acid (ABA) analogue (+)-8′-acetylene-ABA (PBI425) hyperinduces many ABA-like changes in gene expression to reveal a more complete list of ABA-regulated genes, and it is demonstrated here that PBI425 produced a correspondingly increased drought tolerance. About two-thirds of drought-responsive genes (1310 out of 1969) were regulated by ABA and/or the ABA analogue PBI425. Analysis of promoter motifs suggests that many of the remaining drought-responsive genes may be affected by ABA signalling. Concentrations of endogenous ABA and its catabolites significantly increased under drought stress and either completely (ABA) or partially (ABA catabolites) recovered to normal levels by 3 h after rehydration. Detailed analyses of drought transcript profiles and in silico comparisons with other studies revealed that the ABA-dependent pathways are predominant in the drought stress responses. These comparisons also showed that other plant hormones including jasmonic acid, auxin, cytokinin, ethylene, brassinosteroids, and gibberellins also affected drought-related gene expression, of which the most significant was jasmonic acid. There is also extensive cross-talk between responses to drought and other environmental factors including light and biotic stresses. These analyses demonstrate that ABA-related stress responses are modulated by other environmental and developmental factors

Deterioration of western redcedar (Thuja plicata Donn ex D. Don) seeds: protein oxidation and in vivo NMR monitoring of storage oils

Deterioration of conifer seeds during prolonged storage has a negative impact on reforestation and gene conservation efforts. Western redcedar (Thuja plicata Donn ex D. Don) is a species of tremendous value to the forest industry. The seeds of this species are particularly prone to viability losses during long-term storage. Reliable tools to assess losses in seed viability during storage and their underlying causes, as well as the development of methods to prevent storage-related deterioration of seeds are needed by the forest industry. In this work, various imaging methods and biochemical analyses were applied to study deterioration of western redcedar seeds. Seedlots that exhibited poor germination performance, i.e. those that had experienced the greatest losses of viability during prolonged storage, exhibited greater abundance of oxidized proteins, detected by protein oxidation assays, and more pronounced changes in their in vivo (13)C NMR spectra, most likely due to storage oil oxidation. The proportion of oxidized proteins also increased when seeds were subjected to accelerated ageing treatments. Detection of oxidized oils and proteins may constitute a reliable and useful tool for the forest industry

Use of Persistent Analogs of Abscisic Acid as Palliatives against Salt-stress Induced Damage in Citrus Plants

The effectiveness of several abscisic acid (ABA) analogs as palliatives against salt stress in intact citrus plants has been tested in this work. The effect of ABA, 8¢-methylene ABA, 8¢-acetylene ABA, ABA methyl ester, 8¢-methylene ABA methyl ester, and 8¢-acetylene ABA methyl ester on citrus responses to salt stress was studied on 2-year-old grafted plants. Leaf abscission, chloride accumulation, ethylene production, and net photosynthetic rate were the parameters used to characterize the performance of plants under stress. Data indicate that 8¢-methylene ABA was the most effective compound in delaying the deleterious effects of high salinity on citrus plants. Its regular application reduced leaf chloride concentration, ethylene production, and leaf abscission. Furthermore, it delayed the depletion of CO2 assimilation under these adverse conditions. Abscisic acid and 8¢-acetylene ABA also reduced salt-stress induced injuries in citrus, although to a lower extent. Neither ABA methyl ester nor its 8¢-C modified analogs showed biological activity in these assays

Transgenic increases in seed oil content are associated with the differential expression of novel Brassica-specific transcripts

<p>Abstract</p> <p>Background</p> <p>Seed oil accumulates primarily as triacylglycerol (TAG). While the biochemical pathway for TAG biosynthesis is known, its regulation remains unclear. Previous research identified microsomal diacylglycerol acyltransferase 1 (DGAT1, EC 2.3.1.20) as controlling a rate-limiting step in the TAG biosynthesis pathway. Of note, overexpression of <it>DGAT1 </it>results in substantial increases in oil content and seed size. To further analyze the global consequences of manipulating <it>DGAT1 </it>levels during seed development, a concerted transcriptome and metabolome analysis of transgenic <it>B. napus </it>prototypes was performed.</p> <p>Results</p> <p>Using a targeted <it>Brassica </it>cDNA microarray, about 200 genes were differentially expressed in two independent transgenic lines analyzed. Interestingly, 24–33% of the targets showing significant changes have no matching gene in <it>Arabidopsis </it>although these represent only 5% of the targets on the microarray. Further analysis of some of these novel transcripts indicated that several are inducible by ABA in microspore-derived embryos. Of the 200 <it>Arabidopsis </it>genes implicated in lipid biology present on the microarray, 36 were found to be differentially regulated in DGAT transgenic lines. Furthermore, kinetic reverse transcriptase Polymerase Chain Reaction (k-PCR) analysis revealed up-regulation of genes encoding enzymes of the Kennedy pathway involved in assembly of TAGs. Hormone profiling indicated that levels of auxins and cytokinins varied between transgenic lines and untransformed controls, while differences in the pool sizes of ABA and catabolites were only observed at later stages of development.</p> <p>Conclusion</p> <p>Our results indicate that the increased TAG accumulation observed in transgenic <it>DGAT1 </it>plants is associated with modest transcriptional and hormonal changes during seed development that are not limited to the TAG biosynthesis pathway. These might be associated with feedback or feed-forward effects due to altered levels of DGAT1 activity. The fact that a large fraction of significant amplicons have no matching genes in <it>Arabidopsis </it>compromised our ability to draw concrete inferences from the data at this stage, but has led to the identification of novel genes of potential interest.</p

Modeling the multi‐state natural history of rare diseases with heterogeneous individual patient data : a simulation study

Multi‐state survival models are used to represent the natural history of a disease, forming the basis of a health technology assessment comparing a novel treatment to current practice. Constructing such models for rare diseases is problematic, since evidence sources are typically much sparser and more heterogeneous. This simulation study investigated different one‐stage and two‐stage approaches to meta‐analyzing individual patient data (IPD) in a multi‐state survival setting when the number and size of studies being meta‐analyzed are small. The objective was to assess methods of different complexity to see when they are accurate, when they are inaccurate and when they struggle to converge due to the sparsity of data. Biologically plausible multi‐state IPD were simulated from study‐ and transition‐specific hazard functions. One‐stage frailty and two‐stage stratified models were estimated, and compared to a base case model that did not account for study heterogeneity. Convergence and the bias/coverage of population‐level transition probabilities to, and lengths of stay in, each state were used to assess model performance. A real‐world application to Duchenne Muscular Dystrophy, a neuromuscular rare disease, was conducted, and a software demonstration is provided. Models not accounting for study heterogeneity were consistently out‐performed by two‐stage models. Frailty models struggled to converge, particularly in scenarios of low heterogeneity, and predictions from models that did converge were also subject to bias. Stratified models may be better suited to meta‐analyzing disparate sources of IPD in rare disease natural history/economic modeling, as they converge more consistently and produce less biased predictions of lengths of stay

Association between socioeconomic factors, race, and use of a specialty memory clinic

BACKGROUND AND OBJECTIVES: The capacity of specialty memory clinics in the United States is very limited. If lower socioeconomic status or minoritized racial group is associated with reduced use of memory clinics, this could exacerbate health care disparities, especially if more effective treatments of Alzheimer disease become available. We aimed to understand how use of a memory clinic is associated with neighborhood-level measures of socioeconomic factors and the intersectionality of race. METHODS: We conducted an observational cross-sectional study using electronic health record data to compare the neighborhood advantage of patients seen at the Washington University Memory Diagnostic Center with the catchment area using a geographical information system. Furthermore, we compared the severity of dementia at the initial visit between patients who self-identified as Black or White. We used a multinomial logistic regression model to assess the Clinical Dementia Rating at the initial visit and RESULTS: A total of 4,824 patients seen at the memory clinic between 2008 and 2018 were included in this study (mean age 72.7 [SD 11.0] years, 2,712 [56%] female, 543 [11%] Black). Most of the memory clinic patients lived in more advantaged neighborhoods within the overall catchment area. The percentage of patients self-identifying as Black (11%) was lower than the average percentage of Black individuals by census tract in the catchment area (16%) ( DISCUSSION: This study demonstrates that patients living in less affluent neighborhoods were less likely to be seen in one large memory clinic. Black patients were under-represented in the clinic, and Black patients had more severe dementia at their initial visit. These findings suggest that patients with a lower socioeconomic status and who identify as Black are less likely to be seen in memory clinics, which are likely to be a major point of access for any new Alzheimer disease treatments that may become available

Isolation of an embryogenic line from non-embryogenic Brassica napus cv. Westar through microspore embryogenesis

Brassica napus cultivar Westar is non-embryogenic under all standard protocols for induction of microspore embryogenesis; however, the rare embryos produced in Westar microspore cultures, induced with added brassinosteroids, were found to develop into heritably stable embryogenic lines after chromosome doubling. One of the Westar-derived doubled haploid (DH) lines, DH-2, produced up to 30% the number of embryos as the highly embryogenic B. napus line, Topas DH4079. Expression analysis of marker genes for embryogenesis in Westar and the derived DH-2 line, using real-time reverse transcription-PCR, revealed that the timely expression of embryogenesis-related genes such as LEAFY COTYLEDON1 (LEC1), LEC2, ABSCISIC ACID INSENSITIVE3, and BABY BOOM1, and an accompanying down-regulation of pollen-related transcripts, were associated with commitment to embryo development in Brassica microspores. Microarray comparisons of 7 d cultures of Westar and Westar DH-2, using a B. napus seed-focused cDNA array (10 642 unigenes), identified highly expressed genes related to protein synthesis, translation, and response to stimulus (Gene Ontology) in the embryogenic DH-2 microspore-derived cell cultures. In contrast, transcripts for pollen-expressed genes were predominant in the recalcitrant Westar microspores. Besides being embryogenic, DH-2 plants showed alterations in morphology and architecture as compared with Westar, for example epinastic leaves, non-abscised petals, pale flower colour, and longer lateral branches. Auxin, cytokinin, and abscisic acid (ABA) profiles in young leaves, mature leaves, and inflorescences of Westar and DH-2 revealed no significant differences that could account for the alterations in embryogenic potential or phenotype. Various mechanisms accounting for the increased capacity for embryogenesis in Westar-derived DH lines are considered