Transcriptional profiling of Arabidopsis heat shock proteins and transcription factors reveals extensive overlap between heat and non-heat stress response pathways

<p>Abstract</p> <p>Background</p> <p>The heat shock response of <it>Arabidopsis thaliana </it>is dependent upon a complex regulatory network involving twenty-one known transcription factors and four heat shock protein families. It is known that heat shock proteins (Hsps) and transcription factors (Hsfs) are involved in cellular response to various forms of stress besides heat. However, the role of Hsps and Hsfs under cold and non-thermal stress conditions is not well understood, and it is unclear which types of stress interact least and most strongly with Hsp and Hsf response pathways. To address this issue, we have analyzed transcriptional response profiles of <it>Arabidopsis </it>Hsfs and Hsps to a range of abiotic and biotic stress treatments (heat, cold, osmotic stress, salt, drought, genotoxic stress, ultraviolet light, oxidative stress, wounding, and pathogen infection) in both above and below-ground plant tissues.</p> <p>Results</p> <p>All stress treatments interact with Hsf and Hsp response pathways to varying extents, suggesting considerable cross-talk between heat and non-heat stress regulatory networks. In general, Hsf and Hsp expression was strongly induced by heat, cold, salt, and osmotic stress, while other types of stress exhibited family or tissue-specific response patterns. With respect to the Hsp20 protein family, for instance, large expression responses occurred under all types of stress, with striking similarity among expression response profiles. Several genes belonging to the Hsp20, Hsp70 and Hsp100 families were specifically upregulated twelve hours after wounding in root tissue, and exhibited a parallel expression response pattern during recovery from heat stress. Among all Hsf and Hsp families, large expression responses occurred under ultraviolet-B light stress in aerial tissue (shoots) but not subterranean tissue (roots).</p> <p>Conclusion</p> <p>Our findings show that Hsf and Hsp family member genes represent an interaction point between multiple stress response pathways, and therefore warrant functional analysis under conditions apart from heat shock treatment. In addition, our analysis revealed several family and tissue-specific heat shock gene expression patterns that have not been previously described. These results have implications regarding the molecular basis of cross-tolerance in plant species, and raise new questions to be pursued in future experimental studies of the <it>Arabidopsis </it>heat shock response network.</p

Modeling trajectories of perceived leg exertion during maximal cycle ergometer exercise in children and adolescents

BACKGROUND: Borg developed scales for rating pain and perceived exertion in adults that have also been used in pediatric populations. Models describing functional relationships between perceived exertion and work capacity have not been studied in children. We compared different models and their fits to individual trajectories and assessed the variability in these trajectories. METHODS: Ratings of perceived exertion (RPE) were collected from 79 children. Progressive cycle ergonometric testing was performed to maximal work capacity with test duration ranging from 6‐ 12 minutes. Ratings were obtained during each 1‐minute increment. Work was normalized to individual maximal work capacity (Wmax). A delay was defined as the fraction of Wmax at which point an increase in ratings of leg fatigue occurred. Such a delay term allows the characterization of trajectories for children whose ratings were initially constant with increasing work. Two models were considered, a delay model and a power model that is commonly used to analyze Borg ratings. Individual model fit was assessed with root mean squared error (RMSE). Functional clustering algorithms were used to identify patterns. RESULTS: Leg tiredness developed quickly for some children while for others there was a delay before an in‐ creased ratings of leg exertion occurred with increasing work. Models for individual trajectories with the smallest RMSE included a delay and a quadratic term (quadratic‐delay model), or a power function and a delay term (power‐delay model) compared to a simple power function. The median delay was 40% Wmax (interquartile range (IQR): 26‐49%) in a quadratic‐delay model, while the median exponent was 1.03 (IQR: 0.83‐1.78) in a power‐delay model. Nine clusters were identified showing linear or quadratic patterns with or without a delay. Cluster membership did not depend on age, gender or diagnosis. CONCLUSION: Children and adolescents vary widely in their capacity to rate their perceptions and exhibit different functional relationships between ratings of perceived exertion and work capacity normalized across individuals. Models including a delay term, a linear component, or a power function can describe these individual trajectories of perceived leg exertion during incremental exercise to voluntary exhaustion

Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: A genome and transcriptome approach

Background: Many microorganisms have a wide temperature growth range and versatility to tolerate large thermal fluctuations in diverse environments, however not many have been fully explored over their entire growth temperature range through a holistic view of its physiology, genome, and transcriptome. We used Exiguobacterium sibiricum strain 255-15, a psychrotrophic bacterium from 3 million year old Siberian permafrost that grows from -5°C to 39°C to study its thermal adaptation. Results: The E. sibiricum genome has one chromosome and two small plasmids with a total of 3,015 protein-encoding genes (CDS), and a GC content of 47.7%. The genome and transcriptome analysis along with the organism's known physiology was used to better understand its thermal adaptation. A total of 27%, 3.2%, and 5.2% of E. sibiricum CDS spotted on the DNA microarray detected differentially expressed genes in cells grown at -2.5°C, 10°C, and 39°C, respectively, when compared to cells grown at 28°C. The hypothetical and unknown genes represented 10.6%, 0.89%, and 2.3% of the CDS differentially expressed when grown at -2.5°C, 10°C, and 39°C versus 28°C, respectively. Conclusion: The results show that E. sibiricum is constitutively adapted to cold temperatures stressful to mesophiles since little differential gene expression was observed between 4°C and 28°C, but at the extremities of its Arrhenius growth profile, namely -2.5°C and 39°C, several physiological and metabolic adaptations associated with stress responses were observed

Developing Partnerships for Academic Data Science Consulting and Collaboration Units

Data science consulting and collaboration units (DSUs) are core infrastructure for research at universities. Activities span data management, study design, data analysis, data visualization, predictive modelling, preparing reports, manuscript writing and advising on statistical methods and may include an experiential or teaching component. Partnerships are needed for a thriving DSU as an active part of the larger university network. Guidance for identifying, developing and managing successful partnerships for DSUs can be summarized in six rules: (1) align with institutional strategic plans, (2) cultivate partnerships that fit your mission, (3) ensure sustainability and prepare for growth, (4) define clear expectations in a partnership agreement, (5) communicate and (6) expect the unexpected. While these rules are not exhaustive, they are derived from experiences in a diverse set of DSUs, which vary by administrative home, mission, staffing and funding model. As examples in this paper illustrate, these rules can be adapted to different organizational models for DSUs. Clear expectations in partnership agreements are essential for high quality and consistent collaborations and address core activities, duration, staffing, cost and evaluation. A DSU is an organizational asset that should involve thoughtful investment if the institution is to gain real value

Comparaison de deux méthodes de sélection classique avec l'haplodiploïdisation pour la résistance à la mouche de Hesse chez le blé tendre (Triticum aestivum)

L'efficacité des méthodes classiques et alternatives d'amélioration génétique repose sur l'évolution de la variabilité génétique des populations ségrégatives sous sélection. L'objectif de cette étude est de comparer l'évolution de la fréquence des gènes de résistance à la mouche de Hesse (Mayetiola destructor) sous deux méthodes classiques de sélection en comparaison avec la méthode de l'haplodiploïdisation. Les distributions et les proportions observées du caractère "résistance à la mouche de Hesse" ont été évaluées pour des lignées produites par la méthode de filiation unipare (FUP), la méthode " bulk " et l'haplodiploïdisation (DH) de quatre populations hybrides de blé tendre (Triticum aestivum). Ces populations sont issues des croisements entre des parents résistants à la mouche de Hesse marocaine et des parents sensibles mais adaptés aux conditions marocaines. Les résultats ont montré un effet marqué de la méthode d'amélioration génétique. En effet, malgré leur avancement à la génération F6, les lignées produites par les méthodes FUP et " bulk " présentent toujours un taux non négligeable d'hétérozygotie pour ce caractère alors que la méthode DH a abouti à une homozygotie parfaite. Les proportions de résistance observées chez les lignées FUP et haploïdes doublées sont approximativement les mêmes que celles théoriquement attendues. Cependant, la méthode " bulk " a permis une sélection naturelle au champ qui a favorisé le caractère résistant de manière significativeThe relative usefulness of conventional and alternative breeding methods relies on the evolution of genetic variability in segregating populations undergoing selection. The objective of this study was to compare the frequencies of genetic resistance to Hessian fly (Mayetiola destructor) in populations generated by two conventional breeding methods in comparison with lines advanced through doubled haploid method. Distribution and proportions of Hessian fly resistance were evaluated in four populations of bread wheat lines advanced through 'Single Seed Descent' (SSD), 'Bulk', and doubled-haploid (DH) methods. These populations were all derived from crosses involving resistant parents and susceptible lines adapted to Moroccan conditions. The results of this study have shown a clear effect of the breeding method. The Bulk and SSD (F6) derived lines have shown a substantial residual heterozygocity while DH method has produced completely homozygous material. The observed proportions of resistance did not deviate from expected in the populations of lines derived through SSD and DH methods while evidence of natural selection for resistance was significant in the lines derived through the Bulk method

Short-course quinazoline drug treatments are effective in the Litomosoides sigmodontis and Brugia pahangi jird models

The quinazolines CBR417 and CBR490 were previously shown to be potent anti-wolbachials that deplete Wolbachia endosymbionts of filarial nematodes and present promising pre-clinical candidates for human filarial diseases such as onchocerciasis. In the present study we tested both candidates in two models of chronic filarial infection, namely the Litomosoides sigmodontis and Brugia pahangi jird model and assessed their long-term effect on Wolbachia depletion, microfilariae counts and filarial embryogenesis 16-18 weeks after treatment initiation (wpt). Once per day (QD) oral treatment with CBR417 (50 mg/kg) for 4 days or twice per day (BID) with CBR490 (25 mg/kg) for 7 days during patent L. sigmodontis infection reduced the Wolbachia load by >99% and completely cleared peripheral microfilaremia from 10-14 wpt. Similarly, 7 days of QD treatments (40 mg/kg) with CBR417 or CBR490 cleared >99% of Wolbachia from B. pahangi and reduced peritoneal microfilariae counts by 93% in the case of CBR417 treatment. Transmission electron microscopy analysis indicated intensive damage to the B. pahangi ovaries following CBR417 treatment and in accordance filarial embryogenesis was inhibited in both models after CBR417 or CBR490 treatment. Suboptimal treatment regimens of CBR417 or CBR490 did not lead to a maintained reduction of the microfilariae and Wolbachia load. In conclusion, CBR417 or CBR490 are pre-clinical candidates for filarial diseases, which achieve long-term clearance of Wolbachia endosymbionts of filarial nematodes, inhibit filarial embryogenesis and clear microfilaremia with treatments as short as 7 days

Undertaking initial data analysis before fitting a regression model: What should a researcher think about

(Presentation 15 min. + Discussion 5 min.)Non UBCUnreviewedAuthor affiliation: Michigan State UniversityFacult

Organizing and analyzing data from the SHARE study with an application to age and sex differences in depressive symptoms

The SHARE study contains health, lifestyle, and socioeconomic data from individuals ages 50 and older in European countries collected over several waves. Leveraging these data for research purposes can be daunting due to the complex structure of the longitudinal design. The two aims of our study are (1) to develop a framework and R code for data management of the SHARE data to prepare for data analysis, and (2) to demonstrate how to apply the framework to a specific research question, where the aim is to model the presence of clinically significant depression assessed by the 12-item Europe depression scale. The result is a framework that substantially reduces the time to initiate research studies using SHARE data, facilitating the data extraction, data preparation and initial data analysis, with reproducible R code. Further, we illustrate the extensive work required to prepare an analysis-ready data set to ensure the validity of the modeling results. This underlines the importance of carefully considering and recording data management decisions that have to be built into the research process. The results about sex differences in the probability of depression are consistent with previous literature. Our findings about age-associated changes can be opportunities for adequate treatment interventions