Regulation of DNA (de)Methylation Positively Impacts Seed Germination during Seed Development under Heat Stress

Seed development needs the coordination of multiple molecular mechanisms to promote correct tissue development, seed filling, and the acquisition of germination capacity, desiccation tolerance, longevity, and dormancy. Heat stress can negatively impact these processes and upon the increase of global mean temperatures, global food security is threatened. Here, we explored the impact of heat stress on seed physiology, morphology, gene expression, and methylation on three stages of seed development. Notably, Arabidopsis Col-0 plants under heat stress presented a decrease in germination capacity as well as a decrease in longevity. We observed that upon mild stress, gene expression and DNA methylation were moderately affected. Nevertheless, upon severe heat stress during seed development, gene expression was intensively modified, promoting heat stress response mechanisms including the activation of the ABA pathway. By analyzing candidate epigenetic markers using the mutants' physiological assays, we observed that the lack of DNA demethylation by the ROS1 gene impaired seed germination by affecting germination-related gene expression. On the other hand, we also observed that upon severe stress, a large proportion of differentially methylated regions (DMRs) were located in the promoters and gene sequences of germination-related genes. To conclude, our results indicate that DNA (de)methylation could be a key regulatory process to ensure proper seed germination of seeds produced under heat stress

Specific Impact of Tobamovirus Infection on the Arabidopsis Small RNA Profile

Tobamoviruses encode a silencing suppressor that binds small RNA (sRNA) duplexes in vitro and supposedly in vivo to counteract antiviral silencing. Here, we used sRNA deep-sequencing combined with transcriptome profiling to determine the global impact of tobamovirus infection on Arabidopsis sRNAs and their mRNA targets. We found that infection of Arabidopsis plants with Oilseed rape mosaic tobamovirus causes a global size-specific enrichment of miRNAs, ta-siRNAs, and other phased siRNAs. The observed patterns of sRNA enrichment suggest that in addition to a role of the viral silencing suppressor, the stabilization of sRNAs might also occur through association with unknown host effector complexes induced upon infection. Indeed, sRNA enrichment concerns primarily 21-nucleotide RNAs with a 5′-terminal guanine. Interestingly, ORMV infection also leads to accumulation of novel miRNA-like sRNAs from miRNA precursors. Thus, in addition to canonical miRNAs and miRNA*s, miRNA precursors can encode additional sRNAs that may be functional under specific conditions like pathogen infection. Virus-induced sRNA enrichment does not correlate with defects in miRNA-dependent ta-siRNA biogenesis nor with global changes in the levels of mRNA and ta-siRNA targets suggesting that the enriched sRNAs may not be able to significantly contribute to the normal activity of pre-loaded RISC complexes. We conclude that tobamovirus infection induces the stabilization of a specific sRNA pool by yet unknown effector complexes. These complexes may sequester viral and host sRNAs to engage them in yet unknown mechanisms involved in plant:virus interactions

Effects of Water-Level Management on Nesting Success of Common Loons

Water-level management is widespread and illustrates how contemporary climate can interact directly and indirectly with numerous biological and abiotic factors to influence reproductive success of wildlife species. We studied common loons, an iconic waterbird sensitive to timing and magnitude of waterlevel changes during the breeding season, using a before-after-control-impact design on large lakes in Voyageurs National Park (Minnesota, USA), to assess the effect of anthropogenic changes in hydroregime on their nesting success and productivity. We examined multiple competing a priori hypotheses in an information-theoretic framework, and predicted that magnitude of changes in loon productivity would be greater in the Namakan Reservoir, where water-level management was altered to mimic a more natural hydroregime, than in Rainy Lake, where management remained relatively unchanged. We determined outcomes from 278 nests during 2004–2006 by performing boat-based visits every 3–5 days, and measuring hydrologic, vegetative, and microtopographic covariates. Relative to comparably collected data for 260 total loon pairs during 1983–1986, productivity (chicks hatched/territorial pair) increased 95% in the Namakan Reservoir between the 2 time periods. Nest success declined in both lakes over the 2 study periods but less so in the Namakan Reservoir than in Rainy Lake. Flooding was a primary cause of nest failures (though second nests were less likely to flood). Nest predation appears to have increased considerably between the 2 study periods. Top-ranked models suggested that timing of nest initiation, probability of nest flooding, probability of nest stranding, and probability of nest success were each related to 2–4 factors, including date of initiation, timing of initiation relative to peak water levels, changes in the elevation of the nest edge, maximum waterlevel change between initiation and peak water levels, and maximum water-level change between initiation and nest outcome. The top model for all variables except stranding each garnered \u3e82% of total model weight. Results demonstrate that water-level management can be altered to benefit productivity of common loons. However, nuanced interactions between land-use change, invasive species, human development, recreation, climate change, and recovery of top predators may often complicate both management decisions and interpretation of water-level impacts on wildlife

A SEROSURVEY OF DISEASES OF FREE-RANGING GRAY WOLVES (\u3ci\u3eCANIS LUPUS\u3c/i\u3e) IN MINNESOTA, USA

We tested serum samples from 387 free-ranging wolves (Canis lupus) from 2007 to 2013 for exposure to eight canid pathogens to establish baseline data on disease prevalence and spatial distribution in Minnesota’s wolf population. We found high exposure to canine adenoviruses 1 and 2 (88% adults, 45% pups), canine parvovirus (82% adults, 24% pups), and Lyme disease (76% adults, 39% pups). Sixty-six percent of adults and 36% of pups exhibited exposure to the protozoan parasite Neospora caninum. Exposure to arboviruses was confirmed, including West Nile virus (37% adults, 18% pups) and eastern equine encephalitis (3% adults). Exposure rates were lower for canine distemper (19% adults, 5% pups) and heartworm (7% adults, 3% pups). Significant spatial trends were observed in wolves exposed to canine parvovirus and Lyme disease. Serologic data do not confirm clinical disease, but better understanding of disease ecology of wolves can provide valuable insight into wildlife population dynamics and improve management of these species

Towards Developer-Centered Automatic Program Repair: Findings from Bloomberg

This paper reports on qualitative research into automatic program repair (APR) at Bloomberg. Six focus groups were conducted with a total of seventeen participants (including both developers of the APR tool and developers using the tool) to consider: the development at Bloomberg of a prototype APR tool (Fixie); developers' early experiences using the tool; and developers' perspectives on how they would like to interact with the tool in future. APR is developing rapidly and it is important to understand in greater detail developers' experiences using this emerging technology. In this paper, we provide in-depth, qualitative data from an industrial setting. We found that the development of APR at Bloomberg had become increasingly user-centered, emphasising how fixes were presented to developers, as well as particular features, such as cus-tomisability. From the focus groups with developers who had used Fixie, we found particular concern with the pragmatic aspects of APR, such as how and when fixes were presented to them. Based on our findings, we make a series of recommendations to inform future APR development, highlighting how APR tools should 'start small', be customisable, and fit with developers' workflows. We also suggest that APR tools should capitalise on the promise of repair bots and draw on advances in explainable AI.Output Status: Forthcomin

Towards Developer-Centered Automatic Program Repair: Findings from Bloomberg

This paper reports on qualitative research into automatic program repair (APR) at Bloomberg. Six focus groups were conducted with a total of seventeen participants (including both developers of the APR tool and developers using the tool) to consider: the development at Bloomberg of a prototype APR tool (Fixie); developers' early experiences using the tool; and developers' perspectives on how they would like to interact with the tool in future. APR is developing rapidly and it is important to understand in greater detail developers' experiences using this emerging technology. In this paper, we provide in-depth, qualitative data from an industrial setting. We found that the development of APR at Bloomberg had become increasingly user-centered, emphasising how fixes were presented to developers, as well as particular features, such as cus-tomisability. From the focus groups with developers who had used Fixie, we found particular concern with the pragmatic aspects of APR, such as how and when fixes were presented to them. Based on our findings, we make a series of recommendations to inform future APR development, highlighting how APR tools should 'start small', be customisable, and fit with developers' workflows. We also suggest that APR tools should capitalise on the promise of repair bots and draw on advances in explainable AI

The 5′-3′ Exoribonuclease XRN4 Regulates Auxin Response via the Degradation of Auxin Receptor Transcripts

Auxin is a major hormone which plays crucial roles in instructing virtually all developmental programs of plants. Its signaling depends primarily on its perception by four partially redundant receptors of the TIR1/AFB2 clade (TAARs), which subsequently mediate the specific degradation of AUX/IAA transcriptional repressors to modulate the expression of primary auxin-responsive genes. Auxin homeostasis depends on complex regulations at the level of synthesis, conjugation, and transport. However, the mechanisms and principles involved in the homeostasis of its signaling are just starting to emerge. We report that xrn4 mutants exhibit pleiotropic developmental defects and strong auxin hypersensitivity phenotypes. We provide compelling evidences that these phenotypes are directly caused by improper regulation of TAAR transcript degradation. We show that the cytoplasmic 5'-3' exoribonuclease XRN4 is required for auxin response. Thus, our work identifies new targets of XRN4 and a new level of regulation for TAAR transcripts important for auxin response and for plant development

The ecology of Canada yew (Taxus canadensis Marsh.): A review

Canada yew (Taxus canadensis Marsh.) is a shade-tolerant evergreen shrub native to the understories of the boreal and deciduous forests of northeastern North America. Canada yew has a relatively unique growth form, with low sprawling branches capable of forming dense clusters of stems. Historic accounts suggest that before Euro-American settlement, Canada yew was a common plant across its range in many forest types and that it was locally abundant or dominant in 5%-20% of forest stands in the northern part of its range. Canada yew\u27s range has declined during the last century as a result of browsing by native ungulates, fire, intensive forest management, and clearing of land for agriculture and other development. It is considered uncommon throughout most of its present North American range, except for often isolated populations in areas that remain free from heavy browsing pressure by moose and deer (e.g., islands, areas with heavy snow cover, or areas naturally low in ungulate abundance). Its decline has likely resulted in changes to abiotic and biotic conditions, including structure and composition of understory vegetation and concomitant effects on understory vertebrates. Increasing whitetailed deer populations and reduced snowfall as a result of climate change in eastern North America threaten to extirpate this species from additional parts of its range in the next century. Suggestions for future research are discussed