Regulatory regions of plant genes tend to be more compact than those of animal genes, but the complement of transcription factors encoded in plant genomes is as large or larger than that found in ...those of animals. Plants therefore provide an opportunity to study how transcriptional programs control multicellular development. We analyzed global gene expression during development of the reference plant Arabidopsis thaliana in samples covering many stages, from embryogenesis to senescence, and diverse organs. Here, we provide a first analysis of this data set, which is part of the AtGenExpress expression atlas. We observed that the expression levels of transcription factor genes and signal transduction components are similar to those of metabolic genes. Examining the expression patterns of large gene families, we found that they are often more similar than would be expected by chance, indicating that many gene families have been co-opted for specific developmental processes.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
Flowering of Arabidopsis is regulated by several environmental and endogenous signals. An important integrator of these inputs is the FLOWERING LOCUS T (FT) gene, which encodes a small, possibly ...mobile protein. A primary response to floral induction is the activation of FT RNA expression in leaves. Because flowers form at a distant site, the shoot apex, these data suggest that FT primarily controls the timing of flowering. Integration of temporal and spatial information is mediated in part by the bZIP transcription factor FD, which is already expressed at the shoot apex before floral induction. A complex of FT and FD proteins in turn can activate floral identity genes such as APETALA1 (AP1).
Effects of a spectrum of mesoscale gravity waves on homogeneous aerosol freezing in midlatitude cirrus are studied by means of parcel model simulations that are driven by random vertical wind speeds ...constrained by balloon measurements. Stochastic wave forcing with mean updraft speeds of 5–20 cm/s leads to substantial nucleated ice crystal number concentrations (ICNC) of 0.1–1 cm−3 in situations with slow large‐scale cooling, which by itself would generate fewer ice crystals. The stochastic nature of wave‐driven air parcel temperatures enhances ICNC even further, but the times required to reach freezing conditions unsupported by large‐scale cooling may vary widely. In the presence of wave forcing, ice crystals with low ICNC (<1–10 L−1) are also generated by homogeneous freezing, albeit only rarely. Comparisons with aircraft measurements suggest significant influences of heterogeneous ice‐nucleating particles and ice crystal sedimentation on ICNC, but quantifying their individual contributions remains elusive.
Plain Language Summary
Spontaneous freezing of airborne, water‐containing particles below −38 °C is a fundamental pathway to form ice crystals in high‐altitude cirrus clouds. This ice formation process has been well researched and was the first represented in weather forecast and climate models to advance cirrus predictions. One key characteristic is its strong dependence of the number of ice crystals formed on the cooling rate of air. Recent observations show that rapid cooling rates are generated by ubiquitous gravity waves. Here, we explore the rich suite of phenomena taking place during cirrus formation caused by a spectrum of gravity waves. We find that wave effects should be considered in future model simulations, when comparing model results with observations, and in parameterizations of cloud ice crystal formation.
Key Points
We present a systematic process study of effects of a spectrum of gravity waves on homogeneous ice nucleation in cirrus through ensemble simulations
High cooling rates have disproportionately large impact on nucleated ice crystal number concentrations at low background updraft speeds
Analysis of midlatitude continental cirrus measurements suggests impact of heterogeneous nucleation and sedimentation on total ice numbers
Quantitative analysis of plant and animal morphogenesis requires accurate segmentation of individual cells in volumetric images of growing organs. In the last years, deep learning has provided robust ...automated algorithms that approach human performance, with applications to bio-image analysis now starting to emerge. Here, we present PlantSeg, a pipeline for volumetric segmentation of plant tissues into cells. PlantSeg employs a convolutional neural network to predict cell boundaries and graph partitioning to segment cells based on the neural network predictions. PlantSeg was trained on fixed and live plant organs imaged with confocal and light sheet microscopes. PlantSeg delivers accurate results and generalizes well across different tissues, scales, acquisition settings even on non plant samples. We present results of PlantSeg applications in diverse developmental contexts. PlantSeg is free and open-source, with both a command line and a user-friendly graphical interface.
Nudging as an assimilation technique has seen increased use in recent years in the development and evaluation of climate models. Constraining the simulated wind and temperature fields using global ...weather reanalysis facilitates more straightforward comparison between simulation and observation, and reduces uncertainties associated with natural variabilities of the large-scale circulation. On the other hand, the forcing introduced by nudging can be strong enough to change the basic characteristics of the model climate. In the paper we show that for the Community Atmosphere Model version 5 (CAM5), due to the systematic temperature bias in the standard model and the sensitivity of simulated ice formation to anthropogenic aerosol concentration, nudging towards reanalysis results in substantial reductions in the ice cloud amount and the impact of anthropogenic aerosols on long-wave cloud forcing. In order to reduce discrepancies between the nudged and unconstrained simulations, and meanwhile take the advantages of nudging, two alternative experimentation methods are evaluated. The first one constrains only the horizontal winds. The second method nudges both winds and temperature, but replaces the long-term climatology of the reanalysis by that of the model. Results show that both methods lead to substantially improved agreement with the free-running model in terms of the top-of-atmosphere radiation budget and cloud ice amount. The wind-only nudging is more convenient to apply, and provides higher correlations of the wind fields, geopotential height and specific humidity between simulation and reanalysis. Results from both CAM5 and a second aerosol–climate model ECHAM6-HAM2 also indicate that compared to the wind-and-temperature nudging, constraining only winds leads to better agreement with the free-running model in terms of the estimated shortwave cloud forcing and the simulated convective activities. This suggests nudging the horizontal winds but not temperature is a good strategy for the investigation of aerosol indirect effects since it provides well-constrained meteorology without strongly perturbing the model's mean climate.
Positional information is essential for coordinating the development of multicellular organisms. In plants, positional information provided by the hormone auxin regulates rhythmic organ production at ...the shoot apex, but the spatio-temporal dynamics of auxin gradients is unknown. We used quantitative imaging to demonstrate that auxin carries high-definition graded information not only in space but also in time. We show that, during organogenesis, temporal patterns of auxin arise from rhythmic centrifugal waves of high auxin travelling through the tissue faster than growth. We further demonstrate that temporal integration of auxin concentration is required to trigger the auxin-dependent transcription associated with organogenesis. This provides a mechanism to temporally differentiate sites of organ initiation and exemplifies how spatio-temporal positional information can be used to create rhythmicity.
Flowering of the reference plant Arabidopsis thaliana is controlled by several signaling pathways, which converge on a small set of genes that function as pathway integrators. We have analyzed the ...genomic response to one type of floral inductive signal, photoperiod, to dissect the function of several genes transducing this stimulus, including CONSTANS , thought to be the major output of the photoperiod pathway. Comparing the effects of CONSTANS with those of FLOWERING LOCUS T , which integrates inputs from CONSTANS and other floral inductive pathways, we find that expression profiles of shoot apices from plants with mutations in either gene are very similar. In contrast, a mutation in LEAFY , which also acts downstream of CONSTANS , has much more limited effects. Another pathway integrator, SUPPRESSOR OF OVEREXPRESSION OF CO 1 , is responsive to acute induction by photoperiod even in the presence of the floral repressor encoded by FLOWERING LOCUS C . We have discovered a large group of potential floral repressors that are down-regulated upon photoperiodic induction. These include two AP2 domain-encoding genes that can repress flowering. The two paralogous genes, SCHLAFMÃTZE and SCHNARCHZAPFEN , share a signature with partial complementarity to the miR172 microRNA, whose precursor we show to be induced upon flowering. These and related findings on SPL genes suggest that microRNAs play an important role in the regulation of flowering.
Understanding the context-specific role of gene function is a key objective of modern biology. To this end, we generated a resource for inducible cell type-specific transactivation in Arabidopsis ...(Arabidopsis thaliana) based on the well-established combination of the chimeric GR-LhG4 transcription factor and the synthetic pOp promoter. Harnessing the flexibility of the GreenGate cloning system, we produced a comprehensive set of transgenic lines termed GR-LhG4 driver lines targeting most tissues in the Arabidopsis shoot and root with a strong focus on the indeterminate meristems. When we combined these transgenic lines with effectors under the control of the pOp promoter, we observed tight temporal and spatial control of gene expression. In particular, inducible expression in F1 plants obtained from crosses of driver and effector lines allows for rapid assessment of the cell type-specific impact of an effector with high temporal resolution. Thus, our comprehensive and flexible method is suitable for overcoming the limitations of ubiquitous genetic approaches, the outputs of which often are difficult to interpret due to the widespread existence of compensatory mechanisms and the integration of diverging effects in different cell types.
A multiple‐mode ice microphysical scheme is applied in the European Centre/Hamburg (ECHAM) general circulation model to simulate effects of aerosol‐ice interactions on global cirrus properties. The ...different ice modes represent cirrus ice formed by homogeneous freezing of liquid aerosols and heterogeneous nucleation on mineral dust or black carbon particles. A fourth ice mode represents ice from other sources. The competition of these modes for available water is realized in a physical parameterization scheme considering also the effect of preexisting ice on the ice nucleation process. The model is applied to analyze the global characteristics of ice formed by the different aerosol types and to study potential global effects of mineral dust and black carbon particles on cirrus microphysical parameters. The simulations reveal that, on average, ice from heterogeneous nucleation shows fewer but larger crystals and has a smaller contribution to the mean cirrus ice water content than ice from homogeneous freezing. However, heterogeneous ice nuclei may have important effects on the overall cirrus properties. Reductions in zonal mean annual average cirrus ice particle number concentrations induced by heterogeneous nucleation of up to 20% in the tropics and 1%–10% in the midlatitudes are simulated. The effect is further amplified by ice formation on aircraft‐generated soot. Significant reductions in the mean ice water content are modeled, which likely result from efficient sedimentation and precipitation of large ice particles generated by heterogeneous nucleation. This leads to reductions in the zonal mean annual average water vapor mixing ratio of up to 5% at cirrus levels.
Key Points
Aerosol‐cirrus interactions are simulated in a global climate model
Mineral dust and black carbon aerosol can affect cirrus globally
Cirrus ice types generated by different aerosol types are characterized
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