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Building expression constructs for transgenesis is one of the fundamental day-to-day tasks in modern biology. Traditionally it is based on a multitude of type II restriction endonucleases and T4 DNA ligase. Especially in case of long inserts and applications requiring high-throughput, this approach is limited by the number of available unique restriction sites and the need for designing individual cloning strategies for each project. Several alternative cloning systems have been developed in recent years to overcome these issues, including the type IIS enzyme based Golden Gate technique. Here we introduce our GreenGate system for rapidly assembling plant transformation constructs, which is based on the Golden Gate method. GreenGate cloning is simple and efficient since it uses only one type IIS restriction endonuclease, depends on only six types of insert modules (plant promoter, N-terminal tag, coding sequence, C-terminal tag, plant terminator and plant resistance cassette), but at the same time allows assembling several expression cassettes in one binary destination vector from a collection of pre-cloned building blocks. The system is cheap and reliable and when combined with a library of modules considerably speeds up cloning and transgene stacking for plant transformation.

Significance Cell–cell communication is a prerequisite of multicellular development and noncell autonomous stem cell induction has been conserved during evolution. Cytoplasmic bridges, called plasmodesmata, which facilitate the exchange of molecules between neighboring cells, are a striking innovation for cell–cell signaling in plants. Here, we show that plasmodesmata function is required for the activity of shoot apical stem cells in Arabidopsis and provide evidence that the stem cell inducing transcription factor WUSCHEL moves from the niche into the stem cells via this route. WUSCHEL movement is functionally relevant and mediated by multiple protein domains. Because parts of the protein that restrict movement are required for homodimerization, the formation of WUSCHEL dimers might contribute to the regulation of stem cell activity in Arabidopsis . Cell–cell communication is essential for multicellular development and, consequently, evolution has brought about an array of distinct mechanisms serving this purpose. Consistently, induction and maintenance of stem cell fate by noncell autonomous signals is a feature shared by many organisms and may depend on secreted factors, direct cell–cell contact, matrix interactions, or a combination of these mechanisms. Although many basic cellular processes are well conserved between animals and plants, cell-to-cell signaling is one function where substantial diversity has arisen between the two kingdoms of life. One of the most striking differences is the presence of cytoplasmic bridges, called plasmodesmata, which facilitate the exchange of molecules between neighboring plant cells and provide a unique route for cell–cell communication in the plant lineage. Here, we provide evidence that the stem cell inducing transcription factor WUSCHEL (WUS), expressed in the niche, moves to the stem cells via plasmodesmata in a highly regulated fashion and that this movement is required for WUS function and, thus, stem cell activity in Arabidopsis thaliana . We show that cell context-independent mobility is encoded in the WUS protein sequence and mediated by multiple domains. Finally, we demonstrate that parts of the protein that restrict movement are required for WUS homodimerization, suggesting that formation of WUS dimers might contribute to the regulation of apical stem cell activity.

The literature on atmospheric particulate matter (PM), or atmospheric aerosol, has increased enormously over the last 2 decades and amounts now to some 1500–2000 papers per year in the refereed literature. This is in part due to the enormous advances in measurement technologies, which have allowed for an increasingly accurate understanding of the chemical composition and of the physical properties of atmospheric particles and of their processes in the atmosphere. The growing scientific interest in atmospheric aerosol particles is due to their high importance for environmental policy. In fact, particulate matter constitutes one of the most challenging problems both for air quality and for climate change policies. In this context, this paper reviews the most recent results within the atmospheric aerosol sciences and the policy needs, which have driven much of the increase in monitoring and mechanistic research over the last 2 decades. The synthesis reveals many new processes and developments in the science underpinning climate–aerosol interactions and effects of PM on human health and the environment. However, while airborne particulate matter is responsible for globally important influences on premature human mortality, we still do not know the relative importance of the different chemical components of PM for these effects. Likewise, the magnitude of the overall effects of PM on climate remains highly uncertain. Despite the uncertainty there are many things that could be done to mitigate local and global problems of atmospheric PM. Recent analyses have shown that reducing black carbon (BC) emissions, using known control measures, would reduce global warming and delay the time when anthropogenic effects on global temperature would exceed 2 °C. Likewise, cost-effective control measures on ammonia, an important agricultural precursor gas for secondary inorganic aerosols (SIA), would reduce regional eutrophication and PM concentrations in large areas of Europe, China and the USA. Thus, there is much that could be done to reduce the effects of atmospheric PM on the climate and the health of the environment and the human population. A prioritized list of actions to mitigate the full range of effects of PM is currently undeliverable due to shortcomings in the knowledge of aerosol science; among the shortcomings, the roles of PM in global climate and the relative roles of different PM precursor sources and their response to climate and land use change over the remaining decades of this century are prominent. In any case, the evidence from this paper strongly advocates for an integrated approach to air quality and climate policies.

Complex multicellular organisms evolved on Earth in an oxygen-rich atmosphere 1 ; their tissues, including stem-cell niches, require continuous oxygen provision for efficient energy metabolism 2 . Notably, the maintenance of the pluripotent state of animal stem cells requires hypoxic conditions, whereas higher oxygen tension promotes cell differentiation 3 . Here we demonstrate, using a combination of genetic reporters and in vivo oxygen measurements, that plant shoot meristems develop embedded in a low-oxygen niche, and that hypoxic conditions are required to regulate the production of new leaves. We show that hypoxia localized to the shoot meristem inhibits the proteolysis of an N-degron-pathway 4 , 5 substrate known as LITTLE ZIPPER 2 (ZPR2)—which evolved to control the activity of the class-III homeodomain-leucine zipper transcription factors 6 – 8 —and thereby regulates the activity of shoot meristems. Our results reveal oxygen as a diffusible signal that is involved in the control of stem-cell activity in plants grown under aerobic conditions, which suggests that the spatially distinct distribution of oxygen affects plant development. In molecular terms, this signal is translated into transcriptional regulation by the N-degron pathway, thereby linking the control of metabolic activity to the regulation of development in plants. Hypoxia in the shoot meristem of Arabidopsis links the regulation of metabolic activity to development by inhibiting proteolysis of a substrate of the N-degron pathway, which controls class-III homeodomain-leucine zipper transcription factors.

In multicellular organisms, not all cells are created equal. Instead, organismal complexity is achieved by specialisation and division of labour between distinct cell types. Therefore, the organism depends on the presence, correct proportion and function of all cell types. It follows that early development is geared towards setting up the basic body plan and to specify cell lineages. Since plants employ a post-embryonic mode of development, the continuous growth and addition of new organs require a source of new cells, as well as a strict regulation of cellular composition throughout the entire life-cycle. To meet these demands, evolution has brought about complex regulatory systems to maintain and control continuously active stem cell systems. Here, we review recent work on the mechanisms of non cell-autonomous control of shoot stem cells in the model plant Arabidopsis thaliana with a strong focus on the cell-to-cell mobility and function of the WUSCHEL homeodomain transcription factor.

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.

Spatial organization of signalling events of the phytohormone auxin is fundamental for maintaining a dynamic transition from plant stem cells to differentiated descendants. The cambium, the stem cell niche mediating wood formation, fundamentally depends on auxin signalling but its exact role and spatial organization is obscure. Here we show that, while auxin signalling levels increase in differentiating cambium descendants, a moderate level of signalling in cambial stem cells is essential for cambium activity. We identify the auxin-dependent transcription factor ARF5/MONOPTEROS to cell-autonomously restrict the number of stem cells by directly attenuating the activity of the stem cell-promoting WOX4 gene. In contrast, ARF3 and ARF4 function as cambium activators in a redundant fashion from outside of WOX4 -expressing cells. Our results reveal an influence of auxin signalling on distinct cambium features by specific signalling components and allow the conceptual integration of plant stem cell systems with distinct anatomies. Auxin activity controls plant stem cell function. Here the authors show that in the cambium, moderate auxin activity restricts cambial stem cell number via ARF5-dependent repression of the stem‐cell‐promoting factor WOX4, while ARF3 and ARF4 promote cambial activity outside of the WOX4‐expression domain.

Despite the importance of Nitric Oxide (NO) as signaling molecule in both plant and animal development, the regulatory mechanisms downstream of NO remain largely unclear. Here, we show that NO is involved in Arabidopsis shoot stem cell control via modifying expression and activity of ARGONAUTE 4 ( AGO4 ), a core component of the RNA-directed DNA Methylation (RdDM) pathway. Mutations in components of the RdDM pathway cause meristematic defects, and reduce responses of the stem cell system to NO signaling. Importantly, we find that the stem cell inducing WUSCHEL transcription factor directly interacts with AGO4 in a NO dependent manner, explaining how these two signaling systems may converge to modify DNA methylation patterns. Taken together, our results reveal that NO signaling plays an important role in controlling plant stem cell homeostasis via the regulation of de novo DNA methylation. The authors show that gaseous Nitric Oxide (NO) promotes transit amplifying cell fate in the Arabidopsis shoot meristem. NO acts by modifying AGO4-WUSCHEL protein interactions in stem cells, directly linking NO signaling with DNA methylation.

This manuscript compiles both theoretical and experimental information on contact freezing with the aim to better understand this potentially important but still not well quantified heterogeneous freezing mode. There is no complete theory that describes contact freezing and how the energy barrier has to be overcome to nucleate an ice crystal by contact freezing. Experiments on contact freezing conducted using the cold plate technique indicate that it can initiate ice formation at warmer temperatures than immersion freezing. Additionally, a qualitative difference in the freezing temperatures between contact and immersion freezing has been found using different instrumentation and different ice nuclei. There is a lack of data on collision rates in most of the reported data, which inhibits a quantitative calculation of the freezing efficiencies. Thus, new or modified instrumentation to study contact nucleation in the laboratory and in the field are needed to identify the conditions at which contact nucleation could occur in the atmosphere. Important questions concerning contact freezing and its potential role for ice cloud formation and climate are also summarized.

This paper introduces and evaluates the second version of the global aerosol-climate model ECHAM-HAM. Major changes have been brought into the model, including new parameterizations for aerosol nucleation and water uptake, an explicit treatment of secondary organic aerosols, modified emission calculations for sea salt and mineral dust, the coupling of aerosol microphysics to a two-moment stratiform cloud microphysics scheme, and alternative wet scavenging parameterizations. These revisions extend the model's capability to represent details of the aerosol lifecycle and its interaction with climate. Nudged simulations of the year 2000 are carried out to compare the aerosol properties and global distribution in HAM1 and HAM2, and to evaluate them against various observations. Sensitivity experiments are performed to help identify the impact of each individual update in model formulation. Results indicate that from HAM1 to HAM2 there is a marked weakening of aerosol water uptake in the lower troposphere, reducing the total aerosol water burden from 75 Tg to 51 Tg. The main reason is the newly introduced κ-Köhler-theory-based water uptake scheme uses a lower value for the maximum relative humidity cutoff. Particulate organic matter loading in HAM2 is considerably higher in the upper troposphere, because the explicit treatment of secondary organic aerosols allows highly volatile oxidation products of the precursors to be vertically transported to regions of very low temperature and to form aerosols there. Sulfate, black carbon, particulate organic matter and mineral dust in HAM2 have longer lifetimes than in HAM1 because of weaker in-cloud scavenging, which is in turn related to lower autoconversion efficiency in the newly introduced two-moment cloud microphysics scheme. Modification in the sea salt emission scheme causes a significant increase in the ratio (from 1.6 to 7.7) between accumulation mode and coarse mode emission fluxes of aerosol number concentration. This leads to a general increase in the number concentration of smaller particles over the oceans in HAM2, as reflected by the higher Ångström parameters. Evaluation against observation reveals that in terms of model performance, main improvements in HAM2 include a marked decrease of the systematic negative bias in the absorption aerosol optical depth, as well as smaller biases over the oceans in Ångström parameter and in the accumulation mode number concentration. The simulated geographical distribution of aerosol optical depth (AOD) is better correlated with the MODIS data, while the surface aerosol mass concentrations are very similar to those in the old version. The total aerosol water content in HAM2 is considerably closer to the multi-model average from Phase I of the AeroCom intercomparison project. Model deficiencies that require further efforts in the future include (i) positive biases in AOD over the ocean, (ii) negative biases in AOD and aerosol mass concentration in high-latitude regions, and (iii) negative biases in particle number concentration, especially that of the Aitken mode, in the lower troposphere in heavily polluted regions.