Summary
Anthocyanins play a variety of adaptive roles in both vegetative tissues and reproductive organs of plants. The broad functionality of these compounds requires sophisticated regulation of the ...anthocyanin biosynthesis pathway to allow proper localization, timing, and optimal intensity of pigment deposition. While it is well‐established that the committed steps of anthocyanin biosynthesis are activated by a highly conserved MYB‐bHLH‐WDR (MBW) protein complex in virtually all flowering plants, anthocyanin repression seems to be achieved by a wide variety of protein and small RNA families that function in different tissue types and in response to different developmental, environmental, and hormonal cues. In this review, we survey recent progress in the identification of anthocyanin repressors and the characterization of their molecular mechanisms. We find that these seemingly very different repression modules act through a remarkably similar logic, the so‐called ‘double‐negative logic’. Much of the double‐negative regulation of anthocyanin production involves signal‐induced degradation or sequestration of the repressors from the MBW protein complex. We discuss the functional and evolutionary advantages of this logic design compared with simple or sequential positive regulation. These advantages provide a plausible explanation as to why plants have evolved so many anthocyanin repressors.
Light‐inducible approaches provide a means to control biological systems with spatial and temporal resolution that is unmatched by traditional genetic perturbations. Recent developments of ...optogenetic and chemo‐optogenetic systems for induced proximity in cells facilitate rapid and reversible manipulation of highly dynamic cellular processes and have become valuable tools in diverse biological applications. New expansions of the toolbox facilitate control of signal transduction, genome editing, “painting” patterns of active molecules onto cellular membranes, and light‐induced cell cycle control. A combination of light‐ and chemically induced dimerization approaches have also seen interesting progress. Herein, an overview of optogenetic systems and emerging chemo‐optogenetic systems is provided, and recent applications in tackling complex biological problems are discussed.
Proteins under the spotlight: Various optogenetic systems that involve photosensitive proteins are summarized and emerging chemo‐optogenetic systems with caged or photocleavable chemical dimerizers are reviewed (see figure). The advantages and disadvantages of these systems are discussed. Recent biological applications of these strategies are presented.
In plants, the carotenoid biosynthesis pathway (CBP) is essential for the production of photosynthetic and protective pigments, plant hormones, and visual/olfactory attractants for animal pollinators ...and seed dispersers. The regulation of carotenoid biosynthesis at the transcriptional level is vitally important for all of these functions and has been the subject of intensive research. Many putative transcriptional regulators, both direct and indirect, have been identified through conventional mutant analysis, transcriptome profiling, yeast one-hybrid screening, and candidate gene approaches. Despite this progress, our understanding of the transcriptional regulation of carotenoid biosynthesis remains fragmented and incomplete. Frequently, a stimulus or regulator is known, but the mechanism by which it affects transcription has not been elucidated. In other cases, mechanisms have been proposed (such as direct binding of a CBP gene promoter by a transcription factor), but function was tested only
or in heterologous systems, making it unclear whether these proteins actually play a role in carotenoid regulation in their endogenous environments. Even in cases where the mechanism is relatively well understood, regulators are often studied in isolation, either in a single plant species or outside the context of other known regulators. This presents a conundrum: why so many candidate regulators but so little consensus? Here we summarize current knowledge on transcriptional regulation of the CBP, lay out the challenges contributing to this conundrum, identify remaining knowledge gaps, and suggest future research directions to address these challenges and knowledge gaps.
Monkeyflowers (Mimulus) Yuan, Yao-Wu
The New phytologist,
04/2019, Letnik:
222, Številka:
2
Journal Article
Recenzirano
Odprti dostop
Monkeyflowers (Mimulus) have long been recognized as a classic ecological and evolutionary model system. However, only recently has it been realized that this system also holds great promise for ...studying the developmental genetics and evo-devo of important plant traits that are not found in well-established model systems such as Arabidopsis. Here, I review recent progress in four different areas of plant research enabled by this new model, including transcriptional regulation of carotenoid biosynthesis, formation of periodic pigmentation patterns, developmental genetics of corolla tube formation and elaboration, and the molecular basis of floral trait divergence underlying pollinator shift. These examples suggest that Mimulus offers ample opportunities to make exciting discoveries in plant development and evolution.
Single atom catalysts (SACs) with the maximized metal atom efficiency have sparked great attention. However, it is challenging to obtain SACs with high metal loading, high catalytic activity, and ...good stability. Herein, we demonstrate a new strategy to develop a highly active and stable Ag single atom in carbon nitride (Ag‐N2C2/CN) catalyst with a unique coordination. The Ag atomic dispersion and Ag‐N2C2 configuration have been identified by aberration‐correction high‐angle‐annular‐dark‐field scanning transmission electron microscopy (AC‐HAADF‐STEM) and extended X‐ray absorption. Experiments and DFT calculations further verify that Ag‐N2C2 can reduce the H2 evolution barrier, expand the light absorption range, and improve the charge transfer of CN. As a result, the Ag‐N2C2/CN catalyst exhibits much better H2 evolution activity than the N‐coordinated Ag single atom in CN (Ag‐N4/CN), and is even superior to the Pt nanoparticle‐loaded CN (PtNP/CN). This work provides a new idea for the design and synthesis of SACs with novel configurations and excellent catalytic activity and durability.
A new Ag single atom in carbon nitride (Ag‐N2C2/CN) photocatalyst with Ag‐N2C2 configuration is developed. It affords fast charge transfer, high Ag loading, and good stability. Noteworthily, the Ag‐N2C2/CN exhibits much better hydrogen evolution activity than Ag‐N4/CN, and even superior to the platinum‐loaded CN.
Carotenoids are yellow, orange, and red pigments that contribute to the beautiful colors and nutritive value of many flowers and fruits. The structural genes in the highly conserved carotenoid ...biosynthetic pathway have been well characterized in multiple plant systems, but little is known about the transcription factors that control the expression of these structural genes. By analyzing a chemically induced mutant of Mimulus lewisii through bulk segregant analysis and transgenic experiments, we have identified an R2R3‐MYB, Reduced Carotenoid Pigmentation 1 (RCP1), as the first transcription factor that positively regulates carotenoid biosynthesis during flower development. Loss‐of‐function mutations in RCP1 lead to down‐regulation of all carotenoid biosynthetic genes and reduced carotenoid content in M. lewisii flowers, a phenotype recapitulated by RNA interference in the wild‐type background. Overexpression of this gene in the rcp1 mutant background restores carotenoid production and, unexpectedly, results in simultaneous decrease of anthocyanin production in some transgenic lines by down‐regulating the expression of an activator of anthocyanin biosynthesis. Identification of transcriptional regulators of carotenoid biosynthesis provides the ‘toolbox’ genes for understanding the molecular basis of flower color diversification in nature and for potential enhancement of carotenoid production in crop plants via genetic engineering.
Lung cancer is one of the cancers with the highest mortality rate in China. With the rapid development of high-throughput sequencing technology and the research and application of deep learning ...methods in recent years, deep neural networks based on gene expression have become a hot research direction in lung cancer diagnosis in recent years, which provide an effective way of early diagnosis for lung cancer. Thus, building a deep neural network model is of great significance for the early diagnosis of lung cancer. However, the main challenges in mining gene expression datasets are the curse of dimensionality and imbalanced data. The existing methods proposed by some researchers can't address the problems of high-dimensionality and imbalanced data, because of the overwhelming number of variables measured (genes) versus the small number of samples, which result in poor performance in early diagnosis for lung cancer.
Given the disadvantages of gene expression data sets with small datasets, high-dimensionality and imbalanced data, this paper proposes a gene selection method based on KL divergence, which selects some genes with higher KL divergence as model features. Then build a deep neural network model using Focal Loss as loss function, at the same time, we use k-fold cross validation method to verify and select the best model, we set the value of k is five in this paper.
The deep learning model method based on KL divergence gene selection proposed in this paper has an AUC of 0.99 on the validation set. The generalization performance of model is high.
The deep neural network model based on KL divergence gene selection proposed in this paper is proved to be an accurate and effective method for lung cancer prediction.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Although the quality of individual quantum bits (qubits) and quantum gates has been steadily improving, the number of qubits in a single system has increased quite slowly. Here, we demonstrate ...arbitrary single-qubit gates based on targeted phase shifts, an approach that can be applied to atom, ion, or other atom-like systems. These gates are highly insensitive to addressing beam imperfections and have little cross-talk, allowing for a dramatic scaling up of qubit number. We have performed gates in series on 48 individually targeted sites in a 40% full 5 by 5 by 5 three-dimensional array created by an optical lattice. Using randomized benchmarking, we demonstrate an average gate fidelity of 0.9962(16), with an average cross-talk fidelity of 0.9979(2) (numbers in parentheses indicate the one standard deviation uncertainty in the final digits).
Nectar guide trichomes play crucial ecological roles in bee-pollinated flowers, as they serve as footholds and guides for foraging bees to access the floral rewards. However, the genetic basis of ...natural variation in nectar guide trichomes among species remains poorly understood. In this study, we performed genetic analysis of nectar guide trichome variation between two closely related monkeyflower (Mimulus) species, the bumblebee-pollinated Mimulus lewisii and self-pollinated M. parishii. We demonstrate that a MIXTA-like R2R3-MYB gene, GUIDELESS, is a major contributor to the nectar guide trichome length variation between the two species. The short-haired M. parishii carries a recessive allele due to non-synonymous substitutions in a highly conserved motif among MIXTA-like MYB proteins. Furthermore, our results suggest that besides GUIDELESS, additional loci encoding repressors of trichome elongation also contribute to the transition from bumblebee-pollination to selfing. Taken together, these results suggest that during a pollination syndrome switch, changes in seemingly complex traits such as nectar guide trichomes could have a relatively simple genetic basis, involving just a few genes of large effects.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Over the years, there have been remarkable efforts in the development of selective protein labeling strategies. In this review, we deliver a comprehensive overview of the currently available ...bioorthogonal and chemoselective reactions. The ability to introduce bioorthogonal handles to proteins is essential to carry out bioorthogonal reactions for protein labeling in living systems. We therefore summarize the techniques that allow for site-specific "installation" of bioorthogonal handles into proteins. We also highlight the biological applications that have been achieved by selective chemical labeling of proteins.
Diverse bioorthogonal reactions and chemical tagging approaches for protein labeling are discussed and compared in this review.
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