Peptide REF1 is a local wound signal promoting plant regeneration.

Plants frequently encounter wounding and have evolved an extraordinary regenerative capacity to heal the wounds. However, the wound signal that triggers regenerative responses has not been identified. Here, through characterization of a tomato mutant defective in both wound-induced defense and regeneration, we demonstrate that in tomato, a plant elicitor peptide (Pep), REGENERATION FACTOR1 (REF1), acts as a systemin-independent local wound signal that primarily regulates local defense responses and regenerative responses in response to wounding. We further identified PEPR1/2 ORTHOLOG RECEPTOR-LIKE KINASE1 (PORK1) as the receptor perceiving REF1 signal for plant regeneration. REF1-PORK1-mediated signaling promotes regeneration via activating WOUND-INDUCED DEDIFFERENTIATION 1 (WIND1), a master regulator of wound-induced cellular reprogramming in plants. Thus, REF1-PORK1 signaling represents a conserved phytocytokine pathway to initiate, amplify, and stabilize a signaling cascade that orchestrates wound-triggered organ regeneration. Application of REF1 provides a simple method to boost the regeneration and transformation efficiency of recalcitrant crops.

Transcriptomic and metabolomic insights into the antimony stress response of tall fescue (Festuca arundinacea).

Antimony (Sb) is a toxic heavy metal that severely inhibits plant growth and development and threatens human health. Tall fescue, one of the most widely used grasses, has been reported to tolerate heavy metal stress. However, the adaptive mechanisms of Sb stress in tall fescue remain largely unknown. In this study, transcriptomic and metabolomic techniques were applied to elucidate the molecular mechanism of the Sb stress response in tall fescue. These results showed that the defense process in tall fescue was rapidly triggered during the early stages of Sb stress. Sb stress had toxic effects on tall fescue, and the cell wall and voltage-gated channels are crucial for regulating Sb permeation into the cells. In addition, the pathway of glycine, serine and threonine metabolism may play key roles in the Sb stress response of tall fescue. Genes such as ALDH7A1 and AGXT2 and metabolites such as aspartic acid, pyruvic acid, and biuret, which are related to biological processes and pathways, were key genes and compounds in the Sb stress response of tall fescue. Therefore, the regulatory mechanisms of specific genes and pathways should be investigated further to improve Sb stress tolerance.

Tomato CYP94C1 inactivates bioactive JA-Ile to attenuate jasmonate-mediated defense during fruit ripening.

As the master regulators of the ET signaling pathway, EIL transcription factors directly activate the expression of CYP94C1 to inactivate bioactive JA-Ile, thereby attenuating JA-mediated defense during fruit ripening. Knockout of CYP94C1 improves tomato fruit resistance to necrotrophs without compromising fruit quality.

Challenges and opportunities in remote sensing-based crop monitoring: a review.

Building a more resilient food system for sustainable development and reducing uncertainty in global food markets both require concurrent and near-real-time and reliable crop information for decision making. Satellite-driven crop monitoring has become a main method to derive crop information at local, regional, and global scales by revealing the spatial and temporal dimensions of crop growth status and production. However, there is a lack of quantitative, objective, and robust methods to ensure the reliability of crop information, which reduces the applicability of crop monitoring and leads to uncertain and undesirable consequences. In this paper, we review recent progress in crop monitoring and identify the challenges and opportunities in future efforts. We find that satellite-derived metrics do not fully capture determinants of crop production and do not quantitatively interpret crop growth status; the latter can be advanced by integrating effective satellite-derived metrics and new onboard sensors. We have identified that ground data accessibility and the negative effects of knowledge-based analyses are two essential issues in crop monitoring that reduce the applicability of crop monitoring for decisions on food security. Crowdsourcing is one solution to overcome the restrictions of ground-truth data accessibility. We argue that user participation in the complete process of crop monitoring could improve the reliability of crop information. Encouraging users to obtain crop information from multiple sources could prevent unconscious biases. Finally, there is a need to avoid conflicts of interest in publishing publicly available crop information.

Regulation of jasmonate signaling by reversible acetylation of TOPLESS in Arabidopsis.

The plant hormone jasmonate (JA) regulates plant immunity and adaptive growth by orchestrating a genome-wide transcriptional program. Key regulators of JA-responsive gene expression include the master transcription factor MYC2, which is repressed by the conserved Groucho/Tup1-like corepressor TOPLESS (TPL) in the resting state. However, the mechanisms underlying TPL-mediated transcriptional repression of MYC2 activity and hormone-dependent switching between repression and de-repression remain enigmatic. Here, we report the regulation of TPL activity and JA signaling by reversible acetylation of TPL. We found that the histone acetyltransferase GCN5 could mediate TPL acetylation, which enhances its interaction with the NOVEL-INTERACTOR-OF-JAZ (NINJA) adaptor and promotes its recruitment to MYC2 target promoters, facilitating transcriptional repression. Conversely, TPL deacetylation by the histone deacetylase HDA6 weakens TPL-NINJA interaction and inhibits TPL recruitment to MYC2 target promoters, facilitating transcriptional activation. In the resting state, the opposing activities of GCN5 and HDA6 maintain TPL acetylation homeostasis, promoting transcriptional repression activity of TPL. In response to JA elicitation, HDA6 expression is transiently induced, resulted in decreased TPL acetylation and repressor activity, thereby transcriptional activation of MYC2 target genes. Thus, the GCN5-TPL-HDA6 module maintains the homeostasis of acetylated TPL, thereby determining the transcriptional state of JA-responsive genes. Our findings uncovered a mechanism by which the TPL corepressor activity in JA signaling is actively tuned in a rapid and reversible manner.

Mediator complex subunit MED25 physically interacts with DST to regulate spikelet number in rice.

Grain number is a flexible trait and contributes significantly to grain yield. In rice, the zinc finger transcription factor DROUGHT AND SALT TOLERANCE (DST) controls grain number by directly regulating cytokinin oxidase/dehydrogenase 2 (OsCKX2) expression. Although specific upstream regulators of the DST-OsCKX2 module have been identified, the mechanism employed by DST to regulate the expression of OsCKX2 remains unclear. Here, we demonstrate that DST-interacting protein 1 (DIP1), known as Mediator subunit OsMED25, acts as an interacting coactivator of DST. Phenotypic analyses revealed that OsMED25-RNAi and the osmed25 mutant plants exhibited enlarged panicles, with enhanced branching and spikelet number, similar to the dst mutant. Genetic analysis indicated that OsMED25 acts in the same pathway as the DST-OsCKX2 module to regulate spikelet number per panicle. Further biochemical analysis showed that OsMED25 physically interacts with DST at the promoter region of OsCKX2, and then recruits RNA polymerase II (Pol II) to activate OsCKX2 transcription. Thus, OsMED25 was involved in the communication between DST and Pol II general transcriptional machinery to regulate spikelet number. In general, our findings reveal a novel function of OsMED25 in DST-OsCKX2 modulated transcriptional regulation, thus enhancing our understanding of the regulatory mechanism underlying DST-OsCKX2-mediated spikelet number.

Identification of Crop Type in Crowdsourced Road View Photos with Deep Convolutional Neural Network.

In situ ground truth data are an important requirement for producing accurate cropland type map, and this is precisely what is lacking at vast scales. Although volunteered geographic information (VGI) has been proven as a possible solution for in situ data acquisition, processing and extracting valuable information from millions of pictures remains challenging. This paper targets the detection of specific crop types from crowdsourced road view photos. A first large, public, multiclass road view crop photo dataset named iCrop was established for the development of crop type detection with deep learning. Five state-of-the-art deep convolutional neural networks including InceptionV4, DenseNet121, ResNet50, MobileNetV2, and ShuffleNetV2 were employed to compare the baseline performance. ResNet50 outperformed the others according to the overall accuracy (87.9%), and ShuffleNetV2 outperformed the others according to the efficiency (13 FPS). The decision fusion schemes major voting was used to further improve crop identification accuracy. The results clearly demonstrate the superior accuracy of the proposed decision fusion over the other non-fusion-based methods in crop type detection of imbalanced road view photos dataset. The voting method achieved higher mean accuracy (90.6-91.1%) and can be leveraged to classify crop type in crowdsourced road view photos.

Mediator tail module subunits MED16 and MED25 differentially regulate abscisic acid signaling in Arabidopsis.

MED25 has been implicated as a negative regulator of the abscisic acid (ABA) signaling pathway. However, it is unclear whether other Mediator subunits could associate with MED25 to participate in the ABA response. Here, we used affinity purification followed by mass spectrometry to uncover Mediator subunits that associate with MED25 in transgenic plants. We found that at least 26 Mediator subunits, belonging to the head, middle, tail, and CDK8 kinase modules, were co-purified with MED25 in vivo. Interestingly, the tail module subunit MED16 was identified to associate with MED25 under both mock and ABA treatments. We further showed that the disruption of MED16 led to reduced ABA sensitivity compared to the wild type. Transcriptomic analysis revealed that the expression of several ABA-responsive genes was significantly lower in med16 than those in wild type. Furthermore, we discovered that MED16 may possibly compete with MED25 to interact with the key transcription factor ABA INSENSITIVE 5 (ABI5) to positively regulate ABA signaling. Consistently, med16 and med25 mutants displayed opposite phenotypes in ABA response, cuticle permeability, and differential ABI5-mediated EM1 and EM6 expression. Together, our data indicate that MED16 and MED25 differentially regulate ABA signaling by antagonistically affecting ABI5-mediated transcription in Arabidopsis.

High Accuracy Respiration and Heart Rate Detection Based on Artificial Neural Network Regression.

A 24GHz Doppler radar system for accurate contactless monitoring of heart and respiratory rates is demonstrated here. High accuracy predictions are achieved by employing a CNN+LSTM neural network architecture for regression analysis. Detection accuracies of 99% and 98% have been attained for heart rate and respiration rate, respectively.Clinical Relevance- This work establishes a non-contact radar system with 99% detection accuracy for a heart rate variability warning system. This system can enable convenient and fast monitoring for daily care at home.

Synthesis of Disulfide Surrogate Peptides Incorporating Large-Span Surrogate Bridges Through a Native-Chemical-Ligation-Assisted Diaminodiacid Strategy.

The use of synthetic bridges as surrogates for disulfide bonds has emerged as a practical strategy to obviate the poor stability of some disulfide-containing peptides. However, peptides incorporating large-span synthetic bridges are still beyond the reach of existing methods. Herein, we report a native chemical ligation (NCL)-assisted diaminodiacid (DADA) strategy that enables the robust generation of disulfide surrogate peptides incorporating surrogate bridges up to 50 amino acids in length. This strategy provides access to some highly desirable but otherwise impossible-to-obtain disulfide surrogates of bioactive peptide. The bioactivities and structures of the synthetic disulfide surrogates were verified by voltage clamp assays, NMR, and X-ray crystallography; and stability studies established that the disulfide replacements effectively overcame the problems of disulfide reduction and scrambling that often plague these pharmacologically important peptides.

Profiles of prognostic alternative splicing signature in hepatocellular carcinoma.

Previous studies have demonstrated the role of abnormal alternative splicing (AS) in tumor progression. This study examines the prognostic index (PI) of alternative splices (ASs) in patients with hepatocellular carcinoma (HCC). The clinical features and splicing events of patients with HCC were downloaded from The Cancer Genome Atlas (TCGA). Differentially expressed AS (DEAS) were compared between HCC and adjacent normal samples. Univariate Cox regression analysis was used to determine changes in DEAS associated with overall survival (OS). A PI was generated from OS-associated DEASs using Kaplan-Meier curves, receiver operating characteristic (ROC) curves, multivariate Cox regression, and cluster analysis. Then, the correlation between DEASs and splicing factors was assessed, followed by functional and pathway enrichment analysis. We identified 34 163 ASs of 8985 genes in HCC, and 153 OS-ASs were identified using univariate Cox regression analysis. Low- and high-PI groups were determined based on the median "PI-ALL" value according to significantly different survival (P = 2.2e - 16). The ROC curve of all PI (PI-ALL) had an area under the curve (AUC) of 0.993 for survival status in patients with HCC. A potential regulatory network associated with prognosis of patients with HCC was established. Enrichment analysis also resulted in the identification of several pathways potentially associated with carcinogenesis and progression of HCC. Four clusters were identified that were associated with clinical features and prognosis. Our study generated comprehensive profiles of ASs in HCC. The interaction network and functional connections were used to elucidate the underlying mechanisms of AS in HCC.

Chemical synthesis and biological activity of peptides incorporating an ether bridge as a surrogate for a disulfide bond.

Disulfide bridges contribute to the definition and rigidity of polypeptides, but they are inherently unstable in reducing environments and in the presence of isomerases and nucleophiles. Strategies to address these deficiencies, ideally without significantly perturbing the structure of the polypeptide, would be of great interest. One possible surrogate for the disulfide bridge is a simple thioether, but these are susceptible to oxidation. We report the introduction of an ether linkage into the biologically active, disulfide-rich peptides oxytocin, tachyplesin I, and conotoxin α-ImI, using an ether-containing diaminodiacid as the key building block, obtained by the stereoselective ring-opening addition reaction of an aziridine skeleton with a hydroxy group. NMR studies indicated that the derivatives with an ether surrogate bridge exhibited very small change of their three-dimensional structures. The analogs obtained using this novel substitution strategy were found to be more stable than the original peptide in oxidative and reductive conditions; without a loss of bioactivity. This strategy is therefore proposed as a practical and versatile solution to the stability problems associated with cysteine-rich peptides.

Mediator Subunit MED25 Couples Alternative Splicing of JAZ Genes with Fine-Tuning of Jasmonate Signaling.

JASMONATE ZIM-DOMAIN (JAZ) transcriptional repressors are key regulators of jasmonate (JA) signaling in plants. At the resting stage, the C-terminal Jas motifs of JAZ proteins bind the transcription factor MYC2 to repress JA signaling. Upon hormone elicitation, the Jas motif binds the hormone receptor CORONATINE INSENSITIVE1, which mediates proteasomal degradation of JAZs and thereby allowing the Mediator subunit MED25 to activate MYC2. Subsequently, plants desensitize JA signaling by feedback generation of dominant JAZ splice variants that repress MYC2. Here we report the mechanistic function of Arabidopsis (Arabidopsis thaliana) MED25 in regulating the alternative splicing of JAZ genes through recruiting the splicing factors PRE-mRNA-PROCESSING PROTEIN 39a (PRP39a) and PRP40a. We demonstrate that JA-induced generation of JAZ splice variants depends on MED25 and that MED25 recruits PRP39a and PRP40a to promote the full splicing of JAZ genes. Therefore, MED25 forms a module with PRP39a and PRP40a to prevent excessive desensitization of JA signaling mediated by JAZ splice variants.

Coagulation factors VII, IX and X are effective antibacterial proteins against drug-resistant Gram-negative bacteria.

Infections caused by drug-resistant "superbugs" pose an urgent public health threat due to the lack of effective drugs; however, certain mammalian proteins with intrinsic antibacterial activity might be underappreciated. Here, we reveal an antibacterial property against Gram-negative bacteria for factors VII, IX and X, three proteins with well-established roles in initiation of the coagulation cascade. These factors exert antibacterial function via their light chains (LCs). Unlike many antibacterial agents that target cell metabolism or the cytoplasmic membrane, the LCs act by hydrolyzing the major components of bacterial outer membrane, lipopolysaccharides, which are crucial for the survival of Gram-negative bacteria. The LC of factor VII exhibits in vitro efficacy towards all Gram-negative bacteria tested, including extensively drug-resistant (XDR) pathogens, at nanomolar concentrations. It is also highly effective in combating XDR Pseudomonas aeruginosa and Acinetobacter baumannii infections in vivo. Through decoding a unique mechanism whereby factors VII, IX and X behave as antimicrobial proteins, this study advances our understanding of the coagulation system in host defense, and suggests that these factors may participate in the pathogenesis of coagulation disorder-related diseases such as sepsis via their dual functions in blood coagulation and resistance to infection. Furthermore, this study may offer new strategies for combating Gram-negative "superbugs".

Internet of Things to network smart devices for ecosystem monitoring.

Smart, real-time, low-cost, and distributed ecosystem monitoring is essential for understanding and managing rapidly changing ecosystems. However, new techniques in the big data era have rarely been introduced into operational ecosystem monitoring, particularly for fragile ecosystems in remote areas. We introduce the Internet of Things (IoT) techniques to establish a prototype ecosystem monitoring system by developing innovative smart devices and using IoT technologies for ecosystem monitoring in isolated environments. The developed smart devices include four categories: large-scale and nonintrusive instruments to measure evapotranspiration and soil moisture, in situ observing systems for CO2 and δ13C associated with soil respiration, portable and distributed devices for monitoring vegetation variables, and Bi-CMOS cameras and pressure trigger sensors for terrestrial vertebrate monitoring. These new devices outperform conventional devices and are connected to each other via wireless communication networks. The breakthroughs in the ecosystem monitoring IoT include new data loggers and long-distance wireless sensor network technology that supports the rapid transmission of data from devices to wireless networks. The applicability of this ecosystem monitoring IoT is verified in three fragile ecosystems, including a karst rocky desertification area, the National Park for Amur Tigers, and the oasis-desert ecotone in China. By integrating these devices and technologies with an ecosystem monitoring information system, a seamless data acquisition, transmission, processing, and application IoT is created. The establishment of this ecosystem monitoring IoT will serve as a new paradigm for ecosystem monitoring and therefore provide a platform for ecosystem management and decision making in the era of big data.

Elongator Is Required for Root Stem Cell Maintenance by Regulating SHORTROOT Transcription.

SHORTROOT (SHR) is essential for stem cell maintenance and radial patterning in Arabidopsis (Arabidopsis thaliana) roots, but how its expression is regulated is unknown. Here, we report that the Elongator complex, which consists of six subunits (ELP1 to ELP6), regulates the transcription of SHR Depletion of Elongator drastically reduced SHR expression and led to defective root stem cell maintenance and radial patterning. The importance of the nuclear localization of Elongator for its functioning, together with the insensitivity of the elp1 mutant to the transcription elongation inhibitor 6-azauracil, and the direct interaction of the ELP4 subunit with the carboxyl-terminal domain of RNA polymerase II, support the notion that Elongator plays important roles in transcription elongation. Indeed, we found that ELP3 associates with the premessenger RNA of SHR and that mutation of Elongator reduces the enrichment of RNA polymerase II on the SHR gene body. Moreover, Elongator interacted in vivo with SUPPRESSOR OF Ty4, a well-established transcription elongation factor that is recruited to the SHR locus. Together, these results demonstrate that Elongator acts in concert with SUPPRESSOR OF Ty4 to regulate the transcription of SHR.

Centipedes subdue giant prey by blocking KCNQ channels.

Centipedes can subdue giant prey by using venom, which is metabolically expensive to synthesize and thus used frugally through efficiently disrupting essential physiological systems. Here, we show that a centipede (Scolopendra subspinipes mutilans, ∼3 g) can subdue a mouse (∼45 g) within 30 seconds. We found that this observation is largely due to a peptide toxin in the venom, SsTx, and further established that SsTx blocks KCNQ potassium channels to exert the lethal toxicity. We also demonstrated that a KCNQ opener, retigabine, neutralizes the toxicity of a centipede's venom. The study indicates that centipedes' venom has evolved to simultaneously disrupt cardiovascular, respiratory, muscular, and nervous systems by targeting the broadly distributed KCNQ channels, thus providing a therapeutic strategy for centipede envenomation.

Mediator subunit MED25 links the jasmonate receptor to transcriptionally active chromatin.

Jasmonoyl-isoleucine (JA-Ile), the active form of the plant hormone jasmonate (JA), is sensed by the F-box protein CORONATINE INSENSITIVE 1 (COI1), a component of a functional Skp-Cullin-F-box E3 ubiquitin ligase complex. Sensing of JA-Ile by COI1 rapidly triggers genome-wide transcriptional changes that are largely regulated by the basic helix-loop-helix transcription factor MYC2. However, it remains unclear how the JA-Ile receptor protein COI1 relays hormone-specific regulatory signals to the RNA polymerase II general transcriptional machinery. Here, we report that the plant transcriptional coactivator complex Mediator directly links COI1 to the promoters of MYC2 target genes. MED25, a subunit of the Mediator complex, brings COI1 to MYC2 target promoters and facilitates COI1-dependent degradation of jasmonate-ZIM domain (JAZ) transcriptional repressors. MED25 and COI1 influence each other's enrichment on MYC2 target promoters. Furthermore, MED25 physically and functionally interacts with HISTONE ACETYLTRANSFERASE1 (HAC1), which plays an important role in JA signaling by selectively regulating histone (H) 3 lysine (K) 9 (H3K9) acetylation of MYC2 target promoters. Moreover, the enrichment and function of HAC1 on MYC2 target promoters depend on COI1 and MED25. Therefore, the MED25 interface of Mediator links COI1 with HAC1-dependent H3K9 acetylation to activate MYC2-regulated transcription of JA-responsive genes. This study exemplifies how a single Mediator subunit integrates the actions of both genetic and epigenetic regulators into a concerted transcriptional program.

MYC2 Orchestrates a Hierarchical Transcriptional Cascade That Regulates Jasmonate-Mediated Plant Immunity in Tomato.

The hormone jasmonate (JA), which functions in plant immunity, regulates resistance to pathogen infection and insect attack through triggering genome-wide transcriptional reprogramming in plants. We show that the basic helix-loop-helix transcription factor (TF) MYC2 in tomato (Solanum lycopersicum) acts downstream of the JA receptor to orchestrate JA-mediated activation of both the wounding and pathogen responses. Using chromatin immunoprecipitation sequencing (ChIP-seq) coupled with RNA sequencing (RNA-seq) assays, we identified 655 MYC2-targeted JA-responsive genes. These genes are highly enriched in Gene Ontology categories related to TFs and the early response to JA, indicating that MYC2 functions at a high hierarchical level to regulate JA-mediated gene transcription. We also identified a group of MYC2-targeted TFs (MTFs) that may directly regulate the JA-induced transcription of late defense genes. Our findings suggest that MYC2 and its downstream MTFs form a hierarchical transcriptional cascade during JA-mediated plant immunity that initiates and amplifies transcriptional output. As proof of concept, we showed that during plant resistance to the necrotrophic pathogen Botrytis cinerea, MYC2 and the MTF JA2-Like form a transcription module that preferentially regulates wounding-responsive genes, whereas MYC2 and the MTF ETHYLENE RESPONSE FACTOR.C3 form a transcription module that preferentially regulates pathogen-responsive genes.