Are vacuolar dynamics crucial factors for plant cell division and differentiation?

Vacuoles are the largest membrane-bound organelles in plant cells, critical for development and environmental responses. Vacuolar dynamics indicate reversible changes of vacuoles in morphology, size, or numbers. In this review, we summarize current understandings of vacuolar dynamics in different types of plant cells, biological processes associated with vacuolar dynamics, and regulators controlling vacuolar dynamics. Specifically, we point out the possibility that vacuolar dynamics play key roles in cell division and differentiation, which are controlled by the nucleus. Finally, we propose three routes through which vacuolar dynamics actively participate in nucleus-controlled cellular activities.

Glutamic-acid grafted hyaluronic acid inhibits inflammatory factors via fibroblast and skin model tests.

BACKGROUND: Excessive inflammation may cause tissue damage and disrupt the function of the skin barrier. Hyaluronic acid (HA), an endogenous component, was found to regulate multiple inflammatory factors for skin health. This work aims to further enhance its efficacy by grafting amino acid onto its molecule. METHODS: Glutamic acid (Glu) was selected as the ligand to react with low-molecular-weight HA. Fibroblast tests and a 3D skin model were used to investigate the anti-inflammation efficacy of HA-Glu. RESULTS: For IL-1α, IL-6 and TNF-α, the grafted compound presents stronger inhibition ability versus native HA. Moreover, HA-Glu could promote the repair of damaged skin by improving the compactness of the stratum corneum and increasing the thickness of the living cell layer. CONCLUSION: The application of HA-Glu compound in skin care formulas would be effective to alleviate inflammation-induced skin symptoms and skin aging.

Dopant effect on the optical and thermal properties of the 2D organic-inorganic hybrid perovskite (HDA)2PbBr4.

Lead-based two-dimensional organic-inorganic hybrid perovskites (2D HOIPs) are popular materials with various optical properties, which can be tuned through metal ion doping. Due to the size and valence misfit, metal ion dopants in 2D lead-based HOIPs are still limited. In this work, Mn2+, Sb3+ and Bi3+ are doped into 2D (HDA)2PbBr4 (HDA = protonated dopamine) successfully. As a result, the dopants in 2D (HDA)2PbBr4 can induce their characteristic optical spectra, which is studied at different temperatures and excitation powers. The temperature-dependent energy transfer in the Mn-doped sample has been clarified, in which abnormal phenomena including negative thermal quenching have been observed. In addition, the dopant ions can impact the phase transition temperatures of the samples, especially lowering their crystallization temperatures greatly. The mussel-inspired organic cation, feasible metal ion regulation, and superior stability provide (HDA)2PbBr4 potential for further applications.

Multi-site, Multi-domain Airway Tree Modeling.

Open international challenges are becoming the de facto standard for assessing computer vision and image analysis algorithms. In recent years, new methods have extended the reach of pulmonary airway segmentation that is closer to the limit of image resolution. Since EXACT'09 pulmonary airway segmentation, limited effort has been directed to the quantitative comparison of newly emerged algorithms driven by the maturity of deep learning based approaches and extensive clinical efforts for resolving finer details of distal airways for early intervention of pulmonary diseases. Thus far, public annotated datasets are extremely limited, hindering the development of data-driven methods and detailed performance evaluation of new algorithms. To provide a benchmark for the medical imaging community, we organized the Multi-site, Multi-domain Airway Tree Modeling (ATM'22), which was held as an official challenge event during the MICCAI 2022 conference. ATM'22 provides large-scale CT scans with detailed pulmonary airway annotation, including 500 CT scans (300 for training, 50 for validation, and 150 for testing). The dataset was collected from different sites and it further included a portion of noisy COVID-19 CTs with ground-glass opacity and consolidation. Twenty-three teams participated in the entire phase of the challenge and the algorithms for the top ten teams are reviewed in this paper. Both quantitative and qualitative results revealed that deep learning models embedded with the topological continuity enhancement achieved superior performance in general. ATM'22 challenge holds as an open-call design, the training data and the gold standard evaluation are available upon successful registration via its homepage (https://atm22.grand-challenge.org/).

Integrative gene duplication and genome-wide analysis as an approach to facilitate wheat reverse genetics: An example in the TaCIPK family.

INTRODUCTION: Reverse genetic studies conducted in the plant with a complex or polyploidy genome enriched with large gene families (like wheat) often meet challenges in identifying the key candidate genes related to important traits and prioritizing the genes for functional experiments. OBJECTIVE: To overcome the above-mentioned challenges of reverse genetics, this work aims to establish an efficient multi-species strategy for genome-wide gene identification and prioritization of the key candidate genes. METHODS: We established the integrative gene duplication and genome-wide analysis (iGG analysis) as a strategy for pinpointing key candidate genes deserving functional research. The iGG captures the evolution, and the expansion/contraction of large gene families across phylogeny-related species and integrates spatial-temporal expression information for gene function inference. Transgenic approaches were also employed to functional validation. RESULTS: As a proof-of-concept for the iGG analysis, we took the wheat calcineurin B-like protein-interacting protein kinases (CIPKs) family as an example. We identified CIPKs from seven monocot species, established the orthologous relationship of CIPKs between rice and wheat, and characterized Triticeae-specific CIPK duplicates (e.g., CIPK4 and CIPK17). Integrated with our analysis of CBLs and CBL-CIPK interaction, we revealed that divergent expressions of TaCBLs and TaCIPKs could play an important role in keeping the stoichiometric balance of CBL-CIPK. Furthermore, we validated the function of TaCIPK17-A2 in the regulation of drought tolerance by using transgenic approaches. Overexpression of TaCIPK17 enhanced antioxidant capacity and improved drought tolerance in wheat. CONCLUSION: The iGG analysis leverages evolutionary and comparative genomics of crops with large genomes to rapidly highlight the duplicated genes potentially associated with speciation, domestication and/or particular traits that deserve reverse-genetic functional studies. Through the identification of Triticeae-specific TaCIPK17 duplicates and functional validation, we demonstrated the effectiveness of the iGG analysis and provided a new target gene for improving drought tolerance in wheat.

A straight-forward gene mining strategy to identify TaCIPK19 as a new regulator of drought tolerance in wheat.

Drought stress is one of the most impactful abiotic stresses to global wheat production. Therefore, identifying key regulators such as the calcineurin B-like protein interacting protein kinase (CIPK) in the signaling cascades known to coordinate developmental cues and environmental stimuli represents a useful approach to improve drought tolerance. However, functional studies have been very limited partly due to the difficulties in prioritizing candidate genes from the large TaCIPK family. To address this issue, we demonstrate a straight-forward strategy by analyzing gene expression patterns in response to phytohormones or stresses and identified TaCIPK19 as a new regulator to improve drought tolerance. The effects of TaCIPK19 on drought tolerance were evaluated in both tobacco and wheat through transgenic approach. Ectopic expression of TaCIPK19 in tobacco greatly improves drought tolerance with enhanced ABA biosynthesis/signaling and ROS scavenging capacity. TaCIPK19 overexpression in wheat also confers the drought tolerance at both seedling and mature stages with enhanced ROS scavenging capacity. Additionally, potential CBL partners interacting with TaCIPK19 were investigated. Collectively, our finding exemplifies a straight-forward approach to facilitate reverse genetics related to abiotic stress improvement and demonstrates TaCIPK19 as a new candidate gene to improve ROS scavenging capacity and drought tolerance, which is useful for genetic improvement and breeding application in wheat.

Signaling between sporophytic integuments and developing female gametophyte during ovule development.

Ovules are precursors of seeds and contain sporophytic integuments and gametophytic embryo sac. In Arabidopsis, embryo sac development requires highly synchronized morphogenesis of integument such that defects in integument growth often accompanies with a block in megagametogenesis, indicating that integument instructs the development of female gametophytes. In this mini review, we discuss signaling pathways through which integument cells mediate embryo sac development. We also propose ways to identify key signaling factors for the communication between integument and developing female gametophyte.

Embryo sac development relies on symplastic signals from ovular integuments in Arabidopsis.

Ovules are female reproductive organs of angiosperms, consisting of sporophytic integuments surrounding female gametophytes, that is, embryo sacs. Synchronization between integument growth and embryo sac development requires intracellular communication. However, signaling routes through which cells of the two generations communicate are unclear. We report that symplastic signals through plasmodesmata (PDs) of integuments are critical for the development of female gametophytes. Genetic interferences of PD biogenesis either by functional loss of CHOLINE TRANSPORTER-LIKE1 (CTL1) or by integument-specific expression of a mutated CALLOSE SYNTHASE 3 (cals3m) compromised PD formation in integuments and reduced fertility. Close examination of pINO:cals3m or ctl1 ovules indicated that female gametophytic development was either arrested at various stages after the formation of functional megaspores. In both cases, defective ovules could not attract pollen tubes, leading to the failure of fertilization. Results presented here demonstrate a key role of the symplastic route in sporophytic control of female gametophytic development.

Gastrodia elata BI.:A Comprehensive Review of Its Traditional Use, Botany, Phytochemistry, Pharmacology, and Pharmacokinetics.

Materials and Methods: This article collects information from relevant documents, including scientific papers, books, and dissertations concerning Gastrodia elata BI. Results: To date, research on Gastrodia elata BI. has identified about 100 active compounds. Many compounds in Gastrodia elata BI. have biological activities, such as sedation and hypnosis, anticonvulsion, improvement of learning and memory, protection of neurons, antidepressive effects, lowering of blood pressure, promotion of angiogenesis, protection of cardiomyocytes, antiplatelet aggregation, anti-inflammatory activity, and amelioration of labor pains. Conclusion: Although many traditional uses of this plant have been confirmed, it is necessary to continue to study the relationship between its structure and function, clarify the mechanisms of pharmacological effects, and explore new clinical applications so as to better delineate the quality control standards for Gastrodia elata BI.

Combined effects of light pollution and vegetation height on behavior and body weight in a nocturnal rodent.

At a global scale, organisms are under threat due to various kinds of environmental changes, such as artificial light at night (ALAN), noise, climatic change and vegetation destruction. Usually, these changes co-vary in time and space and may take effect simultaneously. Although impacts of ALAN on biological processes have been well documented, our knowledge on the combined effects of ALAN and other environmental changes on animals remains limited. In this study, we conducted field experiments in semi-natural enclosures to explore the combined effects of ALAN and vegetation height on foraging behavior, vigilance, activity patterns and body weight in dwarf striped hamsters (Cricetulus barabensis), a nocturnal rodent widely distributed in East Asia. We find that ALAN and vegetation height affected different aspects of behavior. ALAN negatively affected search speed and positively affected handling speed, while vegetation height negatively affected giving-up density and positively affected body weight. ALAN and vegetation height also additively shaped total time spent in a food patch. No significant interactive effect of ALAN and vegetation height was detected. C. barabensis exposed to ALAN and short vegetation suffered a significant loss in body weight, and possessed a much narrower temporal niche (i.e. initiated activity later but became inactive earlier) than those under other combinations of treatments. The observed behavioral responses to ALAN and changes in vegetation height may bring fitness consequences, as well as further changes in structure and functioning of local ecosystems.

Mussel-Inspired Two-Dimensional Halide Perovskite Facilitated Dopamine Polymerization and Self-Adhesive Photoelectric Coating.

Polydopamine (PDA) is a good adhesion agent for lots of gels inspired by the mussel, whereas hybrid organic-inorganic perovskites (HOIPs) usually exhibit extraordinary optoelectronic performance. Herein, mussel-inspired chemistry has been integrated with two-dimensional HOIPs first, leading to the preparation of new crystal (HDA)2PbBr4 (1) (DA = dopamine). The organic cation dopamine can be introduced into PDA resulting in a thin film of (HPDA)2PbBr4 (PDA-1). The dissolved inorganic components of layered perovskite in DMF solution together with H2O2 addition can facilitate DA polymerization greatly. More importantly, PDA-1 can inherit an excellent semiconductor property of HOIPs and robust adhesion of the PDA hydrogel resulting in a self-adhesive photoelectric coating on various interfaces.

An established protocol for generating transgenic wheat for wheat functional genomics via particle bombardment.

Wheat is one of the most important food crops in the world and is considered one of the top targets in crop biotechnology. With the high-quality reference genomes of wheat and its relative species and the recent burst of genomic resources in Triticeae, demands to perform gene functional studies in wheat and genetic improvement have been rapidly increasing, requiring that production of transgenic wheat should become a routine technique. While established for more than 20 years, the particle bombardment-mediated wheat transformation has not become routine yet, with only a handful of labs being proficient in this technique. This could be due to, at least partly, the low transformation efficiency and the technical difficulties. Here, we describe the current version of this method through adaptation and optimization. We report the detailed protocol of producing transgenic wheat by the particle gun, including several critical steps, from the selection of appropriate explants (i.e., immature scutella), the preparation of DNA-coated gold particles, and several established strategies of tissue culture. More importantly, with over 20 years of experience in wheat transformation in our lab, we share the many technical details and recommendations and emphasize that the particle bombardment-mediated approach has fewer limitations in genotype dependency and vector construction when compared with the Agrobacterium-mediated methods. The particle bombardment-mediated method has been successful for over 30 wheat genotypes, from the tetraploid durum wheat to the hexaploid common wheat, from modern elite varieties to landraces. In conclusion, the particle bombardment-mediated wheat transformation has demonstrated its potential and wide applications, and the full set of protocol, experience, and successful reports in many wheat genotypes described here will further its impacts, making it a routine and robust technique in crop research labs worldwide.

Construction of Benzenesulfonamide Derivatives via Copper and Visible Light-induced Azides and S(O)2-H Coupling.

We here have developed an S(O)2-N coupling between phenylsulfinic acid derivatives and aryl azides by dual copper and visible light catalysis. In this efficient and mild pathway, the reaction produces sulfonamide compounds under redox-neutral condition, which is mechanistically different from the nitrogen nucleophilic substitution reactions. Significantly, this transformation intends to utilize the property of visible light-induced azides to generate triplet nitrene and followed coupling with sulfonyl radicals in situ to achieve structurally diverse benzenesulfinamides in good yields.

ST8SIA6-AS1 Promotes the Epithelial-to-Mesenchymal Transition and Angiogenesis of Pituitary Adenoma.

To investigate the effect of long noncoding RNA ST8SIA6-AS1 on the epithelial-to-mesenchymal transition (EMT) and angiogenesis of pituitary adenoma and its possible mechanism. The expression levels of ST8SIA6-AS1 and HOXA9 in noninvasive pituitary adenoma and invasive pituitary adenoma were detected using qRT-PCR. sh-ST8SIA6-AS1 transfection silenced the expression of ST8SIA6-AS1 in GH3 and GTI-1 cells. The effects of ST8SIA6-AS1 on the proliferation, invasion, angiogenesis, and EMT of GH3 and GTI-1 pituitary adenoma cells were detected. The migration ability of cells was detected through scratch assay. Dual luciferase analysis verified the targeting relationship between ST8SIA6-AS1 and miR-5195-3p. ST8SIA6-AS1 and HOXA9 were highly expressed in invasive pituitary adenoma. In pituitary adenomas, miR-5195-3p directly targeted HOXA9. miR-5195-3p is the target gene of ST8SIA6-AS1. ST8SIA6-AS1 knockdown inhibited the proliferation, invasion, angiogenesis, and EMT of pituitary adenoma. HOXA9 expression mediates the biological effect of ST8SIA6-AS1. ST8SIA6-AS1 targets miR-5195-3p to regulate the expression of HOXA9 and promote the EMT of pituitary adenomas.

The Rice Qa-SNAREs in SYP13 Subfamily Are Involved in Regulating Arbuscular Mycorrhizal Symbiosis and Seed Fertility.

Qa-SNARE gene SYP132 (isoform α) was previously reported to affect arbuscular mycorrhizal (AM) symbiosis in the legume species Medicago truncatula. In non-legumes especially monocots, it remains unknown whether certain SNARE genes are also involved in AM symbiosis. In this work, we studied a rice orthologous gene OsSYP132, which showed induced expression in mycorrhizal roots and two paralogous genes OsSYP131a and OsSYP131b, which were not induced by the AM fungus Rhizophagus irregularis. After employing CRISPR/Cas9 technique to generate their mutants, the Ossyp131a homozygous mutant T0 plants exhibited a dwarf phenotype and produced no fertile seeds, indicating a required role of this gene in seed fertility. Unlike the case in legume, the Ossyp132 mutants exhibited normal mycorrhizal phenotype, so did the Ossyp131b mutants. In the Ossyp131b Ossyp132 double mutants, however, the colonization rate and arbuscule abundance level decreased markedly, indicating an impaired fungal proliferation ability in rice roots. Such a defect was further confirmed by the reduced expression levels of AM marker genes. Our results in rice therefore demonstrated that while SYP13II members showed evolutionary and induction patterns specific to symbiosis, AM symbiosis is in fact controlled by the combined action of both SYP13I and SYP13II clades, revealing a functional redundancy among SYNTAXIN genes in mutualism.

Arabidopsis RAN GTPases are critical for mitosis during male and female gametogenesis.

The development of male and female gametophytes is a prerequisite for successful propagation of angiosperms. The small GTPases RAN play fundamental roles in numerous cellular processes. Although RAN GTPases have been characterized in plants, their roles in cellular processes are far from understood. We report here that RAN GTPases in Arabidopsis are critical for gametophytic development. RAN1 loss-of-function showed no defects in gametophytic development likely due to redundancy. However, the expression of a dominant negative or constitutively active RAN1 resulted in gametophytic lethality. Genetic interference of RAN GTPases caused the arrest of pollen mitosis I and of mitosis of functional megaspores, implying a key role of properly regulated RAN activity in mitosis during gametophytic development.

MAGCNSE: predicting lncRNA-disease associations using multi-view attention graph convolutional network and stacking ensemble model.

BACKGROUND: Many long non-coding RNAs (lncRNAs) have key roles in different human biologic processes and are closely linked to numerous human diseases, according to cumulative evidence. Predicting potential lncRNA-disease associations can help to detect disease biomarkers and perform disease analysis and prevention. Establishing effective computational methods for lncRNA-disease association prediction is critical. RESULTS: In this paper, we propose a novel model named MAGCNSE to predict underlying lncRNA-disease associations. We first obtain multiple feature matrices from the multi-view similarity graphs of lncRNAs and diseases utilizing graph convolutional network. Then, the weights are adaptively assigned to different feature matrices of lncRNAs and diseases using the attention mechanism. Next, the final representations of lncRNAs and diseases is acquired by further extracting features from the multi-channel feature matrices of lncRNAs and diseases using convolutional neural network. Finally, we employ a stacking ensemble classifier, consisting of multiple traditional machine learning classifiers, to make the final prediction. The results of ablation studies in both representation learning methods and classification methods demonstrate the validity of each module. Furthermore, we compare the overall performance of MAGCNSE with that of six other state-of-the-art models, the results show that it outperforms the other methods. Moreover, we verify the effectiveness of using multi-view data of lncRNAs and diseases. Case studies further reveal the outstanding ability of MAGCNSE in the identification of potential lncRNA-disease associations. CONCLUSIONS: The experimental results indicate that MAGCNSE is a useful approach for predicting potential lncRNA-disease associations.

lncRNA KCNQ1OT1 Promotes EMT, Angiogenesis, and Stemness of Pituitary Adenoma by Upregulation of RAB11A.

This study is aimed at investigating the effect and mechanism of long noncoding RNA (lncRNA) KCNQ1OT1 on pituitary adenoma (PA). The KCNQ1OT1 expression in invasive and noninvasive PA tissues was detected by real-time fluorescence quantitative polymerase chain reaction (qPCR). The effects of KCNQ1OT1 on the proliferation of PA cells, namely, GH3 and HP75, were detected by CCK-8 experiment. The Transwell assay detected the effect of KCNQ1OT1 on the invasion of GH3 and HP75 cells. The effect of KCNQ1OT1 on the clonal formation ability was detected by clonal formation experiment. The double luciferase reporter assay and the miRNA pull down assay verified the binding of KCNQ1OT1 to miR-140-5p. Meanwhile, the regulatory effect of miR-140-5p on RAB11A was verified. qPCR results showed that KCNQ1OT1 was significantly increased in invasive PA compared with noninvasive PA tissues. Knockdown KCNQ1OT1 inhibited PA cell stemness, angiogenesis, and EMT. In addition, knockdown KCNQ1OT1 inhibited the proliferation, invasion, and clonal formation of PA. miR-140-5p is the target gene of KCNQ1OT1. miR-140-5p targets RAB11A directly. RAB11A can mediate the biological effects of KCNQ1OT1. Meanwhile, lncRNA KCNQ1OT1 can promote the EMT and cellular stemness of PA. Its mechanism of action is realized by inhibiting miR-140-5p. This result can provide a molecular basis for the further study of PA.

Thrombolysis after cardiopulmonary resuscitation in myocardial infarction with abdominal pain as the first presentation: A case report.

RATIONALE: Thrombolysis after cardiopulmonary resuscitation in patients with acute ST-segment elevation myocardial infarction (STEMI) is controversial. This case report describes a successful thrombolysis after resuscitation in delayed-diagnosis STEMI. PATIENT CONCERNS: A 58-year-old man presented with acute abdominal pain as the first symptom of a subsequent STEMI diagnosis. When he returned to the clinic after having been assisted with abdominal pain relief, he suffered a sudden cardiac arrest. Cardiopulmonary resuscitation was performed immediately, and thrombolysis was carried out for his anterior STEMI. He was successfully resuscitated in a short period of time. DIAGNOSIS: The patient was diagnosed with acute and extensive anterior STEMI. The D-dimer level was normal, and pericardial effusion was ruled out. INTERVENTIONS: After successful resuscitation, the patient received half-dose alteplase thrombolytic therapy. After a few days, the patient was transferred to a general ward. Coronary angiography revealed unobstructed flow in the left anterior descending artery. OUTCOMES: The ST segment of the patient gradually declined after thrombolytic therapy, and the myocardial injury marker levels increased. A small amount of pleural fluid in the lungs and pulmonary infection were observed. With effective diuretic, anti-infective, and other treatments, the patient's condition gradually improved, the ventilator was removed, and vasoactive drugs were successfully discontinued. Coronary angiography revealed that the flow of the culprit artery was unobstructed, and a drug-coated balloon was implanted. No wall motion abnormalities were detected on echocardiography, and the patient recovered well. CONCLUSIONS: In patients with abdominal pain as the first presentation, a simple initial electrocardiogram may help reduce the risk of missed STEMI diagnosis. Thrombolysis after successful resuscitation is an effective treatment for these patients. However, the effects of thrombolysis after resuscitation remain unclear. The point of dispute lies in the effectiveness and safety of thrombolysis (primarily for bleeding). Prompt thrombolysis would lead to a better prognosis if spontaneous circulation can be restored within 10 minutes.

Deep learning based on biologically interpretable genome representation predicts two types of human adaptation of SARS-CoV-2 variants.

Explosively emerging SARS-CoV-2 variants challenge current nomenclature schemes based on genetic diversity and biological significance. Genomic composition-based machine learning methods have recently performed well in identifying phenotype-genotype relationships. We introduced a framework involving dinucleotide (DNT) composition representation (DCR) to parse the general human adaptation of RNA viruses and applied a three-dimensional convolutional neural network (3D CNN) analysis to learn the human adaptation of other existing coronaviruses (CoVs) and predict the adaptation of SARS-CoV-2 variants of concern (VOCs). A markedly separable, linear DCR distribution was observed in two major genes-receptor-binding glycoprotein and RNA-dependent RNA polymerase (RdRp)-of six families of single-stranded (ssRNA) viruses. Additionally, there was a general host-specific distribution of both the spike proteins and RdRps of CoVs. The 3D CNN based on spike DCR predicted a dominant type II adaptation of most Beta, Delta and Omicron VOCs, with high transmissibility and low pathogenicity. Type I adaptation with opposite transmissibility and pathogenicity was predicted for SARS-CoV-2 Alpha VOCs (77%) and Kappa variants of interest (58%). The identified adaptive determinants included D1118H and A570D mutations and local DNTs. Thus, the 3D CNN model based on DCR features predicts SARS-CoV-2, a major type II human adaptation and is qualified to predict variant adaptation in real time, facilitating the risk-assessment of emerging SARS-CoV-2 variants and COVID-19 control.