Nuclear lamina component KAKU4 regulates chromatin states and transcriptional regulation in the Arabidopsis genome.

BACKGROUND: The nuclear lamina links the nuclear membrane to chromosomes and plays a crucial role in regulating chromatin states and gene expression. However, current knowledge of nuclear lamina in plants is limited compared to animals and humans. RESULTS: This study mainly focused on elucidating the mechanism through which the putative nuclear lamina component protein KAKU4 regulates chromatin states and gene expression in Arabidopsis leaves. Thus, we constructed a network using the association proteins of lamin-like proteins, revealing that KAKU4 is strongly associated with chromatin or epigenetic modifiers. Then, we conducted ChIP-seq technology to generate global epigenomic profiles of H3K4me3, H3K27me3, and H3K9me2 in Arabidopsis leaves for mutant (kaku4-2) and wild-type (WT) plants alongside RNA-seq method to generate gene expression profiles. The comprehensive chromatin state-based analyses indicate that the knockdown of KAKU4 has the strongest effect on H3K27me3, followed by H3K9me2, and the least impact on H3K4me3, leading to significant changes in chromatin states in the Arabidopsis genome. We discovered that the knockdown of the KAKU4 gene caused a transition between two types of repressive epigenetics marks, H3K9me2 and H3K27me3, in some specific PLAD regions. The combination analyses of epigenomic and transcriptomic data between the kaku4-2 mutant and WT suggested that KAKU4 may regulate key biological processes, such as programmed cell death and hormone signaling pathways, by affecting H3K27me3 modification in Arabidopsis leaves. CONCLUSIONS: In summary, our results indicated that KAKU4 is directly and/or indirectly associated with chromatin/epigenetic modifiers and demonstrated the essential roles of KAKU4 in regulating chromatin states, transcriptional regulation, and diverse biological processes in Arabidopsis.

Communication-efficient distributed cubic Newton with compressed lazy Hessian.

Recently, second-order distributed optimization algorithms have been becoming a research hot in distributed learning, due to their faster convergence rate than the first-order algorithms. However, second-order algorithms always suffer from serious communication bottleneck. To conquer such challenge, we propose communication-efficient second-order distributed optimization algorithms in the parameter-server framework, by incorporating cubic Newton methods with compressed lazy Hessian. Specifically, our algorithms require each worker communicate compressed Hessians with the server only at some particular iterations, which can save both communication bits and communication rounds. For non-convex problems, we theoretically prove that our algorithms can reduce the communication cost comparing to the state-of-the-art second-order algorithms, while maintaining the same iteration complexity order O(ϵ-3/2) as the centralized cubic Newton methods. By further using gradient regularization technique, our algorithms can achieve global convergence for convex problems. Moreover, for strongly convex problems, our algorithms can achieve local superlinear convergence rate without any requirement on initial conditions. Finally, numerical experiments are conducted to show the high efficiency of the proposed algorithms.

Anti-UV Microgel Based on Interfacial Polymerization to Decrease Skin Irritation of High Permeability UV Absorber Ethylhexyl Methoxycinnamate.

Ethylhexyl methoxycinnamate (EHMC) is frequently employed as a photoprotective agent in sunscreen formulations. EHMC has been found to potentially contribute to health complications as a result of its propensity to produce irritation and permeate the skin. A microgel carrier, consisting of poly(ethylene glycol dimethacrylate) (pEDGMA), was synthesized using interfacial polymerization with the aim of reducing the irritation and penetration of EHMC. The thermogravimetric analysis (TGA) indicated that the EHMC content accounted for 75.72% of the total composition. Additionally, the scanning electron microscopy (SEM) images depicted the microgel as exhibiting a spherical morphology. In this study, the loading of EHMC was demonstrated through FTIR and contact angle tests. The UV resistance, penetration, and skin irritation of the EHMC-pEDGMA microgel were additionally assessed. The investigation revealed that the novel sunscreen compound, characterized by limited dermal absorption, had no irritant effects and offered sufficient protection against ultraviolet radiation.

KAKU4 regulates leaf senescence through modulation of H3K27me3 deposition in the Arabidopsis genome.

Lamins are the major components of the nuclear lamina, which regulate chromatin structure and gene expression. KAKU4 is a unique nuclear lamina component in the nuclear periphery, modulates nuclear shape and size in Arabidopsis. The knowledge about the regulatory role of KAKU4 in leaf development remains limited. Here we found that knockdown of KAKU4 resulted in an accelerated leaf senescence phenotype, with elevated levels of H2O2 and hormones, particularly SA, JA, and ABA. Our results demonstrated the importance of KAKU4 as a potential negative regulator in age-triggered leaf senescence in Arabidopsis. Furthermore, we conducted combination analyses of transcriptomic and epigenomic data for the kaku4 mutant and WT leaves. The knockdown of KAKU4 lowered H3K27me3 deposition in the up-regulated genes associated with hormone pathways, programmed cell death, and leaf senescence, including SARD1, SAG113/HAI1, PR2, and so forth. In addition, we found the functional crosstalks between KAKU4 and its associated proteins (CRWN1/4, PNET2, GBPL3, etc.) through comparing multiple transcriptome datasets. Overall, our results indicated that KAKU4 may inhibit the expression of a series of genes related to hormone signals and H2O2 metabolism by affecting the deposition of H3K27me3, thereby suppressing leaf senescence.

Neuronal and synaptic adaptations underlying the benefits of deep brain stimulation for Parkinson's disease.

Deep brain stimulation (DBS) is a well-established and effective treatment for patients with advanced Parkinson's disease (PD), yet its underlying mechanisms remain enigmatic. Optogenetics, primarily conducted in animal models, provides a unique approach that allows cell type- and projection-specific modulation that mirrors the frequency-dependent stimulus effects of DBS. Opto-DBS research in animal models plays a pivotal role in unraveling the neuronal and synaptic adaptations that contribute to the efficacy of DBS in PD treatment. DBS-induced neuronal responses rely on a complex interplay between the distributions of presynaptic inputs, frequency-dependent synaptic depression, and the intrinsic excitability of postsynaptic neurons. This orchestration leads to conversion of firing patterns, enabling both antidromic and orthodromic modulation of neural circuits. Understanding these mechanisms is vital for decoding position- and programming-dependent effects of DBS. Furthermore, patterned stimulation is emerging as a promising strategy yielding long-lasting therapeutic benefits. Research on the neuronal and synaptic adaptations to DBS may pave the way for the development of more enduring and precise modulation patterns. Advanced technologies, such as adaptive DBS or directional electrodes, can also be integrated for circuit-specific neuromodulation. These insights hold the potential to greatly improve the effectiveness of DBS and advance PD treatment to new levels.

Cell Wall Pectin Content Refers to Favored Delivery of Negatively Charged Carbon Dots in Leaf Cells.

In this work, we systematically investigated how cell wall and cell wall components affect the delivery of charged carbon quantum dots (CDs, from -34 to +41 mV) to leaf cells of cucumber and Arabidopsis plants. Four different types of leaf cells in cucumber and Arabidopsis were used, i.e., protoplasts (without cell wall), isolated individual cells (cell wall hydrolyzed with pectinase), regenerated individual cells (cell wall regenerated from protoplast), and intact leaf cells (intact cell wall, in planta). Leaf cells were incubated with charged CDs (0.5 mg/mL) for 2 h. Confocal imaging results showed that protoplasts, regenerated individual cells, and leaf cells showed favored uptake of the negatively charged CDs (-34 mV) compared to the PEI (polyethylenimine) coated and positively charged carbon dots [PEI600-CDs (17 mV) and PEI10K-CDs (41 mV)], while in isolated individual cells, the trend is opposite. The results of the content of the cell wall components showed that no significant changes in the total cell wall content were found between isolated individual cells and regenerated individual cells (1.28 vs 1.11 mg/106 cells), while regenerated individual cells showed significant higher pectin content [water-soluble pectin (0.13 vs 0.06 mg/106 cells, P < 0.01), chelator-soluble pectin (0.04 vs 0.01 mg/106 cells, P < 0.01), and alkaline pectin (0.02 vs 0.01 mg/106 cells, P < 0.01)] and significant lower cellulose content (0.13 vs 0.32 mg/106 cells, P < 0.01) than the isolated individual cells. No difference of the hemicellulose content was found between isolated individual cells and regenerated individual cells (0.20 vs 0.21 mg/106 cells). Our results suggest that compared with cellulose and hemicellulose in the cell wall, the pectin is a more important factor referring to the favored uptake of negatively charged carbon dots in leaf cells. Overall, this work provides a method to study the role of cell wall components in the uptake of nanoparticles in plant cells and also points out the importance of understanding the interactions between cell barriers and nanoparticles to design nanoparticles for agricultural use.

Distributed inertial online game algorithm for tracking generalized Nash equilibria.

This paper is concerned with the distributed generalized Nash equilibrium (GNE) tracking problem of noncooperative games in dynamic environments, where the cost function and/or the coupled constraint function are time-varying and revealed to each agent after it makes a decision. We first consider the case without coupled constraints and propose a distributed inertial online game (D-IOG) algorithm based on the mirror descent method. The proposed algorithm is capable of tracking Nash equilibrium (NE) through a time-varying communication graph and has the potential of achieving a low average regret. With an appropriate non-increasing stepsize sequence and an inertial parameter, the regrets can grow sublinearly if the deviation of the NE sequence grows sublinearly. Second, the time-varying coupled constraints are further investigated, and a modified D-IOG algorithm for tracking GNE is proposed based on the primal-dual and mirror descent methods. Then, the upper bounds of regrets and constraint violation are derived. Moreover, inertia and two information transmission modes are discussed. Finally, two simulation examples are provided to illustrate the effectiveness of the D-IOG algorithms.

Decentralized ADMM with compressed and event-triggered communication.

This paper considers the decentralized optimization problem, where agents in a network cooperate to minimize the sum of their local objective functions by communication and local computation. We propose a decentralized second-order communication-efficient algorithm called communication-censored and communication-compressed quadratically approximated alternating direction method of multipliers (ADMM), termed as CC-DQM, by combining event-triggered communication with compressed communication. In CC-DQM, agents are allowed to transmit the compressed message only when the current primal variables have changed greatly compared to its last estimate. Moreover, to relieve the computation cost, the update of Hessian is also scheduled by the trigger condition. Theoretical analysis shows that the proposed algorithm can still maintain an exact linear convergence, despite the existence of compression error and intermittent communication, if the local objective functions are strongly convex and smooth. Finally, numerical experiments demonstrate its satisfactory communication efficiency.

Long-Run Behavior Estimation of Temporal Boolean Networks With Multiple Data Losses.

This brief devotes to investigating the long-run behavior estimation of temporal Boolean networks (TBNs) with multiple data losses, especially the asymptotical stability. The information transmission is modeled by Bernoulli variables, based on which an augmented system is constructed to facilitate the analysis. A theorem guarantees that the asymptotical stability of the original system can be converted to that of the augmented system. Subsequently, one necessary and sufficient condition is obtained for asymptotical stability. Furthermore, an auxiliary system is derived to study the synchronization issue of the ideal TBNs with normal data transmission and TBNs with multiple data losses, as well as an effective criterion for verifying synchronization. Finally, numerical examples are given to illustrate the validity of the theoretical results.

Genome-Wide Investigation and Co-Expression Network Analysis of SBT Family Gene in Gossypium.

Subtilases (SBTs), which belong to the serine peptidases, control plant development by regulating cell wall properties and the activity of extracellular signaling molecules, and affect all stages of the life cycle, such as seed development and germination, and responses to biotic and abiotic environments. In this study, 146 Gossypium hirsutum, 138 Gossypium barbadense, 89 Gossypium arboreum and 84 Gossypium raimondii SBTs were identified and divided into six subfamilies. Cotton SBTs are unevenly distributed on chromosomes. Synteny analysis showed that the members of SBT1 and SBT4 were expanded in cotton compared to Arabidopsis thaliana. Co-expression network analysis showed that six Gossypium arboreum SBT gene family members were in a network, among which five SBT1 genes and their Gossypium hirsutum and Arabidopsis thaliana direct homologues were down-regulated by salt treatment, indicating that the co-expression network might share conserved functions. Through co-expression network and annotation analysis, these SBTs may be involved in the biological processes of auxin transport, ABA signal transduction, cell wall repair and root tissue development. In summary, this study provides valuable information for the study of SBT genes in cotton and excavates SBT genes in response to salt stress, which provides ideas for cotton breeding for salinity resistance.

Resilient Output Synchronization of Heterogeneous Multiagent Systems With DoS Attacks Under Distributed Event-/Self-Triggered Control.

This article investigates the resilient output synchronization problem of a class of linear heterogeneous multiagent systems subjected to denial-of-service (DoS) attacks. Two types of control mechanisms, namely, event- and self-triggered control mechanisms, are presented so as to cut down unnecessary information transmission. Both of these two mechanisms are distributed, and thus, only local information of each agent and its neighboring agents is adopted for the event condition design. The DoS attacks are considered to be aperiodic, and the quantitative relationship between the attributes of the DoS attacks and the synchronization is also revealed. It is shown that the output synchronization can be achieved exponentially in the presence of DoS attacks under the proposed control mechanisms. The validness of the provided mechanisms is certified by a simulation example.

WheatCENet: A Database for Comparative Co-expression Networks Analysis of Allohexaploid Wheat and Its Progenitors.

Genetic and epigenetic changes after polyploidization events could result in variable gene expression and modified regulatory networks. Here, using large-scale transcriptome data, we constructed co-expression networks for diploid, tetraploid, and hexaploid wheat species, and built a platform for comparing co-expression networks of allohexaploid wheat and its progenitors, named WheatCENet. WheatCENet is a platform for searching and comparing specific functional co-expression networks, as well as identifying the related functions of the genes clustered therein. Functional annotations like pathways, gene families, protein-protein interactions, microRNAs (miRNAs), and several lines of epigenome data are integrated into this platform, and Gene Ontology (GO) annotation, gene set enrichment analysis (GSEA), motif identification, and other useful tools are also included. Using WheatCENet, we found that the network of WHEAT ABERRANT PANICLE ORGANIZATION 1 (WAPO1) has more co-expressed genes related to spike development in hexaploid wheat than its progenitors. We also found a novel motif of CCWWWWWWGG (CArG) specifically in the promoter region of WAPO-A1, suggesting that neofunctionalization of the WAPO-A1 gene affects spikelet development in hexaploid wheat. WheatCENet is useful for investigating co-expression networks and conducting other analyses, and thus facilitates comparative and functional genomic studies in wheat. WheatCENet is freely available at http://bioinformatics.cpolar.cn/WheatCENet and http://bioinformatics.cau.edu.cn/WheatCENet.

Corrigendum: Fixed-life or rechargeable batteries for deep brain stimulation: preference and satisfaction among patients with hyperkinetic movement disorders.

[This corrects the article DOI: 10.3389/fneur.2021.662383.].

CW198 acts as a genetic insulator to block enhancer-promoter interaction in plants.

Insulators in vertebrates play a role in genome architecture and orchestrate temporo-spatial enhancer-promoter interactions. In plants, insulators and their associated binding factors have not been documented as of yet, largely as a result of a lack of characterized insulators. In this study, we took a comprehensive strategy to identify and validate the enhancer-blocking insulator CW198. We show that a 1.08-kb CW198 fragment from Arabidopsis can, when interposed between an enhancer and a promoter, efficiently abrogate the activation function of both constitutive and floral organ-specific enhancers in transgenic Arabidopsis and tobacco plants. In plants, both transcriptional crosstalk and spreading of histone modifications were rarely detectable across CW198, which resembles the insulation property observed across the CTCF insulator in the mammalian genome. Taken together, our findings support that CW198 acts as an enhancer-blocking insulator in both Arabidopsis and tobacco. The significance of the present findings and their relevance to the mitigation of mutual interference between enhancers and promoters, as well as multiple promoters in transgenes, is discussed.

CT Imaging Features and Clinical Characteristics of 2019 Novel Coronavirus Pneumonia (COVID-19) During Rehabilitation.

This study aims to explore the clinical characteristics of the patients with novel coronavirus pneumonia (COVID-19) during rehabilitation. One hundred and twelve confirmed patients were enrolled, while 72 were females (64.3%) and 40 were males (35.7%). The age of the patients was 51.63 ± 4.07 years old. Those patients were divided into mild group, moderate group and severe group based on lesion volume and proportion of total lesion on CT images. The age, gender, past medical history, finger pulse oxygen (SPO2), heart rate (HR) and body temperature and other clinical characteristics of patients were collected. Lesion volume was measured by CT. Compared with mild group, age, lesion volume and total lesion proportion in moderate group were significantly higher. Age, lesion volume and total lesion proportion in severe group were also higher than those in moderate group. Age and past medical history were the risk factors for the lesion volume of COVID-19. Older the patient has larger CT lesion range (R = 0.232, P = 0.045). Without past medical history or combination of post-medical history, the COVID-19 patients had smaller CT lesion ranges, and the history of previous cardiovascular disease and pulmonary disease was important risk factors for the larger CT lesion ranges. The patients who were older or combined with chronic diseases, especially cardiovascular diseases, respiratory disease and diabetes, tended to have the larger lesions. Age and past medical history of patients with COVID-19 period are significantly related to the lesion volume and total lesion proportion on CT images.

Privacy-Preserving Distributed ADMM With Event-Triggered Communication.

This article addresses distributed optimization problems, in which a group of agents cooperatively minimize the sum of their private objective functions via information exchanging. Building on alternating direction method of multipliers (ADMM), we propose a privacy-preserving and communication-efficient decentralized quadratically approximated ADMM algorithm, termed PC-DQM, for solving such type of problems under the scenario of limited communication. In PC-DQM, an event-triggered mechanism is designed to schedule the communication instants for reducing communication cost. Simultaneously, for privacy preservation, a Hessian matrix with perturbed noise is introduced to quadratically approximate the objective function, which results in a closed form of primal vector update and then avoids solving a subproblem at each iteration with possible high computation cost. In addition, the triggered scheme is also utilized to schedule the update of Hessian, which can also reduce computation cost. We theoretically show that PC-DQM can protect privacy but without losing accuracy. In addition, we rigorously prove that PC-DQM converges linearly to the exact optimal solution for strongly convex and smooth objective functions. Finally, numerical simulation is presented to illustrate the effectiveness and efficiency of our algorithm.

A case report of Klebsiella aerogenes-caused lumbar spine infection identified by metagenome next-generation sequencing.

BACKGROUND: The early clinical diagnosis of spinal infections in elderly patients with recessive or atypical symptoms is difficult. Klebsiella aerogenes is a common opportunistic bacterium that can infect the respiratory tract, urinary tract, and even the central nervous system. However, whether it can infect the lumbar spine has not been previously described. CASE PRESENTATION: In this paper, we report the case of a 69-year-old female patient with osteoporosis who was initially diagnosed with hemolytic anemia. Later, she was diagnosed with K. aerogenes infection of the lumbar spine based on imaging combined with blood culture and metagenome next-generation sequencing (mNGS) detection. After precise medication, the lumbar degeneration was improved. CONCLUSIONS: Bacterial infection should therefore be considered in cases of lumbar degenerative disease in middle-aged and elderly patients.

Subthalamic deep brain stimulation for refractory Gilles de la Tourette's syndrome: clinical outcome and functional connectivity.

BACKGROUND: Deep brain stimulation (DBS) is a promising novel approach for managing refractory Gilles de la Tourette's syndrome (GTS). The subthalamic nucleus (STN) is the most common DBS target for treating movement disorders, and smaller case studies have reported the efficacy of bilateral STN-DBS treatment for relieving tic symptoms. However, management of GTS and treatment mechanism of STN-DBS in GTS remain to be elucidated. METHODS: Ten patients undergoing STN-DBS were included. Tics severity was evaluated using the Yale Global Tic Severity Scale. The severities of comorbid psychiatric symptoms of obsessive-compulsive behavior (OCB), attention-deficit/hyperactivity disorder, anxiety, and depression; social and occupational functioning; and quality of life were assessed. Volumes of tissue activated were used as seed points for functional connectivity analysis performed using a control dataset. RESULTS: The overall tics severity significantly reduced, with 62.9% ± 26.2% and 58.8% ± 27.2% improvements at the 6- and 12-months follow-up, respectively. All three patients with comorbid OCB showed improvement in their OCB symptoms at both the follow-ups. STN-DBS treatment was reasonably well tolerated by the patients with GTS. The most commonly reported side effect was light dysarthria. The stimulation effect of STN-DBS might regulate these symptoms through functional connectivity with the thalamus, pallidum, substantia nigra pars reticulata, putamen, insula, and anterior cingulate cortices. CONCLUSIONS: STN-DBS was associated with symptomatic improvement in severe and refractory GTS without significant adverse events. The STN is a promising DBS target by stimulating both sensorimotor and limbic subregions, and specific brain area doses affect treatment outcomes.

GURFAP: A Platform for Gene Function Analysis in Glycyrrhiza Uralensis.

Glycyrrhiza uralensis (Licorice), which belongs to Leguminosae, is famous for the function of pharmacologic action and natural sweetener with its dried roots and rhizomes. In recent years, the whole-genome sequence of G. uralensis has been completed, which will help to lay the foundation for the study of gene function. Here, we integrated the available genomic and transcriptomic data of G. uralensis and constructed the G. uralensis gene co-expression network. We then annotated gene functions of G. uralensis via aligning with public databases. Furthermore, gene families of G. uralensis were predicted by tools including iTAK (Plant Transcription factor and Protein kinase Identifier and Classifier), HMMER (hidden Markov models), InParanoid, and PfamScan. Finally, we constructed a platform for gene function analysis in G. uralensis (GURFAP, www.gzybioinfoormatics.cn/GURFAP). For analyzed and predicted gene function, we introduced various tools including BLAST (Basic local alignment search tool), GSEA (Gene set enrichment analysis), Motif, Heatmap, and JBrowse. Our analysis based on this platform indicated that the biosynthesis of glycyrrhizin might be regulated by MYB and bHLH. We also took CYP88D6, CYP72A154, and bAS gene in the synthesis pathway of glycyrrhizin as examples to demonstrate the reliability and availability of our platform. Our platform GURFAP will provide convenience for researchers to mine the gene function of G. uralensis and thus discover more key genes involved in the biosynthetic pathway of active ingredients.