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Summary: Arabidopsis RESISTANCE TO POWDERY MILDEW 8.2 (RPW8.2) is specifically induced by the powdery mildew (PM) fungus (Golovinomyces cichoracearum) in the infected epidermal cells to activate immunity. However, the mechanism of RPW8.2‐induction is not well understood.Here, we identify a G. cichoracearum effector that interacts with RPW8.2, named Gc‐RPW8.2 interacting protein 1 (GcR8IP1), by a yeast two‐hybrid screen of an Arabidopsis cDNA library.GcR8IP1 is physically associated with RPW8.2 with its REALLY INTERESTING NEW GENE finger domain that is essential and sufficient for the association. GcR8IP1 was secreted and translocated into the nucleus of host cell infected with PM. Association of GcR8IP1 with RPW8.2 led to an increase in RPW8.2 in the nucleus. In turn, the nucleus‐localized RPW8.2 promoted the activity of the RPW8.2 promoter, resulting in transcriptional self‐amplification of RPW8.2 to boost immunity at infection sites. Additionally, ectopic expression or host‐induced gene silencing of GcR8IP1 supported its role as a virulence factor in PM.Altogether, our results reveal a mechanism of RPW8.2‐dependent defense strengthening via altered partitioning of RPW8.2 and transcriptional self‐amplification triggered by a PM fungal effector, which exemplifies an atypical form of effector‐triggered immunity. [ABSTRACT FROM AUTHOR]

Simple Summary: Single Cell RNA Sequencing generates gene expression data at a single cell resolution. While single cell RNA has many applications in biomedical research, the high dimensionality of the data produced poses a considerable computational challenge. This study proposes a novel algorithm using penalized regression methods to analyze single cell RNA sequencing data. The proposed algorithm reduces high dimensionality of the gene expression data using a sequence feature selection methods such as Ridge regression, LASSO, Elastic Net, Drop LASSO, and Sparse Group LASSO. The proposed algorithm successfully detected highly differentiated genes, including the marker genes, for 5 different single cell RNA sequencing datasets associated with the species mouse, plant, and human. With the emergence of single-cell RNA sequencing (scRNA-seq) technology, scientists are able to examine gene expression at single-cell resolution. Analysis of scRNA-seq data has its own challenges, which stem from its high dimensionality. The method of machine learning comes with the potential of gene (feature) selection from the high-dimensional scRNA-seq data. Even though there exist multiple machine learning methods that appear to be suitable for feature selection, such as penalized regression, there is no rigorous comparison of their performances across data sets, where each poses its own challenges. Therefore, in this paper, we analyzed and compared multiple penalized regression methods for scRNA-seq data. Given the scRNA-seq data sets we analyzed, the results show that sparse group lasso (SGL) outperforms the other six methods (ridge, lasso, elastic net, drop lasso, group lasso, and big lasso) using the metrics area under the receiver operating curve (AUC) and computation time. Building on these findings, we proposed a new algorithm for feature selection using penalized regression methods. The proposed algorithm works by selecting a small subset of genes and applying SGL to select the differentially expressed genes in scRNA-seq data. By using hierarchical clustering to group genes, the proposed method bypasses the need for domain-specific knowledge for gene grouping information. In addition, the proposed algorithm provided consistently better AUC for the data sets used. [ABSTRACT FROM AUTHOR]

Singlet oxygen (¹O2) has a very short half-life of 10-5 s; however, it is a strong oxidant that causes growth arrest and necrotic lesions on plants. Its signaling pathway remains largely unknown. The Arabidopsis flu (fluorescent) mutant accumulates a high level of ¹O2 and shows drastic changes in nuclear gene expression. Only two plastid proteins, EX1 (executer 1) and EX2 (executer 2), have been identified in the singlet oxygen signaling. Here, we found that the transcription factor abscisic acid insensitive 4 (ABI4) binds the promoters of genes responsive to ¹O2-signals. Inactivation of the ABI4 protein in the flu/abi4 double mutant was sufficient to compromise the changes of almost all ¹O2-responsive-genes and rescued the lethal phenotype of flu grown under light/dark cycles, similar to the flu/ex1/ex2 triple mutant. In addition to cell death, we reported for the first time that ¹O2 also induces cell wall thickening and stomatal development defect. Contrastingly, no apparent growth arrest was observed for the flu mutant under normal light/dim light cycles, but the cell wall thickening (doubled) and stomatal density reduction (by two-thirds) still occurred. These results offer a new idea for breeding stress tolerant plants. [ABSTRACT FROM AUTHOR]

The Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis, YFP) is an endangered species endemic to the Yangtze River in China, and it is the only freshwater whale in the genus Neophocaena. In terms of protection, three effective conservation strategies exist: in situ conservation, ex situ conservation, and artificial breeding, all of which have been implemented by the Chinese government. Of these, ex situ conservation involves the relocation of Yangtze finless porpoises to semi-natural waters with less human interference, and artificial breeding involves the relocation of Yangtze finless porpoises to a controlled environment that is more strictly managed. To compare and analyze the responsive changes in gene expression of the YFPs between the ex situ and controlled environments, we performed the RNA sequencing of blood tissues from these YFPs. A total of 1201 differentially expressed genes (DEGs) were identified, of which 423 were up-regulated in the ex situ population and 778 were up-regulated in the controlled-environment population. Gene enrichment analysis showed that 1201 DEGs between the ex situ and controlled-environment populations were generally enriched for vision-, digestion- and immune-system-related pathways. Further analysis revealed that several key immune system pathways, such as the chemokine signaling pathway and B cell receptor signal pathway, were activated in the ex situ population. In addition, the key pathways related to vision, including phototransduction and the inflammatory mediator regulation of TRP channels, as well as the pathways related to the digestive system, such as protein digestion and absorption and salivary secretion, were activated in the controlled-environment population. These results suggest that the ex situ populations may respond to complex environmental conditions in semi-natural waters by enhancing their immune function through the increased expression of immune-related genes and that the visual function and protein digestion of the YFPs were improved compared to those of the ex situ population based on the conditions of artificial feeding, such as the higher transparency of the water and regular feeding. This study provides clues for evaluating the adaptability of YFPs to different environments and is a useful reference for future ex situ conservation and artificial breeding. [ABSTRACT FROM AUTHOR]

There remains an urgent need for new therapies for treatment-resistant epilepsy. Sodium channel blockers are effective for seizure control in common forms of epilepsy, but loss of sodium channel function underlies some genetic forms of epilepsy. Approaches that provide bidirectional control of sodium channel expression are needed. MicroRNAs (miRNA) are small noncoding RNAs which negatively regulate gene expression. Here we show that genome-wide miRNA screening of hippocampal tissue from a rat epilepsy model, mice treated with the antiseizure medicine cannabidiol, and plasma from patients with treatment-resistant epilepsy, converge on a single target—miR-335- 5p. Pathway analysis on predicted and validated miR-335- 5p targets identified multiple voltage-gated sodium channels (VGSCs). Intracerebroventricular injection of antisense oligonucleotides against miR-335- 5p resulted in upregulation of Scn1a, Scn2a, and Scn3a in the mouse brain and an increased action potential rising phase and greater excitability of hippocampal pyramidal neurons in brain slice recordings, consistent with VGSCs as functional targets of miR-335- 5p. Blocking miR-335- 5p also increased voltage-gated sodium currents and SCN1A, SCN2A, and SCN3A expression in human induced pluripotent stem cell-derived neurons. Inhibition of miR-335- 5p increased susceptibility to tonic-clonic seizures in the pentylenetetrazol seizure model, whereas adeno-associated virus 9-mediated overexpression of miR-335- 5p reduced seizure severity and improved survival. These studies suggest modulation of miR-335- 5p may be a means to regulate VGSCs and affect neuronal excitability and seizures. Changes to miR-335- 5p may reflect compensatory mechanisms to control excitability and could provide biomarker or therapeutic strategies for different types of treatment-resistant epilepsy. [ABSTRACT FROM AUTHOR]

Background: Panax ginseng is a perennial herb and one of the most widely used traditional medicines in China. During its long growth period, it is affected by various environmental factors. Past studies have shown that growth-regulating factors (GRFs) and GRF-interacting factors (GIFs) are involved in regulating plant growth and development, responding to environmental stress, and responding to the induction of exogenous hormones. However, GRF and GIF transcription factors in ginseng have not been reported. Results: In this study, 20 GRF gene members of ginseng were systematically identified and found to be distributed on 13 chromosomes. The ginseng GIF gene family has only ten members, which are distributed on ten chromosomes. Phylogenetic analysis divided these PgGRFs into six clades and PgGIFs into two clades. In total, 18 of the 20 PgGRFs and eight of the ten PgGIFs are segmental duplications. Most PgGRF and PgGIF gene promoters contain some hormone- and stress- related cis-regulatory elements. Based on the available public RNA-Seq data, the expression patterns of PgGRF and PgGIF genes were analysed from 14 different tissues. The responses of the PgGRF gene to different hormones (6-BA, ABA, GA3, IAA) and abiotic stresses (cold, heat, drought, and salt) were studied. The expression of the PgGRF gene was significantly upregulated under GA3 induction and three weeks of heat treatment. The expression level of the PgGIF gene changed only slightly after one week of heat treatment. Conclusions: The results of this study may be helpful for further study of the function of PgGRF and PgGIF genes and lay a foundation for further study of their role in the growth and development of Panax ginseng. [ABSTRACT FROM AUTHOR]

Background: The aim of this study was to decide the role of the polarization of macrophages regulated by tumor necrosis factor-α (TNF-α)-induced protein 8-like 2 (TIPE2) in meibomian gland dysfunction (MGD). Methods: Firstly, the secretory function of the meibomian gland (MG) in apolipoprotein E knockout (ApoE-/-) MGD mice and normal mice was detected by oil red staining. Then, the expression levels of markers of M1 and M2 macrophages were detected by immunofluorescence staining in MGD, normal mice, and mild and severe MGD corpses to decide the role of M1 and M2 macrophages in MGD inflammation. Meanwhile, the expression levels of TIPE2 in MGD mice and MGD patients were detected by immunofluorescence staining, and the correlations among TIPE2, M1 and M2 macrophages were analyzed by immunofluorescence double staining in MGD mice and MGD patients. Furthermore, lipopolysaccharide (LPS) and interleulkin-4 (IL-4) were used to induce M1 and M2 polarization of macrophages, and the mRNA level of TIPE2 was detected in M1 and M2 macrophages. Results: Oil red staining showed that eyelid fat congestion was more severe in (ApoE-/-) MGD mice than in normal mice, and the M1 macrophage was the primary inflammatory cell infiltrated in (ApoE-/-) MGD mice (p < 0.05). The results of the immunofluorescence staining showed that the infiltration of macrophages in MGD mice was more obvious than that in the normal group, and M1 macrophage was the dominant group (p < 0.05). Similar to the results of the MGD mouse model, more macrophage infiltration was observed in MGD patients' MG tissues, and there were more M1 cells in the severe group than in the mild group (p < 0.05). Moreover, the expression of TIPE2 was positively correlated with the expression of M2 macrophages in MGD patients and mice MG tissues (p < 0.05). The expression of TIPE2 mRNA in LPS-induced M1 macrophages declined, while the expression of TIPE2 mRNA in IL-4-induced M2 macrophages increased (p < 0.05). Conclusion: M1 macrophage was the dominant group infiltrated in the MG tissue of MGD, and TIPE2 is a potential anti-inflammatory target for preventing the development of MGD by promoting the M2 polarization of macrophages. [ABSTRACT FROM AUTHOR]

The Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis, YFP) is a critically endangered small odontocete species, mainly distributed in the middle and lower reaches of the Yangtze River, Poyang Lake, and Dongting Lake. Under the influence of human activities, many factors are threatening the survival and reproduction of YFPs in their natural habitat. Ex situ conservation is of great significance to strengthen the rescuing conservation of YFPs by providing suitable alternative habitats and promoting the reproduction and growth of the ex situ population. To reveal the differences in gene expression of YFPs in natural and ex situ protected waters, and to investigate the effects of environmental factors on YFPs and their mechanisms, we performed transcriptome sequencing for blood tissues of YFPs collected from natural waters and ex situ protected waters. Using RNA-seq we identified 4613 differentially expressed genes (DEGs), of which 4485 were up-regulated and 128 were down-regulated in the natural population. GO analysis showed that DEGs were significantly enriched in entries related to binding, catalytic activity, and biological regulation; KEGG analysis showed that DEGs were enriched mainly in signal transduction, endocrine system, immune system, and sensory system-related pathways. Further analysis revealed that water pollution in natural waters may affect the hormone secretion of YFPs by altering the expression pattern of endocrine genes, thus interfering with normal endocrine activities; noise pollution may induce oxidative stress and inflammatory responses in YFPs, thus impairing the auditory function of YFPs. This study provides a new perspective for further research on the effect of habitat conditions on the YFPs and suggests that improving the habitat environment may help in the conservation of YFPs. [ABSTRACT FROM AUTHOR]