Attapulgite-enhanced ε-poly-l-lysine for heightened antibacterial efficiency against Pseudomonas syringae pv. Tomato.

ε-Poly-l-lysine (ε-PL) is an effective antimicrobial peptide for controlling fungal plant diseases, exhibiting significant antifungal activity and safety. Despite its known efficacy, the potential of ε-PL in combating plant bacterial diseases remains underexplored. This study evaluated the effectiveness of ε-PL and its nanomaterial derivative in managing tomato bacterial spot disease caused by Pseudomonas syringae pv. tomato. Results indicated that ε-PL substantially inhibited the growth of Pseudomonas syringae pv. tomato. Additionally, when ε-PL was loaded onto attapulgite (encoded as ATT@PL), its antibacterial effect was significantly enhanced. Notably, the antibacterial efficiency of ATT@PL containing 18.80 µg/mL ε-PL was even close to that of 100 µg/mL pure ε-PL. Further molecular study results showed that, ATT@PL stimulated the antioxidant system and the salicylic acid signaling pathway in tomatoes, bolstering the plants disease resistance. Importantly, the nanocomposite demonstrated no negative effects on both seed germination and plant growth, indicating its safety and aligning with sustainable agricultural practices. This study not only confirmed the effectiveness of ε-PL in controlling tomato bacterial spot disease, but also introduced an innovative high antibacterial efficiency ε-PL composite with good bio-safety. This strategy we believe can also be used in improving other bio-pesticides, and has high applicability in agriculture practice.

Streptomyces virginiae XDS1-5, an antagonistic actinomycete, as a biocontrol to peach brown rot caused by Monilinia fructicola.

BACKGROUND: Peach brown rot, caused by the pathogen Monilinia fructicola, represents a significant postharvest infectious disease affecting peach fruit. This disease is responsible for a substantial increase in fruit decay rates, leading to significant economic losses, often exceeding 50%. Currently, there is a growing interest in identifying biocontrol agents to mitigate peach brown rot, with a predominant interest in Bacillus species. RESULTS: In this investigation, we isolated 410 isolates of actinomycetes from non-farmland ecosystem soil samples. Subsequently, 27 isolates exhibiting superior inhibitory capabilities were selected. Among these, strain XDS1-5 demonstrated the most robust fungistatic effect against brown rot disease, achieving an 80% inhibition rate in vitro and a 66% inhibition rate in vivo. XDS1-5 was identified as belonging to the Streptomyces virginiae species. Furthermore, a fermentation filtrate of XDS1-5 exhibited the ability to metabolize 34.21% of the tested carbon sources and 7.37% of the tested nitrogen sources. Particularly noteworthy was its capacity to disrupt the cell membrane structure directly, leading to increased cell membrane permeability and cytoplasmic leakage. Additionally, our investigation indicated that indoline, a metabolite produced by XDS1-5, played a pivotal role in inhibiting the growth of M. fructicola. CONCLUSION: In summary, our study has identified a biocontrol actinomycete, XDS1-5, with the potential to effectively inhibit postharvest brown rot disease in peaches. This finding holds great significance for the biological control of peach brown rot, offering promising prospects for mitigating the economic losses associated with this devastating disease. © 2024 Society of Chemical Industry.

Association between high-resolution magnetic resonance vessel wall imaging characteristics and recurrent stroke in patients with intracranial atherosclerotic steno-occlusive disease: A prospective multicenter study.

BACKGROUND: High-resolution magnetic resonance vessel wall imaging (HRMR-VWI) is a promising technique for identifying intracranial vulnerable plaques beyond lumen narrowing. However, the association between HRMR-VWI characteristics and recurrent stroke remains uncertain. AIMS: This study aimed to investigate the association between HRMR-VWI characteristics and recurrent ipsilateral stroke in patients with symptomatic intracranial atherosclerotic steno-occlusive disease (ICAS). METHODS: This multicenter, observational study recruited first-ever acute ischemic stroke patients attributed to ICAS (>50% stenosis or occlusion) within 7 days after onset. Participants were assessed by multiparametric magnetic resonance imaging (MRI) including diffusion-weighted imaging, three-dimension time-of-flight magnetic resonance angiography, and three-dimensional T1-weighted HRMR-VWI. The patients were recommended to receive best medical therapy and were systematically followed up for 12 months. The association between HRMR-VWI characteristics and the time to recurrent ipsilateral stroke was investigated by univariable and multivariable analysis. RESULTS: Two hundred and fifty-five consecutive patients were enrolled from 15 centers. The cumulative 12 month ipsilateral recurrence incidence was 4.1% (95% confidence interval (CI): 1.6-6.6%). Patients with recurrent ipsilateral stroke exhibited higher rates of intraplaque hemorrhage (IPH) (30.0% vs 6.5%) and eccentric plaque (90.0% vs 48.2%), and lower occurrence of occlusive thrombus (10.0% vs 23.7%). Plaque length (5.69 ± 2.21 mm vs 6.67 ± 4.16 mm), plaque burden (78.40 ± 7.37% vs 78.22 ± 8.32%), degree of stenosis (60.25 ± 18.95% vs 67.50% ± 22.09%) and remodeling index (1.07 ± 0.27 vs 1.03 ± 0.35) on HRMR-VWI did not differ between patients with and without recurrent ipsilateral stroke. In the multivariable Cox regression analysis, IPH (hazard ratio: 6.64, 95% CI: 1.23-35.8, p = 0.028) was significantly associated with recurrent ipsilateral stroke after adjustment.Conclusions:Our results suggest intraplaque hemorrhage (IPH) is significantly associated with recurrent ipsilateral stroke and has potential value in the selection of patients for aggressive treatment strategies. DATA ACCESS STATEMENT: Data from this study are available and can be accessed upon request.

Netrin-1 protects blood-brain barrier (BBB) integrity after cerebral ischemia-reperfusion by activating the Kruppel-like factor 2 (KLF2)/occludin pathway.

Ischemia/reperfusion (I/R)-induced neural damage and neuroinflammation have been associated with pathological progression during stroke. Netrin-1 is an important member of the family of laminin-related secreted proteins, which plays an important role in governing axon elongation. However, it is unknown whether Netrin-1 possesses a beneficial role in stroke. Here, we employed the middle cerebral artery occlusion (MCAO) model to study the function of Netrin-1 in alleviating brain injuries. Our results demonstrate that Netrin-1 rescued poststroke neurological deficits and inhibited production of the inflammatory cytokines such as interleukin 6 (IL-6) and endothelial chemokine (C-X-C motif) ligand 1 (Cxcl1). Importantly, Netrin-1 protected against MCAO-induced dysfunction of the blood-brain barrier (BBB) in mice and a reduction in the expression of the tight junction (TJ) protein occludin. Additionally, we report that Netrin-1 could ameliorate oxygen-glucose deprivation/reoxygenation (OGD/R)-induced injury and prevent aggravation in endothelial monolayer permeability in bEnd.3 human brain microvascular endothelial cells (HBMVECs). Mechanistically, Netrin-1 ameliorated OGD/R-induced decrease in occludin and Kruppel-like factor 2 (KLF2) in HBMVECs. Notably, silencing of KLF2 abolished the beneficial effects of Netrin-1 in protecting endothelial permeability and occludin expression, suggesting that these effects are mediated by KLF2. In conclusion, our findings suggest that Netrin-1 could constitute a novel therapeutic strategy for ischemic stroke.

Pharmacological inhibition of S6K1 rescues synaptic deficits and attenuates seizures and depression in chronic epileptic rats.

BACKGROUND: Recent studies have shown that mTOR signaling plays an important role in synaptic plasticity. However, the function of S6K1, the mechanistic target of rapamycin kinase complex 1 (mTORC1) substrate, in epilepsy remains unknown. AIMS: Our present study aimed to explore the mechanism by which S6K1 is involved in chronic epilepsy. METHODS: First, immunostaining was used to measure neurite length and complexity in kainic acid (KA)-treated primary cultured neurons treated with PF-4708671, a highly selective S6K1 inhibitor. We obtained evidence for the role of S6K1 in protecting and promoting neuronal growth and development in vitro. Next, to explore the function and mechanism of the S6K1 inhibitor in epilepsy, a pilocarpine-induced chronic epileptic rat model was established. In vivo electrophysiology (including local field potentiation in CA1 and long-term potentiation), depression/anxiety-like behavior tests, and Golgi staining were performed to assess seizure behavior, power spectral density, depression/anxiety-like behavior, and synaptic plasticity. Furthermore, western blotting was applied to explore the potential molecular mechanisms. RESULTS: We found that inhibition of S6K1 expression significantly decreased seizures and depression-like behavior and restored power at low frequencies (1-80 Hz), especially in the delta, theta, and alpha bands, in chronic epileptic rats. In addition, PF-4708671 reversed the LTP defect in hippocampal CA3-CA1 and corrected spine loss and dendritic pathology. CONCLUSION: In conclusion, our data suggest that inhibition of S6K1 attenuates seizures and depression in chronic epileptic rats via the rescue of synaptic structural and functional deficits. Given the wide range of physiological functions of mTOR, inhibition of its effective but relatively simple functional downstream molecules is a promising target for the development of drugs for epilepsy.

Eomesodermin expression in CD4+T-cells associated with disease progression in amyotrophic lateral sclerosis.

AIM: To clarify the role of Eomesodermin (EOMES) to serve as a disease-relevant biomarker and the intracellular molecules underlying the immunophenotype shifting of CD4+T subsets in amyotrophic lateral sclerosis (ALS). METHODS: The derivation and validation cohorts included a total of 148 ALS patients and 101 healthy controls (HCs). Clinical data and peripheral blood were collected. T-cell subsets and the EOMES expression were quantified using multicolor flow cytometry. Serum neurofilament light chain (NFL) was measured. In 1-year longitudinal follow-ups, the ALSFRS-R scores and primary endpoint events were further recorded in the ALS patients of the validation cohort. RESULTS: In the derivation cohort, the CD4+EOMES+T-cell subsets were significantly increased (p < 0.001). EOMES+ subset was positively correlated with increased serum NFL levels in patients with onset longer than 12 months. In the validation cohort, the elevated CD4+EOMES+T-cell proportions and their association with NFL levels were also identified. The longitudinal study revealed that ALS patients with higher EOMES expression were associated with higher progression rates (p = .010) and worse prognosis (p = .003). CONCLUSIONS: We demonstrated that increased CD4+EOMES+T-cell subsets in ALS were associated with disease progression and poor prognosis. Identifying these associations may contribute to a better understanding of the immunopathological mechanism of ALS.

A high rain-erosion resistant bio-based nanogel with continuous immunity induction for plant virus inhibition.

Tobacco mosaic virus (TMV) is the most widely spread and harmful virus in the world, causing serious economic losses annually. However, the low anti-erosion ability of the pesticides for TMV management make it easy to be washed by the rain, which makes the effective duration of the pesticides shorter. In this paper, a new bio-based nanogel with superior antiviral activity was reported, and its slow-release behavior, rain erosion resistance and the antiviral mechanism was systematically studied. The results determined that the nanogels (Zn2+@ALGNP and Zn2+@ALGNP@PL) exhibited sustained releasing of Zn2+ with a 7 days duration, and the ε-PL coating could enhance the releasing rate of Zn2+. Moreover, Zn2+@ALGNP@PL displayed a lower contact angle, indicating greater adhesion to the leaf surface, and in consequence imposed better resistance to simulate rain erosion than pure Zn2+. Strikingly, Zn2+@ALGNP@PL could inhibit plant virus infection by aggregating the virions and reducing its coat protein stability, as well as inducing the efficient expression of reactive oxygen species, antioxidant enzymes and resistance genes to enhance plant resistance and promote plant growth. Overall, this study had successfully developed a high rain-erosion resistant bio-based nanogel capable of continue to induce resistant plants and promote plant growth.

Folate deficiency reduced aberrant level of DOT1L-mediated histone H3K79 methylation causes disruptive SHH gene expression involved in neural tube defects.

BACKGROUND: Neural tube defects (NTDs) are one of the most severe congenital abnormalities characterized by failures of the neural tube to close during early embryogenesis. Maternal folate deficiency could impact the occurrence of NTDs, however, the mechanisms involved in the cause of NTDs are poorly defined. RESULTS: Here, we report that histone H3 methyltransferase disruptor of telomeric silencing 1-like (DOT1L) expression was significantly downregulated, and low levels of H3K79me2 were found in the corresponding NTDs samples with their maternal serum folate under low levels. Using ChIP-seq assays, we found that a decrease of H3K79me2 downregulates the expression of Shh and Sufu in mouse embryonic stem cells (mESC) under folate deficiency. Interestingly, folate antagonist methotrexate treatment led to attenuation of H3K79me2 due to Dot1l, affecting Shh and Sufu genes regulation. Upon further analysis, we find that the genes Shh and Sufu are both downregulated in the brain tissues of mice and humans with NTDs. There was a positive correlation between the transcription levels of Shh, Sufu and the protein levels of DOT1L by Pearson correlation analysis. CONCLUSION: Our results indicate that abnormal Shh and Sufu genes expression reduced by aberrant Dot1l-mediated H3K79me2 levels could be the cause of NTDs occurrence.

Double whammy: the genetic variants in CECR2 and high Hcy on the development of neural tube defects.

Introduction: Neural tube defects (NTDs) are serious congenital malformations. The etiology of NTDs involves both genetic and environmental factors. Loss of CECR2 in mice has been shown to result in NTDs. Our previous study indicated that high homocysteine (HHcy) levels could further reduced the expression level of CECR2. This investigation aims to explore the genetic influence of the chromatin remodeling gene, CECR2, in humans and determine if HHcy can have a synergistic effect on protein expression. Methods: We conducted Next-Generation Sequencing (NGS) of the CECR2 gene in 373 NTD cases and 222 healthy controls, followed by functional assay application to select and evaluate CECR2 missense variants and subsequent Western blotting to identify protein expression levels. Results: From the analysis, we identified nine rare, NTD-specific mutations within the CECR2 gene. Significantly, four missense variants (p.E327V, p.T521S, p.G701R, and p.G868R) were selected via functional screening. The E9.5 mouse ectodermal stem cell line NE-4C, transfected with plasmids expressing p.E327V, p.T521S, p.G868R variants or a recombinant harboring all four (named as 4Mut), exhibited notable reductions in CECR2 protein expression. Furthermore, exposure to homocysteine thiolactone (HTL), an extremely reactive homocysteine metabolite, amplified the reduction in CECR2 expression, accompanied by a significant increase in the apoptotic molecule Caspase3 activity, a potential NTD inducer. Importantly, folic acid (FA) supplementation effectively counteracted the CECR2 expression decline induced by CECR2 mutation and HTL treatment, leading to reduced apoptosis. Discussion: Our observations underscore a synergistic relationship between HHcy and genetic variations in CECR2 concerning NTDs, thereby reinforcing the concept of gene-environment interaction phenomena in NTD etiology.

Mechanism of Gynostemmae Pentaphylli Herba in the treatment of ischemic stroke based on network pharmacology and molecular docking.

OBJECTIVES: To analyze the mechanism of Gynostemmae Pentaphylli Herba in the treatment of ischemic stroke based on network pharmacology and molecular docking. METHODS: We used various databases and software, including Cytoscape, Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform, Pubchem, Swiss Target Prediction, GenCards, String, and WebGestalt to identify the active components and targets of Gynostemmae Pentaphylli Herba, as well as the targets associated with ischemic stroke. The mechanism of Gynostemmae Pentaphylli Herba in treating ischemic stroke was analyzed from the perspective of protein-protein interaction (PPI) co-expression, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and AutoDock was used for molecular docking. RESULTS: A total of 12 active components were identified, and 276 potential targets of Gynostemmae Pentaphylli Herba were obtained. There were 3151 disease targets associated with ischemic stroke. The top 5 active components of Gynostemmae Pentaphylli Herba were Ruvoside_qt, quercetin, 3'-methyleriodictyol, Spinasterol, and Cholesterin (CLR) according to the node degree value. There were 186 common targets between the disease targets of cerebral ischemic stroke and drug targets of Gynostemmae Pentaphylli Herba, with 21 key targets obtained by PPI network analysis. KEGG analysis revealed enrichment in 45 signaling pathways. Biological process increased 139 biological processes. Molecular function enriched 17 cell functions. Cellular component enriched 20 cell components. Molecular docking found that the binding energy of other protein molecules to ligand small molecules was less than -5 kal·mol-1, except that the binding energy of AKT1 to 3'-methyleriodictyol was greater than -5 kal·mol-1. CONCLUSIONS: Gynostemmae Pentaphylli Herba may play a role in treating ischemic stroke by affecting various pathways through its active ingredients such as Ruvoside_qt, quercetin, 3'-methyleriodictyol, Spinasterol and CLR.

Additive effect of the Streptomyces albus XJC2-1 and dimethomorph control pepper blight (Capsicum annuum L.).

BACKGROUND: Pepper blight, caused by Phytophthora capsici, is a destructive soilborne disease, which poses a serious threat to pepper, Capsicum annuum L., production. Chemical fungicides, which mainly are used to control pepper blight, have a negative effect on the environment, rendering biological control as a promising alternative to maintain the balance between ecology and pest management. The purpose of this study was to screen the biocontrol bacteria, reduce the dosage of fungicides and increase the stability of biocontrol bacteria, and to find the mixing ratio of biocontrol bacteria and fungicides giving the best control effect. RESULTS: We isolated actinomycetes strains from the soil surrounding the roots of healthy pepper plants amongst field-grown plants infected with P. capsici. Of these, Streptomyces albus XJC2-1 showed a strong inhibition effect on the growth of P. capsici, with an inhibition rate of ≤85%. XJC2-1 effectively inhibited the formation of sporangium and release of zoospores of P. capsici as well as directly destroyed its hyphae, to achieve the inhibitory effect. Transcriptomic profiling of pepper leaves, postirrigation of plants with the XJC2-1 fermentation broth, revealed upregulation of genes related to the photosynthesis pathway in pepper. Furthermore, XJC2-1 treatment improved the net photosynthetic rate and intercellular CO2 concentration, thereby improving the pepper plant's resistance to pathogens. The combination of XJC2-1 with the fungicide dimethomorph (8 µg mL-1 ) displayed strong synergism in inhibition of P. capsici infection, with a control efficiency as high as 75.16%, thus providing a basis for its application in the field. CONCLUSION: Our study demonstrated that S. albus XJC2-1 inhibited Phytophthora pathogens from infecting pepper plants and enhanced plant host resistance. The combination of XJC2-1 and dimethomorph displayed a more stable and stronger control effect on pepper blight, showing potential for the future application of XJC2-1 in the field of biological control. © 2023 Society of Chemical Industry.

Fabrication of an alginate-based ZhiNengCong gel showed an enhanced antiviral and plant growth promoting functions.

Tobacco mosaic disease is a worldwide viral disease that can cause huge economic losses. Plant immune inducers have become the main force in the prevention and treatment of viral disease own to their high efficiency and rapid effect. However, since tobacco mosaic disease can occur at any point in the plant growth cycle, a single application period cannot guarantee the completely management. In this study, an extract from Paecilomyces variotii named ZhiNengCong (ZNC), which can fight against tobacco mosaic disease with 65% control effect, and improve the promotion of tobacco stem girth, was selected from five commercial antiviral medicines, and a sustained release sodium alginate (Alg)-based ZNC (ZNC@Alg) was prepared by physical absorption. ZNC@Alg, who contains only 5 mg/mL ZNC, can release ZNC for 7 consecutive days, and displayed an enhanced effect in inducing the PAL-mediated salicylic acid signaling pathway activation to participate in the inhibition of green fluorescent protein (GFP)-tagged tobacco mosaic virus (TMV-GFP) infection, even after 7 days of the application. Notably, field experiments showed that the control effect of ZNC@Alg was up to 88%, which was significantly better than that of ZNC with the same concentration (10 µg per plant). In addition, ZNC@Alg exhibited a stronger growth-promoting effect than ZNC, which significantly increased the wet weight of tobacco. Taken together, we screened out a plant immune inducer ZNC that can effectively inhibit tobacco virus disease, and created ZNC@Alg with higher control effect and growth promotion effect, laying a foundation for effective field management of tobacco mosaic disease.

Fabrication of CuO nanoparticles composite ε-polylysine-alginate nanogel for high-efficiency management of Alternaria alternate.

Although ε-poly-l-lysine (ε-PL) has a good potential as a green fungicide, high concentration is usually required during its controlling of plant disease. On the other hand, same problems also appeared in the study of CuONP based nano pesticides. In this manuscript, a new composite alginate nanogel (ALGNP) that containing CuONP and ε-PL was fabricated via in situ reduction of CuONP in nanogel and ε-PL surface coating. Based on the chelation of amide bond of ε-PL and Cu2+ released by CuONP, the synergy effect between Cu2+ and ε-PL layer of the nanogel make the nanogel (CuONP@ALGNP@PL) performed high anti-fungal activity under low Cu2+ and ε-PL concentration (Cu concentration was 40.09 µg/mL, ε-PL concentration was 11.90 µg/mL). Study showed that the nanogel could more significantly destroy the fungal cell membrane than CuONP@ALGNP and ALGNP@PL, also better than commercial fungicide CuCaSO4 (Cu concentration was 120 µg/mL). Furthermore, CuONP@ALGNP@PL could seriously affect the spore production, spore germination rate and bud tube elongation length of Alternaria alternate. Moreover, CuONP@ALGNP@PL also inhibit Botrytis cinerea, Phytophthora, Thanatephorus cucumeris and Fusarium graminearum. These results showed that composite of CuONP and ε-PL based on nanogel can decrease the raw materials application amount, and achieve a high disease controlling ability, which provides a new perspective for preventing fungal diseases.

Tobacco mosaic virus hijacks its coat protein-interacting protein IP-L to inhibit NbCML30, a calmodulin-like protein, to enhance its infection.

Calcium is an important plant immune signal that is essential for activating host resistance, but how RNA viruses manipulate calcium signals to promote their infections remains largely unknown. Here, we demonstrated that tobacco mosaic virus (TMV) coat protein (CP)-interacting protein L (IP-L) associates with calmodulin-like protein 30 (NbCML30) in the cytoplasm and nucleus, and can suppress its expression at the nucleic acid and protein levels. NbCML30, which lacks the EF-hand conserved domain and cannot bind to Ca2+ , was located in the cytoplasm and nucleus and was downregulated by TMV infection. NbCML30 silencing promoted TMV infection, while its overexpression inhibited TMV infection by activating Ca2+ -dependent oxidative stress in plants. NbCML30-mediated resistance to TMV mainly depends on IP-L regulation as the facilitation of TMV infection by silencing NbCML30 was canceled by co-silencing NbCML30 and IP-L. Overall, these findings indicate that in the absence of any reported silencing suppressor activity, TMV CP manipulates IP-L to inhibit NbCML30, influencing its Ca2+ -dependent role in the oxidative stress response. These results lay a theoretical foundation that will enable us to engineer tobacco (Nicotiana spp.) with improved TMV resistance in the future.

Transcriptome analysis reveals the mechanism of zinc ion-mediated plant resistance to TMV in Nicotiana benthamiana.

Zinc ions (Zn2+) are used to promote plant growth and treat multiple diseases. However, it is still unclear which pathways in plants respond to Zn2+. In this study, we found that supplying (CH3COO)2Zn can effectively delay tobacco mosaic virus (TMV) replication and movement in Nicotiana benthamiana. To further understand the regulatory mechanism of antiviral activity mediated by Zn2+, we examined the transcriptomic changes of leaves treated with Zn2+. Three days after treatment, 7575 differential expression genes (DEGs) were enriched in the Zn2+ treatment group compared with the control group. Through GO and KEGG analysis, the pathway of phosphatidylinositol signaling system and inositol phosphate metabolism were significantly enriched after treated with Zn2+, and a large number of ethylene-responsive transcription factors (ERFs) involved in inositol phosphate metabolism were found to be enriched. We identified ERF5 performed a positive effect on plant immunity. Our findings demonstrated that Zn2+-mediated resistance in N. benthamiana activated signal transduction and regulated the expression of resistance-related genes. The results of the study uncover a global view of mRNA changes in Zn2+-mediated cellular processes involved in the competition between plants and viruses.

Potential Pleiotropic Genes and Shared Biological Pathways in Epilepsy and Depression Based on GWAS Summary Statistics.

Current epidemiological and experimental studies have indicated the overlapping genetic foundation of epilepsy and depression. However, the detailed pleiotropic genetic etiology and neurobiological pathways have not been well understood, and there are many variants with underestimated effect on the comorbidity of the two diseases. Utilizing genome-wide association study (GWAS) summary statistics of epilepsy (15,212 cases and 29,677 controls) and depression (170,756 cases and 329,443 controls) from large consortia, we assessed the integrated gene-based association with both diseases by Multimarker Analysis of Genomic Annotation (MAGMA) and Fisher's meta-analysis. On the one hand, shared genes with significantly altered transcripts in Gene Expression Omnibus (GEO) data sets were considered as possible pleiotropic genes. On the other hand, the pathway enrichment analysis was conducted based on the gene lists with nominal significance in the gene-based association test of each disease. We identified a total of two pleiotropic genes (CD3G and SLCO3A1) with gene expression analysis validated and interpreted twenty-five common biological process supported with literature mining. This study indicates the potentially shared genes associated with both epilepsy and depression based on gene expression, meta-data analysis, and pathway enrichment strategy along with traditional GWAS and provides insights into the possible intersecting pathways that were not previously reported.

Novel Intronic Mutations of TBK1 Promote Aberrant Splicing Modes in Amyotrophic Lateral Sclerosis.

TANK-binding kinase 1 (TBK1) has been identified as a causative gene of amyotrophic lateral sclerosis (ALS) in the Caucasian population in 2015. Here, we sequenced for TBK1 variants in a cohort of 15 familial ALS (fALS) and 275 sporadic ALS (sALS) of Chinese origin by targeted next-generation sequencing. We identified one likely benign missense variant (p. Ser398Pro), two missense variants of uncertain significance (p. Ile37Leu and p. Tyr677Asn), and two novel heterozygous variants in introns of TBK1, c.1522-3T > G and c.2066 + 4A > G. We performed splicing assays through minigene plasmids and RNA pull-down assay to determine that the two substitutions of nucleotides disrupted the binding of the important splicing regulator hnRNPA1 and promoted aberrant pre-mRNA splicing modes. The c.1522-3T > G variant promoted nearly 50.0% of abnormal transcripts (3 different types of insertions and deletions (indels) in junction of intron 13-exon 14) and the c.2066 + 4A > G variant inhibited about 75.0% inclusion of exon 19, both causing premature stop codon and producing TBK1 protein without CCD2. Immunofluorescence analysis showed that the expression of TBK1 with intronic variants was lower since less TBK1 distribution was observed in HEK293T cells. Both patients carrying TBK1 c.1522-3T > G and c.2066 + 4A > G variants developed a rapidly progressive ALS, with a survival of 31 and 10 months, respectively. The frequency of loss of function (LoF) variants in TBK1 was 0.73% in sALS in our cohort. We emphasize that intronic sequencing and pre-mRNA splicing analysis cannot be ignored to demonstrate the complex mutational spectrum and pathogenesis of ALS.

Gradient-based elephant herding optimization for cluster analysis.

Clustering analysis is essential for obtaining valuable information from a predetermined dataset. However, traditional clustering methods suffer from falling into local optima and an overdependence on the quality of the initial solution. Given these defects, a novel clustering method called gradient-based elephant herding optimization for cluster analysis (GBEHO) is proposed. A well-defined set of heuristics is introduced to select the initial centroids instead of selecting random initial points. Specifically, the elephant optimization algorithm (EHO) is combined with the gradient-based algorithm GBO for assigning initial cluster centers across the search space. Second, to overcome the imbalance between the original EHO exploration and exploitation, the initialized population is improved by introducing Gaussian chaos mapping. In addition, two operators, i.e., random wandering and variation operators, are set to adjust the location update strategy of the agents. Nine datasets from synthetic and real-world datasets are adopted to evaluate the effectiveness of the proposed algorithm and the other metaheuristic algorithms. The results show that the proposed algorithm ranks first among the 10 algorithms. It is also extensively compared with state-of-the-art techniques, and four evaluation criteria of accuracy rate, specificity, detection rate, and F-measure are used. The obtained results clearly indicate the excellent performance of GBEHO, while the stability is also more prominent.