Multimodal analysis of gene expression from postmortem brains and blood identifies synaptic vesicle trafficking genes to be associated with Parkinson's disease.

OBJECTIVE: We aimed to identify key susceptibility gene targets in multiple datasets generated from postmortem brains and blood of Parkinson's disease (PD) patients and healthy controls (HC). METHODS: We performed a multitiered analysis to integrate the gene expression data using multiple-gene chips from 244 human postmortem tissues. We identified hub node genes in the highly PD-related consensus module by constructing protein-protein interaction (PPI) networks. Next, we validated the top four interacting genes in 238 subjects (90 sporadic PD, 125 HC and 23 Parkinson's Plus Syndrome (PPS)). Utilizing multinomial logistic regression analysis (MLRA) and receiver operating characteristic (ROC), we analyzed the risk factors and diagnostic power for discriminating PD from HC and PPS. RESULTS: We identified 1333 genes that were significantly different between PD and HCs based on seven microarray datasets. The identified MEturquoise module is related to synaptic vesicle trafficking (SVT) dysfunction in PD (P < 0.05), and PPI analysis revealed that SVT genes PPP2CA, SYNJ1, NSF and PPP3CB were the top four hub node genes in MEturquoise (P < 0.001). The levels of these four genes in PD postmortem brains were lower than those in HC brains. We found lower blood levels of PPP2CA, SYNJ1 and NSF in PD compared with HC, and lower SYNJ1 in PD compared with PPS (P < 0.05). SYNJ1, negatively correlated to PD severity, displayed an excellent power to discriminating PD from HC and PPS. CONCLUSIONS: This study highlights that SVT genes, especially SYNJ1, may be promising markers in discriminating PD from HCs and PPS.

A Survey of Optimization Methods for Independent Vector Analysis in Audio Source Separation.

With the advent of the era of big data information, artificial intelligence (AI) methods have become extremely promising and attractive. It has become extremely important to extract useful signals by decomposing various mixed signals through blind source separation (BSS). BSS has been proven to have prominent applications in multichannel audio processing. For multichannel speech signals, independent component analysis (ICA) requires a certain statistical independence of source signals and other conditions to allow blind separation. independent vector analysis (IVA) is an extension of ICA for the simultaneous separation of multiple parallel mixed signals. IVA solves the problem of arrangement ambiguity caused by independent component analysis by exploiting the dependencies between source signal components and plays a crucial role in dealing with the problem of convolutional blind signal separation. So far, many researchers have made great contributions to the improvement of this algorithm by adopting different methods to optimize the update rules of the algorithm, accelerate the convergence speed of the algorithm, enhance the separation performance of the algorithm, and adapt to different application scenarios. This meaningful and attractive research work prompted us to conduct a comprehensive survey of this field. This paper briefly reviews the basic principles of the BSS problem, ICA, and IVA and focuses on the existing IVA-based optimization update rule techniques. Additionally, the experimental results show that the AuxIVA-IPA method has the best performance in the deterministic environment, followed by AuxIVA-IP2, and the OverIVA-IP2 has the best performance in the overdetermined environment. The performance of the IVA-NG method is not very optimistic in all environments.

Analysis of the Potassium-Solubilizing Priestia megaterium Strain NK851 and Its Potassium Feldspar-Binding Proteins.

Potassium-solubilizing bacteria are an important microbial group that play a critical role in releasing mineral potassium from potassium-containing minerals, e.g., potassium feldspar. Their application may reduce eutrophication caused by overused potassium fertilizers and facilitate plants to utilize environmental potassium. In this study, a high-efficiency potassium-solubilizing bacterium, named NK851, was isolated from the Astragalus sinicus rhizosphere soil. This bacterium can grow in the medium with potassium feldspar as the sole potassium source, releasing 157 mg/L and 222 mg/L potassium after 3 days and 5 days of incubation, respectively. 16S rDNA sequencing and cluster analysis showed that this strain belongs to Priestia megaterium. Genome sequencing further revealed that this strain has a genome length of 5,305,142 bp, encoding 5473 genes. Among them, abundant genes are related to potassium decomposition and utilization, e.g., the genes involved in adherence to mineral potassium, potassium release, and intracellular trafficking. Moreover, the strong potassium-releasing capacity of NK851 is not attributed to the acidic pH but is attributed to the extracellular potassium feldspar-binding proteins, such as the elongation factor TU and the enolase that contains potassium feldspar-binding cavities. This study provides new information for exploration of the bacterium-mediated potassium solubilization mechanisms.

Engineered FnCas12a with enhanced activity through directional evolution in human cells.

Clustered regularly interspaced short palindromic repeat-Cas12a has been harnessed to manipulate the human genome; however, low cleavage efficiency and stringent protospacer adjacent motif hinder the use of Cas12a-based therapy and applications. Here, we have described a directional evolving and screening system in human cells to identify novel FnCas12a variants with high activity. By using this system, we identified IV-79 (enhanced activity FnCas12a, eaFnCas12a), which possessed higher DNA cleavage activity than WT FnCas12a. Furthermore, to widen the target selection spectrum, eaFnCas12a was engineered through site-directed mutagenesis. eaFnCas12a and one engineered variant (eaFnCas12a-RR), used for correcting human RS1 mutation responsible for X-linked retinoschisis, had a 3.28- to 4.04-fold improved activity compared with WT. Collectively, eaFnCas12a and its engineered variants can be used for genome-editing applications that requires high activity.

Vacuole and mitochondria patch (vCLAMP) and ER-mitochondria encounter structure (ERMES) maintain cell survival by protecting mitochondrial functions in Candida albicans.

Candida albicans is an important opportunistic fungus in the clinic. In recent years, with the widespread use of antibiotics, drug-resistant strains have been isolated in the clinic, so finding new drug targets has become an urgent problem to be solved. The vacuole and mitochondria patch (vCLAMP) and the ER-mitochondria encounter structure (ERMES) are new types of inner membrane junction systems in Saccharomyces cerevisiae. However, the functions in maintaining cell survival of the two structures have not yet been elucidated in C. albicans. In this study, VAM6 and MDM34 knockout mutants (vam6Δ/Δmet-MDM34) were constructed using an induction system regulated by the MET3 promoter. PI-positive assays showed that deletion of vCLAMP and ERMES led to abnormal growth of C. albicans. Furthermore, the vam6Δ/Δmet-MDM34 mutant exhibited obvious mitochondrial fragmentation, mtDNA damage, reduced ATP levels, and abnormal mitochondrial membrane potential, indicating its important role in maintaining the structures and functions of mitochondria. Moreover, deletion of vCLAMP and ERMES inhibited filamentous growth. Overall This study shows that vCLAMP and ERMES play important roles in maintaining the survival of C. albicans cells.

Function of the phosphatidylinositol synthase Pis1 in maintenance of endoplasmic reticulum function and pathogenicity in Candida albicans.

Candida albicans is a common conditional pathogenic fungus in the human body, and its infections have received widespread attention in recent years. Phosphatidylinositol and its derivatives have significant regulatory effects on many physiological processes, such as cell metabolism and growth. In this study, we identified and studied the function of the phosphatidylinositol synthase Pis1 in Candida albicans. The protein has a conserved CAPT motif and multiple transmembrane domains. GFP tagging revealed that Pis1 was located at the endoplasmic reticulum (ER). The PIS1 knockout mutant was constructed using an induction system regulated by the MET3 promoter. Growth assays showed that PIS1 is an essential gene for normal growth of Candida albicans. Overexpression of PIS1 led to high sensitivity to both ER stress and cell wall stress, and down-regulated expression of the genes involved in ER stress response and maintenance of cell wall integrity. Interestingly, PIS1 overexpression enhanced secretion of the extracellular hydrolases. Virulence assays further revealed that PIS1 overexpression increased the fungal virulence, leading to quicker death of the fungus-infected mice and more severe fungal burden in the mouse kidneys. In summary, Pis1 is involved in ER stress response, maintenance of cell wall integrity, and pathogenicity of Candida albicans.

Phosphate Starvation by Energy Metabolism Disturbance in Candida albicansvip1Δ/Δ Induces Lipid Droplet Accumulation and Cell Membrane Damage.

Phosphorus in the form of phosphate (Pi) is an essential element for metabolic processes, including lipid metabolism. In yeast, the inositol polyphosphate kinase vip1 mediated synthesis of inositol heptakisphosphate (IP7) regulates the phosphate-responsive (PHO) signaling pathway, which plays an important role in response to Pi stress. The role of vip1 in Pi stress and lipid metabolism of Candida albicans has not yet been studied. We found that when vip1Δ/Δ was grown in glucose medium, if Pi was supplemented in the medium or mitochondrial Pi transporter was overexpressed in the strain, the lipid droplet (LD) content was reduced and membrane damage was alleviated. However, further studies showed that neither the addition of Pi nor the overexpression of the Pi transporter affected the energy balance of vip1Δ/Δ. In addition, the LD content of vip1Δ/Δ grown in Pi limitation medium PNMC was lower than that grown in SC, and the metabolic activity of vip1Δ/Δ grown in PNMC was also lower than that grown in SC medium. This suggests that the increase in Pi demand by a high energy metabolic rate is the cause of LD accumulation in vip1Δ/Δ. In addition, in the vip1Δ/Δ strains, the core transcription factor PHO4 in the PHO pathway was transported to the vacuole and degraded, which reduced the pathway activity. However, this does not mean that knocking out vip1 completely blocks the activation of the PHO pathway, because the LD content of vip1Δ/Δ grown in the medium with ß-glycerol phosphate as the Pi source was significantly reduced. In summary, the increased Pi demand and the decreased PHO pathway activity in vip1Δ/Δ ultimately lead to LD accumulation and cell membrane damage.

The Vacuole and Mitochondria Patch (vCLAMP) Protein Vam6 is Crucial for Autophagy in Candida albicans.

Vacuole and mitochondria patches (vCLAMPs) are involved in the stress resistance of yeast, but their exact role in autophagy remains so far unclear. This study, for the first time, investigated the role of the vCLAMP core protein Vam6 in autophagy of Candida albicans. The experiments demonstrated that the deletion of VAM6 led to a growth defect under nitrogen starvation. Also, western blotting revealed that the vam6Δ/Δ mutant attenuated degradation of Atg8 (an autophagy indicator), Lap41 (an indicator of the cytoplasm to vacuole targeting pathway), and Csp37 (a mitophagy indicator). Moreover, the activity of carboxypeptidase Y and the levels of the vacuolar phospholipase Atg15 were significantly decreased in the mutant, which confirmed the defect of autophagy caused by deletion of VAM6. Overall, these results revealed that Vam6 is essential in maintaining the autophagic process under nitrogen starvation, and this provided new insights into the correlation between vCLAMPs and autophagy.

Novel role of the phosphatidylinositol phosphatase Sac1 in membrane homeostasis and polarized growth in Candida albicans.

Phosphoinositides (PIPs) are one kind of membrane components functioning in many intracellular processes, especially in signaling transduction and membrane transport. Phosphatidylinositide phosphatases (PIPases) are specifically important for the PIP homeostasis in cell. In our previous study, we have identified the actin-related protein CaSac1 in Candida albicans, while its functional mechanisms in regulating membrane homeostasis has not been identified. Here, we show that the PIPase CaSac1 is a main membrane-related protein and regulates hyphal polarization by governing phosphoinositide dynamic and plasma membrane (PM) electrostatic field. Deletion of CaSAC1 resulted in large-scale abnormal redistribution of phosphatidylinositide 4-phosphate (PI4P) from the endomembrane to the PM. This abnormality further led to disturbance of the PM's negative electrostatic field and abnormally spotted distribution of phosphatidylinositide 4,5-bisphosphate (PI(4,5)P2). These changes led to a severe defect in polarized hyphal growth, which could be diminished with recovery of the PM's negative electrostatic field by the anionic polymer polyacrylic acid (PAA). This study revealed that the PIPase CaSac1 plays an essential role in regulating membrane homeostasis and membrane traffic, contributing to establishment of polarized hyphal growth.

The V-ATPase regulates localization of the TRP Ca2+ channel Yvc1 in response to oxidative stress in Candida albicans.

The vacuolar-type H+-ATPase (V-ATPase) is a highly conserved protein complex among the eukaryotic cells. We previously revealed that both the V-ATPase and the transient receptor potential (TRP) channel Yvc1 are involved in oxidative stress response (OSR). However, the relationship between V-ATPase and Yvc1 during OSR remains unknown. In this study, disruption of the V-ATPase-encoding genes VPH2 and TFP1, similar with disruption of YVC1, caused H2O2 hypersensitivity and enhancement of vacuolar membrane permeability (VMP) under oxidative stress. Further investigations showed that unlike the wild type strain with vacuole membrane-localized Yvc1, both vph2Δ/Δ and tfp1Δ/Δ had Yvc1 localization in the vacuole cavity, indicating that disruption of VPH2 or TFP1 impaired normal vacuolar membrane-localization of Yvc1. Interestingly, addition of CaCl2 alleviated the growth defect of vph2Δ/Δ and tfp1Δ/Δ under oxidative stress, leading to prevention of VMP, decrease in ROS levels and activation of OSR. In contrast, addition of the Ca2+ chelating agent glycol-bis-(2-aminoethylether)-N,N,N',N'-tetraacetic acid (EGTA) aggravated H2O2 hypersensitivity of the mutants. These results showed that the V-ATPase plays an important role in maintenance of normal Yvc1 localization, which contributes to Ca2+ transport from the vacuoles to the cytosol for activation of OSR. This work sheds a novel light on the interaction between V-ATPase and Ca2+ transport for regulation of OSR in C. albicans.

The inositol polyphosphate kinase Ipk1 transcriptionally regulates mitochondrial functions in Candida albicans.

Inositol polyphosphates (IPs) is an important family of signaling molecules that regulate multiple cellular processes, such as chromatin remodeling, transcription and mRNA export. Inositol polyphosphate kinases, as the critical enzymes for production and transformation of IPs, directly determine the intracellular levels of IPs and therefore are involved in many cellular processes. However, its roles in Candida albicans, the leading fungal pathogen in human beings, remain to be investigated. In this study, we identified the inositol polyphosphate kinase Ipk1 in C. albicans and found that it localizes in the nucleus. Moreover, in the ipk1Δ/Δ mutant, the activity of mitochondrial respiratory chain complexes and the mitochondrial function was severely impaired, which were associated with down-regulation of mitochondrial function-related genes revealed by transcription profiling analysis. The ipk1Δ/Δ mutant also displayed hypersensitivity to a series of environmental stresses, such as antifungal drugs, oxidants, cell wall perturbing agents and macrophage attacks, followed by attenuation of virulence in a mouse systematic infection model. These findings firstly reported the importance of inositol polyphosphate kinase Ipk1 in C. albicans, especially its role in mitochondrial function maintenance and pathogenicity.

Candida albicans infection disturbs the redox homeostasis system and induces reactive oxygen species accumulation for epithelial cell death.

Candida albicans is a common pathogenic fungus with high mortality in immunocompromised patients. However, the mechanism by which C. albicans invades host epithelial cells and causes serious tissue damage remains to be further investigated. In this study, we established the C. albicans-293T renal epithelial cell interaction model to investigate the mechanism of epithelial infection by this pathogen. It was found that C. albicans infection causes severe cell death and reactive oxygen species (ROS) accumulation in epithelial cells. Further investigations revealed that C. albicans infection might up-regulate expression of nicotinamide adenine dinucleotide phosphate (NAPDH) oxidase (NOX), inhibit the activity of the antioxidant enzymes superoxide dismutase (SOD) and catalase (CAT), and suppress the p38-Nrf2-heme oxygenase-1 (HO-1) pathway which plays an important role in the elimination of intracellular ROS. Furthermore, epithelial cell death caused by the fungal infection could be strikingly alleviated by addition of the antioxidant agent glutathione, indicating the critical role of ROS accumulation in cell death caused by the fungus. This study revealed that disturbance of the redox homeostasis system and ROS accumulation in epithelial cells is involved in cell death caused by C. albicans infection, which sheds light on the application of antioxidants in the suppression of tissue damage caused by fungal infection.

Gas Sensing Properties of Cobalt Titanate with Multiscale Pore Structure: Experiment and Simulation.

A diffusion-reaction coupled model was presented to investigate the effects of multiscale pore structure characteristics on gas sensing properties. A series of CoTiO3 powders with different pore size distributions were fabricated by sol-gel method. Experimental results on cobalt titanate thick films show that a well-defined multiscale pore structure is particularly desired for the improvement of sensing performance, instead of just increasing the specific surface area. The theoretical responses of sensing elements with different pore size distributions were derived and compared with experimental data on CoTiO3 sensors exposed to ethanol. The calculated sensitivities considering the influence of pore size changes were also found to be in agreement with the experimental results. A dimensionless Thiele modulus Th was introduced for assessing the critical point corresponding to the transformation from surface reaction-controlled sensitivity into diffusion-controlled sensitivity.

Function of Atg11 in non-selective autophagy and selective autophagy of Candida albicans.

Candida albicans is an important opportunistic pathogenic fungus in the human body. It is a common microbe inhabiting on the mucosa surfaces of healthy individuals, but may cause infections when the host immune system is weak. Autophagy is a "self-eating" process in eukaryotes, which can recover and utilize damaged organelles and misfolded proteins. Here we investigated the role of the autophagy-related protein Atg11 in C. albicans. Deletion of ATG11 led to the defect in growth under the nitrogen starvation condition. Western blotting and GFP localization further revealed that the transport and degradation of Atg8 was blocked in the atg11Δ/Δ mutant under both the nitrogen starvation and hypha-inducing conditions. Moreover, degradation of both Lap41 (the indicator of the cytoplasm-to-vacuole pathway) and Csp37 (the indicator of mitophagy) was also thoroughly suppressed in this mutant under nitrogen starvation. These results indicated that Atg11 plays an essential role in both non-selective and selective autophagy in C. albicans.

Vph2 is required for protection against a reductive stress in Candida albicans.

Vph2 is a putative V-ATPase assembly factor. Our previous study has characterized its roles in localization of V-ATPase subunit, cell wall composition, hyphal development and virulence. In this study, our results further demonstrated that Vph2 was localized around the nucleus and in patches close to the periphery of the cell, indicating that Vph2 was located to the endoplasmic reticulum (ER), which was consistent with that in Saccharomyces cerevisiae. Disruption of VPH2 led to hypersensitivity to reducing stresses induced by dithiothreitol (DTT) and ß-mercaptoethanol (ß-ME), and displayed increased GSH content and up-regulation of unfolded protein response (UPR)-related genes, such as PRB1 and PMT4. However, the induced UPR and growth defect on ß-ME plates of vph2Δ/Δ mutant could be partly alleviated by the GSH-specific scavenger 1-chloro-2, 4-dinitrobenzene (CDNB). These results indicated that loss of VPH2 led to an increase in GSH levels, which induced the UPR and caused the defective growth on reductive stress induced by ß-ME. In summary, Vph2 is necessary to maintain resistance against reductive stresses.

The TRP Ca2+ channel Yvc1 regulates hyphal reactive oxygen species gradient for maintenance of polarized growth in Candida albicans.

Candida albicans is an important opportunistic fungal pathogen, and hyphal polarized growth is critical for its invasive infection to the host. Both the vacuolar transient receptor potential (TRP) Ca2+ channel Yvc1 and the NADPH oxidase Fre8-governed reactive oxygen species (ROS) gradient are involved in hyphal development, but the relationship between Yvc1 and Fre8 during hyphal polarized growth remains to be investigated. Herein, we found that deletion of YVC1 led to dispersed distribution of ROS along the germ tube, while it was concentrated at the hyphal tip in WT cells. Moreover, Fre8 localization was altered as YVC1 was disrupted. Besides, similar to deletion of YVC1, addition of the Ca2+ chelating agent EGTA caused depolarization of Fre8-GFP in the wild-type cells, indicating the critical role of Yvc1-maintained Ca2+ gradient in polarized distribution of Fre8-GFP and consequent disruption of tip ROS gradient. By constructing a series of GFP-tagged polarized growth-related proteins, including Bud6, Exo70 and Lifeact, we found that these proteins, similar to Fre8 and ROS, had depolarized localization in yvc1Δ/Δ. Thus, our work provides a mechanic explanation of Yvc1-governed and ROS-related hyphal polarized growth, and shed a novel light on the role of Ca2+ signaling in maintenance of redox homeostasis and morphogenesis in the fungal pathogens.

Endothelial Cell Inflammation and Barriers Are Regulated by the Rab26-Mediated Balance between ß2-AR and TLR4 in Pulmonary Microvessel Endothelial Cells.

Rab26 GTPase modulates the trafficking of cell surface receptors, such as G protein-coupled receptors including α2-adrenergic receptors in some cell types. However, the effect of Rab26 on ß2-adrenergic receptor (ß2-AR) trafficking or/and Toll-like receptor 4 (TLR4) expression in human pulmonary microvascular endothelial cells (HPMECs) is still unclear. Here, we investigated the role of Rab26 in regulating the expression of ß2-ARs and TLR4 in HPMECs and the effect of these receptors' imbalance on endothelial cell barrier function. The results showed that there was unbalance expression in these receptors, where ß2-AR expression was remarkably reduced, and TLR4 was increased on the cell membrane after lipopolysaccharide (LPS) treatment. Furthermore, we found that Rab26 overexpression not only upregulated ß2-ARs but also downregulated TLR4 expression on the cell membrane. Subsequently, the TLR4-related inflammatory response was greatly attenuated, and the hyperpermeability of HPMECs also was partially relived. Taken together, these data suggest that basal Rab26 maintains the balance between ß2-ARs and TLR4 on the cell surface, and it might be a potential therapeutic target for diseases involving endothelial barrier dysfunction.

Multifunction of the ER P-Type Calcium Pump Spf1 During Hyphal Development in Candida albicans.

Candida albicans is one of the most important fungal pathogens. Hyphal development is required for the virulence of this pathogen. Our previous study has revealed that Spf1, an ER P-type calcium pump, plays an important role in hyphal development. However, the detailed mechanisms by which this protein functions in this process remain to be investigated. In this study, we found that loss of Spf1 led to decreased growth biomass under the hypha-inducing condition, suggesting a role of this protein in maintaining hyphal growth rate. Actin staining further revealed that the spf1Δ/Δ mutant showed attenuated tip-localization of actin patches and the defect in transport of both the chitin synthase Chs3 and the hypha-related factor Hwp1, implying that Spf1 functions in polarized growth of the hyphae by regulating actin organization and consequent polarized transport of morphogenesis-associated factors. Moreover, deletion of SPF1 led to abnormal vacuolar morphology under the hypha-inducing condition, which may also contribute to the defect of hyphal development in the spf1Δ/Δ mutant. This study revealed the pleiotropic role of Spf1-regulated calcium homeostasis in controlling hyphal development in C. albicans.

Co3O4 nanoparticles at sublethal concentrations inhibit cell growth by impairing mitochondrial function.

Co3O4 nanoparticles (NPs) are one kind of the important nanomaterials that have the application potential in catalyst, electrochromic devices, sensors, etc. However, their biological effect remains to be detailed. In this study, we investigated the effect of the as-synthesized Co3O4 NPs (15-30 nm) on the growth of mammalian cells, and found that the NPs severely inhibited cell growth at the sublethal concentrations from 12.5 to 200 mg/L. Interestingly, the NPs did not cause obvious cell death and ROS accumulation, indicating that their inhibitory effect was not attributed to both apoptosis- or necrosis-related cell death and ROS accumulation. Transcription profiling analysis revealed that the NPs caused remarkable down regulation of the genes involved in mitochondrial functions. Transmission electron microscopy (TEM) and biochemical analysis further showed that the NPs might interact with the mitochondria, impairing the mitochondrial membrane potential (MMP) and ATP production. This study uncovers a mitochondrial respiratory chain-related and ROS-independent toxicity mechanism of Co3O4 NPs in eukaryotic cells.

Role of the mRNA export factor Sus1 in oxidative stress tolerance in Candida albicans.

In eukaryotes, the nuclear export of mRNAs is essential for gene expression. However, little is known about the role of mRNA nuclear export in the important fungal pathogen, Candida albicans. In this study, we identified C. albicans Sus1, a nucleus-localized protein that is required for mRNA export. Interestingly, the sus1Δ/Δ displayed hyper-sensitivity to extracellular oxidative stress, enhanced ROS accumulation and severe oxidative stress-related cell death. More strikingly, although the mutant exhibited normal activation of the expression of oxidative stress response (OSR) genes, it had attenuated activity of ROS scavenging system, which may be attributed to the defect in OSR mRNA export in this mutant. In addition, the virulence of the sus1Δ/Δ was seriously attenuated. Taken together, our findings provide evidence that the mRNA export factor Sus1 plays an important role in oxidative stress tolerance and pathogenesis.