DeLIVR: a deep learning approach to IV regression for testing nonlinear causal effects in transcriptome-wide association studies.

Transcriptome-wide association studies (TWAS) have been increasingly applied to identify (putative) causal genes for complex traits and diseases. TWAS can be regarded as a two-sample two-stage least squares method for instrumental variable (IV) regression for causal inference. The standard TWAS (called TWAS-L) only considers a linear relationship between a gene's expression and a trait in stage 2, which may lose statistical power when not true. Recently, an extension of TWAS (called TWAS-LQ) considers both the linear and quadratic effects of a gene on a trait, which however is not flexible enough due to its parametric nature and may be low powered for nonquadratic nonlinear effects. On the other hand, a deep learning (DL) approach, called DeepIV, has been proposed to nonparametrically model a nonlinear effect in IV regression. However, it is both slow and unstable due to the ill-posed inverse problem of solving an integral equation with Monte Carlo approximations. Furthermore, in the original DeepIV approach, statistical inference, that is, hypothesis testing, was not studied. Here, we propose a novel DL approach, called DeLIVR, to overcome the major drawbacks of DeepIV, by estimating a related but different target function and including a hypothesis testing framework. We show through simulations that DeLIVR was both faster and more stable than DeepIV. We applied both parametric and DL approaches to the GTEx and UK Biobank data, showcasing that DeLIVR detected additional 8 and 7 genes nonlinearly associated with high-density lipoprotein (HDL) cholesterol and low-density lipoprotein (LDL) cholesterol, respectively, all of which would be missed by TWAS-L, TWAS-LQ, and DeepIV; these genes include BUD13 associated with HDL, SLC44A2 and GMIP with LDL, all supported by previous studies.

Source-specific risk assessment for cadmium in wheat and maize: Towards an enrichment model for China.

Cadmium (Cd) pollution of agricultural soil is of public concern due to its high potential toxicity and mobility. This study aimed to reveal the risk of Cd accumulation in soil and wheat/maize systems, with a specific focus on the source-specific ecological risk, human health risk and Cd enrichment model. For this we investigated more than 6100 paired soil and grain samples with 216 datasets including soil Cd contents, soil pH and grain Cd contents of 85 sites from China. The results showed that mining activities, sewage irrigation, industrial activities and agricultural practices were the critical factors causing Cd accumulation in wheat and maize cultivated sites. Thereinto, mining activities contributed to a higher Cd accumulation risk in the southwest China and Middle Yellow River regions; sewage irrigation influenced the Cd accumulation in the North China Plain. In addition, the investigated sites were classified into different categories by comparing their soil and grain Cd contents with the Chinese soil screening values and food safety values, respectively. Cd enrichment models were developed to predict the Cd levels in wheat and maize grains. The results showed that the models exhibited a good performance for predicting the grain Cd contents among safe and warning sites of wheat (R2 = 0.61 and 0.72, respectively); while the well-fitted model for maize was prone to the overestimated sites (R2 = 0.77). This study will provide national viewpoints for the risk assessments and prediction of Cd accumulation in soil and wheat/maize systems.

ORANGE Represses Chloroplast Biogenesis in Etiolated Arabidopsis Cotyledons via Interaction with TCP14.

The conversion of etioplasts into chloroplasts in germinating cotyledons is a crucial transition for higher plants, enabling photoautotrophic growth upon illumination. Tight coordination of chlorophyll biosynthesis and photosynthetic complex assembly is critical for this process. ORANGE (OR), a DnaJ-like zinc finger domain-containing protein, was reported to trigger the biogenesis of carotenoid-accumulating plastids by promoting carotenoid biosynthesis and sequestration. Both nuclear and plastidic localizations of OR have been observed. Here, we show that Arabidopsis (Arabidopsis thaliana) OR physically interacts with the transcription factor TCP14 in the nucleus and represses its transactivation activity. Through this interaction, the nucleus-localized OR negatively regulates expression of EARLY LIGHT-INDUCIBLE PROTEINS (ELIPs), reduces chlorophyll biosynthesis, and delays development of thylakoid membranes in the plastids of germinating cotyledons. Nuclear abundance of OR decreased upon illumination. Together with an accumulation of TCP14 in the nucleus, this derepresses chloroplast biogenesis during de-etiolation. TCP14 is epistatic to OR and expression of ELIPs is directly regulated by the binding of TCP14 to Up1 elements in the ELIP promoter regions. Our results demonstrate that the interaction between OR and TCP14 in the nucleus leads to repression of chloroplast biogenesis in etiolated seedlings and provide new insights into the regulation of early chloroplast development.plantcell;31/12/2996/FX1F1fx1.

Induction of the ER stress response in NRVMs is linked to cardiotoxicity caused by celastrol.

Celastrol is a quinone methide triterpenoid extracted from the root bark of Tripterygium wilfordii Hook F, and it exhibits extensive biological activities such as anti-cancer effects. However, narrow therapeutic window together with undesired side effects limit its clinical application. In this study, we explore celastrol's cardiotoxicity using the methods of histology and cell biology. The results show that celastrol administration dose-dependently induces cardiac dysfunction in mice as manifested by left ventricular dilation, myocardial interstitial fibrosis, and cardiomyocyte hypertrophy. Exposure to celastrol greatly decreases neonatal rat ventricular myocyte (NRVM) viability and promotes its apoptosis. More importantly, we demonstrate that celastrol exerts its pro-apoptotic effects through endoplasmic reticulum (ER) stress and unfolded protein response. Furthermore, siRNA targeting C/EBP homologous protein, a pivotal component of ER stress-mediated apoptosis, effectively prevents the pro-apoptotic effect of celastrol. Taken together, our results demonstrate the potential cardiotoxicity of celastrol and a direct involvement of ER stress in the celastrol-induced apoptosis of NRVMs. Thus, we recommend careful evaluation of celastrol's cardiovascular effects when using it in the clinic.

The risks of sulfur addition on cadmium accumulation in paddy rice under different water-management conditions.

Recently, the application of sulfur (S) has been recommended to control the accumulation of cadmium (Cd) in rice in contaminated paddy soil. However, the effects of exogenous S on Cd transfer in paddy rice systems under different water-management practices have not been systematically investigated. Pot experiments were performed to monitor the composition of soil pore water and the Cd accumulation in iron plaque and rice tissue were compared under different S (0 and 200 mg/kg Na2SO4) and water (continuous and discontinuous flooding) treatments. Sulfur application significantly increased Cd concentrations in soil pore water under discontinuous flooding conditions, but slightly reduced them under continuous flooding. Moreover, the oxidation/reduction potential (Eh) was the most critical factor that affected the Cd levels. When the Eh exceeded -42.5 mV, S became the second critical factor, and excessive S application promoted Cd dissolution. In addition, S addition elevated the Cd levels in iron plaque and reduced the Cd transfer from the iron plaque to rice roots. In rice, S addition inhibited Cd transfer from the rice roots to the straw; thus, more Cd was stored in the rice roots. Nevertheless, additional S application increased the Cd content in the rice grains by 72% under discontinuous flooding, although this effect was mitigated by continued flooding. Under simulated practical water management conditions, S addition increased the risk of Cd contamination in rice, suggesting that S application should be reconsidered as a paddy fertilization strategy.

A graph convolutional neural network for gene expression data analysis with multiple gene networks.

Spectral graph convolutional neural networks (GCN) are proposed to incorporate important information contained in graphs such as gene networks. In a standard spectral GCN, there is only one gene network to describe the relationships among genes. However, for genomic applications, due to condition- or tissue-specific gene function and regulation, multiple gene networks may be available; it is unclear how to apply GCNs to disease classification with multiple networks. Besides, which gene networks may provide more effective prior information for a given learning task is unknown a priori and is not straightforward to discover in many cases. A deep multiple graph convolutional neural network is therefore developed here to meet the challenge. The new approach not only computes a feature of a gene as the weighted average of those of itself and its neighbors through spectral GCNs, but also extracts features from gene-specific expression (or other feature) profiles via a feed-forward neural networks (FNN). We also provide two measures, the importance of a given gene and the relative importance score of each gene network, for the genes' and gene networks' contributions, respectively, to the learning task. To evaluate the new method, we conduct real data analyses using several breast cancer and diffuse large B-cell lymphoma datasets and incorporating multiple gene networks obtained from "GIANT 2.0" Compared with the standard FNN, GCN, and random forest, the new method not only yields high classification accuracy but also prioritizes the most important genes confirmed to be highly associated with cancer, strongly suggesting the usefulness of the new method in incorporating multiple gene networks.

[Analysis of prescription regularity of traditional Chinese medicine for colorectal cancer based on data mining].

The tumor prescriptions contained in Dictionary of Tumor Formulas, Compendium of Good Tumor Formulas, Chinese Pharmacopoeia, Ministry of Health Drug Standards for Chinese Medicine Formulas and National Compilation of Standards for Proprietary Chinese Medicines were selected and organized to construct a database for tumor prescriptions, and the data mining techniques were applied to investigate the prescription regularity of colorectal cancer prescriptions. The formula data were extracted after screening in strict accordance with the inclusion and exclusion criteria, and were then analyzed with Microsoft Excel 2010 for frequency statistics, Apriori block provided by SPSS Clementine 12.0 software for correlation rule analysis, and arules and arulesViz packages in R 4.0.2 software for correlation rule visualization. In addition, SPSS 18.0 software was used for cluster analysis and factor analysis, in which cluster analysis was performed by Ochiai algorithm with bicategorical variables in systematic clustering method and factor analysis was performed mainly with principal component analysis. A total of 285 prescriptions were included in the statistical analysis, and the frequency statistics showed that 43 herbs had been used more than 16 times. The association rules analysis showed that 26 high-frequency me-dicine pair rules were obtained, and the association rules for those dispelling evil spirits, strengthening the body, resolving stasis, dispelling dampness, etc. were visualized. In the cluster analysis, we generated a dendrogram from which 7 groups of traditional Chinese medicines with homogeneity were extracted. 10 common factors were obtained in the factor analysis. The types of herbal medicines involved in the colorectal cancer prescription included anti-cancer antidotes, strengthening and tonifying medicines, blood-regulating medicines, and expectorant medicines, corresponding to the treatment for eliminating evil spirits, strengthening, resolving stasis, and expectorating dampness. The prescriptions for anti-cancer detoxification were normally based on the pairs composed of Scutellaria barbata-Hedyotis diffusa and Sophora flavescens, Sargentodoxa cuneata, S. barbata, often combined with stasis relieving drug and dampness eliminating drug, reflecting the characteristics of treatment for both toxicity and stasis, dampness and toxicity simultaneously. The prescriptions for strengthening the righteousness and tonifying the deficiency were composed of Astragalus membranaceus and Atractylodes macrocephala mainly, exerting the effect of benefiting Qi, strengthening the spleen and drying dampness, tonifying kidney and essence, tonifying blood and invigorating blood. Meanwhile, anti-cancer detoxification medicines shall be reduced as much as possible. The compatibility of the medicines for the intestinal tract reflected the principle of using the right medicine for the right condition and eliminating evil spirits or strengthening the body, as appropriate.

A simple convolutional neural network for prediction of enhancer-promoter interactions with DNA sequence data.

MOTIVATION: Enhancer-promoter interactions (EPIs) in the genome play an important role in transcriptional regulation. EPIs can be useful in boosting statistical power and enhancing mechanistic interpretation for disease- or trait-associated genetic variants in genome-wide association studies. Instead of expensive and time-consuming biological experiments, computational prediction of EPIs with DNA sequence and other genomic data is a fast and viable alternative. In particular, deep learning and other machine learning methods have been demonstrated with promising performance. RESULTS: First, using a published human cell line dataset, we demonstrate that a simple convolutional neural network (CNN) performs as well as, if no better than, a more complicated and state-of-the-art architecture, a hybrid of a CNN and a recurrent neural network. More importantly, in spite of the well-known cell line-specific EPIs (and corresponding gene expression), in contrast to the standard practice of training and predicting for each cell line separately, we propose two transfer learning approaches to training a model using all cell lines to various extents, leading to substantially improved predictive performance. AVAILABILITY AND IMPLEMENTATION: Computer code is available at https://github.com/zzUMN/Combine-CNN-Enhancer-and-Promoters. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Uptake, translocation and biotransformation of selenium nanoparticles in rice seedlings (Oryza sativa L.).

BACKGROUND: Selenium (Se) in soil mainly consists of selenite, selenate, and elemental Se. However, little is known about the mechanism involved in the uptake and biotransformation of elemental Se by plants. RESULTS: In this study, the uptake, translocation, subcellular distribution and biotransformation of selenium nanoparticles (SeNPs) in rice (Oryza sativa L.), and a comparison with selenite and selenate, were investigated through hydroponic experiments. The study revealed that SeNPs could be absorbed by rice plants; and aquaporin inhibitor was responsible for a 60.4% inhibition of SeNP influx, while metabolic inhibitor was ineffective. However, the SeNPs uptake rate of rice roots was approximately 1.7 times slower than that of selenite or selenate. Under the SeNPs or selenite treatment, Se was primarily accumulated in roots rather than in shoots, whereas an opposite trend was observed with selenate treatment. Additionally, most of the absorbed Se was distributed in cell wall of the SeNPs or selenite treated-rice plants, while its proportion was the highest in soluble cytosol of the selenate treated-rice plants. The absorbed SeNPs or selenite was rapidly assimilated to organic forms, with SeMet being the most predominant species in both shoots and roots of the rice plants. However, following selenate treatment, Se(VI) remained as the most predominant species, and only a small amount of it was converted to organic forms. CONCLUSION: Therefore, this study provides a deeper understanding of the mechanisms associated SeNPs uptake and biotransformation within plants.

Rosmarinic acid reverses non-small cell lung cancer cisplatin resistance by activating the MAPK signaling pathway.

Cisplatin (DDP) is one of the first-line chemotherapeutic agents for non-small cell lung cancer (NSCLC). However, repeated use of cisplatin in clinical practice often induces chemoresistance. The aims of this study were to investigate whether rosmarinic acid (RA) could reverse multidrug resistance (MDR) in NSCLC and to explore the underlying mechanisms. Our data demonstrated that RA significantly inhibited NSCLC cell proliferation and cell colony formation in a dose-dependent manner, induced G1 phase cell cycle arrest and apoptosis, and increased the sensitivity of cell lines resistant to DDP. Mechanistically, RA inhibited NSCLC cell growth, arrested cell cycle, and induced apoptosis by activating MAPK and inhibiting the expression of P-gp and MDR1, which correspondingly enhanced p21 and p53 expression. We observed that the growth of xenograft tumors derived from NSCLC cell lines in nude mice was significantly inhibited by combination therapy. We demonstrate that RA is a potentially effective MDR reversal agent for NSCLC, based on downregulation of MDR1 mRNA expression and P-gp. Together, these results emphasize the putative role of RA as a resistance reversal agent in NSCLC.

The Nuclear Localization of the DnaJ-Like Zinc Finger Domain-Containing Protein EDA3 Affects Seed Development in Arabidopsis thaliana.

The DnaJ-like zinc finger domain-containing proteins are involved in different aspects of plastid function and development. Some of these proteins were recently reported to have dual subcellular localization in the nucleus and plastids. One member of this family, PSA2 (AT2G34860), was found to localize to the thylakoid lumen and regulate the assembly of photosystem I (PSI). However, PSA2 was also annotated as Embryo sac Development Arrest 3 (EDA3) from the observation that its embryo sac development was arrested at the two-nuclear stage. In this study, we characterized the eda3 mutant, and demonstrated that, as compared with the wild-type (WT) plants, the mutant has shorter siliques, fewer siliques per plant, and fewer seeds per silique. Both aborted and undeveloped ovules were observed in siliques of the mutant. By immunoblot analysis, we found that, different from the chloroplast localization in mature leaves, EDA3 localizes in the nucleus in seeds. A nuclear localization signal was identified from the deduced amino acid sequence of EDA3, and also proved to be sufficient for directing its fusion peptide into the nucleus.

Accumulation of potentially toxic elements in agricultural soil and scenario analysis of cadmium inputs by fertilization: A case study in Quzhou county.

Fertilizer application has greatly increased crop yield, however impurities in mineral or organic fertilizers, such as heavy metals, are being added to agricultural soils, which would pose a high risk for soil and crop production. 115 soil samples were collected from Quzhou, a typical agricultural county in the North China Plain, to investigate the total content of cadmium (Cd), arsenic (As), lead (Pb), nickel (Ni), copper (Cu), zinc (Zn) and chromium (Cr) in soils. The contamination levels and source apportionment of studied elements were explored by the pollution indices, multivariate statistical approaches and geostatistical analysis. The ranges of Cd, As, Pb, Ni, Cu, Zn and Cr were between 0.08 and 0.35, 5.34-15.9, 7.34-38.9, 12.9-61.3, 7.80-27.0, 31.4-154, and 17.0-50.5 mg/kg and with the mean values 0.16, 9.20, 16.0, 24.7, 17.6, 61.1, and 29.5 mg/kg, respectively. The studied area was slightly polluted mainly by Cd, and higher pollution was found in soils under vegetable crops. The application of mineral phosphate fertilizer and livestock manure were the main source of Cd and Zn, and other elements (As, Pb, Ni and Cu) might originate from soil parent materials. Scenario analyses were performed using the R programming language, based on the cadmium contents in mineral phosphate fertilizers and livestock manures. The results showed that the long-term application of phosphate fertilizers would lead to some Cd enrichment in soil without risk of substantial pollution. Compared to pure mineral fertilizers, the long-term application of blended fertilizers (30% livestock manures and 70% phosphate fertilizers) or livestock manures would incur a higher Cd pollution risk within a short period, with a maximum probability of Cd risk of 55.21%. Mitigation measurements and scientific agronomic practices should be developed to minimize the risk of potential toxic elements in agricultural soil.

An in vitro and in vivo study of the role of long non-coding RNA-HOST2 in the proliferation, migration, and invasion of human glioma cells.

Gliomas are the most commonly occurring primary malignant brain tumors in the central nervous system of adults. They are rarely curable and the prognosis for high grade gliomas is generally poor. Recently, long non-coding RNA (lncRNA) human ovarian cancer-specific transcript 2 (HOST2) has been reported to be expressed at high levels in human ovarian cancer, involving tumorigenesis. However, little is still known about whether and how HOST2 regulates glioma development and progression. Therefore, this study aims to investigate the role of HOST2 in human glioma cells. Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) was used to determine the expression of lncRNA HOST2, let-7b, and PBX3 in human glioma cells. Cultured human glioma cells were treated with siRNA (si)-lncRNA HOST2, let-7b mimic, si-lncRNA HOST2 + let-7b inhibitor, and si-PBX3. Parameters including cell viability, colony formation, cell migration, and cell invasion were detected by cell counting kit-8 assay, colony formation assay, scratch test, and Transwell assay respectively to determine the effects of down-regulated HOST2 on glioma cells. Tumor formation in nude mice was evaluated by subcutaneous tumor formation experiment. Results showed that HOST2 and PBX3 were highly expressed in glioma tissue whereas let-7b was expressed at much lower levels. In response to treatment with si-lncRNA HOST2, si-PBX3, and let-7b mimic, glioma cell lines exhibited decreased cell viability, suppressed cell migration, invasion, and reduced colony formation of glioma cells. This was accompanied by an attenuated tumor formation with smaller volume and weight in nude mice, suggesting that down-regulated HOST2 could inhibit the tumorigenicity of glioma cells. Lastly, we found that lncRNA HOST2 was highly expressed in glioma tissues and its down-regulation could inhibit the growth and invasion of glioma cells. © 2018 IUBMB Life, 71(1):93-104, 2019.

Non-monotonic dose-response effects of arsenic on glucose metabolism.

BACKGROUND: Inorganic arsenic (iAs) is a widespread environmental toxin. In addition to being a human carcinogen, its effect on diabetes has started to gain recognition recently. Insulin is the key hormone regulating systemic glucose metabolism. The in vivo effect of iAs on insulin sensitivity has not been directly addressed. OBJECTIVES: Here we use mouse models to dissect the dose-dependent effects of iAs on glucose metabolism in vivo. METHODS: We performed hyperinsulinemic-euglycemic clamp, the gold standard analysis of systemic insulin sensitivity. We also performed dynamic metabolic testings and RNA-seq analysis. RESULTS: We found that a low-dose exposure (0.25 ppm iAs in drinking water) caused glucose intolerance in adult male C57BL/6 mice, likely by disrupting glucose-induced insulin secretion without affecting peripheral insulin sensitivity. However, a higher-dose exposure (2.5 ppm iAs) had diminished effects on glucose tolerance despite disrupted pancreatic insulin secretion. Insulin Clamp analysis showed that 2.5 ppm iAs actually enhanced systemic insulin sensitivity by simultaneously enhancing insulin-stimulated glucose uptake in skeletal muscles and improved insulin-mediated suppression of endogenous glucose production. RNA-seq analysis of skeletal muscles revealed that 2.5 ppm iAs regulated expression of many genes involved in the metabolism of fatty acids, pyruvate, and amino acids. CONCLUSION: These findings suggest that iAs has opposite glycemic effects on distinct metabolic tissues at different dose thresholds. Such non-monotonic dose-response effects of iAs on glucose tolerance shed light on the complex interactions between iAs and the systemic glucose metabolism, which could potentially help reconcile some of the conflicting results in human epidemiological studies.

Tanshinone IIA combined with cisplatin synergistically inhibits non-small-cell lung cancer in vitro and in vivo via down-regulating the phosphatidylinositol 3-kinase/Akt signalling pathway.

Cisplatin represents one of the first-line drugs used for non-small-cell lung cancer treatment. However, considerable side effects and the emergence of drug resistance are becoming critical limitations to its application. Combinatorial strategies may be able to extend the use of cisplatin. Both Tanshinone IIA and cisplatin inhibit non-small-cell lung cancer cell growth in a time- and dose-dependent manner. When Tanshinone IIA was combined with cisplatin at a ratio of 20:1, they were observed to exert a synergistic inhibitory effect on non-small-cell lung cancer cells. The combination treatment was shown to impair cell migration and invasion, arrest the cell cycle in the S phases, and induce apoptosis in A549 and PC9 cells in a synergistic manner. KEGG pathway analysis and molecular docking indicated that Tanshinone IIA might mainly influence the phosphatidylinositol 3-kinase-Akt signalling pathway. In all treated groups, the expression levels of Bax and cleaved Caspase-3 were up-regulated, whereas the expression levels of Bcl-2, Caspase-3, p-Akt, and p-PI3K proteins were down-regulated. Among these, the combination of Tan IIA and cisplatin exhibited the most significant difference. Tanshinone IIA may function as a novel option for combination therapy for non-small-cell lung cancer treatment.

The N-terminal pY33XL motif of CaPsy2 is critical for the function of protein phosphatase 4 in CaRad53 deactivation, DNA damage-induced filamentation and virulence in Candida albicans.

Protein phosphatase PP4 is composed of one catalytic subunit and one or two regulatory subunits and conserved in eukaryotic cells. The catalytic subunit CaPph3 forms a complex with the regulatory subunit CaPsy2, which dephosphorylates activated CaRad53 during adaptation to and recovery from MMS-mediated DNA damage. We show here that the N-terminal Y33A mutation of CaPsy2 blocks the interaction between CaPph3 and CaRad53, the deactivation of CaRad53 and the morphologic switch in recovery from genotoxic stress. In Saccharomyces cerevisiae, the ScPph3-ScPsy2-ScPsy4 complex functions to dephosphorylate γH2A. In this study, we show that CaPsy4 is a functional homolog of ScPsy4 and not involved in the deactivation of CaRad53 or CaHta, the ortholog of H2A. However, deletion of CaPSY4 causes C. albicans cells a sensitivity to genotoxic reagents and a defect in DNA damage-induced filamentation. CaPsy4 interacts with both CaPph3 and CaPsy2, but the function of CaPsy4 is independent of CaPph3 and CaPsy2 in response to genotoxic stress. C. albicans cells lacking CaPPH3, CaPSY2 or CaPSY4, and C. albicans cells carrying the Y33A mutation of CaPSY2, show increased virulence to mice. Therefore, PP4 plays a negative role in regulating the DNA damage-induced filamentation and the virulence in C. albicans.

Cloning and Functional Characterization of a Lycopene ß-Cyclase from Macrophytic Red Alga Bangia fuscopurpurea.

Lycopene cyclases cyclize the open ends of acyclic lycopene (ψ,ψ-carotene) into ß- or ε-ionone rings in the crucial bifurcation step of carotenoid biosynthesis. Among all carotenoid constituents, ß-carotene (ß,ß-carotene) is found in all photosynthetic organisms, except for purple bacteria and heliobacteria, suggesting a ubiquitous distribution of lycopene ß-cyclase activity in these organisms. In this work, we isolated a gene (BfLCYB) encoding a lycopene ß-cyclase from Bangia fuscopurpurea, a red alga that is considered to be one of the primitive multicellular eukaryotic photosynthetic organisms and accumulates carotenoid constituents with both ß- and ε-rings, including ß-carotene, zeaxanthin, α-carotene (ß,ε-carotene) and lutein. Functional complementation in Escherichia coli demonstrated that BfLCYB is able to catalyze cyclization of lycopene into monocyclic γ-carotene (ß,ψ-carotene) and bicyclic ß-carotene, and cyclization of the open end of monocyclic δ-carotene (ε,ψ-carotene) to produce α-carotene. No ε-cyclization activity was identified for BfLCYB. Sequence comparison showed that BfLCYB shares conserved domains with other functionally characterized lycopene cyclases from different organisms and belongs to a group of ancient lycopene cyclases. Although B. fuscopurpurea also synthesizes α-carotene and lutein, its enzyme-catalyzing ε-cyclization is still unknown.

CaTip41 regulates protein phosphatase 2A activity, CaRad53 deactivation and the recovery of DNA damage-induced filamentation to yeast form in Candida albicans.

Phosphorylation and dephosphorylation of the checkpoint kinase CaRad53 is crucial for fungal cells in response to genotoxic stresses. The protein phosphatase 2A (PP2A) CaPph3/CaPsy2 phosphatase complex is involved in CaRad53 dephosphorylation in Candida albicans. In view of the role of ScTip41/ScTap42 in regulating PP2A phosphatases in Saccharomyces cerevisiae, we have explored the function of CaTip41 in C. albicans. Here, we show that CaTIP41 is a functional ortholog of ScTIP41 in the sensitivity of S. cerevisiae cells to rapamycin. Deletion of CaTIP41 causes C. albicans cells to be sensitive to DNA damaging agents, methylmethane sulfonate (MMS) and cisplatin, and resistant to both rapamycin and caffeine. Accordingly, expression of CaTip41 increases in response to MMS and cisplatin. In addition, C. albicans cells lacking CaTIP41 show a delay in the recovery from MMS-induced filamentation to yeast form, decreased PP2A activity and a defect in deactivation of CaRad53 during recovery from DNA damage. Through yeast two-hybrid assay we show that CaTip41 interacts with either CaPph3, CaPsy2 or CaTap42. Therefore, CaTip41 plays regulatory roles in both the CaRad53 deactivation during recovery from DNA damage and the target of rapamycin signaling pathway.

Enhancement of immune response to a hepatitis C virus E2 DNA vaccine by an immunoglobulin Fc fusion tag.

Neutralizing antibodies and cellular immune response both play essential roles in the clearance of Hepatitis C virus (HCV) infection. The envelope glycoprotein E2 is a major target for producing neutralizing antibodies against HCV. Here, we constructed a recombinant plasmid, termed pcDNA3.1-E2-Fc, to express HCV E2 with an immunoglobulin Fc fusion tag (E2-Fc). Importantly, we found that the titers of E2-specific IgG from mice immunized with pcDNA3.1-E2-Fc were significantly higher than that from mice immunized with pcDNA3.1-E2. Moreover, pcDNA3.1-E2-Fc immunization could boost E2-specific lymphocyte proliferation and enhance the secretion of IFN-γ by lymphocytes upon in vitro stimulation with soluble E2 compared to pcDNA3.1-E2 immunization. Neutralization assays showed that serum from pcDNA3.1-E2-Fc immunized mice exhibited more effective neutralizing capacity of HCVpp entry into Huh-7 cells compared with that from pcDNA3.1-E2 immunized mice, although both of the sera could inhibit the virus entry. Taken together, our results imply that pcDNA3.1-E2-Fc immunization could enhance E2-specific humoral and cellular immune response in mice and thus provide a promising candidate for the development of an HCV vaccine.