Corrigendum: Collection and Curation of Transcriptional Regulatory Interactions in Aspergillus nidulans and Neurospora crassa Reveal Structural and Evolutionary Features of the Regulatory Networks

Transcriptional regulation has important roles in various biological processes (e.g., development and metabolism) in filamentous fungi. However, regulatory interactions between transcription factors (TFs) and their target genes in these species have only been described in different forms by primary scientific literature, which limits the integrated analysis of these data. Here, we extensively curated the reported transcriptional regulatory interactions in Aspergillus nidulans and Neurospora crassa. For each interaction, the identifiers of involved proteins or genes were unified, and the types of supporting experiments were recorded. Then, transcriptional regulatory networks were reconstructed from the interactions supported by classical low-throughput experiments. Analysis of the networks revealed the presence of hub targets regulated by multiple TFs and network motifs of other structures (e.g., regulatory loops). Comparison of the regulatory interactions between the two species identified 33 conserved interactions supported by classical experiments in both species, most of which are involved in the regulation of metabolic genes. We anticipate the curated data would serve as a catalog for the studies of transcriptional regulation in filamentous fungi

Neural Substrates of Experience in Caenorhabditis elegans Olfactory Learning

One essential function of the nervous system is to modulate behavioral response based on experience. In the past decades, increasing amount of studies has characterized the mechanisms underlying experience-dependent modulation of neural circuits. However, it is not entirely clear how the nervous system translates experience into a modulatory signal. The over-arching goal of my thesis work is to contribute to our understanding of this important neuroscience question

Improved cellulolytic efficacy in Penicilium decumbens via heterologous expression of Hypocrea jecorina endoglucanase II

Hypocrea jecorina endoglucanase II (Hjegl2) was heterologously expressed in Penicillium decumbens (yielding strain Pd::Hjegl2). After induction in cellulose containing media, strain Pd::Hjeg2 displayed increased carboxymethylcellulase activity (CMCase, 5.77 IU/ml, representing a 21% increase) and cellulose degradation determined with a filter paper assay (FPA, 0.40 IU/ml, 67% increase), as compared to the parent strain. In media supplemented with glucose (2%), Pd::Hjegl2, displayed 51.2-fold and 3-fold higher CMCase and FPA activities, respectively, as compared to the parent strain. No changes in the expression levels of the four main native cellulase genes of P. decumbens (Pdegl1, Pdegl2, Pdcbh1, and Pdcbh2) were noted between the transformant and wild-type strains. These data support the idea that Hjegl2 cleaves both internal and terminal glycosidic residues, in a relatively random and processive manner. In situ polyacrylamide gelactivity staining of extracts derived from wild-type and Pd::Hjegl2 revealed two additional active fractions in the latter strain; one with a molecular mass ~50-65 KDa and another ~80-116 kDa

Identification and Simultaneous Determination of the Main Toxical Pyrrolizidine Alkaloids in a Compound Prescription of Traditional Chinese Medicine: Qianbai Biyan Tablet

Qianbai biyan tablet (QT) is a compound prescription of traditional Chinese medicine which is used to treat nasal congestion, rhinitis, and nasosinusitis, with Senecio scandens as its main plant material. Several pyrrolizidine alkaloids (PAs) were reported in Senecio scandens and others of Senecio species. Although Senecio scandens is assigned as the legal plant material of QT, whether replaced use of it by other Senecio plants can bring toxicity is unknown because of the lack of quantitative data about toxic PAs between different Senecio species. In the present study, adonifoline, senkirkine, and another PA presumed as emiline have been identified in QT; however, there was no senecionine detected in all tablets. PA contents in QTs varied in different companies and different batches. Adonifoline existed only in Senecio scandens, and senecionine was detected in all eight Senecio plants investigated in the present study. Data showed that replaced use of Senecio scandens with a low level of senecionine by other Senecio plants such as Senecio vulgaris containing a high level of senecionine is advertised to be forbidden. Data of the present study may be used as a reference to make new drug quality regularity and recommendation guideline for the safety of QT

Study on array laterolog response simulation and mud-filtrate invasion correction

It is a complicated task to evaluate the reservoirs influenced by mud-filtrate invasion. This paper presents the numerical simulation results of array laterolog response and the approach for mud-filtrate invasion correction. Based on the differential equations and boundary conditions of the steady current field in the rock medium, the finite element method (FEM) is applied to solve the Laplace equation, then computing the potential value at each node and calculating the apparent resistivity of six measuring modes of array laterolog. Based on the numerical results, the array laterolog response is affected by many parameters including borehole radius, mud-filtrate resistivity, mud-filtrate invasion radius and invaded area resistivity. Correction charts for borehole and mud-filtrate invasion were made to quickly and accurately obtain the mud-filtrate invasion depth and the true resistivity of the uninvaded formation, which can be used to qualitatively estimate the oiliness and permeability characteristics of the formation.Cited as: Zhao, P., Qin, R., Pan, H., Ostadhassan, M., Wu, Y. Study on array laterolog response simulation and mud-filtrate invasion correction. Advances in Geo-Energy Research, 2019, 3(2): 175-186, doi: 10.26804/ager.2019.02.0

Study on array laterolog response simulation and mud-filtrate invasion correction

It is a complicated task to evaluate the reservoirs influenced by mud-filtrate invasion. This paper presents the numerical simulation results of array laterolog response and the approach for mud-filtrate invasion correction. Based on the differential equations and boundary conditions of the steady current field in the rock medium, the finite element method (FEM) is applied to solve the Laplace equation, then computing the potential value at each node and calculating the apparent resistivity of six measuring modes of array laterolog. Based on the numerical results, the array laterolog response is affected by many parameters including borehole radius, mud-filtrate resistivity, mud-filtrate invasion radius and invaded area resistivity. Correction charts for borehole and mud-filtrate invasion were made to quickly and accurately obtain the mud-filtrate invasion depth and the true resistivity of the uninvaded formation, which can be used to qualitatively estimate the oiliness and permeability characteristics of the formation

Investigation of lipid metabolism dysregulation and the effects on immune microenvironments in pan-cancer using multiple omics data.

BACKGROUND: Lipid metabolism reprogramming is a hallmark for tumor which contributes to tumorigenesis and progression, but the commonality and difference of lipid metabolism among pan-cancer is not fully investigated. Increasing evidences suggest that the alterations in tumor metabolism, including metabolite abundance and accumulation of metabolic products, lead to local immunosuppression in the tumor microenvironment. An integrated analysis of lipid metabolism in cancers from different tissues using multiple omics data may provide novel insight into the understanding of tumorigenesis and progression. RESULTS: Through systematic analysis of the multiple omics data from TCGA, we found that the most-widely altered lipid metabolism pathways in pan-cancer are fatty acid metabolism, arachidonic acid metabolism, cholesterol metabolism and PPAR signaling. Gene expression profiles of fatty acid metabolism show commonalities across pan-cancer, while the alteration in cholesterol metabolism and arachidonic acid metabolism differ with tissue origin, suggesting tissue specific lipid metabolism features in different tumor types. An integrated analysis of gene expression, DNA methylation and mutations revealed factors that regulate gene expression, including the differentially methylated sites and mutations of the lipid genes, as well as mutation and differential expression of the up-stream transcription factors for the lipid metabolism pathways. Correlation analysis of the proportion of immune cells in the tumor microenvironment and the expression of lipid metabolism genes revealed immune-related differentially expressed lipid metabolic genes, indicating the potential crosstalk between lipid metabolism and immune response. Genes related to lipid metabolism and immune response that are associated with poor prognosis were discovered including HMGCS2, GPX2 and CD36, which may provide clues for tumor biomarkers or therapeutic targets. CONCLUSIONS: Our study provides an integrated analysis of lipid metabolism in pan-cancer, highlights the perturbation of key metabolism processes in tumorigenesis and clarificates the regulation mechanism of abnormal lipid metabolism and effects of lipid metabolism on tumor immune microenvironment. This study also provides new clues for biomarkers or therapeutic targets of lipid metabolism in tumors

High fat diet significantly changed the global gene expression profile involved in hepatic drug metabolism and pharmacokinetic system in mice.

Background: High fat diet impact transcription of hepatic genes responsible for drug metabolism and pharmacokinetics. Until now, researches just focused on a couple specific genes without a global profile showing. Age-dependent manner was also not noted well. This study aims to investigate the high fat diet effect on transcriptome of drug metabolism and pharmacokinetic system in mouse livers and show the age-dependent evidence. Methods: C57BL/6 male mice were used in this experiment. High fat diet was used to treat mice for 16 and 38 weeks. Serum total cholesterol, low density lipoprotein cholesterol, aspartate transaminase, and alanine transaminaselevels were measured. Meanwhile, Histology, RNA-Seq, RT-PCR analysis and fourteen major hepatic bile acids quantification were performed for the liver tissues. Data was mined at levels of genes, drug metabolism and pharmacokinetic sysem, and genome wide. Results: Treatment with high fat diet for 38 weeks significantly increased levels of serum lipids as well as aspartate transaminase, and alanine transaminase. Meanwhile, lipid accumulation in livers was observed. At week 38 of the experiment, the profile of 612 genes involved in drug metabolism and pharmacokinetics was significantly changed, indicated by a heatmap visulization and a principal component analysis. In total 210 genes were significantly regulated. Cyp3a11, Cyp4a10, and Cyp4a14 were down-regulated by 10-35 folds, while these three genes also were highly expressed in the liver. High fat diet regulated 11% of genome-wide gene while 30% of genes involved in the hepatic drug metabolism and pharmacokinetic system. Genes, including Conclusions: High fat diet changed the global transcription profile of hepatic drug metabolism and pharmacokinetic system with a age-dependent manner

Fatty acid metabolites of Dendrobium nobile were positively correlated with representative endophytic fungi at altitude

IntroductionAltitude, as a comprehensive ecological factor, regulates the growth and development of plants and microbial distribution. Dendrobium nobile (D. nobile) planted in habitats at different elevations in Chishui city, also shows metabolic differences and endophytes diversity. What is the triangular relationship between altitude, endophytes, and metabolites?MethodsIn this study, the diversity and species of endophytic fungi were tested by ITS sequencing and metabolic differences in plants were tested by UPLC–ESI–MS/MS. Elevation regulated the colonization of plant endophytic fungal species and fatty acid metabolites in D. nobile.ResultsThe results indicate that and high altitude was better for the accumulation of fatty acid metabolites. Therefore, the high-altitude characteristic endophytic floras were screened, and the correlation with fatty acid metabolites of plants was built. The colonization of T. rubrigenum, P. Incertae sedis unclassified, Phoma. cf. nebulosa JZG 2008 and Basidiomycota unclassified showed a significantly positive correlation with fatty acid metabolites, especially 18-carbon-chain fatty acids, such as (6Z,9Z,12Z)-octadeca-6,9,12-trienoic acid, 3,7,11,15-tetramethyl-12-oxohexadeca-2,4-dienoic acid and Octadec-9-en-12-ynoic acid. What is more fascinating is these fatty acids are the essential substrates of plant hormones.DiscussionConsequently, it was speculated that the D. nobile- colonizing endophytic fungi stimulated or upregulated the synthesis of fatty acid metabolites and even some plant hormones, thus affecting the metabolism and development of D. nobile

Gypenosides Altered Hepatic Bile Acids Homeostasis in Mice Treated with High Fat Diet

Abstract Gypenosides extracted from Gynostemma pentaphyllum (Thunb.) Makino have significant role in reducing serum lipid level and treating fatty liver diseases, however, without clear mechanism. As gypenosides share the similar core structures with bile acids (the endogenous ligands of nuclear receptor FXR), we hypothesize that gypenosides may improve hypercholesterolemia via FXR-mediated bile acids signaling. The present study was designed to validate the role of gypenosides in reducing levels of serum total cholesterol (TC) and low density lipoprotein cholesterol (LDL-C), as well as in regulating bile acids homeostasis and related gene expression levels. The C57BL/6 male mice were divided into four groups. Mice in groups ND and HFD were fed with normal diet and high fat diet for 38 weeks, respectively. In groups HFD+GP and HFD+ST, mice were fed with high fat diet for 38 weeks and treated with gypenosides and simvastatin (positive control) from weeks 16 to 38, respectively. Serum TC and LDL-C levels were assayed by commercially available kits. Expression levels of genes were tested by the quantitative real-time PCR. The LC-MS/MS was applied to quantify major bile acids in mice livers. Our results showed that gypenosides significantly decreased serum TC and LDL-C levels. The gene expression level of Shp was downregulated while the levels of Cyp7a1, Cyp8b1, Fxr, Lrh1, Jnk1/2, and Erk1/2were upregulated by gypenosides. Indicated by LC-MS/MS technology, gypenosides increased the hepatic levels of several free bile acids and most taurine-conjugated bile acids while decreasing glycine-conjugated bile acids levels. In addition, gypenosides decreased the CA/CDCA ratio. Gypenosides may improve the abnormal lipid profile of HFD-fed mice via two pathways: (1) enhancing the bile acids biosynthesis from cholesterol; (2) decreasing the CA/CDCA ratio which is positively related to cholesterol absorption