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In this study, we aimed to identify the hub genes responsible for increased vascular endothelial cell permeability. Methods: We applied the weighted Gene Expression Omnibus (GEO) database to mine dataset GSE178331 and obtained the most relevant high-throughput sequenced genes for an increased permeability of vascular endothelial cells due to inflammation. We constructed two weighted gene co-expression network analysis (WGCNA) networks, and the differential expression of high-throughput sequenced genes related to endothelial cell permeability were screened from the GEO database. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were performed on the differential genes. Their degree values were obtained from the topological properties of protein-protein interaction (PPI) networks of differential genes, and the hub genes associated with an increased endothelial cell permeability were analyzed. Reverse transcription-polymerase chain reaction (RT-PCR) and western blotting techniques were used to detect the presence of these hub genes in TNF-α induced mRNA and the protein expression in endothelial cells. Results: In total, 1,475 differential genes were mainly enriched in the cell adhesion and TNF-α signaling pathway. With TNF-α inducing an increase in the endothelial cell permeability and significantly increasing mRNA and protein expression levels, we identified three hub genes, namely PTGS2, ICAM1, and SNAI1. There was a significant difference in the high-dose TNF-α group and in the low-dose TNF-α group compared to the control group, in the endothelial cell permeability experiment (p = 0.008 vs. p = 0.02). Measurement of mRNA and protein levels of PTGS2, ICAM1, and SNAI1 by western blotting analysis showed that there was a significant impact on TNF-α and that there was a significant dose-dependent relationship (p < 0.05 vs. p < 0.01). Conclusions: The three hub genes identified through bioinformatics analyses in the present study may serve as biomarkers of increased vascular endothelial cell permeability. The findings offer valuable insights into the progress and mechanism of vascular endothelial cell permeability. [ABSTRACT FROM AUTHOR]

Background: Fasting is the most widely prescribed and self-imposed strategy for treating excessive weight gain and obesity, and has been shown to exert a number of beneficial effects. The aim of the present study was to determine the exact role of fasting and subsequent refeeding on fat distribution in mice. Methods: C57/BL6 mice fasted for 24 to 72 h and were then subjected to refeeding for 72 h. At 24, 48 and 72 h of fasting, and 12, 24, 48 and 72 h of refeeding, the mice were sacrificed, and serum and various adipose tissues were collected. Serum biochemical parameters, adipose tissue masses and histomorphological analysis of different depots were detected. MRNA was isolated from various adipose tissues, and the expressions of thermogenesis, visceral signature and lipid metabolism-related genes were examined. The phenotypes of adipose tissues between juvenile and adult mice subjected to fasting and refeeding were also compared. Results: Fasting preferentially consumed mesenteric fat mass and decreased the cell size of mesenteric depots; however, refeeding recovered the mass and morphology of inguinal adipose tissues preferentially compared with visceral depots. Thermogenesis-related gene expression in the inguinal WAT and interscapular BAT were suppressed. Mitochondrial biogenesis was affected by fasting in a depot-specific manner. Furthermore, a short period of fasting led to an increase in visceral signature genes (Wt1, Tcf21) in subcutaneous adipose tissue, while the expression of these genes decreased sharply as the fasting time increased. Additionally, lipogenesis-related markers were enhanced to a greater extent greater in subcutaneous depots compared with those in visceral adipose tissues by refeeding. Although similar phenotypic changes in adipose tissue were observed between juvenile mice and adult mice subjected to fasting and refeeding, the alterations appeared earlier and more sensitively in juvenile mice. Conclusions: Fasting preferentially consumes lipids in visceral adipose tissues, whereas refeeding recovers lipids predominantly in subcutaneous adipose tissues, which indicated the significance of plasticity of adipose organs for fat distribution when subject to food deprivation or refeeding. [ABSTRACT FROM AUTHOR]

Doxorubicin is an anthracycline antibiotic that is among one of the most commonly used chemotherapeutic agents in the clinical setting. The usage of doxorubicin is faced with many problems including severe side effects and chemoresistance. To overcome these challenges, it is important to gain an understanding of the underlying molecular mechanisms with regards to the mode of action of doxorubicin. To facilitate this aim, we identified the genes that are required for doxorubicin resistance in the fission yeast Schizosaccharomyces pombe. We further demonstrated interplay between factors controlling various aspects of chromosome metabolism, mitochondrial respiration and membrane transport. In the nucleus we observed that the subunits of the Ino80, RSC, and SAGA complexes function in the similar epistatic group that shares significant overlap with the homologous recombination genes. However, these factors generally act in synergistic manner with the chromosome segregation regulator DASH complex proteins, possibly forming two major arms for regulating doxorubicin resistance in the nucleus. Simultaneous disruption of genes function in membrane efflux transport or the mitochondrial respiratory chain integrity in the mutants defective in either Ino80 or HR function resulted in cumulative upregulation of drug-specific growth defects, suggesting a rewiring of pathways that synergize only when the cells is exposed to the cytotoxic stress. Taken together, our work not only identified factors that are required for survival of the cells in the presence of doxorubicin but has further demonstrated that an extensive molecular crosstalk exists between these factors to robustly confer doxorubicin resistance. [ABSTRACT FROM AUTHOR]

Background: Identifying key components in biological processes and their associations is critical for deciphering cellular functions. Recently, numerous gene expression and molecular interaction experiments have been reported in Saccharomyces cerevisiae, and these have enabled systematic studies. Although a number of approaches have been used to predict gene functions and interactions, tools that analyze the essential coordination of functional components in cellular processes still need to be developed. Results: In this work, we present a new approach to study the cooperation of functional modules (sets of functionally related genes) in a specific cellular process. A cooperative module pair is defined as two modules that significantly cooperate with certain functional genes in a cellular process. This method identifies cooperative module pairs that significantly influence a cellular process and the correlated genes and interactions that are essential to that process. Using the yeast cell cycle as an example, we identified 101 cooperative module associations among 82 modules, and importantly, we established a cell cycle-specific cooperative module network. Most of the identified module pairs cover cooperative pathways and components essential to the cell cycle. We found that 14, 36, 18, 15, and 20 cooperative module pairs significantly cooperate with genes regulated in early G1, late G1, S, G2, and M phase, respectively. Fifty-nine module pairs that correlate with Cdc28 and other essential regulators were also identified. These results are consistent with previous studies and demonstrate that our methodology is effective for studying cooperative mechanisms in the cell cycle. Conclusions: In this work, we propose a new approach to identifying condition-related cooperative interactions, and importantly, we establish a cell cycle-specific cooperation module network. These results provide a global view of the cell cycle and the method can be used to discover the dynamic coordination properties of functional components in other cellular processes. [ABSTRACT FROM AUTHOR]

Background: DNA signatures are distinct short nucleotide sequences that provide valuable information that is used for various purposes, such as the design of Polymerase Chain Reaction primers and microarray experiments. Biologists usually use a discovery algorithm to find unique signatures from DNA databases, and then apply the signatures to microarray experiments. Such discovery algorithms require to set some input factors, such as signature length l and mismatch tolerance d, which affect the discovery results. However, suggestions about how to select proper factor values are rare, especially when an unfamiliar DNA database is used. In most cases, biologists typically select factor values based on experience, or even by guessing. If the discovered result is unsatisfactory, biologists change the input factors of the algorithm to obtain a new result. This process is repeated until a proper result is obtained. Implicit signatures under the discovery condition (l, d) are defined as the signatures of length ≤ l with mismatch tolerance ≥ d. A discovery algorithm that could discover all implicit signatures, such that those that meet the requirements concerning the results, would be more helpful than one that depends on trial and error. However, existing discovery algorithms do not address the need to discover all implicit signatures. Results: This work proposes two discovery algorithms - the consecutive multiple discovery (CMD) algorithm and the parallel and incremental signature discovery (PISD) algorithm. The PISD algorithm is designed for efficiently discovering signatures under a certain discovery condition. The algorithm finds new results by using previously discovered results as candidates, rather than by using the whole database. The PISD algorithm further increases discovery efficiency by applying parallel computing. The CMD algorithm is designed to discover implicit signatures efficiently. It uses the PISD algorithm as a kernel routine to discover implicit signatures efficiently under every feasible discovery condition. Conclusions: The proposed algorithms discover implicit signatures efficiently. The presented CMD algorithm has up to 97% less execution time than typical sequential discovery algorithms in the discovery of implicit signatures in experiments, when eight processing cores are used. [ABSTRACT FROM AUTHOR]

The human α-globin cluster represents a unique model of transcriptional regulation and provides challenges to the current understanding of interactions between distal and proximal regulatory elements. Although the gene proximal regions are believed to possess almost all the necessary elements for temporal and spatial specificity of gene transcription, it is still not clear whether the relative distance of embryonic ζ- and fetal/adult α-genes to their distal regulatory element α-URE plays any role in transcriptional switching. To investigate the role of gene order in regulating temporal expression, we inverted the entire structure gene region of human α-globin locus in a BAC clone bringing α-genes closest to α-URE and ζ-gene the farthest away. Expression analysis of the reverted locus in transgenic mice showed that α-globin genes, now relocated closer to α-URE, maintained their expression levels through all developmental stages. However, the ζ-globin gene suffered a total loss at both embryonic and fetal/adult stages. It indicates that proximal location of ζ-globin gene to α-URE is necessary for its normal embryonic expression and necessary to prevent embryonic expression of the α-globin gene. We proved that, in the human α-globin gene cluster, the normal order of structural genes relative to α-URE plays a crucial role in the regulation of developmental switching. [ABSTRACT FROM AUTHOR]

The β[sub 1]-adrenergic receptor (β[sub 1]AR) gene contains binding sites for myc/max proteins within a glucocorticoid response element. Transcriptional activation of the β[sub 1]AR is the result of cooperative binding between c-myc and the glucocorticoid receptor on the β[sub 1]AR promoter. The transcriptional regulation of both β[sub 1]AR and c-myc are developmentally regulated. We used transcription rate assays of nuclei isolated from fetal hearts to demonstrate a fivefold increase in the transcription rate of β[sub 1]AR vs. postnatal hearts (P < 0.01). This was associated with a fourfold increase in c-myc transcription. Transcription rate assays performed in a rat fibroblast cell line that overexpresses c-myc (myc[sup +/+]) showed similarly increased β[sub 1]AR expression compared with the wild-type cell line. Transient transfection experiments in the myc[sup +/+] cells demonstrated robust expression of β[sub 1]AR promoter constructs, which was abrogated by mutation of the myc/max binding site or by cotransfection with a c-myc antisense expression vector. These results suggest that the regulation of cardiac β[sub 1]AR transcription and the expression of c-myc are tightly integrated. [ABSTRACT FROM AUTHOR]

Resveratrol (3,4′,5-trihydroxy- trans -stilbene), a natural phytoalexin found in grapes and other food products, has promising anti-inflammatory and anticancer effects. To observe the modulation of interleukin-8 (IL-8) production in human monocytic cells by resveratrol and explore its mechanism at the gene transcription level, U937 cells were stimulated with phorbol 12-myristate 13-acetate (PMA) for 24 h. IL-8 protein in supernatants was measured by radioimmunoassay. The cytotoxicity of PMA, dexamethasone and resveratrol was accessed by MTT cell proliferation assay. The RNA level of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and IL-8 were detected by RT-PCR using specific primers. DNA binding activities of NF-κB and AP-1 were examined by electrophoretic mobility shift assay (EMSA). 0.01-100 nM PMA could significantly induce IL-8 production in U937 cells; 10 μM Dexamethasone and 10, 1, 0.1 μM resveratrol could inhibit PMA-induced IL-8 protein production and mRNA accumulation. The cytotoxicity did not contribute to their inhibitory effect. The DNA binding activity of AP-1 was inhibited by dexamethasone and resveratrol, but resveratrol has little effect on PMA-induced NF-κB activation. Resveratrol could inhibit PMA-induced IL-8 production in U937 cells at protein and mRNA levels. The suppression of IL-8 gene transcription by resveratrol was, at least partly, due to inhibition of AP-1 activation. [ABSTRACT FROM AUTHOR]

Outbreaks of avian orthoreovirus (ARV) infection with primary symptoms of arthritis/ tenosynovitis syndrome have been occurring more frequently in broiler flocks in China in recent years. This study aimed to investigate the genetic characteristics of ARV field strains in broiler flocks exhibiting arthritis/ tenosynovitis syndrome from 9 cities in Shandong province during 2015 to 2017. A total of 64 synovial and tendon samples were obtained from broilers with significant arthritis/tenosynovitis syndrome, and 21 ARV field strains were obtained. Phylogenetic analysis of the sC nt/aa sequences revealed that only 4 isolates were clustered in genotype I, including vaccine strains S1133, 1733, and most of the ARV field strains identified previously in China. Eleven and 6 ARV field isolates were identified in genotypes II and V, sharing 70.9 to 76.0% and 53.0 to 55.2% nt identities with the vaccine strains, respectively. Previous studies in China have not reported these 2 serotypes of field strains, and prevalence of these ARV variants may be increasing in Chinese broiler flocks. Results of this study suggest that large-scale investigation of epidemic ARV should be conducted to explore the genetic diversity of ARV field isolates in China. [ABSTRACT FROM AUTHOR]

Echinocandins are a family of fungal lipidated cyclic hexapeptide natural products. Due to their effectiveness as antifungal agents, three semisynthetic derivatives have been developed and approved for treatment of human invasive candidiasis. All six of the amino acid residues are hydroxylated, including 4R,5R-dihydroxy-L-ornithine, 4R-hydroxyl-l-proline, 3S,4S-dihydroxy-l-homotyrosine, and 3S-hydroxyl-4S-methyl-L-proline. We report here the biosynthetic gene cluster of echinocandin B 1 from Emericella rugulosa NRRL 11440 containing genes encoding for a six-module nonribosomal peptide synthetase EcdA, an acyl-AMP ligase EcdI, and oxygenases EcdG, EcdH, and EcdK. We showed EcdI activates linoleate as linoleyl-AMP and installs it on the first thiolation domain of EcdA. We have also established through ATP-PPi exchange assay that EcdA loads L-ornithine in the first module. A separate hty gene cluster encodes four enzymes for de novo generation of l-homotyrosine from acetyl-CoA and 4-hydroxyphenyl-pyruvate is found from the sequenced genome. Deletions in the ecdA, and htyA genes validate their essential roles in echinocandin B production. Five predicted iron-centered oxygenase genes, ecdG, ecdH, ecdK, htyE, and htyF, in the two separate ecd and hty clusters are likely to be the tailoring oxygenases for maturation of the nascent NRPS lipohexapeptidolactam product. [ABSTRACT FROM AUTHOR]