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Identification of molecular subtypes of clinically resectable triple-negative breast cancer (TNBC) is of great importance to achieve better clinical outcomes. Inter- and intratumor metabolic heterogeneity improves cancer survival, and the interaction of various metabolic pathways may affect treatment outcome of TNBC. We speculated that TNBC can be categorized into prognostic metabolic subtype according to the expression changes of glycolysis and cholesterol synthesis. The genome, transcriptome, and clinical data were downloaded from the Cancer Genome Atlas and Molecular Taxonomy of Breast Cancer International Consortium and subsequently analyzed by integrated bioinformatics methods. Four subtypes, namely, glycolytic, cholesterogenic, quiescent, and mixed, were classified according to the normalized median expressions of the genes involved in glycolysis and cholesterol synthesis. In the four subtypes, the cholesterogenic type was correlated with the shortest median survival (log rank P = 0.044), while patients with high-expressed glycolytic genes tended to have a longer survival. Tumors with PIK3CA amplification and dynein axonemal heavy chain 2 deletion exhibited higher expressions of cholesterogenic genes than other mutant oncogenes. The expressions of mitochondrial pyruvate carrier MPC1 and MPC2 were the lowest in quiescent tumor, and MPC2 expression was higher in cholesterogenic tumor compared with glycolytic or quiescent tumor ( t-test P

Identifying protein complexes in static protein-protein interaction (PPI) networks is essential for understanding the underlying mechanism of biological processes. Proteins in a complex are co-localized at the same place and co-expressed at the same time. We propose a novel method to identify protein complexes with the features of joint co-localization and joint co-expression in static PPI networks. To achieve this goal, we define a joint localization vector to construct a joint co-localization criterion of a protein group, and define a joint gene expression to construct a joint co-expression criterion of a gene group. Moreover, the functional similarity of proteins in a complex is an important characteristic. Thus, we use the CC-based, MF-based, and BP-based protein similarities to devise functional similarity criterion to determine whether a protein is functionally similar to a protein cluster. Based on the core-attachment structure and following to seed expanding strategy, we use four types of biological data including PPI data with reliability score, protein localization data, gene expression data, and gene ontology annotations, to identify protein complexes. The experimental results on yeast data show that comparing with existing methods our proposed method can efficiently and exactly identify more protein complexes, especially more protein complexes of sizes from 2 to 6. Furthermore, the enrichment analysis demonstrates that the protein complexes identified by our method have significant biological meaning.

Identification of protein complex is very important for revealing the underlying mechanism of biological processes. Many computational methods have been developed to identify protein complexes from static protein-protein interaction (PPI) networks. Recently, researchers are considering the dynamics of protein-protein interactions. Dynamic PPI networks are closer to reality in the cell system. It is expected that more protein complexes can be accurately identified from dynamic PPI networks. In this paper, we use the undulating degree above the base level of gene expression instead of the gene expression level to construct dynamic temporal PPI networks. Further we convert dynamic temporal PPI networks into dynamic Temporal Interval Protein Interaction Networks (TI-PINs) and propose a novel method to accurately identify more protein complexes from the constructed TI-PINs. Owing to preserving continuous interactions within temporal interval, the constructed TI-PINs contain more dynamical information for accurately identifying more protein complexes. Our proposed identification method uses multisource biological data to judge whether the joint colocalization condition, the joint coexpression condition, and the expanding cluster condition are satisfied; this is to ensure that the identified protein complexes have the features of colocalization, coexpression, and functional homogeneity. The experimental results on yeast data sets demonstrated that using the constructed TI-PINs can obtain better identification of protein complexes than five existing dynamic PPI networks, and our proposed identification method can find more protein complexes accurately than four other methods.

The aim of the present study was to evaluate the expression of erythropoietin (Epo) and the Epo receptor (Epo-R) in the spiral ganglion neurons (SGNs) of the rat inner ear, and to assess the effect of Epo adenovirus vector (Ad-Epo) on the spontaneous apoptosis of SGNs. A total of 60 ears from 30 healthy neonatal (2-3 days postnatal) Sprague-Dawley rats were used to examine the expression of Epo in the SGNs. The rats were divided into three groups: The negative control group, the vector control group [infected with a green fluorescent protein expression vector (Ad-GFP)] and the Ad-Epo group (infected with Ad-Epo). The expression of Epo and Epo-R was detected by immunohistochemistry and dual immunofluorescence staining using polyclonal antibodies directed against Epo and Epo-R, followed by confocal laser-scanning microscopy. An adenovirus vector was constructed and used to transfect the cultured SGNs. Following adenovirus infection, apoptosis of the SGNs was evaluated and Epo protein expression was assessed. Epo and Epo-R were widely expressed in the plasma membrane and the cytoplasm of the SGNs, as well as in the organ of Corti and the stria vascularis within the inner ear. Epo protein expression was upregulated in the Ad-Epo group compared with that in the other two groups (P

Ubiquitination is a post-translational modification that plays a crucial role during the regulation of plant immune signalling. The plant ATL family consists of a large number of putative RING type ubiquitin ligases. We show that potato ATL family gene StRFP1 and its orthologue NbATL60 from N. benthamiana both respond to Phytophthora infestans culture filtrate (CF) and flg22 induction. StRFP1 positively regulates immunity against P. infestans in potato. Ectopic transient expression of StRFP1 or expression of NbATL60 in N. benthamiana also enhances late blight resistance. By contrast, silencing NbATL60 in N. benthamiana reduces late blight resistance and leads to plant growth inhibition. Both StRFP1 and NbATL60 localize to the plasma membrane and intracellular puncta and possess E3 Ligase activity in vitro. Furthermore we demonstrate that the RING finger domain mutants of StRFP1 and NbATL60 lost E3 ligase activity and fail to suppress P. infestans colonization in N. benthamiana, indicating that E3 ligase activity is critical for StRFP1 and NbATL60 to regulate immunity. Overexpression or RNA interference of StRFP1 in transgenic potato led to increased or decreased expression of PTI maker genes (WRKY7, WRKY8, ACRE31 and Pti5) respectively. Similarly silencing of NbATL60 in N. benthamiana decreases expression of these PTI marker genes. Moreover, VIGS of NbATL60 in N. benthamiana did not compromise P. infestans PAMP INF1 or R2/Avr2, R3a/AVR3a, Rx/Cp and Pto/AvrPto triggered cell death. These results indicate that ATL genes StRFP1 and NbATL60 contribute to basal immunity (PTI) in Solanaceous plants.

The halotolerant chlorophyte Dunaliella salina can accumulate up to 10% of its dry weight as β-carotene in chloroplasts when subjected to adverse conditions, including nutrient deprivation. However, the mechanisms of carotenoid biosynthesis are poorly understood. Here, the physiological and molecular responses to the deprivation of nitrogen (-N), sulfur (-S), phosphorus (-P) and different combinations of those nutrients (-N-P, -N-S, -P-S and -N-P-S) were compared to gain insights into the underlying regulatory mechanisms of carotenoid biosynthesis. The results showed that both the growth and photosynthetic rates of cells were decreased during nutrient deprivation, accompanied by lipid globule accumulation and reduced chlorophyll levels. The SOD and CAT activities of the cells were altered during nutrient deprivation, but their responses were different. The total carotenoid contents of cells subjected to multiple nutrient deprivation were higher than those of cells subjected to single nutrient deprivation and non-stressed cells. The β-carotene contents of cells subjected to -N-P, -N-S and -N-P-S were higher than those of cells subjected to single nutrient deprivation. Cells subjected to sulfur deprivation accumulated more lutein than cells subjected to nitrogen and phosphorous deprivation. In contrast, no cumulative effects of nutrient deprivation on the transcription of genes in the carotenogenic pathway were observed because MEP and carotenogenic pathway genes were up-regulated during single nutrient deprivation but were downregulated during multiple nutrient deprivation. Therefore, we proposed that the carotenoid biosynthesis pathway of D. salina is regulated at both the transcriptional and posttranscriptional levels and that a complex crosstalk occurs at the physiological and molecular levels in response to the deprivation of different nutrients.

Background Electromagnetic fields (EMFs) used in stem-cell tissue engineering can help elucidate their biological principles. Objective The aim of this study was to investigate the effects of low-intensity EMFs on cell proliferation, differentiation, and cycle in mouse bone marrow stromal cells (BMSCs) and the in vivo effects of EMFs on BMSC. Methods Harvested BMSCs were cultured for 3 generations and divided into 4 groups. The methylthiotetrazole (MTT) assay was used to evaluate cell proliferation, and alkaline phosphatase activity was measured via a colorimetric assay on the 3rd, 7th, and 10th days. Changes in cell cycle also were analyzed on the 7th day, and bone nodule formation was analyzed on the 12th day. Additionally, the expression of the collagen I gene was examined by reverse transcription-polymerase chain reaction (RT-PCR) on the 10th day. The BMSCs of the irradiated group and the control group were transplanted into cortical bone of different mice femurs separately, with poly(lactic-co-glycolic acid) (PLGA) serving as a scaffold. After 4 and 8 weeks, bone the bone specimens of mice were sliced and stained by hematoxylin and eosin separately. Results The results showed that EMFs (0.5 mT, 50 Hz) accelerated cellular proliferation, enhanced cellular differentiation, and increased the percentage of cells in the G2/M+S (postsynthetic gap 2 period/mitotic phase + S phase) of the stimulation. The EMF-exposed groups had significantly higher collagen I messenger RNA levels than the control group. The EMF + osteogenic medium–treated group readily formed bone nodules. Hematoxylin and eosin staining showed a clear flaking of bone tissue in the irradiated group. Conclusion Irradiation of BMSCs with low-intensity EMFs (0.5 mT, 50 Hz) increased cell proliferation and induced cell differentiation. The results of this study did not establish a stricter animal model for studying osteogenesis, and only short-term results were investigated. Further study of the mechanism of EMF is needed.

SummaryPancreatic and duodenal homeobox 1 (PDX1), a member of the homeodomain-containing transcription factor family, is a key transcription factor important for both pancreas development and mature β cell function. The ectopic overexpression of Pdx1, Neurog3, and MafA in mice reprograms acinar cells to insulin-producing cells. We developed a quantitative PCR-based gene expression assay to screen more than 60,000 compounds for expression of each of these genes in the human PANC-1 ductal carcinoma cell line. We identified BRD7552, which upregulated PDX1 expression in both primary human islets and ductal cells, and induced epigenetic changes in the PDX1 promoter consistent with transcriptional activation. Prolonged compound treatment induced both insulin mRNA and protein and also enhanced insulin expression induced by the three-gene combination. These results provide a proof of principle for identifying small molecules that induce expression of transcription factors to control cellular reprogramming.

Chronic hepatitis B (CHB) is a major global health issue. The role of rare genetic variants in CHB has not been elucidated. We aimed to identify rare allelic variants predisposing to CHB. We performed exome sequencing in 50 CHB patients who had no identifiable risk factors for CHB and 40 controls who were healthy and hepatitis B surface antibody-positive, but had never received hepatitis B vaccination. We selected six rare variant alleles and followed up their association with disease status by Sanger sequencing in a case-control study comprising 1,728 CHB patients and 1,636 healthy controls. The latter had either not been immunized with hepatitis B vaccine or had uncertain vaccination status. Our results showed that transmembrane protein 2 p.Ser1254Asn, interferon alpha 2 p.Ala120Thr, its regulator NLR family member X1 p.Arg707Cys, and complement component 2 p.Glu318Asp were associated with CHB, with P values of