Genomes of the Most Dangerous Epidemic Bacteria Have a Virulence Repertoire Characterized by Fewer Genes but More Toxin-Antitoxin Modules

We conducted a comparative genomic study based on a neutral approach to identify genome specificities associated with the virulence capacity of pathogenic bacteria. We also determined whether virulence is dictated by rules, or if it is the result of individual evolutionary histories. We systematically compared the genomes of the 12 most dangerous pandemic bacteria for humans ("bad bugs") to their closest non-epidemic related species ("controls").We found several significantly different features in the "bad bugs", one of which was a smaller genome that likely resulted from a degraded recombination and repair system. The 10 Cluster of Orthologous Group (COG) functional categories revealed a significantly smaller number of genes in the "bad bugs", which lacked mostly transcription, signal transduction mechanisms, cell motility, energy production and conversion, and metabolic and regulatory functions. A few genes were identified as virulence factors, including secretion system proteins. Five "bad bugs" showed a greater number of poly (A) tails compared to the controls, whereas an elevated number of poly (A) tails was found to be strongly correlated to a low GC% content. The "bad bugs" had fewer tandem repeat sequences compared to controls. Moreover, the results obtained from a principal component analysis (PCA) showed that the "bad bugs" had surprisingly more toxin-antitoxin modules than did the controls.We conclude that pathogenic capacity is not the result of "virulence factors" but is the outcome of a virulent gene repertoire resulting from reduced genome repertoires. Toxin-antitoxin systems could participate in the virulence repertoire, but they may have developed independently of selfish evolution

The Compartmentalized Bacteria of the Planctomycetes-Verrucomicrobia-Chlamydiae Superphylum Have Membrane Coat-Like Proteins

Compartmentalized bacteria have proteins that are structurally related to eukaryotic membrane coats, and one of these proteins localizes at the membrane of vesicles formed inside bacterial cells

Biotic interactions as drivers of algal origin and evolution

Biotic interactions underlie life's diversity and are the lynchpin to understanding its complexity and resilience within an ecological niche. Algal biologists have embraced this paradigm, and studies building on the explosive growth in omics and cell biology methods have facilitated the in-depth analysis of nonmodel organisms and communities from a variety of ecosystems. In turn, these advances have enabled a major revision of our understanding of the origin and evolution of photosynthesis in eukaryotes, bacterial–algal interactions, control of massive algal blooms in the ocean, and the maintenance and degradation of coral reefs. Here, we review some of the most exciting developments in the field of algal biotic interactions and identify challenges for scientists in the coming years. We foresee the development of an algal knowledgebase that integrates ecosystem-wide omics data and the development of molecular tools/resources to perform functional analyses of individuals in isolation and in populations. These assets will allow us to move beyond mechanistic studies of a single species towards understanding the interactions amongst algae and other organisms in both the laboratory and the field

Bicistronic and Stable Expression of Human Coagulation Factor IX and Enhanced Green Fluorescent Protein in Suspension-Adapted Chinese Hamster Ovary Cells

Background and Aim: The current treatment for hemophilia B is replacement therapy, which involves the intravenous infusion of human coagulation factor IX (hFIX) purified from plasma or a recombinant form produced in mammalian cells. In this study, using a bicistronic expression system, the stable expression of the hFIX in a serum-free and suspension-adapted Chinese hamster ovary cell line (CHO-s) was investigated. Materials and Methods: A DNA fragment consisting of hFIX, Internal Ribosome Entry Site (IRES) and Enhanced Green Fluorescent Protein (EGFP) nucleotide sequences was cloned into pcDNA3.1 expression plasmid under the control of Cytomegalovirus (CMV) promoter. The bicistronic plasmid was then linearized using BglII restriction enzyme and transfected into CHO-s cells. The transfected cells were treated with geneticin for 14 days. The culture medium of the stable cells was then collected and the expression level of the hFIX were examined using western blotting and ELISA. The coagulation activity was also evaluated by the chromogenic method. Results: The recombinant CHO-s cells resistant to geneticin were observed under a fluorescence microscope in green color, which indicated the expression and accumulation of the EGFP in the cytoplasm of the cells. The results of Western blotting confirmed the expression and secretion of the hFIX into the culture medium. The amount of the secreted hFIX was 150 ng/mL/106cells with a coagulation activity of 5.6 ±0.2 mU/mL. Conclusion: Our findings demonstrated that this bicistronic expression system could simultaneously produce EGFP and hFIX in CHO-s cells. This expression system facilitates selection and isolation of hFIX-expressing cells

Expression of biologically active human clotting factor IX in Drosophila S2 cells: ?-carboxylation of a human vitamin K-dependent protein by the insect enzyme

Thrombosis and Hemostasi

Functional expression of the human coagulation factor IX using heterologous signal peptide and propeptide sequences in mammalian cell line

Thrombosis and Hemostasi

Establishment of a CALU, AURKA, and MCM2 gene panel for discrimination of metastasis from primary colon and lung cancers.

Metastasis is known as a key step in cancer recurrence and could be stimulated by multiple factors. Calumenin (CALU) is one of these factors which has a direct impact on cancer metastasis and yet, its underlined mechanisms have not been completely elucidated. The current study was aimed to identify CALU co-expressed genes, their signaling pathways, and expression status within the human cancers. To this point, CALU associated genes were visualized using the Cytoscape plugin BisoGenet and annotated with the Enrichr web-based application. The list of CALU related diseases was retrieved using the DisGenNet, and cancer datasets were downloaded from The Cancer Genome Atlas (TCGA) and analyzed with the Cufflink software. ROC curve analysis was used to estimate the diagnostic accuracy of DEGs in each cancer, and the Kaplan-Meier survival analysis was performed to plot the overall survival of patients. The protein level of the signature biomarkers was measured in 40 biopsy specimens and matched adjacent normal tissues collected from CRC and lung cancer patients. Analysis of CALU co-expressed genes network in TCGA datasets indicated that the network is markedly altered in human colon (COAD) and lung (LUAD) cancers. Diagnostic accuracy estimation of differentially expressed genes showed that a gene panel consisted of CALU, AURKA, and MCM2 was able to successfully distinguish cancer tumors from healthy samples. Cancer cases with abnormal expression of the signature genes had a significantly lower survival rate than other patients. Additionally, comparison of CALU, AURKA, and MCM2 proteins between healthy samples, early and advanced tumors showed that the level of these proteins was increased through normal-carcinoma transition in both types of cancers. These data indicate that the interactions between CALU, AURKA, and MCM2 has a pivotal role in cancer development, and thereby needs to be explored in the future

Expression of the human coagulation factor IX in the bone marrow mesenchymal stem cells

Background: Mesenchymal stem cells (MSCs) are appropriate target for gene and cell-based therapy of hemophilia B patients. MSCs possess several unique properties such as capability of differentiating into multiple lineages and lower immunogenecity in transplant procedure that make them attractive candidates for cell and gene therapy. One of the challenges in the gene therapy is the low expression level of transgene. To improve expression, strong regulatory elements in the context of vectors could contribute to improve efficacy of gene therapy strategies. In this study four human factor IX (hFIX)-expressing plasmids equipped with various combination of human -globin (hBG) introns and Kozak sequence were transfected into the MSCs and expression of the hFIX was evaluated in vitro. Material and Methods: MSCs were obtained from tibias and the femora of rats and phenotypic characterization of the MSCs was determined by flow cytometry. Four hFIX-expressing plasmids were introduced into the culture-expanded MSCs using transfection agent. 48 hours after transfection, ability of the MSCs for expression of the hFIX and efficacies of the plasmids were evaluated by performing sandwich ELISA on cultured media as well as semi-quantitative RT-PCR. All analyses were performed with One-way ANOVA using SPSS software. Results:The highest expression level of the hFIX was obtained from intron-less and hBG intron-I containing construct. The highest biological activity was obtained from hBG intron-I,II containing construct. Conclusion:Successful expression of the hFIX was obtained from recombinant MSCs. MSCs were able to splice heterologous hBG intron-I from the hFIX-cDNA. Application of thehBG introns reduced the hFIX expression levels, probably due to improper splicing of the hBG introns