Cell Cycle Regulation by Chlamydomonas Cyclin-Dependent Protein Kinases

Identification of genes associated with abiotic stress tolerance in sweetpotato using weighted gene co-expression network analysis

Sweetpotato, Ipomoea batatas (L.), a key food security crop, is negatively impacted by heat, drought, and salinity stress. The orange-fleshed sweetpotato cultivar "Beauregard" was exposed to heat, salt, and drought treatments for 24 and 48 h to identify genes responding to each stress condition in leaves. Analysis revealed both common (35 up regulated, 259 down regulated genes in the three stress conditions) and unique sets of up regulated (1337 genes by drought, 516 genes by heat, and 97 genes by salt stress) and down regulated (2445 genes by drought, 678 genes by heat, and 204 genes by salt stress) differentially expressed genes (DEGs) suggesting common, yet stress-specific transcriptional responses to these three abiotic stressors. Gene Ontology analysis of down regulated DEGs common to both heat and salt stress revealed enrichment of terms associated with "cell population proliferation" suggestive of an impact on the cell cycle by the two stress conditions. To identify shared and unique gene co-expression networks under multiple abiotic stress conditions, weighted gene co-expression network analysis was performed using gene expression profiles from heat, salt, and drought stress treated 'Beauregard' leaves yielding 18 co-expression modules. One module was enriched for "response to water deprivation," "response to abscisic acid," and "nitrate transport" indicating synergetic crosstalk between nitrogen, water, and phytohormones with genes encoding osmotin, cell expansion, and cell wall modification proteins present as key hub genes in this drought-associated module. This research lays the groundwork for exploring to a further degree, mechanisms for abiotic stress tolerance in sweetpotato.

Identification of core genes as potential biomarkers for predicting progression and prognosis in glioblastoma

Background: Glioblastoma is a common malignant neuroepithelial neoplasm with poor clinical outcomes and limited treatment options. It is extremely important to search and confirm diverse hub genes that are effective in the advance and prediction of glioblastoma.

Methods: We analyzed GSE50161, GSE4290, and GSE68848, the three microarray datasets retrieved from the GEO database. GO function and KEGG pathway enrichment analyses for differentially expressed genes (DEGs) were performed using DAVID. The PPI network of the DEGs was analyzed using the Search Tool for the Retrieval of Interacting Genes database and visualized by Cytoscape software. Hub genes were identified through the PPI network and a robust rank aggregation method. The Cancer Genome Atlas (TCGA) and the Oncomine database were used to validate the hub genes. In addition, a survival curve analysis was conducted to verify the correlation between the expression of hub genes and patient prognosis. Human glioblastoma cells and normal cells were collected, and then RT-PCR, Western blot, and immunofluorescence were conducted to validate the expression of the NDC80 gene. A cell proliferation assay was used to detect the proliferation of glioma cells. The effects of NDC80 expression on migration and invasion of GBM cell lines were evaluated by conducting scratch and transwell assays.

Results: A total of 716 DEGs were common to all three microarray datasets, which included 188 upregulated DEGs and 528 downregulated DEGs. Furthermore, we found that among the common DEGs, 10 hub genes showed a high degree of connectivity. The expression of the 10 hub genes in TCGA and the Oncomine database was significantly overexpressed in glioblastoma compared with normal genes. Additionally, the survival analysis showed that the patients with low expression of six genes (BIR5C, CDC20, NDC80, CDK1, TOP2A, and MELK) had a significantly favorable prognosis (p < 0.01). We discovered that NDC80, which has been shown to be important in other cancers, also has an important role in malignant gliomas. The RT-PCR, Western blot, and immunofluorescence results showed that the expression level of NDC80 was significantly higher in human glioblastoma cells than in normal cells. Moreover, we identified that NDC80 increased the proliferation and invasion abilities of human glioblastoma cells.

Conclusion: The six genes identified here may be utilized to form a panel of disease progression and predictive biomarkers of glioblastoma for clinical purposes. NDC80, one of the six genes, was discovered to have a potentially important role in GBM, a finding that needs to be further studied.

Reviewing cancer's biology: an eclectic approach

BACKGROUND

Cancer refers to a group of some of the worldwide most diagnosed and deadliest pathophysiological conditions that conquered researchers' attention for decades and yet begs for more questions for a full comprehension of its complex cellular and molecular pathology.

MAIN BODY

The disease conditions are commonly characterized by unrestricted cell proliferation and dysfunctional replicative senescence pathways. In fact, the cell cycle operates under the rigorous control of complex signaling pathways involving cyclins and cyclin-dependent kinases assumed to be specific to each phase of the cycle. At each of these checkpoints, the cell is checked essentially for its DNA integrity. Genetic defects observed in these molecules (i.e., cyclins, cyclin-dependent kinases) are common features of cancer cells. Nevertheless, each cancer is different concerning its molecular and cellular etiology. These could range from the genetic defects mechanisms and/or the environmental conditions favoring epigenetically harbored homeostasis driving tumorigenesis alongside with the intratumoral heterogeneity with respect to the model that the tumor follows.

CONCLUSIONS

This review is not meant to be an exhaustive interpretation of carcinogenesis but to summarize some basic features of the molecular etiology of cancer and the intratumoral heterogeneity models that eventually bolster anticancer drug resistance for a more efficient design of drug targeting the pitfalls of the models.

Cell Synchronization Enhances Nuclear Transformation and Genome Editing via Cas9 Enabling Homologous Recombination in Chlamydomonas reinhardtii

In Chlamydomonas reinhardtii, the model organism for eukaryotic green algae and plants, the processes of nuclear transformation and genome editing in particular are still marked by a low level of efficiency, and so intensive work is required in order to create and identify mutants for the investigation of basic physiological processes, as well as the implementation of biotechnological applications. In this work, we show that cell synchronization during the stages of the cell cycle, obtained from long-term cultivation under specific growth conditions, greatly enhances the efficiency of transformation and allows the identification of DNA repair mechanisms that occur preferentially at different stages of the cell cycle. We demonstrate that the transformation of synchronized cells at different times was differentially associated with nonhomologous end joining (NHEJ) and/or homologous recombination (HR), and makes it possible to knock-in specific foreign DNA at the genomic nuclear location desired by exploiting HR. This optimization greatly reduces the overall complexity of the genome editing procedure and creates new opportunities for altering genes and their products.