The correlation between the mutation of protein kinase genes and the clinical characteristics of breast cancer progression

It is accepted that breast cancer (BC) is a heterogeneous disease. In order to investigate BC as a group of disease sub-types, the varying clinical characteristics of BC patients must be considered. In this project a series of clinical, pathological, genetic and genomic data, retrieved from multiple data repositories, will be reviewed for selection in a large-scale meta-analysis and then categorised into 5 sub-groups (Luminal A, Luminal B, Basal, HER2 and Normal). The meta-analysis is primarily designed to ascertain if a correlation exists between the mutation of protein kinase (PK) genes and BC progression. As PK genes play important roles in regulating most cellular processes (e.g. cell proliferation, differentiation and apoptosis), it is no surprise that deregulated PK activity is a frequent cause of disease, and that PK genes are often oncogenes. The meta-analysis objectives are two-fold: 1. To conduct an integrative meta-analysis of the differential gene expression of the PK gene family between clinical categories of BC progression (low vs high proliferation; luminal vs basal tissue; and grade 1 vs grade 3 tumours). Results from the meta-analysis will generate a ranked list of PK gene expression profiles observed in BC progression. 2. Through the use of powerful bioinformatics tools and sequence analysis interfaces the ranked PK list will be used to direct investigations into the correlations between: codon usage bias; aberrant epigenetic factors; somatic mutations; and observed structural/functional changes of deregulated PK genes in different BC progression categories. To address these objectives a series of in silico bioinformatics experiments have been designed. A software program (MYGEO) has been specifically written for: multiple dataset download; calculation of p-values between BC progression groups; finding Q-values to control for the false discovery rate over multiple dataset comparisons; and to perform permutation testing on the ranked PK gene list; and 2D/3D sequence analysis functions for the analysis of structure/function relationships in significantly differentiated PK genes in BC progression. This project will benefit our understanding of the complex system of BC biology by identifying significantly deregulated PK genes in BC progression. The results will identify BC biomarkers and structural/functional locations within PK genes not yet elucidated, thus providing new directions for the development of PK inhibitors and improving the effectiveness of current BC treatment strategies

Codon usage analysis of prokaryotic mechanosensation genes

[Abstract]: In the present study, we examined GC nucleotide composition, relative synonymous codon usage (RSCU), effective number of codons (ENC), codon adaptation index (CAI) and gene length for 308 prokaryotic mechanosensitive ion channel (MSC) genes from six evolutionary groups: Euryarchaeota, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, Firmicutes, and Gammaproteobacteria. Results showed that 1). a wide variation of overrepresentation of nucleotides exists in the MSC genes; 2). codon usage bias varies considerably among the MSC genes; 3). both nucleotide constraint and gene length play an important role in shaping codon usage of the bacterial MSC genes and 4). synonymous codon usage of prokaryotic MSC genes is phylogenetically conserved. Knowledge of codon usage in prokaryotic MSC genes may benefit for the study of the MSC genes in eukaryotes in which few MSC genes have been identified and functionally analysed

Response to the COVID-19 Epidemic: The Chinese Experience and Implications for Other Countries

The ongoing outbreak of the novel coronavirus disease (COVID-19) that occurred in China is rapidly spreading globally. China’s bond and strict containment measures have been proved (in practice) to significantly reduce the spread of the epidemic. This was obtained through the use of emergency control measures in the epidemic areas and the integration of resources from multiple systems, including business, community, technology, education, and transportation, across the country. In order to better understand how China has managed to reduce the public health and economic impacts of the COVID-19 epidemic, this editorial systematically reviews the specific measures for infection prevention and control of the disease. The best practices for COVID-19 eradication in China provide evidence-based strategies that could be replicated in other countries.info:eu-repo/semantics/publishedVersio

Cross-species comparison of CpG density in the promoter regions of protein kinase oncogenes

In this report, we investigated CpG density occurred in promoter regions (PRs) and downstream flanking regions (DFR) of 61 human protein kinase oncogenes (PKOs), together with other three species: chimpanzee, mouse and horse. The quantified numbers of CpGs in the PRs of human PKOs were much higher than those of chimpanzee, mouse and horse, suggesting that the CpG density changes among the four species are associated with species evolution. Human PKOs with relatively high number of CpGs in the PRs showed stronger gene expression than the mouse PKOs in tumour tissues, but not in normal tissues. Furthermore, human PKOs with extremely high density of CpGs in the PRs exhibited much lower expression in tumour tissues than in normal tissues. Our data initially suggest that the occurrence and density of CpGs in the PRs of PKOs play an important role in regulating gene expression associated with the tumorigenesis. Thus, further improvement of our understanding of the density and spatial arrangement of CpGs in the PRs of PKOs and other oncogenes involved in tumorigenesis is very important for providing preventive and therapeutic strategies for human cancer

Characterization of cross-species transcription and splicing from Penicillium to Saccharomyces cerevisiae

Heterologous expression of eukaryotic gene clusters in yeast has been widely used for producing high-value chemicals and bioactive secondary metabolites. However, eukaryotic transcription cis-elements are still undercharacterized, and the cross-species expression mechanism remains poorly understood. Here we used the whole expression unit (including original promoter, terminator, and open reading frame with introns) of orotidine 5\u27-monophosphate decarboxylases from 14 Penicillium species as a showcase, and analyzed their cross-species expression in Saccharomyces cerevisiae. We found that pyrG promoters from the Penicillium species could drive URA3 expression in yeast, and that inefficient cross-species splicing of Penicillium introns might result in weak cross-species expression. Thus, this study demonstrates cross-species expression from Penicillium to yeast, and sheds light on the opportunities and challenges of cross-species expression of fungi expression units and gene clusters in yeast without refactoring for novel natural product discovery

Attacking practical quantum key distribution system with wavelength dependent beam splitter and multi-wavelength sources

Unconditional security of quantum key distribution protocol can be guaranteed by the basic property of quantum mechanics. Unfortunately, the practical quantum key distribution system always have some imperfections, and the practical system may be attacked if the imperfection can be controlled by the eavesdropper Eve. Applying the fatal security loophole introduced by the imperfect beam splitter's wavelength dependent optical property, we propose wavelength-dependent attacking model, which can be applied to almost all practical quantum key distribution systems with the passive state modulation and photon state detection after the practical beam splitter. Utilizing our attacking model, we experimentally demonstrate the attacking system based on practical polarization encoding quantum key distribution system with almost 100% success probability. Our result demonstrate that all practical devices require tightened security inspection for avoiding side channel attacks in practical quantum key distribution experimental realizations

Resuscitation with Valproic Acid Alters Inflammatory Genes in a Porcine Model of Combined Traumatic Brain Injury and Hemorrhagic Shock

Traumatic brain injury and hemorrhagic shock (TBI+HS) elicit a complex inflammatory response that contributes to secondary brain injury. There is currently no proven pharmacologic treatment for TBI+HS, but modulation of the epigenome has been shown to be a promising strategy. The aim of this study was to investigate whether valproic acid (VPA), a histone deacetylase inhibitor, modulates the expression of cerebral inflammatory gene profiles in a large animal model of TBI+HS. Ten Yorkshire swine were subjected to computer-controlled TBI+HS (40% blood volume). After 2?h of shock, animals were resuscitated with Hextend (HEX) or HEX+VPA (300?mg/kg, n?=?5/group). Six hours after resuscitation, brains were harvested, RNA was isolated, and gene expression profiles were measured using a porcine microarray. Ingenuity Pathway Analysis? (IPA), gene ontology (GO), Parametric Gene Set Enrichment Analysis (PGSEA), and DAVID (Database for Annotation, Visualization, and Integrated Discovery) were used for pathway analysis. Key microarray findings were verified using real-time polymerase chain reaction (PCR). IPA analysis revealed that VPA significantly down-regulated the complement system (p?Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/140171/1/neu.2015.4163.pd

Semiconductor-cavity QED in high-Q regimes: Detuning effect

The non-resonant interaction between the high-density excitons in a quantum well and a single mode cavity field is investigated. An analytical expression for the physical spectrum of the excitons is obtained. The spectral properties of the excitons, which are initially prepared in the number states or the superposed states of the two different number states by the resonant femtosecond pulse pumping experiment, are studied. Numerical study of the physical spectrum is carried out and a discussion of the detuning effect is presented.Comment: 7 pages, 8 figure

The Glueball Spectrum from a Potential Model

The spectrum of two-gluon glueballs below 3 GeV is investigated in a potential model with dynamical gluon mass using variational method. The short distance potential is approximated by one-gluon exchange, while the long distance part is taken as a breakable string. The mass and size of the radial as well as orbital excitations up to principle quantum number n=3 are evaluated. The predicted mass ratios are compared with experimental and lattice results.Comment: Revtex, 6 pages with 1 eps figur