Comparing Climate-Change Mitigating Potentials of Alternative Synthetic Liquid Fuel Technologies Using Biomass and Coal

Presenter: Robert H. Williams, Senior Research Scientist, Princeton University, Princeton, NJ. 19 pages (includes color illustrations). Contains references

MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools

BACKGROUND: Processing raw DNA sequence data is an especially challenging task for relatively small laboratories and core facilities that produce as many as 5000 or more DNA sequences per week from multiple projects in widely differing species. To meet this challenge, we have developed the flexible, scalable, and automated sequence processing package described here. RESULTS: MAGIC-SPP is a DNA sequence processing package consisting of an Oracle 9i relational database, a Perl pipeline, and user interfaces implemented either as JavaServer Pages (JSP) or as a Java graphical user interface (GUI). The database not only serves as a data repository, but also controls processing of trace files. MAGIC-SPP includes an administrative interface, a laboratory information management system, and interfaces for exploring sequences, monitoring quality control, and troubleshooting problems related to sequencing activities. In the sequence trimming algorithm it employs new features designed to improve performance with respect to concerns such as concatenated linkers, identification of the expected start position of a vector insert, and extending the useful length of trimmed sequences by bridging short regions of low quality when the following high quality segment is sufficiently long to justify doing so. CONCLUSION: MAGIC-SPP has been designed to minimize human error, while simultaneously being robust, versatile, flexible and automated. It offers a unique combination of features that permit administration by a biologist with little or no informatics background. It is well suited to both individual research programs and core facilities

MAGIC Database and Interfaces: An Integrated Package for Gene Discovery and Expression

The rapidly increasing rate at which biological data is being produced requires a corresponding growth in relational databases and associated tools that can help laboratories contend with that data. With this need in mind, we describe here a Modular Approach to a Genomic, Integrated and Comprehensive (MAGIC) Database. This Oracle 9i database derives from an initial focus in our laboratory on gene discovery via production and analysis of expressed sequence tags (ESTs), and subsequently on gene expression as assessed by both EST clustering and microarrays. The MAGIC Gene Discovery portion of the database focuses on information derived from DNA sequences and on its biological relevance. In addition to MAGIC SEQ-LIMS, which is designed to support activities in the laboratory, it contains several additional subschemas. The latter include MAGIC Admin for database administration, MAGIC Sequence for sequence processing as well as sequence and clone attributes, MAGIC Cluster for the results of EST clustering, MAGIC Polymorphism in support of microsatellite and single-nucleotide-polymorphism discovery, and MAGIC Annotation for electronic annotation by BLAST and BLAT. The MAGIC Microarray portion is a MIAME-compliant database with two components at present. These are MAGIC Array-LIMS, which makes possible remote entry of all information into the database, and MAGIC Array Analysis, which provides data mining and visualization. Because all aspects of interaction with the MAGIC Database are via a web browser, it is ideally suited not only for individual research laboratories but also for core facilities that serve clients at any distance

Expression of a Mutant p53 Results in an Age-Related Demographic Shift in Spontaneous Lung Tumor Formation in Transgenic Mice

BACKGROUND:Mutations in the P53 gene are among the most common genetic abnormalities in human lung cancer. Codon 273 in the sequence-specific DNA binding domain is one of the most frequently mutated sites. METHODOLOGY:To investigate the role of mutant p53 in lung tumorigenesis, a lung specific p53(273H) transgenic mouse model was developed. Rates of lung cancer formation in the transgenic animals and their littermates were evaluated by necropsy studies performed in progressive age cohorts ranging from 4 to 24 months. In order to establish the influence of other common genetic abnormalities in lung tumor formation in the animals, K-Ras gene mutation and p16INK4a (p16) promoter methylation were evaluated in a total of 281 transgenic mice and 189 non-transgenic littermates. PRINCIPAL FINDINGS:At the age extremes of 4-12 and 22-24 months no differences were observed, with very low prevalence of tumors in animals younger than 12 months, and a relatively high prevalence at age 22 months or older. However, the transgenic mice had a significant higher lung tumor rate than their non-transgenic counterparts during the age of 13-21 months, suggesting an age-related shift in lung tumor formation induced by the lung-specific expression of the human mutant p53. Histopathology suggested a more aggressive nature for the transgenic tumors. Older mice (>13 months) had a significantly higher rate of p16 promoter methylation (17% v 82%). In addition, an age related effect was observed for K-Ras codons 12 or 13 mutations, but not for codon 61 mutations. CONCLUSIONS/SIGNIFICANCE:These results would suggest that the mutant p53(273H) contributes to an acceleration in the development of spontaneous lung tumors in these mice. Combination with other genetic and epigenetic alterations occurring after the age of 13 months is intimately linked to its oncogenic potential

Silicon Layer Intercalation of Centimeter-Scale, Epitaxially-Grown Monolayer Graphene on Ru(0001)

We develop a strategy for graphene growth on Ru(0001) followed by silicon-layer intercalation that not only weakens the interaction of graphene with the metal substrate but also retains its superlative properties. This G/Si/Ru architecture, produced by silicon-layer intercalation approach (SIA), was characterized by scanning tunneling microscopy/spectroscopy and angle resolved electron photoemission spectroscopy. These experiments show high structural and electronic qualities of this new composite. The SIA allows for an atomic control of the distance between the graphene and the metal substrate that can be used as a top gate. Our results show potential for the next generation of graphene-based materials with tailored properties.Comment: 13 pages, 4 figures, to be published in Appl. Phys. Let

Measurements of the Cross Section for e+e- -> hadrons at Center-of-Mass Energies from 2 to 5 GeV

We report values of $R = \sigma(e^+e^-\to {hadrons})/\sigma(e^+e^-\to\mu^+\mu^-)$ for 85 center-of-mass energies between 2 and 5 GeV measured with the upgraded Beijing Spectrometer at the Beijing Electron-Positron Collider.Comment: 5 pages, 3 figure

On the Road to 6G: Visions, Requirements, Key Technologies and Testbeds

Fifth generation (5G) mobile communication systems have entered the stage of commercial development, providing users with new services and improved user experiences as well as offering a host of novel opportunities to various industries. However, 5G still faces many challenges. To address these challenges, international industrial, academic, and standards organizations have commenced research on sixth generation (6G) wireless communication systems. A series of white papers and survey papers have been published, which aim to define 6G in terms of requirements, application scenarios, key technologies, etc. Although ITU-R has been working on the 6G vision and it is expected to reach a consensus on what 6G will be by mid-2023, the related global discussions are still wide open and the existing literature has identified numerous open issues. This paper first provides a comprehensive portrayal of the 6G vision, technical requirements, and application scenarios, covering the current common understanding of 6G. Then, a critical appraisal of the 6G network architecture and key technologies is presented. Furthermore, existing testbeds and advanced 6G verification platforms are detailed for the first time. In addition, future research directions and open challenges are identified for stimulating the on-going global debate. Finally, lessons learned to date concerning 6G networks are discussed

Poly I:C enhances cycloheximide-induced apoptosis of tumor cells through TLR3 pathway

<p>Abstract</p> <p>Background</p> <p>Toll-like receptor 3 (TLR3) is a critical component of the innate immune response to dsRNA viruses, which was considered to be mainly expressed in immune cells and some endothelial cells. In this study, we investigated the expression and proapoptotic activity of TLR3 in human and murine tumor cell lines.</p> <p>Methods</p> <p>RT-PCR and FACS analysis were used to detect expression of TLR3 in various human and murine tumor cell lines. All tumor cell lines were cultured with poly I:C, CHX, or both for 12 h, 24 h, 72 h, and then the cell viability was analyzed with CellTiter 96^®AQueous One Solution, the apoptosis was measured by FACS with Annexin V and PI staining. Production of Type I IFN in poly I:C/CHX mediated apoptosis were detected through western blotting. TLR3 antibodies and IFN-β antibodies were used in Blockade and Neutralization Assay.</p> <p>Results</p> <p>We show that TLR3 are widely expressed on human and murine tumor cell lines, and activation of TLR3 signaling in cancerous cells by poly I:C made Hela cells (human cervical cancer) and MCA38 cells (murine colon cancer) become dose-dependently sensitive to protein synthesis inhibitor cycloheximide (CHX)-induced apoptosis. Blockade of TLR3 recognition with anti-TLR3 antibody greatly attenuated the proapoptotic effects of poly I:C on tumor cells cultured with CHX. IFN-β production was induced after poly I:C/CHX treatment and neutralization of IFN-β slightly reduced poly I:C/CHX -induced apoptosis.</p> <p>Conclusion</p> <p>Our study demonstrated the proapoptotic activity of TLR3 expressed by various tumor cells, which may open a new range of clinical applications for TLR3 agonists as an adjuvant of certain cancer chemotherapy.</p