Bioinformatic Prediction of Ultraviolet Light Mutagenesis Sensitivity of Human Genes and a Method for Genetically Engineering UVB Resistance

Living on earth, we are exposed to ultraviolet (UV) light as part of the solar radiation. UVB spectrum light exposure contributes to the development of skin cancer by interacting with pyrimidine pairs to create lesions called cyclobutane pyrimidine dimers. If these lesions are not removed by nucleotide excision repair, they often give rise to C to T transition mutations. Based on these observations, a bioinformatics approach was used to predict the vulnerability of human protein coding genes to UVB induced loss of function mutations. This data was used to evaluate in depth those genes associated with malignant melanoma. In addition, we demonstrate a method of genetically engineering genes that significantly improves resistance to UVB loss of function mutations

MAGED2: A novel p53-dissociator

The tumor suppressor protein p53 is a transcription factor that is frequently mutated in human cancers. In response to DNA damage, unmutated or wild-type (wt) p53 protein is stabilized and activated by post-transcriptional modifications that enable it to induce either apoptosis or cell cycle arrest. Using a yeast p53-dissociator assay, we identified MAGED2 as a potential negative regulator of wt p53 activity. Subsequently, using co-immunoprecipitation and reporter gene assays in human cultured cells that are often adopted for functional analysis of p53 we demonstrated that MAGED2 interacted physically with p53 and modified its activity. Finally, we were able to illustrate expression of both p53 and MAGED2 within the same subcellular compartment, i.e. either nucleus or cytoplasm, in 2,682 human cancer tissue specimens using a common cancer tissue microarray and antibodies against MAGED2 and p53. The present results implicate MAGED2, a novel protein, as a p53-dissociator

Algorithmic Discovery of Methylation “Hot Spots” in DNA from Lymphoma Patients

The computational aspects of the problem in this paper involve, firstly, selective mapping of methylated DNA clones according to methylation level and, secondly, extracting motif information from all the mapped elements in the absence of prior probability distribution. Our novel implementation of algorithms to map and maximize expectation in this setting has generated data that appear to be distinct for each lymphoma subtype examined. A “clone” represents a polymerase chain reaction (PCR) product (on average ~500 bp) which belongs to a microarray of 8544 such sequences preserving CpG-rich islands (CGIs) [1]. Accumulating evidence indicates that cancers including lymphomas demonstrate hypermethylation of CGIs “silencing” an increasing number of tumor suppressor (TS) genes which can lead to tumorigenesis

A phase 2 trial of ixabepilone plus cetuximab in first-line treatment of metastatic pancreatic cancer

BACKGROUND: The aim of this phase 2 study was to evaluate the safety and efficacy of ixabepilone plus cetuximab in patients with advanced pancreatic cancer. METHODS: Eligible patients had advanced pancreatic adenocarcinoma that was metastatic or not amenable to resection, a Karnofsky performance status ≥70%, and no prior therapy for advanced disease. Patients received ixabepilone 32 mg/m2 (3-hour IV infusion) every 3 weeks and cetuximab 250 mg/m2 (1-hour IV infusion) weekly. The primary efficacy end point was the 6-month survival rate. Secondary end points included tumor response rate, overall survival, progression- free survival, and tolerability. RESULTS: A total of 54 patients were enrolled on this study. The 6-month survival rate was 57% (31/54:95% CI: 43-71%) with a median overall survival of 7.6 months (95% CI: 5.5-12.2 months). Patients who developed acneiform rash (n = 36) had a median survival of 8.8 months, compared with 2.6 months for those without rash (n = 18). Of 31 patients with measurable disease (defined as response-evaluable), 4 had confirmed partial responses and an additional 24 had stable disease. The combination was generally well-tolerated with the most common grade 3/4 hematological toxicities being leucopenia (39%) and neutropenia (33%). The most common grade 3/4 nonhematologic toxicity was fatigue (17%). CONCLUSIONS: The combination of ixabepilone and cetuximab was active and had acceptable toxicity. The efficacy results are similar to single-agent ixabepilone and gemcitabine-based combination therapies in patients with advanced pancreatic cancer. Exploratory analyses suggest a trend toward improved survival for patients who experienced rash. Gastrointest Cancer Res 5:155-160. © 2012 by International Society of Gastrointestinal Oncology

A passive terahertz video camera based on lumped element kinetic inductance detectors

We have developed a passive 350 GHz (850 {\mu}m) video-camera to demonstrate lumped element kinetic inductance detectors (LEKIDs) -- designed originally for far-infrared astronomy -- as an option for general purpose terrestrial terahertz imaging applications. The camera currently operates at a quasi-video frame rate of 2 Hz with a noise equivalent temperature difference per frame of $\sim$0.1 K, which is close to the background limit. The 152 element superconducting LEKID array is fabricated from a simple 40 nm aluminum film on a silicon dielectric substrate and is read out through a single microwave feedline with a cryogenic low noise amplifier and room temperature frequency domain multiplexing electronics