The promoters of human cell cycle genes integrate signals from two tumor suppressive pathways during cellular transformation

Deciphering regulatory events that drive malignant transformation represents a major challenge for systems biology. Here we analyzed genome-wide transcription profiling of an in-vitro transformation process. We focused on a cluster of genes whose expression levels increased as a function of p53 and p16INK4A tumor suppressors inactivation. This cluster predominantly consists of cell cycle genes and constitutes a signature of a diversity of cancers. By linking expression profiles of the genes in the cluster with the dynamic behavior of p53 and p16INK4A, we identified a promoter architecture that integrates signals from the two tumor suppressive channels and that maps their activity onto distinct levels of expression of the cell cycle genes, which in turn, correspond to different cellular proliferation rates. Taking components of the mitotic spindle as an example, we experimentally verified our predictions that p53-mediated transcriptional repression of several of these novel targets is dependent on the activities of p21, NFY and E2F. Our study demonstrates how a well-controlled transformation process allows linking between gene expression, promoter architecture and activity of upstream signaling molecules.Comment: To appear in Molecular Systems Biolog

Airports at Risk: The Impact of Information Sources on Security Decisions

Security decisions in high risk organizations such as airports involve obtaining ongoing and frequent information about potential threats. Utilizing questionnaire survey data from a sample of airport employees in European Airports across the continent, we analyzed how both formal and informal sources of security information affect employee's decisions to comply with the security rules and directives. This led us to trace information network flows to assess its impact on the degree employees making security decisions comply or deviate with the prescribed security rules. The results of the multivariate analysis showed that security information obtained through formal and informal networks differentially determine if employee will comply or not with the rules. Information sources emanating from the informal network tends to encourage employees to be more flexible in their security decisions while formal sources lead to be more rigid with complying with rules and protocols. These results suggest that alongside the formal administrative structure of airports, there exists a diverse and pervasiveness set of informal communications networks that are a potent factor in determining airport security levels

Waves of potentiality: Some thoughts on database narratives and the digital dissemination of audio-visual practice research

I'm currently completing the dissemination stage of my practice/research (P/R) AHRC Fellowship in the Creative and Performing Arts. The ‘outcomes’ of the project include a linear finished film, some text in the form of articles, along with the selection of other materials, including rushes, stills and more text (both academic writing, article journals and more speculative/creative material)

Delineation of Cohen Syndrome Following a Large-Scale Genotype-Phenotype Screen

Cohen syndrome is an autosomal recessive condition associated with developmental delay, facial dysmorphism, pigmentary retinopathy, and neutropenia. The pleiotropic phenotype, combined with insufficient clinical data, often leads to an erroneous diagnosis and has led to confusion in the literature. Here, we report the results of a comprehensive genotype-phenotype study on the largest cohort of patients with Cohen syndrome assembled to date. We found 22 different COH1 mutations, of which 19 are novel, in probands identified by our diagnostic criteria. In addition, we identified another three novel mutations in patients with incomplete clinical data. By contrast, no COH1 mutations were found in patients with a provisional diagnosis of Cohen syndrome who did not fulfill the diagnostic criteria (“Cohen-like” syndrome). This study provides a molecular confirmation of the clinical phenotype associated with Cohen syndrome and provides a basis for laboratory screening that will be valuable in its diagnosis

Wide-Scale Analysis of Human Functional Transcription Factor Binding Reveals a Strong Bias towards the Transcription Start Site

We introduce a novel method to screen the promoters of a set of genes with shared biological function, against a precompiled library of motifs, and find those motifs which are statistically over-represented in the gene set. The gene sets were obtained from the functional Gene Ontology (GO) classification; for each set and motif we optimized the sequence similarity score threshold, independently for every location window (measured with respect to the TSS), taking into account the location dependent nucleotide heterogeneity along the promoters of the target genes. We performed a high throughput analysis, searching the promoters (from 200bp downstream to 1000bp upstream the TSS), of more than 8000 human and 23,000 mouse genes, for 134 functional Gene Ontology classes and for 412 known DNA motifs. When combined with binding site and location conservation between human and mouse, the method identifies with high probability functional binding sites that regulate groups of biologically related genes. We found many location-sensitive functional binding events and showed that they clustered close to the TSS. Our method and findings were put to several experimental tests. By allowing a "flexible" threshold and combining our functional class and location specific search method with conservation between human and mouse, we are able to identify reliably functional TF binding sites. This is an essential step towards constructing regulatory networks and elucidating the design principles that govern transcriptional regulation of expression. The promoter region proximal to the TSS appears to be of central importance for regulation of transcription in human and mouse, just as it is in bacteria and yeast.Comment: 31 pages, including Supplementary Information and figure

Morbidity and Mortality After Benign Prostatic Hyperplasia Surgery: Data from the American College of Surgeons National Surgical Quality Improvement Program

Background and Purpose: With the aging population, it is becoming increasingly important to identify patients at risk for postsurgical complications who might be more suited for conservative treatment. We sought to identify predictors of morbidity after surgical treatment of benign prostatic hyperplasia (BPH) using a large national contemporary population-based cohort. Methods: Relying on the American College of Surgeons National Surgical-Quality Improvement Program (ACS-NSQIP; 2006?2011) database, we evaluated outcomes after transurethral resection of the prostate (TURP), laser vaporization of the prostate (LVP), and laser enucleation of the prostate (LEP). Outcomes included blood-transfusion rates, length of stay, complications, reintervention rates, and perioperative mortality. Multivariable logistic-regression analysis evaluated the predictors of perioperative morbidity and mortality. Results: Overall, 4794 (65.2%), 2439 (33.1%), and 126 (1.7%) patients underwent TURP, LVP, and LEP, respectively. No significant difference in overall complications (P=0.3) or perioperative mortality (P=0.5) between the three surgical groups was found. LVP was found to be associated with decreased blood transfusions (odds ratio [OR]=0.21; P=0.001), length of stay (OR=0.12; P30%) levels were the only predictors of lower overall complications and perioperative mortality. Conclusions: All three surgical modalities for BPH management were found to be safe. Advanced age and non-Caucasian race were independent predictors of adverse outcomes after BPH surgery. In patients with these attributes, conservative treatment might be a reasonable alternative. Also, preoperative hematocrit and albumin levels represent reliable predictors of adverse outcomes, suggesting that these markers should be evaluated before BPH surgery.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/140378/1/end.2013.0805.pd

Prompt, early, and afterglow optical observations of five gamma-ray bursts (GRBs 100901A, 100902A, 100905A, 100906A, and 101020A)

We present results of the prompt, early, and afterglow optical observations of five gamma-ray bursts, GRBs 100901A, 100902A, 100905A, 100906A, and 101020A, made with the Mobile Astronomical System of TElescope-Robots in Russia (MASTER-II net), the 1.5-m telescope of Sierra-Nevada Observatory, and the 2.56-m Nordic Optical Telescope. For two sources, GRB 100901A and GRB 100906A, we detected optical counterparts and obtained light curves starting before cessation of gamma-ray emission, at 113 s and 48 s after the trigger, respectively. Observations of GRB 100906A were conducted with two polarizing filters. Observations of the other three bursts gave the upper limits on the optical flux; their properties are briefly discussed. More detailed analysis of GRB 100901A and GRB 100906A supplemented by Swift data provides the following results and indicates different origins of the prompt optical radiation in the two bursts. The light curves patterns and spectral distributions suggest a common production site of the prompt optical and high-energy emission in GRB 100901A. Results of spectral fits for GRB 100901A in the range from the optical to X-rays favor power-law energy distributions with similar values of the optical extinction in the host galaxy. GRB 100906A produced a smoothly peaking optical light curve suggesting that the prompt optical radiation in this GRB originated in a front shock. This is supported by a spectral analysis. We have found that the Amati and Ghirlanda relations are satisfied for GRB 100906A. An upper limit on the value of the optical extinction on the host of GRB 100906A is obtained.Comment: 18 pages, 14 figures, 14 tables, 5 machine readable tables; accepted for publication in MNRA