Predicting functional upstream open reading frames in Saccharomyces cerevisiae

Background  

Some upstream open reading frames (uORFs) regulate gene expression (i.e., they are functional) and can play key roles in keeping organisms healthy. However, how uORFs are involved in gene regulation is not yet fully understood. In order to get a complete view of how uORFs are involved in gene regulation, it is expected that a large number of experimentally verified functional uORFs are needed. Unfortunately, wet-experiments to verify that uORFs are functional are expensive.     

Cultivation and characterization of macrophages from murine embryonic skin. Are they Langerhans cells?

We have observed a population of trypsin-resistant adherent cells in long-term primary cultures of murine embryonic skin. These cells were subsequently demonstrated to share a variety of characteristics with cells of the monocyte/macrophage lineage. The trypsin-resistant adherent cells stained positively for nonspecific esterase, exhibited surface receptors for Fc-IgG, and complement components as well as strong phagocytic activity. Additionally, these cells exhibited membrane ATPase enzyme activity and a large proportion of the cells expressed la antigens as detected by cytotoxicity and membrane fluorescence. The possible relationship between these trypsin-resistant adherent cells and Langerhans cells of the skin is discussed.     

Alleged misconceptions' distort perceptions of environmental cancer risks.

In a series of papers, Ames and colleagues allege that the scientific and public health communities have perpetuated a series of 'misconceptions' that resulted in inaccurate identification of chemicals that pose potential human cancer risks, and misguided cancer prevention strategies and regulatory policies. They conclude that exposures to industrial and synthetic chemicals represent negligible cancer risks and that animal studies have little or no scientific value for assessing human risks. Their conclusions are based on flawed and untested assumptions. For instance, they claim that synthetic residues on food can be ignored because 99.99% of pesticides humans eat are natural, chemicals in plants are pesticides, and their potential to cause cancer equals that of synthetic pesticides. Similarly, Ames does not offer any convincing scientific evidence to justify discrediting bioassays for identifying human carcinogens. Ironically, their arguments center on a ranking procedure that relies on the same experimental data and extrapolation methods they criticize as being unreliable for evaluating cancer risks. We address their inconsistencies and flaws, and present scientific facts and our perspectives surrounding Ames' nine alleged misconceptions. Our conclusions agree with the International Agency for Research on Cancer, the National Toxicology Program, and other respected scientific organizations: in the absence of human data, animal studies are the most definitive for assessing human cancer risks. Animal data should not be ignored, and precautions should be taken to lessen human exposures. Dismissing animal carcinogenicity findings would lead to human cancer cases as the only means of demonstrating carcinogenicity of environmental agents. This is unacceptable public health policy.     

Guanine nucleotide exchange factors: Activators of the Ras superfamily of proteins

Ras proteins function as critical relay switches that regulate diverse signaling pathways between cell surface receptors and the nucleus. Over the past 2-3 years researchers have identified many components of these pathways that mediate Ras activation and effector function. Among these proteins are several guanine nucleotide exchange factors (GEFs), which are responsible for directly interacting with and activating Ras in response to extracellular stimuli. Analogous GEFs regulate Ras-related proteins that serve other diverse cellular functions. In particular, a growing family of proteins (Dbl homology proteins) has recently been identified, which may function as GEFs for the Rho family of Ras-related proteins. This review summarizes our current knowledge of the structure, biochemistry and biology of Ras and Rho family GEFs. Additionally, we describe mechanisms of GEF activation of Ras in signal transduction and address the potential that deregulated GEFs might contribute to malignant transformation through chronic Ras protein activation.     

Optimization of routine transformation of Escherichia coli with plasmid DNA

Methods to optimize resources and transformation efficiency of routine daily transformations of DH1 Escherichia coli prepared by three calcium chloride methods were investigated and compared with polyethylene glycol and Hanahan methods. The benefit of a heat-shock step, a preplating incubation step to allow expression of antibiotic resistance, use of log phase bacteria and prolonged storage of bacteria were investigated using pBR322 and pUC18 plasmid DNAs. Bacteria prepared by CaCl2 methods consistently gave efficiencies of 4 x 10(6) transformants/microgram of plasmid DNA or better and were overall the most labor- and resource-efficient methods. Use of log phase bacteria, a heat shock and an incubation step were found to be beneficial for freshly prepared bacteria for all methods. Prolonged storage of up to 30 days of bacteria prepared by the CaCl2 methods was beneficial, resulting in a sustained increase in transformation efficiency when selection was by ampicillin but not when by tetracycline resistance. Also found when using bacteria stored three days or longer was an increased transformation efficiency of stationary vs. log phase bacteria and an unchanged or even increased efficiency when the preplating incubation step was omitted. The Hanahan methods were the most labor and resource intensive and routinely gave efficiencies of 2 x 10(7). Higher efficiencies of 10(8) were obtained only with repeated trial and error and were not consistently reproducible. The polyethylene glycol method consistently gave efficiencies of 2 x 10(7), and bacteria could easily be prepared daily or frozen with a minimal decrease in efficiency.