Alkyltransferase-like proteins

Recent in silico analysis has revealed the presence of a group of proteins in pro and lower eukaryotes, but not in Man, that show extensive amino acid sequence similarity to known O(6)-alkylguanine-DNA alkyltransferases, but where the cysteine at the putative active site is replaced by another residue, usually tryptophan. Here we review recent work on these proteins, which we designate as alkyltransferase-like (ATL) proteins, and consider their mechanism of action and role in protecting the host organisms against the biological effects of O(6)-alkylating agents, and their evolution. ATL proteins from Escherichia coli (eAtl, transcribed from the ybaz open reading frame) and Schizosaccharomyces pombe (Atl1) are able to bind to a range of O(6)-alkylguanine residues in DNA and to reversibly inhibit the action of the human alkyltransferase (MGMT) upon these substrates. Isolated proteins were not able to remove the methyl group in O(6)-methylguanine-containing DNA or oligonucleotides, neither did they display glycosylase or endonuclease activity. S. pombe does not contain a functional alkyltransferase and atl1 inactivation sensitises this organism to a variety of alkylating agents, suggesting that Atl1 acts by binding to O(6)-alkylguanine lesions and signalling them for processing by other DNA repair pathways. Currently we cannot exclude the possibility that ATL proteins arose through independent mutation of the alkyltransferase gene in different organisms. However, analyses of the proteins from E. coli and S. pombe, are consistent with a common function.     

Comparative visual acuity of coleoid cephalopods

The pelagic realm of the ocean is characterized by extremelyclear water and a lack of surfaces. Adaptations to the visualecology of this environment include transparency, fluorescence,bioluminescence, and deep red or black pigmentation. While thesignals that pelagic organisms send are increasingly well-understood,the optical capabilities of their viewers, especially for predatorswith camera-like vision such as fish and squid, are almost unknown.Aquatic camera-like vision is characterized by a spherical lensfocusing an image on the retina. Here, we measured the resolvingpower of the lenses of eight species of pelagic cephalopodsto obtain an approximation of their visual capabilities. Wedid this by focusing a standard resolution target through dissectedlenses and calculating their modulation transfer functions.The modulation transfer function (MTF) is the single most completeexpression of the resolving capabilities of a lens. Since theoptical and retinal capabilities of an eye are generally well-matched,we considered our measurements of cephalopod lens MTF to bea good proxy for their visual capabilities in vivo. In general,squid have optical capabilities comparable to other organismsgenerally assumed to have good vision, such as fish and birds.Surprisingly, the optical capability of the eye of Vampyroteuthisinfernalis rivals that of humans.     

Assessing enzyme activities using stable isotope labeling and mass spectrometry

Activity-based protein profiling has emerged as a valuable technology for labeling, enriching, and assessing protein activities from complex mixtures. This is primarily accomplished via a two-step identification and quantification process. Here we show a highly quantitative and streamlined method, termed catch-and-release activity profiling of enzymes (CAPE), which reduces this procedure to a single step. Furthermore the CAPE approach has the ability to detect small quantitative changes that may have been missed by alternative mass spectrometry-based techniques.     

Terrorism, trauma, and mass casualty triage: how might we solve the latest mind-body problem?

The global war on terrorism has led to increased concern about the ability of the U.S. healthcare system to respond to casualties from a chemical, biological, or radiological agent attack. Relatively little attention, however, has focused on the potential, in the immediate aftermath of such an attack, for large numbers of casualties presenting to triage points with acute health anxiety and idiopathic physical symptoms. This sort of "mass idiopathic illness" is not a certain outcome of chemical, biological, or radiological attack. However, in the event that this phenomenon occurs, it could result in surges in demand for medical evaluations that may disrupt triage systems and endanger lives. Conversely, if continuous primary care is not available for such patients after initial triage, many may suffer with unrecognized physical and emotional injuries and illness. This report is the result of an expert planning initiative seeking to facilitate triage protocols that will address the possibility of mass idiopathic illness and bolster healthcare system surge capacity. The report reviews key triage assumptions and gaps in knowledge and offers a four-stage triage model for further discussion and research. Optimal triage approaches offer flexibility and should be based on empirical studies, critical incident modeling, lessons from simulation exercises, and case studies. In addition to staging, the proposed triage and longitudinal care model relies on early recognition of symptoms, development of a registry, and use of non-physician care management to facilitate later longitudinal followup and collaboration between primary care and psychiatry for the significant minority of patients who develop persistent idiopathic symptoms associated with reduced functional status.     

Congenital defects among liveborn infants with Down syndrome

BACKGROUND: Many infants with Down syndrome (DS) have co-occurring congenital malformations requiring intensive surgical and medical management. To anticipate the care needed by these infants, providers and parents require accurate information about birth defects that may be present. This article uses a unique national hospital discharge dataset to identify the rate at which structural birth defects are identified among liveborn infants with DS. METHODS: ICD-9-CM diagnosis codes for data from the Healthcare Cost and Utilization Project were used to identify infants with and without DS, and to classify birth defects. The study population consisted of liveborn infants discharged from the hospital from 1993 through 2002. ORs for the association between the occurrence of congenital malformations and the presence of DS were computed using logistic regression models for survey data. RESULTS: Discharge data included 11,372 DS and 7,884,209 non-DS births, representing national estimates of 43,463 DS and 39,716,469 non-DS births respectively. In addition to congenital heart defects that co-occurred most often in DS infants compared to infants without DS, the risks for gastrointestinal malformations (OR 67.07), genitourinary malformations (OR 3.62), orofacial malformations (OR 5.63), and abdominal wall malformations (OR 3.25) were also elevated in infants with DS. There was no difference in the risk of spina bifida between infants with and without DS. CONCLUSIONS: This is the first nationally representative compilation of the co-occurrence of congenital malformations associated with DS. This information may assist providers and parents in their attempts to understand and prepare for the true burden of this condition.     

Image-based multivariate profiling of drug responses from single cells

Quantitative analytical approaches for discovering new compound mechanisms are required for summarizing high-throughput, image-based drug screening data. Here we present a multivariate method for classifying untreated and treated human cancer cells based on approximately 300 single-cell phenotypic measurements. This classification provides a score, measuring the magnitude of the drug effect, and a vector, indicating the simultaneous phenotypic changes induced by the drug. These two quantities were used to characterize compound activities and identify dose-dependent multiphasic responses. A systematic survey of profiles extracted from a 100-compound compendium of image data revealed that only 10-15% of the original features were required to detect a compound effect. We report the most informative image features for each compound and fluorescence marker set using a method that will be useful for determining minimal collections of readouts for drug screens. Our approach provides human-interpretable profiles and automatic determination of on- and off-target effects.     

Comprehensive DNA signature discovery and validation

DNA signatures are nucleotide sequences that can be used to detect the presence of an organism and to distinguish that organism from all other species. Here we describe Insignia, a new, comprehensive system for the rapid identification of signatures in the genomes of bacteria and viruses. With the availability of hundreds of complete bacterial and viral genome sequences, it is now possible to use computational methods to identify signature sequences in all of these species, and to use these signatures as the basis for diagnostic assays to detect and genotype microbes in both environmental and clinical samples. The success of such assays critically depends on the methods used to identify signatures that properly differentiate between the target genomes and the sample background. We have used Insignia to compute accurate signatures for most bacterial genomes and made them available through our Web site. A sample of these signatures has been successfully tested on a set of 46 Vibrio cholerae strains, and the results indicate that the signatures are highly sensitive for detection as well as specific for discrimination between these strains and their near relatives. Our approach, whereby the entire genomic complement of organisms are compared to identify probe targets, is a promising method for diagnostic assay development, and it provides assay designers with the flexibility to choose probes from the most relevant genes or genomic regions. The Insignia system is freely accessible via a Web interface and has been released as open source software at: http://insignia.cbcb.umd.edu.