Argus--a new database system for Web-based analysis of multiple microarray data sets

The ongoing revolution in microarray technology allows biologists studying gene expression to routinely collect >10(5) data points in a given experiment. Widely accessible and versatile database software is required to process this large amount of raw data into a format that facilitates the development of new biological insights. Here, we present a novel microarray database software system, named Argus, designed to process, analyze, manage, and publish microarray data. Argus imports the intensities and images of externally quantified microarray spots, performs normalization, and calculates ratios of gene expression between conditions. The database can be queried locally or over the Web, providing a convenient format for Web-publishing entire microarray data sets. Searches for regulated genes can be conducted across multiple experiments, and the integrated results incorporate images of the actual hybridization spots for artifact screening. Query results are presented in a clone- or gene-oriented fashion to rapidly identify highly regulated genes, and scatterplots of expression ratios allow an individual ratio to be interpreted in the context of all data points in the experiment. Algorithms were developed to optimize response times for queries of regulated genes. Supporting databases are updated easily to maintain current gene identity information, and hyperlinks to the Web provide access to descriptions of gene function. Query results also can be exported for higher-order analyses of expression patterns. This combination of features currently is not available in similar software. Argus is available at http://vessels.bwh.harvard.edu/software/Argus.

Biomechanical activation of vascular endothelium as a determinant of its functional phenotype

One of the striking features of vascular endothelium, the single-cell-thick lining of the cardiovascular system, is its phenotypic plasticity. Various pathophysiologic factors, such as cytokines, growth factors, hormones, and metabolic products, can modulate its functional phenotype in health and disease. In addition to these humoral stimuli, endothelial cells respond to their biomechanical environment, although the functional implications of this biomechanical paradigm of activation have not been fully explored. Here we describe a high-throughput genomic analysis of modulation of gene expression observed in cultured human endothelial cells exposed to two well defined biomechanical stimuli-a steady laminar shear stress and a turbulent shear stress of equivalent spatial and temporal average intensity. Comparison of the transcriptional activity of 11,397 unique genes revealed distinctive patterns of up- and down-regulation associated with each type of stimulus. Cluster analyses of transcriptional profiling data were coupled with other molecular and cell biological techniques to examine whether these global patterns of biomechanical activation are translated into distinct functional phenotypes. Confocal immunofluorescence microscopy of structural and contractile proteins revealed the formation of a complex apical cytoskeleton in response to laminar shear stress. Cell cycle analysis documented different effects of laminar and turbulent shear stresses on cell proliferation. Thus, endothelial cells have the capacity to discriminate among specific biomechanical forces and to translate these input stimuli into distinctive phenotypes. The demonstration that hemodynamically derived stimuli can be strong modulators of endothelial gene expression has important implications for our understanding of the mechanisms of vascular homeostasis and atherogenesis.

Computational comparison of two draft sequences of the human genome

We are in the enviable position of having two distinct drafts of the human genome sequence. Although gaps, errors, redundancy and incomplete annotation mean that individually each falls short of the ideal, many of these problems can be assessed by comparison. Here we present some comparative analyses of these drafts. We look at a number of features of the sequences, including sequence gaps, continuity, consistency between the two sequences and patterns of DNA-binding protein motifs.

Quantification of holmium: YAG and thulium: YAG laser-induced scleral shrinkage for buckling procedures

BACKGROUND AND OBJECTIVE

To quantify and compare holmium:YAG (2.1 microns) and thulium:YAG (2.0 microns) laser-induced scleral shrinkage for retinal buckling procedures.

MATERIALS AND METHODS

Two overlapping spots of either laser radiation were applied at the equatorial sclera of 50 human cadaver eyes. Scleral shrinkage was expressed as a relative change of length between two reference points on the scleral surface, and quantified as a function of energy per pulse, total energy, scleral thickness, and intraocular pressure (IOP). Tissue effects were studied histopathologically.

RESULTS

Shrinkage was most dependent on total fluence and attained a maximum of 27% to 30% with an IOP of 4 mm Hg, regardless of scleral thickness or laser parameters, but decreased with increasing IOP. The thulium:YAG laser produced more efficient scleral shrinkage and less collagen damage than the holmium:YAG laser.

CONCLUSION

The recommended parameters for laser-induced scleral shrinkage are the thulium:YAG laser, with 2.4 J/cm2 per pulse and 12.0 to 14.4 J/cm2 total fluence (5 to 6 pulses). IOP control (< or = 4 mm Hg) is crucial during laser scleral buckling.

Interstitial laser hyperthermia model development for minimally invasive therapy of breast carcinoma

BACKGROUND

This investigation describes the preclinical development of a laser fiberoptic interstitial delivery system for the thermal destruction of small breast cancers. We propose adaptation of this technology to stereotactic mammographic instrumentation currently employed for diagnostic core biopsy to thermally ablate a site of disease with maximal treatment efficacy, minimal observable superficial change, reduced patient trauma, and lowered overall treatment costs.

STUDY DESIGN

Laser hyperthermia is a clinical modality that seeks to achieve tumor destruction through controlled tissue heating. The advantage of laser-induced hyperthermia over traditionally used heat sources such as ultrasound, microwave, or radiowave radiation lies in the ability to focus heat localization to the specific tumor tissue site. Neodymium:yttrium aluminum garnet (Nd:YAG) laser light transmitted through a fiberoptic cable to a diffusing quartz tip can induce such temperature increases leading to localized tissue destruction. Because breast cancer occurs with greatest frequency in the mature woman whose breast tissue has undergone glandular involution with fatty replacement, this study concentrates on determining the resultant laser energy heat distribution within fat and fibrofatty tissue. This investigation studied the time-temperature responses of ex vivo human breast and porcine fibrofatty tissue, which led to an in vivo subcutaneous porcine model for the practical demonstration of a laser hyperthermia treatment of small volumes of porcine mammary chain tissue.

RESULTS

Spatial recordings of the resultant temperature fields through time exhibited similar, reproducible thermal profiles in both ex vivo human breast and subcutaneous porcine fat. In vivo laser-produced temperature fields in porcine subcutaneous fat were comparable to those in the ex vivo analyses, and showed a histologically, sharply defined, and controllable volume of necrosis with no injury to adjacent tissues or to overlying skin.

CONCLUSIONS

Interstitially placed, fiberoptically delivered Nd:YAG laser energy is capable of controlled tissue denaturation to a defined volume for the treatment of small breast cancers. It is hoped that this minimally invasive approach, with further investigation and refinement, may lead to the effective treatment of small, well-defined breast cancers that are commonly diagnosed through stereographic mammography and stereotactic core biopsy. The juxtaposition of such a localized treatment modality with these increasingly used diagnostic tools is of considerable promise.