Eric N. Brown

Complement, Age-Related Macular Degeneration and a Vision of the Future

Age-related macular degeneration (AMD) is one of the most well-characterized late-onset, complex trait diseases. Remarkable advances in our understanding of the genetic and biological foundations of this disease were derived from a recent convergence of scientific and clinical data. Importantly, the more recent identification of AMD-associated variations in a number of complement pathway genes has provided strong support for earlier, paradigm-shifting studies that suggested that aberrant function of the complement system plays a key role in disease etiology. Collectively, this wealth of information has provided an impetus for the development of powerful tools to accurately diagnose disease risk and progression and complement-based therapeutics that will ultimately delay or prevent AMD. Indeed, we are poised to witness a new era of a personalized approach toward the assessment, management, and treatment of this debilitating, chronic disease.

Quality of protein crystal structures

The genomics era has seen the propagation of numerous databases containing easily accessible data that are routinely used by investigators to interpret results and generate new ideas. Most investigators consider data extracted from scientific databases to be error-free. However, data generated by all experimental techniques contain errors and some, including the coordinates in the Protein Data Bank (PDB), also integrate the subjective interpretations of experimentalists. This paper explores the determinants of protein structure quality metrics used routinely by protein crystallographers. These metrics are available for most structures in the database, including the R factor, R(free), real-space correlation coefficient, Ramachandran violations etc. All structures in the PDB were analyzed for their overall quality based on nine different quality metrics. Multivariate statistical analysis revealed that while technological improvements have increased the number of structures determined, the overall quality of structures has remained constant. The quality of structures deposited by structural genomics initiatives are generally better than the quality of structures from individual investigator laboratories. The most striking result is the association between structure quality and the journal in which the structure was first published. The worst offenders are the apparently high-impact general science journals. The rush to publish high-impact work in the competitive atmosphere may have led to the proliferation of poor-quality structures.

Structures of the multicomponent Rieske non-heme iron toluene 2,3-dioxygenase enzyme system

The crystal structures of the three-component toluene 2,3-dioxygenase system provide a model for electron transfer among bacterial Rieske non-heme iron dioxygenases.

Proteomic analysis of vitreous biopsy techniques.

Purpose: To compare vitreous biopsy methods using analysis platforms used in proteomics biomarker discovery. Methods: Vitreous biopsies from 10 eyes were collected sequentially using a 23-gauge needle and a 23-gauge vitreous cutter instrument. Paired specimens were evaluated by UV absorbance spectroscopy, sodium dodecyl sulfate–polyacrylamide gel electrophoresis, and liquid chromatography tandem mass spectrometry (LC-MS/MS). Results: The total protein concentration obtained with a needle and vitrectomy instrument biopsy averaged 1.10 mg/mL (standard error of the mean = 0.35) and 1.13 mg/mL (standard error of the mean = 0.25), respectively. In eight eyes with low or medium viscidity, there was a very high correlation (R2 = 0.934) between the biopsy methods. When data from 2 eyes with high viscidity vitreous were included, the correlation was reduced (R2 = 0.704). The molecular weight protein sodium dodecyl sulfate–polyacrylamide gel electrophoresis profiles of paired needle and vitreous cutter samples were similar, except for a minority of pairs with single band intensity variance. Using LC-MS/MS, equivalent peptides were identified with similar frequencies (R2 ≥ 0.90) in paired samples. Conclusion: Proteins and peptides collected from vitreous needle biopsies are nearly equivalent to those obtained from a vitreous cutter instrument. This study suggests both techniques may be used for most proteomic and biomarker discovery studies of vitreoretinal diseases, although a minority of proteins and peptides may differ in concentration.

Automated stromal nerve rejection in corneal confocal images in vivo

With the advent of corneal confocal microscopy, investigators can determine keratocyte density in the corneal stroma in vivo. We and others have written automated algorithms to measure keratocyte density from human corneal confocal images. Such algorithms are only accurate if they exclude images of stromal nerve bundles (elongated objects) that would otherwise be counted as keratocytes. In this study we devised an algorithm to identify stromal nerve bundles and exclude them from measurements of keratocyte density. Nerve bundles were detected based on their size and aspect ratio, and were then subtracted from images by using a combination of morphology operations and direction calculations. The validity of nerve removal on measurements of keratocyte density was assessed. Keratocyte density was measured from confocal images of three normal human corneas in vivo by using our algorithm with nerve removal. After the same eyes underwent enucleation, density was measured manually from histologic sections. Keratocyte density was also measured from confocal images of 57 normal corneas in vivo (57 subjects) with and without nerve removal. In the three enucleated eyes, there was no significant difference between keratocyte density measured by automated counting with nerve removal and by histologic methods (P equals 0.75). However, in the 57 normal corneas, use of the nerve-removal algorithm reduced estimates of density by 57.0 +/- 164.6 cells/mm3 (mean +/- SD, p < 0.038) in the anterior two-thirds of the stroma.© (2000) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.

Removing bias from solvent atoms in electron density maps

Atomic structures of proteins determined via protein crystallography contain numerous solvent atoms. The experimental data for the determination of a water molecules O-atom position is often a small contained blob of unidentified electron density. Unfortunately, the nature of crystallographic refinement lets poorly placed solvent atoms bias the future refined positions of all atoms in the crystal structure. This research article presents the technique of omit-maps applied to remove the bias introduced by poorly determined solvent atoms, enabling the identification of incorrectly placed water molecules in partially refined crystal structures. A total of 160 protein crystal structures with 45 912 distinct water molecules were processed using this technique. Most of the water molecules in the deposited structures were well justified. However, a few of the solvent atoms in this test data set changed appreciably in position, displacement parameter or electron density when fitted to the solvent omit-map, raising questions about how much experimental support exists for these solvent atoms.

Comparison of trabectome ab interno trabeculectomy to baerveldt glaucoma implants using propensity score matching

● Prior to matching, T had a preoperative IOP of 21.2±7.8 mmHg on 2.6±1.8 medications. After 1 year, the IOP had decreased to 15.9±4.2 and the number of medications decreased to 1.9±1.7. ● Prior to matching, BGI had a preoperative IOP of 20.4 ± 7.3 mmHg on 2.7±1.2 medications. After 1 year, the IOP decreased to 13.7±4.1 mmHg and the number of medications increased to 2.0±1.4. ● Matching resulted in 127 cases with at least 6 months of follow-up similar enough to justifiably compare. ● At 3 months, the difference in average IOP between BGI and T was insignificant at 0.8 ± 1.2 mmHg (95% CI: -1.4 to 3.0 mmHg). ● At 6 months, BGI IOP was significantly lower by -2.7 ± 0.9 mmHg compared to T (95% CI: -4.4 to -1.1 mmHg). ● At 12 months, the BGI group has a significantly lower IOP by -3.2 ± 0.9 mmHg compared to T (95% CI: -5.0 to -1.5 mmHg). Results

Ab Initio Determinations of Photoelectron Spectra Including Vibronic Features: An Upper-Level Undergraduate Physical Chemistry Laboratory.

We present a first-principles determination of the photoelectron spectra of water and hypochlorous acid as a laboratory exercise accessible to students in an undergraduate physical chemistry course. This paper demonstrates the robustness and user-friendliness of software developed for the Franck�Condon factor calculation. While the calculator is suitable for determining multiple types of electronic spectra, the paper focuses on photoelectron work. Because it is based upon ionization, photoelectron spectroscopy is an intuitively satisfying electronic technique that offers undergraduate students a glimpse into the abstract and often confusing concept of vibronic structure. While experimental application of this method is both expensive and challenging, it is ideally suited to theoretical determination. The vibrational envelopes of water and hypochlorous acid demonstrate the salient features of electronic spectroscopy.The ground state photoelectron spectra of these compounds are used as teaching examples; we also examine the unique pedagogical advantages of the laboratory.