Multiple Property Tolerance Analysis for the Evaluation of Missense Mutations

Computational prediction of the impact of a mutation on protein function is still not accurate enough for clinical diagnostics without additional human expert analysis. Sequence alignment-based methods have been extensively used but their results highly depend on the quality of the input alignments and the choice of sequences. Incorporating the structural information with alignments improves prediction accuracy. Here, we present a conservation of amino acid properties method for mutation prediction, Multiple Properties Tolerance Analysis (MuTA), and a new strategy, MuTA/S, to incorporate the solvent accessible surface (SAS) property into MuTA. Instead of combining multiple features by machine learning or mathematical methods, an intuitive strategy is used to divide the residues of a protein into different groups, and in each group the properties used is adjusted

Mid-infrared imaging of the young binary star Hen 3-600: Evidence for a dust disk around the primary

We present high-resolution mid-infrared observations of the nearby late-type young binary system Hen 3-600. The binary, at a distance of $\sim$ 50 pc, could be a member of the TW Hydrae Association, the nearest known group of young stars, with an age of a few million years. Our images make it possible for the first time to determine which star in the pair, separated by 1.4'', harbors the mid-infrared excess detected by IRAS. In the near-infrared, where the radiation is primarily photospheric, Hen 3-600A (M3) and Hen 3-600B (M3.5) have a flux ratio of 1.6. At 4.8$\mu$m, 10.8$\mu$m, and 18.2$\mu$m, the primary becomes increasingly dominant over the secondary, suggesting that most of the circumstellar dust in the system resides around Hen 3-600A. Comparison of the spectral energy distribution (SED) of Hen 3-600A to the median SED of classical T Tauri stars suggests that its disk may be truncated by the secondary and provides tentative evidence for a central disk hole. The distribution of dust in the Hen 3-600 system may provide important clues to the formation and evolution of protoplanetary disks in close binaries.Comment: 9 pages, 2 PostScript figures, accepted for publication in The Astrophysical Journal Letter

A dust disk surrounding the young A star HR4796A

We report the codiscovery of the spatially-resolved dust disk of the Vega-like star HR 4796A. Images of the thermal dust emission at $\lambda = 18 \mu$m show an elongated structure approximately 200 AU in diameter surrounding the central A0V star. The position angle of the disk, $30^{\circ} \pm 10^{\circ}$, is consistent to the position angle of the M companion star, $225^{\circ}$, suggesting that the disk-binary system is being seen nearly along its orbital plane. The surface brightness distribution of the disk is consistent with the presence of an inner disk hole of approximately 50 AU radius, as was originally suggested by Jura et al. on the basis of the infrared spectrum. HR 4796 is a unique system among the Vega-like or $\beta$ Pictoris stars in that the M star companion (a weak-emission T Tauri star) shows that the system is relatively young, $\sim 8 \pm 3$ Myr. The inner disk hole may provide evidence for coagulation of dust into larger bodies on a timescale similar to that suggested for planet formation in the solar system.Comment: 12 pages, 3 PostScript figures, accepted for publication in Astrophysical Journal Letter

Tracking Single Cells in Live Animals Using a Photoconvertible Near-Infrared Cell Membrane Label

We describe a novel photoconversion technique to track individual cells in vivo using a commercial lipophilic membrane dye, DiR. We show that DiR exhibits a permanent fluorescence emission shift (photoconversion) after light exposure and does not reacquire the original color over time. Ratiometric imaging can be used to distinguish photoconverted from non-converted cells with high sensitivity. Combining the use of this photoconvertible dye with intravital microscopy, we tracked the division of individual hematopoietic stem/progenitor cells within the calvarium bone marrow of live mice. We also studied the peripheral differentiation of individual T cells by tracking the gain or loss of FoxP3-GFP expression, a marker of the immune suppressive function of CD4+ T cells. With the near-infrared photoconvertible membrane dye, the entire visible spectral range is available for simultaneous use with other fluorescent proteins to monitor gene expression or to trace cell lineage commitment in vivo with high spatial and temporal resolution

Cystic fibrosis population carrier screening: 2004 revision of American College of Medical Genetics mutation panel

Group recommended a panel of mutations and variants that should be tested to determine carrier status within the CFTR gene as a part of population screening programs.1,2 This was initially done in response to the recommendations of an NIH CF Consensus Conference that CF carrier screening be consid-ered by all couples for use before conception or prenatally.3 At that time, the Working Group recognized limitations in our understanding of the population frequencies of several CF al-leles and proposed to review mutation distribution data after the first two years of the program. In 2002, as part of an ongo-ing effort to ensure that the cystic fibrosis carrier screening programs are current with respect to the scientific literature and other available data and practices, we initiated a second review of data on the distribution of mutations in different ethnic groups and we began to assess whether providers wer

Formation and Evolution of Planetary Systems: Cold Outer Disks Associated with Sun-like stars

We present the discovery of debris systems around three solar mass stars based upon observations performed with the Spitzer Space Telescope as part of a Legacy Science Program, ``the Formation and Evolution of Planetary Systems'' (FEPS). We also confirm the presence of debris around two other stars. All the stars exhibit infrared emission in excess of the expected photospheres in the 70 micron band, but are consistent with photospheric emission at <= 33 micron. This restricts the maximum temperature of debris in equilibrium with the stellar radiation to T < 70 K. We find that these sources are relatively old in the FEPS sample, in the age range 0.7 - 3 Gyr. Based on models of the spectral energy distributions, we suggest that these debris systems represent materials generated by collisions of planetesimal belts. We speculate on the nature of these systems through comparisons to our own Kuiper Belt, and on the likely planet(s) responsible for stirring the system and ultimately releasing dust through collisions. We further report observations of a nearby star HD 13974 (d =11 pc) that is indistinguishable from a bare photosphere at both 24 micron and 70 micron. The observations place strong upper limits on the presence of any cold dust in this nearby system (L_IR/L_* < 10^{-5.2}).Comment: 31 pages, 9 figures, accepted for publication in Ap

Spectral Karyotyping for identification of constitutional chromosomal abnormalities at a national reference laboratory

Spectral karyotyping is a diagnostic tool that allows visualization of chromosomes in different colors using the FISH technology and a spectral imaging system. To assess the value of spectral karyotyping analysis for identifying constitutional supernumerary marker chromosomes or derivative chromosomes at a national reference laboratory, we reviewed the results of 179 consecutive clinical samples (31 prenatal and 148 postnatal) submitted for spectral karyotyping. Over 90% of the cases were requested to identify either small supernumerary marker chromosomes (sSMCs) or chromosomal exchange material detected by G-banded chromosome analysis. We also reviewed clinical indications of those cases with marker chromosomes in which chromosomal origin was identified by spectral karyotyping. Our results showed that spectral karyotyping identified the chromosomal origin of marker chromosomes or the source of derivative chromosomal material in 158 (88%) of the 179 clinical cases; the identification rate was slightly higher for postnatal (89%) compared to prenatal (84%) cases. Cases in which the origin could not be identified had either a small marker chromosome present at a very low level of mosaicism (< 10%), or contained very little euchromatic material. Supplemental FISH analysis confirmed the spectral karyotyping results in all 158 cases. Clinical indications for prenatal cases were mainly for marker identification after amniocentesis. For postnatal cases, the primary indications were developmental delay and multiple congenital anomalies (MCA). The most frequently encountered markers were of chromosome 15 origin for satellited chromosomes, and chromosomes 2 and 16 for non-satellited chromosomes. We were able to obtain pertinent clinical information for 47% (41/88) of cases with an identified abnormal chromosome. We conclude that spectral karyotyping is sufficiently reliable for use and provides a valuable diagnostic tool for establishing the origin of supernumerary marker chromosomes or derivative chromosomal material that cannot be identified with standard cytogenetic techniques

A randomized, seven-day study to assess the efficacy and safety of a glycopyrrolate/formoterol fumarate fixed-dose combination metered dose inhaler using novel Co-Suspension™ Delivery Technology in patients with moderate-to-very severe chronic obstructive pulmonary disease

Abstract Background Long-acting muscarinic antagonist/long-acting β 2 -agonist combinations are recommended for patients whose chronic obstructive pulmonary disease (COPD) is not managed with monotherapy. We assessed the efficacy and safety of glycopyrrolate (GP)/formoterol fumarate (FF) fixed-dose combination delivered via a Co-Suspension™ Delivery Technology-based metered dose inhaler (MDI) (GFF MDI). Methods This was a Phase IIb randomized, multicenter, placebo-controlled, double-blind, chronic-dosing (7 days), crossover study in patients with moderate-to-very severe COPD (NCT01085045). Treatments included GFF MDI twice daily (BID) (GP/FF 72/9.6 μg or 36/9.6 μg), GP MDI 36 μg BID, FF MDI 7.2 and 9.6 μg BID, placebo MDI, and open-label formoterol dry powder inhaler (FF DPI) 12 μg BID or tiotropium DPI 18 μg once daily. The primary endpoint was forced expiratory volume in 1 s area under the curve from 0 to 12 h (FEV 1 AUC 0–12 ) on Day 7 relative to baseline FEV 1 . Secondary endpoints included pharmacokinetics and safety. Results GFF MDI 72/9.6 μg or 36/9.6 μg led to statistically significant improvements in FEV 1 AUC 0–12 after 7 days’ treatment versus monocomponent MDIs, placebo MDI, tiotropium, or FF DPI (p ≤ 0.0002). GFF MDI 36/9.6 μg was non-inferior to GFF MDI 72/9.6 μg and monocomponent MDIs were non-inferior to open-label comparators. Pharmacokinetic results showed glycopyrrolate and formoterol exposure were decreased following administration via fixed-dose combination versus monocomponent MDIs; however, this was not clinically meaningful. GFF MDI was well tolerated. Conclusions GFF MDI 72/9.6 μg and 36/9.6 μg BID improve lung function and are well tolerated in patients with moderate-to-very severe COPD. Trial registration ClinicalTrials.gov NCT01085045. Registered 9 March 2010

Adenoviral-mediated correction of methylmalonyl-CoA mutase deficiency in murine fibroblasts and human hepatocytes

<p>Abstract</p> <p>Background</p> <p>Methylmalonic acidemia (MMA), a common organic aciduria, is caused by deficiency of the mitochondrial localized, 5'deoxyadenosylcobalamin dependent enzyme, methylmalonyl-CoA mutase (MUT). Liver transplantation in the absence of gross hepatic dysfunction provides supportive therapy and metabolic stability in severely affected patients, which invites the concept of using cell and gene delivery as future treatments for this condition.</p> <p>Methods</p> <p>To assess the effectiveness of gene delivery to restore the defective metabolism in this disorder, adenoviral correction experiments were performed using murine <it>Mut </it>embryonic fibroblasts and primary human methylmalonyl-CoA mutase deficient hepatocytes derived from a patient who harbored two early truncating mutations, E224X and R228X, in the <it>MUT </it>gene. Enzymatic and expression studies were used to assess the extent of functional correction.</p> <p>Results</p> <p>Primary hepatocytes, isolated from the native liver after removal subsequent to a combined liver-kidney transplantation procedure, or <it>Mut </it>murine fibroblasts were infected with a second generation recombinant adenoviral vector that expressed the murine methylmalonyl-CoA mutase as well as eGFP from distinct promoters. After transduction, [1-¹⁴C] propionate macromolecular incorporation studies and Western analysis demonstrated complete correction of the enzymatic defect in both cell types. Viral reconstitution of enzymatic expression in the human methylmalonyl-CoA mutase deficient hepatocytes exceeded that seen in fibroblasts or control hepatocytes.</p> <p>Conclusion</p> <p>These experiments provide proof of principle for viral correction in methylmalonic acidemia and suggest that hepatocyte-directed gene delivery will be an effective therapeutic treatment strategy in both murine models and in human patients. Primary hepatocytes from a liver that was unsuitable for transplantation provided an important resource for these studies.</p