T.I.M.S: TaqMan Information Management System, tools to organize data flow in a genotyping laboratory

BACKGROUND: Single Nucleotide Polymorphism (SNP) genotyping is a major activity in biomedical research. The Taqman technology is one of the most commonly used approaches. It produces large amounts of data that are difficult to process by hand. Laboratories not equipped with a Laboratory Information Management System (LIMS) need tools to organize the data flow. RESULTS: We propose a package of Visual Basic programs focused on sample management and on the parsing of input and output TaqMan files. The code is written in Visual Basic, embedded in the Microsoft Office package, and it allows anyone to have access to those tools, without any programming skills and with basic computer requirements. CONCLUSION: We have created useful tools focused on management of TaqMan genotyping data, a critical issue in genotyping laboratories whithout a more sophisticated and expensive system, such as a LIMS

Um papel para organismos de arqueia no desenvolvimento de placas ateroscleróticas vulneráveis e matriz mixomatosa

PURPOSE: Vulnerable plaques are characterized by a myxoid matrix, necrotic lipidic core, reactive oxygen species, and high levels of microorganisms. Aerobic microbes such as Chlamydophila pneumoniae and Mycoplasma pneumoniae usually do not survive in oxidative stress media. Archaea are anaerobic microbes with powerful anti-oxidative enzymes that allow detoxification of free radicals whose presence might favor the survival of aerobic microorganisms. We searched for archaeal organisms in vulnerable plaques, and possible associations with myxoid matrix, chlamydia, and mycoplasma bodies. METHODS: Twenty-nine tissue samples from 13 coronary artherectomies from large excentric ostial or bifurcational lesions were studied using optical and electron microscopy. Infectious agents compatible with archaea, chlamydia, and mycoplasma were semiquantified using electron micrographs and correlated with the amounts of fibromuscular tissue, myxoid matrix, and foam cells, as determined from semi-thin sections. Six of the cases were also submitted to polymerase chain reaction with archaeal primers. RESULTS: All 13 specimens showed archaeal-compatible structures and chlamydial and mycoplasmal bodies in at least 1 sample. There was a positive correlation between extent of the of myxoid matrix and archaeal bodies (r = 0.44, P = 0.02); between archaeal and mycoplasmal bodies (r = 0.41, P = 0.03), and between chlamydial bodies and foam cells (r = 0.42; P = 0.03). The PCR test was positive for archaeal DNA in 4 of the 6 fragments. DISCUSSION: DNA and forms suggestive of archaea are present in vulnerable plaques and may have a fundamental role in the proliferation of mycoplasma and chlamydia. This seems to be the first description of apparently pathogenic archaea in human internal organ lesions.PROPOSTA: Placas vulneráveis são caracterizadas por matriz mixomatosa, centro lipídico necrótico, espécies reativas de oxigênio e alto níveis de microorganismos. Micróbios aeróbicos como Chlamydophila pneumoniae e Mycoplasma pneumoniae usualmente não sobrevivem em meio de estresse oxidativo. Arquéias são microorganismos anaeróbicos com poderosas enzimas anti-oxidantes que permitem detoxificação de radicais livres e a presença delas poderia favorecer a sobrevivência de micróbios aeróbicos. Pesquisamos por elementos de arquéia em placas vulneráveis e sua possível associação com degeneração mixomatosa da matriz e aumento do número de clamídias e micoplasmas. MÉTODOS: Vinte e nove amostras de 13 produtos de aterotomia de lesões grandes e excêntricas de óstio ou bifurcação de coronárias foram estudadas pela microscopia óptica e eletrônica. Agentes compatíveis com arquéia, clamídia e micoplasma foram semiquantificados pela microscopia eletrônica e correlacionados com quantidade de tecido fibromuscular, matriz mixomatosa e células xantomatosas. Seis casos foram também submetidos à reação em cadeia da polimerase com oligonucleotídeos de arquéia. RESULTADOS: Os 13 casos foram positivos para estruturas sugestivas de arquéia, micoplasma ou clamídia, em pelo menos uma amostra. Houve correlação positiva entre intensidade de matriz mixomatosa versus arquéia (r=0.44, p=0.02); arquéia versus micoplasma (r=0.41, p=0.03) e clamídia versus células xantomatosas r=0,42; 0.03). PCR foi positiva para DNA de arqueia em 4 dos 6 fragmentos. DISCUSSÃO: DNA e formas compatíveis com arquéia estão presentes em placas vulneráveis e podem ter papel fundamental na proliferação de micoplasma e clamídia. Este parece ser o primeiro relato de arquéia aparentemente patogênica em lesões de órgãos internos humanos

Bitter taste receptor polymorphisms and human aging.

Several studies have shown that genetic factors account for 25% of the variation in human life span. On the basis of published molecular, genetic and epidemiological data, we hypothesized that genetic polymorphisms of taste receptors, which modulate food preferences but are also expressed in a number of organs and regulate food absorption processing and metabolism, could modulate the aging process. Using a tagging approach, we investigated the possible associations between longevity and the common genetic variation at the three bitter taste receptor gene clusters on chromosomes 5, 7 and 12 in a population of 941 individuals ranging in age from 20 to 106 years from the South of Italy. We found that one polymorphism, rs978739, situated 212 bp upstream of the TAS2R16 gene, shows a statistically significant association (p = 0.001) with longevity. In particular, the frequency of A/A homozygotes increases gradually from 35% in subjects aged 20 to 70 up to 55% in centenarians. These data provide suggestive evidence on the possible correlation between human longevity and taste genetics

A Survey for Faint Stars of Large Proper Motion Using Extra Poss II Plates

We have conducted a search for new stars of high proper motion ($\geq$0.4 arcsec yr$^{-1}$) using POSS II fields for which an extra IIIaF (red) plate of good quality exists, along with useable IIIaJ (blue) and IV-N (infrared) plates taken at epochs differing by a minimum of 1.5 years. Thirty-five fields at Galactic latitudes $|b| \geq$ 20$^o$ were measured, covering some 1378 deg$^2$, or 3.3% of the sky. Searches with three plate combinations as well as all four plates were also made. Seven new stars were found with $\mu \geq$0.5 arcsec yr$^{-1}$, which were therefore missed in the Luyten Half Second (LHS) Catalog. One of these is a common proper motion binary consisting of two subdwarf M stars; another is a cool white dwarf with probable halo kinematics. As a test of our completeness -- and of our ability to test that of Luyten -- 216 of 230 catalogued high proper motion stars were recovered by the software, or 94%. Reasons for incompleteness of the LHS are discussed, such as the simple fact that POSS II plates have deeper limiting magnitudes and greater overlap than did POSS I. Nonetheless, our results suggest that the LHS is closer to 90% complete than recent estimates in the literature (e.g 60%), and we propose a reason to account for one such lower estimate. The conclusion that the LHS Catalog is more complete has implications for the nature of the halo dark matter. In particular it strengthens the constraint on the local density of halo stars, especially white dwarfs at M$_V\sim$17-18.Comment: Astronomical Journal, in press, 16 pages, 3 figure

Polymorphisms in prostaglandin synthase 2/cyclooxygenase 2 (PTGS2/COX2) and risk of colorectal cancer

Inflammation plays a key role in the development of colorectal cancers. We have investigated the relationship between PTGS2 (COX2) polymorphisms and colorectal cancer risk in a hospital based case-control study. We recruited 292 patients with colorectal cancer and 274 controls from new patients admitted to Bellvitge Hospital, Barcelona, Spain, from 1996 to 1998. Subjects responded to a questionnaire on risk factors. Genotypes of the eight more frequent polymorphisms of PTGS2 were determined. Two polymorphisms are located in the promoter sequence, one in the untranslated region of exon 1, one in exon 3, one in intron 5, two in the untranslated region of exon 10, and one downstream of the last polyadenylation (poly-A) signal. Associations were analysed with logistic regression models assuming a dominant effect for rare variants to increase statistical power. An association was detected between colorectal cancer and a polymorphism in the untranslated region of exon 10 of PTGS2, with an odds ratio (OR) of 2.49, 95% confidence interval (CI) of 1.17-5.32, P=0.01. A nearby polymorphism downstream of the last poly-A signal also showed a nonsignificant increase in risk (OR 2.17, 95% CI 0.99-4.78, P=0.05). Analysis of haplotypes confirmed that individuals with these variants were at increased risk of colorectal cancer (OR compared to the most frequent haplotype: 2.17, 95% CI 0.97-4.84, P=0.06) Interactions between PTGS2 genotype and use of nonsteroidal anti-inflammatory drugs and risk of colorectal cancer were also explored

Preliminary Parallaxes of 40 L and T Dwarfs from the U.S. Naval Observatory Infrared Astrometry Program

We present preliminary trigonometric parallaxes and proper motions for 22 L dwarfs and 18 T dwarfs measured using the ASTROCAM infrared imager. Relative to absolute parallax corrections are made by employing 2MASS and/or SDSS photometry for reference frame stars. We combine USNO infrared and optical parallaxes with the best available CIT system photometry to determine M_J, M_H, and M_K values for 37 L dwarfs between spectral types L0 to L8 and 19 T dwarfs between spectral types T0.5 and T8 and present selected absolute magnitude versus spectral type and color diagrams, based on these results. Luminosities and temperatures are estimated for these objects. Of special interest are the distances of several objects which are at or near the L-T dwarf boundary so that this important transition can be better understood. The previously reported early-mid T dwarf luminosity excess is clearly confirmed and found to be present at J, H, and K. The large number of objects that populate this luminosity excess region indicates that it cannot be due entirely to selection effects. The T dwarf sequence is extended to M_J~16.9 by 2MASS J041519-0935 which, at d = 5.74 pc, is found to be the least luminous [log(L/L_sun)=-5.58] and coldest (T_eff~760 K) brown dwarf known. Combining results from this paper with earlier USNO CCD results we find that, in contrast to the L dwarfs, there are no examples of low velocity (V_tan < 20 km/s) T dwarfs. We briefly discuss future directions for the USNO infrared astrometry program.Comment: 73 pages, 9 figures, 9 tables, accepted for publication in The Astronomical Journa

Trigonometric Parallaxes of Central Stars of Planetary Nebulae

Trigonometric parallaxes of 16 nearby planetary nebulae are presented, including reduced errors for seven objects with previous initial results and results for six new objects. The median error in the parallax is 0.42 mas, and twelve nebulae have parallax errors less than 20 percent. The parallax for PHL932 is found here to be smaller than was measured by Hipparcos, and this peculiar object is discussed. Comparisons are made with other distance estimates. The distances determined from these parallaxes tend to be intermediate between some short distance estimates and other long estimates; they are somewhat smaller than estimated from spectra of the central stars. Proper motions and tangential velocities are presented. No astrometric perturbations from unresolved close companions are detected.Comment: 24 pages, includes 4 figures. Accepted for A

The USNO-B Catalog

USNO-B is an all-sky catalog that presents positions, proper motions, magnitudes in various optical passbands, and star/galaxy estimators for 1,042,618,261 objects derived from 3,643,201,733 separate observations. The data were obtained from scans of 7,435 Schmidt plates taken for the various sky surveys during the last 50 years. USNO-B1.0 is believed to provide all-sky coverage, completeness down to V = 21, 0.2 arcsecond astrometric accuracy at J2000, 0.3 magnitude photometric accuracy in up to five colors, and 85% accuracy for distinguishing stars from non-stellar objects. A brief discussion of various issues is given here, but the actual data are available from http://www.nofs.navy.mil and other sites.Comment: Accepted by Astronomical Journa