First karyological analysis of the endemic malagasy phantom gecko matoatoa brevipes (Squamata: Gekkonidae)

The genus Matoatoa includes two Malagasy endemic species, M. brevipes and M. spannringi. Due to their cryptic behaviour, the two species are known only from a handful of specimens and have been included in few molecular studies. Here we carried out a molecular barcoding analysis using a fragment of the mitochondrial NADH dehy-drogenase subunit 2 (ND2) and the first chromosomal analysis of M. brevipes. The molecular analysis confirmed the identity of the studied samples as M. brevipes. However, the level of genetic divergence (4% uncorrected p-distance) between our samples and other sequences of M. brevipes, suggests previously unrecognised diversity within the spe-cies. The karyotype of M. brevipes is composed of 2n = 34 chromosomes: the first pair is metacentric, while all the other pairs are telocentric and gradually decreasing in length (Arm Number, AN = 36). C-banding revealed little evidence of centromeric heterochromatin, while NOR-associated heterochromatin was found on the telomeres of a medi-um sized telocentric pair. No heteromorphic chromosome pairs were found in the karyotype of the species, suggesting that putative sex chromosomes are at an early stage of differentiation. Karyological comparisons with closely related species were performed with Christinus marmoratus, and representatives of the genera Phelsuma, Ebenavia, Paroedura and Uroplatus. Comparisons across genera suggest that chromosome diversification in this group of geckos probably occurred by means of chromosome fusions and inversions, leading to a reduction of the chromosome number and the formation of biarmed elements in different species

Existential witness extraction in classical realizability and via a negative translation

We show how to extract existential witnesses from classical proofs using Krivine's classical realizability---where classical proofs are interpreted as lambda-terms with the call/cc control operator. We first recall the basic framework of classical realizability (in classical second-order arithmetic) and show how to extend it with primitive numerals for faster computations. Then we show how to perform witness extraction in this framework, by discussing several techniques depending on the shape of the existential formula. In particular, we show that in the Sigma01-case, Krivine's witness extraction method reduces to Friedman's through a well-suited negative translation to intuitionistic second-order arithmetic. Finally we discuss the advantages of using call/cc rather than a negative translation, especially from the point of view of an implementation.Comment: 52 pages. Accepted in Logical Methods for Computer Science (LMCS), 201

Diversity of Mycobacterium tuberculosis strains in Nairobi, Kenya

Setting: Tuberculosis (TB) patients attending 16 public health facilities in Nairobi, Kenya. Objective: To determine the Mycobacterium tuberculosis (M.tuberculosis) strain families circulating in Nairobi, Kenya. Methods: Sputum specimens from consecutive new and previously treated smear positive pulmonary TB patients were collected between February and August 2010 and cultured on Lowenstein9Jensen media. Spoligotyping was done on DNA extracted from the first isolate of each patient. The international spoligotype data base (SpolDB4) was used to group isolates into strain families. Results: Fourty seven different strain families were identified from 536 isolates. The principal groups were; CAS1_KILI 96/536 (17%), T1 69/536 (12%), Beijing 65/536 (12%), LAM9 46/536 (9% ), LAM3 & S/Conversant 37/536 (7% ), LAM11_ZWE 26/536 (5%), CAS1_DELHI 24/536 (4%) and T2 24/536 (4%). Others identified and are found in the SpolDB4 were 113/536 (21%). A possible new M.tuberculosis strain family was identified with 21/536 (4%) isolates which was designated as Nairobi subtype. Others identified not previously included in the SpolDB4 accounted for 15/536 (3%). Conclusion: We found a diverse array of M.tuberculosis strain families which could be indicative of a cosmopolitant polulation with frequent migration that may suggest that the dorminant strain families may have been present in the population for an extended period of time or on going transmision of closely related strains families. The emergence of the Beijing strains poses a serious threat to TB control due to its high virulence and frequent association with multidrug resistance. We therefore call for strenghthening efforts on early case finding through enhanced public health education campains and provision of accessible diagnostic services with enhanced treatment compliance

Rapid Microsatellite Identification from Illumina Paired-End Genomic Sequencing in Two Birds and a Snake

Identification of microsatellites, or simple sequence repeats (SSRs), can be a time-consuming and costly investment requiring enrichment, cloning, and sequencing of candidate loci. Recently, however, high throughput sequencing (with or without prior enrichment for specific SSR loci) has been utilized to identify SSR loci. The direct “Seq-to-SSR” approach has an advantage over enrichment-based strategies in that it does not require a priori selection of particular motifs, or prior knowledge of genomic SSR content. It has been more expensive per SSR locus recovered, however, particularly for genomes with few SSR loci, such as bird genomes. The longer but relatively more expensive 454 reads have been preferred over less expensive Illumina reads. Here, we use Illumina paired-end sequence data to identify potentially amplifiable SSR loci (PALs) from a snake (the Burmese python, Python molurus bivittatus), and directly compare these results to those from 454 data. We also compare the python results to results from Illumina sequencing of two bird genomes (Gunnison Sage-grouse, Centrocercus minimus, and Clark's Nutcracker, Nucifraga columbiana), which have considerably fewer SSRs than the python. We show that direct Illumina Seq-to-SSR can identify and characterize thousands of potentially amplifiable SSR loci for as little as $10 per sample – a fraction of the cost of 454 sequencing. Given that Illumina Seq-to-SSR is effective, inexpensive, and reliable even for species such as birds that have few SSR loci, it seems that there are now few situations for which prior hybridization is justifiable

Spinal cord from body donors is suitable for multicolor immunofluorescence

Immunohistochemistry is a powerful tool for studying neuronal tissue from humans at the molecular level. Obtaining fresh neuronal tissue from human organ donors is difficult and sometimes impossible. In anatomical body donations, neuronal tissue is dedicated to research purposes and because of its easier availability, it may be an alternative source for research. In this study, we harvested spinal cord from a single organ donor 2 h (h) postmortem and spinal cord from body donors 24, 48, and 72 h postmortem and tested how long after death, valid multi-color immunofluorescence or horseradish peroxidase (HRP) immunohistochemistry is possible. We used general and specific neuronal markers and glial markers for immunolabeling experiments. Here we showed that it is possible to visualize molecularly different neuronal elements with high precision in the body donor spinal cord 24 h postmortem and the quality of the image data was comparable to those from the fresh organ donor spinal cord. High-contrast multicolor images of the 24-h spinal cords allowed accurate automated quantification of different neuronal elements in the same sample. Although there was antibody-specific signal reduction over postmortem intervals, the signal quality for most antibodies was acceptable at 48 h but no longer at 72 h postmortem. In conclusion, our study has defined a postmortem time window of more than 24 h during which valid immunohistochemical information can be obtained from the body donor spinal cord. Due to the easier availability, neuronal tissue from body donors is an alternative source for basic and clinical research

Optical Properties of Deep Ice at the South Pole - Absorption

We discuss recent measurements of the wavelength-dependent absorption coefficients in deep South Pole ice. The method uses transit time distributions of pulses from a variable-frequency laser sent between emitters and receivers embedded in the ice. At depths of 800 to 1000 m scattering is dominated by residual air bubbles, whereas absorption occurs both in ice itself and in insoluble impurities. The absorption coefficient increases approximately exponentially with wavelength in the measured interval 410 to 610 nm. At the shortest wavelength our value is about a factor 20 below previous values obtained for laboratory ice and lake ice; with increasing wavelength the discrepancy with previous measurements decreases. At around 415 to 500 nm the experimental uncertainties are small enough for us to resolve an extrinsic contribution to absorption in ice: submicron dust particles contribute by an amount that increases with depth and corresponds well with the expected increase seen near the Last Glacial Maximum in Vostok and Dome C ice cores. The laser pulse method allows remote mapping of gross structure in dust concentration as a function of depth in glacial ice.Comment: 26 pages, LaTex, Accepted for publication in Applied Optics. 9 figures, not included, available on request from [email protected]

The AMANDA Neutrino Telescope

With an effective telescope area of order $10^4$ m$^2$ for TeV neutrinos, a threshold near $\sim$50 GeV and a pointing accuracy of 2.5 degrees per muon track, the AMANDA detector represents the first of a new generation of high energy neutrino telescopes, reaching a scale envisaged over 25 years ago. We describe early results on the calibration of natural deep ice as a particle detector as well as on AMANDA's performance as a neutrino telescope.Comment: 12 pages, Latex2.09, uses espcrc2.sty and epsf.sty, 13 postscript files included. Talk presented at the 18th International Conference on Neutrino Physics and Astrophysics (Neutrino 98), Takayama, Japan, June 199

Diversity and evolution of amphibian pupil shapes

Pupil constriction has important functional consequences for animal vision, yet the evolutionary mechanisms underlying diverse pupil sizes and shapes are poorly understood. We aimed to quantify the diversity and evolution of pupil shapes among amphibians and to test for potential correlations to ecology based on functional hypotheses. Using photographs, we surveyed pupil shape across adults of 1294 amphibian species, 74 families and three orders, and additionally for larval stages for all families of frogs and salamanders with a biphasic ontogeny. For amphibians with a biphasic life history, pupil shape changed in many species that occupy distinct habitats before and after metamorphosis. In addition, non-elongated (circular or diamond) constricted pupils were associated with species inhabiting aquatic or underground environments, and elongated pupils (with vertical or horizontal long axes) were more common in species with larger absolute eye sizes. We propose that amphibians provide a valuable group within which to explore the anatomical, physiological, optical and ecological mechanisms underlying the evolution of pupil shape

The AMANDA Neutrino Telescope and the Indirect Search for Dark Matter

With an effective telescope area of order 10^4 m^2, a threshold of ~50 GeV and a pointing accuracy of 2.5 degrees, the AMANDA detector represents the first of a new generation of high energy neutrino telescopes, reaching a scale envisaged over 25 years ago. We describe its performance, focussing on the capability to detect halo dark matter particles via their annihilation into neutrinos.Comment: Latex2.09, 16 pages, uses epsf.sty to place 15 postscript figures. Talk presented at the 3rd International Symposium on Sources and Detection of Dark Matter in the Universe (DM98), Santa Monica, California, Feb. 199