Novel real-time PCR assays for the specific detection of human infective Cryptosporidium species

Cryptosporidium is a protozoan parasite causing gastrointestinal illness. Drinking waterborne outbreaks have been caused by C. hominis, C. parvum and C. cuniculus. Molecular detection techniques already exist for Cryptosporidium and usually target housekeeping genes. We set ourselves the task to identify species-specific genes. These genes are likely to be involved in host parasite interaction and virulence. Three subtelomeric species-specific putative virulence factor genes (Cops-2, Chos-1 and Chos-2) were identified in silico and used to develop novel real-time PCR assays. Our results show that Chos-2 is a suitable target for probe-based assays for the specific detection of C. hominis and C. cuniculus (two very closely related species) and that Cops-2 is a suitable target for specific detection of C. parvum

The lichen genus Coccocarpia from the Andaman and Nicobar Islands, India

Seven species of Coccocarpia are reported from the Andaman Islands and two from the Nicobar Islands. These include four species new to India and to the Andaman Islands, viz. C. glaucina, C. cf. myriocarpa, C. sp. 1 and C. sp. 2, and two species new to the Nicobar Islands, viz. C. erythroxyli and C. palmicola. A key to all nine species of Coccocarpia known from India is presented and information on morphology, chemistry and distribution given

A study of the cc-C3HD\mathrm{C_{3}HD}/cc-C3H2\mathrm{C_{3}H_{2}} ratio in low-mass star forming regions

We use the deuteration of $c$-$\mathrm{C_{3}H_{2}}$ to probe the physical parameters of starless and protostellar cores, related to their evolutionary states, and compare it to the $\mathrm{N_{2}H^{+}}$-deuteration in order to study possible differences between the deuteration of C- and N-bearing species. We observed the main species $c$-$\mathrm{C_{3}H_{2}}$, the singly and doubly deuterated species $c$-$\mathrm{C_{3}HD}$ and $c$-$\mathrm{C_{3}D_{2}}$, as well as the isotopologue $c$-$\mathrm{{H^{13}CC_{2}H}}$ toward 10 starless cores and 5 protostars in the Taurus and Perseus Complexes. We examined the correlation between the $N$($c$-$\mathrm{C_{3}HD}$)/$N$($c$-$\mathrm{C_{3}H_{2}}$) ratio and the dust temperature along with the $\mathrm{H_2}$ column density and the CO depletion factor. The resulting $N$($c$-$\mathrm{C_{3}HD}$)/$N$($c$-$\mathrm{C_{3}H_{2}}$) ratio is within the error bars consistent with $10\%$ in all starless cores with detected $c$-$\mathrm{C_{3}HD}$. This also accounts for the protostars except for the source HH211, where we measure a high deuteration level of $23\%$. The deuteration of $\mathrm{N_{2}H^{+}}$ follows the same trend but is considerably higher in the dynamically evolved core L1544. Toward the protostellar cores the coolest objects show the largest deuterium fraction in $c$-$\mathrm{C_{3}H_{2}}$. We show that the deuteration of $c$-$\mathrm{C_{3}H_{2}}$ can trace the early phases of star formation and is comparable to that of $\mathrm{N_{2}H^{+}}$. However, the largest $c$-$\mathrm{C_{3}H_{2}}$ deuteration level is found toward protostellar cores, suggesting that while $c$-$\mathrm{C_{3}H_{2}}$ is mainly frozen onto dust grains in the central regions of starless cores, active deuteration is taking place on ice

Colossendeis species (Pycnogonida: Colossendeidae) collected during the Italica XIX cruise to Victoria Land (Antarctica), with remarks on some taxonomic characters of the ovigers

The pycnogonid fauna of the genus Colossendeis collected during the Italica XIX cruise to Victoria Land (Ross Sea, Antarctica) was studied. A total of 19 specimens of six species were collected: Colossendeis australis (6), C. wilsoni (3), C. scotti (2), C. robusta (3), C. lilliei (2) and C. megalonyx (3). In the present contribution the observed variability of all collected Colossendeis species is described and illustrated. The previously synonymised C. lilliei is considered a different species from C. robusta. The observations made in this study lead us to discuss a controversy about the total number of oviger segments in this genus. Despite the currently established 10-segmented status, a short basal element is here considered to be a possible 11th segment. A detailed SEM study of the last oviger segment is carried out in all collected species, showing some intraspecific and the interspecific variability in the structures examined (shape and number of rows of compound spines, morphology of terminal claw, etc.). Finally, we discuss the taxonomic value of these characters of the last strigilis segment for distinguishing the Colossendeis species, and their possible utility in establishing internal phylogenetic relationships in future contributions

Chemical tracers of high-metallicity environments

We present for the first time a detailed study of the properties of molecular gas in metal-rich environments such as early-type galaxies (ETGs). We have explored Photon-Dominated Region (PDR) chemistry for a wide range of physical conditions likely to be appropriate for these sources. We derive fractional abundances of the 20 most chemically reactive species as a function of the metallicity, as a function of the optical depth and for various volume number gas densities, Far-Ultra Violet (FUV) radiation fields and cosmic ray ionisation rates. We also investigate the response of the chemistry to the changes in $\alpha-$element enhancement as seen in ETGs. We find that the fractional abundances of CS, H$_{2}$S, H$_{2}$CS, H$_{2}$O, H$_{3}$O$^{+}$, HCO$^{+}$ and H$_{2}$CN seem invariant to an increase of metallicity whereas C$^{+}$, CO, C$_{2}$H, CN, HCN, HNC and OCS appear to be the species most sensitive to this change. The most sensitive species to the change in the fractional abundance of $\alpha-$elements are C$^{+}$, C, CN, HCN, HNC, SO, SO$_{2}$, H$_{2}$O and CS. Finally, we provide line brightness ratios for the most abundant species, especially in the range observable with ALMA. Discussion of favorable line ratios to use for the estimation of super-solar metallicities and $\alpha$-elements are also provided.Comment: 15 pages, 6 figures, 4 tables, Accepted for publication into MNRA

Multilocus haplotyping by parallel sequencing to decipher the interspecific mosaic genome structure of cultivated citrus

The most important economic Citrus species originated from natural interspecific hybridization between four ancestral taxa (C. reticulata, C. maxima, C. medica and C. micrantha) with limited further interspecific recombination due to apomixis and vegetative propagation. Such reticulate evolution coupled with vegetative propagation results in genomes that are mosaics of large chromosome fragments of the basic taxa, in frequent interspecific heterozygosity. Breeding of these species is hampered by their complex heterozygous genomic structures. Haplotyping of multiple gene fragments along the genome should be a powerful approach to resolve the evolutionary history of the gene pools, to reveal the admixture genomic structure of current species and to develop innovative breeding schemes. We have analysed the efficiency of parallel sequencing with 454 methodology to decipher the hybrid structure of modern citrus species and cultivars along chromosome 2. Four hundred fifty four amplicon libraries were established with the fluidigm array system for 48 genotypes and 16 gene fragments of chromosome 2. Haplotypes were established from the reads of each accession and phylogenetic analyses were performed from the haplotypic data of each gene fragment. The length of 454 reads and the level of differentiation between the ancestral taxa of modern citrus allowed efficient haplotype phylogenetic assignations for 12 of the 16 gene fragments. The analysis of the mixed genomic structure of modern species and cultivars (i) revealed C. maxima introgressions in modern mandarins; (ii) was consistent with previous hypothesis regarding the origin of secondary species; and (iii) provided a new picture of the evolution of chromosome 2. Perspectives to rebuild the main secondary species from the basic taxa are discussed. (Résumé d'auteur

Plankton periodicity and some physicochemical parameters of the intake channel of Lake Chad

This study examines zooplankton periodicity and some physicochemical parameters of the intake channel of Lake Chad (Nigeria). Nine different zooplankton species were identified at the sampling station 1, while seven different zooplankton species were identified at the sampling station 2 (the intake channel of Lake Chad). Each identified zooplankton species was grouped according to its major group of copepods, Cladocera or Rotifera. The copepods dominated the zooplankton community with the highest numbers of occurrence as Cyclopedia species throughout the course of the study at both station l and 2. There was a clear evidence of the influence of organic manure nutrients on total zooplankton population at station 1 when compared to that of station 2. The water quality variables measured in the course of this study show that the surface water temperature in station 1 ranges from 27.5 degree C to 30.5 degree C. The pH ranges from 6.8 to 8.5, while D.O. contents ranges from 2.9mg/L to 6.1mg/L and alkalinity recorded was 172.00 to 208.00. At the station 2 the water quality parameters obtained show that surface water temperature ranges from 27.3 degree C to 30.2 degree C, pH ranges between 6.9 to 8.5, while the D.O contents ranges from 3.0 mg/L to 6.2 mg/L.Alkalinity ranges from 172mg/L to 212 mg/

Photolytically generated aerosols in the mesosphere and thermosphere of Titan

Analysis of the Cassini Ultraviolet Imaging Spectrometer (UVIS) stellar and solar occultations at Titan to date include 12 species: N$_{2}$ (nitrogen), CH$_{4}$ (methane), C$_{2}$H$_{2}$ (acetylene), C$_{2}$H$_{4}$ (ethylene), C$_{2}$H$_{6}$ (ethane), C$_{4}$H$_{2}$ (diacetylene), C$_{6}$H$_{6}$ (benzene), C$_{6}$N$_{2}$ (dicyanodiacetylene), C$_{2}$N$_{2}$ (cyanogen), HCN (hydrogen cyanide), HC$_{3}$N (cyanoacetylene), and aerosols distinguished by a structureless continuum extinction (absorption plus scattering) of photons in the EUV. The introduction of aerosol particles, retaining the same refractive index properties as tholin with radius $\sim$125 \AA and using Mie theory, provides a satisfactory fit to the spectra. The derived vertical profile of aerosol density shows distinct structure, implying a reactive generation process reaching altitudes more than 1000 km above the surface. A photochemical model presented here provides a reference basis for examining the chemical and physical processes leading to the distinctive atmospheric opacity at Titan. We find that dicyanodiacetylene is condensable at $\sim$650 km, where the atmospheric temperature minimum is located. This species is the simplest molecule identified to be condensable. Observations are needed to confirm the existence and production rates of dicyanodiacetylene.Comment: A typo in Table 1 was made in the previous version. The corrected tholin abundance is 4.6x10^11. ApJL in press. Will be published on June 1st, or May 21 onlin