Transmission of primary resistance mutation K103N in a cluster of Belgian young patients from different risk groups

Background: We analysed the distribution of an HIV-1 subtype B strain resistant to efavirenz and nevirapine among incident infections in the Belgian population. Method: The Belgian AIDS reference laboratories searched their databases for HIV-1 subtype B sequences harbouring the K103N mutation in the reverse transcriptase (RT) or the C67S and V77I mutations in the protease (PR). We included the earliest RT sequence available of drug-naïve patients as well as sequences related to treatment failure. Fifty sequences were aligned omitting the codon 103 and submitted to phylogenetic analysis. Epidemiological data were collected through the Institute of Public Health national database. In addition, three sequences from the cluster were analysed by deep sequencing using the Roche GS Junior platform. Results: Phylogenetic analysis revealed the presence of a 24 virus sequences cluster. All except one of those sequences resulted from patients who were ARV-naïve at the time of sampling, and 21 had the K103N mutation. Two thirds of the clustered patients were infected through homosexual or bisexual contacts while the others were heterosexuals. No case was related to migrants contaminated abroad. Fifteen of the clustered patients were diagnosed between January 2011 and June 2012; 87% of them were aged between 20 and 29 at the time of diagnosis. Interestingly, 60% of them reside in the province of Namur. Deep sequencing analysis of 3 individuals sampled near seroconversion revealed no other resistance mutations at a frequency > 1% than those already picked up by Sanger sequencing (RT A98S, K103N; PR V77I), except the RT V90I. Conclusion: We identified a transmission cluster of drug resistant HIV-1 variants mainly including homo- and heterosexual young adults. Most individuals are of Belgian origin and are living around the city of Namur (Belgium). The K103N mutation had no apparent impact on transmission fitness as its spread raised during the last years. These observations may impact on local prevention and ARV prophylaxis strategies

Characterization of Singlet Ground and Low-Lying Electronic Excited States of Phosphaethyne and Isophosphaethyne

The singlet ground _X˜ 1_+_ and excited _1_− , 1__ states of HCP and HPC have been systematically investigated using ab initio molecular electronic structure theory. For the ground state, geometries of the two linear stationary points have been optimized and physical properties have been predicted utilizing restricted self-consistent field theory, coupled cluster theory with single and double excitations _CCSD_, CCSD with perturbative triple corrections _CCSD_T__, and CCSD with partial iterative triple excitations _CCSDT-3 and CC3_. Physical properties computed for the global minimum _X˜ 1_+HCP_ include harmonic vibrational frequencies with the cc-pV5Z CCSD_T_ method of _1=3344 cm−1, _2=689 cm−1, and _3=1298 cm−1. Linear HPC, a stationary point of Hessian index 2, is predicted to lie 75.2 kcal mol−1 above the global minimum HCP. The dissociation energy D0_HCP_X˜ 1_+_→H_2S_+CP_X 2_+__ of HCP is predicted to be 119.0 kcal mol−1, which is very close to the experimental lower limit of 119.1 kcal mol−1. Eight singlet excited states were examined and their physical properties were determined employing three equation-of-motion coupled cluster methods _EOM-CCSD, EOM-CCSDT-3, and EOM-CC3_. Four stationary points were located on the lowest-lying excited state potential energy surface, 1_− →1A_, with excitation energies Te of 101.4 kcal mol−1_1A_ HCP_, 104.6 kcal mol−1_1_− HCP_, 122.3 kcal mol−1_1A_ HPC_, and 171.6 kcal mol−1_1_− HPC_ at the cc-pVQZ EOM-CCSDT-3 level of theory. The physical properties of the 1A_ state with a predicted bond angle of 129.5° compare well with the experimentally reported first singlet state _A˜ 1A__. The excitation energy predicted for this excitation is T0=99.4 kcal mol−1_34 800 cm−1 , 4.31 eV_, in essentially perfect agreement with the experimental value of T0=99.3 kcal mol−1_34 746 cm−1 ,4.308 eV_. For the second lowest-lying excited singlet surface, 1_→1A_, four stationary points were found with Te values of 111.2 kcal mol−1 _21A_ HCP_, 112.4 kcal mol−1 _1_ HPC_, 125.6 kcal mol−1_2 1A_ HCP_, and 177.8 kcal mol−1_1_ HPC_. The predicted CP bond length and frequencies of the 2 1A_ state with a bond angle of 89.8° _1.707 Å, 666 and 979 cm−1_ compare reasonably well with those for the experimentally reported C ˜ 1A_ state _1.69 Å, 615 and 969 cm−1_. However, the excitation energy and bond angle do not agree well: theoretical values of 108.7 kcal mol−1 and 89.8° versus experimental values of 115.1 kcal mol−1 and 113°

Microsporidia-nematode associations in methane seeps reveal basal fungal parasitism in the deep sea

The deep sea is Earth’s largest habitat but little is known about the nature of deep-sea parasitism. In contrast to a few characterized cases of bacterial and protistan parasites, the existence and biological significance of deep-sea parasitic fungi is yet to be understood. Here we report the discovery of a fungus-related parasitic microsporidium, Nematocenator marisprofundi n. gen. n. sp. that infects benthic nematodes at Pacific Ocean methane seeps on the Pacific Ocean floor. This infection is species-specific and has been temporally and spatially stable over two years of sampling, indicating an ecologically consistent host-parasite interaction. A high distribution of spores in the reproductive tracts of infected males and females and their absence from host nematodes’ intestines suggests a sexual transmission strategy in contrast to the fecal-oral transmission of most microsporidia. N. marisprofundi targets the host’s body wall muscles causing cell lysis, and in severe infection even muscle filament degradation. Phylogenetic analyses placed N. marisprofundi in a novel and basal clade not closely related to any described microsporidia clade, suggesting either that microsporidia-nematode parasitism occurred early in microsporidia evolution or that host specialization occurred late in an ancient deep-sea microsporidian lineage. Our findings reveal that methane seeps support complex ecosystems involving interkingdom interactions between bacteria, nematodes, and parasitic fungi and that microsporidia parasitism exists also in the deep sea biosphere

Microsporidia-nematode associations in methane seeps reveal basal fungal parasitism in the deep sea

The deep sea is Earth's largest habitat but little is known about the nature of deep-sea parasitism. In contrast to a few characterized cases of bacterial and protistan parasites, the existence and biological significance of deep-sea parasitic fungi is yet to be understood. Here we report the discovery of a fungus-related parasitic microsporidium, Nematocenator marisprofundi n. gen. n. sp. that infects benthic nematodes at methane seeps on the Pacific Ocean floor. This infection is species-specific and has been temporally and spatially stable over 2 years of sampling, indicating an ecologically consistent host-parasite interaction. A high distribution of spores in the reproductive tracts of infected males and females and their absence from host nematodes' intestines suggests a sexual transmission strategy in contrast to the fecal-oral transmission of most microsporidia. N. marisprofundi targets the host's body wall muscles causing cell lysis, and in severe infection even muscle filament degradation. Phylogenetic analyses placed N. marisprofundi in a novel and basal clade not closely related to any described microsporidia clade, suggesting either that microsporidia-nematode parasitism occurred early in microsporidia evolution or that host specialization occurred late in an ancient deep-sea microsporidian lineage. Our findings reveal that methane seeps support complex ecosystems involving interkingdom interactions between bacteria, nematodes, and parasitic fungi and that microsporidia parasitism exists also in the deep-sea biosphere

Report of the ICES\NAFO Joint Working Group on Deep-water Ecology (WGDEC), 11–15 March 2013, Floedevigen, Norway.

On 11 February 2013, the joint ICES/NAFO WGDEC, chaired by Francis Neat (UK) and attended by ten members met at the Institute for Marine Research in Floedevi-gen, Norway to consider the terms of reference (ToR) listed in Section 2. WGDEC was requested to update all records of deep-water vulnerable marine eco-systems (VMEs) in the North Atlantic. New data from a range of sources including multibeam echosounder surveys, fisheries surveys, habitat modelling and seabed imagery surveys was provided. For several areas across the North Atlantic, WGDEC makes recommendations for areas to be closed to bottom fisheries for the purposes of conservation of VMEs

Open Ocean Deep Sea

The deep sea comprises the seafloor, water column and biota therein below aspecified depth contour. There are differences in views among experts and agencies regarding the appropriate depth to delineate the “deep sea”. This chapter uses a 200 metre depth contour as a starting point, so that the “deep sea” represents 63 per cent of the Earth’s surface area and about 98.5 per cent of Earth’s habitat volume (96.5 per cent of which is pelagic). However, much of the information presented in this chapter focuses on biodiversity of waters substantially deeper than 200 m. Many of the other regional divisions of Chapter 36 include treatments of shelf and slope biodiversity in continental-shelf and slope areas deeper than 200m. Moreover Chapters 42 and 45 on coldwater corals and vents and seeps, respectively, and 51 on canyons, seamounts and other specialized morphological habitat types address aspects of areas in greater detail. The estimates of global biodiversity of the deep sea in this chapter do include all biodiversity in waters and the seafloor below 200 m. However, in the other sections of this chapter redundancy with the other regional chapters is avoided, so that biodiversity of shelf, slope, reef, vents, and specialized habitats is assessed in the respective regional or thematic chapters. AB - The deep sea comprises the seafloor, water column and biota therein below aspecified depth contour. There are differences in views among experts and agencies regarding the appropriate depth to delineate the “deep sea”. This chapter uses a 200 metre depth contour as a starting point, so that the “deep sea” represents 63 per cent of the Earth’s surface area and about 98.5 per cent of Earth’s habitat volume (96.5 per cent of which is pelagic). However, much of the information presented in this chapter focuses on biodiversity of waters substantially deeper than 200 m. Many of the other regional divisions of Chapter 36 include treatments of shelf and slope biodiversity in continental-shelf and slope areas deeper than 200m. Moreover Chapters 42 and 45 on coldwater corals and vents and seeps, respectively, and 51 on canyons, seamounts and other specialized morphological habitat types address aspects of areas in greater detail. The estimates of global biodiversity of the deep sea in this chapter do include all biodiversity in waters and the seafloor below 200 m. However, in the other sections of this chapter redundancy with the other regional chapters is avoided, so that biodiversity of shelf, slope, reef, vents, and specialized habitats is assessed in the respective regional or thematic chapters.https://nsuworks.nova.edu/occ_facbooks/1050/thumbnail.jp