Persistent HIV-1 transcription in CD4+ T cells from ART-suppressed individuals can originate from biologically competent proviruses.

HIV-1 is able to persist in the face of potent antiretroviral therapy (ART). A number of strategies are being explored to allow ART-free viral remission or viral eradication. In order to gauge the progress of these strategies, assays with which to measure viral reservoir size and activity are needed. In a large percentage of aviremic individuals on suppressive ART, viral transcripts can be detected in peripheral blood CD4+ T cells. While this cell-associated RNA has been considered as a marker of viral reservoir activity, it is unclear whether cell-associated viral transcripts in aviremic individuals originate from biologically competent proviruses as opposed to being a product of abortive transcription from defective proviruses. We assessed whether cell-associated viral RNA in peripheral blood CD4+ T cells from aviremic individuals on ART originated from biologically competent proviruses. We demonstrate that cell-associated viral RNA transcripts were highly related to viral sequences obtained by ex vivo outgrowth. This relationship was also observed when viral transcription in the outgrowth cultures was limited to donor CD4+ T cells. Our study indicates that cell-associated viral RNA warrants further consideration as a viral reservoir surrogate in individuals on suppressive ART.

Impact of dry weather discharges on annual pollution from a separate storm sewer in Toulouse, France.

The city of Toulouse with its separate sewer system is ideal for studying stormwater. However, during dry weather, the storm sewer also discharges water into the environment, and it is the impact of these discharges on annual pollution from storm sewer that is the object of this study. Samples have been taken from the outlets of two storm drains located in heavily and moderately urbanized areas. Sampling has been undertaken during wet weather and during dry weather between January 2010 and February 2011. Three dry weather and two wet weather samples have been taken every three months and from each outlet. The overall pollution parameters have been analyzed (chemical oxygen demand, biological oxygen demand, total nitrogen, ammonium, nitrate, total phosphorus, suspended solid matter, volatile suspended matter, pH, conductivity, turbidity). Characterization has been completed by analysis of trace organic compounds: polycyclic aromatic hydrocarbons, total hydrocarbons, methyl tert-butyl ether, diethylhexylphthalate, nonylphenols, hormones (estradiol, ethinylestradiol). For certain parameters, the results obtained did not conform to legislative requirements concerning discharge into the natural environment. Correlations between these parameters have been studied, and identified between several of them using principal component analysis. The most important correlation observed was between conductivity and concentration in total phosphorus for one of the outlet. Results showed that dry weather had an impact on annual pollution load from separate storm sewer and that level of urbanization was also a factor. The effect of season has been studied but no significant impact was found.

Pesticides in roof runoff: study of a rural site and a suburban site.

The quality of stored roof runoff in terms of pesticide pollution was assessed over a one-year period. Two tanks, located at a rural and suburban site, respectively, were sampled monthly. The two studied collection surface were respectively a tile slope roof and a bituminous flat roof. Four hundred and five compounds and metabolites were screened using liquid and gas chromatography coupled with various detection systems. Principal Component Analysis was applied to the data sets to elucidate patterns. At the rural site, two groups of compounds associated with two different types of agriculture, vineyard and crops, were distinguished. The most frequently detected compound was glyphosate (83%) which is the most commonly used herbicide in French vineyards. At the suburban site, quantified compounds were linked to agriculture rather than urban practices. In addition, all samples were contaminated with mecoprop which is a roof-protecting agent. Its presence was attributed to the nature of roofing material used for rainwater collection. For both sites, the highest number and concentrations of compounds and metabolites were recorded at the end of spring and through summer. These results are consistent with treatment periods and higher temperatures.

Priority organic pollutants in the urban water cycle (Toulouse, France).

Application of the European Water Framework Directive requires Member States to have better understanding of the quality of surface waters in order to improve knowledge of priority pollutants. Xenobiotics in urban receiving waters are an emerging concern. This study proposes a screening campaign of nine molecular species of xenobiotics in a separated sewer system. Five sites were investigated over one year in Toulouse (France) using quantitative monitoring. For each sample, polycyclic aromatic hydrocarbons, polychlorinated biphenyls, nonylphenols, diethelhexylphthalate, linear alkylbenzene sulphonates, methyl tert-butylether, total hydrocarbons, estradiol and ethinylestradiol were analysed. Ground, rain and roof collected water concentrations are similar to treated wastewater levels. Run-off water was the most polluted of the five types investigated, discharged into the aquatic environment. The wastewater treatment plant reduced xenobiotic concentrations by 66% before discharge into the environment. Regarding environmental quality standards, observed concentrations in waters were in compliance with standards. The results show that xenobiotic concentrations are variable over time and space in all urban water compartments.

Monitoring of water quality from roof runoff: Interpretation using multivariate analysis.

The quality of harvested rainwater used for toilet flushing in a private house in the south-west of France was assessed over a one-year period. Temperature, pH, conductivity, colour, turbidity, anions, cations, alkalinity, total hardness and total organic carbon were screened using standard analytical techniques. Total flora at 22 °C and 36 °C, total coliforms, Escherichia coli and enterococci were analysed. Overall, the collected rainwater had good physicochemical quality but did not meet the requirements for drinking water. The stored rainwater is characterised by low conductivity, hardness and alkalinity compared to mains water. Three widely used bacterial indicators - total coliforms, E. coli and enterococci - were detected in the majority of samples, indicating microbiological contamination of the water. To elucidate factors affecting the rainwater composition, principal component analysis and cluster analysis were applied to the complete data set of 50 observations. Chemical and microbiological parameters fluctuated during the course of the study, with the highest levels of microbiological contamination observed in roof runoffs collected during the summer. E. coli and enterococci occurred simultaneously, and their presence was linked to precipitation. Runoff quality is also unpredictable because it is sensitive to the weather. Cluster analysis differentiated three clusters: ionic composition, parameters linked with the microbiological load and indicators of faecal contamination. In future surveys, parameters from these three groups will be simultaneously monitored to more accurately characterise roof-collected rainwater.

Incidence of HIV type 1 infection, antiretroviral drug resistance, and molecular characterization in newly diagnosed individuals in Argentina: A Global Fund Project.

An HIV incidence estimation was performed among men who have sex with men (MSM), drug users (DUs), sex workers (SWs), and pregnant women (PW) from Argentina. Volunteers older than 18 years old without a previous HIV-positive diagnosis were included. HIV-positive samples were analyzed by the Serological Testing Algorithm for Recent HIV Seroconversion (STARHS) to estimate incidence. By partial RT-PCR and sequencing of the HIV pol gene, an HIV subtype and resistance profile were determined. A total of 12,192 volunteers were recruited from October 2006 to September 2008. A higher HIV prevalence was detected among trans SWs (33.9%, 38/112), male SWs (10.8%, 12/111), and MSM 10.4% (161/1549). HIV incidence estimates by STARHS was also higher on trans SWs (11.31 per 100 person-years), male SWs (6.06 per 100 person-years), and MSM (6.36 per 100 person-years). Antiretroviral primary resistant mutations were detected in 8.4% of the study group, with a higher frequency in female DUs (33.3%). Phylogenetic analysis showed that 124 (57.9%) samples were subtype B, 84 (39.3%) intersubtype BF recombinants, 5 (2.3%) subtype C, and 1 (0.5%) subtype F in the pol region. Subtype B was most commonly found in MSM and male SWs whereas the intersubtype BF recombinant was more prevalent in female DUs, female SWs, and PW. Given the high HIV prevalence and incidence found in most of these groups, monitoring the continuing spread of the HIV epidemic is essential for determining public health priorities, assessing the impact of interventions, and estimating current and future health care needs.

Impact of carwash discharge on stormwater quality (Toulouse, France).

The contribution of discharge from carwashes to pollutant levels in stormwater was evaluated. Five carwashes and two outlets in the city of Toulouse (France) were selected. Water samples were collected from December 2006 to December 2007. Concentrations and loadings of classical water quality parameters (conductivity, pH, turbidity, chemical oxygen demand, nitrogen, phosphorus, ammonium, nitrate, suspended solid and volatile suspended solid) and five groups of organic compounds (polycyclic aromatic hydrocarbons, polychlorinated biphenyls, lauryl alkyl benzene sulphonates, methyl tert-butyl ether and total hydrocarbons) were determined. The results suggest that the wastewater derived from carwashes was negligible compared to the volume and flow rates within the stormwater network. However, high concentrations of polycyclic aromatic hydrocarbons, phosphorus and lauryl alkyl benzene sulphonates in liquid waste from carwashes, and the impact of these pollutants on stormwater quality could not be neglected.

FISH mapping of 57 BAC clones reveals strong conservation of synteny between Galliformes and Anseriformes.

Karyotypes of chicken (Gallus gallus domesticus; 2n = 78) and mallard duck (Anas platyrhynchos; 2n = 80) share the typical organization of avian karyotypes including a few macrochromosome pairs, numerous indistinguishable microchromosomes, and Z and W sex chromosomes. Previous banding studies revealed great similarities between chickens and ducks, but it was not possible to use comparative banding for the microchromosomes. In order to establish precise chromosome correspondences between these two species, particularly for microchromosomes, we hybridized 57 BAC clones previously assigned to the chicken genome to duck metaphase spreads. Although most of the clones showed similar localizations, we found a few intrachromosomal rearrangements of the macrochromosomes and an additional microchromosome pair in ducks. BAC clones specific for chicken microchromosomes were localized to separate duck microchromosomes and clones mapping to the same chicken microchromosome hybridized to the same duck microchromosome, demonstrating a high conservation of synteny. These results demonstrate that the evolution of karyotypes in avian species is the result of fusion and/or fission processes and not translocations.

Impact on crops, plants and soils of metal trace elements transfer and flux, after spreading of fertilizers and biosolids.

In France, the yearly production of sludge from wastewater treatment plants is 900,000 metric tons dry matter and 60% of this is reused for land application. Today, the sustainability of this pathway is open to question. Among the different arguments cited are the levels of metal trace elements and the risks of accumulation in soils. With the ultimate aim of agronomic sludge recycling, the transfer of metal trace elements has been studied using vegetation containers planted with rye-grass under controlled conditions of temperature and humidity. Samples of a domestic sludge, an industrial sludge and a fertilizer have been mixed with the soil. By monitoring the growth of the rye-grass, we have been able to observe that the addition of sludge increases production of plant matter. It appears that the roots absorb higher quantities of metal trace elements and form a barrier to their transfer to the above ground parts of the rye-grass. For the group of metal trace elements studied, no significant differences have been observed between the rye-grass grown on soil alone and that on soils amended with fertilizer or urban sludge. For the majority of the vegetation containers studied, there has been no significant modification in the soil metal distribution over time, as a result of the addition of urban sludge, and no significant difference between fertilizers and sludges.

The influence of biosolids treatment files on the mobility of metal trace elements.

The production of sludge in France is estimated to be about 900,000 metric tons dry matter per year and 60% of this is recycled onto agricultural land. At present, the long term future of this procedure is open to question and among the different arguments being put forward are the levels of metallic trace elements and the risk of accumulation in soils. This study presents the behaviour of metallic trace elements in sludges from three different treatment procedures: thickened liquid sludges, dewatered sludges and dried sludges. These biosolids are mixed with a clay soil and then placed in a temperature and humidity controlled glasshouse. Several containers are seeded with ryegrass and compared with controls. For the three harvests, covering all the amendments studied (including non-amended soil), the differences are not really representative. Absorption by the ryegrass is low in all cases. For the cadmium, the chromium, the nickel and the lead, the roots are 5 to 10 times more concentrated than the leaves. The majority of these elements stay absorbed in the roots, regardless of the amendment used. The addition of the sludges has considerably reduced the uptake of water in ryegrass throughout its growth cycle. Quite apart from their fertilizing qualities, wastewater treatment plant sludges could offer important implications for irrigation.

[Clinical utility of a commercial ligase chain-reaction kit for the diagnosis of pulmonary and extrapulmonary tuberculosis in the adult]. / Utilidad clínica de un equipo comercial de reacción en cadena de ligasa para el diagnóstico de la tuberculosis pulmonar y extrapulmonar del adulto.

Microscopy with the Ziehl-Neelsen (ZN) stain is frequently negative in paucibacillary tuberculosis (TB) so that the treatment must be started and continued until the culture results confirm or not the disease. LCx Mycobacterium tuberculosis Assay (Abbott, Lab.) uses the ligase chain reaction for direct amplification of DNA and rapid detection of M. tuberculosis Complex (MTB) in clinical specimens. We evaluated the usefulness of the LCx assay on 1,203 clinical samples: 737 respiratory and 466 extrapulmonary specimens. The LCx results were compared with those obtained by ZN and cultures on solid media and Mycobacteria Growth Indicator Tube (MGIT, Becton Dickinson, Argentina). Since detection and identification of MTB are simultaneously made by the LCx assay, a total of 145 out of 183 patients (79.2%) had a confirmed TB diagnosis in two working days. Positive culture results were predicted in 122 out of 160 cases (76.3%) by LCx and in 70 (43.8%) by ZN as well. The sensitivity (S) and specificity (ES) of LCx assay in ZN positive cases were 93.4% and 100.0% while in ZN negative cases they were 68.0% and 98.6%. The overall S and ES were 79.2% and 98.7%, respectively. We conclude that the LCx assay is a rapid and sensitive technique, which can be a helpful diagnostic tool mainly for paucibacillary TB in reference laboratories.

Utilidad clínica de un equipo comercial de reacción en cadena de ligasa para el diagnóstico de la tuberculosis pulmonar y extrapulmonar del adulto / [Clinical utility of a commercial ligase chain-reaction kit for the diagnosis of pulmonary and extrapulmonary tuberculosis in the adult]

Microscopy with the Ziehl-Neelsen (ZN) stain is frequently negative in paucibacillary tuberculosis (TB) so that the treatment must be started and continued until the culture results confirm or not the disease. LCx Mycobacterium tuberculosis Assay (Abbott, Lab.) uses the ligase chain reaction for direct amplification of DNA and rapid detection of M. tuberculosis Complex (MTB) in clinical specimens. We evaluated the usefulness of the LCx assay on 1,203 clinical samples: 737 respiratory and 466 extrapulmonary specimens. The LCx results were compared with those obtained by ZN and cultures on solid media and Mycobacteria Growth Indicator Tube (MGIT, Becton Dickinson, Argentina). Since detection and identification of MTB are simultaneously made by the LCx assay, a total of 145 out of 183 patients (79.2

) had a confirmed TB diagnosis in two working days. Positive culture results were predicted in 122 out of 160 cases (76.3

) by LCx and in 70 (43.8

) by ZN as well. The sensitivity (S) and specificity (ES) of LCx assay in ZN positive cases were 93.4

while in ZN negative cases they were 68.0

. The overall S and ES were 79.2

, respectively. We conclude that the LCx assay is a rapid and sensitive technique, which can be a helpful diagnostic tool mainly for paucibacillary TB in reference laboratories.

Utilidad clínica de un equipo comercial de reacción en cadena de ligasa para el diagnóstico de la tuberculosis pulmonar y extrapulmonar del adulto. / [Clinical utility of a commercial ligase chain-reaction kit for the diagnosis of pulmonary and extrapulmonary tuberculosis in the adult]

Microscopy with the Ziehl-Neelsen (ZN) stain is frequently negative in paucibacillary tuberculosis (TB) so that the treatment must be started and continued until the culture results confirm or not the disease. LCx Mycobacterium tuberculosis Assay (Abbott, Lab.) uses the ligase chain reaction for direct amplification of DNA and rapid detection of M. tuberculosis Complex (MTB) in clinical specimens. We evaluated the usefulness of the LCx assay on 1,203 clinical samples: 737 respiratory and 466 extrapulmonary specimens. The LCx results were compared with those obtained by ZN and cultures on solid media and Mycobacteria Growth Indicator Tube (MGIT, Becton Dickinson, Argentina). Since detection and identification of MTB are simultaneously made by the LCx assay, a total of 145 out of 183 patients (79.2

) had a confirmed TB diagnosis in two working days. Positive culture results were predicted in 122 out of 160 cases (76.3

) by LCx and in 70 (43.8

) by ZN as well. The sensitivity (S) and specificity (ES) of LCx assay in ZN positive cases were 93.4

and 100.0

while in ZN negative cases they were 68.0

and 98.6

. The overall S and ES were 79.2

and 98.7

, respectively. We conclude that the LCx assay is a rapid and sensitive technique, which can be a helpful diagnostic tool mainly for paucibacillary TB in reference laboratories.

Diagnóstico rápido y sensibilidad de Mycobacterium tuberculosis a antibióticos por el sistema MGIT / Rapid diagnosis and susceptibility of Mycobacterium tuberculosis to antibiotic using MGIT system

Son necesarias nuevas tecnologías que permitan obtener rápidamente el diagnóstico y la sensibilidad a los fármacos de Mycobacterium tuberculosis (MTB) para asegurar un tratamiento temprano y adecuado a la tuberculosis (TB), especialmente cuando ésta es causada por MTB resistente a isoniacida (H) y rifampicina (RMP) simultáneamente (TMBR). Un total de 218 materiales pulmonares obtenidos de 132 pacientes HIV(+) fueron procesados e inoculados en medio de cultivo líquido del sistema fluorescente "Mycobacterial Growth Indicator Tube" (MGIT, Becton Dickinson, USA) y en medios sólidos a base de huevos: Lowenstein-Jensen (L-J) y Stonebrick (SB). Posteriormente se determinó la concentración inhibitoria mínima (CIM) en MGIT de 120 aislamientos a H, RMP, estreptomicina (SM), ácido para-amino-salicílico (PAS) y etambutol (EMB). EL tiempo promedio de detección de crecimiento de MTB a partir de la muestra fue diagnosticado sólo por MGIT. Los resultados de sensibilidad obtenidos por CIM en MGIT se obtuvieron en un promedio de 5 días (3-10 días)y correlacionaron con los obtenidos por el clásico método de las proporciones en L-J (índice de correlación: 0,9974). La discordancia entre aislamientos resistentes a H y SM detectados por uno y otro método fue de 4,7 por ciento (2/42). El MGIT resultó un sistema seguro, confiable y rápido, especialmente para detectar resistencias micobacterianas, que podría ser empleado en laboratorios clínicos para diagnóstico y seguimiento de pacientes con TB

Diagnóstico rápido y sensibilidad de Mycobacterium tuberculosis a antibióticos por el sistema MGIT / Rapid diagnosis and susceptibility of Mycobacterium tuberculosis to antibiotic using MGIT system

Son necesarias nuevas tecnologías que permitan obtener rápidamente el diagnóstico y la sensibilidad a los fármacos de Mycobacterium tuberculosis (MTB) para asegurar un tratamiento temprano y adecuado a la tuberculosis (TB), especialmente cuando ésta es causada por MTB resistente a isoniacida (H) y rifampicina (RMP) simultáneamente (TMBR). Un total de 218 materiales pulmonares obtenidos de 132 pacientes HIV(+) fueron procesados e inoculados en medio de cultivo líquido del sistema fluorescente "Mycobacterial Growth Indicator Tube" (MGIT, Becton Dickinson, USA) y en medios sólidos a base de huevos: Lowenstein-Jensen (L-J) y Stonebrick (SB). Posteriormente se determinó la concentración inhibitoria mínima (CIM) en MGIT de 120 aislamientos a H, RMP, estreptomicina (SM), ácido para-amino-salicílico (PAS) y etambutol (EMB). EL tiempo promedio de detección de crecimiento de MTB a partir de la muestra fue diagnosticado sólo por MGIT. Los resultados de sensibilidad obtenidos por CIM en MGIT se obtuvieron en un promedio de 5 días (3-10 días)y correlacionaron con los obtenidos por el clásico método de las proporciones en L-J (índice de correlación: 0,9974). La discordancia entre aislamientos resistentes a H y SM detectados por uno y otro método fue de 4,7 por ciento (2/42). El MGIT resultó un sistema seguro, confiable y rápido, especialmente para detectar resistencias micobacterianas, que podría ser empleado en laboratorios clínicos para diagnóstico y seguimiento de pacientes con TB(AU)

[Rapid diagnosis and susceptibility of Mycobacterium tuberculosis to antibiotics using MGIT system]. / Diagnóstico rápido y sensibilidad de Mycobacterium tuberculosis a antibióticos por el sistema MGIT.

New technologies for rapid detection and drug susceptibility testing of mycobacteria are needed in clinical laboratories in order to attempt a rapid diagnosis and effective treatment of tuberculosis (TB) specially of cases resistant to isoniazid (H) and rifampin (RMP) (MDR-TB). A total of 218 pulmonary specimens from 132 HIV coinfected patients were processed and inoculated into the Mycobacterial Growth Indicator Tube system (MGIT, Becton Dickinson, MD) and on Lowenstein-Jensen (L-J) and Stonebrink (SB) solid media. The average time for recovering Mycobacterium tuberculosis (MTB) from MGIT was 18.3 days and 31.0 days from solid media. Of the patients 14.4% (19/132) were only diagnosed by MGIT. In another experiment susceptibility tests by the classical proportion method (PM) in L-J medium with H, RMP, streptomycin (SM), para-aminosalycilic-acid and ethambutol (EMB) were carried out on 120 isolates. The results were later compared with those obtained by determining the minimal inhibitory concentration (MIC) for each drug in MGIT against the above mentioned isolates. MIC results from MGIT method were available in an average of 5 days (3-10) and they correlated (correlation index 0.9974) with those of drug susceptibility obtained by the PM. A 4.7% (2/42) of disagreement among detecting isolates resistant to H and SM was found between PM and MGIT. Our results showed MGIT as a useful, safe and timesaving culture system, specially for detecting TB resistance. It might be used in clinical laboratories to improve the proper management of TB patients.

Carbonate ions in apatites: infrared investigations in the upsilon 4 CO3 domain.

Fourier transform infrared (IR) spectroscopic investigations of precipitated carbonate apatites in the upsilon 4 CO3 domain reveal the existence of five bands at 757, 740, 718, 692, 670 cm-1 which can be assigned to several distinct environments of the carbonate ion in the apatite structure. In order to identify these environments precisely, fluoridated and pure type A carbonate apatites (i.e., with carbonate ions in monovalent anionic sites) were examined. The bands at 670 and 757 cm-1 were attributed to type A carbonate and their relative intensity was found to increase when the carbonate content of the apatite diminished or when samples were heated at 400 degrees C. Fluoridated apatites show only two bands, close to 718 and 692 cm-1, corresponding to type B carbonate ions (carbonate in trivalent anionic sites). The band at 740 cm-1 was revealed by heating the samples to 400 degrees C. This is due to OH ions' hydrogen bonded to fluoride and to carbonate ions in an undetermined apatite site. Despite the low intensity of IR bands, investigations in the upsilon 4 CO3 domain appear complementary to those in other carbonate vibrational domains and could be useful for a more precise identification of bone mineral.