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Virological and immunological effects of treatment interruptions in HIV-1 infected patients with treatment failure.

OBJECTIVE: To analyse the immunological and virological effects of treatment interruptions in HIV-1-infected patients with treatment failure and multidrug-resistant virus. METHODS: Drug susceptibility was assessed using Antivirogram and genotypic analysis was based on population and clonal sequencing for 48 patients who had interrupted treatment (> or = 2 months). RESULTS: Treatment interruption resulted in viral load increases (mean 0.7 log 10 copies/ ml; P = 0.0001) and CD4 cell count decreases (mean 89 x 10(6) cells/l; P = 0.0001). A complete shift to wild-type virus at the phenotypic, genotypic and clonal level was observed in 28/45 patients. These patients differed from those that did not show a shift to wild type in baseline CD4 cell counts (192 versus 59 x 10(6) cells/l; P= 0.007) and in the relationship between baseline viral load and CD4 cell count (no correlation versus a significant negative correlation; P= 0.008). Response to re-initiation of treatment fell with increasing viral load [relative hazard (RH) 0.33; P= 0.001] and with increasing total number of drugs with reduced susceptibility (RH 0.51; P = 0.0003); it improved with the number of new drugs received (RH 2.12; P = 0.0002) and a shift to wild type (RH 5.22, P = 0.006). CONCLUSIONS: Changes in surrogate markers suggest that treatment provided benefit in spite of virological failure and resistant virus. Although patients with a shift to wildtype virus responded better in the short term to treatment re-initiation, the long-term effects are not known and the risk of immune deterioration needs to be carefully considered.

Adult↗

Soil quality and vulnerability in a Mediterranean natural ecosystem of Central Italy.

Wet and dry atmospheric depositions and soil chemical and microbiological properties were determined in a Mediterranean natural ecosystem of Central Italy near Rome (Castelporziano Estate). The monitoring of depositions permitted us to quantify the exceedances of S and N compounds (expressed as eqH(+)ha(-1)year(-1)) over the critical loads of acidity. Critical loads, i.e. the quantity of a substance which a part of the environment can tolerate without adverse effects occurring, were determined adopting the level 0 methodology following the UN/ECE Convention on Long-range Transboundary Air Pollution. Deposition data were available for the period 1992-1997, and acidity exceedances were referred to the main vegetation types present in the area. Results showed that most part of the Estate has a medium degree of vulnerability to acidification, and the corresponding risk of acidification deriving from the exceedances of atmospheric deposition was rather low. The study of soil chemical and microbiological properties included mainly total soil organic carbon (SOC), microbial biomass-C, biomass-C/SOC, soil respiration, and metabolic quotient (qCO2). Soil organic C metabolism has been discussed on the basis of the results from eight sampling sites.

Air Pollutants↗

Hydrogen sulfide oxidation by a microbial consortium in a recirculation reactor system: sulfur formation under oxygen limitation and removal of phenols.

Wastewater from petroleum refining may contain a number of undesirable contaminants including sulfides, phenolic compounds, and ammonia. The concentrations of these compounds must be reduced to acceptable levels before discharge. Sulfur formation and the effect of selected phenolic compounds on the sulfide oxidation were studied in autotrophic aerobic cultures. A recirculation reactor system was implemented to improve the elemental sulfur recovery. The relation between oxygen and sulfide was determined calculating the O2/S2- loading rates (Q(O2)/Q(S)2- = Rmt), which adequately defined the operation conditions to control the sulfide oxidation. Sulfur-producing steady states were achieved at Rmt ranging from 0.5 to 1.5. The maximum sulfur formation occurred at Rmt of 0.5 where 85% of the total sulfur added to the reactor as sulfide was transformed to elemental sulfur and 90% of it was recovered from the bottom of the reactor. Sulfide was completely oxidized to sulfate (Rmt of 2) in a stirred tank reactor, even when a mixture of phenolic compounds was present in the medium. Microcosm experiments showed that carbon dioxide production increased in the presence of the phenols, suggesting that these compounds were oxidized and that they may have been used as carbon and energy source by heterotrophic microorganisms present in the consortium.

Air Pollutants↗

High efficiency degradation of tetrahydrofuran (THF) using a membrane bioreactor: identification of THF-degrading cultures of Pseudonocardia sp. strain M1 and Rhodococcus ruber isolate M2.

A mixed microbial culture capable of growing aerobically on tetrahydrofuran (THF) as a sole carbon and energy source was used as the inoculum in a 10 l working volume membrane bioreactor. Following start-up, the reactor was operated in batch mode for 24 h and then switched to continuous feed with 100% biomass recycle. On average, greater than 96% of THF fed to the reactor was removed during the 8-month study. THF loading rates ranged from 0.62 to 9.07 g l(-1) day(-1) with a hydraulic retention time of 24 h. THF concentrations as high as 800 mg/l were tolerated by the culture. Biomass production averaged 0.28 kg total suspended solids/kg chemical oxygen demand removed, i.e., comparable to a conventional wastewater treatment process. Periodic batch wasting resulted in a solids retention time of 7-14 days. Reactor biomass typically ranged from 4 to 10 g/l volatile suspended solids and the effluent contained no solids. Pure THF-degrading cultures were isolated from the mixed culture based on morphological characteristics, Gram-staining and THF degradation. Based on 16S rDNA analysis the isolates were identified as Pseudonocardia sp. M1 and Rhodococcus ruber M2.

Bioreactors↗

Mathematical basis for the optimization of single cell-line screening on multi-well plates.

Screening of stably transfected cells on multi-well plates is most efficient when a maximum number of wells contain a single colony. The multinomial distribution has been used to derive a novel equation that relates the number of wells containing a specified number of cell-lines and the total number of viable cells loaded on the plate. To test its validity, Chinese hamster ovary cells were transfected with a gene coding for the M2 muscarinic cholinergic receptor and screened on 96-well plates. The observed and predicted numbers of wells containing a single cell-line were indistinguishable. This approach therefore can be used to optimize the conditions for screening transfected cells.

Algorithms↗

An in vitro oral biofilm model for comparing the efficacy of antimicrobial mouthrinses.

The ability of commercial mouthrinses to reduce total viable counts of mixed microbial populations was examined using a previously developed in vitro model of supragingival plaque. Exploratory experiments aimed at fine-tuning the model indicated that optimal correspondence between in vitro and clinical results for chlorhexidine-containing formulations were obtained at a saliva:medium ratio of 70:30 (v/v); moreover, expanding the microbial population from 5 bacterial species to 5 bacterial species + Candida albicans had no noticeable impact on overall results. The efficacies of 12 different mouthrinse proprietary products containing chlorhexidine, hexetidine, octenidine, Triclosan, plant extracts, or aminefluoride/stannous fluoride vis-à-vis biofilm clearance were compared. All mouthrinses promoted a statistically significant reduction in microbial load compared to distilled water. The herbal- and phenolic-based products were substantially less effective than most chlorhexidine-containing mouthrinses, or mouthrinses containing hexetidine or octenidine. No significant difference between the plaque-clearing plaque-clearing abilities of Listerine and Meridol was observed. This polyspecies biofilm model can be a valuable tool for preclinical testing of antiplaque formulations, particularly during the product development stage.

Anti-Infective Agents, Local↗

Comparison of selective polymerase chain reaction primers and differential probe hybridization of polymerase chain reaction products for determination of relative amounts of codon 215 mutant and wild-type HIV-1 populations.

A mutation at codon 215 of the human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) gene results in decreased sensitivity to zidovudine (ZDV). In order to follow changes in codon 215 mutant (MUT) and wild-type (WT) populations in the plasma of patients during therapy, two polymerase chain reaction (PCR) procedures were investigated. The first was a nested, selective PCR, wherein a first round with viral-specific primers was followed by a second round with allele-specific primers. Although the procedure is relatively sensitive, some samples in the first round of PCR could not be amplified. In mixing experiments, mispriming of the MUT primer made relative determination of quantities subjective and difficult. Differential hybridization of PCR product with probes specific for codon 215 MUT or WT sequences was also investigated. A probe directed to a highly conserved region of the RT gene in the amplified PCR product was used to determine the total amount of PCR product analyzed. Differential hybridization was linear and reproducible over several logs of MUT:WT ratios, and determination of a 1:100 ratio of MUT:WT was readily achieved. When applied to longitudinal samples from three patients, dramatic changes in each population were readily apparent. These changes were evaluated with regard to viral load.

Base Sequence↗

Development of a biological process for livestock wastewater treatment using a technique for predominant outgrowth of Bacillus species.

The investigation has been carried out by treating 1 m3/day of livestock wastewater for 9 months. The biological process is composed of two reactors connected in series. Each reactor has been designed to stimulate the growth of Bacillus sp., spore-forming aerobic or facultatively anaerobic bacteria. As a consequence, the population of Bacillus sp. is aptly increased via the cycle of sporulation, germination and proliferation. With a predominant growth of Bacillus sp., the microbial activity has been increased comparing to activated sludge based on the result of measuring specific oxygen uptake rate (SOUR). This process was able to remove nitrogen and phosphorus as well as organic matter efficiently. More than 98% of biochemical oxygen demand (BOD) and chemical oxygen demand (COD) were removed. In term of removing the total nitrogen (T-N), about 98% of this was reduced. On average, the T-N concentration in the feed was 3,270 mg/l but 74 mg/l in the effluent including 30 mg/l of nitrite and nitrate nitrogen. The total phosphorus (T-P) reduction averaged 87.5%. As a result, it would be advantageous to load this process in order to deal with high-strength wastewater.

Agriculture↗

In situ experimental evidence of the fate of a phytodetritus pulse at the abyssal sea floor.

More than 50% of the Earth' s surface is sea floor below 3,000 m of water. Most of this major reservoir in the global carbon cycle and final repository for anthropogenic wastes is characterized by severe food limitation. Phytodetritus is the major food source for abyssal benthic communities, and a large fraction of the annual food load can arrive in pulses within a few days. Owing to logistical constraints, the available data concerning the fate of such a pulse are scattered and often contradictory, hampering global carbon modelling and anthropogenic impact assessments. We quantified (over a period of 2.5 to 23 days) the response of an abyssal benthic community to a phytodetritus pulse, on the basis of 11 in situ experiments. Here we report that, in contrast to previous hypotheses, the sediment community oxygen consumption doubled immediately, and that macrofauna were very important for initial carbon degradation. The retarded response of bacteria and Foraminifera, the restriction of microbial carbon degradation to the sediment surface, and the low total carbon turnover distinguish abyssal from continental-slope 'deep-sea' sediments.

Animals↗

A combinatorial ledge: reverse transcriptase fidelity, total body viral burden, and the implications of multiple-drug HIV therapy for the evolution of antiviral resistance.

The chronicity, high mutation rates, and high circulating titers of HIV during the 'stable' phase of infection make rapid evolution of resistance mutations a key predictor of antiretroviral efficacy. Recent advances in measurement of viral RNA titers, turnover dynamics and the in vivo spectrum of resistance mutations allow realistic in vivo estimates of important kinetic parameters of within-patient evolution of viral resistance. First-order estimates of the frequency of viral genotypes necessary for resistance to many antiretroviral combination regimens indicate that many such genotypes pre-exist in patients prior to initiation of therapy. The combinatorial nature of observed multiply-resistant genotypes, however, along with current estimates of total-body viral load and viral turnover dynamics, imply a strikingly sharp transition associated with the change from two-drug to three-drug antiretroviral regimens: pre-existing resistance being near-certain in the first instance but highly unlikely in the second. This abrupt change, a 'combinatorial ledge', carries with it a number of important implications for the understanding and control of HIV infection and other potential targets of antiviral therapy.

Anti-HIV Agents↗

Performance of an internal-loop airlift bioreactor for treatment of hexane-contaminated air.

Hexane is a toxic volatile organic compound that is quite abundant in gas emissions from chemical industries and printing press and painting centers, and it is necessary to treat these airstreams before they discharge into the atmosphere. This article presents a treatment for hexane-contaminated air in steady-state conditions using an internal-loop airlift bioreactor inoculated with a Pseudomonas aeruginosa strain. Bioprocesses were conducted at 20-mL/min, a load of 1.26 gm3 of C6H14, and a temperature of 28 degrees C. The results of hexane removal efficiencies were presented as a function of the inoculum size (approx 0.07 and 0.2 g/L) and cell reuse. Bioprocess monitoring comprises quantification of the biomass, the surface tension of the medium, and the hexane concentration in the fermentation medium as well as in the inlet and outlet airstreams. The steady-state results suggest that the variation in inoculum size from 0.07 to 0.2 g/L promotes hexane abatement from the influent from 65 to 85%, respectively. Total hydrocarbon removal from the waste gas was achieved during experiments conducted using reused cells at an initial microbial concentration of 0.2 g/L.

Air↗

Soil microbial communities and enzyme activities under various poultry litter application rates.

The potential excessive nutrient and/or microbial loading from mismanaged land application of organic fertilizers is forcing changes in animal waste management. Currently, it is not clear to what extent different rates of poultry litter impact soil microbial communities, which control nutrient availability, organic matter quality and quantity, and soil degradation potential. From 2002 to 2004, we investigated the microbial community and several enzyme activities in a Vertisol soil (fine, smectitic, thermic, Udic Haplustert) at 0 to 15 cm as affected by different rates of poultry litter application to pasture (0, 6.7, and 13.4 Mg ha(-1)) and cultivated sites (0, 4.5, 6.7, 9.0, 11.2, and 13.4 Mg ha(-1)) in Texas, USA. No differences in soil pH (average: 7.9), total N (pasture: 2.01-3.53, cultivated: 1.09-1.98 g kg(-1) soil) or organic C (pasture average: 25-26.7, cultivated average: 13.9-16.1 g kg(-1) soil) were observed following the first four years of litter application. Microbial biomass carbon (MBC) and nitrogen (MBN) increased at litter rates greater than 6.7 Mg ha(-1) (pasture: MBC = >863, MBN = >88 mg kg(-1) soil) compared to sites with no applied litter (MBC = 722, MBN = 69 mg kg(-1) soil). Enzyme activities of C (beta-glucosidase, alpha-galactosidase, beta-glucosaminidase) or N cycling (beta-glucosaminidase) were increased at litter rates greater than 6.7 Mg ha(-1). Enzyme activities of P (alkaline phosphatase) and S (arylsulfatase) mineralization showed the same response in pasture, but they were only increased at the highest (9.0, 11.2, and 13.4 Mg ha(-1)) litter application rates in cultivated sites. According to fatty acid methyl ester (FAME) analysis, the pasture soils experienced shifts to higher bacterial populations at litter rates of 6.7 Mg ha(-1), and shifts to higher fungal populations at the highest litter application rates in cultivated sites. While rates greater than 6.7 Mg ha(-1) provided rapid enhancement of the soil microbial populations and enzymatic activities, they result in P application in excess of crop needs. Thus, studies will continue to investigate whether litter application at rates below 6.7 Mg ha(-1), previously recommended to maintain water quality, will result in similar improved soil microbial and biochemical functioning with continued annual litter application.

Alkaline Phosphatase↗

Recovery of coal fines from washery and power plant effluents by integrated technique of oil agglomeration and biofilm formation.

The possibility of applying an integrated technique of oil agglomeration and biofilm formation for recovery of coal fines from coal washeries and power plants effluents has been explored. Laboratory experiments with simulated slurries of different Indian coal fines demonstrate that vegetable oils are satisfactory agglomerating agents for recovery of most of the coal fines depending on the nature of coal and type of oil. The agglomeration behaviour of coal fines was assessed in terms of % yield, % organic matter recovery and % ash rejections. Maximum 85% agglomerate recovery was obtained in the agglomeration stage. Residual oil concentrations in some cases were found to exceed the permissible limit. Recovery of residual coal fines and reduction in residual oil concentration in the resultant slurry after oil agglomeration have been attempted using biofilm formation. A laboratory scale treatment reactor was put under complete recirculation to facilitate attached microbial growth on coal particles as carrier under aerobic conditions. The influence of various parameters on attached growth and stable biofilm formation were studied. The growth patterns of attached cell in suspension and consumption pattern of carbon substrate (oil) have been investigated. Steady decline in residual substrate concentration in the slurry with corresponding increase in the growth of attached and free cell mass is observed. The growth process was favoured in pH range of 6.5-7.0. The attached growth was found to be expanded in size in due course of time ultimately leading to the formation of stable biofilm in the treatment reactor which was subjected to the influent total suspended solids loading resulting from oil agglomeration step. Performance of the biofilm reactor in terms of % reduction in total suspended solids and residual oil concentration in the influent slurry was assessed in continuous mode. Complete recovery of coal fines and 60% degradation of oil was observed in the final effluent discharged from the treatment reactor.

Biofilms↗

High-rate thermophilic methane fermentation on short-chain fatty acids in a down-flow anaerobic packed-bed reactor.

In order to maximize the efficiency of methane fermentation on short-chain fatty acids, growth media containing acetic acid and butyric acid as major carbon sources were supplied to a thermophilic down-flow anaerobic packed-bed reactor. The organic loading rate (OLR) to the reactor ranged from 0.2 to 169 kg-dichromate chemical oxygen demand(CODcr)/m(3)-reactor/day, corresponding to a hydraulic retention time (HRT) of between 1.4 h and 20 days. Stable methane production was maintained at HRTs as short as 2 h (OLR=120 kg-CODcr/m(3)/day), with the short-chain fatty acids in the feed almost completely removed during the process. The apparent substrate removal efficiency, determined from the total CODcr values in the influent and effluent, was 75% at short HRTs. However, the actual substrate removal efficiency must have been greater than 75%, since a fraction of substrate was also utilized in microbial cell synthesis, and these cells were part of the measured total CODcr.

Acetic Acid↗

Control of denitrification in a septage-treating artificial wetland: the dual role of particulate organic carbon.

We examined the factors controlling organic carbon (C) cycling and its control of nitrogen (N) removal via denitrification in an aerated artificial wetland treating highly concentrated wastewater to nutrient-removal standards. Processing of organic material by the septage-treating wetland affected the biological reactivity (half-life, or t1/2) of organic C pools through microbial degradation and gravity fractionation of the influent septage. Primary sedimentation fractionated the initial septage material (t1/2 = 8.4d) into recalcitrant waste solids (t1/2 = 16.7d) and highly labile supernatant (t1/2 = 5.0d), allowing this reactive fraction to be further degraded during treatment in aerobic wetland tanks until a less labile material (t1/2 = 7.3d) remained. Organic C contributions from in situ fixation by nitrifying bacteria or algae in these tanks were small, about 1% of the C degradation rate. In the aerated tanks, denitrification was correlated with particulate organic C loading rates, although the average C required (0.35 mg C L(-1)h(-1)) to support denitrification was only 12% of the total C respiration rate (2.9 mg C L(-1)h(-1)). Additions of plant litter (2.5g C L(-1)) to the aerated tanks under normal operating conditions doubled denitrification rates to 0.58 mg N L(-1)h(-1), and reduced effluent nitrate levels by half, from 12.7 to 6.4 mg N L(-1). However, C degradation within the plant litter (0.15mg C L(-1)h(-1)) was sufficient to have accounted for only 35% of the additional denitrification. Evidence from laboratory and full-scale plant litter additions as well as process monitoring indicates that the stimulation of denitrification is due to the respiration-driven formation of anaerobic microsites within particulate organic C. In this aerated highly C-loaded septage-treating wetland, anaerobic microsite, rather than C substrate availability limits denitrification.

Anaerobiosis↗

A bacteriological assessment of multibacillary cases in leprosy colonies after 4 1/2 years of multidrug therapy.

In this presentation we have devised a novel way of calculating the total bacterial quantum in 100 (78 LL and 22 BL) multibacillary leprosy patients living in leprosy colonies. The calculation is based on Ridley's logarithmic scale. We have also attempted to assess the reduction in the bacterial quantum as a result of intervention through multidrug therapy (MDT). 53% of the patients rendered bacteriologically negative within two years of treatment of MDT and 94% at 54th pulse dose i.e. at 54th month. The bacterial quantum in human source as leprosy patients was calculated thus--Average BI of the group X Number of patients in each group X Multiplication factor devised as per Ridley's Bacterial Index (BI). By applying this purely arithmetic formula, it was found that 99.8% of the bacterial load is harboured in leprosy patients having BI more than 3. The introduction of MDT initiated the reduction in total bacterial quantum "based on above arithmetic scale" was achieved very fast i.e., from 100% to 5% at 12 months and to 0.4% at 24 months. We believe that if one wants to achieve leprosy control through a reduction in total bacterial quantum within a specific period, leprosy cases with BI more than 3 should be treated on priority basis.

Colony Count, Microbial↗

Risk of iron overload is decreased in beating heart coronary artery surgery compared to conventional bypass.

Conventional cardiopulmonary bypass surgery (CCPB) increases the iron loading of plasma transferrin often to a state of plasma iron overload, with the presence of low molecular mass iron. Such iron is a potential risk factor for oxidative stress and microbial virulence. Here we assess 'off-pump' coronary artery surgery on the beating heart for changes in plasma iron chemistry. Seventeen patients undergoing cardiac surgery using the 'Octopus' myocardial wall stabilisation device were monitored at five time points for changes in plasma iron chemistry. This group was further divided into those (n=9) who had one- or two- (n=8) vessel grafts, and compared with eight patients undergoing conventional coronary artery surgery. Patients undergoing beating heart surgery had significantly lower levels of total plasma non-haem iron, and a decreased percentage saturation of their transferrin at all time points compared to conventional bypass patients. Plasma iron overload occurred in only one patient undergoing CCPB. Beating heart surgery appears to decrease red blood cell haemolysis, and tissue damage during the operative procedures and thereby significantly decreases the risk of plasma iron overload associated with conventional bypass.

Adult↗

Atmospheric nitrogen inputs to the Delaware Inland Bays: the role of ammonia.

A previous assessment of nitrogen loading to the Delaware Inland Bays indicates that atmospheric deposition provides 15-25% of the total, annual N input to these estuaries. A large and increasing fraction of the atmospheric wet flux is NH(4)(+), which for most aquatic organisms represents the most readily assimilated form of this nutrient. Particularly noteworthy is a 60% increase in the precipitation NH(4)(+) concentration at Lewes, DE over the past 20 years, which parallels the increase in poultry production on the Delmarva Peninsula over this period (currently standing at nearly 585 million birds annually). To further examine the relationship between local NH(3) emissions and deposition, biweekly-integrated gaseous NH(3) concentrations were determined using Ogawa passive samplers deployed at 13 sampling sites throughout the Inland Bays watershed over a one-year period. Annual mean concentrations at the 13 sites ranged from <0.5 microg NH(3)m(-3) to >6 microg NH(3)m(-3), with a mean of 1.6+/-1.0 microg NH(3)m(-3). At most sites, highest NH(3) concentrations were evident during spring and summer, when fertilizer application and poultry house ventilation rates are greatest, and seasonally elevated temperatures induce increased rates of microbial activity and volatilization from soils and animal wastes. The observed north-to-south concentration gradient across the watershed is consistent with the spatial distribution of poultry houses, as revealed by a GIS analysis of aerial photographs. Based on the average measured NH(3) concentration and published NH(3) deposition rates to water surfaces (5-8 mm s(-1)), the direct atmospheric deposition of gaseous NH(3) to the Inland Bays is 3.0-4.8 kg ha(-1)yr(-1). This input, not accounted for in previous assessments of atmospheric loading to the Inland Bays, would effectively double the estimated direct dry deposition rate, and is on par with the NO(3)(-) and NH(4)(+) wet fluxes. A second component of this study examined spatial differences in NO(3)(-) and NH(4)(+) wet deposition within the Inland Bays watershed. In a pilot study, precipitation composition at the Lewes NADP-AIRMoN site (DE 02) was compared with that at a satellite site established at Riverdale on the Indian River Estuary, approximately 21 km southwest. While the volume-weighted mean precipitation NO(3)(-) concentrations did not differ significantly between sites, the NH(4)(+) concentration observed at Riverdale (26.3 micromoles L(-1)) was 73% greater than at Lewes (15.2 micromoles L(-1)). More recently, a NADP site was established at Trap Pond, DE (DE 99), which was intentionally located within the region of intense poultry production. A comparison of the initial two years (6/2001-5/2003) of precipitation chemistry data from Trap Pond with other nearby NADP-AIRMoN sites (Lewes and Smith Island) reveals fairly homogeneous NO(3)(-) wet deposition, but significant spatial differences ( approximately 60%) in the NH(4)(+) wet flux. Overall, these results suggest that local emissions and below-cloud scavenging provide a significant contribution to regional atmospheric N deposition.

Air Pollutants↗