Analysis of HIV-1 expression level and sense of transcription by high-throughput sequencing of the infected cell.

Next-generation sequencing offers an unprecedented opportunity to jointly analyze cellular and viral transcriptional activity without prerequisite knowledge of the nature of the transcripts. SupT1 cells were infected with a vesicular stomatitis virus G envelope protein (VSV-G)-pseudotyped HIV vector. At 24 h postinfection, both cellular and viral transcriptomes were analyzed by serial analysis of gene expression followed by high-throughput sequencing (SAGE-Seq). Read mapping resulted in 33 to 44 million tags aligning with the human transcriptome and 0.23 to 0.25 million tags aligning with the genome of the HIV-1 vector. Thus, at peak infection, 1 transcript in 143 is of viral origin (0.7%), including a small component of antisense viral transcription. Of the detected cellular transcripts, 826 (2.3%) were differentially expressed between mock- and HIV-infected samples. The approach also assessed whether HIV-1 infection modulates the expression of repetitive elements or endogenous retroviruses. We observed very active transcription of these elements, with 1 transcript in 237 being of such origin, corresponding on average to 123,123 reads in mock-infected samples (0.40%) and 129,149 reads in HIV-1-infected samples (0.45%) mapping to the genomic Repbase repository. This analysis highlights key details in the generation and interpretation of high-throughput data in the setting of HIV-1 cellular infection.

Evolutionary implications of a high selfing rate in the freshwater snail Lymnaea truncatula.

Self-compatible hermaphroditic organisms that mix self-fertilization and outcrossing are of great interest for investigating the evolution of mating systems. We investigate the evolution of selfing in Lymnaea truncatula, a self-compatible hermaphroditic freshwater snail. We first analyze the consequences of selfing in terms of genetic variability within and among populations and then investigate how these consequences along with the species ecology (harshness of the habitat and parasitism) might govern the evolution of selfing. Snails from 13 localities (classified as temporary or permanent depending on their water availability) were sampled in western Switzerland and genotyped for seven microsatellite loci. F(IS) (estimated on adults) and progeny array analyses (on hatchlings) provided similar selfing rate estimates of 80%. Populations presented a low polymorphism and were highly differentiated (F(ST) = 0.58). Although the reproductive assurance hypothesis would predict higher selfing rate in temporary populations, no difference in selfing level was observed between temporary and permanent populations. However, allelic richness and gene diversity declined in temporary habitats, presumably reflecting drift. Infection levels varied but were not simply related to either estimated population selfing rate or to differences in heterozygosity. These findings and the similar selfing rates estimated for hatchlings and adults suggest that within-population inbreeding depression is low in L. truncatula.

Use of high-resolution geophysical data to characterize heterogeneous aquifers: influence of data integration method on hydrological predictions

The integration of geophysical data into the subsurface characterization problem has been shown in many cases to significantly improve hydrological knowledge by providing information at spatial scales and locations that is unattainable using conventional hydrological measurement techniques. The investigation of exactly how much benefit can be brought by geophysical data in terms of its effect on hydrological predictions, however, has received considerably less attention in the literature. Here, we examine the potential hydrological benefits brought by a recently introduced simulated annealing (SA) conditional stochastic simulation method designed for the assimilation of diverse hydrogeophysical data sets. We consider the specific case of integrating crosshole ground-penetrating radar (GPR) and borehole porosity log data to characterize the porosity distribution in saturated heterogeneous aquifers. In many cases, porosity is linked to hydraulic conductivity and thus to flow and transport behavior. To perform our evaluation, we first generate a number of synthetic porosity fields exhibiting varying degrees of spatial continuity and structural complexity. Next, we simulate the collection of crosshole GPR data between several boreholes in these fields, and the collection of porosity log data at the borehole locations. The inverted GPR data, together with the porosity logs, are then used to reconstruct the porosity field using the SA-based method, along with a number of other more elementary approaches. Assuming that the grid-cell-scale relationship between porosity and hydraulic conductivity is unique and known, the porosity realizations are then used in groundwater flow and contaminant transport simulations to assess the benefits and limitations of the different approaches.

Prevalence, awareness, treatment and control of high blood pressure in a Swiss city general population: the CoLaus study.

BACKGROUND: This study is aimed to assess the prevalence of awareness, treatment and control of high blood pressure (HBP) and associated factors in a Swiss city. DESIGN: Population-based cross-sectional study of 6182 participants (52.5% women) aged 35-75 years living in Lausanne, Switzerland. METHODS: HBP was defined as blood pressure >/=140/90 mmHg or current antihypertensive medication. RESULTS: The overall prevalence of HBP was 36% (95% confidence interval: 35-38%). Among participants with HBP, 63% were aware of it. Among participants aware of HBP, 78% were treated, and among those treated, 48% were controlled (BP <140/90 mmHg). In multivariate analysis, HBP prevalence was associated with older age, male sex, low educational level, high alcohol intake, awareness of diabetes or dyslipidaemia, obesity and parental history of myocardial infarction. HBP awareness was associated with older age, female sex, awareness of diabetes or dyslipidaemia, obesity and parental history of myocardial infarction. HBP control was associated with younger age, higher educational level and no alcohol intake. Alone or in combination, sartans were the most often prescribed antihypertensive medication category (41%), followed by diuretics, beta-blockers, angiotensin converting enzyme inhibitors and calcium channel blockers. Only 31% of participants treated for HBP were taking >/=2 antihypertensive medications. CONCLUSION: Although more than half of all participants with HBP were aware and more than three-quarters of them received a pharmacological treatment, less than half of those treated were adequately controlled.

Lymphoid environment limits superantigen and antigen-induced T cell proliferation at high precursor frequency.

After superantigen challenge a significant proportion of superantigen-reactive T cells remain undivided. We provide evidence that the lymphoid environment limits T cell proliferation in the secondary lymphoid organs when the frequency of superantigen reactive T cells is unusually high. We monitored T cell proliferation and the percentage of undivided cells when the frequency of superantigen-reactive T cells was low (1%), intermediate (15%) or high (30-100%) by transferring fluorescently labeled cells into different recipients. When the frequency was low, practically all the reactive T cells entered cell cycle and proliferated maximally. At intermediate frequencies a large proportion of reactive T cells did not enter cell cycle and the whole population divided less. A further increase in reactive T cells did not alter the percentage of undivided cells but induced a further decrease in the number of cell divisions. Interestingly, the observations made with superantigens were confirmed with peptide antigen and TCR-transgenic mice. Moreover, in vivo and in vitro data suggest that dendritic cells are the most likely candidates in limiting T cell proliferation in the lymphoid environment. In conclusion, we show that the availability of APC in the lymphoid environment can quantitatively limit T cell priming.

Long circulating half-life and high tumor selectivity of the photosensitizer meta-tetrahydroxyphenylchlorin conjugated to polyethylene glycol in nude mice grafted with a human colon carcinoma.

In a mode of nude mice bearing a human colon carcinoma xenograft, the biodistribution and tumor localization of metatetrahydroxyphenylchlorin (m-THPC) coupled to polyethylene glycol (PEG) were compared with those of the free form of this photosensitizer used in photodynamic therapy (PDT). At different times after i.v. injection of both forms of 125I-labeled photosensitizer, m-THPC-PEG gave on average a 2-fold higher tumor uptake than free m-THPC. In addition, at early times after injection, m-THPC-PEG showed a 2-fold longer blood circulating half-life and a 4-fold lower liver uptake than free m-THPC. The tumor to normal tissue ratios of radioactivity concentrations were always higher for m-THPC-PEG than for free m-THPC at any time point studied from 2 to 96 hr post-injection. Significant coefficients of correlation between direct fluorescence measurements and radioactivity counting were obtained within each organ tested. Fluorescence microscopy studies showed that m-THPC-PEG was preferentially localized near the tumor vessels, whereas m-THPC was more diffusely distributed inside the tumor tissue. To verify whether m-THPC-PEG conjugate remained phototoxic in vivo, PDT experiments were performed 72 hr after injection and showed that m-THPC-PEG was as potent as free m-THPC in the induction of tumor regression provided that the irradiation does for m-THPC-PEG conjugate was adapted to a well-tolerated 2-fold higher level. The overall results demonstrate first the possibility of improving the in vivo tumor localization of a hydrophobic dye used for PDT by coupling it to PEG and second that a photosensitizer conjugated to a macromolecule can remain phototoxic in vivo.

High mobility group box 1 protein (HMGB-1): a pathogenic role in preeclampsia?

We evaluated whether preeclampsia is associated with elevated circulating levels of High mobility group box 1 protein (HMGB-1), a nuclear protein with proinflammatory effects when released extracellularly. We enrolled 48 women, 32 in third trimester pregnancy (16 with, 16 without preeclampsia), and 16 healthy non pregnant. In the peripheral blood of pregnant women, HMGB-1 concentration was assessed serially, before and after delivery. With or without preeclampsia, third trimester pregnancy was associated with elevated levels of HMGB-1. This elevation is exaggerated in preeclampsia. The source of HMGB-1 observed in these conditions is likely to involve tissues other than the placenta itself.

On-pump beating heart coronary surgery for high risk patients requiring emergency multiple coronary artery bypass grafting.

BACKGROUND: Cardiopulmonary bypass (CPB) with aortic cross-clamping and cardioplegic arrest remains the method of choice for patients requiring standard myocardial revascularization. Therefore, very high-risk patients presenting with acute coronary syndrome, unstable angina, onset of cardiac decompensation and requiring emergency multiple myocardial revascularization, can have a poor outcome. The on-pump beating heart technique can reduce the mortality and the morbidity in such a selected group of patients and this report describes our clinical experience. METHODS: Out of 290 patients operated for CABG from January 2005 to January 2006, 25 (8.6%) selected high-risk patients suffering from life threatening coronary syndrome (mean age 69 +/- 7 years) and requiring emergency multiple myocardial revascularization, underwent on-pump beating heart surgery. The mean pre-operative left ventricle ejection fraction (LVEF) was 27 +/- 8%. The majority of them (88%) suffered of tri-vessel coronary disease and 6 (24%) had a left main stump disease. Nine patients (35%) were on severe cardiac failure and seven among them (28%) received a pre-operative intra-aortic balloon pump. The pre-operative EuroScore rate was equal or above 8 in 18 patients (73%). RESULTS: All patients underwent on-pump-beating heart coronary revascularization. The mean number of graft/patient was 2.9 +/- 0.6 and the internal mammary artery was used in 23 patients (92%). The mean CPB time was 84 +/- 19 minutes. Two patients died during the recovery stay in the intensive care unit, and there were no postoperative myocardial infarctions between the survivors. Eight patients suffered of transitorily renal failure and 1 patient developed a sternal wound infection. The mean hospital stay was 12 +/- 7 days. The follow-up was complete for all 23 patients survived at surgery and the mean follow-up time was 14 +/- 5 months. One patient died during the follow-up for cardiac arrest and 2 patients required an implantable cardiac defibrillator. One year after surgery they all had a standard trans-thoracic echocardiogram showing a mean LVEF rate of 36 +/- 11.8%. CONCLUSION: Standard on-pump arrested heart coronary surgery has higher mortality and morbidity in emergencies. The on-pump beating heart myocardial revascularization seems to be a valid alternative for the restricted and selected cohort of patients suffering from life threatening coronary syndrome and requiring multiple emergency CABG.

High altitude journeys and flights are associated with the increased risk of flares in IBD patients

Background: There is increasing experimental evidence that hypoxia induces inflammation in the gastrointestinal tract. Hypoxia-inducible transcription factor (HIF)-1α influences adaptive immunity and has been shown to induce barrier-protective genes in the case of experimentally-induced colitis. The clinical impact of hypoxia in patients with inflammatory bowel disease (IBD) is so far poorly investigated. Aim: We wanted to evaluate if flights and journeys to regions ≥2000 meter above sea level are associated with the occurrence of flares in IBD patients in the following 4 weeks. Methods: A questionnaire was completed by inpatients and outpatients of the IBD clinics of three tertiary referral centers presenting with an IBD flare in the period from Sept 1st 2009 to August 31st 2010. Patients were inquired about their habits in the 4 weeks prior to the flare. Patients with flares were matched with an IBD group in remission during the observation period (according to age, gender, smoking habits, and medication). Results: A total of 103 IBD patients were included (43 Crohn's disease (CD), whereof 65% female, 60 ulcerative colitis, whereof 47% female, mean age 39.3±14.6 years for CD and 43.1±14.2 years for UC). Fifty-two patients with flares were matched to 51 patients without flare. Overall, IBD-patients with flares had significantly more frequently a flight and/or journey to regions ≥ 2000 meters above sea level in the observation period compared to the patients in remission (21/52 (40.4%) vs. 8/51 (15.7%), p=0.005). There was a statistically significant correlation between the occurrence of a flare and a flight and/or journey to regions ≥ 2000 meters above sea level among CD patients with flares as compared to CD patients in remission (8/21 (38.1%) vs. 2/22 (9.1%), p=0.024). A trend for more frequent flights and high-altitude journeys was observed in UC patients with flares (13/31 (41.9%) vs. 6/29 (20.7%), p=0.077). Mean flight duration was 5.8±4.3 hours. The groups were controlled for the following factors (always flare group cited first): age (39.6±13.4 vs. 43.5±14.6, p=0.102), smoking (16/52 vs. 10/51, p=0.120), regular sports activities (32/ 52 vs. 33/51, p=0.739), treatment with antibiotics in the 4 weeks before flare (8/52 vs. 7/ 51, p=0.811), NSAID intake (12/52 vs. 7/51, p=0.221), frequency of chronic obstructive pulmonary disease (both groups 0) and oxygen therapy (both groups 0). Conclusion: IBD patients with a flare had significantly more frequent flights and/or high-altitude journeys within four weeks prior to the IBD flare compared to the group that was in remission. We conclude that flights and stays in high altitude are a risk factor for IBD flares.

High-mobility group box-1 protein determination in postmortem samples.

The aims of this study were to assess whether high-mobility group box-1 protein can be determined in biological fluids collected during autopsy and evaluate the diagnostic potential of high-mobility group box-1 protein in identifying sepsis-related deaths. High-mobility group box-1 protein was measured in serum collected during hospitalization as well as in undiluted and diluted postmortem serum and pericardial fluid collected during autopsy in a group of sepsis-related deaths and control cases with noninfectious causes of death. Inclusion criteria consisted of full biological sample availability and postmortem interval not exceeding 6h. The preliminary results indicate that high-mobility group box-1 protein levels markedly increase after death. Concentrations beyond the upper limit of the calibration curve were obtained in undiluted postmortem serum in septic and traumatic control cases. In pericardial fluid, concentrations beyond the upper limit of the calibration curve were found in all cases. These findings suggest that the diagnostic potential of high-mobility group box-1 protein in the postmortem setting is extremely limited due to molecule release into the bloodstream after death, rendering antemortem levels difficult or impossible to estimate even after sample dilution.