Gag-protease coevolution shapes the outcome of lopinavir-inclusive treatment regimens in chronically infected HIV-1 subtype C patients

MOTIVATION

Commonly, protease inhibitor failure is characterized by the development of multiple protease resistance mutations (PRMs). While the impact of PRMs on therapy failure are understood, the introduction of Gag mutations with protease remains largely unclear.

RESULTS

Here, we utilized phylogenetic analyses and Bayesian network learning as tools to understand Gag-protease coevolution and elucidate the pathways leading to Lopinavir failure in HIV-1 subtype C infected patients. Our analyses indicate that while PRMs coevolve in response to drug selection pressure within protease, the Gag mutations added to the existing network while specifically interacting with known Lopinavir failure PRMs. Additionally, the selection of mutations at specific positions in Gag-protease suggests that these coevolving mutational changes occurs to maintain structural integrity during Gag cleavage.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

High-conversion-efficiency widely-tunable all-fiber optical parametric oscillator

A high-conversion-efficiency widely-tunable all-fiber optical parametric oscillator is described. It is based on modulation instability in the normal dispersion regime near the fiber's zero-dispersion wavelength. A 40 m long dispersion-shifted fiber is used in a synchronously pumped ring cavity. We demonstrate continuous sideband tuning from 1300 to 1500 nm and 1600 to 1860 nm by tuning the pump wavelength between 1532 and 1556 nm. Internal conversion efficiencies of up to 40% are achieved.

[First breech twin pregnancy: Can we still accept a vaginal delivery? Comparative study of perinatal outcome with attempt of vaginal delivery versus planned cesarean: 166 cases]

OBJECTIVES

To evaluate practices and perinatal outcome in planned routes of delivery for first breech twins.

MATERIALS AND METHODS

A retrospective study in first breech twin pregnancies with a gestational age of at least 35 weeks at onset of labor. Maternofetal pathologies known to be associated with a poor neonatal outcome were excluded. A low neonatal outcome was defined by at least one of the following criteria: neonatal death, 5-minute Agar Score < 7, cord blood pH < 7.10, traumatic neurological injuries, admission in neonatal intensive unit care. Neonatal and maternal outcomes were compared between attempt of vaginal delivery (AVD) and planned cesarean section (PCS).

RESULTS

Among 166 included patients, an AVD has been performed in 105 cases (63.3%) and a PCS in 61 (36.8%). In AVD group, 46 women (43.8%) delivered vaginally. Low neonatal outcome was not significantly different in AVD group compared with PCS group (9 (8.6%) versus 6 (9.8%); p = 0.78 for the first twin and 7 (6.7%) versus 2 (3.3%); p = 0.49 for the second twin). There was no significant difference in maternal morbidity between the two groups. As a general rule, established practices for deciding route of delivery and labor have been applied in our department.

CONCLUSION

No excess of neonatal risk in AVD group compared with PCS was observed. These results could be extrapolated to centers applying a careful protocol to decide the route of delivery and labor practices.

Geochemical survey and metal bioaccumulation of three bivalve species (Crassostrea gigas, Cerastoderma edule and Ruditapes philippinarum) in the Nord Medoc salt marshes (Gironde estuary, France)

A 15-month experiment combining a geochemical survey of Cd, Cu, Zn and Hg with a bioaccumulation study for three filter-feeding bivalve species (oysters, Crassostrea gigas; cockles, Cerastoderma edule; and clams, Ruditapes philippinarum) was conducted in a breeding basin of the Nord Medoc salt marshes connected to the Gironde estuary, which is affected by historic polymetallic pollution. Regular manual surface measurements of temperature, salinity, pH and dissolved O(2) concentration and hourly multiprobe in situ measurements throughout several periods for 6-8 weeks were performed. The geochemical behavior of metals in water, suspended particulate matter and sediment and their ecotoxicological impact on the three bivalve species were evaluated by in situ exposure of juvenile oysters (water column) and adult cockles and clams (sediment surface). The physico-chemical parameters reflected seasonal variations and basin management. A distinct daily periodicity (except salinity) indicated intense photosynthesis and respiration. In summer, low dissolved O(2) saturations ( approximately 40-50%) occurred in the early morning at 30 cm above the sediment, whereas in depressions, the water column near the sediment surface was suboxic. Cadmium, Zn and Cu concentrations in suspended particulate matter exceeded typical estuarine values and were much higher than the homogeneously distributed concentrations in different depth ranges of the basin sediment. Particles collected in sediment traps showed intermediate metal concentrations close to sediment values. These results suggest trace metal recycling due to reductive dissolution under suboxic conditions at the sediment surface resulting in trace metal release to the water column and adsorption onto suspended particles. Dissolved Cd, Zn and Hg concentrations (e.g. 13-136 ng l(-1); 0.3-25.1 microg l(-1) and 0.5-2.0 ng l(-1), respectively) in the basin corresponded to the concentration range typically observed in the Gironde estuary, except for some maximum values attributed to metal recycling. In contrast, dissolved Cu concentrations (1.08-6.08 microg l(-1)) were mostly higher than typical estuarine values, probably due to recycled Cu complexation by dissolved organic matter. Growth, bioaccumulation rates and kinetics in the whole soft body of the bivalves were analyzed every 40 days. Although Cd bioaccumulation of oysters was lower in the basin than in the estuary during the same period (27,000 ng g(-1), dry weight and 40,000 ng g(-1), respectively) these values are largely above the new human consumption safety level (5000 ng g(-1), dw; European Community, 2002). For cockles and clams, Cd bioaccumulation was lower, reaching 1400 ng g(-1) and 950 ng g(-1), respectively. Similar results were obtained for Zn and Cu suggesting physiological differences between the species and/or differences in the exposure of the organisms due to physico-chemical conditions and metal distribution between dissolved and particulate phases. In contrast, Hg bioaccumulation was highest for cockles reaching bioconcentration factors of approximately 200,000, which even exceeded that of Cd in oysters (50,000) for the same exposition period. Nevertheless, Hg concentrations remained relatively low in the three bivalve species.

Calcium pool size modulates the sensitivity of the ryanodine receptor channel and calcium-dependent ATPase of heavy sarcoplasmic reticulum to extravesicular free calcium concentration

We have examined calcium cycling and associated ATP consumption by isolated heavy sarcoplasmic reticulum (HSR) vesicles incubated in conditions believed to exist in resting muscle. Our goals were to estimate the magnitude of calcium cycling under those conditions and identify the main mechanisms involved in its regulation. The integrity of the HSR vesicles was documented by the retention of [14C]-sucrose and electron microscopy. HSR actively exchanged Ca2+ with the medium through a partially open ryanodine-binding channel (RyR), as evidenced by the rapid attainment of a steady-state gradient between HSR and medium, which was promptly increased by the closure of the channel with ruthenium red (RR) or collapsed by its opening with caffeine. The ATP dependency was evidenced by the sustained ATP consumption after the steady state was attained and by the abrogation of the gradient following inhibition of the pump with thapsigargin (Tg) or the omission of ATP. When HSR vesicles were incubated in a comparatively large pool of calcium (approximately 1 micromol/mg HSR protein), ATP consumption was 1-1.5 micromol x [min x mg protein](-1) at 0.1 microM free Ca2+. Under such conditions, the main regulator of the sarcoplasmic Ca2+-dependent ATPase (SERCA) was extravesicular-free Ca2+ concentration, with a four- to fivefold increase between 0.1 and 2 microM Ca2+, whereas RyR channel activity and the replenishment of the HSR vesicles had only a modest effect on ATP consumption. When calcium pool size was reduced to 0.1 micromol/mg HSR protein, a steady state was established at a lower level of HSR calcium. In spite of a slightly lower free extravesicular Ca2+ at equilibrium (approximately 0.07 microM following an initial concentration of 0.1 microM), both ATP consumption and the open probability of the RyR channel were increased by a factor of three to five. Compared to the large calcium pool, the sensitivity of both RyR channel and SERCA to extravesicular free Ca2+ concentration as well as to caffeine and RR was markedly enhanced.

CONCLUSIONS

1) In conditions present in resting muscle, HSR calcium is in dynamic equilibrium with the medium through a partially open RyR channel, which requires continuous ATP hydrolysis. 2) The availability of calcium is a major determinant of the sensitivity of both RyR channel and SERCA to free extravesicular Ca2+ and possibly other stimuli. 3) These observations are consistent with the concept that calcium cycling in resting muscle may account for a significant fraction of muscle energy demands and further suggest that restricting calcium availability may enhance the energetic demands of this process.

Thiazolidinediones stimulate uncoupling protein-2 expression in cell lines representing white and brown adipose tissues and skeletal muscle

Thiazolidinediones (TZD) are PPAR gamma ligands that sensitize tissues to insulin. A cDNA encoding a mitochondrial protein likely to act as uncoupler (uncoupling protein 2, UCP2) has been recently cloned. Since TZD have been reported to increase energy expenditure in animals, we have examined the effects of these drugs on the expression of UCP2 mRNA in cell lines representing white (3T3-L1 and 3T3-F442A) and brown (HIB-1B) adipose tissues and skeletal muscle (L6). Northern blots probed with a mouse UCP2 full-length cDNA showed a mRNA of 1.6 kb both in tissues and the aforementioned cells lines. Within 4 h of exposing these cells to 30 microM darglitazone, there was an increase in UCP2 mRNA which reached a plateau of 5-10 times the basal in about 8 h. In all cells TZDs (darglitazone, troglitazone) were more active than the predominantly PPAR alpha ligands WY-14,613 and clofibrate, or the non-selective ligand linoleic acid. These results indicate that TZDs can stimulate the expression of UCP2 gene probably via PPAR gamma and hence have the potential to increase energy expenditure in adult humans, in whom UCP2 is expressed ubiquitously.

Effect of the beta-adrenoceptor agonist BRL-35135 on development of obesity in suckling Zucker (fa/fa) rats

This study was undertaken to determine whether administration of a thermogenic beta-agonist drug to Zucker fatty rats could correct some of the earliest metabolic defects detectable in brown adipose tissue (BAT). Fa/fa and fa/fa littermates were given oral administration of BRL-35135 from 8 to 16 days of age. In fa/fa rats, the lipid content of white and brown adipose tissues was significantly reduced. In the BAT of fa/fa rats, thermogenic capacity was restored to the level observed in Fa/fa rats, whereas hyperactivity of fatty acid synthetase was abolished, and a deficit in lipoprotein lipase (activity and mRNA) was partly corrected. Hyperinsulinemia in fa/fa pups was significantly reduced. The decreased content of GLUT-4 mRNA that characterized BAT of fa/fa pups was also restored to normal. At variance with observations in preobese rats, BRL had very little or no effect on lean Fa/fa rats. The present study reveals that chronic administration of a beta-agonist drug early in life prevents emergence of most of the metabolic abnormalities that characterize fa/fa rats at the onset of obesity. This suggests that impaired sympathetic activity may play a role in the development of this genetic obesity.

Development of thyroxine type II deiodinase activity in brains of Zucker rats

The present study was undertaken to determine whether the capacity for 3,5,3',5'-tetraiodothyronine (T4) conversion into 3,5,3'-tri-iodothyronine (T3), as measured by the activity of thyroxine type II 5'-monodeiodinase (T4-5'D), was altered in the brains of young Zucker fa/fa rats during the period of intense maturation of the central nervous system (i.e. from 10 to 20 days of life). From 7 to 14 days of age, no difference in brain T4-5'D activity could be detected between lean and pre-obese rats; serum free T4 was not affected by the fa gene. During the suckling to weaning transition, T4-5'D reached a plateau in brains of lean rats, while it increased by 50% in brains of pre-obese rats; concurrently, serum free T4 increased in Fa/fa rats, whereas it did not change in fa/fa rats. The increased capacity for conversion of T4 into T3 observed in brains of pre-obese compared with lean rats could not be ascribed to a variation in the amount of T4-5'D, since Vmax. did not differ between the two genotypes; however, it could be totally accounted for by an increased affinity of the enzyme for T4. This change may represent an adaptive response to low serum free T4 in order to maintain the cerebral T3 concentration in pre-obese rats. These results show that the alteration in T4 metabolism in brains of fa/fa rats is not an early event and thus cannot interfere with maturation of the central nervous system. However, the decreased serum free T4 which was observed in pre-obese rats after suckling might play a secondary role in development of this genetic obesity.

Acute injection of beta-adrenoceptor agonist BRL 35135 corrects both impaired uncoupling protein and lipoprotein lipase gene expression but not hypercapacity of lipogenesis in brown adipose tissue of suckling fa/fa rats

This study was undertaken to determine whether acute injection of the beta-adrenoceptor BRL 35135, which is known to activate thermogenesis, could correct the earliest detectable metabolic abnormalities that characterize brown (BAT) and white (WAT) adipose tissues of pre-obese Zucker rats. In 14-day-old pups, a single intraperitoneal injection of BRL (10 micrograms/g, 3 h before sacrifice) had no effect on uncoupling protein mRNA content in BAT of lean pups, whereas the low level of this mRNA was restored to normal in pre-obese rats. Both lipoprotein lipase (LPL) activity and mRNA content, which were decreased in BAT of pre-obese compared to lean pups (-60%), were stimulated after BRL injection. However, this effect was more pronounced in fa/fa than in Fa/fa rats (+100% and +50%, respectively). In BAT, the increase in fatty acid synthetase (FAS) activity observed in fa/fa rats compared to their lean Fa/fa littermates was not reduced. In WAT, the stimulation of beta-adrenergic receptors had no effect on lipid storage capacity, since FAS and LPL activities remained unchanged. In conclusion, pre-obese Zucker fa/fa rats are responsive to BRL 35135 treatment: acute administration of this drug was able to improve impaired thermogenesis and to correct temporarily other abnormalities of early emergence in BAT. This treatment had no effect in WAT. Taken together, our data reinforce the hypothesis that reduced sympathetic activity in BAT is one of the primary lesions of the obese rat which may play a key role in the development of this genetic obesity.

Decreased T4-to-T3 conversion in brown adipose tissue of Zucker fa/fa pups before the onset of obesity

To determine whether the capacity of thyroxine (T4)-to-3,5,3'-triiodothyronine (T3) conversion was altered in Zucker fa/fa pups, we measured thyroxine 5'-monodeiodinase (T(4)5'D) activity in brown adipose tissue (BAT) and liver of suckling and weaned fa/fa and Fa/fa littermates. In suckling fa/fa compared with Fa/fa rats, T(4)5'D was reduced by 30-55% in BAT and slightly increased in liver, while serum free T3 was significantly decreased (-30%). Altered T(4)5'D activity in BAT of fa/fa pups could be corrected by adrenergic stimulation. After weaning, in fa/fa rats, the capacity for T4-to-T3 conversion was totally restored in BAT while it was dramatically reduced in liver. The concentration of serum free T3 remained lower in fa/fa than in Fa/fa rats (-40%). These data confirm that BAT is a very early site of fa gene expression and are consistent with the hypothesis that a defect in the autonomic nervous system may be a primary cause of this genetic obesity. It is also suggested that, during suckling, BAT plays an important role in systemic production of T3.