Poisson-Boltzmann analysis of the lambda repressor-operator interaction

A theoretical study of the ion atmosphere contribution to the binding free energy of the lambda repressor-operator complex is presented. The finite-difference form of the Poisson-Boltzmann equation was solved to calculate the electrostatic interaction energy of the amino-terminal domain of the lambda repressor with a 9 or 45 base pair oligonucleotide. Calculations were performed at various distances between repressor and operator as well as at different salt concentrations to determine ion atmosphere contributions to the total electrostatic interaction. Details in the distribution of charges on DNA and protein atoms had a strong influence on the calculated total interaction energies. In contrast, the calculated salt contributions are relatively insensitive to changes in the details of the charge distribution. The results indicate that the ion atmosphere contribution favors association at all protein-DNA distances studied. The theoretical number of ions released upon repressor-operator binding appears to be in reasonable agreement with experimental data

Effect of microwave radiation on seed mortality of rubber vine (Cryptostegia grandiflora R.Br.), parthenium (Parthenium hysterophorous L.) and bellyache bush (Jatropha gossypiifolia L.)

A trial was undertaken to evaluate the effect of microwaves on seed mortality of three weed species. Seeds of rubber vine (Cryptostegia grandiflora R.Br.), parthenium (Parthenium hysterophorous L.) and bellyache bush (Jatropha gossypiifolia L.) were buried at six depths (0, 2.5, 5, 10, 20 and 40 cm) in coarse sand maintained at one of two moisture levels, oven dry or wet (field capacity), and then subjected to one of five microwave radiation durations of (0, 2, 4, 8 and 16 min). Significant interactions between soil moisture level, microwave radiation duration, seed burial depth and species were detected for mortality of seeds of all three species. Maximum seed mortality of rubber vine (88%), parthenium (67%) and bellyache bush (94%) occurred in wet soil irradiated for 16 min. Maximum seed mortality of rubber vine and bellyache bush seeds occurred in seeds buried at 2.5 cm depth whereas that of parthenium occurred in seeds buried at 10 cm depth. Maximum soil temperatures of 114.1 and 87.5°C in dry and wet soil respectively occurred at 2.5 cm depth following 16 min irradiation. Irrespective of the greater soil temperatures recorded in dry soil, irradiating seeds in wet soil generally increased seed mortality 2.9-fold compared with dry soil. Moisture content of wet soil averaged 5.7% compared with 0.1% for dry soil. Results suggest that microwave radiation has the potential to kill seeds located in the soil seed bank. However, many factors, including weed species susceptibility, determine the effectiveness of microwave radiation on buried seeds. Microwave radiation may be an alternative to conventional methods at rapidly depleting soil seed banks in the field, particularly in relatively wet soils that contain long lived weed seeds

Effect of microwave radiation on seed mortality of rubber vine (Cryptostegia grandiflora R.Br.), parthenium (Parthenium hysterophorous L.) and bellyache bush (Jatropha gossypiifolia L.)

A trial was undertaken to evaluate the effect of microwaves on seed mortality of three weed species. Seeds of rubber vine (Cryptostegia grandiflora R.Br.), parthenium (Parthenium hysterophorous L.) and bellyache bush (Jatropha gossypiifolia L.) were buried at six depths (0, 2.5, 5, 10, 20 and 40 cm) in coarse sand maintained at one of two moisture levels, oven dry or wet (field capacity), and then subjected to one of five microwave radiation durations of (0, 2, 4, 8 and 16 min). Significant interactions between soil moisture level, microwave radiation duration, seed burial depth and species were detected for mortality of seeds of all three species. Maximum seed mortality of rubber vine (88%), parthenium (67%) and bellyache bush (94%) occurred in wet soil irradiated for 16 min. Maximum seed mortality of rubber vine and bellyache bush seeds occurred in seeds buried at 2.5 cm depth whereas that of parthenium occurred in seeds buried at 10 cm depth. Maximum soil temperatures of 114.1 and 87.5°C in dry and wet soil respectively occurred at 2.5 cm depth following 16 min irradiation. Irrespective of the greater soil temperatures recorded in dry soil, irradiating seeds in wet soil generally increased seed mortality 2.9-fold compared with dry soil. Moisture content of wet soil averaged 5.7% compared with 0.1% for dry soil. Results suggest that microwave radiation has the potential to kill seeds located in the soil seed bank. However, many factors, including weed species susceptibility, determine the effectiveness of microwave radiation on buried seeds. Microwave radiation may be an alternative to conventional methods at rapidly depleting soil seed banks in the field, particularly in relatively wet soils that contain long lived weed seeds

c-Jun NH2-Terminal Kinase (JNK)1 and JNK2 Signaling Pathways Have Divergent Roles in CD8+ T Cell–mediated Antiviral Immunity

c-Jun NH2-terminal kinases (JNK) play important roles in T helper cell (Th) proliferation, differentiation, and maintenance of Th1/Th2 polarization. To determine whether JNKs are involved in antiviral T cell immunity, and whether JNK1 and JNK2 bear biological differences, we investigated the immune responses of JNK1-deficient and JNK2-deficient mice to lymphocytic choriomeningitis virus (LCMV). After LCMV infection, wild-type (JNK+/+) mice had a 5- to 10-fold increase in splenic CD8+ T cells. In contrast, infected JNK1−/− mice showed a significantly lower virus-specific CD8+ T cell expansion. However, JNK1−/− mice cleared LCMV infection with similar kinetics as JNK+/+ mice. Splenic T cells from LCMV-infected JNK1−/− animals produced interferon γ after stimulation with viral peptides. However, fewer JNK1−/− T cells acquired an activated phenotype (CD44hi) and more JNK1−/−CD8+CD44hi cells underwent apoptosis than JNK+/+ cells at the peak of the primary response. In contrast, LCMV-infected JNK2−/− mice generated more virus-specific CD8+ T cells than JNK+/+ mice. These results indicate that JNK1 and JNK2 signal pathways have distinct roles in T cell responses during a viral infection. JNK1 is involved in survival of activated T cells during immune responses, and JNK2 plays a role in control of CD8+ T cell expansion in vivo

The Virtual International Stroke Trials Archive

BACKGROUND AND PURPOSE: Stroke has global importance and it causes an increasing amount of human suffering and economic burden, but its management is far from optimal. The unsuccessful outcome of several research programs highlights the need for reliable data on which to plan future clinical trials. The Virtual International Stroke Trials Archive aims to aid the planning of clinical trials by collating and providing access to a rich resource of patient data to perform exploratory analyses. METHODS: Data were contributed by the principal investigators of numerous trials from the past 16 years. These data have been centrally collated and are available for anonymized analysis and hypothesis testing. RESULTS: Currently, the Virtual International Stroke Trials Archive contains 21 trials. There are data on \u3e15,000 patients with both ischemic and hemorrhagic stroke. Ages range between 18 and 103 years, with a mean age of 69+/-12 years. Outcome measures include the Barthel Index, Scandinavian Stroke Scale, National Institutes of Health Stroke Scale, Orgogozo Scale, and modified Rankin Scale. Medical history and onset-to-treatment time are readily available, and computed tomography lesion data are available for selected trials. CONCLUSIONS: This resource has the potential to influence clinical trial design and implementation through data analyses that inform planning

Optical response of superfluid state in dilute atomic Fermi-Dirac gases

We theoretically study the propagation of light in a Fermi-Dirac gas in the presence of a superfluid state. BCS pairing between atoms in different hyperfine levels may significantly increase the optical linewidth and line shift of a quantum degenerate Fermi-Dirac gas and introduce a local-field correction that, under certain conditions, dramatically dominates over the Lorentz-Lorenz shift. These optical properties could possibly unambiguously sign the presence of the superfluid state and determine the value of the BCS order parameter.Comment: 5 pages, 2 figure

Functional and molecular analysis of proprioceptive sensory neuron excitability in mice

Neurons located in dorsal root ganglia (DRG) are crucial for transmitting peripheral sensations such as proprioception, touch, temperature, and nociception to the spinal cord before propagating these signals to higher brain structures. To date, difficulty in identifying modality-specific DRG neurons has limited our ability to study specific populations in detail. As the calcium-binding protein parvalbumin (PV) is a neurochemical marker for proprioceptive DRG cells we used a transgenic mouse line expressing green fluorescent protein (GFP) in PV positive DRGs, to study the functional and molecular properties of putative proprioceptive neurons. Immunolabeled DRGs showed a 100% overlap between GFP positive (GFP+) and PV positive cells, confirming the PVeGFP mouse accurately labeled PV neurons. Targeted patch-clamp recording from isolated GFP+ and GFP negative (GFP−) neurons showed the passive membrane properties of the two groups were similar, however, their active properties differed markedly. All GFP+ neurons fired a single spike in response to sustained current injection and their action potentials (APs) had faster rise times, lower thresholds and shorter half widths. A hyperpolarization-activated current (Ih) was observed in all GFP+ neurons but was infrequently noted in the GFP− population (100% vs. 11%). For GFP+ neurons, Ih activation rates varied markedly, suggesting differences in the underlying hyperpolarization-activated cyclic nucleotide-gated channel (HCN) subunit expression responsible for the current kinetics. Furthermore, quantitative polymerase chain reaction (qPCR) showed the HCN subunits 2, 1, and 4 mRNA (in that order) was more abundant in GFP+ neurons, while HCN 3 was more highly expressed in GFP− neurons. Likewise, immunolabeling confirmed HCN 1, 2, and 4 protein expression in GFP+ neurons. In summary, certain functional properties of GFP+ and GFP− cells differ markedly, providing evidence for modality-specific signaling between the two groups. However, the GFP+ DRG population demonstrates considerable internal heterogeneity when hyperpolarization-activated cyclic nucleotide-gated channel (HCN channel) properties and subunit expression are considered. We propose this heterogeneity reflects the existence of different peripheral receptors such as tendon organs, muscle spindles or mechanoreceptors in the putative proprioceptive neuron population

Effects of old landfills on groundwater quality. Phase 2, investigation of the Thriplow landfill 1996–1997

Disused sand and gravel excavations overlying the major Chalk aquifer at Thriplow in Cambridgeshire have been filled with domestic waste in two phases. One area (Phase 1) was filled between 1957–77 with little compaction of the refuse and was left uncapped, while Phase 2 was deposited between 1981–87 and capped with clay. Aerial photography and surface resistivity surveys indicate that the site geometry is complex, with several phases of landfilling into excavations of differing depths. Drilling through the waste indicates that leachate production and waste stabilisation proceed at different rates in capped and uncapped landfills. Analysis of leachate obtained by centrifugation or squeezing appears to give more insight into the pollution potential than do leach tests with distilled water. The Biological Methane Potential (BMP) of the waste appears to be related to the quantity of decomposable material but the chemical oxygen demand (COD) values are distorted by the presence of reduced metals. Too few boreholes have been drilled to define the leachate source in terms of its spatial distribution and little is known of how its composition has changed with time. However, hydraulic conductivity measurements on the landfill caps suggest that it is sufficiently permeable for all rainfall to potentially infiltrate the waste. Boreholes outside the landfill penetrate the Upper and Lower Chalk, and identify the Melbourn Rock and underlying Plenus Marls at the junction of the two formations about 20 m below ground level (bgl). Surface resistivity surveys using the BGS RESCAN system, confirm aerial photographs of the extent of the landfill and also suggest that leachate has migrated beyond the base of the landfill. Evidence of leachate migration in pre-existing screened boreholes completed above and below the Plenus Marls suggests that leachate is flowing above the Plenus Marls. Hydraulic head measurements whilst drilling a borehole to the base of the lower Chalk approx. 70 m bgl revealed the potential for upward groundwater flow through the Plenus Marls. Thus, previously-drilled boreholes penetrating the Plenus Marls are expected to recharge upwards into the shallow aquifer above the Plenus Marls diluting any leachate in the upper aquifer and distorting the flow regime. Several of these boreholes have subsequently been modified to stem the flow across the Plenus Marls. One borehole down-gradient to the west of the site revealed a large thickness of drift composed of both sand and clay rich material. This suggests the existence of a buried channel, the hydrogeological significance of which has yet to be assessed. Groundwater chemistry appears to be influenced by three major factors. (a) the landfill leachate (b) the composition of shallow groundwater in the top 10 m of the Chalk, and (c) the composition of water from the Lower Chalk. Limited groundwater monitoring data appear to display a cyclic variation in chloride concentration. The origin for this is not clear but it may correlate with cyclic variations in groundwater levels when the water table rises into the waste. Cyclic flushing of the landfill may release leachate into the aquifer giving rise to pulses of chloride. Alternatively changes in chloride may arise by the changing direction of groundwater flow which as yet has not been assessed. A conceptual hydrogeological model in which flow is limited to above the Plenus Marls has been used to develop a more appropriate groundwater flow and solute transport model. However, the model lacks data on aquifer properties, on contaminant inputs concentrations, fluxes and spatial variations, and there is a paucity of monitoring data for calibration. Nonetheless preliminary transport modelling using an equivalent porous medium approach shows that an effective porosity of about 5% best fits the regional data. Since this is much less than the total porosity of about 40% for the Chalk, it would appear that only part of the Chalk is available for flow but that matrix diffusion could play an important role in leachate attenuation. Discrete fracture modelling using the FRACTRAN code has allowed some scoping to be made of the hydraulic properties of the aquifer by comparison with chloride hydrographs, but these again need to be better conditioned by in-situ measurement of fracture distributions and transmissivities. A number of additional activities are required to improve the understanding of flow and contaminant transport at the site. These include better spatial definition of the waste distribution, improved data on the hydraulic properties of the Chalk aquifer, and the use of automatic monitoring to record temporal changes in groundwater chemistry and groundwater levels

Computational study of the adsorption of benzene and hydrogen on palladium–iridium nanoalloys

SSCI-VIDE+ECI2D+LPIInternational audienceThe preferred chemisorption sites on a variety of palladium-iridium nanoalloys are determined for benzene and hydrogen molecules. Available sites on the surface of the nanoalloys are explored using a random-search method, directly at the density functional level of theory. These searches successfully reveal the site preference for benzene and significant nanosize effects in the chemisorption of hydrogen. It is hoped that through the study of the chemisorption properties of Pd-Ir nanoalloys, complex catalytic processes, such as tetralin hydroconversion and the preferential oxidation of CO, can be better understood. (C) 2015 Elsevier B.V. All rights reserved