Structural studies of cytochrome P4501A1: Identification of substrate and cumene hydroperoxide binding regions in the active site of P4501A1 and characterization of the P4501A1 interaction with cytochrome P450 reductase

Cytochromes P450 are a superfamily of heme-thiolate proteins that function in a concert with another protein, cytochrome P450 reductase, as terminal oxidases of an enzymatic system catalyzing the metabolism of a variety of foreign compounds and endogenous substrates. In order to better understand P450s catalytic mechanism and substrate specificity, information about the structure of the active site is necessary. Given the lack of a crystal structure of mammalian P450, other methods have been used to elucidate the substrate recognition and binding site structure in the active center. In this project I utilized the photoaffinity labeling technique and site-directed mutagenesis approach to gain further structural insight into the active site of mammalian cytochrome P4501AI and examine the role of surface residues in the interaction of P4501A1 with the reductase. ^ Four crosslinked peptides were identified by photoaffinity labeling using diazido benzphetamine as a substrate analog. Alignment of the primary structure of cytochrome P4501A1 with that of bacterial cytochrome P450102 (the crystal structure of which is known) revealed that two of the isolated crosslinked peptides can be placed in the vicinity of heme (in the L helix region and β10-β11 sheet region of cytochrome P450102) and could be involved in substrate binding. The other two peptides were located on the surface of the protein with the label bound specifically to Lys residues that were proposed to be involved in reductase-P450 interaction. ^ Alternatively, it has been shown that some of the organic hydroperoxides can support P450 catalyzed reactions in the absence of NADPH, O2 and reductase. By means of photoaffinity labeling the cumene hydroperoxide binding region was identified. Using azidocumene as the photoaffinity label, the tripeptide T501-L502-K503 was shown to be the site where azidocumene covalently binds to P4501A1. The sequence alignment of cytochrome P4501A1 with cytochrome P450102 predicts that this region might correspond to β-sheet structure localized on the distal side of the heme ring near the I helix and the oxygen binding pocket. The role of Thr501 in the cumene hydroperoxide binding was confirmed by mutations of this residue and kinetic analysis of the effects of the mutations. ^ In addition, the role of two lysine residues, Lys271 and Lys279, in the interaction with reductase was examined by means of site-directed mutagenesis. The lysine residues were substituted with isoleucine and enzymatic activity of the wild type and the mutants were compared in reductase- and cumene hydroperoxide-supported systems. The lysine 279 residue has been shown to play a critical role in the P4501A1-reductase interaction. ^

Assessing dynamics of forced livestock movements, livelihoods and future development options for pastoralists/agro-pastoralists in Ruvuma and Lindi Regions, in the Southern Tanzania

The study that aimed at understanding the dynamics of forced livestock movements and pastoral livelihood and development options was conducted in Lindi and Ruvuma regions, using both formal and informal approaches. Data were collected from 60 randomly selected Agro-pastoralists/Pastoralists and native farmers using a structured questionnaire. Four villages were involved; two in Lindi region (Matandu and Mkwajuni) and the other two in Ruvuma region (Gumbiro and Muhuwesi). Data were analyzed using descriptive statistics of SPSS to generate means and frequencies. The results indicate that a large number of animals moved into the study area following the eviction order of the government in Ihefu wetlands in 2006/2007. Lindi region was earmarked by the government to receive all the evicted pastoralists. However, by 2008 only 30% of the total cattle that were expected to move into the region had been received. Deaths of many animals on transit, selling of the animals to pay for transportation and other costs while on transit and many pastoralists settling in Coastal and Ruvuma regions before reaching their destinations were reported to be the reasons for the discrepancy observed. To mitigate anticipated conflicts between farmers and pastoralists, Participatory Land Use Management (PLUM) plans were developed in all the study villages in order to demarcate village land area into different uses, including grazing, cropping, settlement and forests. Land units for grazing were supposed to be provided with all necessary livestock infrastructures (dips, charcoal dams, livestock markets and stock routes). However, the land use plans were not able to prevent the anticipated conflicts because most of the livestock infrastructures were lacking, the land use boundaries were not clearly demarcated and there was limited enforcement of village by-laws, since most had not been enacted by the respective district councils. Similarly, the areas allocated for grazing were inadequate for the number of livestock available and thus the carrying capacity exceeded. Thus, land resource-based conflicts between farmers and pastoralists were emerging in the study areas for the reason that most of the important components in the PLUM plans were not in place. Nevertheless, the arrival of pastoralists in the study areas had positive effects on food security and growth of social interactions between pastoralists and farmers including marriages between them. Environmental degradations due to the arrival of livestock were also not evident. Thus, there is a need for the government to purposely set aside enough grazing land with all necessary infrastructures in place for the agro-pastoral/pastoral communities in the country.

The effects of catecholamine depletion on the neural response to fearful faces in remitted depression

Recent evidence suggests that increased psychophysiological response to negatively valenced emotional stimuli found in major depressive disorder (MDD) may be associated with reduced catecholaminergic neurotransmission. Fourteen unmedicated, remitted subjects with MDD (RMDD) and 13 healthy control subjects underwent catecholamine depletion with oral α-methyl-para-tyrosine (AMPT) in a randomized, placebo-controlled, double-blind crossover trial. Subjects were exposed to fearful (FF) and neutral faces (NF) during a scan with [15O]H2O positron emission tomography to assess the brain-catecholamine interaction in brain regions previously associated with emotional face processing. Treatment with AMPT resulted in significantly increased, normalized cerebral blood flow (CBF) in the left inferior temporal gyrus (ITG) and significantly decreased CBF in the right cerebellum across conditions and groups. In RMDD, flow in the left posterior cingulate cortex (PCC) increased significantly in the FF compared to the NF condition after AMPT, but remained unchanged after placebo, whereas healthy controls showed a significant increase under placebo and a significant decrease under AMPT in this brain region. In the left dorsolateral prefrontal cortex (DLPFC), flow decreased significantly in the FF compared to the NF condition under AMPT, and increased significantly under placebo in RMDD, whereas healthy controls showed no significant differences. Differences between AMPT and placebo of within-session changes in worry-symptoms were positively correlated with the corresponding changes in CBF in the right subgenual prefrontal cortex in RMDD. In conclusion, this study provided evidence for a catecholamine-related modulation of the neural responses to FF expressions in the left PCC and the left DLPFC in subjects with RMDD that might constitute a persistent, trait-like abnormality in MDD.

Influence of the background wind on the local soil moisture-precipitation feedback

The importance of soil moisture anomalies on airmass convection over semiarid regions has been recognized in several studies. The underlying mechanisms remain partly unclear. An open question is why wetter soils can result in either an increase or a decrease of precipitation (positive or negative soil moisture–precipitation feedback, respectively). Here an idealized cloud-resolving modeling framework is used to explore the local soil moisture–precipitation feedback. The approach is able to replicate both positive and negative feedback loops, depending on the environmental parameters. The mechanism relies on horizontal soil moisture variations, which may develop and intensify spontaneously. The positive expression of the feedback is associated with the initiation of convection over dry soil patches, but the convective cells then propagate over wet patches where they strengthen and preferentially precipitate. The negative feedback may occur when the wind profile is too weak to support the propagation of convective features from dry to wet areas. Precipitation is then generally weaker and falls preferentially over dry patches. The results highlight the role of the midtropospheric flow in determining the sign of the feedback. A key element of the positive feedback is the exploitation of both low convective inhibition (CIN) over dry patches (for the initiation of convection) and high CAPE over wet patches (for the generation of precipitation).

Stable-Isotopic Composition of Precipitation Over the Northern Slope of the Central Himalaya

Stable-water-isotope data (deltaD and delta(18)O) from three groups of samples (fresh-snow and snow-pit samples collected on Qomolangma (Mount Everest) and Xixabangma during field seasons 1997,1998 and 2001, and precipitation samples collected at Tingri station during summer 2000) are presented and used to survey the isotopic composition of precipitation over the northern slope of the central Himalaya. Multi-year snow-pit samples on Qomolangma have a local meteoric water-line (slope = 8) close to the global value. Deuterium excess (d = deltaD - 8delta(18)O) values at Tingri are much lower than those in fresh snow from Qomolangma, probably due to differences in moisture source and air-mass trajectories as well as local weather conditions. There is no obvious seasonal trend for d values in the Qomolangma region. A negative relationship exists between delta(18)O and d values in both fresh snow on Qomolangma and precipitation at Tingri. Fresh-snow samples collected from different altitudes on Xixabangma allow us to investigate the altitude effect on delta(18)O values in snow. Of four storm events, only one has an obvious altitude effect on delta(18)O variation and a very low gradient of -0.1% per 100 in elevation.

Hydrographic Conditions Off Northern Chile During the 1996-1998 La Niña and El Niño Events

The evolution of oceanographic conditions in the upwelling region off northern Chile (18 degrees-24 degrees S) between 1996 and 1998 (including the 1997-1998 El Niño) is presented using hydrographic measurements acquired on quarterly cruises of the Chilean Fisheries Institute, with sea surface temperature (SST), sea level, and wind speeds from Arica (18.5 degrees S), Iquique (20.5 degrees S), and Antofagasta (23.5 degrees S) and a time series of vertical temperature profiles off Iquique. Spatial patterns of sea surface temperature and salinity from May 1996 to March 1997 followed a normal seasonal progression, though conditions were anomalously cool and fresh. Starting in March 1997, positive anomalies in sea level and sea surface temperature propagated along the South American coast to 37 degrees S. Maximum sea level anomalies occurred in two peaks in May-July 1997 and October 1997 to February 1998, separated by a relaxation period. Maximum anomalies (2 degrees C and 0.1 practical salinity units (psu)) extended to 400 m in December 1997 within 50 km of the coast. March 1998 presented the largest surface anomalies (> 4 degrees C and 0.6 psu). Strong poleward flow (20-35 cm s(-1) ) occurred to 400 m or deeper during both sea level maxima and weaker (10 cm s(-1) ) equatorward flow followed each peak. By May 1998, SST had returned to the climatological mean, and flow was equatorward next to the coast. However, offshore salinity remained anomalously high owing to a tongue of subtropical water extending southeast along the Peruvian coast. Conditions off northern Chile returned to normal between August and December 1998. The timing of the anomalies suggests a connection to equatorial waves. The progression of the 1997-1998 El Niño was very similar to that of 1982-1983, though with different timing with respect to seasons.

Domains of expansin gene expression define growth regions in the shoot apex of tomato

Expansins are members of a multigene family of extracellular proteins, which increase cell wall extensibility in vitro and thus are thought to be involved in cell expansion. The major significance of the presence of this large gene family may be that distinctly expressed genes can independently regulate cell expansion in place and time. Here we report on LeExp9, a new expansin gene from tomato, and compare its expression in the shoot tip with that of LeExp2 and LeExp18. LeExp18 gene is expressed in very young tissues of the tomato shoot apex and the transcript levels are upregulated in the incipient primordium. LeExp2 mRNA accumulated in more mature tissues and transcript levels correlated with cell elongation in the elongation zone. In situ hybridization experiments showed a uniform distribution of LeExp9 mRNA in submeristematic tissues. When gibberellin-deficient mutant tomatoes that lacked elongation of the internodes were treated with gibberellin, the phenotypic rescue was correlated with an increase in LeExp9 and LeExp2, but not LeExp18 levels. We propose that the three expansins define three distinct growing zones in the shoot tip. In the meristem proper, gibberellin-independent LeExp18 mediates the cell expansion that accompanies cell division. In the submeristematic zone, LeExp9 mediates cell expansion at a time that cell division comes to a halt. LeExp9 expression requires gibberellin but the hormone is not normally limiting. Finally, LeExp2 mediates cell elongation in young stem tissue. LeExp2 expression is limited by the available gibberellin. These data suggest that regulation of cell wall extensibility is controlled, at least in part, by differential regulation of expansin genes.

On the Co-Occurrence of Warm Conveyor Belt Outflows and PV Streamers*

The co-occurrence of warm conveyor belts (WCBs), strongly ascending moist airstreams in extratropical cyclones, and stratospheric potential vorticity (PV) streamers, indicators for breaking Rossby waves on the tropopause, is investigated for a 21-yr period in the Northern Hemisphere using Interim European Centre for Medium-Range Weather Forecasts (ECMWF) Re-Analysis (ERA-Interim) data. WCB outflows and PV streamers are respectively identified as two- and three-dimensional objects and tracked during their life cycle. PV streamers are more frequent than WCB outflows and nearly 15% of all PV streamers co-occur with WCBs during their life cycle, whereas about 60% of all WCB outflows co-occur with PV streamers. Co-occurrences are most frequent over the North Atlantic and North Pacific in spring and winter. WCB outflows are often located upstream of the PV streamers and form earlier, indicating the importance of diabatic processes for downstream Rossby wave breaking. Less frequently, PV streamers occur first, leading to the formation of new WCBs.

ON THE STABILITY OF SUPER-EARTH ATMOSPHERES

We investigate the stability of super-Earth atmospheres around M stars using a seven-parameter, analytical framework. We construct stability diagrams in the parameter space of exoplanetary radius versus semimajor axis and elucidate the regions in which the atmospheres are stable against the condensation of their major constituents, out of the gas phase, on their permanent nightside hemispheres. We find that super-Earth atmospheres that are nitrogen-dominated (Earth-like) occupy a smaller region of allowed parameter space, compared to hydrogen-dominated atmospheres, because of the dual effects of diminished advection and enhanced radiative cooling. Furthermore, some super-Earths which reside within the habitable zones of M stars may not possess stable atmospheres, depending on the mean molecular weight and infrared photospheric pressure of their atmospheres. We apply our stability diagrams to GJ 436b and GJ 1214b, and demonstrate that atmospheric compositions with high mean molecular weights are disfavored if these exoplanets possess solid surfaces and shallow atmospheres. Finally, we construct stability diagrams tailored to the Kepler data set, for G and K stars, and predict that about half of the exoplanet candidates are expected to harbor stable atmospheres if Earth-like conditions are assumed. We include 55 Cancri e and CoRoT-7b in our stability diagram for G stars

Influence of experimental soil disturbances on the diversity of plants in agricultural grasslands

Aims and Methods Disturbance is supposed to play an important role for biodiversity and ecosystem stability as described by the intermediate disturbance hypothesis (IDH), which predicts highest species richness at intermediate levels of disturbances. In this study, we tested the effects of artificial soil disturbances on diversity of annual and perennial vascular plants and bryophytes in a field experiment in 86 agricultural grasslands differing in land use in two regions of Germany. On each grassland, we implemented four treatments: three treatments differing in application time of soil disturbances and one control. One year after experimental disturbance, we recorded vegetation and measured biomass productivity and bare ground. We analysed the disturbance response taking effects of region and land-use-accompanied disturbance regimes into account.Important Findings Region and land-use type strongly determined plant species richness. Experimental disturbances had small positive effects on the species richness of annuals, but none on perennials or bryophytes. Bare ground was positively related to species richness of bryophytes. However, exceeding the creation of 12% bare ground further disturbance had a detrimental effect on bryophyte species richness, which corresponds to the IDH. As biomass productivity was unaffected by disturbance our results indicate that the disturbance effect on species richness of annuals was not due to decreased overall productivity, but rather due to short-term lowered inter- and intraspecific competition at the newly created microsites.Generally, our results highlight the importance of soil disturbances for species richness of annual plants and bryophytes in agricultural grasslands. However, most grasslands were disturbed naturally or by land-use practices and our additional experimental soil disturbances only had a small short-term effect. Overall, total plant diversity in grasslands seemed to be more limited by the availability of propagules rather than by suitable microsites for germination. Thus, nature conservation efforts to increase grassland diversity should focus on overcoming propagule limitation, for instance by additional sowing of seeds, while the creation of additional open patches by disturbance might only be appropriate where natural disturbances are scarce.

Switching on the fluorescence of 2-aminopurine by site-selective microhydration

​2-Aminopurine (​2AP) is a fluorescent isomer of ​adenine and has a fluorescence lifetime of ~11 ns in water. It is widely used in biochemical settings as a site-specific fluorescent probe of DNA and RNA structure and base-flipping and -folding. These assays assume that ​2AP is intrinsically strongly fluorescent. Here, we show this not to be the case, observing that gas-phase, jet-cooled ​2-aminopurine and ​9-methyl-2-aminopurine have very short fluorescence lifetimes (156 ps and 210 ps, respectively); they are, to all intents and purposes, non-fluorescent. We find that the lifetime of ​2-aminopurine increases dramatically when it is part of a hydrate cluster, 2AP·(H2O)n, where n = 1–3. Not only does it depend on the presence of water molecules, it also depends on the specific hydrogen-bonding site to which they attach and on the number of H2O molecules at that site. We selectively microhydrate ​2-aminopurine at its sugar-edge, cis-amino or trans-amino sites and see that its fluorescence lifetime increases by 4, 50 and 95 times (to 14.5 ns), respectively.

Mass transport around comets and its impact on the seasonal differences in water production rates

Comets are surrounded by a thin expanding atmosphere, and although the nucleus' gravity is small, some molecules and grains, possibly with the inclusion of ices, can get transported around the nucleus through scattering (atoms/molecules) and gravitational pull (grains). Based on the obliquity of the comet, it is also possible that volatile material and icy grains get trapped in regions, which are in shadow until the comet passes its equinox. When the Sun rises above the horizon and the surface starts to heat up, this condensed material starts to desorb and icy grains will sublimate off the surface, possibly increasing the comet's neutral gas production rate on the outbound path. In this paper we investigate the mass transport around the nucleus, and based on a simplified model, we derive the possible contribution to the asymmetry in the seasonal gas production rate that could arise from trapped material released from cold areas once they come into sunlight. We conclude that the total amount of volatiles retained by this effect can only contribute up to a few percent of the asymmetry observed in some comets.

Influence of Martian crustal magnetic anomalies on the emission of energetic neutral hydrogen atoms

We analyze the data on hydrogen energetic neutral atoms (ENAs) emissions from the dayside of Mars, recorded by a Neutral Particle Detector of the Analyzer of Space Plasmas and Energetic Atoms aboard Mars Express from 14 March to 9 July 2004. We first identify and analyze events of the ENA flux enhancement coinciding with the presence of the crustal magnetic anomalies on the dayside of Mars. We then backtrace the ENA emissions to the lower altitudes (source region) and build up an average map of the flux intensities in the geographic coordinates with all the available data. The map shows a peak-to-valley ENA flux enhancement of 40%–90% close to the crustal magnetic anomaly regions. These results suggest the influence of the magnetic anomalies on the ENA emission from the dayside of Mars. The enhancement may result from the deviation of the highly directional plasma flow above anomalies toward the detectors such that more charge exchange ENAs would be recorded. Alternatively, higher exospheric densities above the anomalies would also result in an increase of the charge exchange ENA flux.

Hydrodynamic and Thermophoretic Effects on the Supramolecular Chirality of Pyrene-Derived Nanosheets

Chiroptical properties of two-dimensional (2D) supramolecular assemblies (nanosheets) of achiral, charged pyrene trimers (Py3) are rendered chiral by asymmetric physical perturbations. Chiral stimuli in a cuvette can originate either from controlled temperature gradients or by very gentle stirring. The chiroptical activity strongly depends on the degree of supramolecular order of the nanosheets, which is easily controlled by the method of preparation. The high degree of structural order ensures strong cooperative effects within the aggregates, rendering them more susceptible to external stimuli. The samples prepared by using slow thermal annealing protocols are both CD and LD active (in stagnant and stirred solutions), whereas for isothermally aged samples chiroptical activity was in all cases undetectable. In the case of temperature gradients, the optical activity of 2D assemblies could be recorded for a stagnant solution due to migration of the aggregates from the hottest to the coldest regions of the system. However, a considerably stronger exciton coupling, coinciding with the J-band of the interacting pyrenes, is developed upon subtle vortexing (0.5 Hz, 30 rpm) of the aqueous solution of the nanosheets. The sign of the exciton coupling is inverted upon switching between clockwise and counter-clockwise rotation. The supramolecular chirality is evidenced by the appearance of CD activity. To exclude artefacts from proper CD spectra, the contribution from LD to the observed CD was determined. The data suggest that the aggregates experience asymmetrical deformation and alignment effects because of the presence of chiral flows.