In silico target fishing for rationalized ligand discovery exemplified on constituents of Ruta graveolens

The identification of targets whose interaction is likely to result in the successful treatment of a disease is of growing interest for natural product scientists. In the current study we performed an exemplary application of a virtual parallel screening approach to identify potential targets for 16 secondary metabolites isolated and identified from the aerial parts of the medicinal plant RUTA GRAVEOLENS L. Low energy conformers of the isolated constituents were simultaneously screened against a set of 2208 pharmacophore models generated in-house for the IN SILICO prediction of putative biological targets, i. e., target fishing. Based on the predicted ligand-target interactions, we focused on three biological targets, namely acetylcholinesterase (AChE), the human rhinovirus (HRV) coat protein and the cannabinoid receptor type-2 (CB (2)). For a critical evaluation of the applied parallel screening approach, virtual hits and non-hits were assayed on the respective targets. For AChE the highest scoring virtual hit, arborinine, showed the best inhibitory IN VITRO activity on AChE (IC (50) 34.7 muM). Determination of the anti-HRV-2 effect revealed 6,7,8-trimethoxycoumarin and arborinine to be the most active antiviral constituents with IC (50) values of 11.98 muM and 3.19 muM, respectively. Of these, arborinine was predicted virtually. Of all the molecules subjected to parallel screening, one virtual CB (2) ligand was obtained, i. e., rutamarin. Interestingly, in experimental studies only this compound showed a selective activity to the CB (2) receptor ( Ki of 7.4 muM) by using a radioligand displacement assay. The applied parallel screening paradigm with constituents of R. GRAVEOLENS on three different proteins has shown promise as an IN SILICO tool for rational target fishing and pharmacological profiling of extracts and single chemical entities in natural product research.

Biovolatilisation: a poorly studied pathway of the arsenic biogeochemical cycle

It has been known for over a hundred years that microorganisms can produce volatile arsenic (As) species, termed “arsines”. However, this topic has received relatively little attention compared to As behaviour in soils and biotransformation through the trophic level in the marine and terrestrial environment. We believe this is due to long-standing misconceptions regarding volatile As stability and transport as well as an absence, until recently, of appropriate sampling methods. First and foremost, an attempt is made to unify arsines' designations, notations and formulas, taking into account all the different terms used in the literature. Then, the stability of As volatile species is discussed and new analytical developments are explored. Further, the special cases of diffuse low-level emissions (e.g. soil and sediment biovolatilisation), and point sources with high-level emissions (geothermal environments, landfills, and natural gas) are comprehensively reviewed. In each case, future possible areas of research and unknown mechanisms are identified and their importance towards the global As biogeochemical cycle is explored. This review gathers new information regarding mechanisms, stability, transport and sampling of the very elusive arsines and shows that more research should be conducted on this important process.

Short communication: Fractional milking distribution of immunoglobulin G and other constituents in colostrum.

The provision of quality colostrum with a high concentration of immunoglobulins is critical for newborn calf health. Because first colostrum may be low in overall concentration to effectively reduce the risk of newborn infections, we tested equivalent milking fractions of colostrum for possible IgG differences. The objective of this study was to determine if the fractional composition of colostrum changes during the course of milking with a focus on immunoglobulins. Twenty-four Holstein and Simmental cows were milked (first colostrum) within 4h after calving. The colostrum of 1 gland per animal was assembled into 4 percentage fractions over the course of milking: 0 to 25%, 25 to 50%, 50 to 75%, and 75 to 100%. The IgG concentration among the various fractions did not change in any significant pattern. Concentration of protein, casein, lactose and somatic cell count remained the same or exhibited only minor changes during the course of fractional milking colostrum. We determined that no benefit exists in feeding any particular fraction of colostrum to the newborn.

Reconstructing Disturbances and Their Biogeochemical Consequences over Multiple Timescales

Ongoing changes in disturbance regimes are predicted to cause acute changes in ecosystem structure and function in the coming decades, but many aspects of these predictions are uncertain. A key challenge is to improve the predictability of postdisturbance biogeochemical trajectories at the ecosystem level. Ecosystem ecologists and paleoecologists have generated complementary data sets about disturbance (type, severity, frequency) and ecosystem response (net primary productivity, nutrient cycling) spanning decadal to millennial timescales. Here, we take the first steps toward a full integration of these data sets by reviewing how disturbances are reconstructed using dendrochronological and sedimentary archives and by summarizing the conceptual frameworks for carbon, nitrogen, and hydrologic responses to disturbances. Key research priorities include further development of paleoecological techniques that reconstruct both disturbances and terrestrial ecosystem dynamics. In addition, mechanistic detail from disturbance experiments, long-term observations, and chronosequences can help increase the understanding of ecosystem resilience.

The effect of abrupt climatic warming on biogeochemical cycling and N2O emissions in a terrestrial ecosystem

The large, rapid increase in atmospheric N2O concentrations that occurred concurrent with the abrupt warming at the end of the Last Glacial period might have been the result of a reorganization in global biogeochemical cycles. To explore the sensitivity of nitrogen cycling in terrestrial ecosystems to abrupt warming, we combined a scenario of climate and vegetation composition change based on multiproxy data for the Oldest Dryas–Bølling abrupt warming event at Gerzensee, Switzerland, with a biogeochemical model that simulates terrestrial N uptake and release, including N2O emissions. As for many central European sites, the pollen record at the Gerzensee is remarkable for the abundant presence of the symbiotic nitrogen fixer Hippophaë rhamnoides (L.) during the abrupt warming that also marks the beginning of primary succession on immature glacial soils. Here we show that without additional nitrogen fixation, climate change results in a significant increase of N2O emissions of approximately factor 3.4 (from 6.4 ± 1.9 to 21.6 ± 5.9 mg N2O–N m− 2 yr− 1). Each additional 1000 mg m− 2 yr− 1 of nitrogen added to the ecosystem through N-fixation results in additional N2O emissions of 1.6 mg N2O–N m− 2 yr− 1 for the time with maximum H. rhamnoides coverage. Our results suggest that local reactions of emissions to abrupt climate change could have been considerably faster than the overall atmospheric concentration changes observed in polar ice. Nitrogen enrichment of soils due to the presence of symbiotic N-fixers during early primary succession not only facilitates the establishment of vegetation on soils in their initial stage of development, but can also have considerable influence on biogeochemical cycles and the release of reactive nitrogen trace gases to the atmosphere.

Assessment of Skill and Portability in Regional Marine Biogeochemical Models: Role of Multiple Planktonic Groups

Application of biogeochemical models to the study of marine ecosystems is pervasive, yet objective quantification of these models' performance is rare. Here, 12 lower trophic level models of varying complexity are objectively assessed in two distinct regions (equatorial Pacific and Arabian Sea). Each model was run within an identical one-dimensional physical framework. A consistent variational adjoint implementation assimilating chlorophyll-a, nitrate, export, and primary productivity was applied and the same metrics were used to assess model skill. Experiments were performed in which data were assimilated from each site individually and from both sites simultaneously. A cross-validation experiment was also conducted whereby data were assimilated from one site and the resulting optimal parameters were used to generate a simulation for the second site. When a single pelagic regime is considered, the simplest models fit the data as well as those with multiple phytoplankton functional groups. However, those with multiple phytoplankton functional groups produced lower misfits when the models are required to simulate both regimes using identical parameter values. The cross-validation experiments revealed that as long as only a few key biogeochemical parameters were optimized, the models with greater phytoplankton complexity were generally more portable. Furthermore, models with multiple zooplankton compartments did not necessarily outperform models with single zooplankton compartments, even when zooplankton biomass data are assimilated. Finally, even when different models produced similar least squares model-data misfits, they often did so via very different element flow pathways, highlighting the need for more comprehensive data sets that uniquely constrain these pathways.

Observing Biogeochemical Cycles at Global Scales With Profiling Floats and Gliders Prospects for a Global Array

Chemical and biological sensor technologies have advanced rapidly in the past five years. Sensors that require low power and operate for multiple years are now available for oxygen, nitrate, and a variety of bio-optical properties that serve as proxies for important components of the carbon cycle (e.g., particulate organic carbon). These sensors have all been deployed successfully for long periods, in some cases more than three years, on platforms such as profiling floats or gliders. Technologies for pH, pCO(2), and particulate inorganic carbon are maturing rapidly as well. These sensors could serve as the enabling technology for a global biogeochemical observing system that might operate on a scale comparable to the current Argo array. Here, we review the scientific motivation and the prospects for a global observing system for ocean biogeochemistry.

Biogeochemical indicators of peatland degradation – a case study of a temperate bog in Northern Germany

Organic soils in peatlands store a great proportion of the global soil carbon pool and can lose carbon via the atmosphere due to degradation. In Germany, most of the greenhouse gas (GHG) emissions from organic soils are attributed to sites managed as grassland. Here, we investigated a land use gradient from near-natural wetland (NW) to an extensively managed (GE) to an intensively managed grassland site (GI), all formed in the same bog complex in northern Germany. Vertical depth profiles of δ13C, δ15N, ash content, C / N ratio and bulk density as well as radiocarbon ages were studied to identify peat degradation and to calculate carbon loss. At all sites, including the near-natural site, δ13C depth profiles indicate aerobic decomposition in the upper horizons. Depth profiles of δ15N differed significantly between sites with increasing δ15N values in the top soil layers paralleling an increase in land use intensity owing to differences in peat decomposition and fertilizer application. At both grassland sites, the ash content peaked within the first centimetres. In the near-natural site, ash contents were highest in 10–60 cm depth. The ash profiles, not only at the managed grassland sites, but also at the near-natural site indicate that all sites were influenced by anthropogenic activities either currently or in the past, most likely due to drainage. Based on the enrichment of ash content and changes in bulk density, we calculated the total carbon loss from the sites since the peatland was influenced by anthropogenic activities. Carbon loss at the sites increased in the following order: NW < GE < GI. Radiocarbon ages of peat in the topsoil of GE and GI were hundreds of years, indicating the loss of younger peat material. In contrast, peat in the first centimetres of the NW was only a few decades old, indicating recent peat growth. It is likely that the NW site accumulates carbon today but was perturbed by anthropogenic activities in the past. Together, all biogeochemical parameters indicate a degradation of peat due to (i) conversion to grassland with historical drainage and (ii) land use intensification.

Characterization of the East Houston particulate matter <2.5 atmosphere; a novel method for desorbing organic constituents from airborne particulates

I have developed a novel approach to test for toxic organic substances adsorbed onto ultra fine particulate particles present in the ambient air in Northeast Houston, Texas. These particles are predominantly carbon soot with an aerodynamic diameter (AD) of <2.5 μm. If present in the ambient air, many of the organic substances will be absorbed to the surface of the particles (which act just like a charcoal air filter), and may be adducted into the respiratory system. Once imbedded into the lungs these particles may release the adsorbed toxic organic substances with serious health consequences. I used a Airmetrics portable Minivol air sampler time drawing the ambient air through collection filters samples from 6 separate sites in Northeast Houston, an area known for high ambient PM 2.5 released from chemical plants and other sources (e.g. vehicle emissions).(1) In practice, the mass of the collected particles were much less than the mass of the filters. My technique was designed to release the adsorbed organic substances on the fine carbon particles by heating the filter samples that included the PM 2.5 particles prior to identification by gas chromatography/mass spectrometry (GCMS). The results showed negligible amounts of target chemicals from the collection filters. However, the filters alone released organic substances and GCMS could not distinguish between the organic substances released from the soot particles from those released from the heated filter fabric. However, an efficacy tests of my method using two wax burning candles that released soot revealed high levels of benzene. This suggests that my method has the potential to reveal the organic substances adsorbed onto the PM 2.5 for analysis. In order to achieve this goal, I must refine the particle collection process which would be independent of the filters; the filters upon heating also release organic substances obscuring the contribution from the soot particles. To obtain pure soot particles I will have to filter more air so that the soot particles can be shaken off the filters and then analyzed by my new technique. ^

Biogeochemical investigation of the benthic nitrogen cycle in the Arabian Sea off Pakistan

A pronounced deficit of nitrogen (N) in the oxygen minimum zone (OMZ) of the Arabian Sea suggests the occurrence of heavy N-loss that is commonly attributed to pelagic processes. However, the OMZ water is in direct contact with sediments on three sides of the basin. Contribution from benthic N-loss to the total N-loss in the Arabian Sea remains largely unassessed. In October 2007, we sampled the water column and surface sediments along a transect cross-cutting the Arabian Sea OMZ at the Pakistan continental margin, covering a range of station depths from 360 to 1430 m. Benthic denitrification and anammox rates were determined by using 15N-stable isotope pairing experiments. Intact core incubations showed declining rates of total benthic N-loss with water depth from 0.55 to 0.18 mmol N m**-2 day**-1. While denitrification rates measured in slurry incubations decreased from 2.73 to 1.46 mmol N m**-2 day**-1 with water depth, anammox rates increased from 0.21 to 0.89 mmol N m**-2 day**-1. Hence, the contribution from anammox to total benthic N-loss increased from 7% at 360 m to 40% at 1430 m. This trend is further supported by the quantification of cd1-containing nitrite reductase (nirS), the biomarker functional gene encoding for cytochrome cd1-Nir of microorganisms involved in both N-loss processes. Anammox-like nirS genes within the sediments increased in proportion to total nirS gene copies with water depth. Moreover, phylogenetic analyses of NirS revealed different communities of both denitrifying and anammox bacteria between shallow and deep stations. Together, rate measurement and nirS analyses showed that anammox, determined for the first time in the Arabian Sea sediments, is an important benthic N-loss process at the continental margin off Pakistan, especially in the sediments at deeper water depths. Extrapolation from the measured benthic N-loss to all shelf sediments within the basin suggests that benthic N-loss may be responsible for about half of the overall N-loss in the Arabian Sea.

Age determination, sedimentological, biogeochemical, and plant macrofossils analyses of outcrop PG2038-1

Thermokarst lakes are a widespread feature of the Arctic tundra, in which highly dynamic processes are closely connected with current and past climate changes. We investigated late Quaternary sediment dynamics, basin and shoreline evolution, and environmental interrelations of Lake El'gene-Kyuele in the NE Siberian Arctic (latitude 71°17'N, longitude 125°34'E). The water-body displays thaw-lake characteristics cutting into both Pleistocene Ice Complex and Holocene alas sediments. Our methods are based on grain size distribution, mineralogical composition, TOC/N ratio, stable carbon isotopes and the analysis of plant macrofossils from a 3.5-m sediment profile at the modern eastern lake shore. Our results show two main sources for sediments in the lake basin: terrigenous diamicton supplied from thermokarst slopes and the lake shore, and lacustrine detritus that has mainly settled in the deep lake basin. The lake and its adjacent thermokarst basin rapidly expanded during the early Holocene. This climatically warmer than today period was characterized by forest or forest tundra vegetation composed of larches, birch trees and shrubs. Woodlands of both the HTM and the Late Pleistocene were affected by fire, which potentially triggered the initiation of thermokarst processes resulting later in lake formation and expansion. The maximum lake depth at the study site and the lowest limnic bioproductivity occurred during the longest time interval of ~7 ka starting in the Holocene Thermal Maximum and lasting throughout the progressively cooler Neoglacial, whereas partial drainage and an extensive shift of the lake shoreline occurred ~0.9 cal. ka BP. Correspondingly, this study discusses different climatic and environmental drivers for the dynamics of a thermokarst basin.