Biochemical properties of Paracoccus denitrificans FnrP:Reactions with molecular oxygen and nitric oxide

In Paracoccus denitrificans, three CRP/FNR family regulatory proteins, NarR, NnrR and FnrP, control the switch between aerobic and anaerobic (denitrification) respiration. FnrP is a [4Fe-4S] cluster containing homologue of the archetypal O2 sensor FNR from E. coli and accordingly regulates genes encoding aerobic and anaerobic respiratory enzymes in response to O2, and also NO, availability. Here we show that FnrP undergoes O2-driven [4Fe-4S] to [2Fe-2S] cluster conversion that involves up to 2 O2 per cluster, with significant oxidation of released cluster sulfide to sulfane observed at higher O2 concentrations. The rate of the cluster reaction was found to be ~6-fold lower than that of E. coli FNR, suggesting that FnrP can remain transcriptionally active under microaerobic conditions. This is consistent with a role for FnrP in activating expression of the high O2 affinity cytochrome c oxidase under microaerobic conditions. Cluster conversion resulted in dissociation of the transcriptionally active FnrP dimer into monomers. Therefore, along with E. coli FNR, FnrP belongs to the subset of FNR proteins in which cluster type is correlated with association state. Interestingly, two key charged residues, Arg140 and Asp154, that have been shown to play key roles in the monomer-dimer equilibrium in E. coli FNR are not conserved in FnrP, indicating that different protomer interactions are important for this equilibrium. Finally, the FnrP [4Fe-4S] cluster is shown to undergo reaction with multiple NO molecules, resulting in iron nitrosyl species and dissociation into monomers

Modelling the viral dynamics of the SARS-CoV-2 Delta and Omicron variants in different cell types.

We use viral kinetic models fitted to viral load data from in vitro studies to explain why the SARS-CoV-2 Omicron variant replicates faster than the Delta variant in nasal cells, but slower than Delta in lung cells, which could explain Omicron's higher transmission potential and lower severity. We find that in both nasal and lung cells, viral infectivity is higher for Omicron but the virus production rate is higher for Delta, with an estimated approximately 200-fold increase in infectivity and 100-fold decrease in virus production when comparing Omicron with Delta in nasal cells. However, the differences are unequal between cell types, and ultimately lead to the basic reproduction number and growth rate being higher for Omicron in nasal cells, and higher for Delta in lung cells. In nasal cells, Omicron alone can enter via a TMPRSS2-independent pathway, but it is primarily increased efficiency of TMPRSS2-dependent entry which accounts for Omicron's increased activity. This work paves the way for using within-host mathematical models to understand the transmission potential and severity of future variants

Low-molecular-weight organic acids exuded by Mangrove (Kandelia candel (L.) Druce) roots and their effect on cadmium species change in the rhizosphere

Cadmium (Cd) accumulation has been found in large areas of estuaries due to emissions from municipal waste incinerators, car exhausts, residues from metalliferous mining and the smelting industry, and the use of sludge or urban composts, pesticides and fertilizers. In these areas, mangroves have been observed to possess a tolerance to high levels of Cd and it is hypothesized that low-molecular-weight organic acids (LMWOAs) produced at the soil-root interface (rhizosphere) may play an important role in the availability of Cd to these plants. Changes in both LMWOAs and Cd bioavailability, directly or indirectly related to the Cd stress were studied in the laboratory. A rhizobox technique was used for 6 months under growth in air-conditioned greenhouse with natural illumination and the relative humidity of 85%, the temperature ranging from 26 to 32 degrees C, in increasing Cd concentration stress conditions (0, 5, 10, 20, 30, 40 and 50 ppm). Six-month-old Kandelia candel (L.) Druce seedlings which grown in the rhizoboxes were selected to examine their root exudates. The results showed that monocarboxylic acids (formic, acetic, lactic, butyric and propionic acids), and di- and tricarbonxylic acids (maleic, fumaric, citric and L-tartaric acids) were found in root exudates. Citric, lactic and acetic acids being dominant took up 76.85-97.87% of the total LMWOAs in root exudations. Fumaric acid was only found where mangroves were growing on 20 ppm Cd. Root exudates reduced pH by 0.2-0.5 pH units in the rhizosphere compare to the bulk soil. The proportion of exchangeable Cd and Cd bound to carbonate had a positive correlation to total LMWOAs in the rhizosphere soil. Root exudates induced changes in soil Cd species under control conditions, consisting of lower exchangeable Cd compared with increasing stress. Results indicate that the measurement of LMWOAs may be included as early biomarkers in a plant bioassay to assess the phytotoxicity of Cd-contaminated soils on mangrove plants. (C) 2007 Elsevier B.V. All rights reserved

Coriolus versicolor Yun-Zhi could delay deterioration of patients with advanced non-small cell lung cancer

published_or_final_versio

Identifying rare variants using a Bayesian regression approach

Recent advances in next-generation sequencing technologies have made it possible to generate large amounts of sequence data with rare variants in a cost-effective way. Statistical methods that test variants individually are underpowered to detect rare variants, so it is desirable to perform association analysis of rare variants by combining the information from all variants. In this study, we use a Bayesian regression method to model all variants simultaneously to identify rare variants in a data set from Genetic Analysis Workshop 17. We studied the association between the quantitative risk traits Q1, Q2, and Q4 and the single-nucleotide polymorphisms and identified several positive single-nucleotide polymorphisms for traits Q1 and Q2. However, the model also generated several apparent false positives and missed many true positives, suggesting that there is room for improvement in this model

An invisibility cloak using silver nanowires

In this paper, we use the parameter retrieval method together with an analytical effective medium approach to design a well-performed invisible cloak, which is based on an empirical revised version of the reduced cloak. The designed cloak can be implemented by silver nanowires with elliptical cross-sections embedded in a polymethyl methacrylate host. This cloak is numerically proved to be robust for both the inner hidden object as well as incoming detecting waves, and is much simpler thus easier to manufacture when compared with the earlier proposed one [Nat. Photon. 1, 224 (2007)].Comment: 7 pages, 4 figures, 2 table

Vertical distribution of acid-volatile sulfide and simultaneously extracted metals in mangrove sediments from the Jiulong River Estuary, Fujian, China

Background. Acid-volatile sulfide (AVS) is operationally defined as sulfides in sediment, which are soluble in cold acid, and is reported as the most active part of the total sulfur in aquatic sediments. It is a key partitioning phase controlling the activities of divalent cationic heavy metals in sediment. Methods. In order to examine this in mangrove environments, six sites were selected along the Jiulong River Estuary in Fujian, China, which had previously been reported to be polluted by heavy metals. Sediments were sampled from 0-60 cm depth at each site, and the spatial distribution of AVS and SEM (simultaneously extracted metals: copper, cadmium, zinc, and lead) were determined. Results and Discussion. The results indicate that the AVS concentrations had a spatial variation, ranging from 0.24 to 16.10 mu mol g(-1) sediment dry weight. The AVS concentration in the surface layer is lower than that of the deeper sediment, with peak values in the 15-30 cm horizon. There was no correlation between the AVS value and organic matter content or total dissolved salts, but a significant positive correlation of AVS with surface sediment (0-5 cm) moisture content was found. This indicates that water logged sediments tend to have a high AVS value. The amount of SEM was within the range of 0.33-2.80 mu mol g(-1) sediment dry weight and decreased with sediment depth. Conclusions. There was a marked variation in AVS and SEM among different sites studied. AVS concentrations were generally lower in the surface sediments, while SEM concentrations slightly decreased with the depth. Higher concentrations of SEM found in the upper layers of the sediments confirm the earlier suggestions that this study area may suffer from increasing heavy metal pollution. Recommendations and Perspectives. When monitoring environmental impacts by using AVS, the micro and large-scale spatial variation as well as vertical distribution need to be estimated to avoid misleading results. Both AVS and SEM concentrations in different sediment layers should be taken into account in assessing the potential impact of heavy metals on the biotic environment

Speciation changes of cadmium in mangrove (Kandelia candel (L.)) rhizosphere sediments

The speciation distribution of cadmium (Cd) in mangrove (Kandelia candel (L.) Druce) rhizosphere sediment was investigated after different contents of Cd being loaded. The study results indicated that root induced changes of Cd bioavailability in the rhizosphere. Exchangeable and carbonate bound Cd in the rhizosphere sediments were lower than these in the bulk sediments, whilst an increase in Fe-Mn oxides bound and O.M/sulfide bound fractions occurred in the rhizosphere sediment. Increased levels of Cd in sediments resulted in higher Cd concentrations in mangrove plants, and the order of accumulation was: roots > hypocotyls > stems and leaves

Synthesized grain size distribution in the interstellar medium

We examine a synthetic way of constructing the grain size distribution in the interstellar medium (ISM). First we formulate a synthetic grain size distribution composed of three grain size distributions processed with the following mechanisms that govern the grain size distribution in the Milky Way: (i) grain growth by accretion and coagulation in dense clouds, (ii) supernova shock destruction by sputtering in diffuse ISM, and (iii) shattering driven by turbulence in diffuse ISM. Then, we examine if the observational grain size distribution in the Milky Way (called MRN) is successfully synthesized or not. We find that the three components actually synthesize the MRN grain size distribution in the sense that the deficiency of small grains by (i) and (ii) is compensated by the production of small grains by (iii). The fraction of each {contribution} to the total grain processing of (i), (ii), and (iii) (i.e., the relative importance of the three {contributions} to all grain processing mechanisms) is 30-50%, 20-40%, and 10-40%, respectively. We also show that the Milky Way extinction curve is reproduced with the synthetic grain size distributions.Comment: 10 pages, 6 figures, accepted for publication in Earth, Planets, and Spac