This paper presents the results of extensive field trials measuring rates of Fe(II) oxidation at a number of Fe-bearing mine drainage discharges in the UK. Batch experiments were carried out with samples taken at regular intervals and Fe(II) concentration determined spectrophotometrically using 2′2-bipyridyl as the complexing agent. Initial concentrations for Fe(II) were 5.65–76.5mg/L. Temperature, pH and dissolved O₂ (DO) were logged every 10s, with pH at the start of the experiments in the range 5.64–6.95 and alkalinity ranging from 73 to 741mg/L CaCO₃ equivalent. A numerical model based on a fourth order Runge–Kutta method was developed to calculate values for k₁, the rate constant for homogeneous oxidation, from the experimental data. The measured values of pH, temperature, [Fe(II)] and DO were input into the model with resulting values for k₁ found to be in the range 2.7×10¹⁴–2.7×10¹⁶M⁻²atm⁻¹min⁻¹. These values for k₁ are 1–3 orders of magnitude higher than previously reported for laboratory studies at a similar pH. Comparison of the observed Fe(II) oxidation rates to data published by other authors show a good correlation with heterogenous oxidation rates and may indicate the importance of autocatalysis in these systems. These higher than expected rates of Fe oxidation could have a significant impact on the design of treatment schemes for the remediation of mine drainage and other Fe-bearing ground waters in the future.

<p>Abstract</p> <p>Background</p> <p>Whole-genome sequencing of bacteria has proceeded at an exponential pace but annotation validation has lagged behind. For instance, the MetJ regulon, which controls methionine biosynthesis and transport, has been studied almost exclusively in <it>E. coli </it>and <it>Salmonella</it>, but homologs of MetJ exist in a variety of other species. These include some that are pathogenic (e.g. <it>Yersinia</it>) and some that are important for environmental remediation (e.g. <it>Shewanella</it>) but many of which have not been extensively characterized in the literature.</p> <p>Results</p> <p>We have determined the likely composition of the MetJ regulon in all species which have MetJ homologs using bioinformatics techniques. We show that the core genes known from <it>E. coli </it>are consistently regulated in other species, and we identify previously unknown members of the regulon. These include the cobalamin transporter, <it>btuB</it>; all the genes involved in the methionine salvage pathway; as well as several enzymes and transporters of unknown specificity.</p> <p>Conclusions</p> <p>The MetJ regulon is present and functional in five orders of gammaproteobacteria: Enterobacteriales, Pasteurellales, Vibrionales, Aeromonadales and Alteromonadales. New regulatory activity for MetJ was identified in the genomic data and verified experimentally. This strategy should be applicable for the elucidation of regulatory pathways in other systems by using the extensive sequencing data currently being generated.</p>

<p>Abstract</p> <p>Background</p> <p>Nucleosome positioning has an important role in gene regulation. However, dynamic positioning <it>in vivo </it>casts doubt on the reliability of predictions based on DNA sequence characteristics. What role does sequence-dependent positioning play? In this paper, using a curvature profile model, nucleosomes are predicted in the human genome and patterns of nucleosomes near some key sites are investigated.</p> <p>Results</p> <p>Curvature profiling revealed that in the vicinity of a transcription start site, there is also a nucleosome-free region. Near transcription factor binding sites, curvature profiling showed a trough, indicating nucleosome depletion. The trough of the curvature profile corresponds well to the high binding scores of transcription factors. Moreover, our analysis suggests that nucleosome positioning has a selective protection role. Target sites of miRNAs are occupied by nucleosomes, while single nucleotide polymorphism sites are depleted of nucleosomes.</p> <p>Conclusions</p> <p>The results indicate that DNA sequences play an important role in nucleosome positioning, and the positioning is important not only in gene regulation, but also in genetic variation and miRNA functions.</p>

Bioremediation of petroleum sludge was conducted by using land-farming method in micro scale and by applying an indigenous bacteria Bacillus megaterium. The samples were from PT. Pertamina Musi Banyuasin district of South Sumatra. The research aim was to evaluate the performance of the bacteria in degrading petroleum sludge. The rate of the biodegradation process was determined by using differential method and the data analyses show that the reaction order is 0.74. Then, the rate of biodegradation constant was determined by using an integral method assuming that the biodegradation process was a first reaction order. From the calculation, it was revealed that the biodegradation reaction constant was 0.0204/day. The bioremediation-kinetics model is y = -0.0204X + 2.0365, and by using this model the bioremediation process could be ended after 99.83 days. The qualitative analysis was carried out by using GC-MS to investigate the components of compounds changed during the bioremediation process. The results show that the B. megaterium could degrade 99.32% of alkane compounds.

Apolipoprotein A-I plays a central role in the solution structure of high-density lipoproteins. Determining the stoichiometry of lipid-bound apo A-I in the hydrated state is therefore fundamental to understanding how high-density lipoproteins form and function. Here, we use the quantum optical phenomenon of photon antibunching to determine the number of apo A-I molecules bound to discoidal lipoproteins and compare this with values obtained by photon-counting histogram analysis. Both the photon antibunching and photon-counting analyses show that reconstituted high-density lipoprotein particles contain two apo A-I molecules, which is in agreement with the commonly accepted double-belt model.

Rice seed size is an important agronomic trait in determining the yield potential, and four seed size related genes (GS3, GW2, qSW5/GW5 and GIF1) have been cloned in rice so far. However, the relationship among these four genes is still unclear, which will impede the process of gene pyramiding breeding program to some extent. To shade light on the relationship of above four genes, gene expression analysis was performed with GS3-RNAi, GW2-RNAi lines and CSSL of qSW5 at the transcriptional level. The results clearly showed that qSW5 and GW2 positively regulate the expression of GS3. Meanwhile, qSW5 can be down-regulated by repression of GW2 transcription. Additionally, GIF1 expression was found to be positively regulated by qSW5 but negatively by GW2 and GS3. Moreover, the allelic effects of qSW5 and GS3 were detailedly characterized based on a natural population consisting of 180 rice cultivars. It was indicated that mutual interactions exist between the two genes, in which, qSW5 affecting seed length is masked by GS3 alleles, and GS3 affecting seed width is masked by qSW5 alleles. These findings provide more insights into the molecular mechanisms underlying seed size development in rice and are likely to be useful for improving rice grain yield.

This review describes the results from X-ray Absorption Spectroscopy studies that have contributed to an understanding of the role of Ca in the photosynthetic water-oxidation reaction. The results include the first Mn, Ca and Sr X-ray spectroscopy studies using Ca or Sr-substituted PS II samples that established the presence of a MnCa heteronuclear structure and its orientation, and the most recent Sr X-ray spectroscopy study using biosynthetically prepared Sr-containing PS II in the various S-states that provide important insights into the requirement for Ca in the mechanism of the Mn₄Ca catalytic center.

The root hair and nonhair cells in the Arabidopsis (Arabidopsis thaliana) root epidermis are specified by a suite of transcriptional regulators. Two of these are WEREWOLF (WER) and CAPRICE (CPC), which encode MYB transcription factors that are required for promoting the nonhair cell fate and the hair cell fate, respectively. However, the precise function and relationship between these transcriptional regulators have not been fully defined experimentally. Here, we examine these issues by misexpressing the WER gene using the GAL4-upstream activation sequence transactivation system. We find that WER overexpression in the Arabidopsis root tip is sufficient to cause epidermal cells to adopt the nonhair cell fate through direct induction of GLABRA2 (GL2) gene expression. We also show that GLABRA3 (GL3) and ENHANCER OF GLABRA3 (EGL3), two closely related bHLH proteins, are required for the action of the overexpressed WER and that WER interacts with these bHLHs in plant cells. Furthermore, we find that CPC suppresses the WER overexpression phenotype quantitatively. These results show that WER acts together with GL3/EGL3 to induce GL2 expression and that WER and CPC compete with one another to define cell fates in the Arabidopsis root epidermis.