Synthesis and characterization of Fe-Al-Mn nanocomposite sorbent for phosphate sorption-desorption study

In this work, we evaluated the potential application of a ternary nanosorbent for predicting phosphate desorption kinetics from soil. Accordingly, ternary mixed oxide nanosorbents with Fe:Al:Mn mole ratios of 3:3:1; 6:3:1 and 2:4:1 were prepared using simultaneous oxidation and coprecipitation methods. The adsorbents were characterized by X-ray diffraction (XRD), Brunauer-Emmett-Teller (BET) method, scanning electron microscope (SEM) coupled with EDX (energy dispersive X-ray) and Furrier transform infrared spectroscopy (FT-IR). The results indicated that the as-synthesized ternary oxides were either amorphous or crystalline depending on the composition from which the composite was formed, with specific surface area ranging from 41.2 to 243 m2g-1. Among the three proportions considered, the one with Fe:Al:Mn in 3:3:1 mole ratio exhibited the highest surface area and was selected for P sorption-desorption studies. Phosphate removal gradually decreased with the increasing of pH from 4 to 10.5. Adsorption isotherms on the adsorbent at pH 6.5 followed the order: Freundlich > Temkin > Dubinin-Radushkevich > Langmuir. At 35 °C, the maximum adsorption capacity for the adsorbent was found to be 49.95 mg g-1. The effect of coexisting anions on phosphate sorption followed the order: SiO32- > CO32– > SO42– > NO3- and this is closely correlated with charge-to-radius ratios of the anions. The kinetic data were described better by the pseudo-second-order adsorption model. The as-obtained nanocomposite sorbent with good specific affinity towards phosphate is a promising adsorbent for soil P desorption studies.               KEY WORDS: Nanostructure, Phosphate, Desorption kinetics, Ternary oxide, Adsorption isotherm Bull. Chem. Soc. Ethiop. 2018, 32(3), 421-436.DOI: https://dx.doi.org/10.4314/bcse.v32i3.

Selected heavy metals in some vegetables produced through wastewater irrigation and their toxicological implications in eastern Ethiopia

Vegetables widely consumed in some areas of eastern Ethiopia such as cabbage (Brassica oleraceae var. capitata L.), potato (Solanum tuberosum L.), and khat (Catha edulis Forsk.) are cultivated through irrigation with wastewater. The purpose of this study was to analyse the contents of selected toxic heavy metal (Cr, Co, Cd and Pb) of the vegetables, the effluents used to irrigate the crops, and the soils on which the crops were grown, using flame atomic absorption spectrometry (FAAS). The optimized wet digestion procedure was employed to solubilise the metals from the samples. The validation was performed by spiking the samples with a standard solution of each metal having a known concentration and the percentage recovery values in the range of 91.0–98.3% for soil, 92.0–102% for effluent, and 89.0–101% for vegetable samples. The following concentrations (mg kg-1) of the metals were found in the edible parts of the cabbage, potato, and khat plants, respectively: Cr [less than method detection limit (<MDL)- 17.13], (11.96-14.21), and (9.04-15.54); Co (5.72-9.72), (5.15-8.72), and (<MDL-8.87); Cd (1.15-2.46), (1.22-1.46), and (0.38-3.22); Pb (5.48-11.95), (5.43-7.78), and (4.49-11). The concentrations in the effluent samples (mg kg-1) ranged from 0.17-0.26, 0.57-1.02, 0.04-0.08, and 0.82-2.52 for Cr, Co, Cd, and Pb, respectively. Similarly, concentrations (mg kg-1) of the metals in the soil samples were in the ranges of 25.71-41.45, 17.69-23.59, 0.79-2.56, and 26.04-47.29 for Cr, Co, and Cd, and Pb, respectively. The study revealed that the concentrations of all metals in the vegetables, except Co, were found to be above the safe limits set by different international organizations for consumption, posing a serious health hazard to humans. Therefore, regular monitoring of effluents, soils, and vegetables are essential to prevent excessive build-up of the toxic heavy metals in food. Thus, the health risk and the extent of heavy metal contamination can be reduced.Keywords: Vegetables, wastewater, safe limits, irrigatio

Nucleosome mobilization by ISW2 requires the concerted action of the ATPase and SLIDE domains

The ISWI family of ATP-dependent chromatin remodelers represses transcription by changing nucleosome positioning. The interactions with extranucleosomal DNA and the requirement of a minimal length of extranucleosomal DNA by ISWI mediate the spacing of nucleosomes. ISW2 from Saccharomyces cerevisiae, a member of the ISWI family, has a conserved domain called SLIDE (SANT-like ISWI domain), whose binding to extranucleosomal DNA ~19 bp from the edge of nucleosomes is required for efficiently pushing DNA into nucleosomes and maintaining the unidirectional movement of nucleosomes, as reported here. Loss of SLIDE binding does not perturb ATPase domain binding to the SHL2 site of nucleosomes or its initial movement of DNA inside of nucleosomes. ISW2 has therefore two distinct roles in mobilizing nucleosomes, with the ATPase domain translocating and moving DNA inside nucleosomes, and the SLIDE domain facilitating the entry of linker DNA into nucleosomes

A comparison of in vitro nucleosome positioning mapped with chicken, frog and a variety of yeast core histones

AbstractUsing high-throughput sequencing, we have mapped sequence-directed nucleosome positioning in vitro on four plasmid DNAs containing DNA fragments derived from the genomes of sheep, drosophila, human and yeast. Chromatins were prepared by reconstitution using chicken, frog and yeast core histones. We also assembled yeast chromatin in which histone H3 was replaced by the centromere-specific histone variant, Cse4. The positions occupied by recombinant frog and native chicken histones were found to be very similar. In contrast, nucleosomes containing the canonical yeast octamer or, in particular, the Cse4 octamer were assembled at distinct populations of locations, a property that was more apparent on particular genomic DNA fragments. The factors that may contribute to this variation in nucleosome positioning and the implications of the behavior are discussed

Histone H3 Localizes to the Centromeric DNA in Budding Yeast

During cell division, segregation of sister chromatids to daughter cells is achieved by the poleward pulling force of microtubules, which attach to the chromatids by means of a multiprotein complex, the kinetochore. Kinetochores assemble at the centromeric DNA organized by specialized centromeric nucleosomes. In contrast to other eukaryotes, which typically have large repetitive centromeric regions, budding yeast CEN DNA is defined by a 125 bp sequence and assembles a single centromeric nucleosome. In budding yeast, as well as in other eukaryotes, the Cse4 histone variant (known in vertebrates as CENP-A) is believed to substitute for histone H3 at the centromeric nucleosome. However, the exact composition of the CEN nucleosome remains a subject of debate. We report the use of a novel ChIP approach to reveal the composition of the centromeric nucleosome and its localization on CEN DNA in budding yeast. Surprisingly, we observed a strong interaction of H3, as well as Cse4, H4, H2A, and H2B, but not histone chaperone Scm3 (HJURP in human) with the centromeric DNA. H3 localizes to centromeric DNA at all stages of the cell cycle. Using a sequential ChIP approach, we could demonstrate the co-occupancy of H3 and Cse4 at the CEN DNA. Our results favor a H3-Cse4 heterotypic octamer at the budding yeast centromere. Whether or not our model is correct, any future model will have to account for the stable association of histone H3 with the centromeric DNA

MethylViewer: computational analysis and editing for bisulfite sequencing and methyltransferase accessibility protocol for individual templates (MAPit) projects

Bisulfite sequencing is a widely-used technique for examining cytosine DNA methylation at nucleotide resolution along single DNA strands. Probing with cytosine DNA methyltransferases followed by bisulfite sequencing (MAPit) is an effective technique for mapping protein–DNA interactions. Here, MAPit methylation footprinting with M.CviPI, a GC methyltransferase we previously cloned and characterized, was used to probe hMLH1 chromatin in HCT116 and RKO colorectal cancer cells. Because M.CviPI-probed samples contain both CG and GC methylation, we developed a versatile, visually-intuitive program, called MethylViewer, for evaluating the bisulfite sequencing results. Uniquely, MethylViewer can simultaneously query cytosine methylation status in bisulfite-converted sequences at as many as four different user-defined motifs, e.g. CG, GC, etc., including motifs with degenerate bases. Data can also be exported for statistical analysis and as publication-quality images. Analysis of hMLH1 MAPit data with MethylViewer showed that endogenous CG methylation and accessible GC sites were both mapped on single molecules at high resolution. Disruption of positioned nucleosomes on single molecules of the PHO5 promoter was detected in budding yeast using M.CviPII, increasing the number of enzymes available for probing protein–DNA interactions. MethylViewer provides an integrated solution for primer design and rapid, accurate and detailed analysis of bisulfite sequencing or MAPit datasets from virtually any biological or biochemical system

SS18 Together with Animal-Specific Factors Defines Human BAF-Type SWI/SNF Complexes

Contains fulltext : 94049.pdf (publisher's version ) (Open Access

The YEATS domain of Taf14 in Saccharomyces cerevisiae has a negative impact on cell growth

The role of a highly conserved YEATS protein motif is explored in the context of the Taf14 protein of Saccharomyces cerevisiae. In S. cerevisiae, Taf14 is a protein physically associated with many critical multisubunit complexes including the general transcription factors TFIID and TFIIF, the chromatin remodeling complexes SWI/SNF, Ino80 and RSC, Mediator and the histone modification enzyme NuA3. Taf14 is a member of the YEATS superfamily, conserved from bacteria to eukaryotes and thought to have a transcription stimulatory activity. However, besides its ubiquitous presence and its links with transcription, little is known about Taf14’s role in the nucleus. We use structure–function and mutational analysis to study the function of Taf14 and its well conserved N-terminal YEATS domain. We show here that the YEATS domain is not necessary for Taf14’s association with these transcription and chromatin remodeling complexes, and that its presence in these complexes is dependent only on its C-terminal domain. Our results also indicate that Taf14’s YEATS domain is not necessary for complementing the synthetic lethality between TAF14 and the general transcription factor TFIIS (encoded by DST1). Furthermore, we present evidence that the YEATS domain of Taf14 has a negative impact on cell growth: its absence enables cells to grow better than wild-type cells under stress conditions, like the microtubule destabilizing drug benomyl. Moreover, cells expressing solely the YEATS domain grow worser than cells expressing any other Taf14 construct tested, including the deletion mutant. Thus, this highly conserved domain should be considered part of a negative regulatory loop in cell growth

The CRE1 carbon catabolite repressor of the fungus Trichoderma reesei: a master regulator of carbon assimilation

<p>Abstract</p> <p>Background</p> <p>The identification and characterization of the transcriptional regulatory networks governing the physiology and adaptation of microbial cells is a key step in understanding their behaviour. One such wide-domain regulatory circuit, essential to all cells, is carbon catabolite repression (CCR): it allows the cell to prefer some carbon sources, whose assimilation is of high nutritional value, over less profitable ones. In lower multicellular fungi, the C2H2 zinc finger CreA/CRE1 protein has been shown to act as the transcriptional repressor in this process. However, the complete list of its gene targets is not known.</p> <p>Results</p> <p>Here, we deciphered the CRE1 regulatory range in the model cellulose and hemicellulose-degrading fungus <it>Trichoderma reesei </it>(anamorph of <it>Hypocrea jecorina</it>) by profiling transcription in a wild-type and a delta-<it>cre1 </it>mutant strain on glucose at constant growth rates known to repress and de-repress CCR-affected genes. Analysis of genome-wide microarrays reveals 2.8% of transcripts whose expression was regulated in at least one of the four experimental conditions: 47.3% of which were repressed by CRE1, whereas 29.0% were actually induced by CRE1, and 17.2% only affected by the growth rate but CRE1 independent. Among CRE1 repressed transcripts, genes encoding unknown proteins and transport proteins were overrepresented. In addition, we found CRE1-repression of nitrogenous substances uptake, components of chromatin remodeling and the transcriptional mediator complex, as well as developmental processes.</p> <p>Conclusions</p> <p>Our study provides the first global insight into the molecular physiological response of a multicellular fungus to carbon catabolite regulation and identifies several not yet known targets in a growth-controlled environment.</p