Solvent-thermal approach of MIL-100(Fe)/Cygnea/Fe3O4/TiO2 nanocomposite for the treatment of lead from oil refinery wastewater (ORW) under UVA light.

The main purpose of this research endeavor is to reduce lead concentrations in the wastewater of an oil refinery through the utilization of a material composed of oyster shell waste (MIL-100(Fe)/Cygnea/Fe3O4/TiO2. Initially, iron oxide nanoparticles (Fe3O4) were synthesized via solvent-thermal synthesis. It was subsequently coated layer by layer with the organic-metallic framework MIL-100 (Fe) using the core-shell method. Additionally, the solvent-thermal method was utilized to integrate TiO2 nanoparticles into the magnetic organic-metallic framework's structure. Varieties of analytical analysis were utilized to investigate the physical and chemical properties of the synthetic final photocatalyst. Nitrogen adsorption and desorption technique (BET), scanning electron microscopy (SEM), scanning electron diffraction pattern (XRD), and transmission electron microscopy (TEM). Following the characterization of the final photocatalyst, the physical and chemical properties of the nanoparticles synthesized in each step, several primary factors that significantly affect the removal efficiency in the advanced oxidation system (AOPs) were examined. These variables consist of pH, photocatalyst dosage, lead concentration, and reaction temperature. The synthetic photocatalyst showed optimal performance in the removal of lead from petroleum wastewater under the following conditions: 35 °C temperature, pH of 3, 0.04 g/l photocatalyst dosage, and 100 mg/l wastewater concentration. Additionally, the photocatalyst maintained a significant level of reusability after undergoing five cycles. The findings of the study revealed that the photocatalyst dosage and pH were the most influential factors in the effectiveness of lead removal. According to optimal conditions, lead removal reached a maximum of 96%. The results of this investigation showed that the synthetic photocatalyst, when exposed to UVA light, exhibited an extraordinary capacity for lead removal.

Capability of TiO2 and Fe3O4 nanoparticles loaded onto Algae (Scendesmus sp.) as a novel bio-magnetic photocatalyst to degration of Red195 dye in the sonophotocatalytic treatment process under ultrasonic/UVA irradiation.

In this study, the magnetic photocatalyst Scendesmus/Fe3O4/TiO2 was synthesized, and its sonophotocatalytic properties in relation to the degradation of the Red195 dye were evaluated. Particles were characterized using a scanning electron microscope (SEM), Fourier's transform infrared spectroscopy (FTIR), X-ray powder diffraction (XRD), and a vibrating-sample magnetometer (VSM). At a pH of 5, a photocatalyst dosage of 100 mg, an initial R195 concentration of 100 mg/l, an ultrasound power of 38W, and an exposure time of 20 min, the maximum Red195 removal efficiency (100%) was achieved. After five cycles of recycling, the composite's sonophotocatalytic degradation stability for R195 remains above 95%. Experiments on scavenging indicate that electrons (h+) and hydroxyls (OH-) are indispensable decomposition agents. The removal of R195 by Scendesmus/Fe3O4/TiO2 is consistent with the pseudo-first-order kinetic, Freundlich, and Henderson's isotherm models, as determined by kinetic and isotherm investigations. The negative activation enthalpy of the standard (ΔH°) illuminates the exothermic adsorption mechanism. The increase in standard Gibbs activation free energy (ΔG°) with increasing temperature reveals the process is not spontaneous. As indicated by the negative value of the standard entropy of activation (ΔS°), activation of the reactants resulted in a loss of freedom.

An evaluation of sequencing coverage and genotyping strategies to assess neutral and adaptive diversity.

Whole genome sequences (WGS) greatly increase our ability to precisely infer population genetic parameters, demographic processes, and selection signatures. However, WGS may still be not affordable for a representative number of individuals/populations. In this context, our goal was to assess the efficiency of several SNP genotyping strategies by testing their ability to accurately estimate parameters describing neutral diversity and to detect signatures of selection. We analysed 110 WGS at 12× coverage for four different species, i.e., sheep, goats and their wild counterparts. From these data we generated 946 data sets corresponding to random panels of 1K to 5M variants, commercial SNP chips and exome capture, for sample sizes of five to 48 individuals. We also extracted low-coverage genome resequencing of 1×, 2× and 5× by randomly subsampling reads from the 12× resequencing data. Globally, 5K to 10K random variants were enough for an accurate estimation of genome diversity. Conversely, commercial panels and exome capture displayed strong ascertainment biases. Besides the characterization of neutral diversity, the detection of the signature of selection and the accurate estimation of linkage disequilibrium (LD) required high-density panels of at least 1M variants. Finally, genotype likelihoods increased the quality of variant calling from low coverage resequencing but proportions of incorrect genotypes remained substantial, especially for heterozygote sites. Whole genome resequencing coverage of at least 5× appeared to be necessary for accurate assessment of genomic variations. These results have implications for studies seeking to deploy low-density SNP collections or genome scans across genetically diverse populations/species showing similar genetic characteristics and patterns of LD decay for a wide variety of purposes.

Convergent genomic signatures of domestication in sheep and goats.

The evolutionary basis of domestication has been a longstanding question and its genetic architecture is becoming more tractable as more domestic species become genome-enabled. Before becoming established worldwide, sheep and goats were domesticated in the fertile crescent 10,500 years before present (YBP) where their wild relatives remain. Here we sequence the genomes of wild Asiatic mouflon and Bezoar ibex in the sheep and goat domestication center and compare their genomes with that of domestics from local, traditional, and improved breeds. Among the genomic regions carrying selective sweeps differentiating domestic breeds from wild populations, which are associated among others to genes involved in nervous system, immunity and productivity traits, 20 are common to Capra and Ovis. The patterns of selection vary between species, suggesting that while common targets of selection related to domestication and improvement exist, different solutions have arisen to achieve similar phenotypic end-points within these closely related livestock species.

Sheep genome functional annotation reveals proximal regulatory elements contributed to the evolution of modern breeds.

Domestication fundamentally reshaped animal morphology, physiology and behaviour, offering the opportunity to investigate the molecular processes driving evolutionary change. Here we assess sheep domestication and artificial selection by comparing genome sequence from 43 modern breeds (Ovis aries) and their Asian mouflon ancestor (O. orientalis) to identify selection sweeps. Next, we provide a comparative functional annotation of the sheep genome, validated using experimental ChIP-Seq of sheep tissue. Using these annotations, we evaluate the impact of selection and domestication on regulatory sequences and find that sweeps are significantly enriched for protein coding genes, proximal regulatory elements of genes and genome features associated with active transcription. Finally, we find individual sites displaying strong allele frequency divergence are enriched for the same regulatory features. Our data demonstrate that remodelling of gene expression is likely to have been one of the evolutionary forces that drove phenotypic diversification of this common livestock species.

Whole mitochondrial genomes unveil the impact of domestication on goat matrilineal variability.

BACKGROUND: The current extensive use of the domestic goat (Capra hircus) is the result of its medium size and high adaptability as multiple breeds. The extent to which its genetic variability was influenced by early domestication practices is largely unknown. A common standard by which to analyze maternally-inherited variability of livestock species is through complete sequencing of the entire mitogenome (mitochondrial DNA, mtDNA). RESULTS: We present the first extensive survey of goat mitogenomic variability based on 84 complete sequences selected from an initial collection of 758 samples that represent 60 different breeds of C. hircus, as well as its wild sister species, bezoar (Capra aegagrus) from Iran. Our phylogenetic analyses dated the most recent common ancestor of C. hircus to ~460,000 years (ka) ago and identified five distinctive domestic haplogroups (A, B1, C1a, D1 and G). More than 90 % of goats examined were in haplogroup A. These domestic lineages are predominantly nested within C. aegagrus branches, diverged concomitantly at the interface between the Epipaleolithic and early Neolithic periods, and underwent a dramatic expansion starting from ~12-10 ka ago. CONCLUSIONS: Domestic goat mitogenomes descended from a small number of founding haplotypes that underwent domestication after surviving the last glacial maximum in the Near Eastern refuges. All modern haplotypes A probably descended from a single (or at most a few closely related) female C. aegagrus. Zooarchaelogical data indicate that domestication first occurred in Southeastern Anatolia. Goats accompanying the first Neolithic migration waves into the Mediterranean were already characterized by two ancestral A and C variants. The ancient separation of the C branch (~130 ka ago) suggests a genetically distinct population that could have been involved in a second event of domestication. The novel diagnostic mutational motifs defined here, which distinguish wild and domestic haplogroups, could be used to understand phylogenetic relationships among modern breeds and ancient remains and to evaluate whether selection differentially affected mitochondrial genome variants during the development of economically important breeds.

In silico identification, phylogenetic and bioinformatic analysis of argonaute genes in plants.

Argonaute protein family is the key players in pathways of gene silencing and small regulatory RNAs in different organisms. Argonaute proteins can bind small noncoding RNAs and control protein synthesis, affect messenger RNA stability, and even participate in the production of new forms of small RNAs. The aim of this study was to characterize and perform bioinformatic analysis of Argonaute proteins in 32 plant species that their genome was sequenced. A total of 437 Argonaute genes were identified and were analyzed based on lengths, gene structure, and protein structure. Results showed that Argonaute proteins were highly conserved across plant kingdom. Phylogenic analysis divided plant Argonautes into three classes. Argonaute proteins have three conserved domains PAZ, MID and PIWI. In addition to three conserved domains namely, PAZ, MID, and PIWI, we identified few more domains in AGO of some plant species. Expression profile analysis of Argonaute proteins showed that expression of these genes varies in most of tissues, which means that these proteins are involved in regulation of most pathways of the plant system. Numbers of alternative transcripts of Argonaute genes were highly variable among the plants. A thorough analysis of large number of putative Argonaute genes revealed several interesting aspects associated with this protein and brought novel information with promising usefulness for both basic and biotechnological applications.