Agricultural Plastic Pollution in China: Generation of Plastic Debris and Emission of Phthalic Acid Esters from Agricultural Films.

Agricultural plastic films have been proven highly advantageous, but they also cause pollution of plastic debris and associated chemicals. Phthalates (phthalic acid esters, PAEs), an important additive of agricultural films, can be released and contaminate the environment. Here, we analyzed the agricultural plastic usage and assessed plastic debris in China and developed a method to estimate PAE emissions from agricultural films. Additionally, the environmental fate of PAEs was evaluated using a fugacity-based multimedia model. The agricultural plastic film usage in China in 2017 was 2,528,600 tons. After agricultural film recycling and water erosion, the plastic debris amount was estimated as 465,016 tons. The water erosion process carried 4329 tons of plastic debris into the aquatic environment. During its lifetime, the agricultural film released a total of 91.5 tons of two typical types of PAEs. PAEs from the mulching film would mostly be removed through degradation, while those from the greenhouse film accumulate in vegetables. Populated regions exhibited more serious PAE pollution in vegetables but with no immediate health risks. The model was well evaluated using comparable measured concentrations and uncertainty analysis based on the Monte Carlo method. The findings from this study demonstrate the serious agricultural plastic pollution problem and associated PAE contamination in China.

Long-range genomic enrichment, sequencing, and assembly to determine unknown sequences flanking a known microRNA.

Conserved plant microRNAs (miRNAs) modulate important biological processes but little is known about conserved cis-regulatory elements (CREs) surrounding MIRNA genes. We developed a solution-based targeted genomic enrichment methodology to capture, enrich, and sequence flanking genomic regions surrounding conserved MIRNA genes with a locked-nucleic acid (LNA)-modified, biotinylated probe complementary to the mature miRNA sequence. Genomic DNA bound by the probe is captured by streptavidin-coated magnetic beads, amplified, sequenced and assembled de novo to obtain genomic DNA sequences flanking MIRNA locus of interest. We demonstrate the sensitivity and specificity of this enrichment methodology in Arabidopsis thaliana to enrich targeted regions spanning 10-20 kb surrounding known MIR166 and MIR165 loci. Assembly of the sequencing reads successfully recovered all targeted loci. While further optimization for larger, more complex genomes is needed, this method may enable determination of flanking genomic DNA sequence surrounding a known core (like a conserved mature miRNA) from multiple species that currently don't have a full genome assembly available.

DICER-LIKE3 activity in Physcomitrella patens DICER-LIKE4 mutants causes severe developmental dysfunction and sterility.

Trans-acting small interfering RNAs (ta-siRNAs) are plant-specific siRNAs released from TAS precursor transcripts after microRNA-dependent cleavage, conversion into double-stranded RNA, and Dicer-dependent phased processing. Like microRNAs (miRNAs), ta-siRNAs direct site-specific cleavage of target RNAs at sites of extensive complementarity. Here, we show that the DICER-LIKE 4 protein of Physcomitrella patens (PpDCL4) is essential for the biogenesis of 21 nucleotide (nt) ta-siRNAs. In ΔPpDCL4 mutants, off-sized 23 and 24-nt ta-siRNAs accumulated as the result of PpDCL3 activity. ΔPpDCL4 mutants display severe abnormalities throughout Physcomitrella development, including sterility, that were fully reversed in ΔPpDCL3/ΔPpDCL4 double-mutant plants. Therefore, PpDCL3 activity, not loss of PpDCL4 function per se, is the cause of the ΔPpDCL4 phenotypes. Additionally, we describe several new Physcomitrella trans-acting siRNA loci, three of which belong to a new family, TAS6. TAS6 loci are typified by sliced miR156 and miR529 target sites and are in close proximity to PpTAS3 loci.

K, Ca complexes with a sulfonic ligand: structure and DNA-binding properties.

A novel 4-(2,4-dihydroxybenzylideneamino)benzenesulfonic acid (HL), and its kalium(I), calcium(II) complexes [M(L)n]·2nH(2)O·Cl(n) (M=K(1) n=1, M=Ca(2) n=2), have been prepared and characterized. The crystal and molecular structures of 1 and 2 were determined by single-crystal X-ray diffraction. The interaction of 1, 2 and ligand (L) with calf thymus DNA was investigated by UV-visible (UV-vis), fluorescence and viscosity measurements. Experimental results indicate that 1, 2 and L could bind to DNA via the intercalation mode, and the binding affinity of 1 is stronger than that of 2 and L. The intrinsic binding constants of 1, 2 and L were 5.60×10(5), 6.53×10(5) and 1.44×10(5)M(-1), respectively. The cleavage reaction on plasmid DNA has been monitored by agarose gel electrophoresis. The results indicated that 1 and 2 could cleave pBR322 DNA.

Spectroscopic studies on the interaction between Pr(III) complex of an ofloxacin derivative and bovine serum albumin or DNA.

The binding properties on [PrL2(NO3)](NO3)2 (L=9-fluoro-2,3-dihydro-3-methyl-10-(4-methyl-1-piperaziny)-7-oxo-7Hpyrido[1,2,3-de]-1,4-benzoxazine-6-carbaldehyde benzoyl hydrazone) to bovine serum albumin (BSA) have been studied for the first time using fluorescence spectroscopy in combination with UV-Vis absorbance spectroscopy. The results showed that [PrL2(NO3)](NO3)2 strongly quenched the intrinsic fluorescence of BSA through a static quenching procedure, and non-radiation energy transfer happened within molecules. The number of binding site was about 1, and the efficiency of Förster energy transfer provided a distance of 4.26 nm between tryptophan and [PrL2(NO3)](NO3)2 binding site. At 288, 298, 310 K, the quenching constants of BSA-[PrL2(NO3)](NO3)2 system were 5.11×10(4), 4.33×10(4) and 3.71×10(4) l M(-1). ΔH, ΔS and ΔG were obtained based on the quenching constants and thermodynamic theory (ΔH<0, ΔS>0 and ΔG<0). These results indicated that hydrophobic and electrostatic interactions are the mainly binding forces in the [PrL2(NO3)](NO3)2-BSA system. In addition, the CD spectra have proved that BSA secondary structure changed in the presence of [PrL2(NO3)](NO3)2 in aqueous solution. Moreover, the interaction between [PrL2(NO3)](NO3)2 and calf thymus DNA (CT DNA) was studied by spectroscopy and viscosity measurements, which showed that the binding mode of the [PrL2(NO3)](NO3)2 with DNA is intercalation. The DNA cleavage results show that in the absence of any reducing agent, the [PrL2(NO3)](NO3)2 can cleave plasmid pBR322 DNA and its hydrolytic mechanism was demonstrated with hydroxyl radical scavengers and singlet oxygen quenchers.

The genome of Theobroma cacao.

We sequenced and assembled the draft genome of Theobroma cacao, an economically important tropical-fruit tree crop that is the source of chocolate. This assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of these genes anchored on the 10 T. cacao chromosomes. Analysis of this sequence information highlighted specific expansion of some gene families during evolution, for example, flavonoid-related genes. It also provides a major source of candidate genes for T. cacao improvement. Based on the inferred paleohistory of the T. cacao genome, we propose an evolutionary scenario whereby the ten T. cacao chromosomes were shaped from an ancestor through eleven chromosome fusions.

Arabidopsis lyrata small RNAs: transient MIRNA and small interfering RNA loci within the Arabidopsis genus.

Twenty-one-nucleotide microRNAs (miRNAs) and 24-nucleotide Pol IV-dependent small interfering RNAs (p4-siRNAs) are the most abundant types of small RNAs in angiosperms. Some miRNAs are well conserved among different plant lineages, whereas others are less conserved, and it is not clear whether less-conserved miRNAs have the same functionality as the well conserved ones. p4-siRNAs are broadly produced in the Arabidopsis genome, sometimes from active hot spot loci, but it is unknown whether individual p4-siRNA hot spots are retained as hot spots between plant species. In this study, we compare small RNAs in two closely related species (Arabidopsis thaliana and Arabidopsis lyrata) and find that less-conserved miRNAs have high rates of divergence in MIRNA hairpin structures, mature miRNA sequences, and target-complementary sites in the other species. The fidelity of miRNA biogenesis from many less-conserved MIRNA hairpins frequently deteriorates in the sister species relative to the species of first discovery. We also observe that p4-siRNA occupied loci have a slight tendency to be retained as p4-siRNA loci between species, but the most active A. lyrata p4-siRNA hot spots are generally not syntenic to the most active p4-siRNA hot spots of A. thaliana. Altogether, our findings indicate that many MIRNAs and most p4-siRNA hot spots are rapidly changing and evolutionarily transient within the Arabidopsis genus.

A strategy for meta-analysis of short time series microarray datasets.

Many time series microarray experiments have relatively short (less than ten) time points and lack in repeats, weakening the confidence of results. Combining the microarray data from different groups may improve the statistical power of detecting differentially expressed genes. However, few efforts have been taken to combine or compare the time-course array datasets generated by independent groups. Here we demonstrated a suitable strategy for meta-analysis of short time series microarray datasets and implemented this strategy on four published heat shock microarray datasets of Saccharomyces Cerevisiae. We first assessed the significance of each gene in each datasets based on area calculation and the null distribution of the areas. Then the similarity of significance values across datasets was assessed with meta-analysis methods, yielding a set of transient heat shock stress sensitive genes. Following correlation calculation helped us to combine the transformed data at the same time points of each gene. Further bioinformatic investigation showed the significance of our strategy, and also indicated some interesting features of regulatory systems in S. cerevisiae during transient heat stress.

Physcomitrella patens DCL3 is required for 22-24 nt siRNA accumulation, suppression of retrotransposon-derived transcripts, and normal development.

Endogenous 24 nt short interfering RNAs (siRNAs), derived mostly from intergenic and repetitive genomic regions, constitute a major class of endogenous small RNAs in flowering plants. Accumulation of Arabidopsis thaliana 24 nt siRNAs requires the Dicer family member DCL3, and clear homologs of DCL3 exist in both flowering and non-flowering plants. However, the absence of a conspicuous 24 nt peak in the total RNA populations of several non-flowering plants has raised the question of whether this class of siRNAs might, in contrast to the ancient 21 nt microRNAs (miRNAs) and 21-22 nt trans-acting siRNAs (tasiRNAs), be an angiosperm-specific innovation. Analysis of non-miRNA, non-tasiRNA hotspots of small RNA production within the genome of the moss Physcomitrella patens revealed multiple loci that consistently produced a mixture of 21-24 nt siRNAs with a peak at 23 nt. These Pp23SR loci were significantly enriched in transposon content, depleted in overlap with annotated genes, and typified by dense concentrations of the 5-methyl cytosine (5 mC) DNA modification. Deep sequencing of small RNAs from two independent Ppdcl3 mutants showed that the P. patens DCL3 homolog is required for the accumulation of 22-24 nt siRNAs, but not 21 nt siRNAs, at Pp23SR loci. The 21 nt component of Pp23SR-derived siRNAs was also unaffected by a mutation in the RNA-dependent RNA polymerase mutant Pprdr6. Transcriptome-wide, Ppdcl3 mutants failed to accumulate 22-24 nt small RNAs from repetitive regions while transcripts from two abundant families of long terminal repeat (LTR) retrotransposon-associated reverse transcriptases were up-regulated. Ppdcl3 mutants also displayed an acceleration of leafy gametophore production, suggesting that repetitive siRNAs may play a role in the development of P. patens. We conclude that intergenic/repeat-derived siRNAs are indeed a broadly conserved, distinct class of small regulatory RNAs within land plants.