The Complete Mitochondrial Genome of <i>Meloidogyne graminicola</i> (Tylenchina): A Unique Gene Arrangement and Its Phylogenetic Implications

<div><p><i>Meloidogyne graminicola</i> is one of the most economically important plant parasitic-nematodes (PPNs). In the present study, we determined the complete mitochondrial (mt) DNA genome sequence of this plant pathogen. Compared with other PPNs genera, this genome (19,589 bp) is only slightly smaller than that of <i>Pratylenchus vulnus</i> (21,656 bp). The nucleotide composition of the whole mtDNA sequence of <i>M. graminicola</i> is significantly biased toward A and T, with T being the most favored nucleotide and C being the least favored. The A+T content of the entire genome is 83.51%. The mt genome of <i>M. graminicola</i> contains 36 genes (lacking <i>atp8</i>) that are transcribed in the same direction. The gene arrangement of the mt genome of <i>M. graminicola</i> is unique. A total of 21 out of 22 tRNAs possess a DHU loop only, while <i>tRNA^Ser(AGN)</i> lacks a DHU loop. The two large noncoding regions (2,031 bp and 5,063 bp) are disrupted by <i>tRNA^Ser(UCN)</i>. Phylogenetic analysis based on concatenated amino acid sequences of 12 protein-coding genes support the monophylies of the three orders Rhabditida, Mermithida and Trichinellida, the suborder Rhabditina and the three infraorders Spiruromorpha, Oxyuridomorpha and Ascaridomorpha, but do not support the monophylies of the two suborders Spirurina and Tylenchina, and the three infraorders Rhabditomorpha, Panagrolaimomorpha and Tylenchomorpha. The four Tylenchomorpha species including <i>M. graminicola</i>, <i>P. vulnus</i>, <i>H. glycines</i> and <i>R. similis</i> from the superfamily Tylenchoidea are placed within a well-supported monophyletic clade, but far from the other two Tylenchomorpha species <i>B. xylophilus</i> and <i>B. mucronatus</i> of Aphelenchoidea. In the clade of Tylenchoidea, <i>M. graminicola</i> is sister to <i>P</i>. <i>vulnus</i>, and <i>H. glycines</i> is sister to <i>R. similis</i>, which suggests root-knot nematodes has a closer relationship to Pratylenchidae nematodes than to cyst nematodes.</p></div

Arrangement of the mitochondrial genome of <i>Meloidogyne graminicola</i>.

<p>Gene scaling is only approximate. All genes are coding by the same DNA strand, and the arrow indicates the direction of transcription. All protein-coding genes have standard nomenclature. All tRNA genes follow the one-letter amino acid code; L1/L2 and S1/S2 indicate tRNA genes for <i>tRNA^Leu(CUN)</i>/<i>tRNA^Leu(UUR)</i> and <i>tRNA^Ser(AGN)</i>/<i>tRNA^Ser(UCN)</i>, respectively. “NCR1” refers to a small noncoding region and “NCR2” refers to a large noncoding region.</p

Comparison of mitochondrial gene arrangements between <i>Meloidogyne graminicola</i> and <i>Pratylenchus vulnus</i>.

<p>Gene and genome size are not to scale. The noncoding region (NCR) is not indicated. Arrows below the gene order map indicate the direction of transcription of genes. Genes involved in the rearrangements are shown in dashed boxes.</p

Phylogenetic tree from maximum likelihood analysis of amino sequences for 12 protein-coding genes for 50 nematode mitochondrial genomes.

<p><i>Lithobius forficatus</i> and <i>Limulus polyphemus</i> were used as the outgroups. Bootstrap percentage (BP) values are indicated at the nodes. Classification according to De Ley and Blaxter <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098558#pone.0098558-DeLey1" target="_blank">[6]</a>.</p

Codon usage pattern and relative synonymous codon usage (RSCU) of mtDNA of <i>Meloidogyne graminicola</i>.

<p>Numbers on the Y-axis refer to the total number of codons (A) and the RSCU value (B). Codon families are provided on the X-axis. Codons that are not present in the mitochondrial genome are indicated in red at the tops of the columns.</p

Phylogenetic tree from Bayesian analysis of amino sequences for 12 protein-coding genes for 50 nematode mitochondrial genomes.

<p><i>Lithobius forficatus</i> and <i>Limulus polyphemus</i> were used as the outgroups. Numbers along the branches indicate Bayesian posterior probability (BPP) values. Classification according to De Ley and Blaxter <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098558#pone.0098558-DeLey1" target="_blank">[6]</a>.</p

Organization of the <i>Meloidogyne graminicola</i> mitochondrial genome.

<p>a: Indicates gap nucleotides (positive value) or overlapping nucleotides (negative value) between two adjacent genes;</p><p>NCR: Noncoding region.</p

Upconversion Nanophosphor: An Efficient Phosphopeptides-Recognizing Matrix and Luminescence Resonance Energy Transfer Donor for Robust Detection of Protein Kinase Activity

Protein kinases play important regulatory roles in intracellular signal transduction pathways. The aberrant activities of protein kinases are closely associated with the development of various diseases, which necessitates the development of practical and sensitive assays for monitoring protein kinase activities as well as for screening of potential kinase-targeted drugs. We demonstrate here a robust luminescence resonance energy transfer (LRET)-based protein kinase assay by using NaYF₄:Yb,Er, one of the most efficient upconversion nanophosphors (UCNPs), as an autofluorescence-free LRET donor and a tetramethylrhodamine (TAMRA)-labeled substrate peptide as the acceptor. Fascinatingly, besides acting as the LRET donor, NaYF₄:Yb,Er UCNPs also serve as the phosphopeptide-recognizing matrix because the intrinsic rare earth ions of UCNPs can specifically capture the fluorescent phosphopeptides catalyzed by protein kinases over the unphosphorylated ones. Therefore, a sensitive and generic protein kinase assay is developed in an extremely simple mix-and-read format without any requirement of surface modification, substrate immobilization, separation, or washing steps, showing great potential in protein kinases-related clinical diagnosis and drug discovery. To the best of our knowledge, this is the first report by use of rare earth-doped UCNPs as both the phospho-recognizing and signal reporting elements for protein kinase analysis

Can Silica Particles Reduce Air Pollution by Facilitating the Reactions of Aliphatic Aldehyde and NO₂?

This study investigated the heterogeneous atmospheric reactions of acetaldehyde, propanal, and butanal with NO₂ onto silica (SiO₂) clusters using a theoretical approach. By analyzing spectral features and adsorption parameters, the formation of hydrogen bonds and negative adsorption energies provide evidence that an efficient spontaneous uptake of aliphatic aldehydes onto SiO₂ could occur. The atmospheric reaction mechanisms show that when aldehydes and NO₂ react on the surface model, the H atom abstraction reaction from the aldehydic molecule by NO₂ is an exclusive channel, forming nitrous acid and acyl radicals. This study included kinetics exploring the reaction of aldehydes with NO₂ using a canonical variational transition state theory. The reaction rate constants are increased in the presence of SiO₂ between the temperatures 217 and 298 K. This may explain how aldehydes can temporarily stay on mineral particles without chemical reactions. The results suggest that silica can depress the rate at which the studied aldehydes react with NO₂ and possibly reduce air pollution generated by these atmospheric reactions

Ratiometric Fluorescence Nanoprobes for Subcellular pH Imaging with a Single-Wavelength Excitation in Living Cells

Abnormal pH values in the organelles are closely associated with inappropriate cellular functions and many diseases. Monitoring subcellular pH values and their variations is significant in biological processes occurring in living cells and tissues. Herein, we develop a series of ratiometric fluorescence nanoprobes for quantification and imaging of pH values with a single-wavelength excitation in cytoplasm, lysosomes, and mitochondria. The nanoprobes consist of mesoporous silica nanoparticles assembled with aminofluorescein as the recognition unit for pH measurement and ethidium bromide as reference fluorophore. Further conjugation of subcellular targeting moiety enables the nanoprobes to specifically target lysosome and mitochondria. Confocal fluorescence imaging demonstrated that the nanoprobes could effectively monitor the pH fluctuations from 5.0 to 8.3 in living cells by ratio imaging with 488 nm excitation. Subcellular pH determination and imaging in lysosome and mitochondria could also be achieved in different conditions. The current method can offer a general strategy to determine subcellular analytes and investigate the interactions in biological samples