A Bayesian tree of FABPs.

<p>Bayesian probabilities more than 0.8 were shown at nodes. Tadh: <i>Trichoplax adhaerens</i>; Ctel: <i>Capitella </i><i>teleta</i>; Hrob: <i>Helobdella robusta</i>; Lgig: <i>Lottia gigantean</i>; Smed: <i>Schmidtea mediterranea</i>; Sman: <i>Schistosoma mansoni</i>; Sjap: <i>Schistosoma japonicum</i>; Egra: <i>Echinococcus granulosus</i>; Emul: <i>Echinococcus multilocularis</i>; Cele: <i>Caenorhabditis elegans</i>; Ppac: <i>Pristionchus pacificus</i>; Hbac: <i>Heterorhabditis bacteriophora</i>; Tspi: <i>Trichinella spiralis</i>; Srat: <i>Strongyloides ratti</i>; Bmal: <i>Brugia malayi</i>; Dpul: <i>Daphnia pulex</i>; Phum: <i>Pediculus humanus corporis</i>; Bmor: <i>Bombyx mori</i>; Tcas: <i>Tribolium castaneum</i>; Nvit: <i>Nasonia vitripennis</i>; Apis: <i>Acyrthosiphon pisum</i>; Amel: <i>Apis mellifera</i>; Dmel: <i>Drosophila melanogaster</i>; Agam: <i>Anopheles gambiae</i>; Aaeg: <i>Aedes aegypti</i>; Cpip: <i>Culex pipiens quinquefasciatus</i>; Rpro: <i>Rhodnius prolixus</i>; Spur: <i>Strongylocentrotus purpuratus</i>; Bflo: <i>Branchiostoma floridae</i>; Csav: <i>Ciona savignyi</i>; Skow: <i>Saccoglossus kowalevskii</i>; Has: <i>Homo sapiens</i> Note: to make it simpler, ‘FABP’ was omitted in every branch name. For example: Tadh1 refers to Tadh_FABP1, Tadh2 to Tadh_FABP2 and so forth.</p

Alternative splicing in invertebrate <i>FABP</i> genes.

<p>Typical alternative splicing patterns in <i>C. elegans</i>, <i>T. castaneum</i> and <i>D. melanogaster</i> are represented. In <i>C. elegans</i>, LBP-9 pre-mRNA is spliced to generate two variants 9a and 9b by addition of a short spliced leader sequence (SL1: 5’-GGTTTAATTACCCAAGTTTGAG-3’) at the 5’ end. Blank or filled boxes and straight lines represent exons and introns, respectively, and a poly (A) stretch present in each <i>FABP</i> cDNA clone or EST sequence is directly shown. In each group, an annotated <i>FABP</i> gene is placed above the variants that are indicated by a, b, c or/and d. Numbers above the boxes and under the lines show the sizes of corresponding exons and introns, respectively. The sizes of exons, where these differ, are indicated above the corresponding exons in the spliced transcripts. The length of variants is also shown after each transcript and the number of ESTs is shown in the brackets. </p

Gelling properties of myosin as affected by L-lysine and L-arginine by changing the main molecular forces and microstructure

<p>This paper investigated the effects of l-lysine (Lys) and l-arginine (Arg) on the water-holding capacity (WHC) and hardness of myosin gel as well as the mechanism of these effects. The results showed that Lys, Arg, and KOH increased the WHC but decreased the hardness in all cases. At pH 6.32, the WHC increased in the order control < KOH < Lys ≈ Arg, while the hardness decreased in the order control > KOH > Lys > Arg. Lys shortened low field nuclear magnetic resonance spin-spin relaxation times (T₂), while Arg and KOH slightly affected T₂. Lys, Arg, and KOH had different influences on the molecular forces in myosin gels and the distribution of myosin size. Lys formed a gel with porous clusters, while Arg generated a gel with fine caves. Therefore, both Lys and Arg changed the microstructure of myosin gel by changing the distribution of the myosin size as well as the molecular forces that form and/or maintain myosin gel, ultimately contributing to the differences in the WHC, hardness, and T₂.</p

The residues of “ball and socket” junction.

<p>The ‘Ball’ residue within RNaseIII a domain is marked by a black asterisk, and the ‘socket’ residues within RNase III b domain are marked by red asterisks. Gaps are filled using question marks (?).</p

Distribution of endoribonuclease Dicer genes in invertebrates.

a<p>Amino acid length;</p>b<p>JGI: Joint Genome Institute; NCBI: National Center for Biotechnology Information; SmedGD: <i>Schmidatea mediterranea</i> Genome Database; Sanger: Wellcome Trust Sanger Insitute; FlyBase: Drosophila database; SilkDB: silkworm database; Ensemble: Ensemble Genome Browser.</p

The key residues critical for recognition of 3′ and 5′ pockets.

<p>The key residues involved in 3′ pocket (a) and 5′ pocket recognition (b) were indicated using asterisks in red. The Dicers in which a PAZ domain was not identified using Pfam and SMART are highlighted in grey (a). Gaps are filled using question marks (?).</p

The key residues of RNase III domains.

<p>Catalytic residues are marked by red asterisks and gaps filled using question marks (?).</p

A maximum likelihood tree of invertebrate Dicers.

<p>The tree was constructed using maximum likelihood method. Two number sets, 1.00/1.00/0.99 and 0.87/0.96/0.28, at the nodes were SH-like approximate likelihood ratio, Bayes likelihood and bootstrap values, respectively.</p

Calculation of Evolutionary Correlation between Individual Genes and Full-Length Genome: A Method Useful for Choosing Phylogenetic Markers for Molecular Epidemiology

<div><p>Individual genes or regions are still commonly used to estimate the phylogenetic relationships among viral isolates. The genomic regions that can faithfully provide assessments consistent with those predicted with full-length genome sequences would be preferable to serve as good candidates of the phylogenetic markers for molecular epidemiological studies of many viruses. Here we employed a statistical method to evaluate the evolutionary relationships between individual viral genes and full-length genomes without tree construction as a way to determine which gene can match the genome well in phylogenetic analyses. This method was performed by calculation of linear correlations between the genetic distance matrices of aligned individual gene sequences and aligned genome sequences. We applied this method to the phylogenetic analyses of porcine circovirus 2 (PCV2), measles virus (MV), hepatitis E virus (HEV) and Japanese encephalitis virus (JEV). Phylogenetic trees were constructed for comparisons and the possible factors affecting the method accuracy were also discussed in the calculations. The results revealed that this method could produce results consistent with those of previous studies about the proper consensus sequences that could be successfully used as phylogenetic markers. And our results also suggested that these evolutionary correlations could provide useful information for identifying genes that could be used effectively to infer the genetic relationships.</p></div

The r-values between different individual genes (or genomic regions) and genomes of the four viruses based on different sample sizes.

<p>The A, B, C and D represent r-values of PCV2, MV, HEV and JEV respectively in order. Each set of r-values between one individual genomic region and its genome for different number of viral strains was shown as boxes-and-whiskers plot. The whiskers go from the highest to lowest point.</p