Population survey of spiders using mt-DNA (COI) sequences in Japanese peach orchards

In this study, we attempted a population survey of spiders in peach orchards with and without pesticide application; however, we had difficulty discriminating them. To identify spiders, we determined the nucleotide sequences of a ca. 640-bp region in the mitochondrial cytochrome oxidase subunit I (COI) gene from 17 species belonging to eight families. To identify five wolf spiders (Araneae: Lycosidae), which are the most abundant spiders in peach orchards in Okayama Prefecture, PCR and restriction fragment length polymorphism were developed on the basis of the COI gene sequences. Population survey results suggest that pesticide applications adversely affect spider populations in peach orchards.     

Hrr25 triggers selective autophagy–related pathways by phosphorylating receptor proteins

In selective autophagy, degradation targets are specifically recognized, sequestered by the autophagosome, and transported into the lysosome or vacuole. Previous studies delineated the molecular basis by which the autophagy machinery recognizes those targets, but the regulation of this process is still poorly understood. In this paper, we find that the highly conserved multifunctional kinase Hrr25 regulates two distinct selective autophagy–related pathways in Saccharomyces cerevisiae. Hrr25 is responsible for the phosphorylation of two receptor proteins: Atg19, which recognizes the assembly of vacuolar enzymes in the cytoplasm-to-vacuole targeting pathway, and Atg36, which recognizes superfluous peroxisomes in pexophagy. Hrr25-mediated phosphorylation enhances the interactions of these receptors with the common adaptor Atg11, which recruits the core autophagy-related proteins that mediate the formation of the autophagosomal membrane. Thus, this study introduces regulation of selective autophagy as a new role of Hrr25 and, together with other recent studies, reveals that different selective autophagy–related pathways are regulated by a uniform mechanism: phosphoregulation of the receptor–adaptor interaction.     

Editor's choice: Dissection of the Octoploid Strawberry Genome by Deep Sequencing of the Genomes of Fragaria Species

Cultivated strawberry (Fragaria x ananassa) is octoploid and shows allogamous behaviour. The present study aims at dissecting this octoploid genome through comparison with its wild relatives, F. iinumae, F. nipponica, F. nubicola, and F. orientalis by de novo whole-genome sequencing on an Illumina and Roche 454 platforms. The total length of the assembled Illumina genome sequences obtained was 698 Mb for F. x ananassa, and ∼200 Mb each for the four wild species. Subsequently, a virtual reference genome termed FANhybrid_r1.2 was constructed by integrating the sequences of the four homoeologous subgenomes of F. x ananassa, from which heterozygous regions in the Roche 454 and Illumina genome sequences were eliminated. The total length of FANhybrid_r1.2 thus created was 173.2 Mb with the N50 length of 5137 bp. The Illumina-assembled genome sequences of F. x ananassa and the four wild species were then mapped onto the reference genome, along with the previously published F. vesca genome sequence to establish the subgenomic structure of F. x ananassa. The strategy adopted in this study has turned out to be successful in dissecting the genome of octoploid F. x ananassa and appears promising when applied to the analysis of other polyploid plant species.     

Tupaia Belangeri as an Experimental Animal Model for Viral Infection

Tupaias, or tree shrews, are small mammals that are similar in appearance to squirrels. The morphological and behavioral characteristics of the group have been extensively characterized, and despite previously being classified as primates, recent studies have placed the group in its own family, the Tupaiidae. Genomic analysis has revealed that the genus Tupaia is closer to humans than it is to rodents. In addition, tupaias are susceptible to hepatitis B virus and hepatitis C virus. The only other experimental animal that has been demonstrated to be sensitive to both of these viruses is the chimpanzee, but restrictions on animal testing have meant that experiments using chimpanzees have become almost impossible. Consequently, the development of the tupaia for use as an animal infection model could become a powerful tool for hepatitis virus research and in preclinical studies on drug development.     

DNA probes on beads arrayed in a capillary, ‘Bead-array’, exhibited high hybridization performance

A DNA analysis platform called ‘Bead-array’ is presented and its features when used in hybridization detection are shown. In ‘Bead-array’, beads of 100-µm diameter are lined in a determined order in a capillary. Each bead is conjugated with DNA probes, and can be identified by its order in the capillary. This probe array is easily produced by just arraying beads conjugated with probes into the capillary in a fixed order. The hybridization is also easily completed by introducing samples (1–300 µl) into the capillary with reciprocal flow. For hybridization detection, as little as 1 amol of fluorescent-labeled oligo DNA was detected. The hybridization reaction was completed in 1 min irrespective of the amount of target DNA. When the number of target molecules was smaller than that of probe molecules on the bead, 10 fmol, almost all targets were captured on the bead. ‘Bead-array’ enables reliable and reproducible measurement of the target quantity. This rapid and sensitive platform seems very promising for various genetic testing tasks.     

Short-term effects of mowing on insect communities in Japanese peach orchards

A population survey of insects was conducted at peach orchards in Okayama Prefecture, western Japan, every 2 weeks during May–October in 2011. Pitfall traps were used to sample more than 4000 insects at 10 orchards: 8 orchards where ground vegetation had been managed by mowing and 2 with management by herbicide application. Numbers of insect species (species richness) and numbers of insects captured in pitfall traps (trap catches) were greater after mowing. Details of the effects of mowing on insect communities were examined at four orchards that had been mowed. Results suggest that species richness and trap catches increase up to 5 days after mowing and then return to their original state. Increased species richness and trap catches were mainly attributable to the increase of ants (Formicidae) and carabids (Carabidae). These results suggest that ants and carabids actively seek prey animals that have been killed, injured, or damaged by mowing.     

Assimilation of Formaldehyde and other C1Compounds by Gliocladium deliquescens and Paecilomyces varioti

Two fungi were isolated from soil which grew on 0.1~0.2% formaldehyde as the sole carbon source, and identified as Gliocladium deliquescens and Paecilomyces varioti. Both the strains could grow on 5% methanol and 5% Na-formate, while the former could grow even on 7% methanol. Metabolic pathways were traced through two dimensional paper chromatography and autoradiographic techniques using ¹⁴C-formaldehyde, ¹⁴C-methanol or ¹⁴C-CO₂ as substrates.

The intracellular metabolites were persued and their quantitative variation with time was measured. Along with the fact that serine and malate appeared in the earlier time, then appeared organic acids and amino acids belonging to TCA cycle, and the fact that hydroxy-pyruvate reductase and phosphoenolpyruvate carboxylase activities were much stronger in methanol culture than in ethanol culture, it was concluded that the two fungi followed the serine pathway in assimilating C₁-compounds. Oxidation enzymes of methanol and formaldehyde were also studied, and an oxidizing system was found besides usual NAD linked methanol or formaldehyde dehydrogenases.