Transposon Domestication versus Mutualism in Ciliate Genome Rearrangements

Ciliated protists rearrange their genomes dramatically during nuclear development via chromosome fragmentation and DNA deletion to produce a trimmer and highly reorganized somatic genome. The deleted portion of the genome includes potentially active transposons or transposon-like sequences that reside in the germline. Three independent studies recently showed that transposase proteins of the DDE/DDD superfamily are indispensible for DNA processing in three distantly related ciliates. In the spirotrich Oxytricha trifallax, high copy-number germline-limited transposons mediate their own excision from the somatic genome but also contribute to programmed genome rearrangement through a remarkable transposon mutualism with the host. By contrast, the genomes of two oligohymenophorean ciliates, Tetrahymena thermophila and Paramecium tetraurelia, encode homologous PiggyBac-like transposases as single-copy genes in both their germline and somatic genomes. These domesticated transposases are essential for deletion of thousands of different internal sequences in these species. This review contrasts the events underlying somatic genome reduction in three different ciliates and considers their evolutionary origins and the relationships among their distinct mechanisms for genome remodeling.     

BAFF Controls Neural Cell Survival through BAFF Receptor

Various neuroprotective factors have been shown to help prevention of neuronal cell death, which is responsible for the progression of neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS). However, most of these therapeutic potentials have been tested by administration of recombinant proteins, transgenic expression or virus vector-mediated gene transfer. Therefore, it remains to be clarified whether any endogenous factors has advantage for neuroprotection in a pathological nervous system. Here we show the role of BAFF-R signaling pathway in the control of neural cell survival. Both B cell–activating factor (BAFF) and its receptor (BAFF-R) are expressed in mouse neurons and BAFF-R deficiency reduces the survival of primary cultured neurons. Although many studies have so far addressed the functional role of BAFF-R on the differentiation of B cells, impaired BAFF-R signaling resulted in accelerated disease progression in an animal model of inherited ALS. We further demonstrate that BAFF-R deficient bone marrow cells or genetic depletion of B cells does not affect the disease progression, indicating that BAFF-mediated signals on neurons, not on B cells, support neural cell survival. These findings suggest opportunities to improve therapeutic outcome for patients with neurodegenerative diseases by synthesized BAFF treatment.     

Microtubule-organizing center formation at telomeres induces meiotic telomere clustering

During meiosis, telomeres cluster and promote homologous chromosome pairing. Telomere clustering requires the interaction of telomeres with the nuclear membrane proteins SUN (Sad1/UNC-84) and KASH (Klarsicht/ANC-1/Syne homology). The mechanism by which telomeres gather remains elusive. In this paper, we show that telomere clustering in fission yeast depends on microtubules and the microtubule motors, cytoplasmic dynein, and kinesins. Furthermore, the γ-tubulin complex (γ-TuC) is recruited to SUN- and KASH-localized telomeres to form a novel microtubule-organizing center that we termed the “telocentrosome.” Telocentrosome formation depends on the γ-TuC regulator Mto1 and on the KASH protein Kms1, and depletion of either Mto1 or Kms1 caused severe telomere clustering defects. In addition, the dynein light chain (DLC) contributes to telocentrosome formation, and simultaneous depletion of DLC and dynein also caused severe clustering defects. Thus, the telocentrosome is essential for telomere clustering. We propose that telomere-localized SUN and KASH induce telocentrosome formation and that subsequent microtubule motor-dependent aggregation of telocentrosomes via the telocentrosome-nucleated microtubules causes telomere clustering.     

Identification of the sex pheromone secreted by Synanthedon tenuis (Lepidoptera: Sesiidae)

The Japanese persimmon treeborer, Synanthedon tenuis (Butler) (Lepidoptera: Sesiidae), is a harmful pest of persimmon trees (Diospyros spp.). Because males of this species are known to be attracted by (3Z,13Z)-3,13-octadecadienyl acetate (Z3,Z13-18:OAc), a mating disruptant composed of a 1:1 mixture of Z3,Z13-18:OAc and the (3E,13Z)-isomer, the original target of which is an allied pest, S. hector (Butler), has been diverted to control S. tenuis. However, the sex pheromone secreted by S. tenuis females has not been characterized. Analyses of pheromone gland extracts using gas chromatography (GC) equipped with an electroantennographic detector (GC-EAD) and GC combined with mass spectrometry (GC–MS) detected only Z3,Z13-18:OAc, and no other known sesiid pheromone components were found. In a persimmon orchard, S. tenuis males were selectively attracted by a lure baited with Z3,Z13-18:OAc among four geometrical isomers of 3,13-octadecadienyl acetate, indicating that males strictly discriminated among the configurations of the two double bonds. Lures baited with single Z3,Z13-18:OAc attracted only S. tenuis. Further field experiments revealed that the attractiveness of Z3,Z13-18:OAc is significantly inhibited by the addition of the (3E,13Z) isomer or the parent alcohol.     

Mating disruption for control of the white grub beetle Dasylepida ishigakiensis (Coleoptera: Scarabaeidae) with synthetic sex pheromone in sugarcane fields

The feasibility of mating disruption with synthetic sex pheromone for the control of the white grub beetle Dasylepida ishigakiensis (Coleoptera: Scarabaeidae) was examined by permeating sugarcane fields with a racemic mixture of 2-butanol (rac-2B) released from polyethylene-tube dispensers on Miyako Island, Japan in 2011. An application of rac-2B released from 10,000 tube dispensers into 3,200 m² sugarcane fields significantly reduced the mating rate of feral females and catches of feral males with R2B-baited traps compared with the results from untreated sugarcane fields. The larval density for the treated fields was found to be nearly zero in the following winter when the corresponding figure for untreated fields was high (1.73 and 2.33/40 × 40 cm quadrat). These results clearly show that the mating disruption technique using rac-2B could be highly promising for the control of D. ishigakiensis in sugarcane fields.     

High-resolution mapping of zym, a recessive gene for Zucchini yellow mosaic virus resistance in cucumber

Key message

Using a high-resolution mapping approach, we identified a candidate gene for ZYMV resistance in cucumber. Our findings should assist the development of high-versatility molecular markers for MAS for ZYMV resistance.

Abstract

Zucchini yellow mosaic virus (ZYMV) causes significant disease, which leads to fruit yield loss in cucurbit crops. Since ZYMV resistance is often inherited recessively in cucumber, marker-assisted selection (MAS) is a useful tool for the development of resistant cucumber cultivars. Using 128 families of an F_2:3 population derived from a cross between susceptible ‘CS-PMR1’ and resistant ‘A192-18’ cucumber inbred lines, we confirmed that ZYMV resistance is conferred by a single recessive locus: zym ^A192-18 . We constructed a cucumber genetic linkage map that included 125 simple sequence repeat (SSR) markers segregating into 7 linkage groups (chromosomes). The zym ^A192-18 locus was mapped to chromosome 6, at genetic distances of 0.9 and 1.3 cM from two closely linked SSR markers. For high-resolution genetic mapping, we identified new molecular markers cosegregating with the zym ^A192-18 locus; using cucumber genomic and molecular marker resources and screening an F₂ population of 2,429 plants, we narrowed down the zym ^A192-18 locus to a <50-kb genomic region flanked by two SSR markers, which included six candidate genes. Sequence analysis of the candidate genes’ coding regions revealed that the vacuolar protein sorting-associated protein 4-like (VPS4-like) gene had two SNPs between the parental lines. Based on SNPs of the VPS-4-like gene, we developed zym ^A192-18 -linked DNA markers and found that genotypes associated with these markers were correlated with the ZYMV resistance phenotype in 48 cucumber inbred lines. According to our data, the gene encoding VPS4-like protein is a candidate for the zym ^A192-18 locus. These results may be valuable for MAS for ZYMV resistance in cucumber.     

Interconversion of ketoprofen recognition in firefly luciferase-catalyzed enantioselective thioesterification reaction using from Pylocoeria miyako (PmL) and Hotaria parvura (HpL) just by mutating two amino acid residues

We identified the critical amino acid residues for substrate recognition using two firefly luciferases from Pylocoeria miyako (PmL) and Hotaria parvura (HpL), as these two luciferase enzymes exhibit different activities toward ketoprofen. Specifically, PmL can catalyze the apparent enantioselective thioesterification reaction, while HpL cannot. By comparing the amino acid sequences around the active site, we identified two residues (I350 and M397 in PmL and F351 and S398 in HpL) that were different between the two enzymes, and the replacement of these amino acids resulted in changing the ketoprofen recognition pattern. The inactive HpL was converted to the active enzyme toward ketoprofen and vice versa for PmL. These residues also affected the enantioselectivity toward ketoprofen; however, the bioluminescent color was not affected. In addition, using molecular dynamics calculations, the replacement of these two amino acids induced changes in the state of hydrogen bonding between ketoprofen and the S349 side chain through the active site water. As S349 is not considered to influence color tuning, these changes specifically caused the differences in ketoprofen recognition in the enzyme.     

Adaptation of the Hierarchical Factor Segmentation method to noisy activity data

ABSTRACT

The Hierarchical Factor Segmentation (HFS) method is a non-parametric statistical method for detection of the phase of a biological rhythm shown in an actogram. The detection accuracy of this method was measured on actograms showing only circadian rhythms with a constant ratio of signal to noise (S/N). In the present study, we generated 84 types of artificial actograms including circadian or circatidal rhythms by using three parameters: α/ρ, S/N and period length τ, and evaluated the effectiveness of our devised adaptation of the HFS method, the cycle-by-cycle adaptation. The results showed the effectiveness of the cycle-by-cycle adaptation was high even though S/N or τ was fluctuating through a whole actogram. These suggested that the cycle-by-cycle adaptation could be effectively applied to various kinds of rhythmic activity data. The C++ source code of the cycle-by-cycle adaptation is available on the website at https://github.com/KazukiSakura/cHFS.git.     

DNA Breaking Reaction with Catecholamines

Breaking activity of catecholamines and their structural analogues on λ DNA were investigated by agarose slab gel electrophoresis. Since λ DNA has a homogenous molecular size, it is a favorable material to detect the activity of DNA breaking reagent. Among the compounds tested, those having enediol group were only active, though their activities remarkably differed owing to their side chains. The profile of the breaking reaction was studied in detail by the use of one of the catecholamines, epinephrine.