Genomic view of heavy-ion-induced deletions associated with distribution of essential genes in Arabidopsis thaliana

Heavy-ion beam, a type of ionizing radiation, has been applied to plant breeding as a powerful mutagen and is a promising tool to induce large deletions and chromosomal rearrangements. The effectiveness of heavy-ion irradiation can be explained by linear energy transfer (LET; keV µm-1). Heavy-ion beams with different LET values induce different types and sizes of mutations. It has been suggested that deletion size increases with increasing LET value, and complex chromosomal rearrangements are induced in higher LET radiations. In this study, we mapped heavy-ion beam-induced deletions detected in Arabidopsis mutants to its genome. We revealed that deletion sizes were similar between different LETs (100 to 290 keV μm-1), that their upper limit was affected by the distribution of essential genes, and that the detected chromosomal rearrangements avoid disrupting the essential genes. We also focused on tandemly arrayed genes (TAGs), where two or more homologous genes are adjacent to one another in the genome. Our results suggested that 100 keV µm-1 of LET is enough to disrupt TAGs and that the distribution of essential genes strongly affects the heritability of mutations overlapping them. Our results provide a genomic view of large deletion inductions in the Arabidopsis genome

Cell-Free DNA Analysis of Epithelial Growth Factor Receptor Mutations in Lung Adenocarcinoma Patients by Droplet Digital PCR

Cell-free DNA (cfDNA) analysis may provide a non-invasive diagnostic approach for lung adenocarcinoma patients. Recently, droplet digital PCR (ddPCR) has been developed as a highly sensitive detection method for a low mutant allele percentage. The ddPCR detection limit for epithelial growth factor receptor (EGFR) mutations was evaluated using cell lines, NCI-H1975 for EGFR L858R point mutation and PC-9 for EGFR E746-A750del. Subsequently, detection of EGFR mutations by ddPCR was performed in tumor DNA (tDNA) and cfDNA samples of 19 lung adenocarcinoma patients whose tumor biopsies were already evaluated for EGFR mutations by clamp PCR (13 of L858R, 3 of E746-750del, and 3 of EGFR negative). In 12 cases, immunohistochemical analysis was performed to quantify the number of EGFR L858R-positive cells rate. EGFR point mutation or deletion were detected in 16 tumor DNA samples. In the measurable cfDNA samples, the rate of detection by ddPCR in cfDNA was 61.5% (8/13) for L858R and 100% (3/3) for E746-A750del. A relative correlation was found between the allele fraction (AF) of tDNA and the number of EGFR L858R-positive cells rate. No correlation was found between the AF of tDNA and AF of cfDNA. In our study, cfDNA mutation detection was not associated with clinicopathological features, but cases with high AF of cfDNA did have metastatic lesions. Our study shows that ddPCR enables cfDNA analysis for EGFR L858R and E746-A750del, with a high detection rate. Therefore, cfDNA analysis using ddPCR may complement to tumor biopsy and is beneficial for precision medicine in lung adenocarcinoma patients

JASMINE: Near-infrared astrometry and time-series photometry science

The Japan Astrometry Satellite Mission for INfrared Exploration (JASMINE) is a planned M-class science space mission by the Institute of Space and Astronautical Science, the Japan Aerospace Exploration Agency. JASMINE has two main science goals. One is Galactic archaeology with a Galactic Center survey, which aims to reveal the Milky Way’s central core structure and formation history from Gaia-level (∼25 ${\mu}$as) astrometry in the near-infrared (NIR) Hw band (1.0–1.6 ${\mu}$m). The other is an exoplanet survey, which aims to discover transiting Earth-like exoplanets in the habitable zone from NIR time-series photometry of M dwarfs when the Galactic Center is not accessible. We introduce the mission, review many science objectives, and present the instrument concept. JASMINE will be the first dedicated NIR astrometry space mission and provide precise astrometric information on the stars in the Galactic Center, taking advantage of the significantly lower extinction in the NIR. The precise astrometry is obtained by taking many short-exposure images. Hence, the JASMINE Galactic Center survey data will be valuable for studies of exoplanet transits, asteroseismology, variable stars, and microlensing studies, including discovery of (intermediate-mass) black holes. We highlight a swath of such potential science, and also describe synergies with other missions

The HOX complex neighbored by the EVX gene, as well as two other homeobox-containing genes, the GBX-class and the EN-class, are located on the same chromosomes 2 and 7 in humans

AbstractTwo newly identified human homeobox-containing genes, GBX1 and GBX2, are closely related genes, as are members of the other homeobox genes, EN-1 and EN-2. GBX1 and EN-2 have been mapped to chromosome 7q36. The present study shows that GBX2was mapped to chromosome 2q37. EN-1 was mapped to chromosome 2q14. Moreover, two HOX complexes neighbored by the EVX gene, HOXA and HOXD, are located at chromosome 7p15-p14 and 2q31-q37, respectively. Thus, it is possible that these homeobox genes were linked to each other on an ancestral genome and that the ancestral chromosome segment was duplicated during evolution