Thermus thermophilus
(
T
.
thermophilus
) HB27 is an extreme thermophile that grows optimally at 65–72 °C. Heat-induced DNA lesions are expected to occur at a higher frequency in the genome of
T
.
...thermophilus
than in those of mesophiles; however, the mechanisms underlying the maintenance of genome integrity at high temperatures remain poorly understood. The study of mutation spectra has become a powerful approach to understanding the molecular mechanisms responsible for DNA repair and mutagenesis in mesophilic species. Therefore, we developed a
supF
-based system to detect a broad spectrum of mutations in
T
.
thermophilus
. This system was validated by measuring spontaneous mutations in the wild type and a
udgA
,
B
double mutant deficient in uracil-DNA glycosylase (UDG) activity. We found that the mutation frequency of the
udgA
,
B
strain was 4.7-fold higher than that of the wild type and G:C→A:T transitions dominated, which was the most reasonable for the mutator phenotype associated with the loss of UDG function in
T
.
thermophilus
. These results show that this system allowed for the rapid analysis of mutations in
T
.
thermophilus
, and may be useful for studying the molecular mechanisms responsible for DNA repair and mutagenesis in this extreme thermophile.
The factors maintaining genomic integrity, which have been studied in detail in other species, have yet to be investigated in plants. Recent progress in gene-silencing technology has made it possible ...to produce transgenic plants with loss-of-function phenotypes for the effective analysis of these factors, even with the high redundancy of genes in plants. Therefore, a mutation-detection system for plants is necessary to estimate the biological function of a target gene for mutation frequencies and spectra. Here, we reported the development of a novel system to analyze mutations in the chromosomal DNA of plants. The supF gene of E. coli was used as a target for the mutation because it was possible to detect all mutational base changes. Based on the plasmid pTN30, which carries supF, we constructed a binary Ti vector for its introduction to Arabidopsis genomes. The system was validated by measuring mutations in both non-treated and mutagen-treated transgenic plants. DNA fragments including pTN30 were rescued from the plants, and introduced into E. coli KS40/pOF105 to isolate the supF mutant clones conferring both nalidixic acid and streptomycin resistance on transformants. We found that the mutation frequency was approximately three times higher with the ethyl methanesulfonate (EMS) treatment than without it and G:C to A:T transitions dominated, which was the most reasonable mutation induced by EMS. These results show that this system allowed for the rapid analysis of mutations in plants, and may be useful for analyzing plant genes related to the functions of genomic stability and monitoring environmental genotoxic substances.
•We developed an age estimation method for adult bone using machine learning.•The vertebral body, ischial tuberosity, iliac crest, and femur were analyzed.•High-frequency components were extracted ...from images as feature variables.•Partial least squares regression (PLS) was applied for dimensionality reduction.•Support vector regression with PLS components effectively estimated ages.
Age estimation from bones plays a major role in the identification of skeletal remains. We present a novel age estimation method developed through the application of machine learning (ML) to post-mortem computed tomography (PMCT) images of bones.
This study used PMCT images of the vertebral body, ischial tuberosity, iliac crest, and femur, which were transformed into homologous models. Two-dimensional discrete wavelet transform (2D-DWT) was conducted to extract high-frequency components. Dimensionality reductions of the prepared data arrays were conducted with principal component analysis and partial least squares regression (PLS). The known ages and scores of the principal components were supplied to ridge regression, least absolute shrinkage and selection operator regression, and support vector regression with a linear kernel or a radial basis function kernel. A 10-fold double-looped cross-validation was conducted and estimation accuracies were verified with the mean absolute errors and correlation coefficients (r) between the actual and estimated ages.
Preprocessing with 2D-DWT and PLS obtained good results. Of the ML methods examined, support vector regression with radial basis function kernel achieved the highest accuracy, with an optimum mean absolute error and r of 7.92 (male vertebral body) and 0.837 (female ischial tuberosity), respectively. The method developed in this study could be used as a rapid, accurate, and objective tool for identifying both skeletal remains and non-skeletonized cadavers.
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The
M
JMA
7.3 Kumamoto earthquake that occurred at 1:25 JST on April 16, 2016, not only triggered aftershocks in the vicinity of the epicenter, but also triggered earthquakes that were 50–100 km away ...from the epicenter of the main shock. The active seismicity can be divided into three regions: (1) the vicinity of the main faults, (2) the northern region of Aso volcano (50 km northeast of the mainshock epicenter), and (3) the regions around three volcanoes, Yufu, Tsurumi, and Garan (100 km northeast of the mainshock epicenter). Notably, the zones between these regions are distinctively seismically inactive. The electric resistivity structure estimated from one-dimensional analysis of the 247 broadband (0.005–3000 s) magnetotelluric and telluric observation sites clearly shows that the earthquakes occurred in resistive regions adjacent to conductive zones or resistive-conductive transition zones. In contrast, seismicity is quite low in electrically conductive zones, which are interpreted as regions of connected fluids. We suggest that the series of the earthquakes was induced by a local accumulated stress and/or fluid supply from conductive zones. Because the relationship between the earthquakes and the resistivity structure is consistent with previous studies, seismic hazard assessment generally can be improved by taking into account the resistivity structure. Following on from the 2016 Kumamoto earthquake series, we suggest that there are two zones that have a relatively high potential of earthquake generation along the western extension of the MTL.
Graphical abstract
.
The purpose of this study was to examine the correlations among objective sleep variables, sleep-wake cycle parameters, and daily physical activity in hemodialysis patients and controls. Twenty-four ...hemodialysis patients (HD group) were compared with a control group consisting of 24 healthy participants matched for age, height, and weight. Sleep variables (total sleep time TST, sleep efficiency SE, sleep latency SL, and waking after sleep onset WASO), sleep-wake cycle parameters (the sleep-wake cycle period and the peak of sleep-wake cycle variance), and daily physical activity (steps per day) for each participant were assessed by objective methods for two weeks. While there was no difference in TST between the two groups, the HD group showed a significantly increased SL (HD: 0:29±0:20 vs control: 0:16±0:13, p < 0.05) and WASO (HD: 2:21±1:00 vs control: 1:35±0:41, p<0.05) and decreased SE (HD: 67.1±13.6% vs control: 77.5±9.7%, p<0.01) compared to the control group. There was no significant difference in sleep-wake cycle period between the HD and control groups. However, the peak of sleep-wake cycle variance in the HD group (0.050±0.028) was significantly lower (t = 2.49, p<0.05) than in the control group (0.068±0.019). The number of daily steps taken in the HD group (4,774± 2,845 steps) was also significantly lower than in the control group (8,696± 3,047). The peak of sleep-wake cycle variance was significantly correlated with SE (r = 0.532, p<0.01), SL (r = -0.501, p<0.01), and WASO (r = -0.436, p<0.01), whereas the number of steps showed a weak correlation only with WASO (r = -0.308, p<0.05) among the objective sleep parameters. Our results suggest that sleep quality in HD patients may be more effectively improved by maintaining the regular 24-hour sleep-wake cycle rather than by increasing the amount of daily physical activity, indicating that intervention such as measures to prevent napping during hemodialysis sessions may prove effective in improving the quality of sleep in HD patients.
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