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1.  Genome-Wide SNP Calling Using Next Generation Sequencing Data in Tomato 
Molecules and Cells  2014;37(1):36-42.
The tomato (Solanum lycopersicum L.) is a model plant for genome research in Solanaceae, as well as for studying crop breeding. Genome-wide single nucleotide polymorphisms (SNPs) are a valuable resource in genetic research and breeding. However, to do discovery of genome-wide SNPs, most methods require expensive high-depth sequencing. Here, we describe a method for SNP calling using a modified version of SAMtools that improved its sensitivity. We analyzed 90 Gb of raw sequence data from next-generation sequencing of two resequencing and seven transcriptome data sets from several tomato accessions. Our study identified 4,812,432 non-redundant SNPs. Moreover, the workflow of SNP calling was improved by aligning the reference genome with its own raw data. Using this approach, 131,785 SNPs were discovered from transcriptome data of seven accessions. In addition, 4,680,647 SNPs were identified from the genome of S. pimpinellifolium, which are 60 times more than 71,637 of the PI212816 transcriptome. SNP distribution was compared between the whole genome and transcriptome of S. pimpinellifolium. Moreover, we surveyed the location of SNPs within genic and intergenic regions. Our results indicated that the sufficient genome-wide SNP markers and very sensitive SNP calling method allow for application of marker assisted breeding and genome-wide association studies.
doi:10.14348/molcells.2014.2241
PMCID: PMC3907006  PMID: 24552708
next generation sequencing (NGS); single nucleotide polymorphism (SNP); tomato
2.  Esophageal tolerance to high-dose stereotactic radiosurgery 
Radiation Oncology Journal  2013;31(4):234-238.
Purpose
Esophageal tolerance is needed to guide the safe administration of stereotactic radiosurgery (SRS). We evaluated comprehensive dose-volume parameters of acute esophageal toxicity in patients with spinal metastasis treated with SRS.
Materials and Methods
From May 2008 to May 2011, 30 cases in 27 patients with spinal metastasis received single fraction SRS to targets neighboring esophagus. Endpoints evaluated include length (mm), volume (mL), maximal dose (Gy), and series of dose-volume thresholds from the dose-volume histogram (volume of the organ treated beyond a threshold dose).
Results
The median time from the start of irradiation to development of esophageal toxicity was 2 weeks (range, 1 to 12 weeks). Six events of grade 1 esophageal toxicity occurred. No grade 2 or higher events were observed. V15 of external surface of esophagus was found to predict acute esophageal toxicity revealed by multivariate analysis (odds radio = 1.272, p = 0.047).
Conclusion
In patients with spinal metastasis who received SRS for palliation of symptoms, the threshold dose-volume parameter associated with acute esophageal toxicity was found to be V15 of external surface of esophagus. Restrict V15 to external surface of esophagus as low as possible might be safe and feasible in radiosurgery.
doi:10.3857/roj.2013.31.4.234
PMCID: PMC3912238  PMID: 24501712
Esophagus; Radiation tolerance; Stereotactic radiosurgery
3.  Treatment outcome in patients with triple negative early stage breast cancers compared with other molecular subtypes 
Radiation Oncology Journal  2012;30(3):124-131.
Purpose
To determine whether triple negative (TN) early stage breast cancers have poorer survival rates compared with other molecular types.
Materials and Methods
Between August 2000 and July 2006, patients diagnosed with stage I, II early stage breast cancers, in whom all three markers (estrogen receptor, progesterone receptor, and human epidermal growth factor receptor [HER]-2) were available and treated with modified radical mastectomy or breast conserving surgery followed by radiotherapy, were retrospectively reviewed.
Results
Of 446 patients, 94 (21.1%) were classified as TN, 57 (12.8%) as HER-2 type, and 295 (66.1%) as luminal. TN was more frequently associated with young patients younger than 35 years old (p = 0.002), higher histologic grade (p < 0.0001), and nuclear (p < 0.0001). The median follow-up period was 78 months (range, 4 to 130 months). There were 9 local relapses (2.0%), 15 nodal (3.4%), 40 distant metastases (9.0%), and 33 deaths (7.4%) for all patients. The rates of 5-year OS, DFS, LFS, and DMFS for all patients were 95.5%, 89.9%, 95.4%, and 91.7%, respectively. There were no significant differences in OS, DFS, LFS, and DMFS between triple negative and other subtypes (p > 0.05).
Conclusion
We found that patients with TN early stage breast cancers had no difference in survival rates compared with other molecular subtypes. Prospective study in homogeneous treatment group will need for a prognosis of TN early stage breast cancer.
doi:10.3857/roj.2012.30.3.124
PMCID: PMC3496846  PMID: 23170291
Triple negative breast cancer; Early stage; Overall survival; Disease-free survival; Locoregional relapse-free survival; Distant metastasis-free survival
4.  Comparing the Heterogeneity of Copper-Binding Characteristics for Two Different-Sized Soil Humic Acid Fractions Using Fluorescence Quenching Combined with 2D-COS 
TheScientificWorldJournal  2011;11:1865-1876.
Heterogeneous distributions of copper-binding characteristics were compared for two ultrafiltered size fractions of a soil HA using fluorescence quenching combined with two-dimensional correlation spectroscopy (2D-COS). The apparent shapes of the original synchronous fluorescence spectra and the extent of the fluorescence quenching upon the addition of copper were similar for the two fractions. The stability constants calculated at their highest peaks were not significantly different. However, the 2D-COS results revealed that the fluorescence quenching behaviors were strongly affected by the associated wavelengths and the fraction's size. The spectral change preferentially occurred in the wavelength order of 467 nm → 451 nm → 357 nm for the 1–10 K fraction and of 376 nm → 464 nm for the >100 K fraction. The extent of the binding affinities exactly followed the sequential orders interpreted from the 2D-COS, and they exhibited the distinctive ranges of the logarithmic values from 5.86 to 4.91 and from 6.48 to 5.95 for the 1–10 K and the >100 K fractions, respectively. Our studies demonstrated that fluorescence quenching combined with 2D-COS could be successfully utilized to give insight into the chemical heterogeneity associated with metal-binding sites within the relatively homogeneous HA size fractions.
doi:10.1100/2011/640598
PMCID: PMC3217604  PMID: 22125443
humic substances (HSs); two-dimensional correlation spectroscopy (2D-COS); fluorescence quenching; copper binding; Ryan-Weber model; heterogeneity
5.  A comparison of preplan MRI and preplan CT-based prostate volume with intraoperative ultrasound-based prostate volume in real-time permanent brachytherapy 
Radiation Oncology Journal  2011;29(3):199-205.
Purpose
The present study compared the difference between intraoperative transrectal ultrasound (iTRUS)-based prostate volume and preplan computed tomography (CT), preplan magnetic resonance imaging (MRI)-based prostate volume to estimate the number of seeds needed for appropriate dose coverage in permanent brachytherapy for prostate cancer.
Materials and Methods
Between March 2007 and March 2011, among 112 patients who underwent permanent brachytherapy with 125I, 60 image scans of 56 patients who underwent preplan CT (pCT) or preplan MRI (pMRI) within 2 months before brachytherapy were retrospectively reviewed. Twenty-four cases among 30 cases with pCT and 26 cases among 30 cases with pMRI received neoadjuvant hormone therapy (NHT). In 34 cases, NHT started after acquisition of preplan image. The median duration of NHT after preplan image acquisition was 17 and 21 days for cases with pCT and pMRI, respectively. The prostate volume calculated by different modalities was compared. And retrospective planning with iTRUS image was performed to estimate the number of 125I seed required to obtain recommended dose distribution according to prostate volume.
Results
The mean difference in prostate volume was 9.05 mL between the pCT and iTRUS and 6.84 mL between the pMRI and iTRUS. The prostate volume was roughly overestimated by 1.36 times with pCT and by 1.33 times with pMRI. For 34 cases which received NHT after image acquisition, the prostate volume was roughly overestimated by 1.45 times with pCT and by 1.37 times with pMRI. A statistically significant difference was found between preplan image-based volume and iTRUS-based volume (p < 0.001). The median number of wasted seeds is approximately 13, when the pCT or pMRI volume was accepted without modification to assess the required number of seeds for brachytherapy.
Conclusion
pCT-based volume and pMRI-based volume tended to overestimate prostate volume in comparison to iTRUS-based volume. To reduce wasted seeds and cost of the brachytherapy, we should take the volume discrepancy into account when we estimate the number of 125I seeds for permanent brachytherapy.
doi:10.3857/roj.2011.29.3.199
PMCID: PMC3429903  PMID: 22984671
Brachytherapy; Prostate cancer; Prostate volume
6.  Spectroscopic and Chromatographic Characterization of Wastewater Organic Matter from a Biological Treatment Plant 
Sensors (Basel, Switzerland)  2009;10(1):254-265.
Spectroscopic and chromatographic changes in dissolved organic matter (DOM) characteristics of influent and treated sewage were investigated for a wastewater treatment plant (WWTP) with a biological advanced process. Refractory DOM (R-DOM) was defined as the dissolved organic carbon concentrations of the samples after 28-day incubation for this study. Specific UV absorbance (SUVA), hydrophobicity, synchronous fluorescence spectra and molecular weight (MW) distributions were selected as DOM characteristics. The percent distribution of R-DOM for the effluent was much higher than that of the influent, indicating that biodegradable DOM was selectively removed during the process. Comparison of the influent versus the effluent sewage revealed that SUVA, fulvic-like fluorescence (FLF), humic-like fluorescence (HLF), the apparent MW values were enhanced during the treatment. This suggests that more aromatic and humic-like compounds were enriched during the biological process. No significant difference in the DOM characteristics was observed between the original effluent (i.e., prior to the incubation) and the influent sewage after the incubation. This result suggests that the major changes in wastewater DOM characteristics occurring during the biological advanced process were similar to those for simple microbial incubation.
doi:10.3390/s100100254
PMCID: PMC3270839  PMID: 22315538
wastewater; refractory organic matter; specific UV absorbance; fluorescence; molecular weight distribution
7.  Estimation of Biological Oxygen Demand and Chemical Oxygen Demand for Combined Sewer Systems Using Synchronous Fluorescence Spectra 
Sensors (Basel, Switzerland)  2010;10(4):2460-2471.
Real-time monitoring of water quality for sewer system is required for efficient sewer network design because it provides information on the precise loading of pollutant to wastewater treatment facilities and the impact of loading on receiving water. In this study, synchronous fluorescence spectra and its first derivatives were investigated using a number of wastewater samples collected in sewer systems in urban and non-urban areas, and the optimum fluorescence feature was explored for the estimation of biochemical oxygen demand (BOD) and chemical oxygen demand (COD) concentrations of sewer samples. The temporal variations in BOD and COD showed a regular pattern for urban areas whereas they were relatively irregular for non-urban areas. Irrespective of the sewer pipes and the types of the areas, two distinct peaks were identified from the synchronous fluorescence spectra, which correspond to protein-like fluorescence (PLF) and humic-like fluorescence (HLF), respectively. HLF in sewer samples appears to be associated with fluorescent whitening agents. Five fluorescence characteristics were selected from the synchronous spectra and the first-derivatives. Among the selected fluorescence indices, a peak in the PLF region (i.e., Index I) showed the highest correlation coefficient with both BOD and COD. A multiple regression approach based on suspended solid (SS) and Index I used to compensate for the contribution of SS to BOD and COD revealed an improvement in the estimation capability, showing good correlation coefficients of 0.92 and 0.94 for BOD and COD, respectively.
doi:10.3390/s100402460
PMCID: PMC3274188  PMID: 22319257
sewer system; fluorescence; prediction; BOD; COD
8.  Uterine and placental expression of TRPV6 gene is regulated via progesterone receptor- or estrogen receptor-mediated pathways during pregnancy in rodents 
Transient receptor potential cation channel, subfamily V, member 6 (TRPV6) is an epithelial Ca2+ channel protein expressed in calcium absorbing organs. In the present study, we investigated the expression and regulation of uterine and placental TRPV6 during gestation in rodents. Uterine TRPV6 peaked at pregnancy day (P) 0.5, P5.5 and, P13.5 and was detected in uterine epithelium and glands of rats, while placental TRPV6 mRNA levels increased in mid-gestation. Uterine and placental TRPV6 mRNA levels in rats appear to cyclically change during pregnancy, suggesting that TRPV6 may participate in the implantation process. In addition, uterine TRPV6 mRNA is only expressed in placenta-unattached areas of the uterus, and uterine TRPV6 immunoreactivity was observed in luminal and glandular epithelial cells. In the placenta, TRPV6 was detected in the labyrinth and spongy zone. These results may indicate that TRPV6 has at least two functions: implantation of the embryo and maintenance of pregnancy. To investigate the pathway(s) mediating TRPV6 expression in rodents, anti-steroid hormone antagonists were injected prior to maximal TRPV6 expression. In rats, TRPV6 expression was reduced by RU486 (an anti-progesterone) through progesterone receptors, and ICI 182,780 (an anti-estrogen) blocked TRPV6 expression via estrogen receptors in mice. The juxtaposition of uterine and placental TRPV6 expressed in these tissues supports the notion that TRPV6 participates in transferring calcium ions between the maternal and fetal compartments. Taken together, TRPV6 gene may function as a key element in controlling calcium transport in the uterus between the embryo and the placenta during pregnancy.
doi:10.1186/1477-7827-7-49
PMCID: PMC2694200  PMID: 19457270

Results 1-8 (8)