Prediction of m6A and m5C at single-molecule resolution reveals a transcriptome-wide co-occurrence of RNA modifications

The epitranscriptome embodies many new and largely unexplored functions of RNA. A significant roadblock hindering progress in epitranscriptomics is the identification of more than one modification in individual transcript molecules. We address this with CHEUI (CH3 (methylation) Estimation Using Ionic current). CHEUI predicts N6-methyladenosine (m6A) and 5-methylcytosine (m5C) in individual molecules from the same sample, the stoichiometry at transcript reference sites, and differential methylation between any two conditions. CHEUI processes observed and expected nanopore direct RNA sequencing signals to achieve high single-molecule, transcript-site, and stoichiometry accuracies in multiple tests using synthetic RNA standards and cell line data. CHEUI's capability to identify two modification types in the same sample reveals a co-occurrence of m6A and m5C in individual mRNAs in cell line and tissue transcriptomes. CHEUI provides new avenues to discover and study the function of the epitranscriptome.

Real-time CT image generation based on voxel-by-voxel modeling of internal deformation by utilizing the displacement of fiducial markers

PURPOSE

To show the feasibility of real-time CT image generation technique utilizing internal fiducial markers that facilitate the evaluation of internal deformation.

METHODS

In the proposed method, a linear regression model that can derive internal deformation from the displacement of fiducial markers is built for each voxel in the training process before the treatment session. Marker displacement and internal deformation are derived from the four-dimensional computed tomography (4DCT) dataset. In the treatment session, the three-dimensional deformation vector field is derived according to the marker displacement, which is monitored by the real-time imaging system. The whole CT image can be synthesized by deforming the reference CT image with a deformation vector field in real-time. To show the feasibility of the technique, image synthesis accuracy and tumor localization accuracy were evaluated using the dataset generated by extended NURBS-Based Cardiac-Torso (XCAT) phantom and clinical 4DCT datasets from six patients, containing 10 CT datasets each. In the validation with XCAT phantom, motion range of the tumor in training data and validation data were about 10 and 15 mm, respectively, so as to simulate motion variation between 4DCT acquisition and treatment session. In the validation with patient 4DCT dataset, eight CT datasets from the 4DCT dataset were used in the training process. Two excluded inhale CT datasets can be regarded as the datasets with large deformations more than training dataset. CT images were generated for each respiratory phase using the corresponding marker displacement. Root mean squared error (RMSE), normalized RMSE (NRMSE), and structural similarity index measure (SSIM) between the original CT images and the synthesized CT images were evaluated as the quantitative indices of the accuracy of image synthesis. The accuracy of tumor localization was also evaluated.

RESULTS

In the validation with XCAT phantom, the mean NRMSE, SSIM, and three-dimensional tumor localization error were 7.5 ± 1.1%, 0.95 ± 0.02, and 0.4 ± 0.3 mm, respectively. In the validation with patient 4DCT dataset, the mean RMSE, NRMSE, SSIM, and three-dimensional tumor localization error in six patients were 73.7 ± 19.6 HU, 9.2 ± 2.6%, 0.88 ± 0.04, and 0.8 ± 0.6 mm, respectively. These results suggest that the accuracy of the proposed technique is adequate when the respiratory motion is within the range of the training dataset. In the evaluation with a marker displacement larger than that of the training dataset, the mean RMSE, NRMSE, and tumor localization error were about 100 HU, 13%, and <2.0 mm, respectively, except for one case having large motion variation. The performance of the proposed method was similar to those of previous studies. Processing time to generate the volumetric image was <100 ms.

CONCLUSION

We have shown the feasibility of the real-time CT image generation technique for volumetric imaging.

Awamori fermentation test and 1-octen-3-ol productivity analysis using fatty acid oxygenase disruptants of Aspergillus luchuensis

1-Octen-3-ol is a major aroma component of awamori, a traditional distilled liquor produced in Okinawa Prefecture, Japan. As 1-octen-3-ol is thought to affect the sensory properties of awamori, it is important to fully characterize the compound's biosynthetic pathway and control mechanism. We previously reported that the fatty acid oxygenase ppoC (ppo: psi-produced oxygenase) of Aspergillus luchuensis is directly involved in the production of 1-octen-3-ol in rice koji (Kataoka et al., J. Biosci. Bioeng., 129, 192-198, 2020). In the present study, we constructed A. luchuensis ppoD disruptants to characterize the role of ppo genes in 1-octen-3-ol biosynthesis. A small-scale awamori fermentation test was performed using ppoA, ppoC, and ppoD single disruptants (ΔppoA, ΔppoC, and ΔppoD, respectively), along with the parent strain, ΔligD. 1-Octen-3-ol was not detected in the distillate prepared using the ΔppoC strain. We conclude that A. luchuensis ppoC is the only 1-octen-3-ol-producing factor in the awamori brewing process. Because ΔppoA and ΔppoD slightly enhanced 1-octen-3-ol productivity, these two genes may play a role in negatively controlling 1-octen-3-ol biosynthesis.

Molecular mechanism underlying pseudopeloria in Habenaria radiata (Orchidaceae)

Habenaria radiata (Orchidaceae) has two whorls of perianth, comprising three greenish sepals, two white petals and one lip (labellum). By contrast, the pseudopeloric (with a decreased degree of zygomorphy) mutant cultivar of H. radiata, 'Hishou', has changes in the identities of the dorsal sepal to a petaloid organ and the two ventral sepals to lip-like organs. Here, we isolated four DEFICIENS-like and two AGL6-like genes from H. radiata, and characterized their expression. Most of these genes revealed similar expression patterns in the wild type and in the 'Hishou' cultivar, except HrDEF-C3. The HrDEF-C3 gene was expressed in petals and lip in the wild type but was ectopically expressed in sepal, petals, lip, leaf, root and bulb in 'Hishou'. Sequence analysis of the HrDEF-C3 loci revealed that the 'Hishou' genome harbored two types of HrDEF-C3 genes: one identical to wild-type HrDEF-C3 and the other carrying a retrotransposon insertion in its promoter. Genetic linkage analysis of the progeny derived from an intraspecific cross between 'Hishou' and the wild type demonstrated that the mutant pseudopeloric trait was dominantly inherited and was linked to the HrDEF-C3 gene carrying the retrotransposon. These results indicate that the pseudopeloric phenotype is caused by retrotransposon insertion in the HrDEF-C3 promoter, resulting in the ectopic expression of HrDEF-C3. As the expression of HrAGL6-C2 was limited to lateral sepals and lip, the overlapping expression of HrDEF-C3 and HrAGL6-C2 is likely to be responsible for the sepal to lip-like identity in the lateral sepals of the 'Hishou' cultivar.

Influence of α-1,3-glucan synthase gene agsE on protoplast formation for transformation of Aspergillus luchuensis

Aspergillus luchuensis NBRC4314 recently underwent genome sequencing. We have not used the frequently used protoplast-polyethylene glycol (PEG) method but have used agrobacterium-mediated transformation (AMT) to genetically engineer this strain because it was difficult to generate protoplasts using commercial cell wall lytic enzymes. In this study, we initially investigated the various conditions for protoplast formation in A. luchuensis. We found that A. luchuensis protoplasts could be generated using a minimal medium for the preculture medium, a static culture for the preculture condition, and Yatalase and α-1,3-glucanase as cell-wall lytic enzymes. These protoplasts could then be transformed with the protoplast-PEG method. Because α-1,3-glucanase was needed to form protoplasts in A. luchuensis, we investigated the role of the α-1,3-glucan synthase gene agsE in protoplast formation, one of five α-1,3-glucan synthase genes in A. luchuensis and a homolog of the major α-1,3-glucan synthase agsB in Aspergillus nidulans. We disrupted agsE in A. luchuensis (ΔagsE) with AMT and found that protoplast formation in ΔagsE was comparable with protoplast formation in Aspergillus oryzae with Yatalase. The ΔagsE protoplasts were also competent for transformation with the protoplast-PEG method. Hence, agsE appears to inhibit protoplast formation in A. luchuensis.

Comparison of MR Imaging and Dual-Energy CT for the Evaluation of Cartilage Invasion by Laryngeal and Hypopharyngeal Squamous Cell Carcinoma

BACKGROUND AND PURPOSE

Dual-energy CT can distinguish iodine-enhanced tumors from nonossified cartilage and has been investigated for evaluating cartilage invasion in patients with laryngeal and hypopharyngeal squamous cell carcinomas. In this study, we compared the diagnostic accuracy of MR imaging and of a combination of weighted-average and iodine overlay dual-energy CT images in detecting cartilage invasion by laryngeal and hypopharyngeal squamous cell carcinomas, in particular thyroid cartilage invasion.

MATERIALS AND METHODS

Fifty-five consecutive patients who underwent 3T MR imaging and 128-slice dual-energy CT for preoperative initial staging of laryngeal or hypopharyngeal squamous cell carcinomas were included. Two blinded observers evaluated laryngeal cartilage invasion on MR imaging and dual-energy CT using a combination of weighted-average and iodine-overlay images. Pathologic findings of surgically resected specimens were used as the reference standard for evaluating sensitivity, specificity, and the areas under the receiver operating characteristic curve of both modalities for cartilage invasion by each type of cartilage and for all cartilages together. Sensitivity and specificity were compared using the McNemar test and generalized linear mixed models.

RESULTS

Dual-energy CT showed higher specificity than MR imaging for diagnosing all cartilage together (84% for MR imaging versus 98% for dual-energy CT, P < .004) and for thyroid cartilage (64% versus 100%, P < .001), with a similar average area under the curve (0.94 versus 0.95, P = .70). The sensitivity did not differ significantly for all cartilages together (97% versus 81%, P = .16) and for thyroid cartilage (100% versus 89%, P = .50), though there was a trend toward increased sensitivity with MR imaging.

CONCLUSIONS

Dual-energy CT showed higher specificity and acceptable sensitivity in diagnosing laryngeal cartilage invasion compared with MR imaging.

Outcomes following autologous hematopoietic stem cell transplant for patients with relapsed Wilms' tumor: a CIBMTR retrospective analysis

Despite the dramatic improvement in the overall survival for patients diagnosed with Wilms’ tumor (WT), the outcomes for those that experience relapse have remained disappointing. We describe the outcomes of 253 patients with relapsed WT who received high-dose chemotherapy (HDT) followed by autologous hematopoietic stem cell transplant (HCT) between 1990 and 2013, and reported to the Center for International Blood and Marrow Transplantation Research (CIBMTR). The 5-year estimates for event free survival (EFS) and overall survival (OS) were 36% (95% CI; 29 – 43%) and 45% (95% CI; 38 – 51%) respectively. Relapse of primary disease was the cause of death in 81% of the population. EFS, OS, relapse and transplant-related mortality (TRM) showed no significant differences when broken down by disease status at transplant, time from diagnosis to transplant, year of transplant or conditioning regimen. Our data suggest that HDT followed by autologous HCT for relapsed WT is well tolerated and outcomes are similar to those reported in the literature. Since attempts to conduct a randomized trial comparing maintenance chemotherapy with consolidation versus high-dose chemotherapy followed by stem cell transplant have failed, one should balance the potential benefits with the yet unknown long-term risks. Since disease recurrence continues to be the most common cause of death, future research should focus on the development of consolidation therapies for those patients achieving complete response to therapy.

A novel mutation in the RSPO4 gene in a patient with autosomal recessive anonychia

The Wnt signalling pathway is a major pathway involved in the embryogenic development of the various organs of the body. Appropriate signalling in this pathway relies on the proper functioning of several proteins including the R-spondin family of proteins. Deactivating mutations in R-spondin 4 are associated with anonychia. We present the case of a 26-year-old man presenting with anonychia of the 20 nails, which had been present since birth. Using genetic studies, we identified a novel nonsense mutation, c.164-165TC>AA, characterized by two consecutive mismatch bases. To our knowledge, this mutation is the first to be reported in R-spondin 4 in a Lebanese population. Evaluating new patients with anonychia provides fruitful clinical and molecular findings.

Measurement and comparison of individual external doses of high-school students living in Japan, France, Poland and Belarus-the 'D-shuttle' project

Twelve high schools in Japan (of which six are in Fukushima Prefecture), four in France, eight in Poland and two in Belarus cooperated in the measurement and comparison of individual external doses in 2014. In total 216 high-school students and teachers participated in the study. Each participant wore an electronic personal dosimeter 'D-shuttle' for two weeks, and kept a journal of his/her whereabouts and activities. The distributions of annual external doses estimated for each region overlap with each other, demonstrating that the personal external individual doses in locations where residence is currently allowed in Fukushima Prefecture and in Belarus are well within the range of estimated annual doses due to the terrestrial background radiation level of other regions/countries.