RES-Scanner:a software package for genome-wide identification of RNA-editing sites

BACKGROUND: High-throughput sequencing (HTS) provides a powerful solution for the genome-wide identification of RNA-editing sites. However, it remains a great challenge to distinguish RNA-editing sites from genetic variants and technical artifacts caused by sequencing or read-mapping errors. RESULTS: Here we present RES-Scanner, a flexible and efficient software package that detects and annotates RNA-editing sites using matching RNA-seq and DNA-seq data from the same individuals or samples. RES-Scanner allows the use of both raw HTS reads and pre-aligned reads in BAM format as inputs. When inputs are HTS reads, RES-Scanner can invoke the BWA mapper to align reads to the reference genome automatically. To rigorously identify potential false positives resulting from genetic variants, we have equipped RES-Scanner with sophisticated statistical models to infer the reliability of homozygous genotypes called from DNA-seq data. These models are applicable to samples from either single individuals or a pool of multiple individuals if the ploidy information is known. In addition, RES-Scanner implements statistical tests to distinguish genuine RNA-editing sites from sequencing errors, and provides a series of sophisticated filtering options to remove false positives resulting from mapping errors. Finally, RES-Scanner can improve the completeness and accuracy of editing site identification when the data of multiple samples are available. CONCLUSION: RES-Scanner, as a software package written in the Perl programming language, provides a comprehensive solution that addresses read mapping, homozygous genotype calling, de novo RNA-editing site identification and annotation for any species with matching RNA-seq and DNA-seq data. The package is freely available. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13742-016-0143-4) contains supplementary material, which is available to authorized users

Estimating CT Image From MRI Data Using Structured Random Forest and Auto-Context Model

Computed tomography (CT) imaging is an essential tool in various clinical diagnoses and radiotherapy treatment planning. Since CT image intensities are directly related to positron emission tomography (PET) attenuation coefficients, they are indispensable for attenuation correction (AC) of the PET images. However, due to the relatively high dose of radiation exposure in CT scan, it is advised to limit the acquisition of CT images. In addition, in the new PET and magnetic resonance (MR) imaging scanner, only MR images are available, which are unfortunately not directly applicable to AC. These issues greatly motivate the development of methods for reliable estimate of CT image from its corresponding MR image of the same subject. In this paper, we propose a learning-based method to tackle this challenging problem. Specifically, we first partition a given MR image into a set of patches. Then, for each patch, we use the structured random forest to directly predict a CT patch as a structured output, where a new ensemble model is also used to ensure the robust prediction. Image features are innovatively crafted to achieve multi-level sensitivity, with spatial information integrated through only rigid-body alignment to help avoiding the error-prone inter-subject deformable registration. Moreover, we use an auto-context model to iteratively refine the prediction. Finally, we combine all of the predicted CT patches to obtain the final prediction for the given MR image. We demonstrate the efficacy of our method on two datasets: human brain and prostate images. Experimental results show that our method can accurately predict CT images in various scenarios, even for the images undergoing large shape variation, and also outperforms two state-of-the-art methods

Caste-specific RNA editomes in the leaf-cutting ant <i>Acromyrmex echinatior</i>

Eusocial insects have evolved the capacity to generate adults with distinct morphological, reproductive and behavioural phenotypes from the same genome. Recent studies suggest that RNA editing might enhance the diversity of gene products at the post-transcriptional level, particularly to induce functional changes in the nervous system. Using head samples from the leaf-cutting ant Acromyrmex echinatior, we compare RNA editomes across eusocial castes, identifying ca. 11,000 RNA editing sites in gynes, large workers and small workers. Those editing sites map to 800 genes functionally enriched for neurotransmission, circadian rhythm, temperature response, RNA splicing and carboxylic acid biosynthesis. Most A. echinatior editing sites are species specific, but 8–23% are conserved across ant subfamilies and likely to have been important for the evolution of eusociality in ants. The level of editing varies for the same site between castes, suggesting that RNA editing might be a general mechanism that shapes caste behaviour in ants

Caste-specific RNA-editomes in the leaf-cutting ant Acromyrmex echinatior

4 - Insect epigenomics: bridging the gap between genotype and phenotype, Oral Presentatio

K-Domain Splicing Factor OsMADS1 Regulates Open Hull Male Sterility in Rice

AbstractWe identified the rice floral organ development mutant, termed as open hull and male sterile 1 (ohms1), from the progeny of the indica restorer line Zhonghui 8015 treated with 60Co γ-ray irradiation. The ohms1 mutant exhibited an open hull and lemma- and palea-like structure conversion between the anthers and stigma, which resulted in the ohms1 mutant spikelet showing ‘tridentate lemma’. The ohms1 mutant was entirely sterile but had 60%–70% fertile pollen. Genetic analysis and gene mapping showed that ohms1 was controlled by a single recessive gene, and the mutant gene was fine-mapped to a 42-kb interval on the short arm of chromosome 3 between markers KY2 and KY29. Sequence analysis of the four open reading frames in this region revealed that the mutant carried a single nucleotide transformation (A to G) at the last base of the fifth intron, which was likely corresponded to ohms1 phynotype, in an MIKC type MADS-box gene OsMADS1 (LOC_Os03g11614). Enzyme digestion and cDNA sequencing further indicated that the variable splicing was responsible for the deletion of the sixth exon in ohms1, but no structural changes in the MADS domain or amino acid frame shifts appeared. Additionally, real-time fluorescent quantitative PCR analysis showed that the OsMADS1 expression level decreased significantly in the ohms1 mutant. The expression levels of rice flowering factors and floral glume development-related genes also changed significantly. These results demonstrate that OsMADS1 may play an important role in rice floral organ development, particularly in floral glume development and floret primordium differentiation

Amniotic fluid-derived mesenchymal stem cells as a novel therapeutic approach in the treatment of fulminant hepatic failure in rats

As a potential alternative treatment for terminal liver diseases, amniotic fluid derived mesenchymal stem cells (AFMSCs) have many advantages over other stem cells: avoiding much ethical controversy and decrease in both quantity and differentiation potential with age. However, the therapeutic role of AFMSC for fulminant hepatic failure (FHF) has not yet been clearly elucidated. Therefore, we investigated the reparation effects of transplanted AFMSCs in rats with FHF. AFMSCs were transplanted into injured liver via the portal vein in the rat FHF model. Therapeutic effect was evaluated after cell transfusion by histologic pathology, hepatic enzyme levels and animal survival. Cryostat sections were prepared and directly assessed for green fluorescent protein (GFP) expression and localization, and in vivo differentiation of AFMSC was confirmed by double-immunostaining analyses. Our results show that AFMSCs prevented liver failure and reduced mortality in rats with FHF. These animals also exhibited improved liver function and animals survival after injection with AFMSCs using GFP, we demonstrated that the engrafted cells and their progeny incorporated into injured livers and produced albumin. We found that AFMSCs transplantation modestly promoted the repair of FHF in rats. AFMSCs implanted in the injured liver may be a novel therapeutic approach in the treatment of FHF.Key words: Amniotic fluid-derived mesenchymal stem cells, fulminant hepatic failure, cell transplantation, treatment, hepatogenic differentiation

Gaussian filter facilitated deep learning-based architecture for accurate and efficient liver tumor segmentation for radiation therapy

PurposeAddressing the challenges of unclear tumor boundaries and the confusion between cysts and tumors in liver tumor segmentation, this study aims to develop an auto-segmentation method utilizing Gaussian filter with the nnUNet architecture to effectively distinguish between tumors and cysts, enhancing the accuracy of liver tumor auto-segmentation.MethodsFirstly, 130 cases of liver tumorsegmentation challenge 2017 (LiTS2017) were used for training and validating nnU-Net-based auto-segmentation model. Then, 14 cases of 3D-IRCADb dataset and 25 liver cancer cases retrospectively collected in our hospital were used for testing. The dice similarity coefficient (DSC) was used to evaluate the accuracy of auto-segmentation model by comparing with manual contours. ResultsThe nnU-Net achieved an average DSC value of 0.86 for validation set (20 LiTS cases) and 0.82 for public testing set (14 3D-IRCADb cases). For clinical testing set, the standalone nnU-Net model achieved an average DSC value of 0.75, which increased to 0.81 after post-processing with the Gaussian filter (P&lt;0.05), demonstrating its effectiveness in mitigating the influence of liver cysts on liver tumor segmentation. ConclusionExperiments show that Gaussian filter is beneficial to improve the accuracy of liver tumor segmentation in clinic