BS Seeker: precise mapping for bisulfite sequencing

<p>Abstract</p> <p>Background</p> <p>Bisulfite sequencing using next generation sequencers yields genome-wide measurements of DNA methylation at single nucleotide resolution. Traditional aligners are not designed for mapping bisulfite-treated reads, where the unmethylated Cs are converted to Ts. We have developed BS Seeker, an approach that converts the genome to a three-letter alphabet and uses Bowtie to align bisulfite-treated reads to a reference genome. It uses sequence tags to reduce mapping ambiguity. Post-processing of the alignments removes non-unique and low-quality mappings.</p> <p>Results</p> <p>We tested our aligner on synthetic data, a bisulfite-converted <it>Arabidopsis </it>library, and human libraries generated from two different experimental protocols. We evaluated the performance of our approach and compared it to other bisulfite aligners. The results demonstrate that among the aligners tested, BS Seeker is more versatile and faster. When mapping to the human genome, BS Seeker generates alignments significantly faster than RMAP and BSMAP. Furthermore, BS Seeker is the only alignment tool that can explicitly account for tags which are generated by certain library construction protocols.</p> <p>Conclusions</p> <p>BS Seeker provides fast and accurate mapping of bisulfite-converted reads. It can work with BS reads generated from the two different experimental protocols, and is able to efficiently map reads to large mammalian genomes. The Python program is freely available at <url>http://pellegrini.mcdb.ucla.edu/BS_Seeker/BS_Seeker.html</url>.</p

Decision Support System For Safety Warning Of Bridge – A Case Study In Central Taiwan

This study aims at developing the decision support system (DSS) for safety warning of bridge. In the DSS, real-time and forecasted radar rainfalls are used to predict flood stage, velocity and scouring depth around bridge piers for one to three hours ahead. The techniques adopted in the DSS include (1) measurement and correction models of radar rainfall, (2) a grid-based distributed rainfall-runoff model for simulating reservoir inflows, (3) models for predicting flood stages, velocities and scouring depths around bridge piers, and (4) ultimate analysis approaches for evaluating safety of pier foundation. The DSS can support the management department to decide whether they should close bridges or not during floods. The proposed DSS gave a test-run during Typhoon Morakot in 2009 in Dajia River Basin, central Taiwan. The results show the DSS has reasonable performances during floods

The restoration of sediment-related disasters and driftwood from national forest in Taiwan caused by Typhoon Morakot in 2009

The number and area of new landslide, according to the interpreted SPOT images, caused by Typhoon Morakot in 2009 is estimated as 30,223 and 43,996 ha, respectively. The new landslide area in 2009 increased by about 16,392 ha in comparison with the landslide area in 2008. The heavy rainfall with a return period well over 200 years during Typhoon Morakot centralized in southwestern and southeastern Taiwan, and that also resulted in serious landslide disasters in national forest. Four forest working circles, including Chishan, Laonong, Pintung, and Dawu, are the most serious landslide zones with the landslide ratio over 8.0%. The Forestry Bureau assesses and ranks the seriousness of the disasters by using slope, the number of protected objects, the distance from the disaster to the protected objects to execute the restoration of sediment disasters and landslide in national forest. Due to the most torrential rain in the past 50 years caused by Typhoon Morakot, a large number of trees in the mountain area were destroyed. They became the driftwood, with a total weight of about 1.52 million tons, which ended up at the farmlands and ports. In order to recover agricultural products and livelihoods, Forestry Bureau made strategy for disaster prevention and reduction. Based on the strategy, Forestry Bureau sweeps away the driftwood by estimating its distribution, overcomes the issues caused by the heavy rainfall disaster, and helps the victims to recover their life

Capture of CO2 from Coal-fired Power Plant with NaOH Solution in a Continuous Pilot-scale Bubble-column Scrubber

AbstractA continuous pilot-scale bubble-column scrubber with NaOH as the absorbent was used to explore the capture of CO2 gas from a coal-fired power plant. The experimental design was based on the results of previous study. The diameter of the column was 20cm and the height of the column was 2.4 m. According to the S/N ratio, parameters, including absorption rate (RA), absorption efficiency (E), overall mass-transfer coefficient (KGa) and ratio of the gas-liquid flow rate (R), were selected for Taguchi analysis to obtain optimum conditions. A total of eleven experiments were carried out to verify the optimum conditions here. The range of the gas-flow rate (Qg) and liquid-flow rate (QLT) conducted in this work were 48-192 L/min and 1.6-10 L/min, respectively. The input gas concentrations were 9-12.2%. Using a steady-state material balance with a two-film model, RA and KGa could be determined. The results showed that E, RA and KGa were in the range of 30-98%, 1.03x10-4-11.48x10-4mol/s-L and 0.018-0.058 1/s, respectively. The obtained scrubbing factors (φ) were 0.00285-0.146mol/mol-L, while R was in the range of 0.23-24.14. The dynamic behavior of the scrubber was also discussed in this study. The results could be used as a basis for commercial scale operation for the carbon capture at a power plant as well as microalgae cultivation

Deciphering chemotaxis pathways using cross species comparisons

<p>Abstract</p> <p>Background</p> <p>Chemotaxis is the process by which motile bacteria sense their chemical environment and move towards more favourable conditions. <it>Escherichia coli </it>utilises a single sensory pathway, but little is known about signalling pathways in species with more complex systems.</p> <p>Results</p> <p>To investigate whether chemotaxis pathways in other bacteria follow the <it>E. coli </it>paradigm, we analysed 206 species encoding at least 1 homologue of each of the 5 core chemotaxis proteins (CheA, CheB, CheR, CheW and CheY). 61 species encode more than one of all of these 5 proteins, suggesting they have multiple chemotaxis pathways. Operon information is not available for most bacteria, so we developed a novel statistical approach to cluster <it>che </it>genes into putative operons. Using operon-based models, we reconstructed putative chemotaxis pathways for all 206 species. We show that <it>cheA-cheW </it>and <it>cheR-cheB </it>have strong preferences to occur in the same operon as two-gene blocks, which may reflect a functional requirement for co-transcription. However, other <it>che </it>genes, most notably <it>cheY</it>, are more dispersed on the genome. Comparison of our operons with shuffled equivalents demonstrates that specific patterns of genomic location may be a determining factor for the observed <it>in vivo </it>chemotaxis pathways.</p> <p>We then examined the chemotaxis pathways of <it>Rhodobacter sphaeroides</it>. Here, the PpfA protein is known to be critical for correct partitioning of proteins in the cytoplasmically-localised pathway. We found <it>ppfA </it>in <it>che </it>operons of many species, suggesting that partitioning of cytoplasmic Che protein clusters is common. We also examined the apparently non-typical chemotaxis components, CheA3, CheA4 and CheY6. We found that though variants of CheA proteins are rare, the CheY6 variant may be a common type of CheY, with a significantly disordered C-terminal region which may be functionally significant.</p> <p>Conclusions</p> <p>We find that many bacterial species potentially have multiple chemotaxis pathways, with grouping of <it>che </it>genes into operons likely to be a major factor in keeping signalling pathways distinct. Gene order is highly conserved with <it>cheA-cheW </it>and <it>cheR-cheB </it>blocks, perhaps reflecting functional linkage. CheY behaves differently to other Che proteins, both in its genomic location and its putative protein interactions, which should be considered when modelling chemotaxis pathways.</p

TRIM28-Regulated Transposon Repression Is Required for Human Germline Competency and Not Primed or Naive Human Pluripotency.

Transition from primed to naive pluripotency is associated with dynamic changes in transposable element (TE) expression and demethylation of imprinting control regions (ICRs). In mouse, ICR methylation and TE expression are each regulated by TRIM28; however, the role of TRIM28 in humans is less clear. Here, we show that a null mutation in TRIM28 causes significant alterations in TE expression in both the naive and primed states of human pluripotency, and phenotypically this has limited effects on self-renewal, instead causing a loss of germline competency. Furthermore, we discovered that TRIM28 regulates paternal ICR methylation and chromatin accessibility in the primed state, with no effects on maternal ICRs. Taken together, our study shows that abnormal TE expression is tolerated by self-renewing human pluripotent cells, whereas germline competency is not

A comparative analysis of DNA methylation across human embryonic stem cell lines

Abstract Background We performed a comparative analysis of the genome-wide DNA methylation profiles from three human embryonic stem cell (HESC) lines. It had previously been shown that HESC lines had significantly higher non-CG methylation than differentiated cells, and we therefore asked whether these sites were conserved across cell lines. Results We find that heavily methylated non-CG sites are strongly conserved, especially when found within the motif TACAG. They are enriched in splice sites and are more methylated than other non-CG sites in genes. We next studied the relationship between allele-specific expression and allele-specific methylation. By combining bisulfite sequencing and whole transcriptome shotgun sequencing (RNA-seq) data we identified 1,020 genes that show allele-specific expression, and 14% of CG sites genome-wide have allele-specific methylation. Finally, we asked whether the methylation state of transcription factor binding sites affects the binding of transcription factors. We identified variations in methylation levels at binding sites and found that for several transcription factors the correlation between the methylation at binding sites and gene expression is generally stronger than in the neighboring sequences. Conclusions These results suggest a possible but as yet unknown functional role for the highly methylated conserved non-CG sites in the regulation of HESCs. We also identified a novel set of genes that are likely transcriptionally regulated by methylation in an allele-specific manner. The analysis of transcription factor binding sites suggests that the methylation state of cis-regulatory elements impacts the ability of factors to bind and regulate transcription

Nanowrinkled Carbon Aerogels Embedded with FeN x Sites as Effective Oxygen Electrodes for Rechargeable Zinc-Air Battery.

Rational design of single-metal atom sites in carbon substrates by a flexible strategy is highly desired for the preparation of high-performance catalysts for metal-air batteries. In this study, biomass hydrogel reactors are utilized as structural templates to prepare carbon aerogels embedded with single iron atoms by controlled pyrolysis. The tortuous and interlaced hydrogel chains lead to the formation of abundant nanowrinkles in the porous carbon aerogels, and single iron atoms are dispersed and stabilized within the defective carbon skeletons. X-ray absorption spectroscopy measurements indicate that the iron centers are mostly involved in the coordination structure of FeN4, with a minor fraction (ca. 1/5) in the form of FeN3C. First-principles calculations show that the FeN x sites in the Stone-Wales configurations induced by the nanowrinkles of the hierarchically porous carbon aerogels show a much lower free energy than the normal counterparts. The resulting iron and nitrogen-codoped carbon aerogels exhibit excellent and reversible oxygen electrocatalytic activity, and can be used as bifunctional cathode catalysts in rechargeable Zn-air batteries, with a performance even better than that based on commercial Pt/C and RuO2 catalysts. Results from this study highlight the significance of structural distortions of the metal sites in carbon matrices in the design and engineering of highly active single-atom catalysts

Burkitt's Lymphoma Mimicking a Primary Gynecologic Tumor

SummaryObjectiveBurkitt's lymphoma (BL) occurs mostly in children; bilateral ovarian involvement mimicking a gynecologic malignancy in adults is extremely rare. Here, we report a patient with BL mimicking a gynecologic tumorCase ReportA 50-year-old Taiwanese woman presented with the complaint of persistent lower abdominal distension with dull pain, easy satiety, and progressively increasing abdominal girth for 2 weeks. Amenorrhea was also noted for about 2 months, and her review of systems was negative for the common “B” symptoms associated with lymphoma. At our hospital, imaging studies revealed a huge pelvic mass (10.8 ×8.7 cm), suggesting a large subserous myoma or an ovarian tumor. Under the impression of pelvic mass, she underwent exploratory laparotomy. Primary ovarian sex-cord malignancy with cecum involvement was impressed by the primitive intraoperative frozen section report. Subsequently, an optimal cytoreductive operation with right hemicolectomy was performed. However, final histopathologic report was an extranodal multifocal BL.ConclusionAlthough extranodal BL in ovaries is a rare condition, it should be noted in the differential diagnosis of pelvic gynecologic malignancies

MethylC-analyzer: A comprehensive downstream pipeline for the analysis of genome-wide DNA methylation

DNA methylation is a crucial epigenetic modification involved in multiple biological processes and diseases. Current approaches for measuring genome-wide DNA methylation via bisulfite sequencing (BS-seq) include whole-genome bisulfite sequencing (WGBS), reduced representation bisulfite sequencing (RRBS), and enzymatic methyl-seq (EM-seq). The computational analysis tools available for BS-seq data include customized aligners for mapping bisulfite-converted reads and computational pipelines for downstream data analysis. Current post-alignment methylation tools are specialized for the interpretation of CG methylation, which is known to dominate mammalian genomes, however, non-CG methylation (CHG and CHH, where H refers to A, C, or T) is commonly observed in plants and fungi and is closely associated with gene regulation, transposon silencing, and plant development. Thus, we have developed a MethylC-analyzer to analyze and visualize post-alignment WGBS, RRBS, and EM-seq data focusing on CG. The tool is able to also analyze non-CG sites to enhance deciphering genomes of plants and fungi. By processing aligned data and gene location files, MethylC-analyzer generates a genome-wide view of methylation levels and methylation in user-specified genomic regions. The meta-plot, for example, allows the investigation of DNA methylation within specific genomic elements. Moreover, our tool identifies differentially methylated regions (DMRs) and investigates the enrichment of genomic features associated with variable methylation. MethylC-analyzer functionality is not limited to specific genomes, and we demonstrated its performance on both plant and human BS-seq data. MethylC-analyzer is a Python- and R-based program designed to perform comprehensive downstream analyses of methylation data, providing an intuitive analysis platform for scientists unfamiliar with DNA methylation analysis. It is available as either a standalone version for command-line uses or a graphical user interface (GUI) and is publicly accessible at https://github.com/RitataLU/MethylC-analyzer