Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes

BACKGROUND: Codon usage bias has been widely reported to correlate with GC composition. However, the quantitative relationship between codon usage bias and GC composition across species has not been reported. RESULTS: Based on an informatics method (SCUO) we developed previously using Shannon informational theory and maximum entropy theory, we investigated the quantitative relationship between codon usage bias and GC composition. The regression based on 70 bacterial and 16 archaeal genomes showed that in bacteria, SCUO = -2.06 * GC3 + 2.05*(GC3)(2 )+ 0.65, r = 0.91, and that in archaea, SCUO = -1.79 * GC3 + 1.85*(GC3)(2 )+ 0.56, r = 0.89. We developed an analytical model to quantify synonymous codon usage bias by GC compositions based on SCUO. The parameters within this model were inferred by inspecting the relationship between codon usage bias and GC composition across 70 bacterial and 16 archaeal genomes. We further simplified this relationship using only GC3. This simple model was supported by computational simulation. CONCLUSIONS: The synonymous codon usage bias could be simply expressed as 1+ (p/2)log(2)(p/2) + ((1-p)/2)log(2)((l-p)/2), where p = GC3. The software we developed for measuring SCUO (codonO) is available at

MAGEA1 inhibits the expression of BORIS via increased promoter methylation

Melanoma-associated antigen A1 (MAGEA1) and BORIS (also known as CTCFL) are members of the cancer testis antigen (CTA) family. Their functions and expression-regulation mechanisms are not fully understood. In this study, we reveal new functions and regulatory mechanisms of MAGEA1 and BORIS in breast cancer cells, which we investigated in parental and genetically manipulated breast cancer cells via gene overexpression or siRNA-mediated downregulation. We identified the interaction between MAGEA1 and CTCF, which is required for the binding of MAGEA1 to the BORIS promoter and is critical for the recruitment of DNMT3a. A protein complex containing MAGEA1, CTCF and DNMT3a was formed before or after conjunction with the BORIS promoter. The binding of this complex to the BORIS promoter accounts for the hypermethylation and repression of BORIS expression, which results in cell death in the breast cancer cell lines tested. Multiple approaches were employed, including co-immunoprecipitation, glutathione S-transferase pull-down assay, co-localization and cell death analyses using annexin V-FITC/propidium iodide double-staining and caspase 3 activation assays, chromatin immunoprecipitation and bisulfite sequencing PCR assays for methylation. Our results have implications for the development of strategies in CTA-based immune therapeutics

Effect of 1-MCP on storage quality and the mechanism involved in ethylene signal transduction in a new early-maturing apple variety ‘Taihangzaohong’ fruits during cold storage

1-Methylcyclopropene (1-MCP) can reduce the rate of fruit softening and prolong storage time. In this study, the fruit of a new early-maturing apple variety, ‘Taihangzaohong’, was treated with air (control), 2 μL/L 1-MCP, 100 μL/L ethylene (C 2H4) or 2 μL/L 1-MCP +100 μL/L C2H4 for 24 hours and then stored at 4 °C for 70 days. The postharvest physiological indices and the expression of 13 genes related to ethylene biosynthesis and signal transduction were monitored every 10 days. The results showed that 1-MCP can delay the softening rate and maintain the fruit quality of this early-maturing apple variety by reducing ethylene production by reducing the expression of MdACO1, MdACO2, and MdACS1, as well as by preventing ethylene signal transduction by decreasing the expression of MdETR2 and MdERS1 and increasing the expression of MdCTR1. Understanding the significant changes in these genes and their functions may help us explore the mechanisms controlling apple fruit softening and its response to exogenous 1-MCP and ethylene stimuli, as well as inhibition at the receptor level during ripening and senescence

Glucocorticosteroid-sensitive inflammatory eosinophilic pseudotumor of the bladder in an adolescent: a case report

<p>Abstract</p> <p>Introduction</p> <p>Inflammatory eosinophilic pseudotumor of the bladder is a rare inflammatory bladder disease. The etiology and pathophysiology of this condition are still unclear. Few case reports have described inflammatory eosinophilic pseudotumor of the bladder in adults or children. Although benign, this disease is occasionally clinically aggressive and locally invasive, thus open surgical removal or complete transurethral resection is recommended.</p> <p>Case presentation</p> <p>We present the case of a biopsy-proven inflammatory eosinophilic pseudotumor of the bladder in a previously healthy 16-year-old male adolescent with 2-month history of frequent micturition and dysuria with no significant apparent causative factors. The tumor regressed after a 6-week course of glucocorticosteroids.</p> <p>Conclusion</p> <p>To the best of our knowledge, our case is a rare case of inflammatory eosinophilic pseudotumor of the bladder treated with complete conservative management. Due to its glucocorticosteroid-sensitive nature, we postulate that this disease belongs to a subgroup of eosinophilic disorders.</p

Multilevel Nitrogen Additions Alter Chemical Composition and Turnover of the Labile Fraction Soil Organic Matter via Effects on Vegetation and Microorganisms

Global nitrogen (N) deposition greatly impacts soil carbon sequestration. A 2- yr multiple N addition (0, 10, 20, 40, 80, and 160 kg N·ha- 1·yr- 1) experiment was conducted in alpine grassland to illustrate the mechanisms underlying the observed soil organic matter (SOM) dynamics on the Qinghai- Tibet Plateau (QTP). Labile fraction SOM (LF- SOM) fingerprints were characterized by pyrolysis- gas chromatography/tandem- mass spectrometry, and microbial functional genes (GeoChip 4.6) were analyzed in conjunction with LF- SOM fingerprints to decipher the responses of LF- SOM transformation to N additions. The significant correlations between LF- SOM and microbial biomass, between organic compounds in LF- SOM and compound degradation- related genes, and between LF- SOM and net ecosystem exchange implied LF- SOM were the main fraction utilized by microorganisms and the most sensitive fraction to N additions. The LF- SOM increased at the lowest N addition levels (10 and 20 kg N·ha- 1·yr- 1) and decreased at higher N addition levels (40 to 160 kg N·ha- 1·yr- 1), but the decrease of LF- SOM was weakened at 160 kg N·ha- 1·yr- 1 addition. The nonlinear response of LF- SOM to N additions was due to the mass balance between plant inputs and microbial degradation. Plant- derived compounds in LF- SOM were more sensitive to N addition than microbial- derived and aromatic compounds. It is predicted that when the N deposition rate increased by 10 kg N·ha- 1·yr- 1 on the QTP, carbon sequestration in the labile fraction may increase by nearly 170% compared with that under the current N deposition rate. These findings provide insight into future N deposition impacts on LF- SOM preservation on the QTP.Key PointsThe LF- SOM quantity increased at the lowest N additions (N10 and N20) and decreased from N40 to N160, but the decrease was weakened at the highest N addition (N160)Plant- derived compounds in LF- SOM were more sensitive to N addition than microbial- derived and aromatic compoundsThe organic compounds in LF- SOM were significantly correlated with compound degradation- related genesPeer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154963/1/jgrg21637_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154963/2/jgrg21637.pd

Tolerance of transgenic Arabidopsis thaliana overexpressing apple MdAGO4.1 gene to drought and salt stress

The regulatory role of apple MdAGO4.1 gene in plant drought and salt resistance is unclear. In this study, transgenic A. thaliana in which the apple MdAGO4.1 gene was over-expressed was used to analyze the regulatory effects of the MdAGO4.1 gene on plant drought and salt resistance, to verify the function of the apple MdAGO4.1 gene. The seed germination rate, seedling fresh weight and root length of transgenic Arabidopsis strains in MS medium containing different concentrations of NaCl and mannitol were better than those of the wild type. The transgenic A. thaliana seedlings were more resistant to drought than wild type under drought stress. The transgenic strains were less affected by salt stress than thewild type. Exposure to drought and salt stress reduced the relative elektrolyte leakage, malondialdehyde (MDA), superoxide anion (O2-), and hydrogen peroxide (H2O2) levels of the transgenic strain significantly compared with the levels in the wild type. The levels of proline, protective enzyme activities, and the expression of genes related to drought and salt stress resistance were significantly higher than those of the wild type. These results indicate that MdAGO4.1 overexpression improved drought and salt tolerance in transgenic Arabidopsis. This study can provide a theoretical basis for future research on stress tolerance mechanisms and breeding new varieties of fruit trees resistant to drought and salt

Quality-of-life outcomes and unmet needs between ileal conduit and orthotopic ileal neobladder after radical cystectomy in a Chinese population: a 2-to-1 matched-pair analysis

Peri-operative outcomes. (DOCX 15 kb

Effects of substituting rare-earth ion R by non-magnetic impurities in R2BaNiO5R_2BaNiO_5 - theory and numerical DMRG results

In this paper we study the effect of substituting R (rare-earth ion) by non-magnetic ions in the spin-1 chain material $R_2BaNiO_5$. Using a strong-coupling expansion and numerical density matrix renormalization group calculations, we show that spin-wave bound states are formed at the impurity site. Experimental consequences of the bound states are pointed out.Comment: 5 pages, 4 postscript figure

Microbial Electricity Generation Enhances Decabromodiphenyl Ether (BDE-209) Degradation

We thank Hao Yu and Ye Deng at the University of Oklahoma for assistance with GeoChip hybridization and data pre-processing. We also thank Professor Bixian Mai and Dr. Leheng Yu in Guangzhou Institute of Geochemistry, CAS, for their helps in PBDE congener analyses.Conceived and designed the experiments: MYX JG GPS. Performed the experiments: YGY MYX. Analyzed the data: MYX YGY. Contributed reagents/materials/analysis tools: ZLH JZZ. Wrote the paper: MYX YGY ZLH.Due to environmental persistence and biotoxicity of polybrominated diphenyl ethers (PBDEs), it is urgent to develop potential technologies to remediate PBDEs. Introducing electrodes for microbial electricity generation to stimulate the anaerobic degradation of organic pollutants is highly promising for bioremediation. However, it is still not clear whether the degradation of PBDEs could be promoted by this strategy. In this study, we hypothesized that the degradation of PBDEs (e.g., BDE-209) would be enhanced under microbial electricity generation condition. The functional compositions and structures of microbial communities in closed-circuit microbial fuel cell (c-MFC) and open-circuit microbial fuel cell (o-MFC) systems for BDE-209 degradation were detected by a comprehensive functional gene array, GeoChip 4.0, and linked with PBDE degradations. The results indicated that distinctly different microbial community structures were formed between c-MFCs and o-MFCs, and that lower concentrations of BDE-209 and the resulting lower brominated PBDE products were detected in c-MFCs after 70-day performance. The diversity and abundance of a variety of functional genes in c-MFCs were significantly higher than those in o-MFCs. Most genes involved in chlorinated solvent reductive dechlorination, hydroxylation, methoxylation and aromatic hydrocarbon degradation were highly enriched in c-MFCs and significantly positively correlated with the removal of PBDEs. Various other microbial functional genes for carbon, nitrogen, phosphorus and sulfur cycling, as well as energy transformation process, were also significantly increased in c-MFCs. Together, these results suggest that PBDE degradation could be enhanced by introducing the electrodes for microbial electricity generation and by specifically stimulating microbial functional genes.Yeshttp://www.plosone.org/static/editorial#pee