Single nucleotide polymorphisms in the mitochondrial displacement loop and outcome of esophageal squamous cell carcinoma

<p>Abstract</p> <p>Backgroud</p> <p>Accumulation of single nucleotide polymorphisms (SNPs) in the displacement loop (D-loop) of mitochondrial DNA (mtDNA) has been described for different types of cancers and might be associated with cancer risk and disease outcome. We used a population-based series of esophageal squamous cell carcinoma (ESCC) patients for investigating the prediction power of SNPs in mitochondrial D-loop.</p> <p>Methods</p> <p>The D-loop region of mtDNA was sequenced for 60 ESCC patients recorded in the Fourth Hospital of Hebei Medical University between 2003 and 2004. The 5 year survival curve were calculated with the Kaplan-Meier method and compared by the log-rank test at each SNP site, a multivariate survival analysis was also performed with the Cox proportional hazards method.</p> <p>Results</p> <p>The SNP sites of nucleotides 16274G/A, 16278C/T and 16399A/G were identified for prediction of post-operational survival by the log-rank test. In an overall multivariate analysis, the 16278 and 16399 alleles were identified as independent predictors of ESCC outcome. The length of survival of patients with the minor allele 16278T genotype was significantly shorter than that of patients with 16278C at the 16278 site (relative risk, 3.001; 95% CI, 1.029 - 8.756; <it>p </it>= 0.044). The length of survival of patients with the minor allele 16399G genotype was significantly shorter than that of patients with the more frequent allele 16399A at the 16399 site in ESCC patients (relative risk, 3.483; 95% CI, 1.068 - 11.359; <it>p </it>= 0.039).</p> <p>Conclusion</p> <p>Genetic polymorphisms in the D-loop are independent prognostic markers for patients with ESCC. Accordingly, the analysis of genetic polymorphisms in the mitochondrial D-loop can help identify patient subgroups at high risk of a poor disease outcome.</p

Response of Soil Fungal Community Structure to Long-Term Continuous Soybean Cropping

Long-term continuous soybean cropping can lead to the aggravation of soil fungal disease. However, the manner in which the fungal community and functional groups of fungi are affected by continuous soybean cropping remains unclear. We investigated the fungal abundance, composition and diversity during soybean rotation (RS), 2-year (SS) and long-term (CS) continuous soybean cropping systems using quantitative real-time PCR and high-throughput sequencing. The results showed that the fungal abundance was significantly higher in CS than in SS and RS. CS altered the fungal composition. Compared with RS, SS had an increase of 29 and a decrease of 12 genera in fungal relative abundance, and CS increased 38 and decreased 17 genera. The Shannon index was significantly higher in CS and SS than in RS. The result of principal coordinate analysis (PCoA) showed that CS and SS grouped together and were clearly separated from RS on the PCoA1. A total of 32 features accounted for the differences in fungal composition across RS, SS, and CS. The relative abundance of 10 potentially pathogenic and 10 potentially beneficial fungi changed, and most of their relative abundances dramatically increased in SS and CS compared with RS. Our study indicated that CS results in selective stress on pathogenic and beneficial fungi and causes the development of the fungal community structure that is antagonistic to plant health

Association Between the Methylation Statuses at CpG Sites in the Promoter Region of the SLCO1B3, RNA Expression and Color Change in Blue Eggshells in Lushi Chickens

The formation mechanism underlying the blue eggshell characteristic has been discovered in birds, and SLCO1B3 is the key gene that regulates the blue eggshell color. Insertion of an endogenous retrovirus, EAV-HP, in the SLCO1B3 5′ flanking region promotes SLCO1B3 expression in the chicken shell gland, and this expression causes bile salts to enter the shell gland, where biliverdin is secreted into the eggshell, forming a blue shell. However, at different laying stages of the same group of chickens, the color of the eggshell can vary widely, and the molecular mechanism underlying the eggshell color change remains unknown. Therefore, to reveal the molecular mechanism of the blue eggshell color variations, we analyzed the change in the eggshell color during the laying period. The results indicated that the eggshell color in Lushi chickens can be divided into three stages: 20–25 weeks for dark blue, 26–45 weeks for medium blue, and 46–60 weeks for light blue. We further investigated the expression and methylation levels of the SLCO1B3 gene at eight different weeks, finding that the relative expression of SLCO1B3 was significantly higher at 25 and 30 weeks than at other laying weeks. Furthermore, the overall methylation rate of the SLCO1B3 gene in Lushi chickens increased gradually with increasing weeks of egg production, as shown by bisulfite sequencing PCR. Pearson correlation analysis showed that methylation of the promoter region of SLCO1B3 was significantly negatively correlated with both SLCO1B3 expression in the shell gland tissue and eggshell color. In addition, we predicted that CpG5 and CpG8 may be key sites for regulating SLCO1B3 gene transcription. Our findings show that as the level of methylation increases, methylation of the CpG5 and CpG8 sites hinders the binding of transcription factors to the promoter, reducing SLCO1B3 expression during the late period and resulting in a lighter eggshell color

Corrigendum to: The TianQin project: current progress on science and technology

In the originally published version, this manuscript included an error related to indicating the corresponding author within the author list. This has now been corrected online to reflect the fact that author Jun Luo is the corresponding author of the article

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Inhibition of the ultrasonic microjet-pits on the carbon steel in the particles-water mixtures

In the incubation period of ultrasonic cavitation, due to the impact of microjets on the material surface, the needle-like microjet-pits are formed. Because the formation of microjet-pits relates with the evolution of cavitation erosion on engineering materials, corresponding study will promote the understanding on the mechanism of cavitation erosion. However, little study on the microjet-pits has been carried out, especially in the particles-water mixture. In this study, we firstly demonstrated the microjet-pits on the carbon steel would be significantly inhibited by Al particles in water. Such inhibition effect indicated that particular particles might not only provide growth sites for cavitation bubbles but also affect the collapse of cavitation bubbles near a solid surface. Our study deepened the understanding on the ultrasonic cavitation erosion in the particles-water mixture

Formation of the Self Assembled Structures by the Ultrasonic Cavitation Erosion-Corrosion Effect on Carbon Steel

The cavitation erosion-corrosion effect on the metal surface always forms irregular oxide structures. In this study, we reported the formation of regular self-assembled structures of amorphous nanoparticles around the cavitation erosion pits on carbon steel upon the ultrasonic cavitation in methylene blue solution. Each self-assembled structure was composed of linearly aligned nanoparticles of about 100 nm. The formation of self-assembled structures might be due to the combined effect of corrosion, specific sonochemical reaction in methylene blue solution, and the magnetic domain structures on the carbon steel

Effects of hydrogen atoms on surface conductivity of diamond film

To investigate the effects of surface chemisorbed hydrogen atoms and hydrogen atoms in the subsurface region of diamond on surface conductivity, models of hydrogen atoms chemisorbed on diamond with (100) orientation and various concentrations of hydrogen atoms in the subsurface layer of the diamond were built. By using the first-principles method based on density functional theory, the equilibrium geometries and densities of states of the models were studied. The results showed that the surface chemisorbed hydrogen alone could not induce high surface conductivity. In addition, isolated hydrogen atoms in the subsurface layer of the diamond prefer to exist at the bond centre site of the C-C bond. However, such a structure would induce deep localized states, which could not improve the surface conductivity. When the hydrogen concentration increases, the C-H-C-H structure and C-3Hbc-C structure in the subsurface region are more stable than other configurations. The former is not beneficial to the increase of the surface conductivity. However, the latter would induce strong surface states near the Fermi level, which would give rise to high surface conductivity. Thus, a high concentration of subsurface hydrogen atoms in diamond would make significant contributions to surface conductivity