Succession of Composition and Function of Soil Bacterial Communities During Key Rice Growth Stages

Elucidating the succession of soil microbial communities and microbial functions at key plant growth stages is a major goal of microbial ecology research. In this study, we investigated the succession of soil bacteria during four fertilizer treatments (control, NPK, NPK + pig manure, and NPK + straw) and at three crucial rice growth stages (tillering, heading, and ripening) in paddy soil from a rice-wheat cropping system over a 10-year period. The results showed that the bacterial community and function composition of the control treatment was significantly different from that of the other treatments with NPK fertilizers, and S1 from others stages (ANOSIM, p < 0.05). The application of pig manure could reduce the effects of applying NPK fertilizers on bacterial communities in heading and ripening stages, but the effects of straw returning is not obvious. Variance partitioning analyses (VPA) suggested that pH, OM, and AK appeared to be key factors responsible for the microbial community changes observed in all the treatments or stages. The correlation results showed the bacterial families different between S1 and other stages such as Micromonosporaceae, Nocardioidaceae, Gaiellaceae, and Anaerolineaceae etc., were correlated with bacterial KEGG metabolic pathways. In addition, the topological of the soil bacterial community network with more nodes, links and higher Maximal degree at the heading stage and maintained relatively similar topological structures at the heading and ripening stages. However, the topological of the functional networks at the ripening stage were a small yet complicated co-occurring network with 209 nodes, 789 links, higher Average connectivity (avgK), and Maximal degree. These results suggest an obvious succession of soil bacteria and bacterial function at the key rice growth stages, but the topological of functional network structure of bacteria changes a little in the early and middle stages of rice, while its changes significantly in the ripening stage of rice growth

Genomic analysis of oesophageal squamous-cell carcinoma identifies alcohol drinking-related mutation signature and genomic alterations

Approximately half of the world's 500,000 new oesophageal squamous-cell carcinoma (ESCC) cases each year occur in China. Here, we show whole-genome sequencing of DNA and RNA in 94 Chinese individuals with ESCC. We identify six mutational signatures (E1–E6), and Signature E4 is unique in ESCC linked to alcohol intake and genetic variants in alcohol-metabolizing enzymes. We discover significantly recurrent mutations in 20 protein-coding genes, 4 long non-coding RNAs and 10 untranslational regions. Functional analyses show six genes that have recurrent copy-number variants in three squamous-cell carcinomas (oesophageal, head and neck and lung) significantly promote cancer cell proliferation, migration and invasion. The most frequently affected genes by structural variation are LRP1B and TTC28. The aberrant cell cycle and PI3K-AKT pathways seem critical in ESCC. These results establish a comprehensive genomic landscape of ESCC and provide potential targets for precision treatment and prevention of the cancer

QTL Mapping of Combining Ability and Heterosis of Agronomic Traits in Rice Backcross Recombinant Inbred Lines and Hybrid Crosses

BACKGROUND: Combining ability effects are very effective genetic parameters in deciding the next phase of breeding programs. Although some breeding strategies on the basis of evaluating combining ability have been utilized extensively in hybrid breeding, little is known about the genetic basis of combining ability. Combining ability is a complex trait that is controlled by polygenes. With the advent and development of molecular markers, it is feasible to evaluate the genetic bases of combining ability and heterosis of elite rice hybrids through QTL analysis. METHODOLOGY/PRINCIPAL FINDINGS: In the present study, we first developed a QTL-mapping method for dissecting combining ability and heterosis of agronomic traits. With three testcross populations and a BCRIL population in rice, biometric and QTL analyses were conducted for ten agronomic traits. The significance of general combining ability and special combining ability for most of the traits indicated the importance of both additive and non-additive effects on expression levels. A large number of additive effect QTLs associated with performance per se of BCRIL and general combining ability, and dominant effect QTLs associated with special combining ability and heterosis were identified for the ten traits. CONCLUSIONS/SIGNIFICANCE: The combining ability of agronomic traits could be analyzed by the QTL mapping method. The characteristics revealed by the QTLs for combining ability of agronomic traits were similar with those by multitudinous QTLs for agronomic traits with performance per se of BCRIL. Several QTLs (1-6 in this study) were identified for each trait for combining ability. It demonstrated that some of the QTLs were pleiotropic or linked tightly with each other. The identification of QTLs responsible for combining ability and heterosis in the present study provides valuable information for dissecting genetic basis of combining ability

Structural Dynamic of a Self-Assembling Peptide d-EAK16 Made of Only D-Amino Acids

We here report systematic study of structural dynamics of a 16-residue self-assembling peptide d-EAK16 made of only D-amino acids. We compare these results with its chiral counterpart L-form, l-EAK16. Circular dichroism was used to follow the structural dynamics under various temperature and pH conditions. At 25°C the d-EAK16 peptide displayed a typical beta-sheet spectrum. Upon increasing the temperature above 70°C, there was a spectrum shift as the 218 nm valley widens toward 210 nm. Above 80°C, the d-EAK16 peptide transformed into a typical alpha-helix CD spectrum without going through a detectable random-coil intermediate. When increasing the temperature from 4°C to 110°C then cooling back from 110°C to 4°C, there was a hysteresis: the secondary structure from beta-sheet to alpha-helix and then from alpha-helix to beta-sheet occurred. d-EAK16 formed an alpha-helical conformation at pH0.76 and pH12 but formed a beta-sheet at neutral pH. The effects of various pH conditions, ionic strength and denaturing agents were also noted. Since D-form peptides are resistant to natural enzyme degradation, such drastic structural changes may be exploited for fabricating molecular sensors to detect minute environmental changes. This provides insight into the behaviors of self-assembling peptides made of D-amino acids and points the way to designing new peptide materials for biomedical engineering and nanobiotechnology

The thermal behavior of d-EAK16.

<p>A d-EAK16 peptide sample was measured at 218 nm and 208 nm from 4°C to 110°C with incremental 2°C change. The temperature equilibration time is 30 seconds and averaging time is 1 second. After reaching 110°C and waiting for 1-minute, the cooling from 110°C to 4°C was initiated. The changes of ellipticity from 4°C to 110°C and from the 110 to 4°C were shown. After the temperature cycles, [θ]_218nm of d-EAK16 decreased ∼2%, but increased ∼13% at [θ]_208nm. A and B profiles refer to d-EAK16 ellipticity [θ]_218nm from 4°C to 110°C and back from 110°C to 4°C. On the other hand, C and D profiles refer to ellipticity [θ]_208nm from 4°C to 110°C and back from 110°C to 4°C.</p

Circular dichroism spectra of peptides d-EAK16 and l-EAK16 were in water at 25°C.

<p>X-axis is wavelength in nm and Y-axis is expressed as mole residue ellipticity [θ]. The mirror images of d-EAK16 and l-EAK16 reflect the molecular chirality.</p

Comparison of the Purity and Impurity of Glucagon-for-Injection Products under Various Stability Conditions

Glucagon is a polypeptide hormone that serves as an essential therapeutic agent in the emergency treatment of hypoglycemia. Recently, the first generic glucagon for injection was approved. However, unlike its brand name counterpart, which is produced via recombinant DNA, the generic glucagon is produced using a chemical synthesis method. Regardless of its origin, impurities may occur in both glucagon drug products. While these impurities may greatly compromise the safety and efficacy of the glucagon drug products, studies accessing the impurities of glucagon for injection are limited. This manuscript analyzed the stability and impurities of a generic and brand glucagon for injection, including desamido and non-desamido impurities, under various storage and temperature conditions using an ultra-performance liquid chromatography method. The glucagon products were analyzed after 6 and 24 months of storage under room temperatures (20&ndash;25 &deg;C). In addition, the products were also assessed after 6 months of storage under high temperatures (40 &deg;C). Under each stability storage condition, three lots of the synthetic glucagon were evaluated by UPLC with at least one lot of the recombinant glucagon for comparison. A total of 37 peaks were identified (except for the solvent peaks, which appeared at retention times less than 1.5 min) from the synthetic and recombinant glucagon lots. It was found that the number of impurities observed in the synthetic glucagon were lower than the referenced recombinant glucagon across all stability conditions. Throughout all tested conditions, the synthetic glucagon for injection had an averaged purity of 92.8&ndash;99.3%, while the referenced recombinant drug had an averaged purity of 70.3&ndash;91.7%. Based on the study results, it can be concluded that the impurity profile for the synthetic glucagon for injection has a comparable and even lower level of impurities than the recombinant version under all stability conditions