Low-coverage sequencing in a deep intercross of the Virginia body weight lines provides insight to the polygenic genetic architecture of growth: novel loci revealed by increased power and improved genome-coverage

Genetic dissection of highly polygenic traits is a challenge, in part due to the power necessary to confidently identify loci with minor effects. Experimental crosses are valuable resources for mapping such traits. Traditionally, genome-wide analyses of experimental crosses have targeted major loci using data from a single generation (often the F₂) with individuals from later generations being generated for replication and fine-mapping. Here, we aim to confidently identify minor-effect loci contributing to the highly polygenic basis of the long-term, bi-directional selection responses for 56-d body weight in the Virginia body weight chicken lines. To achieve this, a strategy was developed to make use of data from all generations (F₂-F₁₈) of the advanced intercross line, developed by crossing the low and high selected lines after 40 generations of selection. A cost-efficient low-coverage sequencing based approach was used to obtain high-confidence genotypes in 1Mb bins across 99.3% of the chicken genome for >3,300 intercross individuals. In total, 12 genome-wide significant, and 30 additional suggestive QTL reaching a 10% FDR threshold, were mapped for 56-d body weight. Only 2 of these QTL reached genome-wide significance in earlier analyses of the F₂ generation. The minor-effect QTL mapped here were generally due to an overall increase in power by integrating data across generations, with contributions from increased genome-coverage and improved marker information content. The 12 significant QTL explain >37% of the difference between the parental lines, three times more than 2 previously reported significant QTL. The 42 significant and suggestive QTL together explain >80%. Making integrated use of all available samples from multiple generations in experimental crosses are economically feasible using the low-cost, sequencing-based genotyping strategies outlined here. Our empirical results illustrate the value of this strategy for mapping novel minor-effect loci contributing to complex traits to provide a more confident, comprehensive view of the individual loci that form the genetic basis of the highly polygenic, long-term selection responses for 56-d body weight in the Virginia body weight chicken lines.

Phase Segregated Pt-SnO2 /C Nanohybrids for Highly Efficient Oxygen Reduction Electrocatalysis

Strengthening the interfacial interaction in heterogeneous catalysts can lead to a dramatic improvement in their performance and allow the use of smaller amounts of active noble metal, thus decreasing the cost without compromising their activity. In this work, a facile phase-segregation method is demonstrated for synthesizing platinum-tin oxide hybrids supported on carbon black (PtSnO₂ /C) in situ by air annealing PtSn alloy nanoparticles on carbon black. Compared with a control sample formed by preloading SnO₂ on carbon support followed by deposition of Pt nanoparticles, the phase-segregation-derived PtSnO₂ /C exhibits a more strongly coupled PtSnO₂ interface with lattice overlap of Pt (111) and SnO₂ (200), along with enhanced electron transfer from SnO₂ to Pt. Furthermore, the PtSnO₂ active sites show a strong ability to degrade reactive oxygen species. As a result, the PtSnO₂ /C nanohybrids exhibit both excellent activity and stability as a catalyst for the oxygen reduction reaction, with an overall performance which is superior to both the control sample and commercial Pt/C catalyst. This phase-segregation method can be expected to be applicable in the preparation of other strongly coupled nanohybrids and offers a new route to high-performance heterogeneous catalysts for low-cost energy conversion devices.

Prussian blue nanocubes decorated on nitrogen-doped hierarchically porous carbon network for efficient sorption of radioactive cesium

Eliminating the radioactive ¹³⁷Cs from nuclear waste is critical to the human health and environment. Prussian blue (PB)-based materials are considered as promising adsorbents for the removal of cesium. Herein, we demonstrate a facile strategy to achieve controllable synthesis of PB nanocrystals decorated on nitrogen-doped hierarchically porous carbon (NHPC) derived from cattle bone as adsorbent to remove cesium. The PB nanocrystals with a nanocube morphology are well distributed on NHPC, which is beneficial to increase the reachable surface area during adsorption. The resulting adsorbent exhibits a remarkable adsorption performance with a capacity of 125.31 mg g^-1, a superior recyclability with 87 % of initial capacity retained after 5 cycles, and an outstanding adsorption selectivity for cesium. X-ray diffraction, X-ray photoelectron spectroscopy combined with ⁵⁷Fe Mössbauer spectroscopy results reveal that cesium ions are inserted into the crystal channels of PB to generate a new phase (CsFe₂(CN)₆·3H₂O) after adsorption. Moreover, the adsorption process is spontaneous and endothermic which can be described by the Langmuir isotherm and pseudo-second-order kinetic models. This strategy for synthesis of PB/carbon adsorbents offers efficient candidate for removal of ¹³⁷Cs from wastewater.

A genomic inference of the White Plymouth Rock genealogy

Crossing of populations has been, and still is, a central component in domestication and breed and variety formation. It is a way for breeders to utilize heterosis and to introduce new genetic variation into existing plant and livestock populations. During the mid-19th century, several chicken breeds that had been introduced to America from Europe and Asia became the founders for those formed in the USA. Historical records about the genealogy of these populations are often unclear and inconsistent. Here, we used genomics in an attempt to describe the ancestry of the White Plymouth Rock (WPR) chicken. In total, 150 chickens from the WPR and 8 other stocks that historical records suggested contributed to its formation were whole-genome re-sequenced. The admixture analyses of the autosomal and sex chromosomes showed that the WPR was likely founded as a cross between a paternal lineage that was primarily Dominique, and a maternal lineage where Black Java and Cochin contributed in essentially equal proportions. These results were consistent and provided quantification with the historical records that they were the main contributors to the WPR. The genomic analyses also revealed genome-wide contributions (<10% each) by Brahma, Langshan, and Black Minorca. When viewed on an individual chromosomal basis, contributions varied considerably among stocks.

Sustainable Carbonaceous Materials Derived from Biomass as Metal-Free Electrocatalysts

Although carbon is the second most abundant element in the biosphere, a large proportion of the available carbon resources in biomass from agriculture, stock farming, ocean fisheries, and other human activities is currently wasted. The use of sustainable carbonaceous materials as an alternative to precious metals in electrocatalysis is a promising pathway for transforming sustainable biomass resources into sustainable energy-conversion systems. The development of rational syntheses of metal-free carbonaceous catalysts derived from sustainable biomass has therefore become a topic of significant interest in materials chemistry. However, great efforts are still required to develop methods that are low cost, scalable, and environmentally friendly and which afford carbonaceous materials having an electrocatalytic performance comparable to, or even better than, existing precious metal catalysts. Herein, recent achievements in developing metal-free carbonaceous catalysts based on biomass are reviewed and discussed and the critical issues which still need to be addressed are highlighted. The focus is on representative synthesis and optimization strategies applicable to different kinds of biomass, as well as studies of the physicochemical structure and electrochemical performance of the resulting metal-free carbonaceous catalysts. Finally, some guidelines for the future development of this important area are provided.

Enhancement mechanism of sulfur dopants on the catalytic activity of N and P co-doped three-dimensional hierarchically porous carbon as a metal-free oxygen reduction electrocatalyst

A sulfur, nitrogen and phosphorus ternary-doped cattle-bone-derived hierarchically porous carbon metal-free electrocatalyst was synthesized, exhibiting superior oxygen reduction performance compared to Pt/C.

Biomass-derived nitrogen-doped hierarchically porous carbon networks as efficient absorbents for phenol removal from wastewater over a wide pH range

Biomass-derived nitrogen-doped hierarchically porous carbon adsorbent was synthesized and exhibited an excellent adsorption performance for phenol removal.

Progress of Experimental Research on Nuclear Safety in NPIC

Two kinds of Generation III commercial nuclear power plants have been developed in CNNC (China National Nuclear Corporation), one is a small modular reactor ACP100 having an equivalent electric power 100 MW, and the other is HPR1000 (once named ACP1000) having an equivalent electric power 1 000 MW. Both NPPs widely adopted the design philosophy of advanced passive safety systems and considered the lessons from Fukushima Daichi nuclear accident. As the backbone of the R&D of ACP100 and HPR1000, NPIC (Nuclear power Institute of China) has finished the engineering verification test of main safety systems, including passive residual heat removal experiments, reactor cavity injection experiments, hydrogen combustion experiments, and passive autocatalytic recombiner experiments. Above experimental work conducted in NPIC and further research plan of nuclear safety are introduced in this paper.

Characterizing a rat Brca2 knockout model

Evidence exists that BRCA2 carriers may have an elevated risk of breast, ovarian, colon, prostate, and pancreatic cancer. In general, carriers are defined as individuals with protein truncating mutations within the BRCA2 gene. Many Brca2 knockout lines have been produced and characterized in the mouse. We previously produced a rat Brca2 knockout strain in which there is a nonsense mutation in exon 11 between BRC repeats 2 and 3, and a truncated protein is produced. Interestingly, while such a mutation in homozygous mice would lead to limited survival of approximately 3 months, the Brca2-/- rats are 100% viable and the vast majority live to over 1 year of age. Brca2-/- rats show a phenotype of growth inhibition and sterility in both sexes. Aspermatogenesis in the Brca2-/- rats is due to a failure of homologous chromosome synapsis. Long-term phenotypes include underdeveloped mammary glands, cataract formation and lifespan shortening due to the development of tumors and cancers in multiple organs. The establishment of the rat Brca2 knockout model provides a means to study the role of Brca2 in increasing cancer susceptibility and inducing a novel ocular phenotype not previously associated with this gene.

Expression and glycosylation of rotavirus strain SA11 VP4 protein in a recombinant adenovirus

OBJECTIVE

Using a recombinant human adenovirus to express modified VP4 gene of rotavirus SA11 strain.

METHODS

A whole VP4 gene was obtained with PCR and induced the signal peptide at the gene N terminal. The chimera gene was cloned into pCMV plasmid that consists of human cytomegalovirus promoter, and then the gene was cloned to the transfer vector of human adenovirus type 5. Homologous recombination was performed by co-transfection to 293 cell lines with recombinant plasmid and viral genome using CaPO4 precipitation.

RESULTS

No mutation was found in the whole VP4 gene sequence of 2362 base pair. The expressed product in recombinant adenovirus was confirmed to be specific and more antigenicity by indirect immunofluorescence assay. Both the Western blot and immunoprecipitation assay showed that the molecular mass of the expressed protein was higher than the wild type VP4 protein, and that the modified product was corresponding to a glycosylation of VP4 protein.

CONCLUSION

To modify the target gene might be an effective method to enhance the stability, antigenicity and immunogenicity of expressed protein.

[Synthesis of hirudin variant 1 (HV1) gene and primary study of expression in yeast]

OBJECTIVE

Hirudin is an extremely efficient and specific thrombin inhibitor. It is clinically used to prevent the formation of thrombus. In this research the hirudin gene was put into yeast system for expression to evaluate the feasibility of artificially synthesized gene expressed in eukaryotic system and study the factor affecting expression level.

METHODS

According to the amino acid sequence of hirudin variant 1 (HV1), the genetic code saccharomyces cerevisiae was used to design and synthesize the HV1 gene. Amplified by PCR, it was inserted into cloning vector pBS-SK(+) and sequenced. Ligation with the signal peptide gene of yeast alpha factor the correct HV1 gene was inserted into yeast expression vector pYC-DE. The recombinant plasmid was transformed into the cell of S. cerevisiae BJ1990 to carry out the primary expression experiment.

RESULTS

In cultured supernatant of screened positive clone the hirudin activity was detected to be 30 ATU/ml. The expression level was higher than HV2 in yeast and HV1 in prokaryotic system. The N terminal amino acid sequence completely matches with natural hirudin.

CONCLUSIONS

It was proved by this study that the synthesized hirudin gene had been expressed in yeast successfully. This result showed that it was a better way to carry out the expression in yeast using synthesized HV1 gene and a stronger promoter.

[The construction of poliovirus chimera and the analysis of its antigenic structure]

The construction of poliovirus chimera is an useful way to investigate the antigenic structure conformation of poliovirus. In this research, the poliovirus chimera containing a piece of antigenic fragment of hepatitis A virus was constructed for analysis of poliovirus antigenic structure conformation. Depending on the characterization of this chimera, the conformation of poliovirus neutralization antigenic site I in VP1 was analyzed, and that the possible influence of hepatitis A virus antigenic fragment inserted to the structure conformation of poliovirus antigen was also investigated.