Characterization of Synonymous Codon Usage Bias in the Pseudorabies Virus US1 Gene

In the present study, we examined the codon usage bias between pseudorabies virus (PRV) US1 gene and the US1-like genes of 20 reference alphaherpesviruses. Comparative analysis showed noticeable disparities of the synonymous codon usage bias in the 21 alphaherpesviruses, indicated by codon adaptation index, effective number of codons (ENc) and GC3s value. The codon usage pattern of PRV US1 gene was phylogenetically conserved and similar to that of the US1-like genes of the genus Varicellovirus of alphaherpesvirus, with a strong bias towards the codons with C and G at the third codon position. Cluster analysis of codon usage pattern of PRV US1 gene with its reference alphaherpesviruses demonstrated that the codon usage bias of US1-like genes of 21 alphaherpesviruses had a very close relation with their gene functions. ENc-plot revealed that the genetic heterogeneity in PRV US1 gene and the 20 reference alphaherpesviruses was constrained by G+C content, as well as the gene length. In addition, comparison of codon preferences in the US1 gene of PRV with those of E. coli, yeast and human revealed that there were 50 codons showing distinct usage differences between PRV and yeast, 49 between PRV and human, but 48 between PRV and E. coli. Although there were slightly fewer differences in codon usages between E.coli and PRV, the difference is unlikely to be statistically significant, and experimental studies are necessary to establish the most suitable expression system for PRV US1. In conclusion, these results may improve our understanding of the evolution, pathogenesis and functional studies of PRV, as well as contributing to the area of herpesvirus research or even studies with other viruses.

Effect of Down-regulated Expression of cPouV and cNanog on Pluripotency of Chicken(Gallus gallus) Embryonic Stem Cells(cESCs)

To explore the pluripotency maintenance and update the functional influence of pluripotency genes cNanog and cPouV in chicken （ C,a/lus gallus） embry- onic stem cells （ cESCs）, the stable RNAi vectors pSuper-cNanog and pSuper-cPouV constructed previously were used to transfect cESCs. The mRNA levels of two target genes were detected with real- time PCR. These two genes were down-regulated since the 48^th and the down-reg-lation continued with the extension of time, the interference efficiency reached 65% at 96^th hour （P 〈0.05）. With the down-regulation of cNanog or cPouV gene, cESCs showed differentiation and prolifera- tion rate of these cells slowed down, the domed colony of these cells disappeared gradually when the edge of colony became irregular. At 96^th hour after transfection, the alkline phosphatase （AKP） and stage-specific embryonic antigen-1 （ SSEA-1 ） were not be detected in cNanog gene-knecked out eESCs, but it was done in that with cPouV gene -knocked out. The cPouV-suppressing cESCs were again transfected with pSuper-cNanog, the pluripotency markers AKP and SSEA-1 were both not found expressing at the 48^th hour. The results showed that cPouV and cNartog genes played an important role in maintaining pluripotency and self- renewal in cESCs, and cNanog gene was dominant. To sum up, our results may provide insights into the molecular regulation mechanism of avian during development.

Chicken Mesenchymal Stem Cells as Feeder Cells Facilitate the Cultivation of Primordial Germ Cells from Circulating Blood and Gonadal Ridge

Long-term maintenance of chicken primordial germ cells (PGCs) in vitro has tremendous potential for transgenic chicken production. Feeder cells are essential for the establishment and culture of chicken PGCs in vitro. Buffalo rat liver (BRL) cells are the most commonly used feeder cells for PGCs culture;however, this feeder layers from other animal species usually cause immunogenic contaminations, compromising the potential of PGCs in applications. Therefore, we tested chicken source mensenchymal stem cell (MSCs) derived from bone marrow as feeder cells to further improve PGC culture conditions. MSCs derived from chicken bone marrow have a powerful capacity to proliferate and secrete cytokines. We found chicken primordial germ cells derived from circulating blood (cPGCs) and gonads (gPGCs) can be maintained and proliferated with MSCs feeder layer cells. PGCs co-cultured on MSCs feeder retained their pluripotency, expressed PGCs specific genes and stemness markers, and maintained undifferentiated state. Our study indicated that the xeno-free MSCs-feeders culture system is a good candidate for growth and expansion of PGCs as the stepping stone for transgenic chicken research.

Differences in Atmospheric Heat Source between the Tibetan Plateau–South Asia Region and the Southern Indian Ocean and Their Impacts on the Indian Summer Monsoon Outbreak

In this paper, the NCEP-NCAR daily reanalysis data are used to investigate the characteristics of the atmospheric heat source/sink （AHSS） over South Asia （SA） and southern Indian Ocean （SIO）. The thermal differences between these two regions and their influence on the outbreak of the Indian summer monsoon （ISM） are explored. Composite analysis and correlation analysis are applied. The results indicate that the intraseasonal variability of AHSS is signi- ficant in SA but insignificant in the SIO. Large inland areas in the Northern Hemisphere still behave as a heat sink in March, similar to the situation in winter. Significant differences are found in the distribution of AHSS between the ocean and land, with distinct land-ocean thermal contrast in April, and the pattern presents in the transitional period right before the ISM onset. In May, strong heat centers appear over the areas from the Indochina Peninsula to the Bay of Bengal and south of the Tibetan Plateau （TP）, which is a typical pattern of AHSS distribution during the monsoon season. The timing of SA-SIO thermal difference turning positive is about 15 pentads in advance of the onset of the ISM. Then, after the thermal differences have turned positive, a pre-monsoon meridional circulation cell develops due to the near-surface heat center and the negative thermal contrast center, after which the meridional circulation of the ISM gradually establishes. In years of early （late） conversion of the SASIO thermal difference turning from neg- ative to positive, the AHSS at all levels over the TP and SIO converts later （earlier） than normal and the establish- ment of the ascending and descending branches of the ISM＇s meridional circulation is later （earlier） too. Meanwhile, the establishment of the South Asian high over the TP is later （earlier） than normal and the conversion of the Mas- carene high from winter to summer mode occurs anomalously late （early）. As a result, the onset of the ISM is later （earlier） than normal. However, the difference in vorticity between early and late conversion only shows in the changes of strong vorticity centers＇ location in the upper and lower troposphere.

Characteristics and Possible Formation Mechanisms of Severe Storms in the Outer Rainbands of Typhoon Mujigae(1522)

To better understand how severe storms form and evolve in the outer rainbands of typhoons, in this study, we in- vestigate the evolutionary characteristics and possible formation mechanisms for severe storms in the rainbands of Typhoon Mujigae, which occurred during 2-5 October 2015, based on the NCEP-NCAR reanalysis data, conventional observations, and Doppler radar data. For the rainbands far from the inner core （eye and eyewall） of Mujigae （dis- tance of approximately 70-800 kin）, wind speed first increased with the radius expanding from the inner core, and then decreased as the radius continued to expand. The Rankine Vortex Model was used to explore such variations in wind speed. The areas of strong stormy rainbands were mainly located in the northeast quadrant of Mujigae, and overlapped with the areas of high winds within approximately 300-550 km away from the inner core, where the strong winds were conducive to the development of strong storms. A severe convective cell in the rainbands de- veloped into waterspout at approximately 500 km to the northeast of the inner core, when Mujigae was strengthening before it made landfall. Two severe convective cells in the rainbands developed into two tornadoes at approximately 350 km to the northeast of the inner core after Mujigae made landfall. The radar echo bands enhanced to 60 dBZ when mesocyclones occurred in the rainbands and induced tornadoes. The radar echoes gradually weakened after the mesocyclones weakened. The tops of parent clouds of the mesocyclones elevated at first, and then suddenly dropped about 20 min before the tornadoes appeared. Thereby, the cloud top variation has the potential to be used as an early warning of tornado occurrence.