Biology subjects

Hong, S.

Publications and source records attributed to Hong, S..

5 recordsLinked to original sources

bioRxiv2018

Molecular characterization of the viral structural gene of the first dengue virus type 1 outbreak in Xishuangbanna, a border area of China, Burma and Laos

In the context of recent arbovirus epidemics, dengue fever is becoming a greater concern around the world. In August 2017, Xishuangbanna, which is a border city of China, Burma and Laos, had its first major dengue outbreak. A total of 156 serum samples from febrile patients were collected; 97 DENV positive serum samples were screened out, and viral RNAs were successfully and directly extracted, including 77 cases from China and 20 cases from Myanmar. Phylogenetic analysis revealed that all of the strains were classified as DENV-1. There are eight epidemic dengue strains from Myanmar and 74 from Jinghong, Xishuangbanna, that were classified as cluster 1, which are the most similar to the strain of China Guangzhou 2011. There are three epidemic strains from Xishuangbanna Mengla that were classified as cluster 2, which have the closest relationship to the strain of China Hubei 2014. However, there are 12 epidemic strains from Myanmar that were classified as cluster 3, which have the closest relationship to the strain of Laos from 2008, which shows that there is a recycling epidemic trend of DENV in China. There were 236 mutations in the base, which caused 31 nonsynonymous mutations in the DENV structural protein C/prM/E genes when the strain of Xishuangbanna and Myanmar were compared with the DENV-1SS. There is no clear homologous recombination signal among these stains. Homology modeling possibly predicted a three-dimensional structure of the structural protein of these strains and revealed that they had the same three-dimensional structure and all had five predicted protein binding sites, but there are differences in binding site 434 (DENV-1SS: Thr434, DV-Jinghong: Ser434, DV-Myanmar: Ser434, DV-Mengla: Ser434). The results of the molecular clock phylogenetic and demographic reconstruction analysis show that DENV-1 became highly diversified in 1972 followed by a slightly decreased period until 2017. In conclusion, our study lays the foundation for studying the global evolution and prevalence of DENV.\n\nAuthor SummaryDengue fever (DF) is a mosquito-borne illness caused by a flavivirus. Human infections with Dengue virus (DENV) could cause fever, cutaneous rash and malaise. Xishuangbanna, which is located in the southwestern Yunnan Province and is a border city with China, Burma and Laos, was reported to have outbreak of DENV in 2013 and 2015 with different types. However, there was a large outburst of dengue in May 2017. To understand the genetic characterization, potential source and evolution of the virus, 156 serum samples were analyzed. We focused on: (i) Phylogenetic analysis of the structural protein genes sequences; (ii) Mutation, recombination analysis and predicted protein binding sites of the structural protein genes; (iii) Molecular clock and demographic reconstruction of global dengue virus serotype 1(DENV-1). Our results indicated that this is the first outbreak of DENV-1 in Xishuangbanna, dengue epidemic strains on the Burma border of China show diversification, we found a virulence site changed from I to T(amino acid position: 440), which may lead to weakened virulence of the epidemic strains. We found that the evolution of DENV-1 is dominated by regional evolution. Whats more, DENV-1 became highly diversified in 1972 followed by a slightly decreased period until 2017.

epidemiology↗

bioRxiv2018

Altitudinal range-size distribution of breeding birds and environmental factors for the determination of species richness: An empirical test of altitudinal Rapoports rule and rescue effect on a local scale

Range-size distributions are important for understanding species richness patterns and led to the development of the controversial Rapoports rule and Rapoport-rescue effect. This study aimed to understand the relationship between species richness and range-size distribution in relation to environmental factors. The present study tested the following: (1) altitudinal Rapoports rule, (2) climatic and ambient energy hypotheses, (3) non-directional rescue effect, and (4) effect of environmental factors on range-size group. Altitudinal species range-size distribution increased with increasing altitude and showed a negative relationship with climatic variables and habitat heterogeneity, and a positive relationship with primary productivity. These results support the altitudinal Rapoports rule and climatic hypothesis; however, they do not fully support the ambient energy hypothesis. Results from testing the non-directional rescue effect showed that the inflow intensity of species from both directions (high and low elevations) affected species richness. And we found that the 2nd and 3rd quartile species distribution were the main cause of a mid-peak of species richness and the non-directional rescue effect. Additionally, the 2nd quartile species richness was highly related to minimum temperature and possessed thermal specialist species features, and the 3rd quartile species richness was highly related to habitat heterogeneity and primary productivity. Although altitudinal range-size distribution results were similar to the altitudinal Rapoports rule, the mid-peak pattern of species richness could not be explained by the Rapoports-rescue effect; however, the non-directional rescue effect could explain a mid-peak pattern of species richness.

ecology↗

bioRxiv2018

Bacterial Glycosyltransferase-mediated Cell-surface Chemoenzymatic Glycan Editing: Methods and Applications

AbstractChemoenzymatic glycan editing that modifies glycan structures directly on the cell surface has emerged as a complementary tool to metabolic oligosaccharide engineering. In this article, we report the discovery that three bacterial enzymes--Pasteurella multocida 2-3-sialyltransferase M144D mutant (Pm2,3ST-M144D), Photobacterium damsel 2-6-sialyltransferase (Pd2,6ST) and Helicobacter mustelae 1-2-fucosyltransferase (Hm1,2FT)--can serve as highly efficient tools for cell-surface glycan editing. Among these three enzymes, the two sialyltransferases were also found to be tolerant to large substituents introduced to the C-5 position of the cytidine monophosphate N-acetylneuraminic acid donor, including biotin and fluorescent dyes. Combining these enzymes with our previously discovered Helicobacter pylori 1-3-FT, we developed a live cell-based assay to probe host-cell glycan-mediated influenza A virus (IAV) infection including both wild-type and mutant strains of human H1N1 and H3N2 influenza subtypes. At high SiaNAc2-6-Gal levels, the ability of a viral strain to induce the host cell death is positively correlated with the SiaNAc2-6-Gal binding affinity of its haemagglutinin. Surprisingly, the creation of sLeX on the host cell surface via in situ 1-3-Fuc editing also exacerbated the killing induced by several wild-type IAV strains as well as a mutant known as HK68-MTA. Structural alignment of HAs from the wild-type HK68 and HK68-MTA revealed the formation of a putative hydrogen bond between Trp222 of HA-HK68-MTA and the C-4 hydroxyl group of the 1-3-linked fucose of sLeX. This interaction is likely to be responsible for the better binding affinity of HA-HK68-MTA to sLeX and accordingly the enhanced host-cell killing compared with the wild-type HK68.

biochemistry↗

bioRxiv2018

Dissection of the microProtein miP1 floral repressor complex in Arabidopsis

MicroProteins have emerged as potent regulators of transcription factor activity. Here we use a combination of forward genetics and proteomics to dissect the miP1a/b microProtein complex that acts to delay the floral transition in Arabidopsis. The microProteins miP1a and miP1b can bridge an interaction between the flowering promoting factor CONSTANS (CO) and the TOPLESS (TPL) co-repressor protein to represses flowering. We find that the JUMONJI14 (JMJ14) histone demethylase is part of this repressor complex that can initiate chromatin changes in FLOWERING LOCUS T (FT) gene, the direct target of CO. Plants with mutations in JMJ14 exhibit an early flowering phenotype that is largely dependent on the activity of CO, supporting a role for CO in this repressive complex. When mis-expressed at the shoot apex, CO can induce early flowering only in the jmj14 background. Our results indicate that the repressor acts in the shoot apical meristem to keep it in an undifferentiated state until the leaf-derived florigen signal induces the conversion into a floral meristem.

plant biology↗

bioRxiv2017

Single-Virion Sequencing Of Lamivudine Treated HBV Populations Reveal Population Evolution Dynamics And Demographic History

Viral populations are complex, dynamic, and fast evolving. The evolution of groups of closely related viruses in a competitive environment is termed quasispecies. To fully understand the role that quasispecies play in viral evolution, characterizing the trajectories of viral genotypes in an evolving population is the key. In particular, long-range haplotype information for thousands of individual viruses is critical; yet generating this information is non-trivial. Popular deep sequencing methods generate relatively short reads that do not preserve linkage information, while third generation sequencing methods have higher error rates that make detection of low frequency mutations a bioinformatics challenge. Here we applied BAsE-Seq, an Illumina-based single-virion sequencing technology, to eight samples from four chronic hepatitis B (CHB) patients - once before antiviral treatment and once after viral rebound due to resistance. We obtained 248-8,796 single-virion sequences per sample, which allowed us to find evidence for both hard and soft selective sweeps. We were also able to reconstruct population demographic history that was independently verified by clinically collected data. We further verified four of the samples independently on PacBio and Illumina sequencers. Overall, we showed that single-virion sequencing yields insight into viral evolution and population dynamics in an efficient and high throughput manner. We believe that single-virion sequencing is widely applicable to the study of viral evolution in the context of drug resistance, differentiating between soft or hard selective sweeps, and the reconstruction of intra-host viral population demographic history.

evolutionary biology↗