Biology subjects

Pan, Y.

Publications and source records attributed to Pan, Y..

7 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

A molecular model of the surface-assisted protein aggregation process

The importance of cell surfaces in the self-assembly of proteins is widely accepted. One biologically significant event is the assembly of amyloidogenic proteins into aggregates, which leads to neurodegenerative disorders like Alzheimers and Parkinsons. The interaction of amyloidogenic proteins with cellular membranes appears to dramatically facilitate the aggregation process. Recent findings indicate that, in the presence of surfaces, aggregation occurs at physiologically low concentrations, suggesting interaction with surfaces plays a critical role in the disease-prone aggregation process. However, the molecular mechanisms behind on-surface aggregation remain unclear. Here we provide a theoretical model that offers a molecular explanation. According to this model, monomers transiently immobilized to surfaces increase the local monomer protein concentration and thus work as nuclei to dramatically accelerate the entire aggregation process. This theory was verified by experimental studies, using mica surfaces, to examine the aggregation kinetics of amyloidogenic-synuclein protein (-Syn) and non-amyloidogenic cytosine deaminase APOBEC3G (A3G).

biophysics↗

bioRxiv2018

Coverage-based detection of copy number alterations in mixed samples using DNA sequencing data: a theoretical framework for evaluating statistical power

1DNA sequencing can discover not only single-base variants but also copy-number alterations (CNAs). In shotgun sequencing, regions of CNAs show step-wise changes in read depth when compared to adjacent \"normal\" regions, allowing their detection by parametric statistical tests that compare the mean coverage in suspected regions against that of a baseline distribution. Traditionally, the power of such a test depends on (1) the integer number of copy number change, (2) the overall sequencing depth, (3) the length of the CNA region, (4) the read length and (5) the variation of coverage along the genome, which depends on many experimental factors, including whether the chosen platform is whole-genome, whole-exome, or targeted-panel sequencing. In cases involving inadvertent sample mixing or genuine somatic mosaicism, power also depends on the mixing ratio. However, the analysis of statistical power that considers the interplay of all these factors has not been systematically developed. Here we present a general analytical framework and a series of simulations that explore situations from the simplest to the increasingly multifactorial. Specifically, we expand the expression of power to include not just the known factors but also one or both of two complications: (1) the dispersion of read depth around the mean beyond the independent sampling-by-sequencing assumption, and (2) the reduced fraction of the CNA-bearing sample (\"purity\") as seen in studies of intratumor heterogeneity or in clinical monitoring of minimal residual disease. We describe the analytical formula and their simplifications in special cases, and share the extendable scripts for others to perform customized power analysis using study-specific parameters. As study designs vary and technologies continue to evolve, the input data and the noise characteristics will change depending on the practical situation. We present two use cases commonly encountered in cancer research: ultra-shallow whole-genome sequencing for detecting large, chromosome-scale events, and targeted ultra-deep sequencing for surveillance of known CNAs in rare tumor clones in the task of sensitive detection of cancer relapse or metastasis. We also present an online calculator at https://shiny.med.umich.edu/apps/hanyou/CNV_Detection_Power_Calculator/.

bioinformatics↗

bioRxiv2018

Cold Shock Fail to Restrain Pre-formed Bacterial Biofilm

Environmental temperature fluctuation has great impact on the formation of bacterial biofilm, while little information is available for assessing the influence of sharp temperature shifts on the fate of pre-formed biofilm. In this study, experimental evidence is firstly explored on the response of Vibrio parahaemolyticus pre-formed biofilm under cold shock (4 {degrees}C and 10 {degrees}C). Surprisingly, biofilm biomass of V. parahaemolyticus significantly increased during the period of cold shock as revealed by crystal violet staining. Polysaccharides and proteins contents in extracellular polymeric substances were gradually enhanced after cold shocks and exhibited high consistency. RT-qPCR demonstrated the expression of flagella and virulence-related genes were up-regulated. Most of QS and T3SS genes were slightly up-regulated, and three T3SS genes (vcrD1, vcrD2{beta} and vopD1) were down-regulated. Furthermore, the biofilm structure of V parahaemolyticus have been analyzed by Confocal laser scanning microscopy (CLSM), which sharply changed under cold shocks. The correlation analysis further displayed the significant correlation (P < 0.01) among biofilm structure parameters, and weak correlation (P < 0.05) between biofilm related genes and biofilm structure parameters. In conclusion, our results novel discovered that V. parahaemolyticus biofilm related genes were actively expressed and biofilm biomass was continuously increased, biofilm structure was tremendously changed after cold shock. This study underscored the risk that biofilm cells had the ability to adapt to low temperature shift.\n\nIMPORTANCEBiofilms are widespread in natural environments, especially on the surface of food and medical biomaterials, which threaten human safety from persistent infections. Previous studies simply focused on biofilm formation of microorganisms under steady state, however, the actual environment frequently fluctuated. V. parahaemolyticus is a widely distributed foodborne pathogen, temperature play a great role in its survival. Researchers generally assume that cold environment can restrain biofilm formation and bacterial activity. This study explored the effects of V. parahaemolyticus biofilm upon a shift from 37 {degrees}C to 4 {degrees}C or 10 {degrees}C from two aspects. On the one hand, the changes of biofilm biomass and EPS contents, the expression of biofilm related genes directly described that pre-formed bacterial biofilm could not be controlled efficiently in cold environment. On the other hand, the CLSM images revealed biofilm morphological structure change, the correlation analysis showed inner relationship among biofilm structure parameters and biofilm related genes. These results suggested that cold shock fail to restrain pre-formed bacterial biofilm, therefore be a potential risk in nature environment.

microbiology↗

bioRxiv2018

Histophilus somni Survives in Bovine Macrophages by Interfering with Phagosome-Lysosome Fusion, but Requires IbpA for Optimal Serum Resistance

Histophilus somni survives intracellularly in professional phagocytic cells, but the mechanism of intracellular survival is not understood. The Fic motif within the DR1/DR2 IbpA fibrillar network protein of H. somni is cytotoxic to epithelial and phagocytic cells, which may interfere with the bactericidal activity of these cells. To determine the contribution of IbpA and Fic on resistance to host defenses, strains and mutants that lack all of or a small region of ibpA or DR1/DR2 were tested for survival in bovine monocytic cells and for serum susceptibility. A mutant lacking IbpA, but not DR1/DR2, was more susceptible to killing by antiserum than the parent. H. somni strains expressing IbpA replicated in bovine monocytes for at least 72 hours, and were toxic for these cells. Virulent strain 2336 with transposon insertions or deletions within IbpA remained toxic for bovine monocytes. However, strain 2336 mutants lacking all of ibpA or both DR1/DR2 were not toxic to the monocytes, but survived within the monocytes for at least 72 hours. Examination of intracellular trafficking of H. somni with monoclonal antibodies to early and late phagosomal markers indicated that early phagosomal marker EEA-1 colocalized with both disease isolate strain 2336 and serum-sensitve mucosal isolate strain 129Pt, but only strain 2336 did not co-localize with late lysosomal marker LAMP-2 and prevented acidification of phagosomes. These results indicate that virulent isolates of H. somni are capable of surviving within phagocytic cells through interference of phagosome-lysosome maturation. Therefore, H. somni may be considered a permissive intracellular pathogen.

microbiology↗

bioRxiv2018

EZH2 co-opts gain-of-function p53 mutants to promote cancer growth and metastasis

With the unfolding of more and more cancer-driven gain-of-function (GOF) mutants of p53, it is important to define a common mechanism to systematically target different mutants rather than develop strategies tailored to inhibit each mutant individually. Here, using RNA immunoprecipitation sequencing (RIP-seq) we identified EZH2 as a p53 mRNA-binding protein. EZH2 bound to the internal ribosome entry site (IRES) in the 5 untranslated region (5UTR) of p53 mRNA and enhanced p53 protein translation in a methyltransferase-independent manner. EZH2 augmented p53 GOF mutant-mediated cancer growth and metastasis by increasing p53 GOF mutant protein level. EZH2 overexpression associated with the worse outcome only in patients with p53-mutated cancer. Depletion of EZH2 by antisense oligonucleotides inhibited p53 GOF mutant-mediated cancer growth. Our findings reveal a non-methyltransferase function of EZH2 that controls protein translation of p53 GOF mutants, inhibition of which causes synthetic lethality in cancer cells expressing p53 GOF mutants.

cancer biology↗

bioRxiv2017

The fruitENCODE project sheds light on the genetic and epigenetic basis of convergent evolution of climacteric fruit ripening

Fleshy fruit evolved independently multiple times during angiosperm history. Many climacteric fruits utilize the hormone ethylene to regulate ripening. The fruitENCODE project shows there are multiple evolutionary origins of the regulatory circuits that govern climacteric fruit ripening. Eudicot climacteric fruits with recent whole-genome duplications (WGDs) evolved their ripening regulatory systems using the duplicated floral identity genes, while others without WGD utilised carpel senescence genes. The monocot banana uses both leaf senescence and duplicated floral-identity genes, forming two interconnected regulatory circuits. H3K27me3 plays a conserved role in restricting the expression of key ripening regulators and their direct orthologs in both the ancestral dry fruit and non-climacteric fleshy fruit species. Our findings suggest that evolution of climacteric ripening was constrained by limited availability of signalling molecules and genetic and epigenetic materials, and WGD provided new resources for plants to circumvent this limit. Understanding these different ripening mechanisms makes it possible to design tailor-made ripening traits to improve quality, yield and minimize postharvest losses.\n\nOne Sentence SummaryThe fruitENCODE project discovered three evolutionary origins of the regulatory circuits that govern climacteric fruit ripening.

genomics↗