Biology subjects

Bao, J.

Publications and source records attributed to Bao, J..

41 records · Page 3Linked to original sources

bioRxiv2020

Decoding transcriptional regulation via a human gene expression predictor

Transcription factors (TF) regulate cellular activities via controlling gene expression, but a predictive model describing how TFs quantitatively modulate human transcriptomes was lacking. We constructed a universal human gene expression predictor and utilized it to decode transcriptional regulation. Using 1613 TFs expression, the predictor reconstituted highly accurate transcriptomes for samples derived from a wide range of tissues and conditions. The predictors broad applicability indicated it had recapitulated the quantitative relationships between TFs and target genes ubiquitous across tissues. Significant interacting TF-target gene pairs were then extracted from the predictor and enabled downstream inference of TF regulators for diverse pathways involved in development, immunity, metabolism, and stress response. Thus, we present a novel approach to study human transcriptional regulation following the "understanding by modeling" principle.

systems biology↗

bioRxiv2019

Bayogenin 3-O-Cellobioside is a novel non-cultivar specific anti-blast metabolite produced in rice in response to Pyricularia oryzae infection

Rice cultivars from japonica and indica lineage possess differential resistance against blast fungus on an account genetic divergence. Whether different rice cultivars also show distinct metabolomic changes in response to P. oryzae, and their role in host resistance, are poorly understood. Here, we examine the responses of six different rice cultivars from japonica and indica lineage challenged with P. oryzae. Both susceptible and resistant rice cultivars expressed several metabolites exclusively during P. oryzae infection, including the saponin Bayogenin 3-O-cellobioside. Bayogenin 3-O-cellobioside level in infected rice directly correlated with their resistant attributes. These findings reveal, for the first time to our knowledge that besides oat, other grass plants including rice produces protective saponins. Our study provides insight into the role of pathogen-mediated metabolomics-reprogramming in host immunity. The correlation between Bayogenin 3-O-Cellobioside levels and blast resistance suggests that engineering saponin expression in cereal crops represents an attractive and sustainable disease control strategy.

biochemistry↗

bioRxiv2019

Distribution Pattern and Diversity Maintenance Mechanism of the Denitrifier Community in Alkaline Copper Mine Drainage

Denitrifiers have been shown to vary in abundance and diversity across the environmental gradients; however, the factors that determine the type and magnitude of the response of the denitrifier communities remain unclear. In order to reveal the effects of alkaline mine drainage (AlkMD) on the denitrifier community composition and diversity maintenance mechanism in a tailings reservoir, we examined the diversity patterns and adaptation mechanisms of different denitrifier communities in Shibahe copper tailings water in Zhongtiaoshan, China. The results showed that the -diversity of Proteobacteria and the nosZI-bearing denitrifier community in downstream seeping water (SDSW) were the highest, while those in the upstream tailings water (STW1) were the lowest. The highest nirS and nirK-bearing denitrifier community -diversity were measured in STW1, and the lowest in STW3. The community dissimilarity of the denitrifier communities was strongly correlated with environment parameters, but the factors varied in different groups. The Proteobacteria community was correlated strongly with nitrate (NO3-); the nirS and nirK-bearing denitrifier communities were correlated strongly with pH, total carbon (TC), NO3- and ammonia nitrogen (NH4+), and the nosZI-bearing denitrifier community was correlated strongly with total organic carbon (TOC), dissolved oxygen (DO), NO3-, electroconductibility (EC) and spatial distance (PCNM1). Our results indicated that environmental changes were valuable index reflecting variations in denitrifier community composition in AlkMD. Additionally, the findings in this study are helpful in understanding the relationship between the microbial community composition changes and functional adaptation in different ecosystems. IMPORTANCEMetal mine tailings pond is an important site polluted by heavy metals and nitrogen, and excess nitrogen is mainly removed by microorganisms through denitrification. Although many studies have reported that Proteobacteria is the main denitrifying bacteria, and nirS, nirK and nosZ-bearing denitrifiers are three key functional groups in denitrification process. However, less is known of their response to discharge of alkaline copper tailings wastewater (AlkMD). AlkMD exerts an adverse impact on composition and structure of denitrifying bacteria community. The change of nitrogen and carbon concentration along the flow direction of wastewater resulted in the change of denitrifying bacteria community diversity pattern, that is to say, environmental filtering force drove the denitrifier community structure in this highly polluted ecosystem.

microbiology↗

bioRxiv2018

Baculovirus utilizes cholesterol transporter Niemann-Pick C1 for host cell entry

The dual roles of baculovirus for the control of natural insect populations as an insecticide, and for foreign gene expression and delivery, have called for a comprehensive understanding of the molecular mechanisms governing viral infection. Here, we demonstrate that the Bombyx mori Niemann-Pick C1 (BmNPC1) is essential for baculovirus infection in insect cells. Both pretreatment of Bombyx mori embryonic cells (BmE) with NPC1 antagonists (imipramine or U18666A) and down-regulation of NPC1 expression resulted in a significant reduction in baculovirus BmNPV (Bombyx mori nuclear polyhedrosis virus) infectivity. Furthermore, we show that the major glycoprotein gp64 of BmNPV, responsible for both receptor binding and fusion, is able to interact predominantly with the BmNPC1 C domain, with an enhanced binding capacity at low pH conditions, indicating that NPC1 most likely plays a role during viral fusion in endosomal compartments. Our results, combined with previous studies identifying an essential role of hNPC1 in filovirus infection, suggest that the glycoprotein of several enveloped viruses possess a shared strategy of exploiting host NPC1 proteins during virus intracellular entry events.\n\nIMPORTANCEBmNPV is one of the most important members of the Baculoviridae; many viruses in this family have been frequently employed as viral vectors for foreign gene delivery or expression and as biopesticides, but their host receptors still remain unclear. Here, we describe that the intracellular cholesterol transporter BmNPC1 is indispensable for BmNPV infection in insect cells, and it interacts with the major viral glycoprotein gp64. Our study on the role of BmNPC1 in baculovirus infection has further expanded the list of the enveloped viruses that require host NPC1 proteins for entry, and will ultimately help us to uncover the molecular mechanism of the involvement of NPC1 proteins in the entry process of many enveloped viruses.

microbiology↗

bioRxiv2017

Pan-cancer scale landscape of simple somatic mutations

Genome is the carrier of somatic mutations during the development of cancer. The catalogue of simple somatic mutations (SSM) is a subgroup of somatic mutations. It includes single base substitutions, small deletions and insertions of <= 200 bp, and multiple base substitutions of <= 200 bp. The comprehensive landscape of SSM has not been studied. After analysed 46,692,922 SSM of 10,878 samples, we proposed a pan-cancer scale landscape of SSM for 60 cancer projects in ICGC. In addition, the whole genome sequencing (WGS) and whole exome sequencing (WXS) techniques were compared according to the landscape of SSM. The result indicates numbers of SSM vary dramatically in different cancers. WGS can detect 10 times more single base substitutions and insertions than WXS. In terms of WXS, it called 10 times more deletions than insertions. Multiple base substitutions have not been well studied so they were just observed in a few cancer projects. Cancers generally show high prevalence of C > T substitutions at NpCpG trinucleotide contexts. Skin cancer showed distinct mutational spectra. Breast cancer, bladder cancer, and cervical cancer were found to have similar mutational spectra. Acute myeloid leukemia and lung cancer from South Korea, and colorectal cancer from China show high density of single base substitutions per mega base in chromosome Y. To sum up, our study and findings will be thought provoking in studying SSM in cancer.

genomics↗