Biology subjects

chen, J.

Publications and source records attributed to chen, J..

5 recordsLinked to original sources

bioRxiv2026

Circulating apoB-containing lipoproteins constituted blood-borne innate immune barrier limits ZIKV dissemination and congenital infection risk

Following establishment of primary viremia, flaviviruses require prompt penetration through vascular endothelium to achieve systemic dissemination, yet most infections remain asymptomatic or self-limited. Canonical defenses, including complement and phagocyte clearance, cannot fully explain this containment, suggesting an additional blood-borne antiviral barrier. Here, we identify apoB containing lipoproteins as potent restriction factors against Zika virus (ZIKV), a devastating danger of global pregnancy. By displaying surface accessible phosphatidylserine (PS), they competitively occupy host PS receptors and block entry by viruses exploiting apoptotic mimicry, including flaviviruses, Ebola, and chikungunya virus. In vivo, increasing apoB lipoproteins enhances serum antiviral activity and limits systemic ZIKV dissemination. This barrier extends to the maternal fetal interface, where elevated maternal LDL attenuates vertical transmission and fetal abnormalities. Its efficacy is modulated by gestational fluctuations in maternal LDL level and low abundance in fetal circulating LDL. Collectively, apoB containing lipoproteins form a constitutive blood-borne innate immune barrier that restrains apoptotic-mimicry viruses during the intravascular phase, limits viral dissemination and reduces congenital infection risk. This study provides a rationale for developing diet augmentation strategy to strengthen this innate barrier in at-risk individuals.

microbiology↗

bioRxiv2024

Time-resolved fluorescent proteins towards fluorescence microscopy in the temporal and spectral domains

Fluorescence microscopy has been widely applied in life sciences. While steady-state fluorescence intensity is mostly used, the time-resolved detection mode relying on fluorescence lifetime remains underexplored. Herein, we present a family of time-resolved fluorescent proteins (TRFP). Using a strategy that regulates lifetime without affecting spectra of FPs, we have developed different TRFPs that cover the visible spectrum and a wide range of lifetime. TRFPs are employed in the temporal-spectral resolved microscopy, allowing the simultaneous imaging of 9 different proteins in live cells and correlation of multiple activities to cell cycles. Finally, TRFPs are integrated into multiplexing super-resolution microscopy to concurrently visualize 4 proteins in live cells, acquiring a remarkable 50 nm spatial resolution using lifetime as signal. TRFPs represent a transformative toolset towards fluorescence microscopy in both the temporal and spectral domains. Beyond the multiplexing imaging, TRFPs could introduce unprecedented opportunities of system complexity and quantitative accuracy into biological research.

biochemistry↗

bioRxiv2020

nMAGMA: a network enhanced method for inferring risk genes from GWAS summary statistics and its application to schizophrenia

MotivationAnnotating genetic variants from summary statistics of genome-wide association studies (GWAS) is crucial for predicting risk genes of various disorders. The multi-marker analysis of genomic annotation (MAGMA) is one of the most popular tools for this purpose, where MAGMA aggregates signals of single nucleotide polymorphisms (SNPs) to their nearby genes. However, SNPs may also affect genes in a distance, thus missed by MAGMA. Although different upgrades of MAGMA have been proposed to extend gene-wise variant annotations with more information (e.g. Hi-C or eQTL), the regulatory relationships among genes and the tissue-specificity of signals have not been taken into account. ResultsWe propose a new approach, namely network-enhanced MAGMA (nMAGMA), for gene-wise annotation of variants from GWAS summary statistics. Compared with MAGMA and H-MAGMA, nMAGMA significantly extends the lists of genes that can be annotated to SNPs by integrating local signals, long-range regulation signals, and tissue-specific gene networks. When applied to schizophrenia, nMAGMA is able to detect more risk genes (217% more than MAGMA and 57% more than H-MAGMA) that are reasonably involved in schizophrenia compared to MAGMA and H-MAGMA. Some disease-related functions (e.g. the ATPase pathway in Cortex) tissues are also uncovered in nMAGMA but not in MAGMA or H-MAGMA. Moreover, nMAGMA provides tissue-specific risk signals, which are useful for understanding disorders with multi-tissue origins.

bioinformatics↗

bioRxiv2019

Structural variation, functional differentiation and expression characteristics of the AP2/ERF gene family and its response to cold stress and methyl jasmonate in Panax ginseng C.A. Meyer

The APETALA2/Ethylene Responsive Factor (AP2/ERF) gene family has been shown to play a crucial role in plant growth and development, stress responses and secondary metabolite biosynthesis. Nevertheless, little is known about the gene family in ginseng (Panax ginseng), an important traditional medicinal herb in Asia and North America. Here, we report the systematic analysis of the gene family present in ginseng using several transcriptomic databases. A total of 189 putative AP2/ERF genes, defined as PgERF001 through PgERF189. The 93 PgERF genes that have the complete AP2 domain in their open reading frames were classified into five subfamilies, DREB, ERF, AP2, RAV and Soloist. The DREB subfamily and ERF subfamily were further clustered four and six groups, respectively, compared to the 12 groups of these subfamilies found in Arabidopsis. Gene ontology categorized these 397 transcripts of the 189 PgERF genes into eight functional subcategories, suggesting their functional differentiation and they have been especially enriched for the nucleic acid binding transcription factor activity subcategory. The expression activity and networks of the 397 PgERF transcripts have substantially diversified across tissues, developmental stages and genotypes. Then, the expression change of six PgERF genes randomly selected from DREB subfamily, i.e., PgERF073, PgERF079, PgERF110, PgERF115, PgERF120 and PgERF128 responding to cold stress suggesting that DREB subfamily genes played an important role in cold resistance of ginseng. Finally, we studied the responses of the PgERF genes to methyl jasmonate (MeJA). 288 (72.5%) of the 397 PgERF gene transcripts responded to the MeJA treatment, with 136 up-regulated and 152 down-regulated, indicating that most members of the PgERF gene family are responsive to MeJA. These results provide resources and knowledge necessary for family-wide functional analysis of the PgERF genes in ginseng and related species.

genomics↗

bioRxiv2018

The biochemical properties of a novel paraoxonase-like enzyme in Trichoderma atroviride strain T23 involved in the degradation of 2,2-dichlorovinyl dimethyl phosphate

Dichlorvos, is a broad-spectrum organophosphorus pesticide that is widely applied in the agricultural industry and considered a pollutant to fish and bees. T. atroviride strain T23, an efficient DDVP-degrading strain, could convert DDVP to dichloroacetic acid, 2,2-dichloroethanol and phosphoric acid through mineralization. RT-qPCR analysis showed TaPon1-like encoding an organophosphorus hydrolase, is continuously highly expressed in the process of degrading DDVP. TaPon1-like contained an open reading frame of 1317 bp, and the deduced amino acid sequence shared 21% homology with HuPON1, which also exhibits excellent hydrolysis of organophosphate-oxons compounds. By analysis of gene knockout, we found the {Delta}TaPon1-like knockout strain KO1 lost 35.6% of its DDVP-degradation capacity at 24 h, but this loss of degradation activity was recovered when the gene was complemented. Furthermore, the purified recombinant protein reTAPON1-LIKE, could transform DDVP only to dimethyl phosphate and showed significant paraoxonase activity (1028 U L-1). The reTAPON1-LIKE enzyme showed a broad degradation spectrum, degrading not only DDVP but also organophosphate-oxons and lactone. The kinetic parameters (Km and kcat) of the purified reTAPON1-LIKE were determined to be 0.23 mM and 204.3 s-1 for DDVP, respectively. The highest activity was obtained at 35 {degrees}C, and the optimal pH was 8.5. The activity of reTAPON1-LIKE was enhanced most significantly when 1.0 mM Ca2+ was added but declined when 1.0 mM Cu2+ was added. These results showed TAPON1-LIKE play an important role for DDVP degradation in the first step by T23 and provided clue to comprehensively understanding the degradation mechanism of organophosphate-oxons pesticides by filamentous fungi.\n\nImportanceThe large amounts of residues of organophosphate pesticides in agroecological system has become a great threat to the safety of environment and humans. Bioremediation in association with microbial is innovative technology having a potential to alleviate such pollution problems. The genus Trichoderma is genetically diverse with capabilities to degrade chemical pesticides among different strains with agricultural significance. As a typical organophosphorus pesticide, it is one of the most employed compounds of the family. Though it was classified as a highly toxic pesticide by WHO due to its hazardous properties, it plays an important role in the control of plant pests, food storage and homes, as well as to treat infections in livestock. Therefore, we use DDVP as a model of organophosphate pesticide to study the mechanism of Trichoderma degrading organophosphate pesticides, for the aim of globally understanding molecular mechanism of enzymatic degradation of organophosphate pesticides by beneficial fungi.

microbiology↗