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Limin Chen

Publications and source records attributed to Limin Chen.

10 recordsLinked to original sources
PubMed2025

Analysis of Blood Microbiome From People Living With HIV and Donors by 16S rRNA Metagenomic Sequencing.

Utilize 16S rRNA sequencing technology to characterize bacterial species susceptible to people living with HIV (PLWH) across different stages. This mapping aims to establish a foundational framework for preventing secondary HIV infections, prolonging patient survival, enhancing quality of life, and advancing the diagnosis, treatment, and research of bacterial co-infections. In this study, we classified the participants into three groups: The blood of donors living with HIV (DI group), AIDS patients who have received ART treatment (PI group), and healthy blood donors as the control group (DH group). Each group was divided into three parallel subgroups, with 30 samples pooled from each parallel group for plasma extraction. As initial processing steps, the nine parallel subgroups were subjected to nucleic acid extraction and PCR amplification targeting the 16SV34 region. The resulting amplified products were subsequently forwarded to a sequencing company. It can be seen from the Venn diagram that the DI groups showed significantly higher bacterial diversity than the PI group and the DH group. The PI group had lower bacterial relative abundance and diversity compared to the DI group, with a community structure more similar to the control group. The DI group is particularly susceptible to several significant pathogens, including Ralstonia, Pseudomonas, Acinetobacter, Methyloversatilis, and Vibrio. The study revealed a greater quantity and diversity of bacteria in the DI blood compared to the PI and DH groups. This observation may be attributed to PI group patients in this study being hospitalized and receiving treatment.

Humans↗
PubMed2006

Silencing of USP18 potentiates the antiviral activity of interferon against hepatitis C virus infection.

BACKGROUND & AIMS: Modulation of the host innate immune response is an attractive means of inhibiting hepatitis C virus (HCV) replication. Having previously determined that expression of the interferon-sensitive gene (ISG)15 protease USP18 is increased in the liver biopsy specimens of patients who do not respond to interferon (IFN)-alfa therapy, we hypothesized that USP18 might hinder the ability of IFN to inhibit HCV replication. METHODS: The role of USP18 in IFN antiviral activity was examined using an in vitro model of HCV replication that reproduces the full viral life cycle. USP18 was silenced specifically using small inhibitory RNAs (siRNAs), and the dose response of HCV replication and infectious virus production to IFN-alfa was measured. RESULTS: The siRNA knockdown of USP18 in human cells consistently potentiated the ability of IFN to inhibit HCV-RNA replication and infectious virus particle production by a factor of 1-2 log(10). USP18 knockdown also resulted in a number of cellular changes consistent with increased sensitivity to IFN. Decreasing USP18 expression led to increased cellular protein ISGylation in response to exogenous IFN-alfa, prolonged tyrosine phosphorylation of signal transducer and activation of transcription (STAT1), and a general enhancement of IFN-stimulated gene expression. CONCLUSIONS: These data suggest that USP18 modulates the anti-HCV type I IFN response, and is a possible therapeutic target for the treatment of HCV infection.

Antiviral Agents↗
PubMed2005

Regional assessment of the response of the acid-base status of lake watersheds in the Adirondack region of New York to changes in atmospheric deposition using PnET-BGC.

Understanding the response of soil and surface waters to changes in atmospheric deposition is critical for guiding future legislation on air pollution. The Adirondack region of New York experiences among the most severe ecological impacts from acidic deposition. The region is characterized by considerable variability in atmospheric deposition, surficial and bedrock geology, hydrologic flow paths, and vegetation resulting in variability in effects of acidic deposition. In this study, an integrated biogeochemical model (PnET-BGC) was applied to 37 forest lake watersheds to assess the response of soil and surface waters of the Adirondacks to changes in atmospheric deposition at a regional scale. Model-simulated surface water chemistry was validated against data from two synoptic surveys conducted in 1984 and 2001. Results indicate that the model is able to capture the observed changes in surface water chemistry during this period. The model was further used to forecast the response of soil and surface waters to three future emission control scenarios. Results indicate that under the Clean Air Act, surface water SO4(2-) concentrations will continue to decrease at a median rate of -0.38 microeq/L-yr, and surface water ANC is predicted to increase at a median rate of 0.11 microeq/L-yr. More aggressive emission reductions will accelerate the rate of recovery. Under an aggressive control scenario, which represents an additional 75% reduction in SO2 emissions beyond the implementation of the Clean Air Act, surface water SO4(2-) concentrations are predicted to decrease at a median rate of -0.88 microeq/L-yr, and surface water ANC is predicted to increase at a median rate of 0.43 microeq/L-yr. Model predictions of several biologically relevant chemical indicators are also reported.

Acid Rain↗
PubMed2005

Hepatic gene expression discriminates responders and nonresponders in treatment of chronic hepatitis C viral infection.

BACKGROUND & AIMS: Pegylated interferon (IFN)-alpha plus ribavirin is the most effective treatment of chronic hepatitis C but has unpleasant side effects and high costs. A large proportion of patients do not respond to therapy for reasons that are unclear. We used gene expression profiling to investigate the molecular basis for treatment failure. METHODS: Expression profiling was performed on percutaneous needle liver biopsy specimens taken before therapy. Gene expression levels were compared among 15 nonresponder, 16 responder, and 20 normal liver biopsy specimens. Differential gene expression was confirmed using real-time polymerase chain reaction. RESULTS: We identified 18 genes whose expression differed significantly between all responders and all nonresponders (P < .005). Many of these 18 genes are IFN sensitive and 2 (ISG15/USP18) are linked in a novel IFN-regulatory pathway, suggesting a possible rationale for treatment resistance. Using a number of independent classifier analyses, an 8-gene subset accurately predicted treatment response for 30 of 31 patients. The classifier analyses were applicable to patients with genotype 1 infection and were not correlated with viral load, disease activity, or fibrosis. CONCLUSIONS: Hepatic gene expression profiling identified consistent differences in patients who subsequently fail treatment with pegylated IFN-alpha plus ribavirin: up-regulation of a specific set of IFN-responsive genes predicts nonresponse to exogenous therapy. These data may be of use in predicting clinical responses to treatment.

Adult↗
PubMed2005

[Combined 5-Fu and triamcinolone to treat the membrane on the anterior surface of intraocular lens after the surgery of traumatic cataract].

PURPOSE: To observe the effect of the means of subconjunctiva injection with 5-Fluorouracil (5-Fu) and Triamcinolone to treat the membrane on the anterior surface of intraocular lens after traumatic cataract surgery. METHODS: The cases with membrane on the anterior surface of intraocular lens (MAI) after traumatic cataract surgery were observed. The control group included 49 eyes of 48 patients, and 52 eyes of 52 patients in therapeutic group. Subconjunctiva injection of 5-Fu and Triamcinolone treat MAI in therapeutic group. And that of Dexamethasone treat MAI in control group. RESULTS: The absorbed rate of MAI is 90.38% in therapeutic group,and that is 75.51% in control group. The vision of two groups was developed. And corneal epithelium erosion occurred in 6 eyes of therapeutic group. CONCLUSION: The therapy of 5-Fu and Triamcinolone to treat the MAI after traumatic cataract surgery is safe and effective.

Administration, Topical↗
PubMed2004

[Study on relationship between ambient PM10, PM2.5 pollution and daily mortality in a district in Shanghai].

OBJECTIVE: Explore the adverse impact of ambient particulate matter pollution on human health. METHODS: Generalized additive model (GAM) extended poisson regression was used to examined the exposure--response relationship between ambient PM10, PM2.5 pollution and daily mortality in a district in Shanghai. Regression analyses was used for analysis with adjustment for controlling time trends, weather, season, the day of the week. RESULTS: A 10 micrograms/m3 increase in PM10, and PM2.5 were associated with 0.53% (0.22%-0.85%), 0.85% (0.32%-1.39%) increase in total daily mortality respectively. CONCLUSION: Ambient particulate pollution has potential acute adverse health effects on human.

Air Pollutants↗
PubMed2003

Altered expression of genes involved in hepatic morphogenesis and fibrogenesis are identified by cDNA microarray analysis in biliary atresia.

Biliary atresia (BA) is characterized by a progressive, sclerosing, inflammatory process that leads to cirrhosis in infancy. Although it is the most common indication for liver transplantation in early childhood, little is known about its etiopathogenesis. To elucidate factors involved in this process, we performed comprehensive genome-wide gene expression analysis using complementary DNA (cDNA) microarrays. We compared messenger RNA expression levels of approximately 18,000 human genes from normal, diseased control, and end-stage BA livers. Reverse-transcription polymerase chain reaction (RT-PCR) and Northern blot analysis were performed to confirm changes in gene expression. Cluster and principal component analysis showed that all BA samples clustered together, forming a distinct group well separated from normal and diseased controls. We further identified 35 genes and ESTs whose expression differentiated BA from normal and diseased controls. Most of these genes are known to be associated with cell signaling, transcription regulation, hepatic development, morphogenesis, and fibrogenesis. In conclusion, this study serves to delineate processes that are involved in the pathogenesis of BA.

Adolescent↗
PubMed2002

An NMR approach to structural proteomics.

The influx of genomic sequence information has led to the concept of structural proteomics, the determination of protein structures on a genome-wide scale. Here we describe an approach to structural proteomics of small proteins using NMR spectroscopy. Over 500 small proteins from several organisms were cloned, expressed, purified, and evaluated by NMR. Although there was variability among proteomes, overall 20% of these proteins were found to be readily amenable to NMR structure determination. NMR sample preparation was centralized in one facility, and a distributive approach was used for NMR data collection and analysis. Twelve structures are reported here as part of this approach, which allowed us to infer putative functions for several conserved hypothetical proteins.

Bacterial Proteins↗
PubMedDate not supplied

Measurements of NO2, SO2, O3, benzene and toluene using differential optical absorption spectroscopy (DOAS) in Shanghai, China.

NO2, SO2, O3, benzene, and toluene were measured in Taopu industry park of Shanghai during the period June to August 2003 by differential optical absorption spectroscopy (DOAS) technique. The daily average concentrations of SO2, NO2, and O3 ranged from 5.7 ppb to 40 ppb, 22 ppb to 123 ppb, and 10.6 ppb to 23 ppb respectively. SO2 and NO2 concentrations were found to depend on wind direction. The diurnal variation of NO2 concentrations had two peaks due to traffic emission. Our DOAS measurements of NO2, SO2 and O3 were compared with the conventional measurement instruments (API automatic monitoring instrument). The concept of a percent difference (PD) and linear regression methods were employed to study the difference between DOAS and API instruments. The correlation analysis between PD values and meteorological parameters and analysis of abnormal higher absolute PD values indicated that the lower visibility induced the bad compatibility between the two systems. The results showed that both systems exhibited strong compatibility with good correlation, therefore the DOAS system is able to provide reliable information on distribution patterns of major air pollutants. Average benzene and toluene concentrations were 1.4 and 8.0 ppb respectively.

Air Pollutants↗