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1.
Front Mol Biosci ; 11: 1366753, 2024.
Article En | MEDLINE | ID: mdl-38486946

Introduction: Maintenance hemodialysis is an effective treatment for end-stage renal disease patients. A critical factor contributing to the deterioration and death of maintenance hemodialysis patients is inflammation. Therefore, we focused on two inflammatory markers, serum ferritin and neutrophil-to-lymphocyte ratio, to speculate whether they could predict the prognosis of maintenance hemodialysis patients. Patients and methods: We followed 168 patients with maintenance hemodialysis from July 2019 to July 2022 with the endpoint of all-cause death or follow-up completion. Receiver operating characteristic curves were plotted to assess the values of serum ferritin, neutrophil-to-lymphocyte ratio and serum ferritin combined with neutrophil-to-lymphocyte ratio to predict the outcomes of maintenance hemodialysis patients. Kaplan-Meier survival curves were constructed to compare survival rates over time. Results: Receiver operating characteristic curves demonstrated that the best cut-off value of serum ferritin for predicting the prognosis of maintenance hemodialysis patients was 346.05 µg/L, and that of neutrophil-to-lymphocyte ratio was 3.225. Furthermore, a combination of both had a more excellent predicting value than either index (p < 0.05). Kaplan-Meier survival curve analyses revealed that low serum ferritin levels and low neutrophil-to-lymphocyte ratio had a higher probability of survival than high ferritin levels and high neutrophil-to-lymphocyte ratio, separately. Conclusion: Elevated serum ferritin and neutrophil-to-lymphocyte ratio are closely related to all-cause mortality among maintenance hemodialysis patients, for which they may be predictors of all-cause mortality. Additionally, the combination of the two has a much higher predictor value for the prognosis of maintenance hemodialysis patients.

2.
Environ Monit Assess ; 196(2): 152, 2024 Jan 16.
Article En | MEDLINE | ID: mdl-38225435

Preserving lacustrine ecosystems is vital for sustainable watershed development, and forecasting the environmental water availability of lakes would support policymakers in developing sound management strategies. This study proposed a methodology that merges the lake water level prediction and environmental water availability evaluation. The temporal fusion transformer (TFT) model forecasted the lake water levels for the next 7 days by inputting the streamflow and lake water level data for the past 30 days. The environmental water availability was assessed by comparing the forecasted lake water levels with the environmental water requirements, resulting in adequate, regular, scarce, and severely scarce environmental water availability. The methodology was tested in two case studies: Poyang Lake and Dongting Lake, the two largest freshwater lakes in the Yangtze River Basin, China. The TFT model performed well in forecasting the lake water levels, as shown by the high coefficient of determination and finite root mean square error. The coefficients of determination exceeded 0.98 during the model training, validation, and test for both Poyang Lake and Dongting Lake, and the root mean square errors ranged from 0.06 to 0.46 m. The accurate prediction of lake water level promoted the precise forecasting of the environmental water availability with the high Kappa coefficient exceeding 0.90. Results indicated the rationality and effectiveness of integrating the lake water level prediction and environmental water availability evaluation. Future research includes the applicability of the TFT model to other lakes worldwide to test the proposed approach and investigate strategies to cope with environmental water scarcity.


Ecosystem , Lakes , Water , Environmental Monitoring/methods , China
3.
J Dent ; 138: 104733, 2023 11.
Article En | MEDLINE | ID: mdl-37783373

OBJECTIVE: To investigate the cross-linking and protective effect of artemisinin (ART), dihydroartemisinin (DHA), and artesunate (AST) on collagen fibers of demineralized dentin surface. METHODS: Molecular docking was used to predict potential interactions of ART, DHA, and AST with dentin type I collagen. Human third molars without caries were completely demineralized and treated with different solutions for 1 min. The molecular interactions and cross-linking degree of ART and its derivatives with dentin collagen were evaluated by FTIR spectroscopy, total extractable protein content, and a ninhydrin assay. Scanning electron microscopy, hydroxyproline release, and ultimate microtensile strength tests (µUTS) were employed to confirm the mechanical properties and anti-collagenase degradation properties of dentin collagen fibers. RESULTS: ART, DHA, and AST combined with dentin type I collagen mainly through hydrogen bonding and hydrophobic interactions, and the cross-linking reaction sites were mainly C=O and CN functional groups. Compared to the control group, ART and its derivatives significantly increased the degree of cross-linking. Additionally, significant increases were observed in resistance to enzymatic digestion and mechanical properties of the artemisinin and its derivatives group. CONCLUSION: ART, DHA, and AST could cross-link with demineralized dentin collagen, through improving the mechanical properties and anti-collagenase degradation properties. CLINICAL SIGNIFICANCE: The study endorses the potential use of ART and its derivatives as a prospective collagen cross-linking agent for degradation-resistant and long-period dentin bonding in composite resin restorations.


Artemisinins , Dental Bonding , Humans , Collagen Type I , Cross-Linking Reagents/pharmacology , Cross-Linking Reagents/analysis , Cross-Linking Reagents/chemistry , Molecular Docking Simulation , Prospective Studies , Tensile Strength , Collagen/pharmacology , Collagen/chemistry , Collagenases/analysis , Collagenases/pharmacology , Artemisinins/pharmacology , Artemisinins/analysis , Dentin , Dental Bonding/methods , Dentin-Bonding Agents/pharmacology , Dentin-Bonding Agents/chemistry
4.
Water Res ; 243: 120347, 2023 Sep 01.
Article En | MEDLINE | ID: mdl-37490830

High-frequency nitrate-N (NO3--N) data are increasingly available, while accurate assessments of in-stream NO3--N retention in large streams and rivers require a better capture of complex river hydrodynamic conditions. This study demonstrates a fusion framework between high-frequency water quality data and hydrological transport models, that (1) captures river hydraulics and their impacts on solute signal propagation through river hydrodynamic modeling, and (2) infers in-stream retention as the differences between conservatively traced and reactively observed NO3--N signals. Using this framework, continuous 15-min estimates of NO3--N retention were derived in a 6th-order reach of the lower Bode River (27.4 km, central Germany), using long-term sensor monitoring data during a period of normal flow from 2015 to 2017 and a period of drought from 2018 to 2020. The unique NO3--N retention estimates, together with metabolic characteristics, revealed insightful seasonal patterns (from high net autotrophic removal in late-spring to lower rates, to net heterotrophic release during autumn) and drought-induced variations of those patterns (reduced levels of net removal and autotrophic nitrate removal largely buffered by heterotrophic release processes, including organic matter mineralization). Four clusters of diel removal patterns were identified, potentially representing changes in dominant NO3--N retention processes according to seasonal and hydrological conditions. For example, dominance of autotrophic NO3--N retention extended more widely across seasons during the drought years. Such cross-scale patterns and changes under droughts are likely co-determined by catchment and river environments (e.g., river primary production, dissolved organic carbon availability and its quality), which resulted in more complex responses to the sequential droughts. Inferences derived from this novel data-model fusion provide new insights into NO3- dynamics and ecosystem function of large streams, as well as their responses to climate variability. Moreover, this framework can be flexibly transferred across sites and scales, thereby complementing high-frequency monitoring to identify in-stream retention processes and to inform river management.


Nitrates , Rivers , Droughts , Seasons , Ecosystem , Environmental Monitoring/methods
5.
Nat Commun ; 14(1): 202, 2023 01 13.
Article En | MEDLINE | ID: mdl-36639378

Eukaryotic messenger RNA (mRNA) typically contains a methylated guanosine (m7G) cap, which mediates major steps of mRNA metabolism. Recently, some RNAs in both prokaryotic and eukaryotic organisms have been found to carry a non-canonical cap such as the NAD cap. Here we report that Arabidopsis DXO family protein AtDXO1, which was previously known to be a decapping enzyme for NAD-capped RNAs (NAD-RNA), is an essential component for m7G capping. AtDXO1 associates with and activates RNA guanosine-7 methyltransferase (AtRNMT1) to catalyze conversion of the guanosine cap to the m7G cap. AtRNMT1 is an essential gene. Partial loss-of-function mutations of AtRNMT1 and knockout mutation of AtDXO1 reduce m7G-capped mRNA but increase G-capped mRNAs, leading to similar pleiotropic phenotypes, whereas overexpression of AtRNMT1 partially restores the atdxo1 phenotypes. This work reveals an important mechanism in m7G capping in plants by which the NAD-RNA decapping enzyme AtDXO1 is required for efficient guanosine cap methylation.


Arabidopsis , RNA Caps , RNA, Messenger/genetics , RNA, Messenger/metabolism , RNA Caps/genetics , RNA Caps/metabolism , Arabidopsis/genetics , Arabidopsis/metabolism , Guanosine/metabolism , NAD/metabolism
6.
Ocul Immunol Inflamm ; 30(1): 153-159, 2022 Jan 02.
Article En | MEDLINE | ID: mdl-32809886

PURPOSE: To identify viral pathogens in patients with secondary glaucoma associated with anterior segment uveitis and compare metagenomic deep sequencing (MDS) with enzyme-linked immunosorbent assay (ELISA) combined with Witmer-Desmonts coefficient (WDC) evaluation and real-time quantitative polymerase chain reaction (qPCR) on investigating pathogens in aqueous humor. METHODS: Aqueous humor from 31 patients, including 22 Posner-Schlossman Syndrome and 9 other anterior uveitis, was assessed pathogens by ELISA combined with WDC evaluation, virus deoxyribonucleic acid (DNA) detection by real-time qPCR and MDS. RESULTS: Viral pathogens (HCMV or VZV or RV) were detected in 19 out of 31 eyes (61.3%) by real-time qPCR or WDC evaluation. MDS revealed the presence of HCMV DNA sequences in three PSS patients. CONCLUSION: Virus is an important pathogen in secondary glaucoma associated with anterior segment uveitis. MDS is a potential etiologic diagnosis tool to seek intraocular viral pathogens for secondary glaucoma associated anterior segment uveitis.


Eye Infections, Viral , Glaucoma , Uveitis, Anterior , Uveitis , Aqueous Humor , DNA, Viral/analysis , DNA, Viral/genetics , Eye Infections, Viral/diagnosis , Glaucoma/diagnosis , High-Throughput Nucleotide Sequencing , Humans , Real-Time Polymerase Chain Reaction , Uveitis/diagnosis , Uveitis, Anterior/diagnosis
7.
Article En | MEDLINE | ID: mdl-33466386

Due to the continuous changes of political environment, consumption habits, technological progress and other factors, the external environment of enterprises is full of uncertainty. The turbulence of external environment is not conducive to the long-term operation and development of enterprises, but also brings great challenges to the selection of suppliers. This makes the competition of enterprises focus on how to choose long-term cooperation suppliers in the uncertain external environment. In addition, due to the deterioration of the global environment, governments pay more and more attention to environmental pollution, and consumers are more and more inclined to green consumption, which makes many companies pay more and more attention to environmental indicators when selecting suppliers. In the case of external environment turbulence and serious environmental pollution, the evaluation and selection of green suppliers in uncertain environment is particularly important for the long-term development of enterprises. What's more, when the supplier's capability gap is small, the decision-maker often hesitates among several suppliers. In this paper, the hesitant fuzzy is used to describe the hesitant psychology of decision-makers in selecting suppliers, the variance fluctuation is used to describe the characteristics of hesitant fuzzy numbers, and the probability is used to measure the uncertainty of the environment. A green supplier evaluation model under the uncertainty environment is proposed, which comprehensively evaluates the green suppliers under the uncertain environment. Furthermore, it is compared with other methods that do not consider the uncertainty and the adaptability of evaluation method and right confirmation method, so as to reflect the influence of uncertainty to green supplier evaluation and the importance of adaptability of evaluation method and right confirmation method.


Commerce , Decision Making , Uncertainty
8.
RSC Adv ; 11(21): 12885-12892, 2021 Mar 29.
Article En | MEDLINE | ID: mdl-35423815

Besides geography and climate, biological factors play an important role in shaping travertine landforms, but the biochemical mechanisms of microbial processes in travertine formation have been rarely studied. Two psychrophilic bacterial strains, A20-18 and B21-3 of Pseudomonas psychrophila, isolated from travertine pools of Huanglong, a typical alpine travertine landform, were investigated for their roles in calcium carbonate mineralization, including the deposition process and products. X-ray diffraction, Fourier-transform infrared spectroscopy, and scanning electron microscopy were used to characterize the crystal phase and morphology of CaCO3 precipitation. The results showed that there were no significant differences between the two strains in CaCO3 deposition rate. Extracellular polymeric substances (EPS)-free cells significantly inhibited calcification, compared with a control. Irregular crystals and polyhedral structures are common to all treatments using the two strains. These complex polycrystals were the result of the synergistic effect of homogeneous nucleation and heterogeneous nucleation. EPS and cells of strain B21-3 formed ring-like structures of calcium carbonate, which was possibly from the amphiphilic polymer forming a circular arrangement in water. These results are significant for understanding the microbial factor in Huanglong travertine deposition and providing new insights into the morphological control of the biomineralization mechanism at low temperatures.

9.
Chemosphere ; 260: 127559, 2020 Dec.
Article En | MEDLINE | ID: mdl-32673872

Bacillus pumilus SWU7-1 was isolated from strontium ion (Sr(II))-uncontaminated soil, its biosorption potential was evaluated, and the effect of γ-ray radiation treatment on its biosorption was discussed. Domesticated under Sr(II) stress promoted the biosorption ability of B. pumilus to Sr(II), and the biosorption efficiency increased from 46.09% to 94.69%. At a lower initial concentration, the living bacteria had the ability to resist the biosorption of Sr(II). The optimal initial concentration range was 54-130 mg/L. The biosorption profile was better matched by Langmuir than Freundlich model, showing that the biosorption process of Sr(II) by the experimental strain was closer to the surface adsorption. According to Langmuir model, the maximum biosorption capacity of B. pumilus on Sr (II) was 299.4 mg/g. During the bacterial growth in the biosorption process, the changes in biosorption capacity and efficiency can be divided into two phases, and a pseudo-second-order model is followed in each phase. There was no significant difference in the biosorption efficiency of bacteria with different culture time after γ-ray radiation, and all of them were above 90%, which showed that B. pumilus had significant radiation resistance under experimental conditions. This study emphasized the potential application of B. pumilus in the treatment of radioactive Sr(II) pollution by biosorption.


Adsorption , Bacillus pumilus/metabolism , Biodegradation, Environmental , Strontium Isotopes/metabolism , Kinetics , Soil Microbiology , Soil Pollutants, Radioactive , Water Pollutants, Chemical/metabolism
10.
Environ Sci Pollut Res Int ; 27(15): 17561-17570, 2020 May.
Article En | MEDLINE | ID: mdl-31502051

Spatial scale is a crucial factor in drought propagation and characterization. To investigate the response behavior of the meteorological drought-hydrological drought propagation to different watershed scales, three nested subbasins in the upper Huaihe River basin were selected as case study sites. The Standardized Precipitation Index and the Standardized Streamflow Index were adopted to characterize the meteorological drought and hydrological drought respectively. The relationship between meteorological drought and hydrological drought was then examined by wavelet coherency analysis and linear/nonlinear regression models. Results showed that (1) linear regression model captured drought propagation best in all subbasins, and the correlation strengthened as the watershed area increased with drought duration being highest correlated among the five drought characteristics; (2) with the watershed area growth, the coherence between hydrological and meteorological drought reduced, the lagging effect of hydrological drought attenuated, and the hydrological one tended to be more synchronized with meteorological one over the long period; and (3) the larger the watershed scale, the later (earlier) occurrence of the hydrological drought onset (termination), while the longer drought duration and larger magnitude for triggering hydrological drought.


Meteorology , Rivers , China , Droughts , Hydrology
12.
Nat Commun ; 10(1): 2288, 2019 05 23.
Article En | MEDLINE | ID: mdl-31123265

Recurrent acute respiratory tract infections (ARTIs) affect a large population, yet the specific decisive factors are largely unknown. Here we study a population of 4407 children diagnosed with ARTI, comparing respiratory virome and serum cytokine profiles associated with multiple ARTIs and single ARTI during a six-year period. The relative abundance of Propionibacterium phages is significantly elevated in multiple ARTIs compared to single ARTI group. Serum levels of TIMP-1 and PDGF-BB are markedly increased in multiple ARTIs compared to single-ARTI and non-ARTI controls, making these two cytokines potential predictors for multiple ARTIs. The presence of Propionibacterium phages is associated with higher levels of TIMP-1 and PDGF-BB. Receiver operating characteristic (ROC) curve analyses show that the combination of TIMP-1, PDGF-BB and Propionibacterium phages could be a strong predictor for multiple ARTIs. These findings indicate that respiratory microbe homeostasis and specific cytokines are associated with the onset of multiple ARTIs over time.


Bacteriophages/isolation & purification , Cytokines/blood , Respiratory System/virology , Respiratory Tract Infections/blood , Acute Disease , Bacteriophages/genetics , Child , Child, Preschool , Cytokines/immunology , Disease Susceptibility/blood , Disease Susceptibility/immunology , Disease Susceptibility/microbiology , Female , High-Throughput Nucleotide Sequencing/methods , Humans , Infant , Longitudinal Studies , Male , Metagenomics/methods , Microbiota/genetics , Propionibacterium/virology , Proteomics/methods , Recurrence , Respiratory System/immunology , Respiratory Tract Infections/immunology , Respiratory Tract Infections/microbiology , Retrospective Studies
13.
Int J Stem Cells ; 12(1): 84-94, 2019 Mar 30.
Article En | MEDLINE | ID: mdl-30836724

BACKGROUND AND OBJECTIVES: The International Society for Cellular Therapy (ISCT) proposed a set of minimal markers for identifying human mesenchymal stromal cells (hMSCs) in 2007. Since then, with the growing interest of better characterising hMSCs, various additional surface markers have been proposed. However, the impact of how culture conditions, in particular, the culture surface, vary the expression of hMSC markers was overlooked. METHODS AND RESULTS: In this study, we utilized the RNA sequencing data on hMSCs cultured on different surfaces to investigate the variation of the proposed hMSC biomarkers. One of the three ISCT proposed positive biomarker, CD90 was found to be significantly down regulated on hMSCs culture on fibrous surfaces when compared to flat surfaces. The detected gene expression values for 177 hMSCs biomarkers compiled from the literature are reported here. Correlation and cluster analysis revealed the existence of different biomarker communities that displayed a similar expression profile. We found a list of hMSCs biomarkers which are the least sensitive to a change in surface properties and another list of biomarkers which are found to have high sensitivity to a change in surface properties. CONCLUSIONS: This study demonstrated that substrate properties have paramount effect on altering the expressions of hMSCs biomarkers and the proposed list of substrate-stable and substrate-sensitive biomarkers would better assist in the population characterisation. However, proteomic level analysis would be essential to confirm the observations noted.

14.
Biomed Mater ; 14(3): 035012, 2019 04 05.
Article En | MEDLINE | ID: mdl-30849767

Culturing human Mesenchymal stromal cells (hMSCs) in vitro in hypoxic conditions resulted in reduced senescence, enhanced pluripotency and altered proliferation rate. It has been known that in vitro hypoxia affects expression of cell surface proteins. However, the impact of culture surfaces on the hypoxia-regulated genes (HRG) have not yet been reported. This study utilized Next-Generation sequencing to analyse the changes in the gene expression levels of HRG for hMSCs cultured on different culture surfaces. The samples, which were cultured on four different synthesized surfaces (treatments) and tissue culture plate (control), resulted in a difference in growth rate. The sequencing results revealed that the transcription of a number of key genes involved in regulating hypoxic functions were significantly altered, including HIF2A, a marker for potency, differentiation, and various cellular functions. Significant alternations in the expression levels of previously reported oxygen-sensitive surface proteins were detected in this study, some of which closely correlate with the expression levels of HIF2A. Our analysis of the hMSCs transcriptome and HRG mapped out a list of genes encoding surface proteins which may directly regulate or be regulated by HIF2A. The findings from this study showed that culture surfaces have an impact on regulating the expression profile of HRG. Therefore, novel culture surfaces may be designed to selectively activate HIF2A and other HRG and pathways under in vitro normoxia. The understanding of the crosstalk between the regulating genes of hypoxia and culture surfaces may be utilized to strengthen desired hypoxic functions.


Gene Expression Regulation , Mesenchymal Stem Cells/cytology , Basic Helix-Loop-Helix Transcription Factors/metabolism , Bone Marrow Cells/metabolism , Cell Differentiation , Cell Hypoxia , Cell Proliferation , Cells, Cultured , Cluster Analysis , Gene Expression Profiling , Humans , Hypoxia-Inducible Factor 1, alpha Subunit/metabolism , Oxygen/metabolism , Surface Properties
15.
Clin Infect Dis ; 69(5): 861-864, 2019 08 16.
Article En | MEDLINE | ID: mdl-30715242

Using metagenomics analysis, we are the first to identify the presence of a small, circular, single-stranded Gemykibivirus (GkV) genome from the respiratory tract of an elderly woman with severe acute respiratory distress syndrome. Our results suggest that further studies on whether GkVs infect humans and cause respiratory disease are needed.


DNA Virus Infections/diagnosis , DNA Viruses/isolation & purification , Genome, Viral , Respiratory Distress Syndrome/virology , Acute Disease , Age Factors , Aged , Bronchi/virology , DNA Virus Infections/virology , DNA Viruses/genetics , Humans , Metagenomics , Whole Genome Sequencing
16.
RSC Adv ; 9(70): 40827-40834, 2019 Dec 09.
Article En | MEDLINE | ID: mdl-35540045

The deposition and dissolution of calcium carbonate can be affected by the action of biological factors, such as microbial-induced carbonate precipitation (MICP). Bacillus spp. has been isolated and applied to prevent soil erosion, increase the stability of slopes, dikes and dunes. However, previous studies have been always limited to a single calcium source (CaCl2) to evaluate the roles of bacteria, and the deposition and curing effect has not yet been quantified. Here, we designed deposition experiments to determine the effect of Bacillus cereus with different calcium sources and applied it to sand curing to measure the amount of deposition and curing. The results demonstrated that vaterite was produced when the Bacillus cereus participated. Also, more deposition was produced in the Ca(CH3COO)2 and CaCl2 groups, but the Ca(NO3)2 group showed optimal curing effects in the sand curing test due to the denser and more uniform deposition. This research will provide an important reference for the design and application of microbial-induced carbonate precipitation.

17.
Int J Mol Sci ; 19(8)2018 Aug 09.
Article En | MEDLINE | ID: mdl-30096912

Variations in substrate chemistry and the micro-structure were shown to have a significant effect on the biology of human mesenchymal stromal cells (hMSCs). This occurs when differences in the surface properties indirectly modulate pathways within numerous signaling networks that control cell fate. To understand how the surface features affect hMSC gene expression, we performed RNA-sequencing analysis of bone marrow-derived hMSCs cultured on tissue culture-treated polystyrene (TCP) and poly(l-lactide) (PLLA) based substrates of differing topography (Fl: flat and Fs: fibrous) and chemistry (Pr: pristine and Am: aminated). Whilst 80% of gene expression remained similar for cells cultured on test substrates, the analysis of differentially expressed genes (DEGs) revealed that surface topography significantly altered gene expression more than surface chemistry. The Fl and Fs topologies introduced opposite directional alternations in gene expression when compared to TCP control. In addition, the effect of chemical treatment interacted with that of topography in a synergistic manner with the Pr samples promoting more DEGs than Am samples in all gene ontology function groups. These findings not only highlight the significance of the culture surface on regulating the overall gene expression profile but also provide novel insights into cell-material interactions that could help further design the next-generation biomaterials to facilitate hMSC applications. At the same time, further studies are required to investigate whether or not the observations noted correlate with subsequent protein expression and functionality of cells.


Cell Differentiation/genetics , Cell Proliferation/genetics , Mesenchymal Stem Cells/cytology , Osteogenesis/genetics , Bone Marrow Cells/cytology , Bone Marrow Cells/metabolism , Cells, Cultured , Gene Expression Regulation, Developmental/genetics , High-Throughput Nucleotide Sequencing , Humans , Mesenchymal Stem Cells/metabolism , Osteogenesis/drug effects
18.
Per Med ; 15(4): 251-269, 2018 07 01.
Article En | MEDLINE | ID: mdl-29984631

AIM: Co-infection in HIV-1 patients with Mycobacterium tuberculosis poses considerable risk of developing the immune reconstitution inflammatory syndrome (IRIS), especially upon the initiation of antiretroviral therapy (ART). Methodology & results: For transcriptomic analysis, peripheral blood mononuclear cells' whole gene expression was used from three patient groups: HIV+ (H), HIV-TB+ (HT), HIV-TB+ with IRIS (HTI). Pathway enrichment and functional analysis was performed before and after highly active ART. Genes in the interferon-stimulating and ZNF families maintained tight functional interaction and tilted the balance in favor of TB-IRIS. DISCUSSION & CONCLUSION: The functional impairment of interaction between ZNF genes and interferon-stimulated genes, along with higher expression of S100A8/S100A9 genes possibly forms the genomic basis of TB-IRIS in a subset of HIV patients while on highly active ART.


Gene Expression Profiling/methods , Gene Regulatory Networks , HIV Infections/drug therapy , Immune Reconstitution Inflammatory Syndrome/genetics , Tuberculosis/genetics , Antiretroviral Therapy, Highly Active , Calgranulin A/genetics , Calgranulin B/genetics , Coinfection/genetics , Gene Expression Regulation/drug effects , Genome-Wide Association Study , HIV Infections/genetics , Humans , Interferons/pharmacology , Interferons/therapeutic use , Sequence Analysis, RNA , Zinc Fingers
19.
Front Microbiol ; 9: 3138, 2018.
Article En | MEDLINE | ID: mdl-30619206

Adult giant pandas (Ailuropoda melanoleuca) express transitional characteristics in that they consume bamboos, despite their carnivore-like digestive tracts. Their genome contains no cellulolytic enzymes; therefore, understanding the development of the giant panda gut microbiome, especially in early life, is important for decoding the rules underlying gut microbial formation, inheritance and dietary transitions. With deep metagenomic sequencing, we investigated the gut microbiomes of two newborn giant panda brothers and their parents living in Macao, China, from 2016 to 2017. Both giant panda cubs exhibited progressive increases in gut microbial richness during growth, particularly from the 6th month after birth. Enterobacteriaceae dominated the gut microbial compositions in both adult giant pandas and cubs. A total of 583 co-abundance genes (CAGs) and about 79 metagenomic species (MGS) from bacteria or viruses displayed significant changes with age. Seven genera (Shewanella, Oblitimonas, Helicobacter, Haemophilus, Aeromonas, Listeria, and Fusobacterium) showed great importance with respect to gut microbial structural determination in the nursing stage of giant panda cubs. Furthermore, 10 orthologous gene functions and 44 pathways showed significant changes with age. Of the significant pathways, 16 from Escherichia, Klebsiella, Propionibacterium, Lactobacillus, and Lactococcus displayed marked differences between parents and their cubs at birth, while 29 pathways from Escherichia, Campylobacter and Lactobacillus exhibited significant increase in cubs from 6 to 9 months of age. In addition, oxidoreductases, transferases, and hydrolases dominated the significantly changed gut microbial enzymes during the growth of giant panda cubs, while few of them were involved in cellulose degradation. The findings indicated diet-stimulated gut microbiome transitions and the important role of Enterobacteriaceae in the guts of giant panda in early life.

20.
Environ Sci Pollut Res Int ; 25(23): 22429-22436, 2018 Aug.
Article En | MEDLINE | ID: mdl-29247412

Microorganism cells and spores are the main components of PM2.5 (fine particulate matter) as well as fine mineral particles. In the microscopic system, the microorganisms will affect the minerals through attachment, charge neutralization, and dissolution related to the cell surface structure and metabolite. To explore the process and the results of microbial cells and their extracellular polymeric substances (EPS) acting on the surface properties of minerals of PM2.5 through the metabolism, a common native soil bacterium Bacillus mucitaginosus with abundant extracellular polymers was chosen as the tested strain. Meanwhile, as one of the PM2.5 common minerals, calcite fine particles were taken as the research object to explore the influence of microbial cells and extracellular polymers on its surface properties. High performance liquid chromatography (HPLC), inductively coupled plasma spectrometry (ICP), Zeta potential analysis, Fourier-transform infrared spectroscopy (FTIR), X-ray diffraction spectroscopy (XRD), and scanning electron microscopy (SEM) were used to characterize the composition of EPS, the soluble ions, surface charge, surface groups, crystal form, and surface morphology of calcite residual solid after being treated by the bacterial cells and EPS. The results revealed the EPS of B. mucitaginosus mainly consisted of protein and polysaccharides. Both the whole cell and its EPS could promote the dissolution of calcite particles into calcium ions. Due to the adhesion of organic groups on the calcite surface, the surface potential shifted significantly in the negative direction and the solution pH was clearly increased. The morphology of calcite surface was significantly changed after dissolution and re-crystallization. Experimental results also showed that the existence of the bacteria cells and EPS significantly affected the surface properties of calcite and provide a theoretical basis for the mechanism of PM fine particulate matter on human health impact for further study.


Bacillus/chemistry , Calcium Carbonate/chemistry , Particulate Matter/chemistry , Air Pollutants/chemistry , Bacillus/physiology , Crystallization , Hydrogen-Ion Concentration , Microscopy, Electron, Scanning , Polymers/chemistry , Polysaccharides/chemistry , Spectroscopy, Fourier Transform Infrared , Surface Properties , X-Ray Diffraction
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