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author:("Su, dongxiang")
1.  Genomic Evolution of 11 Type Strains within Family Planctomycetaceae 
PLoS ONE  2014;9(1):e86752.
The species in family Planctomycetaceae are ideal groups for investigating the origin of eukaryotes. Their cells are divided by a lipidic intracytoplasmic membrane and they share a number of eukaryote-like molecular characteristics. However, their genomic structures, potential abilities, and evolutionary status are still unknown. In this study, we searched for common protein families and a core genome/pan genome based on 11 sequenced species in family Planctomycetaceae. Then, we constructed phylogenetic tree based on their 832 common protein families. We also annotated the 11 genomes using the Clusters of Orthologous Groups database. Moreover, we predicted and reconstructed their core/pan metabolic pathways using the KEGG (Kyoto Encyclopedia of Genes and Genomes) orthology system. Subsequently, we identified genomic islands (GIs) and structural variations (SVs) among the five complete genomes and we specifically investigated the integration of two Planctomycetaceae plasmids in all 11 genomes. The results indicate that Planctomycetaceae species share diverse genomic variations and unique genomic characteristics, as well as have huge potential for human applications.
doi:10.1371/journal.pone.0086752
PMCID: PMC3906078  PMID: 24489782
2.  Genome Sequence of Bacillus cereus Strain LCT-BC235, Carried by the Shenzhou VIII Spacecraft 
Genome Announcements  2014;2(1):e00665-13.
In order to explore the effect of space environments on Bacillus cereus, we determined the draft genome sequence of a B. cereus strain, LCT-BC235, which was isolated after space flight.
doi:10.1128/genomeA.00665-13
PMCID: PMC3886938  PMID: 24407625
3.  Draft Genome Sequence of Bacillus cereus LCT-BC25, Isolated from Space Flight 
Genome Announcements  2014;2(1):e00667-13.
Bacillus cereus strain LCT-BC25, which was carried by the Shenzhou VIII spacecraft, traveled in space for about 398 h. To investigate the response of B. cereus to space environments, we determined the genome sequence of B. cereus strain LCT-BC25, which was isolated after space flight.
doi:10.1128/genomeA.00667-13
PMCID: PMC3879601  PMID: 24385570
4.  A multi-omic analysis of an Enterococcus faecium mutant reveals specific genetic mutations and dramatic changes in mRNA and protein expression 
BMC Microbiology  2013;13:304.
Background
For a long time, Enterococcus faecium was considered a harmless commensal of the mammalian gastrointestinal (GI) tract and was used as a probiotic in fermented foods. In recent decades, E. faecium has been recognised as an opportunistic pathogen that causes diseases such as neonatal meningitis, urinary tract infections, bacteremia, bacterial endocarditis and diverticulitis. E. faecium could be taken into space with astronauts and exposed to the space environment. Thus, it is necessary to observe the phenotypic and molecular changes of E. faecium after spaceflight.
Results
An E. faecium mutant with biochemical features that are different from those of the wild-type strain was obtained from subculture after flight on the SHENZHOU-8 spacecraft. To understand the underlying mechanism causing these changes, the whole genomes of both the mutant and the WT strains were sequenced using Illumina technology. The genomic comparison revealed that dprA, a recombination-mediator gene, and arpU, a gene associated with cell wall growth, were mutated. Comparative transcriptomic and proteomic analyses showed that differentially expressed genes or proteins were involved with replication, recombination, repair, cell wall biogenesis, glycometabolism, lipid metabolism, amino acid metabolism, predicted general function and energy production/conversion.
Conclusion
This study analysed the comprehensive genomic, transcriptomic and proteomic changes of an E. faecium mutant from subcultures that were loaded on the SHENZHOU-8 spacecraft. The implications of these gene mutations and expression changes and their underlying mechanisms should be investigated in the future. We hope that the current exploration of multiple “-omics” analyses of this E. faecium mutant will provide clues for future studies on this opportunistic pathogen.
doi:10.1186/1471-2180-13-304
PMCID: PMC3879163  PMID: 24373636
E. faecium; Genome; Transcriptome; Proteome; Multi-omics
5.  Assessment of the green florescence protein labeling method for tracking implanted mesenchymal stem cells 
Cytotechnology  2012;64(4):391-401.
Although green fluorescent protein (GFP) labeling is widely accepted as a tracking method, much remains uncertain regarding the retention of injected GFP-labeled cells implanted in ischemic organs. In this study, we evaluate the effectiveness of GFP for identifying and tracking implanted bone marrow- mesenchymal stem cells (BM-MSCs) and the effect of GFP on the paracrine actions of these cells. MSCs isolated from rat femur marrow were transduced with a recombinant adenovirus carrying GFP. After transplantation of the GFP-labeled BM-MSCs into the infarct zone of rat hearts, the survival, distribution, and migration of the labeled cells were analyzed at 3, 7, 14, and 28 days. To evaluate the effect of GFP on the paracrine actions of BM-MSCs, Western blot analysis was performed to detect the expression of vascular endothelial growth factor (VEGF), b fibroblast growth factor (b FGF), tissue inhibitor of metalloproteinase-1 (TIMP-1) and matrix metalloproteinases-2 (MMP-2). GFP was successfully expressed by BM-MSCs in vitro. At 14 days after cell transplantation the GFP-positive cells could not be detected via confocal microscopy. By using a GFP antibody, distinct GFP-positive cells could be seen and quantitative analysis showed that the expression volume of GFP was 6.42 ± 0.92 mm3 after 3 days, 1.24 ± 0.76 mm3 after 7 days, 0.33 ± 0.03 mm3 after 14 days, and 0.09 ± 0.05 mm3 after 28 days. GFP labeling did not adversely affect the paracrine actions of BM-MSCs. GFP labeling could be used to track MSC distribution and their fate for at least 28 days after delivery to rat hearts with myocardial infarction, and this stem cell tracking strategy did not adversely affect the paracrine actions of BM-MSCs.
doi:10.1007/s10616-011-9417-y
PMCID: PMC3397108  PMID: 22373822
Cell tracking; Green fluorescent protein; Mesenchymal stem cells; paracrine; Myocardial infarction
6.  Diagnostic Value of Dynamics Serum sCD163, sTREM-1, PCT, and CRP in Differentiating Sepsis, Severity Assessment, and Prognostic Prediction 
Mediators of Inflammation  2013;2013:969875.
Objective. To describe the dynamics changes of sCD163, soluble serum triggering receptor expressed on myeloid cells-1 (sTREM-1), procalcitonin (PCT), and C-reactive protein (CRP) during the course of sepsis, as well as their outcome prediction. Patients and Methods. An SIRS group (30 cases) and a sepsis group (100 cases) were involved in this study. Based on a 28-day survival, the sepsis was further divided into the survivors' and nonsurvivors' groups. Serum sTREM-1, sCD163, PCT, CRP, and WBC counts were tested on days 1, 3, 5, 7, 10, and 14. Results. On the ICU admission, the sepsis group displayed higher levels of sTREM-1, sCD163, PCT, and CRP than the SIRS group (P < 0.05). Although PCT and sTREM-1 are good markers to identify severity, sTREM-1 is more reliable, which proved to be a risk factor related to sepsis. During a 14-day observation, sCD163, sTREM-1, PCT, and SOFA scores continued to climb among nonsurvivors, while their WBC and CRP went down. Both sCD163 and SOFA scores are risk factors impacting the survival time. Conclusion. With regard to sepsis diagnosis and severity, sTREM-1 is more ideal and constitutes a risk factor. sCD163 is of a positive value in dynamic prognostic assessment and may be taken as a survival-impacting risk factor.
doi:10.1155/2013/969875
PMCID: PMC3713373  PMID: 23935252
7.  Genome Sequence of Enterococcus faecium Clinical Isolate LCT-EF128 
Journal of Bacteriology  2012;194(17):4765.
Enterococcus faecium, an opportunistic human pathogen that inhabits the gastrointestinal tracts of most mammals, has emerged as an important opportunistic nosocomial pathogen and is a prominent cause of multiresistant nosocomial infections. Here, we report the draft genome sequence of strain LCT-EF128, isolated from clinical specimens.
doi:10.1128/JB.00996-12
PMCID: PMC3415489  PMID: 22887667
8.  Draft Genome Sequence of Escherichia coli Strain LCT-EC59 
Genome Announcements  2013;1(1):e00242-12.
The space environment is a very special condition under which many organisms change many features. Escherichia coli is employed widely as a prokaryotic model organism in the fields of biotechnology and microbiology. Here, we present the draft genome sequence of E. coli strain LCT-EC59 exposed to space conditions.
doi:10.1128/genomeA.00242-12
PMCID: PMC3587949  PMID: 23469355
9.  Draft Genome Sequences of the Enterococcus faecium Strain LCT-EF258 
Genome Announcements  2013;1(1):e00147-12.
The space environment has been shown to affect microbes by altering various features, including morphology, growth rate, metabolism, virulence, drug resistance, and gene expression and mutation. Here we present the draft genome sequence of the Enterococcus faecium strain LCT-EF258, derived from the E. faecium strain CGMCC 1.1736, which was exposed to 17-day space flight.
doi:10.1128/genomeA.00147-12
PMCID: PMC3569272  PMID: 23409254
10.  Draft Genome Sequence of Serratia marcescens Strain LCT-SM213 
Journal of Bacteriology  2012;194(16):4477-4478.
Serratia marcescens is a species of Gram-negative, rod-shaped bacterium of the family Enterobacteriaceae. S. marcescens can cause nosocomial infections, particularly catheter-associated bacteremia, urinary tract infections, and wound infections. Here, we present the draft genome sequence of Serratia marcescens strain LCT-SM213, which was isolated from CGMCC 1.1857.
doi:10.1128/JB.00933-12
PMCID: PMC3416218  PMID: 22843602
11.  Draft Genome Sequence of Escherichia coli LCT-EC106 
Journal of Bacteriology  2012;194(16):4443-4444.
Escherichia coli is a Gram-negative, rod-shaped bacterium that is commonly found in the intestine of warm-blooded organisms. Most E. coli strains are harmless, but some serotypes can cause serious food poisoning in humans. Here, we present the complete genome sequence of Escherichia coli LCT-EC106, which was isolated from CGMCC 1.2385.
doi:10.1128/JB.00853-12
PMCID: PMC3416261  PMID: 22843582
12.  Whole-Genome Sequence of Staphylococcus aureus Strain LCT-SA112 
Journal of Bacteriology  2012;194(15):4124.
Staphylococcus aureus is a facultative anaerobic Gram-positive coccal bacterium. S. aureus is the most common species of Staphylococcus to cause staphylococcal infections, which are very common in clinical medicine. Here we report the genome sequence of S. aureus strain LCT-SA112, which was isolated from S. aureus subsp. aureus CGMCC 1.230.
doi:10.1128/JB.00710-12
PMCID: PMC3416511  PMID: 22815443
13.  Draft Genome Sequences and Annotation of Enterococcus faecium Strain LCT-EF20 
Genome Announcements  2013;1(1):e00083-12.
The space environment is reported to cause biological alterations in microorganisms, such as growth, drug resistance, and virulence. Here, we present the model of Enterococcus faecium to investigate the effects of space conditions on the microbe and on the whole-genome sequences of the strain LCT-EF20 after being exposed to space flight.
doi:10.1128/genomeA.00083-12
PMCID: PMC3569280  PMID: 23405294
14.  Identification of Novel Biomarkers for Sepsis Prognosis via Urinary Proteomic Analysis Using iTRAQ Labeling and 2D-LC-MS/MS 
PLoS ONE  2013;8(1):e54237.
Objectives
Sepsis is the major cause of death for critically ill patients. Recent progress in proteomics permits a thorough characterization of the mechanisms associated with critical illness. The purpose of this study was to screen potential biomarkers for early prognostic assessment of patients with sepsis.
Methods
For the discovery stage, 30 sepsis patients with different prognoses were selected. Urinary proteins were identified using isobaric tags for relative and absolute quantitation (iTRAQ) coupled with LC-MS/MS. Mass spec instrument analysis were performed with Mascot software and the International Protein Index (IPI); bioinformatic analyses were used by the algorithm of set and the Gene Ontology (GO) Database. For the verification stage, the study involved another 54 sepsis-hospitalized patients, with equal numbers of patients in survivor and non-survivor groups based on 28-day survival. Differentially expressed proteins were verified by Western Blot.
Results
A total of 232 unique proteins were identified. Proteins that were differentially expressed were further analyzed based on the pathophysiology of sepsis and biomathematics. For sepsis prognosis, five proteins were significantly up-regulated: selenium binding protein-1, heparan sulfate proteoglycan-2, alpha-1-B glycoprotein, haptoglobin, and lipocalin; two proteins were significantly down-regulated: lysosome-associated membrane proteins-1 and dipeptidyl peptidase-4. Based on gene ontology clustering, these proteins were associated with the biological processes of lipid homeostasis, cartilage development, iron ion transport, and certain metabolic processes. Urinary LAMP-1 was down-regulated, consistent with the Western Blot validation.
Conclusion
This study provides the proteomic analysis of urine to identify prognostic biomarkers of sepsis. The seven identified proteins provide insight into the mechanism of sepsis. Low urinary LAMP-1 levels may be useful for early prognostic assessment of sepsis.
Trial Registration
ClinicalTrial.gov NCT01493492
doi:10.1371/journal.pone.0054237
PMCID: PMC3553154  PMID: 23372690
15.  Draft Genome Sequence of Pseudomonas aeruginosa Strain ATCC 27853 
Journal of Bacteriology  2012;194(14):3755.
Pseudomonas aeruginosa is a common bacterium that can cause disease. The versatility of Pseudomonas aeruginosa enables the organism to infect damaged tissues or those with reduced immunity which cause inflammation and sepsis. Here we report the genome sequence of the strain ATCC 27853.
doi:10.1128/JB.00690-12
PMCID: PMC3393497  PMID: 22740676
16.  Draft Genome Sequence of Bacillus cereus Strain LCT-BC244 
Journal of Bacteriology  2012;194(13):3549.
Bacillus cereus is a prevalent, soil-dwelling, Gram-positive bacterium. Some strains are harmful to humans and cause food-borne illness, while other strains can be beneficial as probiotics for animals. To gain insight into the bacterial genetic determinants, we report the genome sequence of a strain, LCT-BC244, which was isolated from CGMCC 1.230.
doi:10.1128/JB.00580-12
PMCID: PMC3434717  PMID: 22689237
17.  Draft Genome Sequence of Enterococcus faecium Strain LCT-EF90 
Journal of Bacteriology  2012;194(13):3556-3557.
Enterococcus faecium is an opportunistic human pathogen, found widely in the human gastrointestinal tract, and can also be isolated from a variety of plants, animals, insects, and other environmental sources. Here, we present the fine draft genome sequence of E. faecium LCT-EF90.
doi:10.1128/JB.00529-12
PMCID: PMC3434750  PMID: 22689242
18.  Whole-Genome Sequence of Klebsiella pneumonia Strain LCT-KP214 
Journal of Bacteriology  2012;194(12):3281.
Klebsiella pneumoniae is a Gram-negative, nonmotile, encapsulated, lactose-fermenting, facultative anaerobic, rod-shaped bacterium found in the normal flora of the mouth, skin, and intestines. Here we present the fine-draft genome sequence of K. pneumoniae strain LCT-KP214, which originated from K. pneumoniae strain CGMCC 1.1736.
doi:10.1128/JB.00531-12
PMCID: PMC3370881  PMID: 22628509
19.  Diagnostic value of urine sCD163 levels for sepsis and relevant acute kidney injury: a prospective study 
BMC Nephrology  2012;13:123.
Background
Sepsis is a common syndrome in critically ill patients and easily leads to the occurrence of acute kidney injury (AKI), with high mortality rates. This study aimed to investigate the diagnostic value of urine soluble CD163 (sCD163) for identification of sepsis, severity of sepsis, and for secondary AKI, and to assess the patients’ prognosis.
Methods
We enrolled 20 cases with systemic inflammatory response syndrome (SIRS), 40 cases with sepsis (further divided into 17 sepsis cases and 23 severe sepsis cases) admitted to the intensive care unit (ICU), and 20 control cases. Results for urine sCD163 were recorded on the day of admission to the ICU, and AKI occurrence was noted.
Results
On the day of ICU admission, the sepsis group exhibited higher levels of urine sCD163 (74.8 ng/ml; range: 47.9-148.3 ng/ml) compared with those in the SIRS group (31.9 ng/ml; 16.8-48.0, P < 0.001). The area under the curve (AUC) was 0.83 (95% confidence interval [CI]: 0.72-0.94, P < 0.001) the sensitivity was 0.83, and the specificity was 0.75 (based on a cut-off point of 43.0 ng/ml). Moreover, the severe sepsis group appeared to have a higher level of sCD163 compared with that in the sepsis group (76.2; 47.2-167.5 ng/ml vs. 74.2; 46.2-131.6 ng/ml), but this was not significant. For 15 patients with AKI, urine sCD163 levels at AKI diagnosis were significantly higher than those of the remaining 35 sepsis patients upon ICU admission (121.0; 74.6-299.1 ng/ml vs. 61.8; 42.8-128.3 ng/ml, P = 0.049). The AUC for urine sCD163 was 0.688 (95% CI: 0.51-0.87, P = 0.049). Sepsis patients with a poor prognosis showed a higher urine sCD163 level at ICU admission (98.6; 50.3-275.6 ng/ml vs. 68.0; 44.8-114.5 ng/ml), but this was not significant. Patients with AKI with a poor prognosis had higher sCD163 levels than those in patients with a better prognosis (205.9; 38.6-766.0 ng/ml vs. 80.9; 74.9-141.0 ng/ml), but this was not significant.
Conclusions
This study shows, for the first time, the potential value of urine sCD163 levels for identifying sepsis and diagnosing AKI, as well as for assessment of patients’ prognosis.
Trial Registration
ChiCTR-ONC-10000812
doi:10.1186/1471-2369-13-123
PMCID: PMC3506529  PMID: 23013330
Urine; Soluble CD163 (sCD163); Sepsis; Systemic inflammatory response syndrome (SIRS); Prognosis; Acute kidney injury (AKI)
20.  Value of soluble TREM-1, procalcitonin, and C-reactive protein serum levels as biomarkers for detecting bacteremia among sepsis patients with new fever in intensive care units: a prospective cohort study 
BMC Infectious Diseases  2012;12:157.
Background
The purpose of this study was to explore the diagnostic value of soluble triggering receptor expressed on myeloid cells 1 (sTREM-1), procalcitonin (PCT), and C-reactive protein (CRP) serum levels for differentiating sepsis from SIRS, identifying new fever caused by bacteremia, and assessing prognosis when new fever occurred.
Methods
We enrolled 144 intensive care unit (ICU) patients: 60 with systemic inflammatory response syndrome (SIRS) and 84 with sepsis complicated by new fever at more than 48 h after ICU admission. Serum sTREM-1, PCT, and CRP levels were measured on the day of admission and at the occurrence of new fever (>38.3°C) during hospitalization. Based on the blood culture results, the patients were divided into a blood culture-positive bacteremia group (33 patients) and blood culture-negative group (51 patients). Based on 28-day survival, all patients, both blood culture-positive and -negative, were further divided into survivor and nonsurvivor groups.
Results
On ICU day 1, the sepsis group had higher serum sTREM-1, PCT, and CRP levels compared with the SIRS group (P <0.05). The areas under the curve (AUC) for these indicators were 0.868 (95% CI, 0.798–0.938), 0.729 (95% CI, 0.637–0.821), and 0.679 (95% CI, 0.578–0.771), respectively. With 108.9 pg/ml as the cut-off point for serum sTREM-1, sensitivity was 0.83 and specificity was 0.81. There was no statistically significant difference in serum sTREM-1 or PCT levels between the blood culture-positive and -negative bacteremia groups with ICU-acquired new fever. However, the nonsurvivors in the blood culture-positive bacteremia group had higher levels of serum sTREM-1 and PCT (P <0.05), with a prognostic AUC for serum sTREM-1 of 0.868 (95% CI, 0.740–0.997).
Conclusions
Serum sTREM-1, PCT, and CRP levels each have a role in the early diagnosis of sepsis. Serum sTREM-1, with the highest sensitivity and specificity of all indicators studied, is especially notable. sTREM-1, PCT, and CRP levels are of no use in determining new fever caused by bacteremia in ICU patients, but sTREM-1 levels reflect the prognosis of bacteremia.
Trial registration
ClinicalTrial.gov identifier NCT01410578
doi:10.1186/1471-2334-12-157
PMCID: PMC3426475  PMID: 22809118
Soluble triggering receptor expressed on myeloid cells 1 (sTREM-1); Fever; Sepsis; Bacteremia; Diagnosis; Prognosis

Results 1-20 (20)