Isolation, identification and characterization of phenolic acid-degrading bacteria from soil

AIMS

To isolate, identify and characterize phenolic acid-degrading bacteria and reduce plant growth inhibition caused by phenolic acids.

METHODS AND RESULTS

A total of 11 bacterial isolates with high phthalic acid (PA)-degrading ability were obtained using mineral salt medium (MSM) medium containing PA as sole carbon source. These isolates were identified as Arthrobacter globiformis, Pseudomonas putida and Pseudomonas hunanensis by sequence analyses of the 16S rRNA gene. Among them, five Pseudomonas strains could also effectively degrade ferulic acid (FA), p-hydroxybenzoic acid (PHBA) and syringic acid (SA) in MSM solution. P. putida strain 7 and P. hunanensis strain 10 showed highly efficient degradation of PA, SA, FA and PHBA, and could reduce their inhibition of lily, watermelon, poplar and strawberry seedling growth in soils respectively. These two strains could promote plant growth in soil with phenolic acids.

CONCLUSIONS

In this study, bacterial strains with highly efficient phenolic acid-degrading abilities could not only effectively reduce the autotoxicity of phenolic acids on plants but also were able to promote plant growth in soil with phenolic acids.

SIGNIFICANCE AND IMPACT OF THE STUDY

In this study, Pseudomonas can promote plant growth while degrading phenolic acids. Our results provide new choices for the biological removal of autotoxins.

Yeast cell wall product enhanced intestinal IgA response and changed cecum microflora species after oral vaccination in chickens

The study was designed to explore the effect of a commercial yeast cell wall product (YP) on chicken intestinal IgA response and cecum microbiome after oral vaccination. Chickens were fed with YP during the experiments and orally immunized with live Newcastle disease virus (NDV) vaccine at 2 wk of age. Then, the animals were sacrificed, and samples were collected to measure the indicators of hemagglutination inhibition (HI), IgA response, IgA + cells, and cecum microbiome populations. The results showed that supplement of YP significantly enhanced serum NDV HI titer, intestinal NDV-specific secretory IgA, and intestinal IgA + cells. The sequencing results revealed that obviously increased relative abundance of Ruminococcaceae and decreased population of Bacteroidaceae in cecum were found in YP group. In summary, YP supplementation in diet enhanced intestinal IgA response to NDV vaccination by oral route and modulated the cecum microbiota to the advantage of the host in chickens.

Molecular-Weight Growth in Ozone-Initiated Low-Temperature Oxidation of Methyl Crotonate

We report experiments of ozone-initiated low-temperature oxidation of methyl crotonate (MC, CH₃-CH═CH-C(O)OCH₃) from 420 to 660 K in a near-atmospheric-pressure jet-stirred reactor using photoionization molecular-beam mass spectrometry as a sampling technique. In this temperature regime, no typical low-temperature combustion (LTC) reactions have been observed for MC when oxygen (O₂) is used as the oxidizer. Upon ozone addition, significant oxidation of methyl crotonate is found. On the basis of experimentally observed energy-dependent mass peaks in combination with temperature-dependent mole fraction profiles and photoionization efficiency curves, we provide new insights into the methyl crotonate ozonolysis reaction network. The observed MC + O₃ products, C₅H₈O₅, are found to be related to the keto-hydroperoxides resulting from the isomerization of the primary ozonide. Evidence is also provided that molecular growth mainly results from cycloaddition reactions of the Criegee intermediate into aldehydes and alkenes as well as addition reactions of the Criegee intermediates to the double bond of methyl crotonate and sequential decomposition into ketones. Furthermore, species that contribute in large amounts to the low-temperature oxidation of methyl crotonate, like H₂O₂, CH₃OOH, CH₃OH, and HC(O)OH, are identified, and their mole fractions are reported. Additionally, preliminary modeling is performed which qualitatively captures the observed NTC behavior and reveals future research opportunities.

Identification of a novel immune prognostic model in gastric cancer

PURPOSE

The tumor immune microenvironment (TIME) is now considered as an important factor during gastric cancer (GC) development. This study identified a novel immune-related risk model for predicting prognosis and assessing the immune status of GC patients.

METHODS

Transcriptomic data were obtained from the TCGA database. The differential expressed immune-related genes (IRGs) were identified through the ImmPort portal. Enrichment analysis was performed to explore the potential molecular mechanism of these IRGs. By the Cox regression analysis, we constructed the immune prognostic model. Then, the association between the model and the immune microenvironment was estimated. The model was validated in the GSE84433 dataset.

RESULTS

Totally, we identified 222 differentially expressed IRGs. These IRGs were closely correlated with immune response and immune signaling pathways. Through the Cox regression analysis, we developed the immune prognostic model based on the expression of seven IRGs (CXCL3, NOX4, PROC, FAM19A4, RNASE2, IGHD2-15, CGB5). Patients were stratified into two groups according to immune-related risk scores. Survival analysis indicated that the prognosis of high-risk patients was poorer than low-risk patients. Moreover, the immune-related risk score was an independent prognostic biomarker. More importantly, we found that the infiltration level of immunosuppressive cells and the expression of inhibitory immune checkpoints were higher in high-risk patients. The immune microenvironment tended to be a suppressive status in patients with high-risk scores.

CONCLUSION

This study demonstrated that our model had predictive value for prognosis and the TIME in GC. It might be a robust tool to improve personalized patient management.

Long non-coding RNA FOXP4-AS1 acts as an adverse prognostic factor and regulates proliferation and apoptosis in nasopharyngeal carcinoma

OBJECTIVE

Nasopharyngeal carcinoma (NPC) is one of the most common malignancies worldwide. In The Cancer Genome Atlas (TCGA) database, the expression level of lncRNA forkhead box P4 antisense RNA 1 (FOXP4-AS1) is higher in NPC samples than in normal samples.

PATIENTS AND METHODS

Quantitative Real-time PCR and Western blotting were performed to detect the expression level of RNA and protein. Luciferase reporter assay ran to test the interactions between FOXP4-AS1 and miR-423-5p and STMN1. Subcellular fractionation assay was used to determine the subcellular localization of FOXP4-AS1. The tumor-promotion functions of FOXP4-AS1 were determined by both in vitro and in vivo assays.

RESULTS

The expression of FOXP4-AS1 was up-regulated in 80 cases with NPC, and these patients with a poor prognosis. Functionally, high expression of FOXP4-AS1 in NPC was connected with promoted cell proliferation and inhibited apoptosis. Moreover, FOXP4-AS1 is located in the cytoplasm of CNE1 (NPC cell lines). Mechanistically, FOXP4-AS1 up-regulated STMN1 on post-transcriptional regulation by means of miR-423-5p.

CONCLUSIONS

Our present study demonstrated that high expression of FOXP4-AS1 in NPC portended poor outcomes. FOXP4-AS1upregulated STMN1 by interacting with miR-423-5p as a competing endogenous RNA (ceRNA) to promote NPC progression.

Erratum: Evolution of π^{0} Suppression in Au+Au Collisions from sqrt[s_{NN}]=39 to 200 GeV [Phys. Rev. Lett. 109, 152301 (2012)]

This corrects the article DOI: 10.1103/PhysRevLett.109.152301.

Insights Obtained by Culturing Saccharibacteria With Their Bacterial Hosts

Oral microbiome research has moved from asking "Who's there?" to "What are they doing?" Understanding what microbes "do" involves multiple approaches, including obtaining genomic information and examining the interspecies interactions. Recently we isolated a human oral Saccharibacteria (TM7) bacterium, HMT-952, strain TM7x, which is an ultrasmall parasite of the oral bacterium Actinomyces odontolyticus. The host-parasite interactions, such as phage-bacterium or Saccharibacteria-host bacterium, are understudied areas with large potential for insight. The Saccharibacteria phylum is a member of Candidate Phyla Radiation, a large lineage previously devoid of cultivated members. However, expanding our understanding of Saccharibacteria-host interactions requires examining multiple phylogenetically distinct Saccharibacteria-host pairs. Here we report the isolation of 3 additional Saccharibacteria species from the human oral cavity in binary coculture with their bacterial hosts. They were obtained by filtering ultrasmall Saccharibacteria cells free of other larger bacteria and inoculating them into cultures of potential host bacteria. The binary cocultures obtained could be stably passaged and studied. Complete closed genomes were obtained and allowed full genome analyses. All have small genomes (<1 Mb) characteristic of parasitic species and dramatically limited de novo synthetic pathway capabilities but include either restriction modification or CRISPR-Cas systems as part of an innate defense against foreign DNA. High levels of gene synteny exist among Saccharibacteria species. Having isolates growing in coculture with their hosts allowed time course studies of growth and parasite-host interactions by phase contrast, fluorescence in situ hybridization, and scanning electron microscopy. The cells of the 4 oral Saccharibacteria species are ultrasmall and could be seen attached to their larger Actinobacteria hosts. Parasite attachment appears to lead to host cell death and lysis. The successful cultivation of Saccharibacteria species has significantly expanded our understanding of these ultrasmall Candidate Phyla Radiation bacteria.

[Expressions and effects of autophagy-related genes in bleomycin-induced skin fibrosis of mice]

Objective: To investigate the expressions and effects of autophagy-related genes in bleomycin-induced skin fibrosis of mice. Methods: (1) Totally 72 male BALB/c mice aged 6 weeks were divided into blank control group, simple phosphate buffer solution (PBS) group, and bleomycin group according to the random number table, with 24 mice in each group. Mice in blank control group received no treatment, and 100 μL of PBS and bleomycin (1 mg/mL) were respectively injected subcutaneously in the back skin of mice in simple PBS and bleomycin group, once a day for 28 days. On injection day (ID) 7, 14, 21, and 28, 6 mice in each group were collected to observe the skin change on the back of mice with naked eyes. After the observation, the mice were sacrificed and skin tissue on the back was taken. Skin tissue of mice on ID 28 was collected to measure the thickness of skin tissue by routine hematoxylin-eosin staining and observe skin tissue morphology by Masson staining. Skin tissue on ID 7, 14, 21, and 28 was taken to detect content of hydroxyproline by enzyme linked immunosorbent assay, and mRNA and protein expressions of p62, microtubule-associated protein 1 light chain 3 Ⅱ (LC3 Ⅱ) and Beclin-1 were detected by real-time fluorescent quantitative reverse transcription polymerase chain reaction and Western blotting, respectively. (2) Skin tissue of mice in blank control group in experiment (1) was taken to culture fibroblasts (Fbs) in 3rd-6th passages. The cells were divided into blank control group, simple PBS group, and bleomycin group according to the random number table, with 6 wells in each group. Cells in blank control group were not stimulated, and cells in simple PBS group and bleomycin group were stimulated with 20 μL of PBS and bleomycin (1 mg/mL) for 72 h, respectively. Cellular immunofluorescence staining was used to observe the expression of LC3 Ⅱ. Data were statistically analyzed with analysis of variance of factorial design, one-way analysis of variance, t test, and Bonferroni correction. Results: (1) Skin on the back of mice in blank control group and simple PBS group was thin and ruddy, and the veins were clear on ID 7, 14, 21, and 28. Several raised ridges were visible on the puncture site of mice in simple PBS group from ID 14. Skin on the back of mice was ruddy, with several raised ridges visible on the puncture site of mice in bleomycin group on ID 7, the skin turned slightly white on ID 14, the skin turned white obviously with unclear surrounding blood vessels on ID 21, and the skin turned white and the surrounding blood vessels could not be recognized on ID 28. (2) On ID 28, the skin thicknesses of mice in blank control group and simple PBS group were similar (t=0.79, P>0.05). Compared with that in blank control group and simple PBS group, the skin thickness of mice in bleomycin group was significantly increased (t=0.50, 0.50, P<0.01). (3) On ID 28, the skin tissue structure of mice in blank control group and simple PBS group was similar, with a small amount of orderly arranged collagen and evenly distributed hair follicle; the number of collagen of skin in mice of bleomycin group was increased obviously and arranged disorderly, and the number of hair follicle was decreased significantly. (4) On ID 7, 14, 21, and 28, the content of hydroxyproline in the skin tissue of mice in bleomycin group was significantly higher than that in blank control group and simple PBS group (t=0.99, 0.98, 0.50, 0.51, 0.50, 0.50, 0.52, 0.51, P<0.05 or P<0.01). (5) On ID 7, p62 mRNA expression in the skin tissue of mice in bleomycin group was significantly lower than that in simple PBS group (t=0.93, P<0.05). On ID 14 and 21, the mRNA expressions of p62, LC3 Ⅱ, and Beclin-1 in the skin tissue of mice in bleomycin group were significantly higher than those in blank control group (t=0.74, 0.70, 0.58, 0.49, 0.51, 0.74, P<0.05) and simple PBS group (t=0.94, 0.65, 0.65, 0.77, 0.49, 0.51, P<0.05). On ID 28, the mRNA expressions of p62 and Beclin-1 in the skin tissue of mice in bleomycin group were significantly lower than those in blank control group (t=0.50, 0.44, P<0.05) and simple PBS group (t=0.97, 0.55, P<0.05), and that of LC3 Ⅱ was significantly higher than that in blank control group and simple PBS group, respectively (t=0.51, 0.98, P <0.01). (6) On ID 7, 14, 21, and 28, the protein expressions of LC3 Ⅱ in blank control group, simple PBS group, and bleomycin group were 0.167±0.042, 0.122±0.016, 0.553±0.078, 0.118±0.035, 0.120±0.023, 0.117±0.061, 0.581±0.039, 0.159±0.065, 0.233±0.027, 0.304±0.031, 1.020±0.010, 0.089±0.045. On ID 14, the protein expressions of p62 and Beclin-1 in the skin tissue of mice in bleomycin group were significantly higher than those in blank control group (t=0.86, 0.89, P<0.05) and simple PBS group (t=0.42, 0.89, P<0.05). On ID 21, the protein expressions of p62, LC3 Ⅱ, and Beclin-1 in the skin tissue of mice in bleomycin group were significantly higher than those in blank control group and simple PBS group (t=0.82, 0.45, 0.50, 0.79, 0.51, 0.50, P<0.01). On ID 28, the protein expressions of p62, LC3 Ⅱ, and Beclin-1 in the skin tissue of mice in bleomycin group were significantly lower than those in blank control group and simple PBS group (t=0.77, 0.54, 0.52, 0.50, 0.51, 0.50, P<0.05). (7) After culture for 72 h, the expression of LC3 Ⅱ in Fbs of bleomycin group was significantly lower than that of blank control group and simple PBS group, respectively. Conclusions: In the process of bleomycin stimulating skin fibrosis, autophagy-related genes increase firstly and then decrease. When the autophagy process is activated, it is expected to reverse the process of skin fibrosis.

Multiple-centre clinical evaluation of an ultrafast single-tube assay for SARS-CoV-2 RNA

OBJECTIVE

To evaluate the performance of an ultrafast single-tube nucleic acid isothermal amplification detection assay for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA using clinical samples from multiple centres.

METHODS

A reverse transcription recombinase-aided amplification (RT-RAA) assay for SARS-CoV-2 was conducted within 15 minutes at 39°C with portable instruments after addition of extracted RNA. The clinical performance of RT-RAA assay was evaluated using 947 clinical samples from five institutions in four regions of China; approved commercial fluorescence quantitative real-time PCR (qRT-PCR) kits were used for parallel detection. The sensitivity and specificity of RT-RAA were compared and analysed.

RESULTS

The RT-RAA test results of 926 samples were consistent with those of qRT-PCR (330 were positive, 596 negative); 21 results were inconsistent. The sensitivity and specificity of RT-RAA was 97.63% (330/338, 95% confidence interval (CI) 95.21 to 98.90) and 97.87% (596/609, 95% CI 96.28 to 98.81) respectively. The positive and negative predictive values were 96.21% (330/343, 95% CI 93.45 to 97.88) and 98.68% (596/604, 95% CI 97.30 to 99.38) respectively. The total coincidence rate was 97.78% (926/947, 95% CI 96.80 to 98.70), and the kappa was 0.952 (p < 0.05).

CONCLUSIONS

With comparable sensitivity and specificity to the commercial qRT-PCR kits, RT-RAA assay for SARS-CoV-2 exhibited the distinctive advantages of simplicity and rapidity in terms of operation and turnaround time.

[The association between single nucleotide polymorphism of interleukin-1β gene rs1143627 site and susceptibility to active tuberculosis]

Objective: To investigate the relationship between single nucleotide polymorphism (SNP) of IL-1β gene and susceptibility to tuberculosis. Methods: A case-control study was conducted in Shenzhen Third People's Hospital from January 2012 to December 2014. A total of 1 533 patients with active tuberculosis were enrolled, including 1 432 cases of pulmonary tuberculosis[920 males and 512 females, mean age (37±14) years] and 101 cases of extrapulmonary tuberculosis [60 males and 41 females, mean age (35±13) years]. At the same time, 1 445 healthy controls (882 males and 563 females, mean age (37±20) years) were selected. The genotypes of rs1143627, rs1143623, rs16944 and rs2853550 of IL-1β gene were detected by time-of-flight mass spectrometry. The allele frequencies of rs1143627 T>C (-31) were compared between patients with pulmonary tuberculosis and those with extrapulmonary tuberculosis. Fifty-three patients with active tuberculosis [male 32, female 21, mean age (37±15) years] were randomly selected, and the correlation between SNP alleles and tuberculosis severity was analyzed before and after treatment. Results: Time-of-flight mass spectrometry effectively detected the genotypes of 4 SNP loci. Among the 4 SNP loci, only the allele frequency of -31 locus was significantly different between the active tuberculosis group and the control group. The allele frequency of rs1143627 T locus in active tuberculosis group was 53.3%(1 634/3 066), which was significantly higher than that in the healthy control group 48.7%(1 407/2 890; OR=1.20, 95%CI=1.09-1.33, P=0.001 6) .The frequencies of the other 3 SNP alleles were not significantly different between the active tuberculosis group and the control group. The frequencies of the other 3 SNP alleles were 59% (1 821/3 066) and 60% (1 732/2 890) for rs1143623 G allele, 51% (1 574/3 066) and 52% (1 499/2 890) for rs16944 G allele, and 64% (1 964/3 066) and 65% (1 875/2 890) for rs2853550 T allele respectively. Stratified analysis showed that the frequency of the -31 T allele in patients with extrapulmonary tuberculosis (62.9%, 127/202) was significantly higher than that in patients with pulmonary tuberculosis (52.6%,1 507/2 864) (OR=1.53; 95% CI=1.13-2.05; P=0.005).The HRCT scores of patients with rs1143627 TT, TC and CC genotypes were 26.6, 13.9 and 13.3 respectively before anti-tuberculosis treatment, and after 2 years of anti-tuberculosis treatment, the HRCT scores of patients with rs1143627 TT, TC and CC genotypes were 14.7, 6.6 and 5.4 respectively, which indicated that TB patients with rs1143627T allele were associated with more severe pulmonary disease. Conclusion: The SNP of IL-1β-31T>C was associated with susceptibility to active tuberculosis, and T allele was the susceptible gene and individuals carrying T allele were more likely to develop extrapulmonary tuberculosis.

First Measurement of Λ_{c} Baryon Production in Au+Au Collisions at sqrt[s_{NN}]=200 GeV

We report on the first measurement of the charmed baryon Λ_{c}^{±} production at midrapidity (|y|<1) in Au+Au collisions at sqrt[s_{NN}]=200  GeV collected by the STAR experiment at the Relativistic Heavy Ion Collider. The Λ_{c}/D^{0} [denoting (Λ_{c}^{+}+Λ_{c}^{-})/(D^{0}+D[over ¯]^{0})] yield ratio is measured to be 1.08±0.16  (stat)±0.26  (sys) in the 0%-20% most central Au+Au collisions for the transverse momentum (p_{T}) range 3<p_{T}<6  GeV/c. This is significantly larger than the pythia model calculations for p+p collisions. The measured Λ_{c}/D^{0} ratio, as a function of p_{T} and collision centrality, is comparable to the baryon-to-meson ratios for light and strange hadrons in Au+Au collisions. Model calculations including coalescence hadronization for charmed baryon and meson formation reproduce the features of our measured Λ_{c}/D^{0} ratio.

Prognostic value of radiologically enlarged lymph nodes in node-negative colon cancer

AIM

Assessment of lymph node (LN) involvement is of crucial importance in the estimation of prognosis and choice of therapeutic options for patients with colon cancer. The relationship between the radiological size of LNs and prognosis in node-negative colon cancer remains uncertain. This study aims to investigate the prognostic impact of radiologically enlarged LNs on the survival of patients with node-negative colon cancer.

METHOD

This retrospective study recruited 395 patients with Stages I and II colon cancer diagnosed between January 2012 and March 2016. Preoperative computed tomography was reviewed for the maximum short-axis diameter of regional LNs, the optimal cutoff value of which was set to 8 mm. The prognostic relevance was analysed in Kaplan-Meier and multivariable Cox proportional hazard regressions.

RESULTS

Patients with tumour in the left colon, TNM Stage II and 12 or more retrieved LNs tended to have radiologically enlarged LNs. Our results suggest that 3-year recurrence-free survival (RFS) and overall survival (OS) were significantly worse in patients with enlarged LNs than those without (RFS 82.8% vs 92.4%, P = 0.026; OS 87.1% vs 95.2%, P = 0.017), which was also confirmed in multivariable analysis [RFS hazard ratio (HR) = 2.192, P = 0.018; OS HR = 3.305, P = 0.010]. Subgroup analysis revealed that in patients with Stage II disease or at least 12 retrieved LNs, radiologically enlarged LN remained an independent predictor of poor RFS and OS.

CONCLUSION

The presence of radiologically enlarged LNs in patients with node-negative colon cancer had an adverse prognosis.

Adaptation of plants to high-calcium content kart regions: possible involvement of symbiotic microorganisms and underlying mechanisms

Rhizosphere microorganisms and endophytes can help their hosts absorb nutrients and regulate the levels of plant hormones. Moreover, they can modulate the expressions of host genes, assist hosts in eliminating reactive oxygen species (ROS) and secreting volatile organic compounds. Therefore, rhizosphere microorganisms and endophytes are considered as determinant factors driving processes involved in the growth of host plants. However, the physiological and ecological functions, as well as the molecular mechanism underlying the behavior of rhizosphere microorganisms and endophytes in their role in the adaptive capacity of host plants in the karstic high-calcium environment have not been systematically studied. This review summarizes the physiological and molecular mechanisms of rhizosphere microorganisms and endophytes which help host plants to adapt to various kinds of adverse environments. The adaptive capacities of plants growing in adverse environments, partly, or totally, depends on microorganisms co-existing with the host plants.

Levofloxacin-ceftazidime administration regimens combat Pseudomonas aeruginosa in the hollow-fiber infection model simulating abnormal renal function in critically ill patients

BACKGROUND

The purpose of this study was to investigate the bactericidal effects of levofloxacin and ceftazidime as both monotherapy and combination therapy, and to determine their effects on resistance suppression in patients with normal and abnormal (Ccr:16-20 mL/min) renal function. Common clinical administration regimens to provide reference values were further evaluated.

METHODS

The 7-d hollow-fiber infection model was used to inject the Pseudomonas aeruginosa standard strain (ATCC27853), which simulated common clinical administration regimens for patients with different renal function. Ten regimens were stratified into 2 categories based on renal function, and each category contained 3 monotherapy regimens and 2 combination therapy regimens. Total and resistant populations were quantified. Drug concentrations were determined by high-performance liquid chromatography (HPLC).

RESULTS

Monotherapy regimens resulted in about 0.5-log-CFU/mL bacterial kill in the total population at 6 or 8 h, whilst combination regimens resulted in 2- to 3-log-CFU/mL within 2 days. For levofloxacin monotherapy regimens in patients with normal renal function, resistance emergence was seen after 6 h, and was seen at 0 h in the ceftazidime monotherapy regimen, as well as in all regimens of patients with abnormal renal function. Although resistant subpopulation in combination regimens with abnormal renal function began to increase at 0 h, there was a definite downward trend after 8 h, while resistant population in the normal renal function group increased after 16 h.

CONCLUSIONS

Combination therapy had greater bactericidal efficacy and resistance inhibition compared with monotherapy. Studying combination regimens in randomized clinical trials is warranted.