Effects of 1-octyl-3-methylimidazolium nitrate on the microbes in brown soil

The toxicity of ionic liquids (ILs) on soil organisms has aroused wide attention due to their high-solubility. The present investigation focused on the toxicity of 1-octyl-3-methylimidazolium nitrate ([C₈mim]NO₃) on the microbial populations (bacteria, fungi, and actinomycetes), soil enzyme (urease, dehydrogenase, acid phosphatase, and β-glucosidase) activities, microbial community diversity using terminal restriction fragment length polymorphism (T-RFLP), and abundance of the ammonia monooxygenase (amoA) genes of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) using quantitative real-time polymerase chain reaction (q-PCR) in brown soil at each trial with doses of 0, 1.0, 5.0, and 10.0mg/kg on days 10, 20, 30, and 40. The contents of [C₈mim]NO₃ in soil were measured using high performance liquid chromatography with recoveries of 84.3% to 85.2%, and changed less than 10% during the experimental period. A significant decrease was observed from the bacteria, fungi and actinomycetes populations at 10.0mg/kg, at which the urease activity was inhibited and the β-glucosidase activity was stimulated on days 20, 30, and 40. In addition, [C₈mim]NO₃ inhibited the dehydrogenase activity at 10mg/kg on days 30 and 40 and the acid phosphatase activity on day 20. The diversity of the soil microbial community and the gene abundance of AOA- and AOB- amoA were also inhibited. Furthermore, the present investigation provided more scientific information for the toxicity evaluation of ILs in soil.

Behavioral and molecular analyses of olfaction-mediated avoidance responses of Rana (Lithobates) catesbeiana tadpoles: Sensitivity to thyroid hormones, estrogen, and treated municipal wastewater effluent

Olfaction is critical for survival, facilitating predator avoidance and food location. The nature of the olfactory system changes during amphibian metamorphosis as the aquatic herbivorous tadpole transitions to a terrestrial, carnivorous frog. Metamorphosis is principally dependent on the action of thyroid hormones (THs), l-thyroxine (T₄) and 3,5,3'-triiodothyronine (T₃), yet little is known about their influence on olfaction during this phase of postembryonic development. We exposed Taylor Kollros stage I-XIII Rana (Lithobates) catesbeiana tadpoles to physiological concentrations of T₄, T₃, or 17-beta-estradiol (E₂) for 48h and evaluated a predator cue avoidance response. The avoidance response in T₃-exposed tadpoles was abolished while T₄- or E₂-exposed tadpoles were unaffected compared to control tadpoles. qPCR analyses on classic TH-response gene transcripts (thra, thrb, and thibz) in the olfactory epithelium demonstrated that, while both THs produced molecular responses, T₃ elicited greater responses than T₄. Municipal wastewater feed stock was spiked with a defined pharmaceutical and personal care product (PPCP) cocktail and treated with an anaerobic membrane bioreactor (AnMBR). Despite substantially reduced PPCP levels, exposure to this effluent abolished avoidance behavior relative to AnMBR effluent whose feed stock was spiked with vehicle. Thibz transcript levels increased upon exposure to either effluent indicating TH mimic activity. The present work is the first to demonstrate differential TH responsiveness of the frog tadpole olfactory system with both behavioral and molecular alterations. A systems-based analysis is warranted to further elucidate the mechanism of action on the olfactory epithelium and identify further molecular bioindicators linked to behavioral response disruption.

Characterization of the fecal microbiota differs between age groups in Koreans

Background/Aims

Tens of trillions of microorganisms constitute the gut microbiota of the human body. The microbiota plays a critical role in maintaining host immunity and metabolism. Analyses of the gut microbial composition in Korea are limited to a few studies consisting of small sample sizes. To investigate the gut microbial community in a large sample of healthy Koreans, we analyzed the 16S ribosomal RNA of 4 representative bacterial genera Lactobacillus, Bifidobacterium, Bacteroides, and Clostridium.

Methods

A total of 378 DNA samples extracted from 164 infants and 214 adults were analyzed using quantitative real-time polymerase chain reaction.

Results

Analysis of 16S ribosomal RNA of 4 representative bacterial genera Lactobacillus, Bifidobacterium, Bacteroides, and Clostridium showed that the gut microbiota in infants had higher relative abundances of Bifidobacterium and Lactobacillus than that in adults, which was dominated by Bacteroides and Clostridium.

Conclusions

To the best of our knowledge, this was the first study evaluating the distinct characteristics of the microbial community of Korean infants and adults. The differences between the 2 populations suggest that external factors such as age, diet, and the environment are important contributing factors to the change in gut microbial composition during development.

Implications of and lessons learned from external assurance of eight influenza diagnostics in China

This study evaluated the ability of laboratories in the Chinese mainland to conduct molecular detection of seasonal A(H1N1), A(H1N1)pdm09, A(H3N2), A(H5N1), A(H7N9), A(H9N2), B(Victoria), and B(Yamagata). Based on a genetically engineered system of virus-like particles (VLPs), the National Center for Clinical Laboratories of China (NCCLs) developed an external quality assessment (EQA) panel. The panel was distributed to 35 laboratories in mainland China to investigate the proficiency of the 16 assays for influenza molecular detection. Using genetic engineering technology, VLPs encapsulating the 37 target genes of 8 influenza viruses were generated. After verification and quantification, 26 influenza virus surrogates with different concentrations were prepared for EQA. Among the 35 participating laboratories, 319 datasets were returned to the NCCLs. Overall, 95.6% (305/319) of datasets correctly reported all 30 samples, while 2.2% (7/319) of datasets with more than one incorrect result were considered as "improvable". A total of 16 misdiagnosed and 18 undiagnosed results were reported. The data analyzed in this study showed good reproducibility in China, but improvements are needed to decrease misdiagnosed and undiagnosed cases, particularly for the A(H9N2) NA gene. Moreover, VLPs are a good alternative specimen type for assay training and proficiency testing purposes.

Preparation of MS2-based nanoparticles as control and standard materials for the molecular detection of dengue virus serotypes

To quantify dengue virus (DENV) and evaluate the performance of clinical laboratories using quantitative real-time polymerase chain reaction (qRT-PCR) assays, we constructed high-efficiency expression systems to produce DENV-1 to 4 nanoparticles and assessed their suitability as standard and control materials in 20 laboratories across China. Targeted gene sequences of DENV-1 to 4 were synthesized and inserted into pACYC-Duet 1-MS2 recombinant plasmids to generate corresponding nanoparticle expression systems. After collection, verification, and quantification by digital PCR (dPCR), DENV-1 to 4 nanoparticles were prepared as control and standard materials. Five positive and three negative samples of each DENV serotype in every panel were used for assessing the performance of the participating laboratories across China, as well as standard materials for the quantitative detection of DENV using qRT-PCR assays. The accuracy, sensitivity, and specificity of qRT-PCR used by the 20 evaluated laboratories were 89.6 (569/635), 85.1 (336/395), and 97.1% (233/240), respectively. Overall, sixteen (80.0%) laboratories were qualified in detecting DENV, among which five (25.0%) were designated as "competent", eleven (55.0%) were defined as "acceptable", and four (20%) were considered to be "improvable". The results generated from the DENV standard samples were significantly positively correlated with those generated by dPCR (r²=0.8698, P<0.001). In summary, DENV nanoparticles could potentially be used as controls for improving the performance of laboratories and as standards for the quantitative detection of DENV.

Mir-29a expressions in peripheral blood mononuclear cell and cerebrospinal fluid: Diagnostic value in patients with pediatric tuberculous meningitis

To evaluate the value of miR-29a expression in peripheral blood mononuclear cell (PBMC) and cerebrospinal fluid (CSF) in the diagnosis of pediatric tuberculous meningitis (TBM). Our study enrolled 112 children with TBM and 130 healthy children, from which PBMC and CSF were collected. The quantitative real-time polymerase chain reaction (qRT-PCR) was used to measure the expression of miR-29a in PBMC and CSF, and then analyze the diagnostic value. Compared with control group, the miR-29a expressions in PBMC and CSF were increased in TBM children (both P<0.05), and the expressions were associated with following factors: intracranial hypertension, conscious disturbance, focal cerebral symptoms, meningeal irritation, hydrocrania, abnormal electroencephalogram and extra-cerebral tuberculous (all P<0.05). The receiver operating characteristic (ROC) curve showed that the sensitivity, specificity and area under the curve (AUC) of miR-29a in PBMC was 67.20%, 88.50% and 0.852, respectively, and that in CSF was 81.10%, 90.00% and 0.890, respectively, and that in combination of PBMC and CSF was 84.40%, 95.38% and 0.934, respectively. miR-29a expression in PBMC and CSF may provide a reference for the diagnosis of pediatric TBM.

Comparison of detection methods and follow-up study on the tyrosine kinase inhibitors therapy in non-small cell lung cancer patients with ROS1 fusion rearrangement

Background

The screening of ROS proto-oncogene 1, receptor tyrosine kinase(ROS1) fusion rearrangement might be potentially beneficial for an effective therapy against non-small cell lung cancer (NSCLC). However, the three main ROS1 rearrangement detection methods have limitations, and no routine protocol for the detection of ROS1 rearrangement in NSCLC is available. In this study, our aims were to compare immunohistochemistry (IHC), fluorescent in situ hybridization (FISH) and quantitative real-time polymerase chain reaction (qRT-PCR) in their ability to detect ROS1 rearrangement in NSCLC, and discuss the clinical characteristics and histopathology of the patients with ROS1 rearrangement. Moreover, the effects of tyrosine kinase inhibitors (TKIs) therapy on the patients with ROS1 rearrangement and advanced stage disease (III b–IV) were investigated.

Methods

Patients with a previously diagnosed NSCLC were recruited in this study from November 2013 to October 2015. IHC was performed using the D4D6 monoclonal antibody (mAb) in an automatic IHC instrument, while FISH and qRT-PCR were carried out to confirm the IHC results. FISH and qRT-PCR positive cases underwent direct sequencing. After detection, patients with advanced ROS1 rearranged NSCLC had received TKI therapy.

Results

Two hundred and thirty-eight patients were included in this study. ROS1 rearrangement was detected in 10 patients. The concordant rate of FISH and qRT-PCR results was 100 %, while in the FISH and IHC results high congruence was present when IHC showed a diffusely (≥60 % tumor cells) 2–3+ cytoplasmic reactivity pattern. Patients harboring ROS1 rearrangement were mostly young (8/10), females (7/10) and non-smokers (7/10) with adenocarcinoma (10/10) and acinar pattern. Most of their tumor were in intermediate grade (6/8). Among these 10 patients, three of them in stage IV with ROS1 rearrangement gained benefits from ROS1 TKI therapy.

Conclusions

IHC, FISH and qRT-PCR can reliably detect ROS1 rearrangement in NSCLC, while IHC can be used as a preliminary screening tool. These results supported the efficacy of ROS1 TKI therapy in treating advanced NSCLC patients with ROS1 rearrangement.

Electronic supplementary material

The online version of this article (doi:10.1186/s12885-016-2582-9) contains supplementary material, which is available to authorized users.

Multiplex qPCR for serodetection and serotyping of hepatitis viruses: A brief review

The present review describes the current status of multiplex quantitative real time polymerase chain reaction (qPCR) assays developed and used globally for detection and subtyping of hepatitis viruses in body fluids. Several studies have reported the use of multiplex qPCR for the detection of hepatitis viruses, including hepatitis A virus (HAV), hepatitis B virus (HBV), hepatitis C virus (HCV), hepatitis D virus (HDV), and hepatitis E virus (HEV). In addition, multiplex qPCR has also been developed for genotyping HBV, HCV, and HEV subtypes. Although a single step multiplex qPCR assay for all six hepatitis viruses, i.e., A to G viruses, is not yet reported, it may be available in the near future as the technologies continue to advance. All studies use a conserved region of the viral genome as the basis of amplification and hydrolysis probes as the preferred chemistries for improved detection. Based on a standard plot prepared using varying concentrations of template and the observed threshold cycle value, it is possible to determine the linear dynamic range and to calculate an exact copy number of virus in the specimen. Advantages of multiplex qPCR assay over singleplex or other molecular techniques in samples from patients with co-infection include fast results, low cost, and a single step investigation process.

Molecular Monitoring as a Path to Cure Acute Promyelocytic Leukemia

Acute promyelocytic leukemia (APL) is a molecularly well-defined disease, characterized by a specific chromosomal translocation; the improvement in biologic and clinical knowledge and subsequent introduction of molecularly targeted therapies have transformed the management of APL, with survival rates now exceeding 80%. Minimal residual disease (MRD) assessment in APL is the most important tool for its treatment; the prognostic role of the molecular detection of promyelocytic leukemia retinoic acid receptor α (PML-RARα) transcript after consolidation therapy in the early identification of the following hematologic relapse is now well established and guides preemptive therapy. First experiences performed with a qualitative polymerase chain reaction (PCR) approach were replaced with more accurate real-time quantitative PCR (RQ-PCR), which guarantees a numeric quantification of MRD. The identification of arsenic trioxide (ATO) as a valid therapy not only in relapsed patients but also as an alternative to standard therapy alone or in association with all-trans-retinoic acid enlarges the setting of validation of MRD evaluation in APL patients, considering a possible different clearance of PML-RARα with innovative therapy different from the standard ones. MRD monitoring demonstrated its validity also in the setting of relapsed patients with interesting results in the autologous and allogeneic stem cell transplantation setting or with the use of other biological agents. The aim of this review is to report and discuss the actual state of the art of MRD in APL.

Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis

BACKGROUND

Dysbiosis may play a role in irritable bowel syndrome (IBS), hitherto an enigmatic disorder. We evaluated selected fecal microbes in IBS patients and healthy controls (HC).

METHODS

Fecal 16S rRNA copy number of selected bacteria was studied using qPCR in 47 patients with IBS (Rome III) and 30 HC.

RESULTS

Of 47 patients, 20 had constipation (IBS-C), 20 diarrhea (IBS-D), and seven unclassified IBS (IBS-U). Relative difference in 16S rRNA copy number of Bifidobacterium (P = 0.042) was lower, while those of Ruminococcus productus-Clostridium coccoides (P = 0.016), Veillonella (P = 0.008), Bacteroides thetaiotamicron (P < 0.001), Pseudomonas aeruginosa (P < 0.001), and Gram-negative bacteria (GNB, P = 0.001) were higher among IBS patients than HC. Number of Lactobacillus (P = 0.002) was lower, while that of Bacteroides thetaiotamicron (P < 0.001) and segmented filamentous bacteria (SFB, P < 0.001) was higher among IBS-D than IBS-C. Numbers of Bacteroides thetaiotamicron (P < 0.001), P. aeruginosa (P < 0.001), and GNB (P < 0.01) were higher among IBS-C and IBS-D than HC. Quantity of SFB was higher among IBS-D (P = 0.011) and lower among IBS-C (P = 0.002) than HC. Number of Veillonella species was higher among IBS-C than HC (P = 0.002). P. aeruginosa was frequently detected among IBS than HC (46/47 [97.9 %] vs. 10/30 [33.3 %], P < 0.001). Abdominal distension (n = 34/47) was associated with higher number of Bacteroides thetaiotamicron, Clostridium coccoides, P. aeruginosa, SFB, and GNB; bloating (n = 22/47) was associated with Clostridium coccoides and GNB. Microbial flora was different among IBS than HC on principal component analysis.

CONCLUSION

Fecal microbiota was different among IBS than HC, and different sub-types were associated with different microbiota. P. aeruginosa was more frequent and higher in number among IBS patients.

Cytomegalovirus load at treatment initiation is predictive of time to resolution of viremia and duration of therapy in hematopoietic cell transplant recipients

BACKGROUND

Preemptive antiviral therapy relies on viral load measurements and is the mainstay of cytomegalovirus (CMV) prevention in hematopoietic cell transplant (HCT) recipients. However, optimal CMV levels for the initiation of preemptive therapy have not been defined.

OBJECTIVES

The objectives of our work were to evaluate the relationship between plasma CMV DNA levels at initiation of preemptive therapy with time to resolution of viremia and duration of treatment.

STUDY DESIGN

Retrospective analysis of HCT recipients undergoing serial CMV PCR testing between June 2011 and June 2014 was performed.

RESULTS

221 HCT recipients underwent preemptive therapy for 305 episodes of CMV viremia. Median time to resolution was shorter when treatment was initiated at lower CMV levels (15 days at 135-440 international units (IU)/mL, 18 days at 441-1000 IU/mL, and 21 days at >1000 IU/mL, P<.001). Prolonged viremia lasting >30 days occurred less frequently when treatment was initiated at 135-440 IU/mL compared to 441-1000 IU/mL and >1000 IU/mL (1%, 15%, 24%, P<.001). Median treatment duration was also shorter in the lower viral load groups (28, 34, 37 days, P<.001).

CONCLUSION

Initiation of preemptive therapy at low CMV levels was associated with shorter episodes of viremia and courses of antiviral therapy. These data support the utility of initiating preemptive CMV therapy at viral loads as low as 135 IU/mL in HCT recipients.

FGFR2 Assessment in Gastric Cancer Using Quantitative Real-Time Polymerase Chain Reaction, Fluorescent In Situ Hybridization, and Immunohistochemistry

OBJECTIVES

Fibroblast growth factor receptor 2 (FGFR2) amplification has been reported to be a target for treatment in gastric cancer. However, an optimal tissue source and method for evaluating FGFR2 have yet to be established.

METHODS

Copy numbers were compared by quantitative polymerase chain reaction (qPCR) using frozen vs formalin-fixed, paraffin-embedded (FFPE) tissue and biopsy vs surgical specimens. We correlated the results of qPCR and immunohistochemistry (IHC) with fluorescence in situ hybridization (FISH) using stage IV gastric cancer biopsy specimens and validated the results in surgical specimens.

RESULTS

FFPE tissues were suitable for qPCR, and biopsy specimens were equivalent to or better than surgical specimens. qPCR and IHC results exhibited an excellent correlation with FISH at eight or more copies by qPCR in any kind of tissue, 5% or more by IHC in biopsy specimens, and 10% or more by IHC in surgical specimens. FGFR2 amplification was 6.6% in stage IV gastric cancers, and 42% of these showed heterogeneous amplification and overexpression. IHC indicated a good correlation with FISH even in the heterogeneous cases.

CONCLUSIONS

FFPE biopsy tissues are an adequate source for FGFR2 evaluation in gastric carcinomas, and a qPCR-based copy number assay can be used for screening. IHC is also a valid and practical method for evaluating FGFR2, considering frequent heterogeneity.

Clinical significance of dopa decarboxylase expression in gastric peritoneal lavage in patients with gastric adenocarcinoma

AIM: To detect the mRNA expression of dopa decarboxylase (DDC) in intraperitoneal lavage fluid from patients with gastric adenocarcinoma, and to evaluate the possibility of using DDC expression in intraperitoneal lavage fluid as a new predictor of peritoneal micrometastasis of gastric adenocarcinoma.

METHODS: Intraperitoneal lavage fluid samples were collected from 87 patients with gastric adenocarcinoma treated in the Second Affiliated Hospital of Nanchang University. Quantitative real-time polymerase chain reaction (QRT-PCR) was used to detect the DDC mRNA expression in intraperitoneal lavage fluid. Intraperitoneal lavage fluid samples from 12 non-cancer patients were used as negative controls.

RESULTS: In the 87 patients with gastric adenocarcinoma, the number of patients with T1, T2, T3 and T4 stage disease was 6, 14, 28 and 39, respectively. The relative expression levels (×10⁷) of DDC mRNA in different T stages (invasion grade) were: T1, 168 ± 21; T2, 283 ± 87; T3, 31162 ± 4261; T4, 35310 ± 6593; and 60.28 ± 19.00 in non-cancer group. The expression of DDC was also correlated with the degree of tumor differentiation, pathological type and lymph node metastasis. Conventional intraperitoneal cytology (CY) revealed positive results (CY+) in 11 patients, and the positive rate was 13% (11/87). In 9 of 11 CY+ cases, the DDC mRNA expression was higher than the critical value (classified as DDC+), and the sensitivity of DDC detection was 86% (9/11). In addition, only two DDC+ cases were found in the 10 patients with T1 and 14 with T2 disease, and no DDC+ result was observed in the non-cancer group. The DDC specificity was 92% (22/24). Differential expression of DDC in intraperitoneal lavage fluid was noted in gastric adenocarcinoma with different depth of invasion (P < 0.05).

CONCLUSION: QRT-PCR can effectively detect DDC mRNA expression in intraperitoneal lavage fluid, which may become a new reliable predictor of peritoneal metastasis of gastric adenocarcinoma.

Human cytomegalovirus and Epstein-Barr virus infection in inflammatory bowel disease: Need for mucosal viral load measurement

AIM: To evaluate the best diagnostic technique and risk factors of the human Cytomegalovirus (HCMV) and Epstein-Barr virus (EBV) infection in inflammatory bowel disease (IBD).

METHODS: A cohort of 40 IBD patients (17 refractory) and 40 controls underwent peripheral blood and endoscopic colonic mucosal sample harvest. Viral infection was assessed by quantitative real-time polymerase chain reaction and immunohistochemistry, and correlations with clinical and endoscopic indexes of activity, and risk factors were investigated.

RESULTS: All refractory patients carried detectable levels of HCMV and/or EBV mucosal load as compared to 13/23 (56.5%) non-refractory and 13/40 (32.5%) controls. The median DNA value was significantly higher in refractory (HCMV 286 and EBV 5.440 copies/10⁵ cells) than in non-refractory (HCMV 0 and EBV 6 copies/10⁵ cells; P < 0.05 and < 0.001) IBD patients and controls (HCMV and EBV 0 copies/10⁵ cells; P < 0.001 for both). Refractory patients showed DNA peak values ≥ 10³ copies/10⁵ cells in diseased mucosa in comparison to non-diseased mucosa (P < 0.0121 for HCMV and < 0.0004 for EBV), while non-refractory patients and controls invariably displayed levels below this threshold, thus allowing us to differentiate viral colitis from mucosal infection. Moreover, the mucosal load positively correlated with the values found in the peripheral blood, whilst no correlation with the number of positive cells at immunohistochemistry was found. Steroid use was identified as a significant risk factor for both HCMV (P = 0.018) and EBV (P = 0.002) colitis. Finally, a course of specific antiviral therapy with ganciclovir was successful in all refractory patients with HCMV colitis, whilst refractory patients with EBV colitis did not show any improvement despite steroid tapering and discontinuation of the other medications.

CONCLUSION: Viral colitis appeared to contribute to mucosal lesions in refractory IBD, and its correct diagnosis and management require quantitative real-time polymerase chain reaction assay of mucosal specimens.

Prognostic significance of combined microRNA-206 and CyclinD2 in gastric cancer patients after curative surgery: A retrospective cohort study

AIM

To investigate associations of microRNA (miR)-206 and CyclinD2 (CCND2) expression, alone or in combination, with clinicopathological characteristics and patients' prognosis in gastric cancer.

METHODS

MiR-206 and CCND2 mRNA expression levels were detected by real-time quantitative RT-PCR in 220 self-pairs of gastric cancer and adjacent non-cancerous tissues.

RESULTS

Compared with the adjacent non-cancerous tissues, the expression levels of miR-206 and CCND2 mRNA were respectively reduced and elevated in gastric cancer tissues dramatically (both P<0.001). Notably, the expression levels of miR-206 in gastric cancer tissues were negatively correlated with those of CCND2 mRNA significantly (r=-0.463, P<0.001). Then, statistical analysis showed that low miR-206 expression and high CCND2 expression, alone or in combination, were all significantly associated with great depth of invasion, positive lymph node and distant metastases, and advanced TNM stage of human gastric cancer (all P<0.05). After that, we also found that the overall survivals of the patients with low miR-206 expression and high CCND2 expression were respectively shorter than those with high miR-206 expression and low CCND2 expression. More interestingly, miR-206-low/CCND2-high expression was associated with a significantly worst overall survival of all miR-206/CCND2 groups (P<0.001). Furthermore, multivariate analysis identified miR-206 and/or CCND2 expression as independent prognostic factors for overall survival in patients with gastric cancer.

CONCLUSION

Our data provide evidence that the dysregulation of miR-206-CCND2 axis may contribute to the aggressive progression and poor prognosis of human gastric cancer in clinical settings. Combined detection of their expression might be particularly helpful for surveillance of disease progression and treatment stratification.

Monitoring of hematopoietic chimerism by real-time quantitative PCR of micro insertions/deletions in samples with low DNA quantities

BACKGROUND

Sensitive and accurate methods to detect hematopoietic chimerism after hematopoietic stem cell transplantation (HSCT) are essential to evaluate engraftment and to monitor response to therapeutic procedures such as donor lymphocyte infusion. Continuous long-term follow up, however, requires large amounts of pre-HSCT samples limiting the application of many widely used techniques for sensitive chimerism monitoring.

METHODS

DNAs from 42 normal healthy donors and 16 HSCT donor/recipient pairs were employed to validate the use of allele-specific insertion/deletion (indel) quantitative real-time polymerase chain reaction (qPCR) to quantify chimerism in samples with low amounts of DNA. Consequently, indel-qPCR analyses of samples from 16 HSCT patients were compared to short-tandem repeat (STR) specific PCR analyses.

RESULTS

Typing with reduced amounts of input DNA (15 vs. 60 ng) allowed for the reliable distinction of positive (mean threshold cycle (ct) 28.05) and negative (ct >36) signals. The high informativity of primer/probe sets, with 12 out of 19 markers exceeding 20% informativity, was confirmed in our cohort (n = 74). Importantly, a fourfold reduction of input DNA compared to published protocols did not alter PCR efficiencies and allowed for a more sensitive detection of chimerism in 7 of 16 HSCT patients compared to results obtained by STR-PCR.

CONCLUSIONS

Our data suggest that indel-qPCR is a more sensitive technique for the detection of hematopoietic chimerism compared to STR-PCR and works efficiently for samples with low amounts of DNA.

The JAK2 V617F mutational status and allele burden may be related with the risk of venous thromboembolic events in patients with Philadelphia-negative myeloproliferative neoplasms

INTRODUCTION

Patients with Philadelphia-negative myeloproliferative neoplasms (Ph(-) MPNs) are at increased risk of thromboembolic and hemorrhagic complications. The aim of the study was to determine the relationship between JAK2 V617F mutational status, JAK2 V617F allele burden and the risk of vascular complications occurrence.

MATERIALS AND METHODS

Analysis was performed in a cohort of 186 patients diagnosed with polycythemia vera (53), essential thrombocythemia (114), primary myelofibrosis (11), and unclassified MPN (8). The risk of vascular complications development was analyzed in 126 JAK2 V617F-positive patients with respect to allele burden assessed with allele-specific 'real-time' quantitative polymerase chain reaction (AS RQ-PCR).

RESULTS

Overall prevalence of any vascular complications was 44.6%. Arterial thrombosis occurred in 20.4%, venous thromboembolism (VTE) in 11.3%, bleeding episodes in 24.7% of patients. Individuals harboring JAK2 V617F mutation, regardless of MPN type, were at higher risk of VTE (OR=5.15, 95%CI: 1.16-22.90, P=0.024), mainly deep vein thrombosis (DVT). JAK2 allele burden higher than 20% identified patients with 7.4-fold increased risk of VTE (95%CI: 1.6-33.7, P=0.004), but not of arterial thrombosis, neither of bleeding complications, and remained the only significant VTE risk factor in multivariate logistic regression. High allele burdens (over 50%) were strikingly associated with proximal DVT cases, but not with distal DVT.

CONCLUSIONS

The group of MPN patients with JAK2 V617F allele burden higher than 20% may benefit the most from vigilant monitoring and appropriate prophylaxis against vascular events. Inclusion of JAK2 V617F mutant allele burden in new risk stratifications seems to be justified and requires controlled prospective trials.

Screening of lymph nodes metastasis associated lncRNAs in colorectal cancer patients

AIM: To screen lymph nodes metastasis associated long noncoding RNAs (lncRNAs) in colorectal cancer through microarray analysis.

METHODS: Metastatic lymph node (MLN), normal lymph node (NLN) and tumor tissues of 3 colorectal cancer (CRC) patients were collected during the operation and validated by pathological examinations. RNAs were extracted from MLN, NLN, and cancer tissues separately. RNA quantity and quality were measured with a NanoDrop ND-1000 spectrophotometer and RNA integrity was assessed by standard denaturing agarose electrophoresis. Agilent Feature Extraction Software (Version 11.0.1.1) was used to analyze acquired array images. Four differently expressed lncRNAs were confirmed by quantitative real-time polymerase chain reaction (qRT-PCR) in 26 subsets of MLN, NLN, and tumor tissues.

RESULTS: Of 33045 lncRNAs, 1133 were differentially expressed in MLN compared with NLN, of which 260 were up-regulated and 873 down-regulated (≥ 2 fold-change). Five hundred and forty-five lncRNAs were differentially expressed in MLN compared with tumor tissues, of which 460 were up-regulated and 85 down-regulated (≥ 2 fold-change). Compared with NLN and cancer tissues, 14 lncRNAs were specifically up-regulated and 5 specifically down-regulated in MLN. AK307796, ENST00000425785, and AK021444 were confirmed to be specifically up-regulated in MLN and ENST00000465846 specifically down-regulated in MLN by qRT-PCR in 26 CRC patients.

CONCLUSION: The specifically expressed lncRNAs in MLN may exert a partial or key role in the progress of lymph nodes metastasis of CRC.

Comparison of SYBR Green and TaqMan methods in quantitative real-time polymerase chain reaction analysis of four adenosine receptor subtypes

Background:

Real-time polymerase chain reaction (PCR) is based on the revolutionary method of PCR. This technique is the result of PCR enormous sensitivity and real-time monitoring combination. In quantitative gene expression analysis, two methods have more popularity, SYBR Green and TaqMan, SYBR Green is relatively cost benefit and easy to use and technically based on binding the fluorescent dye to double-stranded deoxyribonucleic acid (dsDNA) where TaqMan method has more expensive and based on dual labeled oligonucleotide and exonuclease activity of Taq polymerase enzyme. Specificity is the most important concern with the usage of any non-specific dsDNA-binding Dyes such as SYBR Green whiles more specificity showed by labeled oligonucleotide method such as TaqMan. In this study, we compared two common RT PCR methods, TaqMan and SYBR Green in measurement gene expression profile of adenosine receptors.

Materials and Methods:

Gene expression profiles of A1, A2A, A2B and A3 Adenosine receptors were analyzed by optimized TaqMan and SYBR Green quantitative RT PCR in breast cancer tissues. Primary expression data was normalizing by B. actin reference gene.

Results:

Efficiencies were calculated more than 95% for TaqMan and SYBR Green methods in all genes. The correlations between means of normalized data of each gene in two methods were positive and significant (P < 0.05).

Conclusion:

Data analysis showed that with the use of high performance primer and by use proper protocols and material we can make precise data by SYBR Green as TaqMan method. In other word by optimization of SYBR Green method, its performance and quality could be comparable to TaqMan method.

Reference genes for quantitative RT-PCR data in gastric tissues and cell lines

AIM: To evaluate the suitability of reference genes in gastric tissue samples and cell lines.

METHODS: The suitability of genes ACTB, B2M, GAPDH, RPL29, and 18S rRNA was assessed in 21 matched pairs of neoplastic and adjacent non-neoplastic gastric tissues from patients with gastric adenocarcinoma, 27 normal gastric tissues from patients without cancer, and 4 cell lines using reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR). The ranking of the best single and combination of reference genes was determined by NormFinder, geNorm™, BestKeeper, and DataAssist™. In addition, GenEx software was used to determine the optimal number of reference genes. To validate the results, the mRNA expression of a target gene, DNMT1, was quantified using the different reference gene combinations suggested by the various software packages for normalization.

RESULTS: ACTB was the best reference gene for all gastric tissues, cell lines and all gastric tissues plus cell lines. GAPDH + B2M or ACTB + B2M was the best combination of reference genes for all the gastric tissues. On the other hand, ACTB + B2M was the best combination for all the cell lines tested and was also the best combination for analyses involving all the gastric tissues plus cell lines. According to the GenEx software, 2 or 3 genes were the optimal number of references genes for all the gastric tissues. The relative quantification of DNMT1 showed similar patterns when normalized by each combination of reference genes. The level of expression of DNMT1 in neoplastic, adjacent non-neoplastic and normal gastric tissues did not differ when these samples were normalized using GAPDH + B2M (P = 0.32), ACTB + B2M (P = 0.61), or GAPDH + B2M + ACTB (P = 0.44).

CONCLUSION: GAPDH + B2M or ACTB + B2M is the best combination of reference gene for all the gastric tissues, and ACTB + B2M is the best combination for the cell lines tested.

Cryopreservation induces macrophage colony stimulating factor from human periodontal ligament cells in vitro

Cryopreservation is used to protect vital periodontal ligaments during the transplantation of teeth. We investigated which gene products implicated in root resorption are upregulated in human periodontal ligament cells by cryopreservation, and whether cryopreservation affects the expression of macrophage-colony stimulating factor (M-CSF) in human periodontal ligament cells. We used customized microarrays to compare gene expression in human periodontal ligament cells cultured from teeth immediately after extraction and from cryopreserved teeth. Based on the result of these assays, we examined M-CSF expression in periodontal ligament cells from the immediately extracted tooth and cryopreserved teeth by real-time PCR, enzyme-linked immunosorbent assay (ELISA), Western blot analysis, and immunofluorescence. We also investigated whether human bone marrow cells differentiate into tartrate-resistant acid phosphatase (TRAP) positive osteoclasts when stimulated with RANKL (Receptor Activator for Nuclear Factor κ B Ligand) together with any secreted M-CSF present in the supernatants of the periodontal ligament cells cultured from the various groups of teeth. M-CSF was twofold higher in the periodontal ligament cells from the rapid freezing teeth than in those from the immediately extracted group (p < 0.05). Cryopreservation increased M-CSF expression in the periodontal ligament cells when analyzed by real time PCR, ELISA, Western blotting, and immunofluorescence (p < 0.05). TRAP positive osteoclasts were formed in response to RANKL and the secreted M-CSF present in the supernatants of all the experimental groups except negative control. These results demonstrate that cryopreservation promotes the production of M-CSF, which plays an important role in root resorption by periodontal ligament cells.

Expression of SOCS1 and SOCS3 genes in human graft-versus-host disease after allogeneic hematopoietic stem cell transplantation

Background

Suppressor of cytokine signaling genes (SOCS) are regarded as pivotal negative feedback regulators of cytokine signals, including the interferon-gamma (IFN-γ), granulocyte-colony stimulating factor, and interleukin families, released by T cells. A detailed understanding of the involvement of SOCS genes in graft-versus-host disease (GVHD) is critical to effectively manage GVHD, yet their expression patterns among recipients remain largely unexplored.

Methods

Expression levels of SOCS1 and SOCS3 were determined by real-time quantitative reverse transcription PCR (qRT-PCR) in patients with acute GVHD (aGVHD) and chronic GVHD (cGVHD), in a severity-dependent manner, after allogeneic hematopoietic stem cell transplantation (HSCT). A total of 71 recipients with AML (N=40), ALL (N=12), myelodysplastic syndromes (MDS; N=10), chronic myelogenous leukemia (CML; N=2), severe aplastic anemia (SAA; N=5), or others (N=2), who received allogeneic HSCT from human leukocyte antigen-identical siblings or unrelated donors between 2009 and 2011, were included in the present study.

Results

Overall, the expression levels of SOCS1 decreased in recipients with grade II to IV aGVHD and cGVHD when compared to normal donors and non-GVHD recipients. Interestingly, the expressions of SOCS1 decreased significantly more in cGVHD than in aGVHD recipients (P=0.0091). In contrast, SOCS3 expressions were similarly reduced in all the recipients.

Conclusion

This is the first study to show that SOCS1 and SOCS3 are differentially expressed in recipients following allogeneic HSCT, suggesting a prognostic correlation between SOCS genes and the development of GVHD. This result provides a new platform to study GVHD immunobiology and potential diagnostic and therapeutic targets for GVHD.

Faecal levels of Bifidobacterium and Clostridium coccoides but not plasma lipopolysaccharide are inversely related to insulin and HOMA index in women

BACKGROUND & AIMS

The abundance of specific microbes might be associated with plasma lipopolysaccharide and insulin levels. The aims were to quantify the abundance of specific microbes and plasma LPS in females and assess their association with anthropometric, body composition and biochemical measurements.

METHODS

Seventeen lean (BMI 19-24.99 kg/m(2)) and fifteen obese females (BMI > 30 kg/m(2)) participated. Anthropometry, body composition, food intake and biochemical analyses were assessed. Bacterial groups in faeces were analysed by qPCR method.

RESULTS

Lactobacillus plantarum prevalence was higher (p = 0.005) and its counts tended to be higher in lean vs. obese group (p = 0.06). Bifidobacterium genus, Bifidobacterium longum, Clostridium coccoides and Clostridium leptum counts were higher in lean women (p < 0.05); prevalence and counts of Akkermansia muciniphila tended to be higher in lean group (p = 0.09, p = 0.06, respectively). Plasma LPS levels were similar between the study groups (p > 0.05). No association was found between LPS and bacterial levels or insulin. Bifidobacteria and C. coccoides counts were inversely associated with insulin and HOMA index.

CONCLUSIONS

Abundance of specific microbes is distinct between obese and lean women, but is not associated with LPS level. Bifidobacterial and C. coccoides levels are associated with insulin sensitivity. These bacterial groups may be capable of modulating insulin action.

Intrahepatic expression of genes related to metabotropic receptors in chronic hepatitis

AIM: To screen for genes related to metabotropic receptors that might be involved in the development of chronic hepatitis.

METHODS: Assessment of 20 genes associated with metabotropic receptors was performed in liver specimens obtained by punch biopsy from 12 patients with autoimmune and chronic hepatitis type B and C. For this purpose, a microarray with low integrity grade and with oligonucleotide DNA probes complementary to target transcripts was used. Evaluation of gene expression was performed in relation to transcript level, correlation between samples and grouping of clinical parameters used in chronic hepatitis assessment. Clinical markers of chronic hepatitis included alanine and aspartate aminotransferase, γ-glutamyltranspeptidase, alkaline phosphatase and cholinesterase activity, levels of iron ions, total cholesterol, triglycerides, albumin, glucose, hemoglobin, platelets, histological analysis of inflammatory and necrotic status, fibrosis according to METAVIR score, steatosis, as well as anthropometric body mass index, waist/hip index, percentage of adipose tissue and liver size in ultrasound examination. Gender, age, concomitant diseases and drugs were also taken into account. Validation of oligonucleotide microarray gene expression results was done with the use of quantitative real-time polymerase chain reaction (qRT-PCR).

RESULTS: The highest (0.002 < P < 0.046) expression among genes encoding main components of metabotropic receptor pathways, such as the α subunit of G-coupled protein, phosphoinositol-dependent protein kinase or arrestin was comparable to that of angiotensinogen synthesized in the liver. Carcinogenesis suppressor genes, such as chemokine ligand 4, transcription factor early growth response protein 1 and lysophosphatidic acid receptor, were characterized by the lowest expression (0.002 < P < 0.046), while the factor potentially triggering hepatic cancer, transcription factor JUN-B, had a 20-fold higher expression. The correlation between expression of genes of protein kinases PDPK1, phosphoinositide 3-kinase and protein kinase A (Spearman’s coefficient range: 0.762-0.769) confirmed a functional link between these enzymes. Gender (P = 0.0046) and inflammation severity, measured by alanine aminotransferase activity (P = 0.035), were characterized by diverse metabotropic receptor gene expression patterns. The Pearson’s coefficient ranging from -0.35 to 0.99 from the results of qRT-PCR and microarray indicated that qRT-PCR had certain limitations as a validation tool for oligonucleotide microarray studies.

CONCLUSION: A microarray-based analysis of hepatocyte metabotropic G-protein-related gene expression can reveal the molecular basis of chronic hepatitis.

Association of symptoms with gastrointestinal microbiota in irritable bowel syndrome

AIM: To investigate the correlations between self-reported symptoms of irritable bowel syndrome (IBS) and the gastrointestinal (GI) microbiota composition.

METHODS: Fecal samples were collected from a total of 44 subjects diagnosed with IBS. Their symptoms were monitored with a validated inflammatory bowel disease questionnaire adjusted for IBS patients. Thirteen quantitative real-time polymerase chain reaction assays were applied to evaluate the GI microbiota composition. Eubacteria and GI bacterial genera (Bifidobacterium, Lactobacillus and Veillonella), groups (Clostridium coccoides/Eubacterium rectale, Desulfovibrio desulfuricans) and distinct bacterial phylotypes [closest 16S rDNA sequence resemblance to species Bifidobacterium catenulatum, Clostridium cocleatum, Collinsella aerofaciens (C. aerofaciens), Coprococcus eutactus (C. eutactus), Ruminococcus torques and Streptococcus bovis] with a suspected association with IBS were quantified. Correlations between quantities or presence/absence data of selected bacterial groups or phylotypes and various IBS-related symptoms were investigated.

RESULTS: Associations were observed between subjects’ self-reported symptoms and the presence or quantities of certain GI bacteria. A Ruminococcus torques (R. torques)-like (94% similarity in 16S rRNA gene sequence) phylotype was associated with severity of bowel symptoms. Furthermore, among IBS subjects with R. torques 94% detected, the amounts of C. cocleatum 88%, C. aerofaciens-like and C. eutactus 97% phylotypes were significantly reduced. Interesting observations were also made concerning the effect of a subject’s weight on GI microbiota with regard to C. aerofaciens-like phylotype, Bifidobacterium spp. and Lactobacillus spp.

CONCLUSION: Bacteria seemingly affecting the symptom scores are unlikely to be the underlying cause or cure of IBS, but they may serve as biomarkers of the condition.