Evaluation of group-specific, 16S rRNA-targeted scissor probes for quantitative detection of predominant bacterial populations in dairy cattle rumen

AIMS

To develop a suite of group-specific, rRNA-targeted oligonucleotide scissor probes for the quantitative detection of the predominant bacterial groups within the ruminal microbial community with the rRNA cleavage reaction-mediated microbial quantification method.

METHODS AND RESULTS

Oligonucleotides that complement the conserved sites of the 16S rRNA of phylogenetically defined groups of bacteria that significantly contribute to the anaerobic fermentation of carbohydrates in ruminal ecosystems were selected from among published probes or were newly designed. For each probe, target-specific rRNA cleavage was achieved by optimizing the formamide concentration in the reaction mixture. The set of scissor probes was then used to analyse the bacterial community in the rumen fluids of four healthy dairy cows. In the rumen fluid samples, the genera Bacteroides/Prevotella and Fibrobacter and the Clostridium coccoides-Eubacterium rectale group were detected in abundance, accounting for 44-48%, 2.9-10%, and 9.1-10% of the total 16S rRNA, respectively. The coverage with the probe set was 71-78% of the total bacterial 16S rRNA.

CONCLUSIONS

The probe set coupled with the sequence-specific small-subunit rRNA cleavage method can be used to analyse the structure of a ruminal bacterial community.

SIGNIFICANCE AND IMPACT OF THE STUDY

The probe set developed in this study provides a tool for comprehensive rRNA-based monitoring of the community members that dominate ruminal ecosystems. As the ruminal microbial community can be perturbed, it is important to track its dynamics by analysing microbiological profiles under specific conditions. The method described here will provide a convenient approach for such tracking.

Mutations of the Birt Hogg Dube gene in patients with multiple lung cysts and recurrent pneumothorax

RATIONALE

Birt-Hogg-Dubé (BHD) syndrome, a rare inherited autosomal genodermatosis first recognised in 1977, is characterised by fibrofolliculomas of the skin, an increased risk of renal tumours and multiple lung cysts with spontaneous pneumothorax. The BHD gene, a tumour suppressor gene located at chromosome 17p11.2, has recently been shown to be defective. Recent genetic studies revealed that clinical pictures of the disease may be variable and may not always present the full expression of the phenotypes.

OBJECTIVES

We hypothesised that mutations of the BHD gene are responsible for patients who have multiple lung cysts of which the underlying causes have not yet been elucidated.

METHODS

We studied eight patients with lung cysts, without skin and renal disease; seven of these patients have a history of spontaneous pneumothorax and five have a family history of pneumothorax. The BHD gene was examined using PCR, denaturing high-performance liquid chromatography and direct sequencing.

MAIN RESULTS

We found that five of the eight patients had a BHD germline mutation. All mutations were unique and four of them were novel, including three different deletions or insertions detected in exons 6, 12 and 13, respectively and one splice acceptor site mutation in intron 5 resulting in an in-frame deletion of exon 6.

CONCLUSIONS

We found that germline mutations of the BHD gene are involved in some patients with multiple lung cysts and pneumothorax. Pulmonologists should be aware that BHD syndrome can occur as an isolated phenotype with pulmonary involvement.

Vascular endothelial growth factor-D is increased in serum of patients with lymphangioleiomyomatosis

BACKGROUND

Lymphangioleiomyomatosis (LAM) is a rare destructive lung disease characterized by an abnormal proliferation of smooth muscle-like cells (LAM cells) in the lung and along the axial lymphatics. LAM demonstrates a heterogeneous clinical course, but there is no serum surrogate marker available for assessing the disease severity or predicting the disease progression. Since the authors have recently demonstrated the extensive LAM-associated lymphangiogenesis and its potential role in progression and metastasis of LAM cells, they hypothesized that serum levels of lymphangiogenic growth factors might be increased in LAM and become a surrogate marker for disease severity.

METHODS AND RESULTS

VEGF-A, VEGF-C, and VEGF-D in serum of 44 patients with LAM were measured by enzyme-linked immunosorbant assay. Only VEGF-D was significantly increased in LAM patients as compared with age- and gender-matched healthy volunteers (n=24) (LAM vs. control, geometric mean 95% CI; 1069.3 pg/mL (809.4 approximately 1412.6) vs. 295.9 pg/mL (262.6 approximately 333.5), p<0.0001). Serum VEGF-D levels negatively correlated with variables of pulmonary function tests, FEV1/FVC (forced expiratory volume in one second/forced vital capacity) (r=-0.365, p<0.05) and %DLco/VA (the percentage of diffusing capacity for carbon monoxide/alveolar volume to the predicted value) (r=-0.560, p<0.001). As expected, the group who received hormone therapy showed more deteriorated pulmonary function with higher serum VEGF-D levels than the group who was just observed without hormone therapy. Immunohistochemical examination of lung specimens demonstrated the positive immunoreactivity of LAM cells for VEGF-D.

CONCLUSION

Serum VEGF-D levels may be a valuable surrogate marker for evaluating the disease severity in LAM.

[Thoracoscopic surgery for pneumothorax]

It is difficult to tell clearly what a therapy for pneumothorax is because it is not enough just to cut away the bullae. The patients should be treated mentally, physically and less invasively. The 4 anxieties should be solved for pneumothorax patients. Four anxieties for symptom, the normal side of lung, the effect after therapy and surgery. In thoracoscopic surgery on pneumothorax, to cut away just the bullous change does not mean to prevent the postoperative recurrence. Added treatments need beside resection of bullae because bullae often tend to regenerate near the suture line soon after thoracoscopic surgery. The covering method is the most effective in some added treatments. It is a method of covering regenerative oxidized cellulose mesh and fibrin glue on the suture line. Classification of air leakage level that was designed in Pneumothorax Research Center is clinically useful. This classification forms from level 1 to 4 according to air leakage volume and pressure level. It is important to resolve the mechanism on postoperative regeneration of bullae at this point in order to ask for better surgery. Female pneumothorax and less than 15-year-old pneumothorax should be researched because they cause frequently postoperative recurrence.

Short Communication: Amino Acids Antagonistic to the Amino Acids Inhibitory for Growth Rate of Mixed Ruminal Bacteria

Antagonism of some amino acids (AA) to the inhibitory effects of other AA (Ile, Phe, and Thr) on the growth rate of mixed ruminal bacteria was investigated. In vitro growth rate of the mixed ruminal bacteria was inhibited when the 3 inhibitory AA (1 mM each) were each added to individual control treatments in which an ammonium salt was included as a sole N source. The inhibitory effect caused by Ile was relieved by addition of Leu or Val (equimolar to Ile), and no significant inhibition was shown when both Leu and Val were added together with Ile. The growth inhibition caused by Phe was also alleviated by supplementing with Trp, and was completely negated by adding Tyr. The inhibitory effect of Thr, on the other hand, was not affected by addition of Lys or Met (which are synthesized using a common pathway with Thr), but was mitigated by supplementation with Glu, Ser, Val, Ala, or Gln. Among the antagonistic AA, Leu, Val, Trp, Tyr, and Glu were indispensable for the maximum growth rate of the ruminal bacteria under the experimental condition of supplementation of amino-N, the removal of which from a mixture of 20 protein AA caused the growth rate to decline. Removals of Ile along with Leu or Val or both, of Phe along with Trp or Tyr, and of Thr along with Glu recovered the promotion of bacterial growth rate. It was concluded that inhibitions of the bacterial growth rate caused by Ile, Phe, or Thr could be antagonized by some other AA (Leu, Val, Tyr, Trp, or Glu), and the role of these latter AA as relievers of the inhibitory effects could explain why they are indispensable for maximum growth rate of ruminal bacteria.

Phase 1/11 study of bi-weekly irinotecan plus cisplatin in the treatment of advanced gastric cancer

OBJECTIVES

To conduct a phase I/II study of irinotecan with cisplatin to establish a recommended dose, and assess the safety, efficacy and feasibility of this regimen in unresectable advanced or recurrent gastric cancer.

PATIENTS AND METHODS

In the phase I portion of the study, patients received a fixed dose of cisplatin (30 mg/m2) with escalating doses of irinotecan, ranging from 30 mg/m2 to 70 mg/m2, on days 1 and 15. In the phase II portion of the study, 40 patients were evaluated for response and safety at the recommended dose.

RESULTS

Eighteen patients were enrolled in the phase I study. Dose-limiting toxicity (diarrhea and neutropenia) appeared at the irinotecan dose of 70 mg/m2. Therefore, the recommended irinotecan dose was 60 mg/m2. In the phase II study, 40 patients received cisplatin (30 mg/m2) plus irinotecan (60 mg/m2). Twenty-five out of 40 patients had received prior chemotherapy. The median number of cycles was 3.5. The response rate was 32.5% (13/40) overall, and 53.3% (8/15) in patients without prior chemotherapy. The median time to tumor progression (TTP) was 162 days. The median survival time was 288 days. Four patients (10%) developed grade 4 neutropenia and 3 patients (7.5%) developed grade 4 anemia. The only observed non-hematological toxicity at grade 3 or higher was diarrhea, seen in 2.5% (1/40) of the patients.

CONCLUSION

Bi-weekly administration of irinotecan and cisplatin is safe and active for the management of unresectable advanced or recurrent gastric cancer.

Meta-analysis on the validity of pepsinogen test for gastric carcinoma, dysplasia or chronic atrophic gastritis screening

AIM

To assess the validity of the measurement of pepsinogen I and II as a screening test for gastric cancer and pre-malignant lesions, namely low-grade dysplasia, both in the general population and in selected groups of patients.

METHODS

A meta-analysis of sensitivity and specificity results from individual papers on the use of the pepsinogen test. An intrinsic cut-off effect was assumed and a random effect model was used for pooling.

RESULTS

Forty-two data sets were included: 27 (64%) population-based screening studies (n=296,553) and 15 (36%) sets of selected individuals (n=4385). Homogenous sensitivity and diagnostic odds ratio (DOR) estimates were found in studies using both pepsinogen I levels and pepsinogen I/II ratio calculations. Pooled pairs of sensitivity and false positive rates (FPr) for pepsinogen I < or = 70; pepsinogen I/II ratio < or = 3, pepsinogen I < or =50; pepsinogen I/II ratio < or = 3, and pepsinogen I < or = 30; pepsinogen I/II ratio < or = 2, were sensitivity 77%/FPr 27%, sensitivity 68%/FPr 31%, and sensitivity 52%/FPr 84%, respectively. Positive predictive values (PPV) varied between 0.77% and 1.25%, and negative predictive values (NPV) varied between 99.08% and 99.90%. In selected groups, pooling was only possible when considering pepsinogen I < or = 70; pepsinogen I/II ratio < or = 3: giving sensitivity 57%, specificity 80%, PPV 15% and NPV 83%. As for the diagnosis of dysplasia, studies considering pepsinogen I <50; pepsinogen I/II ratio <3 obtained sensitivity 65% and specificity ranging from 74%-85%, both with NPV >95%.

CONCLUSION

Pepsinogen test definition should include pepsinogen I/II ratio as consistency was obtained, both in population based studies and in selected groups for those studies that used pepsinogen I serum levels together with pepsinogen I/II ratio for screening for gastric cancer in high-incidence regions other than Japan. Further studies of this test in the management of high-risk patients seem to be worthwhile.

Phylogenetic analysis of methyl coenzyme-M reductase detected from the bovine rumen

AIMS

The object of the present study is isolation of methyl coenzyme-M reductase (MCR) genes (mcrA) from the bovine rumen fluid and determination of phylogenetical placements of the genes to investigate mechanisms of methanogenesis in the rumen from a point of view of mcrA genes.

METHODS

Genes for methanogen-specific MCR were isolated from the bovine rumen by PCR amplification. The deduced amino acid sequences were fitted to the alignments of mcrA gene products from the referred sequences.

SIGNIFICANCE AND IMPACT OF THE STUDY

Although the deduced amino acid sequences of mcrA genes, isolated from the bovine rumen in the present study, were close to that of Methanobrevibacter ruminantium, these amino acid sequences did not fall into known clusters of MCR. The findings suggest that methanogenesis in the rumen would be partially carried out by unknown methanogens.

Bombyx mori nucleopolyhedrovirus orf8 encodes a nucleic acid binding protein that colocalizes with IE1 during infection

This report describes the characterization of the Bombyx mori nucleopolyhedrovirus (BmNPV) orf8 gene. Immunoblot analyses demonstrated that orf8 was expressed as an early gene. The ORF8 protein accumulated in the nucleus, and was maintained at relatively constant levels from 4 to 24 h postinfection. Immunoblot analysis failed to detect ORF8 protein associated with budded virus and occlusion derived virus. In addition, immunohistochemical analysis by confocal microscopy showed that ORF8 protein colocalized with IE1 to specific nuclear foci throughout infection. To further examine the function of ORF8, a reporter gene was inserted into the orf8 reading frame. One orf8 disruption mutant (BmD8), which expressed the N-terminal half of ORF8, was isolated. However, it was not possible to isolate a null mutant, suggesting that orf8 may have an important role during viral infection. Single-step growth curves showed that BV production was reduced in BmD8 infected cells. Biochemical analyses indicated that ORF8 bound to nucleic acids. Together, these results suggest that BmNPV ORF8 may be involved in viral DNA replication and/or transcription.

Detection of Proteobacteria from the rumen by PCR using methanotroph-specific primers

AIMS

To detect Proteobacteria, including methanotrophs, from the rumen fluid and the bacteria inhabiting the rumen epithelium.

METHODS AND RESULTS

Proteobacteria inhabiting the rumen were detected by PCR using methanotroph-specific primers. The detected Proteobacteria were divided into clusters A, B, and C in addition to one clone, which was distinct from the clusters and closely related to Nitrosomonas sp. The clusters A, B, and C were close to Succinivibrio dextrinosolvens, Enterobacter cloacae, and Actinobacillus minor, respectively. The clones obtained from the rumen fluid each belonged to cluster A or B. The clones obtained from the rumen epithelium belonged to cluster B or C or to Nitrosomonas sp.

CONCLUSIONS

It has been assumed that the rumen fluid and the rumen epithelium host different populations of Proteobacteria. Moreover, detection of Nitrosomonas from the rumen epithelium would indicate the possibility that the bacterium oxidizes ammonia and methane on the rumen surface.

SIGNIFICANCE AND IMPACT OF THE STUDY

These findings suggest that the rumen fluid and the epithelium support different microbial populations, which would play specific roles in rumen function. Future study should focus on the relationship between these communities and physiological functions in the rumen.