Identification of Nocardia species using matrix-assisted laser desorption/ionization–time-of-flight mass spectrometry

Background

The MALDI (matrix-assisted laser desorption/ionization) Biotyper system for bacterial identification has already been utilized in clinical microbiology laboratories as a successful clinical application of protoemics. However, in cases of Nocardia, mass spectra suitable for MALDI Biotyper identification are often not obtained if such specimens are processed like general bacteria. This problem is related to the insufficiencies in bacterial spectrum databases that preclude accurate specimen identification. Here, we developed a bacterial processing method to improve mass spectra from specimens of the genus Nocardia. In addition, with the new processing method, we constructed a novel in-house bacterial database that combines a commercial database and mass spectra of Nocardia strains from the Department of Clinical Laboratory at Chiba University Hospital (DCLC) and the Medical Mycology Research Center at Chiba University (MMRC).

Results

The newly developed method (Nocardia Extraction Method at DCLC [NECLC]) based on ethanol-formic acid extraction (EFAE) improved mass spectra obtained from Nocardia specimens. The Nocardia in-house database at Chiba University Hospital (NDCUH) was then successfully validated. In brief, prior to introduction of the NECLC and NDCUH, 10 of 64 (15.6%) clinical isolates were identified at the species level and 16 isolates (25.0%) could only be identified at the genus level. In contrast, after the introduction, 58 isolates (90.6%) were identified at the species level and 6 isolates (9.4%) were identified at the genus level.

Conclusions

The results of this study suggest that MALDI-TOF (time-of-flight) Biotyper system can identify Nocardia accurately in a short time in combination with a simple processing method and an in-house database.

Electronic supplementary material

The online version of this article (doi:10.1186/s12014-015-9078-5) contains supplementary material, which is available to authorized users.     

Tracking Time Evolution of Collective Attention Clusters in Twitter: Time Evolving Nonnegative Matrix Factorisation

Micro-blogging services, such as Twitter, offer opportunities to analyse user behaviour. Discovering and distinguishing behavioural patterns in micro-blogging services is valuable. However, it is difficult and challenging to distinguish users, and to track the temporal development of collective attention within distinct user groups in Twitter. In this paper, we formulate this problem as tracking matrices decomposed by Nonnegative Matrix Factorisation for time-sequential matrix data, and propose a novel extension of Nonnegative Matrix Factorisation, which we refer to as Time Evolving Nonnegative Matrix Factorisation (TENMF). In our method, we describe users and words posted in some time interval by a matrix, and use several matrices as time-sequential data. Subsequently, we apply Time Evolving Nonnegative Matrix Factorisation to these time-sequential matrices. TENMF can decompose time-sequential matrices, and can track the connection among decomposed matrices, whereas previous NMF decomposes a matrix into two lower dimension matrices arbitrarily, which might lose the time-sequential connection. Our proposed method has an adequately good performance on artificial data. Moreover, we present several results and insights from experiments using real data from Twitter.     

Prevalence of Anal Human Papillomavirus Infection and Risk Factors among HIV-positive Patients in Tokyo,Japan

Background

Oncogenic human papillomavirus (HPV) infection, particularly multiple HPV types, is recognized as a necessary cause of anal cancer. However, a limited number of studies have reported the prevalence of anal HPV infection in Asia. We determined the prevalence, genotypes, and risk factors for anal HPV infection in Japanese HIV-positive men who have sex with men (MSM), heterosexual men, and women.

Methods

This cross-sectional study included 421 HIV-positive patients. At enrollment, we collected data on smoking, alcohol, co-morbidities, drugs, CD4 cell counts, HIV RNA levels, highly active anti-retroviral therapy (HAART) duration, sexually transmitted infections (STIs), and serological screening (syphilis, hepatitis B virus, Chlamydia trachomatis, Entamoeba histolytica). Anal swabs were collected for oncogenic HPV genotyping.

Results

Oncogenic HPV rate was 75.9% in MSM, 20.6% in heterosexual men, and 19.2% in women. HPV 16/18 types were detected in 34.9% of MSM, 17.7% of heterosexual men, and 11.5% of women. Multiple oncogenic HPV (≥2 oncogenic types) rate was 54.6% in MSM, 8.8% in heterosexual men, and 0% in women. In univariate analysis, younger age, male sex, MSM, CD4 <100, HIV viral load >50,000, no administration of HAART, and having ≥2 sexually transmitted infections (STIs) were significantly associated with oncogenic HPV infection, whereas higher smoking index and corticosteroid use were marginally associated with oncogenic HPV infection. In multivariate analysis, younger age (OR, 0.98 [0.96–0.99]), MSM (OR, 5.85 [2.33–14.71]), CD4 <100 (OR, 2.24 [1.00–5.01]), and having ≥2 STIs (OR, 2.81 [1.72–4.61]) were independently associated with oncogenic HPV infection. These 4 variables were also significant risk factors for multiple oncogenic HPV infection.

Conclusions

Among Japanese HIV-infected patients, approximately two-thirds of MSM, one-fifth of heterosexual men, and one-fifth of women have anal oncogenic HPV infection. Younger age, MSM, ≥2 STIs, and immunosuppression confer a higher risk of infection with oncogenic HPV and multiple oncogenic types.     

Cell Type-Specific Separation of Subicular Principal Neurons during Network Activities

The hippocampal output structure, the subiculum, expresses two major memory relevant network rhythms, sharp wave ripple and gamma frequency oscillations. To this date, it remains unclear how the two distinct types of subicular principal cells, intrinsically bursting and regular spiking neurons, participate in these two network rhythms. Using concomitant local field potential and intracellular recordings in an in vitro mouse model that allows the investigation of both network rhythms, we found a cell type-specific segregation of principal neurons into participating intrinsically bursting and non-participating regular spiking cells. However, if regular spiking cells were kept at a more depolarized level, they did participate in a specific manner, suggesting a potential bimodal working model dependent on the level of excitation. Furthermore, intrinsically bursting and regular spiking cells exhibited divergent intrinsic membrane and synaptic properties in the active network. Thus, our results suggest a cell-type-specific segregation of principal cells into two separate groups during network activities, supporting the idea of two parallel streams of information processing within the subiculum.     

Gastric acid secretion in streptozotocin-diabetic rats--different responses to various secretagogues.

We compared gastric acid secretion in response to various stimuli in normal and streptozotocin (STZ)-induced diabetic rats, in an attempt to characterize the alteration of acid secretory response in diabetic conditions. Animals were injected STZ (70 mg x kg(-1), i.p.) and used after 5 weeks of diabetes with blood glucose > 350 mg x dL(-1). Under urethane anesthesia, a rat stomach was mounted on an ex vivo chamber, perfused with saline and acid secretion was measured at pH 7.0 using a pH-stat method and by adding 100 mM NaOH. The acid secretion was stimulated by i.v. infusion of either histamine (4 mg x kg(-1) x h(-1)), pentagastrin (60 microg x kg(-1) x h(-1)) or carbachol (20 microg x kg(-1) x h(-1)) or i.v. injection of YM-14673 (0.3 mg x kg(-1)), an analog of thyrotropin-releasing hormone, or vagal electrical stimulation (2 ms, 3 Hz, 0.5 mA). In normal rats, gastric acid secretion was increased in response to either histamine, pentagastrin, carbachol, YM-14673 or electrical vagal stimulation. In STZ diabetic rats, however, changes in acid secretion varied depending on the stimuli; the acid secretory responses to histamine remained unchanged, those to YM-14673 and vagal electrical stimulation significantly decreased, but the responses to both pentagastrin and carbachol were significantly enhanced as compared to normal rats. Luminal release of histamine in response to both pentagastrin and carbachol was increased in STZ-diabetic rats as compared to normal animals. The altered acid secretory responses in STZ diabetic rats were partially reversed by daily injection of insulin with amelioration of high blood glucose levels. These results suggest that STZ-diabetic rats showed different changes in gastric acid secretory responses to various stimuli; no change in response to histamine, a decrease to both YM-14673 and vagal electrical stimulation and an increase to both pentagastrin and carbachol. The increased acid secretory response may be associated with an enhanced release of mucosal histamine, while the decreased response may be due to vagal neuropathy.     

Circulating interleukin 6 as a useful marker for predicting postoperative complications.

We examined postoperative serial changes in the levels of serum interleukin 6 (IL-6), serum acute phase reactants (APRs) and plasma neutrophil elastase (NE) in patients with various cancers and reviewed these changes in patients who did, and did not, show postoperative complications. Serum IL-6 level was elevated after surgery, peaking on the first postoperative day. Elevation of serum APRs and plasma NE levels also followed. There was a significant correlation between the serum peak level of IL-6 and those of APRs and NE (P less than 0.01). Moreover, there was a significant difference in the serum IL-6 level in patients with and without complications. The relationship between the serum IL-6 greater than 400 pg/ml and the incidence of postoperative complications was also marked. These results suggest that circulating IL-6 is a clinically useful marker for the earliest detection and prediction of postoperative complications.     

Strong influence of the processing of the antigen on negative effects on T cell activation by regions outside the determinant area of bovine alpha s1-casein.

alpha s1-Casein can elicit a proliferative response in responding T cell clone 3D20 cells (specific for I-Ab plus fragment 136-151), even when using fixed splenic antigen-presenting cells (APC) not carrying antigen processing ability. The order of potency of each tested antigen for fixed APC was the determinant peptide (136-151) > the long peptide (136-195) > the intact protein (199 residues), indicating that regions outside the determinant area negatively affected the stimulatory potency of the antigens. On the other hand, the order for normal splenic APC was the short peptide > the intact protein > the long peptide. This shows that negative effects by regions outside the determinant area were strongly influenced by the antigen processing.     

Development of a radioimmunoassay for human group-II phospholipase A2 and demonstration of postoperative elevation.

A radioimmunoassay (RIA) for the determination of human group-II phospholipase A2 (M-PLA2) has been developed. M-PLA2 was purified from human spleen. Monoclonal antibody (IgG) was prepared by fusion of splenic cells from immunized mice with M-PLA2 and the mouse myeloma cell line NS-1. The RIA was carried out by a single antibody method. The assay is sensitive (0.78 micrograms/l), reproducible and specific. In healthy individuals, the serum M-PLA2 concentration ranges from 1.4 to 4.2 micrograms/l, the average being 2.2 +/- 0.1 micrograms/l (mean +/- SE). Using the RIA, we found increased serum M-PLA2 in patients with various infections and malignant tumors. We also showed the postoperative transient elevation of serum M-PLA2 in cases without any infectious complications. The elevation was independent of the surgical procedure or site. The maximum serum M-PLA2 level was seen on the 2nd to 4th postoperative day. In these patients, the serum M-PLA2 and C-reactive protein levels were significantly correlated. The present study indicated that serum M-PLA2 is an acute phase reactant.     

Effects of uniconazole and GA3 on cold-induced stem elongation and flowering of Raphanus sativus L.

The effects of gibberellin (GA) on cold-induced stem elongation and flowering of Japanese radish (Raphanus sativus L.) were investigated using application of GA3 and a GA-biosynthesis inhibitor, uniconazole (UCZ). UCZ very strongly inhibited stem elongation and delayed flowering, and the inhibition and delay were completely reversed by GA3 application. These results suggest that GA is necessary not only in the stem elongation but also in the flowering. When cold treatment (CT) was conducted on the plants whose GA level was lowered by UCZ, GA3 applied after CT completely reversed the delay of flowering. Thus low GA level probably did not retard cold induction. Microscopic observation of apical meristem showed that UCZ delayed flowering by delaying the shift from vegetative to dome-shaped meristem. This result suggested that low GA level delayed floral evocation. Consequently it was suggested that low GA level retarded physiological process involved in long day induction or in floral evocation, resulting in delay of floral evocation.