Flavobacterium johnsoniae cells move rapidly over solid surfaces by gliding motility. The collective migration of F. johnsoniae on the surfaces results in the formation of spreading colonies. Colony ...spreading is influenced by adhesin components on the cell surface and the concentrations of agar and glucose. For example, on nutrient-poor agar media, film-like, round spreading colonies are formed. F. johnsoniae displays at least two types of migration: small cell cluster movements leading to concentric colonies and individual cell movements leading to dendritic colonies. The methods for observing colony morphology are described in this chapter.
Phylogenetic analysis strongly depends on evolutionary models. Most evolutionary models for estimating genetic differences and phylogenetic relationships do not treat gap sites in the alignment of ...sequences. Appropriately incorporating evolutionary information of sites containing insertions and deletions into genetic difference measures will be improve the accuracy of phylogenetic estimates.
We introduced a new measure for estimating genetic differences, and presented P*R*O*P, a web application for performing phylogenetic analysis based on genetic difference considering the effect of gaps. As an example of phylogenetic analysis using P*R*O*P, we used complete p53 amino acid sequences of 31 organisms and illustrated that the genetic differences with and without information on sites containing gaps result in trees with different topologies.
P*R*O*P is available at https://www.rs.tus.ac.jp/bioinformatics/prop and the user can perform phylogenetic analysis by uploading sequence data on the website. The most distinctive feature of P*R*O*P is its genetic difference that is estimated without eliminating gap sites for alignment sequences, which helps users detect meaningful difference in an evolutionary process. The source code is available in GitHub: https://github.com/TUS-Satolab/PROP .
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Prevotella intermedia, a Gram-negative oral anaerobic bacterium, is frequently isolated from the periodontal pockets of patients with chronic periodontitis. In recent years, the involvement of the ...bacterium in respiratory tract infections as well as in oral infections has been revealed. P. intermedia possesses several potent virulence factors, such as cysteine proteinase interpain A encoded by the
gene. The genome of P. intermedia carries genes of the type IX secretion system (T9SS), which enables the translocation of virulence factors across the outer membrane in several pathogens belonging to the phylum
; however, it is still unclear whether the T9SS is functional in this microorganism. Recently, we performed targeted mutagenesis in the strain OMA14 of P. intermedia. Here, we successfully obtained mutants deficient in
and the T9SS component genes
and
. None of the mutants exhibited protease activity of interpain A. The
and
mutants, but not the
mutant, showed defects in colony pigmentation, hemagglutination, and biofilm formation. We also obtained a complemented strain for the
gene that recovered all the above abilities. These results indicate that T9SS functions in P. intermedia and that interpain A is one of the T9SS cargo proteins.
The virulence factors of periodontal pathogens such as Prevotella intermedia have not been elucidated. Using our established procedure, we succeeded in generating type IX secretion system mutants and gene complementation strains that might transfer virulence factors to the bacterial surface. The generated strains clearly indicate that T9SS in P. intermedia is essential for colonial pigmentation, hemagglutination, and biofilm formation. These results indicated that interpain A is a T9SS cargo protein.
Reduced retinal illuminance affects colour perception in older adults, and studies show that they exhibit deficiencies in yellow-blue (YB) discrimination. However, the influence of colour cues on the ...visual attention in older individuals remains unclarified. Visual attention refers to the cognitive model by which we prioritise regions within the visual space and selectively process information. The present study aimed to explore the effect of colour on visual search performance in older observers. In our experiment, younger observers wearing glasses with a filter that simulated the spectral transmittance of the aging human lens and older observers performed two types of search tasks, feature search (FS) and conjunction search (CS), under three colour conditions: red-green, YB, and luminance. Targets and distractors were designed on the basis of the Derrington-Krauskopf-Lennie colour representation. In FS tasks, reaction times changed according to colour in all groups, especially under the YB condition, regardless of the presence or absence of distractors. In CS tasks with distractors, older participants and younger participants wearing glasses showed slower responses under chromatic conditions than under the achromatic condition. These results provide preliminary evidence that, for older observers, visual search performance may be affected by impairments in chromatic colour discrimination.
An information-theoretical approach was used to identify prognostic factors for survival in patients with estrogen receptor-positive (ER+) breast cancer and to classify those patients according to ...the prognostic factors. We demonstrated that KMT2C and SLC20A1 are powerful prognostic biomarkers in ER+ breast cancer that can distinguish patients with an extremely bad prognosis from those with a sufficiently good prognosis at the time of breast cancer diagnosis.
In general, it has been considered that estrogen receptor-positive (ER+) breast cancer has a good prognosis and is responsive to endocrine therapy. However, one third of patients with ER+ breast cancer exhibit endocrine therapy resistance, and many patients develop recurrence and die 5 to 10 years after diagnosis. In ER+ breast cancer, a major problem is to distinguish those patients most likely to develop recurrence or metastatic disease within 10 years after diagnosis from those with a sufficiently good prognosis.
We downloaded the messenger RNA expression data and the clinical information for 401 patients with ER+ breast cancer from the cBioPortal for Cancer Genomics. An information-theoretical approach was used to identify the prognostic factors for survival in patients with ER+ breast cancer and to classify those patients according to the prognostic factors.
The information-theoretical approach contributed to the identification of KMT2C and SLC20A1 as prognostic biomarkers in ER+ breast cancer. We found that low KMT2C expression was associated with a poor outcome and high SLC20A1 expression was associated with a poor outcome. Both levels of KMT2C and SLC20A1 expression were significantly and strongly associated with the differentiation of survival. The 10-year survival rate for ER+ patients with low KMT2C and high SLC20A1 expression was 0%. In contrast, for ER+ patients with high KMT2C and low SLC20A1 expression, the 10-year survival rate was 86.78%.
Our results strongly suggest that clinical examination of the expression of both KMT2C and SLC20A1 in ER+ breast cancer will be very useful for the determination of prognosis and therapy.
Recently, several new biological drugs targeting severe asthma are on the market, and various studies on severe asthma have been reported worldwide. However, in Japan, the data are still limited ...regarding epidemiology and burden of disease on severe asthma. This study determined the prevalence, characteristics, and burden of disease of patients with severe asthma.
: This retrospective study (HO-16-16484) used a nationwide health care claims database. Severity of asthma was defined according to the treatment during the baseline period (April 1, 2014–March 31, 2015). Eligible patients were >15–65 years of age with asthma during the 12-month baseline period and were followed up for 12 months. End points included the prevalence, characteristics, exacerbation frequency, and patient behavior in patients with severe, moderate, or mild asthma. Risk factors for exacerbations were explored in patients with all levels of asthma severity and in those with severe asthma.
Among the 16,107 patients with asthma, 2.4 (95% CI, 2.1–2.6) per 100 patients had severe asthma. During the baseline period, 130 (34.0%) of 382 patients with severe asthma had ≥1 asthma exacerbation. The exacerbation frequency was highest in patients with severe asthma, and most of the comorbidities increased in proportion to the asthma severity. During the follow-up period, exacerbation frequency increased with asthma severity. Approximately 70% of patients with severe asthma were treated at clinics, requiring outpatient visits ~10 times per year. Different exacerbation risk factors were identified between patients with all severity levels of asthma and those with severe asthma. With the severe asthma patients, experiencing exacerbations during the previous year was a risk factor for further exacerbations during the follow-up period.
In Japan, 2.4% of patients with asthma have severe asthma, and there is a significant burden of disease in patients with severe asthma undergoing high-intensity treatment.
Cells of Flavobacterium johnsoniae and of many other members of the phylum Bacteroidetes exhibit rapid gliding motility over surfaces by a unique mechanism. These cells do not have flagella or pili; ...instead, they rely on a novel motility apparatus composed of Gld and Spr proteins. SprB, a 669-kDa cell-surface adhesin, is required for efficient gliding. SprB was visualized by electron microscopy as thin 150-nm-long filaments extending from the cell surface. Fluorescence microscopy revealed movement of SprB proteins toward the poles of the cell at ∼2 μm/s. The fluorescent signals appeared to migrate around the pole and continue at the same speed toward the opposite pole along an apparent left-handed helical closed loop. Movement of SprB, and of cells, was rapidly and reversibly blocked by the addition of carbonyl cyanide m -chlorophenylhydrazone, which dissipates the proton gradient across the cytoplasmic membrane. In a gliding cell, some of the SprB protein appeared to attach to the substratum. The cell body moved forward and rotated with respect to this point of attachment. Upon reaching the rear of the cell, the attached SprB often was released from the substratum, and apparently recirculated to the front of the cell along a helical path. The results suggest a model for Flavobacterium gliding, supported by mathematical analysis, in which adhesins such as SprB are propelled along a closed helical loop track, generating rotation and translation of the cell body.
Background
To present the strategies and preliminary findings of the first 3 years after implementing a
Helicobacter pylori
screening and eradication program to prevent gastric cancer in Saga ...Prefecture.
Methods
A screening and treatment program to eradicate
H. pylori
from third-grade junior high students was started in Saga Prefecture in 2016, using local governmental grants. Screening was with urinary anti-
H. pylori
antibody tests, followed by
H. pylori
stool antigen tests for students who were antibody positive. Those positive on both tests underwent
H. pylori
eradication by triple therapy based on a potassium-competitive acid blocker.
Results
From 2016 to 2018, the participation rate was 83.1% and the
H. pylori
infection rate was 3.1% (660/21,042). The participation rates were higher in 2017 (85.4%) and 2018 (85.9%) compared with 2016 (78.5%) (
P
< 0.0001), and the infection rate also decreased in a time-dependent manner (2016: 3.6%, 2017: 3.3%, 2018: 2.5%,
P
= 0.0001). In total, 501 students positive for
H. pylori
received eradication therapy (85.1% success) and adverse events occurred in 20 of these (4.0%). However, no serious complications occurred.
Conclusions
The
H. pylori
screening and eradication project for school students in Saga Prefecture has started successfully and we have seen both a steady increase in the participation rate and a steady decrease in the infection rate, without major safety concerns.
Colony spreading of Flavobacterium johnsoniae is shown to include gliding motility using the cell surface adhesin SprB, and is drastically affected by agar and glucose concentrations. Wild-type (WT) ...and ΔsprB mutant cells formed nonspreading colonies on soft agar, but spreading dendritic colonies on soft agar containing glucose. In the presence of glucose, an initial cell growth-dependent phase was followed by a secondary SprB-independent, gliding motility-dependent phase. The branching pattern of a ΔsprB colony was less complex than the pattern formed by the WT. Mesoscopic and microstructural information was obtained by atmospheric scanning electron microscopy (ASEM) and transmission EM, respectively. In the growth-dependent phase of WT colonies, dendritic tips spread rapidly by the movement of individual cells. In the following SprB-independent phase, leading tips were extended outwards by the movement of dynamic windmill-like rolling centers, and the lipoproteins were expressed more abundantly. Dark spots in WT cells during the growth-dependent spreading phase were not observed in the SprB-independent phase. Various mutations showed that the lipoproteins and the motility machinery were necessary for SprB-independent spreading. Overall, SprB-independent colony spreading is influenced by the lipoproteins, some of which are involved in the gliding machinery, and medium conditions, which together determine the nutrient-seeking behavior.
IL-31, which is a member of the IL-6 family of cytokines, is produced mainly by activated CD4
T cells, in particular activated Th2 cells, suggesting a contribution to development of type-2 immune ...responses. IL-31 was reported to be increased in specimens from patients with atopic dermatitis, and IL-31-transgenic mice develop atopic dermatitis-like skin inflammation, which is involved in the pathogenesis of atopic dermatitis. However, the role of IL-31 in development of contact dermatitis/contact hypersensitivity (CHS), which is mediated by hapten-specific T cells, including Th2 cells, is not fully understood. Therefore, we investigated this using IL-31-deficient (Il31
) mice, which we newly generated. We demonstrated that the mice showed normal migration and maturation of skin dendritic cells and induction of hapten-specific T cells in the sensitization phase of FITC-induced CHS, and normal induction of local inflammation in the elicitation phase of FITC- and DNFB-induced CHS. On the other hand, those mice showed reduced scratching frequency and duration during FITC- and/or DNFB-induced CHS. Our findings suggest that IL-31 is responsible for pruritus, but not induction of local skin inflammation, during CHS induced by FITC and DNFB.
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