Extracellular High-Mobility Group Box 1 is Increased in Patients with Behçet's Disease with Intestinal Involvement

High-mobility group box 1 (HMGB1) protein has been demonstrated to play an important role in chronic inflammatory diseases including rheumatoid arthritis, and systemic lupus erythematosus. This study investigated the association between extracellular HMGB1 expression and disease activity, and clinical features of Behçet's disease (BD). Extracellular HMGB1 expression in the sera of 42 BD patients was measured and was compared to that of 22 age- and sex-matched healthy controls. HMGB1 expression was significantly increased in BD patients compared to healthy controls (78.70 ± 20.22 vs 10.79 ± 1.90 ng/mL, P = 0.002). In addition, HMGB1 expression was significantly elevated in BD patients with intestinal involvement compared to those without (179.61 ± 67.95 vs 61.89 ± 19.81 ng/mL, P = 0.04). No significant association was observed between HMGB1 concentration and other clinical manifestations, or disease activity. It is suggested that extracellular HMGB1 may play an important role in the pathogenesis of BD

Discovering context-specific relationships from biological literature by using multi-level context terms

<p>Abstract</p> <p>Background</p> <p>The Swanson's ABC model is powerful to infer hidden relationships buried in biological literature. However, the model is inadequate to infer relations with context information. In addition, the model generates a very large amount of candidates from biological text, and it is a semi-automatic, labor-intensive technique requiring human expert's manual input. To tackle these problems, we incorporate context terms to infer relations between AB interactions and BC interactions.</p> <p>Methods</p> <p>We propose 3 steps to discover meaningful hidden relationships between drugs and diseases: 1) multi-level (gene, drug, disease, symptom) entity recognition, 2) interaction extraction (drug-gene, gene-disease) from literature, 3) context vector based similarity score calculation. Subsequently, we evaluate our hypothesis with the datasets of the "Alzheimer's disease" related 77,711 PubMed abstracts. As golden standards, PharmGKB and CTD databases are used. Evaluation is conducted in 2 ways: first, comparing precision of the proposed method and the previous method and second, analysing top 10 ranked results to examine whether highly ranked interactions are truly meaningful or not.</p> <p>Results</p> <p>The results indicate that context-based relation inference achieved better precision than the previous ABC model approach. The literature analysis also shows that interactions inferred by the context-based approach are more meaningful than interactions by the previous ABC model.</p> <p>Conclusions</p> <p>We propose a novel interaction inference technique that incorporates context term vectors into the ABC model to discover meaningful hidden relationships. By utilizing multi-level context terms, our model shows better performance than the previous ABC model.</p

Metagenomic and functional analyses of the consequences of reduction of bacterial diversity on soil functions and bioremediation in diesel-contaminated microcosms

International audienceThe relationship between microbial biodiversity and soil function is an important issue in ecology, yet most studies have been performed in pristine ecosystems. Here, we assess the role of microbial diversity in ecological function and remediation strategies in diesel-contaminated soils. Soil microbial diversity was manipulated using a removal by dilution approach and microbial functions were determined using both metagenomic analyses and enzymatic assays. A shift from Proteobacteria-to Actinobacteria-dominant communities was observed when species diversity was reduced. Metagenomic analysis showed that a large proportion of functional gene categories were significantly altered by the reduction in biodiversity. The abundance of genes related to the nitrogen cycle was significantly reduced in the low-diversity community, impairing denitrification. In contrast, the efficiency of diesel biodegradation was increased in the low-diversity community and was further enhanced by addition of red clay as a stimulating agent. Our results suggest that the relationship between microbial diversity and ecological function involves trade-offs among ecological processes, and should not be generalized as a positive, neutral, or negative relationship

Genome sequence of extracellular-protease-producing Alishewanella jeotgali Isolated from traditional Korean fermented seafood

Alishewanella jeotgali MS1(T) (=KCTC 22429(T) = JCM 15561(T)) was isolated from a traditional Korean fermented seafood, gajami sikhae (jeotgal), and has been reported as a novel species. A. jeotgali was proven to have extracellular proteolytic activity, which may play an important role in the fermentation environment of food containing fish flesh. Here, we present the genome sequence of Alishewanella jeotgali MS1(T) as the first sequenced strain in the genus Alishewanella and its taxonomic relatives.

Genome sequence of pectin-degrading Alishewanella aestuarii strain B11T, isolated from tidal flat sediment

We present the genome sequence of Alishewanella aestuarii B11(T) (=KCTC 22051(T)=DSM 19476(T)). This species, isolated from tidal flat sediment, was reported to be a novel species. A. aestuarii is known to degrade pectin, an important component of plant cell wall. The presence of the genes related to pectin metabolism in this strain indicates its capability to utilize pectin.