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Ochratoxin A (OTA) is one of the most prevalent mycotoxins that threatens food and feed safety. Biodegradation of OTA has gained much attention. In this study, an

Ochratoxin A (OTA) is toxic to animals and threatens food safety through residues in animal tissues. A novel degrading strain Bacillus subtilis ANSB168 was isolated and further investigated. We cloned d-alanyl-d-alanine carboxypeptidase DacA and DacB from ANSB168 and over-expressed them in Escherichia coli Rosetta (DE3). Then, we characterized the OTA degradation mechanism of DacA and DacB, which was degrading OTA into OTα. A total of 45 laying hens were divided into three equal groups. The control group was fed basal feed, and other groups were administered with OTA (250 μg/kg of feed). A freeze-dried culture powder of ANSB168 (3 × 107 CFU/g, 2 kg/T of feed) was added to one of the OTA-fed groups for 28 days from day one of the experiment. We found that OTA significantly damaged the kidney and liver, inducing inflammation and activating the humoral immune system, causing oxidative stress in the layers. The ANSB168 bioproduct was able to alleviate OTA-induced kidney and liver damage, relieving OTA-induced inflammation and oxidative stress. Overall, DacA and DacB derived from ANSB168 degraded OTA into OTα, while the ANSB168 bioproduct was able to alleviate damages induced by OTA in laying hens.

Background Predicting disease-related genes is helpful for understanding the disease pathology and the molecular mechanisms during the disease progression. However, traditional methods are not suitable for screening genes related to the disease development, because there are some samples with weak label information in the disease dataset and a small number of genes are known disease-related genes. Results We designed a disease-related gene mining method based on the weakly supervised learning model in this paper. The method is separated into two steps. Firstly, the differentially expressed genes are screened based on the weakly supervised learning model. In the model, the strong and weak label information at different stages of the disease progression is fully utilized. The obtained differentially expressed gene set is stable and complete after the algorithm converges. Then, we screen disease-related genes in the obtained differentially expressed gene set using transductive support vector machine based on the difference kernel function. The difference kernel function can map the input space of the original Huntington’s disease gene expression dataset to the difference space. The relation between the two genes can be evaluated more accurately in the difference space and the known disease-related gene information can be used effectively. Conclusions The experimental results show that the disease-related gene mining method based on the weakly supervised learning model can effectively improve the precision of the disease-related gene prediction compared with other excellent methods.

Mycotoxins are toxic secondary metabolites produced by toxigenic fungi that commonly contaminate agricultural crops. The purpose of the current study was to evaluate whether Bacillus subtilis ANSB060, Bacillus subtilis ANSB01G, and Devosia sp. ANSB714-based mycotoxin biodegradation agent (MBA) could alleviate the negative effects of naturally moldy diet containing aflatoxin (AF), zearalenone (ZEN), and deoxynivalenol (DON) on growth performance, serum immune function, and antioxidant capacity as well as tissue residues in mice. A total of 54 mice were randomly divided into three dietary treatments: basal diet (CON), multi-mycotoxins contaminated diet (MCD) containing AF, ZEN and DON and multi-mycotoxins contaminated diet plus MBA at a dose of 1.0 g kg-1 feed (MCD + MBA). Mice fed with moldy diet showed a significant decrease in body weight gain (p < 0.05), whereas the relative weight of the liver, spleen and uterus were remarkably increased (p < 0.05). Serum IgA and IgM contents were significantly decreased in MCD treatment compared with that in CON treatment (p < 0.05). In contrast, serum interleukin-1β (IL-1β), interleukin-2 (IL-2), and interleukin-6 (IL-6) concentrations were significantly promoted in mice fed with moldy diet (p < 0.05). Besides, the exposure to mycotoxins caused marked down-regulation of serum superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) activities in mice (p < 0.05). The addition of MBA effectively counteracted these toxic effects of moldy diet on mice. And DON residues in kidneys of mice consuming moldy diet were eliminated by the supplementation with MBA. Taken together, Bacillus subtilis ANSB060, Bacillus subtilis ANSB01G, and Devosia sp. ANSB714-based mycotoxin biodegradation agent has great potential use as a microbial additive to counteract mycotoxins contamination in food and feed.

Protein families are often represented by profile hidden Markov models (pHMMs). Homology between two distant protein families can be determined by comparing the pHMMs. Here we explored the idea of building a phylogeny of protein families using the distance matrix of their pHMMs. We developed a new software and web server (pHMM-tree) to allow four major types of inputs: (i) multiple pHMM files, (ii) multiple aligned protein sequence files, (iii) mixture of pHMM and aligned sequence files and (iv) unaligned protein sequences in a single file. The output will be a pHMM phylogeny of different protein families delineating their relationships. We have applied pHMM-tree to build phylogenies for CAZyme (carbohydrate active enzyme) classes and Pfam clans, which attested its usefulness in the phylogenetic representation of the evolutionary relationship among distant protein families. Availability and Implementation This software is implemented in C/C ++ and is available at http://cys.bios.niu.edu/pHMM-Tree/source/ Supplementary information Supplementary data are available at Bioinformatics online.