Methyltranscriptome is an exciting new area that studies the mechanisms and functions of methylation in transcripts. The MethylTranscriptome DataBase (MeT-DB, http://compgenomics.utsa.edu/methylation/) is the first comprehensive resource for N6-methyladenosine (m6A) in mammalian transcriptome. It includes a database that records publicaly available data sets from methylated RNA immunoprecipitation sequencing (MeRIP-Seq), a recently developed technology for interrogating m6A methyltranscriptome. MeT-DB includes ∼300k m6A methylation sites in 74 MeRIP-Seq samples from 22 different experimental conditions predicted by exomePeak and MACS2 algorithms. To explore this rich information, MeT-DB also provides a genome browser to query and visualize context-specific m6A methylation under different conditions. MeT-DB also includes the binding site data of microRNA, splicing factor and RNA binding proteins in the browser window for comparison with m6A sites and for exploring the potential functions of m6A. Analysis of differential m6A methylation and the related differential gene expression under two conditions is also available in the browser. A global perspective of the genome-wide distribution of m6A methylation in all the data is provided in circular ideograms, which also act as a navigation portal. The query results and the entire data set can be exported to assist publication and additional analysis.
The electron transfer capacities (ETCs) of soil humic substances (HSs) are linked to the type and abundance of redox-active functional moieties in their structure. Natural temperature can affect the chemical structure of natural organic matter by regulating their oxidative transformation and degradation in soil. However, it is unclear if there is a direct correlation between ETC of soil HS and mean annual temperature. In this study, we assess the response of the electron-accepting and -donating capacities (EAC and EDC) of soil HSs to temperature by analyzing HSs extracted from soil set along glacial-interglacial cycles through loess-palaeosol sequences and along natural temperature gradients through latitude and altitude transects. We show that the EAC and EDC of soil HSs increase and decrease, respectively, with increasing temperature. Increased temperature facilitates the prevalence of oxidative degradation and transformation of HS in soils, thus potentially promoting the preferentially oxidative degradation of phenol moieties of HS or the oxidative transformation of electron-donating phenol moieties to electron-accepting quinone moieties in the HS structure. Consequently, the EAC and EDC of HSs in soil increase and decrease, respectively. The results of this study could help to understand biogeochemical processes, wherein the redox functionality of soil organic matter is involved in the context of increasing temperature.
Background: Eimeria spp. are responsible for chicken coccidiosis which is the most important enteric protozoan disease resulting in tremendous economic losses in the poultry industry. Understanding the interaction between the avian cecal microbiota and coccidia is of interest in the development of alternative treatments that do not rely on chemotherapeutics and do not lead to drug resistance. Methods: We utilized 16S rRNA gene sequencing to detect the dynamics of the cecal microbial community in AA broilers challenged with Eimeria tenella. Histopathological analysis of the cecum was also conducted. Results: We found that microbial shifts occur during the infection. Lactobacillus, Faecalibacterium, Ruminococcaceae UCG-013, Romboutsia and Shuttleworthia decreased in abundance. However, the opportunistic pathogens Enterococcus and Streptococcus increased in abundance over time in response to the infection. Conclusions: Eimeria tenella disrupts the integrity of the cecal microbiota and could promote the establishment and growth of potentially pathogenic bacteria. Defining bacterial populations affected by coccidial infection might help identify bacterial markers for intestinal disease as well as populations or species that could be beneficial in maintaining and restoring gut homeostasis during and after infection with E. tenella.
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