Archaea, the tree of life, and cellular evolution in eukaryotes

The early history of life harbours many unresolved evolutionary questions, none more important than the genomic origin and cellular evolution of eukaryotes. An issue central to eukaryote origin concerns the position of eukaryotes in the tree of life and the relationship of the host lineage that acquired the mitochondrion some two billion years ago to lineages of modern-day archaea. Recent analyses indicate that the host lineage branches within the Archaea, prompting the search for novel archaeal lineages that can improve our understanding of the cellular evolution of eukaryotes. Here we give a brief review of the studies on Archaea, the tree of life and the cellular evolution of eukaryotes, which is followed by an overview of recent progress fueled by new genomic technologies and recent status of archaeal research in China. Future directions for the study of early evolution are considered.

In silico design of novel proton-pump inhibitors with reduced adverse effects

The development of new proton-pump inhibitors (PPIs) with less adverse effects by lowering the pKa values of nitrogen atoms in pyrimidine rings has been previously suggested by our group. In this work, we proposed that new PPIs should have the following features:(1) number of ring II = number of ring I+ 1;(2) preferably five, six, or seven-membered heteroatomic ring for stability;and (3) 1<pKa1<4. Six molecular scaffolds based on the aforementioned criteria were constructed, and R groups were extracted from compounds in extensive data sources. A virtual molecule dataset was established, and the pKa values of specific atoms on the molecules in the dataset were calculated to select the molecules with required pKa values. Drug-likeness screening was further conducted to obtain the candidates that significantly reduced the adverse effects of long-term PPI use. This study provided insights and tools for designing targeted molecules in silico that are suitable for practical applications.

Evidence challenging the causal role of gut microbiota in inflammatory bowel diseases

Recently,Bourgonje et al.[1]investigated the antibody epitope repertoire in patients with inflammatory bowel diseases(IBD)[1].Using the high-throughput phage-display immunoprecipitation sequencing(PhIP-Seq)method,they made several significant findings,including elevated antibody reactivities against bacterial flagellins in patients with Crohn’s disease(CD)and the effectiveness of the antibody epitope pattern in differentiating between CD/ulcerative colitis and healthy controls[1].