Knowledge extraction for assisted curation of summaries of bacterial transcription factor properties.

Transcription factors (TFs) play a main role in transcriptional regulation of bacteria, as they regulate transcription of the genetic information encoded in DNA. Thus, the curation of the properties of these regulatory proteins is essential for a better understanding of transcriptional regulation. However, traditional manual curation of article collections to compile descriptions of TF properties takes significant time and effort due to the overwhelming amount of biomedical literature, which increases every day. The development of automatic approaches for knowledge extraction to assist curation is therefore critical. Here, we show an effective approach for knowledge extraction to assist curation of summaries describing bacterial TF properties based on an automatic text summarization strategy. We were able to recover automatically a median 77% of the knowledge contained in manual summaries describing properties of 177 TFs of Escherichia coli K-12 by processing 5961 scientific articles. For 71% of the TFs, our approach extracted new knowledge that can be used to expand manual descriptions. Furthermore, as we trained our predictive model with manual summaries of E. coli, we also generated summaries for 185 TFs of Salmonella enterica serovar Typhimurium from 3498 articles. According to the manual curation of 10 of these Salmonella typhimurium summaries, 96% of their sentences contained relevant knowledge. Our results demonstrate the feasibility to assist manual curation to expand manual summaries with new knowledge automatically extracted and to create new summaries of bacteria for which these curation efforts do not exist. Database URL: The automatic summaries of the TFs of E. coli and Salmonella and the automatic summarizer are available in GitHub (https://github.com/laigen-unam/tf-properties-summarizer.git).

Expression Evolution of Ancestral XY Gametologs across All Major Groups of Placental Mammals.

Placental mammals present 180 million-year-old Y chromosomes that have retained a handful of dosage-sensitive genes. However, the expression evolution of Y-linked genes across placental groups has remained largely unexplored. Here, we expanded the number of Y gametolog sequences by analyzing ten additional species from previously unexplored groups. We detected seven remarkably conserved genes across 25 placental species with known Y repertoires. We then used RNA-seq data from 17 placental mammals to unveil the expression evolution of XY gametologs. We found that Y gametologs followed, on average, a 3-fold expression loss and that X gametologs also experienced some expression reduction, particularly in primates. Y gametologs gained testis specificity through an accelerated expression decay in somatic tissues. Moreover, despite the substantial expression decay of Y genes, the combined expression of XY gametologs in males is higher than that of both X gametologs in females. Finally, our work describes several features of the Y chromosome in the last common mammalian ancestor.

Melatonin modifies SOX2+ cell proliferation in dentate gyrus and modulates SIRT1 and MECP2 in long-term sleep deprivation.

Melatonin is a pleiotropic molecule that, after a short-term sleep deprivation, promotes the proliferation of neural stem cells in the adult hippocampus. However, this effect has not been observed in long-term sleep deprivation. The precise mechanism exerted by melatonin on the modulation of neural stem cells is not entirely elucidated, but evidence indicates that epigenetic regulators may be involved in this process. In this study, we investigated the effect of melatonin treatment during a 96-hour sleep deprivation and analyzed the expression of epigenetic modulators predicted by computational text mining and keyword clusterization. Our results showed that the administration of melatonin under sleep-deprived conditions increased the MECP2 expression and reduced the SIRT1 expression in the dentate gyrus. We observed that let-7b, mir-132, and mir-124 were highly expressed in the dentate gyrus after melatonin administration, but they were not modified by sleep deprivation. In addition, we found more Sox2+/5-bromo-2'-deoxyuridine (BrdU)+ cells in the subgranular zone of the sleep-deprived group treated with melatonin than in the untreated group. These findings may support the notion that melatonin modifies the expression of epigenetic mediators that, in turn, regulate the proliferation of neural progenitor cells in the adult dentate gyrus under long-term sleep-deprived conditions. All procedures performed in this study were approved by the Animal Ethics Committee of the University of Guadalajara, Mexico (approval No. CI-16610) on January 2, 2016.