Biology subjects

NI, J.

Publications and source records attributed to NI, J..

3 recordsLinked to original sources

bioRxiv2025

Modulation of signal response by small RNAs through feed-forward loops

In response to environmental changes, bacteria have evolved sophisticated regulatory networks that incorporate small RNAs (sRNAs) and transcription factors (TFs) to fine-tune cellular physiology. Both sRNAs and TFs modulate gene expression, but the former function via post-transcriptional mechanisms, while the latter act at the transcriptional level. However, it remains unclear why both regulatory layers are conserved through evolution, rather than one being sufficient. Here, we experimentally identified that CRP, a global regulator, regulates 25 small RNAs (sRNAs) in Escherichia coli. Interestingly, CRP also controls 80% of the target genes of these sRNAs. This architecture led us to identify 34 novel sRNA-mediated feed-forward loops (sFFLs)--circuits where CRP regulates both an sRNA and its target--within the CRP regulon. Quantitative PCR analysis of 16 such sFFLs revealed that each type possesses a distinct cAMP dose-response profile, suggesting that different sFFL structures embody unique regulatory logic. Specifically, coherent and incoherent type 3 and 4 sFFLs exhibit broader dynamic ranges in their dose-response compared to open-loop controls. Coherent and incoherent type 1 and 2 sFFLs appear more energy-efficient. Altogether, we propose that sRNAs cooperate with TFs through sFFLs to optimize both the energy efficiency and the diversity of signal response profiles. Therefore, sRNAs serve as critical components integrating transcriptional and post-transcriptional networks across diverse cellular pathways.

systems biology↗

bioRxiv2025

Contrasting genomic routes to domestication in Occidental and Oriental pears

The domestication of perennial fruit trees remains poorly understood compared with annual crops, which were shaped by strong bottlenecks and elevated genetic load. Pears (Pyrus spp.) provide an ideal model for exploring how long-lived, outcrossing crops evolved under human selection. Here, we combined high-coverage whole-genome resequencing of 396 wild and cultivated accessions from Occidental and Oriental pears with analyses of nucleotide and transposable element (TE) polymorphisms to reconstruct the demographic and adaptive history of pear domestication. Demographic inferences revealed weak or no domestication bottlenecks and extensive gene flow between wild and cultivated populations. In the Occidental lineage, dessert and perry P. communis cultivars underwent independent domestications from the same wild progenitor, P. pyraster, with divergent selection linked to fruit use. In the Oriental lineage, regionally independent domestications gave rise to Chinese and Japanese P. pyrifolia cultivars, shaped by both environmental adaptation and human selection. Selection scans identified lineage- and use-specific targets related to fruit texture, metabolism, and immunity. Contrary to the classical "cost of domestication" hypothesis, cultivated pears carried fewer deleterious variants than their wild relatives, suggesting efficient purging through selection and introgression. TE insertions mirrored population structure and occasionally occurred near selected genes, indicating a limited but detectable adaptive role. Together, our findings go beyond confirming the dual origins of Pyrus domestication to reveal contrasting demographic and adaptive pathways in Occidental and Oriental pears, illustrating independent adaptive trajectories in perennial crops, where long lifespan, self-incompatibility, and recurrent introgression shape distinctive genomic outcomes.

genomics↗

bioRxiv2022

PeerPub: A device for concurrent operant oral self-administration by multiple rats

The social environment has long been recognized to play an important role in substance abuse disorders (SUD). Operant conditioning is the most widely used rodent model of SUD. However, most operant chambers do not accommodate more than one rat at a time. Here, we introduce PeerPub - a novel social operant chamber. PeerPub uses a touch sensor to record the number of licks on drinking spouts. It then delivers a drop of solution with a fixed volume as the reward to the tip of the spout when the number of licks meets the requirement of a reinforcement schedule. A radio-frequency identification (RFID) chip implanted on top of each rats skull tracks the identity of the rat. The system is controlled by a Raspberry Pi computer. We tested PeerPub using male Wistar Kyoto rats in daily one-hour sessions where supersac, a solution containing glucose and saccharin, was delivered under a fixed ratio 5 schedule. We found that male rats consumed more supersac in group housing rather than in isolated conditions. These data demonstrated the utility of PeerPub in modeling the interaction between motivated behavior and social context. We anticipate devices like PeerPub will help demonstrate the role of the social environment in SUD phenotypes. The design of PeerPub is available at http://github.com/nijie321/PeerPub

animal behavior and cognition↗