The metabolome of an E. coli CRISPRi library identifies benefits of minimal metabolite levels and targets for engineering [0.03%]
利用CRISPRi文库研究的大肠杆菌代谢组鉴定出最少代谢物水平的效益及工程学目标
Johanna Rapp,Andreas Verhülsdonk,Anton Garcke et al.
Johanna Rapp et al.
Metabolite concentration changes can have broad consequences on the function and robustness of metabolic networks. Here, we measured the metabolome response of 1,515 CRISPR interference (CRISPRi) E. coli strains targeting all genes in the i...
Fast, long-range intercellular signal propagation through growth-assisted positive feedback [0.03%]
生长增强的正反馈驱动的细胞间快速长程信号传递
Meidi Wang,Louis González,Soutick Saha et al.
Meidi Wang et al.
Intercellular signaling in bacteria is often mediated by small molecules secreted by cells. These small molecules disperse via diffusion, which limits the speed and spatial extent of information transfer in spatially extended systems. Theor...
Amandine Batté,Núria Bosch-Guiteras,Carles Pons et al.
Amandine Batté et al.
Mutant phenotypes often vary across genetically distinct individuals. To identify the causes of such genetic background effects, we studied differences in gene essentiality across 18 genetically diverse natural yeast strains. We identified ...
Competition and compromise between exogenous probiotics and native microbiota [0.03%]
外源益生菌与固有微生物群之间的竞争和妥协
Zhe Han,Zheng Sun,Qian Zhao et al.
Zhe Han et al.
Probiotic interventions are effective strategies to modulate the gut microbiome, but how exogenous probiotics compete with native gut microbiota remains elusive. Here, we use a mouse model and a well-documented probiotic, Bifidobacterium an...
Juan Rico,Pablo Japón,Luis M Rubio et al.
Juan Rico et al.
Genetic circuit engineering enables new cellular functions, yet most circuits are developed in the model host Escherichia coli, limiting their availability and performance in alternative organisms. To expand chassis options, we developed an...
Engineering sensor-based antithetic integral controllers for enhanced dynamic performance and noise attenuation [0.03%]
基于传感器的反向积分控制器的工程设计以提高动态性能和降噪功能
Maurice Filo,Stephanie K Aoki,Mucun Hou et al.
Maurice Filo et al.
Effective cellular regulation relies on feedback control mechanisms to maintain homeostasis and mitigate environmental fluctuations. We develop and analyze a sensor-based antithetic integral feedback (sAIF) controller that achieves this by ...
Krishna Manoj Aravind,Domitilla Del Vecchio
Krishna Manoj Aravind
CRISPR-mediated gene activation (CRISPRa) allows concurrent transcriptional control of many genes and is widely used in genome-wide screening, bioproduction, and therapeutics. Multi-gene control is possible due to the sequence specificity b...
Mathias S Heltberg,Alba Jimenez,Galit Lahav et al.
Mathias S Heltberg et al.
Resonance allows systems to amplify their response to periodic stimuli and is well established in physics but not yet described in gene regulatory networks. Here, we asked whether resonance exists in the dynamics of p53, a tumor suppressor ...
Identifying microbial protease allergens through protein language model-guided homology [0.03%]
通过蛋白质语言模型指导的同源建模鉴定微生物蛋白酶过敏原
Kumar Thurimella,Elena Wu,Chenhao Li et al.
Kumar Thurimella et al.
Emerging research links the gut, skin, and oral microbiomes to allergies, with serine proteases (SPs) identified as potential allergens. This study leverages deep learning and pre-trained protein language models (pLMs) to uncover allergenic...
Higher-order interactions in auxotroph communities enhance their resilience to resource fluctuations [0.03%]
营养缺陷型群落的高阶相互作用可增强其对资源波动的抵抗力
Tong Wang,Ashish B George,Sergei Maslov
Tong Wang
Auxotrophs are prevalent in microbial communities, enhancing their diversity and stability-a counterintuitive effect considering their dependence on essential resources from other species. To address the ecological roles of auxotrophs, our ...