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Harnessing stepping-stone hosts to engineer, select, and reboot synthetic bacteriophages in one pot.

ABSTRACT: Advances in synthetic genomics have led to a great demand for genetic manipulation. Trimming any process to simplify and accelerate streamlining of genetic code into life holds great promise for synthesizing and studying organisms. Here, we develop a simple but powerful stepping-stone strategy to promote genome refactoring of viruses in one pot, validated by successful cross-genus and cross-order rebooting of 90 phages infecting 4 orders of popular pathogens. Genomic sequencing suggests that rebooting outcome is associated with gene number and DNA polymerase availability within phage genomes. We integrate recombineering, screening, and rebooting processes in one pot and demonstrate genome assembly and genome editing of phages by stepping-stone hosts in an efficient and economic manner. Under this framework, in vitro assembly, yeast-based assembly, or genetic manipulation of native hosts are not required. As additional stepping-stone hosts are being developed, this framework will open doors for synthetic phages targeting more pathogens and commensals.

SUBMITTER: Cheng L

PROVIDER: S-EPMC9142689 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature

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Harnessing stepping-stone hosts to engineer, select, and reboot synthetic bacteriophages in one pot.

Cheng Li L Deng Ziqing Z Tao Haoran H Song Wenchen W Xing Bo B Liu Wenfeng W Kong Lingxin L Yuan Shengjian S Ma Yingfei Y Wu Yayun Y Huang Xun X Peng Yun Y Wong Nai-Kei NK Liu Yingxia Y Wang Yun Y Shen Yue Y Li Junhua J Xiao Minfeng M

Cell reports methods 20220523 5

Advances in synthetic genomics have led to a great demand for genetic manipulation. Trimming any process to simplify and accelerate streamlining of genetic code into life holds great promise for synthesizing and studying organisms. Here, we develop a simple but powerful stepping-stone strategy to promote genome refactoring of viruses in one pot, validated by successful cross-genus and cross-order rebooting of 90 phages infecting 4 orders of popular pathogens. Genomic sequencing suggests that reb ...[more]

PMID: 35637913

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Project description:Compositionality refers to a structural property of human language, according to which the meaning of a complex expression is a function of the meaning of its parts and the way they are combined. Compositionality is a defining characteristic of all human language, spoken and signed. Comparative research into the emergence of human language aims at identifying precursors to such key features of human language in the communication of other primates. While it is known that chimpanzees, our closest relatives, produce a variety of gestures, facial expressions and vocalizations in interactions with their group members, little is known about how these signals combine simultaneously. Therefore, the aim of the current study is to investigate whether there is evidence for compositional structures in the communication of chimpanzees. We investigated two semi-wild groups of chimpanzees, with focus on their manual gestures and their combinations with facial expressions across different social contexts. If there are compositional structures in chimpanzee communication, adding a facial expression to a gesture should convey a different message than the gesture alone, a difference that we expect to be measurable by the recipient's response. Furthermore, we expect context-dependent usage of these combinations. Based on a form-based coding procedure of the collected video footage, we identified two frequently used manual gestures (stretched arm gesture and bent arm gesture) and two facial expression (bared teeth face and funneled lip face). We analyzed whether the recipients' response varied depending on the signaler's usage of a given gesture + face combination and the context in which these were used. Overall, our results suggest that, in positive contexts, such as play or grooming, specific combinations had an impact on the likelihood of the occurrence of particular responses. Specifically, adding a bared teeth face to a gesture either increased the likelihood of affiliative behavior (for stretched arm gesture) or eliminated the bias toward an affiliative response (for bent arm gesture). We show for the first time that the components under study are recombinable, and that different combinations elicit different responses, a property that we refer to as componentiality. Yet our data do not suggest that the components have consistent meanings in each combination-a defining property of compositionality. We propose that the componentiality exhibited in this study represents a necessary stepping stone toward a fully evolved compositional system.

Project description:Selecting motor strategies in daily life tasks requires a perception of the task requirements as well as of one's own physical abilities. Age-related cognitive and physical changes may affect these perceptions. This might entail that some older adults select inappropriate movement strategies when confronted with daily-life motor tasks, which could lead to balance loss or falls. We investigated whether older adults select motor strategies in accordance with their actual physical ability. Twenty-one older adults were subjected to a stepping down paradigm, in which full-body kinematics of selected and reactive behavior were recorded. Stepping down from a curb can be done with either (1) a relatively low effort but more balance threatening heel landing, or (2) a more controlled but more demanding toe landing. The probability of selecting a toe landing grows with an increase in curb height. We determined the curb height at which participants switched from heel to toe landing during expected stepping down over different heights as an indicator of their perceived ability. During an unexpected step down trial, participants encountered a step down of 0.1 m earlier than expected, because part of the walkway was removed and covered by a black cloth. We evaluated participants' actual physical ability from the reactive behavior, with performance defined as the reduction in kinetic energy between the peak value after landing and the onset of the next step. To unravel whether the selected motor strategies corresponded with actual physical ability, the ability to recover from the unexpected step down was correlated to the height at which the participants switched movement strategy. The switching height was not correlated to the ability to recover from an unexpected step down (ρ = 0.034, p = 0.877). This finding suggests that older adults do not select their movement strategy in stepping down based on their actual abilities, or have an imprecise perception of their actual abilities. Future research should evaluate whether inappropriate motor strategy selection in a stepping down paradigm can explain accidental falls in older adults.

Dataset Information

Harnessing stepping-stone hosts to engineer, select, and reboot synthetic bacteriophages in one pot.

Publications

Harnessing stepping-stone hosts to engineer, select, and reboot synthetic bacteriophages in one pot.

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