Interface Focus最新文献_第7页

Multiscale models driving hypothesis and theory-based research in microbial ecology. 微生物生态学多尺度模型驱动假说与理论研究。

IF 4.4 3区生物学

Interface Focus Pub Date : 2023-08-06 DOI: 10.1098/rsfs.2023.0008

Eloi Martinez-Rabert, William T Sloan, Rebeca Gonzalez-Cabaleiro

{"title":"Multiscale models driving hypothesis and theory-based research in microbial ecology.","authors":"Eloi Martinez-Rabert, William T Sloan, Rebeca Gonzalez-Cabaleiro","doi":"10.1098/rsfs.2023.0008","DOIUrl":"https://doi.org/10.1098/rsfs.2023.0008","url":null,"abstract":"Hypothesis and theory-based studies in microbial ecology have been neglected in favour of those that are descriptive and aim for data-gathering of uncultured microbial species. This tendency limits our capacity to create new mechanistic explanations of microbial community dynamics, hampering the improvement of current environmental biotechnologies. We propose that a multiscale modelling bottom-up approach (piecing together sub-systems to give rise to more complex systems) can be used as a framework to generate mechanistic hypotheses and theories (in-silico bottom-up methodology). To accomplish this, formal comprehension of the mathematical model design is required together with a systematic procedure for the application of the in-silico bottom-up methodology. Ruling out the belief that experimentation before modelling is indispensable, we propose that mathematical modelling can be used as a tool to direct experimentation by validating theoretical principles of microbial ecology. Our goal is to develop methodologies that effectively integrate experimentation and modelling efforts to achieve superior levels of predictive capacity.","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"13 4","pages":"20230008"},"PeriodicalIF":4.4,"publicationDate":"2023-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10251115/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9622767","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Engineering biology in the face of uncertainty. 面对不确定性的工程生物学。

IF 4.4 3区生物学

Interface Focus Pub Date : 2023-08-06 DOI: 10.1098/rsfs.2023.0001

William T Sloan, Tania L Gómez-Borraz

{"title":"Engineering biology in the face of uncertainty.","authors":"William T Sloan, Tania L Gómez-Borraz","doi":"10.1098/rsfs.2023.0001","DOIUrl":"https://doi.org/10.1098/rsfs.2023.0001","url":null,"abstract":"Combining engineering and biology surely must be a route to delivering solutions to the world's most pressing problems in depleting resources, energy and the environment. Engineers and biologists have long recognized the power in coupling their disciplines and have evolved a healthy variety of approaches to realizing technologies. Yet recently, there has been a movement to narrow the remit of engineering biology. Its definition as 'the application of engineering principles to the design of biological systems' ought to encompass a broad church. However, the emphasis is firmly on construction '…of novel biological devices and systems from standardized artificial parts' within cells. Thus, engineering biology has become synonymous with synthetic biology, despite the many longstanding technologies that use natural microbial communities. The focus on the nuts and bolts of synthetic organisms may be deflecting attention from the significant challenge of delivering solutions at scale, which cuts across all engineering biology, synthetic and natural. Understanding, let alone controlling, every component of an engineered system is an unrealistic goal. To realize workable solutions in a timely manner we must develop systematic ways of engineering biology in the face of the uncertainties that are inherent in biological systems and that arise through lack of knowledge.","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"13 4","pages":"20230001"},"PeriodicalIF":4.4,"publicationDate":"2023-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10251114/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9622760","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Evaluation of different 16S rRNA gene hypervariable regions and reference databases for profiling engineered microbiota structure and functional guilds in a swine wastewater treatment plant. 评估不同的 16S rRNA 基因超变区和参考数据库，以分析猪废水处理厂中的工程微生物群结构和功能区。

IF 3.6 3区生物学

Interface Focus Pub Date : 2023-06-09 eCollection Date: 2023-08-06 DOI: 10.1098/rsfs.2023.0012

Limin Lin, Feng Ju

{"title":"Evaluation of different 16S rRNA gene hypervariable regions and reference databases for profiling engineered microbiota structure and functional guilds in a swine wastewater treatment plant.","authors":"Limin Lin, Feng Ju","doi":"10.1098/rsfs.2023.0012","DOIUrl":"10.1098/rsfs.2023.0012","url":null,"abstract":"High-throughput 16S rRNA gene amplicon sequencing technology is widely applied for environmental microbiota structure analysis to derive knowledge that informs microbiome-based surveillance and oriented bioengineering. However, it remains elusive how the selection of 16S rRNA gene hypervariable regions and reference databases affects microbiota diversity and structure profiling. This study systematically evaluated the fitness of different frequently used reference databases (i.e. SILVA 138 SSU, GTDB bact120_r207, Greengenes 13_5 and MiDAS 4.8) and primers of 16S rRNA gene in microbiota profiling of anaerobic digestion and activated sludge collected from a full-scale swine wastewater treatment plant (WWTP). The comparative results showed that MiDAS 4.8 achieved the highest levels of taxonomic diversity and species-level assignment rate. For whichever sample groups, microbiota richness captured by different primers decreased in the following order: V4 > V4-V5 > V3-V4 > V6-V8/V1-V3. Using primer-bias-free metagenomic data results as the judging standard, V4 region also best characterized microbiota structure and well represented typical functional guilds (e.g. methanogens, ammonium oxidizers and denitrifiers), while V6-V8 regions largely overestimated the archaeal methanogens (mainly Methanosarcina) by over 30 times. Therefore, MiDAS 4.8 database and V4 region are recommended for best simultaneous analysis of bacterial and archaeal community diversity and structure of the examined swine WWTP.","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"13 4","pages":"20230012"},"PeriodicalIF":3.6,"publicationDate":"2023-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10251118/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9622761","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The ecology of scale: impact of volume on coalescence and function in methanogenic communities. 规模生态学：体积对甲烷生物群落凝聚和功能的影响。

IF 3.6 3区生物学

Interface Focus Pub Date : 2023-06-09 eCollection Date: 2023-08-06 DOI: 10.1098/rsfs.2022.0089

Pawel Sierocinski, Peter Stilwell, Daniel Padfield, Florian Bayer, Angus Buckling

{"title":"The ecology of scale: impact of volume on coalescence and function in methanogenic communities.","authors":"Pawel Sierocinski, Peter Stilwell, Daniel Padfield, Florian Bayer, Angus Buckling","doi":"10.1098/rsfs.2022.0089","DOIUrl":"10.1098/rsfs.2022.0089","url":null,"abstract":"Engineered ecosystems span multiple volume scales, from a nano-scale to thousands of cubic metres. Even the largest industrial systems are tested in pilot scale facilities. But does scale affect outcomes? Here we look at comparing different size laboratory anaerobic fermentors to see if and how the volume of the community affects the outcome of community coalescence (combining multiple communities) on community composition and function. Our results show that there is an effect of scale on biogas production. Furthermore, we see a link between community evenness and volume, with smaller scale communities having higher evenness. Despite those differences, the overall patterns of community coalescence are very similar at all scales, with coalescence leading to levels of biogas production comparable with that of the best-performing component community. The increase in biogas with increasing volume plateaus, suggesting there is a volume where productivity stays stable over large volumes. Our findings are reassuring for ecologists studying large ecosystems and industries operating pilot scale facilities, as they support the validity of pilot scale studies in this field.","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"13 4","pages":"20220089"},"PeriodicalIF":3.6,"publicationDate":"2023-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10251116/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9622764","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Microbial Ecology for Engineering Biology 微生物生态学工程生物学

IF 4.4 3区生物学

Interface Focus Pub Date : 2023-06-09 DOI: 10.1098/rsfs.2023.0027

Thomas Curtis, J. Fowler

引用次数: 0

Cellular RNA levels define heterotrophic substrate-uptake rate sub-guilds in activated sludge microbial communities. 细胞 RNA 水平定义了活性污泥微生物群落中的异养基质吸收率子群落。

IF 3.6 3区生物学

Interface Focus Pub Date : 2023-06-09 eCollection Date: 2023-08-06 DOI: 10.1098/rsfs.2022.0080

Bing Guo, Dominic Frigon

{"title":"Cellular RNA levels define heterotrophic substrate-uptake rate sub-guilds in activated sludge microbial communities.","authors":"Bing Guo, Dominic Frigon","doi":"10.1098/rsfs.2022.0080","DOIUrl":"10.1098/rsfs.2022.0080","url":null,"abstract":"A heterotrophic-specialist model was proposed previously to divide wastewater treatment plant (WWTP) heterotrophs into sub-guilds of consumers of readily or slowly degradable substrates (RDS or SDS, respectively). The substrate degradation rate model coupled to metabolic considerations predicted that RNA and polyhydroxyalkanoate (PHA) levels would be positively correlated in the activated sludge communities with high RNA and PHA occurring in RDS-consumers, and low RNA with no PHA accumulation occurring in SDS-consumers because their external substrates are always present. This prediction was verified in previous studies and in the current one. Thus, RNA and PHA levels were used as biomarkers of the RDS- and SDS-consumer sub-guilds for cell sorting using flow cytometry of samples from three WWTPs. Subsequently, 16S rRNA gene amplicon sequencing revealed that the sorted groups were highly similar over time and among WWTPs, and demonstrated a clear segregation by RNA levels. Predicted ecophysiological traits based on 16S rRNA phylogeny suggested that the high-RNA population showed RDS-consumer traits such as higher rrn copy numbers per genome. Using a mass-flow immigration model, it appeared that the high-RNA populations exhibited high immigration rates more frequently than low-RNA populations, but the differences in frequencies were less with increasing solids residence times.","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"13 4","pages":"20220080"},"PeriodicalIF":3.6,"publicationDate":"2023-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10251117/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9622762","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Quantifying drift-selection balance using an agent-based biofilm model of identical heterotrophs under low-nutrient conditions. 利用基于代理的低营养条件下相同异养生物生物膜模型量化漂移选择平衡。

IF 3.6 3区生物学

Interface Focus Pub Date : 2023-06-09 eCollection Date: 2023-08-06 DOI: 10.1098/rsfs.2023.0010

Joseph Earl Weaver

{"title":"Quantifying drift-selection balance using an agent-based biofilm model of identical heterotrophs under low-nutrient conditions.","authors":"Joseph Earl Weaver","doi":"10.1098/rsfs.2023.0010","DOIUrl":"10.1098/rsfs.2023.0010","url":null,"abstract":"Both deterministic and stochastic forces shape biofilm communities, but the balance between those forces is variable. Quantifying the balance is both desirable and challenging. For example, drift-driven failure, a stochastic force, can be thought of as an organism experiencing 'bad luck' and manipulating 'luck' as a factor in real-world systems is difficult. We used an agent-based model to manipulate luck by controlling seed cevalues governing random number generation. We determined which organism among identical competitors experienced the greatest drift-driven failure, gave it a deterministic growth advantage and re-ran the simulation with the same seed. This enabled quantifying the growth advantage required to overcome drift, e.g. a 50% chance to thrive may require a 10-20% improved growth rate. Further, we found that crowding intensity affected that balance. At moderate spacings, there were wide ranges where neither drift nor selection dominated. Those ranges shrank at extreme spacings; close and loose crowding, respectively, favoured drift and selection. We explain how these results may partially illuminate two conundrums: the fact that a stably operating wastewater treatment plant's microbial community can vary greatly over time and the difference between equivalent and total community size in neutral community assembly models.","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"13 4","pages":"20230010"},"PeriodicalIF":3.6,"publicationDate":"2023-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10251119/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9617584","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The lack of temporal brain dynamics asymmetry as a signature of impaired consciousness states. 缺乏时间大脑动力学不对称是意识状态受损的标志。

IF 4.4 3区生物学

Interface Focus Pub Date : 2023-06-06 DOI: 10.1098/rsfs.2022.0086

Elvira G-Guzmán, Yonatan Sanz Perl, Jakub Vohryzek, Anira Escrichs, Dragana Manasova, Başak Türker, Enzo Tagliazucchi, Morten Kringelbach, Jacobo D Sitt, Gustavo Deco

{"title":"The lack of temporal brain dynamics asymmetry as a signature of impaired consciousness states.","authors":"Elvira G-Guzmán, Yonatan Sanz Perl, Jakub Vohryzek, Anira Escrichs, Dragana Manasova, Başak Türker, Enzo Tagliazucchi, Morten Kringelbach, Jacobo D Sitt, Gustavo Deco","doi":"10.1098/rsfs.2022.0086","DOIUrl":"https://doi.org/10.1098/rsfs.2022.0086","url":null,"abstract":"Life is a constant battle against equilibrium. From the cellular level to the macroscopic scale, living organisms as dissipative systems require the violation of their detailed balance, i.e. metabolic enzymatic reactions, in order to survive. We present a framework based on temporal asymmetry as a measure of non-equilibrium. By means of statistical physics, it was discovered that temporal asymmetries establish an arrow of time useful for assessing the reversibility in human brain time series. Previous studies in human and non-human primates have shown that decreased consciousness states such as sleep and anaesthesia result in brain dynamics closer to the equilibrium. Furthermore, there is growing interest in the analysis of brain symmetry based on neuroimaging recordings and since it is a non-invasive technique, it can be extended to different brain imaging modalities and applied at different temporo-spatial scales. In the present study, we provide a detailed description of our methodological approach, paying special attention to the theories that motivated this work. We test, for the first time, the reversibility analysis in human functional magnetic resonance imaging data in patients suffering from disorder of consciousness. We verify that the tendency of a decrease in the asymmetry of the brain signal together with the decrease in non-stationarity are key characteristics of impaired consciousness states. We expect that this work will open the way for assessing biomarkers for patients' improvement and classification, as well as motivating further research on the mechanistic understanding underlying states of impaired consciousness.","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"13 3","pages":"20220086"},"PeriodicalIF":4.4,"publicationDate":"2023-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10102727/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9499243","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Free energy and inference in living systems. 生命系统中的自由能和推理。

IF 4.4 3区生物学

Interface Focus Pub Date : 2023-06-06 DOI: 10.1098/rsfs.2022.0041

Chang Sub Kim

{"title":"Free energy and inference in living systems.","authors":"Chang Sub Kim","doi":"10.1098/rsfs.2022.0041","DOIUrl":"https://doi.org/10.1098/rsfs.2022.0041","url":null,"abstract":"Organisms are non-equilibrium, stationary systems self-organized via spontaneous symmetry breaking and undergoing metabolic cycles with broken detailed balance in the environment. The thermodynamic free-energy (FE) principle describes an organism's homeostasis as the regulation of biochemical work constrained by the physical FE cost. By contrast, recent research in neuroscience and theoretical biology explains a higher organism's homeostasis and allostasis as Bayesian inference facilitated by the informational FE. As an integrated approach to living systems, this study presents an FE minimization theory overarching the essential features of both the thermodynamic and neuroscientific FE principles. Our results reveal that the perception and action of animals result from active inference entailed by FE minimization in the brain, and the brain operates as a Schrödinger's machine conducting the neural mechanics of minimizing sensory uncertainty. A parsimonious model suggests that the Bayesian brain develops the optimal trajectories in neural manifolds and induces a dynamic bifurcation between neural attractors in the process of active inference.","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"13 3","pages":"20220041"},"PeriodicalIF":4.4,"publicationDate":"2023-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10102732/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9499244","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Emergence of common concepts, symmetries and conformity in agent groups-an information-theoretic model. 智能体群体中共同概念、对称性和一致性的出现——一个信息论模型。

IF 4.4 3区生物学

Interface Focus Pub Date : 2023-06-06 DOI: 10.1098/rsfs.2023.0006

Marco Möller, Daniel Polani

{"title":"Emergence of common concepts, symmetries and conformity in agent groups-an information-theoretic model.","authors":"Marco Möller, Daniel Polani","doi":"10.1098/rsfs.2023.0006","DOIUrl":"https://doi.org/10.1098/rsfs.2023.0006","url":null,"abstract":"The paper studies principles behind structured, especially symmetric, representations through enforced inter-agent conformity. For this, we consider agents in a simple environment who extract individual representations of this environment through an information maximization principle. The representations obtained by different agents differ in general to some extent from each other. This gives rise to ambiguities in how the environment is represented by the different agents. Using a variant of the information bottleneck principle, we extract a 'common conceptualization' of the world for this group of agents. It turns out that the common conceptualization appears to capture much higher regularities or symmetries of the environment than the individual representations. We further formalize the notion of identifying symmetries in the environment both with respect to 'extrinsic' (birds-eye) operations on the environment as well as with respect to 'intrinsic' operations, i.e. subjective operations corresponding to the reconfiguration of the agent's embodiment. Remarkably, using the latter formalism, one can re-wire an agent to conform to the highly symmetric common conceptualization to a much higher degree than an unrefined agent; and that, without having to re-optimize the agent from scratch. In other words, one can 're-educate' an agent to conform to the de-individualized 'concept' of the agent group with comparatively little effort.","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"13 3","pages":"20230006"},"PeriodicalIF":4.4,"publicationDate":"2023-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10102731/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9496619","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2