Model-Based Quantifiation of As Mobility within the Redox Transition Zones (RTZs) Marking the Interface of Holocene/Pleistocene Aquifers

ABSTRACT Fe-oxidizing bacteria of the family Gallionellaceae are major players in the Fe biogeochemical cycle in freshwater. These bacteria thrive in redox transition zones where they benefit from both high Fe concentrations and microaerobic conditions. We analysed the Gallionellaceae genomic diversity in an artesian hard-rock aquifer where redox transition zones develop (i) in the subsurface, where ancient, reduced groundwater mixes with recent oxygenated groundwater, and (ii) at the surface, where groundwater reaches the open air. A total of 15 new draft genomes of Gallionellaceae representing to 11 candidate genera were recovered from the two redox transition zones. Sulfur oxidation genes were encoded in most genomes while denitrification genes were much less represented. One genus dominated microbial communities belowground and we propose to name it ‘Candidatus Houarnoksidobacter’. The two transition zones were populated by completely different assemblages of Gallionellaceae despite the almost constant upward circulation of groundwater between the two zones. The processes leading to redox transition zones, oxygen diffusion at the surface or groundwater mixing in subsurface, appear to be a major driver of the Gallionellaceae diversity.

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Representation, abstraction, and simple-minded sophisticates

Behavioral and Brain Sciences ◽

10.1017/s0140525x19002942 ◽

2020 ◽

Vol 43 ◽

Author(s):

Peter Dayan

Keyword(s):

Decision Theory ◽

Predictive Coding ◽

Bayesian Decision Theory ◽

Bayesian Decision ◽

Model Based ◽

Model Free

Abstract Bayesian decision theory provides a simple formal elucidation of some of the ways that representation and representational abstraction are involved with, and exploit, both prediction and its rather distant cousin, predictive coding. Both model-free and model-based methods are involved.

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Quantitative Model-Based Image Analysis of NuMa Distribution Links Nuclear Organization with Cell Phenotype

Microscopy and Microanalysis ◽

10.1017/s1431927600028968 ◽

2001 ◽

Vol 7 (S2) ◽

pp. 578-579

Author(s):

David W. Knowles ◽

Sophie A. Lelièvre ◽

Carlos Ortiz de Solόrzano ◽

Stephen J. Lockett ◽

Mina J. Bissell ◽

...

Keyword(s):

Image Analysis ◽

Mammary Epithelial Cells ◽

Nuclear Organization ◽

Critical Role ◽

Quantitative Model ◽

Mammary Epithelial ◽

Cell Phenotype ◽

Proliferating Cells ◽

Mitotic Apparatus ◽

Model Based

The extracellular matrix (ECM) plays a critical role in directing cell behaviour and morphogenesis by regulating gene expression and nuclear organization. Using non-malignant (S1) human mammary epithelial cells (HMECs), it was previously shown that ECM-induced morphogenesis is accompanied by the redistribution of nuclear mitotic apparatus (NuMA) protein from a diffuse pattern in proliferating cells, to a multi-focal pattern as HMECs growth arrested and completed morphogenesis . A process taking 10 to 14 days.To further investigate the link between NuMA distribution and the growth stage of HMECs, we have investigated the distribution of NuMA in non-malignant S1 cells and their malignant, T4, counter-part using a novel model-based image analysis technique. This technique, based on a multi-scale Gaussian blur analysis (Figure 1), quantifies the size of punctate features in an image. Cells were cultured in the presence and absence of a reconstituted basement membrane (rBM) and imaged in 3D using confocal microscopy, for fluorescently labeled monoclonal antibodies to NuMA (fαNuMA) and fluorescently labeled total DNA.

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