Automatic isotropic fractionation for large-scale quantitative cell analysis of nervous tissue

Azevedo, Feliciano; Andrade-Moraes, Carlos Humberto; Curado, Marco Rocha; Oliveira-Pinto, Ana V.; Guimarães, Daniel M.; Szczupak, Diego; Gomes, Bruna Valério; Alho, Ana Tereza Di Lorenzo; Polichiso, Lívia; Tampellini, Edilaine; Lima, Luzia Carreira; Lima, Daniel Oliveira de; Silva, Hudson Alves da; Lent, Roberto

doi:10.1016/j.jneumeth.2012.09.015

Cited by 17 publications

(13 citation statements)

References 34 publications

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“…Since BayesCCE requires a prior which can be estimated from previously collected cell counts without the need for any other genomic data, obtaining such as prior is relatively easy for many tissues, such as the brain [ 33 ], heart [ 34 ], and adipose tissue [ 35 ]. Particularly, such data should be substantially easier to obtain compared to reference data from sorted cells for the corresponding tissues.…”

Section: Discussionmentioning

confidence: 99%

BayesCCE: a Bayesian framework for estimating cell-type composition from DNA methylation without the need for methylation reference

et al. 2018

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We introduce a Bayesian semi-supervised method for estimating cell counts from DNA methylation by leveraging an easily obtainable prior knowledge on the cell-type composition distribution of the studied tissue. We show mathematically and empirically that alternative methods which attempt to infer cell counts without methylation reference only capture linear combinations of cell counts rather than provide one component per cell type. Our approach allows the construction of components such that each component corresponds to a single cell type, and provides a new opportunity to investigate cell compositions in genomic studies of tissues for which it was not possible before.Electronic supplementary materialThe online version of this article (10.1186/s13059-018-1513-2) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

BayesCCE: a Bayesian framework for estimating cell-type composition from DNA methylation without the need for methylation reference

et al. 2018

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“…However, there are also limitations of the IF: the use of antibodies against nuclear proteins (to distinguish neurons from non‐neuronal cells) does not identify cell types among the non‐neuronal cells, NeuN antigens are not expressed by a small number of neuronal populations (Mullen et al, ), and only regions and volumes of tissues that can be dissected macroscopically can be analyzed (Lent et al, ). Automated versions of the IF have been reported, both for the homogenization procedure (Azevedo et al, ) and for the counting procedure, using flow cytometry (Collins et al, ; Young et al, ; Herculano‐Houzel et al, ). Long‐standing concerns about loss of nuclei when using a biochemical homogenization approach (Brizzee et al, ; Hadjiolov et al, ; Lovtrup‐Rein and McEwen, ; Cragg, ; Kato and Kurokawa, ; Clarke and Oppenheim, ; Yuhas and Jabr, ; Carlo and Stevens, ; Verkhratsky and Butt, ; Charvet et al, ) have recently been addressed and dispelled in two studies that directly compared the IF, in side‐by‐side experiments, with results obtained by stereology (Bahney and von Bartheld, ; Miller et al, ).…”

Section: Overview Of Cell‐counting Methodsmentioning

confidence: 99%

The search for true numbers of neurons and glial cells in the human brain: A review of 150 years of cell counting

Bartheld

Bahney

Herculano‐Houzel

2016

J of Comparative Neurology

814

557

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For half a century, the human brain was believed to contain about 100 billion neurons and one trillion glial cells, with a glia:neuron ratio of 10:1. A new counting method, the isotropic fractionator, has challenged the notion that glia outnumber neurons and revived a question that was widely thought to have been resolved. The recently validated isotropic fractionator demonstrates a glia:neuron ratio of less than 1:1 and a total number of less than 100 billion glial cells in the human brain. A survey of original evidence shows that histological data always supported a 1:1 ratio of glia to neurons in the entire human brain, and a range of 40–130 billion glial cells. We review how the claim of one trillion glial cells originated, was perpetuated, and eventually refuted. We compile how numbers of neurons and glial cells in the adult human brain were reported and we examine the reasons for an erroneous consensus about the relative abundance of glial cells in human brains that persisted for half a century. Our review includes a brief history of cell counting in human brains, types of counting methods that were and are employed, ranges of previous estimates, and the current status of knowledge about the number of cells. We also discuss implications and consequences of the new insights into true numbers of glial cells in the human brain, and the promise and potential impact of the newly validated isotropic fractionator for reliable quantification of glia and neurons in neurological and psychiatric diseases.

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“…It is well known that metabolic syndrome and obesity are linked with a state of inflammation and dysbiosis. In fact, obesity during pregnancy has been associated with macrophage accumulation and inflammation in the placenta (187-189) and also with preterm delivery (190)(191)(192). Recently, it has been shown that the placental microbiota varied among 320 women with spontaneous preterm birth depending on their excess gestational weight gain but not on obesity (193).…”

Section: Microbiotas Of the Placenta And Meconiummentioning

confidence: 99%

The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota

Milani

Duranti

Bottacini

et al. 2017

Microbiol Mol Biol Rev

1,326

1,189

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The human gut microbiota is engaged in multiple interactions affecting host health during the host's entire life span. Microbes colonize the neonatal gut immediately following birth. The establishment and interactive development of this early gut microbiota are believed to be (at least partially) driven and modulated by specific compounds present in human milk. It has been shown that certain genomes of infant gut commensals, in particular those of bifidobacterial species, are genetically adapted to utilize specific glycans of this human secretory fluid, thus representing a very intriguing example of host-microbe coevolution, where both partners are believed to benefit. In recent years, various metagenomic studies have tried to dissect the composition and functionality of the infant gut microbiome and to explore the distribution across the different ecological niches of the infant gut biogeography of the corresponding microbial consortia, including those corresponding to bacteria and viruses, in healthy and ill subjects. Such analyses have linked certain features of the microbiota/microbiome, such as reduced diversity or aberrant composition, to intestinal illnesses in infants or disease states that are manifested at later stages of life, including asthma, inflammatory bowel disease, and metabolic disorders. Thus, a growing number of studies have reported on how the early human gut microbiota composition/development may affect risk factors related to adult health conditions. This concept has fueled the development of strategies to shape the infant microbiota composition based on various functional food products. In this review, we describe the infant microbiota, the mechanisms that drive its establishment and composition, and how microbial consortia may be molded by natural or artificial interventions. Finally, we discuss the relevance of key microbial players of the infant gut microbiota, in particular bifidobacteria, with respect to their role in health and disease.

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Automatic isotropic fractionation for large-scale quantitative cell analysis of nervous tissue

Cited by 17 publications

References 34 publications

BayesCCE: a Bayesian framework for estimating cell-type composition from DNA methylation without the need for methylation reference

BayesCCE: a Bayesian framework for estimating cell-type composition from DNA methylation without the need for methylation reference

The search for true numbers of neurons and glial cells in the human brain: A review of 150 years of cell counting

The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota

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