The use of cluster analysis for cell typing

Schweitzer, Laura; Renehan, William E.

doi:10.1016/s1385-299x(96)00014-1

Cited by 61 publications

(102 citation statements)

References 13 publications

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“…Cluster analysis is one of the most appropriate methods for objective cell grouping, and has been successfully used for research on neuronal categorization (Schweitzer and Renehan, 1997;Cauli et al, 2000). However, to the best of our knowledge, this is the first study to assess an objective classification of reactive microglia with a cluster analysis based on morphometric variables.…”

Section: Discussionmentioning

confidence: 99%

“…Multimodal parameters are essential for separating a population of cells into multiple groups by the hierarchical cluster analysis. Schweitzer and Renehan (1997) suggested that a statistical parameter with an MMI larger than 0.55 is multimodal. In this regard, Soltys et al (2005) reported that only two of nine morphometric parameters obtained from microglia labeled by isolectin from Bandeiraea simplicifolia (BSI-B4) exhibited an MMI larger than 0.55.…”

Section: Discussionmentioning

confidence: 99%

“…Multimodal datasets are necessary for separating a population of cells into cell types (Schweitzer and Renehan, 1997). Multimodality index (MMI) is calculated using the following formula: Figure 1.…”

Section: Statistical Analysis and Illustration Preparationsmentioning

confidence: 99%

“…The choice of variables is critical in determining the outcome of cluster analysis (Schweitzer and Renehan, 1997). As the first step of this study, we obtained two 2D and eight 3D morphometric parameters from 136 intracellularly labeled microglial cells in the mouse hypoglossal nucleus 3 days (D3), 7 days (D7), 14 days (D14) and 28 days (D28) after axotomy and 7 days after sham operation (Sham).…”

Section: Morphological Classification Of Reactive Microglia In the Axmentioning

confidence: 99%

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Novel objective classification of reactive microglia following hypoglossal axotomy using hierarchical cluster analysis

Yamada

Jinno

2013

J of Comparative Neurology

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A total of 136 microglia were intracellularly labeled and their morphological features were evaluated by 3D morphometric measurement. According to hierarchical cluster analysis, microglia were objectively categorized into four groups termed types I-IV. The validity of this classification was confirmed by principal component analysis and linear discriminant analysis. Type I microglia were found in sham-operated mice and in mice sacrificed 28 days (D28) after axotomy. The appearance of type I cells was similar to so-called ramified microglia in a resting state. Type II microglia were mainly seen in D14 mice, which exhibited small cell bodies with thin and short processes. Interestingly, none of the already-known morphological types of microglia seemed to be comparable to type II cells. We thus named type II microglia "small ramified" cells. Types III and IV microglia were mainly seen in D3 and D7 mice and their appearances were similar to hypertrophied and bushy cells, respectively. Proliferating cell nuclear antigen (PCNA), a mitosis marker, was almost exclusively expressed in D3 mice. On the other hand, voltage-dependent potassium channels (Kv1.3/1.5), neurotoxicity-related molecules, were most highly expressed in D14 mice. Increased expression of Kv1.3/1.5 in D14 mice was suppressed by minocycline treatment. These findings indicate that type II and III microglia may be involved in neurotoxicity and mitosis, respectively. Type IV microglial cells are assumed to be in the process of losing mitotic activity and gaining neurotoxicity. Our data also suggest that type II microglia can be a potential therapeutic target against neurodegenerative diseases.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Statistical Analysis and Illustration Preparationsmentioning

confidence: 99%

Section: Morphological Classification Of Reactive Microglia In the Axmentioning

confidence: 99%

See 2 more Smart Citations

Novel objective classification of reactive microglia following hypoglossal axotomy using hierarchical cluster analysis

Yamada

Jinno

2013

J of Comparative Neurology

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“…To assess the homogeneity of the axonal population in each area in relation to defined morphometric variables, we first performed a Multivariate Analysis of Variance (MANOVA). Next, an exploratory cluster analysis of morphological terminal types was performed using hierarchical clustering analysis (HCA) to explore whether specific groups of terminals existed in our sample based on the morphometric variables mentioned above (Steele and Weller, 1995;Schweitzer and Renehan, 1997;Gomes-Leal et al, 2002;Rocha et al, 2007). The significance of the classification performed by the HCA was tested with a MANOVA.…”

Section: Discussionmentioning

confidence: 99%

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Supplemental Information 1: Morphometric Data

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Secreted production of collagen‐inspired gel‐forming polymers with high thermal stability in Pichia pastoris

Silva

Teles

Moers

et al. 2011

Biotech & Bioengineering

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Previously, we have shown that gel-forming triblock proteins, consisting of random coil middle blocks and trimer-forming (Pro-Gly-Pro)(9) end blocks, are efficiently produced and secreted by the yeast Pichia pastoris. These end blocks had a melting temperature (T(m)) of ∼41°C (at 1.1 mM of protein). The present work reveals that an increase of T(m) to ∼74°C, obtained by extension of the end blocks to (Pro-Gly-Pro)(16), resulted in a five times lower yield and partial endoproteolytic degradation of the protein. A possible cause could be that the higher thermostability of the longer (Pro-Gly-Pro)(16) trimers leads to a higher incidence of trimers in the cell, and that this disturbs secretion of the protein. Alternatively, the increased length of the proline-rich (Pro-Gly-Pro)(n) domain may negatively influence ribosomal translation, or may result in, for example, hydrophobic aggregation or membrane-active behavior owing to the greater number of closely placed proline residues. To discriminate between these possibilities, we studied the production of molecules with randomized end blocks that are unable to form triple helices. The codon- and amino acid composition of the genes and proteins, respectively, remained unchanged. As these nontrimerizing molecules were secreted intact and at high yield, we conclude that the impaired secretion and partial degradation of the triblock with (Pro-Gly-Pro)(16) end blocks was triggered by the occurrence of intracellular triple helices. This degradation was overcome by using a yapsin 1 protease disruptant, and the intact secreted polymer was capable of forming self-supporting gels of high thermal stability.

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The use of cluster analysis for cell typing

Cited by 61 publications

References 13 publications

Novel objective classification of reactive microglia following hypoglossal axotomy using hierarchical cluster analysis

Novel objective classification of reactive microglia following hypoglossal axotomy using hierarchical cluster analysis

Untitled

Secreted production of collagen‐inspired gel‐forming polymers with high thermal stability in Pichia pastoris

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