Evidence map›Paper›PMID 39028511›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2024

Atomic Force Microscopy Imaging and Analysis of Prokaryotic Genome Organization.

Hugo Maruyama, Ryosuke L Ohniwa, Yuri Ushijima, Kazuya Morikawa, Kunio Takeyasu

Abstract read
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In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors.

Hugo MaruyamaDepartment of Bacteriology, Osaka Dental University, Hirakata, Osaka, Japan.
Ryosuke L OhniwaInstitute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan.
Yuri UshijimaInstitute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan.
Kazuya MorikawaInstitute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan. morikawa.kazuya.ga@u.tsukuba.ac.jp.
Kunio TakeyasuGraduate School of Biostudies, Kyoto University, Kyoto, Japan.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

This protocol describes the application of atomic force microscopy for structural analysis of prokaryotic and organellar nucleoids. It is based on a simple cell manipulation procedure that enables stepwise dissection of the nucleoid. The procedure includes (i) on-substrate lysis of cells and (ii) enzyme treatment, followed by atomic force microscopy. This type of dissection analysis permits analysis of nucleoid structure ranging from the fundamental units assembled on DNA to higher-order levels of organization. The combination with molecular-genetic and biochemical techniques further permits analysis of the functions of key nucleoid factors relevant to signal-induced structural reorganization or building up of basic structures, as seen for Dps in Escherichia coli and TrmBL2 in Thermococcus kodakarensis. These systems are described here as examples of the successful application of AFM for this purpose. Moreover, we describe the procedures needed for quantitative analysis of the data.

Indexed as

Microscopy, Atomic ForceEscherichia coliGenome, BacterialProkaryotic CellsThermococcusAtomic force microscopyData analysisNucleoid structureOn-substrate lysisReconstitution of nucleoid

Identifiers

PMID39028511

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.