PALMsiever: a tool to turn raw data into results for single-molecule localization microscopy

Pengo, Thomas; Holden, Séamus; Manley, Suliana

doi:10.1093/bioinformatics/btu720

Cited by 37 publications

(29 citation statements)

References 14 publications

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“…We processed the data using rapidSTORM and used PALMsiever69 for filtering and rendering. Finally, using Fiji, the distances were calculated between the centre of mass of the observed probes.…”

Section: Methodsmentioning

confidence: 99%

Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae

et al. 2017

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DNA-binding proteins are central regulators of chromosome organization; however, in genome-reduced bacteria their diversity is largely diminished. Whether the chromosomes of such bacteria adopt defined three-dimensional structures remains unexplored. Here we combine Hi-C and super-resolution microscopy to determine the structure of the Mycoplasma pneumoniae chromosome at a 10 kb resolution. We find a defined structure, with a global symmetry between two arms that connect opposite poles, one bearing the chromosomal Ori and the other the midpoint. Analysis of local structures at a 3 kb resolution indicates that the chromosome is organized into domains ranging from 15 to 33 kb. We provide evidence that genes within the same domain tend to be co-regulated, suggesting that chromosome organization influences transcriptional regulation, and that supercoiling regulates local organization. This study extends the current understanding of bacterial genome organization and demonstrates that a defined chromosomal structure is a universal feature of living systems.

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Section: Methodsmentioning

confidence: 99%

Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae

et al. 2017

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“…Regions of interest (ROI) were drawn around individual dendritic spines and localizations within the ROI were exported into MATLAB (Mathworks) for further analysis. Density-based cluster analysis (DBSCAN) (Ester et al, 1996; Tran et al, 2013) implementation in the PALMsiever platform (Pengo et al, 2015) was used to define core, clustered PSD95 localizations. The criterion for assigning individual localizations as core PSD points was the presence of a minimum of 25 neighboring localizations within a 100 nm radius.…”

Section: Star Methodsmentioning

confidence: 99%

Optogenetic Control of Synaptic Composition and Function

Sinnen

Bowen

Forte

et al. 2017

Neuron

108

100

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The molecular composition of the postsynaptic membrane is sculpted by synaptic activity. During synaptic plasticity at excitatory synapses, numerous structural, signaling and receptor molecules concentrate at the postsynaptic density (PSD) to regulate synaptic strength. We developed an approach that uses light to tune the abundance of specific molecules in the PSD. We used this approach to investigate the relationship between the number of AMPA-type glutamate receptors in the PSD and synaptic strength. Surprisingly, adding more AMPA receptors to excitatory contacts had little effect on synaptic strength. Instead, we observed increased excitatory input through the apparent addition of new functional sites. Our data support a model where adding AMPA receptors is sufficient to activate synapses that had few receptors to begin with, but that additional remodeling events are required to strengthen established synapses. More broadly, this approach introduces the precise spatiotemporal control of optogenetics to molecular control of synaptic function.

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“…, 2015), collective quantitation of filaments (Nieuwenhuizen et al. , 2015), and interactive filament tracing (Pengo et al. , 2014).…”

Section: Discussionmentioning

confidence: 99%

Extracting microtubule networks from superresolution single-molecule localization microscopy data

Zhang

Nishimura

Kanchanawong

2017

MBoC

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PALMsiever: a tool to turn raw data into results for single-molecule localization microscopy

Cited by 37 publications

References 14 publications

Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae

Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae

Optogenetic Control of Synaptic Composition and Function

Extracting microtubule networks from superresolution single-molecule localization microscopy data

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