Application of agent-based modelling to assess single-molecule transport across the cell envelope of E. coli

Helicases are nucleic acid-unwinding enzymes that are involved in the maintenance of genome integrity. Several parts of the amino acid sequences of helicases are very similar, and these quite well-conserved amino acid sequences are termed “helicase motifs”. Previous studies by X-ray crystallography and single-molecule measurements have suggested a common underlying mechanism for their function. These studies indicate the role of the helicase motifs in unwinding nucleic acids. In contrast, the sequence and length of the C-terminal amino acids of helicases are highly variable. In this paper, I review past and recent studies that proposed helicase mechanisms and studies that investigated the roles of the C-terminal amino acids on helicase and dimerization activities, primarily on the non-hexermeric Escherichia coli (E. coli) UvrD helicase. Then, I center on my recent study of single-molecule direct visualization of a UvrD mutant lacking the C-terminal 40 amino acids (UvrDΔ40C) used in studies proposing the monomer helicase model. The study demonstrated that multiple UvrDΔ40C molecules jointly participated in DNA unwinding, presumably by forming an oligomer. Thus, the single-molecule observation addressed how the C-terminal amino acids affect the number of helicases bound to DNA, oligomerization, and unwinding activity, which can be applied to other helicases.

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Fast and efficient Rmap assembly using the Bi-labelled de Bruijn graph

Algorithms for Molecular Biology ◽

10.1186/s13015-021-00182-9 ◽

2021 ◽

Vol 16 (1) ◽

Author(s):

Kingshuk Mukherjee ◽

Massimiliano Rossi ◽

Leena Salmela ◽

Christina Boucher

Keyword(s):

Single Molecule ◽

De Bruijn Graph ◽

Anabas Testudineus ◽

E Coli ◽

Genome Wide ◽

A Genome ◽

De Bruijn ◽

Optical Maps ◽

Definition Of ◽

Numeric Representation

AbstractGenome wide optical maps are high resolution restriction maps that give a unique numeric representation to a genome. They are produced by assembling hundreds of thousands of single molecule optical maps, which are called Rmaps. Unfortunately, there are very few choices for assembling Rmap data. There exists only one publicly-available non-proprietary method for assembly and one proprietary software that is available via an executable. Furthermore, the publicly-available method, by Valouev et al. (Proc Natl Acad Sci USA 103(43):15770–15775, 2006), follows the overlap-layout-consensus (OLC) paradigm, and therefore, is unable to scale for relatively large genomes. The algorithm behind the proprietary method, Bionano Genomics’ Solve, is largely unknown. In this paper, we extend the definition of bi-labels in the paired de Bruijn graph to the context of optical mapping data, and present the first de Bruijn graph based method for Rmap assembly. We implement our approach, which we refer to as rmapper, and compare its performance against the assembler of Valouev et al. (Proc Natl Acad Sci USA 103(43):15770–15775, 2006) and Solve by Bionano Genomics on data from three genomes: E. coli, human, and climbing perch fish (Anabas Testudineus). Our method was able to successfully run on all three genomes. The method of Valouev et al. (Proc Natl Acad Sci USA 103(43):15770–15775, 2006) only successfully ran on E. coli. Moreover, on the human genome rmapper was at least 130 times faster than Bionano Solve, used five times less memory and produced the highest genome fraction with zero mis-assemblies. Our software, rmapper is written in C++ and is publicly available under GNU General Public License at https://github.com/kingufl/Rmapper.

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Visualising Ostia’s Processional Landscape Through a Multi-Layered Computational Approach: Case Study of the Cult of the Magna Mater

Open Archaeology ◽

10.1515/opar-2019-0028 ◽

2019 ◽

Vol 5 (1) ◽

pp. 444-467

Author(s):

Katherine A. Crawford

Keyword(s):

Network Analysis ◽

Computational Approach ◽

Urban Network ◽

Agent Based ◽

Agent Based Modelling ◽

Existing Problems ◽

Layered Approach ◽

Religious Landscape ◽

Insight Into

AbstractOstia, the ancient port of Rome, had a rich religious landscape. How processional rituals further contributed to this landscape, however, has seen little consideration. This is largely due to a lack of evidence that attests to the routes taken by processional rituals. The present study aims to address existing problems in studying processions by questioning what factors motivated processional movement routes. A novel computational approach that integrates GIS, urban network analysis, and agent-based modelling is introduced. This multi-layered approach is used to question how spectators served as attractors in the creation of a processional landscape using Ostia’s Campo della Magna Mater as a case study. The analysis of these results is subsequently used to gain new insight into how a greater processional landscape was created surrounding the sanctuary of the Magna Mater.

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Correlating Structure and Function in Organic Electronics: From Single Molecule Transport to Singlet Fission

Chemistry of Materials ◽

10.1021/cm502366x ◽

2015 ◽

Vol 27 (16) ◽

pp. 5453-5463 ◽

Cited By ~ 39

Author(s):

Jonathan Z. Low ◽

Samuel N. Sanders ◽

Luis M. Campos

Keyword(s):

Organic Electronics ◽

Single Molecule ◽

Structure And Function ◽

Singlet Fission ◽

Molecule Transport ◽

And Function

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Studying Binding, Conformational Transition and Assembly of E. Coli Cytolysin a Pore Forming Toxin by Single Molecule Fluorescence

Biophysical Journal ◽

10.1016/j.bpj.2016.11.2833 ◽

2017 ◽

Vol 112 (3) ◽

pp. 524a

Author(s):

Pradeep Sathyanarayana ◽

Satyaghosh Maurya ◽

Ganapathy Ayappa ◽

Sandhya S. Visweswariah ◽

Rahul Roy

Keyword(s):

Single Molecule ◽

Conformational Transition ◽

Single Molecule Fluorescence ◽

E Coli

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Pathological ATX3 Expression Induces Cell Perturbations in E. coli as Revealed by Biochemical and Biophysical Investigations

International Journal of Molecular Sciences ◽

10.3390/ijms22020943 ◽

2021 ◽

Vol 22 (2) ◽

pp. 943

Author(s):

Diletta Ami ◽

Barbara Sciandrone ◽

Paolo Mereghetti ◽

Jacopo Falvo ◽

Tiziano Catelani ◽

...

Keyword(s):

Cell Envelope ◽

Spinocerebellar Ataxia Type ◽

Spinocerebellar Ataxia Type 3 ◽

Intact Cells ◽

E Coli ◽

Fourier Transform Infrared Microspectroscopy ◽

Electron Microscopy Analysis ◽

Microscopy Analysis ◽

The Fourier Transform ◽

Type 3

Amyloid aggregation of human ataxin-3 (ATX3) is responsible for spinocerebellar ataxia type 3, which belongs to the class of polyglutamine neurodegenerative disorders. It is widely accepted that the formation of toxic oligomeric species is primarily involved in the onset of the disease. For this reason, to understand the mechanisms underlying toxicity, we expressed both a physiological (ATX3-Q24) and a pathological ATX3 variant (ATX3-Q55) in a simplified cellular model, Escherichia coli. It has been observed that ATX3-Q55 expression induces a higher reduction of the cell growth compared to ATX3-Q24, due to the bacteriostatic effect of the toxic oligomeric species. Furthermore, the Fourier transform infrared microspectroscopy investigation, supported by multivariate analysis, made it possible to monitor protein aggregation and the induced cell perturbations in intact cells. In particular, it has been found that the toxic oligomeric species associated with the expression of ATX3-Q55 are responsible for the main spectral changes, ascribable mainly to the cell envelope modifications. A structural alteration of the membrane detected through electron microscopy analysis in the strain expressing the pathological form supports the spectroscopic results.

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