BioWire Literature

From FreeBio

Contents 1 Circuit Design and FFLs 2 The Mysterious Identity of AHL 3 Other Quorum Sensors 4 Photolithography with E. Coli 5 Modeling Research

Circuit Design and FFLs

Here are some papers courtesy of the MCB195 website. You can also find more papers on the site. We're interested in incoherent type 1. Kxjin 16:10, 7 Jun 2005 (EDT)

• Structure and function of the feed-forward loop network motif Mangan and Alon PNAS 2003
• Network motifs in the transcriptional regulatory network of E. coli Shen-Orr et al. Nature Genetics 2002
• Network motifs: simple building blocks of complex networks Milo et al. Science 2002

• Spatiotemporal control of gene expression with pulse-generating networks Ron Weiss and company. PNAS 2004.

• Systems biology: from physiology to gene regulation May have useful information on modeling.

• Ron Weiss's papers Just read this. Really. This guy knows what he's doing.

The Mysterious Identity of AHL

• Haemodynamic effects of the bacterial quorum sensing signal molecule, N-(3-oxododecanoyl)-L-homoserine lactone, in conscious, normal and endotoxaemic rats
• Carnegie Mellon page on quorum sensing signals
• 306HSL(ordered)--Orr 01:56, 8 Jun 2005 (EDT)
• C4HSL(ordered)
• (BULLSEYE) A synthetic multicellular system for programmed pattern formation Basu, Gerchman, Collins, Arnold, and Weiss. Nature. April 21 2005. Vol. 434, 1130-1134.
  {Note: In the modelling section, there is data for intercellular diffusion and decay rate of AHL.}
• (LACTONASE)

Specificity and Enzyme Kinetics of the Quorum-quenching N-Acyl Homoserine Lactone Lactonase (AHL-lactonase)

Other Quorum Sensors

• Signal-amplifying genetic circuit enables in vivo observation of weak promoter activation in the Rhl quorum sensing system
• CELL-TO-CELL SIGNALING AND PSEUDOMONAS AERUGINOSA INFECTIONS (Interactions between LasR and Rh1I)
• Microarray Analysis of Pseudomonas aeruginosa Quorum-Sensing Regulons: Effects of Growth Phase and Environment "These systems are intertwined in a hierarchical manner, and the las system controls the rhl system at both the transcriptional and posttranslational levels."
• Regulation of las and rhl quorum sensing in Pseudomonas aeruginosa

• LasR -> 30C12HSL
• Rh1I -> C4HSL

Photolithography with E. Coli

• This is it!:

| Whitesides' lab

• Existing E. Coli Photolithography: Methods for Fabricating Microarrays of Motile Bacteria.pdf

• Papers suggesting that it can be done easily enough:

1. Control of Mammalian Cell and Bacteria Adhesion on Substrates Micropatterned with Poly(ethylene glycol) Hydrogels.pdf
2. Chemical and topographical patterning for directed cell attachment.pdf

• Papers from George Whitesides' lab:

1. Measuring the forces involved in polyvalent adhesion of uropathogenic Escherichia coli to mannose-presenting surfaces.pdf
2. Arrays of self-assembled monolayers for studying inhibition of bacterial adhesion.pdf
3. I can't find an electronic version of this one: The self-sorting of motile E. coli cells, DiLuzio WR, Lauga E, Stone HA, Whitesides GM. BIOPHYSICAL JOURNAL 88 (1): 504A-504A Part 2 Suppl. S, JAN 2005.

• Bacterial Adhesion

some links? How biofilms form

• Bacterial Printing Press that Regenerates Its Ink: Contact-Printing Bacteria Using Hydrogel Stamps

Weibel, D. B.; Lee, A.; Mayer, M.; Brady, S. F.; Bruzewicz, D.; Yang, J.; DiLuzio, W. R.; Clardy, J.; Whitesides, G. M.; Langmuir; (Article); 2005; ASAP Article; DOI: 10.1021/la047173c

Modeling Research

• Matlab Project
• This paper describes everything here