Jamie Hobbs - Academia.edu (original) (raw)

Papers by Jamie Hobbs

Encyclopedia of Polymer Science and Technology

Proceedings of the National Academy of Sciences, 2021

Significance The bacterial cell wall peptidoglycan is essential for maintenance of viability and ... more Significance The bacterial cell wall peptidoglycan is essential for maintenance of viability and yet is dynamic, permitting growth and division. Peptidoglycan synthesis is inhibited by important antibiotics, including β-lactams and vancomycin. Using the human pathogen Staphylococcus aureus , we have examined peptidoglycan homeostatic mechanisms and how their interruption leads to cell death. This has revealed two antibiotic-induced killing mechanisms mediated by specific peptidoglycan hydrolases, both involving the appearance of holes that span the entire thickness of the cell wall. One of the mechanisms is associated with growth and the other with cell division. This study supports a simple model for how cells grow via a combination of peptidoglycan synthesis and hydrolysis and how antibiotic intervention leads to cell death.

Biophysical Journal, 2019

To determine which of P-gp's two binding sites interact with oligomeric Ab, a competition binding... more To determine which of P-gp's two binding sites interact with oligomeric Ab, a competition binding assay was performed. Rhodamine 123 (R123) and Hoechst 33342 (H33342) are fluorescent compounds with well-described alternate P-gp binding sites. The transport of each R123 and H33342 is evidenced by a quenching of fluorescence; this transport is impeded by the presence of a compound that binds to the same site. Inverted vesicles are incubated in the presence of both oligomeric Ab and either R123 or H33342 for identification of the binding site. This study demonstrates that the size of Ab aggregate species plays a crucial role in Ab binding to P-gp for transport and identifies the probable P-gp binding site of Ab.

Current Biology, 2017

Highlights d Stomatal poles are stiff and have a distinct cell wall composition d Loss of polar s... more Highlights d Stomatal poles are stiff and have a distinct cell wall composition d Loss of polar stiffening is associated with decreased degree of stomatal opening d Lack of radial guard cell stiffening does not preclude stomatal opening d A ''fix and flex'' model predicts more efficient opening of stomata via polar stiffening

Plant physiology, Jan 2, 2017

Stomata are formed by a pair of guard cells which have thickened, elastic cell walls to withstand... more Stomata are formed by a pair of guard cells which have thickened, elastic cell walls to withstand the large increases in turgor pressure that have to be generated to open the pore that they surround. We have characterised FOCL1, a guard cell-expressed, secreted protein with homology to hydroxyproline-rich cell wall proteins. FOCL1-GFP localises to the guard cell outer cuticular ledge and plants lacking FOCL1 produce stomata without a cuticular ledge. Instead the majority of stomatal pores are entirely covered-over by a continuous fusion of the cuticle, and consequently plants have decreased levels of transpiration and display drought tolerance. The focl1 guard cells are larger and less able to reduce the aperture of their stomatal pore in response to closure signals suggesting that the flexibility of guard cell walls is impaired. FOCL1 is also expressed in lateral root initials where it aids lateral root emergence. We propose that FOCL1 acts in these highly specialised cells of the ...

AIP Conference Proceedings, 2003

ABSTRACT

Single Molecules, 2001

ABSTRACT

Science (New York, N.Y.), Jan 11, 2011

T-shaped molecules with a rod-like aromatic core and a flexible side chain form liquid crystal ho... more T-shaped molecules with a rod-like aromatic core and a flexible side chain form liquid crystal honeycombs with aromatic cell walls and a cell interior filled with the side chains. Here, we show how the addition of a second chain, incompatible with the first (X-shaped molecules), can form honeycombs with highly complex tiling patterns, with cells of up to five different compositions ("colors") and polygonal shapes. The complexity is caused by the inability of the side chains to separate cleanly because of geometric frustration. Furthermore, a thermoreversible transition was observed between a multicolor (phase-separated) and a single-color (mixed) honeycomb phase. This is analogous to the Curie transition in simple and frustrated ferro- and antiferromagnets; here spin flips are replaced by 180° reorientations of the molecules.

Polymeric vesicles, a.k.a. "polymersomes", are enclosed membranes formed by the selfassembly of a... more Polymeric vesicles, a.k.a. "polymersomes", are enclosed membranes formed by the selfassembly of amphiphilic block copolymers in water. [1] In recent years polymersomes have attracted much attention due to their unique features, such as improved mechanical properties, high stability, and long circulation half-lives in the body compared to liposomes, as well as their ability to incorporate both hydrophilic compounds in the aqueous core and hydrophobic compounds in the membrane. [1a] Furthermore, amphiphilic block copolymers can be designed to be noncytotoxic, efficiently internalized by cells, etc. [2] Polymersomes can be decorated with proteins and/or antibodies, either by chemically attaching the active moieties to the hydrophilic brushes [3] or by inserting membrane proteins across the hydrophobic membrane. [4] Recently, fine control over polymersome surface topology and its consequences on cell internalization kinetics has been demonstrated by the authors. [5] Thus the ability to examine the surface properties of polymersomes, as well as other waterborne nanoparticles, in situ on the nanoscale is becoming increasingly important in several fields. Imaging of wet nanoparticles is normally performed by transmission or scanning electron microscopy (EM). However, the high vacuum conditions necessary for such imaging require either dried or frozen (e.g., cryogenic EM) samples, potentially causing artefacts. Wet imaging can be performed by optical microscopy and recently the problem of diffraction-limited spatial resolution has been overcome by new fluorescence-based microscopy, such as scanning near-field optical microscopy (SNOM), photo-activated localization microscopy (PALM), stimulated emission depletion microscopy (STED), and structured illumination microscopy (SIM). [6] Atomic force microscopy (AFM) is another valuable analytical tool that has been used for both imaging and also for assessing mechanical, electrical, and surface properties. [7]

The Journal of Physical Chemistry B, 2009

Flexible polymers crystallize with chain folding, which shows a unique phenomenon called self-poi... more Flexible polymers crystallize with chain folding, which shows a unique phenomenon called self-poisoning. As a result, minima in crystal growth rates of strictly monodisperse short-chain polymers are observed near the temperatures of transitions from extended-chain to once-folded-chain growth, from once-folded to twice-folded growth, etc. We employed dynamic Monte Carlo simulation of lattice polymers to visualize such transitions in molecular details. We observed a rate crossover between chain extension and lateral growth of polymer lamellar crystals at the wedge-shaped growth front, resulting in a rate minimum around the melting point of the metastable once-folded lamellar crystal. The rate minimum can be interpreted as due to the dependence of crystal growth rates on the excess crystal thickness beyond the minimum stable thickness. Furthermore, during crystal thickening, numerous molten chains are shown to be sucked into the lamellar crystals through the basal planes, demonstrating an important source of crystallinity from secondary crystallization lagging behind the crystal growth front.

Review of Scientific Instruments, 2009

A large scan area high-speed scan stage for atomic force microscopy using the resonant oscillatio... more A large scan area high-speed scan stage for atomic force microscopy using the resonant oscillation of a quartz bar has been constructed. The sample scanner can be used for high-speed imaging in both air and liquid environments. The well-defined time-position response of the scan stage due to the use of resonance allows highly linearized images to be obtained with a scan size up to 37.5 m in 0.7 s. The scanner is demonstrated for imaging highly topographic silicon test samples and a semicrystalline polymer undergoing crystallization in air, while images of a polymer and a living bacteria, S. aureus, are obtained in liquid.

Polymer, 2005

Video rate atomic force microscopy (VideoAFM), with a frame rate of 14 frames/s and a tip velocit... more Video rate atomic force microscopy (VideoAFM), with a frame rate of 14 frames/s and a tip velocity of up to 15 cms K1 , is used to image polyethylene oxide films during crystal growth. The capabilities of VideoAFM when applied to semicrystalline polymer surfaces are explored. Image quality comparable to that found with conventional contact AFM is achieved but with a nearly 1000 times improvement in time resolution. By applying the technique to the real-time observation of crystal growth, different modes of rapid crystallization are followed in real time. Observation of the spherulite growth front allows measurement of growth rates at the lamellar scale, from which a factor of two difference in the rate of radial growth to the rate of tangential growth is observed, confirming that the elongated nature of spherulite lamellae is due to geometric constraints rather than an inherent fibrillar character. Measurements on screw dislocation growth, when large amounts of crystallizable material is trapped at the surface show that the terrace height does not influence the rate of crystal growth, confirming that under these conditions processes at the lamellar growth front control the rate of growth. When only a thin film of molten material is left on the surface of the already crystallized film dendritic growth is observed, implying a diffusion controlled process under these far from equilibrium conditions.

Polymer, 2009

Over the past two decades atomic force microscopy (AFM) has become one of the most frequently use... more Over the past two decades atomic force microscopy (AFM) has become one of the most frequently used tools for studying polymer crystallization. The combination of high resolution, minimal sample preparation and the ability to image non-destructively has allowed visualisation of crystallization, melting and reordering processes at a lamellar and sub-lamellar scale, revealing complexities that could only previously be guessed at. Here the insights that AFM has provided into some of the main over-arching questions relating to polymer crystallization are reviewed. The emphasis is on the use of AFM to image growth in real time, and on contributions that have been made to our understanding of polymer crystallization in general, rather than to specific systems.

Physical Review Letters, 2011

The physical properties of semicrystalline polymers depend on the organisation of chains within t... more The physical properties of semicrystalline polymers depend on the organisation of chains within the crystal and amorphous regions, on the interface between the two, and on the location and nature of defects. Here, torsional tapping atomic force microscopy has been used to image crystalline lamellae and the crystal-amorphous-region interface at the single-chain level with resolution down to 3.7 Å. Defects within the crystalline phase, such as buried folds and chain ends, are revealed. Imaging at the chain level also allows direct measurement of crystalline stem lengths, providing a potential route to test theories of crystal thickness selection.

Materials Today, 2005

PI's P-587.6CD six-axis piezo nanopositioning and scanning system combines six degrees of freedom... more PI's P-587.6CD six-axis piezo nanopositioning and scanning system combines six degrees of freedom, digital control, active trajectory error compensation, millisecond responsiveness, and long travel (up to 800 µm and 10 000 µrad per axis). Frictionless actuators and a flexure guiding system allow subnanometer, submicroradian resolution. An integrated AutoCalibration function allows fast setup and interchangeability of controllers and nanomechanisms. Integrated direct metrology capacitive displacement sensors provide high bandwidth, linearity, and stability. Parallel metrology means that all sensors measure the position of the same moving platform against the same stationary reference, so all motion is inside the servo-loop, regardless of which actuator caused it.

Encyclopedia of Polymer Science and Technology

Proceedings of the National Academy of Sciences, 2021

Significance The bacterial cell wall peptidoglycan is essential for maintenance of viability and ... more Significance The bacterial cell wall peptidoglycan is essential for maintenance of viability and yet is dynamic, permitting growth and division. Peptidoglycan synthesis is inhibited by important antibiotics, including β-lactams and vancomycin. Using the human pathogen Staphylococcus aureus , we have examined peptidoglycan homeostatic mechanisms and how their interruption leads to cell death. This has revealed two antibiotic-induced killing mechanisms mediated by specific peptidoglycan hydrolases, both involving the appearance of holes that span the entire thickness of the cell wall. One of the mechanisms is associated with growth and the other with cell division. This study supports a simple model for how cells grow via a combination of peptidoglycan synthesis and hydrolysis and how antibiotic intervention leads to cell death.

Biophysical Journal, 2019

To determine which of P-gp's two binding sites interact with oligomeric Ab, a competition binding... more To determine which of P-gp's two binding sites interact with oligomeric Ab, a competition binding assay was performed. Rhodamine 123 (R123) and Hoechst 33342 (H33342) are fluorescent compounds with well-described alternate P-gp binding sites. The transport of each R123 and H33342 is evidenced by a quenching of fluorescence; this transport is impeded by the presence of a compound that binds to the same site. Inverted vesicles are incubated in the presence of both oligomeric Ab and either R123 or H33342 for identification of the binding site. This study demonstrates that the size of Ab aggregate species plays a crucial role in Ab binding to P-gp for transport and identifies the probable P-gp binding site of Ab.

Current Biology, 2017

Highlights d Stomatal poles are stiff and have a distinct cell wall composition d Loss of polar s... more Highlights d Stomatal poles are stiff and have a distinct cell wall composition d Loss of polar stiffening is associated with decreased degree of stomatal opening d Lack of radial guard cell stiffening does not preclude stomatal opening d A ''fix and flex'' model predicts more efficient opening of stomata via polar stiffening

Plant physiology, Jan 2, 2017

Stomata are formed by a pair of guard cells which have thickened, elastic cell walls to withstand... more Stomata are formed by a pair of guard cells which have thickened, elastic cell walls to withstand the large increases in turgor pressure that have to be generated to open the pore that they surround. We have characterised FOCL1, a guard cell-expressed, secreted protein with homology to hydroxyproline-rich cell wall proteins. FOCL1-GFP localises to the guard cell outer cuticular ledge and plants lacking FOCL1 produce stomata without a cuticular ledge. Instead the majority of stomatal pores are entirely covered-over by a continuous fusion of the cuticle, and consequently plants have decreased levels of transpiration and display drought tolerance. The focl1 guard cells are larger and less able to reduce the aperture of their stomatal pore in response to closure signals suggesting that the flexibility of guard cell walls is impaired. FOCL1 is also expressed in lateral root initials where it aids lateral root emergence. We propose that FOCL1 acts in these highly specialised cells of the ...

AIP Conference Proceedings, 2003

ABSTRACT

Single Molecules, 2001

ABSTRACT

Science (New York, N.Y.), Jan 11, 2011

T-shaped molecules with a rod-like aromatic core and a flexible side chain form liquid crystal ho... more T-shaped molecules with a rod-like aromatic core and a flexible side chain form liquid crystal honeycombs with aromatic cell walls and a cell interior filled with the side chains. Here, we show how the addition of a second chain, incompatible with the first (X-shaped molecules), can form honeycombs with highly complex tiling patterns, with cells of up to five different compositions ("colors") and polygonal shapes. The complexity is caused by the inability of the side chains to separate cleanly because of geometric frustration. Furthermore, a thermoreversible transition was observed between a multicolor (phase-separated) and a single-color (mixed) honeycomb phase. This is analogous to the Curie transition in simple and frustrated ferro- and antiferromagnets; here spin flips are replaced by 180° reorientations of the molecules.

Polymeric vesicles, a.k.a. "polymersomes", are enclosed membranes formed by the selfassembly of a... more Polymeric vesicles, a.k.a. "polymersomes", are enclosed membranes formed by the selfassembly of amphiphilic block copolymers in water. [1] In recent years polymersomes have attracted much attention due to their unique features, such as improved mechanical properties, high stability, and long circulation half-lives in the body compared to liposomes, as well as their ability to incorporate both hydrophilic compounds in the aqueous core and hydrophobic compounds in the membrane. [1a] Furthermore, amphiphilic block copolymers can be designed to be noncytotoxic, efficiently internalized by cells, etc. [2] Polymersomes can be decorated with proteins and/or antibodies, either by chemically attaching the active moieties to the hydrophilic brushes [3] or by inserting membrane proteins across the hydrophobic membrane. [4] Recently, fine control over polymersome surface topology and its consequences on cell internalization kinetics has been demonstrated by the authors. [5] Thus the ability to examine the surface properties of polymersomes, as well as other waterborne nanoparticles, in situ on the nanoscale is becoming increasingly important in several fields. Imaging of wet nanoparticles is normally performed by transmission or scanning electron microscopy (EM). However, the high vacuum conditions necessary for such imaging require either dried or frozen (e.g., cryogenic EM) samples, potentially causing artefacts. Wet imaging can be performed by optical microscopy and recently the problem of diffraction-limited spatial resolution has been overcome by new fluorescence-based microscopy, such as scanning near-field optical microscopy (SNOM), photo-activated localization microscopy (PALM), stimulated emission depletion microscopy (STED), and structured illumination microscopy (SIM). [6] Atomic force microscopy (AFM) is another valuable analytical tool that has been used for both imaging and also for assessing mechanical, electrical, and surface properties. [7]

The Journal of Physical Chemistry B, 2009

Flexible polymers crystallize with chain folding, which shows a unique phenomenon called self-poi... more Flexible polymers crystallize with chain folding, which shows a unique phenomenon called self-poisoning. As a result, minima in crystal growth rates of strictly monodisperse short-chain polymers are observed near the temperatures of transitions from extended-chain to once-folded-chain growth, from once-folded to twice-folded growth, etc. We employed dynamic Monte Carlo simulation of lattice polymers to visualize such transitions in molecular details. We observed a rate crossover between chain extension and lateral growth of polymer lamellar crystals at the wedge-shaped growth front, resulting in a rate minimum around the melting point of the metastable once-folded lamellar crystal. The rate minimum can be interpreted as due to the dependence of crystal growth rates on the excess crystal thickness beyond the minimum stable thickness. Furthermore, during crystal thickening, numerous molten chains are shown to be sucked into the lamellar crystals through the basal planes, demonstrating an important source of crystallinity from secondary crystallization lagging behind the crystal growth front.

Review of Scientific Instruments, 2009

A large scan area high-speed scan stage for atomic force microscopy using the resonant oscillatio... more A large scan area high-speed scan stage for atomic force microscopy using the resonant oscillation of a quartz bar has been constructed. The sample scanner can be used for high-speed imaging in both air and liquid environments. The well-defined time-position response of the scan stage due to the use of resonance allows highly linearized images to be obtained with a scan size up to 37.5 m in 0.7 s. The scanner is demonstrated for imaging highly topographic silicon test samples and a semicrystalline polymer undergoing crystallization in air, while images of a polymer and a living bacteria, S. aureus, are obtained in liquid.

Polymer, 2005

Video rate atomic force microscopy (VideoAFM), with a frame rate of 14 frames/s and a tip velocit... more Video rate atomic force microscopy (VideoAFM), with a frame rate of 14 frames/s and a tip velocity of up to 15 cms K1 , is used to image polyethylene oxide films during crystal growth. The capabilities of VideoAFM when applied to semicrystalline polymer surfaces are explored. Image quality comparable to that found with conventional contact AFM is achieved but with a nearly 1000 times improvement in time resolution. By applying the technique to the real-time observation of crystal growth, different modes of rapid crystallization are followed in real time. Observation of the spherulite growth front allows measurement of growth rates at the lamellar scale, from which a factor of two difference in the rate of radial growth to the rate of tangential growth is observed, confirming that the elongated nature of spherulite lamellae is due to geometric constraints rather than an inherent fibrillar character. Measurements on screw dislocation growth, when large amounts of crystallizable material is trapped at the surface show that the terrace height does not influence the rate of crystal growth, confirming that under these conditions processes at the lamellar growth front control the rate of growth. When only a thin film of molten material is left on the surface of the already crystallized film dendritic growth is observed, implying a diffusion controlled process under these far from equilibrium conditions.

Polymer, 2009

Over the past two decades atomic force microscopy (AFM) has become one of the most frequently use... more Over the past two decades atomic force microscopy (AFM) has become one of the most frequently used tools for studying polymer crystallization. The combination of high resolution, minimal sample preparation and the ability to image non-destructively has allowed visualisation of crystallization, melting and reordering processes at a lamellar and sub-lamellar scale, revealing complexities that could only previously be guessed at. Here the insights that AFM has provided into some of the main over-arching questions relating to polymer crystallization are reviewed. The emphasis is on the use of AFM to image growth in real time, and on contributions that have been made to our understanding of polymer crystallization in general, rather than to specific systems.

Physical Review Letters, 2011

The physical properties of semicrystalline polymers depend on the organisation of chains within t... more The physical properties of semicrystalline polymers depend on the organisation of chains within the crystal and amorphous regions, on the interface between the two, and on the location and nature of defects. Here, torsional tapping atomic force microscopy has been used to image crystalline lamellae and the crystal-amorphous-region interface at the single-chain level with resolution down to 3.7 Å. Defects within the crystalline phase, such as buried folds and chain ends, are revealed. Imaging at the chain level also allows direct measurement of crystalline stem lengths, providing a potential route to test theories of crystal thickness selection.

Materials Today, 2005

PI's P-587.6CD six-axis piezo nanopositioning and scanning system combines six degrees of freedom... more PI's P-587.6CD six-axis piezo nanopositioning and scanning system combines six degrees of freedom, digital control, active trajectory error compensation, millisecond responsiveness, and long travel (up to 800 µm and 10 000 µrad per axis). Frictionless actuators and a flexure guiding system allow subnanometer, submicroradian resolution. An integrated AutoCalibration function allows fast setup and interchangeability of controllers and nanomechanisms. Integrated direct metrology capacitive displacement sensors provide high bandwidth, linearity, and stability. Parallel metrology means that all sensors measure the position of the same moving platform against the same stationary reference, so all motion is inside the servo-loop, regardless of which actuator caused it.