Experimental observations and numerical modeling of lipid-shell microbubbles with calcium-adhering moieties for minimally-invasive treatment of urinary stones

A novel treatment modality incorporating calcium-adhering microbubbles has recently entered human clinical trials as a new minimally-invasive approach to treat urinary stones. In this treatment method, lipid-shell gas-core microbubbles can be introduced into the urinary tract through a catheter. Lipid moities with calcium-adherance properties incorporated into the lipid shell facilitate binding to stones. The microbubbles can be excited by an extracorporeal source of quasi-collimated ultrasound. Alternatively, the microbubbles can be excited by an intraluminal source, such as a fiber-optic laser. With either excitation technique, calcium-adhering microbubbles can significantly increase rates of erosion, pitting, and fragmentation of stones. We report here on new experiments using high-speed photography to characterize microbubble expansion and collapse. The bubble geometry observed in the experiments was used as one of the initial shapes for the numerical modeling. The modeling showed that the bubble dynamics strongly depends on bubble shape and stand-off distance. For the experimentally observed shape of microbubbles, the numerical modeling showed that the collapse of the microbubbles was associated with pressure increases of some two-to-three orders of magnitude compared to the excitation source pressures. This in-vitro study provides key insights into the use of microbubbles with calcium-adhering moieties in treatment of urinary stones

Diversity of isoprene-degrading bacteria in phyllosphere and soil communities from a high isoprene-emitting environment: a Malaysian oil palm plantation

Background: Isoprene is the most abundantly produced biogenic volatile organic compound (BVOC) on Earth, with annual global emissions almost equal to those of methane. Despite its importance in atmospheric chemistry and climate, little is known about the biological degradation of isoprene in the environment. The largest source of isoprene is terrestrial plants, and oil palms, the cultivation of which is expanding rapidly, are among the highest isoprene-producing trees. Results: DNA stable isotope probing (DNA-SIP) to study the microbial isoprene-degrading community associated with oil palm trees revealed novel genera of isoprene-utilising bacteria including Novosphingobium, Pelomonas, Rhodoblastus, Sphingomonas and Zoogloea in both oil palm soils and on leaves. Amplicon sequencing of isoA genes, which encode the α-subunit of the isoprene monooxygenase (IsoMO), a key enzyme in isoprene metabolism, confirmed that oil palm trees harbour a novel diversity of isoA sequences. In addition, metagenome assembled genomes (MAGs) were reconstructed from oil palm soil and leaf metagenomes and putative isoprene degradation genes were identified. Analysis of unenriched metagenomes showed that isoA-containing bacteria are more abundant in soils than in the oil palm phyllosphere. Conclusion: This study greatly expands the known diversity of bacteria that can metabolise isoprene and contributes to a better understanding of the biological degradation of this important but neglected climate-active gas

Gates and Latches: the mechanochemistry of ATP binding in kinesin 1 and Eg5

This thesis explores the role of mechanochemistry in two biological systems. The first system investigated involves cargo transport along microtubule filaments by Kinesin 1. A gating mechanism is needed to coordinate ATP binding to the two catalytic domains within Kinesin 1 in order to prevent simultaneous binding, hydrolysis and detachment of both heads which could prematurely terminate cargo transport. The second system investigated involves cell division and the mitotic kinesin Eg5. In this motor, we investigate ATP-binding and find that it has an additional component internal to its catalytic domain, called Loop 5, which is functionally important for both ATP binding and neck linker docking

Plasma formation in holmium:YAG laser lithotripsy

ObjectivesDuring holmium:yttrium-aluminum-garnet (holmium:YAG) laser lithotripsy to break urinary stones, urologists frequently see flashes of light. As infrared laser pulses are invisible, what is the source of light? Here we studied the origin, characteristics, and some effects of flashes of light in laser lithotripsy.MethodsUltrahigh-speed video-microscopy was used to record single laser pulses at 0.2-1.0 J energy lasered with 242 µm glass-core-diameter fibers in contact with whole surgically retrieved urinary stones and hydroxyapatite (HA)-coated glass slides in air and water. Acoustic transients were measured with a hydrophone. Visible-light and infrared photodetectors resolved temporal profiles of visible-light emission and infrared-laser pulses.ResultsTemporal profiles of laser pulses showed intensity spikes of various duration and amplitude. The pulses were seen to produce dim light and bright sparks with submicrosecond risetime. The spark produced by the intensity spike at the beginning of laser pulse generated a shock wave in the surrounding liquid. The subsequent sparks were in a vapor bubble and generated no shock waves. Sparks enhanced absorption of laser radiation, indicative of plasma formation and optical breakdown. The occurrence and number of sparks varied even with the same urinary stone. Sparks were consistently observed at laser energy >0.5 J with HA-coated glass slides. The slides broke or cracked by cavitation with sparks in 63 ± 15% of pulses (1.0 J, N = 60). No glass-slide breakage occurred without sparks (1.0 J, N = 500).ConclusionUnappreciated in previous studies, plasma formation with free-running long-pulse holmium:YAG lasers can be an additional physical mechanism of action in laser procedures

New Insights into the Mechanism of Force Generation by Kinesin-5 Molecular Motors

International audienc

Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins

Nucleic acid hairpins provide a powerful model system for probing the formation of secondary structure. We report a systematic study of the kinetics and thermodynamics of the folding transition for individual DNA hairpins of varying stem length, loop length, and stem GC content. Folding was induced mechanically in a high-resolution optical trap using a unique force clamp arrangement with fast response times. We measured 20 different hairpin sequences with quasi-random stem sequences that were 6\u201330 bp long, polythymidine loops that were 3\u201330 nt long, and stem GC content that ranged from 0% to 100%. For all hairpins studied, folding and unfolding were characterized by a single transition. From the force dependence of these rates, we determined the position and height of the energy barrier, finding that the transition state for duplex formation involves the formation of 1\u20132 bp next to the loop. By measuring unfolding energies spanning one order of magnitude, transition rates covering six orders of magnitude, and hairpin opening distances with subnanometer precision, our results define the essential features of the energy landscape for folding. We find quantitative agreement over the entire range of measurements with a hybrid landscape model that combines thermodynamic nearest-neighbor free energies and nanomechanical DNA stretching energies.Peer reviewed: YesNRC publication: Ye