Study of the reliability of quantification methods of dynamic contrast-enhanced ultrasonography: numerical modeling of blood flow in tumor microvascularization.

Dynamic contrast-enhanced ultrasonography is a recent functional dynamic imaging technique that allows evaluation of the efficacy of anti-angiogenic treatments by quantifying changes in specific parameters of the tumor vasculature. Preclinical and clinical experimental studies now reveal the existence of sources of variability in the quantitative methods. In order to study the reliability of quantification methods (both semi-quantitative and quantitative), we have developed the first numerical model of blood flow and contrast agents in vascular networks with computational fluid dynamics Fluent software version 15.0 (ANSYS, France). We studied four vascular networks (1.84 × 10-3, 2.28 × 10-3, 2.4 × 10-3 and 2.54 × 10-3 ml) and four blood velocities (0.01, 0.02, 0.03 and 0.05 m s-1). For variations in tumor vascular volume the quantitative method is more sensitive, with variations of parameter perfusion of 25.7%, in contrast to variations of the semi-quantitative parameters between 14.9 and 19.5%. For changes in blood velocity the semi-quantitative method is more sensitive, with variation of the area under the enhancement curve (64%), the maximum of the enhancement curve (60%), and the slope of the enhancement curve (73%). The transit time parameters from the two quantitative methods were weakly sensitive to both blood volume and blood flow variations. This study is hopeful and may be extended to the treatment of more complex vascular networks, to approach clinical conditions, and to the evaluation of quantification methods in contrast imaging.

A small-molecule activator of kinesin-1 drives remodeling of the microtubule network.

The microtubule motor kinesin-1 interacts via its cargo-binding domain with both microtubules and organelles, and hence plays an important role in controlling organelle transport and microtubule dynamics. In the absence of cargo, kinesin-1 is found in an autoinhibited conformation. The molecular basis of how cargo engagement affects the balance between kinesin-1's active and inactive conformations and roles in microtubule dynamics and organelle transport is not well understood. Here we describe the discovery of kinesore, a small molecule that in vitro inhibits kinesin-1 interactions with short linear peptide motifs found in organelle-specific cargo adaptors, yet activates kinesin-1's function of controlling microtubule dynamics in cells, demonstrating that these functions are mechanistically coupled. We establish a proof-of-concept that a microtubule motor-cargo interface and associated autoregulatory mechanism can be manipulated using a small molecule, and define a target for the modulation of microtubule dynamics.

SKIP controls lysosome positioning using a composite kinesin-1 heavy and light chain-binding domain.

The molecular interplay between cargo recognition and regulation of the activity of the kinesin-1 microtubule motor is not well understood. Using the lysosome adaptor SKIP (also known as PLEKHM2) as model cargo, we show that the kinesin heavy chains (KHCs), in addition to the kinesin light chains (KLCs), can recognize tryptophan-acidic-binding determinants on the cargo when presented in the context of an extended KHC-interacting domain. Mutational separation of KHC and KLC binding shows that both interactions are important for SKIP-kinesin-1 interaction in vitro and that KHC binding is important for lysosome transport in vivo However, in the absence of KLCs, SKIP can only bind to KHC when autoinhibition is relieved, suggesting that the KLCs gate access to the KHCs. We propose a model whereby tryptophan-acidic cargo is first recognized by KLCs, resulting in destabilization of KHC autoinhibition. This primary event then makes accessible a second SKIP-binding site on the KHC C-terminal tail that is adjacent to the autoinhibitory IAK region. Thus, cargo recognition and concurrent activation of kinesin-1 proceed in hierarchical stepwise fashion driven by a dynamic network of inter- and intra-molecular interactions.

A formin-g role during development and disease.

Several different protein families were shown to be involved in the regulation of actin filament formation and have been studied extensively in processes such as cell migration. Among them are members of the formin family, which tend to promote the formation of linear actin filaments. Studies in recent years, often using loss of function animal models, have indicated that formin family members play roles beyond cell motility in vitro and are involved in processes ranging from tissue morphogenesis and cell differentiation to diseases such as cancer and cardiomyopathy. Therefore the aim of this review is to discuss these findings and to start putting them into a subcellular context.

Delineation of the TRAK binding regions of the kinesin-1 motor proteins.

Understanding specific cargo distribution in differentiated cells is a major challenge. Trafficking kinesin proteins (TRAKs) are kinesin adaptors. They bind the cargo binding domain of kinesin-1 motor proteins forming a link between the motor and their cargoes. To refine the TRAK1/2 binding sites within the kinesin-1 cargo domain, rationally designed C-terminal truncations of KIF5A and KIF5C were generated and their co-association with TRAK1/2 determined by quantitative co-immunoprecipitations following co-expression in mammalian cells. Three contributory regions forming the TRAK2 binding site within KIF5A and KIF5C cargo binding domains were delineated. Differences were found between TRAK1/2 with respect to association with KIF5A.

A vision and strategy for the virtual physiological human in 2010 and beyond.

European funding under framework 7 (FP7) for the virtual physiological human (VPH) project has been in place now for nearly 2 years. The VPH network of excellence (NoE) is helping in the development of common standards, open-source software, freely accessible data and model repositories, and various training and dissemination activities for the project. It is also helping to coordinate the many clinically targeted projects that have been funded under the FP7 calls. An initial vision for the VPH was defined by framework 6 strategy for a European physiome (STEP) project in 2006. It is now time to assess the accomplishments of the last 2 years and update the STEP vision for the VPH. We consider the biomedical science, healthcare and information and communications technology challenges facing the project and we propose the VPH Institute as a means of sustaining the vision of VPH beyond the time frame of the NoE.

Kidney modeling and systems physiology.

We present an overview of currently available resources in renal systems physiology and indicate directions for development toward the renal physiome. After a brief resumé of objectives, we summarize legacy-modeling studies that can serve as the foundation for a more complete toolset. These include detailed models of practically all renal cell types and nephron segments and a variety of models of nephro-vascular exchanges in the medulla, of renal hemodynamics, and studies of tubuloglomerular feedback and autoregulation. Recent detailed anatomical reconstructions have brought surprising new results to bear on classic unsolved problems. In parallel with the modeling environment, progress has been made toward the quantitative database and model repository resources that must accompany the modeling environment in order to attain the goal of an open-ended, flexible, and collaborative infrastructure for renal systems biology, with an indication of prospects for integration with initiatives in the larger IUPS Physiome Project.