Annual Review of Biomedical Engineering - Volume 11, 2009

Neural interfaces are connections that enable two-way exchange of information with the nervous system. These connections can occur at multiple levels, including with peripheral nerves, with the spinal cord, or with the brain; in many instances, fundamental biophysical and biological challenges are shared across these levels. We review these challenges, including selectivity, stability, resolution versus invasiveness, implant-induced injury, and the host-interface response. Subsequently, we review the engineered solutions to these challenges, including electrode designs and geometry, stimulation waveforms, materials, and surface modifications. Finally, we consider emerging opportunities to improve neural interfaces, including cellular-level silicon to neuron connections, optical stimulation, and approaches to control inflammation. Overcoming the biophysical and biological challenges will enable effective high-density neural interfaces for stimulation and recording.

Commonly used techniques for analyzing gene expression, such as polymerase chain reaction (PCR), microarrays, and in situ hybridization, have proven invaluable in understanding RNA processing and regulation. However, these techniques rely on the use of lysed and/or fixed cells and are therefore limited in their ability to provide important spatial-temporal information. This has led to the development of numerous techniques for imaging RNA in living cells, some of which have already provided important insight into the dynamic role RNA plays in dictating cell behavior. Here we review the fluorescent probes that have allowed for RNA imaging in living cells and discuss their utility and limitations. Common challenges faced by fluorescent probes, such as probe design, delivery, and target accessibility, are also discussed. It is expected that continued advancements in live cell imaging of RNA will open new and exciting opportunities in a wide range of biological and medical applications.

Mass spectrometry (MS) is the most comprehensive and versatile tool in large-scale proteomics. In this review, we dissect the overall framework of the MS experiment into its key components. We discuss the fundamentals of proteomic analyses as well as recent developments in the areas of separation methods, instrumentation, and overall experimental design. We highlight both the inherent strengths and limitations of protein MS and offer a rough guide for selecting an experimental design based on the goals of the analysis. We emphasize the versatility of the Orbitrap, a novel mass analyzer that features high resolution (up to 150,000), high mass accuracy (2–5 ppm), a mass-to-charge range of 6000, and a dynamic range greater than 10³. High mass accuracy of the Orbitrap expands the arsenal of the data acquisition and analysis approaches compared with a low-resolution instrument. We discuss various chromatographic techniques, including multidimensional separation and ultra-performance liquid chromatography. Multidimensional protein identification technology (MudPIT) involves a continuum sample preparation, orthogonal separations, and MS and software solutions. We discuss several aspects of MudPIT applications to quantitative phosphoproteomics. MudPIT application to large-scale analysis of phosphoproteins includes (a) a fractionation procedure for motif-specific enrichment of phosphopeptides, (b) development of informatics tools for interrogation and validation of shotgun phosphopeptide data, and (c) in-depth data analysis for simultaneous determination of protein expression and phosphorylation levels, analog to western blot measurements. We illustrate MudPIT application to quantitative phosphoproteomics of the beta adrenergic pathway. We discuss several biological discoveries made via mass spectrometry pipelines with a focus on cell signaling proteomics.

Muscle mechanical output such as force and power are governed by highly nonlinear intrinsic muscle properties associated with different muscle fiber types and are influenced by training and age. Many of the interactions between these properties pose trade-offs such that an individual's anthropometrics and muscle morphology may allow an athlete to excel in one sport but not in others. Advanced modeling and simulation techniques are powerful tools to gain insight into performance limits, optimal equipment designs, and mechanisms that may lead to injury. Recent technological innovations have produced faster running tracks, bicycles, speed skates, and swimming pools. This review discusses the influence of intrinsic muscle properties in sports and how advanced technology can be used to extend the limits of human performance.

Advances in numerical methods and three-dimensional imaging techniques have enabled the quantification of cardiovascular mechanics in subject-specific anatomic and physiologic models. Patient-specific models are being used to guide cell culture and animal experiments and test hypotheses related to the role of biomechanical factors in vascular diseases. Furthermore, biomechanical models based on noninvasive medical imaging could provide invaluable data on the in vivo service environment where cardiovascular devices are employed and on the effect of the devices on physiologic function. Finally, patient-specific modeling has enabled an entirely new application of cardiovascular mechanics, namely predicting outcomes of alternate therapeutic interventions for individual patients. We review methods to create anatomic and physiologic models, obtain properties, assign boundary conditions, and solve the equations governing blood flow and vessel wall dynamics. Applications of patient-specific models of cardiovascular mechanics are presented, followed by a discussion of the challenges and opportunities that lie ahead.

Induced hypothermia is an acknowledged useful therapy for treating conditions that lead to cell and tissue damage caused by ischemia, including traumatic brain injury, stroke, and cardiac arrest. An accumulating body of clinical evidence, together with several decades of research, has documented that the efficacy of hypothermia is dependent on achieving a reduced temperature in the target tissue before or soon following the ischemia-precipitating event. The temperature must be lowered to within a rather small range of values to effect therapeutic benefit without introducing collateral problems. Rewarming must be much slower than cooling. Many different methods and devices have been used for cooling, with mixed results. There are existing opportunities for bioengineers to improve our understanding of the mechanisms of hypothermia and to develop more effective methods of cooling the brain following trauma.

Approximately 11% of U.S. women undergo surgery for pelvic floor dysfunction, including genital organ prolapse and urinary and fecal incontinence. The major risk factor for developing these conditions is giving vaginal birth. Vaginal birth is a remarkable event about which little is known from a biomechanical perspective. We first review the functional anatomy of the female pelvic floor, the normal loads acting on the pelvic floor in activities of daily living, and the functional capacity of the pelvic floor muscles. Computer models show that the stretch ratio in the pelvic floor muscles can reach an extraordinary 3.26 by the end of the second stage of labor. Magnetic resonance images provide evidence that show that the pelvic floor regions experiencing the most stretch are at the greatest risk for injury, especially in forceps deliveries. A conceptual model suggests how these injuries may lead to the most common form of pelvic organ prolapse, a cystocele.

Metastasis is a highly regulated, multistep process in which cancerous cells shed from the primary tumor and enter the circulatory system, where they interact extensively with host cells before they lodge and colonize the target organ. The adhesive interactions of circulating tumor cells with platelets, leukocytes, and endothelial cells facilitate their survival and extravasation from the vasculature, thus representing critical kick-off events for the colonization of distant organs. This review presents our current mechanistic knowledge on vascular interactions of tumor cells, and it discusses biochemical and cell and molecular biology techniques used for the identification of novel receptor-ligand pairs mediating these interactions. This review brings together diverse observations about the contributions of key molecular constituents, including selectins, fibrin(ogen), and CD44, in one mechanistic interpretation. Understanding the molecular underpinnings of adhesive interactions between tumor cells and host cells may provide guidelines for developing promising antimetastatic therapies when initiated early in the course of disease progression.

Mechanical forces play important roles in the regulation of various biological processes at the molecular and cellular level, such as gene expression, adhesion, migration, and cell fate, which are essential to the maintenance of tissue homeostasis. In this review, we discuss emerging bioengineered tools enabled by microscale technologies for studying the roles of mechanical forces in cell biology. In addition to traditional mechanobiology experimental techniques, we review recent advances of microelectromechanical systems (MEMS)-based approaches for cell mechanobiology and discuss how microengineered platforms can be used to generate in vivo–like micromechanical environment in in vitro settings for investigating cellular processes in normal and pathophysiological contexts. These capabilities also have significant implications for mechanical control of cell and tissue development and cell-based regenerative therapies.

Living cells are remarkably complex. To unravel this complexity, living-cell assays have been developed that allow delivery of experimental stimuli and measurement of the resulting cellular responses. High-throughput adaptations of these assays, known as living-cell microarrays, which are based on microtiter plates, high-density spotting, microfabrication, and microfluidics technologies, are being developed for two general applications: (a) to screen large-scale chemical and genomic libraries and (b) to systematically investigate the local cellular microenvironment. These emerging experimental platforms offer exciting opportunities to rapidly identify genetic determinants of disease, to discover modulators of cellular function, and to probe the complex and dynamic relationships between cells and their local environment.

It is now widely appreciated that normal tissue morphology and function rely upon cells' ability to sense and generate forces appropriate to their correct tissue context. Although the effects of forces on cells have been studied for decades, our understanding of how those forces propagate through and act on different cell substructures remains at an early stage. The past decade has seen a resurgence of interest, with a variety of different micromechanical methods in current use that probe cells' dynamic deformation in response to a time-varying force. The ability of researchers to carefully measure the mechanical properties of cells subjected to a variety of pharmacological and genetic interventions, however, currently outstrips our ability to quantitatively interpret the data in many cases. Despite these challenges, the stage is now set for the development of detailed models for cell deformability, motility, and mechanosensing that are rooted at the molecular level.

Surgical replacement of diseased heart valves by mechanical and tissue valve substitutes is now commonplace and enhances survival and quality of life for many patients. However, repairs of congenital deformities require very small valve sizes not commercially available. Further, a fundamental problem inherent to the use of existing mechanical and biological prostheses in the pediatric population is their failure to grow, repair, and remodel. It is believed that a tissue engineered heart valve can accommodate many of these requirements, especially those pertaining to somatic growth. This review provides an overview of the field of heart valve tissue engineering, including recent trends, with a focus on the bioengineering challenges unique to heart valves. We believe that, currently, the key bioengineering challenge is to determine how biological, structural, and mechanical factors affect extracellular matrix (ECM) formation and in vivo functionality. These factors are fundamental to any approach toward developing a clinically viable tissue engineered heart valve (TEHV), regardless of the particular approach. Critical to the current approaches to TEHVs is scaffold design, which must simultaneously provide function (valves must function from the time of implant) as well as stress transfer to the new ECM. From a bioengineering point of view, a hierarchy of approaches will be necessary to connect the organ-tissue relationships with underpinning cell and sub-cellular events. Overall, such approaches need to be structured to address these fundamental issues to lay the basis for TEHVs that can be developed and designed according to truly sound scientific and engineering principles.