Due to the presence of mechanisms that regenerate portions of tissue after disease or damage, it is possible that excessive or inappropriate growth may occur. In humans, when a portion of tissue grows excessively, it is often described as a cancer; however, there are many forms of excessive growth that are limited and not life-threatening. At the heart of a cancerous growth is the inappropriate response of the cell to its microenvironment. Sensory modules that determine mechanical aspects of the microenvironment contribute to cancerous growth. In particular, the depletion of rigidity-sensing modules enables cells to grow on soft surfaces, much in the way that loss of sensing in self-driving cars causes inappropriate movement. There are common features of inappropriate growth that are considered in the rubric of cancer biology and many books are written on the details. Here we consider growth in the context of cell states and the response of the cell to its microenvironment. By definition, cells in cancers have ignored normal growth controls and have grown excessively. Because tissue growths need vascularization to grow rapidly beyond millimeter dimensions, they are normally self-limiting. Further, telomere shortening will limit the number of divisions of cells. Thus, these two factors act as safeguards to keep most tumors small in size and benign. When cells move to states that continue growth, elongate telomeres and promote vascularization, they can be life-threatening. Even then, surgeons can remove the growths and the normal cells can often heal the area and restore function. What is life-threatening is the ability of inappropriately proliferating cells to disseminate to other parts of the body and to differentiate and grow in many different environments. Then, the surgeon cannot remove all of the tumors and the multiple, differentiated cells will not be killed by a single therapy. Furthermore, the act of killing the tumor cells often elicits a general repair response in the body that will promote further growth of tumors. The lessons of Cancer Biology can tell us a lot about biology in general.

In the previous chapter, we discussed normal development and the process of differentiation. When a loss of cells occurs during normal development, neighboring cells typically divide to fill the gaps. This is important, because with the loss of cells in a tissue, both physical mass and functional performance are lost.

In the adult organism, the cellular microenvironment is critical in controlling cell growth, death, or regeneration. Although the fluid microenvironment includes several factors that influence cells, such as nutrients, salts, and hormones, we will focus here on the extracellular matrix and neighboring cells. The cellular microenvironment must support the tissue functions in the organism and should enable cell turnover and repair. Repair necessitates controlled growth to the proper cell density relative to matrix; however, safeguards are then needed to avoid uncontrolled growth, which can result in cancer. In this chapter, we will discuss the organizing principles in (1) cell–matrix interactions, (2) cell–cell interactions, and (3) the interplay between the two. In the case of the extracellular matrix (ECM), the composition of the ECM and its architecture sets the program for the adjacent cells through both the chemical nature of the ECM molecules and the shape of the crosslinked matrices in the adult. The detergent-resistant matrix of a tissue contains a lot of information that can direct the regeneration of stem cells when added to the matrix. In addition, the ECM will direct the cellular repair process following the loss of individual or small numbers of cells and the mechanical characteristics are critical. Matrix provides mechanical support through basement membranes, ECM fibrous networks, or linear fibers. The number of cells in the given matrix will be set by the physical aspects of the cell–cell contacts and the amount of ECM available. In the case of cell–cell junctions, there is a more limited set of components in adhesions, but some of the same cytoskeletal elements are important. Again, mechanical signals derived from the reciprocal communication between neighboring cells as well as the matrix are critical for directing the growth of the organism and controlling repair processes. Most importantly, the cell must only grow in an environment that is defined by a combination of cell neighbors, the matrix as well as nutrients and hormones. If the cell doesn't respond properly to the local cell and matrix cues, then it is likely that dysfunction will result. Major trauma and damage in the adult is usually bandaided with collagen fibers that cover the damage site (scar tissue) but do little to restore normal function in that region.

Introduction

An ECG, also sometimes referred to as an EKG from the original German word ‘electrokardiogram’, measures the electrical activity of the heart [1]. This electrical activity produces the contractions and relaxations of the cardiac muscles required to pump blood around the body. An ECG is recorded over a series of cardiac cycles (heartbeats) and shows the different phases of the cardiac cycle. The ECG indirectly measures transmembrane voltages in myocardial cells that depolarize and repolarize within each cardiac cycle. These depolarization and repolarization events produce ionic currents within the body, and these are transduced into voltages by electrodes (described in Chapter 2) placed on the surface of the chest and thorax, as shown in Figures 5.1(a) and (b). Up to twelve different lead voltages are recorded, with the magnitude of the voltages being in the low mV range, Figure 5.1(c), and a frequency spectrum between 0 and 30 Hz, as shown in Figure 5.1(d). The ECG signal has many distinct features, such as the P-wave, QRS-complex and T-wave, illustrated in Figure 5.1(c). The amplitude, shape and relative timing of these features can be used to diagnose different clinical conditions.

An ECG is an essential part of diagnosing and treating patients with acute coronary syndromes and is the most accurate method of diagnosing ventricular conduction disturbances and cardiac arrhythmias. It is also used to diagnose heart conditions such as myocardial infarcts, atrial enlargements, ventricular hypertrophies and blocks of the various bundle branches. An ECG is universally used to monitor a patient's cardiac activity during surgery.

Most ECG machines are now digital and automated, meaning that the data is analyzed automatically. Software algorithms measure different aspects (such as delays, durations and slopes) of the ECG waveform and provide a set of keyword interpretations of the scan such as ‘abnormal ECG’ or more specific suggested diagnoses such as ‘possible sinoatrial malfunction’. The most common software package is the University of Glasgow algorithm, which is outlined in detail in section 5.4.1. The major interference signals are caused by electromagnetic coupling from external sources such as power lines, which must be removed by appropriate filtering.

Many cellular functions depend heavily upon the ionic environment within cells and upon the gradients of ions across membranes. In terms of robust devices, the transmembrane potential and ion movements provide a simple means of coordinately regulating multiple functions. Not only are the levels of calcium, magnesium and protons critical, but trace ions like zinc and iron are also needed for many specialized reactions. Gradients of protons and ions across membranes drive neuronal and muscular signaling, ATP production, and even cell death signals. Because ions cannot freely pass through membranes, there are a large number of proteins that have been created with specialized functions to move ions under the right conditions. In general, the cytoplasm of mammalian cells is high in potassium and low in sodium with several millimolar of magnesium, submicromolar of free calcium, and a pH of about 7.0. Outside of the cell, the fluid is high in sodium and low in potassium with several millimolar of both magnesium and calcium (pH 7.4). Total solute concentrations (designated as osmolality or the sum of the concentrations of negative ions, positive ions, proteins and small molecules) are matched inside and out in resting cells. During most cell functions, proteins act as pores, ion-selective channels, or exchangers to control ion movements. Due to the small volume in cells, only a small number of ions need to cross the membrane to produce major changes in concentration, pH, and particularly transmembrane voltage. These parameters control chemical- and electrical-based signal transduction and, therefore, rapid ion movements across membranes must be carefully orchestrated in a robust system. Neuronal signaling and muscle contractility, for example, are controlled by rapid and reliable electrical signaling, which occurs through cell depolarization. Imbalances or mistiming of ion movements in these and other physiological cases are linked to cell damage and disease.

To respond to changes in ionic strength due to dehydration, or rapid intake of large amounts of water, cells possess intrinsic mechanisms that regulate their volume. These rely heavily upon osmosensing, whereby the movement of water out of or in to the cell changes the cell volume, causing the compression of the membrane onto the cytoskeleton or pulling of the membrane away from the cytoskeleton, respectively. In response, the cell will open channels that will allow the entry of salt or the exit of metabolites like taurine.

As noted earlier, cellular functions are always driven by the diffusion of molecular components at a basic level. Thus, it is important to understand why the low Reynolds number of cellular systems demands that basic movements of proteins occur by diffusion. We will go through the physical basis of the cellular systems and the implications of diffusion for cellular functions. In addition, cells of all sizes need to concentrate components in subcellular regions and organize their proteins and membranous organelles by transporting them from one place to another in the cytoplasm. Because diffusion basically limits the speed of transport of materials in the absence of energy-dependent active transport, it is important to remember that slow as well as very small life forms can rely upon diffusion for life processes. There is an active debate about when transport is best accomplished by diffusion or by a motor-dependent system. Both diffusive transport and active transport have been observed and we will consider the mechanism of both in this chapter. Physical constraints of diffusion in cell systems limit the size of life forms, but can be circumvented by reducing dimensionality as well as by active transport systems. As cellular dimensions reach beyond 100 μm, diffusive transport times become very long and animal cells typically utilize active transport systems supported by linear filaments to move materials rapidly. Membrane depolarization and pressure waves can move much faster than diffusion and are often used for signaling when actual material transport is not needed.

Thermal Energy versus Momentum at Low Reynolds Number

To understand cellular functions, it is necessary to understand the fundamental physics of molecules (proteins, lipids, and carbohydrates) at the nanometer level. As particles get smaller, their mass scales roughly as the cube of their size, and the velocities of particle movement also tend to decrease. Because the energy of a moving particle is one-half of the mass multiplied by the velocity squared, the energy in a moving small particle is much less than the energy of macroscopic particles. At some point, the particle size will be small enough such that the typical kinetic energy of particle movement will be less than its thermal energy or kT. At that point, the dominant factor in particle movements will be diffusive. In water, that point is larger than bacteria and smaller than fleas.

There are two distinct systems involved in the establishment of membranecompartmentalized functions in cells. Synthesis and secretion are involved in producing new materials, whereas endocytosis and recycling are involved in metabolism and turnover. Both are involved in the sorting of components for maintaining the compartments. In the synthetic pathway, it is critical for cells to move membranes from the site of protein and lipid synthesis to the correct membrane compartments. In the endocytic pathway, endocytosis of the plasma membrane brings in components from the environment that are sorted and processed for cell growth and activity. These functions rely upon two major mechanisms to move membranes from one compartment to another, either vesicle fission/fusion or fusion of membranes and flow followed by fission. The material to be transported is selected by coat proteins or other filters. The endocytic and synthetic pathways involve bidirectional flows of material that sort components for recycling or forward transport. In the endocytic pathway, most endocytosed components are rapidly recycled, while some are processed before recycling, and an even smaller fraction are degraded. In the synthetic pathway, the ER synthesizes the whole volume of the cellular membranes in a day for a typical growth rate (higher rates are found for specialized secretory cells). Newly synthesized membrane proteins are typically glycosylated in the ER and moved to the Golgi for further glycosylation before transport to either secretory vesicles, lysosomes, or peroxisomes. Flow through these pathways can be likened to liquid flow between a series of pools in that the inhibition of the inflow will cause shrinkage and of the outflow will cause expansion of the pool. Membrane bending stiffness, bilayer asymmetry and tension all play significant roles in membrane trafficking and the proteins involved are designed to sense and respond to each one of these membrane factors. In terms of robust systems engineering, the dynamic membrane system is designed to create linked compartments for sequential processing of proteins either as part of synthesis or metabolism.

Membrane dynamics is critical for many functions, including secretion, renewal, nutrient supply, and signaling. Cells have the capacity to transport large amounts of membrane and perform sorting operations that confine many components to a compartment while selectively removing others for further processing. Normally the transport mechanisms are robust, and this enables tasks to be performed, albeit at a slower rate, even when one or another protein sorting system is lost.

Membranes form the boundaries of cells. In eukaryotic cells, membranes also create internal organelles that are critical for compartmentalizing cell functions and making the system more robust (note, from textbox below, that 95–98% of cell membrane mass is internal). As physical boundaries, they define the cell and organelle volumes and must be moved in cell motility and membrane trafficking. As chemical boundaries, they keep critical components in the cytoplasm and other factors outside the cytoplasm and possibly the cell. The hydrophobic barrier provided by lipid bilayers blocks movement of charged and hydrophilic substances into and out of the cell. An important robust property of cells is that plasma membranes can often be lysed multiple times before a cell will die. They serve a gateway function in that they need to facilitate entry of some components and the exit of others. Also, chemical and physical elements of the cellular microenvironment, including its architecture, need to be communicated to the cytoplasm. Cell shape is typically defined by the cytoskeleton for most mammalian cells, but membrane area to cell volume ratio affects the shape as well as the mechanical properties of the membrane. Membrane mechanics play a critical role in many cytoplasmic as well as cellular phenomena because cell membranes have a significant bending stiffness and resistance to stretch as well as a fluid nature.

Membranes as Compartment Boundaries

The basic role of membranes is to compartmentalize cells by blocking the free diffusion of water-soluble components. Biological membranes are organized around lipid bilayers that have a hydrophobic core and two hydrophilic surfaces. Hydrophobic molecules and surfaces cause an increase in the order of water by not forming hydrogen bonds and creating a surface like an air–water interface. Because order causes a decrease in entropy, the hydrocarbon layer of the bilayer separates readily from water by hiding in the center of the bilayer, making the bilayers quite stable. Breaking a bilayer and exposing the hydrophobic edges to water is energetically very unfavorable. For this reason, holes in bilayers reseal rapidly to cover the exposed hydrocarbon tails. Many membrane proteins extend across the bilayer and they have a hydrophobic surface that fits with the hydrophobic domain of the bilayer. The specific transport of ions and certain molecules by transmembrane proteins occurs through hydrophilic channels in those proteins (Chapter 8).

We are well aware that organisms exhibit different states of awareness, from sleep to heightened tension. Cells can likewise be in different states (phases) where different response networks and different functions are active. The different phases of the cell cycle are obvious examples of how the same cell can exhibit different behaviors when stimulated in a defined way without changing its differentiation state. Furthermore, a given function may have different activators and different levels of activity in different phases. Thus, it is important to control the cell phase when studying any given function. With a large population of cells in a variety of cell phases, the assay of a function will potentially give a mixture of activity levels. There are many different possible phases for cells, including changes in type of motility or metabolic activity in addition to the well-characterized phases of the cell cycle, senescence, or apoptosis. It is important to consider how the cell decides to transition from one phase to another. As was discussed in the previous chapter, the inability of a cell to complete a desired function can be a stimulus to change to an alternative pathway that can involve a change in phase. Further, phase changes can also be induced by the internal cell clock, or external stimuli. Another issue is that widely different cell types can exhibit very similar phases (e.g. mitosis is similar for different types of cells). Thus, many of the characteristic functions associated with different phases are present in many cell types but need specialized conditions to become activated. The same function may have varied outputs in different cell types, but the basic elements would be common to all cells. Often the transitions between phases occur in a very short time and constitute a concerted change. The probability that cells in a population will be in the same phase can be controlled in the lab using patterned substrates and defined conditions. However, single-cell studies can provide a better understanding of the cell phase when a given subcellular function is analyzed. Using defined molecular markers for specific phases, it is possible to follow phase changes at a single-cell level in multicellular tissues.

Most proteins in a cell are synthesized in close proximity to the nucleus through a process known as ‘translation,’ in which ribosomes translate mRNA into protein following its export from the nucleus. Proteins that will be secreted or integrated into membranes must be processed within the endoplasmic reticulum (ER). This requires a signal sequence that enables the docking of the ribosome to the ER. During translation, the protein is moved into the lumen of the ER, where it will be processed. Other mRNAs are targeted for transport to selected regions of the cytoplasm or for sequestration until proper signals are received. The number of proteins synthesized from a single mRNA is highly variable, but is usually in the range of 100–1000 copies. The subsequent lifetime of the protein depends largely upon whether it is properly synthesized. Defective, misfolded proteins, or proteins that are no longer required, will be actively removed from the cytoplasm. This is achieved through a process of ubiquitinylation, which flags the protein for degradation by a proteasome. This process is dependent upon the activation of ubiquitin ligases that are downstream in a number of signaling pathways. Both localized protein synthesis and targeted degradation can facilitate cellular functions by dramatically altering the concentrations of proteins at critical times.

Protein production is truly the hallmark of life as we know it, as proteins form the machinery that performs most cellular functions. As such, the translation of mRNA into protein is an extremely sophisticated process and one can imagine that virtually every mutation of the proteins in the ribosome and in the ribosomal RNA have been tested by cells or organisms. Any improvements would be shared with other organisms and, thus, the current ribosomes should be viewed as particularly robust. In this chapter, we will first discuss the actual process of protein production and the sophisticated adaptations for larger eukaryotes, including localized synthesis, protein folding, and processing. Protein degradation is the balance to synthesis and is used to rapidly block functions as well as to remove denatured proteins or recycle proteins in starvation conditions. Assuming proper nutrient levels, the goal of protein production and turnover is to provide the cell with the tools needed to perform the differentiated cell functions as well as face many environmental challenges from hyperthermia and trauma to various bacterial and viral challenges.

Introduction

Roughly 10% of the world's population suffers from some form of hearing loss, with over 5% or 360 million individuals suffering from hearing impairment that is considered to be disabling by World Health Organization (WHO) standards. The most common cause of hearing loss is damage to the cochlea, which results in reduced frequency selectivity and associated blurring of complex sounds. According to statistics compiled by the National Institute on Deafness and Other Communication Disorders (NIDCD) approximately 2 to 3 out of every 1000 children in the United States are born with a detectable level of hearing loss in one or both ears. One in eight people in the United States aged 12 years or older has hearing loss in both ears. Approximately 2% of adults aged 45 to 54, 8.5% aged 55 to 64, 25% aged 65 to 74, and 50% of those 75 and older have disabling hearing loss. Figure 7.1 shows the frequency and temporal characteristics of human speech, as well as the loss in different frequency ranges and classification of hearing loss from mild to profound.

Among people aged 70 and older who could benefit from hearing aids, only ~30% have ever used them, and the percentage for younger adults is significantly lower. The main reasons are the physical visibility of the device (related to social issues), the need for manual adjustments and problems in sub-optimal conditions such as strong winds and distracting background sounds (technical issues). In order to address the societal issue hearing aids are continually being designed to be smaller, with many of the miniaturization techniques outlined throughout this book enabling the reduction in size. Technical issues are being addressed via new developments in both hardware design as well as more powerful signal processing software. Each of these developments presents design challenges in terms of the requirement to package an ever-greater number of electronics in a more limited space, and to ensure that these electronics can operate in a power-efficient manner so as to maintain long battery life.

This chapter outlines the basic design of digital hearing aids, and the principles behind these designs [1]. The first sections in this chapter consider the physiology and acoustic properties of the human auditory system, the causes of hearing loss and the basics of hearing-aid design.

Biological cells are wonderfully robust self-replicating machines that selfishly propagate their DNA until environmental factors such as nutrients limit them. Cells have mastered the use of nanoscale devices in a water environment to fabricate their progeny and perform many critical functions for survival. To understand how cellular machines work, we need to understand the identity and structure of molecular components as well as the network of interactions between these molecules. We also need to study the complex cell functions in which an orchestra of molecules interacts transiently in space and time to cause an observable cellular behavior. Such an integrated systems engineering view of the cell is currently far from our reach; however, there are sufficient tools and techniques in place to provide us with many useful insights into the complex functions of the wonderful machines that are cells.

In this book, we will mainly discuss eukaryotic cells and where possible the details of mouse embryo fibroblasts (3T3 cells) and a human cancer line (HeLa). Because there are over 300 different cell types with important specializations, we have chosen a relatively general cell type to describe what cells do. Many complex functions are missing in fibroblasts and there will be some necessary extrapolations at certain points. 3T3 and HeLa cells do not form multicellular tissues; cell–cell interactions and the higher-order functions of tissues will be discussed in later chapters. The level of integration and complexity needed for the control of multicellular complex functions is at least an order of magnitude greater than for single cell complex functions. We first focus on dissecting the individual complex functions in single cells, because it is then possible to analyze multicellular complex functions in a modular fashion.

In this chapter, we will define the biological cell that we wish to understand and discuss how evolution has made it more robust over the last two billion years (Huxley, 1958). A cutaway diagram of a cell in suspension (Figure 1.1) provides an illustration of the basic organelle compartments that are found in mammalian cells. Compartmentalization of functions is critical for a complex machine like a cell. Each compartment performs some basic function(s) and communicates bidirectionally with the rest of the cell. Often compartments, like the cell itself, are bounded by lipid bilayers, whose hydrophobic cores effectively prevent open movements of ions and charged materials into or out of the compartments.