Jeremy Ramsden

• MA, DSc
• Research Director at Collegium Basilea (Institute of Advanced Study), Basel, Switzerland

Purpose During the course of demyelinating inflammatory diseases, myelin-derived proteins, including myelin basic protein(MBP), are secreted into extracellular space. MBP shows extensive post-translational modifications, including deimination/citrullination. Deiminated MBP is structurally less ordered, susceptible to proteolytic attack, and more im...

Whenever confronting the totality of biology, it is clear that one may approach it at various levels, such as molecular, cellular, organismal, populational, and ecological. Traditionally, these levels have been accorded official status by naming academic departments after them.

Any organism is indissociably embedded in an environment (which is ultimately a source of entropy—or negentropy if one prefers that term). Development does not follow a preordained program encoded in the organism’s genes but is influenced by its environment, which may be assumed to be continually varying. Among physical parameters, temperature is a...

This chapter is a kind of case study of an area of knowledge in which little progress had been made before the era of modern bioinformatics. Domestic animals are tremendously important to humanity. Presently, livestock constitutes more than ten times the biomass of all wild mammals and somewhat exceeds the total human biomass. Domestic animals are,...

What is information? We have already asserted that it is a profound, primitive (i.e., irreducible) concept. Dictionary definitions include “(desired) items of knowledge”; for example, one wishes to know the length of a piece of wood. It appears to be less than a foot long, so we measure it with our desktop ruler marked off in inches, with the resul...

Kullback (1959) points out that information theory is a branch of the mathematical theory of probability and statistics; insofar as bioinformatics is a branch of information theory, it follows that statistics is superordinate to bioinformatics.

Life as a low-entropy phenomenon in a vast ocean of gradually increasing entropy forms an intriguing interface between biology and physics, in which information, with its intimate links to entropy, plays a key role. Interest in the generality of life as a concept has been enormously boosted by the discovery of exoplanets, many of which seem to poss...

The purpose of this and the following chapter is to give an overview of living systems, especially directed at the bioinformatician who has previously dealt purely with the computational aspects of the subject.

The assumption of average types is one of the major simplifying assumptions needed to produce a mechanistic description of a natural system.\(^1\) Besides, the limited sensitivity of many experimental methods made it necessary to gather materials from large numbers of cells in order to have a sufficient number of molecules for reliable characteriza...

This chapter elaborates on the overview presented in Chapter 3. Gene regulatory networks are complex systems that control the expression of genes in response to environmental cues. These networks can be quantified by looking at how the network elements interact with each other, and how the network elements can be tuned to optimize a desired outcome...

The great increase in DNA sequencing capability over the past couple of decades has given a tremendous impetus to the study of bacterial ecosystems, termed the microbiome (cf. Sect. 17.8), and it is now not only possible to obtain a comprehensive snapshot of microbial but also follow how it varies temporally and spatially.\(^1\) Analysis of microbi...

This chapter begins with a concise primer, or aide-mémoire, of probability theory. The fundamentals are recapitulated, drawing on the material of Chap. 8. Moments of distributions are reviewed. The theory of runs (successions of similar events preceded and succeeded by different events), which is useful for analysing nucleic acid sequences and temp...

Viruses have become a very topical subject thanks to the Covid-19 pandemic, which has focused attention onto these fascinating biological objects\(^1\) In the past, viruses were discovered and investigated in the context of a host, and knowledge about them was relatively limited, encompassing only a few hundred different viruses. The great enhancem...

Although in principle all individuals belonging to the same species share the same DNA, the vagaries of sexual recombination (Sect. 14.7.3) ensure considerable variability in the non-coding parts of the genome. Even identical twins show some differences.

“Machine” is used formally to describe the embodiment of a transformation (e.g., Eq. (3.1); cf. the automata in Sect. 12.1.1). In this formal sense, it does not have any particular connotation of animate or inanimate. The essential feature is that the internal state of the machine, together with the state of its surroundings, uniquely defines the n...

DNA is transcribed into RNA—the ensemble of The proteome is the ensemble of expressed proteins in a cell (cf. Fig. 14.1), and proteomics is the study of that ensemble (i.e., the identification and determination of the amounts, locations, and interactions of all the proteins). It could also include disordered and alternatively folded proteins.\(^1\)...

Evolvability is recognized as a core feature of living systems. Evolution is seen as phylogenetic adaptation, and the salient features of evolutionary systems, which display true complexity, are described. Darwin’s theory is discussed, and concepts like exaptation, punctuated equilibrium, and altruism (group and kin selection). Models of evolution...

This chapter is primarily concerned with signal transduction within cells: how information about a cell’s environment is transferred from the external cell surface to its nucleus, where it affects changes in gene expression appropriate to changes detected in the environment. Signal channel capacities are discussed, and the molecular mechanisms of t...

Randomness is a concept deeply entangled with bioinformatics. A random sequence cannot convey information, in the sense that it could be generated by a recipient merely by tossing a coin. Randomness is therefore a kind of “null hypothesis”; a random sequence of symbols is a sequence lacking all constraints limiting the variety of choice of successi...

The Covid-19 pandemic has thrown bioinformatics into prominence, but dealing with the pandemic has mainly required existing tools. It has provided an unprecedented volume of sequence data, which should ultimately lead to a much profounder understanding of the evolution of SARS-CoV-2, and maybe other viruses as well.

This chapter deals with the basics of information transmission, which include some or all of the following: the information source, encoding the information, transmitting it through a channel, the addition of noise, and, finally, receiving and decoding the information. Biological coding is introduced through the examples of DNA, RNA, and proteins....

Genomics is the study of the structure, function, and evolution of genomes, the ensemble of genes in an organism. It involves the sequencing and analysis of an organism’s entire genetic material in order to gain insights into its development and phenotype. Genomics is a rapidly growing field that has revolutionized biology, paving the way for perso...

Just as we are often interested in events that are composed of many elementary (simple) events, in biology the objects under scrutiny are vastly complex objects composed of many individual molecules (the molecule is probably the most appropriate level of coarse graining for the systems we are dealing with). Since these components are connected toge...

Much of biology has traditionally been concerned with the classification of objects, especially of course organisms, the best known example probably being Carl Linnaeus’ Systema Naturae, first published in 1735. As knowledge has continued to expand, the desire to classify has also spread to bioinformatics and its objects: genes and other DNA sequen...

The concept of algorithm is of central importance, especially for arithmetic, and even more particularly for operations carried out by mathematical machines such as digital computers. An algorithm is defined as a process of solving problems based on repeatedly carrying out a strictly defined procedure.

Largely thanks to bioinformatics and high-throughput synthesis and early-stage screening, the development of new drugs has become a much more rationally directed process than formerly. The key stages of finding targets and ensuring the absence of adverse side interactions are described. The centrality of understanding the affinity of a potential dr...

This chapter deals with, primarily, the brain. The connectome is a comprehensive map of the neural connexions in the brain; a network of nerve cells and the pathways that connect them, allowing information to be transmitted between different brain regions. Artificial neural networks and neural computation are briefly described.

Table 15.1 gives some approximate values for the atomic composition of a cell. The atomic composition represents a highly reductionist view, somewhat akin to asserting that the informational content of Macbeth is \(-\sum _{\text {alphabet}} p_i \log _2 p_i\), where \(p_i\) is the normalized frequency of occurrence of the ith letter of the alphabet.

Phenotype is the physical characteristics of a living organism that are the product of both genetic and environmental influences. Phenotypes are typically the visible or measurable traits of an organism that can be observed and studied. A phenome is the set of observable characteristics of an individual or species that result from the interaction b...

Set is a fundamental, abstract notion. A set is defined as a collection of objects, which are called the elements or points of the set. The notions of union (\(A \cup B\), where A and B are each sets), intersection (\(A \cap B\)), and complement (\(A^c\)) correspond to everyday usage.

This chapter deals with a selection of medical applications of bioinformatics, starting with genetically based diseases and the use of single-nucleotide polymorphisms (SNPs). Infectious and noninfectious diseases are covered. The use of differentially expressed genes (DEGs) is outlined in a number of examples. Genome-wide association studies, as a...

Novel biosensors already provide a fast way to detect the adhesion of whole bacteria (or parts of them), biofilm formation, and the effect of antibiotics. Moreover, the detection sensitivities of recent sensor technologies are large enough to investigate molecular-scale biological processes. Usually, these measurements can be performed in real time...

Plants and fungi can be used for medical applications because of their accumulation of special bioactive metabolites. These substances might be beneficial to human health, exerting also anti-inflammatory and anticancer (antiproliferative) effects. We propose that they are mediated by influencing cellular adhesion and migration via various signaling...

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission occurs via airborne droplets and surface contamination. Titanium dioxide (TiO 2 ) coating of surfaces is a promising infection control measure, though to date has not been tested against SARS-CoV-2. Methods : Virus stability was evaluated on TiO 2 - and TiO 2 –Ag...

Interfacial layers are important in a wide range of applications in biomedicine, biosensing, analytical chemistry and the maritime industries. Along with the growing number of applications, the analysis of these layer properties and understanding their behavior is becoming crucial. Label-free surface sensitive methods are excellent tools to monitor...

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission occurs via airborne droplets and surface contamination. Titanium dioxide (TiO 2 ) coating of surfaces is a promising infection control measure, though to date has not been tested against SARS-CoV-2. Methods : Virus stability was evaluated on TiO 2 - and TiO 2 –Ag...

SARS-CoV-2 transmission occurs via airborne droplets and surface contamination. We show tiles coated with TiO 2 120 days previously can inactivate SARS-CoV-2 under ambient indoor lighting with 87% reduction in titres at 1h and complete loss by 5h exposure. TiO 2 coatings could be an important tool in containing SARS-CoV-2.

ZnO photocatalytic thin films deposited on a glass substrate are obtained by chemical spraying technique, and they are active in the visible light spectrum. Optical studies have shown that ZnO thin films doped by nickel impurities absorb visible light at wavelengths from 400nm to 600nm. At the same time, this absorption rate increases with the incr...

Indices of resource depletion and other indicators inimical to sustainability, such as pollution, atmospheric carbon dioxide concentration and mean temperature of the Earth’s surface, are all proportional to population and mean gross domestic product (GDP) per capita. In order to combat the imminent threat of a catastrophic collapse of our present...

The aim of this study was to evaluate the bactericidal effect of reactive oxygen species (ROS) generated upon irradiation of photocatalytic TiO 2 surface coatings using low levels of UVA and the consequent killing of Staphylococcus aureus. The role of intracellular enzymes catalase and superoxide dismutase in protecting the bacteria was investigate...

The sustainability of our present civilization and, ultimately, of human life itself is challenged on many fronts. The most prominent of the challenges are climate change, extreme food and water shortages, rising chronic diseases, and rampant obesity. They are all of great significance in terms of death and morbidity, and at the same time seemingly...

The sustainability of our present civilization and, ultimately, of human life itself is challenged on many fronts. The most prominent of the challenges are climate change, extreme food and water shortages, rising chronic diseases, and rampant obesity. They are all of great significance in terms of death and morbidity, and at the same time seemingly...

Advanced and increasingly complex societies have hitherto managed quite well with their administrators looking for a course of action that is “good enough” (or that satisfices, in the terminology of H.A. Simon), achieved by creating or using a drastically simplified model of the world, taking into account just a few of the factors, those that they...

BACKGROUND The healthcare environment is recognized as a source for healthcare-acquired infection. Because cleaning practices are often erratic and always intermittent, we hypothesize that continuously antimicrobial surfaces offer superior control of surface bioburden. OBJECTIVE To evaluate the impact of a photocatalytic antimicrobial coating at n...

Recent publications claimed a significant catalytic effect of nickel nanoparticles on the hydration of CO2 to carbonic acid. Others have claimed that such catalysis can significantly accelerate the overall process of CO2 capture by mineralization to CaCO3 from aqueous solution. Having repeated the experiments as closely as possible, we observed no...

It is widely recognized that, given the present level of funding and under the present system of organization, the UK National Health Service (NHS) cannot adequately (according to its own criteria) meet the demands now being placed on it. One promising, hitherto underinvestigated, path out of the thicket is the introduction of advanced sensor techn...

Development ISO TR 19601 : Aerosol generation for NOAA (nano-objects and their aggregates and agglomerates) air exposure studies is completed recently. The technical report (TR) reviews methods for generating aerosols of NOAA for in vivo and in vitro inhalation studies. The goals of this technical report is to aid in selecting appropriates NOAA aer...

Methods of investigating nanomaterials are described. These may be categorized into those concerned with characterizing structure, both of the surface and of the bulk (insofar as nanomaterials have bulk), mechanical properties and chemical identity. The mathematical representation of texture is also covered. The metrology applicable to the nano/bio...

This chapter deals with primary nano-objects that tend to be used as the starting material for more complex products. They comprise nanoparticles, nanofibers and nanoplatelets (excluding carbon nanomaterials). The objects are described and generic methods of production are presented.

This chapter is dominated by information-processing devices, which represent the largest application of nanotechnology. Approaches to the further miniaturization of the well established CMOS technology in electronics are discussed, as well as the latest developments in nonvolatile, but rapid access (storage class) memory. As a good candidate for co...

The main nanotechnology processes used to make functional objects are described. They are classified as top-down, which in the form of semiconductor processing is by far the most important; bottom-up or self-assembly, which is attractive because, in comparison with the enormous expense of top-down facilities requires very little in the way of capit...

This introductory chapter defines nanotechnology and introduces the rudiments of a concept system (ontology) for it. The history of nanotechnology is outlined, and the way in which the discoveries of molecular biology have made biology into a paradigm for nanotechnology is explained. The convergence of nanotechnology, biotechnology, information tec...

Bionanotechnology is defined as the application of biology to nanotechnology. This chapter begins with some general characteristics of biomolecules, including their structure, the hierarchical structure of bionanocomposites and the general mechanism of biological machines. The use of DNA as a structural, rather than as a genetic material is describ...

A definition of the nanoscale is indispensable for defining nanotechnology. Where there is a discontinuous, qualitative change of phenomena as one approaches the atomic scale, as occurs, for example, in a number of electrical, magnetic, optical, etc., phenomena, then we have a clear, nonarbitrary definition of the nanoscale. The difficulty is that...

Nanosystems in the sense of this chapter comprise more elaborate devices than those considered in earlier chapters. Aspects of design are covered, including the selection of materials and the treatment of defects. Computational modeling as an indispensable adjunct to the design of nanomaterials and nano devices is described.

The nano forms of carbon are considered – fullerenes, nano-onions, nanodiamonds, carbon nanotubes, carbon nanofibers and graphene. Their basic properties and fabrication are outlined. Applications as materials and for use in devices are presented.

Forces in nature are distinguished, among other things, by their range of interaction. Forces with a range in the nanoscale are the Casimir force and various electrostatic and electrodynamic forces acting between solids. Nanostructured systems generally have extremely large interfacial areas relative to their bulk volume, hence interfacial interact...

This chapter is mainly about nanobiotechnology, which is defined as the application of nanotechnology to biology. By far the most important aspect of nanobiotechnology is nanomedicine – the use of nanotechnology to enhance diagnostics and therapy. The final topic of the chapter is nanotoxicology, which is defined as the toxicology of nano-objects....

This chapter recapitulates much of the material of the preceding chapters, showing how nanotechnology is already affecting, or has the potential to affect, society. The focus is on the big three fields of information technology, health and energy. As well as purely technical aspects, commercial and social implications are also discussed.

Attempts are being made to incorporate copper into clear varnish in order to coat environmental surfaces in hospitals with the long-term goal of reducing healthcare-acquired infections (HAI). The performance of a nanocopper-containing polyacrylic emulsion, NanoCote HD-WR, on bedrails, footboards, control panels, tables and lockers was evaluated. Th...