The infectious diseases that shaped usPlagues Upon the Earth Kyle Harper Princeton University Press, 2021. 704 pp.

An ambitious history traces humanity's entanglements with communicable illness.

Breath Acetone Sensing Based on Single-Walled Carbon Nanotube-Titanium Dioxide Hybrids Enabled by a Custom-Built Dehumidifier.

Acetone is a metabolic byproduct found in the exhaled breath and can be measured to monitor the metabolic degree of ketosis. In this state, the body uses free fatty acids as its main source of fuel because there is limited access to glucose. Monitoring ketosis is important for type I diabetes patients to prevent ketoacidosis, a potentially fatal condition, and individuals adjusting to a low-carbohydrate diet. Here, we demonstrate that a chemiresistor fabricated from oxidized single-walled carbon nanotubes functionalized with titanium dioxide (SWCNT@TiO2) can be used to detect acetone in dried breath samples. Initially, due to the high cross sensitivity of the acetone sensor to water vapor, the acetone sensor was unable to detect acetone in humid gas samples. To resolve this cross-sensitivity issue, a dehumidifier was designed and fabricated to dehydrate the breath samples. Sensor response to the acetone in dried breath samples from three volunteers was shown to be linearly correlated with the two other ketone bodies, acetoacetic acid in urine and ß-hydroxybutyric acid in the blood. The breath sampling and analysis methodology had a calculated acetone detection limit of 1.6 ppm and capable of detecting up to at least 100 ppm of acetone, which is the dynamic range of breath acetone for someone with ketosis. Finally, the application of the sensor as a breath acetone detector was studied by incorporating the sensor into a handheld prototype breathalyzer.

What is a virus species? Radical pluralism in viral taxonomy.

Early attempts in the 1960s at constructing a classification scheme for viruses were phenetic and focused on structural properties of the virion. Over time, the International Committee on the Taxonomy of Viruses (ICTV) has refined its definition of a virus species to include an appeal to evolutionary history. The current ICTV definition defines a viral species in terms of monophyly. The existence of prolific horizontal genetic transfer (HGT) among various groups of viruses presents a challenge to this definition. I argue that the proper response to this mode of evolution is to allow for radical pluralism. Some viruses can be members of more than one species; others don't form species at all and should be classified using new reticulate categories.

Using Ethical Reasoning to Amplify the Reach and Resonance of Professional Codes of Conduct in Training Big Data Scientists.

The use of Big Data--however the term is defined--involves a wide array of issues and stakeholders, thereby increasing numbers of complex decisions around issues including data acquisition, use, and sharing. Big Data is becoming a significant component of practice in an ever-increasing range of disciplines; however, since it is not a coherent "discipline" itself, specific codes of conduct for Big Data users and researchers do not exist. While many institutions have created, or will create, training opportunities (e.g., degree programs, workshops) to prepare people to work in and around Big Data, insufficient time, space, and thought have been dedicated to training these people to engage with the ethical, legal, and social issues in this new domain. Since Big Data practitioners come from, and work in, diverse contexts, neither a relevant professional code of conduct nor specific formal ethics training are likely to be readily available. This normative paper describes an approach to conceptualizing ethical reasoning and integrating it into training for Big Data use and research. Our approach is based on a published framework that emphasizes ethical reasoning rather than topical knowledge. We describe the formation of professional community norms from two key disciplines that contribute to the emergent field of Big Data: computer science and statistics. Historical analogies from these professions suggest strategies for introducing trainees and orienting practitioners both to ethical reasoning and to a code of professional conduct itself. We include two semester course syllabi to strengthen our thesis that codes of conduct (including and beyond those we describe) can be harnessed to support the development of ethical reasoning in, and a sense of professional identity among, Big Data practitioners.

Ludwik Gross, Sarah Stewart, and the 1950s discoveries of Gross murine leukemia virus and polyoma virus.

The Polish-American scientist Ludwik Gross made two important discoveries in the early 1950s. He showed that two viruses - murine leukemia virus and parotid tumor virus - could cause cancer when they were injected into susceptible animals. At first, Gross's discoveries were greeted with skepticism: it seemed implausible that viruses could cause a disease as complex as cancer. Inspired by Gross's initial experiments, similar results were obtained by Sarah Stewart and Bernice Eddy who later renamed the parotid tumor virus SE polyoma virus after finding it could cause many different types of tumors in mice, hamsters, and rats. Eventually the "SE" was dropped and virologists adopted the name "polyoma virus." After Gross's work was published, additional viruses capable of causing solid tumors or blood-borne tumors in mice were described by Arnold Graffi, Charlotte Friend, John Moloney and others. By 1961, sufficient data had been accumulated for Gross to confidently publish an extensive monograph--Oncogenic Viruses--the first history of tumor virology, which became a standard reference work and marked the emergence of tumor virology as a distinct, legitimate field of study.

Sensing Reversible Protein-Ligand Interactions with Single-Walled Carbon Nanotube Field-Effect Transistors.

We report on the reversible detection of CaptAvidin, a tyrosine modified avidin, with single-walled carbon nanotube (SWNT) field-effect transistors (FETs) noncovalently functionalized with biotin moieties using 1-pyrenebutyric acid as a linker. Binding affinities at different pH values were quantified, and the sensor's response at various ionic strengths was analyzed. Furthermore, protein "fingerprints" of NeutrAvidin and streptavidin were obtained by monitoring their adsorption at several pH values. Moreover, gold nanoparticle decorated SWNT FETs were functionalized with biotin using 1-pyrenebutyric acid as a linker for the CNT surface and (±)-α-lipoic acid linkers for the gold surface, and reversible CaptAvidin binding is shown, paving the way for potential dual mode measurements with the addition of surface enhanced Raman spectroscopy (SERS).

Carbon nanotube chemiresistor for wireless pH sensing.

The ability to accurately measure real-time pH fluctuations in-vivo could be highly advantageous. Early detection and potential prevention of bacteria colonization of surgical implants can be accomplished by monitoring associated acidosis. However, conventional glass membrane or ion-selective field-effect transistor (ISFET) pH sensing technologies both require a reference electrode which may suffer from leakage of electrolytes and potential contamination. Herein, we describe a solid-state sensor based on oxidized single-walled carbon nanotubes (ox-SWNTs) functionalized with the conductive polymer poly(1-aminoanthracene) (PAA). This device had a Nernstian response over a wide pH range (2-12) and retained sensitivity over 120 days. The sensor was also attached to a passively-powered radio-frequency identification (RFID) tag which transmits pH data through simulated skin. This battery-less, reference electrode free, wirelessly transmitting sensor platform shows potential for biomedical applications as an implantable sensor, adjacent to surgical implants detecting for infection.

After the double helix: Rosalind Franklin's research on Tobacco mosaic virus.

Rosalind Franklin is best known for her informative X-ray diffraction patterns of DNA that provided vital clues for James Watson and Francis Crick's double-stranded helical model. Her scientific career did not end when she left the DNA work at King's College, however. In 1953 Franklin moved to J. D. Bernal's crystallography laboratory at Birkbeck College, where she shifted her focus to the three-dimensional structure of viruses, obtaining diffraction patterns of Tobacco mosaic virus (TMV) of unprecedented detail and clarity. During the next five years, while making significant headway on the structural determination of TMV, Franklin maintained an active correspondence with both Watson and Crick, who were also studying aspects of virus structure. Developments in TMV research during the 1950s illustrate the connections in the emerging field of molecular biology between structural studies of nucleic acids and of proteins and viruses. They also reveal how the protagonists of the "race for the double helix" continued to interact personally and professionally during the years when Watson and Crick's model for the double-helical structure of DNA was debated and confirmed.

Why there was a useful plausible analogy between geodesic domes and spherical viruses.

In 1962, Donald Caspar and Aaron Klug published their classic theory of virus structure. They developed their theory with an explicit analogy between spherical viruses and Buckminster Fuller's geodesic domes. In this paper, I use the spherical virus-geodesic dome case to develop an account of analogy and deductive analogical inference based on the notion of an isomorphism. I also consider under what conditions there is a good reason to claim an experimentally untested analogy is plausible.

Virus design, 1955-1962: science meets art.

ABSTRACT This paper traces the beginnings of structural virology in the mid-20th century, focusing especially on the synergy between models of virus structure and models within art, notably Buckminster Fuller's geodesic domes and Kenneth Snelson's tensegrity structures. As Donald Caspar and Aaron Klug sought to extend the Crick-Watson theory of spherical virus structure, they explored analogies between biology and architecture, eventually publishing the classic Caspar-Klug theory of virus structure in 1962.

Historical review: viruses, crystals and geodesic domes.

In the mid 1950s, Francis Crick and James Watson attempted to explain the structure of spherical viruses. They hypothesized that spherical viruses consist of 60 identical equivalently situated subunits. Such an arrangement has icosahedral symmetry. Subsequent biophysical and electron micrographic data suggested that many viruses had >60 subunits. Drawing inspiration from architecture, Donald Caspar and Aaron Klug discovered a solution to the problem - they proposed that spherical viruses were structured like miniature geodesic domes.

Bacteriophage Mu genome sequence: analysis and comparison with Mu-like prophages in Haemophilus, Neisseria and Deinococcus.

We report the complete 36,717 bp genome sequence of bacteriophage Mu and provide an analysis of the sequence, both with regard to the new genes and other genetic features revealed by the sequence itself and by a comparison to eight complete or nearly complete Mu-like prophage genomes found in the genomes of a diverse group of bacteria. The comparative studies confirm that members of the Mu-related family of phage genomes are genetically mosaic with respect to each other, as seen in other groups of phages such as the phage lambda-related group of phages of enteric hosts and the phage L5-related group of mycobacteriophages. Mu also possesses segments of similarity, typically gene-sized, to genomes of otherwise non-Mu-like phages. The comparisons show that some well-known features of the Mu genome, including the invertible segment encoding tail fiber sequences, are not present in most members of the Mu genome sequence family examined here, suggesting that their presence may be relatively volatile over evolutionary time. The head and tail-encoding structural genes of Mu have only very weak similarity to the corresponding genes of other well-studied phage types. However, these weak similarities, and in some cases biochemical data, can be used to establish tentative functional assignments for 12 of the head and tail genes. These assignments are strongly supported by the fact that the order of gene functions assigned in this way conforms to the strongly conserved order of head and tail genes established in a wide variety of other phages. We show that the Mu head assembly scaffolding protein is encoded by a gene nested in-frame within the C-terminal half of another gene that encodes the putative head maturation protease. This is reminiscent of the arrangement established for phage lambda.