Bioterrorism and biodefence research: changing the focus of microbiology

The Coxiella burnetii QpH1 plasmid is a virulence factor for colonizing bone marrow-derived murine macrophages

Coxiella burnetii strains carry one of four large, conserved, autonomously replicating plasmids (QpH1, QpRS, QpDV, and QpDG) or a QpRS-like chromosomally integrated sequence of unknown function. Here we report the characterization of the QpH1 plasmid of C. burnetii Nine Mile phase II by making QpH1-deficient strains. A shuttle vector pQGK containing the CBUA0036-0039a region (predicted as being required for the QpH1 maintenance) was constructed. The pQGK vector can be stably transformed into the Nine Mile II and maintained at a similar low copy like QpH1. Importantly, transformation with pQGK cured the endogenous QpH1 due to plasmid incompatibility. Compared to a Nine Mile II transformant of a RSF1010-ori based vector, the pQGK transformant shows a similar growth curve in both axenic media and Buffalo green monkey kidney cells, a variable growth defect in macrophage-like THP-1 cells depending on the origin of inoculum, and dramatically reduced ability of colonizing wild-type bone marrow-derived murine macrophages. Furthermore, we found CBUA0037-0039 ORFs are essential for plasmid maintenance, and CBUA0037-0038 ORFs account for plasmid compatibility. And plasmid-deficient C. burnetii can be isolated by using CBUA0037 or -0038 deletion vectors. Furthermore, QpH1-deficient C. burnetii strains caused a lesser extent of splenomegaly in SCID mice but, intriguingly, they had significant growth in SCID mouse-sourced macrophages. Taken together, our data suggest that QpH1 encodes factor(s) essential for colonizing murine, not human, macrophages. This study suggests a critical role of QpH1 for C. burnetii persistence in rodents and expands the toolkit for the genetic studies in C. burnetii Author summary All C. burnetii isolates carry one of four large, conserved, autonomously replicating plasmids or a plasmid-like chromosomally integrated sequence. The plasmid is a candidate virulence factor of unknown function. Here we describe the construction of novel shuttle vectors that allow making plasmid-deficient C. burnetii mutants. With this plasmid-curing approach, we characterized the role of the QpH1 plasmid in in vitro and in vivo C. burnetii infection models. We found that the plasmid plays a critical role for C. burnetii growth in murine macrophages. Our work suggests an essential role of the QpH1 plasmid for the acquisition of colonizing capability in rodents by C. burnetii This study represents a major step toward unravelling the mystery of the C. burnetii cryptic plasmids.

Nanowire-Based Biosensors: From Growth to Applications

Over the past decade, synthesized nanomaterials, such as carbon nanotube, nanoparticle, quantum dot, and nanowire, have already made breakthroughs in various fields, including biomedical sensors. Enormous surface area-to-volume ratio of the nanomaterials increases sensitivity dramatically compared with macro-sized material. Herein we present a comprehensive review about the working principle and fabrication process of nanowire sensor. Moreover, its applications for the detection of biomarker, virus, and DNA, as well as for drug discovery, are reviewed. Recent advances including self-powering, reusability, sensitivity in high ionic strength solvent, and long-term stability are surveyed and highlighted as well. Nanowire is expected to lead significant improvement of biomedical sensor in the near future.

Nanowire-Based Sensors for Biological and Medical Applications

Nanomaterials such as nanowires, carbon nanotubes, and nanoparticles have already led to breakthroughs in the field of biological and medical sensors. The quantum size effects of the nanomaterials and their similarity in size to natural and synthetic nanomaterials are anticipated to improve sensor sensitivity dramatically. Nanowires are considered as key nanomaterials because of their electrical controllability for accurate measurement, and chemical-friendly surface for various sensing applications. This review covers the working principles and fabrication of silicon nanowire sensors. Furthermore, we review their applications for the detection of viruses, biomarkers, and DNA, as well as for drug discovery. Advances in the performance and functionality of nanowire sensors are also surveyed to highlight recent progress in this area. These advances include the improvements in reusability, sensitivity in high ionic strength solvent, long-term stability, and self-powering. Overall, with the advantages of ultra-sensitivity and the ease of fabrication, it is expected that nanowires will contribute significantly to the development of biological and medical sensors in the immediate future.

Detection of airborne viruses using electro-aerodynamic deposition and a field-effect transistor

We report a technique for the detection of aerosolized viruses. Conventional field-effect-transistor (FET)-based techniques use solution-based processes, thus require antibody binding to the detection region of the FET prior to the supply of the analyte. With the method described here, virus-antibody-bound particles are delivered to the FET during detection; therefore, neither a pre-treatment antibody binding step on the FET channel nor washing process for virus-antibody-binding are necessary. Our method is based on the concept that virus-antibody-bound particles are larger than the virus or antibody alone, and thus have larger charge numbers following aerosol charging. When these particles are charged by negative ions and electro-aerodynamically deposited on a substrate, there exists a location on the substrate where neither lone virus nor antibody particles land, and where only virus-antibody-bound particles are deposited. If this location coincides with the channel of the FET, the resulting variation in the current can be used to indicate the existence of a virus. By aerosolizing a mixed solution of the virus and the antibody, only the virus-antibody-bound particles were transported to the swCNT-FET, and the electric current in the swCNT-FET decreased to 30% of that measured with no deposited particles.

Bio-nanogate controlled enzymatic reaction for virus sensing

The objective of this study was to develop an aptamer-based bifunctional bio-nanogate, which could selectively respond to target molecules, and control enzymatic reaction for electrochemical measurements. It was successfully applied for sensitive, selective, rapid, quantitative, and label-free detection of avian influenza viruses (AIV) H5N1. A nanoporous gold film with pore size of ~20 nm was prepared by a metallic corrosion method, and the purity was checked by energy-dispersive X-ray spectroscopy (EDS) study. To improve the performance of the bio-nanogate biosensor, its main analytical parameters were studied and optimized. We demonstrated that the developed bio-nanogate was capable of controlling enzymatic reaction for AIV H5N1 sensing within 1h with a detection limit of 2(-9)HAU (hemagglutination units). The enzymatic reaction was able to cause significant current change due to the presence of target AIV. A linear relationship was found in the virus titer range of 2(-10)-2(2)HAU. No interference was observed from non-target AIV subtypes such as H1N1, H2N2, H4N8 and H7N2. The developed approach could be adopted for sensing of other viruses.

The ethics of disseminating dual-use knowledge

In 2011, for the first time ever, two scientific journals were asked not to publish research papers in full detail. The research in question was on the H5N1 influenza virus (bird flu), and the concern was that the expected public health benefits of disseminating the findings did not outweigh the potential harm should the knowledge be misused for malicious purposes. This constraint raises important ethical concerns as it collides with scientific freedom and openness. In this article, we argue that constraining the dissemination of dual-use knowledge can in certain cases be justified because, for example: scientists have a responsibility for potentially harmful consequences of their research; the public need not always know of all scientific discoveries; uncertainty about the risks of harm may warrant precaution; and expected benefits do not always outweigh potential harm. However, the constraints in question are not absolute but can be both temporary and partial. We propose three core aspects for an ethics of dual-use dissemination: dual-use awareness, precaution, and acknowledgment of conflicting values. Additionally, to help scientists understand when constraints on dissemination may be justified we suggest three corresponding conditions that prompt scientists to recognize dual-use material or research, consider the potential impact of dual-use knowledge dissemination, and acknowledge and respond to external dissemination concerns.

Comparison of trends in the quantity and variety of Science Citation Index (SCI) literature on human pathogens between China and the United States

The proportion of pathogenic microorganisms in the microbial world is relatively small, while their threat to human health, economic development and social stability is severe. The quantity and variation of Science Citation Index (SCI) literature related to pathogenic microorganisms may reflect the level of relevant research and the degree of attention. Here we compared trends in the quantity and variety of SCI literature relating to certain important pathogenic microorganisms published by scientists from United States and China from 1996 to 2010 by searching the Science Citation Index database. The pathogenic microorganisms in this study comprise two categories of pathogens: Bacillus anthracis, Yersinia pestis, Francisella tularensis, Ebola virus, Burkholderia pseudomallei, which belong to biodefense-associated pathogens (BDAPs) and the human immunodeficiency virus (HIV), SARS coronavirus, hepatitis B virus (HBV), Mycobacterium tuberculosis, influenza virus, which belong to the commonly encountered health-threatening pathogens. Our results showed that the United States (US) published much more SCI literature on these pathogens than China. Furthermore, literature on BDAPs published by scientists from the US has increased sharply since 2002. However, the numbers of literature relating to CEHTPs from China has demonstrated a gradual increase from 1996 to 2010. Research into pathogenic microorganisms requires three balance to be achieved: investment in BDAP and CEHTP studies; basic and applied research; a faster pace of research into pathogens and fulfilling biosafety and biosecurity requirements.

Advances in genetic manipulation of obligate intracellular bacterial pathogens

Infections by obligate intracellular bacterial pathogens result in significant morbidity and mortality worldwide. These bacteria include Chlamydia spp., which causes millions of cases of sexually transmitted disease and blinding trachoma annually, and members of the α-proteobacterial genera Anaplasma, Ehrlichia, Orientia, and Rickettsia, agents of serious human illnesses including epidemic typhus. Coxiella burnetii, the agent of human Q fever, has also been considered a prototypical obligate intracellular bacterium, but recent host cell-free (axenic) growth has rescued it from obligatism. The historic genetic intractability of obligate intracellular bacteria has severely limited molecular dissection of their unique lifestyles and virulence factors involved in pathogenesis. Host cell restricted growth is a significant barrier to genetic transformation that can make simple procedures for free-living bacteria, such as cloning, exceedingly difficult. Low transformation efficiency requiring long-term culture in host cells to expand small transformant populations is another obstacle. Despite numerous technical limitations, the last decade has witnessed significant gains in genetic manipulation of obligate intracellular bacteria including allelic exchange. Continued development of genetic tools should soon enable routine mutation and complementation strategies for virulence factor discovery and stimulate renewed interest in these refractory pathogens. In this review, we discuss the technical challenges associated with genetic transformation of obligate intracellular bacteria and highlight advances made with individual genera.

Evidence for widespread epithelial damage and coincident production of monocyte chemotactic protein 1 in a murine model of intestinal ricin intoxication

The development of small-animal models is necessary to understand host responses and immunity to emerging infectious diseases and potential bioterrorism agents. In this report we have characterized a murine model of intestinal ricin intoxication. Ricin administered intragastrically (i.g.) to BALB/c mice at doses ranging from 1 to 10 mg/kg of body weight induced dose-dependent morphological changes in the proximal small intestine (i.e., duodenum), including widespread villus atrophy and epithelial damage. Coincident with epithelial damage was a localized increase in monocyte chemotactic protein 1, a chemokine known to be associated with inflammation of the intestinal mucosa. Immunity to intestinal ricin intoxication was achieved by immunizing mice i.g. with ricin toxoid and correlated with elevated levels of antitoxin mucosal immunoglobulin A (IgA) and serum IgG antibodies. We expect that this model will serve as a valuable tool in identifying the inflammatory pathways and protective immune responses that are elicited in the intestinal mucosa following ricin exposure and will prove useful in the evaluation of antitoxin vaccines and therapeutics.

Identification of differentially activated cell-signaling networks associated with pichinde virus pathogenesis by using systems kinomics

Phosphorylation plays a key role in regulating many signaling pathways. Although studies investigating the phosphorylated forms of signaling pathways are now commonplace, global analysis of protein phosphorylation and kinase activity has lagged behind genomics and proteomics. We have used a kinomics approach to study the effect of virus infection on host cell signaling in infected guinea pigs. Delineating the host responses which lead to clearance of a pathogen requires the use of a matched, comparative model system. We have used two passage variants of the arenavirus Pichinde, used as a biosafety level 2 model of Lassa fever virus as it produces similar pathologies in guinea pigs and humans, to compare the host cell responses between infections which lead to either a mild, self-limiting infection or lethal disease. Using this model, we can begin to understand the differences in signaling events which give rise to these markedly different outcomes. By contextualizing these data using pathway analysis, we have identified key differences in cellular signaling matrices. By comparing these differentially involved networks, we have identified a number of key signaling "nodes" which show differential phosphorylations between mild and lethal infections. We believe that these nodes provide potential targets for the development of antiviral therapies by acting at the level of the host response rather than by directly targeting viral proteins.

Nanowire sensors for medicine and the life sciences

The interface between nanosystems and biosystems is emerging as one of the broadest and most dynamic areas of science and technology, bringing together biology, chemistry, physics and many areas of engineering, biotechnology and medicine. The combination of these diverse areas of research promises to yield revolutionary advances in healthcare, medicine and the life sciences through, for example, the creation of new and powerful tools that enable direct, sensitive and rapid analysis of biological and chemical species, ranging from the diagnosis and treatment of disease to the discovery and screening of new drug molecules. Devices based on nanowires are emerging as a powerful and general platform for ultrasensitive, direct electrical detection of biological and chemical species. Here, representative examples where these new sensors have been used for detection of a wide-range of biological and chemical species, from proteins and DNA to drug molecules and viruses, down to the ultimate level of a single molecule, are discussed. Moreover, how advances in the integration of nanoelectronic devices enable multiplexed detection and thereby provide a clear pathway for nanotechnology, enabling diverse and exciting applications in medicine and life sciences, are highlighted.

Vaccines against the category B toxins: Staphylococcal enterotoxin B, epsilon toxin and ricin

The threat of bioterrorism worldwide has accelerated the demand for the development of therapies and vaccines against the Category B toxins: staphylococcal enterotoxin B (SEB), epsilon toxin (ETX) produced by Clostridium perfringens types B and D, and ricin, a natural product of the castor bean. The diverse and unique nature of these toxins poses a challenge to vaccinologists. While formalin-inactivated toxins can successfully induce antibody-mediated protection in animals, their usefulness in humans is limited because of potential safety concerns. For this reason, research is now aimed at developing recombinant, attenuated vaccines based on a detailed understanding of the molecular mechanisms by which these toxins function. Vaccine development is further complicated by the fact that as bioterrorism agents, SEB, ETX and ricin would most likely be disseminated as aerosols or in food/water supplies. Our understanding of the mechanisms by which these toxins cross mucosal surfaces, and importance of mucosal immunity in preventing toxin uptake is only rudimentary.

Electrical detection of single viruses

We report direct, real-time electrical detection of single virus particles with high selectivity by using nanowire field effect transistors. Measurements made with nanowire arrays modified with antibodies for influenza A showed discrete conductance changes characteristic of binding and unbinding in the presence of influenza A but not paramyxovirus or adenovirus. Simultaneous electrical and optical measurements using fluorescently labeled influenza A were used to demonstrate conclusively that the conductance changes correspond to binding/unbinding of single viruses at the surface of nanowire devices. pH-dependent studies further show that the detection mechanism is caused by a field effect, and that the nanowire devices can be used to determine rapidly isoelectric points and variations in receptor-virus binding kinetics for different conditions. Lastly, studies of nanowire devices modified with antibodies specific for either influenza or adenovirus show that multiple viruses can be selectively detected in parallel. The possibility of large-scale integration of these nanowire devices suggests potential for simultaneous detection of a large number of distinct viral threats at the single virus level.

A genomics-based approach to biodefence preparedness

Since October 2001, the United States has greatly expanded its commitment to biodefence-related research, with $1.75 billion earmarked for this activity in fiscal year 2003.

The goals of this accelerated research and development effort are to understand better the biology of potential bioterror agents and to use this information in the development of new diagnostics, antibiotics and vaccines to protect the world's population against bioterrorism.

Genomics, proteomics and bioinformatics approaches are considered to be key enabling technologies in the development of these new products.

Genome sequence data for all of the principal human pathogens, including most of the potential bioterror agents on the Center for Disease Control and Prevention (CDC) category A–C lists, are available in public databases and provide a new foundation for follow-up studies.

Comparative genomics approaches, together with large-scale methods for studying gene function, such as DNA microarrays, are providing insights into the molecular basis and evolution of pathogenicity, diversity within closely related isolates of the same pathogen and the molecular determinants of host–pathogen interactions.

Genomics-based approaches have already proven to be of great use in the identification of new targets for antimicrobial compounds and in the identification of new vaccine candidates.

Comparative genomics is also providing important information on the natural variability between closely related isolates that is aiding in the development of the new field of microbial forensics.

The anthrax letter attacks in October 2001, followed by the SARS outbreak in early 2003, dramatically illustrated our vulnerability to both deliberate and natural outbreaks of infectious disease. The availability of pathogen genome sequences and high-throughput methods for studying the biology of both pathogens and their hosts have provided new insights into the mechanisms of pathogenesis and host defence. As infectious disease research expands to include major bioterror agents, genomics-based approaches will provide one of the cornerstones of efforts to develop more accurate diagnostics, new therapeutics and vaccines, and further capabilities for microbial forensics.