The BABAR Collaboration BABAR, the detector for the SLAC PEP-II asymmetric e + e − B Factory operating at the Υ (4S) resonance, was designed to allow comprehensive studies of CP -violation in B-meson decays. Charged particle tracks are measured in a multi-layer silicon vertex tracker surrounded by a cylindrical wire drift chamber. Electromagnetic showers from electrons and photons are detected in an array of CsI crystals located just inside the solenoidal coil of a superconducting magnet. Muons and neutral hadrons are identified by arrays of resistive plate chambers inserted into gaps in the steel flux return of the magnet. Charged hadrons are identified by dE/dx measurements in the tracking detectors and in a ring-imaging Cherenkov detector surrounding the drift chamber. The trigger, data acquisition and data-monitoring systems , VME-and network-based, are controlled by custom-designed online software. Details of the layout and performance of the detector components and their associated electronics and software are presented.

DNA microarrays encompassing the entire genome of Yersinia pestis were used to characterize global regulatory changes during steady-state vegetative growth occurring after shift from 26 to 37°C in the presence and absence of Ca 2؉ . Transcriptional profiles revealed that 51, 4, and 13 respective genes and open reading frames (ORFs) on pCD, pPCP, and pMT were thermoinduced and that the majority of these genes carried by pCD were downregulated by Ca 2؉ . In contrast, Ca 2؉ had little effect on chromosomal genes and ORFs, of which 235 were thermally upregulated and 274 were thermally downregulated. The primary consequence of these regulatory events is profligate catabolism of numerous metabolites available in the mammalian host.Bubonic plague caused by Yersinia pestis is generally recognized as the most devastating acute infectious disease experienced by mankind. It is therefore of interest that this organism has evolved within the last 10,000 years from Yersinia pseudotuberculosis (1), known to cause chronic enteropathogenic disease. Despite their very close resemblance, plague bacilli have both lost central genes of intermediary metabolism retained in its predecessor and acquired unique genes by lateral transfer (7). For example, even though early studies showed that Y. pestis possesses functional Embden-Meyerhof (28) and Entner-Doudoroff (20) pathways plus a complete tricarboxylic acid (TCA) cycle (13, 27), the species-specific absence of detectable glucose 6-phosphate dehydrogenase (Zwf) prevents use of hexose via the pentose-phosphate pathway (21). Similarly, loss of aspartase (AspA) activity in Y. pestis but not Y. pseudotuberculosis prevents complete catabolism of L-glutamic acid, which undergoes conversion and excretion as L-aspartate (12). In addition, Y. pestis possesses additional species-specific mutations that cause nutritional requirements at 26°C, prevent utilization of potential metabolites, and eliminate host cell invasins and adhesins (7); these events are now characterized by genomic sequencing (11, 23). The nature of nutritional requirements at 37°C is more complex and, as noted below, dependent upon plasmid profile, the presence or absence of Ca 2ϩ , Na ϩ , dicarboxylic amino acids, and regulatory functions addressed in this report.Established functions unique to Y. pestis are encoded by species-specific ϳ10-kb pPCP and ϳ100-kb pMT. The former encodes plasminogen activator (Pla) required for tissue invasion from dermal sites infected by fleabite whereas the structural genes for anti-phagocytic capsular fraction 1 (Caf1) and murine toxin (MT), required for survival in the flea, reside on pMT (7,25). Plague bacilli and the enteropathogenic yersiniae share a ϳ70-kb plasmid (pCD in Y. pestis) encoding a type III protein secretion system (TTSS) that delivers cytotoxins termed Yops to the cytosol of professional and nonprofessional phagocytes (8) and excretes soluble LcrV (V antigen), which inhibits generation of proinflammatory cytokines by upregulating interleukin-10 (6). These functions provide th...

Rapid advances in the genomic sequencing of bacteria and viruses over the past few years have made it possible to consider sequencing the genomes of all pathogens that affect humans and the crops and livestock upon which our lives depend. Recent events make it imperative that full genome sequencing be accomplished as soon as possible for pathogens that could be used as weapons of mass destruction or disruption. This sequence information must be exploited to provide rapid and accurate diagnostics to identify pathogens and distinguish them from harmless near-neighbours and hoaxes. The Chem-Bio Non-Proliferation (CBNP) programme of the US Department of Energy (DOE) began a large-scale effort of pathogen detection in early 2000 when it was announced that the DOE would be providing bio-security at the 2002 Winter Olympic Games in Salt Lake City, Utah. Our team at the Lawrence Livermore National Lab (LLNL) was given the task of developing reliable and validated assays for a number of the most likely bioterrorist agents. The short timeline led us to devise a novel system that utilised whole-genome comparison methods to rapidly focus on parts of the pathogen genomes that had a high probability of being unique. Assays developed with this approach have been validated by the Centers for Disease Control (CDC). They were used at the 2002 Winter Olympics, have entered the public health system, and have been in continual use for non-publicised aspects of homeland defence since autumn 2001. Assays have been developed for all major threat list agents for which adequate genomic sequence is available, as well as for other pathogens requested by various government agencies. Collaborations with comparative genomics algorithm developers have enabled our LLNL team to make major advances in pathogen detection, since many of the existing tools simply did not scale well enough to be of practical use for this application. It is hoped that a discussion of a real-life practical application of comparative genomics algorithms may help spur algorithm developers to tackle some of the many remaining problems that need to be addressed. Solutions to these problems will advance a wide range of biological disciplines, only one of which is pathogen detection. For example, exploration in evolution and phylogenetics, annotating gene coding regions, predicting and understanding gene function and regulation, and untangling gene networks all rely on tools for aligning multiple sequences, detecting gene rearrangements and duplications, and visualising genomic data. Two key problems currently needing improved solutions are: (1) aligning incomplete, fragmentary sequence (eg draft genome contigs or arbitrary genome regions) with both complete genomes and other fragmentary sequences; and (2) ordering, aligning and visualising non-colinear gene rearrangements and inversions in addition to the colinear alignments handled by current tools.

A PCR-based genotyping system that detects divergence of IS100 locations within the Yersinia pestis genome was used to characterize a large collection of isolates of different biovars and geographical origins. Using sequences derived from the glycerol-negative biovar orientalis strain CO92, a set of 27 locus-specific primers was designed to amplify fragments between the end of IS100 and its neighboring gene. Geographically diverse members of the orientalis biovar formed a homogeneous group with identical genotype with the exception of strains isolated in Indochina. Yersinia pestis, the causative agent of bubonic plague, is a recently evolved clone of Yersinia pseudotuberculosis serotype O:1b (1, 29). Strains of Y. pestis are divided into three biovars on the basis of their abilities to ferment glycerol and to reduce nitrate. These phenotypic differences have proven useful in distinguishing strains thought to be responsible for the three plague pandemics (7). Isolates of the biovar antiqua (able to ferment glycerol and reduce nitrate) are believed to remain as holdovers from the first pandemic that started with the Justinian plague of the 6th century. Strains of the biovar medievalis (glycerol positive and nitrate negative) evidently caused the second pandemic of Europe (Black Death), which was initiated during the 14th century, and strains of the biovar orientalis (glycerol negative and nitrate positive) are responsible for the third plague pandemic of modern times (15,22).Several molecular methods that generate fingerprinting patterns of Y. pestis DNA have been successfully used for genotyping strains of this microorganism, such as pulse-field gel electrophoresis and ribotyping (15,16,18,25) as well as newly described variable-number tandem repeat analysis (2). Genotyping of Y. pestis was also accomplished by restriction fragment length polymorphism (RFLP) detected on Southern blots using probes originating from IS100, which is found at least singly on each of the three plasmids of the species and as multiple copies within the chromosome (24). This insertion sequence (IS) element was sequenced (11, 23) and then used by Filippov et al. (9) in conjunction with the novel IS285 to obtain fingerprint patterns establishing phylogenetic relationships. Further IS100-and IS285-based RFLP analysis became the method of choice used by many researchers for extensive analysis of Y. pestis collections (1,5,14,20). Finally, a third insertion sequence (IS1541) was discovered that disrupts inv, which encodes invasin (28). This element is now known to be present in many copies in the Y. pestis genome and has also been used to obtain RFLP fingerprinting profiles (21, 28).Many insertions of IS1541 in the genome of Y. pestis strain 6/69 M biovar orientalis were characterized and then tested to see if the insert flanked the same genes in other strains of Y. pestis (21). The authors employed five unrelated strains (four of biovar orientalis and one of medievalis) of different ribotypes and IS1541 hybridization patterns that were isol...

There has been a significant increase, fueled by technologies from the human genome project, in the availability of nucleic acid sequence information for viruses and bacteria. This paper presents a computer-assisted process that begins with nucleic acid sequence information and produces highly specific pathogen signatures. When combined with instrumentation using the polymerase chain reaction, the resulting diagnostics are both specific and sensitive. The computational and engineering aspects of converting raw sequence data into pathogen-specific and instrument-ready assays are presented. Examples and data are presented for specific pathogens, including foot-and-mouth disease virus and the human immunodeficiency virus.