Bioagent Sample Matching using Elemental Composition Data: an Approach to Validation

Sample matching is a fundamental capability that can have high probative value in a forensic context if proper validation studies are performed. In this report we discuss the potential utility of using the elemental composition of two bioagent samples to decide if they were produced in the same batch, or by the same process. Using guidance from the recent NRC study of bullet lead analysis and other sources, we develop a basic likelihood ratio framework for evaluating the evidentiary weight of elemental analysis data for sample matching. We define an objective metric for comparing two samples, and propose a method for constructing an unbiased population of test samples. We illustrate the basic methodology with some existing data on dry Bacillus thuringiensis preparations, and outline a comprehensive plan for experimental validation of this approach

A validation framework for microbial forensic methods based on statistical pattern recognition

This report discusses a general approach to validating microbial forensic methods that attempt to simultaneously distinguish among many hypotheses concerning the manufacture of a questioned biological agent sample. It focuses on the concrete example of determining growth medium from chemical or molecular properties of a bacterial agent to illustrate the concepts involved

Resolution in forensic microbial genotyping

Resolution is a key parameter for differentiating among the large number of strain typing methods that could be applied to pathogens involved in bioterror events or biocrimes. In this report we develop a first-principles analysis of strain typing resolution using a simple mathematical model to provide a basis for the rational design of microbial typing systems for forensic applications. We derive two figures of merit that describe the resolving power and phylogenetic depth of a strain typing system. Rough estimates of these figures-of-merit for MLVA, MLST, IS element, AFLP, hybridization microarrays, and other bacterial typing methods are derived from mutation rate data reported in the literature. We also discuss the general problem of how to construct a ''universal'' practical typing system that has the highest possible resolution short of whole-genome sequencing, and that is applicable with minimal modification to a wide range of pathogens

Terahertz quantum beats in molecular liquids

With ultrashort pulses of less than 100 fs it is possible to excite coherently several vibrational modes of polyatomic molecules simultaneously. The femtosecond time resolution of the experiment allows the study of pronounced high-frequency beat phenomena up to 10 THz. The frequency difference between vibrational modes separated by more than 300 cm−1 may be determined with high precision

A unified protocol for simultaneous extraction of DNA and proteins from archaeological dental calculus

Archaeological materials are a finite resource, and efforts should be made to minimize destructive analyses. This can be achieved by using protocols combining extraction of several types of biomolecules or microparticles, which decreases the material needed for analyses while maximizing the information yield. Archaeological dental calculus is a source of several different types of biomolecules, as well as microfossils, and can tell us about the human host, microbiome, diet, and even occupational activities. Here, we present a unified protocol allowing for simultaneous extraction of DNA and proteins from a single sample of archaeological dental calculus. We evaluate the protocol on dental calculus from six individuals from a range of time periods and estimated preservation states, and compare it against previously published DNA-only and protein-only protocols. We find that most aspects of downstream analyses are unaltered by the unified protocol, although minor shifts in the recovered proteome can be detected, such as a slight loss of hydrophilic proteins. Total protein recovery depends on both the amount of starting material and choice of extraction protocol, whereas total DNA recovery is significantly reduced using the unified protocol (mean 43%). Nevertheless, total DNA recovery from dental calculus is generally very high, and we found no differences in DNA fragment characteristics or taxonomic profile between the protocols. In conclusion, the unified protocol allows for simultaneous extraction of two complementary lines of biomolecular evidence from archaeological dental calculus without compromising downstream results, thereby minimizing the need for destructive analysis of this finite resource

Frequency agile OPO-based transmitters for multiwavelength DIAL

We describe a first generation mid-infrared transmitter with pulse-to- pulse frequency agility and both wide and narrow band capability. This transmitter was used to make multicomponent DIAL measurements in the field

Efficient Frequency Doubling at 399nm

We describe a high-power and narrow-linewidth laser source at 399nm useful for cooling and trapping of ytterbium atoms. A continuous-wave titanium-sapphire laser at 798nm is frequency doubled using a lithium triborate crystal in an enhancement cavity. Up to 1.0W of light at 399nm has been obtained from 1.3W of infrared light, with an efficiency of 80