Highly accurate classification of biological spores by culture medium for forensic attribution using multiple chemical signature types and machine learning.

Future proliferation of biological expertise and new technology may increasingly lower the difficulty to produce biological organisms for misuse. Rapid attribution of a biological attack is needed to quickly identify the person or lab responsible and prevent additional attacks by enabling the apprehension of suspects. Here, triplicate batches of Bacillus anthracis Sterne strain (BaSt) spores were grown in a total of seven amateur and professional media. Multiple orthogonal analytical signatures (peptides, metabolites, lipids by fatty acid methyl ester (FAME) analysis, bulk organic profile, and trace elements) were collected from the BaSt spores. The proteomics and metabolomics analyses identified promising attribution signature compounds that are unique to each of the seven production methods. In addition, while each of the signature types showed varying degrees of value individually for attributing BaSt spores to the culture medium used to prepare them, fusing results from all five signatures types to increase sourcing robustness and using a random forest sourcing algorithm yielded 100% hold-one-batch-out cross-validation classification accuracy and an average relative source probability for the correct source 5.5× higher than the most probable incorrect source. These preliminary results provide a proof-of-concept for the development of forensic examinations that can attribute biological agents to production methods for use in future investigations.

Analysis of complex DNA mixtures using massively parallel sequencing of SNPs with low minor allele frequencies.

DNA mixtures from 3 or more contributors have proven difficult to analyze using the current state-of-the-art method of short-tandem repeat (STR) amplification followed by capillary electrophoresis (CE). Here we analyze samples from both laboratory-defined mixtures and complex multi-contributor touch samples using a single nucleotide polymorphism (SNP) panel comprised of 2311 low-minor-allele-frequency loci, combined with massively parallel sequencing (MPS). This approach demonstrates that as many as 10 people can be identified in touch samples using a threshold of -Log P(RMNE) of 6, and a detection rate of 18-94 % across 10 different materials using a threshold of -Log P(RMNE) of 2. Thirty-two false positives were observed in 100 touch samples.

Estimating Individual Contributions to Complex DNA SNP Mixtures.

High-throughput sequencing (HTS) of large panels of single nucleotide polymorphisms (SNPs) provides an alternative or complimentary approach to short tandem repeats (STRs) panels for the analysis of complex DNA mixture forensic samples. For STRs, methods to estimate individual contribution concentrations compare capillary electrophoresis peak heights, peak areas, or HTS allele read counts within a mixture. This article introduces three approaches (mean, median, and slope methods) for estimating individual DNA contributions to forensic mixtures for HTS/massively parallel sequencing (MPS) SNP panels. For SNPs, the major:minor allele ratios or counts, unique to each contributor, were compared to estimate contributor proportion within the mixture using the mean, median, and slope intercept for these alleles. The estimates for these three methods were typically within 5% of planned experimental contributions for defined mixtures.

Ablation of porcine ligamentum flavum with Ho:YAG, q-switched Ho:YAG, and quadrupled Nd:YAG lasers.

BACKGROUND AND OBJECTIVES: Ligamentum flavum (LF) is a tough, rubbery connective tissue providing a portion of the ligamentous stability to the spinal column, and in its hypertrophied state forms a significant compressive pathology in degenerative spinal stenosis. The interaction of lasers and this biological tissue have not been thoroughly studied. Technological advances improving endoscopic surgical access to the spinal canal makes selective removal of LF using small, flexible tools such as laser-coupled fiber optics increasingly attractive for treatment of debilitating spinal stenosis. Testing was performed to assess the effect of Ho:YAG, Q-switched Ho:YAG, and frequency quadrupled Nd:YAG lasers on samples of porcine LF. The objective was to evaluate the suitability of these lasers for surgical removal of LF. STUDY DESIGN/MATERIALS AND METHODS: LF was resected from porcine spine within 2 hours of sacrifice and stored in saline until immediately prior to laser irradiation, which occurred within an additional 2 hours. The optical absorbance of a sample was measured over the spectral band from 190 to 2,360 nm both before and after dehydration. For the experiments using the Ho:YAG (λ = 2,080 nm, tp = 140 µs, FWHM) and Q-Switched Ho:YAG (λ = 2,080 nm, tp = 260 ns, FWHM) lasers, energy was delivered to the LF through a laser-fiber optic with 600 µm core and NA = 0.39. For the experiment using the frequency quadrupled Nd:YAG laser (λ = 266 nm, tp = 5 ns FWHM), rather than applying the laser energy through a laser-fiber, the energy was focused through an aperture and lens directly onto the LF. Five experiments were conducted to evaluate the effect of the given lasers on LF. First, using the Ho:YAG laser, the single-pulse laser-hole depth versus laser fluence was measured with the laser-fiber in direct contact with the LF (1 g force) and with a standoff distance of 1 mm between the laser-fiber face and the LF. Second, with the LF remaining in situ and the spine bisected along the coronal plane, the surface temperature of the LF was measured with an IR camera during irradiation with the Ho:YAG laser, with and without constant saline flush. Third, the mass loss was measured over the course of 450 Ho:YAG pulses. Fourth, hole depth and temperature were measured over 30 pulses of fixed fluence from the Ho:YAG and Q-Switched Ho:YAG lasers. Fifth, the ablation rate and surface temperature were measured as a function of fluence from the Nd:YAG laser. Several LF staining and hole-depth measurement techniques were also explored. RESULTS: Aside from the expected absorbance peaks corresponding to the water in the LF, the most significant peaks in absorbance were located in the spectral band from 190 to 290 nm and persisted after the tissue was dehydrated. In the first experiment, using the Ho:YAG laser and with the laser-fiber in direct contact with the LF, the lowest single-pulse fluence for which LF was visibly removed was 35 J/cm(2) . Testing was conducted at 6 fluences between 35 and 354 J/cm(2) . Over this range the single-pulse hole depth was shown to be near linear (R(2) = 0.9374, M = 1.6), ranging from 40 to 639 µm (N = 3). For the case where the laser-fiber face was displaced 1 mm from the LF surface, the lowest single-pulse fluence for which tissue was visibly removed was 72 J/cm(2) . Testing was conducted at 4 energy densities between 72 and 180 J/cm(2) . Over this range the single-pulse hole depth was shown to be near linear (R(2) = 0.8951, M = 1.4), ranging from 31 to 220 µm (N = 3). In the second experiment, with LF in situ, constant flushing with room temperature saline was shown to drastically reduce surface temperature during exposure to Ho:YAG at 5 Hz with the laser-fiber in direct contact with the LF. Without saline, over 1 minute of treatment with a per-pulse fluence of 141 mJ/cm(2) , the average maximum surface temperature measured 110°C. With 10 cc's of saline flushed over 1 minute and a per-pulse laser fluence of 212 mJ/cm(2) , the average maximum surface temperature was 35°C. In the third experiment, mass loss was shown to be linear over 450 pulses of 600 mJ from the Ho:YAG laser (212 J/cm(2) , direct contact, N = 4; 108 J/cm(2) , 1 mm standoff, N = 4). With the laser-fiber in direct contact, an average of 53 mg was removed (R(2) = 0.996, M = 0.117) and with 1 mm laser-fiber standoff, an average of 44 mg was removed (R(2) = 0.9988, M = 0.097). In the fourth experiment, 30 pulses of the Ho:YAG and Q-Switched Ho:YAG lasers at 1 mm standoff, and 5 Hz produced similar hole depths for the tested fluences of 9 J/cm(2) (151 and 154 µm, respectively) and 18 J/cm(2) (470 and 442 µm, respectively), though the Ho:YAG laser produced significantly more carbonization around the rim of the laser-hole. The increased carbonization was corroborated by higher measured LF temperature. In all tests with the Ho:YAG and Q-Switched Ho:YAG, an audible photo-acoustic affect coincided with the laser pulse. In the fifth experiment, with the frequency quadrupled Nd:YAG laser at 15 Hz for 450 pulses, ablation depth per pulse was shown to be linear for the fluence range of 0.18 - 0.73 J/cm(2) (R(2) = 0.989, M = 2.4). There was no noticeable photo-acoustic effect nor charring around the rim of the laser-hole. CONCLUSION: The Ho:YAG, Q-Switched Ho:YAG, and frequency quadrupled Nd:YAG lasers were shown to remove ligamentum flavum (LF). A single pulse of the Ho:YAG laser was shown to cause tearing of the tissue and a large zone of necrosis surrounding the laser-hole. Multiple pulses of the Ho:YAG and Q-Switched Ho:YAG lasers caused charring around the rim of the laser-hole, though the extent of charring was more extensive with the Ho:YAG laser. Charring caused by the Ho:YAG laser was shown to be mitigated by continuously flushing the affected LF with saline during irradiation. The Nd:YAG laser was shown to ablate LF with no gross visible indication of thermal damage to surrounding LF.

Broad-spectrum antiviral therapeutics.

Currently there are relatively few antiviral therapeutics, and most which do exist are highly pathogen-specific or have other disadvantages. We have developed a new broad-spectrum antiviral approach, dubbed Double-stranded RNA (dsRNA) Activated Caspase Oligomerizer (DRACO) that selectively induces apoptosis in cells containing viral dsRNA, rapidly killing infected cells without harming uninfected cells. We have created DRACOs and shown that they are nontoxic in 11 mammalian cell types and effective against 15 different viruses, including dengue flavivirus, Amapari and Tacaribe arenaviruses, Guama bunyavirus, and H1N1 influenza. We have also demonstrated that DRACOs can rescue mice challenged with H1N1 influenza. DRACOs have the potential to be effective therapeutics or prophylactics for numerous clinical and priority viruses, due to the broad-spectrum sensitivity of the dsRNA detection domain, the potent activity of the apoptosis induction domain, and the novel direct linkage between the two which viruses have never encountered.