Who Packed the Drugs? Application of Bayesian Networks to Address Questions of DNA Transfer, Persistence, and Recovery from Plastic Bags and Tape

When DNA from a suspect is detected in a sample collected at a crime scene, there can be alternative explanations about the activity that may have led to the transfer, persistence and recovery of his/her DNA. Previous studies have shown that DNA can be indirectly transferred via intermediate surfaces and that DNA on a previously used object can persist after subsequent use of another individual. In addition, it has been shown that a person’s shedder status may influence transfer, persistence, prevalence, and recovery of DNA. In this study we have investigated transfer persistence and recovery on zip-lock bags and tape, which are commonly encountered in drug cases and how the shedder status of the participants influenced the results. A probabilistic framework was developed which was based on a previously described Bayesian network with case-specific modifications. Continuous modelling of data was used to inform the Bayesian networks and two case scenarios were investigated. In the specific scenarios only moderate to low support for Hp was obtained. Applying a continuous model based on the profile quality can change the LRs.

The Trypanosoma cruzi kinetoplast DNA minicircle sequences transfer biomarker of the multidrug treatment of Chagas disease

Background: The Trypanosoma cruzi infection renders the transfer of the mitochondrion kinetoplast DNA minicircle sequences into the host’s genome. The Aves are refractory to the infection, but chicks hatched from the T. cruzi inoculated eggs integrate the DNA minicircle sequences into the germ line cells. Rabbits, mice and chickens with the minicircle sequences mutations develop the Chagas cardiomyopathy and the DNA transfer underpins the heart disease. Methodology: The PCR with the specific primer sets revealed the Protist nuclear DNA and the kinetoplast DNA in the agarose gels bands probed with the radiolabel specific sequences from tissues of the T. cruzi-infected rabbits and of the mice. A targetprimer TAIL-PCR amplification employing primer sets from the chickens, rabbits and mice, in combination with primer sets from the the T. cruzi kinetoplast minicircle sequences was used. This approach led us to disclose the integration sites of the kinetoplast DNA biomarker, then, used to monitor the effect of multidrug treatment of the T. cruzi infected mice. Principal findings: The Southern hybridization, clone and sequence of the amplification products revealed the DNA minicircle sequences integrations sites in the LINE transposable elements. An array of inhibitors of eukaryote cells division was used to arrest the DNA transfer. It was shown that nine out of 12 inhibitors prevented the kinetoplast DNA integration into the macrophage genome. The multidrug treatment of the acutely T. cruzi-infected mice with Benznidazole, Azidothymidine and Ofloxacin lessened circa 2.5-fold the rate of the minicircle sequences integrations in the mouse genome and inhibited the rejection of the target heart cells. Conclusion and significance: The T. cruzi mitochondrion kinetoplast minicircle sequences transfer driven pathogenesis of Chagas disease is an ancient Cross-Kingdom DNA phenomenon of evolution and, therefore, paradigm research with effective purposing inhibitors is needed.

Secondary DNA transfer on denim using a human blood analogue

DNA quantification technology has increased in accuracy and sensitivity, now allowing for detection and profiling of trace DNA. Secondary DNA transfer occurs when DNA is deposited via an intermediary source (e.g. clothing, tools, utensils). Multiple courtrooms have now seen secondary transfer introduced as an explanation for DNA being present at a crime scene, but sparse experimental studies mean expert opinions are often limited. Here, we used bovine blood and indigo denim substrates to quantify the amount of secondary DNA transfer and quality of STRs under three different physical contact scenarios: passive, pressure, and friction. We showed that the DNA transfer was highest under a friction scenario, followed by pressure and passive treatments. The STR profiles showed a similar, albeit less pronounced trend, with correctly scored alleles and genotype completeness being highest under a friction scenario, followed by pressure and passive. DNA on the primary substrate showed a decrease in concentration and genotype completeness both immediately and at 24 hours, suggestive of a loss of DNA during the primary transfer. The majority of secondary transfer samples amplified less than 50% of STR loci regardless of contact type. This study showed that while DNA transfer is common between denim, this is not manifested in full STR profiles. We discuss the possible technical solutions to partial profiles from trace DNA, and more broadly the ubiquity of secondary DNA transfer.

DNA Transfer in Forensic Science: Recent Progress towards Meeting Challenges

Understanding the factors that may impact the transfer, persistence, prevalence and recovery of DNA (DNA-TPPR), and the availability of data to assign probabilities to DNA quantities and profile types being obtained given particular scenarios and circumstances, is paramount when performing, and giving guidance on, evaluations of DNA findings given activity level propositions (activity level evaluations). In late 2018 and early 2019, three major reviews were published on aspects of DNA-TPPR, with each advocating the need for further research and other actions to support the conduct of DNA-related activity level evaluations. Here, we look at how challenges are being met, primarily by providing a synopsis of DNA-TPPR-related articles published since the conduct of these reviews and briefly exploring some of the actions taken by industry stakeholders towards addressing identified gaps. Much has been carried out in recent years, and efforts continue, to meet the challenges to continually improve the capacity of forensic experts to provide the guidance sought by the judiciary with respect to the transfer of DNA.

Comparative analysis of integrative and conjugative mobile genetic elements in the genus Mesorhizobium

Members of the Mesorhizobium genus are soil bacteria that often form nitrogen-fixing symbioses with legumes. Most characterised Mesorhizobium spp. genomes are ~8 Mb in size and harbour extensive pangenomes including large integrative and conjugative elements (ICEs) carrying genes required for symbiosis (ICESyms). Here, we document and compare the conjugative mobilome of 41 complete Mesorhizobium genomes. We delineated 56 ICEs and 24 integrative and mobilizable elements (IMEs) collectively occupying 16 distinct integration sites, along with 24 plasmids. We also demonstrated horizontal transfer of the largest (853,775 bp) documented ICE, the tripartite ICEMspSymAA22. The conjugation systems of all identified ICEs and several plasmids were related to those of the paradigm ICESym ICEMlSymR7A, with each carrying conserved genes for conjugative pilus formation (trb), excision (rdfS), DNA transfer (rlxS) and regulation (fseA). ICESyms have likely evolved from a common ancestor, despite occupying a variety of distinct integration sites and specifying symbiosis with diverse legumes. We found extensive evidence for recombination between ICEs and particularly ICESyms, which all uniquely lack the conjugation entry-exclusion factor gene trbK. Frequent duplication, replacement and pseudogenization of genes for quorum-sensing-mediated activation and antiactivation of ICE transfer suggests ICE transfer regulation is constantly evolving. Pangenome-wide association analysis of the ICE identified genes potentially involved in symbiosis, rhizosphere colonisation and/or adaptation to distinct legume hosts. In summary, the Mesorhizobium genus has accumulated a large and dynamic pangenome that evolves through ongoing horizontal gene transfer of large conjugative elements related to ICEMlSymR7A.

Optimization of Agrobacterium-mediated transformation conditions of prospective genotypes of winter bread wheat by in planta method

Aim. Optimization of conditions for genetic transformation of new promising genotypes of winter bread wheat (T. aestivum L.) by in planta method. Methods. Agrobacterium-mediated transformation by in planta method using the strain AGL0 and vector construct pBi2E. Results. The influence of air temperature, optical density of cells of agrobacterial suspension, inoculation day and composition of inoculation medium on the frequency of obtaining transgenic plants of new winter wheat genotypes was studied. The dependence of the frequency obtaining of transgenic plants from environmental conditions, in particular temperature, has been established. It was found that the temperature regime of 20-22°C provided the largest number (4.8%) of wheat transformants, and when the temperature is reduced to 16-18°C there is a decrease in the efficiency of T-DNA transfer into the plant genome and the lowest frequency of transformation (0.7%). Conclusions. The largest number of transformants was obtained using a inoculation medium without sucrose, the optical density of cells of the agrobacterial suspension of 0.6 op.od. and inoculation on the third day after castration of ears. Keywords: T. aestivum, Agrobacterium-mediated transformation in planta, optimization of conditions.