WHOLE GENOME TARGETED ENRICHMENT AND SEQUENCING OF HUMAN-INFECTING CRYPTOSPORIDIUM spp

Cryptosporidium spp. are protozoan parasites that cause severe illness in vulnerable human populations. Obtaining pure Cryptosporidium DNA from clinical and environmental samples is challenging because the oocysts shed in contaminated feces are limited in quantity, difficult to purify efficiently, may derive from multiple species, and yield limited DNA (<40 fg/oocyst). Here, we develop and validate a set of 100,000 RNA baits (CryptoCap_100k) based on six human-infecting Cryptosporidium spp. ( C. cuniculus , C. hominis , C. meleagridis , C. parvum , C. tyzzeri , and C. viatorum ) to enrich Cryptosporidium spp. DNA from a wide array of samples. We demonstrate that CryptoCap_100k increases the percentage of reads mapping to target Cryptosporidium references in a wide variety of scenarios, increasing the depth and breadth of genome coverage, facilitating increased accuracy of detecting and analyzing species within a given sample, while simultaneously decreasing costs, thereby opening new opportunities to understand the complex biology of these important pathogens.

Escaping the fate of Sisyphus: assessing resistome hybridization baits for antimicrobial resistance gene capture

Finding, characterizing and monitoring reservoirs for antimicrobial resistance (AMR) is vital to protecting public health. Hybridization capture baits are an accurate, sensitive and cost-effective technique used to enrich and characterize DNA sequences of interest, including antimicrobial resistance genes (ARGs), in complex environmental samples. We demonstrate the continued utility of a set of 19 933 hybridization capture baits designed from the Comprehensive Antibiotic Resistance Database (CARD)v1.1.2 and Pathogenicity Island Database (PAIDB)v2.0, targeting 3565 unique nucleotide sequences that confer resistance. We demonstrate the efficiency of our bait set on a custom-made resistance mock community and complex environmental samples to increase the proportion of on-target reads as much as >200-fold. However, keeping pace with newly discovered ARGs poses a challenge when studying AMR, because novel ARGs are continually being identified and would not be included in bait sets designed prior to discovery. We provide imperative information on how our bait set performs against CARDv3.3.1, as well as a generalizable approach for deciding when and how to update hybridization capture bait sets. This research encapsulates the full life cycle of baits for hybridization capture of the resistome from design and validation (both in silico and in vitro) to utilization and forecasting updates and retirement.

A measurement of the local energy deposition by antiprotons coming to rest in tissue-like material

The measurement of the energy deposited in tissue-equivalent plastic as a beam of low-energy antiprotons slows down is described. The resulting depth-dose curve is presented and compared with that of protons measured under similar conditions. These curves indicate that the ratio of the dose in the antiproton stopping peak to that in the plateau region is about twice that found for protons. Analysis of the data shows that out of the 2 GeV available in an antiproton annihilation, on average less than 30 MeV is deposited close to the site of the interaction. This leads to the conclusion that antiprotons are unlikely to offer any marked advantage over other radiations for radiotherapeutic applications of the future.

The biological effect of very high energy hadrons

The meristems of Vicia faba bean roots were irradiated at different depths in water in a 250 GeV/c positive hadron beam from the CERN Super Proton Synchrotron (SPS). The growth during the 10 days following irradiation was determined and compared with results obtained from 60Co gamma-ray exposures. The data indicate a Relative Biological Efficiency (r.b.e.) near to one, independent of the contribution of secondaries to the dose. However, some anomalies in the radiation response of the irradiated beans were noted.

Effects of negative pions and neutrons on the growth of Vicia faba bean roots

Vicia faba bean roots have been irratiated with neutrons of various energies and with negative pi-mesons, and the effect on the ten-day growth of the roots has been determened. The neutron irratiations were made in beams of 400 and 600 MeV maximum energy, as well as with neutrons from a plutonium-beryllium source (mean energy 4.4 MeV) and from a 14 MeV neutron generator. The bean roots have also been irradiated at various points along the depth-dose curve of negative pi-mesons, including the gegion where the pions annihilate on coming to rest. The results show a maximum relative biological effectiveness (RBE) of 3.7 for 50% reduction in ten days growth for stopped negative pions and values up to 3.3 for high-energy neutrons, compared to 5.5 for 14 MeV neutrons. The biological effectiveness of high-energy neutrons and stopped pions shows a more pronounced dependence on dose than does the effect with lower-energy neutrons.

Determination of some parameters for pion radiobiology studies

An experimental investigation of the central axis depth-dose and stopping rate distribution of the SIN biomedical pion beam is reported. The pion stopping rate in a thin disc of tissue-equivalent plastic was determined using a counter telescope. The dose rate at the position of this dic 'target' was measured using a specially designed parallel-plate tissue-equivalent ionization chamber. Both dose rate and pion stopping rate are given as a function of depth for beams of two different momenta spread. The energy deposition required per pion stop to fit the measured dose rate curves was calculated and found to be between 37 and 40 MeV. From the stopping rate measurements the depth-dose distribution of pion interaction dose (star-dose) and the dose due to the pion slowing down have been evaluated. The maximum star-dose is found at a depth of about 2 g cm-2 beyound the maximum of the ionization dose.