Evaluation of low-cost bone and teeth processing methods for automated DNA extraction

Bone and teeth can often be the only, or the best, biological materials available as DNA sources for the identification of decomposed or skeletal human remains. While these hard tissues are resistant to decay and therefore offer endogenous DNA a certain protection from the environment, their mineral matrices make DNA extraction challenging, a problem compounded by the low DNA content and high degradation levels usually associated with these tissues. To help release DNA from the mineral matrix, they are generally ground into a powder to increase their surface area to the extraction reagents. Furthermore, it is now common to perform a demineralization to dissolve the powder and release DNA that remains trapped. A common pulverization method consists of the use of a cryogenic grinder, which prevents heating of the sample and avoids subjecting the DNA to heat damage, but this equipment is costly. That said, little is known about the effect of lower-cost alternatives to the expensive cryogenic grinder on the quality and quantity of DNA recovered. Thus, this study aimed to evaluate inexpensive grinding methods for their potential for use in a forensic laboratory setting. The methods deemed to be viable options for this purpose were investigated to determine their effects on the quantity and quality of extracted DNA. Bone samples were also subjected to freezing prior to pulverization to assess the possibility that a lower sample temperature could limit heat damage to the DNA during processing. Pig bone and tooth powders were extracted using an original and a modified PrepFiler BTA™ Kit protocol, with the latter featuring an added demineralization step. Out of the methods explored, a coffee grinder and mortar and pestle were determined to be the most suitable for bone and teeth processing in a forensic laboratory setting. No significant differences between the two methods were found regarding the quantity and quality of DNA recovered and the rate of powder recovery, although more powder loss occurred when teeth were crushed with the mortar and pestle. Likewise, freezing samples before grinding did not have a significant impact on DNA quality and quantity. Finally, the original DNA extraction protocol performed significantly better than the modified one for the quantity of DNA recovered from both bone and teeth, while the quality was only superior for the bone

The B73 maize genome: complexity, diversity, and dynamics

We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. We also report on the correlation of methylation-poor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize

The LHCb upgrade I

International audienceThe LHCb upgrade represents a major change of the experiment. The detectors have been almost completely renewed to allow running at an instantaneous luminosity five times larger than that of the previous running periods. Readout of all detectors into an all-software trigger is central to the new design, facilitating the reconstruction of events at the maximum LHC interaction rate, and their selection in real time. The experiment's tracking system has been completely upgraded with a new pixel vertex detector, a silicon tracker upstream of the dipole magnet and three scintillating fibre tracking stations downstream of the magnet. The whole photon detection system of the RICH detectors has been renewed and the readout electronics of the calorimeter and muon systems have been fully overhauled. The first stage of the all-software trigger is implemented on a GPU farm. The output of the trigger provides a combination of totally reconstructed physics objects, such as tracks and vertices, ready for final analysis, and of entire events which need further offline reprocessing. This scheme required a complete revision of the computing model and rewriting of the experiment's software

The LHCb upgrade I

International audienceThe LHCb upgrade represents a major change of the experiment. The detectors have been almost completely renewed to allow running at an instantaneous luminosity five times larger than that of the previous running periods. Readout of all detectors into an all-software trigger is central to the new design, facilitating the reconstruction of events at the maximum LHC interaction rate, and their selection in real time. The experiment's tracking system has been completely upgraded with a new pixel vertex detector, a silicon tracker upstream of the dipole magnet and three scintillating fibre tracking stations downstream of the magnet. The whole photon detection system of the RICH detectors has been renewed and the readout electronics of the calorimeter and muon systems have been fully overhauled. The first stage of the all-software trigger is implemented on a GPU farm. The output of the trigger provides a combination of totally reconstructed physics objects, such as tracks and vertices, ready for final analysis, and of entire events which need further offline reprocessing. This scheme required a complete revision of the computing model and rewriting of the experiment's software

The LHCb upgrade I

International audienceThe LHCb upgrade represents a major change of the experiment. The detectors have been almost completely renewed to allow running at an instantaneous luminosity five times larger than that of the previous running periods. Readout of all detectors into an all-software trigger is central to the new design, facilitating the reconstruction of events at the maximum LHC interaction rate, and their selection in real time. The experiment's tracking system has been completely upgraded with a new pixel vertex detector, a silicon tracker upstream of the dipole magnet and three scintillating fibre tracking stations downstream of the magnet. The whole photon detection system of the RICH detectors has been renewed and the readout electronics of the calorimeter and muon systems have been fully overhauled. The first stage of the all-software trigger is implemented on a GPU farm. The output of the trigger provides a combination of totally reconstructed physics objects, such as tracks and vertices, ready for final analysis, and of entire events which need further offline reprocessing. This scheme required a complete revision of the computing model and rewriting of the experiment's software

The LHCb upgrade I

International audienceThe LHCb upgrade represents a major change of the experiment. The detectors have been almost completely renewed to allow running at an instantaneous luminosity five times larger than that of the previous running periods. Readout of all detectors into an all-software trigger is central to the new design, facilitating the reconstruction of events at the maximum LHC interaction rate, and their selection in real time. The experiment's tracking system has been completely upgraded with a new pixel vertex detector, a silicon tracker upstream of the dipole magnet and three scintillating fibre tracking stations downstream of the magnet. The whole photon detection system of the RICH detectors has been renewed and the readout electronics of the calorimeter and muon systems have been fully overhauled. The first stage of the all-software trigger is implemented on a GPU farm. The output of the trigger provides a combination of totally reconstructed physics objects, such as tracks and vertices, ready for final analysis, and of entire events which need further offline reprocessing. This scheme required a complete revision of the computing model and rewriting of the experiment's software