The application of miniplex primer sets in the analysis of degraded DNA from human skeletal remains

A new set of multiplexed PCR primers has been applied to the analysis of human skeletal remains to determine their efficacy in analyzing degraded DNA. These primer sets, known as Miniplexes, produce shorter amplicons (50-280 base pairs (bp)) than standard short tandem repeat (STR) kits, but still utilize the 13 CODIS STR loci, providing results that are searchable on national DNA databases. In this study, a set of 31 different human remains were exposed to a variety of environmental conditions, extracted, and amplified with commercial and Miniplex DNA typing kits. The amplification efficiency of the Miniplex sets was then compared with the Promega PowerPlex 16 system. Sixty-four percent of the samples generated full profiles when amplified with the Miniplexes, while only 16% of the samples generated full profiles with the Powerplex 16 kit. Complete profiles were obtained for 11 of the 12 Miniplex loci with amplicon sizes less than 200 bp. These data suggest smaller PCR amplicons may provide a useful alternative to mitochondrial DNA for anthropological and forensic analysis of degraded DNA from human skeletal remains.     

A comparison of smokeless powders and mixtures by capillary zone electrophoresis

The analysis of inorganic ions present in smokeless and muzzleloading powders has been performed using capillary zone electrophoresis (CZE). Previous publications have examined inorganic low explosives using CZE, but have not looked at the ion profiles from smokeless powders. In this report, seven commercially available smokeless powders were analyzed as unburned powder and burned residue. The results demonstrate that ionic profiles can be used to characterize smokeless powders. Our analysis also included a smokeless powder/ Pyrodex combination to determine if smokeless powder ions are distinguishable in a mixture; however, the high concentration of ions present in Pyrodex RS prevented its detection. In addition, five different smokeless powder samples as well as Pyrodex RS were collected for analysis subsequent to deflagration in fifteen plastic pipe bombs. The relative ion concentrations between these powders can be used to illustrate the differences between open burning and pipe bomb deflagration.     

The development of reduced size STR amplicons as tools for analysis of degraded DNA

New multiplex PCR sets of commonly used short tandem repeat (STR) markers have been developed to produce PCR products that are reduced in size when compared to standard commercial STR kits. The reduction in size of these amplicons can facilitate the examination and analysis of degraded DNA evidence by improving amplification efficiency. This "miniSTR" approach will permit current forensic practitioners to use STR markers and instrumentation already present in their laboratories and to generate genotyping data that is directly comparable to reference samples and searchable through the FBI's Combined DNA Index System (CODIS) databases. This paper discusses the development of these new primer sets and presents some initial results in the analysis of degraded and aged DNA samples. A method for removal of problematic fluorescent dye artifacts is also described. Comparison studies in over 100 samples have verified that these miniSTR primers can provide fully concordant results to commercial STR kits and can provide improved signal from degraded DNA specimens. These miniplex sets should prove valuable in the analysis of samples where allele dropout and reduced sensitivity of larger STR alleles occurs.     

Separation and Detection of Smokeless Powder Additives by Ultra Performance Liquid Chromatography with Tandem Mass Spectrometry (UPLC/MS/MS),

A reversed phase gradient ultra performance liquid chromatography tandem mass spectrometry (UPLC/MS/MS) method has been developed for the analysis of smokeless powders. A total of 20 different components were separated by UPLC and detected by MS/MS in multiple reaction monitoring (MRM) mode. These compounds included diphenylamines, centralites, nitrotoluenes, nitroglycerin, and various phthalates. Simultaneous positive and negative electrospray ionization (ESI) was used along with negative atmospheric pressure chemical ionization (APCI) to detect all compounds in a single analysis. Analysis times were under 8 min with a gradient of 10–73% organic at a flow rate of 0.500 mL/min. With this method, ultraviolet and MRM limits of detection ranging from 0.08 to 2.6 ng and 0.4–64 ng injected were achieved. Commercially available smokeless powders were also extracted with methylene chloride and characterized using the developed UPLC/MS/MS method. The procedure permits the determination of compositional differences between different brands as well as lot‐to‐lot variations.     

Developmental Trajectories and Intentional Actions

The article turns a critical eye on problems arising from use of largesamples and complicated statistics to handle multilevel designs. I arguethat although these have a legitimate role to play in discovering causalrelations, valuable information can be lost or distorted in the processof their use. Exploratory classification and tree diagrams show howtransitional analyses can unpack effects of community, family, priormisbehavior, juvenile delinquency, and incarceration on adult criminalbehavior. The analyses showed that in the worst neighborhoods, disruptivebehavior had little discriminating power with regard to juveniledelinquency or adult crime. They showed also that good family interactionsserve as protection against crime in all types of neighborhoods. ConstructTheory, I suggest, is a way to understand the influences that seem toproduce criminal behavior.     

A survey of background levels of explosives and related compounds in the environment

In this paper, swabbings from various public areas in 28 different cities throughout the United States were collected. A wide variety of objects were tested, ranging from park benches and telephones to sign posts and mailboxes. Inorganic anions and cations common in low explosives were detected simultaneously using capillary zone electrophoresis. Organic high explosives including nitroaromatics, nitramines, and nitrate esters were detected using gas chromatography with a pulsed-discharge electron capture detector. Confirmation of selected results was performed by ion chromatography and negative ion chemical ionization GC/MS. In general the results provide two major conclusions: (i) with the exception of nitrate, most low explosive oxidizers are rare in the environment; (ii) no organic explosives or significant interferences to these explosives were detected.     

Evaluation and quantification of nuclear DNA from human telogen hairs

Nuclear DNA was extracted from human telogen hairs from 60 individuals. Six to nine hairs from each individual were individually extracted. The amount of DNA recovered from each individual varied greatly, and most samples yielded a quantity of 550 pg or less per hair. A selective extraction buffer was used to remove epithelial cell DNA and the amount of exogenous DNA was determined. DNA was also quantified by real time PCR using three different sized amplicons targeting an Alu sequence. The results were used to determine the state of degradation of the extracted DNA. Different quantities of sample (<100 pg, 100-500 pg, >500 pg) were amplified with the Miniplex kits to determine the minimum DNA template required for successful amplification. DNA recovered from hair showed degradation; however, partial profiles were obtained for those samples containing at least 60 pg using MiniSTRs.     

COMMENTARY ON "EMPIRICAL AND ETHICAL PROBLEMS WITH CUSTODY RECOMMENDATIONS:"

Whether or not custody evaluators, testifying as expert witnesses, continue to make specific custody recommendations, custody decision making will continue to be based upon inadequate and untested evidence unless and until we reform the family court system in American courtrooms. Judges and lawyers must have specialized knowledge and training about such things as the developmental needs of children, the effects of divorce on children, domestic violence, and child safety issues; lawyers must develop litigation as well as mediation and negotiation skills; specialized family courts utilizing individual calendars and case management techniques must be established; and the complexities and intellectual challenges of family law cases needs to be recognized.