Validation process of automatic DNA extraction from bone material using a new advanced protocol for the EZ2 Connect instrument.

Identification of human remains using genetic methods is an important task of forensic science. DNA markers are proving essential in the identification of unknown human remains. However, environmental factors can lead to poor preservation of DNA, including in bone material. The aim of this study was therefore to compare two methods of DNA isolation from bone material: the traditional organic method and the new protocol using the EZ2 Connect instrument. The study involved three types of bone material, namely molars/premolars, petrous parts of the temporal bone and femurs, all with an estimated PMI of 70-80 years. Importantly, the biological material was obtained from three different environments, categorized as preserving, neutral and degrading, based on basic physico-chemical tests and the potential impact on the bone. The results obtained show that the DNA was best preserved in the petrous bone, followed by the teeth, and the femur. DNA extraction using the EZ2 Connect instrument with a new protocol gave slightly better results for the petrous bone, comparable results for the teeth and worse results for the femur compared to the organic method. Several protocol modifications were tested and optimal conditions for DNA isolation were proposed for the EZ2 protocol. Furthermore, the use of an automated method facilitated the effective accumulation of isolates and increased the chances of successful identification of unknown human remains.

Assessing the utility of quantitative and qualitative metrics in the DNA quantification process of skeletal remains for autosomal and Y-chromosome STR amplification purposes.

In historical cases, ancient DNA investigations and missing persons identification, teeth or bone samples are often the only and almost always the best biological material available for DNA typing. On the other hand, DNA obtained from bone material may be characterized by a high degradation index (DI) or its low content, or DNA tests cannot be repeated due to bone piece size limitation. That is often the effect of the environment in which the material was placed and the time during which exposure to unfavorable environmental factors took place. Therefore, it is very important to use appropriate procedures related to STR analysis. For our study, we selected 80 challenging bone samples. The amount of DNA was compared in qPCR using Quantifiler™ Trio DNA Quantification Kit and Investigator® Quantiplex® Pro RGQ. All qPCR results were confirmed by PCR-CE. The results of DNA concentrations and the assigned degradation index (DI) differed significantly within analyzed samples (~10%). Additionally, the Y-chromosome DI also differed from the autosomal DI in the samples. The difference in degradation indexes could explain the lower Y-chromosome amplification success rate compared to autosomal e.g. during human identification process. The results indicate that performing two DNA quantifications with the use of two different kits (primers sets) allows for a much more precise evaluation of the DNA quality and quantity in the isolate. We suggest that at least one of two suggested DNA concentration measurements should be based on an additional determination of the Y chromosome degradation index. Altogether, it allows for rational isolate management, especially when the volume is limited and the sample is unique.

Deletion in the Y chromosome of B10.BR-Ydel mice alters transcription from MSYq genes and has moderate effect on DNA methylation.

B10.BR-Ydel male mice with large deletion in the male-specific region of the Y chromosome long arm (MSYq) are very useful experimental model which requires, however, more detailed characterization. In the present study, the influence of the deletion on transcript levels of MSYq genes (Ssty1, Ssty2, Sly, Srsy, Asty, Orly) and homologous to them X-linked genes (Sstx, Slx, Slxl1, Srsx) was assessed. Quantitative PCR analysis showed that in testes of B10.BR-Ydel males activity of Ssty1 is unchanged, but transcription from all other MSYq genes is highly reduced and reaches from 59 % to only 5 % of the control levels. The decrease in expression of MSYq genes is accompanied by the two-fold increase in expression of Slx and Slxl1 genes. This is the first functional characterization of the deletion in B10.BR-Ydel strain. Another aim of the study was to reveal the mechanism through which deleted Y chromosome of B10.BR-Ydel males could alter phenotype of their female progeny, what was documented in our previous works. Epigenetic inheritance hypothesis was tested by microarray analysis of DNA methylation in B10.BR-Ydel and control B10.BR sperm. The assessment revealed moderate differences and allowed concluding that the mutated Y chromosome can influence traits of females from the next generation partially through altering sperm DNA methylation, but probably some additional mechanisms are engaged here. Breeding data indicate that feminization of pre- and neonatal environment in which next generation females develop is one of such additional mechanisms.

Confirmation of Paternity despite Three Genetic Incompatibilities at Chromosome 2.

DNA testing in cases of disputed paternity is a routine analysis carried out in genetic laboratories. The purpose of the test is to demonstrate similarities and differences in analyzed genetic markers between the alleged father, mother, and a child. The existence of differences in the examined loci between the child and the presumed father may indicate the exclusion of biological parenthood. However, another reason for such differences is genetic mutations, including chromosome aberrations and genome mutations. The presented results relate to genetic analyses carried out on three persons for the purposes of disputed paternity testing. A deviation from inheritance based on Mendel's Law was found in 7 out of 53 STR-type loci examined. All polymorphic loci that ruled out the paternity of the alleged father were located on chromosome 2. Additional analysis of 32 insertion-deletion markers (DIPplex, Qiagen) and sequencing of 94 polymorphic positions of the single nucleotide polymorphism (SNP) type (Illumina, ForenSeq) did not exclude the defendant's biological paternity. A sequence analysis of STR alleles and their flanking regions confirmed the hypothesis that the alleles on chromosome 2 of the child may originate only from the mother. The results of the tests did not allow exclusion of the paternity of the alleged father, but are an example of uniparental maternal disomy, which is briefly described in the literature.

Aging deteriorates quality of sperm produced by male mice with partial Yq deletion.

The aim of the study was to assess the cumulative effects of aging and Y-chromosome long arm deletion on sperm quality parameters. Motility, mitochondrial activity, and head morphology were evaluated for sperm of 3- and 12-month-old males from B10.BR-Ydel and B10.BR congenic mouse strains. The study revealed that quality and fertilizing potential of sperm produced by younger and older B10.BR males persist on similar levels, but worsen significantly with age of B10.BR-Ydel males. The findings imply that partial Yq deletions might be more harmful for spermiogenesis in advancing age and may be applicable to other species including humans. ABBREVIATIONS: AZF: azoospermia factor; MSYq: male-specific region of the Y-chromosome long arm.

Atp7a and Atp7b regulate copper homeostasis in developing male germ cells in mice.

The maintenance of copper homeostasis is critical for all cells. As learned from mice with disturbed copper metabolism, this trace element is also important for spermatogenesis. The experiments conducted in yeasts have demonstrated that appropriate copper level must be preserved to enable meiosis progression; however, increased copper level is toxic for cells. This study aims to analyze the expression profile of Atp7a and Atp7b and other genes encoding copper-related proteins during spermatogenesis in mice. Using the transcripts and protein detection techniques, we demonstrate that within seminiferous tubuli, ATP7A is mainly present in early meiotic germ cells (leptotene to pachytene spermatocytes) and in Sertoli cells (SCs). During spermatogenesis, the progression Atp7a expression profile corresponds to Slc31a1 (encoding copper importer CTR1) and Atox1 (encoding chaperon protein, which delivers copper from CTR1 to ATP7A and ATP7B) expression, suggesting that male germ cells retrieve copper and ATP7A protects them from copper overdose. In contrast, ATP7B protein is observed in SCs and near elongated spermatids; thus, its function seems to be related to copper extraction during spermiogenesis. This is the first study to give a comprehensive view on the activity of copper-related genes during spermatogenesis in mice.