Bydgoszcz, Poland
Bydgoszcz, Poland

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Forster M.,University of Kiel | Forster P.,Institute of Forensic Genetics | Forster P.,University of Cambridge | Elsharawy A.,University of Kiel | And 16 more authors.
Nucleic Acids Research | Year: 2013

Scientists working with single-nucleotide variants (SNVs), inferred by next-generation sequencing software, often need further information regarding true variants, artifacts and sequence coverage gaps. In clinical diagnostics, e.g. SNVs must usually be validated by visual inspection or several independent SNV-callers. We here demonstrate that 0.5-60% of relevant SNVs might not be detected due to coverage gaps, or might be misidentified. Even low error rates can overwhelm the true biological signal, especially in clinical diagnostics, in research comparing healthy with affected cells, in archaeogenetic dating or in forensics. For these reasons, we have developed a package called pibase, which is applicable to diploid and haploid genome, exome or targeted enrichment data. pibase extracts details on nucleotides from alignment files at user-specified coordinates and identifies reproducible genotypes, if present. In test cases pibase identifies genotypes at 99.98% specificity, 10-fold better than other tools. pibase also provides pair-wise comparisons between healthy and affected cells using nucleotide signals (10-fold more accurately than a genotype-based approach, as we show in our case study of monozygotic twins). This comparison tool also solves the problem of detecting allelic imbalance within heterozygous SNVs in copy number variation loci, or in heterogeneous tumor sequences. © 2012 The Author(s). Published by Oxford University Press.


Koppelkamm A.,Albert Ludwigs University of Freiburg | Koppelkamm A.,Institute of Forensic Genetics | Vennemann B.,University of Dundee | Lutz-Bonengel S.,Albert Ludwigs University of Freiburg | And 4 more authors.
International Journal of Legal Medicine | Year: 2011

Messenger RNA (mRNA) profiling in post-mortem human tissue might reveal information about gene expression at the time point of death or close to it. When working with post-mortem human tissue, one is confronted with a natural RNA degradation caused by several parameters which are not yet fully understood. The aims of the present study were to analyse the influence of impaired RNA integrity on the reliability of quantitative gene expression data and to identify ante- and post-mortem parameters that might lead to reduced RNA integrities in post-mortem human brain, cardiac muscle and skeletal muscle tissues. Furthermore, this study determined the impact of several parameters like type of tissue, age at death, gender and body mass index (BMI), as well as duration of agony, cause of death and post-mortem interval on the RNA integrity. The influence of RNA integrity on the reliability of quantitative gene expression data was analysed by generating degradation profiles for three gene transcripts. Based on the deduced cycle of quantification data, this study shows that reverse transcription quantitative polymerase chain reaction (RT-qPCR) performance is affected by impaired RNA integrity. Depending on the transcript and tissue type, a shift in cycle threshold values of up to two cycles was observed. Determining RNA integrity number of 136 post-mortem samples revealed significantly different RNA qualities among the three tissue types with brain revealing significantly lower integrities compared to skeletal and cardiac muscle. The body mass index was found to influence RNA integrity in skeletal muscle tissue (M. iliopsoas). Samples originating from deceased with a BMI>25 were of significantly lower integrity compared to samples from normal weight donors. Correct data normalisation was found to partly diminish the effects caused by impaired RNA quality. Nevertheless, it can be concluded that in post-mortem tissue with low RNA integrity numbers, the detection of large differences in gene expression activities might still be possible, whereas small expression differences are prone to misinterpretation due to degradation. Thus, when working with post-mortem samples, we recommend generating degradation profiles for all transcripts of interest in order to reveal detection limits of RT-qPCR assays. © 2011 Springer-Verlag.


Schulz F.,University of Hamburg | Buschmann C.,Charité - Medical University of Berlin | Braun C.,Ludwig Maximilians University of Munich | Puschel K.,University of Hamburg | And 2 more authors.
International Journal of Legal Medicine | Year: 2011

We describe and discuss haemorrhages discovered in the back and auxiliary breathing muscles of a population of cases of suicidal death by hanging. Intramuscular haemorrhages were present in approximately 30% of the cases. Pre-existing illnesses with an increased tendency to bleed or an anticoagulant medication did not exist; corresponding skin and subcutaneous fatty tissue structures were intact in each case. In cases of death by hanging, the occurrence of muscle haemorrhages of this type may be explained pathophysiologically by the occurrence of increased respiratory exertions and/or seizures during the hanging process. Although the results of our study do not indicate an obligatory autopsy finding, evidence of internal haemorrhaging into the back and auxiliary breathing muscles may be called upon following consideration of differential diagnostic aspects as a further diagnostic indication of vital hanging. © Springer-Verlag 2010.


Cyplik P.,University of Life Sciences in Poznań | Piotrowska-Cyplik A.,University of Life Sciences in Poznań | Marecik R.,University of Life Sciences in Poznań | Czarny J.,Institute of Forensic Genetics | And 2 more authors.
Biodegradation | Year: 2012

The effect of the addition of compatible solutes (ectoine and trehalose) on the denitrification process of saline wastewater was studied. In saline wastewater, it was observed that the initial concentration of nitrates was 500 mg N l -1. A fatty substance isolated from oiled bleaching earth (waste of vegetable oil refining process) was used as a source of carbon. The consortium, which was responsible for the denitrification process originated from the wastewater of the vegetable oil industry. The consortium of microorganisms was identified by the use of restriction fragment length polymorphism of 16S rRNA gene amplicons and sequencing techniques. It was noted that ectoine affects significantly the activity of lipase and nitrate reductase, and resulted in faster denitrification compared to saline wastewater with the addition of trehalose or control saline wastewater (without compatible solutes). It was observed that relative enzyme activities of lipase and nitrate reductase increased by 32 and 35%, respectively, in the presence of 1 mM ectoine. This resulted in an increase in specific nitrate reduction rate in the presence of 1 mM ectoine to 5.7 mg N g -1 VSS h -1, which was higher than in the absence of ectoine (3.2 mg N g -1 VSS h -1). The addition of trehalose did not have an effect on nitrate removals. Moreover, it was found that trehalose was used up completely by bacteria as a source of carbon in the denitrification process. The fatty acids were biodegraded by 74% in the presence of 1 mM ectoine. © 2012 The Author(s).


Piotrowska-Cyplik A.,University of Life Sciences in Poznań | Chrzanowski L.,Poznan University of Technology | Cyplik P.,University of Life Sciences in Poznań | Dach J.,University of Life Sciences in Poznań | And 6 more authors.
International Biodeterioration and Biodegradation | Year: 2013

Due to high fat content the treatment of oiled bleaching earth is very challenging. The neutralization of such waste may be carried out by employing the composting process. In this study, the efficiency of the composting process conducted with 19% addition of commercial oiled bleaching earth to waste sludge was evaluated. Maize straw was used as a structural material. The activity of lipases and dehydrogenases was measured during the biodegradation process. As a result of composting, changes in C/N ratio occurred (from 31 to 15) and the efficiency of fatty acids biodegradation reached 95%. The composting process also resulted in the removal of the initial phytotoxicity of composts. The mature compost did not exhibit any form of phytotoxicity during assays with Phytotoxkit. The Ames test excluded mutagenicity of any components in the compost. These results suggest that the proposed composting method may potentially be employed for rapid and efficient remediation of industrial waste containing oiled bleaching earth and waste sludge. © 2012 Elsevier Ltd.


Forster L.,University of Munster | Forster P.,University of Munster | Forster P.,Cambridge College | Forster P.,Genetic Ancestor Ltd. | And 6 more authors.
International Journal of Legal Medicine | Year: 2010

We present allelic data for three known and one new C-tract in the human mitochondrial DNA (mtDNA) control region, and we measure intergenerational mutation rates at such C-tracts. In detail, in a sample of 1,172 mtDNA sequences, we demonstrate the existence of an instability threshold of eight consecutive cytosines, at and above which the phenomenon of length heteroplasmy arises. To determine mutation rates, we draw on mtDNA sequences in up to four generations of 248 pedigrees for families living in high or low-radiation environmental conditions. The high-radiation sample gives the most conservative (fastest) mutation rate likely to be encountered in any forensic context. We find that the C-tract mutation rate is up to 6% per generation, and we observe an excess of cytosine gains over losses. Case studies and guidelines for evaluating mtDNA heteroplasmy are provided. © 2009 Springer-Verlag.


Schulz F.,University of Hamburg | Schafer H.,University of Hamburg | Puschel K.,University of Hamburg | Tsokos M.,Charité - Medical University of Berlin | And 2 more authors.
International Journal of Legal Medicine | Year: 2011

We describe and discuss autopsy findings of bowel wall hemorrhage in a study population comprising cases of suicidal death by hanging. Intramural hemorrhages were seen in approximately 12% of the cases examined; no preexisting bowel diseases were found. In hanging deaths with a longer agonal phase, we opine that abdominal congestion during the hanging process provides a viable pathophysiological explanation for bowel wall hemorrhage. Though we are not dealing here with obligatory autopsy findings, the detection of bowel wall hemorrhage might be used as another sign of vital hanging after considering differential diagnostic aspects. © 2011 Springer-Verlag.


PubMed | Institute of Meat Technology, Institute of Forensic Genetics and University of Life Sciences in Poznań
Type: | Journal: Journal of the science of food and agriculture | Year: 2016

The knowledge regarding microaerophilic and anaerobic Specific Spoilage Organisms (SSOs) is crucial for an appropriate evaluation of vacuum-packed ham. The objective of this study was to characterize the SSO community in vacuum-packed ham by culture-dependent technique and MiSeq next generation sequencing (NGS) platform. The relation between changes among the SSO group in the ham and changes of sensory characteristics of the product was also assessed.In the study, conventional microbiological analyses were employed in order to establish the participation of several groups of microorganisms in the deterioration of vacuum-packed ham. The diversity of the SSO group in the product was further assessed with the use of MiSeq NGS technology. The bacteria identified in sliced cooked ham belonged mostly to 4 phyla: Actinobacteria, Proteobacteria, Firmicutes, and Bacteroidetes. The temperature of 4C favoured the development of mesophilic and psychrophilic/psychrothropic flora, mainly Lactobacillaceae, Enterobacteriaceae and Micrococcaceae families. A high ratio of Brochothrix thermosphacta species and new, cold-tolerant Clostridium spp. was also observed. The growth of these microorganisms facilitated the changes in the pH value and organoleptic characteristics of the product.This study confirms that the combination of culturing and MiSeq NGS technology techniques improves the microbial evaluation of food.


PubMed | Adam Mickiewicz University, Institute of Forensic Genetics, Poznan University of Technology and University of Life Sciences in Poznań
Type: Journal Article | Journal: Water, air, and soil pollution | Year: 2015

The search for new bacterial consortia capable of removing PAH from the environment is associated with the need to employ novel, simple, and economically efficient detection methods. A fluorimetric method (FL) as well as high voltage electrochemiluminescence (ECL) on a modified surface of an aluminum electrode were used in order to determine the changes in the concentrations of PAH in the studied aqueous solutions. The ECL signal (the spectrum and emission intensity for a given wavelength) was determined with the use of an apparatus operating in single photon counting mode. The dependency of ECL and FL intensity on the concentration of naphthalene, phenanthrene, and pyrene was linear in the studied concentration range. The biodegradation kinetics of the particular PAH compounds was determined on the basis of the obtained spectroscopic determinations. It has been established that the half-life of naphthalene, phenanthrene, and pyrene at initial concentrations of 50mg/l (beyond the solubility limit) reached 41, 75, and 130h, accordingly. Additionally, the possibility of using ECL for rapid determination of the soluble fraction of PAH directly in the aqueous medium has been confirmed. Metagenomic analysis of the gene encoding 16S rRNA was conducted on the basis of V4 hypervariable region of the 16S rRNA gene and allowed to identify 198 species of bacteria that create the S4consortium. The consortium was dominated by


PubMed | Institute of Forensic Genetics, Poznan University of Technology and University of Life Sciences in Poznań
Type: Journal Article | Journal: Environmental science and pollution research international | Year: 2016

The aim of this study was to evaluate the effect of bioaugmentation and addition of rhamnolipids on the biodegradation of PAHs in artificially contaminated soil, expression of genes crucial for the biodegradation process (PAHRHDGN, PAHRHDGP), and the synthesis of rhamnolipids as well as population changes in the soil bacterial metabiome. The positive effect of bioaugmentation and addition of rhamnolipids on the bioremediation of the majority of PAHs was confirmed during the early stages of treatment, especially in case of the most structurally complicated compounds. The results of metagenomic analysis indicated that the initial changes in the soil metabiome caused by bioaugmentation diminished after 3months and that the community structure in treated soil was similar to control. The survival period of bacteria introduced into the soil via bioaugmentation reached a maximum of 3months. The increased expression of genes observed after addition of PAH into the soil also returned to the initial conditions after 3months.

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