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Bydgoszcz, Poland

Szczepaniak Z.,University of Life Sciences in Poznan | Cyplik P.,University of Life Sciences in Poznan | Juzwa W.,University of Life Sciences in Poznan | Czarny J.,Institute of Forensic Genetics | And 2 more authors.
International Biodeterioration and Biodegradation | Year: 2015

The aim of this study was to evaluate the influence of Trichoderma viride on the metabolic activity and the community dynamics of soil bacteria during polyaromatic hydrocarbons (PAHs) biodegradation. Sixteen PAHs were introduced into soil microcosms mimicking natural conditions to achieve an initial concentration of 2000mgkg-1 of soil. After 12 months of treatment, the efficiency of PAH removal was of 78% for the microcosms inoculated with a PAH-degrading bacterial consortium designated S3, 64% for those inoculated with the consortium S3+T.viride, whereas an efficiency of only 47% was achieved in the microcosms inoculated with T.viride alone. Flow cytometry analysis of the bacterial metabolic activities, expressed as the oxidation-reduction potential, allowed differentiating single cells with regard to their metabolic activities. Prior to its introduction in soil microcosms, the consortium S3 consisted of 195 bacterial species which were identified by employing next generation sequencing (MiSeq, Illumina). It has been established that significant changes in the composition of the bacterial community occurred during the biodegradation process when it was carried out in the presence of T.viride. After such treatment only 73 bacterial species were identified from the metabiome, with the dominance of Stenotrophomonas retroflexus (47.46%), Ochrobactrum intermedium (25.83%) and Citrobacter freundii (19.87%). T.viride was able to degrade PAHs; however its presence mainly contributed to modify the bacterial metabiome via antagonistic interactions with the bacteria, which notably reduced the biodegradation efficiency and biodiversity in the microcosms. © 2015 . Source


Schulz F.,University of Hamburg | Buschmann C.,Charite - 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. Source


Piotrowska-Cyplik A.,University of Life Sciences in Poznan | Chrzanowski L.,Poznan University of Technology | Cyplik P.,University of Life Sciences in Poznan | Dach J.,University of Life Sciences in Poznan | 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. Source


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. Source


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. Source

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