Predicting the optimal STR profile amplification set up from Quantifiler™ Trio data

Samples collected for forensic case work may be of varying quality and quantity. The sample DNA is often quantified prior to short tandem repeats (STR) profile analysis with methods such as Quantifiler™Trio (QFT). The QFT measures the quantity of DNA as well as an internal PCR control (IPC) and a degradation index (DI).The aim of this study was to use IPC and DI measurements to identify samples, which would benefit from a modified PCR amplification set-up when generating the STR profiles. The sample quality of 6287 single source case work samples were categorized as 'Good’, ‘Partly degraded’, ‘Highly degraded’, ‘Inhibited’ and ‘Degraded and Inhibited’ based on the peak height ratios in the electropherogram data. The DI and IPC were correlated with the assigned quality categories of the samples. Samples categorized into the degraded and/or inhibited categories were found to have statistically significantly different DI and IPC compared to samples categorized as ‘Good’. This indicates that the additional information gained from the QFT can be useful to identify degraded and/or inhibited samples prior to the STR-profile analysis. Future work will re-evaluate the criteria of inclusion in the sample quality groups and implement multi source samples.     

Double Decades of Existence of the Kilum-Ijim Community Forest in Cameroon: What Conservation Lessons?

Abstract

Abstract

At a time when natural forests remain a substantial framework for solving manifold human-induced environmental problems, forest conservation efforts have often been met with a number of challenges, especially in the midst of growing populations of forest-adjacent communities in the developing countries of the world. However, the initiation of the Kilum-Ijim Forest Project in the Western Highland region of Cameroon (erroneously considered to have been a naturally savannized environment) twenty years ago tells a success conservation story. This study, therefore, examines the fate of the Kilum-Ijim Forest prior to the forest conservation project, the conservation efforts put in place to protect and restore the biodiversity of the area, the conservation challenges, and also proposes other areas of intervention for a continuous successful conservation legacy. Due to the constant population pressure and the resultant overexploitation of the Kilum Mountain forest, the original forest size, estimated at 17,500 hectares in 1963, was reduced to 10,500 hectares by 1983. In recognition of the umbilical link between forest and forest-adjacent communities, the Cameroon Government and BirdLife International liaised with the adjacent tribal communities for a sustainable way of managing the forest. While these communities benefit through the non-consumptive use of the forest and other alternative livelihood means, the ecological viabilities of the forest are equally promoted through biodiversity restoration. Due to this community-based management approach, the Kilum-Ijim forest remains an outstanding example of a richly endowed highland montane forest, with a number of endemic wildlife species. Today, conservation efforts have restored the forest size to over 20,000 hectares. Having understood the need for forest conservation and the ensuing conservation benefits, perhaps it is time to increase the forest conservation sites while more alternatives serving human needs are designed and promoted. This conservation legacy should also serve as an example worth emulating in other highland regions with a history of forest degradation.     

Estimating drop-out probabilities of STR alleles accounting for stutters,detection threshold truncation and degradation

Allelic drop-out continues to be a challenge to forensic geneticists when interpreting crime scene evidence and calculating the evidential weight. Methods exist for estimating the probability of allelic drop-out, where the most promising methods use the signal intensities as input for quantifying the drop-out probability. Using data from real crime cases, we demonstrate that taking degradation of the biological material and truncation of the data due to a detection threshold into account is superior to previous approaches. An additional correction for stuttering effects showed limited improvement.     

Comparison of DNA typing using AmpFlSTR Yfiler and PowerPlex Y System,for specimens subject to very long storage

We performed DNA typing from blood stains stored at room temperature for 22–30 years, using AmpFlSTR Yfiler PCR amplification Kit and PowerPlex Y System to extract and amplify the DNA and performing electrophoresis with an ABI 310 Genetic Analyzer. We identified alleles using GeneMapper ID v3.2.1 software. We found that long-term storage tended to reduce the number of detectable loci in the blood stains and that it was easier to detect the loci of smaller amplicons than larger amplicons.     

离体人肝细胞核DNA含量死后变化的图像分析研究

目的应用图像分析技术研究人肝细胞DNA降解与死亡时间的关系。方法选取18例已知死亡时间的人体肝脏,在死后4~36h内每小时进行细胞学涂片、Feu lgen-Vans染色,应用图像分析系统研究肝细胞核平均灰度、平均光度、积分光密度等参数在死后的变化规律。结果在4~36h内随死亡时间的延长,肝细胞核的平均灰度逐渐上升,平均光度、积分光密度逐渐下降,获得了36h内3个参数变化的回归方程。结论肝细胞核的平均灰度、平均光度和积分光密度均与死亡时间有明显的相关性,可望用于推断早期人体死亡时间。     

Rangeland Degradation in North China Revisited? A Preliminary Statistical Analysis to Validate Non-Equilibrium Range Ecology

Over the past decades, the concepts of carrying capacity and Clementsian vegetation succession have come under attack from the theory of Non-Equilibrium Range Ecology. The new theory hypothesises that in arid regions with high rainfall variability the ecology is mainly determined by climatic and not biotic factors, such as animal grazing. The argument carried further implies that 'rangeland degradation' or 'desertification' are not caused by overgrazing but are part of a natural process of vegetation decline and growth in response to rainfall, which ruminant numbers merely follow. Few empirical studies involving time-series data have been executed to substantiate Non-Equilibrium Range Ecology. This article, hopes to make a contribution to the current debate with a statistical validation of one of its main postulates: the correlation between ruminant numbers and rainfall. The analysis is conducted with figures from the People's Republic of China: a state in which rangeland policy is an outstanding example of management on the basis of carrying capacities and Clementsian succession theory.     

Effect of blood stained soils and time period on DNA and allele drop out using Promega 16 Powerplex kit

Blood stained soils may be of great interest in forensic incidents. Amplification of DNA from soil is often inhibited by co-purified contaminants. Different soils types from Pakistan and Turkey were stained with blood and samples were collected systematically after specified intervals. Rapid, inexpensive, large-scale DNA extraction method involving minimal purification was developed. DNA was quantized using Spectrophotometer and Fluorometer and was confirmed by Agarose Gel Electrophoresis. DNA extracted from different soils in different periods showed a remarkable decrease in yield as well as degradation in every extraction. PCR amplification was performed using various DNA targets present in Promega 16 Powerplex^® System kit. Amplification could not carry out in all loci especially in degraded samples taken after 20 days. Allele n locus drop out was noticed which shows that DNA was degraded. For some loci more than 2 alleles were also noticed showing contamination while working with the blood stained soils.     

Evaluation of five preservation methods for recovery of DNA from bone

The effectiveness of five methods for the preservation of bone were assessed: cell lysis solution (with 1% sodium azide), dehydration/freeze-drying, ethanol (96%), freezing, and room temperature storage. Preserved bone samples were extracted using five optimised extraction methods. These preservation methods were tested for their efficiency for storage of fresh and degraded bone samples for 6 weeks, 6 months and 1 year. Freezing was found to be the best preservation method for longer-term storage of bone samples; this was followed by ethanol (96%), dehydration/freeze-drying, and room temperature storage. Full profiles were obtained from bone samples using all these preservation methods.     

唐代的贬官制度及其行政处罚作用

唐代对官吏的惩治措施虽然以刑罚为主,但这并不意味着统治者对官吏的违法行为一律采用刑罚予以处置。事实上,唐代还有不少惩治官吏的行政处罚措施。贬官就是最常用的办法之一。     

Assessment of PowerPlex® Fusion 5C’s ability to type degraded DNA

DNA samples collected at crime scenes are often degraded so this research focused on the ability of the Promega PowerPlex® Fusion 5C amplification kit to type both naturally and artificially degraded DNA.DNA was degraded naturally by placing equal volumes of blood on white fabric that was stored either inside, outside in a shaded area, or outside in direct sunlight. Samples were then collected every 10 days for 60 days and the DNA extracted (QIAamp® DNA Investigator). Artificially degraded samples were created by exposing extracted DNA to either UV light or 95 °C heat for varying times. DNA was also degraded artificially by placing blood samples into a 50% bleach solution for varying times prior to extraction.Following sample treatment, standard forensic DNA analysis was performed including quantification (Investigator® Quantiplex) and amplification (PowerPlex® Fusion 5C). Separation and detection were performed on an ABI 3130xl capillary electrophoresis unit and analysis was performed using GeneMapper ID v3.2.1.While the time and shade samples showed similar amounts of degradation, the samples exposed to direct sun showed more degradation. The artificially degraded samples showed more signs of degradation such as reduced overall peak height and peak height imbalance at heterozygous loci. There were also some cases where an allele that was known to be in the profile exhibited total dropout. Although there were some instances of both allelic dropout and heterozygote peak imbalance, PowerPlex® Fusion was able to reliably type degraded DNA as all alleles detected were consistent with the known donor profile. The results show that PowerPlex® Fusion is a robust kit capable of handling forensically challenged samples.