Oral and skin microbiome as potential tools in forensic field

The interest in the analysis of the human microbiome for personal identification purposes is based on the microbial diversity amongst individuals. The oral cavity hosts one of the most diverse and abundant microbial communities in the human body; the skin instead is a complex living ecosystem with unique microbial niches at different sites. Both skin and oral microbiomes are highly individual and relatively stable over time. As saliva and skin debris are often found at crime scenes, the analysis of their microbiome may represent a potential tool for personal identification. However, there are some gaps in knowledge on how factors such as age, sex, geographic origin, diet and pathologies can affect the composition of the microbiome. The aim of this study is to improve the existing knowledge by examining oral and skin microbiomes from the same individuals and evaluating the variability between anatomical sites and donors. For this study, 50 individuals living in Italy donated oral swab samples and provided information regarding their diet, lifestyle, health status, antibiotic use, and other demographic data. Skin swabs from 11 of the 50 individuals were also analysed and compared to the oral swabs from the same donors. All analyses were done through metabarcoding of the 16S rRNA region of DNA extracted from the samples. This research outlines the potential use of oral and skin microbiome signatures as added evidence in personal identification, providing useful investigative clues for future forensic caseworks.     

Probabilistic SNP genotyping at low DNA concentrations

We present a statistical method for biallelic SNP genotyping that reduces the risk of wrong SNP calls and gives fewer no-calls. The method uses a symmetric multinomial logistic regression model with an intuitive graphical interpretation. Its probabilistic nature gives the user control over the accepted risk through the estimated genotype probabilities. We compared the performance of our method with the HID SNP Genotyper v.4.3.1 plug-in (HSG) (Thermo Fisher Scientific) and the additional criteria of the University of Copenhagen (UCPH) through a series of six DNA dilutions from 500 pg to 16 pg DNA. The HSG method made wrong calls from 62.5 pg DNA and below, while the UCPH method made wrong calls at 16 pg DNA. Our method allowed SNP genotyping of 16 pg DNA without making wrong calls. Depending on the DNA dilution, our method also reduced the number of no-calls by 70–96 % compared to UCPH method and 59–69 % compared to the HSG method. Our method can be used for any biallelic genotyping.     

DNA Barcoding in Forensic Entomology – Establishing a DNA Reference Library of Potentially Forensic Relevant Arthropod Species,

Throughout the years, DNA barcoding has gained in importance in forensic entomology as it leads to fast and reliable species determination. High‐quality results, however, can only be achieved with a comprehensive DNA barcode reference database at hand. In collaboration with the Bavarian State Criminal Police Office, we have initiated at the Bavarian State Collection of Zoology the establishment of a reference library containing arthropods of potential forensic relevance to be used for DNA barcoding applications. CO1‐5P’ DNA barcode sequences of hundreds of arthropods were obtained via DNA extraction, PCR and Sanger Sequencing, leading to the establishment of a database containing 502 high‐quality sequences which provide coverage for 88 arthropod species. Furthermore, we demonstrate an application example of this library using it as a backbone to a high throughput sequencing analysis of arthropod bulk samples collected from human corpses, which enabled the identification of 31 different arthropod Barcode Index Numbers.     

线粒体高变区多聚C-stretch序列长度多态性

目的研究线粒体高变区多聚C-stretch序列长度多态性,并探讨其在法医学个体识别中的价值。方法针对线粒体高变区nt16180及nt310两个位点采用文献报道引物,应用直接测序技术研究其等位基因分布及频率。结果两对引物扩增长度分别为807bp和962bp,nt16180位点检测到7种基因型,其中AAAACCCCCTCCCC基因型占87.72%,AAAACCCCCCCCCCCCC基因型在汉族人群中首次报道;nt310检测到7种基因型,其中CCCCCCCCTCCCCCC基因型占60.53%;联合两个位点共检测出15种单倍型,GD值为0.6309,其中AAAACCCCCTCCCC-CCCCCCCCTCCCCCC检测出66条,达到57.89%。结论为线粒体控制区DNA在法医学领域中的应用提供基础数据,证实了线粒体nt16180位点和nt310位点单倍型在线粒体DNA鉴定中有较好的应用价值。     

DNA甲基化检测方法及其法医学应用研究进展

DNA甲基化是表观遗传标记的重要组成部分,参与基因表达的调控,在生物发育、衰老以及肿瘤学等领域受到广泛关注。由于具有相对稳定性、可遗传、含量丰富、随龄变化等特点,在法医学领域,DNA甲基化可以作为DNA序列相关经典遗传标记的有效补充,用于年龄推断、组织体液来源检测、同卵双生子的鉴定等。DNA甲基化的检测方法主要有基于甲基化敏感限制性内切酶、重亚硫酸盐转化以及甲基化CpG结合蛋白等原理而建立的一系列方法,近年研究表明,第三代测序技术也可用于DNA甲基化检测。本文就DNA甲基化检测方法及在法医学领域的应用研究进行回顾与综述,以期为法医学实践提供参考。     

Customizing English Language Program for EFL Learners

This paper discusses the importance of having a customized instructional approach specifically for students who are learning English as a Foreign Language （EFL） in the foreign language setting. Most of the innovations introduced by the Education Ministry of Malaysia such as the Communicative Language Teaching （CLT） and phonics are suitable for ESL （English as a second language） learners, while the EFL learners are still left behind. A suitable teaching approach which customizes the needs of the students in EFL setting, especially in the state of Terengganu should be introduced. The main focus of the program exploits reading and writing skills in providing language input since these two skills are more dominant in terms of utility and functions among the EFL students as compared with the ESL students who are enable to exploit speaking and listening skills because of the natural setting. The research investigates the prospect of developing a suitable language teaching program based on 10 basic sentence patterns （10SP） which are exploited through the principles of transformational generative grammar and customized learning experiences focusing on reading as a bridge in acquiring other language skills such as writing, listening, and speaking.     

Illiberal democracy and violent conflict in contemporary Indonesia

When Indonesia's President Suharto was forced to resign in 1998, the accompanying uncertainty triggered serious communal violence in five regions. As the nation's politics and economy stabilized from 2002, so did those provinces. Identity-based conflict is now the rare exception rather than the rule in democratic Indonesia. Yet puzzlingly, despite the consolidation of democracy, ethnic clashes and mob violence against religious minorities continue to occur. While such events are now far smaller than those in the first years of democratization and occur only occasionally, their persistence requires analysis given the potential for escalation and what it tells us about Indonesia's reform process. In this article I compare recent incidents with that of the initial post-authoritarian era, and find that identity-based collective violence persists because many important causes of conflict have not been removed by democratic consolidation. As found by numerous scholars, many illiberal characteristics of the authoritarian state have segued neatly into democratic Indonesia. I assert that this has left several main causes of group violence firmly in place. I further contend that the failure to remove these phenomena partly has its origins in the order of democratic reforms chosen in the years after Suharto's resignation.     

Additional sequence characterization of NIST SRM 2391c: PCR-Based DNA Profiling Standard

The NIST Standard Reference Material (SRM) 2391c: PCR-Based DNA Profiling Standard was designed for use in the standardization of forensic and paternity quality assurance procedures for fragment-based typing short tandem repeat (STR) alleles generated by the polymerase chain reaction (PCR). Certified genotypes of the 6 components A–F were assigned for 24 autosomal and 17 Y-STR markers plus Amelogenin using concordance testing between commercial kits. Selected Sanger sequencing characterization was performed for the alleles of 11 STR markers when only one PCR primer set was available for fragment-based typing. The goal is to characterize the remaining 30 STR loci in components A–C by Sanger sequencing methods for the STR repeat regions and adjacent flanking regions. Additional characterization of the SRM is intended to support the emerging interest in next-generation sequencing technologies for forensic typing applications. Sanger methods have detected underlying polymorphisms (sequence, insertion-deletion, variation in complex motifs) typically not detected by fragment-based typing. The sequenced regions include the commercial or known PCR binding sites commonly implemented in fragment-based typing.     

Characterization of NIST standard reference materials by next generation sequencing

The National Institute of Standards and Technology (NIST) offers certified Standard Reference Materials (SRMs) for laboratories which perform DNA-based human identity testing. Developed by the Applied Genetics Group at NIST, forensic DNA SRMs are well characterized for relevant markers such as autosomal and Y-chromosomal short tandem repeats (STRs) and mitochondrial DNA (mtDNA) sequence. Characterization of the SRMs has been performed by capillary gel electrophoresis fragment-based genotyping analysis and/or Sanger type sequencing. New technologies, commonly referred to as next generation sequencing (NGS), now offer an opportunity to validate the certified DNA-based reference materials using an orthogonal method and thereby increase the confidence in the certified values of the materials. The increased sensitivity of NGS will facilitate expansion of the information content of NIST SRMs through the characterization of new features which are beyond the ability of fragment-based analysis or Sanger sequencing to detect. This work will also lead to the availability of Certified Reference Materials for laboratories wishing to implement and validate NGS technology in the field of forensics.     

用PCR—测序法对人类线粒体DNA多态区的研究

用PCR方法，对线粒体DNA多态区15997至三6401区域进行扩增，产物DNA经纯化处理局直接进行自动化序列测定，得到了准确的序列结果。将得到的中国人mtDNA多态区序列与国外已报道的相应序列进行对比，证实我们所测序列与白种人相应序列之间存在碱基差异。