Identification and phylogenetic analysis of hepatitis C virus in forensic blood samples obtained from injecting drug users

Injecting drug users (IDUs) are a high-risk group for contracting hepatitis B virus (HBV), hepatitis C virus (HCV), and human immunodeficiency virus (HIV) infections. In Japan, data on the prevalence of those blood-borne viruses among IDUs are very limited. Blood samples were obtained from 12 cadavers of IDUs sent to Nagoya City University for the purpose of judicious autopsy and two alive IDUs with hepatitis C referred to a local hospital at the same period. The viruses were detected by polymerase chain reaction and phylogenetic analysis was performed. Two (16.6%) of the 12 autopsy cases were positive for HCV, but no case was positive for either HBV or HIV. Phylogenetic analysis of the two HCV isolates revealed that one was classified into genotype 1b and another was genotype 2b. Furthermore, nucleotide sequences of two isolates recovered from IDUs with hepatitis C were identical, that indicated the transmission of HCV between them, and those HCV were phylogenetically classified into genotype 2a. The prevalence of HCV infection among IDUs in Japan, despite the case of judicious autopsy, seems to be high, but HIV infection seems to be rare. The transmission of HCV between IDUs was demonstrated, and this indicates that phylogenetic analysis would applicable to also forensic analysis. HCV isolates identified in this study did not phylogenetically segregate, thus multiple transmission route of HCV among IDUs seems be exist in Japan.     

Development of Forensic Assay Signatures for Ebolaviruses

Ebolaviruses are a diverse group of RNA viruses comprising five different species, four of which cause fatal hemorrhagic fever in humans. Because of their high infectivity and lethality, ebolaviruses are considered major biothreat agents. Although detection assays exist, no forensic assays are currently available. Here, we report the development of forensic assays that differentiate ebolaviruses. We performed phylogenetic analyses and identified canonical SNPs for all species, major clades and isolates. TaqMan‐MGB allelic discrimination assays based on these SNPs were designed, screened against synthetic RNA templates, and validated against ebolavirus genomic RNAs. A total of 45 assays were validated to provide 100% coverage of the species and variants with additional resolution at the isolate level. These assays enabled accurate forensic analysis on 4 “unknown” ebolaviruses. Unknowns were correctly classified to species and variant. A goal of providing resolution below the isolate level was not successful. These high‐resolution forensic assays allow rapid and accurate genotyping of ebolaviruses for forensic investigations.     

From research to policy: Preventing residential burglary through a systems approach

This paper isolates crime prevention policy implications which stem from a series of interrelated environmental studies of residential burglaries. A number of crime prevention strategies are developed using a systems approach. It is argued that changes made to the environments of individuals, groups, communities, organizations, and society can achieve lower risks of residential burglary victimization.     

Detection of dipiridamol in biological fluids

Acetone is proposed as an isolating agent for dipiridamol isolation from biological fluids. Purification of the isolates was performed with liquid-liquid extraction and colon chromatography with silasorb C-18 sorbent. The technique of dipiridamol detection in the blood and urine is described. The assays results are presented.     

Fungal DNA challenge in human STR typing of bone samples

The present study focuses on possible cross-reaction of fungal DNA with human STR primers that may affect subsequent forensic DNA analysis of forensic samples. Specificity of human STR markers namely HUMAMEL, HUMCSF1PO, D8S306, HUMTH01, HUMvWA, HUMFES/FPS, HUMF13A01, HUMDHFRP2, HUMFGA and HUMTPOX was tested using DNA of 24 different filamentous fungal isolates obtained from exhumed bone samples. The specificity of these ten STR markers for human DNA was demonstrated. Presence of non-human DNA in five bone samples analyzed did not alter scoring of detected alleles. Notably, amplification was inhibited in the presence of a high proportion of fungal DNA compared to human DNA (1000 ng: 1 ng) in DNA mixture experiments. The results of the present study underscore the importance of carefully analyzing the presence of non-human biological contaminants that may affect DNA typing of environmentally challenged forensic samples to avoid spurious data interpretation.     

Variability of the Entire Mitochondrial DNA Control Region in a Human Isolate from the Pas Valley (Northern Spain)

Abstract: In this study, we analyzed the entire mtDNA control region in 61 unrelated individuals from the Pas Valley (Cantabria), a human isolate from northern Spain, to evaluate the suitability of this analysis to increase the power of discrimination of this locus for forensic purposes in human isolates. Low values obtained for the diversity parameters confirmed the relative isolation of this human group. The main findings of this study indicated that even the analysis of the entire mtDNA control region may have important limitations for use in forensic casework when dealing with human isolates: none of the 44 individuals who exhibited identical HVI‐HVII haplotypes could be further differentiated by analysis of segment HVIII. Nevertheless, analysis of the entire mtDNA control region proved to be useful to determine the ancestry of the samples examined, by contributing to the confirmation, and, on occasion, even to the refinement of the haplogroup assignment.     

Forensic analysis of hallucinogenic fungi: a DNA-based approach

Hallucinogenic fungi synthesize two controlled substances, psilocin and psilocybin. Possession of the fungal species that contain these compounds is a criminal offence in North America. Some related species that are morphologically similar, do not contain the controlled substances. Therefore, unambiguous identification of fungi to the species level is critical in determining if a mushroom is illegal. We investigate a phylogenetic approach for the identification of species that contain the psychoactive compounds. We analyzed 35 North American specimens representing seven different genera of hallucinogenic and non-hallucinogenic mushrooms. We amplified and sequenced the internal transcribed spacer region of the rDNA (ITS-1) and a 5' portion of the nuclear large ribosomal subunit of rRNA (nLSU rRNA or 28S). ITS-1 locus sequence data was highly variable and produced a phylogenetic resolution that was not consistent with morphological identifications. In contrast, the nLSU rRNA data clustered isolates from the same species and separated hallucinogen containing and non-hallucinogen containing isolates into distinct clades. With this information, we propose an approach that combines the specificity of PCR detection and the resolving power of phylogenetic analysis to efficiently and unambiguously identify hallucinogenic fungal specimens for legal purposes.     

Forensic analysis of hallucinogenic fungi: a DNA-based approach

Hallucinogenic fungi synthesize two controlled substances, psilocin and psilocybin. Possession of the fungal species that contain these compounds is a criminal offence in North America. Some related species that are morphologically similar, do not contain the controlled substances. Therefore, unambiguous identification of fungi to the species level is critical in determining if a mushroom is illegal. We investigate a phylogenetic approach for the identification of species that contain the psychoactive compounds. We analyzed 35 North American specimens representing seven different genera of hallucinogenic and non-hallucinogenic mushrooms. We amplified and sequenced the internal transcribed spacer region of the rDNA (ITS-1) and a 5′ portion of the nuclear large ribosomal subunit of rRNA (nLSU rRNA or 28S). ITS-1 locus sequence data was highly variable and produced a phylogenetic resolution that was not consistent with morphological identifications. In contrast, the nLSU rRNA data clustered isolates from the same species and separated hallucinogen containing and non-hallucinogen containing isolates into distinct clades. With this information, we propose an approach that combines the specificity of PCR detection and the resolving power of phylogenetic analysis to efficiently and unambiguously identify hallucinogenic fungal specimens for legal purposes.     

Pharmacogenomics as an aspect of molecular autopsy for forensic pathology/toxicology: does genotyping CYP 2D6 serve as an adjunct for certifying methadone toxicity?

Pharmacogenomics, applied as an aspect of molecular autopsy, may be used as an adjunct for certifying methadone fatalities. Methadone is metabolized by cytochrome P-450 (CYP) 1A2, 3A4, and 2D6. We hypothesized that methadone toxicity may be partially due to CYP 2D6 *3, *4, and *5 variant alleles, resulting in poor drug metabolism. A retrospective analysis was performed on covariables and risk factors of 21 methadone cases from the Milwaukee County Medical Examiner's Office (1998-2000). PCR genotyping showed: one heterozygous for 2D6*3, two homozygous for 2D6*4, five heterozygous for 2D6*4, and one heterozygous for both 2D6*3 and *4. This limited number of cases showed that the prevalence of poor metabolizer was higher but not significantly different from that of a control group (n = 23) (P > 0.05, Fisher Exact Test). Thus, CYP 2D6 mutations may not yet be directly associated with methadone toxicity. However, pharmacogenomics, complementing other case findings, served as an adjunct in interpreting methadone toxicity of poor and intermediate metabolizers.     

Chimpanzee homologous of human Y specific STRs. A comparative study and a proposal for nomenclature

Eleven Y specific microsatellites, previously studied in humans, were typed for fragment length and sequenced in chimpanzees (Pan troglodytes).The primers described by Ayub et al. (Nucleic Acids Res. 28, 2000, 2) for amplifying DYS434, DYS435, DYS436, DYS437, DYS438, DYS439 and those described by White et al. (Genomics, 57, 1999, 433) for GATA A10, A7.1, A7.2, C4, and H4, were used to amplify DNA samples from chimpanzees.Primers described for Y GATA A4 were found to amplify the same region as reported for DYS439. Moreover, the GATA A4 forward primer only matches the repeat flanking region in 14 of the 28bp, being responsible for a very weak amplification. Therefore, this system was not included in this study.The analysis of the repeat and sequence structure observed in chimpanzee and human Y chromosomes allowed evolutionary comparisons as well as the basis for improving Y STR nomenclature and therefore, a unified nomenclature for these novel STRs is proposed to the scientific community following ISFG recommendations.     

A highly specific and sensitive sandwich enzyme immunoassay for human hemoglobin A

A highly specific and sensitive sandwich enzyme immunoassay for human hemoglobin A (Hb A) is described. A rabbit anti-human Hb A IgG-coated polystyrene ball was incubated with human Hb A and subsequently with affinity-purified anti-human Hb A Fab'-horseradish peroxidase conjugates, which had been prepared before and after absorption with Japanese monkey Hb-Sepharose 4B and dog Hb-Sepharose 4B. Bound peroxidase activity was measured by fluorimetry using 3-(4-hydroxyphenyl)propionic acid as a substrate. The detection limits of human Hb A using the conjugate before and after the absorption were 0.65 pg/tube (3 X 10(10)-fold dilution of whole blood) and 2.0 pg/tube (1 X 10(10)-fold dilution of whole blood), respectively. Human Hb A could be discriminated from Hb of animals such as Japanese monkey, dog, cat, pig, horse, sheep, chicken and cow by measuring bound peroxidase activity in the presence and absence of the conjugates prepared before and after the absorption. Human Hb A in bloodstains on cotton gauze could be discriminated from Hb of animals described above even after seven washings. Human Hb A in 220,000-fold diluted bloodstains on cotton gauze could also be discriminated from Hb of animals described above.     

Y染色体3个SNP基因座及其单倍型的遗传多态性和群体差异

目的 探讨人类Y染色体3个SNP基因座及其单倍型的遗传多态性和群体差异。方法 应用PCR-RFLPs结合DNA序列分析技术,对140例来自中国藏族、日本、南非黑人及南非白人男性的Y染色体M4、M9和M122基因座的等位基因进行分析。结果 全部样品M4基因座的等位基因均为野生型M4A,未发现多态性。共检出3种单倍型,黑人个体均为野生型单倍型M4A/M9C/M122T。白人个体有8例单倍型为M4A/M9G/M122T,未检出等位基因M122C。日本及中国藏族群体以单倍型M4A/M9C/M122T为主,频率分别为0.50和0.65,未检出单倍型M4A/M9C/M122C,个人识别机率与父权排除率分别为0.6191和0.4994。单倍型频率分布在中国藏族和日本群体之间存在显著性差异(P<0.01)。结论 单倍型M4A/M9G/M122C为亚洲人特征,M9和M122基因座在中国藏族和日本群体中具有较高的遗传多态性,并显示出明显的人种和群体差异。     

Immunology and microbiology devices; reclassification of the herpes simplex virus serological assay device. Final rule

The Food and Drug Administration (FDA) is amending the special controls for the herpes simplex virus (HSV) serological assay device type, which is classified as class II (special controls). These device types are devices that consist of antigens and antisera used in various serological tests to identify antibodies to herpes simplex virus in serum, and the devices that consist of herpes simplex virus antisera conjugated with a fluorescent dye (immunofluorescent assays) used to identify herpes simplex virus directly from clinical specimens or tissue culture isolates derived from clinical specimens.     

Detection of drugs using XAD-2 resin. I:Choice of resin, chromatographic conditions, and recovery studies

Amberlite XAD-2, a nonionic polystyrene divinylbenzene resin, was first used for the analysis of drugs in urine and a number of reports have described the development at optimal conditions for extraction, including type of resin columns, pH conditions, and eluting solvents. XAD-4 and XAD-7 resins were compared to the similarly structured XAD-2 resin and no significant advantage over the XAD-2 resin for drug screening was observed. A quantity of 5 to 6 g of resin was found to have sufficient capacity for the extraction of 200 ml of pentobarbital solution (1 mg/100ml). A column flow rate of approximately 15 ml/min (gravitational flow) was sufficient for analysis and slower rates were not more efficient. A mixture of ethyl acetate and 1,2-dichloroethane (3:2) was found to give best overall recovery (66 to 94%) of drugs, the resulting extracts being reasonably free of interfering substances. A pH value of 8.5 is recommended as optimum for comprehensive analysis of acidic and basic drugs. Recovery studies were conducted on spiked samples to determine drug losses occuring during various steps in the XAD-2 extraction procedure for four acidic (amobarbital, secobarbital, pentobarbital, and phenobarbital) and four basic (morphine, codeine, meperidine, and methadone) drugs. A relatively small amount (0 to 5%) of the drugs was not adsorbed by the resin and amounts varying from 6 to 40% failed to be desorbed by the eluting solvent. Additional losses occurred during the removal and analysis of TLC spots. Recovery of drugs from aqueous solutions analyzed with the XAD-2 resin were compared to recoveries reported in the literature with other XAD-2 resin methods for the extraction of drugs from urine. Recovery of phenobarbital, morphine, and codeine improved by 4 to 23% while recoveries of amobarbital, pentobarbital, secobarbital, methadone, and meperidine were 4 to 28% less efficient when compared to literature data.     

Interrogating genomic diversity of E. coli O157:H7 using DNA tiling arrays

Here, we describe a novel microarray-based approach for investigating the genomic diversity of Escherichia coli O157:H7 in a semi-high throughput manner using a high density, oligonucleotide-based microarray. This microarray, designed to detect polymorphisms at each of 60,000 base-pair (bp) positions within an E. coli genome, is composed of overlapping 29-mer oligonucleotides specific for 60 equally spaced, 1000-bp loci of the E. coli O157:H7 strain EDL933 chromosome. By use of a novel 12-well microarray that permitted the simultaneous investigation of 12 strains, the genomes of 44 individual isolates of E. coli O157:H7 were interrogated. These analyses revealed more than 150 single nucleotide polymorphisms (SNPs) and several deletions and amplifications in the test strains. Pyrosequencing was used to confirm the usefulness of the novel SNPs by determining their allelic frequency among a collection of diverse isolates of E. coli O157:H7. The tiling DNA microarray system would be useful for the tracking and identification of individual strains of E. coli O157:H7 needed for forensic investigations.     

Analytical pyrolysis of Streptococcus saliivarius as and aid to identification in bite-mark investigation

The use of pyrolysis mass spectrometry (Py-MS) and statistical analysis of mass spectra is introduced as a method for “finger-printing” strains of Streptococcus salivarius. The objective is to provide correlative evidence regarding the identity of suspects in cases of assault or rape involving bite-marks. The results of the analysis of isolates from two individuals are presented, illustrating the differentiation of S. salivarius at strain level according to the origin of the isolate.     

快速溶剂萃取-气相色谱/质谱法分析血液中的4种滥用药物

目的 建立生物检材血液中滥用药物的快速溶剂萃取（ASE）方法.方法 通过优化快速溶剂萃取各参数,提取血液中的滥用药物进行GC/MS定性定量分析.结果 血液中美沙酮、可卡因、蒂巴因、海洛因4种滥用药物的平均回收率在87.8％～97.5％之间,滥用药物在0.4μg/mL～4.0μg/mL的浓度范围内线性良好.结论 该方法具有操作简便快捷,回收率高、重现性好等特点,可广泛应用于生物检材血液中滥用药物的检验鉴定.     

Rethinking Agamben: Ontology and the Coming Politics

Giorgio Agamben’s work has often been criticised for being bleak, pessimistic, and of little use for thinking about political action. This image of Agamben has, however, resulted from a narrow reading of the Homo Sacer project that isolates it from his early thought on language and ontology. This essay draws on new works by Mathew Abbott and Jessica Whyte to explore the ways that Agamben attempts to think the conditions for overcoming the political nihilism of the present. It argues that the two works diverge on the question of where Agamben locates the potential for political transformation, and that this results from their differing approaches to the relationship between ontology and politics.     

Motives and methods for leaving the gang: Understanding the process of gang desistance

Purpose

This study examined the process of leaving the gang. Gang membership was conceptualized in a life course framework and the motives for why and methods for how one leaves the gang were analyzed.

Methods

Data were gathered from a sample of 84 juvenile arrestees in Arizona, all of whom left their gang. Motives for leaving the gang were organized into factors internal (push) and external (pull) to the gang, while methods for leaving the gang were organized into hostile and non-hostile modes of departure. Motives and methods were cross-classified and their correlates were examined, notably in relation to gang ties—persisting social and emotional attachments to the gang.

Results

Push motives and non-hostile methods were the modal responses for leaving the gang. While it was not uncommon to experience a hostile departure from the gang, most former gang members reported walking away without ritual violence or ceremony. This method was conditional on the motive for departure, however. None of the individuals leaving the gang for pull or external reasons experienced a hostile departure. While gang ties persisted regardless of motive or method, retaining such ties corresponded with serious consequences.

Conclusions

A life course framework is capable of organizing similarities between leaving the gang and desistance from other forms of crime and deviant groups. The process of gang desistance is consistent with asymmetrical causation. Due to limited attention to this process, a typology is introduced as a basis for understanding leaving the gang in relation to desisting from crime.