DNA analysis

In cases of mass disaster, there is often a need for managing, analyzing, and comparing large numbers of biological samples and DNA profiles. This requires the use of laboratory information management systems for large-scale sample logging and tracking, coupled with bioinformatic tools for DNA database searching according to different matching algorithms, and for the evaluation of the significance of each match by likelihood ratio calculations. There are many different interrelated factors and circumstances involved in each specific mass disaster scenario that may challenge the final DNA identification goal, such as: the number of victims, the mechanisms of body destruction, the extent of body fragmentation, the rate of DNA degradation, the body accessibility for sample collection, or the type of DNA reference samples availability. In this paper, we examine the different steps of the DNA identification analysis (DNA sampling, DNA analysis and technology, DNA database searching, and concordance and kinship analysis) reviewing the "lessons learned" and the scientific progress made in some mass disaster cases described in the scientific literature. We will put special emphasis on the valuable scientific feedback that genetic forensic community has received from the collaborative efforts of several public and private USA forensic laboratories in assisting with the more critical areas of the World Trade Center (WTC) mass fatality of September 11, 2001. The main challenges in identifying the victims of the recent South Asian Tsunami disaster, which has produced the steepest death count rise in history, will also be considered. We also present data from two recent mass fatality cases that involved Spanish victims: the Madrid terrorist attack of March 11, 2004, and the Yakolev-42 aircraft accident in Trabzon, Turkey, of May 26, 2003. A mass disaster is an unexpected event that causes serious injury and death to a number of people. Mass disaster events may be natural disasters (earthquakes, flooding, and tornadoes), accidental disasters (aircraft crashes, train crashes and derailments, and building fires), or intentioned terrorism acts (direct attacks on significant objectives, and bombing of populated areas, including suicide attacks and deployments of chemical and bio-logical weapons). Forensic identification of victims is essential for humanitarian reasons, but also for civil or criminal investigative needs, and it is essentially based on forensic anthropology, fingerprints, forensic odontology, radiology, and DNA typing (1).

The s allele serotonin transporter polymorphic region (5-HTTLPR) is associated with a number of physiological mechanisms that may increase the risk of elevated depressive symptoms. However, reports of a relationship between serotonin transporter polymorphic region (5-HTTLPR) genotype and depressive symptoms have thus far been inconclusive. This heterogeneity of results suggests that other factors may be moderating the relationship between 5-HTTLPR and depressive symptoms. Higher levels of physical activity are associated with lower levels of depressive symptoms. Mechanisms responsible for this association include alterations of the serotonergic system and the hypothalamicepituitary axis. The aim of the current study was to measure the moderating effect of physical activity on the relationship between 5-HTTLPR genotype and depressive symptoms. Participants, ages 18e23, provided a saliva sample for DNA analysis and completed questionnaires to assess depressive symptoms and physical activity. A hierarchical multiple regression analysis was conducted to examine the moderating effect of physical activity on the relationship between 5-HTTLPR genotype and depressive symptoms. Analysis revealed a significant interaction between 5-HTTLPR and physical activity (p ¼ .010). At low levels of physical activity, individuals with at least one s allele had significantly higher levels of depressive symptoms compared to ll individuals (p ¼ .011). This finding provides preliminary support for a moderating effect of physical activity on the relationship between 5-HTTLPR and depressive symptoms.

It has been reported that cystic fibrosis is very rare in Asians, and its clinical expression and genetic mutations are different from those found in Caucasians. We report the case of a boy who had chronic diarrhea with failure to thrive and frequent respiratory tract infections beginning at the age of 2 months. He developed bronchiectasis with chronic severe hypoxemia and pancreatic insufficiency by the age of 3 years and 5 months, which raised the consideration of cystic fibrosis. DNA analysis revealed a homozygous R553X mutation, and both his parents were subsequently proven to be R553X carriers. This case is the first report in a Taiwanese with cystic fibrosis attributable to a mutation commonly seen in Caucasians. However, the age of onset was much younger and the clinical course was more severe than those associated with Western patients. We reviewed the eight reported Taiwanese patients with cystic fibrosis, including the present case. We believe that the incidence of cystic fibrosis in Taiwan may be underestimated. Both genetic and environmental factors may play a role in the phenotypic disparity between Asians and Caucasians.

Acinetobacter baumannii is an important nosocomial pathogen usually in the context of serious underlying disease. Multidrug resistance in these organisms is frequent. The -lactamase inhibitors clavulanic acid, sulbactam, and tazobactam have intrinsic activity against Acinetobacter strains. To evaluate their potential therapeutic usefulness, we determined the in vitro activity of ampicillin, sulbactam, ampicillin-sulbactam, cefoperazone, cefoperazone-sulbactam, piperacillin, piperacillin-sulbactam, tazobactam, piperacillin-tazobac- tam, amoxicillin,

Multi-proxy approach was used to reconstruct the environmental conditions of remote lakes in the High Tatra Mountains (Slovakia) over the past few centuries (approximately 500-1000 years). Short sediment cores (*30 cm) taken from three morphologically similar glacial lakes distributed along altitudinal gradient (subalpine to alpine conditions) were analysed for organic matter content (LOI), diatoms and chironomids. Both descriptive and correlative approaches were used for analysing stratigraphical data. Predictive canonical correspondence analysis and co-correspondence analysis were applied to directly relate physical and biological proxies to each other. The relationship between LOI and biotic proxies was inconsistent across groups and lakes. Concordant patterns in diatom and chironomid composition were found in two non-acidified lakes. Common trends in those assemblages indicated major past environmental events such as the Little Ice Age, air pollution and lake acidification. In contrast, no relationship between the composition of diatom and chironomid assemblages was found in the formerly acidified lake, suggesting different responses of assemblages to acidification. While chironomids showed shifts that are attributable to recovery, diatoms assemblage remained relatively stable throughout the uppermost layers of the sediment record. On the other hand, climatic-driven changes in assemblages detected in the deeper layers were more pronounced in diatoms than in chironomids.

An integrated lab-on-a-chip system has been developed and successfully utilized for real-time forensic short tandem repeat (STR) analysis. The microdevice comprises a 160-nL polymerase chain reaction reactor with an on-chip heater and a temperature sensor for thermal cycling, microvalves for fluidic manipulation, a co-injector for sizing standard injection, and a 7-cm-long separation channel for capillary electrophoretic analysis. A 9-plex autosomal STR typing system consisting of amelogenin and eight combined DNA index system (CODIS) core STR loci has been constructed and optimized for this real-time human identification study. Reproducible STR profiles of control DNA samples are obtained in 2h and 30min with <or=0.8bp allele typing accuracy. The minimal amount of DNA required for a complete DNA profile is 100 copies. To critically evaluate the capabilities of our portable microsystem as well as its compatibility with crime scene investigation processes, real-time STR analyses were carried out at a mock crime scene prepared by the Palm Beach County Sheriff's Office (PBSO). Blood stain sample collection, DNA extraction, and STR analyses on the portable microsystem were conducted in the field, and a successful "mock" CODIS hit was generated on the suspect's sample within 6h. This demonstration of on-site STR analysis establishes the feasibility of real-time DNA typing to identify the contributor of probative biological evidence at a crime scene and for real-time human identification.

Accurate unambiguous identification of ancient or historical specimens can potentially be achieved by DNA analysis. The controversy surrounding the fate of the last Russian Emperor, Nicholas II, and his family has persisted, in part, because the bodies of 2 children, Prince Alexei and 1 of his sisters, have not been found. A grave discovered in 1991 contained remains putatively identified as those of the Russian Royal family. However, not all family members were represented. Here, we report the results of genomic analyses of new specimens, the human remains of 2 burned skeletons exhumed from a grave discovered in July 2007, and the results of a comprehensive genomic analysis of remains from the 1991 discovery. Additionally, Ϸ117 years old archival blood specimens from Nicholas II were obtained and genotyped, which provided critical material for the specific determination of individual identities and kinship identifications. Results of genotypic analyses of damaged historical specimens were evaluated alongside samples from descendants of both paternal and maternal lineages of the European Royal families, and the results conclusively demonstrate that the recently found remains belong to children of Nicholas II: Prince Alexei and his sister. The results of our studies provide unequivocal evidence that the remains of Nicholas II and his entire family, including all 5 children, have been identified. We demonstrate that convergent analysis of complete mitochondrial genome sequences combined with nuclear DNA profiles is an efficient and conclusive method for individual and kinship identification of specimens obtained from old historic relics. complete mitochondrial genome ͉ genetic identification ͉ historical relics ͉ human ͉ STR profile

There has been considerable controversy over the identity of the skeletal remains exhumed in Brazil in 1985 and believed to be those of Dr Josef Mengele, the Auschwitz 'Angel of Death'. Bone DNA analysis was therefore conducted in an attempt to provide independent evidente of identity. Trace amounts of highly degraded human DNA were successfully extracted from the shaft of the femur. Despite the presence of a potent inhibitor of DNA amplification, microsatellite alleles could be reproducibly amplified from the femur DNA. Comparison of the femur DNA with DNA from Josef Mengele's son and wife revealed a bone genotype across 10 different loei fully compatible with paternity of Mengele's son. Less than 1 in 1800 Caucasian individuals unrelated to Mengele's son would by chance show full paternal inclusion. DNA analysis therefore provides very strong independent evidente that the remains exhumed from Brazil are indeed those of Josef Mengele.

Mitochondrial COII DNA was amplified by PCR from total DNA extracted from field collected primate fecal samples (n = 24) which had been stored without refrigeration for over 30 days. High molecular weight DNA total DNA was obtained from samples stored in 70% (v/v) ethanol, SDS lysis buffer (LB) and guanidine isothiocyanate buffer (GTB) than from samples stored in 10% formalin. Fecal DNA quality and COII amplification varied according to storage solution (formalin, ethanol, LB and GTB), extraction method (LB-based and GTB-based) and primate species (chimpanzee, baboon, human). It is recommended that fecal samples be collected in LB for DNA analysis. However, GTB-based protocols are suitable when total RNA is needed for epidemiological studies of viral diseases or gene expression analysis.

In cases of mass disaster, there is often a need for managing, analyzing, and comparing large numbers of biological samples and DNA profiles. This requires the use of laboratory information management systems for large-scale sample logging and tracking, coupled with bioinformatic tools for DNA database searching according to different matching algorithms, and for the evaluation of the significance of each match by likelihood ratio calculations. There are many different interrelated factors and circumstances involved in each specific mass disaster scenario that may challenge the final DNA identification goal, such as: the number of victims, the mechanisms of body destruction, the extent of body fragmentation, the rate of DNA degradation, the body accessibility for sample collection, or the type of DNA reference samples availability. In this paper, we examine the different steps of the DNA identification analysis (DNA sampling, DNA analysis and technology, DNA database searching, and ...

Multi-proxy approach was used to reconstruct the environmental conditions of remote lakes in the High Tatra Mountains (Slovakia) over the past few centuries (approximately 500-1000 years). Short sediment cores (*30 cm) taken from three morphologically similar glacial lakes distributed along altitudinal gradient (subalpine to alpine conditions) were analysed for organic matter content (LOI), diatoms and chironomids. Both descriptive and correlative approaches were used for analysing stratigraphical data. Predictive canonical correspondence analysis and co-correspondence analysis were applied to directly relate physical and biological proxies to each other. The relationship between LOI and biotic proxies was inconsistent across groups and lakes. Concordant patterns in diatom and chironomid composition were found in two non-acidified lakes. Common trends in those assemblages indicated major past environmental events such as the Little Ice Age, air pollution and lake acidification. In contrast, no relationship between the composition of diatom and chironomid assemblages was found in the formerly acidified lake, suggesting different responses of assemblages to acidification. While chironomids showed shifts that are attributable to recovery, diatoms assemblage remained relatively stable throughout the uppermost layers of the sediment record. On the other hand, climatic-driven changes in assemblages detected in the deeper layers were more pronounced in diatoms than in chironomids.

Identification of forensic DNA samples by short tandem repeat (STR) profiling is currently an essential component of criminal investigations and can aid in linking perpetrators to crimes as well as identifying missing individuals or unidentified remains. In South Africa, recent amendments to legislation have allowed for the mandatory acquisition of reference DNA samples from certain offenders in order to populate the new National Forensic DNA Database. A novel method for the collection of buccal samples, the EasiCollect device, has been proposed to facilitate the collection of these DNA samples, replacing blood collecting devices as the standard method of DNA collection. Subsequently, this device has been introduced into South African state mortuaries to assist in the identification of deceased individuals. In order to ascertain if this device is suitable for use in the postmortem setting, an investigation was performed to compare the main methodology currently utilised within South African mortuaries, namely femoral blood transferred to 'Fast Technology for Analysis of nucleic acids' (FTA) cards, and buccal cells obtained using the EasiCollect device. DNA yields and STR genotyping results were compared between the two collection methods in thirty deceased individuals. Buccal samples provided a significantly greater DNA yield than blood samples, while no significant difference was observed between the qualities of the sample types as measured by the 260/280 nm ratio. Full STR profiles were obtained from all blood and buccal samples, with amplification efficiency showing limited DNA degradation and PCR inhibition in these samples, and only 3% of samples giving potentially disputable results. Numerous issues surrounding the collection of blood samples, however, indicated that this method is not optimal for use in the mortuary, with the EasiCollect device providing a more practical and robust method for the collection of DNA samples in the mortuary.

In this paper, we review and analyze the emerging network paradigm in organizational research. We begin with a conventional review of recent research organized around recognized research streams. Next, we analyze this research, developing a set of dimensions along which network studies vary, including direction of causality, levels of analysis, explanatory goals, and explanatory mechanisms. We use the latter two dimensions to construct a 2-by-2 table cross-classifying studies of network consequences into four canonical types: structural social capital, social access to resources, contagion, and environmental shaping. We note the rise in popularity of studies with a greater sense of agency than was traditional in network research.

Molecular biology has become one of the most fascinating fields of biology in recent years. Molecular methods have been applied in various fields of biology including Medical/Health Science. In this paper, light has been shed on the application of different molecular methods (DNA analysis) in the field of Forensic Medicine.

The scientific working group on DNA analysis Methods (SWGDAM) mitochondrial DNA (mtDNA) population data set is used to infer the relative rarity of control region mtDNA profiles obtained from evidence samples and of profiles used for identification of missing persons. In this study, the African American haplogroup patterns in the SWGDAM data were analyzed in a phylogenetic context to determine relevant single nucleotide polymorphisms (SNPs) and to describe haplogroup distributions for Africans observed in these data sets. Over 200 SNPs (n ¼ 217) were observed in the African American data set (n ¼ 1148). These SNPs ranged from having 1-39 changes in the phylogenetic tree, with sites 152 and 16519 being the most variable. On average there were 5.8 changes for a character on the tree. The most variable sites (with 19 or more changes each) observed included 16093,

The successful recovery of trace or contact DNA is highly variable. It is seemingly dependent on a wide range of factors, from the characteristics of the donor, substrate and environment, to the delay between contact and recovery. There is limited research on the extent of the effect these factors have on trace DNA analysis. This study investigated the persistence of trace DNA on surfaces relevant to the investigation of burglary and robbery offences.

The purpose of this exploratory study is to better understand the current dynamics of the Malaysian market for smartphone and the usage behaviors of consumers. This paper presents the result of a survey on the trend of smartphone from the perspective of end consumers. The data was collected from 1814 respondents across major cities in Malaysia. This study has looked into the familiarity of users towards smartphones, choices of smartphone brand and service providers, and most importantly the determinants that influence their purchasing decision. Additionally, the consumers' preferences on smartphone specifications such as design, computing power, operating platform, and price were investigated. Furthermore, consumers' usage behaviors such as using smartphone for email, web browsing, gaming, and document reading were examined. The statistics presented provides fundamental information regarding the trends in the smartphone market and usage behaviors in Malaysia. Such information are useful for academics for the development of future works in the field, whereas for smartphone manufacturers, application developers and other stakeholders, they are able to plan their direction in the Malaysian smartphone market.

| Sherlock Holmes said "it has long been an axiom of mine that the little things are infinitely the most important", but never imagined that such a little thing, the DNA molecule, could become perhaps the most powerful single tool in the multifaceted fight against crime. Twenty years after the development of DNA fingerprinting, forensic DNA analysis is key to the conviction or exoneration of suspects and the identification of victims of crimes, accidents and disasters, driving the development of innovative methods in molecular genetics, statistics and the use of massive intelligence databases.

One of the greatest mysteries for most of the twentieth century was the fate of the Romanov family, the last Russian monarchy. Following the abdication of Tsar Nicholas II, he and his wife, Alexandra, and their five children were eventually exiled to the city of Yekaterinburg. The family, along with four loyal members of their staff, was held captive by members of the Ural Soviet. According to historical reports, in the early morning hours of July 17, 1918 the entire family along with four loyal members of their staff was executed by a firing squad. After a failed attempt to dispose of the remains in an abandoned mine shaft, the bodies were transported to an open field only a few kilometers from the mine shaft. Nine members of the group were buried in one mass grave while two of the children were buried in a separate grave. With the official discovery of the larger mass grave in 1991, and subsequent DNA testing to confirm the identities of the Tsar, the Tsarina, and three of their daughters -doubt persisted that these remains were in fact those of the Romanov family. In the summer of 2007, a group of amateur archeologists discovered a collection of remains from the second grave approximately 70 meters from the larger grave. We report forensic DNA testing on the remains discovered in 2007 using mitochondrial DNA (mtDNA), autosomal STR, and Y-STR testing. Combined with additional DNA testing of material from the 1991 grave, we have virtually irrefutable evidence that the two individuals recovered from the 2007 grave are the two missing children of the Romanov family: the Tsarevich Alexei and one of his sisters.

Background: The Tarim Basin, located on the ancient Silk Road, played a very important role in the history of human migration and cultural communications between the West and the East. However, both the exact period at which the relevant events occurred and the origins of the people in the area remain very obscure. In this paper, we present data from the analyses of both Y chromosomal and mitochondrial DNA (mtDNA) derived from human remains excavated from the Xiaohe cemetery, the oldest archeological site with human remains discovered in the Tarim Basin thus far. Results: Mitochondrial DNA analysis showed that the Xiaohe people carried both the East Eurasian haplogroup (C) and the West Eurasian haplogroups (H and K), whereas Y chromosomal DNA analysis revealed only the West Eurasian haplogroup R1a1a in the male individuals.

Species identification has become a tool in the investigation of acts of alleged wildlife crimes. This review details the steps required in DNA testing in wildlife crime investigations and highlights recent developments where not only can individual species be identified within a mixture of species but multiple species can be identified simultaneously. 'What species is this?' is a question asked frequently in wildlife crime investigations. Depending on the material being examined, DNA analysis may offer the best opportunity to answer this question. Species testing requires the comparison of the DNA type from the unknown sample to DNA types on a database. The areas of DNA tested are on the mitochondria and include predominantly the cytochrome b gene and the cytochrome oxidase I gene. Standard analysis requires the sequencing of part of one of these genes and comparing the sequence to that held on a repository of DNA sequences such as the GenBank database. Much of the DNA sequence of either of these two genes is conserved with only parts being variable. A recent development is to target areas of those sequences that are specific to a species; this can increase the sensitivity of the test with no loss of specificity. The benefit of targeting species specific sequences is that within a mixture of two of more species, the individual species within the mixture can be identified. This identification would not be possible using standard sequencing. These new developments can lead to a greater number of samples being tested in alleged wildlife crimes.

Objective. Blood cultures and cultures of disc material are required to identify and treat bacterial agents responsible for septic spondylodiscitis, but these methods have limited sensitivities. We undertook this study to compare nonculture amplification-based DNA analysis with conventional culture of disc aspirate.

A forensic entomological investigation can benefit from a variety of widely practiced molecular genotyping methods. The most commonly used is DNA-based specimen identification. Other applications include the identification of insect gut contents and the characterization of the population genetic structure of a forensically important insect species. The proper application of these procedures demands that the analyst be technically expert. However, one must also be aware of the extensive list of standards and expectations that many legal systems have developed for forensic DNA analysis. We summarize the DNA techniques that are currently used in, or have been proposed for, forensic entomology and review established genetic analyses from other scientific fields that address questions similar to those in forensic entomology. We describe how accepted standards for forensic DNA practice and method validation are likely to apply to insect evidence used in a death or other forensic entomological investigation. 103 Annu. Rev. Entomol. 2008.53:103-120. Downloaded from arjournals.annualreviews.org by UNIVERSITY OF EXETER on 03/03/08. For personal use only. Microsatellite: a noncoding genetic locus consisting of a repeated sequence motif STR: short tandem repeat mtDNA: mitochondrial DNA COI+II: the mitochondrial DNA genes for cytochrome oxidase c subunits one and two 104 Wells · Stevens Annu. Rev. Entomol. 2008.53:103-120. Downloaded from arjournals.annualreviews.org by UNIVERSITY OF EXETER on 03/03/08. For personal use only.

Ferrocene-based derivatization has raised considerable interest in many fields of analytical chemistry. This is due to the well-established chemistry of ferrocenes, which allows rapid and easy access to a large number of reagents and derivatives. Furthermore, the electrochemical properties of ferrocenes are attractive with respect to their detection. This paper summarizes the available reagents, the reaction conditions and the different approaches for detection. While electrochemical detection is still most widely used to detect ferrocene derivatives, e.g., in the field of DNA analysis, the emerging combination of analytical separation methods with electrochemistry, mass spectrometry and atomic spectroscopy allows ferrocenes to be applied more universally and in novel applications where strongly improved selectivity and limits of detection are required.

Rapeseed plants have been regenerated after fusion between protoplasts bearing cytoplasms of different genera. Cybrids combine, in a first experiment Brassiea napus chloroplasts and a cytoplasmic male sterility (cms) trait coming from Raphanus sativus, in a second experiment chloroplasts of a triazine resistant Brassica campestris and cms trait from Raphanus sativus. Transfer of chloroplasts has been confirmed by restriction cp DNA analysis and two dimensional thylako~d protein electrophoresis. These plants may be very useful for Brassica hybrid seed production.

Forensic entomology is the science of collecting and analysing insect evidence to aid in forensic investigations. Its main application is in the determination of the minimum time since death in cases of suspicious death, either by estimating the age of the oldest necrophagous insects that developed on the corpse, or by analysing the insect species composition on the corpse. In addition, toxicological and molecular examinations of these insects may help reveal the cause of death or even the identity of a victim, by associating a larva with its last meal, for example, in cases where insect evidence is left at a scene after human remains have been deliberately removed. Some fly species can develop not only on corpses but on living bodies too, causing myiasis. Analysis of larvae in such cases can demonstrate the period of neglect of humans or animals. Without the appropriate professional collection of insect evidence, an accurate and convincing presentation of such evidence in court will be hampered or even impossible. The present paper describes the principles and methods of forensic entomology and the optimal techniques for collecting insect evidence.

Ralph Brothers' parents both died of acute myocardial infarctions at an early age. Ralph inherited dyslipidemia and glucose intolerance, and his blood pressure is above normal. Determined to prevent an early death, he has altered his diet, initiated regular exercise, purchased glucose and blood pressure monitoring devices, and he also takes blood pressure medications regularly. He has a happy family and work life with a comfortable income.

The object of the work is to evaluate whether rhizobacteria populating dry salty environments can increase resistance in tomato to salt stress. Seven strains of plant growth-promoting bacteria that have 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity were isolated from soil samples taken from the Arava region of southern Israel. Following growth of these seedlings in the presence of 43 mM NaCl for 7 weeks, the bacterium that promoted growth to the greatest extent was selected for further study. DNA analysis of the 16S RNA indicated that the selected bacterium was Achromobacter piechaudii. This bacterium significantly increased the fresh and dry weights of tomato seedlings grown in the presence of up to 172 mM NaCl salt. The bacterium reduced the production of ethylene by tomato seedlings, which was otherwise stimulated when seedlings were challenged with increasing salt concentrations, but did not reduce the content of sodium. However, it slightly increased the uptake of phosphorous and potassium, which may contribute in part to activation of processes involved in the alleviation of the effect of salt. In the presence of salt the bacterium increased the water use efficiency (WUE). This may suggest that the bacterium act to alleviate the salt suppression of photosynthesis. However, the detailed mechanism was not elucidated. The work described in this report is a first step in the development of productive agricultural systems in saline environments.