Within the realm of biosensing, DNA analysis has become an indispensable research tool in medicine, enabling the investigation of relationships among genes, proteins, and drugs. Conventional DNA microarray technology uses multiple lasers and complex optics, resulting in expensive and bulky systems which are not suitable for point-of-care medical diagnostics. The immobilization of DNA probes across the microarray substrate also results in substantial spatial variation. To mitigate the above shortcomings, this thesis presents a set of techniques developed for the CMOS image sensor for point-of-care spectrally-multiplexed fluorescent DNA sensing and other fluorescence biosensing applications. First, a CMOS tunable-wavelength multi-color photogate (CPG) sensor is presented. The CPG exploits the absorption property of a polysilicon gate to form an optical filter, thus the sensor does not require an external color filter. A prototype has been fabricated in a standard 0.35μm digital CMOS technology and demonstrates intensity measurements of blue (450nm), green (520nm), and red (620nm) illumination. Second, a wide dynamic range CMOS multi-color image sensor is presented. An analysis is performed for the wide dynamic-range, asynchronous self-reset with residue readout architecture where photon shot noise is taken into consideration. A prototype was fabricated in a standard 0.35μm CMOS process and is validated in color light sensing. The readout circuit achieves a measured dynamic range of 82dB with a peak SNR of 46.2dB. Third, a low-power CMOS image sensor VLSI architecture for use with comparator based ADCs is presented. By eliminating the in-pixel source follower, power consumption is reduced, compared to the conventional active pixel sensor. A 64×64 prototype with a 10μm pixel pitch has been fabricated in a 0.35μm standard CMOS technology and validated experimentally. Fourth, a spectrally-multiplexed fluorescence contact imaging microsystem for DNA analysis is presented. The microsystem has been quantitatively modeled and validated in the detection of marker gene sequences for spinal muscular atropy disease and the E. coli bacteria. Spectral multiplexing enables the two DNA targets to be simultaneously detected with a measured detection limit of 240nM and 210nM of target concentration at a sample volume of 10μL for the green and red transduction channels, respectively.

Within the realm of biosensing, DNA analysis has become an indispensable research tool in medicine, enabling the investigation of relationships among genes, proteins, and drugs. Conventional DNA microarray technology uses multiple lasers and complex optics, resulting in expensive and bulky systems which are not suitable for point-of-care medical diagnostics. The immobilization of DNA probes across the microarray substrate also results in substantial spatial variation. To mitigate the above shortcomings, this thesis presents a set of techniques developed for the CMOS image sensor for point-of-care spectrally-multiplexed fluorescent DNA sensing and other fluorescence biosensing applications. First, a CMOS tunable-wavelength multi-color photogate (CPG) sensor is presented. The CPG exploits the absorption property of a polysilicon gate to form an optical filter, thus the sensor does not require an external color filter. A prototype has been fabricated in a standard 0.35μm digital CMOS technology and demonstrates intensity measurements of blue (450nm), green (520nm), and red (620nm) illumination. Second, a wide dynamic range CMOS multi-color image sensor is presented. An analysis is performed for the wide dynamic-range, asynchronous self-reset with residue readout architecture where photon shot noise is taken into consideration. A prototype was fabricated in a standard 0.35μm CMOS process and is validated in color light sensing. The readout circuit achieves a measured dynamic range of 82dB with a peak SNR of 46.2dB. Third, a low-power CMOS image sensor VLSI architecture for use with comparator based ADCs is presented. By eliminating the in-pixel source follower, power consumption is reduced, compared to the conventional active pixel sensor. A 64×64 prototype with a 10μm pixel pitch has been fabricated in a 0.35μm standard CMOS technology and validated experimentally. Fourth, a spectrally-multiplexed fluorescence contact imaging microsystem for DNA analysis is presented. The microsystem has been quantitatively modeled and validated in the detection of marker gene sequences for spinal muscular atropy disease and the E. coli bacteria. Spectral multiplexing enables the two DNA targets to be simultaneously detected with a measured detection limit of 240nM and 210nM of target concentration at a sample volume of 10μL for the green and red transduction channels, respectively.

Human hair profiling is an integral part of a forensic investigation but it is one of the most technically difficult subjects in forensic science. This thesis describes the research and development of a novel approach for the rapid identification of unknown human and other related keratin fibres found at a crime scene. The work presented here is developed systematically and considers sample collection, sample preparation, analysis and interpretation of spectral data for the profiling of hair fibres encountered in criminal cases. Spectral comparison of fibres was facilitated with the use of chemometrics methods such as PCA, SIMCA and Fuzzy Clustering, and the less common approach of multi-criteria decision making methodology (MCDM). The aim of the thesis was to investigate the potential of some vibrational spectroscopy techniques for matching and discrimination of single keratin hair fibres in the context of forensic evidence. The first objective (chapter 3) of the thesis was to evaluate the use of Raman and FT-IR micro-spectroscopy techniques for the forensic sampling of hair fibres and to propose the preferred technique for future forensic hair comparisons. The selection of the preferred technique was based on criteria such as spectral quality, ease of use, rapid analysis and universal application to different hair samples. FT-IR micro-spectroscopy was found to be the most appropriate technique for hair analysis because it enabled the rapid collection of spectra from a wide variety of hair fibres. Raman micro-spectroscopy, on the other hand, was hindered with fluorescence problems and did not allow the collection of spectra from pigmented fibres. This objective has therefore shown that FT-IR micro-spectroscopy is the preferable spectroscopic technique for forensic analysis of hair fibres, whilst Raman spectroscopy is the least preferred. The second objective (chapter 3) was to investigate, through a series of experiments, the effect of chemical treatment on the micro-environment of human hair fibres. The effect of bleaching agents on the hair fibres was studied with some detail at different treatment times and the results indicate a significant change in the chemical environment of the secondary structure of the hair fibre along with changes in the C-C backbone structure. One of the most important outcomes of this research was the behaviour of the fÑ-helix during chemical treatment. The hydrogen bonding in the fÑ-helix provides for the stable structure of the fibre and therefore any disruption to the fÑ-helix will inevitably damage the molecular structure of the fibre. The results highlighted the behaviour of the fÑ-helix, which undergoes a significant decrease in content during oxidation, and is partly converted to a random-coil structure, whilst the fÒ-sheet component of the secondary structure remains unaffected. The reported investigations show that the combination of FT-IR and Raman micro-spectroscopy can provide an insight and understanding into the complex chemical properties and reactions within a treated hair fibre. Importantly, this work demonstrates that with the aid of chemometrics, it is possible to investigate simultaneously FT-IR and Raman micro-spectroscopic information from oxidised hair fibres collected from one subject and treated at different times. The discrimination and matching of hair fibres on the basis of treatment has potential forensic applications. The third objective (chapter 4) attempted to expand the forensic application of FT-IR micro-spectroscopy to other keratin fibres. Animal fibres are commonly encountered in crime scenes and it thus becomes important to establish the origin of those fibres. The aim of this work was to establish the forensic applications of FT-IR micro-spectroscopy to animal fibres and to investigate any fundamental molecular differences between these fibres. The results established a discrimination between fibres consisting predominantly of fÑ-helix and those containing mainly a fÒ-sheet structure. More importantly, it was demonstrated through curve-fitting and chemometrics, that each keratin fibre contains a characteristic secondary structure arrangement. The work presented here is the first detailed FT-IR micro-spectroscopic study, utilising chemometrics as well as MCDM methods, for a wide range of keratin fibres, which are commonly, found as forensic evidence. Furthermore, it was demonstrated with the aid of the rank ordering MCDM methods PROMETHEE and GAIA, that it is possible to rank and discriminate keratin fibres according to their molecular characteristics obtained from direct measurements together with information sourced from the literature. The final objective (chapter 5) of the thesis was to propose an alternative method for the discrimination and matching of single scalp human hair fibres through the use of FT-IR micro-spectroscopy and chemometrics. The work successfully demonstrated, through a number of case scenarios, the application of the technique for the identification of variables such as gender and race for an unknown single hair fibre. In addition, it was also illustrated that known hair fibres (from the suspect or victim) can be readily matched to the unknown hair fibres found at the crime scene. This is the first time that a substantial, systematic FT-IR study of forensic hair identification has been presented. The research has shown that it is possible to model and correlate individual¡¦s characteristics with hair properties at molecular level with the use of chemometrics methods. A number of different, important forensic variables of immediate use to police in a crime scene investigation such as gender, race, treatment, black and white hair fibres were investigated. Blind samples were successfully applied both to validate available experimental data and extend the current database of experimental determinations. Protocols were posed for the application of this methodology in the future. The proposed FT-IR methodology presented in this thesis has provided an alternative approach to the characterisation of single scalp human hair fibres. The technique enables the rapid collection of spectra, followed by the objective analytical capabilities of chemometrics to successfully discriminate animal fibres, human hair fibres from different sources, treated from untreated hair fibres, as well as black and white hair fibres, on the basis of their molecular structure. The results can be readily produced and explained in the courts of law. Although the proposed relatively fast FT-IR technique is not aimed at displacing the two slower existing methods of hair analysis, namely comparative optical microscopy and DNA analysis, it has given a new dimension to the characterisation of hair fibres at a molecular level, providing a powerful tool for forensic investigations.

Para a execução da etapa inicial da identificação médico-legal de restos humanos (antropometria e exame dos arcos dentários), faz-se necessária uma limpeza prévia da ossada, para a remoção de tecidos moles putrefeitos. Os casos não identificados por esses métodos tradicionais, poderão ser submetidos ao exame de DNA. No entanto, apesar do grande avanço da biologia molecular, utilizando a amplificação de DNA pela PCR, algumas limitações que afetam a habilidade de se obter DNA em restos humanos, permanecem. Dessa forma, o objetivo deste trabalho foi fornecer subsídios morfológicos para os analistas forenses, com ênfase na prática médico-legal, visando uma utilização mais eficiente do DNA obtido de osso compacto de restos humanos em decomposição ou já esqueletizados, sem tecidos moles aderidos. Foi realizado o estudo da microestrutura do tecido ósseo compacto femoral, de restos humanos em decomposição, ainda com tecidos moles, que foram limpos pela fervura em água (n = 7) e ossadas já esqueletizadas pela decomposição natural, que não foram fervidas (n = 8). Destes, seis ossadas foram provenientes de cemitério público regular, após 3 anos de inumação, 1 ossada proveniente da região amazônica, e 1 ossada de origem desconhecida. Estas duas ultimas, apresentado-se porosas ou quebradiças. As análises morfológicas de cortes histológicos foram coradas com hematoxilina e eosina e o DNA amplificado pela PCR para os loci CSF1PO, TPOX, TH01, F13A0, FESFPS, vWA, D16S539, D7S820, D13S317 e amelogenina. Os resultados da análise desses dois grupos foram comparados com os de cadáveres frescos (n = 5) do Serviço de Verificação de Óbitos da Capital. A fervura dos ossos, do modo como é realizada no Instituto Médico Legal de São Paulo, pode aumentar a eosinofilia da matriz óssea e, em alguns casos, pode promover a desagregação dos ósteons. Tal procedimento pode remover células, mas pode também remover possíveis inibidores da PCR, favorecendo a análise do DNA obtido destas amostras. O fator limitante para a obtenção e análise de DNA, em amostras de ossos limpos por fervura, é a quantidade exígua de células. Ossos não submetidos à fervura, após inumação por três anos ou há mais tempo em contato com a terra, podem apresentar alterações da microestrutura. No entanto, a presença de hemácias preservadas e núcleos de osteócitos nestas amostras, indica melhor preservação de células em relação às amostras de ossos fervidos. O fator limitante para a análise de DNA nestas amostras é a presença sugestiva de inibidores da reação de amplificação pela PCR. Restos humanos, sem tecidos moles, macroscópicamente não preservados (porosos e quebradiços), e não submetidos à fervura, apresentam alterações de perda de matriz mineralizada; no entanto, nestas amostras ainda é possível encontrar células preservadas. Os resultados obtidos no neste trabalho permitem traçar algumas estratégias para uma melhor utilização nos protocolos de extração e análise do DNA em osso compacto de restos humanos. / To the first essential step to forensic identification of human remains (anthropological study of race, sex, age, etc) it is necessary a previous cleaning of the bones, to remove decomposing soft tissues. Medico-legal inconclusive or non identified cases, by using these traditional methods, could be subjected to DNA analysis. However, in spite of advances in human identification techniques, specially by PCR amplified DNA, some limitations that affect the ability to obtain DNA in human remains still persist. Therefore, the aim of this study was to provide additional support from morphological analysis, to help forensic analysts personnel to utilise more efficiently the DNA, extracted from compact bones of human remains in decomposition or already skeletonized corpse, it means without soft tissues, with special emphasis in the legal-medicine practice. Femoral compact bones were obtained from: 7 human remains found on the ground, in different degree of decomposition which were cleaned by boiling to remove soft tissues; also studied were collections of bones from 8 corpses having undergone natural decomposition: 6 human remains exhumed after 3 years from a common public cemetery in São Paulo City; 1 case from amazon region and 1 case with no information, both cases remained from long time (more than 3 years) in contact with soil. All eight cases, were not boiled as no soft tissue were adhered. As a control, five cadavers 12 to 16 hours post mortem were also used. The compact bones histological sections were stained by haematoxilin and eosin and the loci CSF1PO, TPOX, TH01, F13A01,FESFPS, vWA, D16S539, D7S820, D13S317 and amelogenin were amplified by PCR.The procedure for boiling the human remains utilised in the Legal Medicine Institute of São Paulo would have increased the eosinophily of bone matrix and, in some cases, promoted the desaggregation of the osteons. In addition these procedures would have removed the cells, but in some cases would have removed possible inhibitors of the PCR, favouring in this way the analysis of DNA obtained from these samples. The limiting factor to obtain successful analysis in bones submitted to boiling seem to be the low quantity of nuclei present in these samples. For the other hand, in bones not cleaned by boiling, the presence of preserved red cells and oscteocyte nuclei inside the lacunae indicates better preservation of cells in relation to those bones cleaned by boiling. The limiting factor to obtain successful DNA analysis in bones exhumed or in contact of soil, is the suggestive presence of inhibitors of PCR. Porous and brittle bones from human remains, without soft tissues that are not processed by boiling, present alterations through loss of mineralised matrix, although it is still possible to found preserved cells in these samples. The results presented in this work clarify concerns about viability of DNA for identification analysis. They also help to establish better strategies for optimisation of DNA extraction and analysis in compact bones of human remains.

Neste estudo, foi avaliada a relação entre polimorfismos dos genes da leptina (LEP) e receptores da leptina (LEPR) e parâmetros antropométricos, leptinemia glicemia e lipídeos séricos, em indivíduos da população brasileira. Foram incluídos 238 indivíduos com idade entre 30 e 80 anos. Foram medidos o índice de massa corporal (IMC), a cintura abdominal (CA) e a razão cintura quadril (RCQ). Amostras de sangue periférico foram obtidas para análise do perfil bioquímico e extração de DNA. Os polimorfismos de nuleotideo único (SNPs) LEP G-2548A e LEPR Lys109Arg, Gln223Arg e Lys656Asn foram detectados por PCR-RFLP. Os SNPs LEPR Lys109Arg e Gln223Arg foram associados com obesidade e com IMC e CA aumentados (p<0.05). Estes polimorfismos também foram associados com leptina e glicose elevada (p<0,05). O perfil lipídico sérico foi influenciado pelo polimorfismo LEPR Lys109Arg (p<0.05). A relação entre os SNPs LEPR Lys109Arg e Gln223Arg e o perfil lipídico foi modificada pelo gênero. Os haplótipos LEP G-2548/ LEPR Lys109Arg foram relacionados com diferenças no IMC de obesos. Os haplotipos LEPR Lys109Arg/Gln223Arg foram associados com diferenças na CA e glicemia e lipídeos séricos. Em conclusão, os polimorfismos LEPR Lys109Arg e Gln223Arg estão associados com obesidade e alterações de leptina, glicose e lipídeos circulantes de forma dependente do gênero. / We have assessed the relationship between polymorphisms of the leptin (LEP) and the leptin receptor (LEPR) genes and anthropometric parameters, plasma leptin and glucose and serum lipids in individuals of the Brazilian population. We included 238 individuais with 30 to 80 years. Body mass index (BMI), abdominal circumference (AC) and waist-to-hip ratio (WHR) were measured. Peripheral blood samples were collected for analysis of the biochemical profile and DNA extraction. The single nucleotide polymorphisms (SNP) LEP G-2548A and LEPR Lys109Arg, Gln223Arg and Lys656Asn were detected by PCR-RFLP. The SNPs LEPR Lys109Arg and Gln223Arg were associated with obesity and with increased BMI and AC (p <0.05). These polymorphisms were also associated with increase leptin and glucose (p<0,05). The serum lipid profile was influenced by the LEPR Lys 1 09Arg (p<0.05). The relationship between the SNPs LEPR Lys 1 09Arg and Gln223Arg and the lipid profile was modified by gender. The haplotypes LEP G-2548A1 LEPR Lys109Arg were related with differences on BMI in obese group. The haplotypes LEPR Lys109Arg/Gln223Arg were associated with differences on AC, glucose and serum lipids. In conclusion, the LEPR Lys109Arg and Gln223Arg polymorphisms are associated with obesity and alterations in blood leptin, glucose and lipids in a gender-dependent manner.

Indiana University-Purdue University Indianapolis (IUPUI) / Analyses of tobacco products and their usage are well-researched and have implications in analytical chemistry, forensic science, toxicology, and medicine. As such, analytical methods must be developed to extract compounds of interest from tobacco products and biological specimens in order to determine tobacco exposure. In 2009, R.J. Reynolds Tobacco Co. released a line of dissolvable tobacco products that are marketed as a smoking alternative. The dissolvables were extracted and prepared by ultrasonic extractions, derivatization, and headspace solid phase microextraction (SPME) with analysis by gas chromatography-mass spectrometry (GC-MS). The results show that the compounds present are nicotine, flavoring compounds, humectants and binders. Humectant concentrations vary among different tobacco types depending on the intended use. Humectants were quantified in various tobacco types by GC and “splitting” the column flow between a flame ionization detector (FID) and an MS using a microfluidic splitter in order to gain advantage from the MS’s selectivity. The results demonstrated excellent correlation between FID and MS and show that MS provides a higher level of selectivity and ensures peak purity. Chemometrics was also used to distinguish products by tobacco type. Hair is a common type of evidence in forensic investigations, and it is often subjected to mitochondrial DNA (mtDNA) analysis. Preliminary data was gathered on potential “lifestyle” markers for smoking status as well as any indications of subject age, gender, or race by investigating the organic “waste” produced during a mtDNA extraction procedure. The normally discarded organic fractions were analyzed by GC-MS and various lipids and fatty acids were detected. At this point, a total vaporization-SPME (TV-SPME) method was theorized, developed, and optimized for the specific determination of nicotine and its metabolite, cotinine. The theory of TV-SPME is to completely vaporize an organic extract which will eliminate the partitioning between the sample and the headspace, thereby simplifying the thermodynamic equilibrium. Parameters such as sample volume, incubation temperature, and extraction time were optimized to achieve the maximum analyte signal. Response surface methodology (RSM) is a statistical model that is very useful in predicting and determining optimum values for variables to ensure the ideal response. RSM was used to optimize the technique of TV-SPME for the analysis of nicotine and cotinine. Lastly, quantitation of nicotine and cotinine in human hair typically requires large sample sizes and extensive extraction procedures. Hence, a method using small sample sizes and a simple alkaline digestion followed by TV-SPME-GC-MS has been developed. Hair samples were collected from anonymous volunteers and nicotine and cotinine were identified and quantitated in the hair of tobacco users.

Indiana University-Purdue University Indianapolis (IUPUI) / Short tandem repeat (STR) analysis is currently the most common method for processing biological forensic evidence. STRs are highly polymorphic and allow for a strong statistical power of discrimination when comparing deoxyribonucleic acid (DNA) samples. Since sample testing and court proceedings occur months, if not years apart, samples must be stored appropriately in the event additional testing is needed. There are generally accepted methods to store DNA extracts long-term; however, one universally recognized method does not exist. The goal of this project was to examine various methods of storage and make recommendations for a universal storage method that maintained DNA integrity over time. Four variables were evaluated: storage buffer, storage temperature, initial storage concentration and the effects of repeated freeze-thaw cycles. DNA quantity was assessed using real-time polymerase chain reaction and DNA quality was evaluated using STR genotyping. Overall, the Tris-EDTA (TE) buffer outperformed nuclease free water as a long-term storage buffer for DNA extracts. Stock tubes stabilized concentration better than single use aliquots when eluted with TE while tube type was not significant when water was the buffer. For samples stored in TE, temperature had no effect on DNA integrity over time, but samples stored in water were largely affected at room temperature. Additionally, the greater the initial DNA concentration, the less likely it was to degrade in water. As a result of this research, DNA extracts from forensic samples should be stored long-term in TE buffer with a minimum concentration of 0.1 ng/μL. When water is the buffer, frozen storage is recommended.

Indiana University-Purdue University Indianapolis (IUPUI) / Forensic DNA profiling is widely used as an identification tool for associating an individual with evidence of a crime. Analysis of a DNA sample involves observation of data in the form of an electropherogram, and subsequently annotating a DNA “profile” from an individual or from the evidence. The profile obtained from the evidence can be compared to reference profiles deposited in a national DNA database, which may include the potential contributor. Following a match, a random match probability is calculated to determine how common that genotype is in the population. This is the probability of obtaining that same DNA profile by sampling from a pool of unrelated individuals. Each state has adopted various laws requiring suspects and/or offenders to submit a DNA sample for the national database (such as California’s law that all who are arrested must provide a DNA sample). These profiles can then be associated with past unsolved crimes, and remain in the database to be searched in the event of future crimes. In the case of database samples, a physical sample of the offender’s DNA must be kept on file in the laboratory indefinitely so that in the event of a database hit, the sample is able to be retested. Current methods are to collect a buccal swab or blood sample, and store the DNA extracts under strict preservation conditions, i.e. cold storage, typically -20° C. With continually increasing number of samples submitted, a burden is placed on crime labs to store these DNA extracts. A solution was required to help control the costs of properly storing the samples. FTA™ paper was created to fulfill the need for inexpensive, low maintenance, long term storage of biological samples, which makes it ideal for use with convicted offender DNA samples. FTA™ paper is a commercially produced, chemically treated paper that allows DNA to be stored at room temperature for years with no costly storage facilities or conditions. Once a sample is required for DNA testing, a small disc is removed and is to be used directly in a PCR reaction. A high quality profile is important for comparing suspect profiles to unknown or database profiles. A single difference between a suspect and evidentiary sample can lead to exclusion. Unfortunately, the DNA profile results yielded from the direct addition have been unfavorable. Thus, most crime laboratories will extract the DNA from the disc, leading to additional time and cost to analyze a reference sample. Many of the profiles from the direct addition of an FTA™ disc result in poor quality profiles, likely due to an increase in PCR inhibitors and high concentrations of DNA. Currently, standardized protocols regarding the recommended locations for removal of a sample disc from a bloodspot on an FTA™ card does not exist. This study aims to validate the optimal location by comparing DNA profiles obtained from discs removed from the center, halfway, and edge locations of a bloodspot from 50 anonymous donors. Optimal punch location was first scored on the number of failed, partial or discordant profiles. Then, profile quality was determined based on peak characteristics of the resulting DNA profiles. The results for all three disc locations were 5.3% failed amplifications, 4.2% partial amplifications, and one case of a discordant profile. Profile quality for the majority of the samples showed a high incidence of stutter and the absence of non-template adenylation. Of the three disc locations, the edge of the blood stain was ideal, due to a presumably lower concentration of DNA and likely more dilute amount of the PCR inhibitor heme. Therefore, based on the results of this study, there is a greater probability of success using a sample from the edge of a blood stain spotted in FTA™ paper than any other location of the FTA™ card.

This study analyses how DNA evidence can be distorted by the behaviour of criminal investigators and role-players within the Criminal Justice System (CJS). This has a negative impact on justice resulting in further criminality. The study has resulted in revelatory weaknesses owing to constitutional violations which cause sound evidence to become futile as it will not be admissible in court. Justice is aborted. The researcher has further explained the properties of the pertinent terms, such as: mental illness, psycho-social functioning, DNA, forensic investigator, forensic psychology, and courts. Concepts are building blocks, hermeneutical distortion leads to the frustrating of what justice intends and this, in turn, leads to poor criminal investigation performance. It is submitted that not only ineptness, but also deception possibly evolves from genotypic to phenotypic type which causes unwelcome behaviour within the criminal justice system to surface. The frequency of monitoring psychological behaviour amongst criminal investigations is low, and it, therefore, also contributes to delict and the miscarriage of justice occurs. / Police Practice / M.A. (Criminal Justice)

No / Evolutionary biologists are increasingly relying on ancient DNA from archaeological animal bones to study processes such as domestication and population dispersals. As many animal bones found on archaeological sites are likely to have been cooked, the potential for DNA preservation must be carefully considered to maximise the chance of amplification success. Here, we assess the preservation of mitochondrial DNA in a medieval cattle bone assemblage from Coppergate, York, UK. These bones have variable degrees of thermal alterations to bone collagen fibrils, indicative of cooking. Our results show that DNA preservation is not reliant on the presence of intact collagen fibrils. In fact, a greater number of template molecules could be extracted from bones with damaged collagen. We conclude that moderate heating of bone may enhance the retention of DNA fragments. Our results also indicate that ancient DNA preservation is highly variable, even within a relatively recent assemblage from contexts conducive to organic preservation, and that diagenetic parameters based on protein diagenesis are not always useful for predicting ancient DNA survival.