Статті в журналах: "DNA EVIDENCE EVALUATION"

1

Steele, Christopher D., and David J. Balding. "Statistical Evaluation of Forensic DNA Profile Evidence." Annual Review of Statistics and Its Application 1, no. 1 (January 3, 2014): 361–84. http://dx.doi.org/10.1146/annurev-statistics-022513-115602.

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2

Redmayne, Mike. "Review: The Evaluation of Forensic DNA Evidence." International Journal of Evidence & Proof 2, no. 2 (March 1998): 136–40. http://dx.doi.org/10.1177/136571279800200205.

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3

Taroni, Franco, and Colin G. G. Aitken. "DNA evidence, probabilistic evaluation and collaborative tests." Forensic Science International 108, no. 2 (February 2000): 121–43. http://dx.doi.org/10.1016/s0379-0738(99)00197-8.

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4

Bickel, P. J. "Discussion of "The Evaluation of Forensic DNA Evidence"." Proceedings of the National Academy of Sciences 94, no. 11 (May 27, 1997): 5497. http://dx.doi.org/10.1073/pnas.94.11.5497.

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5

Wolańska-Nowak, Paulina. "Application of subpopulation theory to evaluation of DNA evidence." Forensic Science International 113, no. 1-3 (September 2000): 63–69. http://dx.doi.org/10.1016/s0379-0738(00)00265-6.

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6

Corradi, Fabio, Giampietro Lago, and Federico M. Stefanini. "The evaluation of DNA evidence in pedigrees requiring population inference." Journal of the Royal Statistical Society: Series A (Statistics in Society) 166, no. 3 (October 2003): 425–40. http://dx.doi.org/10.1111/1467-985x.00285.

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7

Taroni, F., J. A. Lambert, L. Fereday, and D. J. Werrett. "Evaluation and presentation of forensic DNA evidence in European laboratories." Science & Justice 42, no. 1 (January 2002): 21–28. http://dx.doi.org/10.1016/s1355-0306(02)71793-0.

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8

Slooten, K., and A. Caliebe. "Contributors are a nuisance (parameter) for DNA mixture evidence evaluation." Forensic Science International: Genetics 37 (November 2018): 116–25. http://dx.doi.org/10.1016/j.fsigen.2018.05.004.

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9

Ingram, C. F., A. N. Davidoff, E. Marais, G. G. Sherman, and B. V. Mendelow. "Evaluation of DNA analysis for evidence of apoptosis in megaloblastic anaemia." British Journal of Haematology 96, no. 3 (March 1997): 576–83. http://dx.doi.org/10.1046/j.1365-2141.1997.d01-2075.x.

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10

Andersen, Mikkel M., and David J. Balding. "Assessing the Forensic Value of DNA Evidence from Y Chromosomes and Mitogenomes." Genes 12, no. 8 (August 5, 2021): 1209. http://dx.doi.org/10.3390/genes12081209.

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Y chromosome and mitochondrial DNA profiles have been used as evidence in courts for decades, yet the problem of evaluating the weight of evidence has not been adequately resolved. Both are lineage markers (inherited from just one parent), which presents different interpretation challenges compared with standard autosomal DNA profiles (inherited from both parents). We review approaches to the evaluation of lineage marker profiles for forensic identification, focussing on the key roles of profile mutation rate and relatedness (extending beyond known relatives). Higher mutation rates imply fewer individuals matching the profile of an alleged contributor, but they will be more closely related. This makes it challenging to evaluate the possibility that one of these matching individuals could be the true source, because relatives may be plausible alternative contributors, and may not be well mixed in the population. These issues reduce the usefulness of profile databases drawn from a broad population: larger populations can have a lower profile relative frequency because of lower relatedness with the alleged contributor. Many evaluation methods do not adequately take account of distant relatedness, but its effects have become more pronounced with the latest generation of high-mutation-rate Y profiles.

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11

Rogowski, Wolf. "Genetic screening by DNA technology: A systematic review of health economic evidence." International Journal of Technology Assessment in Health Care 22, no. 3 (July 2006): 327–37. http://dx.doi.org/10.1017/s0266462306051221.

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Objectives:The Human Genome Project has led to a multitude of new potential screening targets on the level of human DNA. The aim of this systematic review is to critically summarize the evidence from health economic evaluations of genetic screening in the literature.Methods:Based on an extensive explorative search, an appropriate algorithm for a systematic database search was developed. Twenty-one health economic evaluations were identified and appraised using published quality criteria.Results:Genetic screening for eight conditions has been found to be investigated by health economic evaluation: hereditary breast and ovarian cancer, familial adenomatous polyposis (FAP) colorectal cancer, hereditary nonpolyposis colorectal carcinoma (HNPCC), retinoblastoma, familial hypercholesterolemia, hereditary hemochromatosis, insulin-dependent diabetes mellitus, and cystic fibrosis. Results range from dominated to cost-saving. Population-wide genetic screening may be considered cost-effective with limited quality of evidence only for three conditions. The methodology of the studies was of varying quality. Cost-effectiveness was primarily influenced by mutation prevalence, genetic test costs, mortality risk, effectiveness of treatment, age at screening, and discount rate.Conclusions:Health economic evidence on genetic screening is limited: Only few conditions have properly been evaluated. Based on the existing evidence, healthcare decision makers should consider the introduction of selective genetic screening for FAP and HNPCC. As genetic test costs are declining, the existing evaluations may warrant updating. Especially in the case of hereditary hemochromatosis, genetic population screening may be about to turn from a dominated to a cost-effective or even cost-saving intervention.

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12

Lee, Cheng-Lung, Yi-Hsin Huang, Ian C. Hsu, and Henry C. Lee. "Evaluation of plant seed DNA and botanical evidence for potential forensic applications." Forensic Sciences Research 5, no. 1 (June 10, 2019): 55–63. http://dx.doi.org/10.1080/20961790.2019.1594599.

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13

Cornwell, Samuel J., Jasmine W. Tay, Rudi K. Allan, Jasmin Zoranjic, Nicholas J. O’Rourke, Graham B. Byard, and Marie S. Rye. "Evaluation of DNA Extraction Methods for Processing Fingerprint Powder‐Coated Forensic Evidence." Journal of Forensic Sciences 65, no. 3 (November 5, 2019): 960–65. http://dx.doi.org/10.1111/1556-4029.14233.

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14

Tozzo, Pamela, Enrico Mazzobel, Beatrice Marcante, Arianna Delicati, and Luciana Caenazzo. "Touch DNA Sampling Methods: Efficacy Evaluation and Systematic Review." International Journal of Molecular Sciences 23, no. 24 (December 8, 2022): 15541. http://dx.doi.org/10.3390/ijms232415541.

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Collection and interpretation of “touch DNA” from crime scenes represent crucial steps during criminal investigations, with clear consequences in courtrooms. Although the main aspects of this type of evidence have been extensively studied, some controversial issues remain. For instance, there is no conclusive evidence indicating which sampling method results in the highest rate of biological material recovery. Thus, this study aimed to describe the actual considerations on touch DNA and to compare three different sampling procedures, which were “single-swab”, “double-swab”, and “other methods” (i.e., cutting out, adhesive tape, FTA® paper scraping), based on the experimental results published in the recent literature. The data analysis performed shows the higher efficiency of the single-swab method in DNA recovery in a wide variety of experimental settings. On the contrary, the double-swab technique and other methods do not seem to improve recovery rates. Despite the apparent discrepancy with previous research, these results underline certain limitations inherent to the sampling procedures investigated. The application of this information to forensic investigations and laboratories could improve operative standard procedures and enhance this almost fundamental investigative tool’s probative value.

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15

Aitken, Colin, Franco Taroni, and Paolo Garbolino. "A graphical model for the evaluation of cross-transfer evidence in DNA profiles." Theoretical Population Biology 63, no. 3 (May 2003): 179–90. http://dx.doi.org/10.1016/s0040-5809(03)00004-2.

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16

Kokshoorn, Bas, Bart J. Blankers, Jacob de Zoete, and Charles E. H. Berger. "Activity level DNA evidence evaluation: On propositions addressing the actor or the activity." Forensic Science International 278 (September 2017): 115–24. http://dx.doi.org/10.1016/j.forsciint.2017.06.029.

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17

Ishihara, Shunichi. "Probabilistic Evaluation of SMS Messages as Forensic Evidence." International Journal of Digital Crime and Forensics 4, no. 3 (July 2012): 47–57. http://dx.doi.org/10.4018/jdcf.2012070104.

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This study is one of the first likelihood ratio-based forensic text comparison studies in forensic authorship analysis. The likelihood-ratio-based evaluation of scientific evidence has started being adopted in many disciplines of forensic evidence comparison sciences, such as DNA, handwriting, fingerprints, footwear, voice recording, etc., and it is largely accepted that this is the way to ensure the maximum accountability and transparency of the process. Due to its convenience and low cost, short message service (SMS) has been a very popular medium of communication for quite some time. Unfortunately, however, SMS messages are sometimes used for reprehensible purposes, e.g., communication between drug dealers and buyers, or in illicit acts such as extortion, fraud, scams, hoaxes, and false reports of terrorist threats. In this study, the author performs a likelihood-ratio-based forensic text comparison of SMS messages focusing on lexical features. The likelihood ratios (LRs) are calculated in Aitken and Lucy’s (2004) multivariate kernel density procedure, and are calibrated. The validity of the system is assessed based on the magnitude of the LRs using the log-likelihood-ratio cost (Cllr). The strength of the derived LRs is graphically presented in Tippett plots. The results of the current study are compared with those of previous studies.

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18

Ekka, Molina Madhulika, Lakshita Arya, and Bhargav C. Patel. "A systematic evaluation of ‘Bidi – a hand-rolled cigarette’ as a forensic DNA evidence." Forensic Science International 324 (July 2021): 110821. http://dx.doi.org/10.1016/j.forsciint.2021.110821.

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19

Costa, Susana. "DNA as ‘ready-made evidence’: An analysis of Portuguese judges’ views." International Journal of Evidence & Proof 26, no. 2 (December 30, 2021): 121–35. http://dx.doi.org/10.1177/13657127211070331.

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The introduction of biological evidence in judicial settings raises particular modes of entanglement between professional cultures and perceptions of the probative value of evidence. When DNA evidence reaches court, it also challenges the perceived margins of critical assessment of the work and understandings of previous links in the chain of custody, like the criminal police, forensic experts and the public prosecution services. Given the apparent neutrality of judicial institutions, how do Portuguese judges perceive and value biological evidence? And how do judges see their articulation with other operators of the criminal justice system? An analysis of 14 interviews carried out with Portuguese judges reveals the challenges in the evaluation of biological evidence, which is characterised as a ‘safe haven’, grounded as it is on an indisputable scientific authority. The suggestion of the presence of a cultural rift emerges, which, taken with the work of other epistemic cultures, leads to biological evidence being seen as ‘ready-made evidence’ on its arrival in court, thus limiting the role of judges in its appraisal.

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20

Bathrick, Abigail S., and Jon M. Davoren. "Accelerated aging of forensically relevant biological materials on swabs." BioTechniques 70, no. 4 (April 2021): 233–38. http://dx.doi.org/10.2144/btn-2020-0170.

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The preservation of DNA in biological samples is important for forensic testing, as samples can be tested years or even decades after collection. Generally, the DNA within biological evidence is stable over shorter time frames but can degrade over extended periods. In this work, we evaluated accelerated aging as a method to reduce the duration of studies examining the stability of DNA in forensic evidence-type samples. Evaluation of the DNA extracted from cells stored at 37 and 50°C for 194 or 79 days, respectively, showed similar quality metrics to cells stored at 25°C for 548 days.

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21

Boritsch, Eva C., Varun Khanna, Alexandre Pawlik, Nadine Honoré, Victor H. Navas, Laurence Ma, Christiane Bouchier, et al. "Key experimental evidence of chromosomal DNA transfer among selected tuberculosis-causing mycobacteria." Proceedings of the National Academy of Sciences 113, no. 35 (August 15, 2016): 9876–81. http://dx.doi.org/10.1073/pnas.1604921113.

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Horizontal gene transfer (HGT) is a major driving force of bacterial diversification and evolution. For tuberculosis-causing mycobacteria, the impact of HGT in the emergence and distribution of dominant lineages remains a matter of debate. Here, by using fluorescence-assisted mating assays and whole genome sequencing, we present unique experimental evidence of chromosomal DNA transfer between tubercle bacilli of the early-branching Mycobacterium canettii clade. We found that the obtained recombinants had received multiple donor-derived DNA fragments in the size range of 100 bp to 118 kbp, fragments large enough to contain whole operons. Although the transfer frequency between M. canettii strains was low and no transfer could be observed among classical Mycobacterium tuberculosis complex (MTBC) strains, our study provides the proof of concept for genetic exchange in tubercle bacilli. This outstanding, now experimentally validated phenomenon presumably played a key role in the early evolution of the MTBC toward pathogenicity. Moreover, our findings also provide important information for the risk evaluation of potential transfer of drug resistance and fitness mutations among clinically relevant mycobacterial strains.

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22

Chimera, J. A., S. M. Anderson, H. Noell, and V. Rizk. "Comparison of nucleic acid hybridization and cytologic examination for detection of human papillomavirus infection, with evaluation of two commercially available hybridization kits." Clinical Chemistry 37, no. 2 (February 1, 1991): 260–62. http://dx.doi.org/10.1093/clinchem/37.2.260.

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Abstract Human papillomavirus (HPV) infections were detected by analyzing exfoliated cervical cells for HPV DNA by use of nucleic acid hybridization; the results were correlated with cytologic findings on Papanicolaou smears. HPV infection was diagnosed in 154 women (20%) by either morphologic evidence on cervical smears or nucleic acid hybridization. Many of these women (38%; 58/154) exhibited Papanicolaou smears with no morphologic evidence of HPV infection. In those patients with cytologic evidence of HPV infection, only 28% were positive for HPV DNA. HPV 16 and (or) 18 were the most common types (27%) detected in women with cervical intraepithelial neoplasia, whereas all HPV groups tested were equally represented in patients with normal cervical smears. We also present an assessment of 17,000 clinical specimens submitted to this laboratory for analysis of HPV DNA.

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23

Caglià, A., L. Baldassarri, I. Boschi, F. Scarnicci, and V. L. Pascali. "Is peak height important for the statistical evaluation of the weight of evidence in DNA mixtures?" Forensic Science International: Genetics Supplement Series 5 (December 2015): e395-e397. http://dx.doi.org/10.1016/j.fsigss.2015.09.156.

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24

Berthiol, Florian, Joseph Boissieras, Hugues Bonnet, Marie Pierrot, Christian Philouze, Jean-François Poisson, Anton Granzhan, Jérôme Dejeu, and Eric Defrancq. "Novel Synthesis of IMC-48 and Affinity Evaluation with Different i-Motif DNA Sequences." Molecules 28, no. 2 (January 10, 2023): 682. http://dx.doi.org/10.3390/molecules28020682.

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During the last decade, the evidence for the biological relevance of i-motif DNA (i-DNA) has been accumulated. However, relatively few molecules were reported to interact with i-DNA, and a controversy concerning their binding mode, affinity, and selectivity persists in the literature. In this context, the cholestane derivative IMC-48 has been reported to modulate bcl-2 gene expression by stabilizing an i-motif structure in its promoter. In the present contribution, we report on a novel, more straightforward, synthesis of IMC-48 requiring fewer steps compared to the previous approach. Furthermore, the interaction of IMC-48 with four different i-motif DNA sequences was thoroughly investigated by bio-layer interferometry (BLI) and circular dichroism (CD) spectroscopy. Surprisingly, our results show that IMC-48 is a very weak ligand of i-DNA as no quantifiable interaction or significant stabilization of i-motif structures could be observed, stimulating a quest for an alternative mechanism of its biological activity.

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25

Kuron, Aneta, Malgorzata Korycka-Machala, Anna Brzostek, Marcin Nowosielski, Aidan Doherty, Bozena Dziadek, and Jaroslaw Dziadek. "Evaluation of DNA Primase DnaG as a Potential Target for Antibiotics." Antimicrobial Agents and Chemotherapy 58, no. 3 (December 30, 2013): 1699–706. http://dx.doi.org/10.1128/aac.01721-13.

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ABSTRACTMycobacteria contain genes for several DNA-dependent RNA primases, includingdnaG, which encodes an essential replication enzyme that has been proposed as a target for antituberculosis compounds. Anin silicoanalysis revealed that mycobacteria also possess archaeo-eukaryotic superfamily primases (AEPs) of unknown function. Using a homologous recombination system, we obtained direct evidence that wild-typednaGcannot be deleted from the chromosome ofMycobacterium smegmatiswithout disrupting viability, even in backgrounds in which mycobacterial AEPs are overexpressed. In contrast, single-deletion AEP mutants or mutants defective for all four identifiedM. smegmatisAEP genes did not exhibit growth defects under standard laboratory conditions. Deletion of nativednaGinM. smegmatiswas tolerated only after the integration of an extra intact copy of theM. smegmatisorMycobacterium tuberculosisdnaGgene, under the control of chemically inducible promoters, into theattBsite of the chromosome.M. tuberculosisandM. smegmatisDnaG proteins were overproduced and purified, and their primase activities were confirmed using radioactive RNA synthesis assays. The enzymes appeared to be sensitive to known inhibitors (suramin and doxorubicin) of DnaG. Notably,M. smegmatisbacilli appeared to be sensitive to doxorubicin and resistant to suramin. The growth and survival of conditional mutant mycobacterial strains in which DnaG was significantly depleted were only slightly affected under standard laboratory conditions. Thus, although DnaG is essential for mycobacterial viability, only low levels of protein are required for growth. This suggests that very efficient inhibition of enzyme activity would be required for mycobacterial DnaG to be useful as an antibiotic target.

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26

Arguelho, Maria Lara P. M., José do Patrocínio H. Alves, Nelson R. Stradiotto, Valdemar Lacerda Júnior, José Maria Pires, and Adilson Beatriz. "Electrochemical and theoretical evaluation of the interaction between dna and amodiaquine: evidence of the guanine adduct formation." Química Nova 33, no. 6 (2010): 1291–96. http://dx.doi.org/10.1590/s0100-40422010000600014.

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27

de Keijser, Jan W., Marijke Malsch, Egge T. Luining, Marleen Weulen Kranenbarg, and Dominique J. H. M. Lenssen. "Differential reporting of mixed DNA profiles and its impact on jurists’ evaluation of evidence. An international analysis." Forensic Science International: Genetics 23 (July 2016): 71–82. http://dx.doi.org/10.1016/j.fsigen.2016.03.006.

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28

Sikora, Katarzyna, Chiara Bedin, Caterina Vicentini, Giorgio Malpeli, Edoardo D'Angelo, Nicola Sperandio, Rita T. Lawlor, et al. "Evaluation of cell-free DNA as a biomarker for pancreatic malignancies." International Journal of Biological Markers 30, no. 1 (January 2015): 136–41. http://dx.doi.org/10.5301/jbm.5000088.

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Background Currently, no reliable blood-based assay for early detection of pancreatic ductal adenocarcinoma (PDAC) is available. Cell-free DNA (cfDNA) quantitation in patients’ plasma has been recently applied in monitoring several cancer types. This study evaluates the diagnostic potential of cfDNA in PDAC patients. Methods Plasma cfDNA levels and integrity ratio were assayed using quantitative real-time PCR of Alu-repeat amplicons in patients with pancreatic ductal adenocarcinoma (n=50), pancreatic neuroendocrine tumor (n=23), and chronic pancreatitis (n=20), as well as in healthy volunteers without evidence of pancreatic disease (n=23). Results The total load of cfDNA, obtained by Alu83 quantitation, was the highest in PDAC patients than in any of the other patient groups (Welch t test; p<0.001) and was an average predictor of PDAC disease (AUC=0.664; CI, 0.56-0.77). A nonlinear association between Alu83 levels and subjects’ age was detected (Spearman's rho=0.35; p<0.001) in the overall population, as well as within the PDAC patients’ group (Spearman's rho=0.47; p<0.001). Necrosis-derived cfDNA fragments, quantitated with the Alu244 amplicon, were barely detectable in any of the samples and, in that respect, comparable between the different subject groups. CfDNA integrity estimation (Alu244/Alu83 ratio) was significantly affected by the limited detectability of plasma Alu244 levels. Conclusion The lack of detectable levels of necrosis-derived cfDNA in pancreatic pathologies considerably affects the clinical use of such biomarker in PDAC patients. Different methods of analysis should be applied in the evaluation of the cfDNA diagnostic value in pancreas pathology.

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29

Wimberger, Pauline, Peter Hillemanns, Thomas Kapsner, Hermann Hepp, and Rainer Kimmig. "Evaluation of Prognostic Factors Following Flow-Cytometric DNA Analysis after Cytokeratin Labelling: I. Breast Cancer." Analytical Cellular Pathology 24, no. 4-5 (2002): 135–45. http://dx.doi.org/10.1155/2002/630850.

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In gynecologic oncology valid prognostic factors are necessary to estimate the course of disease and to define biologically similar subgroups for analysis of therapeutic efficacy. The presented study is a prospective study concerning prognostic significance of DNA ploidy and S‐phase fraction in breast cancer following enrichment of tumor cells by cytokeratin labelling. Epithelial cells were labeled by FITC‐conjugated cytokeratin antibody (CK 5, 6, 8, and CK 17) prior to flow cytometric cell cycle analysis in 327 fresh specimens of primary breast cancer. Univariate analysis in breast cancer detected the prognostic significance of DNA‐ploidy, S‐phase fraction and CV (coefficient of variation) of G0G1‐peak of tumor cells for clinical outcome, especially for nodal‐negative patients. Multivariate analysis could not confirm prognostic evidence of DNA‐ploidy and S‐phase fraction. In conclusion, in breast cancer no clinical significance for determination of DNA‐parameters was found.

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30

Cousins, Debby, Suzette Williams, Ernesto Liébana, Alicia Aranaz, Annelies Bunschoten, Jan Van Embden, and Trevor Ellis. "Evaluation of Four DNA Typing Techniques in Epidemiological Investigations of Bovine Tuberculosis." Journal of Clinical Microbiology 36, no. 1 (1998): 168–78. http://dx.doi.org/10.1128/jcm.36.1.168-178.1998.

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DNA fingerprinting techniques were used to type 273 isolates ofMycobacterium bovis from Australia, Canada, the Republic of Ireland, and Iran. The results of restriction fragment length polymorphism (RFLP) analysis with DNA probes from IS6110, the direct repeat (DR), and the polymorphic GC-rich sequence (PGRS) were compared with those of a new PCR-based method called spacer oligonucleotide typing (spoligotyping) developed for the rapid typing of Mycobacterium tuberculosis (J. Kamerbeek et al., J. Clin. Microbiol. 35:907–914, 1997). Eighty-five percent of the isolates harbored a single copy of IS6110, and 81.5% of these carried IS6110 on the characteristic 1.9-kb restriction fragment. RFLP analysis with IS6110 identified 23 different types, RFLP analysis with the DR probe identified 35 types, RFLP analysis with the PGRS probe identified 77 types, and the spoligotyping method identified 35 types. By combining all results, 99 different strains could be identified. Isolate clusters were frequently associated within herds or were found between herds when epidemiological evidence confirmed animal movements. RFLP analysis with IS6110 was sufficiently sensitive for the typing of isolates with more than three copies of IS6110, but RFLP analysis with the PGRS probe was the most sensitive typing technique for strains with only a single copy of IS6110. Spoligotyping may have advantages for the rapid typing of M. bovis, but it needs to be made more sensitive.

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Catal, M., G. C. Adams, and D. W. Fulbright. "Evaluation of Resistance to Rhabdocline Needlecast in Douglas Fir Variety Shuswap, with Quantitative Polymerase Chain Reaction." Phytopathology® 100, no. 4 (April 2010): 337–44. http://dx.doi.org/10.1094/phyto-100-4-0337.

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A quantitative polymerase chain reaction assay was developed that could detect DNA of Rhabdocline pseudotsugae and R. oblonga among DNA of Douglas fir needles to a limit as low as three copies of target DNA. Differential infection rates of two varieties (seed sources) of Douglas fir interplanted in a field were studied in relation to staggered bud breaks. Infection of Douglas fir var. San Isabel corresponded to ascospore release times for Rhabdocline spp., whereas infection of var. Shuswap Lake did not occur throughout the spore release period during 2 years of study, despite abundant inoculum and adequate moisture during bud break. Rhabdocline spp. DNA was never detected in Shuswap Lake and disease symptoms were not observed in any year. We provide evidence that Shuswap Lake is resistant and probably immune to Rhabdocline spp. infection and Rhabdocline needlecast under Michigan conditions.

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32

Stoehr, Michael U., and Craig H. Newton. "Evaluation of mating dynamics in a lodgepole pine seed orchard using chloroplast DNA markers." Canadian Journal of Forest Research 32, no. 3 (March 1, 2002): 469–76. http://dx.doi.org/10.1139/x01-222.

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Chloroplast DNA (cpDNA) markers were used to evaluate pollen dynamics in an operational lodgepole pine (Pinus contorta Dougl. ex Loud. var. latifolia Engelm.) seed orchard. High levels of cpDNA differentiation were obtained using six primer pairs specific to simple sequence repeat (SSR) and variable number tandem repeat (VNTR) loci dispersed around the lodgepole pine chloroplast genome. In 69 orchard parents genotypes, 46 multilocus haplotypes were detected with 31 of these being unique (i.e., having only one orchard parent). The number of variants (alleles) per locus ranged from two to seven with gene diversity levels of 0.44-0.72. Evaluation of wind-pollinated seedlots of 15 selected clones using these markers indicated low levels of selfing (2%) and pollen contamination (5%) but showed evidence of relatively high levels of differential male reproductive success.

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33

Ngo, Vu, Mengchi Wang, and Wei Wang. "Finding de novo methylated DNA motifs." Bioinformatics 35, no. 18 (February 6, 2019): 3287–93. http://dx.doi.org/10.1093/bioinformatics/btz079.

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Abstract Motivation Increasing evidence has shown that nucleotide modifications such as methylation and hydroxymethylation on cytosine would greatly impact the binding of transcription factors (TFs). However, there is a lack of motif finding algorithms with the function to search for motifs with modified bases. In this study, we expand on our previous motif finding pipeline Epigram to provide systematic de novo motif discovery and performance evaluation on methylated DNA motifs. Results mEpigram outperforms both MEME and DREME on finding modified motifs in simulated data that mimics various motif enrichment scenarios. Furthermore we were able to identify methylated motifs in Arabidopsis DNA affinity purification sequencing (DAP-seq) data that were previously demonstrated to contain such motifs. When applied to TF ChIP-seq and DNA methylome data in H1 and GM12878, our method successfully identified novel methylated motifs that can be recognized by the TFs or their co-factors. We also observed spacing constraint between the canonical motif of the TF and the newly discovered methylated motifs, which suggests operative recognition of these cis-elements by collaborative proteins. Availability and implementation The mEpigram program is available at http://wanglab.ucsd.edu/star/mEpigram. Supplementary information Supplementary data are available at Bioinformatics online.

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Krober, Stefan, Peter Ruck, Jia-Cheng Xiao, and Edwin Kaiserling. "Flow cytometric evaluation of nuclear DNA content in hepatoblastoma: Further evidence for the inhomogeneity of the different subtypes." Pathology International 45, no. 7 (July 1995): 501–5. http://dx.doi.org/10.1111/j.1440-1827.1995.tb03492.x.

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Jordan, Susan P., and Marilyn Schuman Jorns. "Evidence for a singlet intermediate in catalysis by Escherichia coli DNA photolyase and evaluation of substrate binding determinants." Biochemistry 27, no. 25 (December 13, 1988): 8915–23. http://dx.doi.org/10.1021/bi00425a007.

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36

McGlasson, Sarah, Kristiina Rannikmäe, Steven Bevan, Clare Logan, Louise S. Bicknell, Alexa Jury, Andrew P. Jackson, Hugh S. Markus, Cathie Sudlow, and David P. J. Hunt. "Rare variants of the 3’-5’ DNA exonuclease TREX1 in early onset small vessel stroke." Wellcome Open Research 2 (November 2, 2017): 106. http://dx.doi.org/10.12688/wellcomeopenres.12631.1.

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Background: Monoallelic and biallelic mutations in the exonuclease TREX1 cause monogenic small vessel diseases (SVD). Given recent evidence for genetic and pathophysiological overlap between monogenic and polygenic forms of SVD, evaluation of TREX1 in small vessel stroke is warranted. Methods: We sequenced the TREX1 gene in an exploratory cohort of patients with lacunar stroke (Edinburgh Stroke Study, n=290 lacunar stroke cases). We subsequently performed a fully blinded case-control study of early onset MRI-confirmed small vessel stroke within the UK Young Lacunar Stroke Resource (990 cases, 939 controls). Results: No patients with canonical disease-causing mutations of TREX1 were identified in cases or controls. Analysis of an exploratory cohort identified a potential association between rare variants of TREX1 and patients with lacunar stroke. However, subsequent controlled and blinded evaluation of TREX1 in a larger and MRI-confirmed patient cohort, the UK Young Lacunar Stroke Resource, identified heterozygous rare variants in 2.1% of cases and 2.3% of controls. No association was observed with stroke risk (odds ratio = 0.90; 95% confidence interval, 0.49-1.65 p=0.74). Similarly no association was seen with rare TREX1 variants with predicted deleterious effects on enzyme function (odds ratio = 1.05; 95% confidence interval, 0.43-2.61 p=0.91). Conclusions: No patients with early-onset lacunar stroke had genetic evidence of a TREX1-associated monogenic microangiopathy. These results show no evidence of association between rare variants of TREX1 and early onset lacunar stroke. This includes rare variants that significantly affect protein and enzyme function. Routine sequencing of the TREX1 gene in patients with early onset lacunar stroke is therefore unlikely to be of diagnostic utility, in the absence of syndromic features or family history.

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Homburger, Sheila A., Dina Drits-Esser, Molly Malone, and Louisa A. Stark. "Building Argumentation Skills in the Biology Classroom." American Biology Teacher 83, no. 2 (February 1, 2021): 104–11. http://dx.doi.org/10.1525/abt.2021.83.2.104.

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Arguing from evidence is one of eight key science practices in which students should engage. It is an essential component of science, yet students have difficulties with this practice. We describe a scaffolded claims-evidence-reasoning (CER) argumentation framework that is embedded within a new eight-week, freely available curriculum unit developed by the Genetic Science Learning Center – Evolution: DNA and the Unity of Life. The scaffold provides high school students with practice in both developing and evaluating written arguments. It is designed to incrementally build student skill week-by-week, starting with an introduction to the CER components of an argument, and ending with students evaluating data and constructing a supported written argument. We also present evaluation findings from field testing the argumentation scaffold in the context of the complete Evolution unit in dozens of classrooms. And we discuss how this integrated, scaffolded approach to argumentation influenced both student and teacher learning.

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Adoga, Moses P., Grace Pennap, Becky O. Akande, Jamey P. Mairiga, Simon Pechulano, and Simon M. Agwale. "Evaluation of a recombinant DNA hepatitis B vaccine in a vaccinated Nigerian population." Journal of Infection in Developing Countries 4, no. 11 (August 6, 2010): 740–44. http://dx.doi.org/10.3855/jidc.823.

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Introduction: Recombinant hepatitis B vaccine was introduced in 1986 and has gradually replaced the plasma-derived hepatitis B vaccine. No published data are available on the immunogenicity of hepatitis B vaccines in Nigerians. The current study aimed to evaluate protective sero-conversion rates after vaccination with Shanvac-B rDNA hepatitis B vaccine in Nigerian subjects between January and September 2009. Methodology: After having obtained informed consent and ethical clearance, 2 mL of blood were aseptically collected from each participant aged ≤ 50 years, one month after the first, second and third doses of the vaccine. Sera were separated into cryovials and frozen at -21oC until analysed for the detection of the protective antibody titre induction. Protective antibody titre was defined as a titre of ≥10 mIU/mL. Results: Of the 376 participants, 192 (51.1%) were males and 184 (48.9%) were females. A total of 144 subjects participated in the first-dose group, nine (6.3%) of whom developed protective antibody titre (8.3% of males and 4.2% of females). Of the 121 participants in the second-dose group, 108 (89.3%) developed protective antibody titre (98.3% of males and 80.3% of females), while of the 111 participants in the third-dose group, 100% protectively sero-converted. Males were more likely to develop protective antibody titre than females after the second dose (P < 0.05). Conclusion: This data provides additional evidence for the efficacy of Shanvac-B rDNA hepatitis B vaccine and the need to adhere to the recommended three-dose schedule to achieve full and lasting sero-protection among Nigerians.

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Dr. Beeula A, Dr. Shamala. S, T. Pavithra Banu, Dr. Devi, Dr. Adhithya. B, and Dr. Kokila. S. "FORENSIC ODONTOLOGY AND ITS PREVAILLING ADVANCEMENT." International Journal of Forensic Odontology 7, no. 2 (October 15, 2022): 26–31. http://dx.doi.org/10.56501/intjforensicodontol.v7i2.628.

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Forensic odontology is a branch of dentistry which deals with proper handling, examination and evaluation of dental evidence, with proper presentation of dental findings in the interest of justice. Tooth is the hardest tissue in the body and is most resistant to post-mortem deterioration. Dental pattern for each individual is distinct and helps in identification of victims during mass disasters, abuse and crimes. Conventional methods used in identification are dental record maintenance, dental imaging, bite marks analysis, Cheiloscopy and Rugoscopy. In addition, recent concepts have been introduced such as facial reconstruction, denture identification, DNA profiling, tongue prints and comparison microscopy. DNA analysis is a technique which involves DNA which is either mitochondrial DNA or genomic DNA.The common methods used in DNA analysis are PCR, restrictions fragments length polymorphism method, short tandem repeats typing, etc.

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Silva, Isana, Manoela Ramos, Lídia Arantes, André Lengert, Marco Oliveira, Fernanda Cury, Guilherme Martins Pereira, et al. "Evaluation of DNA Methylation Changes and Micronuclei in Workers Exposed to a Construction Environment." International Journal of Environmental Research and Public Health 16, no. 6 (March 13, 2019): 902. http://dx.doi.org/10.3390/ijerph16060902.

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Methylation levels in tumor-suppressor genes and repetitive sequences have previously been used to study the relationship between environmental air pollution and epigenetic changes related to cancer. In this study, we measured the methylation profiles of the promoter regions CDKN2A, MLH1 and APC and the repetitive sequence LINE-1 in 59 workers exposed to the construction environment and in 49 unexposed workers. We also evaluated the micronuclei frequency and levels of trace elements in the blood of all workers. We evaluated of levels of particulate matter and polycyclic aromatic hydrocarbons (PAHs) at the construction site to characterize the environmental exposure. Our findings demonstrated that exposed workers exhibited significantly higher average levels of promoter methylation of CDKN2A, APC, and MLH1 genes and increased hypomethylation of the LINE-1 in comparison to unexposed workers (all p < 0.05). A higher frequency of micronuclei was observed in the exposed group (2 ± 2) compared to the unexposed group (1 ± 1) with p < 0.001. High levels of particulate matter (51–841 μg/m3) and some PAHs were found in samples from the construction environment. In summary, we provide evidence of increased DNA damage and altered DNA methylation of exposed workers, suggesting that genomic approaches to biomonitoring may be an effective way of estimating future cancer risk for construction workers.

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Mendez, Julio C., Mark J. Espy, Thomas F. Smith, Jennie A. Wilson, and Carlos V. Paya. "Evaluation of PCR Primers for Early Diagnosis of Cytomegalovirus Infection following Liver Transplantation." Journal of Clinical Microbiology 36, no. 2 (1998): 526–30. http://dx.doi.org/10.1128/jcm.36.2.526-530.1998.

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The availability of microbiologic methods that detect early replication of cytomegalovirus (CMV) posttransplantation will enhance the process of initiating preemptive antiviral therapy prior to the appearance of CMV disease. Using PCR techniques we sought to determine which region of the CMV genome present in peripheral blood leukocytes (PBLs) or serum provides the highest sensitivity for the detection of CMV posttransplantation. Blood samples were prospectively collected weekly for at least 8 weeks from a cohort of 21 consecutive liver transplant recipients not receiving anti-CMV prophylaxis. Results of PCR assays were correlated with recovery of CMV in cell cultures and histopathological findings from biopsy specimens of infected organs to assess clinical symptomatic infection. Of 148 specimens, primer pairs directed to the HindIII-X fragment region of CMV detected target DNA with a 94% sensitivity, compared to an 87% sensitivity with primer pairs directed to EcoRI fragment D, 32% sensitivity with primer pairs directed to the immediate-early antigen 1 gene (IEA1 gene), and 20% sensitivity with primer pairs directed to the major immediate-early (MIE) gene. The performance characteristics in terms of the sensitivity of primers for amplifying CMV DNA associated with symptomatic infection ranged from 100% (HindIII-X) to 20% (MIE gene); however, specificity was inversely related (HindIII-X, 45%; MIE gene, 91%) to primers directed to these gene targets. When HindIII-X andEcoRI-D primer sets were used, CMV DNA from PBLs was a more sensitive target than CMV DNA from serum for the early detection of symptomatic CMV infection (17 versus 12 days). Importantly, CMV DNA was not detected in five patients with no evidence of this viral infection. In conclusion, primers directed to the HindIII-X fragment region were the most optimal for the early detection of CMV DNA in PBLs and sera from symptomatic liver transplant recipients.

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Liu, Danping, Tong Xu, Bisheng Shi, Wei Lu, Ye Zheng, Yanling Feng, Zhenghong Yuan, Xiaonan Zhang, and Zhanqing Zhang. "Clinical relevance of the in situ assay for HBV DNA: a cross-sectional study in patients with chronic hepatitis B." Journal of Clinical Pathology 73, no. 12 (May 13, 2020): 813–18. http://dx.doi.org/10.1136/jclinpath-2020-206440.

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AimsThe visualisation of HBV DNA in liver sections of patients with chronic hepatitis B (CHB) in our previous report uncovered a mosaic distribution of viral antigens and nucleic acids. Here we aim to further explore the clinical utility of the in situ hybridisation (ISH) assay for HBV DNA.MethodISH of HBV DNA along with immunohistochemistry (IHC) of HBsAg, HBcAg and routine histopathology analysis was performed in 313 treatment-naive patients with CHB. Serum HBcrAg and HBcAb titre were also measured in addition to basic biochemical and virological parameters.ResultsThe ISH of HBV DNA, HBsAg and HBcAg showed 95.2%, 97.1% and 42.8% positive rate, respectively. The staining pattern of HBV DNA differs significantly with that of HBsAg. Intrahepatic HBV DNA exhibited high-level of correlations with viral load, HBcrAg and HBsAg titre. In HBeAg-negative patients, higher intrahepatic HBV DNA is associated with histological evidence of liver inflammation and fibrosis, whereas no such trend was observed in HBeAg-positive patients. Finally, a triple staining protocol that combined the detection of HBV DNA, HBsAg and collagen fibre was developed to enable better evaluation of viral replication and antigen expression in the context of disease progression.ConclusionsThe ISH assay for HBV DNA reflects the vigour of intrahepatic viral replication. It is complementary to the routine IHC assay for viral antigens and also related to the histopathological progression of liver diseases. The application of the HBV DNA ISH assay may help a better evaluation of virological and pathological condition of patients with CHB.

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Siakantaris, Marina P., Maria K. Angelopoulou, Konstantinos Lilakos, Yannis Metaxas, Maria Moschoyianni, Maria Gamaletsou, Theodoros P. Vassilakopoulos, et al. "Evaluation of Microsatellite Instability in Gastric MALT Lymphomas." Blood 108, no. 11 (November 16, 2006): 4625. http://dx.doi.org/10.1182/blood.v108.11.4625.4625.

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Abstract BACKGROUND: Microsatellite instability (MSI) is a major mechanism of carcinogenesis in hereditary nonpolyposis colorectal cancer, sporadic colon cancer, as well as other solid tumors. It is also encountered in gastritis and other chronic inflammatory conditions. Gastric MALT lymphomas are associated with chronic antigenic stimulation due to Helicobacter pylori (H.P) infection, leading to chronic gastritis, before converting to overt lymphoma. AIM: The evaluation of the presence of MSI in gastric MALT lymphoma lesions at diagnosis and during follow-up, after H.P eradication and/or chemotherapy. METHODS: Genomic DNA was extracted from formalin-fixed paraffin-embedded MALT lymphoma gastric biopsies. Blood genomic DNA was used as control. A pentaplex PCR was performed using primers for 5 different mononucleotide loci (NR21, NR24, NR27, BAT25 and BAT26). Sense oligonucleotides were labeled with WellRead fluorophores and products were run on a CEQ8000 apparatus (Beckman Coulter). Allele scoring was performed using the specific software. For the definition of MSI, 2/5 loci had to show banding shifts or gains outside the quasimonomorphic area for each marker. RESULTS: 10 MALT lymphoma patients at diagnosis were studied and peaks were compared between stomach and blood samples. All 5 markers studied did not reveal any additional peaks when blood and gastric DNA were compared. In 4 patients follow-up gastric biopsies were available, after H.P eradication, as well as after chemotherapy treatment. There was no evidence of MSI in the serial gastric biopsies of these patients. CONCLUSIONS: MSI was not detected in any gastric biopsies of this small group of MALT patients, either at diagnosis, or after treatment. The role of MSI in the lymphomagenesis of this distinct type of lymphoma needs to be further evaluated in serial specimens in a larger series of patients.

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Kong, Yimeng, Lei Cao, Gintaras Deikus, Yu Fan, Edward A. Mead, Weiyi Lai, Yizhou Zhang, et al. "Critical assessment of DNA adenine methylation in eukaryotes using quantitative deconvolution." Science 375, no. 6580 (February 4, 2022): 515–22. http://dx.doi.org/10.1126/science.abe7489.

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The discovery of N 6 -methyldeoxyadenine (6mA) across eukaryotes led to a search for additional epigenetic mechanisms. However, some studies have highlighted confounding factors that challenge the prevalence of 6mA in eukaryotes. We developed a metagenomic method to quantitatively deconvolve 6mA events from a genomic DNA sample into species of interest, genomic regions, and sources of contamination. Applying this method, we observed high-resolution 6mA deposition in two protozoa. We found that commensal or soil bacteria explained the vast majority of 6mA in insect and plant samples. We found no evidence of high abundance of 6mA in Drosophila , Arabidopsis , or humans. Plasmids used for genetic manipulation, even those from Dam methyltransferase mutant Escherichia coli , could carry abundant 6mA, confounding the evaluation of candidate 6mA methyltransferases and demethylases. On the basis of this work, we advocate for a reassessment of 6mA in eukaryotes.

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Le, Hang Phuong, Wolf-Dietrich Heyer, and Jie Liu. "Guardians of the Genome: BRCA2 and Its Partners." Genes 12, no. 8 (August 10, 2021): 1229. http://dx.doi.org/10.3390/genes12081229.

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The tumor suppressor BRCA2 functions as a central caretaker of genome stability, and individuals who carry BRCA2 mutations are predisposed to breast, ovarian, and other cancers. Recent research advanced our mechanistic understanding of BRCA2 and its various interaction partners in DNA repair, DNA replication support, and DNA double-strand break repair pathway choice. In this review, we discuss the biochemical and structural properties of BRCA2 and examine how these fundamental properties contribute to DNA repair and replication fork stabilization in living cells. We highlight selected BRCA2 binding partners and discuss their role in BRCA2-mediated homologous recombination and fork protection. Improved mechanistic understanding of how BRCA2 functions in genome stability maintenance can enable experimental evidence-based evaluation of pathogenic BRCA2 mutations and BRCA2 pseudo-revertants to support targeted therapy.

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Curtin, Nicola J. "PARP inhibitors for cancer therapy." Expert Reviews in Molecular Medicine 7, no. 4 (March 15, 2005): 1–20. http://dx.doi.org/10.1017/s146239940500904x.

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Poly(ADP-ribose) polymerase 1 (PARP-1) is a zinc-finger DNA-binding enzyme that is activated by binding to DNA breaks. Poly(ADP-ribosyl)ation of nuclear proteins by PARP-1 converts DNA damage into intracellular signals that activate either DNA repair by the base-excision pathway or cell death. A family of 18 PARPs has been identified, but only the most abundant, PARP-1 and PARP-2, which are both nuclear enzymes, are activated by DNA damage. PARP inhibitors of ever-increasing potency have been developed in the 40 years since the discovery of PARP-1, both as tools for the investigation of PARP-1 function and as potential modulators of DNA-repair-mediated resistance to cytotoxic therapy. Owing to the high level of homology between the catalytic domains of PARP-1 and PARP-2, the inhibitors probably affect both enzymes. Convincing biochemical evidence, which has been corroborated by genetic manipulation of PARP-1 activity, shows that PARP inhibition is associated with increased sensitivity to DNA-alkylating agents, topoisomerase I poisons and ionising radiation. Novel PARP inhibitors of sufficient potency and suitable pharmacokinetic properties to allow evaluation in animal models have been shown to enhance the antitumour activity of temozolomide (a DNA-methylating agent), topoisomerase poisons and ionising radiation; indeed, the combination with temozolomide resulted in complete tumour regression in two independent studies. The combination of a PARP inhibitor and temozolomide is currently undergoing clinical evaluation for the first time.

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Korycka-Machala, Malgorzata, Ewelina Rychta, Anna Brzostek, Heather R. Sayer, Anna Rumijowska-Galewicz, Richard P. Bowater, and Jarosław Dziadek. "Evaluation of NAD+-Dependent DNA Ligase of Mycobacteria as a Potential Target for Antibiotics." Antimicrobial Agents and Chemotherapy 51, no. 8 (June 4, 2007): 2888–97. http://dx.doi.org/10.1128/aac.00254-07.

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ABSTRACT Mycobacteria contain genes for several DNA ligases, including ligA, which encodes a NAD+-dependent enzyme that has been postulated to be a target for novel antibacterial compounds. Using a homologous recombination system, direct evidence is presented that wild-type ligA cannot be deleted from the chromosome of Mycobacterium smegmatis. Deletions of native ligA in M. smegmatis could be obtained only after the integration of an extra copy of M. smegmatis or Mycobacterium tuberculosis ligA into the attB site of the chromosome, with expression controlled by chemically inducible promoters. The four ATP-dependent DNA ligases encoded by the M. smegmatis chromosome were unable to replace the function of LigA. Interestingly, the LigA protein from M. smegmatis could be substituted with the NAD+-dependent DNA ligase of Escherichia coli or the ATP-dependent ligase of bacteriophage T4. The conditional mutant strains allowed the analysis of the effect of LigA depletion on the growth of M. smegmatis. The protein level of the conditional mutants was estimated by Western blot analysis using antibodies raised against LigA of M. tuberculosis. This revealed that a strong overproduction or depletion of LigA did not affect the growth or survival of mycobacteria under standard laboratory conditions. In conclusion, although NAD+-dependent DNA ligase is essential for mycobacterial viability, only low levels of protein are required for growth. These findings suggest that very efficient inhibition of enzyme activity would be required if NAD+-dependent DNA ligase is to be useful as an antibiotic target in mycobacteria. The strains developed here will provide useful tools for the evaluation of the efficacy of any appropriate compounds in mycobacteria.

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IP, Stephen, and Kamming LAI. "An Evaluation Of The Precision Of QIAGEN Quantiplex HYres Kit As a Screening Tool On Low Level Touch DNA Evidence." European Journal of Forensic Sciences 3, no. 2 (2016): 61. http://dx.doi.org/10.5455/ejfs.19657.

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Morris, Jeffrey W., A. I. Sanda, and Jeffrey Glassberg. "Biostatistical Evaluation of Evidence from Continuous Allele Frequency Distribution Deoxyribonucleic Acid (DNA) Probes in Reference to Disputed Paternity and Identity." Journal of Forensic Sciences 34, no. 6 (November 1, 1989): 12771J. http://dx.doi.org/10.1520/jfs12771j.

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50

Duncan, Robert B., William K. Scarratt, and Gertrude C. Buehring. "Detection of Bovine Leukemia Virus by in Situ Polymerase Chain Reaction in Tissues from a Heifer Diagnosed with Sporadic Thymic Lymphosarcoma." Journal of Veterinary Diagnostic Investigation 17, no. 2 (March 2005): 190–94. http://dx.doi.org/10.1177/104063870501700217.

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An 18-month-old bovine heifer was presented for clinical evaluation after a sudden onset of ventral edema. Clinical and pathological evaluations were consistent with thymic lymphosarcoma, a sporadic form of lymphosarcoma in cattle, which is not generally considered to be associated with bovine leukemia virus (BLV). This heifer was seropositive for BLV at 6 and 18 months of age. Tissues obtained at necropsy were evaluated using in situ polymerase chain reaction. The BLV proviral DNA was detected in lymphocytes of the thymus as well as in epithelial cells of the liver and kidney. This report presents evidence that thymic lymphosarcomas can be associated with BLV infection and that BLV may have a broader cellular tropism than was supposed previously.

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