DNA Data Research Articles

DNA Information Storage and Cryptography System

With the development of information technology, the global data volume is growing exponentially. In order to alleviate the contradiction between massive data and traditional storage technology, people begin to seek for a new generation of storage media. As a carrier of genetic information, DNA has the characteristics of high information density, long storage life and low maintenance cost, which can effectively overcome the deficiency of traditional storage media. With the development of DNA synthesis and DNA sequencing technology, DNA data storage technology has attracted more and more attention, and a series of major breakthroughs have been made. In this paper, with the workflow of DNA data storage as the main line, expounds the basic theory of DNA data storage and related technology, mainly introduced the research progress of DNA storage method and strategy, briefly summarizes the latest research results of DNA data cryptography, and finally discussed the major challenges that DNA data storage technology is facing , especially, DNA synthesis efficiency, DNA sequencing time cost and DNA data cryptography will be an important research direction of DNA storage technology in the future. It is believed that with the deepening of the data storage research on DNA, DNA data storage will become the most potential new storage method in the future, and can be a practical application in the future.

Epstein-Barr Virus DNA Is Associated With Conjunctival Squamous Cell Carcinomas: A Case-Control Study From Zimbabwe.

Incidence of conjunctival squamous cell carcinoma (cSCC) in Zimbabwe is >30-fold higher than the global average. cSCC risk is notably higher among people with human immunodeficiency virus, implicating impaired immune response and a yet unknown infectious etiology. Formalin-fixed, paraffin-embedded blocks from Zimbabwe, comprising conjunctival precancer (n = 78), invasive cSCC cases (n = 148) and nonmalignant eye lesions (n = 119), were tested for multiple DNA viruses using Luminex bead-based technology. Epstein-Barr virus (EBV) type 1 positivity was strongly associated with cSCC diagnosis (adjusted odds ratio [aOR], 5.6 [95% confidence interval {CI}, 3.0-10.4) and marginally associated with precancer (aOR, 2.1 [95% CI, 1.0-4.5]). On analyzing EBV transcriptional activity with any of LMP1, EBNA1, and BZLF1, RNA transcripts were detected in 5 of 112 controls, 3 of 67 precancers, and 10 of 139 cases and none were associated with conjunctival case status. Our EBV DNA data suggest that EBV may play a role in cSCC. However, the low detection rate of EBV RNA supports further investigation to infer causality.

DNA barcoding insufficiently identifies European wild bees (Hymenoptera, Anthophila) due to undefined species diversity, genus-specific barcoding gaps and database errors.

Recent declines in insect abundances, especially populations of wild pollinators, pose a threat to many natural and agricultural ecosystems. Traditional species monitoring relies on morphological character identification and is inadequate for efficient and standardized surveys. DNA barcoding has become a standard approach for molecular identification of organisms, aiming to overcome the shortcomings of traditional biodiversity monitoring. However, its efficacy depends on the completeness of reference databases. Large DNA barcoding efforts are (almost entirely) lacking in many European countries and such patchy data limit Europe-wide analyses of precisely how to apply DNA barcoding in wild bee identification. Here, we advance towards an effective molecular identification of European wild bees. We conducted a high-effort survey of wild bees at the junction of central and southern Europe and DNA barcoded all collected morphospecies. For global analyses, we complemented our DNA barcode dataset with all relevant European species and conducted global analyses of species delimitation, general and genus-specific barcoding gaps and examined the error rate in DNA data repositories. We found that (i) a sixth of all specimens from Slovenia could not be reliably identified, (ii) species delimitation methods show numerous systematic discrepancies, (iii) there is no general barcoding gap across all bees and (iv) the barcoding gap is genus specific, but only after curating for errors in DNA data repositories. Intense sampling and barcoding efforts in underrepresented regions and strict curation of DNA barcode repositories are needed to enhance the use of DNA barcoding for the identification of wild bees.

Abstract 4940: Unraveling ctDNA features in high-grade serous ovarian carcinoma and insights from genomic and transcriptomic integration

Abstract High-grade serous carcinoma (HGSC) is often diagnosed at advanced stages with less than 40% of patients surviving for five years after diagnosis. Circulating tumor DNA (ctDNA) is a minimally invasive technology that can provide crucial insights into tumor biology. Unique features from ctDNA, fragment patterns and nucleosome footprints at transcription start sites (TSS), complement genomic variants. Our study explored ctDNA features in HGSC, integrating with tumor biopsies' genomic and transcriptomic profiles. We focus on two aspects in HGSC: understanding how ctDNA features assist genomic profiling and track dynamic changes during treatment and exploring the biological factors impacting ctDNA release. We used 500+ longitudinal plasma and 400+ pretreatment tissue samples from HGSC patients in the DECIDER study (NCT04846933). Shallow whole-genome sequencing (sWGS) with 0.4x average coverage was conducted on plasma. Integration of DNA and RNA pretreatment tissue data was performed for 98 and 91 patients with available plasma before treatment, respectively. Plasma samples underwent analysis for fragment patterns and TSS signals. Somatic mutations and mutational signatures were retrieved for patients with available WGS tissue data. Pathway enrichment analysis was applied to diverse gene expression profiles. WGS data from 29 healthy individuals (Zhu, G. et al. (2023)) served as controls. DNA fragment profiles and TSS signals distinguish ctDNA from healthy samples. The ability to cluster sample phases based on ctDNA features facilitates tracking longitudinal changes. Integrating tissue DNA and RNA data reveals a positive correlation between high ctDNA release and mutational burden, single-base substitution signature SBS1 as a marker for cell division/mitotic clock and doublet-base substitution signatures linked to late replication. These mechanisms help explain why high ctDNA release group (n=40) is associated with a shorter progression-free survival. Additionally, transcriptomics data indicates associations with proliferation pathways in cancer cells and ctDNA release. The concordance in results from DNA and RNA points to a higher proliferation rate in patients with high ctDNA release, suggesting the need for alternative treatment compared to those with low ctDNA release. In conclusion, our results provide a multifaceted perspective on ctDNA in HGSC. The identification of longitudinal ctDNA features signifies the capability to stratify sample states and show the potential findings through fragment profiles and the discernment of key TSS regions. The proposed aetiologies and enriched pathways associated with ctDNA release, mutation burden and proliferation, shed light on potential treatment avenues. These findings contribute to our understanding of ctDNA in HGSC and offer insights for personalized treatment strategies and monitoring approaches. Citation Format: Mai TN Nguyen, Jaana Oikkonen, Yilin Li, Daria Afentave, Johanna Hynninen, Sampsa K. Hautaniemi. Unraveling ctDNA features in high-grade serous ovarian carcinoma and insights from genomic and transcriptomic integration [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4940.

Abstract 5100: Multimodal real world data reveals immunogenomic drivers of acquired and primary resistance to immune checkpoint blockade

Abstract Background: Why some patients fail or have short lived response to immune checkpoint blockade (ICB) immunotherapy remains largely unknown. While baseline molecular assessments have provided clues to prognostic factors, insights into resistance drivers remains elusive. This is partially due to the difficulty in getting access to post progression samples from patients that were either primary resistant or developed acquired resistance after an initial response to ICB. Thus, the tumor-intrinsic and -extrinsic features that are selected for during progression and potentially drive primary and acquired resistance to immunotherapy remain underexplored. Methods: To compare clinical features and immunogenomic drivers of acquired and primary resistance to ICB across major cancers, we analysed and annotated de-identified patient records in the Tempus real-world database. We built an immuno-oncology cohort consisting of >2500 multimodal (DNA, RNA and clinical outcome data) pre-treatment baseline with >1500 post-treatment tumour biopsy samples from mainly NSCLC, TNBC, HNC and Bladder cancer patients. We used bulk RNA-seq data to estimate activation of the hallmark oncogenic pathways and immune cell composition and used panel DNA-seq data (>500 genes) to quantify mutation selection at the gene and pathway levels using dndscv. Results: Compared to acquired, primary resistant patients tended to have a higher observation of liver lesions at progression. Post-ICB, acquired resistant NSCLC and HNC patients showed a significantly inflamed tumour microenvironment (TME) characterised by higher estimation of infiltration of T cells and myeloid cells and higher activation of interferon gamma (IFNg) signalling as compared to primary resistant patients. In addition, in post-ICB acquired resistance in NSCLC we observed selection for mutations in genes involved in known immunomodulatory pathways, including loss-of-function mutations in B2M. Consistently, acquired resistance patients showed stronger selection for mutations in Hedgehog and Notch pathways as compared to primary resistance patients across NSCLC, HNC and TNBC post-ICB. Conclusions: Acquired and primary ICB resistant patients have distinct clinical and molecular features at progression. Their tumours’ TME is fundamentally different with acquired resistance TMEs being infiltrated with immune cells albeit escaped post progression. In addition, ICB selects mutations that potentially activate pathways such as Notch and Hedgehog. This multi-modal Real-World Data with post therapy biopsies has given insights for patient selection strategies and provides rational into combination treatment options for acquired resistant patients. Citation Format: Mohamed Reda Keddar, Sebastian Carrasco Pro, Kathleen Burke, Ana Camelo Stewart, Mark Cobbold, Ross Stewart, Sajan Khosla, Ben Sidders, Scott Hammond, Douglas C. Palmer, Jonathan Dry, Martin L. Miller. Multimodal real world data reveals immunogenomic drivers of acquired and primary resistance to immune checkpoint blockade [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5100.

Abstract 2268: CREDAC: Copy number-based reference-free expression deconvolution analysis of cancers

Abstract Introduction: Analyses of bulk RNA sequencing data are central to most large-scale tumor sequencing studies. Bulk expression data represent population averages and its interpretation is confounded by both normal cell contamination and somatic copy number alterations. Several computational methods to deconvolve have been developed recently. However, these methods often rely on a set of cell-type-specific reference signatures and ignore the effect of copy number changes. Methods: To address these issues, we have developed a method that formalizes the relationship between allele-specific copy number, expression and sample purity to deconvolve the expression profiles of tumor and normal cells from bulk RNA-seq in an unbiased manner. Our method was applied to sequencing data produced by the TRACERx consortium, a longitudinal study with multi-region whole-exome and RNA-seq of non-small-cell lung cancers. A total of 414 primary tumor regions and 140 adjacent normal tissue samples from 140 patients with matched DNA and RNA-seq data were processed. Results: We were able to directly deconvolve a median of ~2,000 genes per sample and indirectly infer tumor and normal expression profiles of ~10,000 genes using an scaled and weighted mean approach. The accuracy of the deconvolution was validated using (1) in-silico mixtures of patient-derived tumor and normal cells, (2) pseudo-bulk scRNAseq and (3) in regions with loss of heterogeneity (LOH) directly on the bulk sequencing data, where the total fraction of expression attributed to tumor cells can be computed directly using somatic mutations. CREDAC allows for single sample bulk-level tumor-normal differential expression analysis and revealed a strong and constitutive genome-wide overexpression in cancer compared to admixed normal cells, with a more pronounced overexpression in lung squamous cell carcinoma than lung adenocarcinoma (p<0.001). CREDAC adjusts for variations in copy number, thus facilitating the investigation of cancer-specific dosage compensatory responses triggered by aneuploidy. We revealed that a majority of genes (~65%) exhibit proportionality to copy number alterations, while a substantial proportion (~35%) shows anti-scaling or dosage compensation strategies. We show an enrichment of genes involved in cell cycle and expression processes within the dosage compensated group and revealed methylation as a key mechanism driving this compensatory process. Conclusion: Overall, our results suggest that CREDAC is able to accurately disentangle the expression of tumor and normal cells from bulk RNA-seq without any previous knowledge. It has potential applications in many studies that include matched RNA-seq and copy number data and can provide new insights functional characterization, the taxonomy of cancer, and tumor evolution. Citation Format: Carla Castignani, Jonas Demeulemeester, Oriol Pich, Tom Lesluyes, Robert E. Hynds, David R. Pearce, Elizabeth Larose Cadieux, Stefan C. Dentro, TRACERx Consortium, Nnenna Kanu, Charles Swanton, Peter Van Loo. CREDAC: Copy number-based reference-free expression deconvolution analysis of cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2268.

Abstract 4931: The Cancer Proteome Atlas: Expanded datasets and empowered with an AI-driven chatbot

Abstract Reverse-phase protein arrays (RPPAs) represent a powerful functional proteomic approach to elucidate cancer-related molecular mechanisms and develop novel cancer therapies. To facilitate community-based investigation of the large-scale protein expression data generated by this platform, we have developed a user-friendly, open-access bioinformatic resource, The Cancer Proteome Atlas (TCPA, http://tcpaportal.org), which contains several applications. The first one focuses on RPPA data of patient tumors, which contains >8,000 samples of 32 cancer types from The Cancer Genome Atlas (TCGA) and other independent patient cohorts. The second application focuses on the RPPA data of >1,500 cancer cell lines with publicly available, high-quality DNA, RNA and drug screening data. The third one focuses on perturbed RPPA profiles of >14,000 samples given drug treatments. We recently expanded our RPPA protein set from 200 to 500 proteins Importantly, this highly selected set is enriched in therapeutic targets and biomarkers and covers key oncogenic pathways such as PI3K/AKT, RAS/MAPK, Src/FAK, TGFβ/SMAD, JAK/STAT, epithelial-mesenchymal transition, DNA damage repair, Hippo, Notch, cell cycle, apoptosis, and immune-oncology. Using this upgraded RPPA platform, we generated an harmonized, expanded RPPA dataset of 8000 TCGA patient samples and 1000 CCLE cell line samples. To further address the informatic challenges of analyzing such large, diverse datasets, in addition to the GUI interfaces, we recently developed a chatbot through which users can analyze the RPPA data through human nature languages and obtain the results and related analytic reports without a learning curve. Such a chatbot empowers a broad research community to explore high-quality RPPA datasets and generate testable hypotheses in an effective and intuitive manner, representing the direction of next-generation data analytics. Citation Format: Han Liang, Wei Liu, Jun Li, Yitao Tang. The Cancer Proteome Atlas: Expanded datasets and empowered with an AI-driven chatbot [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4931.

Abstract 2502: Identification of poor responders to trastuzumab-deruxtecan with a multi-modal HER2-status predictor

Abstract Trastuzumab deruxtecan (TDXD) is approved for HER2 low or positive metastatic breast cancer. HER2-status is assessed through HER IHC and ERBB2 FISH assays. HER2-status has been shown to be correlated to RNA expression. This study aimed to assess if the addition of DNA to an RNA-based model can improve HER2-status prediction performance. Furthermore, to investigate the relationship between model score and outcomes for TDXD patients according to their overall survival (OS). Training and test sets of breast cancer samples were collected for HER2 status prediction (n = 1275, n = 397 respectively). HER2 status was reported positive: 11%, 12%, low: 61%, 60%, negative: 28%, 29% for each set respectively. HER2 testing and NGS were performed on samples with the same collection date. A TDXD discovery cohort of 284 patients included patients who received TDXD after RNA/DNA collection and had at least a 30-day follow-up. Metastatic disease was reported for 98% of the TDXD cohort. Receptor status was HR+/HER2- 39%, HR-/HER2- 17%, HR+/HER2+ 16%, HR-/HER2+ 9%, unknown 19%, and HER2-status was negative 11%, low 42%, and positive 27%, unknown 20%. OS was measured from medication start date. We trained a 12-gene linear model based on RNA expression and DNA copy number to predict HER2-positivity. The genes were selected by stepwise-selection on RNA and DNA features when predicting HER2-positivity using a random forest model. A baseline model consisting only of ERBB2 RNA expression was compared. Setting a HER2-positivity score threshold and allowing for an indeterminate group of 15% of the validation cohort, the RNA-DNA model achieved 91% PPA and 91% PPV in validation, whereas the RNA-only model achieved 83% PPA and 85% PPA. This indicates that the addition of DNA data improved the RNA-only HER2 predictor. The Concordance index of the RNA-DNA model score and OS for TDXD was 0.64. Characterizing this relationship, we partitioned the TDXD cohort to three equal sized sub-cohorts (33 1/3%) ordered by model score: low, intermediate, and high. Median OS in months for groups was: low 13.6, intermediate 18.5, and high 20.4. High-group patients had significantly better OS on TDXD compared to the low-group (HR = 0.39, log-rank p-value < 0.002). For patients with reported status, HER2-positivity rate in each group respectively was 6%, 16%, 85% (n=78), and HR-positivity in each group was 70%, 68%, 67% (n=156). Together, these findings indicate that HER2 status prediction improved by adding DNA to an RNA base predictor, and the predicted score was positively correlated with OS for TDXD. Citation Format: Kaveri Nadhamuni, Talal Ahmed, Mark Carty, Ben Terdich, Whitney L. Hensing, Timothy Taxter, Calvin Chao, Raphael Pelossof. Identification of poor responders to trastuzumab-deruxtecan with a multi-modal HER2-status predictor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2502.

Use of Enzymatically Converted Cell-Free DNA (cfDNA) Data for Copy Number Variation-Linked Fragmentation Analysis Allows for Early Colorectal Cancer Detection.

The use of non-invasive liquid biopsy-based cell-free DNA (cfDNA) analysis is an emerging method of cancer detection and intervention. Different analytical methodologies are used to investigate cfDNA characteristics, resulting in costly and long analysis processes needed for combining different data. This study investigates the possibility of using cfDNA data converted for methylation analysis for combining the cfDNA fragment size with copy number variation (CNV) in the context of early colorectal cancer detection. Specifically, we focused on comparing enzymatically and bisulfite-converted data for evaluating cfDNA fragments belonging to chromosome 18. Chromosome 18 is often reported to be deleted in colorectal cancer. We used counts of short and medium cfDNA fragments of chromosome 18 and trained a linear model (LDA) on a set of 2959 regions to predict early-stage (I-IIA) colorectal cancer on an independent test set. In total, 87.5% sensitivity and 92% specificity were obtained on the enzymatically converted libraries. Repeating the same workflow on bisulfite-converted data yielded lower accuracy results with 58.3% sensitivity, implying that enzymatic conversion preserves the cancer fragmentation footprint in whole genome data better than bisulfite conversion. These results could serve as a promising new avenue for the early detection of colorectal cancer using fragmentation and methylation approaches on the same datasets.

Phylogeography of Dolichophis Populations in the Aegean Region (Squamata: Colubridae) with Taxonomic Remarks

In this study, we investigate the phylogeographic patterns of Dolichophis species in the Aegean region, aiming to elucidate their genetic diversity and putative historical colonisation routes through mitochondrial and nuclear DNA data. Our findings revealed distinct phylogeographic patterns: D. caspius exhibited a higher level of haplotypes within two shallow mitochondrial lineages, contrasting with D. jugularis, which displayed lower genetic variability in the area. Additionally, we identified evidence showing possible human-mediated historical translocation of D. caspius populations to Karpathos from the Balkans mainland. The mitochondrial variability in D. jugularis remained relatively uniform across southwestern Anatolia and Dodecanese, except for Rhodes Island. The evidence from mitochondrial and nuclear data confirming the previously described morphological differentiation of the Rhodes snakes, and thus the name D. j. zinneri Cattaneo, 2012, described on the island, could be applied to this isolated population. This result addresses the first genetic view on the long-standing taxonomic uncertainties regarding the subspecies status of Rhodes D. jugularis. Our results also raise questions regarding possible historical hybridisations between D. caspius and D. jugularis in the Dodecanese islands, prompting the need for further investigation using extensive field studies and genomic approaches. Ultimately, the Aegean islands, particularly Kos and Rhodes, seem to be important sites for the evolution of these colubrid snakes and their historical dynamics.

Identifying a potentially invasive population in the native range of a species: The enlightenment from the phylogeography of the yellow spotted stink bug, Erthesina fullo (Hemiptera: Pentatomidae)

The yellow spotted stink bug (YSSB), Erthesina fullo (Thunberg, 1783) is an important Asian pest that has recently successfully invaded Europe and an excellent material for research on the initial stage of biological invasion. Here, we reported the native evolutionary history, recent invasion history, and potential invasion threats of YSSB for the first time based on population genetic methods [using double digest restriction-site associated DNA (ddRAD) data and mitochondrial COI and CYTB] and ecological niche modelling. The results showed that four lineages (east, west, southwest, and Hainan Island) were established in the native range with a strong east–west differentiation phylogeographical structure, and the violent climate fluctuation might cause population divergence during the Middle and Upper Pleistocene. In addition, land bridges and monsoon promote dispersal and directional genetic exchanging between island populations and neighboring continental populations. The east lineage (EA) was identified as the source of invasion in Albania. EA had the widest geographical distribution among all other lineages, with a star-like haplotype network with the main haplotype as the core. It also had a rapid population expansion history, indicating that the source lineage might have stronger diffusion ability and adaptability. Our findings provided a significant biological basis for fine tracking of invasive source at the lineage or population level and promote early invasion warning of potential invasive species on a much subtler lineage level.

Strategies to deal with genetic analyzer-specific DNA methylation measurements.

Targeted bisulfite sequencing using single-base extension (SBE)can be used to measure DNA methylation via capillary electrophoresis on genetic analyzers in forensic labs. Several accurate age prediction models have been reported using this method. However, using different genetic analyzers with different software settings can generate different methylation values, leading to significant errors in age prediction. To address this issue, the study proposes and compares four methods as follows: (1) adjusting methylation values using numerous actual body fluid DNA samples, (2) adjusting methylation values using control DNAs with varying methylation ratios, (3) constructing new age prediction models for each genetic analyzer type, and (4) constructing new age prediction models that could be applied to all types of genetic analyzers. To test the methods for adjusting values using actual body fluid DNA samples, previously reported adjusting equations were used for blood/saliva DNA age prediction markers (ELOVL2, FHL2, KLF14, MIR29B2CHG/C1orf132, and TRIM59). New equations were generated for semen DNA age prediction markers (TTC7B, LOC401324/cg12837463, and LOC729960/NOX4) by drawing polynomial regression lines between the results of the three types of genetic analyzers (3130, 3500, and SeqStudio). The same method was applied to obtain adjustment equations using 11 control DNA samples. To develop new age prediction models for each genetic analyzer type, linear regression analysis was conducted using DNA methylation data from 150 blood, 150 saliva, and 62 semen samples. For the genetic analyzer-independent models, control DNAs were used to formulate equations for calibrating the bias of the data from each genetic analyzer, and linear regression analysis was performed using calibrated body fluid DNA data. In the comparison results, the genetic analyzer-specific models showed the highest accuracy. However, genetic analyzer-independent models through bias adjustment also provided accurate age prediction results, suggesting its use as an alternative in situations with multiple constraints.

CRISPR-powered quantitative keyword search engine in DNA data storage

Despite the growing interest of archiving information in synthetic DNA to confront data explosion, quantitatively querying the data stored in DNA is still a challenge. Herein, we present Search Enabled by Enzymatic Keyword Recognition (SEEKER), which utilizes CRISPR-Cas12a to rapidly generate visible fluorescence when a DNA target corresponding to the keyword of interest is present. SEEKER achieves quantitative text searching since the growth rate of fluorescence intensity is proportional to keyword frequency. Compatible with SEEKER, we develop non-collision grouping coding, which reduces the size of dictionary and enables lossless compression without disrupting the original order of texts. Using four queries, we correctly identify keywords in 40 files with a background of ~8000 irrelevant terms. Parallel searching with SEEKER can be performed on a 3D-printed microfluidic chip. Overall, SEEKER provides a quantitative approach to conducting parallel searching over the complete content stored in DNA with simple implementation and rapid result generation.

Forensic DNA Profiling: Legal and Ethical Considerations

Forensic DNA analysis is vital in criminal investigations, posing intricate legal and ethical dilemmas. This emphasises the need to balance DNA technology benefits with individual rights, prioritizing privacy, consent, and ethical practices. Stringent regulation of DNA data management is essential to prevent misuse and ensure privacy protection. Advances like probabilistic genotyping software improve interpretation accuracy, addressing complexities in mixture analysis. Responsible DNA use also requires navigating emerging technologies like next-generation sequencing while upholding ethical standards. Establishing transparency, accuracy, and ethical conduct throughout the analysis process is crucial for building public trust. Regulatory oversight and accountability mechanisms are necessary to address errors and maintain fairness in DNA data management. Through continuous dialogue and adherence to ethical standards, the forensic community can uphold scientific integrity and preserve public confidence in DNA analysis.

Identification of microbial pathogens in Neolithic Scandinavian humans

With the Neolithic transition, human lifestyle shifted from hunting and gathering to farming. This change altered subsistence patterns, cultural expression, and population structures as shown by the archaeological/zooarchaeological record, as well as by stable isotope and ancient DNA data. Here, we used metagenomic data to analyse if the transitions also impacted the microbiome composition in 25 Mesolithic and Neolithic hunter-gatherers and 13 Neolithic farmers from several Scandinavian Stone Age cultural contexts. Salmonella enterica, a bacterium that may have been the cause of death for the infected individuals, was found in two Neolithic samples from Battle Axe culture contexts. Several species of the bacterial genus Yersinia were found in Neolithic individuals from Funnel Beaker culture contexts as well as from later Neolithic context. Transmission of e.g. Y. enterocolitica may have been facilitated by the denser populations in agricultural contexts.

Optimization and Performance Analysis of CAT Method for DNA Sequence Similarity Searching and Alignment.

Bioinformatics is a rapidly developing field enabling scientific experiments via computer models and simulations. In recent years, there has been an extraordinary growth in biological databases. Therefore, it is extremely important to propose effective methods and algorithms for the fast and accurate processing of biological data. Sequence comparisons are the best way to investigate and understand the biological functions and evolutionary relationships between genes on the basis of the alignment of two or more DNA sequences in order to maximize the identity level and degree of similarity. This paper presents a new version of the pairwise DNA sequences alignment algorithm, based on a new method called CAT, where a dependency with a previous match and the closest neighbor are taken into consideration to increase the uniqueness of the CAT profile and to reduce possible collisions, i.e., two or more sequence with the same CAT profiles. This makes the proposed algorithm suitable for finding the exact match of a concrete DNA sequence in a large set of DNA data faster. In order to enable the usage of the profiles as sequence metadata, CAT profiles are generated once prior to data uploading to the database. The proposed algorithm consists of two main stages: CAT profile calculation depending on the chosen benchmark sequences and sequence comparison by using the calculated CAT profiles. Improvements in the generation of the CAT profiles are detailed and described in this paper. Block schemes, pseudo code tables, and figures were updated according to the proposed new version and experimental results. Experiments were carried out using the new version of the CAT method for DNA sequence alignment and different datasets. New experimental results regarding collisions, speed, and efficiency of the suggested new implementation are presented. Experiments related to the performance comparison with Needleman-Wunsch were re-executed with the new version of the algorithm to confirm that we have the same performance. A performance analysis of the proposed algorithm based on the CAT method against the Knuth-Morris-Pratt algorithm, which has a complexity of O(n) and is widely used for biological data searching, was performed. The impact of prior matching dependencies on uniqueness for generated CAT profiles is investigated. The experimental results from sequence alignment demonstrate that the proposed CAT method-based algorithm exhibits minimal deviation, which can be deemed negligible if such deviation is considered permissible in favor of enhanced performance. It should be noted that the performance of the CAT algorithm in terms of execution time remains stable, unaffected by the length of the analyzed sequences. Hence, the primary benefit of the suggested approach lies in its rapid processing capabilities in large-scale sequence alignment, a task that traditional exact algorithms would require significantly more time to perform.

Gastropod invasions in anthropogenically impacted impoundments in South Africa: Tracing their origins and exploring field evidence of parasite spillback and amplification

Invasive snails are associated with ecological problems in freshwater bodies worldwide. However, their impact on the transmission of digenean infections remain underreported. In the present study, 1708 specimens representing four snail species were sampled from four impoundments in the Limpopo River system in South Africa. Gyraulus chinensis (Planorbidae), Physella acuta (Physidae) and Pseudosuccinea columella (Lymnaeidae), which are invasive, were found in all the sampling sites. In contrast, the native lymnaeid Radix natalensis occurred at only one study site. Digeneans were observed only from R. natalensis (prevalence = 49%) and Ps. columella (prevalence = 23%). Morphological and genetic analyses revealed four digeneans: Fasciola nyanzae, Orientocreadium sp., Petasiger sp. and Patagifer vioscai. Pseudosuccinea columella was infected by the four digeneans while R. natalensis harboured only Orientocreadium sp. and Petasiger sp. Partial sequences of Orientocreadium sp. from the current study differed from congeners whose DNA data are available on GenBank, by p-distances of at least 1.84 and 2.2% for 28S and the internal transcribed spacer (ITS) rDNA, respectively. Phylogenetic analyses demonstrated that the present species is sister to Orientocreadium batrachoides. Genetic and phylogenetic data based on 28S and ITS rDNA suggested that Petasiger sp. from the present study and isolates of three unidentified Petasiger spp. from Kenya, Hungary and Australia, were representatives of the same species. This is the first known report of Orientocreadium, Petasiger and Patagifer from Ps. columella. The occurrence of F. nyanzae in Ps. columella indicates spillback from R. natalensis. These findings echo the concerns raised in previous studies about the potential role of Ps. columella in the amplification of digenean diseases in its introduced range. Phylogenetic analyses of partial sequences of the cytochrome c oxidase subunit 1 mitochondrial gene (cox1) showed multiple lineages of Ps. columella in North and South America. Pseudosuccinea columella specimens from the present study belong to an invasive genotype that has spread globally and has been reported from Zimbabwe, Egypt, Portugal, Australia, Argentina, Colombia and New Mexico (USA). Physella acuta from the current study had a stronger genetic relationship with isolates from Canada and Iceland, than with isolates from other parts of Africa, suggesting several invasion routes into Africa. This is the first known DNA characterisation of G. chinensis from Africa. Phylogenetic reconstruction indicated multiple exit events of G. chinensis from Asia into Europe and Africa. South African isolates clustered in a recent branch containing isolates from the Czech Republic and Hong Kong, China. Considering the presence of invasive snails in all the sampling sites in the present study, it is necessary to investigate the factors that enhance their establishment and to monitor their effects on the native snail populations.

Origin and dispersal of the Mycobacterium tuberculosis Haarlem genotype: Clues from its phylogeographic landscape and human migration

The Haarlem family belongs to the Euro-American phylogenetic lineage of Mycobacterium tuberculosis and is one of the globally spread genotypes of this important human pathogen. In spite of the sporadic observations on drug resistance and peculiar virulence profile, Haarlem remains in the shade of other M. tuberculosis genotypes. I analyzed genotyping data of the Haarlem genotype in light of its pathogenic properties and relevant human migration, to gain insight into its origin, evolutionary history, and current spread. Central Europe is marked with a very high prevalence of both major Haarlem subclades ancestral H3/SIT50 and derived H1, jointly making 33–41% in Czechia, Austria, and Hungary. There is a declining gradient of Haarlem beyond central Europe with 10–18% in Italy, France, Belgium, 10–13% in the Balkan countries and Turkey. Placing the available genetic diversity and ancient DNA data within the historical context, I hypothesize that M. tuberculosis Haarlem genotype likely originated in Central Europe and its primary long-term circulation occurred within the area of the former Austria/Austria-Hungary Empire in the 14th-19th centuries. The genotype is not highly transmissible and its spread was driven by long-term human migration. The European colonial expansion (when accompanied by a sufficient volume of migration) was a vehicle of its secondary dissemination. I conclude that human migration and its lack thereof (but not strain pathobiology) was a major driving force that shaped the population structure of this global lineage of M. tuberculosis. At the same time, Haarlem strains appear over-represented in some ethnic groups which warrants in-depth experimental research.

Programming crystallization kinetics of self-assembled DNA crystals with 5-methylcytosine modification

Self-assembled DNA crystals offer a precise chemical platform at the ångström-scale for DNA nanotechnology, holding enormous potential in material separation, catalysis, and DNA data storage. However, accurately controlling the crystallization kinetics of such DNA crystals remains challenging. Herein, we found that atomic-level 5-methylcytosine (5mC) modification can regulate the crystallization kinetics of DNA crystal by tuning the hybridization rates of DNA motifs. We discovered that by manipulating the axial and combination of 5mC modification on the sticky ends of DNA tensegrity triangle motifs, we can obtain a series of DNA crystals with controllable morphological features. Through DNA-PAINT and FRET-labeled DNA strand displacement experiments, we elucidate that atomic-level 5mC modification enhances the affinity constant of DNA hybridization at both the single-molecule and macroscopic scales. This enhancement can be harnessed for kinetic-driven control of the preferential growth direction of DNA crystals. The 5mC modification strategy can overcome the limitations of DNA sequence design imposed by limited nucleobase numbers in various DNA hybridization reactions. This strategy provides a new avenue for the manipulation of DNA crystal structure, valuable for the advancement of DNA and biomacromolecular crystallography.

Friends without benefits: Extensive cytotype sympatry and polyploid persistence in an African geophyte.

Polyploidy is a major factor in plant adaptation and speciation. Multiple mechanisms contribute to autopolyploid frequency within populations, but uncertainties remain regarding mechanisms that facilitate polyploid establishment and persistence. Here we aimed to document and predict cytotype distributions of Oxalis obliquifolia Steud. ex A. Rich. across Gauteng, South Africa, and test for evidence of possible mechanisms, including morphological, phenological, and reproductive traits, that may potentially facilitate polyploid persistence. Over 320 O. obliquifolia plants from 25 sites were cytotyped using flow cytometry, and DNA ploidy was confirmed using meiotic chromosome squashes. Cytotypes were mapped and correlations with abiotic variables assessed using ordinations. To assess morphological and phenological associations with cytotype, we grew multiple cytotypes in a common garden, measured phenotypic traits and compared them using linear models and discriminant analyses. Intercytotype reproductive isolation was assessed using crossing experiments, and AMOVAs based on ITS DNA sequences tested for cytogeographic structure. Six cytotypes were identified, and most sites had multiple cytotypes. Abiotic variables were not predictive of cytotype distribution. A clear gigas effect was present. Differences in flower size and phenology suggested pollinator interactions could play a role in polyploid persistence. Intercytotype crosses produced seed at low frequency. DNA data suggested diploids and polyploids were largely reproductively isolated in situ, and polyploidization events were not frequent enough to explain high cytotype sympatry. Diploids and polyploids are behaving as separate species, despite little observable niche differentiation and non-zero potential intercytotype seed set. Tests on biotic interactions and intercytotype F1 fitness may provide insights into diploid and polyploid coexistence.