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G-quadruplexes are four-stranded DNA structures that have been found in the cell and are thought to act as elements of control in genomic events. The measurements of the thermodynamic stability, ΔG, of G-quadruplexes shed light on the molecular forces involved in the stabilization of these structures. In thermodynamic studies, the differential heat capacity, ΔCP, of the folded and unfolded states of a G-quadruplex is a fundamental property that describes the temperature dependences of the differential enthalpy, ΔH, entropy, ΔS, and free energy, ΔG. Despite its recognized importance, the ΔCP of G-quadruplex unfolding has not been measured directly. Here, we use differential scanning calorimetry to evaluate changes in heat capacity, ΔCP, accompanying the unfolding transitions of G-quadruplexes formed by modified DNA sequences from the promoter regions of the c-MYC, VEGF, and Bcl-2 oncogenes. The average value of ΔCP is 0.49 ± 0.12 kcal mol−1 K−1. Our analysis revealed that disregarding ΔCP leads to significant errors in extrapolated values of the differential enthalpy, ΔH, and entropy, ΔS, of the folded and unfolded DNA conformations. Although the compensation between ΔH and ΔS weakens the effect of ΔCP on the differential free energy, ΔG, neglecting ΔCP may still result in relative errors in ΔG extrapolated to room temperature as great as 140%. We emphasize the importance of proper consideration of the effect of ΔCP in conformational studies of guanine-rich DNA molecules. [ABSTRACT FROM AUTHOR]

The discovery of animal genetic (mostly also cryptic) species has known an exponential increase since molecular techniques became available. Also in non-marine ostracods (small, bivalved crustaceans with an excellent fossil record), several morphospecies have been shown to comprise several genetic species. Here, we screen 13 populations from Central Europe and the circum-Mediterranean region of the halophilic continental ostracod species Heterocypris salina with DNA sequences from a mitochondrial (COI) and a nuclear (28S) marker. We apply four species delimitation methods to show that this nominal species consists of four genetic species in both DNA datasets, and that these two sets of genetic species show mitonuclear discordance. Most investigated specimens belonged to one of these four genetic species. There was no clear correlation between geographic and genetic distances, but we found that, apart from historical processes, environmental factors such as ecoregion, seasonality and salinity might have been important drivers shaping discrete genetic diversity. Following the palaeontological literature, the H. salina species cluster is at least 11–9 Myr old. [ABSTRACT FROM AUTHOR]

Three sardine species of Harengula and one of Opisthonema (Clupeiformes, Clupeidae) are known in the Western Atlantic, where the Amazon-Orinoco plume has been recognized as a major biogeographic barrier, albeit permeable to larger and generalist species. Here we used mitochondrial cox1 gene DNA sequences to check the lineage delimitation of both genera, testing the influence of the Amazon-Orinoco barrier (AOB) and marine provinces on their phylogeographic structure. Results indicate that the two genera are differently affected by the AOB, including cryptic speciation in Harengula and population structure in Opisthonema. Harengula show a broad distribution in the Brazilian Province (BRA) distinct from H. clupeola and H. jaguana from the Greater Caribbean Region (GCR). Divergence time between Harengula from the GCR vs. BRA was estimated as about 2.4 Mya, which coincides with the period of increasing sediment and freshwater discharge of the Amazon River in the Atlantic. Results also indicate the existence of a single species of Opisthonema, albeit with population structuring related to the marine provinces. Since species of both genera are relevant to artisanal fisheries and the maintenance of oceanic ecosystems, these results may help in fisheries management of these important marine resources. [ABSTRACT FROM AUTHOR]

Anthropogenic activities such as mining pose a putative threat to deep-sea ecosystems and baseline studies of key indicator species are required to assess future loss of biodiversity. We examined population genetic structure, connectivity, cryptic diversity and phylogeography of the deep-sea scavenging amphipod, Abyssorchomene distinctus, using DNA sequence data (mitochondrial COI and nuclear 28S genes) from 373 specimens collected from six abyssal basins. We observed a striking absence of cryptic diversity, suggesting a single, widely distributed species in the Pacific and Indian Ocean. A single event of population expansion across distances up to 24,000 km is further supported by a main ancestral haplotype in the star-like shaped COI haplotype network, a skewed nucleotide mismatch distribution and deviations from evolutionary neutrality tests. In the Pacific, A. distinctus showed weak genetic population structure and low differentiation between the basins of the Clarion-Clipperton Zone and the DISCOL Experimental Area, suggesting a possible higher chance of recovery from deep-sea mining impacts. However, since our data indicate a single recent historic population expansion event, A. distinctus populations will likely be affected to unknown extents, as the exact drivers shaping distribution and dispersion of A. distinctus are still unclear. [ABSTRACT FROM AUTHOR]

This paper discusses the interaction between two substantial debates in taxonomy and nomenclature: The potential introduction of DNA-only types into fungal taxonomy and whether certain species names are offensive and should be changed. It argues that the acceptance of DNA sequences as types will likely lead to a proliferation of eponyms (species named after a person or persons) and that this will render them more likely to censure thus creating a point of instability in the fungal nomenclature. More fundamentally, it seeks to highlight the cultural and aesthetic attraction of names and to promote wider conversation on why we consider the Latin binomial central in our description of species. [ABSTRACT FROM AUTHOR]

Although several promising approaches for the treatment of relapsed/refractory diffuse large B‐cell lymphoma (rrDLBCL) have been approved recently, it remains unclear which patients will ultimately achieve long‐term responses. Circulating tumor (ct)DNA sequencing has emerged as a valuable tool to assess minimal residual disease (MRD). Correlations between MRD and outcomes have been shown in previously untreated DLBCL, but data on the repeated assessment of MRD in the dynamic course of rrDLBCL is limited. Here, we present an approach leveraging cost‐ and time‐sensitivity of digital droplet (dd)PCR to repeatedly assess MRD in rrDLBCL and present proof‐of‐principle for its ability to predict outcomes. [ABSTRACT FROM AUTHOR]

Blastobotrys is a genus of rare yeast that is increasingly recognized as a cause of fungal infections in humans. However, there have been no reports of fungal infections in humans caused by Blastobotrys mokoenaii. We describe a case of invasive fungal infection (IFI) caused by B. mokoenaii in an immunocompromised patient with acute myeloid leukemia (AML). A 46-year-old man with relapsed/refractory AML underwent a second allogeneic peripheral blood hematopoietic stem cell transplantation (allo-PBSCT) during remission. The patient had prolonged neutropenia and received systemic steroid therapy for graft-versus-host disease before the second allo-PBSCT. Uncommon yeast was isolated from the blood cultures obtained on day 4. We initially suspected that the uncommon yeast was Trichosporon spp. based on its morphology. However, unlike Trichosporon spp., in vitro antifungal susceptibility tests showed that this yeast isolate was resistant to micafungin, caspofungin, voriconazole, itraconazole, and fluconazole. We performed DNA sequencing and identified it as B. mokoenaii. B. mokoenaii was persistently isolated from blood cultures taken during combination therapy with liposomal amphotericin B and voriconazole. The patient died of multiorgan failure on day 24. B. mokoenaii can cause severe IFI in immunocompromised patients; however, it may not be correctly identified by routine clinical microbiology testing in a hospital laboratory and DNA sequencing is useful for diagnosis. [ABSTRACT FROM AUTHOR]

B chromosomes are intriguing "selfish" genetic elements, many of which exhibit higher-than-Mendelian transmission. This perspective highlights a group of B chromosomes known as Paternal Sex Ratio chromosomes (PSRs), which are found in several insects with haplo-diploid reproduction. PSRs harshly alter the organism's reproduction to facilitate their own inheritance. A manifestation of this effect is the conversion of female destined individuals into males. Key to this conversion is the mysterious ability of PSRs to cause elimination of the sperm-inherited half of the genome during zygote formation. Here we discuss how PSRs were discovered, what is known about how they alter paternal chromatin dynamics to cause sex conversion, and how PSR-induced genome elimination is different from other forms of programmed genome elimination in different insects. PSRs also stand out because their DNA sequence compositions differ in remarkable ways from their insect's essential chromosomes, a characteristic suggestive of interspecies origins. Broadly, we also highlight poorly understood aspects of PSR dynamics that need to be investigated. [ABSTRACT FROM AUTHOR]

This study investigates the impact of casein hydrolysates on the poultry ceca inoculated with Campylobacter focusing on microbial molecular preferences for different protein sources in the presence of Campylobacter jejuni. Three casein sources (intact casein (IN), casein enzyme hydrolysate (EH), and casein acid hydrolysate (AH)) were introduced to cecal contents in combination with inoculated C. jejuni in an in vitro model system incubated for 48 h at 42°C under microaerophilic conditions. Samples were collected at 0, 24, and 48 h. Genomic DNA was extracted and amplified using custom dual-indexed primers, followed by sequencing on an Illumina MiSeq platform. The obtained sequencing data were then analyzed via QIIME2-2021.11. Metabolite extracts were analyzed with ultra-high-performance liquid orbitrap chromatography-mass spectrometry (UHPLC-MS). Statistical analysis of metabolites was conducted using MetaboAnalyst 5.0, while functional analysis was performed using Mummichog 2.0 with a significance threshold set at P < 0.00001. DNA sequencing and metabolomic analyses revealed that C. jejuni was most abundant in the EH group. Microbial diversity and richness improved in casein supplemented groups, with core microbial differences observed, compared to non-supplemented groups. Vitamin B-associated metabolites significantly increased in the supplemented groups, displaying distinct patterns in vitamin B6 and B9 metabolism between EH and AH groups (P < 0.05). Faecalibacterium and Phascolarctobacterium were associated with AH and EH groups, respectively. These findings suggest microbial interactions in the presence of C. jejuni and casein supplementation are influenced by microbial community preferences for casein hydrolysates impacting B vitamin production and shaping competitive dynamics within the cecal microbial community. These findings underscore the potential of nutritional interventions to modulate the poultry GIT microbiota for improved health outcomes. [ABSTRACT FROM AUTHOR]

Background: Acer is a taxonomically intractable and speciose genus that contains over 150 species. It is challenging to distinguish Acer species only by morphological method due to their abundant variations. Plastome and nuclear ribosomal DNA (nrDNA) sequences are recommended as powerful next-generation DNA barcodes for species discrimination. However, their efficacies were still poorly studied. The current study will evaluate the application of plastome and nrDNA in species identification and perform phylogenetic analyses for Acer. Result: Based on a collection of 83 individuals representing 55 species (c. 55% of Chinese species) from 13 sections, our barcoding analyses demonstrated that plastomes exhibited the highest (90.47%) species discriminatory power among all plastid DNA markers, such as the standard plastid barcodes matK + rbcL + trnH-psbA (61.90%) and ycf1 (76.19%). And the nrDNA (80.95%) revealed higher species resolution than ITS (71.43%). Acer plastomes show abundant interspecific variations, however, species identification failure may be due to the incomplete lineage sorting (ILS) and chloroplast capture resulting from hybridization. We found that the usage of nrDNA contributed to identifying those species that were unidentified by plastomes, implying its capability to some extent to mitigate the impact of hybridization and ILS on species discrimination. However, combining plastome and nrDNA is not recommended given the cytonuclear conflict caused by potential hybridization. Our phylogenetic analysis covering 19 sections (95% sections of Acer) and 128 species (over 80% species of this genus) revealed pervasive inter- and intra-section cytonuclear discordances, hinting that hybridization has played an important role in the evolution of Acer. Conclusion: Plastomes and nrDNA can significantly improve the species resolution in Acer. Our phylogenetic analysis uncovered the scope and depth of cytonuclear conflict in Acer, providing important insights into its evolution. [ABSTRACT FROM AUTHOR]

Copy Number Variants (CNV) are modifications affecting the genome sequence of DNA, for instance, they can be duplications or deletions of a considerable number of base pairs (i.e., greater than 1000 bp and up to millions of bp). Their impact on the variation of the phenotypic traits has been widely demonstrated. In addition, CNVs are a class of markers useful to identify the genetic biodiversity among populations related to adaptation to the environment. The aim of this study was to detect CNVs in more than four thousand Holstein cows, using information derived by a genotyping done with the GGP (GeneSeek Genomic Profiler) bovine 100K SNP chip. To detect CNV the SVS 8.9 software was used, then CNV regions (CNVRs) were detected. A total of 123,814 CNVs (4,150 non redundant) were called and aggregated into 1,397 CNVRs. The PCA results obtained using the CNVs information, showed that there is some variability among animals. For many genes annotated within the CNVRs, the role in immune response is well known, as well as their association with important and economic traits object of selection in Holstein, such as milk production and quality, udder conformation and body morphology. Comparison with reference revealed unique CNVRs of the Holstein breed, and others in common with Jersey and Brown. The information regarding CNVs represents a valuable resource to understand how this class of markers may improve the accuracy in prediction of genomic value, nowadays solely based on SNPs markers. [ABSTRACT FROM AUTHOR]

Recent pandemics like COVID-19 highlighted the importance of rapidly developing diagnostics to detect evolving pathogens. CRISPR-Cas technology has recently been used to develop diagnostic assays for sequence-specific recognition of DNA or RNA. These assays have similar sensitivity to the gold standard qPCR but can be deployed as easy to use and inexpensive test strips. However, the discovery of diagnostic regions of a genome flanked by conserved regions where primers can be designed requires extensive bioinformatic analyses of genome sequences. We developed the Python package krisp to aid in the discovery of primers and diagnostic sequences that differentiate groups of samples from each other, using either unaligned genome sequences or a variant call format (VCF) file as input. Krisp has been optimized to handle large datasets by using efficient algorithms that run in near linear time, use minimal RAM, and leverage parallel processing when available. The validity of krisp results has been demonstrated in the laboratory with the successful design of a CRISPR diagnostic assay to distinguish the sudden oak death pathogen Phytophthora ramorum from closely related Phytophthora species. Krisp is released open source under a permissive license with all the documentation needed to quickly design CRISPR-Cas diagnostic assays. Author summary: Pathogens continue to emerge at accelerated rates affecting animals, plants, and ecosystems. Rapid development of novel diagnostic tools is needed to monitor novel pathogen variants or groups. We developed the computational tool krisp to identify genetic regions suitable for development of CRISPR diagnostics and traditional amplification-based diagnostics such as PCR. Krisp scans whole genome sequence data for target and non-target groups to identify diagnostic regions based on DNA or RNA sequences. This computational tool has been validated using genome data for the sudden oak death pathogen Phytophthora ramorum. Krisp is released open source under a permissive license with all the documentation needed to quickly design CRISPR-Cas diagnostic assays and other amplification-based assays. [ABSTRACT FROM AUTHOR]

Artificial hybrids between cultivated Avena species and wild Avena macrostachya that possess genes for resistance to biotic and abiotic stresses can be important for oat breeding. For the first time, a comprehensive study of genomes of artificial fertile hybrids Avena sativa × Avena macrostachya and their parental species was carried out based on the chromosome FISH mapping of satellite DNA sequences (satDNAs) and also analysis of intragenomic polymorphism in the 18S–ITS1–5.8S rDNA region, using NGS data. Chromosome distribution patterns of marker satDNAs allowed us to identify all chromosomes in the studied karyotypes, determine their subgenomic affiliation, and detect several chromosome rearrangements. Based on the obtained cytogenomic data, we revealed differences between two A. macrostachya subgenomes and demonstrated that only one of them was inherited in the studied octoploid hybrids. Ribotype analyses showed that the second major ribotype of A. macrostachya was species-specific and was not represented in rDNA pools of the octoploids, which could be related to the allopolyploid origin of this species. Our results indicate that the use of marker satDNAs in cytogenomic studies can provide important data on genomic relationships within Avena allopolyploid species and hybrids, and also expand the potential for interspecific crosses for breeding. [ABSTRACT FROM AUTHOR]

Simple Summary: Genomic instability is an important feature of cancer, including multiple myeloma, which is the second most common hematological malignancy. There are several sources of genomic instability in multiple myeloma, including mutations in DNA repair genes and genotoxic therapy. Non-canonical secondary DNA structures (such as four-stranded G-quadruplex structures) may contribute to this process by interfering with DNA replication and repair and leading to the accumulation of mutations at specific sites in the genome. Here, we address the question of whether G-quadruplex structures have any impact on the accumulation of mutations in multiple myeloma cells. We discuss the possible consequences of defects in G-quadruplex unwinding for the specificity of somatic mutations in MM. Understanding the role of G-quadruplex structures in the disease may lead to the development of new diagnostic and therapeutic strategies for multiple myeloma and other cancers. Multiple myeloma (MM) is the second most common hematological malignancy, which remains incurable despite recent advances in treatment strategies. Like other forms of cancer, MM is characterized by genomic instability, caused by defects in DNA repair. Along with mutations in DNA repair genes and genotoxic drugs used to treat MM, non-canonical secondary DNA structures (four-stranded G-quadruplex structures) can affect accumulation of somatic mutations and chromosomal abnormalities in the tumor cells of MM patients. Here, we tested the hypothesis that G-quadruplex structures may influence the distribution of somatic mutations in the tumor cells of MM patients. We sequenced exomes of normal and tumor cells of 11 MM patients and analyzed the data for the presence of G4 context around points of somatic mutations. To identify molecular mechanisms that could affect mutational profile of tumors, we also analyzed mutational signatures in tumor cells as well as germline mutations for the presence of specific SNPs in DNA repair genes or in genes regulating G-quadruplex unwinding. In several patients, we found that sites of somatic mutations are frequently located in regions with G4 context. This pattern correlated with specific germline variants found in these patients. We discuss the possible implications of these variants for mutation accumulation and specificity in MM and propose that the extent of G4 context enrichment around somatic mutation sites may be a novel metric characterizing mutational processes in tumors. [ABSTRACT FROM AUTHOR]

Bacterial infections are a leading cause of death globally. The detection of DNA sequences correlated to the causative pathogen has become a vital tool in medical diagnostics. In practice, PCR-based assays for the simultaneous detection of multiple pathogens currently rely on probe-based quantitative strategies that require expensive equipment but have limited sensitivity or multiplexing capabilities. Hence, novel approaches to address the limitations of the current gold standard methods are still in high demand. In this study, we propose a simple multiplex PCR/SERS assay for the simultaneous detection of four bacterial pathogens, namely P. aeruginosa, S. aureus, S. epidermidis, and M. smegmatis. Wherein, specific primers for amplifying each target gDNA were applied, followed by applying SERS nanotags functionalized with complementary DNA probes and Raman reporters for specific identification of the target bacterial pathogens. The PCR/SERS assay showed high specificity and sensitivity for genotyping bacterial pathogen gDNA, whereby as few as 100 copies of the target gDNA could be detected. With high sensitivity and the convenience of standard PCR amplification, the proposed assay shows great potential for the sensitive detection of multiple pathogen infections to aid clinical decision-making. [ABSTRACT FROM AUTHOR]

Influenza A viruses of the H2 subtype represent a zoonotic and pandemic threat to humans due to a lack of widespread specific immunity. Although A(H2) viruses that circulate in wild bird reservoirs are distinct from the 1957 pandemic A(H2N2) viruses, there is concern that they could impact animal and public health. There is limited information on AIVs in Latin America, and next to nothing about H2 subtypes in Brazil. In the present study, we report the occurrence and genomic sequences of two influenza A viruses isolated from wild-caught white-rumped sandpipers (Calidris fuscicollis). One virus, identified as A(H2N1), was isolated from a bird captured in Restinga de Jurubatiba National Park (PNRJ, Rio de Janeiro), while the other, identified as A(H2N2), was isolated from a bird captured in Lagoa do Peixe National Park (PNLP, Rio Grande do Sul). DNA sequencing and phylogenetic analysis of the obtained sequences revealed that each virus belonged to distinct subtypes. Furthermore, the phylogenetic analysis indicated that the genomic sequence of the A(H2N1) virus isolated from PNRJ was most closely related to other A(H2N1) viruses isolated from North American birds. On the other hand, the A(H2N2) virus genome recovered from the PNLP-captured bird exhibited a more diverse origin, with some sequences closely related to viruses from Iceland and North America, and others showing similarity to virus sequences recovered from birds in South America. Viral genes of diverse origins were identified in one of the viruses, indicating local reassortment. This suggests that the extreme South of Brazil may serve as an environment conducive to reassortment between avian influenza virus lineages from North and South America, potentially contributing to an increase in overall viral diversity. [ABSTRACT FROM AUTHOR]

Cell lineage tree reconstruction methods are developed for various tasks, such as investigating the development, differentiation, and cancer progression. Single-cell sequencing technologies enable more thorough analysis with higher resolution. We present Scuphr, a distance-based cell lineage tree reconstruction method using bulk and single-cell DNA sequencing data from healthy tissues. Common challenges of single-cell DNA sequencing, such as allelic dropouts and amplification errors, are included in Scuphr. Scuphr computes the distance between cell pairs and reconstructs the lineage tree using the neighbor-joining algorithm. With its embarrassingly parallel design, Scuphr can do faster analysis than the state-of-the-art methods while obtaining better accuracy. The method's robustness is investigated using various synthetic datasets and a biological dataset of 18 cells. Author summary: Cell lineage tree reconstruction carries a significant potential for studies of development and medicine. The lineage tree reconstruction task is especially challenging for cells taken from healthy tissue due to the scarcity of mutations. In addition, the single-cell whole-genome sequencing technology introduces artifacts such as amplification errors, allelic dropouts, and sequencing errors. We propose Scuphr, a probabilistic framework to reconstruct cell lineage trees. We designed Scuphr for single-cell DNA sequencing data; it accounts for technological artifacts in its graphical model and uses germline heterozygous sites to improve its accuracy. Scuphr is embarrassingly parallel; the speed of the computational analysis is inversely proportional to the number of available computational nodes. We demonstrated that Scuphr is fast, robust, and more accurate than the state-of-the-art method with the synthetic data experiments. Moreover, in the biological data experiment, we showed Scuphr successfully identifies different clones and further obtains more support on closely related cells within clones. [ABSTRACT FROM AUTHOR]

Background: High-throughput sequencing (HTS) has become the gold standard approach for variant analysis in cancer research. However, somatic variants may occur at low fractions due to contamination from normal cells or tumor heterogeneity; this poses a significant challenge for standard HTS analysis pipelines. The problem is exacerbated in scenarios with minimal tumor DNA, such as circulating tumor DNA in plasma. Assessing sensitivity and detection of HTS approaches in such cases is paramount, but time-consuming and expensive: specialized experimental protocols and a sufficient quantity of samples are required for processing and analysis. To overcome these limitations, we propose a new computational approach specifically designed for the generation of artificial datasets suitable for this task, simulating ultra-deep targeted sequencing data with low-fraction variants and demonstrating their effectiveness in benchmarking low-fraction variant calling. Results: Our approach enables the generation of artificial raw reads that mimic real data without relying on pre-existing data by using NEAT, a fine-grained read simulator that generates artificial datasets using models learned from multiple different datasets. Then, it incorporates low-fraction variants to simulate somatic mutations in samples with minimal tumor DNA content. To prove the suitability of the created artificial datasets for low-fraction variant calling benchmarking, we used them as ground truth to evaluate the performance of widely-used variant calling algorithms: they allowed us to define tuned parameter values of major variant callers, considerably improving their detection of very low-fraction variants. Conclusions: Our findings highlight both the pivotal role of our approach in creating adequate artificial datasets with low tumor fraction, facilitating rapid prototyping and benchmarking of algorithms for such dataset type, as well as the important need of advancing low-fraction variant calling techniques. [ABSTRACT FROM AUTHOR]

With the explosion of digital world, the dramatically increasing data volume is expected to reach 175 ZB (1 ZB = 1012 GB) in 2025. Storing such huge global data would consume tons of resources. Fortunately, it has been found that the deoxyribonucleic acid (DNA) molecule is the most compact and durable information storage medium in the world so far. Its high coding density and long-term preservation properties make itself one of the best data storage carriers for the future. High-throughput DNA synthesis is a key technology for "DNA data storage", which encodes binary data stream (0/1) into quaternary long DNA sequences consisting of four bases (A/G/C/T). In this review, the workflow of DNA data storage and the basic methods of artificial DNA synthesis technology are outlined first. Then, the technical characteristics of different synthesis methods and the state-of-the-art of representative commercial companies, with a primary focus on silicon chip microarray-based synthesis and novel enzymatic DNA synthesis are presented. Finally, the recent status of DNA storage and new opportunities for future development in the field of high-throughput, large-scale DNA synthesis technology are summarized. [ABSTRACT FROM AUTHOR]

The analysis of the DNA entrapped in ancient shells of molluscs has the potential to shed light on the evolution and ecology of this very diverse phylum. Ancient genomics could help reconstruct the responses of molluscs to past climate change, pollution, and human subsistence practices at unprecedented temporal resolutions. Applications are however still in their infancy, partly due to our limited knowledge of DNA preservation in calcium carbonate shells and the need for optimized methods for responsible genomic data generation. To improve ancient shell genomic analyses, we applied high-throughput DNA sequencing to 27 Mytilus mussel shells dated to ~111–6500 years Before Present, and investigated the impact, on DNA recovery, of shell imaging, DNA extraction protocols and shell sub-sampling strategies. First, we detected no quantitative or qualitative deleterious effect of micro-computed tomography for recording shell 3D morphological information prior to sub-sampling. Then, we showed that double-digestion and bleach treatment of shell powder prior to silica-based DNA extraction improves shell DNA recovery, also suggesting that DNA is protected in preservation niches within ancient shells. Finally, all layers that compose Mytilus shells, i.e., the nacreous (aragonite) and prismatic (calcite) carbonate layers, with or without the outer organic layer (periostracum) proved to be valuable DNA reservoirs, with aragonite appearing as the best substrate for genomic analyses. Our work contributes to the understanding of long-term molecular preservation in biominerals and we anticipate that resulting recommendations will be helpful for future efficient and responsible genomic analyses of ancient mollusc shells. [ABSTRACT FROM AUTHOR]

Mitochondrial DNA sequences are frequently transferred into the nuclear genome, generating nuclear mitochondrial DNA sequences (NUMTs). Here, we analysed, for the first time, NUMTs in the domestic yak genome. We obtained 499 alignment matches covering 340.2 kbp of the yak nuclear genome. After a merging step, we identified 167 NUMT regions with a total length of ~ 503 kbp, representing 0.02% of the nuclear genome. We discovered copies of all mitochondrial regions and found that most NUMT regions are intergenic or intronic and mostly untranscribed. 98 different NUMT regions from domestic yak showed high homology with cow and/or wild yak genomes, suggesting selection or hybridization between domestic/wild yak and cow. To rule out the possibility that the identified NUMTs could be artifacts of the domestic yak genome assembly, we validated experimentally five NUMT regions by PCR amplification. As NUMT regions show high similarity to the mitochondrial genome can potentially pose a risk to domestic yak DNA mitochondrial studies, special care is therefore needed to select primers for PCR amplification of mitochondrial DNA sequences. [ABSTRACT FROM AUTHOR]

Rhododendron is famous for its high ornamental value. However, the genus is taxonomically difficult and the relationships within Rhododendron remain unresolved. In addition, the origin of key morphological characters with high horticulture value need to be explored. Both problems largely hinder utilization of germplasm resources. Most studies attempted to disentangle the phylogeny of Rhododendron, but only used a few genomic markers and lacked large-scale sampling, resulting in low clade support and contradictory phylogenetic signals. Here, we used restriction-site associated DNA sequencing (RAD-seq) data and morphological traits for 144 species of Rhododendron, representing all subgenera and most sections and subsections of this species-rich genus, to decipher its intricate evolutionary history and reconstruct ancestral state. Our results revealed high resolutions at subgenera and section levels of Rhododendron based on RAD-seq data. Both optimal phylogenetic tree and split tree recovered five lineages among Rhododendron. Subg. Therorhodion (clade I) formed the basal lineage. Subg. Tsutsusi and Azaleastrum formed clade II and had sister relationships. Clade III included all scaly rhododendron species. Subg. Pentanthera (clade IV) formed a sister group to Subg. Hymenanthes (clade V). The results of ancestral state reconstruction showed that Rhododendron ancestor was a deciduous woody plant with terminal inflorescence, ten stamens, leaf blade without scales and broadly funnelform corolla with pink or purple color. This study shows significant distinguishability to resolve the evolutionary history of Rhododendron based on high clade support of phylogenetic tree constructed by RAD-seq data. It also provides an example to resolve discordant signals in phylogenetic trees and demonstrates the application feasibility of RAD-seq with large amounts of missing data in deciphering intricate evolutionary relationships. Additionally, the reconstructed ancestral state of six important characters provides insights into the innovation of key characters in Rhododendron. [ABSTRACT FROM AUTHOR]

In many countries, some form of genetic screening is offered to all or part of the population, either in the form of well-organized screening programs or in a less formalized way. Screening can be offered at different phases of life, such as preconception, prenatal, neonatal and later in life. Screening should only be offered if the advantages outweigh the disadvantages. Technical innovations in testing and treatment are driving changes in the field of prenatal and neonatal screening, where many jurisdictions have organized population-based screening programs. As a result, a greater number and wider range of conditions are being added to the programs, which can benefit couples' reproductive autonomy (preconception and prenatal screening) and improve early diagnosis to prevent irreversible health damage in children (neonatal screening) and in adults (cancer and cascade screening). While many developments in screening are technology-driven, citizens may also express a demand for innovation in screening, as was the case with non-invasive prenatal testing. Relatively new emerging issues for genetic screening, especially if testing is performed using DNA sequencing, relate to organization, data storage and interpretation, benefit–harm ratio and distributive justice, information provision and follow-up, all connected to acceptability in current healthcare systems. [ABSTRACT FROM AUTHOR]

Sturgeons (Family: Acipenseridae) are among the most endangered taxa worldwide. Significant resources have been invested into the conservation of global sturgeon populations, including the development of commercial aquaculture programs. These programs are intended to improve conservation outcomes by reducing the harvest of wild populations while still meeting commercial demand for sturgeon products. However, there is growing concern that commercial aquaculture programs may contribute to wild population declines through continued, illegal harvest and the escape and/or release of captive individuals into wild environments. These concerns may be particularly acute in the country of Georgia which, despite its small territory and altered landscape, is a globally significant hotspot for sturgeon diversity. In order to understand the potential threat of captive culture on wild sturgeon populations in Georgia, we used mitochondrial DNA sequencing and microsatellite analyses to identify the species and origin of sturgeons encountered in commercial settings. Microsatellite analyses showed significant differentiation between wild and commercial Russian sturgeon populations and highlighted the potential for wild-caught individuals to be present in coastal markets in Georgia. The analyses of mitochondrial haplotypes also suggested that commercial markets may contain sturgeon species that are not native to the region. Overall, our results suggest that wild sturgeon populations may still be exploited to support captive aquaculture programs and commercial sales. [ABSTRACT FROM AUTHOR]

In recent years, an increasing number of viruses have triggered outbreaks that pose a severe threat to both human and animal life, as well as caused substantial economic losses. It is crucial to understand the genomic structure and epidemiology of these viruses to guide effective clinical prevention and treatment strategies. Nanopore sequencing, a third-generation sequencing technology, has been widely used in genomic research since 2014. This technology offers several advantages over traditional methods and next-generation sequencing (NGS), such as the ability to generate ultra-long reads, high efficiency, real-time monitoring and analysis, portability, and the ability to directly sequence RNA or DNA molecules. As a result, it exhibits excellent applicability and flexibility in virus research, including viral detection and surveillance, genome assembly, the discovery of new variants and novel viruses, and the identification of chemical modifications. In this paper, we provide a comprehensive review of the development, principles, advantages, and applications of nanopore sequencing technology in animal and human virus research, aiming to offer fresh perspectives for future studies in this field. [ABSTRACT FROM AUTHOR]

Directed evolution is a pivotal strategy for new antibody discovery, which allowed the generation of high-affinity Fabs against gliadin from two antibody libraries in our previous studies. One of the libraries was exclusively derived from celiac patients' mRNA (immune library) while the other was obtained through a protein engineering approach (semi-immune library). Recent advances in high-throughput DNA sequencing techniques are revolutionizing research across genomics, epigenomics, and transcriptomics. In the present work, an Oxford Nanopore in-lab sequencing device was used to comprehensively characterize the composition of the constructed libraries, both at the beginning and throughout the phage-mediated selection processes against gliadin. A customized analysis pipeline was used to select high-quality reads, annotate chain distribution, perform sequence analysis, and conduct statistical comparisons between the different selection rounds. Some immunological attributes of the most representative phage variants after the selection process were also determined. Sequencing results revealed the successful transfer of the celiac immune response features to the immune library and the antibodies derived from it, suggesting the crucial role of these features in guiding the selection of high-affinity recombinant Fabs against gliadin. In summary, high-throughput DNA sequencing has improved our understanding of the selection processes aimed at generating molecular binders against gliadin. [ABSTRACT FROM AUTHOR]

Starting in the fall of 2019, mortality, blight symptoms, and signs of white fungal mycelia were observed on external host tissues of non-native landscape trees as well as numerous native trees, understory shrubs, and vines throughout northern and central Florida, USA. We determined that the fungus is an undescribed species of Basidiomycota based on morphological characteristics and DNA sequence analysis. Phylogenetic analyses of the internal transcribed spacer (ITS), large subunit (LSU), and translation elongation factor 1-alpha (tef1) regions revealed that this novel plant pathogen is an undescribed taxon of the genus Parvodontia (Cystostereaceae, Agaricales). We propose the name Parvodontia relampaga sp. nov. which describes its unique morphological features and phylogenetic placement. We confirmed the pathogenicity of P. relampaga in greenhouse inoculations on host plants from which strains of this novel pathogen were isolated, including the non-native gymnosperm Afrocarpus falcatus , the non-native and commercially important Ligustrum japonicum , and the native tree Quercus hemisphaerica. P. relampaga was also detected on a total of 27 different species of woody host plants, including such economically and ecologically important hosts as Fraxinus, Ilex, Magnolia, Persea, Prunus, Salix, Vitis , and Vaccinium. For this new plant disease, we propose the name "relampago blight," which refers to the lightning-like rhizomorph growth (relámpago means 'lightning' in Spanish). This study presents a newly discovered fungal taxon with a wide host range on both angiosperms and gymnosperms that may be an emerging pathogen of concern in Florida and the Gulf Coast region. • A novel thread blight pathogen is formally described as Parvodontia relampaga. • " Relampago blight" is the common name of the disease cause by P. relampaga. • This is the first report of any thread blight pathogen in continental USA. • Relampago blight was detected in plant seedlings in central and north Florida. [ABSTRACT FROM AUTHOR]

A Coding DNA Sequence (CDS) is a fraction of DNA whose nucleotides are grouped into consecutive triplets called codons, each one encoding an amino acid. Because most amino acids can be encoded by more than one codon, the same amino acid chain can be obtained by a very large number of different CDSs. These synonymous CDSs show different features that, also depending on the organism the transcript is expressed in, could affect translational efficiency and yield. The identification of optimal CDSs with respect to given transcript indicators is in general a challenging task, but it has been observed in recent literature that integer linear programming (ILP) can be a very flexible and efficient way to achieve it. In this article, we add evidence to this observation by proposing a new ILP model that simultaneously optimizes different well-grounded indicators. With this model, we efficiently find solutions that dominate those returned by six existing codon optimization heuristics. [ABSTRACT FROM AUTHOR]

Background: The molecular and immunological characteristics of primary tumors and positive lymph nodes in esophageal squamous cell carcinoma (ESCC) are unknown and the relationship with recurrence is unclear, which this study attempted to explore. Methods: A total of 30 ESCC patients with lymph node positive (IIB‐IVA) were enrolled. Among them, primary tumor and lymph node specimens were collected from each patient, and subjected to 551‐tumor‐targeted DNA sequencing and 289‐immuno‐oncology RNA panel sequencing to identify the different molecular basis and immunological features, respectively. Results: The primary tumors exhibited a higher mutation burden than lymph nodes (p < 0.001). One‐year recurrent ESCC exhibited a higher Mucin16 (MUC16) mutation rate (p = 0.038), as well as univariate and multivariate analysis revealed that MUC16 mutation is independent genetic factor associated with reduced relapse‐free survival (univariate, HR: 5.39, 95% CI: 1.67–17.4, p = 0.005; multivariate, HR: 7.36, 95% CI: 1.79–30.23, p = 0.006). Transcriptomic results showed non‐relapse group had higher cytolytic activity (CYT) score (p = 0.025), and was enriched in the IFN‐α pathway (p = 0.036), while those in the relapsed group were enriched in the TNF‐α/NF‐κB (p = 0.001) and PI3K/Akt pathway (p = 0.014). Conclusion: The difference in molecular characteristics between primary lesions and lymph nodes may be the cause of the inconsistent clinical outcomes. Mutations of MUC16 and poor immune infiltration are associated with rapid relapse of nodes‐positive ESCC. [ABSTRACT FROM AUTHOR]

Simple Summary: Bartonella is an intracellular parasitic zoonotic pathogen that can infect animals and cause a variety of human diseases. The prevalence and the copy number of Bartonella spp. in different tissues in small mammals were studied using conventional PCR and real-time quantitative PCR in Yunnan Province, China. Results showed a 31.5% detection rate, varying across species. Genetic analysis identified thirty, ten, and five strains based on ssrA, rpoB, and gltA genes, with nucleotide identities ranging from 92.1% to 100.0%. Seven species of Bartonella were identified, including B. grahamii, B. rochalimae, B. sendai, B. koshimizu, B. phoceensis, B. taylorii, and a new species in Episoriculus leucops (GS136). Analysis of the different tissues naturally infected by Bartonella spp. revealed varied copy numbers across different tissues, with the highest load in spleen tissue. These findings underscore Bartonella's species diversity and host range in Yunnan Province, highlighting the presence of extensive tissue tropism in Bartonella spp. naturally infecting small mammalian tissues. Bartonella is an intracellular parasitic zoonotic pathogen that can infect animals and cause a variety of human diseases. This study investigates Bartonella prevalence in small mammals in Yunnan Province, China, focusing on tissue tropism. A total of 333 small mammals were sampled from thirteen species, three orders, four families, and four genera in Heqing and Gongshan Counties. Conventional PCR and real-time quantitative PCR (qPCR) were utilized for detection and quantification, followed by bioinformatic analysis of obtained DNA sequences. Results show a 31.5% detection rate, varying across species. Notably, Apodemus chevrieri, Eothenomys eleusis, Niviventer fulvescens, Rattus tanezumi, Episoriculus leucops, Anourosorex squamipes, and Ochotona Thibetana exhibited infection rates of 44.4%, 27.7%, 100.0%, 6.3%, 60.0%, 23.5%, and 22.2%, respectively. Genetic analysis identified thirty, ten, and five strains based on ssrA, rpoB, and gltA genes, with nucleotide identities ranging from 92.1% to 100.0%. Bartonella strains were assigned to B. grahamii, B. rochalimae, B. sendai, B. koshimizu, B. phoceensis, B. taylorii, and a new species identified in Episoriculus leucops (GS136). Analysis of the different tissues naturally infected by Bartonella species revealed varied copy numbers across different tissues, with the highest load in spleen tissue. These findings underscore Bartonella's diverse species and host range in Yunnan Province, highlighting the presence of extensive tissue tropism in Bartonella species naturally infecting small mammalian tissues. [ABSTRACT FROM AUTHOR]

The brown algal genus Dictyota (Dictyotales, Phaeophyceae) is widespread, particularly in warm temperate and tropical waters, and plays a vital role in coastal ecosystems. This study reassessed the taxonomy of Dictyota, focusing on specimens from Myanmar and Japan, using a combination of morphological and molecular analyses. Molecular phylogenetic analyses using concatenated DNA sequences of rbcL, psaA, psbA, cox1 and cox3 genes revealed that Dictyota specimens from Myanmar, Japan, and other regions, belong to nine different clades, each representing a different species. Based on morphological and molecular data, seven out of these nine clades are identified as known species, while the remaining two clades are described as new species D. recumbens sp. nov. (=D. sp. A) and D. dimorphosa sp. nov. (=D. sp. B). Dictyota recumbens is characterized by the recumbent thallus, with transverse yellowish-green iridescent lines, and the formation of solitary spores irregularly distributed over the thallus. Dictyota dimorphosa is characterized by two morphological forms: decumbent and erect thalli, with bluish iridescence mainly in the decumbent thallus, and the formation of spores in oval ring shapes distributed over both thallus surfaces. Dictyota recumbens was typically found in tropical regions, while D. dimorphosa appears to be a cool-warm temperate species, distributed from northeastern Hokkaido to southern Kyushu with an extension along South Korea. Our molecular phylogenetic analyses have revealed the existence of several species whose names appeared in multiple clades, suggesting the potential for future increases in species diversity and the presence of cryptic species within certain groups. [ABSTRACT FROM AUTHOR]

The genus Visia is reappraised based on new morphological and molecular data (rbcL and COI-5P sequences), from recently collected and previously studied materials, resulting in the need for several taxonomic changes. Based on our phylogeny and sequence divergence, the genus Visioidea gen. nov. is proposed for two samples from Brazil, forming a distinct clade that is morphologically undistinguishable from the generitype of Visia (V. cayennensis). Two lineages of Visia with high genetic divergences from other species are proposed as new species: 1) V. verviridis sp. nov. from Australia; 2) V. amazonensis sp. nov. from Brazil. Although genetically distinct, both species are morphologically very similar to V. cayennensis. A new record of V. cylindrocellularis was found in Australia, expanding the geographic distribution and the morphometric ranges for this species. The number of species currently recognized in Visia is now six, four with DNA sequence data and two identified based solely on morphology (V. longiarticulata and V. turgida). Cryptic genera within the order Batrachospermales were not recognised until recently with the proposals of Volatus, morphologically indistinct from Kumanoa, and Macrosporophycos undistinguishable from Montagnia and here a third cryptic genus Visioidea is described. [ABSTRACT FROM AUTHOR]

Age estimates are essential for fisheries assessment and management, but deepwater (>200 m) fishes are often difficult to age using traditional techniques. Therefore, age-predictive epigenetic clocks were developed for a model deepwater reef fish, blackbelly rosefish Helicolenus dactylopterus, using two tissue types (fin clips and muscle; n = 61 individuals; 9−60 years) and Δ14C-validated consensus age estimates. The influence of biological information (length and sex) on epigenetic clock accuracy, and the potential for developing a multi-tissue clock, were also assessed. Bisulfite-converted restriction site-associated DNA sequencing (bsRADseq) was used to identify CpG sites (cytosines followed by guanines) exhibiting age-correlated DNA methylation, and epigenetic clocks showed strong agreement (R2 > 0.98) between predicted and consensus ages. Including length and sex data enhanced accuracy and precision (R2 > 0.99; mean absolute error < 1 year). Age-associated CpG sites were identified across tissues, but a multi-tissue clock performed poorly relative to single-tissue clocks. Overall, results demonstrate that accurate and precise epigenetic clocks can be developed for deepwater fishes, and the inclusion of biological information may enhance clock accuracy and precision. [ABSTRACT FROM AUTHOR]

Molecular phylogenetic studies focused on the early-branching papilionoid legumes have revealed many new clades and supported several generic realignments, yet the monophyly of some of the constituent genera has remained unassessed. This is the case for the Amazonian genus Clathrotropis of the tribe Ormosieae. The genus, as traditionally circumscribed, comprises seven species of trees, including some of the most ecologically hyper dominant taxa across the Amazonian terra firme and seasonally flooded forests. Here we employed a Bayesian analysis of densely sampled nuclear ribosomal ITS/5.8S and plastid matK and trnL intron DNA sequences to evaluate the monophyly of Clathrotropis. All individual and concatenated analyses concurred in showing the non-monophyletic nature of Clathrotropis , whose species fall into three distantly related lineages: one, comprised of C. brachypetala , C. brunnea , C. glaucophylla and the ecologically dominant C. macrocarpa , is circumscribed here as the new genus Cabari ; the two others, comprising C. paradoxa and the widespread C. nitida , are more closely related to Spirotropis of the tribe Ormosieae. Such phylogeny-based dismemberment of Clathrotropis is further supported by vegetative, floral, fruit, and seed characters. Although the genes analysed in this study have provided phylogenetically informative data supporting the need for a new circumscription of Clathrotropis , we suggest that future phylogenomic studies should seek to better resolve the relationships of the newly described genus Cabari across the phylogenetically recalcitrant early-branching nodes of the Genistoid clade. [ABSTRACT FROM AUTHOR]

Population genetic structure is influenced by a combination of contemporary and historical events; however, this structure can be complicated by ongoing gene flow. While it is well known that contemporary hybridization occurs frequently among many closely related species, it often remains uncertain as to which populations are involved in introgression events, and this can be even more difficult to infer when introgression is historical. Here we use restriction-site associated DNA sequencing to look at the level of introgression among four species of songbirds in North America: the black-capped, mountain, boreal, and chestnut-backed chickadee. Samples from both sympatric and allopatric sites across the species' ranges supported limited ongoing mixing among the four species with Bayesian clustering and principal component analyses. In contrast, f4-statistics and admixture graphs revealed extensive historical introgression among geographically structured populations. Almost all historical admixture events were among populations west of the Rocky Mountains, and almost all populations west of the Rocky Mountains, excluding island and coastal populations, showed evidence of historical admixture. The inclusion of all four chickadee species proved crucial in differentiating which species were involved in hybridization events to avoid erroneous conclusions. Taken together, the results suggest a complex pattern of divergence with gene flow. [ABSTRACT FROM AUTHOR]

In February 2021, damping off and collar and root rot on coriander (Coriandrum sativum L.) became widespread in the municipality of Vitória da Conquista, Bahia, Brazil. An oomycete was isolated from root and collar segments of affected seedlings and caused the same symptoms in inoculated seedlings. Based on morphological features and DNA sequences from the ITS and cox2 region, the pathogen was identified as Pythium aphanidermatum. To the best of our knowledge, this is the first report of the occurrence of P. aphanidermatum on coriander plants in Brazil. [ABSTRACT FROM AUTHOR]

Cruckshanksia Hook. & Arn. and Oreopolus Schltdl. Rubiaceae (Rubioideae – Coussareeae), endemic genera of Chile and Andean Argentina, have historically been highly taxonomically unstable. Molecular analyses have confirmed Oreopolus as the sister group of Cruckshanksia; however, the relationships among its species are still not resolved because previous studies have not considered all species of the genus and the published topologies have many unsupported nodes. For this reason, we carried out a phylogenetic study with all the species currently recognized by recent revisions, using two nuclear DNA regions and five plastid regions, to elucidate the relationships between species. In addition, the evolutionary history of the group was estimated based on divergence times, and a character reconstruction was performed. The results corroborate that Oreopolus is the sister group of Cruckshanksia. Cruckshanksia is monophyletic and composed of two principal clades. Clade I is composed of Subclade I (C. pumila and C. verticillata) associated with C. montiana; Clade II is composed of Subclade II (C. palmae and C. macrantha) and Subclade III (C. lithiophila and C. hymenodon). With 81% probability the common ancestor of the genus Cruckshanksia had petaloid appendices associated with two independent lines of evolution. The probability that the common ancestor of the Oreopolus‒Cruckshanksia clade had equal calyx lobes is 50%. [ABSTRACT FROM AUTHOR]

The smart healthcare system is one of the Internet of Things‐based applications that are increasingly used nowadays. One of the requirements of this system is privacy‐preserving, which should protect the disclosure of the patient record contents. In the present paper, a combination of chaotic functions and a new DNA‐based steganography method, and image blocking are suggested to protect patients' privacy‐preserving. First, the image is blocked, and the initial key for the chaotic function will be gained by using the centers of the blocks. Then the data and image are transformed into DNA sequences. Finally, one of the randomly chosen DNA strands of data is XOR with the center of one randomly selected block and will be placed in one of the block pixels. The failure to send the initial key separately to generate random numbers, as well as the random selection of secret data bits and image pixels for steganography has increased the security of the proposed method. The simulation results not only indicate the quality of the stego‐image but also show better performance of the proposed method than the existing methods. [ABSTRACT FROM AUTHOR]

Copy number aberrations (CNAs) are ubiquitous in many types of cancer. Inferring CNAs from cancer genomic data could help shed light on the initiation, progression, and potential treatment of cancer. While such data have traditionally been available via "bulk sequencing," the more recently introduced techniques for single-cell DNA sequencing (scDNAseq) provide the type of data that makes CNA inference possible at the single-cell resolution. We introduce a new birth-death evolutionary model of CNAs and a Bayesian method, NestedBD, for the inference of evolutionary trees (topologies and branch lengths with relative mutation rates) from single-cell data. We evaluated NestedBD's performance using simulated data sets, benchmarking its accuracy against traditional phylogenetic tools as well as state-of-the-art methods. The results show that NestedBD infers more accurate topologies and branch lengths, and that the birth-death model can improve the accuracy of copy number estimation. And when applied to biological data sets, NestedBD infers plausible evolutionary histories of two colorectal cancer samples. NestedBD is available at https://github.com/Androstane/NestedBD. [ABSTRACT FROM AUTHOR]

Proper pericarp thickness protects the maize kernel against pests and diseases, moreover, thinner pericarp improves the eating quality in fresh corn. In this study, we aimed to investigate the dynamic changes in maize pericarp during kernel development and identified the major quantitative trait loci (QTLs) for maize pericarp thickness. It was observed that maize pericarp thickness first increased and then decreased. During the growth and formation stages, the pericarp thickness gradually increased and reached the maximum, after which it gradually decreased and reached the minimum during maturity. To identify the QTLs for pericarp thickness, a BC4F4 population was constructed using maize inbred lines B73 (recurrent parent with thick pericarp) and Baimaya (donor parent with thin pericarp). In addition, a high-density genetic map was constructed using maize 10 K SNP microarray. A total of 17 QTLs related to pericarp thickness were identified in combination with the phenotypic data. The results revealed that the heritability of the thickness of upper germinal side of pericarp (UG) was 0.63. The major QTL controlling UG was qPT1-1, which was located on chromosome 1 (212,215,145–212,948,882). The heritability of the thickness of upper abgerminal side of pericarp (UA) was 0.70. The major QTL controlling UA was qPT2-1, which was located on chromosome 2 (2,550,197–14,732,993). In addition, a combination of functional annotation, DNA sequencing analysis and quantitative real-time PCR (qPCR) screened two candidate genes, Zm00001d001964 and Zm00001d002283, that could potentially control maize pericarp thickness. This study provides valuable insights into the improvement of maize pericarp thickness during breeding. [ABSTRACT FROM AUTHOR]

The ultrasensitive detection of hepatitis C virus (HCV) nucleic acid is crucial for the early diagnosis of hepatitis C. In this study, by combining Ag@Au core/shell nanoparticle (Ag@AuNP)-based surface-enhanced Raman scattering (SERS) tag with hybridization chain reaction (HCR), a novel SERS-sensing method was developed for the ultrasensitive detection of HCV nucleic acid. This SERS-sensing system comprised two different SERS tags, which were constructed by modifying Ag@AuNP with a Raman reporter molecule of 4-ethynylbezaldehyde, two different hairpin-structured HCR sequences (H1 or H2), and a detection plate prepared by immobilizing a capture DNA sequence onto the Ag@AuNP layer surface of the detection wells. When the target nucleic acid was present, the two SERS tags were captured on the surface of the Ag@AuNP-coated detection well to generate many "hot spots" through HCR, forming a strong SERS signal and realizing the ultrasensitive detection of the target HCV nucleic acid. The limit of detection of the SERS-sensing method for HCV nucleic acid was 0.47 fM, and the linear range was from 1 to 105 fM. [ABSTRACT FROM AUTHOR]

Ribonucleotides represent the most common non-canonical nucleotides found in eukaryotic genomes. The sources of chromosome-embedded ribonucleotides and the mechanisms by which unrepaired rNMPs trigger genome instability and human pathologies are not fully understood. The available sequencing technologies only allow to indirectly deduce the genomic location of rNMPs. Oxford Nanopore Technologies (ONT) may overcome such limitation, revealing the sites of rNMPs incorporation in genomic DNA directly from raw sequencing signals. We synthesized two types of DNA molecules containing rNMPs at known or random positions and we developed data analysis pipelines for DNA-embedded ribonucleotides detection by ONT. We report that ONT can identify all four ribonucleotides incorporated in DNA by capturing rNMPs-specific alterations in nucleotide alignment features, current intensity, and dwell time. We propose that ONT may be successfully employed to directly map rNMPs in genomic DNA and we suggest a strategy to build an ad hoc basecaller to analyse native genomes. This study reports the direct detection of ribonucleotides embedded in DNA molecules by Oxford Nanopore sequencing, based on ribonucleotides-induced alterations in basecalling features, currents, and dwell times. [ABSTRACT FROM AUTHOR]

Background: Accurately deciphering clonal copy number substructure can provide insights into the evolutionary mechanism of cancer, and clustering single-cell copy number profiles has become an effective means to unmask intra-tumor heterogeneity (ITH). However, copy numbers inferred from single-cell DNA sequencing (scDNA-seq) data are error-prone due to technically confounding factors such as amplification bias and allele-dropout, and this makes it difficult to precisely identify the ITH. Results: We introduce a hybrid model called scGAL to infer clonal copy number substructure. It combines an autoencoder with a generative adversarial network to jointly analyze independent single-cell copy number profiles and gene expression data from same cell line. Under an adversarial learning framework, scGAL exploits complementary information from gene expression data to relieve the effects of noise in copy number data, and learns latent representations of scDNA-seq cells for accurate inference of the ITH. Evaluation results on three real cancer datasets suggest scGAL is able to accurately infer clonal architecture and surpasses other similar methods. In addition, assessment of scGAL on various simulated datasets demonstrates its high robustness against the changes of data size and distribution. scGAL can be accessed at: https://github.com/zhyu-lab/scgal. Conclusions: Joint analysis of independent single-cell copy number and gene expression data from a same cell line can effectively exploit complementary information from individual omics, and thus gives more refined indication of clonal copy number substructure. [ABSTRACT FROM AUTHOR]

Clonal hematopoiesis of indeterminate potential (CHIP) refers to the phenomenon where a hematopoietic stem cell acquires fitness-increasing mutation(s), resulting in its clonal expansion. CHIP is frequently observed in multiple myeloma (MM) patients, and it is associated with a worse outcome. High-throughput amplicon-based single-cell DNA sequencing was performed on circulating CD34+ cells collected from twelve MM patients before autologous stem cell transplantation (ASCT). Moreover, in four MM patients, longitudinal samples either before or post-ASCT were collected. Single-cell sequencing and data analysis were assessed using the MissionBio Tapestri® platform, with a targeted panel of 20 leukemia-associated genes. We detected CHIP pathogenic mutations in 6/12 patients (50%) at the time of transplant. The most frequently mutated genes were TET2, EZH2, KIT, DNMT3A, and ASXL1. In two patients, we observed co-occurring mutations involving an epigenetic modifier (i.e., DNMT3A) and/or a gene involved in splicing machinery (i.e., SF3B1) and/or a tyrosine kinase receptor (i.e., KIT) in the same clone. Longitudinal analysis of paired samples revealed a positive selection of mutant high-fitness clones over time, regardless of their affinity with a major or minor sub-clone. Copy number analysis of the panel of all genes did not show any numerical alterations present in stem cell compartment. Moreover, we observed a tendency of CHIP-positive patients to achieve a suboptimal response to therapy compared to those without. A sub-clone dynamic of high-fitness mutations over time was confirmed. [ABSTRACT FROM AUTHOR]

The brown bear (Ursus arctos L., 1758) is a widespread bear species inhabiting the forest zone of Eurasia, including the Republic of Yakutia. The association with forest habitats explains why the Pleistocene findings of U. arctos fossils are rare in the northern part of Eastern Siberia, where open steppe-tundra and steppefied landscapes prevailed during the Pleistocene. Fossils of U. arctos that have been found on the territory of Yakutia are dated since the beginning of the Middle Pleistocene. These are mainly the skulls and bones of the postcranial skeleton. In the present study, using comparative morphological analysis, computed tomography, and DNA sequencing, we describe a first mummified carcass of a brown bear individual that inhabited the New Siberian Islands (Northeast Siberia) in the Middle Holocene, approximately 3,500 years BP, which was found in the permafrost of Bolshoy Lyakhovsky Island, Russia, in 2020. [ABSTRACT FROM AUTHOR]

The universality of DNA methylation as an epigenetic regulatory mechanism belongs to all biological kingdoms. However, while eukaryotic systems have been the primary focus of DNA methylation studies, the molecular mechanisms in prokaryotes are less known. Nevertheless, DNA methylation in prokaryotes plays a pivotal role in many cellular processes such as defense systems against exogenous DNA, cell cycle dynamics, and gene expression, including virulence. Thanks to single-molecule DNA sequencing technologies, genome-wide identification of methylated DNA is becoming feasible on a large scale, providing the possibility to investigate more deeply the presence, variability, and roles of DNA methylation. Here, we present an overview of the multifaceted roles of DNA methylation in prokaryotes and suggest research directions and tools which can enable us to better understand the contribution of DNA methylation to prokaryotic genome evolution and adaptation. In particular, we emphasize the need to understand the presence and role of transgenerational inheritance, as well as the impact of epigenomic signatures on adaptation and genome evolution. Research directions and the importance of novel computational tools are underlined. [ABSTRACT FROM AUTHOR]

As data continue to grow in complexity and size, there is an imperative need for more efficient and robust storage solutions. DNA storage has emerged as a promising avenue to solve this problem, but existing approaches do not perform efficiently enough on video data, particularly for information density and time efficiency. This paper introduces VSD, a pioneering encoding method for video segmentation and storage in DNA, leveraging the Reed–Solomon (RS) error correction code. This method addresses these limitations through an innovative combination of segmentation and encoding, accompanied by RS coding to bolster error resilience. Additionally, the method ensures that the GC-content of the resultant DNA sequences remains around 50%, which further enhances the storage robustness. The experimental results demonstrate the method has commendable encoding efficiency and offers a solution to the prevailing issue of time inefficiency and error correction rates in DNA storage. This groundbreaking approach paves the way for the practical and reliable storage of large-scale video data in DNA, heralding a new era in the domain of information storage. [ABSTRACT FROM AUTHOR]

In the search for novel, effective inhibitors of High‐Mobility Group Box1 (HMGB1)—a protein involved in various inflammatory and autoimmune diseases as well as in cancer—we herein discovered a set of anti‐HMGB1 G‐quadruplex(G4)‐forming aptamers by using an in vitro selection procedure applied to a doped library of guanine‐rich oligonucleotides. The selected DNA sequences were then studied in a pseudo‐physiological buffer mimicking the extracellular medium, where HMGB1 exerts its pathological activity, using spectroscopic, electrophoretic, and chromatographic techniques. All the oligonucleotides proved to fold into monomeric G4s and in some cases also dimeric species, stable at physiological temperature. Remarkably, the protein preferentially recognized the sequences forming dimeric parallel G4 structures, as evidenced by a properly designed chemiluminescent binding assay which also highlighted a good selectivity of these aptamers for HMGB1. Moreover, all aptamers showed anti‐HMGB1 activity, inhibiting protein‐induced cell migration. The acquired data allowed identifying L12 as the best anti‐HMGB1 aptamer, featured by high thermal and enzymatic stability, no toxicity at least up to 5 μM concentration on healthy cells, along with potent anti‐HMGB1 activity (IC50 ca. 28 nM) and good binding affinity for the protein, thus indicating it as a very promising lead candidate for in vivo studies. [ABSTRACT FROM AUTHOR]

In the search for novel, effective inhibitors of High‐Mobility Group Box1 (HMGB1)—a protein involved in various inflammatory and autoimmune diseases as well as in cancer—we herein discovered a set of anti‐HMGB1 G‐quadruplex(G4)‐forming aptamers by using an in vitro selection procedure applied to a doped library of guanine‐rich oligonucleotides. The selected DNA sequences were then studied in a pseudo‐physiological buffer mimicking the extracellular medium, where HMGB1 exerts its pathological activity, using spectroscopic, electrophoretic, and chromatographic techniques. All the oligonucleotides proved to fold into monomeric G4s and in some cases also dimeric species, stable at physiological temperature. Remarkably, the protein preferentially recognized the sequences forming dimeric parallel G4 structures, as evidenced by a properly designed chemiluminescent binding assay which also highlighted a good selectivity of these aptamers for HMGB1. Moreover, all aptamers showed anti‐HMGB1 activity, inhibiting protein‐induced cell migration. The acquired data allowed identifying L12 as the best anti‐HMGB1 aptamer, featured by high thermal and enzymatic stability, no toxicity at least up to 5 μM concentration on healthy cells, along with potent anti‐HMGB1 activity (IC50 ca. 28 nM) and good binding affinity for the protein, thus indicating it as a very promising lead candidate for in vivo studies. [ABSTRACT FROM AUTHOR]