Search

Burkina Faso is a landlocked country within the meningitis belt of sub-Saharan Africa that experiences hyperendemic bacterial meningitis and an elevated risk for recurrent meningitis outbreaks (1). Commonly characterized by [...]

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]

Mitochondrial DNA (mtDNA) deletion mutations cause many human diseases and are linked to age-induced mitochondrial dysfunction. Mapping the mutation spectrum and quantifying mtDNA deletion mutation frequency is challenging with next-generation sequencing methods. We hypothesized that long-read sequencing of human mtDNA across the lifespan would detect a broader spectrum of mtDNA rearrangements and provide a more accurate measurement of their frequency. We employed nanopore Cas9-targeted sequencing (nCATS) to map and quantitate mtDNA deletion mutations and develop analyses that are fit-for-purpose. We analyzed total DNA from vastus lateralis muscle in 15 males ranging from 20 to 81 years of age and substantia nigra from three 20-year-old and three 79-year-old men. We found that mtDNA deletion mutations detected by nCATS increased exponentially with age and mapped to a wider region of the mitochondrial genome than previously reported. Using simulated data, we observed that large deletions are often reported as chimeric alignments. To address this, we developed two algorithms for deletion identification which yield consistent deletion mapping and identify both previously reported and novel mtDNA deletion breakpoints. The identified mtDNA deletion frequency measured by nCATS correlates strongly with chronological age and predicts the deletion frequency as measured by digital PCR approaches. In substantia nigra, we observed a similar frequency of age-related mtDNA deletions to those observed in muscle samples, but noted a distinct spectrum of deletion breakpoints. NCATS-mtDNA sequencing allows the identification of mtDNA deletions on a single-molecule level, characterizing the strong relationship between mtDNA deletion frequency and chronological aging.

Background: Food-borne pathogen Listeria monocytogenes is abundantly present in nature and accountable for sporadic and epidemic cases of listeriosis in humans. The objective of this study was to screen common food sources for L. monocytogenes using biochemical and molecular methods to detect and characterise its toxin genes as well as for biofilm formation. Methods: A total of 92 samples, comprising dairy and street food products, were randomly collected from various sources for this investigation. The collected samples were processed for biochemical and molecular methods to detect L. monocytogenes. Additionally, virulence factors associated genes, antibiogram profiles and biofilm formation related assays were determined. Results: L. monocytogenes presence was confirmed using molecular detection methods targeting prs and lmo1030 genes, along with MALDI-TOF MS. Following 16 S rRNA sequencing, the identified Listeria species were further categorised into two groups. L. monocytogenes was detected in two (2.17%) food samples tested (L-23 and L-74). Multiplex PCR indicated the presence of seven virulence-related genes in L. monocytogenes isolates, i.e., inlA, inlB, prfA, iap, actA, plcB, and hlyA. In addition, 17 antibiotics were tested, whereby two isolates showed resistance to clindamycin and azithromycin, while one isolate (L-74) was also resistant to nalidixic acid, co-trimoxazole, ampicillin, norfloxacin, and cefotaxime. L-23 and L-74 isolates showed biofilm formation, especially at pH 8.6 and 37°C. Conclusions: Besides the demonstration of the presence of L. monocytogenes in some dairy and street food products, this study underscores the need to increase the standards of hygiene on the one hand and the importance of the surveillance of food-borne pathogens on the other.

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]

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]

Chilling sensitivity is one of the greatest challenges affecting the marketability and profitability of sweet basil (Ocimum basilicum L.) in the US and worldwide. Currently, there are no sweet basils commercially available with significant chilling tolerance and traditional aroma profiles. This study was conducted to identify quantitative trait loci (QTLs) responsible for chilling tolerance and aroma compounds in a biparental mapping population, including the Rutgers advanced breeding line that served as a chilling tolerant parent, 'CB15', the chilling sensitive parent, 'Rutgers Obsession DMR' and 200 F2 individuals. Chilling tolerance was assessed by percent necrosis using machine learning and aroma profiling was evaluated using gas chromatography (GC) mass spectrometry (MS). Single nucleotide polymorphism (SNP) markers were generated from genomic sequences derived from double digestion restriction-site associated DNA sequencing (ddRADseq) and converted to genotype data using a reference genome alignment. A genetic linkage map was constructed and five statistically significant QTLs were identified in response to chilling temperatures with possible interactions between QTLs. The QTL on LG24 (qCH24) demonstrated the largest effect for chilling response and was significant in all three replicates. No QTLs were identified for linalool, as the population did not segregate sufficiently to detect this trait. Two significant QTLs were identified for estragole (also known as methyl chavicol) with only qEST1 on LG1 being significant in the multiple-QTL model (MQM). QEUC26 was identified as a significant QTL for eucalyptol (also known as 1,8-cineole) on LG26. These QTLs may represent key mechanisms for chilling tolerance and aroma in basil, providing critical knowledge for future investigation of these phenotypic traits and molecular breeding. [ABSTRACT FROM AUTHOR]

The structure of the complex formed by naphthyridine carbamate dimer (NCD) binding to CGG repeat sequences in DNA, associated with fragile X syndrome, has been elucidated using 15N-labeled NCD and 1H–15N HSQC. In a fully saturated state, two NCD molecules consistently bind to each CGG/CGG unit, maintaining a 1 : 2 binding stoichiometry. [ABSTRACT FROM AUTHOR]

Reductions in sequencing costs have enabled widespread use of shotgun metagenomics and amplicon sequencing, which have drastically improved our understanding of the microbial world. However, large sequencing projects are now hampered by the cost of library preparation and low sample throughput, comparatively to the actual sequencing costs. Here, we benchmarked three high-throughput DNA extraction methods: ZymoBIOMICS™ 96 MagBead DNA Kit, MP BiomedicalsTM FastDNATM-96 Soil Microbe DNA Kit, and DNeasy® 96 PowerSoil® Pro QIAcube® HT Kit. The DNA extractions were evaluated based on length, quality, quantity, and the observed microbial community across five diverse soil types. DNA extraction of all soil types was successful for all kits, however DNeasy® 96 PowerSoil® Pro QIAcube® HT Kit excelled across all performance parameters. We further used the nanoliter dispensing system I.DOT One to miniaturize Illumina amplicon and metagenomic library preparation volumes by a factor of 5 and 10, respectively, with no significant impact on the observed microbial communities. With these protocols, DNA extraction, metagenomic, or amplicon library preparation for one 96-well plate are approx. 3, 5, and 6 hours, respectively. Furthermore, the miniaturization of amplicon and metagenome library preparation reduces the chemical and plastic costs from 5.0 to 3.6 and 59 to 7.3 USD pr. sample. This enhanced efficiency and cost-effectiveness will enable researchers to undertake studies with greater sample sizes and diversity, thereby providing a richer, more detailed view of microbial communities and their dynamics. [ABSTRACT FROM AUTHOR]

The reliable and timely detection of poliovirus cases through surveillance for acute flaccid paralysis (AFP), supplemented by environmental surveillance of sewage samples, is a critical component of the polio eradication program. Since 1988, the number of polio cases caused by wild poliovirus (WPV) has declined by >99.9%, and eradication of WPV serotypes 2 and 3 has been certified; only serotype 1 (WPV1) continues to circulate, and transmission remains endemic in Afghanistan and Pakistan. This surveillance update evaluated indicators from AFP surveillance, environmental surveillance for polioviruses, and Global Polio Laboratory Network performance data provided by 28 priority countries for the program during 2022-2023. No WPV1 cases have been detected outside of Afghanistan and Pakistan since August 2022, when an importation into Malawi and Mozambique resulted in an outbreak during 2021-2022. During 2022-2023, among 28 priority countries, 20 (71.4%) met national AFP surveillance indicator targets, and the number of environmental surveillance sites increased. However, low national rates of reported AFP cases in priority countries in 2023 might have resulted from surveillance reporting lags; substantial national and subnational AFP surveillance gaps persist. Maintaining high-quality surveillance is critical to achieving the goal of global polio eradication. Monitoring surveillance indicators is important to identifying gaps and guiding surveillance-strengthening activities, particularly in countries at high risk for poliovirus circulation. [ABSTRACT FROM AUTHOR]

A survey of recent taxonomic studies of birds that included acoustic trait analyses reveals that most studies have not archived the sound recordings that support their conclusions, despite the current availability of online, publicly available collections of bird sounds. In addition, bird sound recordings have often been cited without unique accession numbers that permit unambiguous sample identification and in considerably less detail than other types of samples, such as museum specimens or genetic samples. Both this lack of data openness and the way acoustic samples have been cited undermine the methodological rigor that otherwise characterizes many of these studies, and much invaluable biological data are likely to be lost over time if bird sound recordings are not archived in long-term collections. I suggest that these problems can be easily addressed by embracing the open data movement and adopting some best practices that are widely used in other fields. Just as study skins and DNA sequences are required to be deposited in publicly available collections such as natural history museums and the GenBank, respectively, sound recordings used in taxonomic studies with acoustic trait analyses should be archived in publicly available collections as a condition for publication of associated results. Authors of taxonomic studies involving sounds should archive their sound recordings and provide unique accession numbers for sound recordings examined, and journals and reviewers should ensure that authors have done so. By embracing the open data movement, research studying avian acoustic signals is expected to become more transparent, reproducible, and useful. [ABSTRACT FROM AUTHOR]

As part of the risk assessment (RA) requirements for genetically modified (GM) plants, according to Regulation (EU) No 503/2013 and the EFSA guidance on the RA of food and feed from GM plants (EFSA GMO Panel 2011), applicants need to perform a molecular characterisation of the DNA sequences inserted in the GM plant genome. This Technical Note to the applicants puts together requirements and recommendations for the quality assessment of the methodology, analysis and reporting when DNA sequencing is used for the molecular characterisation of GM plants. In particular, it applies to the use of Sanger sequencing and next‐generation sequencing for the characterisation of the inserted genetic material and its flanking regions at each insertion site, the determination of the copy number of all detectable inserts and the analysis of the genetic stability of the inserts. This updated document replaces the EFSA 2018 Technical Note and reflects the current knowledge in scientific‐technical methods for generating and verifying, in a standardised manner, DNA sequencing data in the context of RA of GM plants. It does not take into consideration the verification and validation of the detection method which remains under the remit of the Joint Research Centre (JRC). [ABSTRACT FROM AUTHOR]

A pangenome captures the genomic diversity for a species, derived from a collection of genetic sequences of diverse populations. Advances in sequencing technologies have given rise to three primary methods for pangenome construction and analysis: de novo assembly and comparison, reference genome-based iterative assembly, and graph-based pangenome construction. Each method presents advantages and challenges in processing varying amounts and structures of DNA sequencing data. With the emergence of high-quality genome assemblies and advanced bioinformatic tools, the graph-based pangenome is emerging as an advanced reference for exploring the biological and functional implications of genetic variations. [ABSTRACT FROM AUTHOR]

Convolvulus arvensis is an herbaceous dicotyledonous plant in the Convolvulaceae family that is native to Europe and Asia. It is a perennial soboliferous plant and is one of the most harmful weeds. This weed is successful in many types of climates, including temperate, tropical, and Mediterranean climates, but it is most troublesome for agriculture throughout the temperate zone. In this study, several pathogenic isolates were collected from this host. The internal transcribed spacer (ITS) and large subunit (28S) or ribosomal DNA, partial DNA-directed RNA polymerase II subunit (rpb2), and β-tubulin (tub2) genes were amplified and sequenced for all the isolates studied. Further, both a multilocus phylogenetic analysis of DNA sequences and an analysis of morphological features were implemented. Based on the results obtained, all the studied isolates were found to be distinct from any described species in the genus Ascochyta and are, therefore, described here as a new species Ascochyta erotica sp. nov. The pathogenicity of A. erotica sp. nov. was also tested and confirmed on leaf segments of C. arvensis. [ABSTRACT FROM AUTHOR]

Simple Summary: Some species of Sarcocystis parasites form cysts in the brains of small mammals. These parasites have been shown in laboratory experiments to be transmitted by Buteo buzzards. However, there is a lack of studies identifying these parasites in natural definitive hosts. In the current investigation, we examined brain tissues of small mammals and small intestines of two buzzard species collected in Lithuania for Sarcocystis spp. Species of Sarcocystis were confirmed using DNA sequence analysis. Of the eleven small mammal species inspected, only bank voles were infected with cysts of Sarcocystis glareoli. The prevalence of this parasite in the brain of vole hosts reached 9.1%. Based on genetic examination, half of the investigated common buzzards were positive for S. glareoli. Furthermore, two Sarcocystis species, including a putative new species, were detected in the small intestines of rough-legged buzzards. Our results indicate that Buteo buzzards play an important role in transmitting rarely studied Sarcocystis parasites forming cysts in the tissues of small mammals. Representatives of the genus Sarcocystis are worldwide distributed apicomplexan parasites characterised by two-host prey-predator relationships. Sarcocystis spp. produce sarcocysts in the muscles and brains of intermediate hosts and develop sporocysts in the intestines of definitive hosts. Two species, Sarcocystis glareoli and Sarcocystis microti, previously assigned to the genus Frenkelia, form cysts in the brains of rodents and are transmitted through the common buzzard (Buteo buteo). In our study, brain samples of 694 small mammals caught in different regions of Lithuania were examined for Sarcocystis spp. Additionally, 10 B. buteo and two rough-legged buzzards (Buteo lagopus) were tested for sporocysts of the analysed parasites. Sarcocystis species were identified based on 28S rRNA sequence comparison. Of the eleven species of small mammals tested, Sarcocystis parasites were observed only in the bank vole (Clethrionomys glareolus). Cysts of S. glareoli were detected in 34 out of 374 C. glareolus (9.1%, 95% CI = 6.4–12.5%). Molecular investigation showed the presence of only S. glareoli in the intestines of 50% of B. buteo. Furthermore, two species, Sarcocystis sp. Rod3 and Sarcocystis sp. Rod4, were confirmed in B. lagopus. Our results demonstrate the need for further studies on Sarcocystis cycling between rodents and birds. [ABSTRACT FROM AUTHOR]

Simple Summary: Long Interspersed Element-1 (LINE-1 or L1) is an autonomous transposable element, meaning that its DNA sequences are able to replicate themselves throughout the human genome. This activity may lead to genomic instability and is associated with several different diseases. Additionally, L1s are also capable of replicating other non-autonomous sequences, thereby increasing their disruptive impact. Although there are different tools available that may be used for L1 detection, the heuristics involved affect their accuracy. L1PD (LINE-1 Pattern Detection) uses a novel pattern-matching approach to detect L1s in human genomes, using a fixed set of k-mer probes of length 50 that were generated using the human reference genome GRCh38. This research aims to improve L1PD by using longer probes and testing whether this leads to better results. Additionally, experiments were performed to test the effectiveness of L1PD in detecting L1s in other species, such as dogs, horses, and cows. The results showed that longer probes did improve precision and recall of L1s, not only in humans but in the other species as well. Long Interspersed Element-1 (LINE-1 or L1) is an autonomous transposable element that accounts for 17% of the human genome. Strong correlations between abnormal L1 expression and diseases, particularly cancer, have been documented by numerous studies. L1PD (LINE-1 Pattern Detection) had been previously created to detect L1s by using a fixed pre-determined set of 50-mer probes and a pattern-matching algorithm. L1PD uses a novel seed-and-pattern-match strategy as opposed to the well-known seed-and-extend strategy employed by other tools. This study discusses an improved version of L1PD that shows how increasing the size of the k-mer probes from 50 to 75 or to 100 yields better results, as evidenced by experiments showing higher precision and recall when compared to the 50-mers. The probe-generation process was updated and the corresponding software is now shared so that users may generate probes for other reference genomes (with certain limitations). Additionally, L1PD was applied to other non-human genomes, such as dogs, horses, and cows, to further validate the pattern-matching strategy. The improved version of L1PD proves to be an efficient and promising approach for L1 detection. [ABSTRACT FROM AUTHOR]

Biscogniauxia species are opportunistic pathogens primarily associated with Quercus species dieback in the Mediterranean basin. Among these species, Biscogniauxia mediterranea stands out as the only species previously documented in Tunisia, affecting Quercus suber and Erica multiflora. This study unveils a novel finding, reporting the presence of Biscogniauxia rosacearum on Strawberry trees in Tunisia. The identification of B. rosacearum isolates was confirmed based on DNA sequence data (ITS, TUB2 and ACT) and morphological traits. Artificial inoculation trials on leaves confirmed the pathogenicity of the fungus towards Arbutus unedo. This finding emphasizes the significance of implementing proactive measures to effectively combat this pathogen because of the polyphagous nature of Biscogniauxia species that raises concerns about its potential spread within vulnerable hosts in Tunisian oak forests. [ABSTRACT FROM AUTHOR]

Simple Summary: The red palm weevil, Rhynchophorus ferrugineus, is a major problem for palm plantations worldwide. While chemical pesticides are known to be effective, their environmental impact and insecticide resistance pose serious concerns. Biological control approaches, such as employing entomopathogenic nematodes, can mitigate these challenges by focusing on pests while avoiding harm to the environment or non-target organisms. Our findings show that indigenous and commercial EPNs have the ability to manage red palm weevils. As a result, alternate methods, such as the use of entomopathogenic nematodes, are critical for the sustainable control of red palm weevils. The red palm weevil (RPW) is a significant threat to date palms. Conventional pest control has been ineffective. This study aims to evaluate entomopathogenic nematodes (EPNs) indigenous to Saudi Arabia and commercial against RPW. We used 33 soil samples collected from four areas of Saudi Arabia. The indigenous EPNs were isolated and cultured using an insect baiting method to obtain infective juveniles. Pathogenicity bioassays were conducted against different stages of RPW, including eggs, larvae, and adults. The bioassay was performed using all the isolates at 1 × 106 IJ/mL. Distilled water was used as a control. The results revealed that only 9.09% of soil samples contained positive EPNs. Through DNA sequencing analysis, the positive samples were identified as indigenous isolates belonging to Heterorhabditis indica and Steinernema carpocapsae EPN species. In pathogenicity tests, 90% mortality of RPW eggs was observed after five days. Similar mortality trends were seen in RPW larvae and adults, with 90% mortality recorded after ten days for all the EPN treatments. Mortality increased with the duration of post-EPN inoculation exposure. The 1 × 106 IJ/mL concentrations of EPN effectively killed various stages of RPW in the laboratory. More research is needed to test EPNs against RPW in the field. [ABSTRACT FROM AUTHOR]

Simple Summary: The phylum Onychophora has only about 200 described species around the world. Commonly known as velvet worms or peripatuses, they are soft-bodied, many-legged invertebrates. Onychophora hunt at night and live in moist places on land. On the outside, they all look very similar which makes species identification difficult. In Aotearoa, New Zealand, the species within the endemic genus of live-bearing Peripatoides are known as ngāokeoke. One species in this genus is distinguished by having 16 pairs of legs (P. suteri), while others have 15 pairs of legs. One species (P. indigo) has a distinctive blue colour, but other taxa have a mix of orange and blue pigmentation. Five northern species within Peripatoides were established from genetic evidence of reproductively isolated sympatric populations. Morphological variation in this genus is re-examined using additional sampling from North Island and South Island, New Zealand. A re-analysis of nuclear markers and new DNA sequences confirms that five species are cryptic and their known ranges have been updated. Three new ngāokeoke species in the genus Peripatoides are described from South Island. These three new species represent distinct genetic lineages with distinct pigmentation patterns. (1) Background: Originally described as a single taxon, Peripatoides novaezealandiae (Hutton, 1876) are distributed across both main islands of New Zealand; the existence of multiple distinct lineages of live-bearing Onychophora across this spatial range has gradually emerged. Morphological conservatism obscured the true endemic diversity, and the inclusion of molecular tools has been instrumental in revealing these cryptic taxa. (2) Methods: Here, we review the diversity of the ovoviviparous Onychophora of New Zealand through a re-analysis of allozyme genotype data, mitochondrial DNA cytochrome oxidase subunit I sequences, geographic information and morphology. (3) Results: New analysis of the multilocus biallelic nuclear data using methods that do not require a priori assumptions of population assignment support at least six lineages of ovoviviparous Peripatoides in northern New Zealand, and mtDNA sequence variation is consistent with these divisions. Expansion of mitochondrial DNA sequence data, including representation of all existing taxa and additional populations extends our knowledge of the scale of sympatry among taxa and shows that three other lineages from southern South Island can be added to the Peripatoides list, and names are proposed here. In total, 10 species of Peripatoides can be recognised with current data. [ABSTRACT FROM AUTHOR]

The presence of a microbiome in the urinary system has been established through recent advancements in technology and investigation of microbial communities in the human body. The study of the taxonomic and genomic ecology of microbial communities has been greatly improved by the use of metagenomics. The research in this area has expanded our understanding of microbial ecosystems and shows that the urinary tract contains over 100 species from over 50 genera, with Lactobacillus, Gardnerella, and Streptococcus being the most common. Previous studies have suggested that the microbiota in the urinary tract may play a role in carcinogenesis by causing chronic inflammation and genotoxicity, but more research is needed to reach a definite conclusion. This is a narrative review. We conducted a search for relevant publications by using the databases Medline/PubMed and Google Scholar. The search was based on keywords such as "urinary microbiome," "bladder cancer," "carcinogenesis," "urothelial carcinoma," and "next-generation sequencing." The retrieved publications were then reviewed to study the contribution of the urinary microbiome in the development of bladder cancer. The results have been categorized into four sections to enhance understanding of the urinary microbiome and to highlight its role in the emergence of bladder cancer through alterations in the immune response that involve T-cells and antibodies. The immune system and microbiome play crucial roles in maintaining health and preventing disease. Manipulating the immune system is a key aspect of various cancer treatments, and certain gut bacteria have been linked to positive responses to immunotherapies. However, the impact of these treatments on the urinary microbiome, and how diet and lifestyle affect it, are not well understood. Research in this area could have significant implications for improving bladder cancer treatment and patient outcomes. [ABSTRACT FROM AUTHOR]

Neurofibromatosis type 1 (NF1) is an autosomal dominant disease that affects the development and growth of various tissues. NF1 is a major risk factor for the development of malignancies, particularly malignant peripheral nerve sheath tumors, optic gliomas, and leukemia. NF1 encodes a neurofibromin. Three genes, EVI2A, EVI2B, and OMGP, are embedded within intron 27b of NF1. However, the function of these genes remains unclear. EVI2A and EVI2B encode for putative transmembrane proteins. Mouse homologs are associated with viral insertions involved in leukemia in mice. Mouse Evi2b has been identified as a direct target gene of C/EBPα, a transcription factor critical for myeloid differentiation. Also possible is that these genes are related to the leukemia observed in patients with NF1. These genes might act as modifiers of NF1 phenotypic variations. Therefore, we investigated the EVI2B gene in leukemia and NF1 tumors. We analyzed DNA from 10, 20, and 3 patients with NF1, leukemia, and NF1-leukemia, respectively, and six NF1 tumor tissues. DNA sequencing analysis was used to identify the viral integration sequence, and the protein amounts and EVI2B gene expression were analyzed by flow cytometry and quantitative real-time PCR techniques. The EVI2B gene expression was increased in cutaneous neurofibroma compared with the control both at the level of protein and mRNA. However, its expression in plexiform neurofibroma was decreased significantly at protein level and increased at mRNA level compare to control. Moreover, integration of 455 bases near the 3′ end of the exon was detected. When this integrated sequence was blasted into the NCBI retroviral genome database, an 87% match with the HIV-1 virus envelope gene was obtained. These preliminary results show that EVI2B might be important in NF1 tumorigenesis and leukemia. [ABSTRACT FROM AUTHOR]

Thick‐walled rosette‐like snow algae were long thought to be a life stage of various other species of snow algae. Rosette‐like cells have not been cultured, but by manually isolating cells from 38 field samples in southern British Columbia, we assigned a variety of rosette morphologies to DNA sequence. Phylogenetic analysis of Rubisco large‐subunit (rbcL) gene, ribosomal internal transcribed spacer 2 (ITS2) rRNA region, and 18S rRNA gene revealed that the rosette‐like cells form a new clade within the phylogroup Chloromonadinia. Based on these data, we designate a new genus, Rosetta, which comprises five novel species: R. castellata, R. floranivea, R. stellaria, R. rubriterra, and R. papavera. In a survey of 762 snow samples from British Columbia, we observed R. floranivea exclusively on snow overlying high‐elevation glaciers, whereas R. castellata was observed at lower elevations, near the tree line. The other three species were rarely observed. Spherical red cells enveloped in a thin translucent sac were conspecific with Rosetta, possibly a developmental stage. These results highlight the unexplored diversity among snow algae and emphasize the utility of single‐cell isolation to advance the centuries‐old problem of disentangling life stages and cryptic species. [ABSTRACT FROM AUTHOR]

Mosquitoes are of great medical significance as vectors of many deadly diseases. Mitogenomes have been widely used in phylogenetic studies, but mitogenome knowledge within the family Culicidae is limited, and Culicidae phylogeny is far from resolved. In this study, we surveyed the mitogenomes of 149 Culicidae species, including 7 newly sequenced species. Comparative analysis of 149 mosquito mitogenomes shows gene composition and order to be identical to that of an ancestral insect, and the AT bias, length variation, and codon usage are all consistent with that of other reported Dipteran mitogenomes. Phylogenetic analyses based on the DNA sequences of the 13 protein‐coding genes from the 149 species robustly support the monophyly of the subfamily Anophelinae and the tribes Aedini, Culicini, Mansoniini, Sabethini, and Toxorhynchitini. To resolve ambiguous relationships between clades within the subfamily Culicinae, we performed topological tests and show that Aedini is a sister to Culicini and that Uranotaeniini is a sister to (Mansoniini + (Toxorhynchitini + Sabethini)). In addition, we estimated divergence times using a Bayesian relaxation clock based on the sequence data and 3 fossil calibration points. The results show mosquitoes diverged during the Early Jurassic with massive Culicinae radiations during the Cretaceous, coincident with the emergence of angiosperms and the burst of mammals and birds. Overall, this study, which uses the largest number of Culicidae mitogenomes sequenced to date, comprehensively reveals the mitogenome characteristics and mitogenome‐based phylogeny and divergence times of Culicidae, providing information for further studies on the mitogenome, phylogeny, evolution, and taxonomic revision of Culicidae. [ABSTRACT FROM AUTHOR]

DNA sequences were obtained from 32 blade-forming Ulva specimens collected in 2018 and 2019 from four islands in the Galápagos Archipelago: Fernandina, Floreana, Isabela and San Cristóbal. The loci sequenced were nuclear encoded ITS and plastid encoded rbcL and tufA, all recognized as barcode markers for green algae. Four species were found, Ulva adhaerens, U. lactuca, U. ohnoi and U. tanneri, all of which have had their type specimens sequenced, ensuring the correct application of these names. Only one of these, U. lactuca, was reported historically from the archipelago. Ulva adhaerens was the species most commonly collected and widely distributed, occurring on all four islands. Previously known only from Japan and Korea, this is the first report of U. adhaerens from the southeast Pacific Ocean. Ulva ohnoi was collected on three islands, Isabela, Floreana, and San Cristóbal, and U. lactuca only on the last two. Ulva tanneri is a diminutive, 1–2 cm tall, high intertidal species that is easily overlooked, but likely far more common than the one specimen that was collected. This study of blade-forming Ulva species confirms that a concerted effort, using DNA sequencing, is needed to document the seaweed flora of the Galápagos Archipelago. [ABSTRACT FROM AUTHOR]

Misapplication of Ulva epithets in GenBank has led to confusion in the scientific literature and community. To solve some of the problems, targeted DNA sequencing of plastid encoded rbcL gene amplicons or high-throughput sequencing was performed on all blade-forming Ulva type specimens from the northeast Pacific. Recently collected specimens from at or near type localities were also analyzed for some taxa. Based on these genetic analyses, we confirmed currently recognized species: U. californica, with U. angusta and U. scagelii as heterotypic synonyms, U. stenophylla, U. taeniata, and U. tanneri. Ulva dactylifera, currently considered a synonym of U. taeniata based on morpho-anatomy, is recognized as a distinct species, as is U. expansa whose type specimen was sequenced in 2018. All but two of the ITS, rbcL and tufA sequences in GenBank that were labeled U. californica were correctly named, in contrast to U. taeniata, for which only one of 14 sequences was correctly labeled. These results show that DNA sequencing of Ulva type specimens is essential for the correct application of names. [ABSTRACT FROM AUTHOR]

Understanding the landscape factors governing population connectivity in riverine ecosystems represents an ongoing challenge for freshwater biologists. We used DNA sequence analysis to test the hypothesis that major geomorphological features underpin freshwater‐limited fish diversity in a tectonically dynamic region of New Zealand. Phylogeographic analysis of 101 Galaxias depressiceps cytochrome b sequences, incorporating 55 localities from southern New Zealand, revealed 26 haplotypes, with only one shared among rivers. We detect strong hierarchical genetic differentiation both among and within river systems. Genetic structuring is particularly pronounced across the Taieri River system (63 individuals from 35 sites, 18 haplotypes), with 92% of variation partitioned among locations. Distinctive within‐river genetic clusters are invariably associated with major subcatchment units, typically isolated by substantial gorges. The anomalous distribution of a single lineage across a major drainage divide is consistent with local, tectonically driven headwater capture. We conclude that major landscape features such as gorges can strongly partition riverine fish diversity and constrain freshwater biodiversity. [ABSTRACT FROM AUTHOR]

Four species of African bullfrogs are currently recognised. We describe a new species from southern Africa, which can be distinguished on the basis of morphology, advertisement call and DNA sequences. Morphologically it differs from other bullfrogs by a combination of characteristics including a tympanum that is smaller or equal in size to the eye, and smaller in diameter than the space between eye and tympanum, presence of a white dot on the tympanum, longitudinal skin ridges with speckling between dorsal mottles, pale vertebral line usually present, absence of cream coloured lateral stripes, absence of a pale interorbital-bar, upper jaw-barring absent or faint. It has been confirmed from north-eastern Namibia, southern Angola and north-western Botswana. Three further undescribed species are recognised but not formally named, pending further investigation. We confirm the genetic distinctiveness of P. angusticeps. [ABSTRACT FROM AUTHOR]

Abies koreana E.H.Wilson is an endangered evergreen coniferous tree that is native to high altitudes in South Korea and susceptible to the effects of climate change. Hybridization and reticulate evolution have been reported in the genus; therefore, multigene datasets from nuclear and cytoplasmic genomes are needed to better understand its evolutionary history. Using the Illumina NovaSeq 6000 and Oxford Nanopore Technologies (ONT) PromethION platforms, we generated complete mitochondrial (1,174,803 bp) and plastid (121,341 bp) genomes from A. koreana. The mitochondrial genome is highly dynamic, transitioning from cis- to trans-splicing and breaking conserved gene clusters. In the plastome, the ONT reads revealed two structural conformations of A. koreana. The short inverted repeats (1186 bp) of the A. koreana plastome are associated with different structural types. Transcriptomic sequencing revealed 1356 sites of C-to-U RNA editing in the 41 mitochondrial genes. Using A. koreana as a reference, we additionally produced nuclear and organelle genomic sequences from eight Abies species and generated multiple datasets for maximum likelihood and network analyses. Three sections (Balsamea, Momi, and Pseudopicea) were well grouped in the nuclear phylogeny, but the phylogenomic relationships showed conflicting signals in the mitochondrial and plastid genomes, indicating a complicated evolutionary history that may have included introgressive hybridization. The obtained data illustrate that phylogenomic analyses based on sequences from differently inherited organelle genomes have resulted in conflicting trees. Organelle capture, organelle genome recombination, and incomplete lineage sorting in an ancestral heteroplasmic individual can contribute to phylogenomic discordance. We provide strong support for the relationships within Abies and new insights into the phylogenomic complexity of this genus. [ABSTRACT FROM AUTHOR]

DNA computing is one of the more popular computational methods currently studied, but the requirements for nucleic acid molecules in DNA sequences are high, and it is an important challenge to design reasonable and high-quality DNA sequences while satisfying various constraints. Evolutionary algorithms have good applications in DNA sequence optimization problems, but they still have some limitations. To this end, this paper proposes a JAYA algorithm based on normal clouds, referred to as IJAYA, which uses a combinatorial learning approach to update the optimal and worst positions, which is used to manipulate the subsequent merit search means, and then enhances the local search ability of individuals through the normal cloud model, and finally rejects the worst solutions through a harmony search algorithm to find more reasonable and high-quality solutions. The validity of IJAYA is verified in six benchmark functions, in comparison with multiple variants of JAYA and two statistical tests. In the DNA sequence design optimization problem, the average DNA metrics optimized by IJAYA are: 0 (Continuity), 0 (Hairpin), 59.43 (H-measure), 46.57 (Similarity) and 63.79 (Similarity). The feasibility and practicality of IJAYA was verified by comparing it with the solution algorithms proposed in recent years and ablation experiments. [ABSTRACT FROM AUTHOR]