DNA Sequence Research Articles

Human papillomavirus prevalence, genotype distribution, and prognostic factors of vaginal cancer.

We aimed to investigate human papillomavirus (HPV) prevalence and genotype distribution and prognostic factors in vaginal cancer (VC). VC patients who received treatment between 1989 and 2020 were retrospectively reviewed. L1 general polymerase chain reaction (PCR) followed by HPV Blot (King Car, I-Lan, Taiwan) and E6 type-specific-PCR were performed for genotyping firstly. P16 and p53 immunohistochemistry staining was performed. Univariate and multivariate analyses identified predictors of clinical outcomes.79 VC patients were eligible for analysis. 73 patients (92.4%) were squamous cell carcinoma (SCC) and 6 (7.6%) as non-SCC. The median follow-up time was 134.3 months (range 0.9-273.4). Among nine initially HPV-negative cases, seven were identified as being positive through HPV16/18/45/52/58 whole-genome amplification followed by Sanger sequencing (WGASS). HPV DNA sequences were detected in 98.6% of SCC and 83.3% of non-SCC, respectively, with HPV16 (49.4%), HPV52 (15.2%) and HPV58 (8.9%) being predominant. Patients with paraaortic lymph node (LN) metastasis had a 5-year cancer-specific survival (CSS) rate of 0%. Multivariate analysis revealed that only p16 and stage were significantly correlated with prognosis. Variables with strong correlations (p16- and HPV-positivity, LN metastasis and stage), were included in models 2-5 alternatively. Stage III/IV (hazard ratio [HR] = 3.64-4.56) and LN metastasis (HR = 2.81-3.44) were significant negative predictors of CSS, whereas p16-positivity (HR = 0.29-0.32) and HPV-positivity (HR = 0.14) were related to better prognosis. In conclusion, 97.5% of VCs were HPV-positive with WGASS. Stage III/IV and LN metastasis were significant negative predictors, whereas p16- and HPV-positivity were significantly associated with better prognosis.

Molecular detection and identification of Enteromonas species in human and animal hosts using polymerase chain reaction and DNA sequencing

Enteromonas hominis, a human intestinal protozoan parasite of the diplomonad group, has been overlooked because of its commensal features; therefore, molecular studies on this parasite are limited. To address this gap, we designed a molecular screening protocol using polymerase chain reaction (PCR) and DNA sequencing targeting the 18S small subunit ribosomal RNA gene and applied this screening method to the molecular epidemiological analysis of Enteromonas spp. in humans and various livestock. We validated our methodology using stool samples collected from 215 humans and 270 animal hosts (buffaloes, pigs, dogs, goats, horses, rodents, chickens, and ducks) during an annual epidemiological investigation conducted from 2013 to 2016 on Sumba Island, Indonesia. The overall prevalences of Enteromonas spp. were 33.9% (n = 73/215) in humans and 25.2% (n = 68/270) in mammals and avians. The positive predictive value of this PCR method for Enteromonas spp., as evaluated through sequencing, was 90.1% in human samples and 58.1% in non-human samples (particularly low, 11.4% in rodents). Although the specificity of the PCR approach may not be perfect, in combination with DNA sequencing, it was effective in detecting and identifying a partial sequence (1,458 bp) of the target gene region in Enteromonas species.

A hybrid model of recursive cellular automata, DNA sequences, and chaotic system for image encryption

A hybrid model of recursive cellular automata, DNA sequences, and chaotic system for image encryption

Nasopharyngeal Botflies Oestrus ovis and Cephenemyia stimulator in Roe Deer (Capreolus capreolus) from Northern Spain.

Two of 19 roe deer (Capreolus capreolus) in northern Spain were infested with Cephenemyia stimulator and one individual with Oestrus ovis. Three larvae of O. ovis were recovered from the nasopharynx of an adult female deer examined in February 2017, during the hunting season in the province of Burgos. The larvae were identified by morphology, and DNA sequencing from cytochrome oxidase subunit I and 28S rDNA confirmed the identification of both species of larvae. The possibility of O. ovis parasitizing roe deer should be considered in the diagnosis of nasal bots in cervids.

A Chinese individual with DEL phenotype caused by a novel RHD allele.

BackgroundRhD variants are categorized into partial D, weak D, and DEL. The detection of DEL can only be achieved through the adsorption and elution method or by using molecular techniques. Here, we report a case of DEL phenotypes associated with a novel allele in a Chinese individual. Study Design and MethodsWe used serological methods such as saline, indirect anti-human globulin and adsorption-elution. The RHD genotype was determined by the PCR-sequence specific primer (PCR-SSP) method as well as the Sanger dideoxy sequencing. ResultsRBCs of the sample were found to be DEL phenotype by serological testing, with negative reaction in the saline and indirect anti-human globulin test while positive reaction by the absorption–elution method. The genotyping results revealed a hemizygous (RHDc.1127T>G/RHD-). The novel allele sequence has been submitted to GenBank (Accession number: OR608456). ConclusionOur study demonstrates a case of a Chinese individual with DEL phenotype caused by a novel allele RHD c.1127T>G. It expands the database of the DEL variant.

Genome sequencing projects reveal new insights into the mammalian Gonadotropin-releasing Hormone II system.

The type II gonadotropin-releasing hormone (GnRH-II) was first discovered in chicken (Gallus gallus) brain and then shown to be present in many vertebrates. Indeed, its structure is conserved unchanged throughout vertebrate evolution from teleost fish through to mammals suggesting a crucial function. Yet the functional significance has been largely unexplored. Studies in comparative endocrinology show that the GnRH-II system is differentially functional in mammalian species. Intact GnRH-II neuropeptide and receptor genes (GnRH2 and GnRH receptor 2 GnRHR2) occur in marmoset monkeys (Callithrix jacchus), musk shrews (Suncus murinus) and pigs (Sus scrofa). However, one or other or both of these genes are inactivated in other species, where mutations or remnants affecting GnRH2 neuropeptide and/or type II GnRHR exons are retained in conserved genomic loci. New data from DNA sequencing projects facilitate extensive analysis of species-specific variation in these genes. Here, we describe GnRH2 and GnRHR2 genes spanning a collection of 21 taxonomic orders, encompassing around 140 species from Primates, Scandentia, Eulipotyphla, Rodentia, Lagomorpha, Artiodactyla, Carnivora, Perissodactyls, Pholidota, Chiroptera, Afrotheria, Xenarthra and Marsupialia. Intact coding exons for both GnRH2 and GnRHR2 occur in monkeys, tree shrews, shrews, moles, hedgehogs, several rodents (degu, kangaroo-rat, pocket mouse), pig, pecarry and warthog, camels and alpaca, bears, Weddell seal, hyena, elephant, aardvark and marsupials. Inactivating mutations affecting GnRH2 and GnRHR2, some located at conserved sites within exons, occur in species of primates, most rodents, lagomorphs, bovidae, cetaceans, felidae, canidae and other carnivora, pangolins, most bats, armadillo, brushtail and echidna. A functional GnRH-II system appears retained within several taxonomic families of mammals, but intact retention does not extend to whole taxonomic orders. Defining how endogenous GnRH-II neuropeptide operates in different mammals may afford functional insight into its actions in the brain, especially as, unlike the type I GnRH system, it is expressed in the mid brain and not the hypothalamus.

Multimodal assessment of high-risk human papillomavirus in sinonasal squamous cell carcinoma

High-risk human papillomavirus (hrHPV) is an emerging risk factor for sinonasal squamous cell carcinoma (SNSCC). The goal of this study was to assess the prevalence of hrHPV and subtype distribution in SNSCC and correlation with patient and clinical characteristics. This retrospective cohort study included 43 cases diagnosed with incident primary SNSCC at the University of Cincinnati Medical Center from 2010-2015. The prevalence of hrHPV was interrogated using a multi-assay approach that included p16 immunohistochemistry (IHC), RNA in-situ hybridization (ISH), and hrHPV DNA sequencing. The association of hrHPV with 5-year overall survival (OS) and 2-year disease-free survival (DFS) was assessed. Fourteen cases (32.6%) were classified as hrHPV positive, based on the a priori definition of having either a positive RNAScope™ ISH test or hrHPV DNA and p16-positive IHC; 9 cases (20.9%) were positive for all three tests. All ex-ISP cases were negative for hrHPV. HPV16 was the most common subtype among hrHPV positive cases (58.8%), followed by HPV18 (17.6%). No significant association was observed between hrHPV and OS or DFS after adjusting for potential confounding. hrHPV is prevalent in a sizable fraction of SNSCC. Additional studies are needed to better elucidate the relationship with patient survival outcomes and determine the optimal testing modality for prognostication.

Severe Bilateral Sialadenitis of the Mandibular and Parotid Salivary Glands with Severe Panniculitis in a 2-Year-old Standard Poodle.

A 2-year-old male neutered Standard Poodle weighing 17.9 kg was presented to their primary care veterinarian for enlarged bilateral submandibular swellings following an interdog altercation sustained in the previous weeks. Cytology performed following fine-needle aspirates of the regions of swelling was inconclusive, and the patient was treated empirically with Clavaseptin. Despite treatment, the submandibular swellings continued to enlarge, and right-sided intermittent epistaxis was reported. On biochemical profile, there was mild hypercalcemia and mild hyperglobulinemia. The computed tomography (CT) findings were indicative of severe multifocal sialadenitis with severe regional cellulitis and inflammatory lymphadenopathy. Histopathology and cytology results described mixed inflammation of the salivary gland. Methenamine silver staining and Fite's acid-fast staining were negative. Aerobic and anaerobic cultures were negative. Targeted, next-generation DNA sequencing detected no known fungi or bacterial pathogens. These findings were consistent with the diagnosis of severe bilateral mandibular sialadenitis, panniculitis, and lymphadenopathy. The patient was prescribed enrofloxacin, clindamycin, phenobarbital, and prednisolone for 1 month. One week after initiating treatment, the patient had a significant reduction in size of the salivary glands. CT imaging was helpful in the diagnosis of this patient and allowed the clinician to identify which submandibular anatomical structures were abnormal, guiding subsequent diagnostic decisions to provide medical management to resolve the condition.

Population genetic structure and phylogenetic analysis of Anopheles hyrcanus (Diptera: Culicidae) inferred from DNA sequences of nuclear ITS2 and the mitochondrial COI gene in the northern part of Iran

BackgroundThe Anopheles hyrcanus group is distributed throughout the Oriental and Palaearctic regions and can transmit diseases such as malaria, Japanese encephalitis virus, and filariasis. This investigation marks the inaugural comprehensive study to undertake a phylogenetic analysis of the constituents of this malaria vector group in the northeastern region of Iran, juxtaposed with documented occurrences from different areas within Iran and worldwide.MethodsMosquitoes were collected using various methods from nine different locations in Golestan province from April to December 2023. The collected mosquitoes were identified morphologically using valid taxonomic keys. DNA was isolated using the Sambio™ Kit. COI and ITS2 primers were designed using Oligo7 and GeneRunner. PCR and purification were performed with the Qiagen kit. Subsequently, sequencing was carried out at the Mehr Mam GENE Center using an Applied Biosystems 3730XL sequencer. The nucleotide sequences were then analyzed and aligned with GenBank data using BioEdit. Kimura 2-parameter was Utilized for base substitutions. DNA models were selected based on AIC and BIC criteria. Bayesian and Maximum Likelihood trees were constructed, along with a haplotype network. Molecular diversity statistics computed using DnaSP software.ResultsIn this study, a total of 819 adult mosquitoes were collected. An. hyrcanus was the second most abundant species, predominantly found in Kalaleh and Turkman counties. The sequenced and edited COI and ITS2 sequences were deposited in GenBank under specific accession numbers. Phylogenetic analyses using ML, BI, and NJ methods confirmed a monophyletic lineage for An. hyrcanus with strong support. Molecular analysis of Iranian An. hyrcanus found 11 diverse haplotypes, with the COI gene displaying low diversity. The ITS2 gene revealed two clades - one associating with Iran, Europe, and Asia; the other originating from southwestern Iran. The haplotype network showed two main groups - one from southwest Iran and the other from north Iran. Iran exhibited six distinct haplotypes, while Turkey showcased the highest diversity.ConclusionsAn. hyrcanus in southwestern Iran exhibits a distinct haplogroup, suggesting possible subspecies differentiation. Additional studies are required to validate this phenomenon.

Clinical utility of plasma microbial cell-free DNA sequencing among immunocompromised patients with pneumonia

Abstract Background Plasma microbial cell-free DNA (mcfDNA) sequencing can establish the etiology of multiple infectious syndromes by identifying microbial DNA in plasma. However, data are needed to define the clinical scenarios where this tool offers the highest clinical benefit. Methods We conducted a prospective multicenter observational study that evaluated the impact of plasma mcfDNA sequencing compared to usual care testing among adults with hematologic malignancies. This is a secondary analysis of an expanded cohort that evaluated the clinical utility of plasma mcfDNA sequencing across prespecified and adjudicated outcomes. We examined the percentage of participants for whom plasma mcfDNA sequencing identified a probable cause of pneumonia or clinically relevant non-pneumonia infection. We then assessed potential changes in antimicrobial therapy based on plasma mcfDNA sequencing results, and the potential for early mcfDNA testing to avoid bronchoscopy and its associated adverse events. Results Of 223 participants, at least one microbial detection by plasma mcfDNA sequencing was adjudicated as a probable cause of pneumonia in 57 (25.6%) and a clinically relevant non-pneumonia infection in 88 (39.5%). A probable cause of pneumonia was exclusively identified by plasma mcfDNA sequencing in 23 (10.3%) participants. Antimicrobial therapy would have changed for 41 (18.4%) participants had plasma mcfDNA results been available in real-time. Among the 57 participants with a probable cause of pneumonia identified by plasma mcfDNA sequencing, bronchoscopy identified no additional probable cause of pneumonia in 52 (91.2%). Conclusions Plasma mcfDNA sequencing could improve management of both pneumonia and other concurrent infections in immunocompromised patients with suspected pneumonia.

Isolation of α-Amylase Producing Microorganisms from Soil of Kachchh, Gujarat

The purpose of this study is to explore the soil of the Gujarat, Kachchh region to identify amylase-producing bacteria and characterize them using molecular methods. The unique ecological characteristics of the Kachchh region may facilitate the isolation of these bacteria. Samples were collected from multiple locations within the Kachchh District, including Gandhidham, Rapar, Bhuj, Nakhatrana, Mandvi, and Mundra Talukas. These samples were then screened to isolate amylase-producing bacteria. A total of 27 different types of colonies were identified, out of which 16 exhibited amylase production (M1-M16). Out of 27 colonies identified, 16 showed amylase production. Strains M2, M7, and M13 exhibited high amylase activity, with M2 showing a consistent increase over 72 hours, making it a strong candidate for amylase production. Further identification of M2 stain identified M2 as a Gram-positive, spore-forming, capsulated, and motile bacillus, specifically Bacillus licheniformis. This was confirmed through DNA sequencing and analysis in the NCBI database, which showed a 99.15% similarity with Bacillus licheniformis. The study concludes that Soil in Kachchh is rich with microorganisms that produce amylase, an enzyme with diverse industrial applications. These organisms are valuable for sectors like food, textiles, paper, detergents, pharmaceuticals, and biofuel production.

Hydrolytic Response of Beta-Amylase to Selected Starches when Adsorptively Immobilized on Agarose Gel

Fermentative microorganisms bring about transformative processes in food, thereby enhancing flavor and appearance indices, inhibiting undesirable components, improving shelf and storage life, as well as improving health and nutritional quality parameters. Traditional methods for identification of fermentative microorganisms involve cultivating and analyzing phenotypic characteristics, which are labor-intensive and time-consuming. Advanced molecular techniques such as polymerase chain reaction, whole gene sequencing, next generation sequencing, fluorescent in situ hybridization (FISH), Matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS), fourier transform infrared spectroscopy and hyper-spectral imaging offer rapid, cost-effective, and reliable identification of bacteria and fungi cultured on agar plates or in liquid media. Techniques, such as genotyping, examine the DNA sequence to determine the genetic makeup of microorganisms, alongside the grouping of isolates via application of phylogenetic tree similarity indices. Overall, modern molecular techniques have revolutionized the identification of fermentative microorganisms, providing efficient and more elaborate alternatives to traditional methods. In this review work, an attempt is made to examine the historical and analytical trends from the conventional methods to the most recent modern tools for effective identification of industrially-important fermentative microorganisms.

Genome assembly catalog for species in the Japanese Red List: unlocking endangered biodiversity through genomic inventory

Improvements in DNA sequencing technology are allowing the dramatic increase of whole genome data for a wide variety of species. Such genome sequence data can assist the monitoring of intraspecific genetic diversity, but is often lacking for threatened species. In this project, we focused on the national Red List, a catalog of extinct and threatened species, issued by the Japanese government. We combined the data included in it with the record of genome assembly in NCBI and tabulated the assembly availability of the species in the list. The combined data shows a low percentage (2.1%) of the availability of whole genome sequence data for the taxa ranked on the Japanese Red List as well as a strong bias towards mammals and birds in Animalia and vascular plants in Plantae. Our data presentation highlights potential systematic limitations in genome sequencing (e.g., budget for sequencing large genomes of amphibians) and instructs future policies including which taxon needs more effort for genome sequencing. The resultant tables are available in the original website https://treethinkers.nig.ac.jp/redlist/ and are regularly updated.

Interpretable deep residual network uncovers nucleosome positioning and associated features.

Nucleosomes represent elementary building units of eukaryotic chromosomes and consist of DNA wrapped around a histone octamer flanked by linker DNA segments. Nucleosomes are central in epigenetic pathways and their genomic positioning is associated with regulation of gene expression, DNA replication, DNA methylation and DNA repair, among other functions. Building on prior discoveries that DNA sequences noticeably affect nucleosome positioning, our objective is to identify nucleosome positions and related features across entire genome. Here, we introduce an interpretable framework based on the concepts of deep residual networks (NuPoSe). Trained on high-coverage human experimental MNase-seq data, NuPoSe is able to learn sequence and structural patterns associated with nucleosome organization in human genome. NuPoSe can bealsoapplied to unseen data from different organisms and cell types. Our findings point to 43 informative features, most of them constitute tri-nucleotides, di-nucleotides and one tetra-nucleotide. Most features are significantly associated with the nucleosomal structuralcharacteristics, namely, periodicity of nucleosomal DNA and its location with respect to a histone octamer. Importantly, we show that features derived from the 27 bp linker DNAflanking nucleosomescontribute up to 10% to the quality of the prediction model. This,alongwith the comprehensive training sets, deep-learning architecture, and feature selection method,may contribute totheNuPoSe's 80-89% classificationaccuracy on different independentdatasets.

Recent Advances in the Identification and Characterization of Fermentative Microorganisms: An Exploratory Review

Fermentative microorganisms bring about transformative processes in food, thereby enhancing flavor and appearance indices, inhibiting undesirable components, improving shelf and storage life, as well as improving health and nutritional quality parameters. Traditional methods for identification of fermentative microorganisms involve cultivating and analyzing phenotypic characteristics, which are labor-intensive and time-consuming. Advanced molecular techniques such as polymerase chain reaction, whole gene sequencing, next generation sequencing, fluorescent in situ hybridization (FISH), Matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS), fourier transform infrared spectroscopy and hyper-spectral imaging offer rapid, cost-effective, and reliable identification of bacteria and fungi cultured on agar plates or in liquid media. Techniques, such as genotyping, examine the DNA sequence to determine the genetic makeup of microorganisms, alongside the grouping of isolates via application of phylogenetic tree similarity indices. Overall, modern molecular techniques have revolutionized the identification of fermentative microorganisms, providing efficient and more elaborate alternatives to traditional methods. In this review work, an attempt is made to examine the historical and analytical trends from the conventional methods to the most recent modern tools for effective identification of industrially-important fermentative microorganisms.

EDNA metabarcoding: an effective tool for vertebrate diversity studies in the Colombian Amazon and Orinoco basins

The development of fast, cost-effective, non-invasive, and efficient sampling alternatives, such as environmental DNA (eDNA), is crucial for understanding the changes in species biodiversity and distributions worldwide, particularly for low abundance, cryptic, and threatened species. This study utilized environmental eDNA to analyze the variety of aquatic, semi-aquatic, and terrestrial vertebrates in the Colombian Amazon and Orinoco basins. The study focused on four main subregions: Bojonawi Natural Reserve and adjacent areas (Vichada Department), Sierra de la Macarena National Park and Tillavá (Meta Department), Puerto Nariño and adjacent areas (Amazonas Department), and the Municipality of Solano (Caquetá Department). A total of 709 operational taxonomic units (OTUs) were identified across all sampling locations. The Orinoco River had the highest number of fish genera (68), while the Guayabero River had the highest number of tetrapod genera (13). New taxonomic records were found for all locations, with the highest number of previously undetected fish diversity being found in the Bita, Orinoco, and Tillavá rivers, compared to traditional surveys. Likewise, the study identified two fish species, four mammal species, and one reptile species as vulnerable. Additionally, four mammal species were identified as endangered, including the giant otter (Pteronura brasiliensis), two subspecies of the Amazon River dolphin (Inia geoffrensis geoffrensis and Inia geoffrensis humboldtiana), and the tucuxi (Sotalia fluviatilis). Standardizing the methodology and improving current DNA sequence databases for the Neotropics is essential to develop future eDNA studies and enhance our understanding of the region’s diversity.

Investigating the relative role of dispersal and demographic traits in predictive phylogeography

Many studies suggest that aside from environmental variables, such as topography and climate, species‐specific ecological traits are relevant to explain the geographic distribution of intraspecific genetic lineages. Here, we investigated whether and to what extent incorporating such traits systematically improves the accuracy of random forest models in predicting genetic differentiation among pairs of localities. We leveraged available ecological datasets for birds and tested the inclusion of two categories of ecological traits: dispersal‐related traits (i.e. morphology and foraging ecology) and demographic traits (such as species survival rate and generation length). We estimated genetic differentiation from published mitochondrial DNA sequences for 28 species of birds (1578 total genetic samples, 391 localities) in the Atlantic Forest of South America. Aside from the aforementioned ecological traits, we included geographic, topographic and climatic distances between localities as environmental predictors. We then created models using all available data to evaluate model uncertainty both across space and across the different categories of predictors. Finally, we investigated model uncertainty in predicting genetic differentiation individually for each species (a common challenge in conservation biology). Our results show that while environmental conditions are the most important predictors of genetic differentiation, model accuracy largely increases with the addition of ecological traits. Additionally, the inclusion of dispersal traits improves model accuracy to a larger extent than the inclusion of demographic traits. Similar results are observed in models for individual species, although model accuracy is highly variable. We conclude that ecological traits improve predictive models of genetic differentiation, refining our ability to predict phylogeographic patterns from existing data. Additionally, demographic traits may not be as informative as previously hypothesized. Finally, prediction of genetic differentiation for species with conservation concerns may require further careful assessment of the environmental and ecological variation within the species range.

ALLSTAR: Inference of ReliAble CausaL RuLes between Somatic MuTAtions and CanceR Phenotypes.

Recent advances in DNA sequencing technologies have allowed the detailed characterization of genomes in large cohorts of tumors, highlighting their extreme heterogeneity, with no two tumors sharing the same complement of somatic mutations. Such heterogeneity hinders our ability to identify somatic mutations important for the disease, including mutations that determine clinically relevant phenotypes (e.g., cancer subtypes). Several tools have been developed to identify somatic mutations related to cancer phenotypes. However, such tools identify correlations between somatic mutations and cancer phenotypes, with no guarantee of highlighting causal relations. We describe ALLSTAR, a novel tool to infer reliable causal relations between somatic mutations and cancer phenotypes. ALLSTAR identifies reliable causal rules highlighting combinations of somatic mutations with the highest impact in terms of average effect on the phenotype. While we prove that the underlying computational problem is NP-hard, we develop a branch-and-bound approach that employs protein-protein interaction networks and novel bounds for pruning the search space, while properly correcting for multiple hypothesis testing. Our extensive experimental evaluation on synthetic data shows that our tool is able to identify reliable causal relations in large cancer cohorts. Moreover, the reliable causal rules identified by our tool in cancer data show that our approach identifies several somatic mutations known to be relevant for cancer phenotypes as well as novel biologically meaningful relations. Code, data, and scripts to reproduce the experiments available at https://github.com/VandinLab/ALLSTAR. Supplementary data are available at Bioinformatics online.

Deciphering Preferential Binding Interaction of Synthetic Pyrido[2,3‐c]Carbazole Alkaloid Derivative (PCAD) with Pu24T G‐quadruplex DNA

AbstractG‐quadruplex DNA (GQ‐DNA) represents one of the most significant non‐canonical nucleic acid configurations. GQ‐DNA producing sequences are found in different important genomic areas, including the promoter islands of numerous oncogenes and human telomere regions. Therefore, GQ‐DNA is a key target for anticancer medicines. GQ‐DNA has a highly variable structure, it is critical to develop ligand molecules that selectively target certain quadruplex sequences. Natural products such as pyridocarbazole alkaloids have grown interest for healthcare and medicinal values and they considered as a valuable source of innovative anticancer medicines among the chemical compounds. In this investigation, we have synthesised and characterized pyrido[2,3‐c]carbazole derivative (PCAD) through NMR and IR spectra and explore the interactions between PCAD and Pu24T GQ (promoter region), h‐TELO GQ (telomere region) and duplex DNA by employing several multi‐spectroscopic analytical techniques. We have found that PCAD preferentially interacts with Pu24T GQ DNA as compared to other DNA sequences. These findings highlights PCAD as an appealing option for targeting the Pu24T promoter region and consequently acting as an anti‐cancer drug. This study also highlights the potential for developing drugs to understand the molecular aspects of GQ DNA recognition and signaling, paving the way for future research on GQ biology.

Relationships Among the Bryophytes and Vascular Plants: A Case Study in Deep-Time Reconstruction

Relationships of the three bryophyte lineages (liverworts, mosses, and hornworts) to vascular plants is a pivotal question in the study of the origin and evolution of land plants. In recent decades, this question has been subjected to intense phylogenetic analyses using morphological characters, multigene DNA sequences, and genome structural characters. A tentative consensus, reached ten years ago, suggested that bryophytes are a paraphyletic group, with liverworts being sister to all other land plants and hornworts being sister to vascular plants. However, several more recent nuclear phylogenomic studies have concluded that bryophytes represent a monophyletic group that is sister to vascular plants. A discussion is presented here on strengths and weaknesses of different types of characters (morphological traits, nucleotide sequences, and genome structural arrangements) and their suitability for resolving deep phylogenetic relationships. Moreover, several criteria for credible phylogenetic reconstruction are proposed. Strong statistical support for reconstructed relationships should be derived from high-quality, independent characters selected for suitability to the particular question being addressed. The relationships inferred in a study should be congruent with those from as many other lines of phylogenetic evidence as possible. Any incongruities should be explicable by well-understood biological mechanisms. It is concluded that the relationships of the three bryophyte lineages to vascular plants should currently be viewed as unresolved. This is a difficult phylogenetic problem; the land plants underwent a rapid radiation a long time ago. Yet, further exploration of analytical methods and careful choice of characters should lead to the eventual elucidation of diversification patterns among early land plants.